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Michael Galperin

Research Profile

Genes & Molecular Sequences

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TOP 3
Xosé M Fernández-Suárez; Michael Galperin
The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection.
Michael Galperin; Sergei L Mekhedov; Pere Puigbo; Sergey Smirnov; Yuri I Wolf; Daniel J Rigden
Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes.
Armen Y Mulkidjanian; Andrew Yu Bychkov; Daria V Dibrova; Michael Galperin; Eugene V Koonin
Open questions on the origin of life at anoxic geothermal fields.

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All Publications

2013: Xosé M Fernández-Suárez; Michael Galperin
The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection.
Nucleic acids research 2013;41(Database issue):D1-7.
2012: Michael Galperin; Sergei L Mekhedov; Pere Puigbo; Sergey Smirnov; Yuri I Wolf; Daniel J Rigden
Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes.
Environmental microbiology 2012;14(11):2870-90.
2012: Armen Y Mulkidjanian; Andrew Yu Bychkov; Daria V Dibrova; Michael Galperin; Eugene V Koonin
Open questions on the origin of life at anoxic geothermal fields.
Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life 2012;42(5):507-16.
2012: Daria V Dibrova; Michael Galperin; Eugene V Koonin; Michail Y Chudetsky; Armen Y Mulkidjanian
The role of energy in the emergence of biology from chemistry.
Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life 2012;42(5):459-68.
2011: Pascale Gaudet; Amos Bairoch; Dawn Field; Susanna-Assunta Sansone; Chris Taylor; Teresa K Attwood; Alex Bateman; Judith A Blake; Carol Bult; J Michael Cherry; Rex Chisholm; Guy Cochrane; Charles E Cook; Janan T Eppig; Michael Galperin; Robert Gentleman; Carole A Goble; Takashi Gojobori; John M Hancock; Douglas G Howe; Tadashi Imanishi; Janet Kelso; David Landsman; Suzanna E Lewis; Ilene Karsch Mizrachi; Sandra Orchard; B F Francis Ouellette; Shoba Ranganathan; Lorna Richardson; Philippe Rocca-Serra; Paul N Schofield; Damian Smedley; Christopher Southan; Tin W Tan; Tatiana Tatusova; Patricia L Whetzel; Owen R White; Chisato Yamasaki
Towards BioDBcore: a community-defined information specification for biological databases.
Database : the journal of biological databases and curation 2011;2011():baq027.
2011: Michael Galperin; Guy R Cochrane
The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection.
Nucleic acids research 2011;39(Database issue):D1-6.
2011: Pascale Gaudet; Amos Bairoch; Dawn Field; Susanna-Assunta Sansone; Chris Taylor; Teresa K Attwood; Alex Bateman; Judith A Blake; Carol Bult; J Michael Cherry; Rex Chisholm; Guy Cochrane; Charles E Cook; Janan T Eppig; Michael Galperin; Robert Gentleman; Carole Goble; Takashi Gojobori; John M Hancock; Douglas G Howe; Tadashi Imanishi; Janet Kelso; David Landsman; Suzanna E Lewis; Ilene Karsch Mizrachi; Sandra Orchard; B F Francis Ouellette; Shoba Ranganathan; Lorna Richardson; Philippe Rocca-Serra; Paul N Schofield; Damian Smedley; Christopher Southan; Tin Wee Tan; Tatiana Tatusova; Patricia L Whetzel; Owen R White; Chisato Yamasaki
Towards BioDBcore: a community-defined information specification for biological databases.
Nucleic acids research 2011;39(Database issue):D7-10.
2010: Anatoli Tchigvintsev; Xiaohui Xu; Alexander Singer; Changsoo Chang; Greg Brown; Michael Proudfoot; Hong Cui; Robert Flick; Wayne F Anderson; Andrzej Joachimiak; Michael Galperin; Alexei Savchenko; Alexander F Yakunin
Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases.
Journal of molecular biology 2010;402(3):524-38.
