Selected Publications

The following is a list of selected publications from the Computational & Synthetic Biology group.

  1. N. Alon, C. Colbourn, A. Ling, M. Tompa, "Equireplicate Balanced Binary Codes for Oligo Arrays", SIAM Journal on Discrete Mathematics, vol. 14 (2001) 481-497.   Supplement.
  2. P. Anandam, E. Torarinsson, W. Ruzzo, "Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies", Bioinformatics, vol. 25 (2009) 668-9. Pubmed 19136551.   Supplement.
  3. M. Bar, S. Wyman, B. Fritz, J. Qi, K. Garg, R. Parkin, E. Kroh, A. Bendoraite, P. Mitchell, A. Nelson, W. Ruzzo, C. Ware, J. Radich, R. Gentleman, H. Ruohola-Baker, M. Tewari, "MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries", Stem Cells, vol. 26 (2008) 2496-505. Pubmed 18583537.
  4. M. Barrett, K. Yeung, W. Ruzzo, L. Hsu, P. Blount, R. Sullivan, H. Zarbl, J. Delrow, P. Rabinovitch, B. Reid, "Transcriptional analyses of Barrett's metaplasia and normal upper GI mucosae", Neoplasia, vol. 4 (2002) 121-8. Pubmed 11896567.
  5. J. Barrick, N. Sudarsan, Z. Weinberg, W. Ruzzo, R. Breaker, "6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter", RNA, vol. 11 (2005) 774-84. Pubmed 15811922.
  6. M. Biggin, "MyoD, a lesson in widespread DNA binding", Dev. Cell, vol. 18 (2010) 505-6. Pubmed 20412764.
  7. M. Blanchette, "A comparative analysis method for detecting binding sites in coding regions", RECOMB03: Seventh Annual International Conference on Computational Molecular Biology, (2003) 57-66.
  8. M. Blanchette, "Algorithms for phylogenetic footprinting", RECOMB01: Fifth Annual International Conference on Computational Molecular Biology (Best Student Paper Award), (2001) 49-58.
  9. M. Blanchette, S. Kwong, M. Tompa, "An Empirical Comparison of Tools for Phylogenetic Footprinting", Third IEEE Symposium on Bioinformatics and Bioengineering, (2003) 69-78.   Supplement.
  10. M. Blanchette, B. Schwikowski, M. Tompa, "Algorithms for phylogenetic footprinting", J. Comput. Biol., vol. 9 (2002) 211-23. Pubmed 12015878.
  11. M. Blanchette, B. Schwikowski, M. Tompa, "An exact algorithm to identify motifs in orthologous sequences from multiple species", Proc Int Conf Intell Syst Mol Biol, vol. 8 (2000) 37-45. Pubmed 10977064.
  12. M. Blanchette, S. Sinha, "Separating real motifs from their artifacts", Bioinformatics, vol. 17 Suppl 1 (2001) S30-8. Pubmed 11472990.   Supplement.
  13. M. Blanchette, M. Tompa, "Discovery of regulatory elements by a computational method for phylogenetic footprinting", Genome Res., vol. 12 (2002) 739-48. Pubmed 11997340.   Supplement.
  14. M. Blanchette, M. Tompa, "FootPrinter: A program designed for phylogenetic footprinting", Nucleic Acids Res., vol. 31 (2003) 3840-2. Pubmed 12824433.
  15. G. Bongiovanni, G. Gambosi, R. Petreschi, J. Redstone, W. Ruzzo, "Algorithms for a Simple Point Placement Problem", Algorithms and Complexity, 4th Italian Conference, CIAC 2000, Springer Lecture Notes in Computer Science, vol. 1767 (2000) 32-43.
  16. J. Buhler, "Efficient large-scale sequence comparison by locality-sensitive hashing", Bioinformatics, vol. 17 (2001) 419-28. Pubmed 11331236.   Supplement.
