Pavel Pevzner

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Comparative genomics reveals birth and death of fragile regions in mammalian evolution
    Max A Alekseyev
    Department of Computer Science and Engineering, University of South Carolina, 301 Main St, Columbia, SC 29208, USA
    Genome Biol 11:R117. 2010
  2. pmc Identifying repeat domains in large genomes
    Degui Zhi
    Bioinformatics Program, University of California, San Diego, CA 92093 0419, USA
    Genome Biol 7:R7. 2006
  3. doi request reprint Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"
    Pavel A Pevzner
    Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, Mail Code 0404, La Jolla, CA 92093 0404, USA
    Science 321:1040; author reply 1040. 2008
  4. pmc Genome rearrangements in mammalian evolution: lessons from human and mouse genomes
    Pavel Pevzner
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093 0114, USA
    Genome Res 13:37-45. 2003
  5. pmc Neuropeptidomic components generated by proteomic functions in secretory vesicles for cell-cell communication
    Vivian Hook
    University of California, San Diego, La Jolla, 92093 0744, USA
    AAPS J 12:635-45. 2010
  6. pmc Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers
    Paul Medvedev
    Department of Computer Science and Engineering, University of California, San Diego, California, USA
    J Comput Biol 18:1625-34. 2011
  7. ncbi request reprint Correcting base-assignment errors in repeat regions of shotgun assembly
    Degui Zhi
    Bioinformatics Program, University of California, San Diego, La Jolla 92093, USA
    IEEE/ACM Trans Comput Biol Bioinform 4:54-64. 2007
  8. ncbi request reprint De novo identification of repeat families in large genomes
    Alkes L Price
    Department of Computer Science and Engineering, University of California San Diego La Jolla, CA 92093 0114, USA
    Bioinformatics 21:i351-8. 2005
  9. ncbi request reprint Peptide sequence tags for fast database search in mass-spectrometry
    Ari Frank
    Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0114, USA
    J Proteome Res 4:1287-95. 2005
  10. pmc Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases
    Sangtae Kim
    Department of Computer Science and Engineering, University of California San Diego, La Jolla CA 92093, USA
    J Proteome Res 7:3354-63. 2008

Research Grants

  1. Algorithms & Software for Computational Mass Spectrometry
    Pavel Pevzner; Fiscal Year: 2007
  2. Computer Mass-Spectrometry
    Pavel Pevzner; Fiscal Year: 2004
  3. A New Approach to Fragment Assembly in DNA Sequencing
    Pavel Pevzner; Fiscal Year: 2003

Detail Information

Publications67

  1. pmc Comparative genomics reveals birth and death of fragile regions in mammalian evolution
    Max A Alekseyev
    Department of Computer Science and Engineering, University of South Carolina, 301 Main St, Columbia, SC 29208, USA
    Genome Biol 11:R117. 2010
    ..Although nearly all recent studies supported the existence of fragile regions in mammalian genomes, the most comprehensive phylogenomic study of mammals raised some doubts about their existence...
  2. pmc Identifying repeat domains in large genomes
    Degui Zhi
    Bioinformatics Program, University of California, San Diego, CA 92093 0419, USA
    Genome Biol 7:R7. 2006
    ..Our method recovers documented mosaic repeat structures and suggests additional putative ones. Our method is useful for elucidating the evolutionary history of repeats and annotating de novo generated repeat libraries...
  3. doi request reprint Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"
    Pavel A Pevzner
    Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, Mail Code 0404, La Jolla, CA 92093 0404, USA
    Science 321:1040; author reply 1040. 2008
    ..We argue that the reported T. rex peptides may represent statistical artifacts and call for complete data release to enable experimental and computational verification of their findings...
  4. pmc Genome rearrangements in mammalian evolution: lessons from human and mouse genomes
    Pavel Pevzner
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093 0114, USA
    Genome Res 13:37-45. 2003
    ..Because these graphs provide important insights into rearrangement scenarios, we introduce a new visualization tool that allows one to view breakpoint graphs superimposed with genomic dot-plots...
