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Kira Makarova

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Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Comparative genomics of defense systems in archaea and bacteria.
Evgeny Klimuk; Rob Lavigne; Kira S Makarova; Natalia Akulenko; Pieter-Jan Ceyssens; Ivan Volchenkov; Konstantin Severinov
Host RNA polymerase inhibitors encoded by ϕKMV-like phages of Pseudomonas.
Mircea Podar; David E Graham; Eugene V Koonin; Kira S Makarova; Yuri I Wolf; Anna-Louise Reysenbach
Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park.

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All Publications

2013: Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Comparative genomics of defense systems in archaea and bacteria.
Nucleic acids research 2013;41(8):4360-77.
2013: Evgeny Klimuk; Rob Lavigne; Kira S Makarova; Natalia Akulenko; Pieter-Jan Ceyssens; Ivan Volchenkov; Konstantin Severinov
Host RNA polymerase inhibitors encoded by ϕKMV-like phages of Pseudomonas.
Virology 2013;436(1):67-74.
2013: Mircea Podar; David E Graham; Eugene V Koonin; Kira S Makarova; Yuri I Wolf; Anna-Louise Reysenbach
Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park.
Biology direct 2013;8(1):9.
2012: Boguslaw Nocek; Konstantin Severinov; Anton Tikhonov; Gaston Vondenhoff; Min Zhou; Arthur Van Aerschot; Wayne F Anderson; Gyorgy Babnigg; Minyi Gu; Keehwan Kwon; Kira S Makarova; Andrzej Joachimiak
Structural and functional characterization of microcin C resistance peptidase MccF from Bacillus anthracis.
Journal of molecular biology 2012;420(4-5):366-83.
2012: Nobuto Takeuchi; Yuri I Wolf; Kira S Makarova; Eugene V Koonin
Nature and intensity of selection pressure on CRISPR-associated genes.
Journal of bacteriology 2012;194(5):1216-25.
2012: Sonia Paytubi; Catherine H Botting; Shirley Graham; Eugene V Koonin; Huanting Liu; Kira S Makarova; Stephen McMahon; James H Naismith; Malcolm F White
Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(7):E398-405.
2012: Yuri I Wolf; Natalya Yutin; Kira S Makarova; Eugene V Koonin
Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.
Biology direct 2012;7():46.
2012: Kira S Makarova; Vivek Anantharaman; L Aravind; Eugene V Koonin
Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes.
Biology direct 2012;7():40.
2012: Maud M Swanson; Lesley Torrance; Peter J Cock; David W Hopkins; Eugene V Koonin; Kira S Makarova; Brian Reavy; Michael E Taliansky
Novel bacteriophages containing a genome of another bacteriophage within their genomes.
PloS one 2012;7(7):e40683.
2012: Kira S Makarova; Eugene V Koonin; Zvi Kelman
The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes.
Biology direct 2012;7():7.
2011: Domink Esser; Theresa Kouril; Todd Lowe; Kira S Makarova; Dietmar Schomburg; Sonja-Verena Albers; Patricia P Chan; Pawel Sierocinski; John van der Oost; Melanie Zaparty; Bettina Siebers
Functional curation of the Sulfolobus solfataricus P2 and S. acidocaldarius 98-3 complete genome sequences.
Extremophiles : life under extreme conditions 2011;15(6):711-2.
2011: Kira S Makarova; Sagi Snir; Yuri I Wolf; Eugene V Koonin
Defense islands in bacterial and archaeal genomes and prediction of novel defense systems.
Journal of bacteriology 2011;193(21):6039-56.
2011: Kira S Makarova; Daniel H Haft; Rodolphe Barrangou; Stan J J Brouns; Emmanuelle Charpentier; Philippe HORVATH; Sylvain Moineau; Francisco J M Mojica; Yuri I Wolf; Alexander F Yakunin; John van der Oost; Eugene V Koonin
Evolution and classification of the CRISPR-Cas systems.
Nature reviews. Microbiology 2011;9(6):467-77.