2010: Armen Y Mulkidjanian; Michael Galperin
On the abundance of zinc in the evolutionarily old protein domains.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(36):E137; author reply E138.
2010: Michael Galperin; Eugene V Koonin
From complete genome sequence to 'complete' understanding?
Trends in biotechnology 2010;28(8):398-406.
2010: Daria V Dibrova; Michael Galperin; Armen Y Mulkidjanian
Characterization of the N-ATPase, a distinct, laterally transferred Na+-translocating form of the bacterial F-type membrane ATPase.
Bioinformatics (Oxford, England) 2010;26(12):1473-6.
2010: Michael Galperin; Roger Higdon; Eugene Kolker
Interplay of heritage and habitat in the distribution of bacterial signal transduction systems.
Molecular bioSystems 2010;6(4):721-8.
2010: Michael Galperin
Diversity of structure and function of response regulator output domains.
Current opinion in microbiology 2010;13(2):150-9.
2010: Marina V Omelchenko; Michael Galperin; Yuri I Wolf; Eugene V Koonin
Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution.
Biology direct 2010;5():31.
2010: Guy Cochrane; Michael Galperin
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources.
Nucleic acids research 2010;38(Database issue):D1-4.
2009: Michelle A Allen; Federico M Lauro; Timothy J Williams; Dominic Burg; Khawar S Siddiqui; Davide De Francisci; Kevin W Y Chong; Oliver Pilak; Hwee H Chew; Matthew Z De Maere; Lily Ting; Marilyn Katrib; Charmaine Ng; Kevin R Sowers; Michael Galperin; Iain J Anderson; Natalia Ivanova; Eileen Dalin; Michele Martinez; Alla Lapidus; Loren Hauser; Miriam Land; Torsten Thomas; Ricardo Cavicchioli
The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation.
The ISME journal 2009;3(9):1012-35.
2009: Xuehua Wan; Jason R Tuckerman; Jennifer A Saito; Tracey Allen K Freitas; James S Newhouse; Judith R Denery; Michael Galperin; Gonzalo Gonzalez; Marie-Alda Gilles-Gonzalez; Maqsudul Alam
Globins synthesize the second messenger bis-(3'-5')-cyclic diguanosine monophosphate in bacteria.
Journal of molecular biology 2009;388(2):262-70.
2009: Armen Y Mulkidjanian; Michael Galperin; Eugene V Koonin
Co-evolution of primordial membranes and membrane proteins.
Trends in biochemical sciences 2009;34(4):206-15.
2009: Urs Jenal; Michael Galperin
Single domain response regulators: molecular switches with emerging roles in cell organization and dynamics.
Current opinion in microbiology 2009;12(2):152-60.
2009: Michael Galperin
Microbial genomics as pursuit of happiness.
Microbial biotechnology 2009;2(2):135-6.
2009: Armen Y Mulkidjanian; Michael Galperin
On the origin of life in the zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth.
Biology direct 2009;4():27.
2009: Víctor de Lorenzo; Michael Galperin
Microbial systems biology: bottom up and top down.
FEMS microbiology reviews 2009;33(1):1-2.
2009: Michael Galperin; Guy R Cochrane
Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009.
Nucleic acids research 2009;37(Database issue):D1-4.
2008: Michael Galperin
Sorting out the mix in microbial genomics.
Environmental microbiology 2008;10(12):3187-92.
2008: Michael Galperin
The quest for biofuels fuels genome sequencing.
Environmental microbiology 2008;10(10):2471-5.
2008: Daniel J Rigden; Michael Galperin
Sequence analysis of GerM and SpoVS, uncharacterized bacterial 'sporulation' proteins with widespread phylogenetic distribution.
Bioinformatics (Oxford, England) 2008;24(16):1793-7.
2008: Michael Galperin
New feel for new phyla.
Environmental microbiology 2008;10(8):1927-33.
2008: Armen Y Mulkidjanian; Pavel Dibrov; Michael Galperin
The past and present of sodium energetics: may the sodium-motive force be with you.
