Publications

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Glenn Tesler.
Multi de Bruijn sequences,
Journal of Combinatorics, 8 no. 3 (2017), 439-474.
Journal, Software
Roy Ronen, Glenn Tesler, Ali Akbari, Shay Zakov, Noah A. Rosenberg, and Vineet Bafna.
Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele,
PLoS Genetics, 11 no. 9 (2015), e1005527 (electronic, 27 pages).
Journal, PreCIOSS software
Roy Ronen, Glenn Tesler, Ali Akbari, Shay Zakov, Noah A. Rosenberg, and Vineet Bafna.
Haplotype Allele Frequency (HAF) Score: Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Adaptive Allele,
in Teresa M. Przytycka (Ed.), Proceedings of RECOMB 2015, Lecture Notes in Computer Science, Vol. 9029, pp. 276-280. Springer, Cham, 2015.
Abstract, PreCIOSS software
Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey A. Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey D. Prjibelski, Alexey Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Scott R. Clingenpeel, Tanja Woyke, Jeffrey S. Mclean, Roger Lasken, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner.
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products,
Journal of Computational Biology, 20 no 10 (Oct. 2013): 714-737.
Journal
Jeffrey S. McLean, Mary-Jane Lombardo, Jonathan H. Badger, Anna Edlund, Mark Novotny, Joyclyn Yee-Greenbaum, Nikolay Vyahhi, Adam P. Hall, Youngik Yang, Christopher L. Dupont, Michael G. Ziegler, Hamidreza Chitsaz, Andrew E. Allen, Shibu Yooseph, Glenn Tesler, Pavel A. Pevzner, Robert M. Friedman, Kenneth H. Nealson, J. Craig Venter, and Roger S. Lasken,
Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum,
Proceedings of the National Academy of Sciences U.S.A., 110 no. 26 (2013), E2390-E2399. Published online ahead of print June 10, 2013.
Journal
Jeffrey S. McLean, Mary-Jane Lombardo, Michael G. Ziegler, Mark Novotny, Joyclyn Yee-Greenbaum, Jonathan H. Badger, Glenn Tesler, Sergey Nurk, Valery Lesin, Daniel Brami, Adam P. Hall, Anna Edlund, Lisa Z. Allen, Scott Durkin, Sharon Reed, Francesca Torriani, Kenneth H. Nealson, Pavel A. Pevzner, Robert Friedman, J. Craig Venter, and Roger S. Lasken,
Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform,
Genome Research, 23 no. 5 (2013) 867-877. Published online ahead of print April 5, 2013.
Journal
Related material: JCVI press release, San Diego Union-Tribune (April 9, 2013)
Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey Prjibelsky, Alexey Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey McLean, Roger Lasken, Scott R. Clingenpeel, Tanja Woyke, Glenn Tesler, Max A. Alekseyev, Pavel A. Pevzner,
Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads,
in Proceedings of RECOMB 2013, Lecture Notes in Computer Science, Vol. 7821, pp. 158-170 (2013).
Abstract
Paul Loriaux, Glenn Tesler, Alexander Hoffman,
Characterizing the Relationship between Steady State and Response Using Analytical Expressions for the Steady States of Mass Action Models,
PLoS Computational Biology 9 no. 2 (2013), e1002901 (electronic, 19 pages). Published online February 28, 2013.
JournalPysub software
Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler,
QUAST: quality assessment tool for genome assemblies,
Bioinformatics, 29 no. 8 (2013), 1072-1075.
JournalQUAST software
Mark Chaisson and Glenn Tesler,
Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR): Theory and Application,
BMC Bioinformatics (2012), 13:238.
JournalBLASR software
Son K. Pham, Dmitry Anitpov, Alexander Sirotkin, Glenn Tesler, Pavel A. Pevzner, and Max A. Alekseyev,
Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly,
Journal of Computational Biology, 20 no. 4 (2013), 359-371. Online ahead of print July 17, 2012.
