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	1.	Research Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing Vivek Anantharaman, Kira S Makarova, A Maxwell Burroughs, Eugene V Koonin, L Aravind Biology Direct 2013, 8:15 (15 June 2013) Abstract \| Provisional PDF
	2.	Research Two novel PIWI families: roles in inter-genomic conflicts in bacteria and mediator-dependent modulation of transcription in eukaryotes A Maxwell Burroughs, Lakshminarayan M Iyer, L Aravind Biology Direct 2013, 8:13 (8 June 2013) Abstract \| Provisional PDF \| PubMed
	3.	Research article Clustering cliques for graph-based summarization of the biomedical research literature Han Zhang, Marcelo Fiszman, Dongwook Shin, Bartlomiej Wilkowski, Thomas C Rindflesch BMC Bioinformatics 2013, 14:182 (7 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	4.	Research article GeneRIF indexing: sentence selection based on machine learning Antonio J Jimeno-Yepes, J Caitlin Sticco, James G Mork, Alan R Aronson BMC Bioinformatics 2013, 14:171 (31 May 2013) Abstract \| Provisional PDF \| PubMed
	5.	Methodology article NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data Nak-Kyeong Kim, Rasika V Jayatillake, John L Spouge BMC Genomics 2013, 14:349 (25 May 2013) Abstract \| Full text \| PDF \| PubMed
	6.	Research article Domain analysis of symbionts and hosts (DASH) in a genome-wide survey of pathogenic human viruses Mileidy W Gonzalez, John L Spouge BMC Research Notes 2013, 6:209 (24 May 2013) Abstract \| Full text \| PDF \| PubMed
	7.	Research Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies Natalya Yutin, Didier Raoult, Eugene V Koonin Virology Journal 2013, 10:158 (23 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A phylogenomic analysis found that giant viruses, virophages and transposable elements have a complex evolutionary relationship, suggesting that viruses evolved from non-viral mobile genetic elements and vice versa, on more than one occasion.
	8.	Research article Combining MEDLINE and publisher data to create parallel corpora for the automatic translation of biomedical text Antonio Jimeno Yepes, Élise Prieur-Gaston, Aurélie Névéol BMC Bioinformatics 2013, 14:146 (30 April 2013) Abstract \| Full text \| PDF \| PubMed
	9.	Editorial Biology Direct: celebrating 7 years of open, published peer review Eugene V Koonin, Laura F Landweber, David J Lipman Biology Direct 2013, 8:11 (30 April 2013) Abstract \| Full text \| PDF \| PubMed
	10.	Research Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar, Kira S Makarova, David E Graham, Yuri I Wolf, Eugene V Koonin, Anna-Louise Reysenbach Biology Direct 2013, 8:9 (22 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The genome of the first terrestrial member of the Nanoarchaeota and comparisons with the marine Nanoarchaeum equitans reveals stages in the evolution of archaeal symbiosis and parasitism
	11.	Anniversary Update Seeing the Tree of Life behind the phylogenetic forest Pere Puigbò, Yuri I Wolf, Eugene V Koonin BMC Biology 2013, 11:46 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
	12.	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.
	13.	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.
	14.	Research article Genome-wide associations of signaling pathways in glioblastoma multiforme Stefan Wuchty, Alexei Vazquez, Serdar Bozdag, Peter O Bauer BMC Medical Genomics 2013, 6:11 (28 March 2013) Abstract \| Full text \| PDF \| PubMed
	15.	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
	16.	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”.
	17.	Discovery notes AID/APOBEC cytosine deaminase induces genome-wide kataegis Artem G Lada, Alok Dhar, Robert J Boissy, Masayuki Hirano, Aleksandr A Rubel, Igor B Rogozin, Youri I Pavlov Biology Direct 2012, 7:47 (18 December 2012) Abstract \| Full text \| PDF \| PubMed
	18.	Research Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer Yuri I Wolf, Kira S Makarova, Natalya Yutin, Eugene V Koonin Biology Direct 2012, 7:46 (14 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of the updated set of orthologs in 120 archaeal genomes reveals a complex history of gene exchange with no major "highways" of horizontal gene transfer.
	19.	Hypothesis Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes Kira S Makarova, Vivek Anantharaman, L Aravind, Eugene V Koonin Biology Direct 2012, 7:40 (14 November 2012) Abstract \| Full text \| PDF \| PubMed
	20.	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
	21.	Research article Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis Sunghwan Kim, Evan E Bolton, Stephen H Bryant Journal of Cheminformatics 2012, 4:28 (7 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary \| Graphical abstract In the latest article in the PubChem3D series, the effects of employing multiple diverse conformers per compound on 3D similarity computation are investigated, which may help to build search and analysis tools that exploit 3D molecular similarity between compounds in PubChem
	22.	Research Thematic clustering of text documents using an EM-based approach Sun Kim, W Wilbur Journal of Biomedical Semantics 2012, 3(Suppl 3):S6 (5 October 2012) Abstract \| Full text \| PDF \| PubMed
	23.	Research Finding biomedical categories in Medline^® Lana Yeganova, Won Kim, Donald C Comeau, W John Wilbur Journal of Biomedical Semantics 2012, 3(Suppl 3):S3 (5 October 2012) Abstract \| Full text \| PDF \| PubMed
	24.	Discovery notes Proteorhodopsin genes in giant viruses Natalya Yutin, Eugene V Koonin Biology Direct 2012, 7:34 (4 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Some giant viruses encode previously unknown proteorhodopsins that are predicted to affect signal transduction in infected protists and might have substantial ecological impact.