Biochimica et biophysica acta 2008;1777(7-8):985-92.
2008: Michael Galperin
Genomes of model organisms: know thy tools.
Environmental microbiology 2008;10(6):1383-91.
2008: Michael Galperin
Telling bacteria: do not LytTR.
Structure (London, England : 1993) 2008;16(5):657-9.
2008: Michael Galperin
The dawn of synthetic genomics.
Environmental microbiology 2008;10(4):821-5.
2008: Michael Galperin
Social bacteria and asocial eukaryotes.
Environmental microbiology 2008;10(2):281-8.
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: 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: Michael Galperin
The Molecular Biology Database Collection: 2008 update.
Nucleic acids research 2008;36(Database issue):D2-4.
2007: Michael Galperin
Some bacteria degrade explosives, others prefer boiling methanol.
Environmental microbiology 2007;9(12):2905-10.
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: Michael Galperin
Dark matter in a deep-sea vent and in human mouth.
Environmental microbiology 2007;9(10):2385-91.
2007: Armen Y Mulkidjanian; Michael Galperin
Physico-chemical and evolutionary constraints for the formation and selection of first biopolymers: towards the consensus paradigm of the abiogenic origin of life.
Chemistry & biodiversity 2007;4(9):2003-15.
2007: Michael Galperin
Genomics against flatulence.
Environmental microbiology 2007;9(8):1869-77.
2007: Michael Galperin
Linear chromosomes in bacteria: no straight edge advantage?
Environmental microbiology 2007;9(6):1357-62.
2007: Michael Galperin
Mycobacterial genomes for all tastes: from BCG to biodegradation of naphtalene and pyrene.
Environmental microbiology 2007;9(4):839-45.
2007: Daniela Bumbaca; James E Littlejohn; Hannah Nayakanti; Alexander H Lucas; Daniel J Rigden; Michael Galperin; Mark J Jedrzejas
Genome-based identification and characterization of a putative mucin-binding protein from the surface of Streptococcus pneumoniae.
Proteins 2007;66(3):547-58.
2007: Michael Galperin
Using archaeal genomics to fight global warming and clostridia to fight cancer.
Environmental microbiology 2007;9(2):279-86.
2007: Michael Galperin; Anastasia N Nikolskaya
Identification of sensory and signal-transducing domains in two-component signaling systems.
Methods in enzymology 2007;422():47-74.
2007: Michael Galperin
The Molecular Biology Database Collection: 2007 update.
Nucleic acids research 2007;35(Database issue):D3-4.
2007: Mark D'Souza; Elizabeth M Glass; Mustafa H Syed; Yi Zhang; Alexis Rodriguez; Natalia Maltsev; Michael Galperin
Sentra: a database of signal transduction proteins for comparative genome analysis.
Nucleic acids research 2007;35(Database issue):D271-3.
2006: Michael Galperin
The fuzzy border between a cell and an organelle.
Environmental microbiology 2006;8(12):2062-7.
2006: Michael Galperin; Eugene Kolker
New metrics for comparative genomics.
Current opinion in biotechnology 2006;17(5):440-7.
2006: Michael Galperin
A square archaeon, the smallest eukaryote and the largest bacteria.
Environmental microbiology 2006;8(10):1683-7.
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: Michael Galperin
Sampling of microbial diversity by complete genomes.
Environmental microbiology 2006;8(8):1313-7.
2006: Michael Galperin
Structural classification of bacterial response regulators: diversity of output domains and domain combinations.
Journal of bacteriology 2006;188(12):4169-82.
2006: Michael Galperin
Genomes to aid in bioremediation of dry cleaning solvents, mothballs and more.
Environmental microbiology 2006;8(6):949-55.
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: Michael Galperin
The minimal genome keeps growing.
Environmental microbiology 2006;8(4):569-73.
2006: Michael Galperin
Protecting sausages with bacteria instead of salt.
Environmental microbiology 2006;8(2):185-92.
2006: Michael Galperin
The Molecular Biology Database Collection: 2006 update.
