| | Other Issues: previous | next | latest | archiveDiscovery Notes The prokaryotic V4R domain is the likely ancestor of a key component of the eukaryotic vesicle transport system Mircea Podar, Mark A Wall, Kira S Makarova, and Eugene V Koonin PMCID: PMC2253512 Orphan SelD proteins and selenium-dependent molybdenum hydroxylases Daniel H Haft and William T Self PMCID: PMC2276186 MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases Lakshminarayan M Iyer, Saraswathi Abhiman, and L Aravind PMCID: PMC2292703 Endogenous retroviruses of the chicken genome Ahsan Huda, Nalini Polavarapu, I King Jordan, and John F McDonald PMCID: PMC2329609 An intragenic distribution bias of DNA uptake sequences in Pasteurellaceae and Neisseriae Mark WJ van Passel PMCID: PMC2346458 U12 intron positions are more strongly conserved between animals and plants than U2 intron positions Malay Kumar Basu, Wojciech Makalowski, Igor B Rogozin, and Eugene V Koonin PMCID: PMC2426677 cpRAS: a novel circularly permuted RAS-like GTPase domain with a highly scattered phylogenetic distribution Marek Elias and Marian Novotny PMCID: PMC2430557 Accumulation of GC donor splice signals in mammals Alexander Churbanov, Stephen Winters-Hilt, Eugene V Koonin, and Igor B Rogozin PMCID: PMC2490688 A highly conserved family of inactivated archaeal B family DNA polymerases Igor B Rogozin, Kira S Makarova, Youri I Pavlov, and Eugene V Koonin PMCID: PMC2527604 A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases Lakshminarayan M Iyer, Saraswathi Abhiman, and L Aravind PMCID: PMC2579912 Transduplication resulted in the incorporation of two protein-coding sequences into the Turmoil-1 transposable element of C. elegans Noa Sela, Adi Stern, Wojciech Makalowski, Tal Pupko, and Gil Ast PMCID: PMC2572040 Synaptic enrichment of microRNAs in adult mouse forebrain is related to structural features of their precursors Neil R Smalheiser PMCID: PMC2588566 Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination Lakshminarayan M Iyer, AM Burroughs, and L Aravind PMCID: PMC2588565 A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya Céline Brochier-Armanet, Simonetta Gribaldo, and Patrick Forterre PMCID: PMC2621148 Editorials Mathematical Biology in Biology Direct Andrei Yakovlev PMCID: PMC2216004 Dr. Andrei Yakovlev: Visionary, Leader, Iconoclast Yuriy Gusev, Leonid Hanin, Lev Klebanov, Alex Tsodikov, Nikolay M Yanev, and Alexander Zorin PMCID: PMC2287165 Hypothesis Occurrence of cancer at multiple sites: Towards distinguishing multigenesis from metastasis Wei-Kang Zhang, Chun Zhang, Jing J Zhang, and Shi V Liu PMCID: PMC2373780 Erwin Schroedinger, Francis Crick and epigenetic stability Vasily V Ogryzko PMCID: PMC2413215 An extension of the coevolution theory of the origin of the genetic code Massimo Di Giulio PMCID: PMC2538516 A new model defines the minimal set of polymorphism in HLA-DQ and -DR that determines susceptibility and resistance to autoimmune diabetes Christian S Parry and Bernard R Brooks PMCID: PMC2590596 Exon definition as a potential negative force against intron losses in evolution Deng-Ke Niu PMCID: PMC2614967 On the brink between extinction and persistence Cino Pertoldi, Lars A Bach, and Volker Loeschcke PMCID: PMC2613133 Are we degenerate tetraploids? More genomes, new facts Amir Ali Abbasi PMCID: PMC2615429 Research The control of CD4+CD25+Foxp3+ regulatory T cell survival Pushpa Pandiyan and Michael J Lenardo PMCID: PMC2270257 Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series Igor B Rogozin, Karen Thomson, Miklós Csürös, Liran Carmel, and Eugene V Koonin PMCID: PMC2292158 Evolution of complexity in RNA-like replicator systems Nobuto Takeuchi