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Alla Lapidus

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K Dimitri Kits; Martin Klotz; Aurélie Lajus; M L Land; Alla Lapidus; S Lucas; Claudine Médigue; J Colin Murrell; Huub J M Op den Camp; S Pitluck; Françoise Bringel; D Bruce; Jan-Fang Cheng; A Copeland; Alan A DiSpirito; Lynne Goodwin; Loren Hauser; Mike S M Jetten; Marina G Kalyuzhnaya; Stéphane Vuilleumier; Tanja Woyke; Ahmet Zeytun; Lisa Y Stein
Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8.
James G Elkins; Lynne A Goodwin; Scott D Hamilton-Brehm; Cliff S Han; James Han; Loren Hauser; Natalia N Ivanova; Nikos C Kyrpides; Miriam L Land; Alla Lapidus; Susan Lucas; Natalia Mikhailova; Ioanna Pagani; Lin Peters; Sam Pitluck; Roxanne Tapia; Tanja Woyke; David Bruce; Jan-Fang Cheng; Karen W Davenport; John C Detter; Robert W Cottingham
Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T.
Caroline M Plugge; Lars Rohlin; Johannes C M Scholten; Alfons J M Stams; Daan C Swarts; Petra Worm; Astrid H Paulitsch-Fuchs; Bryan R Crable; Eugene Goltsman; Robert P Gunsalus; Anne M Henstra; Edwin Kim; Alla Lapidus; Athanasios Lykidis; Erin McDonald; Michael J McInerney
Complete genome sequence of Syntrophobacter fumaroxidans strain (MPOB(T)).

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All Publications

2013: K Dimitri Kits; Martin Klotz; Aurélie Lajus; M L Land; Alla Lapidus; S Lucas; Claudine Médigue; J Colin Murrell; Huub J M Op den Camp; S Pitluck; Françoise Bringel; D Bruce; Jan-Fang Cheng; A Copeland; Alan A DiSpirito; Lynne Goodwin; Loren Hauser; Mike S M Jetten; Marina G Kalyuzhnaya; Stéphane Vuilleumier; Tanja Woyke; Ahmet Zeytun; Lisa Y Stein
Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8.
Genome announcements 2013;1(2):e0017013.
2013: James G Elkins; Lynne A Goodwin; Scott D Hamilton-Brehm; Cliff S Han; James Han; Loren Hauser; Natalia N Ivanova; Nikos C Kyrpides; Miriam L Land; Alla Lapidus; Susan Lucas; Natalia Mikhailova; Ioanna Pagani; Lin Peters; Sam Pitluck; Roxanne Tapia; Tanja Woyke; David Bruce; Jan-Fang Cheng; Karen W Davenport; John C Detter; Robert W Cottingham
Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T.
Genome announcements 2013;1(2):e0016213.
2012: Caroline M Plugge; Lars Rohlin; Johannes C M Scholten; Alfons J M Stams; Daan C Swarts; Petra Worm; Astrid H Paulitsch-Fuchs; Bryan R Crable; Eugene Goltsman; Robert P Gunsalus; Anne M Henstra; Edwin Kim; Alla Lapidus; Athanasios Lykidis; Erin McDonald; Michael J McInerney
Complete genome sequence of Syntrophobacter fumaroxidans strain (MPOB(T)).
Standards in genomic sciences 2012;7(1):91-106.
2012: David A Mead; Galina Ovchinnikova; Sam Pitluck; Thomas Schoenfeld; Roxanne Tapia; Tanja Woyke; Xiaojing Zhang; David Bruce; Catherine Brumm; Yun-Juan Chang; Jan-Fang Cheng; Olga Chertkov; Alex Copeland; John C Detter; Lynne A Goodwin; Cliff S Han; Loren J Hauser; Rebecca Hochstein; Natalia N Ivanova; Nikos C Kyrpides; Miriam Land; Alla Lapidus; Susan Lucas; Phillip Brumm
Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park.
Standards in genomic sciences 2012;6(3):381-400.
2012: Shivakumara Siddaramappa; Roxanne Tapia; Tanja Woyke; Jun Yan; Matt Nolan; Galina Ovchinnikova; Len Pennacchio; Sam Pitluck; Fred A Rainey; Kimberly S Bowman; David Bruce; Jean F Challacombe; Yun-Juan Chang; Milton S da Costa; Hajnalka Daligault; Susana F Delano; Chris Detter; Lynne Goodwin; Lance D Green; James Han; Shunsheng Han; Loren Hauser; Nikos C Kyrpides; Miriam Land; Alla Lapidus; William M Moe
Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to "Dehalococcoides" strains.
Standards in genomic sciences 2012;6(2):251-64.