2011: Valera V Peremyslov; Todd C Mockler; Sergei A Filichkin; Samuel E Fox; Pankaj Jaiswal; Kira S Makarova; Eugene V Koonin; Valerian V Dolja
Expression, splicing, and evolution of the myosin gene family in plants.
Plant physiology 2011;155(3):1191-204.
2011: Damir Mukhamedyarov; Konstantin Severinov; Kira S Makarova; Konstantin Kuznedelov
Francisella RNA polymerase contains a heterodimer of non-identical α subunits.
BMC molecular biology 2011;12():50.
2011: Bettina Siebers; Britta Tjaden; Mathias von Jan; Melanie Zaparty; Sonja-Verena Albers; Steve D Bell; Fabian Blombach; Hans-Peter Klenk; Arnulf Kletzin; Nikos Kyrpides; Christa Lanz; Kira S Makarova; André Plagens; Günter Raddatz; Markus Rampp; Andrea Rosinus; Stephan C Schuster; Reinhard Hensel
The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota.
PloS one 2011;6(10):e24222.
2011: Kira S Makarova; Yuri I Wolf; L Aravind; Eugene V Koonin
Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems.
Biology direct 2011;6():38.
2010: Kira S Makarova; Natalya Yutin; Stephen D Bell; Eugene V Koonin
Evolution of diverse cell division and vesicle formation systems in Archaea.
Nature reviews. Microbiology 2010;8(10):731-41.
2010: Elizabeth M Fozo; Kira S Makarova; Svetlana A Shabalina; Natalya Yutin; Eugene V Koonin; Gisela Storz
Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families.
Nucleic acids research 2010;38(11):3743-59.
2010: Kira S Makarova; Eugene V Koonin
Archaeal ubiquitin-like proteins: functional versatility and putative ancestral involvement in tRNA modification revealed by comparative genomic analysis.
Archaea (Vancouver, B.C.) 2010;2010():.
2010: Kira S Makarova; Eugene V Koonin
Two new families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea.
Biology direct 2010;5():33.
2009: Fabian Blombach; Kira S Makarova; Jeannette Marrero; Bettina Siebers; Eugene V Koonin; John van der Oost
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.
Biology direct 2009;4():39.
2009: Kira S Makarova; Yuri I Wolf; John van der Oost; Eugene V Koonin
Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements.
Biology direct 2009;4():29.
2009: Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes.
Biology direct 2009;4():19.
2009: Tahir Tahirov; Kira S Makarova; Igor Rogozin; Youri I Pavlov; Eugene V Koonin
Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors.
Biology direct 2009;4():11.
2008: Stan J J Brouns; Matthijs M Jore; Magnus Lundgren; Edze R Westra; Rik J H Slijkhuis; Ambrosius Snijders; Mark J Dickman; Kira S Makarova; Eugene V Koonin; John van der Oost
Small CRISPR RNAs guide antiviral defense in prokaryotes.
Science (New York, N.Y.) 2008;321(5891):960-4.
2008: Natalya Yutin; Kira S Makarova; Sergei L Mekhedov; Yuri I Wolf; Eugene V Koonin
The deep archaeal roots of eukaryotes.
Molecular biology and evolution 2008;25(8):1619-30.
2008: Natalia Beloglazova; Greg Brown; Matthew D Zimmerman; Michael Proudfoot; Kira S Makarova; Marina Kudritska; Samvel Kochinyan; Shuren Wang; Maksymilian Chruszcz; Wladek Minor; Eugene V Koonin; Aled M Edwards; Alexei Savchenko; Alexander F Yakunin
A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats.
The Journal of biological chemistry 2008;283(29):20361-71.
2008: James G Elkins; Mircea Podar; David E Graham; Kira S Makarova; Yuri Wolf; Lennart Randau; Brian P Hedlund; Céline Brochier-Armanet; Victor Kunin; Iain Anderson; Alla Lapidus; Eugene Goltsman; Kerrie Barry; Eugene V Koonin; Phil Hugenholtz; Nikos Kyrpides; Gerhard Wanner; Paul Richardson; Martin Keller; Karl O Stetter
A korarchaeal genome reveals insights into the evolution of the Archaea.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(23):8102-7.
