Michael Brudno

Nilgun Donmez, Michael Brudno: SCARPA: scaffolding reads with practical algorithms. Bioinformatics 29(4): 428-434 (2013)

Yue Jiang, Yadong Wang, Michael Brudno: PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants. Bioinformatics 28(20): 2576-2583 (2012)

Marc Fiume, Eric J. M. Smith, Andrew Brook, Dario Strbenac, Brian Turner, Aziz M. Mezlini, Mark D. Robinson, Shoshana J. Wodak, Michael Brudno: Savant Genome Browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Research 40(Web-Server-Issue): 615-621 (2012)

Matei David, Misko Dzamba, Dan Lister, Lucian Ilie, Michael Brudno: SHRiMP2: Sensitive yet Practical Short Read Mapping. Bioinformatics 27(7): 1011-1012 (2011)

Orion Buske, Misko Dzamba, Justin Foong, Lynette Lau, Marc Fiume, Christian Marshall, Susan Walker, Aparna Prasad, Michael Brudno: Variant detection and the Autism sequencing project. BMC Bioinformatics 12(S-11): A4 (2011)

H. Andrés Lagar-Cavilla, Joseph Andrew Whitney, Roy Bryant, Philip Patchin, Michael Brudno, Eyal de Lara, Stephen M. Rumble, M. Satyanarayanan, Adin Scannell: SnowFlock: Virtual Machine Cloning as a First-Class Cloud Primitive. ACM Trans. Comput. Syst. 29(1): 2 (2011)

Nilgun Donmez, Michael Brudno: Hapsembler: An Assembler for Highly Polymorphic Genomes. RECOMB 2011: 38-52

Joseph Andrew Whitney, Judice L. Y. Koh, Michael Costanzo, Grant Brown, Charles Boone, Michael Brudno: Clustering with Overlap for Genetic Interaction Networks via Local Search Optimization. WABI 2011: 326-338

Adrian V. Dalca, Michael Brudno: Genome variation discovery with high-throughput sequencing data. Briefings in Bioinformatics 11(1): 3-14 (2010)

Adrian V. Dalca, Stephen M. Rumble, Samuel Levy, Michael Brudno: VARiD: A variation detection framework for color-space and letter-space platforms. Bioinformatics [ISMB] 26(12): 343-349 (2010)

Marc Fiume, Vanessa Williams, Andrew Brook, Michael Brudno: Savant: genome browser for high-throughput sequencing data. Bioinformatics 26(16): 1938-1944 (2010)

Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, Süleyman Cenk Sahinalp: Session Introduction. Pacific Symposium on Biocomputing 2010: 302-304

Seunghak Lee, Eric P. Xing, Michael Brudno: MoGUL: Detecting Common Insertions and Deletions in a Population. RECOMB 2010: 357-368

Michael Brudno, Paul Medvedev, Jens Stoye, Francisco M. de la Vega: A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). Bioinformatics 25(21): 2863-2864 (2009)

Paul Medvedev, Michael Brudno: Maximum Likelihood Genome Assembly. Journal of Computational Biology 16(8): 1101-1116 (2009)

Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend Sidow, Michael Brudno: SHRiMP: Accurate Mapping of Short Color-space Reads. PLoS Computational Biology 5(5) (2009)

Horacio Andrés Lagar-Cavilla, Joseph Andrew Whitney, Adin Matthew Scannell, Philip Patchin, Stephen M. Rumble, Eyal de Lara, Michael Brudno, Mahadev Satyanarayanan: SnowFlock: rapid virtual machine cloning for cloud computing. EuroSys 2009: 1-12

Seunghak Lee, Elango Cheran, Michael Brudno: A robust framework for detecting structural variations in a genome. ISMB 2008: 59-67

Gerald Quon, Yee Whye Teh, Esther T. Chan, Timothy R. Hughes, Michael Brudno, Quaid Morris: A mixture model for the evolution of gene expression in non-homogeneous datasets. NIPS 2008: 1297-1304

Michael Brudno, Bernard M. E. Moret, C. Randal Linder, Tandy Warnow: Session Introduction. Pacific Symposium on Biocomputing 2008: 1-2

Adrian V. Dalca, Michael Brudno: FRESCO: Flexible Alignment with Rectangle Scoring Schemes. Pacific Symposium on Biocomputing 2008: 3-14

Paul Medvedev, Michael Brudno: Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads. RECOMB 2008: 50-64

Vladimir Yanovski, Stephen M. Rumble, Michael Brudno: Read Mapping Algorithms for Single Molecule Sequencing Data. WABI 2008: 38-49

Michael Brudno, Alexander Poliakov, Simon Minovitsky, Igor Ratnere, Inna Dubchak: Multiple whole genome alignments and novel biomedical applications at the VISTA portal. Nucleic Acids Research 35(Web-Server-Issue): 669-674 (2007)

Paul Medvedev, Konstantinos Georgiou, Gene Myers, Michael Brudno: Computability of Models for Sequence Assembly. WABI 2007: 289-301

Galina Yu. Kovaleva, Georgii A. Bazykin, Michael Brudno, Mikhail S. Gelfand: Comparative Genomics of Transcriptional Regulation in Yeasts and its Application to Identification of a Candidate Alpha-isopropylmalate Transporter. J. Bioinformatics and Computational Biology 4(5): 981-998 (2006)

Nameeta Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, E. Wes Bethel, Edward M. Rubin, Bernd Hamann, Inna Dubchak: Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics 20(5): 636-643 (2004)

Michael Brudno, Rasmus Steinkamp, Burkhard Morgenstern: The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences. Nucleic Acids Research 32(Web-Server-Issue): 41-44 (2004)

Chuong B. Do, Michael Brudno, Serafim Batzoglou: PROBCONS: Probabilistic Consistency-Based Multiple Alignment of Amino Acid Sequences. AAAI 2004: 703-708

Mukund Sundararajan, Michael Brudno, Kerrin Small, Arend Sidow, Serafim Batzoglou: Chaining Algorithms for Alignment of Draft Sequence. WABI 2004: 326-337

Leila Taher, Oliver Rinner, Saurabh Garg, Alexander Sczyrba, Michael Brudno, Serafim Batzoglou, Burkhard Morgenstern: AGenDA: homology-based gene prediction. Bioinformatics 19(12): 1575-1577 (2003)

Michael Brudno, Michael Chapman, Berthold Göttgens, Serafim Batzoglou, Burkhard Morgenstern: Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics 4: 66 (2003)

Michael Brudno, Sanket Malde, Alexander Poliakov, Chuong B. Do, Olivier Couronne, Inna Dubchak, Serafim Batzoglou: Glocal alignment: finding rearrangements during alignment. ISMB (Supplement of Bioinformatics) 2003: 54-62

Michael Brudno, Burkhard Morgenstern: Fast and Sensitive Alignment of Large Genomic Sequences. CSB 2002: 138-

Chris Mayor, Michael Brudno, Jody R. Schwartz, Alexander Poliakov, Edward M. Rubin, Kelly A. Frazer, Lior Pachter, Inna Dubchak: VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16(11): 1046-1047 (2000)

I. Dralyuk, Michael Brudno, Mikhail S. Gelfand, Manfred Zorn, Inna Dubchak: ASDB: database of alternatively spliced genes. Nucleic Acids Research 28(1): 296-297 (2000)