Pavel Pevzner
Chief Advisor
Publications
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TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats Bioinformatics, 2020 -
The string decomposition problem and its applications to centromere analysis and assembly Bioinformatics, 2020 -
The String Decomposition problem and its applications to centromere analysis and assembly (talk), 2020 -
TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats (talk), 2020 -
Plasmid detection and assembly in genomic and metagenomic data sets Genome Research, 2019 -
BiosyntheticSPAdes: Reconstructing Biosynthetic Gene Clusters From Assembly Graphs Genome Research, 2019 -
cloudSPAdes: Assembly of Synthetic Long Reads Using de Bruijn graphs Bioinformatics, 2019 -
cloudSPAdes: Assembly of Synthetic Long Reads Using de Bruijn graphs (talk), 2019 -
Variable Identification and De Novo Sequencing of Cyclopeptides via Computational Processing of Tandem Mass Spectra (talk), 2018 -
SPAdes Family of Tools for Genome Assembly and Analysis: What’s New? (poster), 2018 -
SPAdes Family of Tools for Genome Assembly and Analysis: Current Status (poster), 2018 -
metaSPAdes: a new versatile de novo metagenomics assembler. Genome Research, 2017 -
Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads. The Journal of Immunology, 2017 -
Dereplication of peptidic natural products through database search of mass spectra. Nature Chemical Biology, 2017 -
Reconstructing antibody repertoires from error-prone immunosequencing datasets (talk), 2017 -
Identification of novel peptidic antibiotics via large scale scoring of mass spectra against natural products databases (poster), 2017 -
AntEvolo: a novel approach for clonal analysis of antibody repertoires (poster), 2017 -
SPAdes: is there anything new we could develop? (talk), 2017 -
SPAdes Family of Tools for Genome Assembly and Analysis: What’s New? (poster), 2017 -
VarQuest: modification-tolerant identification of novel variants of peptidic antibiotics and other natural products. (poster), 2017 -
Identification of novel peptidic antibiotics via large scale scoring of mass spectra against natural products databases (poster), 2017 -
SPAdes Family of Tools for Genome Assembly and Analysis: What’s New? (poster), 2017 -
From Metagenome Sequencing to Genome Mining for New Antibiotics (talk), 2017 -
hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics, 2016 -
Top-down analysis of protein samples by de novo sequencing techniques. Bioinformatics, 2016 -
TruSPAdes: barcode assembly of TruSeq synthetic long reads. Nature Methods, 2016 -
SPArcle: Identifying Microbial Genome Variations with Colored de Bruijn Graphs. Manuscript in preparation., 2016 -
plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data. Bioinformatics, 2016 -
A novel toolkit for analysis of adaptive immune repertoires using immunosequencing and mass spectra data. Poster., 2016 -
Assembling Short Reads from Jumping Libraries with Large Insert Sizes. Bioinformatics, 2015 -
IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Bioinformatics, 2015 -
dipSPAdes: assembler for highly polymorphic diploid genomes. Journal of Computational Biology, 2015 -
De novo sequencing of peptides from top-down tandem mass spectra. Journal of Proteome Research, 2015 -
IgTools: a toolkit for analysis of antibody repertoire from immunosequencing and mass spectra data. Poster on Immunogenomics 2015. Huntsville, USA, 2015 -
ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinformatics, 2014 -
Characterization of Cyanobacterial Hydrocarbon Composition and Distribution of Biosynthetic Pathways. PLoS One, 2014 -
New Frontiers of Genome Assembly with SPAdes 3.0. (poster), 2014 -
What is the difference between the breakpoint graph and the de Bruijn graph? BMC Genomics, 2014 -
dipSPAdes: assembler for highly polymorphic diploid genomes. In Sharan, Roded (eds.) RECOMB 2014, LNCS (8394). pp. 265-279. Springer, Heidelberg, 2014 -
dipSPAdes: assembler for highly polymorphic diploid genomes. Talk., 2014 -
Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. Journal of Computational Biology, 2013 -
Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proceedings of the National Academy of Sciences, 2013 -
Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. Genome Research, 2013 -
Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly. Journal of Computational Biology, 2013 -
Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads. Lecture Notes in Computer Science, 2013 -
Using uneven coverage depth in bacterial single-cell repeat resolution. (poster), 2013 -
BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics, 2013 -
MORPH-PRO: a novel algorithm and web server for protein morphing. Algorithms for molecular biology, 2013 -
BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics, 2013 -
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology, 2012 -
From de Bruijn Graphs to Rectangle Graphs for Genome Assembly. Lecture Notes in Bioinformatics, 2012 -
Path-Extend: An Approach for Repeat Resolution in de novo Genome Assembly. , 2012 -
Genomic insights into secondary metabolism of the natural product-rich cyanobacterium Moorea bouillonii. Planta Medica, 2012 -
Peptide Sequence Tags for Top-Down Spectra. (poster, session TP25), 2012 -
Pathset Graphs: A Novel Approach for Comprehensive Utilization of Mate-Pairs in Genome Assembly. Lecture Notes in Computer Science, 2012 -
Peptide Sequence Tags for Top-Down Spectra. (talk), 2012 -
BioInformatics and genome assemblies — Challenges for Russia and for the world community. , 2012 -
De novo sequencing of peptide antibiotics. (talk), 2011 -
The Birth and Death of Fragile Regions in Human Genome. (highlight track paper), 2011 -
Bayesian Evaluation of de novo Genome Assembly. (poster), 2011 -
Expandable de novo genome assembler for short-read sequence data. (HiTSeq poster), 2011 -
Protein Identification Using Top-Down Spectra. (poster), 2011 -
Multiplex De Novo Sequencing of Peptide Antibiotics. (paper, talk), 2011 -
Blocked Pattern Matching Problem and its Applications in Proteomics. (paper, talk), 2011 -
Paired de Bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. (paper, talk), 2011 -
How Will the Human Genome Evolve in the Next Million Years? (talk), 2011 -
Genome rearrangements: from biological problems to combinatorial algorithms (and back). , 2011 -
Вычислительная протеомика. , 2011 -
Genome Rearrangements: from Biological Problems to Combinatorial Algorithms. , 2010