2008: Dror Avisar; Alexey I Prokhnevsky; Kira S Makarova; Eugene V Koonin; Valerian V Dolja
Myosin XI-K Is required for rapid trafficking of Golgi stacks, peroxisomes, and mitochondria in leaf cells of Nicotiana benthamiana.
Plant physiology 2008;146(3):1098-108.
2008: Jimmy Saw; Bruce W Mountain; Lu Feng; Marina V Omelchenko; Shaobin Hou; Jennifer A Saito; Matthew B Stott; Dan Li; Guang Zhao; Junli Wu; Michael Galperin; Eugene V Koonin; Kira S Makarova; Yuri I Wolf; Daniel J Rigden; Peter F Dunfield; Lei Wang; Maqsudul Alam
Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1.
Genome biology 2008;9(11):R161.
2008: Mircea Podar; Iain Anderson; Kira S Makarova; James G Elkins; Natalia Ivanova; Mark A Wall; Athanasios Lykidis; Kostantinos Mavromatis; Hui Sun; Matthew Hudson; Wenqiong Chen; Cosmin Deciu; Don Hutchison; Jonathan R Eads; Abraham Anderson; Fillipe Fernandes; Ernest Szeto; Alla Lapidus; Nikos Kyrpides; Milton H Saier; Paul M Richardson; Reinhard Rachel; Harald Huber; Jonathan Eisen; Eugene V Koonin; Martin Keller; Karl O Stetter
A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans.
Genome biology 2008;9(11):R158.
2008: Igor Rogozin; Kira S Makarova; Youri I Pavlov; Eugene V Koonin
A highly conserved family of inactivated archaeal B family DNA polymerases.
Biology direct 2008;3():32.
2008: Shaobin Hou; Kira S Makarova; Jimmy Saw; Pavel Senin; Benjamin V Ly; Zhemin Zhou; Yan Ren; Jianmei Wang; Michael Galperin; Marina V Omelchenko; Yuri I Wolf; Natalya Yutin; Eugene V Koonin; Matthew B Stott; Bruce W Mountain; Michelle A Crowe; Angela Smirnova; Peter F Dunfield; Lu Feng; Lei Wang; Maqsudul Alam
Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia.
Biology direct 2008;3():26.
2008: Armen Y Mulkidjanian; Michael Galperin; Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Evolutionary primacy of sodium bioenergetics.
Biology direct 2008;3():13.
2008: Mircea Podar; Mark A Wall; Kira S Makarova; Eugene V Koonin
The prokaryotic V4R domain is the likely ancestor of a key component of the eukaryotic vesicle transport system.
Biology direct 2008;3():2.
2008: Angela M Marcobal; David Sela; Yuri I Wolf; Kira S Makarova; david mills
Role of hypermutability in the evolution of the genus Oenococcus.
Journal of bacteriology 2008;190(2):564-70.
2007: Armen Y Mulkidjanian; Kira S Makarova; Michael Galperin; Eugene V Koonin
Inventing the dynamo machine: the evolution of the F-type and V-type ATPases.
Nature reviews. Microbiology 2007;5(11):892-9.
2007: Kira S Makarova; Eugene V Koonin
Evolutionary genomics of lactic acid bacteria.
Journal of bacteriology 2007;189(4):1199-208.
2007: Eugene V Koonin; Kira S Makarova; James G Elkins
Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota".
Biology direct 2007;2():38.
2007: Kira S Makarova; Alexander V Sorokin; Pavel Novichkov; Yuri I Wolf; Eugene V Koonin
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.
Biology direct 2007;2():33.
2007: Kira S Makarova; Marina V Omelchenko; Elena K Gaidamakova; Vera Y Matrosova; Alexander Vasilenko; Min Zhai; Alla Lapidus; Alex Copeland; Edwin Kim; Miriam Land; Konstantinos Mavrommatis; Samuel Pitluck; Paul M Richardson; Chris Detter; Thomas S Brettin; Elizabeth Saunders; Barry Lai; Bruce Ravel; Kenneth M Kemner; Yuri I Wolf; Alexei Sorokin; Anna V Gerasimova; Mikhail S Gelfand; James K Fredrickson; Eugene V Koonin; Michael J Daly
Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks.
