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	76.	Research Mathematical modeling of tumor therapy with oncolytic viruses: Regimes with complete tumor elimination within the framework of deterministic models Artem S Novozhilov, Faina S Berezovskaya, Eugene V Koonin, Georgy P Karev Biology Direct 2006, 1:6 (17 February 2006) Abstract \| Full text \| PDF \| PubMed
	77.	Research Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution Marina V Omelchenko, Michael Y Galperin, Yuri I Wolf, Eugene V Koonin Biology Direct 2010, 5:31 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Almost 10% of the biochemical reactions in the Enzyme Commission nomenclature are catalyzed by two or more enzymes with different structural folds and hence independent evolutionary origins.
	78.	Research article The crosstalk between EGF, IGF, and Insulin cell signaling pathways - computational and experimental analysis Rafal Zielinski, Pawel F Przytycki, Jie Zheng, David Zhang, Teresa M Przytycka, Jacek Capala BMC Systems Biology 2009, 3:88 (4 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	79.	Research article Automated annotation of chemical names in the literature with tunable accuracy Jun D Zhang, Lewis Y Geer, Evan E Bolton, Stephen H Bryant Journal of Cheminformatics 2011, 3:52 (22 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary \| Graphical abstract An automated chemical name annotation system has been developed to annotate small molecule names in scientific abstracts with the aim of reproducing MeSH term annotations on biomedical and chemical literature
	80.	Research article PubChem3D: conformer ensemble accuracy Sunghwan Kim, Evan E Bolton, Stephen H Bryant Journal of Cheminformatics 2013, 5:1 (7 January 2013) Abstract \| Full text \| PDF \| PubMed \| Graphical abstract
	81.	Research Small but versatile: the extraordinary functional and structural diversity of the β-grasp fold A Maxwell Burroughs, S Balaji, Lakshminarayan M Iyer, L Aravind Biology Direct 2007, 2:18 (2 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	82.	Discovery notes ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-type retroposons Lakshminarayan M Iyer, L Aravind Biology Direct 2012, 7:39 (12 November 2012) Abstract \| Full text \| PDF \| PubMed
	83.	Research article *Comparative genomics of Thermus thermophilus* and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance** Marina V Omelchenko, Yuri I Wolf, Elena K Gaidamakova, Vera Y Matrosova, Alexander Vasilenko, Min Zhai, Michael J Daly, Eugene V Koonin, Kira S Makarova BMC Evolutionary Biology 2005, 5:57 (20 October 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	84.	Research A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes Diana Chernikova, Sam Motamedi, Miklós Csürös, Eugene V Koonin, Igor B Rogozin Biology Direct 2011, 6:26 (19 May 2011) Abstract \| Full text \| PDF \| PubMed
	85.	Research Comparative genomic analysis of fungal genomes reveals intron-rich ancestors Jason E Stajich, Fred S Dietrich, Scott W Roy Genome Biology 2007, 8:R223 (19 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of intron gain and loss in fungal genomes provides support for an intron-rich fungus-animal ancestor.
	86.	Methodology article Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures Andrew F Neuwald, Christopher J Lanczycki, Aron Marchler-Bauer BMC Bioinformatics 2012, 13:144 (22 June 2012) Abstract \| Full text \| PDF \| PubMed
	87.	Research Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol ε and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors Tahir H Tahirov, Kira S Makarova, Igor B Rogozin, Youri I Pavlov, Eugene V Koonin Biology Direct 2009, 4:11 (18 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	88.	Research article PubChem3D: Diversity of shape Evan E Bolton, Sunghwan Kim, Stephen H Bryant Journal of Cheminformatics 2011, 3:9 (21 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Graphical abstract
	89.	Research Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape Artem S Novozhilov, Yuri I Wolf, Eugene V Koonin Biology Direct 2007, 2:24 (23 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	90.	Research Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family Natalya Yutin, Philippe Colson, Didier Raoult, Eugene V Koonin Virology Journal 2013, 10:106 (4 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Clusters of orthologous genes for mimiviruses (mimiCOGs) were constructed and used for comprehensive phylogenetic analysis of large dsDNA viruses, finding that two Phycodnaviruses actually belong in the Mimiviridae.
	91.	Research Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels Asba Tasneem, Lakshminarayan M Iyer, Eric Jakobsson, L Aravind Genome Biology 2004, 6:R4 (20 December 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Acetylcholine receptor type ligand-gated ion channels are well known in animals. Homologs are identified in prokaryotes that may act as chemotactic receptors.
	92.	Research Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome Jie Zheng, Pavel P Khil, R Daniel Camerini-Otero, Teresa M Przytycka Genome Biology 2010, 11:R103 (20 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An algorithm called LDsplit was developed to identify polymorphisms associated with meiotic recombination hotspots.
	93.	Research Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution Maxim Y Wolf, Yuri I Wolf, Eugene V Koonin Biology Direct 2008, 3:40 (7 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	94.	Opinion Comparative genomics of archaea: how much have we learned in six years, and what's next? Kira S Makarova, Eugene V Koonin Genome Biology 2003, 4:115 (16 July 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary With 16 complete archaeal genomes sequenced to date, comparative genomics has revealed a conserved core of 313 genes that are represented in all sequenced archaeal genomes, plus a variable 'shell' that is prone to lineage-specific gene loss and horizontal gene exchange.
	95.	Research Post-radiation increase in VEGF enhances glioma cell motility in vitro Whoon Kil, Philip J Tofilon, Kevin Camphausen Radiation Oncology 2012, 7:25 (22 February 2012) Abstract \| Full text \| PDF \| PubMed \| F1000 Medicine \| F1000 Biology
	96.	Editorial A community experiment with fully open and published peer review Eugene V Koonin, Laura F Landweber, David J Lipman Biology Direct 2006, 1:1 (31 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 2 comments
	97.	Research The gene normalization task in BioCreative III Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illes Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova, Patrick Ruch, Martin Romacker, Fabio Rinaldi, Sanmitra Bhattacharya, Padmini Srinivasan, Hongfang Liu, Manabu Torii, Sergio Matos, David Campos, Karin Verspoor, Kevin M Livingston, W Wilbur BMC Bioinformatics 2011, 12(Suppl 8):S2 (3 October 2011) Abstract \| Full text \| PDF \| PubMed
	98.	Research article PubChem3D: Shape compatibility filtering using molecular shape quadrupoles Sunghwan Kim, Evan E Bolton, Stephen H Bryant Journal of Cheminformatics 2011, 3:25 (20 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Graphical abstract
	99.	Research New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system Vivek Anantharaman, L Aravind Genome Biology 2003, 4:R81 (26 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequence profile analysis of the RelE- and ParE-type post-segregational cell killing (PSK) toxins from diverse bacteria and archaea has unified these proteins into a single superfamily. Further comparative analysis suggests that the core of the eukaryotic nonsense-mediated RNA decay system has probably evolved from a PSK-related system.
	100.	Report GENETAG: a tagged corpus for gene/protein named entity recognition Lorraine Tanabe, Natalie Xie, Lynne H Thom, Wayne Matten, W John Wilbur BMC Bioinformatics 2005, 6(Suppl 1):S3 (24 May 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central