  17. J. Buhler, "Provably sensitive indexing strategies for biosequence similarity search", J. Comput. Biol., vol. 10 (2003) 399-417. Pubmed 13677335.   Supplement.
  18. J. Buhler, T. Ideker, D. Haynor, "Dapple: Improved Techniques for Finding Spots on DNA Microarrays", University of Washington Department of Computer Science & Engineering Technical Report UW-CSE-2000-08-05, (2000)   Supplement.
  19. J. Buhler, M. Tompa, "Finding motifs using random projections", J. Comput. Biol., vol. 9 (2002) 225-42. Pubmed 12015879.   Supplement.
  20. Y. Cao, Z. Yao, D. Sarkar, M. Lawrence, G. Sanchez, M. Parker, K. MacQuarrie, J. Davison, M. Morgan, W. Ruzzo, R. Gentleman, S. Tapscott, "Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming", Dev. Cell, vol. 18 (2010) 662-74. Pubmed 20412780.   Supplement.
  21. X. Chen, M. Tompa, "Comparative assessment of methods for aligning multiple genome sequences", Nat. Biotechnol., vol. 28 (2010) 567-72. Pubmed 20495551.   Supplement.
  22. C. Colbourn, A. Ling, M. Tompa, "Construction of optimal quality control for oligo arrays", Bioinformatics, vol. 18 (2002) 529-35. Pubmed 12016050.
  23. G. Dantas, A. Watters, B. Lunde, Z. Eletr, N. Isern, T. Roseman, J. Lipfert, S. Doniach, M. Tompa, B. Kuhlman, B. Stoddard, G. Varani, D. Baker, "Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution", J. Mol. Biol., vol. 362 (2006) 1004-24. Pubmed 16949611.
  24. C. Diorio, R. Rao, "Neural circuits in silicon", Nature, vol. 405 (2000) 891-2. Pubmed 10879514.
  25. J. Eisen, R. Coyne, M. Wu, D. Wu, M. Thiagarajan, J. Wortman, J. Badger, Q. Ren, P. Amedeo, K. Jones, L. Tallon, A. Delcher, S. Salzberg, J. Silva, B. Haas, W. Majoros, M. Farzad, J. Carlton, R. Smith, J. Garg, R. Pearlman, K. Karrer, L. Sun, G. Manning, N. Elde, A. Turkewitz, D. Asai, D. Wilkes, Y. Wang, H. Cai, K. Collins, A. Stewart, S. Lee, K. Wilamowska, Z. Weinberg, W. Ruzzo, D. Wloga, J. Gaertig, J. Frankel, C. Tsao, M. Gorovsky, P. Keeling, R. Waller, N. Patron, M. Cherry, N. Stover, C. Krieger, C. Toro, H. Ryder, S. Williamson, R. Barbeau, E. Hamilton, E. Orias, "Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote", PLoS Biol., vol. 4 (2006) e286. Pubmed 16933976.   Supplement.
  26. A. Fong, Z. Yao, J. Zhong, Y. Cao, W. Ruzzo, R. Gentleman, S. Tapscott, "Genetic and epigenetic determinants of neurogenesis and myogenesis", Dev. Cell, vol. 22 (2012) 721-35. Pubmed 22445365.
  27. L. Geng, Z. Yao, L. Snider, A. Fong, J. Cech, J. Young, S. Maarel, W. Ruzzo, R. Gentleman, R. Tawil, S. Tapscott, "DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy", Dev. Cell, vol. 22 (2012) 38-51. Pubmed 22209328.
  28. L. Giacani, C. Godornes, M. Puray-Chavez, C. Guerra-Giraldez, M. Tompa, S. Lukehart, A. Centurion-Lara, "TP0262 is a modulator of promoter activity of tpr Subfamily II genes of Treponema pallidum ssp. pallidum", Mol. Microbiol., vol. 72 (2009) 1087-99. Pubmed 19432808.