  5. pmc Neuropeptidomic components generated by proteomic functions in secretory vesicles for cell-cell communication
    Vivian Hook
    University of California, San Diego, La Jolla, 92093 0744, USA
    AAPS J 12:635-45. 2010
    ..Knowledge of the entire repertoire of neuropeptides that regulate physiological systems will provide novel insight into regulatory mechanisms in health, disease, and therapeutics...
  6. pmc Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers
    Paul Medvedev
    Department of Computer Science and Engineering, University of California, San Diego, California, USA
    J Comput Biol 18:1625-34. 2011
    ..Through assembly results on simulated perfect data, we argue that this can effectively improve the contig sizes in assembly...
  7. ncbi request reprint Correcting base-assignment errors in repeat regions of shotgun assembly
    Degui Zhi
    Bioinformatics Program, University of California, San Diego, La Jolla 92093, USA
    IEEE/ACM Trans Comput Biol Bioinform 4:54-64. 2007
    ..We demonstrate that EULER-AIR is a software tool that can be used to find and correct base-assignment errors in a genome assembly project...
  8. ncbi request reprint De novo identification of repeat families in large genomes
    Alkes L Price
    Department of Computer Science and Engineering, University of California San Diego La Jolla, CA 92093 0114, USA
    Bioinformatics 21:i351-8. 2005
    ..We develop a new method for de novo identification of repeat families via extension of consensus seeds; our method enables a rigorous definition of repeat boundaries, a key issue in repeat analysis...
  9. ncbi request reprint Peptide sequence tags for fast database search in mass-spectrometry
    Ari Frank
    Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0114, USA
    J Proteome Res 4:1287-95. 2005
    ..Our tag generating algorithm along with our de novo sequencing algorithm PepNovo can be accessed via the URL http://peptide.ucsd.edu/...
  10. pmc Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases
    Sangtae Kim
    Department of Computer Science and Engineering, University of California San Diego, La Jolla CA 92093, USA
    J Proteome Res 7:3354-63. 2008
    ..We therefore argue that the generating function approach has the potential to increase the number of peptide identifications in MS/MS searches...
  11. ncbi request reprint Comparative genomics reveals unusually long motifs in mammalian genomes
    Neil C Jones
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
    Bioinformatics 22:e236-42. 2006
    ....
  12. pmc De novo repeat classification and fragment assembly
    Pavel A Pevzner
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
    Genome Res 14:1786-96. 2004
    ..Our key algorithmic idea also leads to new approaches to multiple alignment and fragment assembly. In particular, we show that our FragmentGluer assembler improves on Phrap and ARACHNE in assembly of BACs and bacterial genomes...
  13. pmc Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra
    Sangtae Kim
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
    Mol Cell Proteomics 8:53-69. 2009
    ..We show that such searches allow one to correct sequencing errors and find programmed frameshifts...
  14. ncbi request reprint Identification of post-translational modifications by blind search of mass spectra
    Dekel Tsur
    Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0404, USA
    Nat Biotechnol 23:1562-7. 2005
    ..We also argue that MS-Alignment reveals some uncharacterized modifications that warrant further experimental validation...
  15. pmc Breakpoint graphs and ancestral genome reconstructions
    Max A Alekseyev
    Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093 0404, USA
    Genome Res 19:943-57. 2009
    ..MGRA also generates the rearrangement-based characters guiding the phylogenetic tree reconstruction when the phylogeny is unknown...
  16. pmc SEQuel: improving the accuracy of genome assemblies
    Roy Ronen
    Bioinformatics Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
    Bioinformatics 28:i188-96. 2012
    ..Fundamental to the algorithm behind SEQuel is the positional de Bruijn graph, a graph structure that models k-mers within reads while incorporating the approximate positions of reads into the model...