Nucleic acids research 2006;34(Database issue):D3-5.
2006: Michael Galperin; Olga V Moroz; Keith S Wilson; Alexey G Murzin
House cleaning, a part of good housekeeping.
Molecular microbiology 2006;59(1):5-19.
2006: Dorit Amikam; Michael Galperin
PilZ domain is part of the bacterial c-di-GMP binding protein.
Bioinformatics (Oxford, England) 2006;22(1):3-6.
2005: Michael Galperin
More cool news from marine bacteria.
Environmental microbiology 2005;7(12):1864-7.
2005: Rahim Habibian; Judith Dzioba; Jeannie Barrett; Michael Galperin; Peter C Loewen; Pavel Dibrov
Functional analysis of conserved polar residues in Vc-NhaD, Na+/H+ antiporter of Vibrio cholerae.
The Journal of biological chemistry 2005;280(47):39637-43.
2005: Michael Galperin
The secret of being cool.
Environmental microbiology 2005;7(10):1499-504.
2005: Alexey Teplyakov; Galina Obmolova; John Toedt; Michael Galperin; Gary L Gilliland
Crystal structure of the bacterial YhcH protein indicates a role in sialic acid catabolism.
Journal of bacteriology 2005;187(16):5520-7.
2005: Ute Römling; Mark Gomelsky; Michael Galperin
C-di-GMP: the dawning of a novel bacterial signalling system.
Molecular microbiology 2005;57(3):629-39.
2005: Michael Galperin
To finish or not to finish?
Environmental microbiology 2005;7(8):1061-4.
2005: Michael Galperin
The vibrio that sheds light.
Environmental microbiology 2005;7(6):757-60.
2005: Michael Galperin
On the bottom of the deep blue sea.
Environmental microbiology 2005;7(4):453-8.
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: Eugene Kolker; Alex F Picone; Michael Galperin; Margaret F Romine; Roger Higdon; Kira S Makarova; Natali Kolker; Gordon A Anderson; Xiaoyun Qiu; Kenneth J Auberry; Gyorgy Babnigg; Alex S Beliaev; Paul Edlefsen; Dwayne A Elias; Yuri A Gorby; Ted Holzman; Joel A Klappenbach; Konstantinos T Konstantinidis; Miriam L Land; Mary S Lipton; Lee-Ann McCue; Matthew Monroe; Ljiljana Pasa-Tolic; Grigoriy Pinchuk; Samuel Purvine; Margrethe H Serres; Sasha Tsapin; Brian A Zakrajsek; Wenhong Zhu; Jizhong Zhou; Frank W Larimer; Charles E Lawrence; Monica Riley; Frank R Collart; John R Yates; Richard D Smith; Carol S Giometti; Kenneth H Nealson; James K Fredrickson; James M Tiedje
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(6):2099-104.
2005: Michael Galperin
Life is not defined just in base pairs.
Environmental microbiology 2005;7(2):149-52.
2005: Michael Galperin
A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts.
BMC microbiology 2005;5():35.
2005: Michael Galperin
The Molecular Biology Database Collection: 2005 update.
Nucleic acids research 2005;33(Database issue):D5-24.
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 Galperin
Genomes back-to-back: when sequencing race is a good thing.
Environmental microbiology 2004;6(12):1205-9.
2004: Daniel J Rigden; Michael Galperin
The DxDxDG motif for calcium binding: multiple structural contexts and implications for evolution.
Journal of molecular biology 2004;343(4):971-84.
2004: Olga V Moroz; Maria Harkiolaki; Michael Galperin; Alexei A Vagin; Dolores González-Pacanowska; Keith S Wilson
The crystal structure of a complex of Campylobacter jejuni dUTPase with substrate analogue sheds light on the mechanism and suggests the "basic module" for dimeric d(C/U)TPases.
Journal of molecular biology 2004;342(5):1583-97.
2004: Michael Galperin
The bugs that came in from the cold.
Environmental microbiology 2004;6(10):1001-4.
