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		Research 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, Frank Eisenhaber Biology Direct 2008, 3:23 (3 June 2008) Abstract \| Full text \| PDF \| PubMed
		Research Classifying transcription factor targets and discovering relevant biological features Dustin T Holloway, Mark Kon, Charles DeLisi Biology Direct 2008, 3:22 (30 May 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
		Discovery notes cpRAS: a novel circularly permuted RAS-like GTPase domain with a highly scattered phylogenetic distribution Marek Elias, Marian Novotny Biology Direct 2008, 3:21 (29 May 2008) Abstract \| Full text \| PDF \| PubMed
		Research Splign: algorithms for computing spliced alignments with identification of paralogs Yuri Kapustin, Alexander Souvorov, Tatiana Tatusova, David Lipman Biology Direct 2008, 3:20 (21 May 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Discovery notes U12 intron positions are more strongly conserved between animals and plants than U2 intron positions Malay Basu, Wojciech Makalowski, Igor B Rogozin, Eugene V Koonin Biology Direct 2008, 3:19 (14 May 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research The look-ahead effect of phenotypic mutations Dion J Whitehead, Claus O Wilke, David Vernazobres, Erich Bornberg-Bauer Biology Direct 2008, 3:18 (14 May 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research 14-3-3 theta binding to cell cycle regulatory factors is enhanced by HIV-1 Vpr Diane L Bolton, Robert A Barnitz, Keiko Sakai, Michael J Lenardo Biology Direct 2008, 3:17 (29 April 2008) Abstract \| Full text \| PDF \| PubMed
		Research The origin and evolution of the ribosome Temple F Smith, Jung C Lee, Robin R Gutell, Hyman Hartman Biology Direct 2008, 3:16 (22 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Hypothesis Erwin Schroedinger, Francis Crick and epigenetic stability Vasily V Ogryzko Biology Direct 2008, 3:15 (17 April 2008) Abstract \| Full text \| PDF \| PubMed \| 1 comment
		Hypothesis Occurrence of cancer at multiple sites: Towards distinguishing multigenesis from metastasis Wei-Kang Zhang, Chun Zhang, Jing J Zhang, Shi V Liu Biology Direct 2008, 3:14 (11 April 2008) Abstract \| Full text \| PDF \| PubMed
		Research Evolutionary primacy of sodium bioenergetics Armen Y Mulkidjanian, Michael Y Galperin, Kira S Makarova, Yuri I Wolf, Eugene V Koonin Biology Direct 2008, 3:13 (1 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology
		Discovery notes An intragenic distribution bias of DNA uptake sequences in Pasteurellaceae and Neisseriae Mark WJ van Passel Biology Direct 2008, 3:12 (27 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Evolution of complexity in RNA-like replicator systems Nobuto Takeuchi, Paulien Hogeweg Biology Direct 2008, 3:11 (27 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Editorial Dr. Andrei Yakovlev: Visionary, Leader, Iconoclast Yuriy Gusev, Leonid Hanin, Lev Klebanov, Alex Tsodikov, Nikolay M Yanev, Alexander Zorin Biology Direct 2008, 3:10 (26 March 2008) Abstract \| Full text \| PDF \| PubMed
		Discovery notes Endogenous retroviruses of the chicken genome Ahsan Huda, Nalini Polavarapu, I King Jordan, John F McDonald Biology Direct 2008, 3:9 (24 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Discovery notes MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases Lakshminarayan M Iyer, Saraswathi Abhiman, L Aravind Biology Direct 2008, 3:8 (17 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research 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, Eugene V Koonin Biology Direct 2008, 3:7 (17 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Homoplasy denotes the same (parallel) mutations occurring independently in different lineages. It is a scourge of phylogenetic methods. Here, however, it is shown that homoplasy is also an interesting evolutionary phenomenon. Homplasy seems, at least, in part, to underlie the so-called homologous series of phenotypic variation occurring in different, particularly, closely related lineages, an effect first described by the famous Russian geneticict Vavilov some 90 years ago.