2012: Mahajabeen Padamsee; Robert Riley; Sourabha Shantappa; Joseph W Spatafora; Manfred Binder; Alex Boyd; Ana M Calvo; Kentaro Furukawa; Igor V Grigoriev; Cedar Hesse; David S Hibbett; Stefan Hohmann; Timothy Y James; T K Arun Kumar; Kurt LaButti; Alla Lapidus; Erika Lindquist; Susan Lucas; David J McLaughlin; Kari Miller; M Catherine Aime
The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction.
Fungal genetics and biology : FG & B 2012;49(3):217-26.
2012: Konstantinos Mavromatis; Daniel J Quest; Tanja Woyke; Miriam L Land; Alla Lapidus; Thomas S Brettin; Alicia Clum; Alex Copeland; Robert W Cottingham; Lynne Goodwin; Hans Peter Klenk; Nikos Kyrpides
The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.
PloS one 2012;7(12):e48837.
2012: Hitoshi Suzuki; Khajamohiddin Syed; Patricia A vanKuyk; Ad Wiebenga; Jagjit S Yadav; Asaf Salamov; Masahiro Samejima; Mamdouh Abou-Zaid; Andrea Aerts; Kerrie Barry; Pedro Coutinho; Ronald P de Vries; Yunchen Gong; Igor V Grigoriev; Bernard Henrissat; Chiaki Hori; Kiyohiko Igarashi; Kurt LaButti; Alla Lapidus; Erika Lindquist; Susan Lucas; Jacqueline MacDonald; Radhakrishnan Mahadevan; Emma R Master
Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize.
BMC genomics 2012;13():444.
2011: Rich Boden; Jan-Fang Cheng; Michael Cunliffe; Lynne Goodwin; Cliff Han; James Han; Loren Hauser; Natalia Ivanova; Mike S.M. Jetten; K Dimitri Kits; Martin Klotz; Nikos Kyrpides; Miriam L Land; Alla Lapidus; Susan Lucas; Natalia Mikhailova; Hélène Moussard; Ioanna Pagani; Lin Peters; Sam Pitluck; Julie Scanlan; Lisa Stein; Roxanne Tapia; Hazuki Teshima; Stéphane Vuilleumier; Tanja Woyke; J Colin Murrell
Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09.
Journal of bacteriology 2011;193(24):7001-2.
2011: Mette M Svenning; Stéphane Vuilleumier; Ingvild Wartiainen; Françoise Bringel; David Bruce; Jan-Fang Cheng; Lynne Goodwin; Cliff S Han; James Han; Loren Hauser; Brittany Held; Anne Grethe Hestnes; Natalia Ivanova; Marina G Kalyuzhnaya; Martin Klotz; Aurélie Lajus; Miriam L Land; Alla Lapidus; Susan Lucas; Claudine Médigue; Matt Nolan; Sam Pitluck; Anja Spang; Lisa Y Stein; Tanja Woyke
Genome sequence of the Arctic methanotroph Methylobacter tundripaludum SV96.
Journal of bacteriology 2011;193(22):6418-9.
2011: Garret Suen; Roxanne Tapia; Tanja Woyke; Julie Boyum; David Bruce; Jan-Feng Cheng; Olga Chertkov; Alex Copeland; Chris Detter; John C Detter; Lynne A Goodwin; Cliff S Han; Loren J Hauser; Natalia N Ivanova; Nikos C Kyrpides; Miriam L Land; Alla Lapidus; Susan Lucas; David Mead; Galina Ovchinnikova; Sam Pitluck; David M Stevenson; Paul J Weimer
Complete genome of the cellulolytic ruminal bacterium Ruminococcus albus 7.
Journal of bacteriology 2011;193(19):5574-5.
2011: Christopher E Ellison; Brian Foster; Igor V Grigoriev; David J Jacobson; Alla Lapidus; Erika A Lindquist; Donald O Natvig; Robert Riley; Jason E Stajich; Andrea Aerts; John W Taylor
Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma.
Genetics 2011;189(1):55-69.
2011: Dana J Wohlbach; Robert Zinkel; Venkatesh Balan; Kerrie W Barry; Alicia Clum; Bruce E Dale; Igor V Grigoriev; Christa Gunawan; Thomas W Jeffries; Mingjie Jin; Alan Kuo; Kurt M Labutti; Alla Lapidus; Erika A Lindquist; Susan Lucas; Jasmyn L Pangilinan; Katlyn M Potts; Asaf Salamov; Trey K Sato; Hui Sun; Audrey P Gasch
Comparative genomics of xylose-fermenting fungi for enhanced biofuel production.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(32):13212-7.