  17. pmc Representing and comparing protein structures as paths in three-dimensional space
    Degui Zhi
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 3102, USA
    BMC Bioinformatics 7:460. 2006
    ..Most existing formulations of protein structure comparison are based on detailed atomic level descriptions of protein structures and bypass potential insights that arise from a higher-level abstraction...
  18. ncbi request reprint Shotgun protein sequencing by tandem mass spectra assembly
    Nuno Bandeira
    Computer Science and Engineering Department, University of California, San Diego, Department 0114, 9500 Gilman Drive, La Jolla, California 92093 0114, USA
    Anal Chem 76:7221-33. 2004
    ..We show that this approach not only extends the length of reconstructed amino acid sequences but also dramatically improves the quality of de novo peptide sequencing, even for low mass accuracy MS/MS data...
  19. pmc A novel method for multiple alignment of sequences with repeated and shuffled elements
    Benjamin Raphael
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093 0114, USA
    Genome Res 14:2336-46. 2004
    ..In addition, ABA is useful in the alignment of genomic sequences that contain duplications and inversions. We provide several examples illustrating the applications of ABA...
  20. doi request reprint Interpreting top-down mass spectra using spectral alignment
    Ari M Frank
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093 0404, USA
    Anal Chem 80:2499-505. 2008
    ....
  21. doi request reprint DRIMM-Synteny: decomposing genomes into evolutionary conserved segments
    Son K Pham
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
    Bioinformatics 26:2509-16. 2010
    ..However, the number of genes shared among all genomes quickly decreases with the increase in the number of genomes...
  22. ncbi request reprint Reconstructing tumor genome architectures
    Benjamin J Raphael
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093 0114, USA
    Bioinformatics 19:ii162-71. 2003
    ..Our results assist in the ongoing ESP analysis of MCF7 tumors by suggesting additional ESP experiments for the completion of a reliable reconstruction of the MCF7 tumor genome, and by focusing BAC re-sequencing efforts...
  23. ncbi request reprint Colored de Bruijn graphs and the genome halving problem
    Max A Alekseyev
    Department of Computer Science and Engineering, University of California at San Diego, La Jolla 92093 0114, USA
    IEEE/ACM Trans Comput Biol Bioinform 4:98-107. 2007
    ..The generalized breakpoint graphs make the El-Mabrouk-Sankoff result more transparent and promise to be useful in future studies of genome rearrangements...
  24. pmc False discovery rates of protein identifications: a strike against the two-peptide rule
    Nitin Gupta
    Bioinformatics Program and Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
    J Proteome Res 8:4173-81. 2009
    ..We further extend the generating function approach (originally proposed for evaluating matches between a peptide and a single spectrum) to evaluating matches between a protein and an entire spectral data set...
  25. pmc Protein identification by spectral networks analysis
    Nuno Bandeira
    Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 104:6140-5. 2007
    ..In addition to speed, our approach provides a unique paradigm for identifying posttranslational modifications by means of spectral networks analysis...
  26. pmc De novo fragment assembly with short mate-paired reads: Does the read length matter?
    Mark J Chaisson
    Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA
    Genome Res 19:336-46. 2009
    ....
  27. pmc Multi-spectra peptide sequencing and its applications to multistage mass spectrometry
    Nuno Bandeira
    Department of Computer Science and Engineering, University of California, San Diego, USA
    Bioinformatics 24:i416-23. 2008
    ..We describe a de novo peptide sequencing algorithm aimed at this experimental protocol and show that it improves the sequencing accuracy on both tandem and multistage mass spectrometry...
  28. ncbi request reprint Unrestrictive identification of post-translational modifications through peptide mass spectrometry
    Stephen Tanner
    Bioinformatics Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
    Nat Protoc 1:67-72. 2006
    ..This protocol requires you to type out several commands, so you may wish to enlist the help of a colleague familiar with the computer's command-line interface. A typical MS run of up to 25,000 scans can be searched and analyzed in 3 h...