2004: Michael Galperin
Looking at big brothers for clues.
Environmental microbiology 2004;6(8):767-8.
2004: Daniel J Rigden; Luciane V Mello; Michael Galperin
The PA14 domain, a conserved all-beta domain in bacterial toxins, enzymes, adhesins and signaling molecules.
Trends in biochemical sciences 2004;29(7):335-9.
2004: Michael Galperin; Alan J M Baker
From biofouling to bioremediation: the good, the bad and the vague.
Current opinion in biotechnology 2004;15(3):167-9.
2004: Michael Galperin
Bacterial signal transduction network in a genomic perspective.
Environmental microbiology 2004;6(6):552-67.
2004: Michael Galperin
Metagenomics: from acid mine to shining sea.
Environmental microbiology 2004;6(6):543-5.
2004: Michael Galperin
All bugs, big and small.
Environmental microbiology 2004;6(5):435-7.
2004: Pavel Dibrov; Elena Dibrov; Grant N Pierce; Michael Galperin
Salt in the wound: a possible role of Na+ gradient in chlamydial infection.
Journal of molecular microbiology and biotechnology 2004;8(1):1-6.
2004: Daniela Bumbaca; James E Littlejohn; Hannah Nayakanti; Daniel J Rigden; Michael Galperin; Mark J Jedrzejas
Sequence analysis and characterization of a novel fibronectin-binding repeat domain from the surface of Streptococcus pneumoniae.
Omics : a journal of integrative biology 2004;8(4):341-56.
2004: Michael Galperin; Eugene V Koonin
'Conserved hypothetical' proteins: prioritization of targets for experimental study.
Nucleic acids research 2004;32(18):5452-63.
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: Michael Galperin
The Molecular Biology Database Collection: 2004 update.
Nucleic acids research 2004;32(Database issue):D3-22.
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: Daniel J Rigden; Mark J Jedrzejas; Olga V Moroz; Michael Galperin
Structural diversity of calcium-binding proteins in bacteria: single-handed EF-hands?
Trends in microbiology 2003;11(7):295-7.
2003: Armen Y Mulkidjanian; Dmitry A Cherepanov; Michael Galperin
Survival of the fittest before the beginning of life: selection of the first oligonucleotide-like polymers by UV light.
BMC evolutionary biology 2003;3():12.
2003: Daniel J Rigden; Mark J Jedrzejas; Michael Galperin
Amidase domains from bacterial and phage autolysins define a family of gamma-D,L-glutamate-specific amidohydrolases.
Trends in biochemical sciences 2003;28(5):230-4.
2003: Daniel J Rigden; Mark J Jedrzejas; Michael Galperin
An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands.
FEMS microbiology letters 2003;221(1):103-10.
2003: Georges N Cohen; Valérie Barbe; Didier Flament; Michael Galperin; Roland Heilig; Odile Lecompte; Olivier Poch; Daniel Prieur; Joël Quérellou; Raymond Ripp; Jean-Claude Thierry; John van der Oost; Jean Weissenbach; Yvan Zivanovic; Patrick Forterre
An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi.
Molecular microbiology 2003;47(6):1495-512.
2003: Boris G Mirkin; Trevor I Fenner; Michael Galperin; Eugene V Koonin
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes.
BMC evolutionary biology 2003;3():2.
2003: I King Jordan; Katrin Henze; Natalie Fedorova Abrams; Eugene V Koonin; Michael Galperin
Phylogenomic analysis of the Giardia intestinalis transcarboxylase reveals multiple instances of domain fusion and fission in the evolution of biotin-dependent enzymes.
Journal of molecular microbiology and biotechnology 2003;5(3):172-89.
2003: Daniel J Rigden; Michael Galperin; Mark J Jedrzejas
Analysis of structure and function of putative surface-exposed proteins encoded in the Streptococcus pneumoniae genome: a bioinformatics-based approach to vaccine and drug design.
Critical reviews in biochemistry and molecular biology 2003;38(2):143-68.
