M Tompa

Summary

Affiliation: University of Washington
Country: USA

Publications

  1. pmc MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes
    Shane Neph
    Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195 2350, USA
    Nucleic Acids Res 34:W366-8. 2006
  2. pmc Measuring the accuracy of genome-size multiple alignments
    Amol Prakash
    Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195 2350, USA
    Genome Biol 8:R124. 2007
  3. pmc PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences
    Saurabh Sinha
    Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10021, USA
    BMC Bioinformatics 5:170. 2004
  4. pmc How accurately is ncRNA aligned within whole-genome multiple alignments?
    Adrienne X Wang
    Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195, USA
    BMC Bioinformatics 8:417. 2007
  5. pmc Algorithms for locating extremely conserved elements in multiple sequence alignments
    Huei Hun E Tseng
    Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195 2350, USA
    BMC Bioinformatics 10:432. 2009
  6. ncbi request reprint Assessing computational tools for the discovery of transcription factor binding sites
    Martin Tompa
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195 2350, USA
    Nat Biotechnol 23:137-44. 2005
  7. ncbi request reprint Discovery of regulatory elements in vertebrates through comparative genomics
    Amol Prakash
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195 2350, USA
    Nat Biotechnol 23:1249-56. 2005
  8. ncbi request reprint Construction of optimal quality control for oligo arrays
    Charles J Colbourn
    Department of Computer Science and Engineering, Arizona State University, Tempe, AZ 85287 5406, USA
    Bioinformatics 18:529-35. 2002
  9. ncbi request reprint An exact algorithm to identify motifs in orthologous sequences from multiple species
    M Blanchette
    Department of Computer Science and Engineering, University of Washington, Seattle 98195 2350, USA
    Proc Int Conf Intell Syst Mol Biol 8:37-45. 2000
  10. ncbi request reprint A statistical method for finding transcription factor binding sites
    S Sinha
    Department of Computer Science and Engineering, University of Washington, Seattle 98195 2350, USA
    Proc Int Conf Intell Syst Mol Biol 8:344-54. 2000