2011: A Christine Munk; Sam Pitluck; Susan Reslewic; Paul Richardson; Gary P Roberts; Manfred Rohde; Jeremy Schmutz; Roxanne Tapia; Yaoping Zhang; Kerrie Barry; Thomas S Brettin; David Bruce; Alex Copeland; Tijana Glavina Del Rio; John C Detter; Paul Gilna; Markus Göker; Nancy Hammon; Cliff Han; Sanjay Israni; Hans-Peter Klenk; Nikos C Kyrpides; Miriam Land; Alla Lapidus; Frank W Larimer; Susan Lucas; Konstantinos Mavromatis; David C Schwartz
Complete genome sequence of Rhodospirillum rubrum type strain (S1).
Standards in genomic sciences 2011;4(3):293-302.
2011: Lisa Y Stein; Françoise Bringel; Alan A DiSpirito; Sukkyun Han; Mike S.M. Jetten; Marina G Kalyuzhnaya; K Dimitri Kits; Martin G Klotz; Huub J M Op den Camp; Jeremy D Semrau; Stéphane Vuilleumier; David C Bruce; Jan-Fang Cheng; Karen W Davenport; Lynne Goodwin; Shunsheng Han; Loren Hauser; Aurélie Lajus; Miriam L Land; Alla Lapidus; Susan Lucas; Claudine Médigue; Sam Pitluck; Tanja Woyke
Genome sequence of the methanotrophic alphaproteobacterium Methylocystis sp. strain Rockwell (ATCC 49242).
Journal of bacteriology 2011;193(10):2668-9.
2011: Mark W J van Passel; Ravi Kant; Airi Palva; Alex Copeland; Susan Lucas; Alla Lapidus; Tijana Glavina del Rio; Sam Pitluck; Eugene Goltsman; Alicia Clum; Hui Sun; Jeremy Schmutz; Frank W Larimer; Miriam L Land; Loren Hauser; Nikolaos Kyrpides; Natalia Mikhailova; P Paul Richardson; Peter H Janssen; Willem M de Vos; Hauke Smidt
Genome sequence of the verrucomicrobium Opitutus terrae PB90-1, an abundant inhabitant of rice paddy soil ecosystems.
Journal of bacteriology 2011;193(9):2367-8.
2011: Steven D Brown; Cynthia C Gilmour; Amy M Kucken; Judy D Wall; Dwayne A Elias; Craig C Brandt; Mircea Podar; Olga Chertkov; Brittany Held; David C Bruce; John C Detter; Roxanne Tapia; Cliff S Han; Lynne A Goodwin; Jan-Fang Cheng; Samuel Pitluck; Tanja Woyke; Natalia Mikhailova; Natalia N Ivanova; James Han; Susan Lucas; Alla Lapidus; Miriam L Land; Loren Hauser; Anthony V Palumbo
Genome sequence of the mercury-methylating strain Desulfovibrio desulfuricans ND132.
Journal of bacteriology 2011;193(8):2078-9.
2011: Joseph K.-H. Tang; Kerrie Barry; Olga Chertkov; Eileen Dalin; Cliff S Han; Loren J Hauser; Barbara M Honchak; Lauren E Karbach; Miriam L Land; Alla Lapidus; Frank W Larimer; Natalia Mikhailova; Beverly K Pierson; Samuel Pitluck; Robert E Blankenship
Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus.
BMC genomics 2011;12():334.
2010: Lisa Y Stein; Sukhwan Yoon; Jeremy D Semrau; Alan A DiSpirito; Andrew Crombie; J Colin Murrell; Stéphane Vuilleumier; Marina G Kalyuzhnaya; Huub J M Op den Camp; Françoise Bringel; D Bruce; J-F Cheng; A Copeland; Lynne Goodwin; Shunsheng Han; Loren Hauser; Mike S.M. Jetten; Aurélie Lajus; M L Land; Alla Lapidus; S Lucas; Claudine Médigue; S Pitluck; Tanja Woyke; Ahmet Zeytun; Martin G Klotz
Genome sequence of the obligate methanotroph Methylosinus trichosporium strain OB3b.
Journal of bacteriology 2010;192(24):6497-8.
2009: Paul J McMurdie; Sebastian F Behrens; Jochen A Müller; Jonathan Göke; Kirsti M Ritalahti; Ryan Wagner; Eugene Goltsman; Alla Lapidus; Susan Holmes; Frank E Loeffler; Alfred M Spormann
Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides.
PLoS genetics 2009;5(11):e1000714.
2009: Mark J McBride; Gary Xie; Eric C Martens; Alla Lapidus; Bernard Henrissat; Ryan G Rhodes; Eugene Goltsman; Wei Wang; Jian Xu; David W Hunnicutt; Andrew M Staroscik; Timothy R Hoover; Yi-Qiang Cheng; Jennifer L Stein
Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis.
