| | Other Issues: previous | next | latest | archiveCorrespondence Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni: comment Morgane Thomas-Chollier and Valérie Ledent PMCID: PMC2246111 Genomics Research: World Survey of Public Funding Jennifer Reineke Pohlhaus and Robert M Cook-Deegan PMCID: PMC2576262 Database RGST - Rat Gene Symbol Tracker, a database for defining official rat gene symbols Greta Petersen and Fredrik Ståhl PMCID: PMC2265274 A Caenorhabditis motif compendium for studying transcriptional gene regulation Christoph Dieterich and Ralf J Sommer PMCID: PMC2248174 The RAST Server: Rapid Annotations using Subsystems Technology Ramy K Aziz, Daniela Bartels, Aaron A Best, Matthew DeJongh, Terrence Disz, Robert A Edwards, Kevin Formsma, Svetlana Gerdes, Elizabeth M Glass, Michael Kubal, Folker Meyer, Gary J Olsen, Robert Olson, Andrei L Osterman, Ross A Overbeek, Leslie K McNeil, Daniel Paarmann, Tobias Paczian, Bruce Parrello, Gordon D Pusch, Claudia Reich, Rick Stevens, Olga Vassieva, Veronika Vonstein, Andreas Wilke, and Olga Zagnitko PMCID: PMC2265698 MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters Philip J Law, Clotilde Claudel-Renard, Fourie Joubert, Abraham I Louw, and Dave K Berger PMCID: PMC2277412 DATFAP: A Database of Primers and Homology Alignments for Transcription Factors from 13 Plant Species Jakob Fredslund PMCID: PMC2322997 PRRDB: A comprehensive database of Pattern-Recognition Receptors and their ligands Sneh Lata and Gajendra P S Raghava PMCID: PMC2346480 RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina Ravi Kiran Reddy Kalathur, Nicolas Gagniere, Guillaume Berthommier, Laetitia Poidevin, Wolfgang Raffelsberger, Raymond Ripp, Thierry Léveillard, and Olivier Poch PMCID: PMC2386825 SjTPdb: integrated transcriptome and proteome database and analysis platform for Schistosoma japonicum Feng Liu, Ping Chen, Shu-Jian Cui, Zhi-Qin Wang, and Ze-Guang Han PMCID: PMC2447853 WildSilkbase: An EST database of wild silkmoths KP Arunkumar, Archana Tomar, Takaaki Daimon, Toru Shimada, and J Nagaraju PMCID: PMC2483293 PRFdb: A database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals Ashton T Belew, Nicholas L Hepler, Jonathan L Jacobs, and Jonathan D Dinman PMCID: PMC2483730 SoyXpress: A database for exploring the soybean transcriptome Kei Chin Christine Cheng and Martina V Strömvik PMCID: PMC2536680 MGDD: Mycobacterium tuberculosis Genome Divergence Database Anchal Vishnoi, Alok Srivastava, Rahul Roy, and Alok Bhattacharya PMCID: PMC2518163 Fungal cytochrome P450 database Jongsun Park, Seungmin Lee, Jaeyoung Choi, Kyohun Ahn, Bongsoo Park, Jaejin Park, Seogchan Kang, and Yong-Hwan Lee PMCID: PMC2542383 SCUD: Saccharomyces Cerevisiae Ubiquitination Database Won-Chul Lee, Minho Lee, Jin Woo Jung, Kwang Pyo Kim, and Dongsup Kim PMCID: PMC2567349 CoGemiR: A comparative genomics microRNA database Vincenza Maselli, Diego Di Bernardo, and Sandro Banfi PMCID: PMC2567348 DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions Jingkai Yu, Svetlana Pacifico, Guozhen Liu, and Russell L Finley, Jr PMCID: PMC2572628 RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration Gelio Alves, Aleksey Y Ogurtsov, and Yi-Kuo Yu PMCID: PMC2605478 NemaPath: online exploration of KEGG-based metabolic pathways for nematodes Todd Wylie, John Martin, Sahar Abubucker, Yong Yin, David Messina, Zhengyuan Wang, James P McCarter, and Makedonka Mitreva PMCID: PMC2588608 Software SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels Mathijs A Sanders, Roel GW Verhaak, Wendy MC Geertsma-Kleinekoort, Saman Abbas, Sebastiaan Horsman, Peter J van der Spek, Bob Löwenberg, and Peter JM Valk PMCID: PMC2235842 A software framework for microarray and gene expression object model (MAGE-OM) array design annotation Matloob Qureshi and Alasdair Ivens PMCID: PMC2358904 Linking Cytoscape and the corynebacterial reference database CoryneRegNet Jan Baumbach and Leonard Apeltsin PMCID: PMC2375448 T2D-Db: An integrated platform to study the molecular basis of Type 2 diabetes Shipra Agrawal, Nevenka Dimitrova, Prasanthi Nathan, K Udayakumar, S Sai Lakshmi, S Sriram, N Manjusha, and Urmi Sengupta PMCID: PMC2491641 Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT Jost Neigenfind, Gabor Gyetvai, Rico Basekow, Svenja Diehl, Ute Achenbach, Christiane Gebhardt, Joachim Selbig, and Birgit Kersten PMCID: PMC2566320 Human MLPA Probe Design (H-MAPD): a probe design tool for both electrophoresis-based and bead-coupled human multiplex ligation-dependent probe amplification assays Jizu Zhi and Eli Hatchwell PMCID: PMC2547856 BOV – a web-based BLAST output visualization tool Rajesh Gollapudi, Kashi Vishwanath Revanna, Chris Hemmerich, Sarah Schaack, and Qunfeng Dong PMCID: PMC2566317 BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams Tim Hulsen, Jacob de Vlieg, and Wynand Alkema PMCID: PMC2584113 Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources Evert Jan Blom, Rainer Breitling, Klaas Jan Hofstede, Jos BTM Roerdink, Sacha AFT van Hijum, and Oscar P Kuipers PMCID: PMC2585105 ProSeeK: A web server for MLPA probe design Lorena Pantano, Lluís Armengol, Sergi Villatoro, and Xavier Estivill PMCID: PMC2625369 Research Articles Genome-wide analysis of the interaction between the endosymbiotic bacterium Wolbachia and its Drosophila host Zhiyong Xi, Laurent Gavotte, Yan Xie, and Stephen L Dobson PMCID: PMC2253531 Codon usage suggests that translational selection has a major impact on protein expression in trypanosomatids David Horn PMCID: PMC2217535 Switch-like genes populate cell communication pathways and are enriched for extracellular proteins Adam Ertel and Aydin Tozeren PMCID: PMC2257939 Persistence drives gene clustering in bacterial genomes Gang Fang, Eduardo PC Rocha, and Antoine Danchin PMCID: PMC2234087 A first glimpse at the transcriptome of Physarum polycephalum Gernot Glöckner, Georg Golderer, Gabriele Werner-Felmayer, Sonja Meyer, and Wolfgang Marwan PMCID: PMC2258281 Profiling expression changes caused by a segmental aneuploid in maize Irina Makarevitch, Ronald L Phillips, and Nathan M Springer PMCID: PMC2254597 Identification of novel homologous microRNA genes in the rhesus macaque genome Junming Yue, Yi Sheng, and Kyle E Orwig PMCID: PMC2254598 Halibut mitochondrial genomes contain extensive heteroplasmic tandem repeat arrays involved in DNA recombination Kenneth A Mjelle, Bård O Karlsen, Tor E Jørgensen, Truls Moum, and Steinar D Johansen PMCID: PMC2248175 Using 454 technology for long-PCR based sequencing of the complete mitochondrial genome from single Haemonchus contortus (Nematoda) Aaron R Jex, Min Hu, D Timothy J Littlewood, Andrea Waeschenbach, and Robin B Gasser PMCID: PMC2254599 Genetic and genomic analysis modeling of germline c-MYC overexpression and cancer susceptibility Xavier Solé, Pilar Hernández, Miguel López de Heredia, Lluís Armengol, Benjamín Rodríguez-Santiago, Laia Gómez, Christopher A Maxwell, Fernando Aguiló, Enric Condom, Jesús Abril, Luis Pérez-Jurado, Xavier Estivill, Virginia Nunes, Gabriel Capellá, Stephen B Gruber, Víctor Moreno, and Miguel Angel Pujana PMCID: PMC2244606 Computational analysis of splicing errors and mutations in human transcripts Yerbol Z Kurmangaliyev and Mikhail S Gelfand PMCID: PMC2234086 Virulence factor rtx in Legionella pneumophila, evidence suggesting it is a modular multifunctional protein Giuseppe D'Auria, Núria Jiménez, Francesc Peris-Bondia, Carmen Pelaz, Amparo Latorre, and Andrés Moya PMCID: PMC2257941 The midgut transcriptome of Lutzomyia longipalpis: comparative analysis of cDNA libraries from sugar-fed, blood-fed, post-digested and Leishmania infantum chagasi-infected sand flies Ryan C Jochim, Clarissa R Teixeira, Andre Laughinghouse, Jianbing Mu, Fabiano Oliveira, Regis B Gomes, Dia-Eldin Elnaiem, and Jesus G Valenzuela PMCID: PMC2249575 Strand bias structure in mouse DNA gives a glimpse of how chromatin structure affects gene expression Kenneth J Evans PMCID: PMC2266913 A pig multi-tissue normalised cDNA library: large-scale sequencing, cluster analysis and 9K micro-array resource generation Agnès Bonnet, Eddie Iannuccelli, Karine Hugot, Francis Benne, Maria F Bonaldo, Marcelo B Soares, François Hatey, and Gwenola Tosser-Klopp PMCID: PMC2257943 Transcriptional co-expression and co-regulation of genes coding for components of the oxidative phosphorylation system Corina van Waveren and Carlos T Moraes PMCID: PMC2268925 Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family Nicolas Joannin, Saraswathi Abhiman, Erik L Sonnhammer, and Mats Wahlgren PMCID: PMC2257938 Systematic identification of stem-loop containing sequence families in bacterial genomes Luca Cozzuto, Mauro Petrillo, Giustina Silvestro, Pier Paolo Di Nocera, and Giovanni Paolella PMCID: PMC2267715 Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce Nathalie Pavy, Betty Pelgas, Stéphanie Beauseigle, Sylvie Blais, France Gagnon, Isabelle Gosselin, Manuel Lamothe, Nathalie Isabel, and Jean Bousquet PMCID: PMC2246113 Annotation and analysis of a large cuticular protein family with the R&R Consensus in Anopheles gambiae R Scott Cornman, Toru Togawa, W Augustine Dunn, Ningjia He, Aaron C Emmons, and Judith H Willis PMCID: PMC2259329 Repeats and EST analysis for new organisms Ketil Malde and Inge Jonassen PMCID: PMC2258282 Identification and investigation of ORFans in the viral world Yanbin Yin and Daniel Fischer PMCID: PMC2245933 DArT markers: diversity analyses and mapping in Sorghum bicolor Emma S Mace, Ling Xia, David R Jordan, Kirsten Halloran, Dipal K Parh, Eric Huttner, Peter Wenzl, and Andrzej Kilian PMCID: PMC2270266 Genetic marker anchoring by six-dimensional pools for development of a soybean physical map Xiaolei Wu, Guohua Zhong, Seth D Findley, Perry Cregan, Gary Stacey, and Henry T Nguyen PMCID: PMC2259328 Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference Tae-Sung Kim, James G Booth, Hugh G Gauch, Jr, Qi Sun, Jongsun Park, Yong-Hwan Lee, and Kwangwon Lee PMCID: PMC2257937 Microarray analysis of the in vivo sequence preferences of a minor groove binding drug Todd T Eckdahl, Adam D Brown, Steven N Hart, Kelly J Malloy, Martha Shott, Gloria Yiu, Laura L Mays Hoopes, and Laurie J Heyer PMCID: PMC2254601 The mitochondrial genome of the hexactinellid sponge Aphrocallistes vastus: Evidence for programmed translational frameshifting Rafael D Rosengarten, Erik A Sperling, Maria A Moreno, Sally P Leys, and Stephen L Dellaporta PMCID: PMC2267718 Global mRNA expression analysis in myosin II deficient strains of Saccharomyces cerevisiae reveals an impairment of cell integrity functions José F Rodríguez-Quiñones, Rafael A Irizarry, Nitza L Díaz-Blanco, Félix E Rivera-Molina, Diana Gómez-Garzón, and José R Rodríguez-Medina PMCID: PMC2253530 Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea Fengfeng Zhou, Victor Olman, and Ying Xu PMCID: PMC2246112 Discovery of genes implicated in whirling disease infection and resistance in rainbow trout using genome-wide expression profiling Melinda R Baerwald, Amy B Welsh, Ronald P Hedrick, and Bernie May PMCID: PMC2257940 Development of a human mitochondrial oligonucleotide microarray (h-MitoArray) and gene expression analysis of fibroblast cell lines from 13 patients with isolated F1Fo ATP synthase deficiency Alena Čížková, Viktor Stránecký, Robert Ivánek, Hana Hartmannová, Lenka Nosková, Lenka Piherová, Markéta Tesařová, Hana Hansíková, Tomáš Honzík, Jiří Zeman, Petr Divina, Andrea Potocká, Jan Paul, Wolfgang Sperl, Johannes A Mayr, Sara Seneca, Josef Houštĕk, and Stanislav Kmoch PMCID: PMC2267714 SNPs and Hox gene mapping in Ciona intestinalis Luigi Caputi, Marco Borra, Nikos Andreakis, Elio Biffali, and Paolo Sordino PMCID: PMC2262895 Comparative analysis of the Photorhabdus luminescens and the Yersinia enterocolitica genomes: uncovering candidate genes involved in insect pathogenicity Ralf Heermann and Thilo M Fuchs PMCID: PMC2266911 Probing regulon of ArcA in Shewanella oneidensis MR-1 by integrated genomic analyses Haichun Gao, Xiaohu Wang, Zamin K Yang, Timothy Palzkill, and Jizhong Zhou PMCID: PMC2262068 Genomic DNA from animals shows contrasting strand bias in large and small subsequences Kenneth J Evans PMCID: PMC2267173 Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice Dong Wang, Yinghui Guo, Changai Wu, Guodong Yang, Yingying Li, and Chengchao Zheng PMCID: PMC2267713 Systematic sequencing of mRNA from the Antarctic krill (Euphausia superba) and first tissue specific transcriptional signature Cristiano De Pittà, Cristiano Bertolucci, Gabriella M Mazzotta, Filippo Bernante, Giorgia Rizzo, Barbara De Nardi, Alberto Pallavicini, Gerolamo Lanfranchi, and Rodolfo Costa PMCID: PMC2270838 Amplification biases: possible differences among deviating gene expressions Séverine A Degrelle, Christelle Hennequet-Antier, Hélène Chiapello, Karine Piot-Kaminski, Francois Piumi, Stéphane Robin, Jean-Paul Renard, and Isabelle Hue PMCID: PMC2257942 Comparative secretome analysis suggests low plant cell wall degrading capacity in Frankia symbionts Juliana E Mastronunzio, Louis S Tisa, Philippe Normand, and David R Benson PMCID: PMC2266912 Relationship between mRNA secondary structure and sequence variability in Chloroplast genes: possible life history implications Neeraja M Krishnan, Hervé Seligmann, and Basuthkar J Rao PMCID: PMC2276208 High frequency of microsatellites in S. cerevisiae meiotic recombination hotspots Andrew TM Bagshaw, Joel PW Pitt, and Neil J Gemmell PMCID: PMC2267716 Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region Yong-hui Jiang, Kekio Wauki, Qian Liu, Jan Bressler, Yanzhen Pan, Catherine D Kashork, Lisa G Shaffer, and Arthur L Beaudet PMCID: PMC2268926 Computational prediction and molecular confirmation of Helitron transposons in the maize genome Chunguang Du, Jason Caronna, Limei He, and Hugo K Dooner PMCID: PMC2267711 New miRNAs cloned from neuroblastoma Elena A Afanasyeva, Agnes Hotz-Wagenblatt, Karl-Heinz Glatting, and Frank Westermann PMCID: PMC2254388 Glioma cells on the run – the migratory transcriptome of 10 human glioma cell lines Tim Demuth, Jessica L Rennert, Dominique B Hoelzinger, Linsey B Reavie, Mitsutoshi Nakada, Christian Beaudry, Satoko Nakada, Eric M Anderson, Amanda N Henrichs, Wendy S McDonough, David Holz, Anna Joy, Richard Lin, Kuang H Pan, Chih J Lih, Stan N Cohen, and Michael E Berens PMCID: PMC2275271 Identification of protein secretion systems and novel secreted proteins in Rhizobium leguminosarum bv. viciae Martin Krehenbrink and J Allan Downie PMCID: PMC2275737 Genome-wide transcriptome analysis reveals that a pleiotropic antibiotic regulator, AfsS, modulates nutritional stress response in Streptomyces coelicolor A3(2) Wei Lian, Karthik P Jayapal, Salim Charaniya, Sarika Mehra, Frank Glod, Yun-Seung Kyung, David H Sherman, and Wei-Shou Hu PMCID: PMC2267785 Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding Steven G Ralph, Hye Jung E Chun, Dawn Cooper, Robert Kirkpatrick, Natalia Kolosova, Lee Gunter, Gerald A Tuskan, Carl J Douglas, Robert A Holt, Steven JM Jones, Marco A Marra, and Jörg Bohlmann PMCID: PMC2270264 Insights into the Musa genome: Syntenic relationships to rice and between Musa species Magali Lescot, Pietro Piffanelli, Ana Y Ciampi, Manuel Ruiz, Guillaume Blanc, Jim Leebens-Mack, Felipe R da Silva, Candice MR Santos, Angélique D'Hont, Olivier Garsmeur, Alberto D Vilarinhos, Hiroyuki Kanamori, Takashi Matsumoto, Catherine M Ronning, Foo Cheung, Brian J Haas, Ryan Althoff, Tammy Arbogast, Erin Hine, Georgios J Pappas, Jr, Takuji Sasaki, Manoel T Souza, Jr, Robert NG Miller, Jean-Christophe Glaszmann, and Christopher D Town PMCID: PMC2270835 Characterization of a newly developed chicken 44K Agilent microarray Xianyao Li, Hsin-I Chiang, James Zhu, Scot E