  29. J. Gorodkin, I. Hofacker, E. Torarinsson, Z. Yao, J. Havgaard, W. Ruzzo, "De novo prediction of structured RNAs from genomic sequences", Trends Biotechnol., vol. 28 (2010) 9-19. Pubmed 19942311.   Supplement.
  30. P. Hsieh, R. Kenagy, E. Mulvihill, J. Jeanette, X. Wang, C. Chang, Z. Yao, W. Ruzzo, S. Justice, K. Hudkins, C. Alpers, S. Berceli, A. Clowes, "Bone morphogenetic protein 4: potential regulator of shear stress-induced graft neointimal atrophy", J. Vasc. Surg., vol. 43 (2006) 150-8. Pubmed 16414402.   Supplement.
  31. T. Ideker, V. Thorsson, J. Ranish, R. Christmas, J. Buhler, J. Eng, R. Bumgarner, D. Goodlett, R. Aebersold, L. Hood, "Integrated genomic and proteomic analyses of a systematically perturbed metabolic network", Science, vol. 292 (2001) 929-34. Pubmed 11340206.
  32. J. Jaeger, R. Sengupta, W. Ruzzo, "Improved gene selection for classification of microarrays", Pac Symp Biocomput, (2003) 53-64. Pubmed 12603017.
  33. D. Jones, W. Ruzzo, X. Peng, M. Katze, "A new approach to bias correction in RNA-Seq", Bioinformatics, vol. 28 (2012) 921-8. Pubmed 22285831.
  34. D. Jones, W. Ruzzo, X. Peng, M. Katze, "Compression of next-generation sequencing reads aided by highly efficient de novo assembly", , (Submitted)
  35. A. Keller, M. Schummer, L. Hood, W. Ruzzo, "Bayesian Classification of DNA Array Expression Data", University of Washington Department of Computer Science & Engineering Technical Report UW-CSE-00-08-01, (2000)
  36. E. Knouf, K. Garg, J. Arroyo, Y. Correa, D. Sarkar, R. Parkin, K. Wurz, K. O'Briant, A. Godwin, N. Urban, W. Ruzzo, R. Gentleman, C. Drescher, E. Swisher, M. Tewari, "An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription", Nucleic Acids Res., vol. 40 (2012) 499-510. Pubmed 21917857.
  37. N. Li, M. Tompa, "Analysis of computational approaches for motif discovery", Algorithms for molecular biology : AMB, vol. 1 (2006) 8. Pubmed 16722558.
  38. M. Mandal, M. Lee, J. Barrick, Z. Weinberg, G. Emilsson, W. Ruzzo, R. Breaker, "A glycine-dependent riboswitch that uses cooperative binding to control gene expression", Science, vol. 306 (2004) 275-9. Pubmed 15472076.
  39. K. Miller, G. Schalk, E. Fetz, M. Nijs, J. Ojemann, R. Rao, "Cortical activity during motor execution, motor imagery, and imagery-based online feedback", Proc. Natl. Acad. Sci. U.S.A., vol. 107 (2010) 4430-5. Pubmed 20160084.
  40. E. Mulvihill, J. Jaeger, R. Sengupta, W. Ruzzo, C. Reimer, S. Lukito, S. Schwartz, "Atherosclerotic plaque smooth muscle cells have a distinct phenotype", Arterioscler. Thromb. Vasc. Biol., vol. 24 (2004) 1283-9. Pubmed 15142862.   Supplement.
  41. S. Neph, M. Tompa, "MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes", Nucleic Acids Res., vol. 34 (2006) W366-8. Pubmed 16845027.   Supplement.
  42. C. Olson, M. Kim, C. Clauson, B. Kogon, C. Ebeling, S. Hauck, W. Ruzzo, "Hardware Acceleration of Short Read Mapping", FCCM 2012: The 20th Annual IEEE International Symposium on Field-Programmable Custom Computing Machines, (2012)
  43. H. Park, K. Guinn, M. Harrell, R. Liao, M. Voskuil, M. Tompa, G. Schoolnik, D. Sherman, "Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis", Mol. Microbiol., vol. 48 (2003) 833-43. Pubmed 12694625.