Applied and environmental microbiology 2009;75(21):6864-75.
2009: Kevin Penn; Caroline Jenkins; Markus Nett; Daniel W Udwary; Erin A Gontang; Ryan P McGlinchey; Brian Foster; Alla Lapidus; Sheila Podell; Eric E Allen; Bradley S Moore; Paul R Jensen
Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria.
The ISME journal 2009;3(10):1193-203.
2009: Federico M Lauro; Diane McDougald; Torsten Thomas; Timothy J Williams; Suhelen Egan; Scott Rice; Matthew Z DeMaere; Lily Ting; Haluk Ertan; Justin Johnson; Steve Ferriera; Alla Lapidus; Iain Anderson; Nikos Kyrpides; A Christine Munk; Chris Detter; Cliff S Han; Mark V Brown; Frank Thomson Robb; Staffan Kjelleberg; Ricardo Cavicchioli
The genomic basis of trophic strategy in marine bacteria.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(37):15527-33.
2009: Ravi D Barabote; Gary Xie; David H Leu; Philippe Normand; Anamaria Necsulea; Vincent Daubin; Claudine Médigue; William S Adney; Xin Clare Xu; Alla Lapidus; Rebecca E Parales; Chris Detter; Petar Pujic; David Bruce; Celine Lavire; Jean F Challacombe; Thomas S Brettin; Alison M Berry
Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations.
Genome research 2009;19(6):1033-43.
2009: Iain J Anderson; Magdalena Sieprawska-Lupa; Eugene Goltsman; Alla Lapidus; Alex Copeland; Tijana Glavina Del Rio; Hope Tice; Eileen Dalin; Kerrie Barry; Sam Pitluck; Loren Hauser; Miriam Land; Susan Lucas; Paul Richardson; William B Whitman; Nikos Kyrpides
Complete genome sequence of Methanocorpusculum labreanum type strain Z.
Standards in genomic sciences 2009;1(2):197-203.
2009: Iain J Anderson; Magdalena Sieprawska-Lupa; Alla Lapidus; Matt Nolan; Alex Copeland; Tijana Glavina Del Rio; Hope Tice; Eileen Dalin; Kerrie Barry; Elizabeth Saunders; Cliff Han; Thomas Brettin; John C Detter; David Bruce; Natalia Mikhailova; Sam Pitluck; Loren Hauser; Miriam Land; Susan Lucas; Paul Richardson; William B Whitman; Nikos Kyrpides
Complete genome sequence of Methanoculleus marisnigri Romesser et al. 1981 type strain JR1.
Standards in genomic sciences 2009;1(2):189-96.
2009: Kennan Kellaris Salinero; Keith Keller; William S Feil; Helene Feil; Stephan Trong; Genevieve Di Bartolo; Alla Lapidus
Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation.
BMC genomics 2009;10():351.
2009: Iain Anderson; Luke E Ulrich; Boguslaw Lupa; Dwi Susanti; Iris Porat; Sean D Hooper; Athanasios Lykidis; Magdalena Sieprawska-Lupa; Lakshmi Dharmarajan; Eugene Goltsman; Alla Lapidus; Elizabeth Saunders; Cliff Han; Miriam Land; Susan Lucas; Biswarup Mukhopadhyay; William B Whitman; Carl Woese; James Bristow; Nikos Kyrpides
Genomic characterization of methanomicrobiales reveals three classes of methanogens.
PloS one 2009;4(6):e5797.
2009: Konstantinos Mavromatis; Natalia Ivanova; Iain Anderson; Athanasios Lykidis; Sean D Hooper; Hui Sun; Victor Kunin; Alla Lapidus; Philip Hugenholtz; Bharat Patel; Nikos Kyrpides
Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii.
PloS one 2009;4(1):e4192.
2008: Dylan Chivian; Eoin L Brodie; Eric J Alm; David E Culley; Paramvir S Dehal; Todd Z DeSantis; Thomas M Gihring; Alla Lapidus; Li-Hung Lin; Stephen R Lowry; Duane P Moser; Paul M Richardson; Gordon Southam; Greg Wanger; Lisa M Pratt; Gary L Andersen; Terry C Hazen; Fred J Brockman; Adam P Arkin; Tullis C Onstott
Environmental genomics reveals a single-species ecosystem deep within Earth.
Science (New York, N.Y.) 2008;322(5899):275-8.
2008: Marina G Kalyuzhnaya; Alla Lapidus; Natalia Ivanova; Alex Copeland; Alice C McHardy; Ernest Szeto; Asaf Salamov; Igor V Grigoriev; dominic suciu; Samuel R Levine; Victor M Markowitz; Isidore Rigoutsos; Susannah G Tringe; David C Bruce; Paul M Richardson; Mary E Lidstrom; Ludmila Chistoserdova
High-resolution metagenomics targets specific functional types in complex microbial communities.