Dowd, and Huaijun Zhou PMCID: PMC2262898 Comparative genomic analysis of novel conserved peptide upstream open reading frames in Drosophila melanogaster and other dipteran species Celine A Hayden and Giovanni Bosco PMCID: PMC2276209 Evolution of the chicken Toll-like receptor gene family: A story of gene gain and gene loss Nicholas D Temperley, Sofia Berlin, Ian R Paton, Darren K Griffin, and David W Burt PMCID: PMC2275738 Fungi have three tetraspanin families with distinct functions Karine Lambou, Didier Tharreau, Annegret Kohler, Catherine Sirven, Mélanie Marguerettaz, Crystel Barbisan, Adrienne C Sexton, Ellen M Kellner, Francis Martin, Barbara J Howlett, Marc J Orbach, and Marc-Henri Lebrun PMCID: PMC2278132 Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia Ashleen Shadeo, Raj Chari, Kim M Lonergan, Andrea Pusic, Dianne Miller, Tom Ehlen, Dirk Van Niekerk, Jasenka Matisic, Rebecca Richards-Kortum, Michele Follen, Martial Guillaud, Wan L Lam, and Calum MacAulay PMCID: PMC2277413 Origin and evolution of candidate mental retardation genes on the human X chromosome (MRX) Margaret L Delbridge, Daniel A McMillan, Ruth J Doherty, Janine E Deakin, and Jennifer A Marshall Graves PMCID: PMC2276207 Genomic organization, sequence divergence, and recombination of feline immunodeficiency virus from lions in the wild Jill Pecon-Slattery, Carrie L McCracken, Jennifer L Troyer, Sue VandeWoude, Melody Roelke, Kerry Sondgeroth, Christiaan Winterbach, Hanlie Winterbach, and Stephen J O'Brien PMCID: PMC2270836 All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues Julian M Rozenberg, Andrey Shlyakhtenko, Kimberly Glass, Vikas Rishi, Maxim V Myakishev, Peter C FitzGerald, and Charles Vinson PMCID: PMC2267717 Transcriptomic dissection of tongue squamous cell carcinoma Hui Ye, Tianwei Yu, Stephane Temam, Barry L Ziober, Jianguang Wang, Joel L Schwartz, Li Mao, David T Wong, and Xiaofeng Zhou PMCID: PMC2262071 In silico discovery of transcription regulatory elements in Plasmodium falciparum Jason A Young, Jeffery R Johnson, Chris Benner, S Frank Yan, Kaisheng Chen, Karine G Le Roch, Yingyao Zhou, and Elizabeth A Winzeler PMCID: PMC2268928 Activation of counter-regulatory mechanisms in a rat renal acute rejection model Bayram Edemir, Sunil M Kurian, Martin Eisenacher, Detlef Lang, Carsten Müller-Tidow, Gert Gabriëls, Daniel R Salomon, and Eberhard Schlatter PMCID: PMC2262896 Human glycolipid transfer protein (GLTP) genes: organization, transcriptional status and evolution Xianqiong Zou, Taeowan Chung, Xin Lin, Margarita L Malakhova, Helen M Pike, and Rhoderick E Brown PMCID: PMC2262070 Analysis of the retinal gene expression profile after hypoxic preconditioning identifies candidate genes for neuroprotection Markus Thiersch, Wolfgang Raffelsberger, Rico Frigg, Marijana Samardzija, Andreas Wenzel, Olivier Poch, and Christian Grimm PMCID: PMC2270833 Gene expression patterns within cell lines are predictive of chemosensitivity Brian Z Ring, Stella Chang, L Winston Ring, Robert S Seitz, and Douglas T Ross PMCID: PMC2263043 Mobile phone radiation might alter protein expression in human skin Anu Karinen, Sirpa Heinävaara, Reetta Nylund, and Dariusz Leszczynski PMCID: PMC2258283 Effect of thyroid hormone concentration on the transcriptional response underlying induced metamorphosis in the Mexican axolotl (Ambystoma) Robert B Page, Stephen R Voss, Amy K Samuels, Jeramiah J Smith, Srikrishna Putta, and Christopher K Beachy PMCID: PMC2262897 Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor Emma Laing, Khushwant Sidhu, and Simon J Hubbard PMCID: PMC2276206 Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci Giovanna Vaccarelli, Maria C Miccoli, Rachele Antonacci, Graziano Pesole, and Salvatrice Ciccarese PMCID: PMC2270265 Molecular characterization, tissue expression and sequence variability of the barramundi (Lates calcarifer) myostatin gene Christian De Santis, Brad S Evans, Carolyn Smith-Keune, and Dean R Jerry PMCID: PMC2292173 Circadian regulation of a limited set of conserved microRNAs in Drosophila Maocheng Yang, Jung-Eun Lee, Richard W Padgett, and Isaac Edery PMCID: PMC2263044 Genome-wide analysis of the rice and arabidopsis non-specific lipid transfer protein (nsLtp) gene families and identification of wheat nsLtp genes by EST data mining Freddy Boutrot, Nathalie Chantret, and Marie-Françoise Gautier PMCID: PMC2277411 A Bayesian Change point model for differential gene expression patterns of the DosR regulon of Mycobacterium tuberculosis Yi Zhang, Kim A Hatch, Lorenz Wernisch, and Joanna Bacon PMCID: PMC2275270 Dissecting microregulation of a master regulatory network Amit U Sinha, Vivek Kaimal, Jing Chen, and Anil G Jegga PMCID: PMC2289817 Developmentally regulated expression, alternative splicing and distinct sub-groupings in members of the Schistosoma mansoni venom allergen-like (SmVAL) gene family Iain W Chalmers, Andrew J McArdle, Richard MR Coulson, Marissa A Wagner, Ralf Schmid, Hirohisa Hirai, and Karl F Hoffmann PMCID: PMC2270263 Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta Naoki Osada, Katsuyuki Hashimoto, Yosuke Kameoka, Makoto Hirata, Reiko Tanuma, Yasuhiro Uno, Itsuro Inoue, Munetomo Hida, Yutaka Suzuki, Sumio Sugano, Keiji Terao, Jun Kusuda, and Ichiro Takahashi PMCID: PMC2287170 Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues Tatiana Popova, Detlev Mennerich, Andreas Weith, and Karsten Quast PMCID: PMC2268927 Links between core promoter and basic gene features influence gene expression Sandra Moshonov, Rofa Elfakess, Michal Golan-Mashiach, Hadar Sinvani, and Rivka Dikstein PMCID: PMC2279122 Gene conversion in the rice genome Shuqing Xu, Terry Clark, Hongkun Zheng, Søren Vang, Ruiqiang Li, Gane Ka-Shu Wong, Jun Wang, and Xiaoguang Zheng PMCID: PMC2277409 Annotation of expressed sequence tags for the East African cichlid fish Astatotilapia burtoni and evolutionary analyses of cichlid ORFs Walter Salzburger, Susan CP Renn, Dirk Steinke, Ingo Braasch, Hans A Hofmann, and Axel Meyer PMCID: PMC2279125 Coral life history and symbiosis: Functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata Jodi A Schwarz, Peter B Brokstein, Christian Voolstra, Astrid Y Terry, David J Miller, Alina M Szmant, Mary Alice Coffroth, and Mónica Medina PMCID: PMC2291459 A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy Xiangrong Kong, Valeria Mas, and Kellie J Archer PMCID: PMC2276496 Global gene expression analysis of early response to chemotherapy treatment in ovarian cancer spheroids Sylvain L'Espérance, Magdalena Bachvarova, Bernard Tetu, Anne-Marie Mes-Masson, and Dimcho Bachvarov PMCID: PMC2279123 New insights into the Saccharomyces cerevisiae fermentation switch: Dynamic transcriptional response to anaerobicity and glucose-excess Joost van den Brink, Pascale Daran-Lapujade, Jack T Pronk, and Johannes H de Winde PMCID: PMC2292174 Gene array and real time PCR analysis of the adrenal sensitivity to adrenocorticotropic hormone in pig Dominique Hazard, Laurence Liaubet, Magali SanCristobal, and Pierre Mormède PMCID: PMC2289818 Protein abundance profiling of the Escherichia coli cytosol Yasushi Ishihama, Thorsten Schmidt, Juri Rappsilber, Matthias Mann, F Ulrich Hartl, Michael J Kerner, and Dmitrij Frishman PMCID: PMC2292177 Sequencing and analysis of the gene-rich space of cowpea Michael P Timko, Paul J Rushton, Thomas W Laudeman, Marta T Bokowiec, Edmond Chipumuro, Foo Cheung, Christopher D Town, and Xianfeng Chen PMCID: PMC2279124 Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes Jon Bohlin, Eystein Skjerve, and David W Ussery PMCID: PMC2289816 Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array Sayan Das, Prasanna R Bhat, Chinta Sudhakar, Jeffrey D Ehlers, Steve Wanamaker, Philip A Roberts, Xinping Cui, and Timothy J Close PMCID: PMC2270837 An integrated genetic and physical map of homoeologous chromosomes 12 and 26 in Upland cotton (G. hirsutum L.) Zhanyou Xu, Russell J Kohel, Guoli Song, Jaemin Cho, Jing Yu, Shuxun Yu, Jeffrey Tomkins, and John Z Yu PMCID: PMC2270834 Altered expression patterns of lipid metabolism genes in an animal model of HCV core-related, nonobese, modest hepatic steatosis Ming-Ling Chang, Chau-Ting Yeh, Jeng-Chang Chen, Chau-Chun Huang, Shi-Ming Lin, I-Shyan Sheen, Dar-In Tai, Chia-Ming Chu, Wei-Pin Lin, Ming-Yu Chang, Chun-Kai Liang, Cheng-Tang Chiu, and Deng-Yn Lin PMCID: PMC2287171 Search for the genes involved in oocyte maturation and early embryo development in the hen Sebastien Elis, Florence Batellier, Isabelle Couty, Sandrine Balzergue, Marie-Laure Martin-Magniette, Philippe Monget, Elisabeth Blesbois, and Marina S Govoroun PMCID: PMC2322995 Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica Zuly E Parra, Michelle L Baker, Jennifer Hathaway, April M Lopez, Jonathan Trujillo, Alana Sharp, and Robert D Miller PMCID: PMC2275272 Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions Katsuhiko Murakami, Tadashi Imanishi, Takashi Gojobori, and Kenta Nakai PMCID: PMC2292176 Comparative mapping of Brassica juncea and Arabidopsis thaliana using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes Priya Panjabi, Arun Jagannath, Naveen C Bisht, K Lakshmi Padmaja, Sarita Sharma, Vibha Gupta, Akshay K Pradhan, and Deepak Pental PMCID: PMC2277410 Comprehensive transcriptional profiling of prion infection in mouse models reveals networks of responsive genes Garrett Sorensen, Sarah Medina, Debra Parchaliuk, Clark Phillipson, Catherine Robertson, and Stephanie A Booth PMCID: PMC2294129 Arsenic-induced changes in the gene expression of lung epithelial L2 cells: implications in carcinogenesis Tisha Posey, Tingting Weng, Zhongming Chen, Narendranath R Chintagari, Pengcheng Wang, Nili Jin, Heidi Stricker, and Lin Liu PMCID: PMC2292705 Annotated ESTs from various tissues of the brown planthopper Nilaparvata lugens: A genomic resource for studying agricultural pests Hiroaki Noda, Sawako Kawai, Yoko Koizumi, Kageaki Matsui, Qiang Zhang, Shigetoyo Furukawa, Michihiko Shimomura, and Kazuei Mita PMCID: PMC2311293 LEA (Late Embryogenesis Abundant) proteins and their encoding genes in Arabidopsis thaliana Michaela Hundertmark and Dirk K Hincha PMCID: PMC2292704 The adaptive evolution of the mammalian mitochondrial genome Rute R da Fonseca, Warren E Johnson, Stephen J O'Brien, Maria João Ramos, and Agostinho Antunes PMCID: PMC2375446 Evolution of the hepcidin gene in primates Ludovica Segat, Alessandra Pontillo, Michele Milanese, Alessandro Tossi, and Sergio Crovella PMCID: PMC2294130 Transcriptome analysis of grain development in hexaploid wheat Yongfang Wan, Rebecca L Poole, Alison K Huttly, Claudia Toscano-Underwood, Kevin Feeney, Sue Welham, Mike J Gooding, Clare Mills, Keith J Edwards, Peter R Shewry, and Rowan AC Mitchell PMCID: PMC2292175 Bioinformatics prediction of overlapping frameshifted translation products in mammalian transcripts Sebastien Ribrioux, Adrian Brüngger, Birgit Baumgarten, Klaus Seuwen, and Markus R John PMCID: PMC2329644 Transcriptomic analysis of the dialogue between Pseudorabies virus and porcine epithelial cells during infection Laurence Flori, Claire Rogel-Gaillard, Marielle Cochet, Gaetan Lemonnier, Karine Hugot, Patrick Chardon, Stéphane Robin, and François Lefèvre PMCID: PMC2335119 Can subtle changes in gene expression be consistently detected with different microarray platforms? Paola Pedotti, Peter AC 't Hoen, Erno Vreugdenhil, Geert J Schenk, Rolf HAM Vossen, Yavuz Ariyurek, Mattias de Hollander, Rowan Kuiper, Gertjan JB van Ommen, Johan T den Dunnen, Judith M Boer, and Renée X de Menezes PMCID: PMC2335120 Analyzing stochastic transcription to elucidate the nucleoid's organization Alessandra Riva, Anne-Sophie Carpentier, Frédérique Barloy-Hubler, Angélique Chéron, and Alain Hénaut PMCID: PMC2270832 Salmon louse (Lepeophtheirus salmonis) transcriptomes during post molting maturation and egg production, revealed using EST-sequencing and microarray analysis Christiane Eichner, Petter Frost, Bjarte Dysvik, Inge Jonassen, Bjørn Kristiansen, and Frank Nilsen PMCID: PMC2329643 Evolution of hedgehog and hedgehog-related genes, their origin from Hog proteins in ancestral eukaryotes and discovery of a novel Hint motif Thomas R Bürglin PMCID: PMC2362128 Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria Abel D González Pérez, Evelyn González González, Vladimir Espinosa Angarica, Ana Tereza R Vasconcelos, and Julio Collado-Vides PMCID: PMC2329645 Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping Marine Douaud, Katia Fève, Marie Gerus, Valérie Fillon, Suzanne Bardes, David Gourichon, Deborah A Dawson, Olivier Hanotte, Terry Burke, Florence Vignoles, Mireille Morisson, Michèle Tixier-Boichard, Alain Vignal, and Frédérique Pitel PMCID: PMC2275740 The Songbird Neurogenomics (SoNG) Initiative: Community-based tools and strategies for study of brain gene function and evolution Kirstin Replogle, Arthur P Arnold, Gregory F Ball, Mark Band, Staffan Bensch, Eliot A Brenowitz, Shu Dong, Jenny Drnevich, Margaret Ferris, Julia M George, George Gong, Dennis Hasselquist, Alvaro G Hernandez, Ryan Kim, Harris A Lewin, Lei Liu, Peter V Lovell, Claudio V Mello, Sara Naurin, Sandra Rodriguez-Zas, Jyothi Thimmapuram, Juli Wade, and David F Clayton PMCID: PMC2329646 Organization and differential expression of the GACA/GATA tagged somatic and spermatozoal transcriptomes in Buffalo Bubalus bubalis Jyoti Srivastava, Sanjay Premi, Sudhir Kumar, and Sher Ali PMCID: PMC2346481 An indicator of cancer: downregulation of Monoamine Oxidase-A in multiple organs and species Leszek A Rybaczyk, Meredith J Bashaw, Dorothy R Pathak, and Kun Huang PMCID: PMC2311292 Comparative genomic analysis of Mycobacterium avium subspecies obtained from multiple host species Michael L Paustian, Xiaochun Zhu, Srinand Sreevatsan, Suelee Robbe-Austerman, Vivek Kapur, and John P Bannantine PMCID: PMC2323391 Estimating the extent of horizontal gene transfer in metagenomic sequences Javier Tamames and Andrés Moya PMCID: PMC2324111 Topological comparison of methods for predicting transcriptional cooperativity in yeast Daniel Aguilar and Baldo Oliva PMCID: PMC2315657 Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: Focus on point miscalls and artefactual expansions Mark J Mandel, Eric V Stabb, and Edward G Ruby PMCID: PMC2330054 Construction of a BAC library and mapping BAC clones to the linkage map of Barramundi, Lates calcarifer Chun Ming Wang, Loong Chueng Lo, Felicia Feng, Ping Gong, Jian Li, Ze Yuan Zhu, Grace Lin, and Gen Hua Yue PMCID: PMC2329641 Comparative analysis of the acute response of the trout, O. mykiss, head kidney to in vivo challenge with virulent and attenuated infectious hematopoietic necrosis virus and LPS-induced inflammation Simon MacKenzie, Joan C Balasch, Beatriz Novoa, Laia Ribas, Nerea Roher, Aleksei Krasnov, and Antonio Figueras PMCID: PMC2291046 cDNA-AFLP analysis of plant and pathogen genes expressed in grapevine infected with Plasmopara viticola Marianna Polesani, Filomena Desario, Alberto Ferrarini, Anita Zamboni, Mario Pezzotti, Andreas Kortekamp, and Annalisa Polverari PMCID: PMC2292706 Identification and characterization of PhoP regulon members in Yersinia pestis biovar Microtus Yingli Li, He Gao, Long Qin, Bei Li, Yanping Han, Zhaobiao Guo, Yajun Song, Junhui Zhai, Zongmin Du, Xiaoyi Wang, Dongsheng Zhou, and Ruifu Yang PMCID: PMC2322996 Impaired barrier function by dietary fructo-oligosaccharides (FOS) in rats is accompanied by increased colonic mitochondrial gene expression Wendy Rodenburg, Jaap Keijer, Evelien Kramer, Carolien Vink, Roelof van der Meer, and Ingeborg MJ Bovee-Oudenhoven PMCID: PMC2311291 A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1 Christof Francke, Robert Kerkhoven, Michiel Wels, and Roland J Siezen PMCID: PMC2329647 Brain