List of works by Pavel A. Pevzner

A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria

scientific article published on 06 January 2021

A family of small, cyclic peptides buried in preproalbumin since the Eocene epoch

scientific article published on 28 February 2018

A new approach to evaluating statistical significance of spectral identifications

scientific article published on 8 March 2013

A novel method for multiple alignment of sequences with repeated and shuffled elements

scientific article published on November 2004

Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer

scientific article

Algorithm for identification of fusion proteins via mass spectrometry.

scientific article published in January 2008

American Gut: an Open Platform for Citizen Science Microbiome Research

article

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

scientific article published on August 2010

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

scientific article published on 7 October 2007

Application of de novo sequencing tools to study abiogenic peptide formations by tandem mass spectrometry. The case of homo-peptides from glutamic acid complicated by substitutions of hydrogen by sodium or potassium atoms.

scientific article

Are there rearrangement hotspots in the human genome?

scientific article

Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads

Assembling short reads from jumping libraries with large insert sizes

scientific article published on 3 June 2015

Assembling single-cell genomes and mini-metagenomes from chimeric MDA products

scientific article

Assembly of long error-prone reads using de Bruijn graphs

scientific article published on 12 December 2016

Assembly of long, error-prone reads using repeat graphs

scientific article published on 01 April 2019

Automated assembly of centromeres from ultra-long error-prone reads

scientific article published on 14 July 2020

Automated de novo protein sequencing of monoclonal antibodies

scientific article published on December 2008

Automated genome mining of ribosomal peptide natural products

scientific article

BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs

scientific article published on 03 June 2019

Breakpoint graphs and ancestral genome reconstructions

scientific article published on 13 February 2009

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

scientific article

Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways

scientific article (publication date: 2014)

Clustering millions of tandem mass spectra

scientific article published on 8 December 2007

Colored de Bruijn graphs and the genome halving problem

scientific article published on January 2007

Combinatorial algorithms for design of DNA arrays.

scientific article

Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry".

scientific article

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

scientific article

Comparative genomics reveals birth and death of fragile regions in mammalian evolution

scientific article published on 30 November 2010

Comparative genomics reveals unusually long motifs in mammalian genomes.

scientific article published in July 2006

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

scientific article

Competencies: A Cure for Pre-Med Curriculum

scientific article published on 01 November 2011

Computing has changed biology--biology education must catch up.

scientific article

Corepressor-dependent silencing of chromosomal regions encoding neuronal genes

scientific article (publication date: 29 November 2002)

Correcting base-assignment errors in repeat regions of shotgun assembly.

scientific article

Cycloquest: identification of cyclopeptides via database search of their mass spectra against genome databases

scientific article

Cytotoxic veraguamides, alkynyl bromide-containing cyclic depsipeptides from the marine cyanobacterium cf. Oscillatoria margaritifera. ⬇️

scientific article

DRIMM-Synteny: decomposing genomes into evolutionary conserved segments

scientific article published on 24 August 2010

De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments

scientific article published on 18 December 2019

De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra

scientific article

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

scientific article published on 3 December 2008

De novo peptide sequencing and identification with precision mass spectrometry

scientific article published on January 2007

De novo protein sequencing by combining top-down and bottom-up tandem mass spectra.

scientific article

De novo repeat classification and fragment assembly

scientific article published on September 2004

Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes

article

Decoding the Genomic Architecture of Mammalian and Plant Genomes: Synteny Blocks and Large-scale Duplications

article

Decoding the fine-scale structure of a breast cancer genome and transcriptome

scientific article

Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach

scientific article

Dereplication and de novo sequencing of nonribosomal peptides

scientific article published on 13 July 2009

Dereplication of microbial metabolites through database search of mass spectra

scientific article published in Nature Communications

Dereplication of peptidic natural products through database search of mass spectra

scientific article

Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks

scientific article

Detection and analysis of ancient segmental duplications in mammalian genomes

scientific article published on 07 May 2018

Does trypsin cut before proline?