Nature biotechnology 2008;26(9):1029-34.
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: Iain Anderson; Jason Rodriguez; Dwi Susanti; Iris Porat; Claudia Reich; Luke E Ulrich; James G Elkins; Kostas Mavromatis; Athanasios Lykidis; Edwin Kim; Linda S Thompson; Matt Nolan; Miriam Land; Alex Copeland; Alla Lapidus; Susan Lucas; Chris Detter; Igor B Zhulin; Gary J Olsen; William B Whitman; Biswarup Mukhopadhyay; James Bristow; Nikos Kyrpides
Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction.
Journal of bacteriology 2008;190(8):2957-65.
2008: Sandrine Auger; Nathalie Galleron; Elena Bidnenko; S Dusko Ehrlich; Alla Lapidus; Alexei Sorokin
The genetically remote pathogenic strain NVH391-98 of the Bacillus cereus group is representative of a cluster of thermophilic strains.
Applied and environmental microbiology 2008;74(4):1276-80.
2008: Stefan M Sievert; Kathleen M Scott; Martin Klotz; Patrick S G Chain; Loren Hauser; James Hemp; Michael Hügler; Miriam Land; Alla Lapidus; Frank W Larimer; Susan Lucas; Stephanie Malfatti; Folker Meyer; Ian Paulsen; Qinghu Ren; Jörg Simon
Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans.
Applied and environmental microbiology 2008;74(4):1145-56.
2008: Alla Lapidus; Eugene Goltsman; Sandrine Auger; Nathalie Galleron; Béatrice Ségurens; Carole Dossat; Miriam Land; Veronique Broussolle; Julien Brillard; Marie-Helene Guinebretiere; Vincent Sanchis; Christophe Nguen-The; Didier Lereclus; Paul Richardson; Patrick Wincker; Jean Weissenbach; S Dusko Ehrlich; Alexei Sorokin
Extending the Bacillus cereus group genomics to putative food-borne pathogens of different toxicity.
Chemico-biological interactions 2008;171(2):236-49.
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.
2007: Gregory C Kettler; Adam C Martiny; Katherine Huang; Jeremy Zucker; Maureen L Coleman; Sebastien Rodrigue; Feng Chen; Alla Lapidus; Steven Ferriera; Justin Johnson; Claudia Steglich; George M Church; Paul Richardson; Sallie W Chisholm
Patterns and implications of gene gain and loss in the evolution of Prochlorococcus.
PLoS genetics 2007;3(12):e231.
2007: Daniel W Udwary; Lisa Zeigler; Ratnakar N Asolkar; Vasanth Singan; Alla Lapidus; William Fenical; Paul R Jensen; Bradley S Moore
Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(25):10376-81.
2007: Konstantinos Mavromatis; Natalia Ivanova; Kerrie W Barry; Harris Shapiro; Eugene Goltsman; Alice C McHardy; Isidore Rigoutsos; Asaf Salamov; Frank Korzeniewski; Miriam Land; Alla Lapidus; Igor V Grigoriev; Paul Richardson; Philip Hugenholtz; Nikos Kyrpides
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.
Nature methods 2007;4(6):495-500.
2007: Ludmila Chistoserdova; Alla Lapidus; Cliff Han; Lynne Goodwin; Liz Saunders; Thomas S Brettin; Roxanne Tapia; Paul Gilna; Susan Lucas; Paul M Richardson; Mary E Lidstrom
Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy.
Journal of bacteriology 2007;189(11):4020-7.
2007: Athanasios Lykidis; Konstantinos Mavromatis; Natalia Ivanova; Iain Anderson; Miriam Land; Genevieve DiBartolo; Michele Martinez; Alla Lapidus; Susan Lucas; Alex Copeland; Paul Richardson; David B Wilson; Nikos Kyrpides
Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX.
Journal of bacteriology 2007;189(6):2477-86.
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.
2007: Philippe Normand; Pascal Lapierre; Louis S Tisa; J Peter Gogarten; Nicole Alloisio; Emilie Bagnarol; Carla A Bassi; Alison M Berry; Derek M Bickhart; Nathalie Choisne; Arnaud Couloux; Benoit Cournoyer; Stéphane Cruveiller; Vincent Daubin; Nadia Demange; Maria Pilar Francino; Eugene Goltsman; Ying Huang; Olga R Kopp; Laurent Labarre; Alla Lapidus; Celine Lavire; Joelle Marechal; Michele Martinez; Juliana E Mastronunzio; Beth C Mullin; James Niemann; Pierre Pujic; Tania Rawnsley; Zoe Rouy; Chantal Schenowitz; Anita Sellstedt; Fernando Tavares; Jeffrey Tomkins; David Vallenet; Claudio Valverde; Luis G Wall; Ying Wang; Claudine Medigue; David R Benson
Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.
