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	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.