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	1.	Software Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction Jian Ye, George Coulouris, Irena Zaretskaya, Ioana Cutcutache, Steve Rozen, Thomas L Madden BMC Bioinformatics 2012, 13:134 (18 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	2.	Hypothesis The ancient Virus World and evolution of cells Eugene V Koonin, Tatiana G Senkevich, Valerian V Dolja Biology Direct 2006, 1:29 (19 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology
	3.	Research article Utilization of the PICO framework to improve searching PubMed for clinical questions Connie Schardt, Martha B Adams, Thomas Owens, Sheri Keitz, Paul Fontelo BMC Medical Informatics and Decision Making 2007, 7:16 (15 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	4.	Review The origin and early evolution of eukaryotes in the light of phylogenomics Eugene V Koonin Genome Biology 2010, 11:209 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics and new phylogenies of eukaryote groups suggest a scenario in which the mitochondrial endosymbiosis triggered the origin of eukaryotes.
	5.	Research Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics Dapeng Zhang, Robson F de Souza, Vivek Anantharaman, Lakshminarayan M Iyer, L Aravind Biology Direct 2012, 7:18 (25 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comprehensive dissection of polymorphic and related secreted toxin systems uncovers nearly 240 toxin and immunity domains with implications for intra-organismal conflict, kin discrimination, pathogenesis and emergence of eukaryotic sub-cellular systems.
	6.	Review Origin and evolution of spliceosomal introns Igor B Rogozin, Liran Carmel, Miklos Csuros, Eugene V Koonin Biology Direct 2012, 7:11 (16 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
	7.	Review A unified phylogeny-based nomenclature for histone variants Paul B Talbert, Kami Ahmad, Geneviève Almouzni, Juan Ausió, Frederic Berger, Prem L Bhalla, William M Bonner, W Cande, Brian P Chadwick, Simon W L Chan, George A M Cross, Liwang Cui, Stefan I Dimitrov, Detlef Doenecke, José M Eirin-López, Martin A Gorovsky, Sandra B Hake, Barbara A Hamkalo, Sarah Holec, Steven E Jacobsen, Kinga Kamieniarz, Saadi Khochbin, Andreas G Ladurner, David Landsman, John A Latham, Benjamin Loppin, Harmit S Malik, William F Marzluff, John R Pehrson, Jan Postberg et al. Epigenetics & Chromatin 2012, 5:7 (31 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In response to an urgent need to rationalize the current schemes for naming histone variants, researchers from over 30 institutions worldwide have developed consistent but flexible naming rules that are informative and database-searchable.
	8.	Hypothesis The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life Eugene V Koonin Biology Direct 2007, 2:15 (31 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
	9.	Opinion Is evolution Darwinian or/and Lamarckian? Eugene V Koonin, Yuri I Wolf Biology Direct 2009, 4:42 (11 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Darwinian and Lamarckian mechanisms are both important for evolution and seem to belong to different parts of the broad range of complex interactions between genotypes and environment.
	10.	Software BLAST+: architecture and applications Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden BMC Bioinformatics 2009, 10:421 (15 December 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary With the advent of more complete genomes BLAST has been re-written to include a new set of command line searches and a new modular structure, giving substantial speed improvements for long queries and an improved user interface.
	11.	Research Lower short- and long-term mortality associated with overweight and obesity in a large cohort study of adult intensive care unit patients Swapna Abhyankar, Kira Leishear, Fiona M Callaghan, Dina Demner-Fushman, Clement J McDonald Critical Care 2012, 16:R235 (18 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Overweight and obese patients have significantly lower mortality rates than normal weight patients, both 30 days and one year after ICU admission, supporting the theory that obesity has a “protective effect”.
	12.	Research article The COG database: an updated version includes eukaryotes Roman L Tatusov, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Boris Kiryutin, Eugene V Koonin, Dmitri M Krylov, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Sridhar Rao, Sergei Smirnov, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin, Darren A Natale BMC Bioinformatics 2003, 4:41 (11 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology
	13.	Opinion Does the central dogma still stand? Eugene V Koonin Biology Direct 2012, 7:27 (23 August 2012) Abstract \| Full text \| PDF \| PubMed
	14.	Research On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth Armen Y Mulkidjanian, Michael Y Galperin Biology Direct 2009, 4:27 (24 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The relatively high zinc content of living cells and its role as cofactor in many key enzymes and RNA structures might reflect the origin of life in zinc-rich environments.