  29. ncbi request reprint Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins
    Nuno Bandeira
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
    Mol Cell Proteomics 6:1123-34. 2007
    ....
  30. pmc Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes
    Nitin Gupta
    Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA
    Genome Res 18:1133-42. 2008
    ..We therefore argue that complementing DNA sequencing projects by comparative proteogenomics projects can be a viable approach to improve both genomic and proteomic annotations...
  31. pmc Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation
    Nitin Gupta
    Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA
    Genome Res 17:1362-77. 2007
    ..This study demonstrates that complementing every genome sequencing project by an MS/MS project would significantly improve both genome and proteome annotations for a reasonable cost...
  32. pmc Clustering millions of tandem mass spectra
    Ari M Frank
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093 0404, USA
    J Proteome Res 7:113-22. 2008
    ..Our open source software MS-Clustering is available for download at http://peptide.ucsd.edu or can be run online at http://proteomics.bioprojects.org/MassSpec...
  33. doi request reprint Algorithm for identification of fusion proteins via mass spectrometry
    Julio Ng
    Bioinformatics Program, University of California, San Diego, La Jolla, California 92093 0419, USA
    J Proteome Res 7:89-95. 2008
    ..We further illustrate how this approach can be modified for human exons prediction...
  34. pmc Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass spectrometry
    Nitin Gupta
    Bioinformatics Program, University of California San Diego, La Jolla, CA 92093, USA
    Proteomics 10:2833-44. 2010
    ..Finally, we show that comparative analysis of multiple proteases can be used to detect putative in vivo proteolytic sites on a proteome-wide scale...
  35. pmc De novo peptide sequencing and identification with precision mass spectrometry
    Ari M Frank
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093 0404, USA
    J Proteome Res 6:114-23. 2007
    ..Our de novo sequencing software is available for download at http://peptide.ucsd.edu/...
  36. ncbi request reprint Splicing graphs and EST assembly problem
    Steffen Heber
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, 92093 0114, USA
    Bioinformatics 18:S181-8. 2002
    ..A better approach would be to represent all splicing variants for a given gene in a way that captures the relationships between different splicing variants...
  37. ncbi request reprint Finding subtle motifs by branching from sample strings
    Alkes Price
    Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093 0114, USA
    Bioinformatics 19:ii149-55. 2003
    ..Our PatternBranching and ProfileBranching algorithms achieve favorable results relative to other motif finding algorithms. Availability: http://www-cse.ucsd.edu/groups/bioinformatics/software.html..
  38. pmc Whole-genome analysis of Alu repeat elements reveals complex evolutionary history
    Alkes L Price
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093 0114, USA
    Genome Res 14:2245-52. 2004
    ..We apply a novel method to identify and statistically validate 213 Alu subfamilies. We build an evolutionary tree of these subfamilies and conclude that the history of Alu evolution is more complex than previous studies had indicated...
  39. ncbi request reprint Reconstructing tumor amplisomes
    Benjamin J Raphael
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093 0114, USA
    Bioinformatics 20:i265-73. 2004
    ....
  40. pmc Are there rearrangement hotspots in the human genome?
    Max A Alekseyev
    Department of Computer Science and Engineering, University of California San Diego, San Diego, California, United States of America
    PLoS Comput Biol 3:e209. 2007
    ..In particular, we demonstrate that (1) even if transpositions were a dominant force in mammalian evolution, the arguments in favor of FBM still stand, and (2) the "gene deletion" argument against FBM is flawed...
  41. ncbi request reprint InsPecT: identification of posttranslationally modified peptides from tandem mass spectra
    Stephen Tanner
    Department of Bioengineering and Computer Science Department, APM 3832, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093 0114, USA
    Anal Chem 77:4626-39. 2005
    ..The tool was used to identify a number of novel modifications in different data sets, including many phosphopeptides in data provided by Alliance for Cellular Signaling that were missed by other tools...
