Biology Direct

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A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action

Kira S Makarova, Nick V Grishin, Svetlana A Shabalina, Yuri I Wolf and Eugene V Koonin*

Biology Direct 2006, 1:7 doi:10.1186/1745-6150-1-7

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Proceedings   Open Access

Genomic analysis reveals Lactobacillus sanfranciscensis as stable element in traditional sourdoughs

Rudi F Vogel, Melanie Pavlovic, Matthias A Ehrmann, Arnim Wiezer, Heiko Liesegang, Stefanie Offschanka, Sonja Voget, Angel Angelov, Georg Böcker, Wolfgang Liebl Microbial Cell Factories 2011, 10(Suppl 1):S6 (30 August 2011)

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Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems

Kira S Makarova, L Aravind, Yuri I Wolf, Eugene V Koonin Biology Direct 2011, 6:38 (14 July 2011)

Research article   Open Access Highly Accessed

Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi

Kounthéa Phok, Annick Moisan, Dana Rinaldi, Nicolas Brucato, Agamemnon J Carpousis, Christine Gaspin, Béatrice Clouet-d'Orval BMC Genomics 2011, 12:312 (13 June 2011)

Commentary   Open Access

Taming of the shrewd: novel eukaryotic genes from RNA viruses

Eugene V Koonin BMC Biology 2010, 8:2 (12 January 2010)

Eugene Koonin comments on the recent finding that integrated copies of non-retroviral RNA virus genes are widely spread in fungal genomes and proposes a role for these acquired genes in antiviral immunity.

Opinion   Open Access Highly Accessed

Is evolution Darwinian or/and Lamarckian?

Eugene V Koonin, Yuri I Wolf Biology Direct 2009, 4:42 (11 November 2009)

This article is part of a collection on Evolutionary Biology 150...

Darwinian and Lamarckian mechanisms are both important for evolution and seem to belong to different parts of the broad range of complex interactions between genotypes and environment.

Correction   Open Access

Hypothesis for heritable, anti-viral immunity in crustaceans and insects

Timothy W Flegel Biology Direct 2009, 4:36 (1 October 2009)

Hypothesis   Open Access

Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements

Kira S Makarova, Yuri I Wolf, John van der Oost, Eugene V Koonin Biology Direct 2009, 4:29 (25 August 2009)

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Community-wide analysis of microbial genome sequence signatures

Gregory J Dick, Anders F Andersson, Brett J Baker, Sheri L Simmons, Brian C Thomas, A Pepper Yelton, Jillian F Banfield Genome Biology 2009, 10:R85 (21 August 2009)

Genome signatures are used to identify and cluster sequences de novo from an acid biofilm microbial community metagenomic dataset, revealing information about the low-abundance community members.

Research article   Open Access

Gain and loss of an intron in a protein-coding gene in Archaea: the case of an archaeal RNA pseudouridine synthase gene

Shin-ichi Yokobori, Takashi Itoh, Shigeo Yoshinari, Norimichi Nomura, Yoshihiko Sako, Akihiko Yamagishi, Tairo Oshima, Kiyoshi Kita, Yoh-ichi Watanabe BMC Evolutionary Biology 2009, 9:198 (11 August 2009)

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Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content

Fumito Maruyama, Mitsuhiko Kobata, Ken Kurokawa, Keishin Nishida, Atsuo Sakurai, Kazuhiko Nakano, Ryota Nomura, Shigetada Kawabata, Takashi Ooshima, Kenta Nakai, Masahira Hattori, Shigeyuki Hamada, Ichiro Nakagawa BMC Genomics 2009, 10:358 (5 August 2009)

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The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens

Muktak Aklujkar, Julia Krushkal, Genevieve DiBartolo, Alla Lapidus, Miriam L Land, Derek R Lovley BMC Microbiology 2009, 9:109 (27 May 2009)

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Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1

Jimmy H Saw, Bruce W Mountain, Lu Feng, Marina V Omelchenko, Shaobin Hou, Jennifer A Saito, Matthew B Stott, Dan Li, Guang Zhao, Junli Wu, Michael Y Galperin, Eugene V Koonin, Kira S Makarova, Yuri I Wolf, Daniel J Rigden, Peter F Dunfield, Lei Wang, Maqsudul Alam Genome Biology 2008, 9:R161 (17 November 2008)

Sequencing of the complete genome of Anoxybacillus flavithermus reveals enzymes that are required for silica adaptation and biofilm formation.

Research   Open Access Highly Accessed

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia

Shaobin Hou, Kira S Makarova, Jimmy HW Saw, Pavel Senin, Benjamin V Ly, Zhemin Zhou, Yan Ren, Jianmei Wang, Michael Y Galperin, Marina V Omelchenko, Yuri I Wolf, Natalya Yutin, Eugene V Koonin, Matthew B Stott, Bruce W Mountain, Michelle A Crowe, Angela V Smirnova, Peter F Dunfield, Lu Feng, Lei Wang, Maqsudul Alam Biology Direct 2008, 3:26 (1 July 2008)

Genome sequence of a methanotrophic member of the bacterial phylum Verrucomicrobia reveals adaptations to the methane utilization under acidic conditions and supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a superphylum

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Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

Kira S Makarova, Alexander V Sorokin, Pavel S Novichkov, Yuri I Wolf, Eugene V Koonin Biology Direct 2007, 2:33 (27 November 2007)

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Hitting bacteria at the heart of the central dogma: sequence-specific inhibition

Louise Rasmussen, Hans Sperling-Petersen, Kim Mortensen Microbial Cell Factories 2007, 6:24 (10 August 2007)

Software   Open Access

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats

Charles Bland, Teresa L Ramsey, Fareedah Sabree, Micheal Lowe, Kyndall Brown, Nikos C Kyrpides, Philip Hugenholtz BMC Bioinformatics 2007, 8:209 (18 June 2007)

Database   Open Access

The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

Ibtissem Grissa, Gilles Vergnaud, Christine Pourcel BMC Bioinformatics 2007, 8:172 (23 May 2007)

Research   Open Access

Evolutionary conservation of sequence and secondary structures in CRISPR repeats

Victor Kunin, Rotem Sorek, Philip Hugenholtz Genome Biology 2007, 8:R61 (18 April 2007)

The categorisation and structural analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) sequences from 195 microbial genomes show that repeats from diverse organisms can be grouped based on sequence similarity, and that some groups have pronounced secondary structures with compensatory base changes.

Software   Open Access

PILER-CR: Fast and accurate identification of CRISPR repeats

Robert C Edgar BMC Bioinformatics 2007, 8:18 (20 January 2007)

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The ancient Virus World and evolution of cells

Eugene V Koonin, Tatiana G Senkevich, Valerian V Dolja Biology Direct 2006, 1:29 (19 September 2006)

Research   Open Access

The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like β-grasp domains

Lakshminarayan M Iyer, A Maxwell Burroughs, L Aravind Genome Biology 2006, 7:R60 (19 July 2006)

A systematic analysis of prokaryotic ubiquitin-related beta-grasp fold proteins provides new insights into the Ubiquitin family functional history.