Works by Pevzner, Pavel A.

Results: 70

plasmidSPAdes: assembling plasmids from whole genome sequencing data.

Published in:

Bioinformatics, 2016, v. 32, n. 22, p. 3380, doi. 10.1093/bioinformatics/btw493

By:

Antipov, Dmitry;
Hartwick, Nolan;
Shen, Max;
Mikhail Raiko;
Lapidus, Alla;
Pevzner, Pavel A.

Publication type:

Article

Top-down analysis of protein samples by de novo sequencing techniques.

Published in:

Bioinformatics, 2016, v. 32, n. 18, p. 2753, doi. 10.1093/bioinformatics/btw307

By:

Vyatkina, Kira;
Pevzner, Pavel A.;
Si Wu;
Dekker, Lennard J. M.;
VanDuijn, Martijn M.;
Luider, Theo M.;
Xiaowen Liu;
Tolić, Nikola;
Paša-Tolic, Ljiljana

Publication type:

Article

HYBRIDSPADES: an algorithm for hybrid assembly of short and long reads.

Published in:

Bioinformatics, 2016, v. 32, n. 7, p. 1009, doi. 10.1093/bioinformatics/btv688

By:

Antipov, Dmitry;
Korobeynikov, Anton;
McLean, Jeffrey S.;
Pevzner, Pavel A.

Publication type:

Article

Assembling short reads from jumping libraries with large insert sizes.

Published in:

Bioinformatics, 2015, v. 31, n. 20, p. 3262, doi. 10.1093/bioinformatics/btv337

By:

Vasilinetc, Irina;
Prjibelski, Andrey D.;
Gurevich, Alexey;
Korobeynikov, Anton;
Pevzner, Pavel A.

Publication type:

Article

IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i53, doi. 10.1093/bioinformatics/btv238

By:

Safonova, Yana;
Bonissone, Stefano;
Kurpilyansky, Eugene;
Starostina, Ekaterina;
Lapidus, Alla;
Stinson, Jeremy;
DePalatis, Laura;
Sandoval, Wendy;
Lill, Jennie;
Pevzner, Pavel A.

Publication type:

Article

ExSPAnder: a universal repeat resolver for DNA fragment assembly.

Published in:

Bioinformatics, 2014, v. 30, n. 12, p. i293, doi. 10.1093/bioinformatics/btu266

By:

Prjibelski, Andrey D.;
Vasilinetc, Irina;
Bankevich, Anton;
Gurevich, Alexey;
Krivosheeva, Tatiana;
Nurk, Sergey;
Pham, Son;
Korobeynikov, Anton;
Lapidus, Alla;
Pevzner, Pavel A.

Publication type:

Article

UniNovo: a universal tool for de novo peptide sequencing.

Published in:

Bioinformatics, 2013, v. 29, n. 16, p. 1953, doi. 10.1093/bioinformatics/btt338

By:

Jeong, Kyowon;
Kim, Sangtae;
Pevzner, Pavel A.

Publication type:

Article

SEQuel: improving the accuracy of genome assemblies.

Published in:

Bioinformatics, 2012, v. 28, n. 12, p. i188, doi. 10.1093/bioinformatics/bts219

By:

Ronen, Roy;
Boucher, Christina;
Chitsaz, Hamidreza;
Pevzner, Pavel

Publication type:

Article

Error correction of high-throughput sequencing datasets with non-uniform coverage.

Published in:

Bioinformatics, 2011, v. 27, n. 13, p. i137, doi. 10.1093/bioinformatics/btr208

By:

Medvedev, Paul;
Scott, Eric;
Kakaradov, Boyko;
Pevzner, Pavel

Publication type:

Article

DRIMM-Synteny: decomposing genomes into evolutionary conserved segments.

Published in:

Bioinformatics, 2010, v. 26, n. 20, p. 2509, doi. 10.1093/bioinformatics/btq465

By:

Pham, Son K.;
Pevzner, Pavel A.

Publication type:

Article

Multi-spectra peptide sequencing and its applications to multistage mass spectrometry.

Published in:

Bioinformatics, 2008, v. 24, n. 13, p. i416, doi. 10.1093/bioinformatics/btn184

By:

Bandeira, Nuno;
Olsen, Jesper V.;
Mann, Matthias;
Pevzner, Pavel A.

Publication type:

Article

Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution.

Published in:

Nature Genetics, 2007, v. 39, n. 11, p. 1361, doi. 10.1038/ng.2007.9

By:

Zhaoshi Jiang;
Haixu Tang;
Ventura, Mario;
Cardone, Maria Francesca;
Marques-Bonet, Tomas;
Xinwei She;
Pevzner, Pavel A.;
Eichler, Evan E.