  44. D. Patterson, K. Yasuhara, W. Ruzzo, "Pre-mRNA secondary structure prediction aids splice site prediction", Pac Symp Biocomput, (2002) 223-34. Pubmed 11928478.
  45. A. Prakash, M. Blanchette, S. Sinha, M. Tompa, "Motif discovery in heterogeneous sequence data", Pac Symp Biocomput, (2004) 348-59. Pubmed 14992516.
  46. A. Prakash, M. Tompa, "Assessing the discordance of multiple sequence alignments", IEEE/ACM Trans Comput Biol Bioinform, vol. 6 (2009) 542-51. Pubmed 19875854.
  47. A. Prakash, M. Tompa, "Discovery of regulatory elements in vertebrates through comparative genomics", Nat. Biotechnol., vol. 23 (2005) 1249-56. Pubmed 16211068.   Supplement.
  48. A. Prakash, M. Tompa, "Measuring the accuracy of genome-size multiple alignments", Genome Biol., vol. 8 (2007) R124. Pubmed 17594489.   Supplement.
  49. A. Prakash, M. Tompa, "Statistics of local multiple alignments", Bioinformatics, vol. 21 Suppl 1 (2005) i344-50. Pubmed 15961477.
  50. R. Rao, D. Ballard, "Predictive coding in the visual cortex: a functional interpretation of some extra-classical receptive-field effects", Nat. Neurosci., vol. 2 (1999) 79-87. Pubmed 10195184.
  51. J. Redstone, W. Ruzzo, "Algorithms for Ordering DNA Probes on Chromosomes", University of Washington Department of Computer Science & Engineering Technical Report UW-CSE-98-12-04, (1998)
  52. E. Regulski, R. Moy, Z. Weinberg, J. Barrick, Z. Yao, W. Ruzzo, R. Breaker, "A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism", Mol. Microbiol., vol. 68 (2008) 918-32. Pubmed 18363797.
  53. E. Rocke, "A Hybrid Scoring Function for Protein Multiple Alignment", Proceedings of the 2nd Workshop on Algorithms in Bioinformatics, (2002)
  54. E. Rocke, M. Tompa, "An Algorithm for Finding Novel Gapped Motifs in DNA Sequences", RECOMB98: Proceedings of the Second Annual International Conference on Computational Molecular Biology, (1998) 228-233.   Supplement.
  55. W. Ruzzo, M. Tompa, "A linear time algorithm for finding all maximal scoring subsequences", Proc Int Conf Intell Syst Mol Biol, (1999) 234-41. Pubmed 10786306.
  56. G. Seelig, D. Soloveichik, D. Zhang, E. Winfree, "Enzyme-free nucleic acid logic circuits", Science, vol. 314 (2006) 1585-8. Pubmed 17158324.
  57. G. Seelig, B. Yurke, E. Winfree, "Catalyzed relaxation of a metastable DNA fuel", J. Am. Chem. Soc., vol. 128 (2006) 12211-20. Pubmed 16967972.
  58. S. Seemann, S. Sunkin, M. Hawrylycz, W. Ruzzo, J. Gorodkin, "Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain", BMC Genomics, vol. 13 (2012) 214. Pubmed 22651826.
  59. R. Sengupta, M. Tompa, "Quality control in manufacturing oligo arrays: a combinatorial design approach", J. Comput. Biol., vol. 9 (2002) 1-22. Pubmed 11911792.
  60. M. Shnyreva, W. Weaver, M. Blanchette, S. Taylor, M. Tompa, D. Fitzpatrick, C. Wilson, "Evolutionarily conserved sequence elements that positively regulate IFN-gamma expression in T cells", Proc. Natl. Acad. Sci. U.S.A., vol. 101 (2004) 12622-7. Pubmed 15304658.