PloS one 2007;2(9):e955.
2006: Kira S Makarova; Nick V Grishin; Eugene V Koonin
The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria.
Bioinformatics (Oxford, England) 2006;22(21):2581-4.
2006: Armen Y Mulkidjanian; Eugene V Koonin; Kira S Makarova; Sergei L Mekhedov; Alexei Sorokin; Yuri I Wolf; Alexis Dufresne; Frédéric Partensky; Henry Burd; Denis Kaznadzey; Robert Haselkorn; Michael Galperin
The cyanobacterial genome core and the origin of photosynthesis.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(35):13126-31.
2006: Kira S Makarova; Eugene V Koonin; Robert Haselkorn; Michael Galperin
Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion.
Bioinformatics (Oxford, England) 2006;22(11):1297-301.
2006: Nina Marinsek; Elizabeth R Barry; Kira S Makarova; Isabelle Dionne; Eugene V Koonin; Steve Bell
GINS, a central nexus in the archaeal DNA replication fork.
EMBO reports 2006;7(5):539-45.
2006: Kira S Makarova; Nick V Grishin; Svetlana A Shabalina; Yuri I Wolf; Eugene V Koonin
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.
Biology direct 2006;1():7.
2006: Elena Smirnova; Elysa B Goldberg; Kira S Makarova; Lin Lin; William J Brown; Catherine L Jackson
ATGL has a key role in lipid droplet/adiposome degradation in mammalian cells.
EMBO reports 2006;7(1):106-13.
2005: Kira S Makarova; Eugene V Koonin
Evolutionary and functional genomics of the Archaea.
Current opinion in microbiology 2005;8(5):586-94.
2005: Debabrota Ghosal; Marina V Omelchenko; Elena K Gaidamakova; Vera Y Matrosova; Alexander Vasilenko; Amudhan Venkateswaran; Min Zhai; Heather M Kostandarithes; Hassan Brim; Kira S Makarova; Lawrence P Wackett; James K Fredrickson; Michael J Daly
How radiation kills cells: survival of Deinococcus radiodurans and Shewanella oneidensis under oxidative stress.
FEMS microbiology reviews 2005;29(2):361-75.
2005: Olga V Moroz; Alexey G Murzin; Kira S Makarova; Eugene V Koonin; Keith S Wilson; Michael Galperin
Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential "house-cleaning" functions.
Journal of molecular biology 2005;347(2):243-55.
2005: Marina V Omelchenko; Yuri I Wolf; Elena K Gaidamakova; Vera Y Matrosova; Alexander Vasilenko; Min Zhai; Michael J Daly; Eugene V Koonin; Kira S Makarova
Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance.
BMC evolutionary biology 2005;5():57.
2005: Kira S Makarova; Yuri I Wolf; Sergei L Mekhedov; Boris G Mirkin; Eugene V Koonin
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell.
Nucleic acids research 2005;33(14):4626-38.
2004: Shaobin Hou; Jimmy Saw; Kit Shan Lee; Tracey Allen K Freitas; Claude Belisle; Yutaka Kawarabayasi; Stuart P Donachie; Alla Pikina; Michael Galperin; Eugene V Koonin; Kira S Makarova; Marina V Omelchenko; Alexei Sorokin; Yuri I Wolf; Qing X Li; Young-Soo Keum; Sonia Campbell; Judith Denery; Shin-Ichi Aizawa; Satoshi Shibata; Alexander Malahoff; Maqsudul Alam
Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(52):18036-41.
2004: Michael J Daly; Elena K Gaidamakova; Vera Y Matrosova; Alexander Vasilenko; Min Zhai; Amudhan Venkateswaran; M Hess; Marina V Omelchenko; Heather M Kostandarithes; Kira S Makarova; Lawrence P Wackett; James K Fredrickson; Debabrota Ghosal
Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance.
