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	1.	Research article Comparison of RefSeq protein-coding regions in human and vertebrate genomes Jessica H Fong, Terence D Murphy, Kim D Pruitt BMC Genomics 2013, 14:654 (25 September 2013) Abstract \| Full text \| PDF \| PubMed
	2.	Research article Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila Penelope Coggill, Ruth Y Eberhardt, Robert D Finn, Yuanyuan Chang, Lukasz Jaroszewski, Adam Godzik, Debanu Das, Qingping Xu, Herbert L Axelrod, L Aravind, Alexey G Murzin, Alex Bateman BMC Bioinformatics 2013, 14:265 (3 September 2013) Abstract \| Full text \| PDF \| PubMed
	3.	Discovery notes Novel autoproteolytic and DNA-damage sensing components in the bacterial SOS response and oxidized methylcytosine-induced eukaryotic DNA demethylation systems L Aravind, Swadha Anand, Lakshminarayan M Iyer Biology Direct 2013, 8:20 (15 August 2013) Abstract \| Full text \| PDF \| PubMed
	4.	Research Parabolic replicator dynamics and the principle of minimum Tsallis information gain Georgy P Karev, Eugene V Koonin Biology Direct 2013, 8:19 (11 August 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Adequate theoretical description of the dynamics of realistic systems of prebiotic replicators requires the use of a form of the Maximum Entropy Principle in which the minimized quantity is Tsallis entropy, a generalization of the better known Shannon entropy function.
	5.	Research article MeSH indexing based on automatically generated summaries Antonio J Jimeno-Yepes, Laura Plaza, James G Mork, Alan R Aronson, Alberto Díaz BMC Bioinformatics 2013, 14:208 (26 June 2013) Abstract \| Full text \| PDF \| PubMed
	6.	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 Burroughs, Eugene V Koonin, L Aravind Biology Direct 2013, 8:15 (15 June 2013) Abstract \| Full text \| PDF \| PubMed
	7.	Research Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in eukaryotes A Burroughs, Lakshminarayan M Iyer, L Aravind Biology Direct 2013, 8:13 (8 June 2013) Abstract \| Full text \| PDF \| PubMed
	8.	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
	9.	Research article GeneRIF indexing: sentence selection based on machine learning Antonio J Jimeno-Yepes, J Sticco, James G Mork, Alan R Aronson BMC Bioinformatics 2013, 14:171 (31 May 2013) Abstract \| Full text \| PDF \| PubMed
	10.	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
	11.	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
	12.	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 \| Cited on BioMed Central \| 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.
	13.	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
	14.	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
	15.	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
	16.	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
	17.	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.
	18.	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.
	19.	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
	20.	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
	21.	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 \| Cited on BioMed Central \| 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”.
	22.	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
	23.	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.
	24.	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 \| Cited on BioMed Central
	25.	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