Journal
Son K. Pham, Dmitry Anitpov, Alexander Sirotkin, Glenn Tesler, Pavel A. Pevzner, and Max A. Alekseyev,
Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly,
in Benny Chor (Ed.), Proceedings of RECOMB 2012, Lecture Notes in Bioinformatics, Vol. 7262, pp. 200-212. Springer, Heidelberg, 2012.
Abstract
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey Gurevich, Mikhail Dvorkin, Alexander Kulikov, Valery Lesin, Sergey Nikolenko, Son Pham, Andrey Prjibelski, Alexey Pyshkin, Alexander Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max Alekseyev and Pavel Pevzner.
SPAdes: a New Genome Assembly Algorithm and its Applications to Single-Cell Sequencing,
Journal of Computational Biology, 19 no. 5 (2012), 455-477.
AbstractSPAdes software
Phillip E.C. Compeau, Pavel A. Pevzner, and Glenn Tesler,
How to apply de Bruijn graphs to genome assembly,
Nature Biotechnology, 29 no. 11 (2011), 987-991.
Abstract
Paul Medvedev, Son Pham, Mark Chaisson, Glenn Tesler, Pavel Pevzner,
Paired de Bruijn Graphs: a Novel Approach for Incorporating Mate Pair Information into Genome Assemblers,
Journal of Computational Biology, 18 no. 11 (2011), 1625-1634.
Abstract
Hamidreza Chitsaz, Joyclyn L. Yee-Greenbaum, Glenn Tesler, Mary-Jane Lombardo, Christopher L. Dupont, Jonathan H. Badger, Mark Novotny, Douglas B. Rusch, Louise J. Fraser, Niall A. Gormley, Ole Schulz-Trieglaff, Geoffrey P. Smith, Dirk J. Evers, Pavel A. Pevzner, Roger S. Lasken,
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets,
Nature Biotechnology 29 (2011), 915-921.
Advance online publication, 18 Sep 2011.
AbstractDatasets and Software
Paul Medvedev, Son Pham, Mark Chaisson, Glenn Tesler, Pavel Pevzner,
Paired de Bruijn Graphs: a Novel Approach for Incorporating Mate Pair Information into Genome Assemblers,
in V. Bafna and S.C. Sahinalp (Eds.), Proceedings of RECOMB 2011, Lecture Notes in Bioinformatics, Vol. 6577, pp. 238-251. Springer, Heidelberg, 2011.
Abstract
Dumitru Brinza, Matthew Schutz, Glenn Tesler, Vineet Bafna,
RAPID detection of gene-gene interactions in genome-wide association studies,
Bioinformatics, 26 no. 22 (2010), 2856-2862.
JournalRAPID software
Qian Peng, Max Alekseyev, Glenn Tesler, Pavel A. Pevzner,
Decoding the Genomic Architecture of Mammalian and Plant Genomes: Synteny Blocks and Large-Scale Duplications,
Communications in Information and Systems, 10 no. 1 (2010), 1-22.
Journal
Qian Peng, Max Alekseyev, Glenn Tesler, Pavel A. Pevzner,
Decoding the Genomic Architecture of Mammalian and Plant Genomes: Synteny Blocks and Large-Scale Duplications,
9th Workshop on Algorithms in Bioinformatics, WABI 2009,
Lecture Notes in Computer Science / Lecture Notes in Bioinformatics, Vol. 5724, Springer Verlag, 2009, pp. 220-232.
Abstract
Guillaume Bourque and Glenn Tesler,
``Computational Tools for the Analysis of Rearrangements in Mammalian Genomes'' in Bioinformatics, Volume I: Data, Sequence Analysis and Evolution (Jonathan M. Keith, Ed.), Methods in Molecular Biology, Vol. 452, Humana Press, 2008, 431-455.
Online article, Amazon
Glenn Tesler and Dannie Durand (Guest Editors),
Special Issue on the RECOMB Satellite Workshop on Comparative Genomics 2007, Journal of Computational Biology, 15 no. 8 (2008).
Preface (written by Glenn Tesler and Dannie Durand), pp. 943-946.
