| | 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 Biol Direct. 2008; 3: 2. Published online 2008 January 25. doi: 10.1186/1745-6150-3-2.PMCID: PMC2253512 Orphan SelD proteins and selenium-dependent molybdenum hydroxylases Daniel H Haft and William T Self Biol Direct. 2008; 3: 4. Published online 2008 February 20. doi: 10.1186/1745-6150-3-4.PMCID: PMC2276186 MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases Lakshminarayan M Iyer, Saraswathi Abhiman, and L Aravind Biol Direct. 2008; 3: 8. Published online 2008 March 17. doi: 10.1186/1745-6150-3-8.PMCID: PMC2292703 Endogenous retroviruses of the chicken genome Ahsan Huda, Nalini Polavarapu, I King Jordan, and John F McDonald Biol Direct. 2008; 3: 9. Published online 2008 March 24. doi: 10.1186/1745-6150-3-9.PMCID: PMC2329609 An intragenic distribution bias of DNA uptake sequences in Pasteurellaceae and Neisseriae Mark WJ van Passel Biol Direct. 2008; 3: 12. Published online 2008 March 27. doi: 10.1186/1745-6150-3-12.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 Biol Direct. 2008; 3: 19. Published online 2008 May 14. doi: 10.1186/1745-6150-3-19.PMCID: PMC2426677 cpRAS: a novel circularly permuted RAS-like GTPase domain with a highly scattered phylogenetic distribution Marek Elias and Marian Novotny Biol Direct. 2008; 3: 21. Published online 2008 May 29. doi: 10.1186/1745-6150-3-21.PMCID: PMC2430557 Accumulation of GC donor splice signals in mammals Alexander Churbanov, Stephen Winters-Hilt, Eugene V Koonin, and Igor B Rogozin Biol Direct. 2008; 3: 30. Published online 2008 July 9. doi: 10.1186/1745-6150-3-30.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 Biol Direct. 2008; 3: 32. Published online 2008 August 6. doi: 10.1186/1745-6150-3-32.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 Biol Direct. 2008; 3: 39. Published online 2008 October 4. doi: 10.1186/1745-6150-3-39.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 Biol Direct. 2008; 3: 41. Published online 2008 October 8. doi: 10.1186/1745-6150-3-41.PMCID: PMC2572040 Synaptic enrichment of microRNAs in adult mouse forebrain is related to structural features of their precursors Neil R Smalheiser Biol Direct. 2008; 3: 44. Published online 2008 October 29. doi: 10.1186/1745-6150-3-44.PMCID: PMC2588566 Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination Lakshminarayan M Iyer, AM Burroughs, and L Aravind Biol Direct. 2008; 3: 45. Published online 2008 November 3. doi: 10.1186/1745-6150-3-45.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 Biol Direct. 2008; 3: 54. Published online 2008 December 23. doi: 10.1186/1745-6150-3-54.PMCID: PMC2621148 Editorials Mathematical Biology in Biology Direct Andrei Yakovlev Biol Direct. 2008; 3: 1. Published online 2008 January 16. doi: 10.1186/1745-6150-3-1.PMCID: PMC2216004 Dr. Andrei Yakovlev: Visionary, Leader, Iconoclast Yuriy Gusev, Leonid Hanin, Lev Klebanov, Alex Tsodikov, Nikolay M Yanev, and Alexander Zorin Biol Direct. 2008; 3: 10. Published online 2008 March 26. doi: 10.1186/1745-6150-3-10.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 Biol Direct. 2008; 3: 14. Published online 2008 April 11. doi: 10.1186/1745-6150-3-14.PMCID: PMC2373780 Erwin Schroedinger, Francis Crick and epigenetic stability Vasily V Ogryzko Biol Direct. 2008; 3: 15. Published online 2008 April 17. doi: 10.1186/1745-6150-3-15.PMCID: PMC2413215 An extension of the coevolution theory of the origin of the genetic code Massimo Di Giulio Biol Direct. 2008; 3: 37. Published online 2008 September 5. doi: 10.1186/1745-6150-3-37.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 Biol Direct. 2008; 3: 42. Published online 2008 October 14. doi: 10.1186/1745-6150-3-42.PMCID: PMC2590596 Exon definition as a potential negative force against intron losses in evolution Deng-Ke Niu Biol Direct. 2008; 3: 46. Published online 2008 November 13. doi: 10.1186/1745-6150-3-46.PMCID: PMC2614967 On the brink between extinction and persistence Cino Pertoldi, Lars A Bach, and Volker Loeschcke Biol Direct. 2008; 3: 47. Published online 2008 November 19. doi: 10.1186/1745-6150-3-47.PMCID: PMC2613133 Are we degenerate tetraploids? More genomes, new facts Amir Ali Abbasi Biol Direct. 2008; 3: 50. Published online 2008 December 10. doi: 10.1186/1745-6150-3-50.PMCID: PMC2615429 Research The control of CD4+CD25+Foxp3+ regulatory T cell survival Pushpa Pandiyan and Michael J Lenardo Biol Direct. 2008; 3: 6. Published online 2008 February 27. doi: 10.1186/1745-6150-3-6.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 Biol Direct. 