	15.	Research A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action Kira S Makarova, Nick V Grishin, Svetlana A Shabalina, Yuri I Wolf, Eugene V Koonin Biology Direct 2006, 1:7 (16 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Computational analysis shows that CRISPR repeats and associated Cas proteins in prokaryotes might act in conjunction as a RNA-silencing mechanism against plasmids and viruses, similar to the eukaryotic RNA-interference system.
	16.	Research Domain enhanced lookup time accelerated BLAST Grzegorz M Boratyn, Alejandro A Schäffer, Richa Agarwala, Stephen F Altschul, David J Lipman, Thomas L Madden Biology Direct 2012, 7:12 (17 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DELTA-BLAST is a new BLAST alignment tool for sensitive protein searches that uses conserved domain models to construct a position specific scoring matrix.
	17.	Research article PubMed related articles: a probabilistic topic-based model for content similarity Jimmy Lin, W John Wilbur BMC Bioinformatics 2007, 8:423 (30 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	18.	Research AceView: a comprehensive cDNA-supported gene and transcripts annotation Danielle Thierry-Mieg, Jean Thierry-Mieg Genome Biology 2006, 7(Suppl 1):S12 (7 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	19.	Hypothesis The Biological Big Bang model for the major transitions in evolution Eugene V Koonin Biology Direct 2007, 2:21 (20 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 2 comments
	20.	Research Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems Kira S Makarova, L Aravind, Yuri I Wolf, Eugene V Koonin Biology Direct 2011, 6:38 (14 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	21.	Methodology Advancing translational research with the Semantic Web Alan Ruttenberg, Tim Clark, William Bug, Matthias Samwald, Olivier Bodenreider, Helen Chen, Donald Doherty, Kerstin Forsberg, Yong Gao, Vipul Kashyap, June Kinoshita, Joanne Luciano, M Scott Marshall, Chimezie Ogbuji, Jonathan Rees, Susie Stephens, Gwendolyn T Wong, Elizabeth Wu, Davide Zaccagnini, Tonya Hongsermeier, Eric Neumann, Ivan Herman, Kei-Hoi Cheung BMC Bioinformatics 2007, 8(Suppl 3):S2 (9 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology
	22.	Methodology article Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation Leonid Zaslavsky, Yiming Bao, Tatiana A Tatusova BMC Bioinformatics 2008, 9:237 (16 May 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	23.	Research *Mediation of Drosophila* autosomal dosage effects and compensation by network interactions** John H Malone, Dong-Yeon Cho, Nicolas R Mattiuzzo, Carlo G Artieri, Lichun Jiang, Ryan K Dale, Harold E Smith, Jennifer McDaniel, Sarah Munro, Marc Salit, Justen Andrews, Teresa M Przytycka, Brian Oliver Genome Biology 2012, 13:R28 (24 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comprehensive RNA-seq analysis of autosomal dosage effects and compensation in 21 autosomal deficiency Drosophila lines
	24.	Methodology Increasing peptide identifications and decreasing search times for ETD spectra by pre-processing and calculation of parent precursor charge Viswanadham Sridhara, Dina L Bai, An Chi, Jeffrey Shabanowitz, Donald F Hunt, Stephen H Bryant, Lewis Y Geer Proteome Science 2012, 10:8 (9 February 2012) Abstract \| Full text \| PDF \| PubMed
	25.	Research The origins of phagocytosis and eukaryogenesis Natalya Yutin, Maxim Y Wolf, Yuri I Wolf, Eugene V Koonin Biology Direct 2009, 4:9 (26 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Archaeal ancestors of eukaryotes might have possessed a primitive, actin-based cytoskeleton that would facilitate engulfment of bacteria, in particular, the proto-mitochondrial endosymbiont.