  61. S. Sinha, "Discriminative motifs", J. Comput. Biol., vol. 10 (2003) 599-615. Pubmed 12935347.
  62. S. Sinha, "PhyME: a software tool for finding motifs in sets of orthologous sequences", Methods Mol. Biol., vol. 395 (2007) 309-18. Pubmed 17993682.
  63. S. Sinha, M. Blanchette, M. Tompa, "PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences", BMC Bioinformatics, vol. 5 (2004) 170. Pubmed 15511292.
  64. S. Sinha, M. Tompa, "A statistical method for finding transcription factor binding sites", Proc Int Conf Intell Syst Mol Biol, vol. 8 (2000) 344-54. Pubmed 10977095.   Supplement.
  65. S. Sinha, M. Tompa, "Discovery of novel transcription factor binding sites by statistical overrepresentation", Nucleic Acids Res., vol. 30 (2002) 5549-60. Pubmed 12490723.   Supplement.
  66. S. Sinha, M. Tompa, "Performance Comparison of Algorithms for Finding Transcription Factor Binding Sites", 3rd IEEE Symposium on Bioinformatics and Bioengineering, (2003) 214-220.   Supplement.
  67. S. Sinha, M. Tompa, "YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation", Nucleic Acids Res., vol. 31 (2003) 3586-8. Pubmed 12824371.   Supplement.
  68. D. Soloveichik, G. Seelig, E. Winfree, "DNA as a universal substrate for chemical kinetics", Proc. Natl. Acad. Sci. U.S.A., vol. 107 (2010) 5393-8. Pubmed 20203007.
  69. M. Tompa, "An exact method for finding short motifs in sequences, with application to the ribosome binding site problem", Proc Int Conf Intell Syst Mol Biol, (1999) 262-71. Pubmed 10786309.
  70. M. Tompa, "Computational Motif Discovery", Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, (2005)
  71. M. Tompa, "Identifying functional elements by comparative DNA sequence analysis", Genome Res., vol. 11 (2001) 1143-4. Pubmed 11435394.
  72. M. Tompa, "Lecture Notes on Biological Sequence Analysis", University of Washington Department of Computer Science & Engineering Technical Report 2000-06-01, (2000)   Supplement.
  73. M. Tompa, N. Li, T. Bailey, G. Church, B. De Moor, E. Eskin, A. Favorov, M. Frith, Y. Fu, J. Kent, V. Makeev, A. Mironov, W. Noble, G. Pavesi, G. Pesole, M. Régnier, N. Simonis, S. Sinha, G. Thijs, J. Helden, M. Vandenbogaert, Z. Weng, C. Workman, C. Ye, Z. Zhu, "Assessing computational tools for the discovery of transcription factor binding sites", Nat. Biotechnol., vol. 23 (2005) 137-44. Pubmed 15637633.   Supplement.
  74. E. Torarinsson, Z. Yao, E. Wiklund, J. Bramsen, C. Hansen, J. Kjems, N. Tommerup, W. Ruzzo, J. Gorodkin, "Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions", Genome Res., vol. 18 (2008) 242-51. Pubmed 18096747.
  75. H. Tseng, M. Tompa, "Algorithms for locating extremely conserved elements in multiple sequence alignments", BMC Bioinformatics, vol. 10 (2009) 432. Pubmed 20021665.
  76. H. Tseng, Z. Weinberg, J. Gore, R. Breaker, W. Ruzzo, "Finding non-coding RNAs through genome-scale clustering", J Bioinform Comput Biol, vol. 7 (2009) 373-88. Pubmed 19340921.
  77. A. Wang, W. Ruzzo, M. Tompa, "How accurately is ncRNA aligned within whole-genome multiple alignments?", BMC Bioinformatics, vol. 8 (2007) 417. Pubmed 17963514.   Supplement.
