A
Alla Lapidus
Researcher at Saint Petersburg State University
Publications - 408
Citations - 33491
Alla Lapidus is an academic researcher from Saint Petersburg State University. The author has contributed to research in topics: Genome & Whole genome sequencing. The author has an hindex of 77, co-authored 396 publications receiving 29182 citations. Previous affiliations of Alla Lapidus include Joint Genome Institute & United States Department of Energy.
Papers
More filters
Journal ArticleDOI
The complete genome sequence of the Gram-positive bacterium Bacillus subtilis
F. Kunst,Naotake Ogasawara,Ivan Moszer,Alessandra M. Albertini,G. Alloni,Vasco Azevedo,M. G. Bertero,M. G. Bertero,Philippe Bessières,Bolotin Ap,S. Borchert,Rainer Borriss,L. Boursier,Alain Brans,M. Braun,S. C. Brignell,Sierd Bron,S. Brouillet,S. Brouillet,Carlo V. Bruschi,B. Caldwell,V. Capuano,Noel Carter,Soo Keun Choi,J.-J. Codani,Ian F. Connerton,Nicola J. Cummings,Richard A. Daniel,François Denizot,Kevin M. Devine,A. Düsterhöft,Stanislav Dusko Ehrlich,P. T. Emmerson,K. D. Entian,Jeff Errington,C. Fabret,Eugenio Ferrari,D. Foulger,C. Fritz,Masaya Fujita,Yasutaro Fujita,S. Fuma,Alessandro Galizzi,Nathalie Galleron,Sa Youl Ghim,Philippe Glaser,André Goffeau,E. J. Golightly,Guido Grandi,G. Guiseppi,BJ Guy,Kazuko Haga,Jacques Haiech,Colin R. Harwood,Alain Hénaut,H. Hilbert,Siger Holsappel,S. Hosono,Marie-Françoise Hullo,Mitsuhiro Itaya,Louis M. Jones,Bernard Joris,Dimitri Karamata,Y. Kasahara,M. Klaerr-Blanchard,Carsten Klein,Y. Kobayashi,P. Koetter,G. Koningstein,Susanne Krogh,Miyuki Kumano,Kanako Kurita,Alla Lapidus,S. Lardinois,J. Lauber,Vladimir Lazarevic,Simon Ming-Yuen Lee,Alain Levine,H. Liu,S. Masuda,Catherine Mauël,Claudine Médigue,Claudine Médigue,N. Medina,Rafael P. Mellado,Motoki Mizuno,D. Moestl,S. Nakai,Michiel A. Noback,David Noone,Mary O'Reilly,K. Ogawa,A. Ogiwara,B. Oudega,S.-H. Park,Victor Parro,Thomas Pohl,Daniel Portetelle,Steffen Porwollik,A. M. Prescott,E. Presecan,Petar Pujic,Bénédicte Purnelle,Georges Rapoport,M. Rey,Stacey Reynolds,Michael A. Rieger,Carlo Rivolta,Eduardo P. C. Rocha,Eduardo P. C. Rocha,B. Roche,Matthias Rose,Yoshito Sadaie,Toshitada Sato,E. Scanlan,S. Schleich,R. Schroeter,F Scoffone,Junichi Sekiguchi,Agnieszka Sekowska,Simone J. Séror,Pascale Serror,B.-S. Shin,Blazenka Soldo,Alexei Sorokin,E. Tacconi,T. Takagi,Hideyuki Takahashi,Ken-Ichi Takemaru,Michio Takeuchi,A. Tamakoshi,Tetsu Tanaka,Peter Terpstra,Angelo Tognoni,Valentina Tosato,Shigeki Uchiyama,Micheline Vandenbol,Françoise Vannier,A. Vassarotti,Alain Viari,R. Wambutt,E. Wedler,H. Wedler,T. Weitzenegger,P. Winters,Anil Wipat,Hiroki Yamamoto,Kunio Yamane,K. Yasumoto,Katsunori Yata,K. Yoshida,Hisashi Yoshikawa,Emmanuelle Zumstein,Hiroshi Yoshikawa,Antoine Danchin +154 more
TL;DR: Bacillus subtilis is the best-characterized member of the Gram-positive bacteria, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.
