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	1.	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
	2.	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”.
	3.	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
	4.	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.
	5.	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
	6.	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
	7.	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
	8.	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
	9.	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
	10.	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 \| 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.
	11.	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
	12.	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
	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 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 \| 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.
	15.	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.
	16.	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 \| Provisional PDF \| PubMed
	17.	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
	18.	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
	19.	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
	20.	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.
	21.	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
	22.	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
	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.	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.
	25.	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