Genome research 2007;17(1):7-15.
2006: Kathleen M Scott; Stefan M Sievert; Fereniki N Abril; Lois A Ball; Chantell J Barrett; Rodrigo A Blake; Amanda J Boller; Patrick S G Chain; Justine A Clark; Carisa R Davis; Chris Detter; Kimberly F Do; Kimberly P Dobrinski; Brandon I Faza; Kelly A Fitzpatrick; Sharyn K Freyermuth; Tara L Harmer; Loren J Hauser; Michael Hügler; Cheryl A Kerfeld; Martin Klotz; William W Kong; Miriam Land; Alla Lapidus; Frank W Larimer; Dana L Longo; Susan Lucas; Stephanie A Malfatti; Steven E Massey; Darlene D Martin; zoe (mckiness) mccuddin; Folker Meyer; Jessica L Moore; Luis H Ocampo; John H Paul; Ian Paulsen; Douglas K Reep; Qinghu Ren; Rachel L Ross; Priscila Y Sato; Phaedra Thomas; Lance E Tinkham; Gary T Zeruth
The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2.
PLoS biology 2006;4(12):e383.
2006: Dennis L Maeder; Iain Anderson; Thomas S Brettin; David Bruce; Paul Gilna; Cliff S Han; Alla Lapidus; William W Metcalf; Elizabeth Saunders; Roxanne Tapia; Kevin R Sowers
The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes.
Journal of bacteriology 2006;188(22):7922-31.
2006: Laura E Williams; Chris Detter; Kerrie W Barry; Alla Lapidus; Anne O Summers
Facile recovery of individual high-molecular-weight, low-copy-number natural plasmids for genomic sequencing.
Applied and environmental microbiology 2006;72(7):4899-906.
2006: Xiaodong Bai; Jianhua Zhang; Adam Ewing; Sally A Miller; Agnes Jancso-Radek; Dmitriy V Shevchenko; Kiryl Tsukerman; Theresa Walunas; Alla Lapidus; John W Campbell; Saskia A Hogenhout
Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts.
Journal of bacteriology 2006;188(10):3682-96.
2005: Marina G Kalyuzhnaya; Olivier Nercessian; Alla Lapidus; Ludmila Chistoserdova
Fishing for biodiversity: novel methanopterin-linked C transfer genes deduced from the Sargasso Sea metagenome.
Environmental microbiology 2005;7(12):1909-16.
2005: Iain Anderson; Alexei Sorokin; Vinayak Kapatral; Gary Reznik; Anamitra Bhattacharya; Natalia Mikhailova; Henry Burd; Victor Joukov; Denis Kaznadzey; Theresa Walunas; Niels Larsen; Gordon Pusch; Konstantinos Liolios; Yuri Grechkin; Alla Lapidus; Eugene Goltsman; Lien Chu; Michael Fonstein; S Dusko Ehrlich; Ross Overbeek; Nikos Kyrpides; Natalia Ivanova
Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis.
FEMS microbiology letters 2005;250(2):175-84.
2005: Susan Reslewic; Shiguo Zhou; Michael Place; Yaoping Zhang; Adam Briska; Steve Goldstein; Chris Churas; Rod Runnheim; Dan Forrest; Alex Lim; Alla Lapidus; Cliff S Han; Gary P Roberts; David C Schwartz
Whole-genome shotgun optical mapping of Rhodospirillum rubrum.
Applied and environmental microbiology 2005;71(9):5511-22.
2005: Helene Feil; William S Feil; Patrick S G Chain; Frank W Larimer; Genevieve DiBartolo; Alex Copeland; Athanasios Lykidis; Stephen Trong; Matt Nolan; Eugene Goltsman; James Thiel; Stephanie Malfatti; Joyce E Loper; Alla Lapidus; John C Detter; Miriam Land; Paul M Richardson; Nikos Kyrpides; Natalia Ivanova; Steven E Lindow
Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(31):11064-9.
2005: Aharon Oren; Frank W Larimer; Paul Richardson; Alla Lapidus; Laszlo N Csonka
How to be moderately halophilic with broad salt tolerance: clues from the genome of Chromohalobacter salexigens.
Extremophiles : life under extreme conditions 2005;9(4):275-9.