	25.	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
	26.	Research article In silico identification and characterization of the ion transport specificity for P-type ATPases in the Mycobacterium tuberculosis complex Lorena Novoa-Aponte, Andrés León-Torres, Miyer Patiño-Ruiz, Jenifer Cuesta-Bernal, Luz-Mary Salazar, David Landsman, Leonardo Mariño-Ramírez, Carlos-Yesid Soto BMC Structural Biology 2012, 12:25 (3 October 2012) Abstract \| Full text \| PDF \| PubMed
	27.	Opinion Does the central dogma still stand? Eugene V Koonin Biology Direct 2012, 7:27 (23 August 2012) Abstract \| Full text \| PDF \| PubMed
	28.	Research Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes Natalya Yutin, Eugene V Koonin Virology Journal 2012, 9:161 (14 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Research confirming that the Nucleo-Cytoplasmic Large DNA viruses, from smallpox to mimivirus, evolved from a single common ancestor. Interestingly a number of core genes, carrying out the same function in these diverse viruses, were unrelated to each other but were instead independently acquired from their eukaryotic hosts. This remarkable example of convergent evolution reveals a complex genetic history for an important group of viruses.
	29.	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.
	30.	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
	31.	Proceedings Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots Min Wu, Chee-Keong Kwoh, Teresa M Przytycka, Jing Li, Jie Zheng Proteome Science 2012, 10(Suppl 1):S11 (21 June 2012) Abstract \| Full text \| PDF \| PubMed
	32.	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
	33.	Technical Note New finite-size correction for local alignment score distributions Yonil Park, Sergey Sheetlin, Ning Ma, Thomas L Madden, John L Spouge BMC Research Notes 2012, 5:286 (12 June 2012) Abstract \| Full text \| PDF \| PubMed
	34.	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.
	35.	Technical Note CytoITMprobe: a network information flow plugin for Cytoscape Aleksandar Stojmirović, Alexander Bliskovsky, Yi-Kuo Yu BMC Research Notes 2012, 5:237 (15 May 2012) Abstract \| Full text \| PDF \| PubMed
	36.	Research article *The Physalis peruviana* leaf transcriptome: assembly, annotation and gene model prediction** Gina A Garzón-Martínez, Z Zhu, David Landsman, Luz S Barrero, Leonardo Mariño-Ramírez BMC Genomics 2012, 13:151 (25 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	37.	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
	38.	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.
	39.	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
	40.	Discovery notes Archaeal origin of tubulin Natalya Yutin, Eugene V Koonin Biology Direct 2012, 7:10 (29 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Probable ancestors of eukaryotic tubulins, denoted artubulins, were discovered in two genomes of thaumarchaeota of the genus Nitrosoarchaeum.
	41.	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
	42.	Research article Automatic identification and normalization of dosage forms in drug monographs Jiao Li, Zhiyong Lu BMC Medical Informatics and Decision Making 2012, 12:9 (15 February 2012) Abstract \| Full text \| PDF \| PubMed
	43.	Research The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes Kira S Makarova, Eugene V Koonin, Zvi Kelman Biology Direct 2012, 7:7 (13 February 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomic analysis reveals diverged orthologs of eukaryotic CDC45 protein and bacterial RecJ nuclease in nearly all archaeal genomes; the CMG complex is conserved in both archaea and eukaryotes, and appears to be an essential component of the ancestral DNA replication machinery.
	44.	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
	45.	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
	46.	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
	47.	Research article Constructing a semantic predication gold standard from the biomedical literature Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, Thomas C Rindflesch BMC Bioinformatics 2011, 12:486 (20 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	48.	Research article A unified framework for managing provenance information in translational research Satya S Sahoo, Vinh Nguyen, Olivier Bodenreider, Priti Parikh, Todd Minning, Amit P Sheth BMC Bioinformatics 2011, 12:461 (29 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	49.	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
	50.	Research article Francisella RNA polymerase contains a heterodimer of non-identical α subunits Damir Mukhamedyarov, Kira S Makarova, Konstantin Severinov, Konstantin Kuznedelov BMC Molecular Biology 2011, 12:50 (22 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Unlike all other known bacterial genera, Francisella possesses two rpoA genes, encoding two non-identical alpha subunits of the RNA polymerase, and both subunits must be present in the same enzyme to ensure robust transcription activity.