Publication type:

Article

De novo identification of repeat families in large genomes.

Published in:

Bioinformatics, 2005, v. 21, p. i351, doi. 10.1093/bioinformatics/bti1018

By:

Price, Alkes L.;
Jones, Neil C.;
Pevzner, Pavel A.

Publication type:

Article

De novo identification of repeat families in large genomes.

Published in:

Bioinformatics, 2005, v. 21, n. 1, p. i351

By:

Pavel A. Pevzner

Publication type:

Article

Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians.

Published in:

Bioinformatics, 2004, v. 20, n. 14, p. 2159, doi. 10.1093/bioinformatics/bth217

By:

Pavel A. Pevzner

Publication type:

Article

Fragment assembly with short reads.

Published in:

Bioinformatics, 2004, v. 20, n. 13, p. 2067, doi. 10.1093/bioinformatics/bth205

By:

Mark Chaisson;
Pavel Pevzner;
Haixu Tang

Publication type:

Article

Reconstructing tumor amplisomes.

Published in:

Bioinformatics, 2004, v. 20, n. suppl_1, p. i265, doi. 10.1093/bioinformatics/bth931

By:

Raphael, Benjamin J.;
Pevzner, Pavel A.

Publication type:

Article

Reconstructing tumor amplisomes.

Published in:

Bioinformatics, 2004, v. 20, p. i265, doi. 10.1093/bioinformatics/bth931

By:

Raphael, Benjamin J.;
Pevzner, Pavel A.

Publication type:

Article

Finding composite regulatory patterns in DNA sequences.

Published in:

Bioinformatics, 2002, v. 18, p. S354, doi. 10.1093/bioinformatics/18.suppl_1.S354

By:

Eskin, Eleazar;
Pevzner, Pavel A.

Publication type:

Article

Splicing graphs and EST assembly problem.

Published in:

Bioinformatics, 2002, v. 18, p. S181, doi. 10.1093/bioinformatics/18.suppl_1.S181

By:

Heber, Steffen;
Alekseyev, Max;
Sze, Sing-Hoi;
Tang, Haixu;
Pevzner, Pavel A.

Publication type:

Article

Fragment assembly with double-barreled data.

Published in:

Bioinformatics, 2001, v. 17, p. 225, doi. 10.1093/bioinformatics/17.suppl_1.s225

By:

Pevzner, Pavel A.;
Tang, Haixu

Publication type:

Article

A new approach to sequence comparison: normalized sequence alignment.

Published in:

Bioinformatics, 2001, v. 17, n. 4, p. 327, doi. 10.1093/bioinformatics/17.4.327

By:

Arslan, Abdullah N.;
Eğecioğlu, Ömer;
Pevzner, Pavel A.

Publication type:

Article

Algorithms and software for support of gene identification experiments.

Published in:

Bioinformatics, 1998, v. 14, n. 1, p. 14, doi. 10.1093/bioinformatics/14.1.14

By:

Sze, Sing‐Hoi;
Roytberg, Michael;
Gelfand, Mikhail;
Mironov, Andrey;
Astakhova, Tatiana;
Pevzner, Pavel

Publication type:

Article

Publisher Correction: Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery.

Published in:

2021

By:

Behsaz, Bahar;
Bode, Edna;
Gurevich, Alexey;
Shi, Yan-Ni;
Grundmann, Florian;
Acharya, Deepa;
Caraballo-Rodríguez, Andrés Mauricio;
Bouslimani, Amina;
Panitchpakdi, Morgan;
Linck, Annabell;
Guan, Changhui;
Oh, Julia;
Dorrestein, Pieter C.;
Bode, Helge B.;
Pevzner, Pavel A.;
Mohimani, Hosein

Publication type:

Correction Notice

viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-021-02566-x

By:

Antipov, Dmitry;
Rayko, Mikhail;
Kolmogorov, Mikhail;
Pevzner, Pavel A.

Publication type:

Article

Characterization of Cyanobacterial Hydrocarbon Composition and Distribution of Biosynthetic Pathways.

Published in:

PLoS ONE, 2014, v. 9, n. 1, p. 1, doi. 10.1371/journal.pone.0085140

By:

Coates, R. Cameron;
Podell, Sheila;
Korobeynikov, Anton;
Lapidus, Alla;
Pevzner, Pavel;
Sherman, David H.;
Allen, Eric E.;
Gerwick, Lena;
Gerwick, William H.

Publication type:

Article

Single Cell Genome Amplification Accelerates Identification of the Apratoxin Biosynthetic Pathway from a Complex Microbial Assemblage.

