Michael Brudno -- Publications

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  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 Res. 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, Morgenstern, B. Fast and sensitive alignment of large genomic sequences.  Proceedings of the IEEE Computer Society Bioinformatics Conference (CSB) 2002.
  6. 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 Res. 13:721-731, 2003.
  7. Cooper GM, Brudno M, Green ED, Batzoglou S, Sidow A. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Res. 13:813-820, 2003.
  8. 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.
  9. Taher L, Rinner O, Garg S, Sczyrba A, Brudno M, Batzoglou S, Morgenstern B. AgenDA: homology-based gene prediction. Bioinformatics 19:1575-1577, 2003.
  10. Brudno M, Chapman M, GĀšttgens B, Batzoglou S, Morgenstern B. Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics 4:66, 2003.
  11. 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.
  12. Rat Genome Sequencing Project Consortium (RGSPC). Genome sequence of the Brown Norway Rat yields insights into mammalian evolution. Nature 428:493–521, 2004.
  13. Cooper GM, Brudno M, Stone ES, Dubchak I, Batzoglou S, Sidow A. Characterization of evolutionary rates and constraints in three mammalian genomes. Genome Res. 14:539–48, 2004.
  14. 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 Res. 14:685–692, 2004.
  15. Brudno M, Steinkamp R, Morgenstern B. The CHAOS/DIALIGN WWW server for multiple sequence alignment. Nucleic Acids Research 32:W41 – W44, 2004.
  16. 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
  17. 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.
  18. The ENCODE Consortium. The ENCODE (ENCylopedia Of DNA Elements) Project. Science, 306: 636–640, 2004.
  19. Do CB, Mahabhashyam M, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple alignment of amino acid sequences. Genome Res. 15: 330–340, 2005
  20. 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
  21. 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.
  22. 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
  23. 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
  24. Bazykin GA, Kondrashov FA, Brudno M, Poliakov A, Dubchak I, Kondrashov AS. Extensive parallelism in protein evolution. Biology Direct . 2:20 2007
  25. 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
  26. Dalca AV, Brudno M. FRESCO: Flexible Alignment with Rectangle Scoring Schemes Proceedings of the Pacific Symposium on Biocomputing (PSB) 13:3-14 2008
  27. 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
  28. 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.