Whole issue (edited by Glenn Tesler and Dannie Durand).
Glenn Tesler,
Distribution of Segment Lengths in Genome Rearrangements,
Electronic Journal of Combinatorics, 15 (2008), no. 1, Research Paper R105, 56 pp. (electronic).
Abstract and article
Software
Glenn Tesler and Guillaume Bourque,
``Computational Tools for the Analysis of Rearrangements in Mammalian Genomes'' in Phylogenomics (William J. Murphy, Ed.), Methods in Molecular Biology, Vol. 422, Humana Press, 2007, 145-170.
Amazon
Glenn Tesler and Dannie Durand (Editors),
Comparative Genomics,
RECOMB 2007 International Workshop, RECOMB-CG 2007, San Diego, CA, USA, September 16-18, 2007. Proceedings,

Lecture Notes in Computer Science / Lecture Notes in Bioinformatics, Vol. 4751, Springer-Verlag, 2007.
Book, Online edition, Amazon
Pontius, et al. (26 coauthors, including G. Tesler),
Initial sequence and comparative analysis of the cat genome,
Genome Research, 17 no. 11 (2007), 1675-1689.
Abstract
Related material: UCSD press release (November 9, 2007)
Glenn Tesler,
Book review: Algebraic Statistics for Computational Biology (Edited by Lior Pachter and Bernd Sturmfels),
Briefings in Bioinformatics, 8 no. 2 (2007) 138-139.
Abstract
Guillaume Bourque, Glenn Tesler and Pavel A. Pevzner,
The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction,
Genome Research, 16 no. 3 (2006) 311-313.
Abstract
Qian Peng, Pavel A. Pevzner, Glenn Tesler,
The Fragile Breakage versus Random Breakage Models of Chromosome Evolution,
PLoS Computational Biology, 2 no. 2 (2006): e14 (electronic, 12 pages).
Article
Murphy, et al. (25 coauthors, including G. Tesler),
Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps,
Science, 309 no. 5734 (2005), 613-617. (22 July 2005 issue.)
Abstract
Related material: UCSD press release (July 21, 2005) and 2nd copy, UIUC press release (July 21, 2005), Texas A&M press release (July 21, 2005), San Diego Union-Tribune (July 22, 2005, page B2), New York Times (August 30, 2005, Science section).
Guillaume Bourque, Evgeny M. Zdobnov, Peer Bork, Pavel A. Pevzner, and Glenn Tesler,
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages,
Genome Research, 15 no. 1 (2005), 98-110.
Abstract
Hillier, et al. (175 coauthors, including G. Tesler),
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution,
Nature, 432 (2004), 695-716.
Journal
Related material: UCSD press release, NIH press release, Union-Tribune articles (Dec. 10 and 15, 2004).
P.A. Pevzner, H. Tang and G. Tesler,
De novo repeat classification and fragment assembly,
Genome Research, 14 no. 9 (2004), 1786-1789.
Abstract
Pavel A. Pevzner, Haixu Tang and Glenn Tesler,
De novo repeat classification and fragment assembly,
RECOMB '04: Proceedings of the eighth annual international conference on Resaerch in computational molecular biology, San Diego, CA (2004) 213-222.
Abstract and article
Gibbs, et al. (237 coauthors, including G. Tesler),
Genome sequence of the Brown Norway rat yields insights into mammalian evolution,
Nature, 428 (2004), 493-521.
Journal
Related material: UCSD press release (March 31, 2004), NIH press release (March 31, 2004).
G. Bourque, P.A. Pevzner and G. Tesler,
Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes,
Genome Research, 14 no. 4 (2004), 507-516.
Abstractdata
We also authored the cover illustration for this issue!
G. Bourque, W. Murphy, M. Krzywinski, P. Pevzner, and G. Tesler, Genome Research, 14 no. 4 (2004), cover.
At journalenlargement
G. Andelfinger, C. Hitte, L. Etter, R. Guyon, G. Bourque, G. Tesler, P. Pevzner, E. Kirkness, F. Galibert and D. W. Benson,
Detailed four-way comparative mapping and gene order analysis of the canine ctvm locus reveals evolutionary chromosome rearrangements, Genomics, 83 (2004), 1053-1062.