		Research The control of CD4⁺CD25⁺Foxp3⁺regulatory T cell survival Pushpa Pandiyan, Michael J Lenardo Biology Direct 2008, 3:6 (27 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology
		Review Molecular chaperones and selection against mutations Katarzyna Tomala, Ryszard Korona Biology Direct 2008, 3:5 (26 February 2008) Abstract \| Full text \| PDF \| PubMed
		Discovery notes Orphan SelD proteins and selenium-dependent molybdenum hydroxylases Daniel H Haft, William T Self Biology Direct 2008, 3:4 (20 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 2 comments
		Review Predicting the conformations of peptides and proteins in early evolution E James Milner-White, Michael J Russell Biology Direct 2008, 3:3 (28 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Discovery 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, Eugene V Koonin Biology Direct 2008, 3:2 (25 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Editorial Mathematical Biology in Biology Direct Andrei Yakovlev Biology Direct 2008, 3:1 (16 January 2008) Abstract \| Full text \| PDF \| PubMed
		Research Epigenetic hereditary transcription profiles II, aging revisited Johannes WIM Simons Biology Direct 2007, 2:39 (28 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Discovery notes Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota" Eugene V Koonin, Kira S Makarova, James G Elkins Biology Direct 2007, 2:38 (14 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central

	All
		Research 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, Frank Eisenhaber Biology Direct 2008, 3:23 (3 June 2008) Abstract \| Full text \| PDF \| PubMed
		Research Classifying transcription factor targets and discovering relevant biological features Dustin T Holloway, Mark Kon, Charles DeLisi Biology Direct 2008, 3:22 (30 May 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
		Discovery notes cpRAS: a novel circularly permuted RAS-like GTPase domain with a highly scattered phylogenetic distribution Marek Elias, Marian Novotny Biology Direct 2008, 3:21 (29 May 2008) Abstract \| Full text \| PDF \| PubMed
		Research Splign: algorithms for computing spliced alignments with identification of paralogs Yuri Kapustin, Alexander Souvorov, Tatiana Tatusova, David Lipman Biology Direct 2008, 3:20 (21 May 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Discovery notes U12 intron positions are more strongly conserved between animals and plants than U2 intron positions Malay Basu, Wojciech Makalowski, Igor B Rogozin, Eugene V Koonin Biology Direct 2008, 3:19 (14 May 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research The look-ahead effect of phenotypic mutations Dion J Whitehead, Claus O Wilke, David Vernazobres, Erich Bornberg-Bauer Biology Direct 2008, 3:18 (14 May 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research 14-3-3 theta binding to cell cycle regulatory factors is enhanced by HIV-1 Vpr Diane L Bolton, Robert A Barnitz, Keiko Sakai, Michael J Lenardo Biology Direct 2008, 3:17 (29 April 2008) Abstract \| Full text \| PDF \| PubMed
		Research The origin and evolution of the ribosome Temple F Smith, Jung C Lee, Robin R Gutell, Hyman Hartman Biology Direct 2008, 3:16 (22 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Hypothesis Erwin Schroedinger, Francis Crick and epigenetic stability Vasily V Ogryzko Biology Direct 2008, 3:15 (17 April 2008) Abstract \| Full text \| PDF \| PubMed \| 1 comment
		Hypothesis Occurrence of cancer at multiple sites: Towards distinguishing multigenesis from metastasis Wei-Kang Zhang, Chun Zhang, Jing J Zhang, Shi V Liu Biology Direct 2008, 3:14 (11 April 2008) Abstract \| Full text \| PDF \| PubMed
		Research Evolutionary primacy of sodium bioenergetics Armen Y Mulkidjanian, Michael Y Galperin, Kira S Makarova, Yuri I Wolf, Eugene V Koonin Biology Direct 2008, 3:13 (1 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology
		Discovery notes An intragenic distribution bias of DNA uptake sequences in Pasteurellaceae and Neisseriae Mark WJ van Passel Biology Direct 2008, 3:12 (27 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Evolution of complexity in RNA-like replicator systems Nobuto Takeuchi, Paulien Hogeweg Biology Direct 2008, 3:11 (27 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Editorial Dr. Andrei Yakovlev: Visionary, Leader, Iconoclast Yuriy Gusev, Leonid Hanin, Lev Klebanov, Alex Tsodikov, Nikolay M Yanev, Alexander Zorin Biology Direct 2008, 3:10 (26 March 2008) Abstract \| Full text \| PDF \| PubMed
		Discovery notes Endogenous retroviruses of the chicken genome Ahsan Huda, Nalini Polavarapu, I King Jordan, John F McDonald Biology Direct 2008, 3:9 (24 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Discovery notes MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases Lakshminarayan M Iyer, Saraswathi Abhiman, L Aravind Biology Direct 2008, 3:8 (17 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research 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, Eugene V Koonin Biology Direct 2008, 3:7 (17 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Homoplasy denotes the same (parallel) mutations occurring independently in different lineages. It is a scourge of phylogenetic methods. Here, however, it is shown that homoplasy is also an interesting evolutionary phenomenon. Homplasy seems, at least, in part, to underlie the so-called homologous series of phenotypic variation occurring in different, particularly, closely related lineages, an effect first described by the famous Russian geneticict Vavilov some 90 years ago.
		Research The control of CD4⁺CD25⁺Foxp3⁺regulatory T cell survival Pushpa Pandiyan, Michael J Lenardo Biology Direct 2008, 3:6 (27 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology
		Review Molecular chaperones and selection against mutations Katarzyna Tomala, Ryszard Korona Biology Direct 2008, 3:5 (26 February 2008) Abstract \| Full text \| PDF \| PubMed
		Discovery notes Orphan SelD proteins and selenium-dependent molybdenum hydroxylases Daniel H Haft, William T Self Biology Direct 2008, 3:4 (20 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 2 comments
		Review Predicting the conformations of peptides and proteins in early evolution E James Milner-White, Michael J Russell Biology Direct 2008, 3:3 (28 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Discovery 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, Eugene V Koonin Biology Direct 2008, 3:2 (25 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Editorial Mathematical Biology in Biology Direct Andrei Yakovlev Biology Direct 2008, 3:1 (16 January 2008) Abstract \| Full text \| PDF \| PubMed
		Research Epigenetic hereditary transcription profiles II, aging revisited Johannes WIM Simons Biology Direct 2007, 2:39 (28 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Discovery notes Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota" Eugene V Koonin, Kira S Makarova, James G Elkins Biology Direct 2007, 2:38 (14 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central