gene expression profiles of Cln1 and Cln5 deficient mice unravels common molecular pathways underlying neuronal degeneration in NCL diseases Carina von Schantz, Juha Saharinen, Outi Kopra, Jonathan D Cooper, Massimiliano Gentile, Iiris Hovatta, Leena Peltonen, and Anu Jalanko PMCID: PMC2323392 Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens Amy J Powell, Gavin C Conant, Douglas E Brown, Ignazio Carbone, and Ralph A Dean PMCID: PMC2330156 The unique genomic properties of sex-biased genes: Insights from avian microarray data Judith E Mank, Lina Hultin-Rosenberg, Matthew T Webster, and Hans Ellegren PMCID: PMC2294128 Losing helena: The extinction of a drosophila line-like element Rita Rebollo, Emmanuelle Lerat, Liliana Lopez Kleine, Christian Biémont, and Cristina Vieira PMCID: PMC2330053 An original SERPINA3 gene cluster: Elucidation of genomic organization and gene expression in the Bos taurus 21q24 region Patrick Pelissier, Didier Delourme, Agnes Germot, Xavier Blanchet, Samira Becila, Abderrahman Maftah, Hubert Leveziel, Ahmed Ouali, and Laure Bremaud PMCID: PMC2373789 Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs Hirokazu Chiba, Riu Yamashita, Kengo Kinoshita, and Kenta Nakai PMCID: PMC2335122 A novel method of differential gene expression analysis using multiple cDNA libraries applied to the identification of tumour endothelial genes John MJ Herbert, Dov Stekel, Sharon Sanderson, Victoria L Heath, and Roy Bicknell PMCID: PMC2346479 Comparative transcriptome analysis of Arabidopsis thaliana infested by diamond back moth (Plutella xylostella) larvae reveals signatures of stress response, secondary metabolism, and signalling Jürgen Ehlting, Sunita G Chowrira, Nathalie Mattheus, Dana S Aeschliman, Gen-Ichiro Arimura, and Jörg Bohlmann PMCID: PMC2375910 Detailed characterization of the mouse embryonic stem cell transcriptome reveals novel genes and intergenic splicing associated with pluripotency Galih Kunarso, Kee-Yew Wong, Lawrence W Stanton, and Leonard Lipovich PMCID: PMC2375908 Microarray analysis of E9.5 reduced folate carrier (RFC1; Slc19a1) knockout embryos reveals altered expression of genes in the cubilin-megalin multiligand endocytic receptor complex Janee Gelineau-van Waes, Joyce R Maddox, Lynette M Smith, Michael van Waes, Justin Wilberding, James D Eudy, Linda K Bauer, and Richard H Finnell PMCID: PMC2383917 Hidden layers of human small RNAs Hideya Kawaji, Mari Nakamura, Yukari Takahashi, Albin Sandelin, Shintaro Katayama, Shiro Fukuda, Carsten O Daub, Chikatoshi Kai, Jun Kawai, Jun Yasuda, Piero Carninci, and Yoshihide Hayashizaki PMCID: PMC2359750 Analyses of murine GBP homology clusters based on in silico, in vitro and in vivo studies Alexandra Kresse, Carolin Konermann, Daniel Degrandi, Cornelia Beuter-Gunia, Jan Wuerthner, Klaus Pfeffer, and Sandra Beer PMCID: PMC2387175 Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes Stefanie Schindler, Karol Szafranski, Michael Hiller, Gul Shad Ali, Saiprasad G Palusa, Rolf Backofen, Matthias Platzer, and Anireddy SN Reddy PMCID: PMC2375911 Novel and nodulation-regulated microRNAs in soybean roots Senthil Subramanian, Yan Fu, Ramanjulu Sunkar, W Brad Barbazuk, Jian-Kang Zhu, and Oliver Yu PMCID: PMC2335117 Structure and expression pattern of Oct4 gene are conserved in vole Microtus rossiaemeridionalis Sergey P Medvedev, Alexander I Shevchenko, Eugene A Elisaphenko, Tatyana B Nesterova, Neil Brockdorff, and Suren M Zakian PMCID: PMC2410140 Analysis of Aspergillus nidulans metabolism at the genome-scale Helga David, İlknur Ş Özçelik, Gerald Hofmann, and Jens Nielsen PMCID: PMC2386489 Complex evolution of the DAL5 transporter family Linda Hellborg, Megan Woolfit, Mattias Arthursson-Hellborg, and Jure Piškur PMCID: PMC2329640 The human ABC transporter pseudogene family: Evidence for transcription and gene-pseudogene interference Armin P Piehler, Marit Hellum, Jürgen J Wenzel, Ellen Kaminski, Kari Bente Foss Haug, Peter Kierulf, and Wolfgang E Kaminski PMCID: PMC2329642 Gene expression pattern of functional neuronal cells derived from human bone marrow mesenchymal stromal cells Tatiana Tondreau, Marielle Dejeneffe, Nathalie Meuleman, Basile Stamatopoulos, Alain Delforge, Philippe Martiat, Dominique Bron, and Laurence Lagneaux PMCID: PMC2358905 Genome-wide search reveals a novel GacA-regulated small RNA in Pseudomonas species Nicolas González, Stephan Heeb, Claudio Valverde, Elisabeth Kay, Cornelia Reimmann, Thomas Junier, and Dieter Haas PMCID: PMC2375449 Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution Darren K Griffin, Lindsay B Robertson, Helen G Tempest, Alain Vignal, Valérie Fillon, Richard PMA Crooijmans, Martien AM Groenen, Svetlana Deryusheva, Elena Gaginskaya, Wilfrid Carré, David Waddington, Richard Talbot, Martin Völker, Julio S Masabanda, and Dave W Burt PMCID: PMC2375447 Overlapping genes in the human and mouse genomes Chaitanya R Sanna, Wen-Hsiung Li, and Liqing Zhang PMCID: PMC2335118 Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli Anders Ståhlberg, Karin Elbing, José Manuel Andrade-Garda, Björn Sjögreen, Amin Forootan, and Mikael Kubista PMCID: PMC2335116 Transcriptional regulation by Poly(ADP-ribose) polymerase-1 during T cell activation Luis Saenz, Juan J Lozano, Rut Valdor, Alberto Baroja-Mazo, Pablo Ramirez, Pascual Parrilla, Pedro Aparicio, Lauro Sumoy, and José Yélamos PMCID: PMC2375913 How many human genes can be defined as housekeeping with current expression data? Jiang Zhu, Fuhong He, Shuhui Song, Jing Wang, and Jun Yu PMCID: PMC2396180 Transcriptome architecture across tissues in the pig André LJ Ferraz, Ana Ojeda, Manel López-Béjar, Lana T Fernandes, Anna Castelló, Josep M Folch, and Miguel Pérez-Enciso PMCID: PMC2335121 Non-random retention of protein-coding overlapping genes in Metazoa Giulia Soldà, Mikita Suyama, Paride Pelucchi, Silvia Boi, Alessandro Guffanti, Ermanno Rizzi, Peer Bork, Maria Luisa Tenchini, and Francesca D Ciccarelli PMCID: PMC2330155 Marked variation in predicted and observed variability of tandem repeat loci across the human genome Colm T O'Dushlaine and Denis C Shields PMCID: PMC2364633 Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening Paolo Bagnaresi, Anna Moschella, Ottavio Beretta, Federico Vitulli, Paolo Ranalli, and Pierdomenico Perata PMCID: PMC2358903 Major histocompatibility complex (Mhc) class Ib gene duplications, organization and expression patterns in mouse strain C57BL/6 Masato Ohtsuka, Hidetoshi Inoko, Jerzy K Kulski, and Shinichi Yoshimura PMCID: PMC2375909 Gene expression analyses in Atlantic salmon challenged with infectious salmon anemia virus reveal differences between individuals with early, intermediate and late mortality Sven Martin Jørgensen, Sergey Afanasyev, and Aleksei Krasnov PMCID: PMC2387173 Genome-wide subcellular localization of putative outer membrane and extracellular proteins in Leptospira interrogans serovar Lai genome using bioinformatics approaches Wasna Viratyosin, Supawadee Ingsriswang, Eakasit Pacharawongsakda, and Prasit Palittapongarnpim PMCID: PMC2387172 A systematic survey in Arabidopsis thaliana of transcription factors that modulate circadian parameters Shigeru Hanano, Ralf Stracke, Marc Jakoby, Thomas Merkle, Malgorzata A Domagalska, Bernd Weisshaar, and Seth J Davis PMCID: PMC2410138 Deep Sequencing of Chicken microRNAs Joan Burnside, Ming Ouyang, Amy Anderson, Erin Bernberg, Cheng Lu, Blake C Meyers, Pamela J Green, Milos Markis, Grace Isaacs, Emily Huang, and Robin W Morgan PMCID: PMC2375912 Prediction and analysis of nucleosome exclusion regions in the human genome Ahmed Radwan, Akmal Younis, Peter Luykx, and Sawsan Khuri PMCID: PMC2386137 Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel Mehar S Khatkar, Frank W Nicholas, Andrew R Collins, Kyall R Zenger, Julie AL Cavanagh, Wes Barris, Robert D Schnabel, Jeremy F Taylor, and Herman W Raadsma PMCID: PMC2386485 A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data Hua Li, Dongxiao Zhu, and Malcolm Cook PMCID: PMC2397416 Mining small RNA structure elements in untranslated regions of human and mouse mRNAs using structure-based alignment Mugdha Khaladkar, Jianghui Liu, Dongrong Wen, Jason TL Wang, and Bin Tian PMCID: PMC2413145 Burkholderia pseudomallei genome plasticity associated with genomic island variation Sarinna Tumapa, Matthew TG Holden, Mongkol Vesaratchavest, Vanaporn Wuthiekanun, Direk Limmathurotsakul, Wirongrong Chierakul, Edward J Feil, Bart J Currie, Nicholas PJ Day, William C Nierman, and Sharon J Peacock PMCID: PMC2386483 Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse Tao Peng, Chenghai Xue, Jianning Bi, Tingting Li, Xiaowo Wang, Xuegong Zhang, and Yanda Li PMCID: PMC2432081 Importance of the interferon-α system in murine large intestine indicated by microarray analysis of commensal bacteria-induced immunological changes Kaori Munakata, Masahiro Yamamoto, Naoko Anjiki, Mitsue Nishiyama, Sachiko Imamura, Seiichi Iizuka, Kiyoe Takashima, Atsushi Ishige, Kyoji Hioki, Yasuyuki Ohnishi, and Kenji Watanabe PMCID: PMC2408602 Multiple expressed MHC class II loci in salmonids; details of one non-classical region in Atlantic salmon (Salmo salar) Håvard Harstad, Morten F Lukacs, Hege G Bakke, and Unni Grimholt PMCID: PMC2386828 Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots Elke Mangelsen, Joachim Kilian, Kenneth W Berendzen, Üner H Kolukisaoglu, Klaus Harter, Christer Jansson, and Dierk Wanke PMCID: PMC2390551 The abundant extrachromosomal DNA content of the Spiroplasma citri GII3-3X genome Colette Saillard, Patricia Carle, Sybille Duret-Nurbel, Raphaël Henri, Nabil Killiny, Sébastien Carrère, Jérome Gouzy, Joseph-Marie Bové, Joël Renaudin, and Xavier Foissac PMCID: PMC2386487 ERK1 and ERK2 MAPK are key regulators of distinct gene sets in zebrafish embryogenesis SF Gabby Krens, Maximiliano Corredor-Adámez, Shuning He, B Ewa Snaar-Jagalska, and Herman P Spaink PMCID: PMC2390552 Transcriptome analysis identifies pathways associated with enhanced maternal performance in QSi5 mice Palaniappan Ramanathan, Ian C Martin, Margaret Gardiner-Garden, Peter C Thomson, Rosanne M Taylor, Christopher J Ormandy, Christopher Moran, and Peter Williamson PMCID: PMC2386486 Differences in mtDNA haplogroup distribution among 3 Jewish populations alter susceptibility to T2DM complications Jeanette Feder, Ilana Blech, Ofer Ovadia, Shirly Amar, Julio Wainstein, Itamar Raz, Sarah Dadon, Dan E Arking, Benjamin Glaser, and Dan Mishmar PMCID: PMC2386827 Altered gene expression in the superior temporal gyrus in schizophrenia Nikola A Bowden, Rodney J Scott, and Paul A Tooney PMCID: PMC2386488 Genome sequence surveys of Brachiola algerae and Edhazardia aedis reveal microsporidia with low gene densities Bryony AP Williams, Renny CH Lee, James J Becnel, Louis M Weiss, Naomi M Fast, and Patrick J Keeling PMCID: PMC2387174 Identification of novel vascular markers through gene expression profiling of tumor-derived endothelium Carmen Ghilardi, Giovanna Chiorino, Romina Dossi, Zsuzsanna Nagy, Raffaella Giavazzi, and MariaRosa Bani PMCID: PMC2410137 Comparative analysis of sequence features involved in the recognition of tandem splice sites Ralf Bortfeldt, Stefanie Schindler, Karol Szafranski, Stefan Schuster, and Dirk Holste PMCID: PMC2423196 Stage-specific gene expression during urediniospore germination in Puccinia striiformis f. sp tritici Yonghong Zhang, Zhipeng Qu, Wenming Zheng, Bo Liu, Xiaojie Wang, Xiaodan Xue, Liangsheng Xu, Lili Huang, Qingmei Han, Jie Zhao, and Zhensheng Kang PMCID: PMC2386484 Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A Steven L Salzberg, Daniel D Sommer, Michael C Schatz, Adam M Phillippy, Pablo D Rabinowicz, Seiji Tsuge, Ayako Furutani, Hirokazu Ochiai, Arthur L Delcher, David Kelley, Ramana Madupu, Daniela Puiu, Diana Radune, Martin Shumway, Cole Trapnell, Gudlur Aparna, Gopaljee Jha, Alok Pandey, Prabhu B Patil, Hiromichi Ishihara, Damien F Meyer, Boris Szurek, Valerie Verdier, Ralf Koebnik, J Maxwell Dow, Robert P Ryan, Hisae Hirata, Shinji Tsuyumu, Sang Won Lee, Pamela C Ronald, Ramesh V Sonti, Marie-Anne Van Sluys, Jan E Leach, Frank F White, and Adam J Bogdanove PMCID: PMC2432079 Genomic imprinting of IGF2 in marsupials is methylation dependent Betty R Lawton, Benjamin R Carone, Craig J Obergfell, Gianni C Ferreri, Christina M Gondolphi, John L VandeBerg, Ikhide Imumorin, Rachel J O'Neill, and Michael J O'Neill PMCID: PMC2386826 Circadian genomics of the chick pineal gland in vitro Stephen P Karaganis, Vinod Kumar, Phillip D Beremand, Michael J Bailey, Terry L Thomas, and Vincent M Cassone PMCID: PMC2405806 Analysis of the distribution of functionally relevant rare codons Michael Widmann, Marie Clairo, Jürgen Dippon, and Jürgen Pleiss PMCID: PMC2391168 In vivo gene expression profiling of human intestinal epithelial cells: analysis by laser microdissection of formalin fixed tissues Michael D George, Jan Wehkamp, Robert J Kays, Christian M Leutenegger, Sadiah Sabir, Irina Grishina, Satya Dandekar, and Charles L Bevins PMCID: PMC2394537 Genomics of an extreme psychrophile, Psychromonas ingrahamii Monica Riley, James T Staley, Antoine Danchin, Ting Zhang Wang, Thomas S Brettin, Loren J Hauser, Miriam L Land, and Linda S Thompson PMCID: PMC2405808 Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES293 (West Pacific) strains Rose Ann Cattolico, Michael A Jacobs, Yang Zhou, Jean Chang, Melinda Duplessis, Terry Lybrand, John McKay, Han Chuan Ong, Elizabeth Sims, and Gabrielle Rocap PMCID: PMC2410131 Loss of p24 function in Drosophila melanogaster causes a stress response and increased levels of NF-κB-regulated gene products Kara A Boltz and Ginger E Carney PMCID: PMC2396179 Genomic and bioinformatics analysis of human adenovirus type 37: New insights into corneal tropism Christopher M Robinson, Fatemeh Shariati, Allison F Gillaspy, David W Dyer, and James Chodosh PMCID: PMC2397415 A universal DNA mini-barcode for biodiversity analysis Isabelle Meusnier, Gregory AC Singer, Jean-François Landry, Donal A Hickey, Paul DN Hebert, and Mehrdad Hajibabaei PMCID: PMC2396642 Complete Sequence and Analysis of the Mitochondrial Genome of Hemiselmis andersenii CCMP644 (Cryptophyceae) Eunsoo Kim, Christopher E Lane, Bruce A Curtis, Catherine Kozera, Sharen Bowman, and John M Archibald PMCID: PMC2397417 Global analysis of aberrant pre-mRNA splicing in glioblastoma using exon expression arrays Hannah C Cheung, Keith A Baggerly, Spiridon Tsavachidis, Linda L Bachinski, Valerie L Neubauer, Tamara J Nixon, Kenneth D Aldape, Gilbert J Cote, and Ralf Krahe PMCID: PMC2410136 Biocomputational prediction of small non-coding RNAs in Streptomyces Josef Pánek, Jan Bobek, Karel Mikulík, Marek Basler, and Jiří Vohradský PMCID: PMC2422843 Expansion of signaling genes for adaptive immune system evolution in early vertebrates Kinya Okada and Kiyoshi Asai PMCID: PMC2391169 How Athila retrotransposons survive in the Arabidopsis genome Antonio Marco and Ignacio Marín PMCID: PMC2410132 Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling Arthur G Hunt, Ruqiang Xu, Balasubrahmanyam Addepalli, Suryadevara Rao, Kevin P Forbes, Lisa R Meeks, Denghui Xing, Min Mo, Hongwei Zhao, Amrita Bandyopadhyay, Lavanya Dampanaboina, Amanda Marion, Carol Von Lanken, and Qingshun Quinn Li PMCID: PMC2391170 Extensive expansion and diversification of the chemokine gene family in zebrafish: Identification of a novel chemokine subfamily CX Hisayuki Nomiyama, Kunio Hieshima, Naoki Osada, Yoko Kato-Unoki, Kaori Otsuka-Ono, Sumio Takegawa, Toshiaki Izawa, Akio Yoshizawa, Yutaka Kikuchi, Sumio Tanase, Retsu Miura, Jun Kusuda, Miki Nakao, and Osamu Yoshie PMCID: PMC2416438 A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers Thomas Moen, Ben Hayes, Matthew Baranski, Paul R Berg, Sissel