Search | Genome Research

Analyzing rare mutations in metagenomes assembled using long and accurate reads

Marcus W. Fedarko
Mikhail Kolmogorov
Pavel A. Pevzner

First Published November 23, 2022

Fast and accurate mapping of long reads to complete genome assemblies with VerityMap

Andrey V. Bzikadze
Alla Mikheenko
Pavel A. Pevzner

First Published November 15, 2022

Automated annotation of human centromeres with HORmon

Olga Kunyavskaya
Tatiana Dvorkina
Andrey V. Bzikadze
Ivan A. Alexandrov
Pavel A. Pevzner

First Published May 11, 2022

Gene prediction in the immunoglobulin loci

Vikram Sirupurapu
Yana Safonova
Pavel A. Pevzner

First Published May 11, 2022

Variations in antibody repertoires correlate with vaccine responses

Yana Safonova
Sung Bong Shin
Luke Kramer
James Reecy
Corey T. Watson
Timothy P.L. Smith
Pavel A. Pevzner

First Published March 31, 2022

V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s

Yana Safonova
Pavel A. Pevzner

First Published September 18, 2020

BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs

Dmitry Meleshko
Hosein Mohimani
Vittorio Tracanna
Iman Hajirasouliha
Marnix H. Medema
Anton Korobeynikov
Pavel A. Pevzner

First Published June 3, 2019

Plasmid detection and assembly in genomic and metagenomic data sets

Dmitry Antipov
Mikhail Raiko
Alla Lapidus
Pavel A. Pevzner

First Published May 2, 2019

Selfish mutations dysregulating RAS-MAPK signaling are pervasive in aged human testes

Geoffrey J. Maher
Hannah K. Ralph
Zhihao Ding
Nils Koelling
Hana Mlcochova
Eleni Giannoulatou Pawan Dhami Dirk S. Paul Stefan H. Stricker
... [+4 authors] ...,
Stephan Beck
Gilean McVean
Andrew O.M. Wilkie
Anne Goriely

First Published October 24, 2018

Detection and analysis of ancient segmental duplications in mammalian genomes

Lianrong Pu
Yu Lin
Pavel A. Pevzner

First Published May 7, 2018

metaSPAdes: a new versatile metagenomic assembler

Sergey Nurk
Dmitry Meleshko
Anton Korobeynikov
Pavel A. Pevzner

First Published March 15, 2017

Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform" > Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform

Jeffrey S. McLean
Mary-Jane Lombardo
Michael G. Ziegler
Mark Novotny
Joyclyn Yee-Greenbaum
Jonathan H. Badger Glenn Tesler Sergey Nurk Valery Lesin Daniel Brami Adam P. Hall Anna Edlund Lisa Z. Allen Scott Durkin Sharon Reed Francesca Torriani Kenneth H. Nealson
... [+12 authors] ...,
Pavel A. Pevzner
Robert Friedman
J. Craig Venter
Roger S. Lasken

First Published April 5, 2013

A functional methylome map of ulcerative colitis

Robert Häsler
Zhe Feng
Liselotte Bäckdahl
Martina E. Spehlmann
Andre Franke
Andrew Teschendorff Vardhman K. Rakyan Thomas A. Down Gareth A. Wilson
... [+4 authors] ...,
Andrew Feber
Stephan Beck
Stefan Schreiber
Philip Rosenstiel

First Published July 23, 2012

Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors

Andrew Feber
Gareth A. Wilson
Lu Zhang
Nadege Presneau
Bernadine Idowu
Thomas A. Down Vardhman K. Rakyan Luke A. Noon Alison C. Lloyd Elia Stupka Vassia Schiza
... [+6 authors] ...,
Andrew E. Teschendorff
Gary P. Schroth
Adrienne Flanagan
Stephan Beck