Research Grants

  1. Discovering Motifs From Orthologous Sequences
    Martin Tompa; Fiscal Year: 2004

Detail Information

Publications26

  1. pmc MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes
    Shane Neph
    Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195 2350, USA
    Nucleic Acids Res 34:W366-8. 2006
    ..The software is called MicroFootPrinter and is available at http://bio.cs.washington.edu/software.html...
  2. pmc Measuring the accuracy of genome-size multiple alignments
    Amol Prakash
    Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195 2350, USA
    Genome Biol 8:R124. 2007
    ..We identify 9.7% (21 Mbp) of the human chromosome 1 alignment as suspiciously aligned. We present independent evidence that many of these suspicious regions represent misalignments...
  3. pmc PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences
    Saurabh Sinha
    Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10021, USA
    BMC Bioinformatics 5:170. 2004
    ..This paper addresses the problem of discovering transcription factor binding sites in heterogeneous sequence data, which includes regulatory sequences of one or more genes, as well as their orthologs in other species...
  4. pmc How accurately is ncRNA aligned within whole-genome multiple alignments?
    Adrienne X Wang
    Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195, USA
    BMC Bioinformatics 8:417. 2007
    ..At present, the accuracy of whole-genome multiple alignments, particularly in noncoding regions, has not been thoroughly evaluated...
  5. pmc Algorithms for locating extremely conserved elements in multiple sequence alignments
    Huei Hun E Tseng
    Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195 2350, USA
    BMC Bioinformatics 10:432. 2009
    ..In 2004, Bejerano et al. announced the startling discovery of hundreds of "ultraconserved elements", long genomic sequences perfectly conserved across human, mouse, and rat. Their announcement stimulated a flurry of subsequent research...
  6. ncbi request reprint Assessing computational tools for the discovery of transcription factor binding sites
    Martin Tompa
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195 2350, USA
    Nat Biotechnol 23:137-44. 2005
    ..The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools...
  7. ncbi request reprint Discovery of regulatory elements in vertebrates through comparative genomics
    Amol Prakash
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195 2350, USA
    Nat Biotechnol 23:1249-56. 2005
    ..The results provide a glimpse into the wealth of information that comparative genomics can yield and suggest the need for further improvement of genome-wide comparative computational techniques...
  8. ncbi request reprint Construction of optimal quality control for oligo arrays
    Charles J Colbourn
    Department of Computer Science and Engineering, Arizona State University, Tempe, AZ 85287 5406, USA
    Bioinformatics 18:529-35. 2002
    ..Oligo arrays are important experimental tools for the high throughput measurement of gene expression levels. During production of oligo arrays, it is important to identify any faulty manufacturing step...
  9. ncbi request reprint An exact algorithm to identify motifs in orthologous sequences from multiple species
    M Blanchette
    Department of Computer Science and Engineering, University of Washington, Seattle 98195 2350, USA
    Proc Int Conf Intell Syst Mol Biol 8:37-45. 2000
    ..We then discuss experimental results on finding promoters of the rbcS gene for a family of 10 plants, on finding promoters of the adh gene for 12 Drosophila species, and on finding promoters of several chloroplast encoded genes...
  10. ncbi request reprint A statistical method for finding transcription factor binding sites
    S Sinha
    Department of Computer Science and Engineering, University of Washington, Seattle 98195 2350, USA
    Proc Int Conf Intell Syst Mol Biol 8:344-54. 2000
    ..We discuss the results of experiments in which this algorithm was used to locate candidate binding sites in several well studied pathways of S. cerevisiae, as well as gene clusters from some of the hybridization microarray experiments...
  11. pmc Discovery of regulatory elements by a computational method for phylogenetic footprinting
    Mathieu Blanchette
    Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195 2350, USA
    Genome Res 12:739-48. 2002
    ..We report the results of this algorithm on several data sets of interest. A large number of known functional binding sites are identified by our method, but we also find several highly conserved motifs for which no function is yet known...
  12. pmc A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes
    Zizhen Yao
    Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA
    PLoS Comput Biol 3:e126. 2007
    ..Of the ncRNA candidates not in Rfam, we find compelling evidence that some of them are functional, and analyze several potential ribosomal protein leaders in depth...
  13. ncbi request reprint Algorithms for phylogenetic footprinting
    Mathieu Blanchette
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, WA 98195 2350, USA
    J Comput Biol 9:211-23. 2002
    ..Each technique is implemented and successfully identifies a number of known binding sites, as well as several highly conserved but uncharacterized regions. The program is available at http://bio.cs.washington.edu/software.html...
  14. ncbi request reprint Quality control in manufacturing oligo arrays: a combinatorial design approach
    Rimli Sengupta
    Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195 2350, USA
    J Comput Biol 9:1-22. 2002
    ..Our results improve over prior work in guaranteeing coverage of all protocol steps and in being able to tolerate a greater number of unreliable probe intensities...
  15. ncbi request reprint Statistics of local multiple alignments
    Amol Prakash
    Department of Computer Science and Engineering Box 352350 University of Washington Seattle, WA 98195 2350, USA
    Bioinformatics 21:i344-50. 2005
    ..We demonstrate its usefulness in distinguishing high and moderate quality multiple alignments from low quality ones, with supporting experiments on orthologous vertebrate promoter sequences...
  16. pmc Discovery of novel transcription factor binding sites by statistical overrepresentation
    Saurabh Sinha
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, WA 98195 2350, USA
    Nucleic Acids Res 30:5549-60. 2002
    ..cerevisiae, where the algorithm suggests many promising novel transcription factor binding sites. The program is available at http://bio.cs.washington.edu/software.html...
  17. doi request reprint Comparative assessment of methods for aligning multiple genome sequences
    Xiaoyu Chen
    Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA
    Nat Biotechnol 28:567-72. 2010
    ..Our assessment reveals that constructing accurate whole-genome multiple sequence alignments remains a significant challenge, particularly for noncoding regions and distantly related species...
  18. pmc TP0262 is a modulator of promoter activity of tpr Subfamily II genes of Treponema pallidum ssp. pallidum
    Lorenzo Giacani
    Department of Medicine, University of Washington, Seattle, WA 98104, USA
    Mol Microbiol 72:1087-99. 2009
    ..This is the first characterization of a T. pallidum transcriptional modulator that influences tpr promoter activity...
  19. pmc Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases
    Kai Wang
    Department of Genetics, Rosetta Inpharmatics, Seattle, Washington, USA
    PLoS Comput Biol 5:e1000616. 2009
    ..Taken together, our approach represents a novel step forward in integrating gene co-expression networks from multiple large scale datasets to leverage not only common information but also differences that are dataset-specific...
  20. ncbi request reprint Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution
    Gautam Dantas
    Department of Biochemistry, University of Washington, Seattle 98195, USA
    J Mol Biol 362:1004-24. 2006
    ..The symmetric self-association between two identical mis-translated CFr sub-domains to generate an extremely stable structure parallels a mechanism for natural protein-fold evolution by modular recombination of protein sub-structures...
  21. pmc Evolutionarily conserved sequence elements that positively regulate IFN-gamma expression in T cells
    Maria Shnyreva
    Department of Immunology, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 101:12622-7. 2004
    ..Like IFN-gamma expression, these histone modifications were T-bet-dependent in CD4+ cells, but not CD8+ T cells. These findings define two distal regulatory elements associated with T cell subset-specific IFN-gamma expression...
  22. pmc Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis
    Heui Dong Park
    Department of Pathobiology, University of Washington, Seattle, WA 98195, USA
    Mol Microbiol 48:833-43. 2003
    ..Together, these results demonstrate that Rv3133c/DosR is a transcription factor of the two-component response regulator class, and that it is the primary mediator of a hypoxic signal within M. tuberculosis...
  23. pmc Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline
    Zasha Weinberg
    Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520 8103, USA
    Nucleic Acids Res 35:4809-19. 2007
    ..These candidate RNAs add to the growing list of RNA motifs involved in multiple cellular processes, and suggest that many additional RNAs remain to be discovered...
  24. ncbi request reprint Finding motifs using random projections
    Jeremy Buhler
    Department of Computer Science, Box 1045, Washington University, One Brookings Drive, St Louis, MO 63130, USA
    J Comput Biol 9:225-42. 2002
    ..We also test the performance of our algorithm on realistic biological examples, including transcription factor binding sites in eukaryotes and ribosome binding sites in prokaryotes...
  25. pmc FootPrinter: A program designed for phylogenetic footprinting
    Mathieu Blanchette
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 31:3840-2. 2003
    ..The software is called FootPrinter and is available at http://bio.cs.washington.edu/software.html...
  26. pmc YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation
    Saurabh Sinha
    Center for Studies in Physics and Biology, Box 25, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Nucleic Acids Res 31:3586-8. 2003
    ..More specifically, YMF enumerates all motifs in the search space and is guaranteed to produce those motifs with greatest z-scores. This note describes the YMF web software, available at http://bio.cs.washington.edu/software.html...

Research Grants3

  1. Discovering Motifs From Orthologous Sequences
    Martin Tompa; Fiscal Year: 2004
    ..3. Algorithms to discover secondary structure motifs in orthologous RNA molecules will be developed. 4. Algorithms that identify exons from syntenic genomic sequences of multiple species will be developed. ..