2005: Jeremy Foster; Mehul Ganatra; Ibrahim H Kamal; Jennifer Ware; Kira Makarova; Natalia Ivanova; Anamitra Bhattacharyya; Vinayak Kapatral; Sanjay Kumar; Janos Posfai; Tamas Vincze; Jessica Ingram; Laurie Moran; Alla Lapidus; Marina V Omelchenko; Nikos Kyrpides; Elodie Ghedin; Shiliang Wang; Eugene Goltsman; Victor Joukov; Olga Ostrovskaya; Kiryl Tsukerman; Mikhail Mazur; Donald Comb; Eugene Koonin; Barton Slatko
The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode.
PLoS biology 2005;3(4):e121.
2004: Alexander Bolotin; Benoit Quinquis; Pierre Renault; Alexei Sorokin; S Dusko Ehrlich; Saulius Kulakauskas; Alla Lapidus; Eugene Goltsman; Michael Mazur; Gordon Pusch; Michael Fonstein; Ross Overbeek; Nikos Kyrpides; Bénédicte Purnelle; Deborah Prozzi; Katrina Ngui; David Masuy; Frédéric Hancy; Sophie Burteau; Marc Boutry; Jean Delcour; André Goffeau; Pascal Hols
Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus.
Nature biotechnology 2004;22(12):1554-8.
2004: Ludmila Chistoserdova; Cheryl Jenkins; Marina G Kalyuzhnaya; Christopher J Marx; Alla Lapidus; Julia A Vorholt; James T Staley; Mary E Lidstrom
The enigmatic planctomycetes may hold a key to the origins of methanogenesis and methylotrophy.
Molecular biology and evolution 2004;21(7):1234-41.
2004: Michael W Rey; Preethi Ramaiya; Beth A Nelson; Shari D Brody-Karpin; Elizabeth J Zaretsky; Maria Tang; Alfredo Lopez de Leon; Henry Xiang; Veronica Gusti; Ib Groth Clausen; Peter B Olsen; Michael D Rasmussen; Jens T Andersen; Per L Jørgensen; Thomas S Larsen; Alexei Sorokin; Alexander Bolotin; Alla Lapidus; Nathalie Galleron; S Dusko Ehrlich; Randy M Berka
Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species.
Genome biology 2004;5(10):R77.
2003: Vinayak Kapatral; Natalia Ivanova; Iain Anderson; Gary Reznik; Anamitra Bhattacharyya; Warren Gardner; Natalia Mikhailova; Alla Lapidus; Niels Larsen; Mark D'Souza; Theresa Walunas; Robert Haselkorn; Ross Overbeek; Nikos Kyrpides
Genome analysis of F. nucleatum sub spp vincentii and its comparison with the genome of F. nucleatum ATCC 25586.
Genome research 2003;13(6A):1180-9.
2003: Ludmila Chistoserdova; Sung-Wei Chen; Alla Lapidus; Mary E Lidstrom
Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view.
Journal of bacteriology 2003;185(10):2980-7.
2003: Natalia Ivanova; Alexei Sorokin; Iain Anderson; Nathalie Galleron; Benjamin Candelon; Vinayak Kapatral; Anamitra Bhattacharyya; Gary Reznik; Natalia Mikhailova; Alla Lapidus; Lien Chu; Michael Mazur; Eugene Goltsman; Niels Larsen; Mark D'Souza; Theresa Walunas; Yuri Grechkin; Gordon Pusch; Robert Haselkorn; Michael Fonstein; S Dusko Ehrlich; Ross Overbeek; Nikos Kyrpides
Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis.
Nature 2003;423(6935):87-91.
2002: Alla Lapidus; Nathalie Galleron; Jens Tønne Andersen; Per Linå Jørgensen; S Dusko Ehrlich; Alexei Sorokin
Co-linear scaffold of the Bacillus licheniformis and Bacillus subtilis genomes and its use to compare their competence genes.
FEMS microbiology letters 2002;209(1):23-30.
1997: Haike Antelmann; Susanne Engelmann; Roland Schmid; Alexei Sorokin; Alla Lapidus; Michael Hecker
Expression of a stress- and starvation-induced dps/pexB-homologous gene is controlled by the alternative sigma factor sigmaB in Bacillus subtilis.
Journal of bacteriology 1997;179(23):7251-6.
1997: Alla Lapidus; Nathalie Galleron; Alexei Sorokin; S Dusko Ehrlich
Sequencing and functional annotation of the Bacillus subtilis genes in the 200 kb rrnB-dnaB region.
Microbiology (Reading, England) 1997;143 ( Pt 11)():3431-41.
1996: Alexei Sorokin; Alla Lapidus; V Capuano; N Galleron; P Pujic; S Dusko Ehrlich
A new approach using multiplex long accurate PCR and yeast artificial chromosomes for bacterial chromosome mapping and sequencing.
Genome research 1996;6(5):448-53.
1991: A N Markaryan; S V Mashko; L V Kukel; Alla Lapidus; A N Bach; A M Egorov
Construction of expression vectors for gene fusions on the model of beta-galactosidase-human fibroblast beta-interferon for the purpose of immunoenzyme assay.
