Pavel Pevzner

Pavel Pevzner

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Pavel Pevzner

Pavel Pevzner

Publications by authors named "Pavel Pevzner"

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100Publications

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BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs.

Genome Res 2019 08 3;29(8):1352-1362. Epub 2019 Jun 3.

Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia, 19904.

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http://dx.doi.org/10.1101/gr.243477.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6673720PMC
August 2019

cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs.

Bioinformatics 2019 Jul;35(14):i61-i70

Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.

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http://dx.doi.org/10.1093/bioinformatics/btz349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612831PMC
July 2019

Plasmid detection and assembly in genomic and metagenomic data sets.

Genome Res 2019 06 2;29(6):961-968. Epub 2019 May 2.

Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg 199004, Russia.

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http://dx.doi.org/10.1101/gr.241299.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6581055PMC
June 2019

Assembly of long, error-prone reads using repeat graphs.

Nat Biotechnol 2019 05 1;37(5):540-546. Epub 2019 Apr 1.

Department of Computer Science and Engineering, University of California, San Diego, CA, USA.

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http://dx.doi.org/10.1038/s41587-019-0072-8DOI Listing
May 2019

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

Front Immunol 2019 3;10:987. Epub 2019 May 3.

Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, United States.

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https://www.frontiersin.org/article/10.3389/fimmu.2019.00987
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http://dx.doi.org/10.3389/fimmu.2019.00987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6516046PMC
May 2019

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

Cell Syst 2018 08 25;7(2):192-200.e3. Epub 2018 Jul 25.

Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1016/j.cels.2018.06.009DOI Listing
August 2018

Detection and analysis of ancient segmental duplications in mammalian genomes.

Genome Res 2018 06 7;28(6):901-909. Epub 2018 May 7.

Department of Computer Science and Engineering, University of California at San Diego, San Diego, California 92093, USA.

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http://dx.doi.org/10.1101/gr.228718.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991524PMC
June 2018

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

Nat Microbiol 2018 03 22;3(3):319-327. Epub 2018 Jan 22.

Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia.

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http://dx.doi.org/10.1038/s41564-017-0094-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5951390PMC
March 2018

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

Plant Direct 2018 Feb 28;2(2). Epub 2018 Feb 28.

The University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Crawley, Perth 6009, Australia.

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http://dx.doi.org/10.1002/pld3.42DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6223261PMC
February 2018

The Antibody Repertoire of Colorectal Cancer.

Mol Cell Proteomics 2017 Dec 18;16(12):2111-2124. Epub 2017 Oct 18.

¶Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92037

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http://www.mcponline.org/lookup/doi/10.1074/mcp.RA117.000397
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http://dx.doi.org/10.1074/mcp.RA117.000397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5724175PMC
December 2017

Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads.

J Immunol 2017 11 4;199(9):3369-3380. Epub 2017 Oct 4.

Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg University, St. Petersburg, Russia 199034.

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http://dx.doi.org/10.4049/jimmunol.1700485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5661950PMC
November 2017

metaSPAdes: a new versatile metagenomic assembler.

Genome Res 2017 05 15;27(5):824-834. Epub 2017 Mar 15.

Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia 199004.

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http://dx.doi.org/10.1101/gr.213959.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411777PMC
May 2017

Single-molecule protein identification by sub-nanopore sensors.

PLoS Comput Biol 2017 05 9;13(5):e1005356. Epub 2017 May 9.

Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5423552PMC
May 2017

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

J Proteomics 2017 04 27;159:67-76. Epub 2017 Feb 27.

Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Spectroswiss Sàrl, EPFL Innovation Park, 1015 Lausanne, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.jprot.2017.02.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478168PMC
April 2017

Dereplication of peptidic natural products through database search of mass spectra.

Nat Chem Biol 2017 Jan 31;13(1):30-37. Epub 2016 Oct 31.

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1038/nchembio.2219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5409158PMC
January 2017

Assembly of long error-prone reads using de Bruijn graphs.

Proc Natl Acad Sci U S A 2016 12 12;113(52):E8396-E8405. Epub 2016 Dec 12.

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92092;

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http://dx.doi.org/10.1073/pnas.1604560113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5206522PMC
December 2016

Spatial Molecular Architecture of the Microbial Community of a Lichen.

mSystems 2016 Nov-Dec;1(6). Epub 2016 Dec 20.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA; Department of Chemistry and Biochemistry, University of California, San Diego, California, USA; Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1128/mSystems.00139-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5183598PMC
December 2016

plasmidSPAdes: assembling plasmids from whole genome sequencing data.

Bioinformatics 2016 11 27;32(22):3380-3387. Epub 2016 Jul 27.

Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btw493DOI Listing
November 2016

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

Bioinformatics 2016 09 14;32(18):2753-9. Epub 2016 May 14.

Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, St Petersburg, Russia Department of Computer Science and Engineering, University of California, San Diego, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6280873PMC
September 2016

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

Authors:
Mingxun Wang Jeremy J Carver Vanessa V Phelan Laura M Sanchez Neha Garg Yao Peng Don Duy Nguyen Jeramie Watrous Clifford A Kapono Tal Luzzatto-Knaan Carla Porto Amina Bouslimani Alexey V Melnik Michael J Meehan Wei-Ting Liu Max Crüsemann Paul D Boudreau Eduardo Esquenazi Mario Sandoval-Calderón Roland D Kersten Laura A Pace Robert A Quinn Katherine R Duncan Cheng-Chih Hsu Dimitrios J Floros Ronnie G Gavilan Karin Kleigrewe Trent Northen Rachel J Dutton Delphine Parrot Erin E Carlson Bertrand Aigle Charlotte F Michelsen Lars Jelsbak Christian Sohlenkamp Pavel Pevzner Anna Edlund Jeffrey McLean Jörn Piel Brian T Murphy Lena Gerwick Chih-Chuang Liaw Yu-Liang Yang Hans-Ulrich Humpf Maria Maansson Robert A Keyzers Amy C Sims Andrew R Johnson Ashley M Sidebottom Brian E Sedio Andreas Klitgaard Charles B Larson Cristopher A Boya P Daniel Torres-Mendoza David J Gonzalez Denise B Silva Lucas M Marques Daniel P Demarque Egle Pociute Ellis C O'Neill Enora Briand Eric J N Helfrich Eve A Granatosky Evgenia Glukhov Florian Ryffel Hailey Houson Hosein Mohimani Jenan J Kharbush Yi Zeng Julia A Vorholt Kenji L Kurita Pep Charusanti Kerry L McPhail Kristian Fog Nielsen Lisa Vuong Maryam Elfeki Matthew F Traxler Niclas Engene Nobuhiro Koyama Oliver B Vining Ralph Baric Ricardo R Silva Samantha J Mascuch Sophie Tomasi Stefan Jenkins Venkat Macherla Thomas Hoffman Vinayak Agarwal Philip G Williams Jingqui Dai Ram Neupane Joshua Gurr Andrés M C Rodríguez Anne Lamsa Chen Zhang Kathleen Dorrestein Brendan M Duggan Jehad Almaliti Pierre-Marie Allard Prasad Phapale Louis-Felix Nothias Theodore Alexandrov Marc Litaudon Jean-Luc Wolfender Jennifer E Kyle Thomas O Metz Tyler Peryea Dac-Trung Nguyen Danielle VanLeer Paul Shinn Ajit Jadhav Rolf Müller Katrina M Waters Wenyuan Shi Xueting Liu Lixin Zhang Rob Knight Paul R Jensen Bernhard O Palsson Kit Pogliano Roger G Linington Marcelino Gutiérrez Norberto P Lopes William H Gerwick Bradley S Moore Pieter C Dorrestein Nuno Bandeira

Nat Biotechnol 2016 08;34(8):828-837

Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.

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http://dx.doi.org/10.1038/nbt.3597DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5321674PMC
August 2016

Immunoglobulin Classification Using the Colored Antibody Graph.

J Comput Biol 2016 06 5;23(6):483-94. Epub 2016 May 5.

2 Department of Computer Science and Engineering, University of California San diego , La Jolla, California.

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http://www.liebertpub.com/doi/10.1089/cmb.2016.0010
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http://dx.doi.org/10.1089/cmb.2016.0010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4904161PMC
June 2016

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

Bioinformatics 2016 04 20;32(7):1009-15. Epub 2015 Nov 20.

Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, Department of Computer Science and Engineering, University of California, San Diego, USA and.

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http://dx.doi.org/10.1093/bioinformatics/btv688DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907386PMC
April 2016

TruSPAdes: barcode assembly of TruSeq synthetic long reads.

Nat Methods 2016 Mar 1;13(3):248-50. Epub 2016 Feb 1.

Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia.

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http://dx.doi.org/10.1038/nmeth.3737DOI Listing
March 2016

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

Nat Prod Rep 2016 Jan;33(1):73-86

Department of Computer Science and Engineering, University of California, San Diego, USA.

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http://dx.doi.org/10.1039/c5np00050eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5590107PMC
January 2016

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

J Proteome Res 2016 Jan 17;15(1):144-51. Epub 2015 Dec 17.

