Simple Rearrangement using Length-Weighted Inversions (2008)
Lina Dong, Saurabh Sethia, Pavel Sumazin
Abstract. Recent studies of genome rearrangement indicate a high proportion of short inversion events in genome evolution. This data motivates genome rearrangement models that reward short inversions...
Andrew D Smith, Pavel Sumazin, Michael Q Zhang
www.molecularsystemsbiology.com
Andrew D Smith, Pavel Sumazin, Michael Q Zhang
The identification of genomic regulatory patterns such as transcription factor binding sites is among the most important immediate challenges in genome science. Computational discovery of regulatory...
Adam A. Margolin, Teresa Palomero, Pavel Sumazin, Andrea Califano, Adolfo Ferrando, Gustavo A. Stolovitzky
ChIP-on-chip has emerged as a powerful tool to dissect the complex network of regulatory interactions between transcription factors and their targets. However, most ChIP-on-chip analysis methods use...
Shift Error Detection in Standardized Exams (Extended Abstract) (2007)
Computer-graded multiple choice examinations are a familiar and dreaded part of most student's lives. Many test takers are particularly fearful of form-lling
Michael A. Bender, Giridhar Pemmasani, Steven Skiena, Pavel Sumazin
We study the problem of nding least common ancestors (LCA) in trees and directed acyclic graphs (DAGs). We present a very simple optimal algorithm for the LCA problem in trees. We thus dispel the...
A Model for Analyzing Black-Box Optimization (Extended Abstract) (2007)
Vinhthuy Phan, Steven Skiena, Pavel Sumazin
The design of heuristics for NP-hard problems is perhaps the most active area of research in the theory of combinatorial algorithms. However, practitioners more often resort to local improvement...
Shift Error Detection in Standardized Exams (Extended Abstract) (2007)
Computer-graded multiple choice examinations are a familiar and dreaded part of most student's lives. Many test takers are particularly fearful of form-lling
DWE: discriminating word enumerator (2005)
Pavel Sumazin, Gengxin Chen, Naoya Hata, Andrew D. Smith, Michael Q. Zhang
Motivation: Tissue-specific transcription-factor binding sites give insight into tissue-specific transcription regulation. Results: We describe a word-counting-based tool for de novo tissue-specific...
Andrew D. Smith, Pavel Sumazin, Debopriya Das, Michael Q. Zhang
Vol. 21 Suppl. 1 2005, pages i403–i412 doi:10.1093/bioinformatics/bti1043
Lowest common ancestors in trees and directed acyclic graphs (2005)
Michael A. Bender, Martín Farach-colton, Giridhar Pemmasani, Steven Skiena, Pavel Sumazin
We study the problem of finding lowest common ancestors (LCA) in trees and directed acyclic graphs (DAGs). Specifically, we extend the LCA problem to DAGs and study the LCA variants that arise in...
Similarity of position frequency matrices for transcription factor binding sites (2005)
Schones, Dustin E., Sumazin, Pavel, Zhang, Michael Q.
Motivation: Transcription-factor binding sites (TFBS) in promoter sequences of higher eukaryotes are commonly modeled using position frequency matrices (PFM). The ability to compare PFMs representing...
Mining ChIP-chip data for transcription factor and cofactor binding sites (2005)
Smith, Andrew D., Sumazin, Pavel, Das, Debopriya, Zhang, Michael Q.
Motivation: Identification of single motifs and motif pairs that can be used to predict transcription factor localization in ChIP-chip data, and gene expression in tissue-specific microarray data....
DWE: Discriminating Word Enumerator (2005)
Sumazin, Pavel, Chen, Gengxin, Hata, Naoya, Smith, Andrew D., Zhang, Theresa, Zhang, Michael Q.
Motivation: Tissue-specific transcription factor binding sites give insight into tissue-specific transcription regulation. Results: We describe a word-counting-based tool for de novo tissue-specific...
DWE: discriminating word enumerator (2004)
Sumazin, Pavel, Chen, Gengxin, Hata, Naoya, Smith, Andrew D., Zhang, Theresa, Zhang, Michael Q.
Motivation: Tissue-specific transcription-factor binding sites give insight into tissue-specific transcription regulation. Results: We describe a word-counting-based tool for de novo tissue-specific...
Similarity of position frequency matrices for transcription factor binding sites (2004)
Schones, Dustin E., Sumazin, Pavel, Zhang, Michael Q.