Journal ArticleDOI
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Robert M. Bowers,Nikos C. Kyrpides,Ramunas Stepanauskas,Miranda Harmon-Smith,Devin F. R. Doud,T. B. K. Reddy,Frederik Schulz,Jessica K. Jarett,Adam R. Rivers,Adam R. Rivers,Emiley A. Eloe-Fadrosh,Susannah G. Tringe,Susannah G. Tringe,Natalia Ivanova,Alex Copeland,Alicia Clum,Eric D. Becraft,Rex R. Malmstrom,Bruce W. Birren,Mircea Podar,Peer Bork,George M. Weinstock,George M. Garrity,Jeremy A. Dodsworth,Shibu Yooseph,Granger G. Sutton,Frank Oliver Gloeckner,Jack A. Gilbert,William C. Nelson,Steven J. Hallam,Sean P. Jungbluth,Sean P. Jungbluth,Thijs J. G. Ettema,Scott Tighe,Konstantinos T. Konstantinidis,Wen Tso Liu,Brett J. Baker,Thomas Rattei,Jonathan A. Eisen,Brian P. Hedlund,Katherine D. McMahon,Noah Fierer,Rob Knight,Robert D. Finn,Guy Cochrane,Ilene Karsch-Mizrachi,Gene W. Tyson,Christian Rinke,Alla Lapidus,Folker Meyer,Pelin Yilmaz,Donovan H. Parks,A. M. Eren,Lynn M. Schriml,Jillian F. Banfield,Philip Hugenholtz,Tanja Woyke +56 more
TL;DR: Two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences are presented, including the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum information about a Metagenome-Assembled Genomes (MIMAG), including estimates of genome completeness and contamination.
Journal ArticleDOI
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products
Sergey Nurk,Anton Bankevich,Dmitry Antipov,Alexey Gurevich,Anton Korobeynikov,Alla Lapidus,Andrey D. Prjibelski,Alex Pyshkin,Alexander Sirotkin,Yakov Sirotkin,Ramunas Stepanauskas,Scott Clingenpeel,Tanja Woyke,Jeffrey S. McLean,Roger S. Lasken,Glenn Tesler,Max A. Alekseyev,Pavel A. Pevzner +17 more
TL;DR: Applications of the single-cell assembler SPAdes to a new approach for capturing and sequencing "microbial dark matter" that forms small pools of randomly selected single cells and further sequences all genomes from the mini-metagenome at once.
Journal ArticleDOI
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.
Dongying Wu,Dongying Wu,Philip Hugenholtz,Konstantinos Mavromatis,Rüdiger Pukall,Eileen Dalin,Natalia Ivanova,Victor Kunin,Lynne Goodwin,Martin Wu,Brian J. Tindall,Sean D. Hooper,Amrita Pati,Athanasios Lykidis,Stefan Spring,Iain Anderson,Patrik D'haeseleer,Patrik D'haeseleer,Adam Zemla,Mitchell Singer,Alla Lapidus,Matt Nolan,Alex Copeland,Cliff Han,Feng Chen,Jan Fang Cheng,Susan Lucas,Cheryl A. Kerfeld,Elke Lang,Sabine Gronow,Patrick S. G. Chain,Patrick S. G. Chain,David Bruce,Edward M. Rubin,Nikos C. Kyrpides,Hans-Peter Klenk,Jonathan A. Eisen,Jonathan A. Eisen +37 more
TL;DR: The results strongly support the need for systematic ‘phylogenomic’ efforts to compile a phylogeny-driven ‘Genomic Encyclopedia of Bacteria and Archaea’ in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come.
Journal ArticleDOI
Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis
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 Bent Larsen,Mark D'Souza,Theresa L. Walunas,Yuri Grechkin,Gordon D. Pusch,Robert Haselkorn,Michael Fonstein,S. Dusko Ehrlich,Ross Overbeek,Nikos C. Kyrpides +22 more
TL;DR: The sequencing and analysis of the type strain B. cereus ATCC 14579 together with the gapped genome of B. anthracis A2012 enables the comparative analysis to clarify the phylogeny of the cereus group, and the latter to determine plasmid-independent species-specific markers.