Abstract
W.J. Murphy, G. Bourque, G. Tesler, P. Pevzner, S.J. O'Brien,
Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps, Human Genomics, 1 no. 1 (2003), 30-40.
Abstract
P. Pevzner and G. Tesler,
Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution,
Proceedings of the National Academy of Sciences U.S.A., 100 no. 13 (2003), 7672-7677.
Abstract

Related material: UCSD press release (June 16, 2003), (Oct. 10, 2003), North County Times (June 29, 2003), PNAS commentary (Sep. 30, 2003), Discover Magazine (Nov. 2003).
Pavel Pevzner and Glenn Tesler,
Transforming men into mice: the Nadeau-Taylor chromosomal breakage model revisited,
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biology, Berlin, Germany, (2003), 247-256.
Abstract and article
P. Pevzner and G. Tesler,
Genome Rearrangements in Mammalian Evolution: Lessons from Human and Mouse Genomes,
Genome Research, 13 no. 1 (2003), 37-45.
Abstract and preprintGRIMM-Synteny software
G. Tesler,
Efficient algorithms for multichromosomal genome rearrangements,
Journal of Computer and System Sciences, 65 no. 3 (2002), 587-609.
Abstract and preprint
Waterston, et al. (222 coauthors, including G. Tesler),
Initial sequencing and comparative analysis of the mouse genome,
Nature, 420 (2002), 520-562.
Journal

Related material: UCSD press release (Dec. 4, 2002)*, NIH press release, Nature mouse genome web site, San Diego Union-Tribune (Dec. 5, 2002)* (U-T print version included front page photo not available online).
* Articles include interviews with Pavel Pevzner and Glenn Tesler.
G. Tesler,
GRIMM: genome rearrangements web server,
Bioinformatics, 18 no. 3 (2002), 492-493.
Abstract and preprintGRIMM and MGR websites and software
F. Bergeron, A.M. Garsia, and G. Tesler,
Multiple Left Regular Representations Generated by Alternants,
Journal of Combinatorial Theory, Series A, 91 no. 1-2 (2000), 49-83.
Abstract and preprint
F. Bergeron, A.M. Garsia, M. Haiman and G. Tesler,
Identities and Positivity Conjectures for some remarkable Operators in the Theory of Symmetric Functions,
Methods and Applications of Analysis, 6 no. 3 (1999), 363-420.
Abstract and preprint
A.M. Garsia, M. Haiman and G. Tesler,
Explicit Plethystic Formulas for Macdonald q,t-Kostka Coefficients,
Séminaire Lotharingien de Combinatoire, B42m (1999), 45 pp. (electronic).
Abstract and paper
G. Tesler,
Matchings in Graphs on Non-orientable Surfaces,
Journal of Combinatorial Theory, Series B, 78 (2000), 198-231.
Abstract and preprint
F. Bergeron, N. Bergeron, A. Garsia, M. Haiman and G. Tesler,
Lattice Diagram Polynomials and Extended Pieri Rules,
Advances in Mathematics, 142 no. 2 (1999), 244-334.
Abstract and preprint
G. Tesler,
Isotypic Decompositions of Lattice Determinants,
Journal of Combinatorial Theory, Series A, 85 (1999), 208-227.
Abstract and preprint
A. Garsia and G. Tesler,
Plethystic Formulas for Macdonald q,t-Kostka Coefficients,
Advances in Mathematics, 123 no. 2 (1996), 143-222.
Abstract and preprintSoftware
G. Tesler,
Semi-primary Lattices and Tableau Algorithms,
Ph.D. thesis, Massachusetts Institute of Technology, 1995.
Abstract and thesis
G. Tesler,
The Kekulé Covalent Bond Arrangements of C60,
Advances in Applied Mathematics 14 (1993), 217-225.
Abstract and preprint