and Paulien Hogeweg PMCID: PMC2390529 Evolutionary primacy of sodium bioenergetics Armen Y Mulkidjanian, Michael Y Galperin, Kira S Makarova, Yuri I Wolf, and Eugene V Koonin PMCID: PMC2359735 The origin and evolution of the ribosome Temple F Smith, Jung C Lee, Robin R Gutell, and Hyman Hartman PMCID: PMC2386862 14-3-3 theta binding to cell cycle regulatory factors is enhanced by HIV-1 Vpr Diane L Bolton, Robert A Barnitz, Keiko Sakai, and Michael J Lenardo PMCID: PMC2390528 The look-ahead effect of phenotypic mutations Dion J Whitehead, Claus O Wilke, David Vernazobres, and Erich Bornberg-Bauer PMCID: PMC2423361 Splign: algorithms for computing spliced alignments with identification of paralogs Yuri Kapustin, Alexander Souvorov, Tatiana Tatusova, and David Lipman PMCID: PMC2440734 Classifying transcription factor targets and discovering relevant biological features Dustin T Holloway, Mark Kon, and Charles DeLisi PMCID: PMC2441612 On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation Wing-Cheong Wong, Marie Loh, and Frank Eisenhaber PMCID: PMC2453111 In silico regulatory analysis for exploring human disease progression Dustin T Holloway, Mark Kon, and Charles DeLisi PMCID: PMC2464594 Genetic characterization of Hawaiian isolates of Plasmodium relictum reveals mixed-genotype infections Susan I Jarvi, Margaret EM Farias, and Carter T Atkinson PMCID: PMC2464593 Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia Shaobin Hou, Kira S Makarova, Jimmy HW Saw, Pavel Senin, Benjamin V Ly, Zhemin Zhou, Yan Ren, Jianmei Wang, Michael Y Galperin, Marina V Omelchenko, Yuri I Wolf, Natalya Yutin, Eugene V Koonin, Matthew B Stott, Bruce W Mountain, Michelle A Crowe, Angela V Smirnova, Peter F Dunfield, Lu Feng, Lei Wang, and Maqsudul Alam PMCID: PMC2474590 Detection of co-eluted peptides using database search methods Gelio Alves, Aleksey Y Ogurtsov, Siwei Kwok, Wells W Wu, Guanghui Wang, Rong-Fong Shen, and Yi-Kuo Yu PMCID: PMC2483259 A family of GFP-like proteins with different spectral properties in lancelet Branchiostoma floridae Diana Baumann, Malcolm Cook, Limei Ma, Arcady Mushegian, Erik Sanders, Joel Schwartz, and C Ron Yu PMCID: PMC2467403 The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner Nicolas Glansdorff, Ying Xu, and Bernard Labedan PMCID: PMC2478661 Origin of the nucleus and Ran-dependent transport to safeguard ribosome biogenesis in a chimeric cell Gáspár Jékely PMCID: PMC2503971 Critical role for BIM in T cell receptor restimulation-induced death Andrew L Snow, João B Oliveira, Lixin Zheng, Janet K Dale, Thomas A Fleisher, and Michael J Lenardo PMCID: PMC2529272 A nitty-gritty aspect of correlation and network inference from gene expression data Lev B Klebanov and Andrei Yu Yakovlev PMCID: PMC2569917 Same-strand overlapping genes in bacteria: compositional determinants of phase bias Niv Sabath, Dan Graur, and Giddy Landan PMCID: PMC2542354 CAIcal: A combined set of tools to assess codon usage adaptation Pere Puigbò, Ignacio G Bravo, and Santiago Garcia-Vallve PMCID: PMC2553769 Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution Maxim Y Wolf, Yuri I Wolf, and Eugene V Koonin PMCID: PMC2572155 Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift? Richard W Jobson and Yin-Long Qiu PMCID: PMC2584032 The evolution of domain-content in bacterial genomes Nacho Molina and Erik van Nimwegen PMCID: PMC2615428 Reviews Predicting the conformations of peptides and proteins in early evolution. A review article submitted to Biology Direct E James Milner-White and Michael J Russell PMCID: PMC2241844 Molecular chaperones and selection against mutations Katarzyna Tomala and Ryszard Korona PMCID: PMC2267774 |