Science (New York, N.Y.) 2004;306(5698):1025-8.
2004: Thijs J G Ettema; Kira S Makarova; Gera L Jellema; Hinco J Gierman; Eugene V Koonin; Martijn A Huynen; WILLEM DE VOS; John van der Oost
Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism.
Journal of bacteriology 2004;186(22):7754-62.
2004: Igor Rogozin; Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes.
Briefings in bioinformatics 2004;5(2):131-49.
2004: Lakshminarayan M Iyer; Kira S Makarova; Eugene V Koonin; L Aravind
Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging.
Nucleic acids research 2004;32(17):5260-79.
2004: Eugene Kolker; Kira S Makarova; Svetlana A Shabalina; Alex F Picone; Samuel O Purvine; Ted Holzman; Tim Cherny; David Armbruster; Robert munson; Grigory Kolesov; Dmitrij Frishman; Michael Galperin
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae.
Nucleic acids research 2004;32(8):2353-61.
2004: Anu Raghunathan; Nathan Price; Michael Galperin; Kira S Makarova; Samuel O Purvine; Alex F Picone; Tim Cherny; Tao Xie; Thomas J Reilly; Robert munson; Ryan E Tyler; Brian Akerley; Arnold L. Smith; Bernhard Ø Palsson; Eugene Kolker
In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.
Omics : a journal of integrative biology 2004;8(1):25-41.
2004: Eugene V Koonin; Natalie Fedorova Abrams; John D Jackson; Aviva R Jacobs; Dmitri M Krylov; Kira S Makarova; Raja Mazumder; Sergei L Mekhedov; Anastasia N Nikolskaya; B Sridhar Rao; Igor Rogozin; Sergei Smirnov; Alexander V Sorokin; Alexander V Sverdlov; Sona Vasudevan; Yuri I Wolf; Jodie Yin; Darren A Natale
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes.
Genome biology 2004;5(2):R7.
2003: Kira S Makarova; Eugene V Koonin
Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis.
FEMS microbiology letters 2003;227(1):17-23.
2003: Alexis Dufresne; Marcel Salanoubat; Frédéric Partensky; François Artiguenave; Ilka M Axmann; Valérie Barbe; Simone Duprat; Michael Galperin; Eugene V Koonin; Florence Le Gall; Kira S Makarova; Martin Ostrowski; Sophie Oztas; Catherine Robert; Igor Rogozin; David J Scanlan; Nicole Tandeau de Marsac; Jean Weissenbach; Patrick Wincker; Yuri I Wolf; Wolfgang Hess
Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(17):10020-5.
2003: Eugene Kolker; Samuel O Purvine; Michael Galperin; Sergey Stolyar; David R Goodlett; Alexey I Nesvizhskii; Andrew Keller; Tao Xie; Jimmy K Eng; Eugene Yi; Leroy Hood; Alex F Picone; Tim Cherny; Brian C Tjaden; Andrew F Siegel; Thomas J Reilly; Kira S Makarova; Bernhard Ø Palsson; Arnold L. Smith
Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.
Journal of bacteriology 2003;185(15):4593-602.
2003: Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Potential genomic determinants of hyperthermophily.
Trends in genetics : TIG 2003;19(4):172-6.
2003: Yongqing Liu; ali khawwam; Marina V Omelchenko; Alex S Beliaev; Amudhan Venkateswaran; Julia Stair; Liyou Wu; Dorothea K Thompson; Dong Xu; Igor Rogozin; Elena K Gaidamakova; Min Zhai; Kira S Makarova; Eugene V Koonin; Michael J Daly
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(7):4191-6.
2003: Igor Rogozin; Vladimir N Babenko; Natalie Fedorova Abrams; John D Jackson; Aviva R Jacobs; Dmitri M Krylov; Kira S Makarova; Raja Mazumder; Sergei L Mekhedov; Boris G Mirkin; Anastasia N Nikolskaya; B Sridhar Rao; Sergei Smirnov; Alexander V Sorokin; Alexander V Sverdlov; Sona Vasudevan; Yuri I Wolf; Jodie Yin; Darren A Natale; Eugene V Koonin
Evolution of eukaryotic gene repertoire and gene structure: discovering the unexpected dynamics of genome evolution.