First Published February 1, 2011

Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer

Andrew E. Teschendorff
Usha Menon
Aleksandra Gentry-Maharaj
Susan J. Ramus
Daniel J. Weisenberger
Hui Shen Mihaela Campan Houtan Noushmehr Christopher G. Bell A. Peter Maxwell David A. Savage Elisabeth Mueller-Holzner Christian Marth Gabrijela Kocjan Simon A. Gayther Allison Jones Stephan Beck
... [+12 authors] ...,
Wolfgang Wagner
Peter W. Laird
Ian J. Jacobs
Martin Widschwendter

First Published March 10, 2010

Breakpoint graphs and ancestral genome reconstructions

Max A. Alekseyev
Pavel A. Pevzner

First Published February 13, 2009

De novo fragment assembly with short mate-paired reads: Does the read length matter?

Mark J. Chaisson
Dumitru Brinza
Pavel A. Pevzner

First Published December 3, 2008

Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex

Diego Ottaviani
Elliott Lever
Richard Mitter
Tania Jones
Tim Forshew
Rossitza Christova Eleni M. Tomazou Vardhman K. Rakyan Stephen A. Krawetz
... [+4 authors] ...,
Adrian E. Platts
Badmavady Segarane
Stephan Beck
Denise Sheer

First Published October 10, 2008

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

Vardhman K. Rakyan
Thomas A. Down
Natalie P. Thorne
Paul Flicek
Eugene Kulesha
Stefan Gräf Eleni M. Tomazou Liselotte Bäckdahl Nathan Johnson Marlis Herberth Kevin L. Howe David K. Jackson Marcos M. Miretti Heike Fiegler John C. Marioni Ewan Birney
... [+11 authors] ...,
Tim J.P. Hubbard
Nigel P. Carter
Simon Tavaré
Stephan Beck

First Published June 24, 2008

Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes

Nitin Gupta
Jamal Benhamida
Vipul Bhargava
Daniel Goodman
Elisabeth Kain
Ian Kerman Ngan Nguyen Noah Ollikainen Jesse Rodriguez Jian Wang Mary S. Lipton
... [+6 authors] ...,
Margaret Romine
Vineet Bafna
Richard D. Smith
Pavel A. Pevzner

First Published April 21, 2008

Short read fragment assembly of bacterial genomes

Mark J. Chaisson
Pavel A. Pevzner

First Published December 14, 2007

Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation

Nitin Gupta
Stephen Tanner
Navdeep Jaitly
Joshua N. Adkins
Mary Lipton
Robert Edwards Margaret Romine
... [+2 authors] ...,
Andrei Osterman
Vineet Bafna
Richard D. Smith
Pavel A. Pevzner

First Published August 9, 2007

The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction

Guillaume Bourque
Glenn Tesler
Pavel A. Pevzner

First Published March 1, 2006

KIR) loci in primates" > Single haplotype analysis demonstrates rapid evolution of the killer immunoglobulin-like receptor (KIR) loci in primates

Jennifer G. Sambrook
Arman Bashirova
Sophie Palmer
Sarah Sims
John Trowsdale
Laurent Abi-Rached
Peter Parham
Mary Carrington
Stephan Beck

First Published January 3, 2005

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages

Guillaume Bourque
Evgeny M. Zdobnov
Peer Bork
Pavel A. Pevzner
Glenn Tesler

First Published December 8, 2004

Alu repeat elements reveals complex evolutionary history" > Whole-genome analysis of Alu repeat elements reveals complex evolutionary history

Alkes L. Price
Eleazar Eskin
Pavel A. Pevzner

First Published November 1, 2004

Complete MHC Haplotype Sequencing for Common Disease Gene Mapping

C. Andrew Stewart
Roger Horton
Richard J.N. Allcock
Jennifer L. Ashurst
Alexey M. Atrazhev
Penny Coggill Ian Dunham Simon Forbes Karen Halls Joanna M.M. Howson Sean J. Humphray Sarah Hunt Andrew J. Mungall Kazutoyo Osoegawa Sophie Palmer Anne N. Roberts Jane Rogers Sarah Sims Yu Wang Laurens G. Wilming John F. Elliott Pieter J. de Jong
... [+17 authors] ...,
Stephen Sawcer
John A. Todd
John Trowsdale
Stephan Beck