Motivation: Transcription-factor binding sites in promoter sequences of higher eukaryotes are commonly modeled using position frequency matrices. The ability to compare position frequency matrices...
DWE: discriminating word enumerator (2004)
Sumazin, Pavel, Chen, Gengxin, Hata, Naoya, Smith, Andrew D., Zhang, Theresa, Zhang, Michael Q.
Motivation: Tissue-specific transcription-factor binding sites give insight into tissue-specific transcription regulation. Results: We describe a word-counting-based tool for de novo tissue-specific...
Similarity of position frequency matrices for transcription factor binding sites (2004)
Schones, Dustin E., Sumazin, Pavel, Zhang, Michael Q.
Motivation: Transcription-factor binding sites in promoter sequences of higher eukaryotes are commonly modeled using position frequency matrices. The ability to compare position frequency matrices...
A time-sensitive system for black-box combinatorial optimization (2002)
Vinhthuy Phan, Pavel Sumazin, Steven Skiena
When faced with a combinatorial optimization problem, practitioners often turn to black-box search heuristics such as simulated annealing and genetic algorithms. In black-box optimization, the...
A time-sensitive system for black-box combinatorial optimization (2002)
Vinhthuy Phan, Pavel Sumazin, Steven Skiena
When faced with a combinatorial optimization problem, practitioners often turn to black-box search heuristics such as simulated annealing and genetic algorithms. In black-box optimization, the...
Deconvolving sequence variation in mixed DNA populations (2002)
Andy Wildenberg, Steven Skiena, Pavel Sumazin
The need for DNA sequencing did not end with the successful public and private projects to sequence the human genome. Indeed, attention is shifting from de
Deconvolving sequence variation in mixed DNA populations (2002)
Andy Wildenberg, Steven Skiena, Pavel Sumazin
We present an original approach to identifying sequence variants in a mixed DNA population from sequence trace data. The heart of the method is based on parsimony: given a wildtype DNA sequence, a...
Finding least common ancestors in directed acyclic graphs (2001)
Michael A. Bender, Giridhar Pemmasani, Steven Skiena, Pavel Sumazin
One of the fundamental algorithmic problems on trees is how to nd the least common ancestor (LCA)
Shift error detection in standardized exams (2000)
ABSTRACT: Hundreds of millions of multiple choice exams are given every year in the United States. These exams permit formfilling shift errors, where an absent-minded mismarking displaces a long run...
Detecting and correcting shift errors in standardized exams (2000)
Hundreds of millions multiple choice exams are given every year in the United States. Form filling shift errors, where a single absent-minded mismarking displaces a long run of correct answers, can...
Identifying tissue-selective transcription factor binding sites in vertebrate promoters
Smith, Andrew D., Sumazin, Pavel, Zhang, Michael Q.
We present a computational method aimed at systematically identifying tissue-selective transcription factor binding sites. Our method focuses on the differences between sets of promoters that are...
DNA motifs in human and mouse proximal promoters predict tissue-specific expression
Smith, Andrew D., Sumazin, Pavel, Xuan, Zhenyu, Zhang, Michael Q.
Comprehensive identification of cis-regulatory elements is necessary for accurately reconstructing gene regulatory networks. We studied proximal promoters of human and mouse genes with differential...
Identifying tissue-selective transcription factor binding sites in vertebrate promoters
Smith, Andrew D., Sumazin, Pavel, Zhang, Michael Q.
We present a computational method aimed at systematically identifying tissue-selective transcription factor binding sites. Our method focuses on the differences between sets of promoters that are...
DNA motifs in human and mouse proximal promoters predict tissue-specific expression
Smith, Andrew D., Sumazin, Pavel, Xuan, Zhenyu, Zhang, Michael Q.
Comprehensive identification of cis-regulatory elements is necessary for accurately reconstructing gene regulatory networks. We studied proximal promoters of human and mouse genes with differential...
Tissue-specific regulatory elements in mammalian promoters
Smith, Andrew D, Sumazin, Pavel, Zhang, Michael Q
Transcription factor-binding sites and the cis-regulatory modules they compose are central determinants of gene expression. We previously showed that binding site motifs and modules in proximal...
Margolin, Adam A., Palomero, Teresa, Sumazin, Pavel, Califano, Andrea, Ferrando, Adolfo A., Stolovitzky, Gustavo
ChIP-on-chip has emerged as a powerful tool to dissect the complex network of regulatory interactions between transcription factors and their targets. However, most ChIP-on-chip analysis methods use...