Department of Computer Science and Engineering, UCSD , 9500 Gilman Drive, La Jolla, California, United States.

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http://dx.doi.org/10.1021/acs.jproteome.5b00610DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6020058PMC
January 2016

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

Appl Environ Microbiol 2015 Dec 18;81(24):8265-76. Epub 2015 Sep 18.

Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA

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http://dx.doi.org/10.1128/AEM.01659-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644660PMC
December 2015

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

J Proteome Res 2015 Nov 13;14(11):4450-62. Epub 2015 Oct 13.

Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University , 7-9 Universitetskaya nab., Saint Petersburg 199034, Russia.

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http://dx.doi.org/10.1021/pr501244vDOI Listing
November 2015

Assembling short reads from jumping libraries with large insert sizes.

Bioinformatics 2015 Oct 3;31(20):3262-8. Epub 2015 Jun 3.

Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St.Petersburg State University, 199004, Department of Computer Science and Engineering, University of California, San Diego, CA 92093-0404, USA.

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http://bioinformatics.oxfordjournals.org/content/early/2015/
Web Search
http://bioinformatics.oxfordjournals.org/content/early/2015/
Web Search
http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btv337DOI Listing
October 2015

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

J Proteome Res 2015 Sep 21;14(9):3555-67. Epub 2015 Jul 21.

Department of Biomedical Informatics, Vanderbilt University , Nashville, Tennessee 37203, United States.

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http://dx.doi.org/10.1021/acs.jproteome.5b00264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868822PMC
September 2015

dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.

J Comput Biol 2015 Jun 3;22(6):528-45. Epub 2015 Mar 3.

1Algorithmic Biology Laboratory, St. Petersburg Academic University, Russian Academy of Sciences, St. Petersburg, Russia.

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http://dx.doi.org/10.1089/cmb.2014.0153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4449708PMC
June 2015

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

Bioinformatics 2015 Jun;31(12):i53-61

Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542777PMC
June 2015

Proteogenomics.

Proteomics 2014 Dec;14(23-24):2631-2

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http://dx.doi.org/10.1002/pmic.201470173DOI Listing
December 2014

Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways.

PLoS One 2014 27;9(1):e85140. Epub 2014 Jan 27.

Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America ; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0085140PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3903477PMC
November 2014

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

Nat Commun 2014 Oct 31;5:5277. Epub 2014 Oct 31.

Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/ncomms6277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5036525PMC
October 2014

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

J Nat Prod 2014 Aug 12;77(8):1902-9. Epub 2014 Aug 12.

†Department of Electrical and Computer Engineering, ‡Department of Chemistry and Biochemistry, §Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, ⊥Skaggs School of Pharmacy and Pharmaceutical Sciences, and ∥Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, United States.

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http://dx.doi.org/10.1021/np500370cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4143176PMC
August 2014

Automated genome mining of ribosomal peptide natural products.

ACS Chem Biol 2014 Jul 23;9(7):1545-51. Epub 2014 May 23.

Department of Electrical and Computer Engineering, University of California San Diego , La Jolla, California 92093, United States.

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http://dx.doi.org/10.1021/cb500199hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4215869PMC
July 2014

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

J Proteome Res 2014 Jul 18;13(7):3241-8. Epub 2014 Jun 18.

Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis , 535 West Michigan Street, IT 475, Indianapolis, Indiana 46202, United States.

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http://dx.doi.org/10.1021/pr401300mDOI Listing
July 2014

ExSPAnder: a universal repeat resolver for DNA fragment assembly.

Bioinformatics 2014 Jun;30(12):i293-301

Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USAAlgorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu266DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058921PMC
June 2014

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

Proteomics 2014 May 13;14(10):1211-22. Epub 2014 Apr 13.

Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratories, Richland, WA, USA.

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http://doi.wiley.com/10.1002/pmic.201300378
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http://dx.doi.org/10.1002/pmic.201300378DOI Listing
May 2014

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

J Proteome Res 2013 Dec 15;12(12):5830-8. Epub 2013 Nov 15.

Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis , Indianapolis, IN 46202, United States.

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http://dx.doi.org/10.1021/pr400849yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905687PMC
December 2013

UniNovo: a universal tool for de novo peptide sequencing.

Bioinformatics 2013 Aug 12;29(16):1953-62. Epub 2013 Jun 12.

Department of Electrical and Computer Engineering and Department of Computer Science and Engineering, University of California-San Diego, CA 92093, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt338DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3722526PMC
August 2013

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

Algorithms Mol Biol 2013 Jul 11;8(1):19. Epub 2013 Jul 11.