scientific article

Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps

scientific article

EULER-PCR: finishing experiments for repeat resolution.

scientific article published in January 2002

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

scientific article published on 8 April 2004

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

scientific article

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

scientific article

ExSPAnder: a universal repeat resolver for DNA fragment assembly

scientific article

False discovery rates of protein identifications: a strike against the two-peptide rule

scientific article published on September 2009

Finding composite regulatory patterns in DNA sequences

scientific article published on 01 January 2002

Finding subtle motifs by branching from sample strings

scientific article

Fragment assembly with short reads

scientific article

From de Bruijn Graphs to Rectangle Graphs for Genome Assembly

Gapped spectral dictionaries and their applications for database searches of tandem mass spectra

scientific article

Genome Halving Problem Revisited

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

scientific article published on 5 April 2013

Genome rearrangements in mammalian evolution: lessons from human and mouse genomes

scientific article (publication date: 2003)

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

Genome-scale evolution: reconstructing gene orders in the ancestral species.

scientific article

Genome-wide analysis of bacterial promoter regions

scientific article published on 01 January 2003

How bioinformatics and open data can boost basic science in countries and universities with limited resources

scientific article published on 01 March 2019

How many signal peptides are there in bacteria?

scientific article published on April 2013

How to apply de Bruijn graphs to genome assembly

scientific article (publication date: 8 November 2011)

Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution

scientific article

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

scientific article published on 27 November 2005

Identification of post-translational modifications via blind search of mass-spectra

scientific article published on January 2005

Identification of ultramodified proteins using top-down tandem mass spectra.

scientific article

Identifying repeat domains in large genomes

scientific article

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

scientific article published on June 2015

Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis

scientific article

Immunoglobulin Classification Using the Colored Antibody Graph

scientific article published on 05 May 2016

Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra.

scientific article published on 22 January 2018

Inference of Diversity Genes and Analysis of Non-canonical V(DD)J Recombination in Immunoglobulins

article

Initial sequencing and comparative analysis of the mouse genome

scientific article

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

scientific article

Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery

scientific article published on 28 May 2021

Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides

scientific article published on June 2009

Interpreting top-down mass spectra using spectral alignment.

scientific article published on 27 February 2008

Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity

scientific article published on 25 July 2018

Limited Lifespan of Fragile Regions in Mammalian Evolution

MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection

scientific article published on 10 January 2018

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

scientific article

MS-GF+ makes progress towards a universal database search tool for proteomics

scientific article published on 31 October 2014

Mass spectrometry-based neuropeptidomics of secretory vesicles from human adrenal medullary pheochromocytoma reveals novel peptide products of prohormone processing

scientific article

MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities

scientific article published on 16 October 2019

Modeling and characterization of multi-charge mass spectra for peptide sequencing.

scientific article published in December 2006

Multi-break rearrangements and chromosomal evolution

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

scientific article

Multiplex de novo sequencing of peptide antibiotics

scientific article published on 28 October 2011

N-terminal protein processing: a comparative proteogenomic analysis

scientific article published on 23 September 2012

NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery

scientific article

Neuropeptidomic components generated by proteomic functions in secretory vesicles for cell-cell communication

scientific article

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads

scientific article published on 31 October 2019

Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers

scientific article published on 14 October 2011

Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly

Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly

scientific article published on 17 July 2012

PepNovo: de novo peptide sequencing via probabilistic network modeling

scientific article

Peptide sequence tags for fast database search in mass-spectrometry.

scientific article published in July 2005

Plasmid detection and assembly in genomic and metagenomic data sets

scientific article published on 02 May 2019

Preface: 2nd Satellite Meeting on Bioinformatics Education, Research in Computational Molecular Biology (RECOMB-BE 2010).

scientific article published on 12 May 2011

Protein identification by spectral networks analysis

scholarly article

Protein identification using top-down.

