Michael Brudno — Publications

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Journal Papers

  1. Dralyuk I, Brudno M, Gelfand M, Zorn M, Dubchak I. ASDB: database of alternatively spliced genes. Nucleic Acids Res. 28:296-7. 2000
  2. Dubchak I, Brudno M, Pachter LS, Loots GG, Mayor C, Rubin EM, Frazer K. Active conservation of noncoding sequences revealed by 3-way species comparisons. Genome Research. 10:1304-6. 2000
  3. Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer K, Pachter LS, Dubchak I VISTA: Visualizing global DNA sequence alignments of arbitrary length. Bioinformatics, 16:1046-1047. 2000
  4. Brudno M, Gelfand MS, Spengler S, Zorn M, Dubchak I, Conboy JG Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing. Nucleic Acids Res. 29:2338-48 2001
  5. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S. LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Research. 13:721-731, 2003.
  6. Cooper GM, Brudno M, Green ED, Batzoglou S, Sidow A. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Research. 13:813-820, 2003.
  7. Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S. Glocal alignment: finding rearrangements during alignment. Special Issue on the Proceedings of the ISMB 2003, Bioinformatics 19: 54i-62i, 2003.
  8. Taher L, Rinner O, Garg S, Sczyrba A, Brudno M, Batzoglou S, Morgenstern B. AgenDA: homology-based gene prediction. Bioinformatics 19:1575-1577, 2003.
  9. Brudno M, Chapman M, G?ttgens B, Batzoglou S, Morgenstern B. Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics 4:66, 2003.
  10. Shan N, Couronne O, Pennacchio LA, Brudno M, Batzoglou S, Joy S, Bethel W, Rubin EM, Hamann B, Dubchak I. Phylo-VISTA: an interactive visualization tool for multiple DNA sequence alignments. Bioinformatics 20: 636-643, 2004.
  11. Rat Genome Sequencing Project Consortium (RGSPC). Genome sequence of the Brown Norway Rat yields insights into mammalian evolution. Nature 428:493–521, 2004.
  12. Cooper GM, Brudno M, Stone ES, Dubchak I, Batzoglou S, Sidow A. Characterization of evolutionary rates and constraints in three mammalian genomes. Genome Research. 14:539–48, 2004.
  13. Brudno M, Poliakov A, Salamov A, Cooper GM, Sidow A, Rubin EM, Solovyev V, Batzoglou S, Dubchak I. Automated whole-genome multiple alignment of Rat, Mouse, and Human. Genome Research. 14:685–692, 2004.
  14. Brudno M, Steinkamp R, Morgenstern B. The CHAOS/DIALIGN WWW server for multiple sequence alignment. Nucleic Acids Research 32:W41 – W44, 2004.
  15. The ENCODE Consortium. The ENCODE (ENCylopedia Of DNA Elements) Project. Science, 306: 636–640, 2004.
  16. Do CB, Mahabhashyam M, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple alignment of amino acid sequences. Genome Res. 15: 330–340, 2005
  17. Kovaleva G., Bazykin G., Brudno M., Gelfand M. Comparative genomics of transcriptional regulation in yeasts and its application to identification of a candidate alpha-isopropylmalate transporter. Journal of Bioinformatics and Computational Biology 4:981-998, 2006
  18. Small KS, Brudno M, Hill MM, Sidow A. Extreme genomic variation in a natural population. Proc Natl Acad Sci USA. 104(13):5698-703. 2007.
  19. Small KS, Brudno M, Hill MM, Sidow A. A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. Genome Biol. 8(3):R41 2007
  20. Brudno M., Poliakov A., Minovitsky S., Ratnere I., Dubchak I. Multiple whole genome alignments and novel biomedical applications at the VISTA portal. Nucleic Acids Research, 35:W669-74 2007
  21. Bazykin GA, Kondrashov FA, Brudno M, Poliakov A, Dubchak I, Kondrashov AS. Extensive parallelism in protein evolution. Biology Direct . 2:20 2007
  22. Lee S, Cheran E, Brudno M. A Robust Framework for Detecting Structural Variations in a Genome Proceedings of the 16th Annual International Conference on Intelligent Systems in Molecular Biology (ISMB) 2008.
  23. Donmez N, Bazykin G, Brudno M, Kondrashov AS. Polymorphism due to multiple amino acid substitutions at a codon site within Ciona savignyi. Genetics 181:685-690 2009
  24. Dubchak I, Poliakov A, Kislyuk A, Brudno M. Multiple Whole Genome alignment without a Reference Sequence. Genome Research, 19:682-689 2009
  25. Chan ET, Quon GT, Chua G, Babak T, Trochesset M, Zirngibl RA, Aubin J, Ratcliffe M, Wilde A, Brudno M, Morris QD, Hughes TR. Conservation of core gene expression invertebrate tissues. Journal of Biology, 8:33 2009
  26. Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M. SHRiMP: Accurate Mapping of Short Color-space Reads. PLoS Computational Biology, 5:5 2009
  27. Medvedev P, Brudno M. Maximum Likelihood Genome Assembly. Journal of Computational Biology , 16:968-983 2009
  28. Lee S, Hormozdiari F, Alkan C, Brudno M. MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nature Methods , 6:473-474 2009
  29. Medvedev P, Stanciu M, Brudno M. Computational methods for discovering structural variation with next generation sequencing. Nature Methods , 6:S13-20 2009 (Review).
  30. Dalca A, Brudno M. Genome Variation Discovery with High Throughput Sequencing Data. Briefings in Bionformatics, 11:3-14 2010 (Review).
  31. Costanzo M and 52 others. The Genetic Landscape of a Cell. Science, 327:425-431 2010
  32. Dalca, A, Rumble SM, Levy S, Brudno M. VARiD: A Variation Detection Framework for Colorspace and Letterspace platforms. Proceedings of the 18th Conference on Intelligent Systems in Molecular Biology (ISMB); Bioinformatics , 26:i343-i349 2010
  33. Fiume M, Williams V, Brook A, Brudno M. Savant: Genome Browser for High Throughput Sequencing Data. Bioinformatics, 26:1938-1944 2010
  34. Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M. Detecting Copy Number Variation with Mated Short Reads. Genome Research (Accepted) 2010
  35. Lagar-Cavilla A, Whitney JA, Bryant R, Patchin P, Brudno M, de Lara E. SnowFlock: Virtual Machine Cloning as a First Class Cloud Primitive. Transactions on Computer Systems (Accepted) 2010