2003: Anastasia N Nikolskaya; Armen Y Mulkidjanian; Iwona Beech; Michael Galperin
MASE1 and MASE2: two novel integral membrane sensory domains.
Journal of molecular microbiology and biotechnology 2003;5(1):11-6.
2003: Judith Dzioba; Claudia C Häse; Khoosheh K Gosink; Michael Galperin; Pavel Dibrov
Experimental verification of a sequence-based prediction: F(1)F(0)-type ATPase of Vibrio cholerae transports protons, not Na(+) ions.
Journal of bacteriology 2003;185(2):674-8.
2003: Igor B Zhulin; Anastasia N Nikolskaya; Michael Galperin
Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea.
Journal of bacteriology 2003;185(1):285-94.
2002: Daniel J Rigden; Vladimir V Mosolov; Michael Galperin
Sequence conservation in the chagasin family suggests a common trend in cysteine proteinase binding by unrelated protein inhibitors.
Protein science : a publication of the Protein Society 2002;11(8):1971-7.
2002: Anastasia N Nikolskaya; Michael Galperin
A novel type of conserved DNA-binding domain in the transcriptional regulators of the AlgR/AgrA/LytR family.
Nucleic acids research 2002;30(11):2453-9.
2001: Michael Galperin; M J Jedrzejas
Conserved core structure and active site residues in alkaline phosphatase superfamily enzymes.
Proteins 2001;45(4):318-24.
2001: I King Jordan; D A Natale; E V Koonin; Michael Galperin
Independent evolution of heavy metal-associated domains in copper chaperones and copper-transporting atpases.
Journal of molecular evolution 2001;53(6):622-33.
2001: Michael Galperin; Tatiana A Gaidenko; Armen Y Mulkidjanian; Michiko M Nakano; Chester W Price
MHYT, a new integral membrane sensor domain.
FEMS microbiology letters 2001;205(1):17-23.
2001: Michael Galperin; Anastasia N Nikolskaya; Eugene V Koonin
Novel domains of the prokaryotic two-component signal transduction systems.
FEMS microbiology letters 2001;203(1):11-21.
2001: Claudia C Häse; Natalie Fedorova Abrams; Michael Galperin; Pavel Dibrov
Sodium ion cycle in bacterial pathogens: evidence from cross-genome comparisons.
Microbiology and molecular biology reviews : MMBR 2001;65(3):353-70, table of contents.
2001: Michael Galperin
Conserved 'hypothetical' proteins: new hints and new puzzles.
Comparative and functional genomics 2001;2(1):14-8.
2001: Michael Galperin; Eugene V Koonin
Comparative genome analysis.
Methods of biochemical analysis 2001;43():359-92.
2001: Roman L Tatusov; Darren A Natale; I V Garkavtsev; Tatiana Tatusova; Uma Shankavaram; B Sridhar Rao; Boris Kiryutin; Michael Galperin; Natalie Fedorova Abrams; Eugene V Koonin
The COG database: new developments in phylogenetic classification of proteins from complete genomes.
Nucleic acids research 2001;29(1):22-8.
2000: Michael Galperin; Nick V Grishin
The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase.
Proteins 2000;41(2):238-47.
2000: I King Jordan; D A Natale; Michael Galperin
Copper chaperones in bacteria: association with copper-transporting ATPases.
Trends in biochemical sciences 2000;25(10):480-1.
2000: Michael Galperin; Eugene V Koonin
Who's your neighbor? New computational approaches for functional genomics.
Nature biotechnology 2000;18(6):609-13.
2000: LB Sánchez; Michael Galperin; Miklós Müller
Acetyl-CoA synthetase from the amitochondriate eukaryote Giardia lamblia belongs to the newly recognized superfamily of acyl-CoA synthetases (Nucleoside diphosphate-forming).
The Journal of biological chemistry 2000;275(8):5794-803.
2000: Michael Galperin; L Aravind; Eugene V Koonin
Aldolases of the DhnA family: a possible solution to the problem of pentose and hexose biosynthesis in archaea.