Algorithmic Biology Laboratory, Saint Petersburg Academic University, Saint Petersburg, Russia.

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http://dx.doi.org/10.1186/1748-7188-8-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738870PMC
July 2013

A new approach to evaluating statistical significance of spectral identifications.

J Proteome Res 2013 Apr 8;12(4):1560-8. Epub 2013 Mar 8.

Department of Electrical and Computer Engineering and ‡Department of Computer Science and Engineering, University of California-San Diego , San Diego, California 92093.

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http://dx.doi.org/10.1021/pr300453tDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5590104PMC
April 2013

How many signal peptides are there in bacteria?

Environ Microbiol 2013 Apr;15(4):983-90

Technische Universität München, Department of Genome-Oriented Bioinformatics, 85354, Freising, Germany.

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http://dx.doi.org/10.1111/1462-2920.12105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3621014PMC
April 2013

N-terminal protein processing: a comparative proteogenomic analysis.

Mol Cell Proteomics 2013 Jan 23;12(1):14-28. Epub 2012 Sep 23.

Bioinformatics Program, University of California San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1074/mcp.M112.019075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3536895PMC
January 2013

Unexpected diversity of signal peptides in prokaryotes.

MBio 2012 Nov 20;3(6). Epub 2012 Nov 20.

Division of Biological Sciences, Pacific Northwest National Laboratory, Richland, Washington, USA.

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http://dx.doi.org/10.1128/mBio.00339-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509430PMC
November 2012

Protein identification using top-down.

Mol Cell Proteomics 2012 Jun 25;11(6):M111.008524. Epub 2011 Oct 25.

Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, San Diego, California 92093, USA.

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http://dx.doi.org/10.1074/mcp.M111.008524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3433905PMC
June 2012

SEQuel: improving the accuracy of genome assemblies.

Bioinformatics 2012 Jun;28(12):i188-96

Bioinformatics Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371851PMC
June 2012

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

J Comput Biol 2011 Nov 14;18(11):1625-34. Epub 2011 Oct 14.

Department of Computer Science and Engineering, University of California, San Diego, California, USA.

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http://dx.doi.org/10.1089/cmb.2011.0151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216098PMC
November 2011

Multiplex de novo sequencing of peptide antibiotics.

J Comput Biol 2011 Nov 28;18(11):1371-81. Epub 2011 Oct 28.

Department of Electrical and Computer Engineering, University of California San Diego, San Diego, California 92092, USA.

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http://dx.doi.org/10.1089/cmb.2011.0158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216106PMC
November 2011

How to apply de Bruijn graphs to genome assembly.

Nat Biotechnol 2011 Nov 8;29(11):987-91. Epub 2011 Nov 8.

Department of Mathematics, University of California San Diego, La Jolla, California, USA.

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http://www.nature.com/articles/nbt.2023
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http://dx.doi.org/10.1038/nbt.2023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5531759PMC
November 2011

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

J Proteome Res 2011 Oct 7;10(10):4505-12. Epub 2011 Sep 7.

Department of Electrical and Computer Engineering, University of California, San Diego, California, United States.

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http://dx.doi.org/10.1021/pr200323aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242011PMC
October 2011

Sequencing cyclic peptides by multistage mass spectrometry.

Proteomics 2011 Sep 9;11(18):3642-50. Epub 2011 Aug 9.

Department of Electrical and Computer Engineering, UC San Diego, CA, USA.

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http://dx.doi.org/10.1002/pmic.201000697DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398611PMC
September 2011

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

J Comput Biol 2011 Jul 12;18(7):865. Epub 2011 May 12.

Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093-0404, USA.

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http://dx.doi.org/10.1089/cmb.2011.007pDOI Listing
July 2011

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

Bioinformatics 2011 Jul;27(13):i137-41

Department of Computer Science and Engineering, University of California, San Diego, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117386PMC
July 2011

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

J Am Soc Mass Spectrom 2011 Jul 5;22(7):1111-20. Epub 2011 May 5.

Bioinformatics Program, University of California San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1007/s13361-011-0139-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3220955PMC
July 2011

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

Genome Biol 2010 30;11(11):R117. Epub 2010 Nov 30.

Department of Computer Science & Engineering, University of South Carolina, 301 Main St, Columbia, SC 29208, USA.

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http://dx.doi.org/10.1186/gb-2010-11-11-r117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156956PMC
June 2011

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

Mol Cell Proteomics 2011 Jun 28;10(6):M110.002220. Epub 2011 Mar 28.

Department of Electrical and Computer Engineering, University of California, San Diego, CA, USA.