Kjøglum, Ben F Koop, Willie S Davidson, Stig W Omholt, and Sigbjørn Lien PMCID: PMC2405805 The complete mitochondrial genomes for three Toxocara species of human and animal health significance Ming-Wei Li, Rui-Qing Lin, Hui-Qun Song, Xiang-Yun Wu, and Xing-Quan Zhu PMCID: PMC2396643 Comparative analysis of transcriptional profiling of CD3+, CD4+ and CD8+ T cells identifies novel immune response players in T-Cell activation Min Wang, Dirk Windgassen, and Eleftherios T Papoutsakis PMCID: PMC2396644 Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA Nalini Polavarapu, Leonardo Mariño-Ramírez, David Landsman, John F McDonald, and I King Jordan PMCID: PMC2397414 SNP discovery and molecular evolution in Anopheles gambiae, with special emphasis on innate immune system Anna Cohuet, Sujatha Krishnakumar, Frédéric Simard, Isabelle Morlais, Anastasios Koutsos, Didier Fontenille, Michael Mindrinos, and Fotis C Kafatos PMCID: PMC2405807 Sequence features of HLA-DRB1 locus define putative basis for gene conversion and point mutations Jenny von Salomé and Jyrki P Kukkonen PMCID: PMC2408603 Photorhabdus luminescens genes induced upon insect infection Anna Münch, Lavinia Stingl, Kirsten Jung, and Ralf Heermann PMCID: PMC2422844 PPARalpha-mediated effects of dietary lipids on intestinal barrier gene expression Heleen M de Vogel-van den Bosch, Meike Bünger, Philip J de Groot, Hanneke Bosch-Vermeulen, Guido JEJ Hooiveld, and Michael Müller PMCID: PMC2408604 Genomic analysis of post-mating changes in the honey bee queen (Apis mellifera) Sarah D Kocher, Freddie-Jeanne Richard, David R Tarpy, and Christina M Grozinger PMCID: PMC2413142 Insight into the sialome of the castor bean tick, Ixodes ricinus Jindřich Chmelař, Jennifer M Anderson, Jianbing Mu, Ryan C Jochim, Jesus G Valenzuela, and Jan Kopecký PMCID: PMC2410133 Uncovering rate variation of lateral gene transfer during bacterial genome evolution Weilong Hao and G Brian Golding PMCID: PMC2426709 MicroRNA-encoding long non-coding RNAs Shunmin He, Hua Su, Changning Liu, Geir Skogerbø, Housheng He, Dandan He, Xiaopeng Zhu, Tao Liu, Yi Zhao, and Runsheng Chen PMCID: PMC2410135 A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS) Hana Šimková, Jan Šafář, Pavla Suchánková, Pavlína Kovářová, Jan Bartoš, Marie Kubaláková, Jaroslav Janda, Jarmila Číhalíková, Rohit Mago, Tamas Lelley, and Jaroslav Doležel PMCID: PMC2410134 Simultaneous gene expression profiling in human macrophages infected with Leishmania major parasites using SAGE Fatma Z Guerfali, Dhafer Laouini, Lamia Guizani-Tabbane, Florence Ottones, Khadija Ben-Aissa, Alia Benkahla, Laurent Manchon, David Piquemal, Sondos Smandi, Ons Mghirbi, Thérèse Commes, Jacques Marti, and Koussay Dellagi PMCID: PMC2430024 Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen Sherene Loi, Benjamin Haibe-Kains, Christine Desmedt, Pratyaksha Wirapati, Françoise Lallemand, Andrew M Tutt, Cheryl Gillet, Paul Ellis, Kenneth Ryder, James F Reid, Maria G Daidone, Marco A Pierotti, Els MJJ Berns, Maurice PHM Jansen, John A Foekens, Mauro Delorenzi, Gianluca Bontempi, Martine J Piccart, and Christos Sotiriou PMCID: PMC2423197 Gene expression analysis of embryonic stem cells expressing VE-cadherin (CD144) during endothelial differentiation Vesna Nikolova-Krstevski, Manoj Bhasin, Hasan H Otu, Towia Libermann, and Peter Oettgen PMCID: PMC2440556 Evolutionary origin of regulatory regions of retrogenes in Drosophila Yongsheng Bai, Claudio Casola, and Esther Betrán PMCID: PMC2413143 Gene discovery in an invasive tephritid model pest species, the Mediterranean fruit fly, Ceratitis capitata Ludvik M Gomulski, George Dimopoulos, Zhiyong Xi, Marcelo B Soares, Maria F Bonaldo, Anna R Malacrida, and Giuliano Gasperi PMCID: PMC2427042 Cloning, characterization, and expression of microRNAs from the Asian malaria mosquito, Anopheles stephensi Edward Andrew Mead and Zhijian Tu PMCID: PMC2430712 Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae Wanwipa Vongsangnak, Peter Olsen, Kim Hansen, Steen Krogsgaard, and Jens Nielsen PMCID: PMC2413144 Correlation of mRNA and protein levels: Cell type-specific gene expression of cluster designation antigens in the prostate Laura E Pascal, Lawrence D True, David S Campbell, Eric W Deutsch, Michael Risk, Ilsa M Coleman, Lillian J Eichner, Peter S Nelson, and Alvin Y Liu PMCID: PMC2413246 Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth Ju-Hoon Lee, VN Karamychev, SA Kozyavkin, D Mills, AR Pavlov, NV Pavlova, NN Polouchine, PM Richardson, VV Shakhova, AI Slesarev, B Weimer, and DJ O'Sullivan PMCID: PMC2430713 Identification and characteristics of microRNAs from Bombyx mori Ping-an He, Zuoming Nie, Jianqing Chen, Jian Chen, Zhengbing Lv, Qing Sheng, Songping Zhou, Xiaolian Gao, Lingyin Kong, Xiangfu Wu, Yongfeng Jin, and Yaozhou Zhang PMCID: PMC2435238 Stabilization of the genome of the mismatch repair deficient Mycobacterium tuberculosis by context-dependent codon choice Roger M Wanner, Carolin Güthlein, Burkhard Springer, Erik C Böttger, and Martin Ackermann PMCID: PMC2430213 Relationship between metabolic and genomic diversity in sesame (Sesamum indicum L.) Hernán Laurentin, Astrid Ratzinger, and Petr Karlovsky PMCID: PMC2440766 In silico identification of genes involved in selenium metabolism: evidence for a third selenium utilization trait Yan Zhang, Anton A Turanov, Dolph L Hatfield, and Vadim N Gladyshev PMCID: PMC2432076 Genomic Organization of Zebrafish microRNAs Elizabeth J Thatcher, Jordan Bond, Ima Paydar, and James G Patton PMCID: PMC2427041 Genome-wide gene expression profiling analysis of Leishmania major and Leishmania infantum developmental stages reveals substantial differences between the two species Annie Rochette, Frédéric Raymond, Jean-Michel Ubeda, Martin Smith, Nadine Messier, Sébastien Boisvert, Philippe Rigault, Jacques Corbeil, Marc Ouellette, and Barbara Papadopoulou PMCID: PMC2453527 Pyrosequencing as a method for SNP identification in the rhesus macaque (Macaca mulatta) Jessica A Satkoski, RS Malhi, S Kanthaswamy, RY Tito, VS Malladi, and DG Smith PMCID: PMC2443142 The complete mitochondrial genome sequence of the hydrothermal vent galatheid crab Shinkaia crosnieri (Crustacea: Decapoda: Anomura): A novel arrangement and incomplete tRNA suite Jin-Shu Yang and Wei-Jun Yang PMCID: PMC2442616 Validation of oligoarrays for quantitative exploration of the transcriptome Vigdis Nygaard, Fang Liu, Marit Holden, Winston P Kuo, Jeff Trimarchi, Lucila Ohno-Machado, Connie L Cepko, Arnoldo Frigessi, Ingrid K Glad, Mark A van de Wiel, Eivind Hovig, and Heidi Lyng PMCID: PMC2430212 Smoking-induced gene expression changes in the bronchial airway are reflected in nasal and buccal epithelium Sriram Sridhar, Frank Schembri, Julie Zeskind, Vishal Shah, Adam M Gustafson, Katrina Steiling, Gang Liu, Yves-Martine Dumas, Xiaohui Zhang, Jerome S Brody, Marc E Lenburg, and Avrum Spira PMCID: PMC2435556 Evolution and potential function of fibrinogen-like domains across twelve Drosophila species Sumit Middha and Xinguo Wang PMCID: PMC2429915 Insights and inferences about integron evolution from genomic data Diana R Nemergut, Michael S Robeson, Robert F Kysela, Andrew P Martin, Steven K Schmidt, and Rob Knight PMCID: PMC2426708 Activation of peroxisome proliferator-activated receptor alpha in human peripheral blood mononuclear cells reveals an individual gene expression profile response Mark Bouwens, Lydia A Afman, and Michael Müller PMCID: PMC2430976 The SIDER2 elements, interspersed repeated sequences that populate the Leishmania genomes, constitute subfamilies showing chromosomal proximity relationship Jose M Requena, Cristina Folgueira, Manuel C López, and M Carmen Thomas PMCID: PMC2424063 Developing and applying a gene functional association network for anti-angiogenic kinase inhibitor activity assessment in an angiogenesis co-culture model Yuefeng Chen, Tao Wei, Lei Yan, Frank Lawrence, Hui-Rong Qian, Timothy P Burkholder, James J Starling, Jonathan M Yingling, and Jianyong Shou PMCID: PMC2435557 Genome-wide survey of allele-specific splicing in humans Victoria Nembaware, Bukiwe Lupindo, Katherine Schouest, Charles Spillane, Konrad Scheffler, and Cathal Seoighe PMCID: PMC2427040 Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus Jennifer Owen, B Ann Hedley, Claus Svendsen, Jodie Wren, Martijs J Jonker, Peter K Hankard, Linsey J Lister, Stephen R Stürzenbaum, A John Morgan, David J Spurgeon, Mark L Blaxter, and Peter Kille PMCID: PMC2440553 The RHNumtS compilation: Features and bioinformatics approaches to locate and quantify Human NumtS Daniela Lascaro, Stefano Castellana, Giuseppe Gasparre, Giovanni Romeo, Cecilia Saccone, and Marcella Attimonelli PMCID: PMC2447851 Modelling and measuring single cell RNA expression levels find considerable transcriptional differences among phenotypically identical cells Tatiana Subkhankulova, Michael J Gilchrist, and Frederick J Livesey PMCID: PMC2429916 Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data Alexei A Sharov, Shinji Masui, Lioudmila V Sharova, Yulan Piao, Kazuhiro Aiba, Ryo Matoba, Li Xin, Hitoshi Niwa, and Minoru SH Ko PMCID: PMC2424064 Functional characterization of endogenous siRNA target genes in Caenorhabditis elegans Suvi Asikainen, Liisa Heikkinen, Garry Wong, and Markus Storvik PMCID: PMC2440555 The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571 Kyung-Bum Lee, Philippe De Backer, Toshihiro Aono, Chi-Te Liu, Shino Suzuki, Tadahiro Suzuki, Takakazu Kaneko, Manabu Yamada, Satoshi Tabata, Doris M Kupfer, Fares Z Najar, Graham B Wiley, Bruce Roe, Tim T Binnewies, David W Ussery, Wim D'Haeze, Jeroen Den Herder, Dirk Gevers, Danny Vereecke, Marcelle Holsters, and Hiroshi Oyaizu PMCID: PMC2443382 Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences Wan-Lin Su, Barmak Modrek, Debraj GuhaThakurta, Stephen Edwards, Jyoti K Shah, Amit V Kulkarni, Archie Russell, Eric E Schadt, Jason M Johnson, and John C Castle PMCID: PMC2432077 Highly plastic genome of Microcystis aeruginosa PCC 7806, a ubiquitous toxic freshwater cyanobacterium Lionel Frangeul, Philippe Quillardet, Anne-Marie Castets, Jean-François Humbert, Hans CP Matthijs, Diego Cortez, Andrew Tolonen, Cheng-Cai Zhang, Simonetta Gribaldo, Jan-Christoph Kehr, Yvonne Zilliges, Nadine Ziemert, Sven Becker, Emmanuel Talla, Amel Latifi, Alain Billault, Anthony Lepelletier, Elke Dittmann, Christiane Bouchier, and Nicole Tandeau de Marsac PMCID: PMC2442094 Gene expression in developing watermelon fruit W Patrick Wechter, Amnon Levi, Karen R Harris, Angela R Davis, Zhangjun Fei, Nurit Katzir, James J Giovannoni, Ayelet Salman-Minkov, Alvaro Hernandez, Jyothi Thimmapuram, Yaakov Tadmor, Vitaly Portnoy, and Tova Trebitsh PMCID: PMC2440768 Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes Flavio Mignone, Anna Anselmo, Giacinto Donvito, Giorgio P Maggi, Giorgio Grillo, and Graziano Pesole PMCID: PMC2442843 Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins Muhammad Nauman Aftab, Housheng He, Geir Skogerbø, and Runsheng Chen PMCID: PMC2442092 Transcriptome analysis of Loxosceles laeta (Araneae, Sicariidae) spider venomous gland using expressed sequence tags Matheus de F Fernandes-Pedrosa, Inácio de LM Junqueira-de-Azevedo, Rute M Gonçalves-de-Andrade, Leonardo S Kobashi, Diego D Almeida, Paulo L Ho, and Denise V Tambourgi PMCID: PMC2440767 The first generation of a BAC-based physical map of Brassica rapa Jeong-Hwan Mun, Soo-Jin Kwon, Tae-Jin Yang, Hye-Sun Kim, Beom-Soon Choi, Seunghoon Baek, Jung Sun Kim, Mina Jin, Jin A Kim, Myung-Ho Lim, Soo In Lee, Ho-Il Kim, Hyungtae Kim, Yong Pyo Lim, and Beom-Seok Park PMCID: PMC2432078 The patatin-like lipase family in Gallus gallus Jani Saarela, Gerlinde Jung, Marcela Hermann, Johannes Nimpf, and Wolfgang J Schneider PMCID: PMC2435558 The highest-copy repeats are methylated in the small genome of the early divergent vascular plant Selaginella moellendorffii Agnes P Chan, Admasu Melake-Berhan, Kimberly O'Brien, Stephanie Buckley, Hui Quan, Dan Chen, Matthew Lewis, Jo Ann Banks, and Pablo D Rabinowicz PMCID: PMC2442089 Phenotypic and genetic characterization of a novel phenotype in pigs characterized by juvenile hairlessness and age dependent emphysema Camilla S Bruun, Claus B Jørgensen, Lene Bay, Susanna Cirera, Henrik E Jensen, Páll S Leifsson, Jens Nielsen, Knud Christensen, and Merete Fredholm PMCID: PMC2474626 Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures Jason M Bechtel, Thomas Wittenschlaeger, Trisha Dwyer, Jun Song, Sasi Arunachalam, Sadeesh K Ramakrishnan, Samuel Shepard, and Alexei Fedorov PMCID: PMC2442090 Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories Michael J Boedigheimer, Russell D Wolfinger, Michael B Bass, Pierre R Bushel, Jeff W Chou, Matthew Cooper, J Christopher Corton, Jennifer Fostel, Susan Hester, Janice S Lee, Fenglong Liu, Jie Liu, Hui-Rong Qian, John Quackenbush, Syril Pettit, and Karol L Thompson PMCID: PMC2453529 Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition Wei Zhu, Shu Ouyang, Marina Iovene, Kimberly O'Brien, Hue Vuong, Jiming Jiang, and C Robin Buell PMCID: PMC2442093 Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping François L Luro, Gilles Costantino, Javier Terol, Xavier Argout, Thierry Allario, Patrick Wincker, Manuel Talon, Patrick Ollitrault, and Raphael Morillon PMCID: PMC2435559 Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants Lingkang Huang, Alexandra N Heinloth, Zhao-Bang Zeng, Richard S Paules, and Pierre R Bushel PMCID: PMC2478688 Venezuelan equine encephalitis virus infection causes modulation of inflammatory and immune response genes in mouse brain Anuj Sharma, Bhaskar Bhattacharya, Raj K Puri, and Radha K Maheshwari PMCID: PMC2440554 Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae): Unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer Jean-Simon Brouard, Christian Otis, Claude Lemieux, and Monique Turmel PMCID: PMC2442088 Genome-wide transcriptional changes induced by phagocytosis or growth on bacteria in Dictyostelium Alessio Sillo, Gareth Bloomfield, Alessandra Balest, Alessandra Balbo, Barbara Pergolizzi, Barbara Peracino, Jason Skelton, Alasdair Ivens, and Salvatore Bozzaro PMCID: PMC2443395 Relative effects of mutability and selection on single nucleotide polymorphisms in transcribed regions of the human genome Ivan P Gorlov, Olga Y Gorlova, and Christopher I Amos PMCID: PMC2442617 Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins Phillip Hahn, Jens Böse, Stefanie Edler, and Andreas Lengeling PMCID: PMC2453528 Double feature selection and cluster analyses in mining of microarray data from cotton Magdy S Alabady, Eunseog Youn, and Thea A Wilkins PMCID: PMC2441630 ESTs from the microsporidian Edhazardia aedis Erin E Gill, James J Becnel, and Naomi M Fast PMCID: PMC2474625 Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria Haïtham Sghaier, Kaïs Ghedira, Alia Benkahla, and Insaf Barkallah PMCID: PMC2441631 The trypanosome transcriptome is remodelled during differentiation but displays limited responsiveness within life stages V Lila Koumandou, Senthil Kumar A Natesan, Tatiana Sergeenko, and Mark C Field PMCID: PMC2443814 Functional genomics reveals increases in cholesterol biosynthetic genes and highly unsaturated fatty acid biosynthesis after dietary substitution of fish oil with vegetable oils in Atlantic salmon (Salmo salar) Michael J Leaver, Laure AN Villeneuve, Alex Obach, Linda Jensen, James E Bron, Douglas R Tocher, and John B Taggart PMCID: PMC2459193 Expressed sequence tags from Peromyscus testis and placenta tissue: Analysis, annotation, and utility for mapping Julie L Weston Glenn, Chin-Fu Chen, Adrienne Lewandowski, Chun-Huai Cheng, Clifton M Ramsdell, Rebecca Bullard-Dillard, Jianguo Chen, Michael J Dewey, and Travis