2008; 3: 7. Published online 2008 March 17. doi: 10.1186/1745-6150-3-7.PMCID: PMC2292158 Evolution of complexity in RNA-like replicator systems Nobuto Takeuchi and Paulien Hogeweg Biol Direct. 2008; 3: 11. Published online 2008 March 27. doi: 10.1186/1745-6150-3-11.PMCID: PMC2390529 Evolutionary primacy of sodium bioenergetics Armen Y Mulkidjanian, Michael Y Galperin, Kira S Makarova, Yuri I Wolf, and Eugene V Koonin Biol Direct. 2008; 3: 13. Published online 2008 April 1. doi: 10.1186/1745-6150-3-13.PMCID: PMC2359735 The origin and evolution of the ribosome Temple F Smith, Jung C Lee, Robin R Gutell, and Hyman Hartman Biol Direct. 2008; 3: 16. Published online 2008 April 22. doi: 10.1186/1745-6150-3-16.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 Biol Direct. 2008; 3: 17. Published online 2008 April 29. doi: 10.1186/1745-6150-3-17.PMCID: PMC2390528 The look-ahead effect of phenotypic mutations Dion J Whitehead, Claus O Wilke, David Vernazobres, and Erich Bornberg-Bauer Biol Direct. 2008; 3: 18. Published online 2008 May 14. doi: 10.1186/1745-6150-3-18.PMCID: PMC2423361 Splign: algorithms for computing spliced alignments with identification of paralogs Yuri Kapustin, Alexander Souvorov, Tatiana Tatusova, and David Lipman Biol Direct. 2008; 3: 20. Published online 2008 May 21. doi: 10.1186/1745-6150-3-20.PMCID: PMC2440734 Classifying transcription factor targets and discovering relevant biological features Dustin T Holloway, Mark Kon, and Charles DeLisi Biol Direct. 2008; 3: 22. Published online 2008 May 30. doi: 10.1186/1745-6150-3-22.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 Biol Direct. 2008; 3: 23. Published online 2008 June 3. doi: 10.1186/1745-6150-3-23.PMCID: PMC2453111 In silico regulatory analysis for exploring human disease progression Dustin T Holloway, Mark Kon, and Charles DeLisi Biol Direct. 2008; 3: 24. Published online 2008 June 18. doi: 10.1186/1745-6150-3-24.PMCID: PMC2464594 Genetic characterization of Hawaiian isolates of Plasmodium relictum reveals mixed-genotype infections Susan I Jarvi, Margaret EM Farias, and Carter T Atkinson Biol Direct. 2008; 3: 25. Published online 2008 June 25. doi: 10.1186/1745-6150-3-25.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 Biol Direct. 2008; 3: 26. Published online 2008 July 1. doi: 10.1186/1745-6150-3-26.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 Biol Direct. 2008; 3: 27. Published online 2008 July 2. doi: 10.1186/1745-6150-3-27.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 Biol Direct. 2008; 3: 28. Published online 2008 July 3. doi: 10.1186/1745-6150-3-28.PMCID: PMC2467403 The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner Nicolas Glansdorff, Ying Xu, and Bernard Labedan Biol Direct. 2008; 3: 29. Published online 2008 July 9. doi: 10.1186/1745-6150-3-29.PMCID: PMC2478661 Origin of the nucleus and Ran-dependent transport to safeguard ribosome biogenesis in a chimeric cell Gáspár Jékely Biol Direct. 2008; 3: 31. Published online 2008 July 24. doi: 10.1186/1745-6150-3-31.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 Biol Direct. 2008; 3: 34. Published online 2008 August 20. doi: 10.1186/1745-6150-3-34.PMCID: PMC2529272 A nitty-gritty aspect of correlation and network inference from gene expression data Lev B Klebanov and Andrei Yu Yakovlev Biol Direct. 2008; 3: 35. Published online 2008 August 20. doi: 10.1186/1745-6150-3-35.PMCID: PMC2569917 Same-strand overlapping genes in bacteria: compositional determinants of phase bias Niv Sabath, Dan Graur, and Giddy Landan Biol Direct. 2008; 3: 36. Published online 2008 August 21. doi: 10.1186/1745-6150-3-36.PMCID: PMC2542354 CAIcal: A combined set of tools to assess codon usage adaptation Pere Puigbò, Ignacio G Bravo, and Santiago Garcia-Vallve Biol Direct. 2008; 3: 38. Published online 2008 September 16. doi: 10.1186/1745-6150-3-38.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 Biol Direct. 2008; 3: 40. Published online 2008 October 7. doi: 10.1186/1745-6150-3-40.PMCID: PMC2572155 Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift? Richard W Jobson and Yin-Long Qiu Biol Direct. 2008; 3: 43. Published online 2008 October 21. doi: 10.1186/1745-6150-3-43.PMCID: PMC2584032 The evolution of domain-content in bacterial genomes Nacho Molina and Erik van Nimwegen Biol Direct. 2008; 3: 51. Published online 2008 December 11. doi: 10.1186/1745-6150-3-51.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 Biol Direct. 2008; 3: 3. Published online 2008 January 28. doi: 10.1186/1745-6150-3-3.PMCID: PMC2241844 Molecular chaperones and selection against mutations Katarzyna Tomala and Ryszard Korona Biol Direct. 2008; 3: 5. Published online 2008 February 26. doi: 10.1186/1745-6150-3-5.PMCID: PMC2267774 |