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	126.	Research article Genome trees constructed using five different approaches suggest new major bacterial clades Yuri I Wolf, Igor B Rogozin, Nick V Grishin, Roman L Tatusov, Eugene V Koonin BMC Evolutionary Biology 2001, 1:8 (23 October 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Five different methods of phylogenetic reconstruction suggest novel high-level bacterial clades, despite confounding factors such as lateral gene transfer and gene loss.
	127.	Minireview Reconstructing prokaryotic transcriptional regulatory networks: lessons from actinobacteria Thiago M Venancio, L Aravind Journal of Biology 2009, 8:29 (15 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Venancio and Aravind review recent studies, including one in BMC Systems Biology, that offer new ways to reconstruct transcriptional regulatory networks in previously uncharacterised prokaryotes, such as the actinobacteria.
	128.	Method Predicting domain-domain interactions using a parsimony approach Katia S Guimarães, Raja Jothi, Elena Zotenko, Teresa M Przytycka Genome Biology 2006, 7:R104 (9 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new parsimony approach for the prediction of domain-domain interactions is presented and demonstrated to provide improvement in prediction coverage and accuracy.
	129.	Research Mathematical modeling of tumor therapy with oncolytic viruses: effects of parametric heterogeneity on cell dynamics Georgy P Karev, Artem S Novozhilov, Eugene V Koonin Biology Direct 2006, 1:30 (3 October 2006) Abstract \| Full text \| PDF \| PubMed
	130.	Research article Duplicated genes evolve slower than singletons despite the initial rate increase I King Jordan, Yuri I Wolf, Eugene V Koonin BMC Evolutionary Biology 2004, 4:22 (6 July 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Following gene duplication there is a period of rapid evolution, which then slows down in cases where the original gene has an important biological function and the duplicate is retained.
	131.	Research article Identification and characterization of pseudogenes in the rice gene complement Françoise Thibaud-Nissen, Shu Ouyang, C Robin Buell BMC Genomics 2009, 10:317 (16 July 2009) Abstract \| Full text \| PDF \| PubMed
	132.	Research Detection of co-eluted peptides using database search methods Gelio Alves, Aleksey Y Ogurtsov, Siwei Kwok, Wells W Wu, Guanghui Wang, Rong-Fong Shen, Yi-Kuo Yu Biology Direct 2008, 3:27 (2 July 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The "one peptide per spectrum" dogma cannot hold true due to limited chromatographic separation resulting in mass spectra containing co-eluted peptides with high probability; this issue is numerically investigated.
	133.	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
	134.	Research Exceptional error minimization in putative primordial genetic codes Artem S Novozhilov, Eugene V Koonin Biology Direct 2009, 4:44 (19 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	135.	Research Reconstructing the ubiquitin network - cross-talk with other systems and identification of novel functions Thiago M Venancio, S Balaji, Lakshminarayan M Iyer, L Aravind Genome Biology 2009, 10:R33 (30 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A computational model of the yeast Ubiquitin system highlights interesting biological features including functional interactions between components and interplay with other regulatory mechanisms.
	136.	Discovery notes Novel eukaryotic enzymes modifying cell-surface biopolymers Vivek Anantharaman, L Aravind Biology Direct 2010, 5:1 (7 January 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	137.	Discovery notes Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Crenarchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea Fabian Blombach, Kira S Makarova, Jeannette Marrero, Bettina Siebers, Eugene V Koonin, John Oost Biology Direct 2009, 4:39 (14 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary While Archaea are thought to possess a single RNA polymerase type resembling in its subunit composition eukaryotic RNAP II, the identified archaeal RPC34 orhtolog implicates functional specialization of archaeal RNAPs.
	138.	Research The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases L Aravind, Eugene V Koonin Genome Biology 2001, 2:research0007-research0007.8 (19 February 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequence-profile analysis shows that the DNA repair protein AlkB, the extracellular matrix protein leprecan, the disease-resistance-related protein EGL-9 and several uncharacterized proteins define novel families of enzymes of the 2OG-Fe(II) oxygenase superfamily. This allows the prediction of catalytic activity for a wide range of biochemically uncharacterized proteins from eukaryotes and bacteria.
	139.	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
	140.	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
	141.	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
	142.	Discovery notes OST-HTH: a novel predicted RNA-binding domain Vivek Anantharaman, Dapeng Zhang, L Aravind Biology Direct 2010, 5:13 (19 March 2010) Abstract \| Full text \| PDF \| PubMed
	143.	Discovery notes Accumulation of GC donor splice signals in mammals Alexander Churbanov, Stephen Winters-Hilt, Eugene V Koonin, Igor B Rogozin Biology Direct 2008, 3:30 (9 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Reconstruction of the evolution of donor splice sites in mammals reveals accumulation of minor GC sites that could contribute to the evolution of alternative splicing.
	144.	Software askMEDLINE: a free-text, natural language query tool for MEDLINE/PubMed Paul Fontelo, Fang Liu, Michael Ackerman BMC Medical Informatics and Decision Making 2005, 5:5 (10 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary A new plain text search tool for clinicians, researchers and other information seekers which will translate a question into an efficient search of MEDLINE/PubMed.
	145.	Research Overview of the BioCreative III Workshop Cecilia N Arighi, Zhiyong Lu, Martin Krallinger, Kevin B Cohen, W Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H Wu BMC Bioinformatics 2011, 12(Suppl 8):S1 (3 October 2011) Abstract \| Full text \| PDF \| PubMed
	146.	Research Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series Igor B Rogozin, Karen Thomson, Miklós Csürös, Liran Carmel, Eugene V Koonin Biology Direct 2008, 3:7 (17 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Homoplasy denotes the same (parallel) mutations occurring independently in different lineages. It is a scourge of phylogenetic methods. Here, however, it is shown that homoplasy is also an interesting evolutionary phenomenon. Homplasy seems, at least, in part, to underlie the so-called homologous series of phenotypic variation occurring in different, particularly, closely related lineages, an effect first described by the famous Russian geneticict Vavilov some 90 years ago.
	147.	Discovery notes Presence of a classical RRM-fold palm domain in Thg1-type 3'- 5'nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains Vivek Anantharaman, Lakshminarayan M Iyer, L Aravind Biology Direct 2010, 5:43 (30 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	148.	Research article Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases Lakshminarayan M Iyer, Eugene V Koonin, L Aravind BMC Structural Biology 2003, 3:1 (28 January 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The discovery that RNA-dependent RNA polymerases, which are solely eukaryotic, share a domain with a subunit of DNA-dependent RNA polymerases, which are universal, sheds light on the evolutionary relationships and origins of polymerases.
	149.	Research A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain L Aravind, Lakshminarayan M Iyer, Detlef D Leipe, Eugene V Koonin Genome Biology 2004, 5:R30 (16 April 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This study characterizes the KAP protein family - a newly identified sub-group of the P-loop NTPases, which have transmembrane helices inserted into the P-loop NTPase domain. Their unusual phyletic distribution suggests KAP proteins were transferred from bacteria to animals by horizontal gene transfer.
	150.	Research article Developing and validating predictive decision tree models from mining chemical structural fingerprints and high–throughput screening data in PubChem Lianyi Han, Yanli Wang, Stephen H Bryant BMC Bioinformatics 2008, 9:401 (25 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central