C Glenn PMCID: PMC2443383 Differential gene expression of the honey bee Apis mellifera associated with Varroa destructor infection M Navajas, A Migeon, C Alaux, ML Martin-Magniette, GE Robinson, JD Evans, S Cros-Arteil, D Crauser, and Y Le Conte PMCID: PMC2447852 Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells Seraya Maouche, Odette Poirier, Tiphaine Godefroy, Robert Olaso, Ivo Gut, Jean-Phillipe Collet, Gilles Montalescot, and François Cambien PMCID: PMC2464609 Proteomic profile of dormant Trichophyton Rubrum conidia Wenchuan Leng, Tao Liu, Rui Li, Jian Yang, Candong Wei, Wenliang Zhang, and Qi Jin PMCID: PMC2443143 A physical map of human Alu repeats cleavage by restriction endonucleases Murat A Abdurashitov, Victor N Tomilov, Valery A Chernukhin, and Sergey Kh Degtyarev PMCID: PMC2443384 The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali' Michael Kube, Bernd Schneider, Heiner Kuhl, Thomas Dandekar, Katja Heitmann, Alexander M Migdoll, Richard Reinhardt, and Erich Seemüller PMCID: PMC2459194 Expression profiling of a high-fertility mouse line by microarray analysis and qPCR Jens Vanselow, Gerd Nürnberg, Dirk Koczan, Martina Langhammer, Hans-Jürgen Thiesen, and Norbert Reinsch PMCID: PMC2443385 RAWUL: A new ubiquitin-like domain in PRC1 Ring finger proteins that unveils putative plant and worm PRC1 orthologs Luis Sanchez-Pulido, Damien Devos, Zinmay R Sung, and Myriam Calonje PMCID: PMC2447854 Microarray analysis identifies a common set of cellular genes modulated by different HCV replicon clones Anna Rita Ciccaglione, Cinzia Marcantonio, Elena Tritarelli, Paola Tataseo, Alessandro Ferraris, Roberto Bruni, Bruno Dallapiccola, Germano Gerosolimo, Angela Costantino, and Maria Rapicetta PMCID: PMC2474623 Meta-Analysis Approach identifies Candidate Genes and associated Molecular Networks for Type-2 Diabetes Mellitus Axel Rasche, Hadi Al-Hasani, and Ralf Herwig PMCID: PMC2515154 Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: Identification of genes absent from epidemic strains Audrey J King, Tamara van Gorkom, Jeroen LA Pennings, Han GJ van der Heide, Qiushui He, Dimitri Diavatopoulos, Kees Heuvelman, Marjolein van Gent, Karin van Leeuwen, and Frits R Mooi PMCID: PMC2481270 High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome Evandro Novaes, Derek R Drost, William G Farmerie, Georgios J Pappas, Jr, Dario Grattapaglia, Ronald R Sederoff, and Matias Kirst PMCID: PMC2483731 The topology of the bacterial co-conserved protein network and its implications for predicting protein function Anis Karimpour-Fard, Sonia M Leach, Lawrence E Hunter, and Ryan T Gill PMCID: PMC2488357 A preliminary analysis of genome structure and composition in Gossypium hirsutum Wangzhen Guo, Caiping Cai, Changbiao Wang, Liang Zhao, Lei Wang, and Tianzhen Zhang PMCID: PMC2481271 The complete mitochondrial genome of the Antarctic springtail Cryptopygus antarcticus (Hexapoda: Collembola) Antonio Carapelli, Sara Comandi, Peter Convey, Francesco Nardi, and Francesco Frati PMCID: PMC2483729 High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example Gustavo A de Souza, Hiwa Målen, Tina Søfteland, Gisle Sælensminde, Swati Prasad, Inge Jonassen, and Harald G Wiker PMCID: PMC2483986 Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays Catriona Rennie, Harry A Noyes, Stephen J Kemp, Helen Hulme, Andy Brass, and David C Hoyle PMCID: PMC2475537 The ORFeome of Staphylococcus aureus v 1.1 Christina J Brandner, Richard H Maier, Daryl S Henderson, Helmut Hintner, Johann W Bauer, and Kamil Önder PMCID: PMC2474624 Meta-analysis of nasopharyngeal carcinoma microarray data explores mechanism of EBV-regulated neoplastic transformation Xia Chen, Shuang Liang, WenLing Zheng, ZhiJun Liao, Tao Shang, and WenLi Ma PMCID: PMC2491640 Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly Navinder Saini, Jeffry Shultz, and David A Lightfoot PMCID: PMC2478686 Topoisomerase II inhibition involves characteristic chromosomal expression patterns Susanne Reymann and Jürgen Borlak PMCID: PMC2488358 Altered gene expression changes in Arabidopsis leaf tissues and protoplasts in response to Plum pox virus infection Mohan Babu, Jonathan S Griffiths, Tyng-Shyan Huang, and Aiming Wang PMCID: PMC2478689 Immunity related genes in dipterans share common enrichment of AT-rich motifs in their 5' regulatory regions that are potentially involved in nucleosome formation Jesus Hernandez-Romano, Francisco J Carlos-Rivera, Heladia Salgado, Hector Lamadrid-Figueroa, Veronica Valverde-Garduño, Mario H Rodriguez, and Jesus Martinez-Barnetche PMCID: PMC2491644 The Hypocrea jecorina (Trichoderma reesei) hypercellulolytic mutant RUT C30 lacks a 85 kb (29 gene-encoding) region of the wild-type genome Verena Seidl, Christian Gamauf, Irina S Druzhinina, Bernhard Seiboth, Lukas Hartl, and Christian P Kubicek PMCID: PMC2483294 Cross-platform comparison of SYBR® Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study Emi Arikawa, Yanyang Sun, Jie Wang, Qiong Zhou, Baitang Ning, Stacey L Dial, Lei Guo, and Jingping Yang PMCID: PMC2491643 Polymorphisms in the selenoprotein S gene: lack of association with autoimmune inflammatory diseases Alfonso Martínez, Jose Luis Santiago, Jezabel Varadé, Ana Márquez, José Ramón Lamas, Juan Luis Mendoza, Hermenegildo de la Calle, Manuel Díaz-Rubio, Emilio G de la Concha, Benjamín Fernández-Gutiérrez, and Elena Urcelay PMCID: PMC2491642 An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters Michiel Wels, Tom Groot Kormelink, Michiel Kleerebezem, Roland J Siezen, and Christof Francke PMCID: PMC2494555 The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae) Paola Salvato, Mauro Simonato, Andrea Battisti, and Enrico Negrisolo PMCID: PMC2488359 Low nucleosome occupancy is encoded around functional human transcription factor binding sites Floris Daenen, Frans van Roy, and Pieter J De Bleser PMCID: PMC2490708 Structure and properties of transcriptional networks driving selenite stress response in yeasts Hélène Salin, Vivienne Fardeau, Eugenia Piccini, Gaelle Lelandais, Véronique Tanty, Sophie Lemoine, Claude Jacq, and Frédéric Devaux PMCID: PMC2515152 Transcriptional profiling in C. elegans suggests DNA damage dependent apoptosis as an ancient function of the p53 family Sebastian Greiss, Björn Schumacher, Kaj Grandien, Jonathan Rothblatt, and Anton Gartner PMCID: PMC2491638 Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions? Albert Pallejà, Eoghan D Harrington, and Peer Bork PMCID: PMC2478687 Genetic interaction network of the Saccharomyces cerevisiae type 1 phosphatase Glc7 Michael R Logan, Thao Nguyen, Nicolas Szapiel, James Knockleby, Hanting Por, Megan Zadworny, Michael Neszt, Paul Harrison, Howard Bussey, Craig A Mandato, Jackie Vogel, and Guillaume Lesage PMCID: PMC2481269 Evolutionary conservation of zinc finger transcription factor binding sites in promoters of genes co-expressed with WT1 in prostate cancer Kurtis Eisermann, Sunpreet Tandon, Anton Bazarov, Adina Brett, Gail Fraizer, and Helen Piontkivska PMCID: PMC2515153 Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis Marcel Scheideler, Christian Elabd, Laure-Emmanuelle Zaragosi, Chiara Chiellini, Hubert Hackl, Fatima Sanchez-Cabo, Sunaina Yadav, Kalina Duszka, Gerald Friedl, Christine Papak, Andreas Prokesch, Reinhard Windhager, Gerard Ailhaud, Christian Dani, Ez-Zoubir Amri, and Zlatko Trajanoski PMCID: PMC2492879 Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: A three factor design Alessandro Fazio, Michael C Jewett, Pascale Daran-Lapujade, Roberta Mustacchi, Renata Usaite, Jack T Pronk, Christopher T Workman, and Jens Nielsen PMCID: PMC2500033 Parasitization by the wasp Eretmocerus mundus induces transcription of genes related to immune response and symbiotic bacteria proliferation in the whitefly Bemisia tabaci Assaf Mahadav, Dan Gerling, Yuval Gottlieb, Henryk Czosnek, and Murad Ghanim PMCID: PMC2488360 Growth rate regulated genes and their wide involvement in the Lactococcus lactis stress responses Clémentine Dressaire, Emma Redon, Helene Milhem, Philippe Besse, Pascal Loubière, and Muriel Cocaign-Bousquet PMCID: PMC2526093 Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803 Zhigang Zhang, Ninad D Pendse, Katherine N Phillips, James B Cotner, and Arkady Khodursky PMCID: PMC2491639 Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies Riccardo Papa, Clayton M Morrison, James R Walters, Brian A Counterman, Rui Chen, Georg Halder, Laura Ferguson, Nicola Chamberlain, Richard ffrench-Constant, Durrell D Kapan, Chris D Jiggins, Robert D Reed, and William O McMillan PMCID: PMC2515155 Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region Martin Kircher, Christoph Bock, and Martina Paulsen PMCID: PMC2500034 Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology Alessandro Botton, Giulio Galla, Ana Conesa, Christian Bachem, Angelo Ramina, and Gianni Barcaccia PMCID: PMC2515857 Deciphering downstream gene targets of PI3K/mTOR/p70S6K pathway in breast cancer Henna Heinonen, Anni Nieminen, Matti Saarela, Anne Kallioniemi, Juha Klefström, Sampsa Hautaniemi, and Outi Monni PMCID: PMC2496917 Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array Gregory AC Singer, Jiejun Wu, Pearlly Yan, Christoph Plass, Tim HM Huang, and Ramana V Davuluri PMCID: PMC2527337 A fragmented metazoan organellar genome: the two mitochondrial chromosomes of Hydra magnipapillata Oliver Voigt, Dirk Erpenbeck, and Gert Wörheide PMCID: PMC2518934 Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening Ross N Crowhurst, Andrew P Gleave, Elspeth A MacRae, Charles Ampomah-Dwamena, Ross G Atkinson, Lesley L Beuning, Sean M Bulley, David Chagne, Ken B Marsh, Adam J Matich, Mirco Montefiori, Richard D Newcomb, Robert J Schaffer, Björn Usadel, Andrew C Allan, Helen L Boldingh, Judith H Bowen, Marcus W Davy, Rheinhart Eckloff, A Ross Ferguson, Lena G Fraser, Emma Gera, Roger P Hellens, Bart J Janssen, Karin Klages, Kim R Lo, Robin M MacDiarmid, Bhawana Nain, Mark A McNeilage, Maysoon Rassam, Annette C Richardson, Erik HA Rikkerink, Gavin S Ross, Roswitha Schröder, Kimberley C Snowden, Edwige JF Souleyre, Matt D Templeton, Eric F Walton, Daisy Wang, Mindy Y Wang, Yanming Y Wang, Marion Wood, Rongmei Wu, Yar-Khing Yauk, and William A Laing PMCID: PMC2515324 Spatial and temporal expression of the 23 murine Prolactin/Placental Lactogen-related genes is not associated with their position in the locus David G Simmons, Saara Rawn, Alastair Davies, Martha Hughes, and James C Cross PMCID: PMC2527339 High-resolution array copy number analyses for detection of deletion, gain, amplification and copy-neutral LOH in primary neuroblastoma tumors: Four cases of homozygous deletions of the CDKN2A gene Helena Carén, Jennie Erichsen, Linda Olsson, Charlotta Enerbäck, Rose-Marie Sjöberg, Jonas Abrahamsson, Per Kogner, and Tommy Martinsson PMCID: PMC2527340 Expression patterns of transcribed human endogenous retrovirus HERV-K(HML-2) loci in human tissues and the need for a HERV Transcriptome Project Aline Flockerzi, Alessia Ruggieri, Oliver Frank, Marlies Sauter, Esther Maldener, Bernd Kopper, Bernd Wullich, Wolfgang Seifarth, Nikolaus Müller-Lantzsch, Christine Leib-Mösch, Eckart Meese, and Jens Mayer PMCID: PMC2525661 Correlation between the secondary structure of pre-mRNA introns and the efficiency of splicing in Saccharomyces cerevisiae Sanja Rogic, Ben Montpetit, Holger H Hoos, Alan K Mackworth, BF Francis Ouellette, and Philip Hieter PMCID: PMC2536676 Gene-based microsatellite development for mapping and phylogeny studies in eggplant Anikò Stàgel, Ezio Portis, Laura Toppino, Giuseppe Leonardo Rotino, and Sergio Lanteri PMCID: PMC2527019 Selective inhibition of yeast regulons by daunorubicin: A transcriptome-wide analysis Marta Rojas, Marta Casado, José Portugal, and Benjamin Piña PMCID: PMC2536678 Transcriptional profiling of putative human epithelial stem cells Salih S Koçer, Petar M Djurić, Mónica F Bugallo, Sanford R Simon, and Maja Matic PMCID: PMC2536675 Conserved upstream open reading frames in higher plants Michael K Tran, Carolyn J Schultz, and Ute Baumann PMCID: PMC2527020 Effects of increased milking frequency on gene expression in the bovine mammary gland Erin E Connor, Stephen Siferd, Theodore H Elsasser, Christina M Evock-Clover, Curtis P Van Tassell, Tad S Sonstegard, Violet M Fernandes, and Anthony V Capuco PMCID: PMC2518935 Integrative analysis of RUNX1 downstream pathways and target genes Joëlle Michaud, Ken M Simpson, Robert Escher, Karine Buchet-Poyau, Tim Beissbarth, Catherine Carmichael, Matthew E Ritchie, Frédéric Schütz, Ping Cannon, Marjorie Liu, Xiaofeng Shen, Yoshiaki Ito, Wendy H Raskind, Marshall S Horwitz, Motomi Osato, David R Turner, Terence P Speed, Maria Kavallaris, Gordon K Smyth, and Hamish S Scott PMCID: PMC2529319 Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis Curtis M Nelson, Michael J Herron, Roderick F Felsheim, Brian R Schloeder, Suzanne M Grindle, Adela Oliva Chavez, Timothy J Kurtti, and Ulrike G Munderloh PMCID: PMC2527338 Transcriptome analysis of a respiratory Saccharomycescerevisiae strain suggests the expression of its phenotype is glucose insensitive and predominantly controlled by Hap4, Cat8 and Mig1 Nicklas Bonander, Cecilia Ferndahl, Petter Mostad, Martin DB Wilks, Celia Chang, Louise Showe, Lena Gustafsson, Christer Larsson, and Roslyn M Bill PMCID: PMC2536679 Gene networks driving bovine milk fat synthesis during the lactation cycle Massimo Bionaz and Juan J Loor PMCID: PMC2547860 Trait correlated expression combined with expression QTL analysis reveals biological pathways and candidate genes affecting water holding capacity of muscle Siriluck Ponsuksili, Elisabeth Jonas, Eduard Murani, Chirawath Phatsara, Tiranun Srikanchai, Christina Walz, Manfred Schwerin, Karl Schellander, and Klaus Wimmers PMCID: PMC2529315 Peripheral arterial occlusive disease: Global gene expression analyses suggest a major role for immune and inflammatory responses Shijun Fu, Haiguang Zhao, Jiantao Shi, Arhat Abzhanov, Keith Crawford, Lucila Ohno-Machado, Jianqin Zhou, Yanzhi Du, Winston Patrick Kuo, Ji Zhang, Mier Jiang, and Jason Gang Jin PMCID: PMC2529314 Differential control of Zap1-regulated genes in response to zinc deficiency in Saccharomyces cerevisiae Chang-Yi Wu, Amanda J Bird, Lisa M Chung, Michael A Newton, Dennis R Winge, and David J Eide PMCID: PMC2535606 Sequence conservation and combinatorial complexity of Drosophila neural precursor cell enhancers Thomas Brody, Wayne Rasband, Kevin Baler, Alexander Kuzin, Mukta Kundu, and Ward F Odenwald PMCID: PMC2529316 Evidence of the role of tick subolesin in gene expression José de la Fuente, Christine Maritz-Olivier, Victoria Naranjo, Patricia Ayoubi, Ard M Nijhof, Consuelo Almazán, Mario Canales, José M Pérez de la Lastra, Ruth C Galindo, Edmour F Blouin, Christian Gortazar, Frans Jongejan, and Katherine M Kocan PMCID: PMC2518936 Identification of the transcriptional response of human intestinal mucosa to Lactobacillus plantarum WCFS1 in vivo Freddy J Troost, Peter van Baarlen, Patrick Lindsey, Andrea Kodde, Willem M de Vos, Michiel Kleerebezem, and Robert-Jan M Brummer PMCID: PMC2519092 Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability Martin H van Vliet, Fabien Reyal, Hugo M Horlings, Marc J van de Vijver, Marcel JT Reinders, and Lodewyk FA Wessels PMCID: PMC2527336 Novel functional view of the crocidolite asbestos-treated A549 human lung epithelial transcriptome reveals an intricate network of pathways with opposing functions Joan M Hevel, Laura C Olson-Buelow, Balasubramanian Ganesan, John R Stevens, Jared P Hardman, and Ann E Aust PMCID: PMC2533023 Altered gene expression in highly purified enterocytes from patients with active coeliac disease Suzanne Bracken, Greg Byrne, Jacinta