  42. pmc Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution
    Pavel Pevzner
    Department of Computer Science and Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0114, USA
    Proc Natl Acad Sci U S A 100:7672-7. 2003
    ..Our results suggest a model of chromosome evolution that postulates that mammalian genomes are mosaics of fragile regions with high propensity for rearrangements and solid regions with low propensity for rearrangements...
  43. pmc Dereplication and de novo sequencing of nonribosomal peptides
    Julio Ng
    Bioinformatics Program, University of California San Diego, La Jolla, California, USA
    Nat Methods 6:596-9. 2009
    ..We also developed an algorithm for comparative NRP dereplication that establishes similarities between newly isolated and previously identified similar but nonidentical NRPs, substantially reducing dereplication efforts...
  44. pmc Short read fragment assembly of bacterial genomes
    Mark J Chaisson
    Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA
    Genome Res 18:324-30. 2008
    ....
  45. ncbi request reprint PepNovo: de novo peptide sequencing via probabilistic network modeling
    Ari Frank
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093 0114, USA
    Anal Chem 77:964-73. 2005
    ..PepNovo can be accessed via the URL http://www-cse.ucsd.edu/groups/bioinformatics/software.html...
  46. ncbi request reprint Corepressor-dependent silencing of chromosomal regions encoding neuronal genes
    Victoria V Lunyak
    Howard Hughes Medical Institute HHMI, Department of Computer Science and Engineering, School of Medicine, University of California, San Diego, 9500 Gilman Drive, Room 345, La Jolla, CA 92093 0648, USA
    Science 298:1747-52. 2002
    ....
  47. pmc The fragile breakage versus random breakage models of chromosome evolution
    Qian Peng
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
    PLoS Comput Biol 2:e14. 2006
    ..Finally, we study the link between rearrangements and regulatory regions and argue that long regulatory regions and inhomogeneity of gene distribution in mammalian genomes may be responsible for the breakpoint reuse phenomenon...
  48. pmc Mass spectrometry-based neuropeptidomics of secretory vesicles from human adrenal medullary pheochromocytoma reveals novel peptide products of prohormone processing
    Nitin Gupta
    Bioinformatics Graduate Program, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
    J Proteome Res 9:5065-75. 2010
    ..The global peptidomic approach of this study demonstrates the complexity of diverse neuropeptides present in human secretory vesicles for cell-cell communication...
  49. pmc Error correction of high-throughput sequencing datasets with non-uniform coverage
    Paul Medvedev
    Department of Computer Science and Engineering, University of California, San Diego, CA, USA
    Bioinformatics 27:i137-41. 2011
    ....
  50. ncbi request reprint Fragment assembly with short reads
    Mark Chaisson
    Bioinformatics Program, University of California San Diego, La Jolla, CA 92093, USA
    Bioinformatics 20:2067-74. 2004
    ..Modern assembly programs and error correction routines have been tuned to work well with current read technology but were not designed for assembly of short reads...
  51. ncbi request reprint Scalable heuristics for design of DNA probe arrays
    Andrew B Kahng
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
    J Comput Biol 11:429-47. 2004
    ..Finally, we give lower bounds that offer insights into the amount of available further improvements...
  52. ncbi request reprint Does trypsin cut before proline?
    Jesse Rodriguez
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
    J Proteome Res 7:300-5. 2008
    ..Our approach can be applied to analyze any protease, and we further argue that specificity rules for other enzymes should also be re-evaluated based on statistical evidence derived from large MS/MS data sets...
  53. pmc Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides
    Wei Ting Liu
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 0636, USA
    Anal Chem 81:4200-9. 2009
    ....
  54. pmc Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification
    Sangtae Kim
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
    Mol Cell Proteomics 8:1391-400. 2009
    ..In addition, spectral profiles also enable intuitive visualization of all high scoring de novo reconstructions of tandem mass spectra...