scientific article

Proteogenomics

scientific article published on 01 December 2014

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

scientific article published on 13 April 2014

Rapid validation of protein identifications with the borderline statistical confidence via de novo sequencing and MS BLAST searches.

scientific article

Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads

scientific article published on 4 October 2017

Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes

scientific article published on April 2004

Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps

scientific article

Reconstructing tumor amplisomes

scientific article published on August 2004

Reconstructing tumor genome architectures

scientific article published in October 2003

Representing and comparing protein structures as paths in three-dimensional space.

scientific article

SEQuel: improving the accuracy of genome assemblies

scientific article

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing

scientific article

Scalable heuristics for design of DNA probe arrays.

scientific article

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

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

scientific article

Sequencing cyclic peptides by multistage mass spectrometry

scientific article

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

scientific article (publication date: 9 August 2016)

Short read fragment assembly of bacterial genomes

scientific article published on 14 December 2007

Shotgun protein sequencing by tandem mass spectra assembly

scientific article published in December 2004

Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins.

scientific article published on 19 April 2007

Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage

scientific article

Single cells within the Puerto Rico trench suggest hadal adaptation of microbial lineages.

scientific article published on 18 September 2015

Single-molecule protein identification by sub-nanopore sensors

scientific article

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen

scientific article (publication date: 20 December 2016)

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

scientific article

Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra

scientific article published on 14 August 2008

Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases

scientific article published on 03 July 2008

Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification

scientific article published on 02 March 2009

SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra.

scientific article published on 2 December 2015

Splicing graphs and EST assembly problem

scientific article published in January 2002

Synergistic allelochemicals from a freshwater cyanobacterium ⬇️

scientific article

TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats

scientific article published on 01 July 2020

Target-decoy approach and false discovery rate: when things may go wrong

scientific article published on 5 May 2011

Telomere-to-telomere assembly of a complete human X chromosome

scientific article published on 14 July 2020

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

scientific article published on 03 August 2004

The antibody repertoire of colorectal cancer.

scientific article published on 18 October 2017

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

scientific article published in March 2006

The fragile breakage versus random breakage models of chromosome evolution

scientific article

The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search

scientific article

The string decomposition problem and its applications to centromere analysis and assembly

scientific article published on 01 July 2020

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

scientific article published on 29 March 2021

Top-down analysis of immunoglobulin G isotypes 1 and 2 with electron transfer dissociation on a high-field Orbitrap mass spectrometer

scientific article

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

scientific article

Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions.

scientific article

TruSPAdes: barcode assembly of TruSeq synthetic long reads

scientific article published in February 2016

Ultra-low input single tube linked-read library method enables short-read second-generation sequencing systems to generate highly accurate and economical long-range sequencing information routinely

scientific article published on 15 June 2020

Unexpected diversity of signal peptides in prokaryotes

scientific article published on 20 November 2012

UniNovo: a universal tool for de novo peptide sequencing

scientific article

Unrestrictive identification of post-translational modifications through peptide mass spectrometry

scientific article

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

scientific article published on 18 September 2020

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

scientific article

Whole Genome Duplications and Contracted Breakpoint Graphs

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

scientific article

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

scientific article (publication date: November 2004)

Whole-genome sequencing and assembly with high-throughput, short-read technologies

scientific article published on 30 May 2007

cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs

scientific article published on 01 July 2019

dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes

scientific article published on 3 March 2015

hybridSPAdes: an algorithm for hybrid assembly of short and long reads

scientific article published on 20 November 2015

metaFlye: scalable long-read metagenome assembly using repeat graphs

scientific article published on 05 October 2020

metaSPAdes: a new versatile metagenomic assembler

scientific article

metaviralSPAdes: assembly of viruses from metagenomic data

scientific article published on 15 May 2020

plasmidSPAdes: assembling plasmids from whole genome sequencing data

scientific article

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