Kelly, John Jackson, and Conleth Feighery PMCID: PMC2533024 Proteome changes in the skin of the grape cultivar Barbera among different stages of ripening Alfredo S Negri, Bhakti Prinsi, Mara Rossoni, Osvaldo Failla, Attilio Scienza, Maurizio Cocucci, and Luca Espen PMCID: PMC2529320 Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors LO Baumbusch, J Aarøe, FE Johansen, J Hicks, H Sun, L Bruhn, K Gunderson, B Naume, VN Kristensen, K Liestøl, A-L Børresen-Dale, and OC Lingjærde PMCID: PMC2547478 Construction of a comparative genetic map in faba bean (Vicia faba L.); conservation of genome structure with Lens culinaris Simon R Ellwood, Huyen TT Phan, Megan Jordan, James Hane, Anna M Torres, Carmen M Avila, Serafín Cruz-Izquierdo, and Richard P Oliver PMCID: PMC2533332 Characterization of hemizygous deletions in Citrus using array-Comparative Genomic Hybridization and microsynteny comparisons with the poplar genome Gabino Ríos, Miguel A Naranjo, Domingo J Iglesias, Omar Ruiz-Rivero, Marion Geraud, Antonio Usach, and Manuel Talón PMCID: PMC2533677 LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice Hao Wang and Jin-Song Liu PMCID: PMC2533021 Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobili Norihiro Futamura, Yasushi Totoki, Atsushi Toyoda, Tomohiro Igasaki, Tokihiko Nanjo, Motoaki Seki, Yoshiyuki Sakaki, Adriano Mari, Kazuo Shinozaki, and Kenji Shinohara PMCID: PMC2568000 The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements Tomàs Marques-Bonet, Ze Cheng, Xinwei She, Evan E Eichler, and Arcadi Navarro PMCID: PMC2542386 Isolation and analysis of the genetic diversity of repertoires of VSG expression site containing telomeres from Trypanosoma brucei gambiense, T. b. brucei and T. equiperdum Rosanna Young, Jesse E Taylor, Ayako Kurioka, Marion Becker, Edward J Louis, and Gloria Rudenko PMCID: PMC2533676 Complete genome of Phenylobacterium zucineum – a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562 Yingfeng Luo, Xiaoli Xu, Zonghui Ding, Zhen Liu, Bing Zhang, Zhiyu Yan, Jie Sun, Songnian Hu, and Xun Hu PMCID: PMC2529317 Multiple actions of lysophosphatidic acid on fibroblasts revealed by transcriptional profiling Catelijne Stortelers, Ron Kerkhoven, and Wouter H Moolenaar PMCID: PMC2536681 Dynamic RNA profiling in Plasmodium falciparum synchronized blood stages exposed to lethal doses of artesunate Onguma Natalang, Emmanuel Bischoff, Guillaume Deplaine, Caroline Proux, Marie-Agnès Dillies, Odile Sismeiro, Ghislaine Guigon, Serge Bonnefoy, Jintana Patarapotikul, Odile Mercereau-Puijalon, Jean-Yves Coppée, and Peter H David PMCID: PMC2536677 A human genome-wide library of local phylogeny predictions for whole-genome inference problems Srinath Sridhar and Russell Schwartz PMCID: PMC2556685 Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays Alexandra Graf, Brigitte Gasser, Martin Dragosits, Michael Sauer, Germán G Leparc, Thomas Tüchler, David P Kreil, and Diethard Mattanovich PMCID: PMC2533675 Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken Martin G Elferink, Amélie AA Vallée, Annemieke P Jungerius, Richard PMA Crooijmans, and Martien AM Groenen PMCID: PMC2542384 Rapid functional diversification in the structurally conserved ELAV family of neuronal RNA binding proteins Marie-Laure Samson PMCID: PMC2529313 Diversity in genomic organisation, developmental regulation and distribution of the murine PR72/B" subunits of protein phosphatase 2A Karen Zwaenepoel, Justin V Louis, Jozef Goris, and Veerle Janssens PMCID: PMC2529318 Comparison of prognostic gene expression signatures for breast cancer Benjamin Haibe-Kains, Christine Desmedt, Fanny Piette, Marc Buyse, Fatima Cardoso, Laura van't Veer, Martine Piccart, Gianluca Bontempi, and Christos Sotiriou PMCID: PMC2533026 Transcriptome analysis reveals response regulator SO2426-mediated gene expression in Shewanella oneidensis MR-1 under chromate challenge Karuna Chourey, Wei Wei, Xiu-Feng Wan, and Dorothea K Thompson PMCID: PMC2535785 Catalogue of epidermal genes: Genes expressed in the epidermis during larval molt of the silkworm Bombyx mori Shun Okamoto, Ryo Futahashi, Tetsuya Kojima, Kazuei Mita, and Haruhiko Fujiwara PMCID: PMC2542385 Differential screening identifies transcripts with depot-dependent expression in white adipose tissues Yu Wu, Ji Young Kim, Shengli Zhou, and Cynthia M Smas PMCID: PMC2547859 Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution Wilfried Haerty, Carlo Artieri, Navid Khezri, Rama S Singh, and Bhagwati P Gupta PMCID: PMC2533025 Identification of genes and pathways associated with aluminum stress and tolerance using transcriptome profiling of wheat near-isogenic lines Mario Houde and Amadou Oury Diallo PMCID: PMC2551624 Comparative mapping of quantitative trait loci associated with waterlogging tolerance in barley (Hordeum vulgare L.) Haobing Li, René Vaillancourt, Neville Mendham, and Meixue Zhou PMCID: PMC2533678 Hepatocyte RXRalpha deficiency in matured and aged mice: impact on the expression of cancer-related hepatic genes in a gender-specific manner Minglei Guo, Lei Gong, Lin He, Lois Lehman-McKeeman, and Yu-Jui Yvonne Wan PMCID: PMC2547858 Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome Nicole L Quinn, Natasha Levenkova, William Chow, Pascal Bouffard, Keith A Boroevich, James R Knight, Thomas P Jarvie, Krzysztof P Lubieniecki, Brian A Desany, Ben F Koop, Timothy T Harkins, and William S Davidson PMCID: PMC2532694 Gene organization, evolution and expression of the microtubule-associated protein ASAP (MAP9) Magali Venoux, Karine Delmouly, Ollivier Milhavet, Sophie Vidal-Eychenié, Dominique Giorgi, and Sylvie Rouquier PMCID: PMC2551623 Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation Kyung Eun Lee, Seungyoon Nam, Eun-ah Cho, Ikjoo Seong, Jin-Kyung Limb, Sanghyuk Lee, and Jaesang Kim PMCID: PMC2556353 A map of the class III region of the sheep major histocompatibilty complex J Qin, C Mamotte, NE Cockett, JD Wetherall, and DM Groth PMCID: PMC2566321 Short Tandem Repeats in Human Exons: A Target for Disease Mutations Bo Eskerod Madsen, Palle Villesen, and Carsten Wiuf PMCID: PMC2543027 Microarray analysis of toxicogenomic effects of Ortho-phenylphenol in Staphylococcus aureus Hyeung-Jin Jang, Chantal Nde, Freshteh Toghrol, and William E Bentley PMCID: PMC2562396 The protein-phosphatome of the human malaria parasite Plasmodium falciparum Jonathan M Wilkes and Christian Doerig PMCID: PMC2559854 Novel genome polymorphisms in BCG vaccine strains and impact on efficacy Andrea S Leung, Vanessa Tran, Zuowei Wu, Xuping Yu, David C Alexander, George Fu Gao, Baoli Zhu, and Jun Liu PMCID: PMC2553098 Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011 Claudio Valverde, Jonathan Livny, Jan-Philip Schlüter, Jan Reinkensmeier, Anke Becker, and Gustavo Parisi PMCID: PMC2573895 Transcriptomic analysis of the exit from dormancy of Aspergillus fumigatus conidia Claude Lamarre, Sergueï Sokol, Jean-Paul Debeaupuis, Christine Henry, Céline Lacroix, Philippe Glaser, Jean-Yves Coppée, Jean-Marie François, and Jean-Paul Latgé PMCID: PMC2556354 Transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in liver: Comparison of rat and mouse Paul C Boutros, Rui Yan, Ivy D Moffat, Raimo Pohjanvirta, and Allan B Okey PMCID: PMC2559853 Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures David T Pride and Thomas Schoenfeld PMCID: PMC2556352 Gene expression profiling in hepatic tissue of newly weaned pigs fed pharmacological zinc and phytase supplemented diets Michelle M Martínez-Montemayor, Gretchen M Hill, Nancy E Raney, Valencia D Rilington, Robert J Tempelman, Jane E Link, Christopher P Wilkinson, Antonio M Ramos, and Catherine W Ernst PMCID: PMC2566318 Development of genomic resources for Citrus clementina: Characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences Javier Terol, M Angel Naranjo, Patrick Ollitrault, and Manuel Talon PMCID: PMC2561056 Global identification of bursicon-regulated genes in Drosophila melanogaster Shiheng An, Songjie Wang, Lawrence I Gilbert, Brenda Beerntsen, Mark Ellersieck, and Qisheng Song PMCID: PMC2566319 Comparative genomics of small RNA regulatory pathway components in vector mosquitoes Corey L Campbell, William C Black, IV, Ann M Hess, and Brian D Foy PMCID: PMC2566310 Interspecies data mining to predict novel ING-protein interactions in human Paul MK Gordon, Mohamed A Soliman, Pinaki Bose, Quang Trinh, Christoph W Sensen, and Karl Riabowol PMCID: PMC2565686 The genome of Aeromonas salmonicida subsp. salmonicida A449: insights into the evolution of a fish pathogen Michael E Reith, Rama K Singh, Bruce Curtis, Jessica M Boyd, Anne Bouevitch, Jennifer Kimball, Janet Munholland, Colleen Murphy, Darren Sarty, Jason Williams, John HE Nash, Stewart C Johnson, and Laura L Brown PMCID: PMC2556355 POEM, A 3-dimensional exon taxonomy and patterns in untranslated exons Keith Knapp, Ashley Chonka, and Yi-Ping Phoebe Chen PMCID: PMC2561055 Analysis of the goldfish Carassius auratus olfactory epithelium transcriptome reveals the presence of numerous non-olfactory GPCR and putative receptors for progestin pheromones Nikolay N Kolmakov, Michael Kube, Richard Reinhardt, and Adelino VM Canario PMCID: PMC2556351 The information highways of a biotechnological workhorse – signal transduction in Hypocrea jecorina Monika Schmoll PMCID: PMC2566311 Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals Nao Nishida, Asako Koike, Atsushi Tajima, Yuko Ogasawara, Yoshimi Ishibashi, Yasuka Uehara, Ituro Inoue, and Katsushi Tokunaga PMCID: PMC2566316 Heat stress-responsive transcriptome analysis in heat susceptible and tolerant wheat (Triticum aestivum L.) by using Wheat Genome Array Dandan Qin, Haiyan Wu, Huiru Peng, Yingyin Yao, Zhongfu Ni, Zhenxing Li, Chunlei Zhou, and Qixin Sun PMCID: PMC2614437 Genome sequencing and analysis reveals possible determinants of Staphylococcus aureus nasal carriage Karthikeyan Sivaraman, Nitya Venkataraman, Jennifer Tsai, Scott Dewell, and Alexander M Cole PMCID: PMC2566312 Differential SAGE analysis in Arabidopsis uncovers increased transcriptome complexity in response to low temperature Stephen J Robinson and Isobel AP Parkin PMCID: PMC2568001 Identification of transcripts involved in meiosis and follicle formation during ovine ovary development Adrienne Baillet, Béatrice Mandon-Pépin, Cédric Cabau, Elodie Poumerol, Eric Pailhoux, and Corinne Cotinot PMCID: PMC2566313 Analysis of Porcine Transcriptional Response to Salmonella enterica serovar Choleraesuis suggests novel targets of NFkappaB are activated in the Mesenteric Lymph Node Yanfang Wang, Oliver P Couture, Long Qu, Jolita J Uthe, Shawn MD Bearson, Daniel Kuhar, Joan K Lunney, Dan Nettleton, Jack CM Dekkers, and Christopher K Tuggle PMCID: PMC2570369 The rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana Felipe F Aceituno, Nick Moseyko, Seung Y Rhee, and Rodrigo A Gutiérrez PMCID: PMC2566314 Identifying gene regulatory modules of heat shock response in yeast Wei-Sheng Wu and Wen-Hsiung Li PMCID: PMC2575218 Evolution of the holozoan ribosome biogenesis regulon Seth J Brown, Michael D Cole, and Albert J Erives PMCID: PMC2570694 Gene expression profiling of liver from dairy cows treated intra-mammary with lipopolysaccharide Li Jiang, Peter Sørensen, Christine Røntved, Lotte Vels, and Klaus L Ingvartsen PMCID: PMC2576255 Using gene expression databases for classical trait QTL candidate gene discovery in the BXD recombinant inbred genetic reference population: Mouse forebrain weight Lu Lu, Lai Wei, Jeremy L Peirce, Xusheng Wang, Jianhua Zhou, Ramin Homayouni, Robert W Williams, and David C Airey PMCID: PMC2570693 Organogenic nodule development in hop (Humulus lupulus L.): Transcript and metabolic responses Ana M Fortes, Filipa Santos, Young H Choi, Marta S Silva, Andreia Figueiredo, Lisete Sousa, Fernando Pessoa, Bartolomeu A Santos, Mónica Sebastiana, Klaus Palme, Rui Malhó, Rob Verpoorte, and Maria S Pais PMCID: PMC2573896 Molecular architecture of the fruit fly's airway epithelial immune system Christina Wagner, Kerstin Isermann, Heinz Fehrenbach, and Thomas Roeder PMCID: PMC2566315 Antigen stimulation of peripheral blood mononuclear cells from Mycobacterium bovis infected cattle yields evidence for a novel gene expression program Kieran G Meade, Eamonn Gormley, Cliona O'Farrelly, Stephen D Park, Eamon Costello, Joseph Keane, Yingdong Zhao, and David E MacHugh PMCID: PMC2569068 Cross-species comparison of biological themes and underlying genes on a global gene expression scale in a mouse model of colorectal liver metastasis and in clinical specimens Obul Reddy Bandapalli, Christoph Kahlert, Victoria Hellstern, Luis Galindo, Peter Schirmacher, Jürgen Weitz, and Karsten Brand PMCID: PMC2573898 The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae Roy Gross, Carlos A Guzman, Mohammed Sebaihia, Vítor AP Martins dos Santos, Dietmar H Pieper, Ralf Koebnik, Melanie Lechner, Daniela Bartels, Jens Buhrmester, Jomuna V Choudhuri, Thomas Ebensen, Lars Gaigalat, Stefanie Herrmann, Amit N Khachane, Christof Larisch, Stefanie Link, Burkhard Linke, Folker Meyer, Sascha Mormann, Diana Nakunst, Christian Rückert, Susanne Schneiker-Bekel, Kai Schulze, Frank-Jörg Vorhölter, Tetyana Yevsa, Jacquelyn T Engle, William E Goldman, Alfred Pühler, Ulf B Göbel, Alexander Goesmann, Helmut Blöcker, Olaf Kaiser, and Rosa Martinez-Arias PMCID: PMC2572626 Quality assessment parameters for EST-derived SNPs from catfish Shaolin Wang, Zhenxia Sha, Tad S Sonstegard, Hong Liu, Peng Xu, Benjaporn Somridhivej, Eric Peatman, Huseyin Kucuktas, and Zhanjiang Liu PMCID: PMC2570692 Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice Meenu Kapoor, Rita Arora, Tenisha Lama, Aashima Nijhawan, Jitendra P Khurana, Akhilesh K Tyagi, and Sanjay Kapoor PMCID: PMC2576257 The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains Siyuan Ren, Guang Yang, Youyu He, Yiguo Wang, Yixue Li, and Zhengjun Chen PMCID: PMC2576256 Splice-mediated Variants of Proteins (SpliVaP) – data and characterization of changes in signatures among protein isoforms due to alternative splicing Matteo Floris, Massimiliano Orsini, and Thangavel Alphonse Thanaraj PMCID: PMC2573899 Selection and mutation on microRNA target sequences during rice evolution Xingyi Guo, Yijie Gui, Yu Wang, Qian-Hao Zhu, Chris Helliwell, and Longjiang Fan PMCID: PMC2567346 Unassigned MURF1 of kinetoplastids codes for NADH dehydrogenase subunit 2 Sivakumar Kannan and Gertraud Burger PMCID: PMC2572627 Promoter-sharing by different genes in human genome – CPNE1 and RBM12 gene pair as an example Wanling Yang, Ping Ng, Minghui Zhao, Thomas KF Wong, Siu-Ming Yiu, and Yu Lung Lau PMCID: PMC2568002 Adrenaline modulates the global transcriptional profile of Salmonella revealing a role in the antimicrobial peptide and oxidative stress resistance responses MH Karavolos, H Spencer, DM Bulmer, A Thompson, K Winzer, P Williams, JCD Hinton, and CM Anjam Khan PMCID: PMC2576261 Deciphering the genetic basis for polyketide variation among mycobacteria producing mycolactones Sacha J Pidot, Hui Hong, Torsten Seemann, Jessica L Porter, Marcus J Yip, Artem Men, Matthew Johnson, Peter Wilson, John K Davies, Peter F Leadlay, and Timothy P Stinear PMCID: PMC2569948 Preferred and avoided codon pairs in three domains of life Age Tats, Tanel Tenson, and Maido Remm PMCID: PMC2585594 Prediction of evolutionarily conserved interologs in Mus musculus Sailu Yellaboina, Dawood B Dudekula, and Minoru SH Ko PMCID: PMC2571111 Retrocopy contributions to the evolution of the human genome Robert Baertsch, Mark Diekhans, W James Kent, David Haussler, and Jürgen Brosius PMCID: PMC2584115 A comparative computational analysis of nonautonomous Helitron elements between maize and rice Michael Sweredoski, Leah DeRose-Wilson, and