Published in:

PLoS ONE, 2011, v. 6, n. 4, p. 1, doi. 10.1371/journal.pone.0018565

By:

Grindberg, Rashel V.;
Ishoey, Thomas;
Brinza, Dumitru;
Esquenazi, Eduardo;
Coates, R. Cameron;
Wei-ting Liu;
Gerwick, Lena;
Dorrestein, Pieter C.;
Pevzner, Pavel;
Lasken, Roger;
Gerwick, William H.

Publication type:

Article

How many signal peptides are there in bacteria?

Published in:

Environmental Microbiology, 2013, v. 15, n. 4, p. 983, doi. 10.1111/1462-2920.12105

By:

Ivankov, Dmitry N.;
Payne, Samuel H.;
Galperin, Michael Y.;
Bonissone, Stefano;
Pevzner, Pavel A.;
Frishman, Dmitrij

Publication type:

Article

Are There Rearrangement Hotspots in the Human Genome?

Published in:

PLoS Computational Biology, 2007, v. 3, n. 11, p. e209, doi. 10.1371/journal.pcbi.0030209

By:

Alekseyev, Max A.;
Pevzner, Pavel A.

Publication type:

Article

The Fragile Breakage versus Random Breakage Models of Chromosome Evolution.

Published in:

PLoS Computational Biology, 2006, v. 2, n. 2, p. 0100, doi. 10.1371/journal.pcbi.0020014

By:

Qiang Peng;
Pevzner, Pavel A.;
Tesler, Glenn

Publication type:

Article

Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing.

Published in:

Proteomics, 2007, v. 7, n. 14, p. 2318, doi. 10.1002/pmic.200700003

By:

Waridel, Patrice;
Frank, Ari;
Thomas, Henrik;
Surendranath, Vineeth;
Sunyaev, Shamil;
Pevzner, Pavel;
Shevchenko, Andrej

Publication type:

Article

Dereplication of microbial metabolites through database search of mass spectra.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-06082-8

By:

Mohimani, Hosein;
Gurevich, Alexey;
Shlemov, Alexander;
Mikheenko, Alla;
Korobeynikov, Anton;
Cao, Liu;
Shcherbin, Egor;
Nothias, Louis-Felix;
Dorrestein, Pieter C.;
Pevzner, Pavel A.

Publication type:

Article

Automated de novo protein sequencing of monoclonal antibodies.

Published in:

Nature Biotechnology, 2008, v. 26, n. 12, p. 1336, doi. 10.1038/nbt1208-1336

By:

Bandeira, Nuno;
Pham, Victoria;
Pevzner, Pavel;
Arnott, David;
Lill, Jennie R

Publication type:

Article

Identification of post-translational modifications by blind search of mass spectra.

Published in:

Nature Biotechnology, 2005, v. 23, n. 12, p. 1562, doi. 10.1038/nbt1168

By:

Tsur, Dekel;
Tanner, Stephen;
Zandi, Ebrahim;
Bafna, Vineet;
Pevzner, Pavel A.

Publication type:

Article

SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs.

Published in:

PeerJ, 2024, p. 1, doi. 10.7717/peerj.18050

By:

Tolstoganov, Ivan;
Chen, Zhoutao;
Pevzner, Pavel;
Korobeynikov, Anton

Publication type:

Article

Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-23502-4

By:

Behsaz, Bahar;
Bode, Edna;
Gurevich, Alexey;
Shi, Yan-Ni;
Grundmann, Florian;
Acharya, Deepa;
Caraballo-Rodríguez, Andrés Mauricio;
Bouslimani, Amina;
Panitchpakdi, Morgan;
Linck, Annabell;
Guan, Changhui;
Oh, Julia;
Dorrestein, Pieter C.;
Bode, Helge B.;
Pevzner, Pavel A.;
Mohimani, Hosein

Publication type:

Article

Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-21350-w

By:

Yutin, Natalya;
Benler, Sean;
Shmakov, Sergei A.;
Wolf, Yuri I.;
Tolstoy, Igor;
Rayko, Mike;
Antipov, Dmitry;
Pevzner, Pavel A.;
Koonin, Eugene V.

Publication type:

Article

What is the difference between the breakpoint graph and the de Bruijn graph?

Published in:

BMC Genomics, 2014, v. 15, p. 1, doi. 10.1186/1471-2164-15-S6-S6

By:

Yu Lin;
Nurk, Sergey;
Pevzner, Pavel A.

Publication type:

Article

ORFograph: search for novel insecticidal protein genes in genomic and metagenomic assembly graphs.

Published in:

Microbiome, 2021, v. 9, n. 1, p. 1, doi. 10.1186/s40168-021-01092-z

By:

Dvorkina, Tatiana;
Bankevich, Anton;
Sorokin, Alexei;
Yang, Fan;
Adu-Oppong, Boahemaa;
Williams, Ryan;
Turner, Keith;
Pevzner, Pavel A.