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http://dx.doi.org/10.1074/mcp.M110.002220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3108828PMC
June 2011

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

J Nat Prod 2011 May 13;74(5):928-36. Epub 2011 Apr 13.

Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States.

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http://pubs.acs.org/doi/abs/10.1021/np200077f
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3103610PMC
May 2011

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

Nat Methods 2011 May 15;8(7):587-91. Epub 2011 May 15.

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1038/nmeth.1609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3128193PMC
May 2011

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

PLoS One 2011 Apr 12;6(4):e18565. Epub 2011 Apr 12.

Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3075265PMC
April 2011

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

Mol Cell Proteomics 2010 Dec 9;9(12):2840-52. Epub 2010 Sep 9.

Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1074/mcp.M110.003731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3101864PMC
December 2010

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

Mol Cell Proteomics 2010 Dec 20;9(12):2772-82. Epub 2010 Sep 20.

Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA.

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M110.002766
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3101958PMC
December 2010

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

J Proteome Res 2010 Oct;9(10):5065-75

Bioinformatics Graduate Program, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1021/pr100358bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000314PMC
October 2010

DRIMM-Synteny: decomposing genomes into evolutionary conserved segments.

Bioinformatics 2010 Oct 24;26(20):2509-16. Epub 2010 Aug 24.

Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.

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October 2010

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

Proteomics 2010 Aug;10(15):2833-44

Bioinformatics Program, University of California San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1002/pmic.200900821DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3220954PMC
August 2010

Synergistic allelochemicals from a freshwater cyanobacterium.

Proc Natl Acad Sci U S A 2010 Jun 7;107(25):11183-8. Epub 2010 Jun 7.

CIIMAR/CIMAR-LA, Center for Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.

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http://dx.doi.org/10.1073/pnas.0914343107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2895120PMC
June 2010

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

J Proteome Res 2009 Sep;8(9):4173-81

Bioinformatics Program and Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1021/pr9004794DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398614PMC
September 2009

Dereplication and de novo sequencing of nonribosomal peptides.

Nat Methods 2009 Aug 13;6(8):596-9. Epub 2009 Jul 13.

Bioinformatics Program, University of California San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1038/nmeth.1350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754211PMC
August 2009

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

Science 2009 Jul;325(5940):541-2

Department of Computer Science, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1173876
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July 2009

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

Mol Cell Proteomics 2009 Jun 2;8(6):1391-400. Epub 2009 Mar 2.

Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1074/mcp.M800535-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690493PMC
June 2009

Breakpoint graphs and ancestral genome reconstructions.

Genome Res 2009 May 13;19(5):943-57. Epub 2009 Feb 13.

Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093-0404, USA.

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http://dx.doi.org/10.1101/gr.082784.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675983PMC
May 2009

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

Genome Res 2009 Feb 3;19(2):336-46. Epub 2008 Dec 3.

Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.079053.108
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652199PMC
February 2009

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

Mol Cell Proteomics 2009 Jan 14;8(1):53-69. Epub 2008 Aug 14.

Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1074/mcp.M800103-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2621003PMC
January 2009

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

J Proteome Res 2008 Aug 3;7(8):3354-63. Epub 2008 Jul 3.

Department of Computer Science and Engineering, University of California San Diego, La Jolla CA 92093, USA.

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http://pubs.acs.org/doi/abs/10.1021/pr8001244
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689316PMC
August 2008

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

Science 2008 Aug;321(5892):1040; author reply 1040

Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, Mail Code 0404, La Jolla, CA 92093-0404, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1155006
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August 2008

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

Bioinformatics 2008 Jul;24(13):i416-23

Department of Computer Science and Engineering, University of California, San Diego, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718660PMC
http://dx.doi.org/10.1093/bioinformatics/btn184DOI Listing
July 2008

Interpreting top-down mass spectra using spectral alignment.

Anal Chem 2008 Apr 27;80(7):2499-505. Epub 2008 Feb 27.

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093-0404, USA.

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http://dx.doi.org/10.1021/ac702324uDOI Listing
April 2008

Short read fragment assembly of bacterial genomes.

Genome Res 2008 Feb 14;18(2):324-30. Epub 2007 Dec 14.

Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1101/gr.7088808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2203630PMC
February 2008

Does trypsin cut before proline?

J Proteome Res 2008 Jan 8;7(1):300-5. Epub 2007 Dec 8.

Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1021/pr0705035DOI Listing
January 2008

Algorithm for identification of fusion proteins via mass spectrometry.

J Proteome Res 2008 Jan;7(1):89-95

Bioinformatics Program, University of California, San Diego, La Jolla, California 92093-0419, USA.

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http://dx.doi.org/10.1021/pr070214gDOI Listing
January 2008