  55. pmc Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis
    Wei Ting Liu
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 107:16286-90. 2010
    ....
  56. ncbi request reprint Finding composite regulatory patterns in DNA sequences
    Eleazar Eskin
    Department of Computer Science, Columbia University, New York, 10027 NY, USA
    Bioinformatics 18:S354-63. 2002
    ..We demonstrate that MITRA performs well for both monad and composite patterns by presenting experiments over biological and synthetic data...
  57. pmc The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction
    Guillaume Bourque
    Information and Mathematical Sciences, Genome Institute of Singapore, 138672 Singapore
    Genome Res 16:311-3. 2006
  58. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  59. ncbi request reprint Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution
    Zhaoshi Jiang
    Department of Genome Sciences, University of Washington School of Medicine and the Howard Hughes Medical Institute, 1705 NE Pacific Street, Seattle, Washington 98195, USA
    Nat Genet 39:1361-8. 2007
    ....
  60. ncbi request reprint Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps
    William J Murphy
    Department of Veterinary Integrative Biosciences, Texas A and M University, College Station, TX 77843, USA
    Science 309:613-7. 2005
    ..We found that segmental duplications populate the majority of primate-specific breakpoints and often flank inverted chromosome segments, implicating their role in chromosomal rearrangement...
  61. pmc Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
    Guillaume Bourque
    Genome Institute of Singapore, Singapore 138672, Republic of Singapore
    Genome Res 15:98-110. 2005
    ....
  62. ncbi request reprint Mammalian phylogenomics comes of age
    William J Murphy
    Basic Research Laboratory, SAIC Frederick, Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA
    Trends Genet 20:631-9. 2004
    ....
  63. pmc Genome-scale evolution: reconstructing gene orders in the ancestral species
    Guillaume Bourque
    Department of Mathematics, University of Southern California, California 90089, USA
    Genome Res 12:26-36. 2002
    ..In particular, our analysis suggests a new improved rearrangement scenario for a very difficult Campanulaceae cpDNA dataset and a putative rearrangement scenario for human, mouse and cat genomes...
  64. pmc Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes
    Guillaume Bourque
    Centre de Recherches Mathématiques, Universite de Montreal, Canada H3C 3J7
    Genome Res 14:507-16. 2004
    ..Our analysis implies that the rate of rearrangements is much higher in murid rodents than in the human lineage and confirms the existence of rearrangement hot-spots in all three lineages...
  65. ncbi request reprint Combinatorial algorithms for design of DNA arrays
    Sridhar Hannenhalli
    Department of Mathematics, University of Southern California, Los Angeles 90089 1113, USA
    Adv Biochem Eng Biotechnol 77:1-19. 2002
    ..We also address the difficult problem of finding an arrangement which minimizes the border length and come up with a new idea of threading that significantly reduces the border length as compared to standard designs...
  66. ncbi request reprint Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians
    Pavel A Pevzner
    Bioinformatics 20:2159-61. 2004

Research Grants10

  1. Algorithms & Software for Computational Mass Spectrometry
    Pavel Pevzner; Fiscal Year: 2007
    ..However, computational analysis of mass spectromtery data remains a significant bottleneck. This proposed research addresses computational challenges in the analysis of mass spectromtery data. ..
  2. Computer Mass-Spectrometry
    Pavel Pevzner; Fiscal Year: 2004
    ..We also propose to implement MS-ALIGNMENT, MS-SEQUENCING, and MS-GENESEARCH software tools as a web server available for mass-spectrometry researchers. ..
  3. A New Approach to Fragment Assembly in DNA Sequencing
    Pavel Pevzner; Fiscal Year: 2003
    ..This reduction allows one to generate provably optimal error-free fragment assemblies. The main goal of this proposal is to scale up EULER for assembly of eukaryotic genomes. ..