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	101.	Research The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like β-grasp domains Lakshminarayan M Iyer, A Maxwell Burroughs, L Aravind Genome Biology 2006, 7:R60 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic analysis of prokaryotic ubiquitin-related beta-grasp fold proteins provides new insights into the Ubiquitin family functional history.
	102.	Research *Mutational hotspots in the TP53* gene and, possibly, other tumor suppressors evolve by positive selection** Galina V Glazko, Vladimir N Babenko, Eugene V Koonin, Igor B Rogozin Biology Direct 2006, 1:4 (31 January 2006) Abstract \| Full text \| PDF \| PubMed
	103.	Software OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression Lawrence Hunter, Zhiyong Lu, James Firby, William A Baumgartner, Helen L Johnson, Philip V Ogren, K Bretonnel Cohen BMC Bioinformatics 2008, 9:78 (31 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	104.	Software Coalescent: an open-source and scalable framework for exact calculations in coalescent theory Susanta Tewari, John L Spouge BMC Bioinformatics 2012, 13:257 (3 October 2012) Abstract \| Full text \| PDF \| PubMed
	105.	Research Evolution of DNA ligases of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes: a case of hidden complexity Natalya Yutin, Eugene V Koonin Biology Direct 2009, 4:51 (18 December 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	106.	Short report *Female Anopheles gambiae* antennae: increased transcript accumulation of the mosquito-specific odorant-binding-protein OBP2** Seth A Hoffman, Lakshminarayanan Aravind, Soundarapandian Velmurugan Parasites & Vectors 2012, 5:27 (6 February 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The odorant binding protein, OBP2, had increased transcript accumulation in the antennae of female vs. male Anopheles gambiae. suggesting it may play a role in female feeding and breeding behavior. Image: Heads, mouthparts and antennae of female (left) and male (right) Anopheles gambiae
	107.	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
	108.	Discovery notes Predicted class-I aminoacyl tRNA synthetase-like proteins in non-ribosomal peptide synthesis L Aravind, Robson F de Souza, Lakshminarayan M Iyer Biology Direct 2010, 5:48 (2 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two class-I aminoacyl-tRNA-synthetase homologs, the cyclic dipeptide synthases and a paralogous Met-tRNA-synthetase, are shown to be involved as peptide ligases in non-ribosomal biosynthesis of novel peptide metabolites.
	109.	Research article The relationship of protein conservation and sequence length David J Lipman, Alexander Souvorov, Eugene V Koonin, Anna R Panchenko, Tatiana A Tatusova BMC Evolutionary Biology 2002, 2:20 (1 November 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Proteins conserved across kingdoms are likely to be longer than more divergent proteins, suggesting evolutionary trends in favour of shortness.
	110.	Methodology Fast 3D shape screening of large chemical databases through alignment-recycling Fabien Fontaine, Evan Bolton, Yulia Borodina, Stephen H Bryant Chemistry Central Journal 2007, 1:12 (6 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	111.	Opinion Back to Bermuda: how is science best served? Deanna M Church, LaDeana W Hillier Genome Biology 2009, 10:105 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two bovine genome assemblies from the same data suggest it is time to revisit the spirit of the Bermuda and Fort Lauderdale agreements.
	112.	Research article Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families Ratna R Thangudu, Malini Manoharan, N Srinivasan, Frédéric Cadet, R Sowdhamini, Bernard Offmann BMC Structural Biology 2008, 8:55 (26 December 2008) Abstract \| Full text \| PDF \| PubMed
	113.	Discovery notes Two new families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea Kira S Makarova, Eugene V Koonin Biology Direct 2010, 5:33 (7 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	114.	Software Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites Parsa Hosseini, Ivan Ovcharenko, Benjamin F Matthews Plant Methods 2013, 9:12 (11 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary This article describes a software tool that can identify transcription factor binding sites from amongst large collections of promoter sequences by integrating a number of different approaches. The method is able to identify more over-represented binding site sequences than other common approaches.
	115.	Opinion The mammalian transcriptome and the function of non-coding DNA sequences Svetlana A Shabalina, Nikolay A Spiridonov Genome Biology 2004, 5:105 (25 March 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Many non-coding sequences transcribed from the mammalian genome are proving to have important regulatory roles, but the functions of the majority remain mysterious.
	116.	Research article Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation Antonio J Jimeno-Yepes, Bridget T McInnes, Alan R Aronson BMC Bioinformatics 2011, 12:223 (2 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	117.	Database Virus variation resources at the National Center for Biotechnology Information: dengue virus Wolfgang Resch, Leonid Zaslavsky, Boris Kiryutin, Michael Rozanov, Yiming Bao, Tatiana A Tatusova BMC Microbiology 2009, 9:65 (2 April 2009) Abstract \| Full text \| PDF \| PubMed
	118.	Research Transposable element derived DNaseI-hypersensitive sites in the human genome Leonardo Mariño-Ramírez, I King Jordan Biology Direct 2006, 1:20 (20 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology
	119.	Research Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes Vivek Anantharaman, L Aravind Genome Biology 2003, 4:R11 (3 February 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Detailed analysis of the N1pC/P60 peptidases showed that these proteins define a large superfamily encompassing several diverse groups of proteins. Evolutionary analysis of this superfamily shows that it comprises four major families, with diverse domain architectures in each of them.
	120.	Research article Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA Nalini Polavarapu, Leonardo Mariño-Ramírez, David Landsman, John F McDonald, I King Jordan BMC Genomics 2008, 9:226 (17 May 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	121.	Research article Genome trees constructed using five different approaches suggest new major bacterial clades Yuri I Wolf, Igor B Rogozin, Nick V Grishin, Roman L Tatusov, Eugene V Koonin BMC Evolutionary Biology 2001, 1:8 (23 October 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Five different methods of phylogenetic reconstruction suggest novel high-level bacterial clades, despite confounding factors such as lateral gene transfer and gene loss.
	122.	Method Predicting domain-domain interactions using a parsimony approach Katia S Guimarães, Raja Jothi, Elena Zotenko, Teresa M Przytycka Genome Biology 2006, 7:R104 (9 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new parsimony approach for the prediction of domain-domain interactions is presented and demonstrated to provide improvement in prediction coverage and accuracy.
	123.	Research Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ Marina V Omelchenko, Kira S Makarova, Yuri I Wolf, Igor B Rogozin, Eugene V Koonin Genome Biology 2003, 4:R55 (29 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics and phylogenetic analysis have been used to examine horizontal transfer of entire operons versus displacement of individual genes within operons by horizontally acquired orthologs and independent assembly of the same or similar operons from genes with different phylogenetic affinities.
	124.	Minireview Reconstructing prokaryotic transcriptional regulatory networks: lessons from actinobacteria Thiago M Venancio, L Aravind Journal of Biology 2009, 8:29 (15 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Venancio and Aravind review recent studies, including one in BMC Systems Biology, that offer new ways to reconstruct transcriptional regulatory networks in previously uncharacterised prokaryotes, such as the actinobacteria.
	125.	Research article Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs Hani Z Girgis, Ivan Ovcharenko BMC Bioinformatics 2012, 13:25 (7 February 2012) Abstract \| Full text \| PDF \| PubMed