FEMS microbiology letters 2000;183(2):259-64.
2000: Darren A Natale; Uma Shankavaram; Michael Galperin; Yuri I Wolf; L Aravind; Eugene V Koonin
Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs).
Genome biology 2000;1(5):RESEARCH0009.
2000: Darren A Natale; Michael Galperin; Roman L Tatusov; Eugene V Koonin
Using the COG database to improve gene recognition in complete genomes.
Genetica 2000;108(1):9-17.
2000: Roman L Tatusov; Michael Galperin; Darren A Natale; Eugene V Koonin
The COG database: a tool for genome-scale analysis of protein functions and evolution.
Nucleic acids research 2000;28(1):33-6.
1999: Michael Galperin; Eugene V Koonin
Searching for drug targets in microbial genomes.
Current opinion in biotechnology 1999;10(6):571-8.
1999: Michael Galperin; D A Natale; L Aravind; Eugene V Koonin
A specialized version of the HD hydrolase domain implicated in signal transduction.
Journal of molecular microbiology and biotechnology 1999;1(2):303-5.
1999: Michael Galperin
Bioinformatics for all! ABRF meeting: Bioinformatics and Biomolecular Technologies: linking genomes, proteomes and biochemistry, Durham, North Carolina, USA, 19-22 March 1999. Association of Biomolecular Resource Facilities.
Trends in genetics : TIG 1999;15(7):257-8.
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.
1999: Michael Galperin; Eugene V Koonin
Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes.
Genetica 1999;106(1-2):159-70.
1998: Jesus G Valenzuela; Rosane Charlab; Michael Galperin; José M C Ribeiro
Purification, cloning, and expression of an apyrase from the bed bug Cimex lectularius. A new type of nucleotide-binding enzyme.
The Journal of biological chemistry 1998;273(46):30583-90.
1998: Michael Galperin; Amos Bairoch; Eugene V Koonin
A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases.
Protein science : a publication of the Protein Society 1998;7(8):1829-35.
1998: Michael Galperin; Steven E Brenner
Using metabolic pathway databases for functional annotation.
Trends in genetics : TIG 1998;14(8):332-3.
1998: Michael Galperin; DR Walker; Eugene V Koonin
Analogous enzymes: independent inventions in enzyme evolution.
Genome research 1998;8(8):779-90.
1998: Eugene V Koonin; Roman L Tatusov; Michael Galperin
Beyond complete genomes: from sequence to structure and function.
Current opinion in structural biology 1998;8(3):355-63.
1998: L Aravind; Michael Galperin; Eugene V Koonin
The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold.
Trends in biochemical sciences 1998;23(4):127-9.
1998: Michael Galperin; Eugene V Koonin
Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption.
In silico biology 1998;1(1):55-67.
1997: Eugene V Koonin; Michael Galperin
Prokaryotic genomes: the emerging paradigm of genome-based microbiology.
Current opinion in genetics & development 1997;7(6):757-63.
1997: Michael Galperin; Eugene V Koonin
A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity.
Protein science : a publication of the Protein Society 1997;6(12):2639-43.
1997: Eugene V Koonin; AR Mushegian; Michael Galperin; DR Walker
Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea.
Molecular microbiology 1997;25(4):619-37.
1997: Michael Galperin; E V Koonin
Sequence analysis of an exceptionally conserved operon suggests enzymes for a new link between histidine and purine biosynthesis.
Molecular microbiology 1997;24(2):443-5.
1995: Michael Galperin; M Lassiter; Y Ma; K G Taylor; Ronald J Doyle
Chemiluminescent detection of dextran bound to streptococcal glucan-binding lectin.
Analytical biochemistry 1995;225(1):185-7.
1992: J S Singh; Michael Galperin; D Drake; K G Taylor; Ronald J Doyle
Chelating agents inhibit activity and prevent expression of streptococcal glucan-binding lectins.
Infection and immunity 1992;60(9):3807-13.