Conference & Workshop Papers

  1. Brudno M, Morgenstern, B. Fast and sensitive alignment of large genomic sequences.  Proceedings of the IEEE Computer Society Bioinformatics Conference (CSB) 2002.
  2. Do CB, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple alignment of amino acid sequences. Proceedings of the Nineteenth National Conference on Artificial Intelligence (AAAI) 703-708 2004
  3. Sundararajan M, Brudno M, Small K, Sidow A, Batzoglou S. Chaining algorithms for alignment of draft sequence. Proceedings of the fourth Workshop on Algorithms in Bioinformatics (WABI) 289-301 2004.
  4. Medvedev P, Georgiou K, Myers EW, Brudno M. Computability and equivalence of models for genome assembly. Proceedings of  Workshop on Algorithms in Bioinformatics (WABI): 289-301 2007
  5. Dalca AV, Brudno M. FRESCO: Flexible Alignment with Rectangle Scoring Schemes Proceedings of the Pacific Symposium on Biocomputing (PSB) 13:3-14 2008
  6. Medvedev P, Brudno M. Ab initio Whole Genome Shotgun Assembly with Mated Short Reads Proceedings of the 12th Annual Research in Computational Biology Conference (RECOMB) 2008
  7. Yanovsky V, Rumble SR, Brudno M. Read Mapping Algorithms for Single Molecule Sequencing Data Proceedings of Workshop on Algorithms in Bioinformatics (WABI) 2008
  8. Quon G, The YW, Chan ET, Hughes TR, Brudno M, Morris QD. A mixture model for the evolution of gene expression in non-homogeneous datasets. Proceedings of The Neural Information Processing Systems Conference (NIPS) 2008.
  9. Lagar-Cavilla A, Whitney JA, Scannel A, Rumble SM, Patchin P, de Lara E, Brudno M, Satyanarayanan, M. SnowFlock: Rapid Virtual Machine Cloning for Cloud Computing. Proceedings of the European Conference on Computer Systems (Eurosys) 2009
  10. Patchin P, Lagar-Cavilla HA, de Lara E, Brudno M. Adding the Easy Button to the Cloud with Snowflock and MPI. 3rd Workshop on System-level Virtualization for High Performance Computing?(HPCVirt) 2009
  11. Lee S, Xing EP, Brudno M. MoGUL: Detecting Common Insertions and Deletions in a Population. Proceedings of the 14th Annual Research in Computational Biology Conference (RECOMB), 2010