Brandon S Gaut PMCID: PMC2575219 The SWI/SNF protein ATRX co-regulates pseudoautosomal genes that have translocated to autosomes in the mouse genome Michael A Levy, Andrew D Fernandes, Deanna C Tremblay, Claudia Seah, and Nathalie G Bérubé PMCID: PMC2577121 Characterization of ten novel Ty1/copia-like retrotransposon families of the grapevine genome Cédric Moisy, Keith E Garrison, Carole P Meredith, and Frédérique Pelsy PMCID: PMC2576258 RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes Henri Grosjean, Christine Gaspin, Christian Marck, Wayne A Decatur, and Valérie de Crécy-Lagard PMCID: PMC2584109 Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function Hoa T Tran, Julia Krushkal, Frances M Antommattei, Derek R Lovley, and Robert M Weis PMCID: PMC2577667 Toxicogenomic response of Pseudomonas aeruginosa to ortho-phenylphenol Chantal W Nde, Hyeung-Jin Jang, Freshteh Toghrol, and William E Bentley PMCID: PMC2577666 Differential gene expression profiles are dependent upon method of peripheral blood collection and RNA isolation Adam L Asare, Svetlana A Kolchinsky, Zhong Gao, Richard Wang, Khadir Raddassi, Katarzyna Bourcier, and Vicki Seyfert-Margolis PMCID: PMC2573897 Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription Rebecca L Poole, Gary LA Barker, Kay Werner, Gaia F Biggi, Jane Coghill, J George Gibbings, Simon Berry, Jim M Dunwell, and Keith J Edwards PMCID: PMC2584110 High-throughput cell-based screening reveals a role for ZNF131 as a repressor of ERalpha signaling Xiao Han, Jinhai Guo, Weiwei Deng, Chenying Zhang, Peige Du, Taiping Shi, and Dalong Ma PMCID: PMC2577665 Complete mitochondrial DNA sequence of oyster Crassostrea hongkongensis-a case of "Tandem duplication-random loss" for genome rearrangement in Crassostrea? Ziniu Yu, Zhengpeng Wei, Xiaoyu Kong, and Wei Shi PMCID: PMC2576254 Global analysis of gene expression changes during retinoic acid-induced growth arrest and differentiation of melanoma: comparison to differentially expressed genes in melanocytes vs melanoma Mary Estler, Goran Boskovic, James Denvir, Sarah Miles, Donald A Primerano, and Richard M Niles PMCID: PMC2572629 Genomics and proteomics of immune modulatory effects of a butanol fraction of echinacea purpurea in human dendritic cells Chien-Yu Wang, Vanisree Staniforth, Ming-Tsang Chiao, Chia-Chung Hou, Han-Ming Wu, Kuo-Chen Yeh, Chun-Houh Chen, Pei-Ing Hwang, Tuan-Nan Wen, Lie-Fen Shyur, and Ning-Sun Yang PMCID: PMC2571112 Prioritizing genes of potential relevance to diseases affected by sex hormones: an example of Myasthenia Gravis Mandeep Kaur, Sebastian Schmeier, Cameron R MacPherson, Oliver Hofmann, Winston A Hide, Stephen Taylor, Nick Willcox, and Vladimir B Bajic PMCID: PMC2592250 PwRn1, a novel Ty3/gypsy-like retrotransposon of Paragonimus westermani: molecular characters and its differentially preserved mobile potential according to host chromosomal polyploidy Young-An Bae, Jong-Sook Ahn, Seon-Hee Kim, Mun-Gan Rhyu, Yoon Kong, and Seung-Yull Cho PMCID: PMC2582038 The dual transcriptional regulator CysR in Corynebacterium glutamicum ATCC 13032 controls a subset of genes of the McbR regulon in response to the availability of sulphide acceptor molecules Christian Rückert, Johanna Milse, Andreas Albersmeier, Daniel J Koch, Alfred Pühler, and Jörn Kalinowski PMCID: PMC2580772 A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis) Steven G Ralph, Hye Jung E Chun, Natalia Kolosova, Dawn Cooper, Claire Oddy, Carol E Ritland, Robert Kirkpatrick, Richard Moore, Sarah Barber, Robert A Holt, Steven JM Jones, Marco A Marra, Carl J Douglas, Kermit Ritland, and Jörg Bohlmann PMCID: PMC2579922 Identification of drought-responsive genes in roots of upland rice (Oryza sativa L) Aline R Rabello, Cléber M Guimarães, Paulo HN Rangel, Felipe R da Silva, Daniela Seixas, Emanuel de Souza, Ana CM Brasileiro, Carlos R Spehar, Márcio E Ferreira, and Ângela Mehta PMCID: PMC2605477 p53 induces distinct epigenetic states at its direct target promoters Lukas Vrba, Damian J Junk, Petr Novak, and Bernard W Futscher PMCID: PMC2585595 Species-specific regulation of PXR/CAR/ER-target genes in the mouse and rat liver elicited by o, p'-DDT Naoki Kiyosawa, Joshua C Kwekel, Lyle D Burgoon, Edward Dere, Kurt J Williams, Colleen Tashiro, Brock Chittim, and Timothy R Zacharewski PMCID: PMC2577663 Ploidy status and copy number aberrations in primary glioblastomas defined by integrated analysis of allelic ratios, signal ratios and loss of heterozygosity using 500K SNP Mapping Arrays Paul J Gardina, Ken C Lo, Walter Lee, John K Cowell, and Yaron Turpaz PMCID: PMC2576260 Disturbances in metabolic, transport and structural genes in experimental colonic inflammation in the rat: a longitudinal genomic analysis Olga Martínez-Augustin, Manel Merlos, Antonio Zarzuelo, María Dolores Suárez, and Fermín Sánchez de Medina PMCID: PMC2577662 Design and analysis of mismatch probes for long oligonucleotide microarrays Ye Deng, Zhili He, Joy D Van Nostrand, and Jizhong Zhou PMCID: PMC2576263 Copy number variations (CNVs) identified in Korean individuals Tae-Wook Kang, Yeo-Jin Jeon, Eunsu Jang, Hee-Jin Kim, Jeong-Hwan Kim, Jong-Lyul Park, Siwoo Lee, Yong Sung Kim, Jong Yeol Kim, and Seon-Young Kim PMCID: PMC2576253 Transcriptional response of Mexican axolotls to Ambystoma tigrinum virus (ATV) infection Jennifer D Cotter, Andrew Storfer, Robert B Page, Christopher K Beachy, and S Randal Voss PMCID: PMC2584114 Local and systemic gene expression responses of Atlantic salmon (Salmo salar L.) to infection with the salmon louse (Lepeophtheirus salmonis) Stanko Skugor, Kevin Alan Glover, Frank Nilsen, and Aleksei Krasnov PMCID: PMC2582245 In silico identification and molecular characterization of genes predominantly expressed in the fish oocyte Julien Bobe, Thaovi Nguyen, Sophie Mahé, and Philippe Monget PMCID: PMC2584112 Comparative analysis of the time-dependent functional and molecular changes in spinal cord degeneration induced by the G93A SOD1 gene mutation and by mechanical compression Andrea Malaspina, Natasa Jokic, Wenlong L Huang, and John V Priestley PMCID: PMC2585103 Matching curated genome databases: a non trivial task Stéphane Descorps-Declère, Matthieu Barba, and Bernard Labedan PMCID: PMC2596144 Meta-analysis of genome-wide expression patterns associated with behavioral maturation in honey bees Heather A Adams, Bruce R Southey, Gene E Robinson, and Sandra L Rodriguez-Zas PMCID: PMC2582039 Changes induced by dietary energy intake and divergent selection for muscle fat content in rainbow trout (Oncorhynchus mykiss), assessed by transcriptome and proteome analysis of the liver Catherine-Ines Kolditz, Gilles Paboeuf, Maïena Borthaire, Diane Esquerré, Magali SanCristobal, Florence Lefèvre, and Françoise Médale PMCID: PMC2612026 Histone deacetylase inhibitors: A new mode for inhibition of cholesterol metabolism Sridar V Chittur, Niquiche Sangster-Guity, and Paulette J McCormick PMCID: PMC2613157 Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform Joan Cerdà, Jaume Mercadé, Juan José Lozano, Manuel Manchado, Angèle Tingaud-Sequeira, Antonio Astola, Carlos Infante, Silke Halm, Jordi Viñas, Barbara Castellana, Esther Asensio, Pedro Cañavate, Gonzalo Martínez-Rodríguez, Francesc Piferrer, Josep V Planas, Francesc Prat, Manuel Yúfera, Olga Durany, Francesc Subirada, Elisabet Rosell, and Tamara Maes PMCID: PMC2612027 Microarray analysis of Foxa2 mutant mouse embryos reveals novel gene expression and inductive roles for the gastrula organizer and its derivatives Owen J Tamplin, Doris Kinzel, Brian J Cox, Christine E Bell, Janet Rossant, and Heiko Lickert PMCID: PMC2605479 A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite, Plasmodium falciparum Karine G Le Roch, Jeffrey R Johnson, Hugues Ahiboh, Duk-Won D Chung, Jacques Prudhomme, David Plouffe, Kerstin Henson, Yingyao Zhou, William Witola, John R Yates, Choukri Ben Mamoun, Elizabeth A Winzeler, and Henri Vial PMCID: PMC2596145 Genomic plasticity of the immune-related Mhc class I B region in macaque species Maxime Bonhomme, Gaby GM Doxiadis, Corrine MC Heijmans, Virginie Vervoort, Nel Otting, Ronald E Bontrop, and Brigitte Crouau-Roy PMCID: PMC2584111 Multiple genome alignment for identifying the core structure among moderately related microbial genomes Ikuo Uchiyama PMCID: PMC2615449 Establishing an adjusted p-value threshold to control the family-wide type 1 error in genome wide association studies Priya Duggal, Elizabeth M Gillanders, Taura N Holmes, and Joan E Bailey-Wilson PMCID: PMC2621212 Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats Thomas Wicker, Apurva Narechania, Francois Sabot, Joshua Stein, Giang TH Vu, Andreas Graner, Doreen Ware, and Nils Stein PMCID: PMC2584661 The prediction of protein-protein interaction networks in rice blast fungus Fei He, Yan Zhang, Hao Chen, Ziding Zhang, and You-Liang Peng PMCID: PMC2601049 Evolution of conserved secondary structures and their function in transcriptional regulation networks Hai-Bing Xie, David M Irwin, and Ya-Ping Zhang PMCID: PMC2584662 mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft Darren Magda, Philip Lecane, Julia Prescott, Patricia Thiemann, Xuan Ma, Patricia K Dranchak, Donna M Toleno, Krishna Ramaswamy, Kimberly D Siegmund, and Joseph G Hacia PMCID: PMC2612029 Isolation, characterization and comparison of Atlantic and Chinook salmon growth hormone 1 and 2 Kristian R von Schalburg, Ryosuke Yazawa, Johan de Boer, Krzysztof P Lubieniecki, Benjamin Goh, Christopher A Straub, Marianne R Beetz-Sargent, Adrienne Robb, William S Davidson, Robert H Devlin, and Ben F Koop PMCID: PMC2584663 Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identify novel genes expressed during vegetative, infectious, and reproductive growth Burton H Bluhm, Braham Dhillon, Erika A Lindquist, Gert HJ Kema, Stephen B Goodwin, and Larry D Dunkle PMCID: PMC2596140 Comparative genomics of wild type yeast strains unveils important genome diversity Laura Carreto, Maria F Eiriz, Ana C Gomes, Patrícia M Pereira, Dorit Schuller, and Manuel AS Santos PMCID: PMC2588607 Gene expression profiling in chicken heterophils with Salmonella enteritidis stimulation using a chicken 44 K Agilent microarray Hsin-I Chiang, Christina L Swaggerty, Michael H Kogut, Scot E Dowd, Xianyao Li, Igal Y Pevzner, and Huaijun Zhou PMCID: PMC2588606 Temporal and functional profile of the transcriptional regulatory network in the early regenerative response to partial hepatectomy in the rat Egle Juskeviciute, Rajanikanth Vadigepalli, and Jan B Hoek PMCID: PMC2613928 The transcriptomic signature of fasting murine liver Milka Sokolović, Aleksandar Sokolović, Diederik Wehkamp, Emiel Ver Loren van Themaat, Dirk R de Waart, Lisa A Gilhuijs-Pederson, Yuri Nikolsky, Antoine HC van Kampen, Theodorus BM Hakvoort, and Wouter H Lamers PMCID: PMC2588605 Linking gene regulation and the exo-metabolome: A comparative transcriptomics approach to identify genes that impact on the production of volatile aroma compounds in yeast Debra Rossouw, Tormod Næs, and Florian F Bauer PMCID: PMC2585593 The complete mitochondrial genome of the sexual oribatid mite Steganacarus magnus: genome rearrangements and loss of tRNAs Katja Domes, Mark Maraun, Stefan Scheu, and Stephen L Cameron PMCID: PMC2588462 Analysis of the largest tandemly repeated DNA families in the human genome Peter E Warburton, Dan Hasson, Flavia Guillem, Chloe Lescale, Xiaoping Jin, and Gyorgy Abrusan PMCID: PMC2588610 Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L.) David P Horvath, Wun S Chao, Jeffrey C Suttle, Jyothi Thimmapuram, and James V Anderson PMCID: PMC2605480 Identifying Positioned Nucleosomes with Epigenetic Marks in Human from ChIP-Seq Yong Zhang, Hyunjin Shin, Jun S Song, Ying Lei, and X Shirley Liu PMCID: PMC2596141 Expression of the cytochrome P450s, CYP6P3 and CYP6M2 are significantly elevated in multiple pyrethroid resistant populations of Anopheles gambiae s.s. from Southern Benin and Nigeria Rousseau F Djouaka, Adekunle A Bakare, Ousmane N Coulibaly, Martin C Akogbeto, Hilary Ranson, Janet Hemingway, and Clare Strode PMCID: PMC2588609 Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches Foo Cheung, Joe Win, Jillian M Lang, John Hamilton, Hue Vuong, Jan E Leach, Sophien Kamoun, C André Lévesque, Ned Tisserat, and C Robin Buell PMCID: PMC2612028 Genomic characterization of putative allergen genes in peach/almond and their synteny with apple Lin Chen, Shuiming Zhang, Eudald Illa, Lijuan Song, Shandong Wu, Werner Howad, Pere Arús, Eric van de Weg, Kunsong Chen, and Zhongshan Gao PMCID: PMC2621206 Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: A genome and transcriptome approach Debora F Rodrigues, Natalia Ivanova, Zhili He, Marianne Huebner, Jizhong Zhou, and James M Tiedje PMCID: PMC2615787 Genome-wide survey of prokaryotic serine proteases: Analysis of distribution and domain architectures of five serine protease families in prokaryotes Lokesh P Tripathi and R Sowdhamini PMCID: PMC2605481 Genome-wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis Tongtong Xue, Dong Wang, Shizhong Zhang, Juergen Ehlting, Fei Ni, Stephen Jakab, Chengchao Zheng, and Yuan Zhong PMCID: PMC2612031 A genome-wide Asian genetic map and ethnic comparison: The GENDISCAN study Young Seok Ju, Hansoo Park, Mi-Kyeong Lee, Jong-Il Kim, Joohon Sung, Sung-Il Cho, and Jeong-Sun Seo PMCID: PMC2612022 New insights into the origin of the B genome of hexaploid wheat: Evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides Jérome Salse, Véronique Chagué, Stéphanie Bolot, Ghislaine Magdelenat, Cécile Huneau, Caroline Pont, Harry Belcram, Arnaud Couloux, Soazic Gardais, Aurélie Evrard, Béatrice Segurens, Mathieu Charles, Catherine Ravel, Sylvie Samain, Gilles Charmet, Nathalie Boudet, and Boulos Chalhoub PMCID: PMC2612700 Differential replication dynamics for large and small Vibrio chromosomes affect gene dosage, expression and location Rikard Dryselius, Kaori Izutsu, Takeshi Honda, and Tetsuya Iida PMCID: PMC2612033 Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure Robert S Coyne, Mathangi Thiagarajan, Kristie M Jones, Jennifer R Wortman, Luke J Tallon, Brian J Haas, Donna M Cassidy-Hanley, Emily A Wiley, Joshua J Smith, Kathleen Collins, Suzanne R Lee, Mary T Couvillion, Yifan Liu, Jyoti Garg, Ronald E Pearlman, Eileen P Hamilton, Eduardo Orias, Jonathan A Eisen, and Barbara A Methé PMCID: PMC2612030 LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice Hao Wang, Zhao Xu, and Hongjie Yu PMCID: PMC2612701 Genomic islands from five strains of Burkholderia pseudomallei Apichai Tuanyok, Benjamin R Leadem, Raymond K Auerbach, Stephen M Beckstrom-Sternberg, James S Beckstrom-Sternberg, Mark Mayo, Vanaporn Wuthiekanun, Thomas S Brettin, William C Nierman, Sharon J Peacock, Bart J Currie, David M Wagner, and Paul Keim PMCID: PMC2612704 Recent CR1 non-LTR retrotransposon activity in coscoroba reveals an insertion site preference Judy St John and Thomas W Quinn PMCID: PMC2612034 Genome plasticity of Vibrio parahaemolyticus: microevolution of the 'pandemic group' Haihong Han, Hin-chung Wong, Biao Kan, Zhaobiao Guo, Xiaotao Zeng, Shengjun Yin, Xiumei Liu, Ruifu Yang, and Dongsheng Zhou PMCID: PMC2612023 Dissecting an alternative splicing analysis workflow for GeneChip® Exon 1.0 ST Affymetrix arrays Cristina Della Beffa, Francesca Cordero, and Raffaele A Calogero PMCID: PMC2612032 A novel custom high density-comparative genomic hybridization array detects common rearrangements as well as deep intronic mutations in dystrophinopathies Matteo Bovolenta, Marcella Neri, Sergio Fini, Marina Fabris, Cecilia Trabanelli, Anna Venturoli, Elena Martoni, Elena Bassi, Pietro Spitali, Simona Brioschi, Maria S Falzarano, Paola Rimessi, Roberto Ciccone, Emma Ashton, Joanne