First Published May 12, 2004

Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes

Guillaume Bourque
Pavel A. Pevzner
Glenn Tesler

First Published April 1, 2004

Genome-Scale Evolution: Reconstructing Gene Orders in the Ancestral Species

Guillaume Bourque
Pavel A. Pevzner

First Published January 1, 2002

Assembling Puzzles from Preassembled Blocks

Pavel A. Pevzner

First Published September 1, 2001

Characterization of Clustered MHC-Linked Olfactory Receptor Genes in Human and Mouse

Ruth M. Younger
Claire Amadou
Graeme Bethel
Anke Ehlers
Kirsten Fischer Lindahl
Simon Forbes Roger Horton Sarah Milne Andrew J. Mungall
... [+4 authors] ...,
John Trowsdale
Armin Volz
Andreas Ziegler
Stephan Beck

First Published March 13, 2001

Efficiency of Database Search for Identification of Mutated and Modified Proteins via Mass Spectrometry

Pavel A. Pevzner
Zufar Mulyukov
Vlado Dancik
Chris L Tang

First Published February 1, 2001

MHC-Linked Olfactory Receptor Loci Exhibit Polymorphism and Contribute to Extended HLA/OR-Haplotypes

Anke Ehlers
Stephan Beck
Simon A. Forbes
John Trowsdale
Armin Volz
Ruth Younger
Andreas Ziegler

First Published December 1, 2000

Construction of a High-Resolution 2.5-Mb Transcript Map of the Human 6p21.2–6p21.3 Region Immediately Centromeric of the Major Histocompatibility Complex

Nicos Tripodis
Sophie Palmer
Sam Phillips
Sarah Milne
Stephan Beck
Jiannis Ragoussis

First Published April 1, 2000

Estimation of Distances and Map Construction Using Radiation Hybrids

William Newell
Stephan Beck
Hans Lehrach
Andrew Lyall

First Published May 1, 1998

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Your search for returned 35 results

Analyzing rare mutations in metagenomes assembled using long and accurate reads

Fast and accurate mapping of long reads to complete genome assemblies with VerityMap

Automated annotation of human centromeres with HORmon

Gene prediction in the immunoglobulin loci

Variations in antibody repertoires correlate with vaccine responses

V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s

BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs

Plasmid detection and assembly in genomic and metagenomic data sets

Selfish mutations dysregulating RAS-MAPK signaling are pervasive in aged human testes

Detection and analysis of ancient segmental duplications in mammalian genomes

metaSPAdes: a new versatile metagenomic assembler

Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform" > Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform

A functional methylome map of ulcerative colitis

Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors

Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer

Breakpoint graphs and ancestral genome reconstructions

De novo fragment assembly with short mate-paired reads: Does the read length matter?

Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes

Short read fragment assembly of bacterial genomes

Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation

The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction

KIR) loci in primates" > Single haplotype analysis demonstrates rapid evolution of the killer immunoglobulin-like receptor (KIR) loci in primates

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages

Alu repeat elements reveals complex evolutionary history" > Whole-genome analysis of Alu repeat elements reveals complex evolutionary history

Complete MHC Haplotype Sequencing for Common Disease Gene Mapping

Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes

Genome-Scale Evolution: Reconstructing Gene Orders in the Ancestral Species

Assembling Puzzles from Preassembled Blocks

Characterization of Clustered MHC-Linked Olfactory Receptor Genes in Human and Mouse

Efficiency of Database Search for Identification of Mutated and Modified Proteins via Mass Spectrometry

MHC-Linked Olfactory Receptor Loci Exhibit Polymorphism and Contribute to Extended HLA/OR-Haplotypes

Construction of a High-Resolution 2.5-Mb Transcript Map of the Human 6p21.2–6p21.3 Region Immediately Centromeric of the Major Histocompatibility Complex

Estimation of Distances and Map Construction Using Radiation Hybrids

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Your search for returned 35 results