Cold Spring Harbor symposia on quantitative biology 2003;68():293-301.
2003: Marina V Omelchenko; Kira S Makarova; Yuri I Wolf; Igor Rogozin; Eugene V Koonin
Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ.
Genome biology 2003;4(9):R55.
2003: Kira S Makarova; Eugene V Koonin
Comparative genomics of Archaea: how much have we learned in six years, and what's next?
Genome biology 2003;4(8):115.
2003: Vladimir A Ponomarev; Kira S Makarova; L Aravind; Eugene V Koonin
Gene duplication with displacement and rearrangement: origin of the bacterial replication protein PriB from the single-stranded DNA-binding protein Ssb.
Journal of molecular microbiology and biotechnology 2003;5(4):225-9.
2003: Eugene V Koonin; Kira S Makarova; Igor Rogozin; Laetitia Davidovic; Marie-Claude Letellier; Luca Pellegrini
The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers.
Genome biology 2003;4(3):R19.
2002: Igor Rogozin; Kira S Makarova; Darren A Natale; Alexey N Spiridonov; Roman L Tatusov; Yuri I Wolf; Jodie Yin; Eugene V Koonin
Congruent evolution of different classes of non-coding DNA in prokaryotic genomes.
Nucleic acids research 2002;30(19):4264-71.
2002: Kira S Makarova; L Aravind; Eugene V Koonin
SWIM, a novel Zn-chelating domain present in bacteria, archaea and eukaryotes.
Trends in biochemical sciences 2002;27(8):384-6.
2002: Igor Rogozin; Kira S Makarova; Janos Murvai; Eva Czabarka; Yuri I Wolf; Roman L Tatusov; Laszlo A Szekely; Eugene V Koonin
Connected gene neighborhoods in prokaryotic genomes.
Nucleic acids research 2002;30(10):2212-23.
2002: Marina V Omelchenko; Kira S Makarova; Eugene V Koonin
Recurrent intragenomic recombination leading to sequence homogenization during the evolution of the lipoyl-binding domain.
FEMS microbiology letters 2002;209(2):255-60.
2002: Alexei I Slesarev; Katja V Mezhevaya; Kira S Makarova; Nikolai Polushin; Olga V Shcherbinina; Vera V Shakhova; Galina I Belova; L Aravind; Darren A Natale; Igor Rogozin; Roman L Tatusov; Yuri I Wolf; Karl O Stetter; Andrei Malykh; Eugene V Koonin; Sergei A Kozyavkin
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(7):4644-9.
2002: Kira S Makarova; L Aravind; Nick V Grishin; Igor Rogozin; Eugene V Koonin
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.
Nucleic acids research 2002;30(2):482-96.
2001: J Nölling; G Breton; Marina V Omelchenko; Kira S Makarova; Qiandong Zeng; R Gibson; H M Lee; J Dubois; D Qiu; J Hitti; Yuri I Wolf; Roman L Tatusov; F Sabathe; Lynn Doucette-Stamm; P Soucaille; Michael J Daly; george bennett; Eugene V Koonin; D R Smith
Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum.
Journal of bacteriology 2001;183(16):4823-38.
2001: I King Jordan; Kira S Makarova; John L Spouge; Yuri I Wolf; Eugene V Koonin
Lineage-specific gene expansions in bacterial and archaeal genomes.
Genome research 2001;11(4):555-65.
2001: Kira S Makarova; L Aravind; Yuri I Wolf; Roman L Tatusov; KW Minton; Eugene V Koonin; Michael J Daly
Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics.
Microbiology and molecular biology reviews : MMBR 2001;65(1):44-79.
2001: Kira S Makarova; V A Ponomarev; Eugene V Koonin
Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins.
Genome biology 2001;2(9):RESEARCH 0033.
2001: Eugene V Koonin; Kira S Makarova; L Aravind
Horizontal gene transfer in prokaryotes: quantification and classification.