McCauley, Shu Yau, Stephen Abbs, Francesco Muntoni, Luciano Merlini, Francesca Gualandi, and Alessandra Ferlini PMCID: PMC2612025 Differential expression profiling of components associated with exoskeletal hardening in crustaceans Anna V Kuballa and Abigail Elizur PMCID: PMC2612702 Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans Fabrice Armougom and Didier Raoult PMCID: PMC2625370 Resequencing microarray probe design for typing genetically diverse viruses: human rhinoviruses and enteroviruses Zheng Wang, Anthony P Malanoski, Baochuan Lin, Carolyn Kidd, Nina C Long, Kate M Blaney, Dzung C Thach, Clark Tibbetts, and David A Stenger PMCID: PMC2607299 Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations Gloria Levicán, Juan A Ugalde, Nicole Ehrenfeld, Alejandro Maass, and Pilar Parada PMCID: PMC2607301 Properties of non-coding DNA and identification of putative cis-regulatory elements in Theileria parva Xiang Guo and Joana C Silva PMCID: PMC2612703 Chemical-genetic profile analysis in yeast suggests that a previously uncharacterized open reading frame, YBR261C, affects protein synthesis Md Alamgir, Veronika Eroukova, Matthew Jessulat, Jianhua Xu, and Ashkan Golshani PMCID: PMC2613417 Overcoming function annotation errors in the Gram-positive pathogen Streptococcus suis by a proteomics-driven approach Manuel J Rodríguez-Ortega, Inmaculada Luque, Carmen Tarradas, and José A Bárcena PMCID: PMC2613929 A cross-species transcriptomics approach to identify genes involved in leaf development Nathaniel Robert Street, Andreas Sjödin, Max Bylesjö, Petter Gustafsson, Johan Trygg, and Stefan Jansson PMCID: PMC2621207 EST analysis of male accessory glands from Heliconius butterflies with divergent mating systems James R Walters and Richard G Harrison PMCID: PMC2621208 High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families Gyorgy Szittya, Simon Moxon, Dulce M Santos, Runchun Jing, Manuel PS Fevereiro, Vincent Moulton, and Tamas Dalmay PMCID: PMC2621214 Insights into the genome sequence of a free-living Kinetoplastid: Bodo saltans (Kinetoplastida: Euglenozoa) Andrew P Jackson, Michael A Quail, and Matthew Berriman PMCID: PMC2621209 Mononucleotide repeats are asymmetrically distributed in fungal genes Mark WJ van Passel and Leo H de Graaff PMCID: PMC2621210 Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications Jorge Valdés, Inti Pedroso, Raquel Quatrini, Robert J Dodson, Herve Tettelin, Robert Blake, II, Jonathan A Eisen, and David S Holmes PMCID: PMC2621215 High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies Jean-Marc Aury, Corinne Cruaud, Valérie Barbe, Odile Rogier, Sophie Mangenot, Gaelle Samson, Julie Poulain, Véronique Anthouard, Claude Scarpelli, François Artiguenave, and Patrick Wincker PMCID: PMC2625371 A first generation whole genome RH map of the river buffalo with comparison to domestic cattle M Elisabete J Amaral, Jason R Grant, Penny K Riggs, Nedenia B Stafuzza, Edson A Rodrigues Filho, Tom Goldammer, Rosemarie Weikard, Ronald M Brunner, Kelli J Kochan, Anthony J Greco, Jooha Jeong, Zhipeng Cai, Guohui Lin, Aparna Prasad, Satish Kumar, G Pardha Saradhi, Boby Mathew, M Aravind Kumar, Melissa N Miziara, Paola Mariani, Alexandre R Caetano, Stephan R Galvão, Madhu S Tantia, Ramesh K Vijh, Bina Mishra, ST Bharani Kumar, Vanderlei A Pelai, Andre M Santana, Larissa C Fornitano, Brittany C Jones, Humberto Tonhati, Stephen Moore, Paul Stothard, and James E Womack PMCID: PMC2625372 Methodology Articles Viral genome sequencing by random priming methods Appolinaire Djikeng, Rebecca Halpin, Ryan Kuzmickas, Jay DePasse, Jeremy Feldblyum, Naomi Sengamalay, Claudio Afonso, Xinsheng Zhang, Norman G Anderson, Elodie Ghedin, and David J Spiro PMCID: PMC2254600 A highly sensitive and specific system for large-scale gene expression profiling Guohong Hu, Qifeng Yang, Xiangfeng Cui, Gang Yue, Marco A Azaro, Hui-Yun Wang, and Honghua Li PMCID: PMC2267712 Accounting for one-channel depletion improves missing value imputation in 2-dye microarray data Cecilia Ritz and Patrik Edén PMCID: PMC2267710 Genome-wide analysis of antisense transcription with Affymetrix exon array Xijin Ge, Wendy S Rubinstein, Yong-chul Jung, and Qingfa Wu PMCID: PMC2257944 A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes Ben Carter, Guanghui Wu, Martin J Woodward, and Muna F Anjum PMCID: PMC2262894 A novel method to quantify local CpG methylation density by regional methylation elongation assay on microarray Dingdong Zhang, Yan Wang, Yunfei Bai, Qinyu Ge, Yingjuan Qiao, Junfeng Luo, Chao Jia, and Zuhong Lu PMCID: PMC2262069 High-throughput mammalian two-hybrid screening for protein-protein interactions using transfected cell arrays Andrea Fiebitz, Lajos Nyarsik, Bernard Haendler, Yu-Hui Hu, Florian Wagner, Sabine Thamm, Hans Lehrach, Michal Janitz, and Dominique Vanhecke PMCID: PMC2254387 The Sterolgene v0 cDNA microarray: a systemic approach to studies of cholesterol homeostasis and drug metabolism Tadeja Režen, Peter Juvan, Klementina Fon Tacer, Drago Kuzman, Adrian Roth, Denis Pompon, Lawrence P Aggerbeck, Urs A Meyer, and Damjana Rozman PMCID: PMC2262072 Multiplex-Ready PCR: A new method for multiplexed SSR and SNP genotyping Matthew J Hayden, Thao M Nguyen, Amanda Waterman, and Kenneth J Chalmers PMCID: PMC2275739 Complementary RNA amplification methods enhance microarray identification of transcripts expressed in the C. elegans nervous system Joseph D Watson, Shenglong Wang, Stephen E Von Stetina, W Clay Spencer, Shawn Levy, Phillip J Dexheimer, Nurith Kurn, Joe Don Heath, and David M Miller, III PMCID: PMC2263045 Quantitative Single-letter Sequencing: a method for simultaneously monitoring numerous known allelic variants in single DNA samples Baptiste Monsion, Hervé Duborjal, and Stéphane Blanc PMCID: PMC2276495 Microarray analysis of defined Mycobacterium tuberculosis populations using RNA amplification strategies Simon J Waddell, Ken Laing, Claire Senner, and Philip D Butcher PMCID: PMC2276497 A genome-wide SNP panel for mapping and association studies in the rat Isaäc J Nijman, Sylvia Kuipers, Mark Verheul, Victor Guryev, and Edwin Cuppen PMCID: PMC2266910 Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis Amarendra S Yavatkar, Yong Lin, Jermaine Ross, Yang Fann, Thomas Brody, and Ward F Odenwald PMCID: PMC2268679 Systematic identification of cell cycle regulated transcription factors from microarray time series data Chao Cheng and Lei M Li PMCID: PMC2315658 An anatomy ontology to represent biological knowledge in Dictyostelium discoideum Pascale Gaudet, Jeffery G Williams, Petra Fey, and Rex L Chisholm PMCID: PMC2323390 On detection and assessment of statistical significance of Genomic Islands Raghunath Chatterjee, Keya Chaudhuri, and Probal Chaudhuri PMCID: PMC2362129 A gene sets approach for identifying prognostic gene signatures for outcome prediction Seon-Young Kim and Yong Sung Kim PMCID: PMC2364634 Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants Matthieu G Conte, Sylvain Gaillard, Gaetan Droc, and Christophe Perin PMCID: PMC2377279 Improved microarray gene expression profiling of virus-infected cells after removal of viral RNA Matthijs Raaben, Penn Whitley, Diane Bouwmeester, Robert A Setterquist, Peter JM Rottier, and Cornelis AM de Haan PMCID: PMC2397413 Optimal control and analysis of two-color genomotyping experiments using bacterial multistrain arrays Francisco R Pinto, Sandra I Aguiar, J Melo-Cristino, and Mário Ramirez PMCID: PMC2410139 Sequence polymorphism can produce serious artefacts in real-time PCR assays: hard lessons from Pacific oysters Nicolas Taris, Robert P Lang, and Mark D Camara PMCID: PMC2424065 Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study Wei Sun, Shinsheng Yuan, and Ker-Chau Li PMCID: PMC2432080 Identification of SNPs and INDELS in swine transcribed sequences using short oligonucleotide microarrays Steve R Bischoff, Shengdar Tsai, Nicholas E Hardison, Abby M York, Brad A Freking, Dan Nonneman, Gary Rohrer, and Jorge A Piedrahita PMCID: PMC2442091 Exploiting orthologue diversity for systematic detection of gain-of-function phenotypes Maria Luisa Martelli, Claudio Isella, Alessia Mira, Limin Fu, Daniela Cantarella, and Enzo Medico PMCID: PMC2435555 Combination of native and denaturing PAGE for the detection of protein binding regions in long fragments of genomic DNA Kristel Kaer, Kert Mätlik, Madis Metsis, and Mart Speek PMCID: PMC2435560 A simple and accurate SNP scoring strategy based on typeIIS restriction endonuclease cleavage and matrix-assisted laser desorption/ionization mass spectrometry Sun Pyo Hong, Seung Il Ji, Hwanseok Rhee, Soo Kyeong Shin, Sun Young Hwang, Seung Hwan Lee, Soong Deok Lee, Heung-Bum Oh, Wangdon Yoo, and Soo-Ok Kim PMCID: PMC2442615 Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley Hana Šimková, Jan T Svensson, Pascal Condamine, Eva Hřibová, Pavla Suchánková, Prasanna R Bhat, Jan Bartoš, Jan Šafář, Timothy J Close, and Jaroslav Doležel PMCID: PMC2453526 A genome-wide 20 K citrus microarray for gene expression analysis M Angeles Martinez-Godoy, Nuria Mauri, Jose Juarez, M Carmen Marques, Julia Santiago, Javier Forment, and Jose Gadea PMCID: PMC2483987 Between-groups within-gene heterogeneity of residual variances in microarray gene expression data Joaquim Casellas and Luis Varona PMCID: PMC2488361 A method for detecting epistasis in genome-wide studies using case-control multi-locus association analysis Javier Gayán, Antonio González-Pérez, Fernando Bermudo, María Eugenia Sáez, Jose Luis Royo, Antonio Quintas, Jose Jorge Galan, Francisco Jesús Morón, Reposo Ramirez-Lorca, Luis Miguel Real, and Agustín Ruiz PMCID: PMC2533022 Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray Hongying Jiang, Ming Yi, Jianbing Mu, Louie Zhang, Al Ivens, Leszek J Klimczak, Yentram Huyen, Robert M Stephens, and Xin-zhuan Su PMCID: PMC2543026 Haplotype block partitioning as a tool for dimensionality reduction in SNP association studies Cristian Pattaro, Ingo Ruczinski, Danièle M Fallin, and Giovanni Parmigiani PMCID: PMC2547855 Multiple displacement amplification for complex mixtures of DNA fragments Muhammad Shoaib, Sonia Baconnais, Undine Mechold, Eric Le Cam, Marc Lipinski, and Vasily Ogryzko PMCID: PMC2553422 A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome Lucie Hanriot, Céline Keime, Nadine Gay, Claudine Faure, Carole Dossat, Patrick Wincker, Céline Scoté-Blachon, Christelle Peyron, and Olivier Gandrillon PMCID: PMC2562395 A novel reverse transduction adenoviral array for the functional analysis of shRNA libraries Angelika Oehmig, Andrea Klotzbücher, Maria Thomas, Frank Weise, Ursula Hagner, Ralf Brundiers, Dirk Waldherr, Andreas Lingnau, Achim Knappik, Michael HG Kubbutat, Thomas O Joos, and Hansjürgen Volkmer PMCID: PMC2559852 A MITE-based genotyping method to reveal hundreds of DNA polymorphisms in an animal genome after a few generations of artificial selection Aurélie Bonin, Margot Paris, Laurence Després, Guillaume Tetreau, Jean-Philippe David, and Andrzej Kilian PMCID: PMC2579443 Improved generation of rat gene knockouts by target-selected mutagenesis in mismatch repair-deficient animals Ruben van Boxtel, Pim W Toonen, Mark Verheul, Henk S van Roekel, Isaac J Nijman, Victor Guryev, and Edwin Cuppen PMCID: PMC2567347 Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer Roberta Bordoni, Raoul Bonnal, Ermanno Rizzi, Paola Carrera, Sara Benedetti, Laura Cremonesi, Stefania Stenirri, Alessio Colombo, Cristina Montrasio, Sara Bonalumi, Alberto Albertini, Luigi Rossi Bernardi, Maurizio Ferrari, and Gianluca De Bellis PMCID: PMC2569949 Improved coverage of cDNA-AFLP by sequential digestion of immobilized cDNA Arne Weiberg, Dirk Pöhler, Burkhard Morgenstern, and Petr Karlovsky PMCID: PMC2577664 Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients Wynn L Walker, Isaac H Liao, Donald L Gilbert, Brenda Wong, Katherine S Pollard, Charles E McCulloch, Lisa Lit, and Frank R Sharp PMCID: PMC2576259 In silico microarray probe design for diagnosis of multiple pathogens Ravi Vijaya Satya, Nela Zavaljevski, Kamal Kumar, Elizabeth Bode, Susana Padilla, Leonard Wasieloski, Jeanne Geyer, and Jaques Reifman PMCID: PMC2596143 Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization Stephane Flibotte and Donald G Moerman PMCID: PMC2577661 Enhanced cross-species utility of conserved microsatellite markers in shorebirds Clemens Küpper, Terry Burke, Tamás Székely, and Deborah A Dawson PMCID: PMC2588463 An optimized procedure for the design and evaluation of Ecotilling assays Stefan Coassin, Anita Brandstätter, and Florian Kronenberg PMCID: PMC2586031 A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes Stefan Kurtz, Apurva Narechania, Joshua C Stein, and Doreen Ware PMCID: PMC2613927 Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays Amandine Bemmo, David Benovoy, Tony Kwan, Daniel J Gaffney, Roderick V Jensen, and Jacek Majewski PMCID: PMC2585104 A new strategy for faster urinary biomarkers identification by Nano-LC-MALDI-TOF/TOF mass spectrometry K Benkali, P Marquet, JP Rérolle, Y Le Meur, and LN Gastinel PMCID: PMC2596142 Application of dissociation curve analysis to radiation hybrid panel marker scoring: generation of a map of river buffalo (B. bubalis) chromosome 20 Kelli J Kochan, M Elisabete J Amaral, Richa Agarwala, Alejandro A Schäffer, and Penny K Riggs PMCID: PMC2621213 Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs Fumihito Miura, Noriko Kawaguchi, Mikio Yoshida, Chihiro Uematsu, Keiji Kito, Yoshiyuki Sakaki, and Takashi Ito PMCID: PMC2612024 A toolbox for epitope-tagging and genome-wide location analysis in Candida albicans Hugo Lavoie, Adnane Sellam, Christopher Askew, André Nantel, and Malcolm Whiteway PMCID: PMC2607300 Evaluating genome-wide DNA methylation changes in mice by Methylation Specific Digital Karyotyping Kathy Boon, John K Tomfohr, Nathaniel W Bailey, Stavros Garantziotis, Zhuowei Li, David M Brass, Shuichiro Maruoka, John W Hollingsworth, and David A Schwartz PMCID: PMC2621211 Corrections Coral life history and symbiosis: Functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata Jodi A Schwarz, Peter B Brokstein, Christian Voolstra, Astrid Y Terry, Chitra F Manohar, David J Miller, Alina M Szmant, Mary Alice Coffroth, and Mónica Medina PMCID: PMC2559851 Corrects: Jodi A Schwarz, et al. Coral life history and symbiosis: Functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata. BMC Genomics. 2008; 9: 97. The complete mitochondrial genome sequence of the hydrothermal vent galatheid crab Shinkaia crosnieri (Crustacea: Decapoda: Anomura): A novel arrangement and incomplete tRNA suite Jin-Shu Yang, Hiromichi Nagasawa, Yoshihiro Fujiwara, Shinji Tsuchida, and Wei-Jun Yang PMCID: PMC2582037 Corrects: Jin-Shu Yang, et al. The complete mitochondrial genome sequence of the hydrothermal vent galatheid crab Shinkaia crosnieri (Crustacea: Decapoda: Anomura): A novel arrangement and incomplete tRNA suite. BMC Genomics. 2008; 9: 257. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A Steven L Salzberg, Daniel D Sommer, Michael C Schatz, Adam M Phillippy, Pablo D Rabinowicz, Seiji Tsuge, Ayako Furutani, Hirokazu Ochiai, Arthur L Delcher, David Kelley, Ramana Madupu, Daniela Puiu, Diana Radune, Martin Shumway, Cole Trapnell, Gudlur Aparna, Gopaljee Jha, Alok Pandey, Prabhu B Patil, Hiromichi Ishihara, Damien F Meyer, Boris Szurek, Valerie Verdier, Ralf Koebnik, J Maxwell Dow, Robert P Ryan, Hisae Hirata, Shinji Tsuyumu, Sang Won Lee, Young-Su Seo, Malinee Sriariyanum, Pamela C Ronald, Ramesh V Sonti, Marie-Anne Van Sluys, Jan E Leach, Frank F White, and Adam J Bogdanove PMCID: PMC2588604 Corrects: Steven L Salzberg, et al. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics. 2008; 9: 204. |
