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Pavel Sumazin |
Research Interests
Transcription Regulation, Computational Molecular Biology, Combinatorial Algorithms and Optimization.Software
Comprehensive Regulatory Element Analysis and DiscoveryDiscriminating Matrix Enumerator
Discriminating Word Enumerator
MatCompare
Discrete Optimizer
Publications
Tissue-specific regulatory elements in mammalian promoters, Andrew D. Smith, Pavel Sumazin and Michael Q. Zhang. Molecular Systems Biology, 3(73), 2007. [pdf, html] Supporting Information [pdf]TCat: the catalog of tissue-specific regulatory motifs [html]
DNA motifs in human and mouse proximal promoters predict tissue-specific expression, Andrew D. Smith, Pavel Sumazin, Zhenyu Xuan and Michael Q. Zhang. Proceedings of the National Academy of Sciences USA, 103(16):6275-6280, 2006. [pdf, html]
Supporting Information [pdf]; Promoters, transcripts, motifs, modules and predictive models [html]
Mining ChIP-chip Data for Transcription Factor and Cofactor Binding Sites, Andrew D. Smith, Pavel Sumazin, Debopriya Das and Michael Q. Zhang. Bioinformatics, 21 Suppl 1:i403-i412, 2005. [pdf]
Presented at the Thirteenth International Conference on Intelligent Systems for Molecular Biology (ISMB), Detroit, MI, 2005.
Identifying tissue-selective transcription factor binding sites in vertebrate promoters, Andrew D. Smith, Pavel Sumazin, Michael Q. Zhang. Proceedings of the National Academy of Sciences USA, 102(5):1560-1565, 2005. [html, pdf]
Supporting Information (PNAS site) [html]
Highlights appeared in Nature Reviews Drug Discovery and Nature Reviews Genetics, February and March 2005. [html]
DWE: Discriminant Word Enumerator, Pavel Sumazin, Gengxin Chen, Naoya Hata, Andrew D. Smith, Theresa Zhang and Michael Q. Zhang. Bioinformatics, 21(1):31-38, 2005. [pdf]
Similarity of Position Frequency Matrices for Transcription Factor Binding Sites, Dustin Schones, Pavel Sumazin and Michael Q. Zhang. Bioinformatics, 21(3):307-313, 2005. [pdf]
Genome-wide Prediction and Analysis of Function-Specific Transcription Factor Binding Sites, Fan Long, Hong Liu, Chang Hahn, Pavel Sumazin, Michael Q. Zhang and Asher Zilberstein. In Silico Biology, 4(4):395-410, 2004. [html]
All-Pairs Lowest Common Ancestors in Trees and Directed Acyclic Graphs, Michael Bender, Martin Farach-Colton, Giri Pemmasani and Steven Skiena, Pavel Sumazin. Journal of Algorithms, 57(2): 75-94, 2005. [pdf]
Preliminary versions in SODA 2001 and LATIN 2002:
The Level Ancestor Problem Simplified, Michael Bender, Martin Farach-Colton. In Proceeding of Latin American Theoretical INformatics (LATIN) 2002: 508-515. [postscript]
All-Pairs Least Common Ancestors in Directed Acyclic Graphs, Michael Bender, Giri Pemmasani and Steven Skiena, Pavel Sumazin. In Proceeding of the Twelfth ACM-SIAM Symposium on Discrete Algorithms (SODA), 2001, 845-854. [postscript]
Shift-Error Detection and Correction in SAT exams, Steve Skiena, Pavel Sumazin. Submitted.
Shift Error Detection in Standardized Exams, Steve Skiena, Pavel Sumazin. Journal of Discrete Algorithms 2(2): 313-331, 2004. [postscript]
Preliminary version appeared in Proceeding of the 11th Annual Symposium on Combinatorial Pattern Matching (CPM), Montreal Canada, June 2000, 264-276. [postscript]
Cited by Karen W. Arenson, The New York Times, April 2006. [html]
Simple Rearrangement using Length-Weighted Inversions, Lina Dong, Saurabh Sethia, Pavel Sumazin. Technical Report PDX-CS-TR-06-01, first submitted September 2003. [pdf]
Deconvolving Sequence Variation in Mixed DNA Populations, Andy Wildenberg, Steven Skiena and Pavel Sumazin. Journal of Computational Biology, 2003;10(3-4):635-652. [pdf]
Preliminary version appeared in Proceeding of the 6th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Washington DC, April 2002, 311-320. [postscript]
A Model for Analyzing Black-Box Optimization, Vinhthuy Phan, Steven Skiena and Pavel Sumazin. In Proceedings of the 2003 Workshop on Algorithms and Data Structures (WADS), Ottawa, Canada, July 2003, Lecture Notes in Computer Science, Volume 2748, 424-438. [postscript]
A Time-Sensitive System for Black-Box Combinatorial Optimization, Vinhthuy Phan, Pavel Sumazin and Steven Skiena. In Proceeding of the 4th Workshop on Algorithm Engineering and Experiments (ALENEX), San Francisco, California, January 2002, 16-28. [postscript]
Algorithm Visualization
Algorithm visualizations are contributed by Portland State University undergraduate students.Alignment Computation Visualization by Mike Zapp, Sirisha Pagadala, Jaswant Tawdekar and Alexander Weitzer.
Tree LCA algorithms by Zack Ramjan, Muhammad Ahsun Yusuf and Muhammad Karamutullah.
Links
Andrew D SmithISMB2007 tutorial
CREAD