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	1.	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
	2.	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
	3.	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
	4.	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
	5.	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.
	6.	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.
	7.	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
	8.	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
	9.	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”.
	10.	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
	11.	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.
	12.	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
	13.	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
	14.	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
	15.	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
	16.	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
	17.	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.
	18.	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
	19.	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
	20.	Opinion Does the central dogma still stand? Eugene V Koonin Biology Direct 2012, 7:27 (23 August 2012) Abstract \| Full text \| PDF \| PubMed
	21.	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.
	22.	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.
	23.	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
	24.	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
	25.	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