  78. K. Wang, M. Narayanan, M. Tompa, J. Zhu, E. Schadt, "Inter-Species Comparison of Liver Co-expression Networks Elucidates Traits Associated with Common Human Diseases", 5th Annual RECOMB Satellite on Regulatory Genomics and 4th Annual RECOMB Satellite on Systems Biology, (2008)
  79. K. Wang, M. Narayanan, H. Zhong, M. Tompa, E. Schadt, J. Zhu, "Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases", PLoS Comput. Biol., vol. 5 (2009) e1000616. Pubmed 20019805.
  80. Z. Weinberg, J. Barrick, Z. Yao, A. Roth, J. Kim, J. Gore, J. Wang, E. Lee, K. Block, N. Sudarsan, S. Neph, M. Tompa, W. Ruzzo, R. Breaker, "Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline", Nucleic Acids Res., vol. 35 (2007) 4809-19. Pubmed 17621584.   Supplement.
  81. Z. Weinberg, E. Regulski, M. Hammond, J. Barrick, Z. Yao, W. Ruzzo, R. Breaker, "The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches", RNA, vol. 14 (2008) 822-8. Pubmed 18369181.
  82. Z. Weinberg, W. Ruzzo, "Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy", Bioinformatics, vol. 20 Suppl 1 (2004) i334-41. Pubmed 15262817.   Supplement.
  83. Z. Weinberg, W. Ruzzo, "Faster Genome Annotation of Non-coding RNA Families Without Loss of Accuracy", Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004), (2004) pp 243-251.   Supplement.
  84. Z. Weinberg, W. Ruzzo, "Sequence-based heuristics for faster annotation of non-coding RNA families", Bioinformatics, vol. 22 (2006) 35-9. Pubmed 16267089.   Supplement.
  85. Z. Yao, J. Barrick, Z. Weinberg, S. Neph, R. Breaker, M. Tompa, W. Ruzzo, "A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes", PLoS Comput. Biol., vol. 3 (2007) e126. Pubmed 17616982.   Supplement.
  86. Z. Yao, W. Ruzzo, "A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data", BMC Bioinformatics, vol. 7 Suppl 1 (2006) S11. Pubmed 16723004.
  87. Z. Yao, Z. Weinberg, W. Ruzzo, "CMfinder--a covariance model based RNA motif finding algorithm", Bioinformatics, vol. 22 (2006) 445-52. Pubmed 16357030.   Supplement.
  88. K. Yeung, M. Barrett, J. Delrow, P. Blount, L. Hsu, W. Ruzzo, B. Reid, P. Rabinovitch, "Expression analysis of Barrett's epithelium and normal gastrointestinal tissues", University of Washington Department of Computer Science & Engineering Technical Report UW-CSE-00-11-01, (2000)
  89. K. Yeung, C. Fraley, A. Murua, A. Raftery, W. Ruzzo, "Model-based clustering and data transformations for gene expression data", Bioinformatics, vol. 17 (2001) 977-87. Pubmed 11673243.   Supplement.
  90. K. Yeung, D. Haynor, W. Ruzzo, "Validating clustering for gene expression data", Bioinformatics, vol. 17 (2001) 309-18. Pubmed 11301299.   Supplement.
  91. K. Yeung, W. Ruzzo, "Principal component analysis for clustering gene expression data", Bioinformatics, vol. 17 (2001) 763-74. Pubmed 11590094.   Supplement.
  92. D. Zhang, G. Seelig, "Dynamic DNA nanotechnology using strand-displacement reactions", Nat Chem, vol. 3 (2011) 103-13. Pubmed 21258382.
  93. R. Giancarlo, D. Sankoff, E. Rocke, "Using Suffix Trees for Gapped Motif Discovery", Combinatorial Pattern Matching, 11th Annual Symposium, vol. 1848 (2000)