Annals of the New York Academy of Sciences 1991;646():125-35.
1991: Dimitry A Chistiakov; S G Arsenian; Eleonora Braga; Alla Lapidus; IuI Kozlov; S V Mashko; Valery V Nosikov; E D Sverdlov; Vladimir G Debabov
[Elimination of introns from the interleukin 1 beta genome by DNA amplification and expression of interleukin 1 beta in Escherichia coli].
Molekuliarnaia biologiia 1991;25(5):1273-84.
1991: S V Mashko; A V Mochulsky; Sergei V Kotenko; M I Lebedeva; Alla Lapidus; N A Mochulskaya; Lara Izotova; VP Veiko; Y P Vinetsky; S A Ketlinsky
Use of a dual-origin temperature-controlled amplifiable replicon for optimization of human interleukin-1 beta synthesis in Escherichia coli.
Gene 1991;97(2):259-66.
1990: S V Mashko; VP Veiko; Alla Lapidus; M I Lebedeva; A V Mochulsky; I I Shechter; M E Trukhan; K I Ratmanova; B A Rebentish; V E Kaluzhsky
TGATG vector: a new expression system for cloned foreign genes in Escherichia coli cells.
Gene 1990;88(1):121-6.
1990: S V Mashko; Sergei V Kotenko; V P Veĭko; M I Lebedeva; Alla Lapidus; A V Mochul'skiĭ; I I Shekhter; Lara Izotova; Iu P Vinetskiĭ; Vladimir G Debabov
[The use of the TGATG vector for expression in Escherichia coli cells of cloned cDNA copy of human interleukin-1beta gene].
Doklady Akademii nauk SSSR 1990;312(1):233-6.
1990: Alla Lapidus; A V Mochul'skii; S M Podkovyrov; M I Lebedeva; A A Antipin; Lara Izotova; O P Zagnit'ko; G S Komolova; A A Klesov; VP Veiko
Expression of the hAng gene in Escherichia coli; isolation and characterization of human recombinant Ser-(-1) angiogenin.
Biomedical science 1990;1(6):597-604.
1988: M E Trukhan; R L Gorovits; M I Lebedeva; Alla Lapidus; S V Mashko
[Effectiveness of expression of chloramphenicol acetyltransferase gene controlled by foreign regulatory regions in Escherichia coli. III. Relative effectiveness of cloned promoters of Escherichia coli and coliphages].
Molekuliarnaia biologiia 1988;22(4):1033-44.
1987: S V Mashko; Alla Lapidus; M E Trukhan; M I Lebedeva; S M Podkovyrov
[Creation of artificial hybrid operons with partially overlapping genes to achieve an expression of heterologous genes in Escherichia coli cells].
Molekuliarnaia biologiia 1987;21(5):1297-309.
1987: S V Mashko; Alla Lapidus; M E Trukhan; N A Stashchuk; Vladimir G Debabov
[Effectiveness of translation coupling in hybrid operons].
Molekuliarnaia biologiia 1987;21(5):1310-21.
1987: A Iu Chistoserdov; M R Eremashvili; S V Mashko; Alla Lapidus; M A Skvortsova
[Expression of the human interferon alpha F gene in the obligate methylotroph Methylobacillus flagellatum KT and Pseudomonas putida].
Molekuliarnaia genetika, mikrobiologiia i virusologiia 1987;(8):36-41.
1987: S V Mashko; M I Lebedeva; S M Podkovyrov; Alla Lapidus; M E Trukhan
[Optimization of the gene expression for human alpha F- and beta 1-interferons in Escherichia coli cells].
Antibiotiki i meditsinskaia biotekhnologiia = Antibiotics and medical biotechnology / Ministerstvo meditsinskoĭ promyshlennosti SSSR 1987;32(4):248-54.
1987: S V Mashko; S M Podkovyrov; M E Trukhan; M I Lebedeva; Alla Lapidus
[Effectiveness of expression of the chloramphenicol acetyltransferase gene controlled by foreign regulator regions in Escherichia coli cells. II. Molecular cloning of promoters].
Molekuliarnaia biologiia 1987;21(1):73-86.
1984: S V Mashko; Alla Lapidus; M I Lebedeva; S M Podkovyrov; T G Plotnikova
[Achievement of highly efficient expression of cloned genes by constructing hybrid operons].
Doklady Akademii nauk SSSR 1984;278(6):1491-6.
1982: E M Khurges; L V Gening; IuI Kozlov; L P Kochetova; Alla Lapidus
[Isolation and study of hybrid plasmids carrying Escherichia coli threonine operon genes].
Genetika 1982;18(10):1620-30.