Publication type:

Article

Thousands of previously unknown phages discovered in whole-community human gut metagenomes.

Published in:

Microbiome, 2021, v. 9, n. 1, p. 1, doi. 10.1186/s40168-021-01017-w

By:

Benler, Sean;
Yutin, Natalya;
Antipov, Dmitry;
Rayko, Mikhail;
Shmakov, Sergey;
Gussow, Ayal B.;
Pevzner, Pavel;
Koonin, Eugene V.

Publication type:

Article

Neuropeptidomic Components Generated by Proteomic Functions in Secretory Vesicles for Cell-Cell Communication.

Published in:

AAPS Journal, 2010, v. 12, n. 4, p. 635, doi. 10.1208/s12248-010-9223-z

By:

Hook, Vivian;
Bark, Steven;
Gupta, Nitin;
Lortie, Mark;
Lu, Weiya;
Bandeira, Nuno;
Funkelstein, Lydiane;
Wegrzyn, Jill;
O'Connor, Daniel;
Pevzner, Pavel

Publication type:

Article

Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra.

Published in:

Nature Methods, 2011, v. 8, n. 7, p. 587, doi. 10.1038/nmeth.1609

By:

Frank, Ari M.;
Monroe, Matthew E.;
Shah, Anuj R.;
Carver, Jeremy J.;
Bandeira, Nuno;
Moore, Ronald J.;
Anderson, Gordon A.;
Smith, Richard D.;
Pevzner, Pavel A.

Publication type:

Article

Dereplication and de novo sequencing of nonribosomal peptides.

Published in:

Nature Methods, 2009, v. 6, n. 8, p. 596, doi. 10.1038/nmeth.1350

By:

Julio Ng;
Bandeira, Nuno;
Wei-Ting Liu;
Ghassemian, Majid;
Simmons, Thomas L.;
Gerwick, William H.;
Linington, Roger;
Dorrestein, Pieter C.;
Pevzner, Pavel A.

Publication type:

Article

Proteogenomics.

Published in:

Proteomics, 2014, v. 14, n. 23/24, p. 2631, doi. 10.1002/pmic.201470173

By:

Pandey, Akhilesh;
Pevzner, Pavel A.

Publication type:

Article

Quantitative analysis of human salivary gland-derived intact proteome using top-down mass spectrometry.

Published in:

Proteomics, 2014, v. 14, n. 10, p. 1211, doi. 10.1002/pmic.201300378

By:

Wu, Si;
Brown, Joseph N.;
Tolić, Nikola;
Meng, Da;
Liu, Xiaowen;
Zhang, Haizhen;
Zhao, Rui;
Moore, Ronald J.;
Pevzner, Pavel;
Smith, Richard D.;
Paša‐Tolić, Ljiljana

Publication type:

Article

Sequencing cyclic peptides by multistage mass spectrometry.

Published in:

Proteomics, 2011, v. 11, n. 18, p. 3642, doi. 10.1002/pmic.201000697

By:

Mohimani, Hosein;
Yang, Yu-Liang;
Liu, Wei-Ting;
Hsieh, Pei-Wen;
Dorrestein, Pieter C.;
Pevzner, Pavel A.

Publication type:

Article

Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass spectrometry.

Published in:

Proteomics, 2010, v. 10, n. 15, p. 2833, doi. 10.1002/pmic.200900821

By:

Gupta, Nitin;
Hixson, Kim K.;
Culley, David E.;
Smith, Richard D.;
Pevzner, Pavel A.

Publication type:

Article

MS-GFþ makes progress towards a universal database search tool for proteomics.

Published in:

Nature Communications, 2014, v. 5, n. 10, p. 5277, doi. 10.1038/ncomms6277

By:

Kim, Sangtae;
Pevzner, Pavel A.

Publication type:

Article

MORPH-PRO: a novel algorithm and web server for protein morphing.

Published in:

Algorithms for Molecular Biology, 2013, v. 8, n. 1, p. 1, doi. 10.1186/1748-7188-8-19

By:

Castellana, Natalie E.;
Lushnikov, Andrey;
Rotkiewicz, Piotr;
Sefcovic, Natasha;
Pevzner, Pavel A.;
Godzik, Adam;
Vyatkina, Kira

Publication type:

Article

The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome.

Published in:

Nucleic Acids Research, 2004, v. 32, n. 13, p. 3977, doi. 10.1093/nar/gkh731

By:

Leipzig, Jeremy;
Pevzner, Pavel;
Heber, Steffen

Publication type:

Article