Annual review of microbiology 2001;55():709-42.
2001: Kira S Makarova; A A Mironov; M S Gelfand
Conservation of the binding site for the arginine repressor in all bacterial lineages.
Genome biology 2001;2(4):RESEARCH0013.
2001: I King Jordan; Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Gene conversions in genes encoding outer-membrane proteins in H. pylori and C. pneumoniae.
Trends in genetics : TIG 2001;17(1):7-10.
2000: L Aravind; Kira S Makarova; Eugene V Koonin
SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.
Nucleic acids research 2000;28(18):3417-32.
2000: Amudhan Venkateswaran; S C McFarlan; Debabrota Ghosal; KW Minton; Alexander Vasilenko; Kira S Makarova; Lawrence P Wackett; Michael J Daly
Physiologic determinants of radiation resistance in Deinococcus radiodurans.
Applied and environmental microbiology 2000;66(6):2620-6.
2000: Kira S Makarova; L Aravind; Eugene V Koonin
A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae.
Trends in biochemical sciences 2000;25(2):50-2.
2000: Kira S Makarova; L Aravind; Michael J Daly; Eugene V Koonin
Specific expansion of protein families in the radioresistant bacterium Deinococcus radiodurans.
Genetica 2000;108(1):25-34.
1999: Kira S Makarova; Yuri I Wolf; Owen R White; KW Minton; Michael J Daly
Short repeats and IS elements in the extremely radiation-resistant bacterium Deinococcus radiodurans and comparison to other bacterial species.
Research in microbiology 1999;150(9-10):711-24.
1999: Kira S Makarova; Nick V Grishin
Thermolysin and mitochondrial processing peptidase: how far structure-functional convergence goes.
Protein science : a publication of the Protein Society 1999;8(11):2537-40.
1999: Kira S Makarova; Nick V Grishin
The Zn-peptidase superfamily: functional convergence after evolutionary divergence.
Journal of molecular biology 1999;292(1):11-7.
1999: Kira S Makarova; L Aravind; Eugene V Koonin
A superfamily of archaeal, bacterial, and eukaryotic proteins homologous to animal transglutaminases.
Protein science : a publication of the Protein Society 1999;8(8):1714-9.
1999: Kira S Makarova; L Aravind; Michael Galperin; Nick V Grishin; Roman L Tatusov; Yuri I Wolf; Eugene V Koonin
Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.
Genome research 1999;9(7):608-28.
1996: Iu I Vul'f; Kira S Makarova; VA Ratner
[Evolution modes of eukaryote retrotransposons].
Genetika 1996;32(1):35-41.
1995: Kira S Makarova; Iu I Vul'f; I A Seledtsov; VA Ratner
[Evolution of gypsy-group retrotransposons: phylogenetic analysis of domains included in the pol-polyprotein].
Genetika 1995;31(12):1614-29.
1995: I A Seledtsov; Iu I Vul'f; Kira S Makarova
[Multiple alignment of biopolymer sequences, based on the search for statistically significant common segments].
Molekuliarnaia biologiia 1995;29(5):1023-39.
1993: V V Solovyev; Kira S Makarova
A novel method of protein sequence classification based on oligopeptide frequency analysis and its application to search for functional sites and to domain localization.
Computer applications in the biosciences : CABIOS 1993;9(1):17-24.
1992: Kira S Makarova; A V Mazin; Y I Wolf; V V Soloviev
DIROM: an experimental design interactive system for directed mutagenesis and nucleic acids engineering.
Computer applications in the biosciences : CABIOS 1992;8(5):425-31.
1992: V V Solov'ev; Kira S Makarova
[Search for functional domain boundaries and localization of functional sites based on oligopeptide vocabularies].
Molekuliarnaia biologiia 1992;26(2):341-53.
1992: Kira S Makarova; Iu V Bul'f; A V Mazin; V V Solov'ev
["DIROM"--an interactive system for planning experiments on directed mutagenesis and design of artificial genes].
Molekuliarnaia biologiia 1992;26(1):93-103.