Saurabh Sinha

Summary

Affiliation: University of Illinois
Country: USA

Publications

  1. pmc Genome scan for cis-regulatory DNA motifs associated with social behavior in honey bees
    Saurabh Sinha
    Department of Computer Science, Institute of Genomic Biology, University of Illinois at Urbana Champaign, 201 North Goodwin Avenue, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 103:16352-7. 2006
  2. pmc MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules
    Saurabh Sinha
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
    PLoS Comput Biol 3:e216. 2007
  3. ncbi request reprint On counting position weight matrix matches in a sequence, with application to discriminative motif finding
    Saurabh Sinha
    Department of Computer Science, University of Illinois Urbana Champaign, 201 N Goodwin Ave, Urbana, IL 61801, USA
    Bioinformatics 22:e454-63. 2006
  4. pmc Stubb: a program for discovery and analysis of cis-regulatory modules
    Saurabh Sinha
    Department of Computer Science, University of Illinois, Urbana Champaign, NY, USA
    Nucleic Acids Res 34:W555-9. 2006
  5. pmc Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution
    Xin He
    Department of Computer Science, University of Illinois Urbana Champaign, Urbana, IL, USA
    PLoS Comput Biol 5:e1000299. 2009
  6. pmc Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances
    Jaebum Kim
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
    PLoS Comput Biol 6:e1000652. 2010
  7. pmc Incorporating chromatin accessibility data into sequence-to-expression modeling
    Pei Chen Peng
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, Illinois
    Biophys J 108:1257-67. 2015
  8. doi request reprint Evaluating thermodynamic models of enhancer activity on cellular resolution gene expression data
    Abul Hassan Samee
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, IL, USA
    Methods 62:79-90. 2013
  9. pmc Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development
    Majid Kazemian
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, IL, USA, Laboratory of Molecular Immunology and Immunology Center, National Heart Lung and Blood Institute, National Institutes of Health, MD, USA, Program in Gene Function and Expression, University of Massachusetts Medical School, MA, USA, Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School, MA, USA, Department of Molecular Medicine, University of Massachusetts Medical School, MA, USA and Institute of Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA
    Nucleic Acids Res 41:8237-52. 2013
  10. pmc Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy
    Qiong Cheng
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, IL, USA
    PLoS Genet 9:e1003571. 2013

Collaborators

Detail Information

Publications47

  1. pmc Genome scan for cis-regulatory DNA motifs associated with social behavior in honey bees
    Saurabh Sinha
    Department of Computer Science, Institute of Genomic Biology, University of Illinois at Urbana Champaign, 201 North Goodwin Avenue, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 103:16352-7. 2006
    ....
  2. pmc MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules
    Saurabh Sinha
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
    PLoS Comput Biol 3:e216. 2007
    ..Our work will fill in this void and enable more reliable analysis of CRM evolution...
  3. ncbi request reprint On counting position weight matrix matches in a sequence, with application to discriminative motif finding
    Saurabh Sinha
    Department of Computer Science, University of Illinois Urbana Champaign, 201 N Goodwin Ave, Urbana, IL 61801, USA
    Bioinformatics 22:e454-63. 2006
    ..We finally use the algorithm on genes predictive of social behavior in the honey bee, and find interesting motifs...
  4. pmc Stubb: a program for discovery and analysis of cis-regulatory modules
    Saurabh Sinha
    Department of Computer Science, University of Illinois, Urbana Champaign, NY, USA
    Nucleic Acids Res 34:W555-9. 2006
    ..The web server may be accessed at the URL http://stubb.rockefeller.edu/...
  5. pmc Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution
    Xin He
    Department of Computer Science, University of Illinois Urbana Champaign, Urbana, IL, USA
    PLoS Comput Biol 5:e1000299. 2009
    ..Our approach is implemented as software, EMMA (Evolutionary Model-based cis-regulatory Module Analysis), ready to be applied in a broad biological context...
  6. pmc Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances
    Jaebum Kim
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
    PLoS Comput Biol 6:e1000652. 2010
    ..We also apply the framework to find motifs associated with socially regulated gene sets in the honeybee, Apis mellifera, using comparisons with Nasonia, a solitary species, to identify honeybee-specific associations...
  7. pmc Incorporating chromatin accessibility data into sequence-to-expression modeling
    Pei Chen Peng
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, Illinois
    Biophys J 108:1257-67. 2015
    ..It also calls for future advances in modeling accessibility levels from sequence and the transregulatory context, so as to predict accurately the effect of cis and trans perturbations on gene expression. ..
  8. doi request reprint Evaluating thermodynamic models of enhancer activity on cellular resolution gene expression data
    Abul Hassan Samee
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, IL, USA
    Methods 62:79-90. 2013
    ..Finally, we show how fitting quantitative models on data sets comprising a handful of enhancers, as reported in earlier work, may lead to unreliable models...
  9. pmc Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development
    Majid Kazemian
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, IL, USA, Laboratory of Molecular Immunology and Immunology Center, National Heart Lung and Blood Institute, National Institutes of Health, MD, USA, Program in Gene Function and Expression, University of Massachusetts Medical School, MA, USA, Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School, MA, USA, Department of Molecular Medicine, University of Massachusetts Medical School, MA, USA and Institute of Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA
    Nucleic Acids Res 41:8237-52. 2013
    ..This study demonstrates how DNA-binding motifs can be used to produce a comprehensive map of sequence signatures for different mechanisms of combinatorial TF action. ..
  10. pmc Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy
    Qiong Cheng
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, IL, USA
    PLoS Genet 9:e1003571. 2013
    ....
  11. pmc A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data
    Xin He
    Department of Computer Science, University of Illinois at Urbana Champaign, Champaign, Illinois, United States of America
    PLoS ONE 4:e8155. 2009
    ..How transcription factors (TFs) interact with cis-regulatory sequences and interact with each other is a fundamental, but not well understood, aspect of gene regulation...
  12. pmc Evolution of regulatory sequences in 12 Drosophila species
    Jaebum Kim
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
    PLoS Genet 5:e1000330. 2009
    ....
  13. pmc Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison
    Majid Kazemian
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Nucleic Acids Res 39:9463-72. 2011
    ..We make our program available as downloadable source code, and as a plugin for a genome browser installed on our servers...
  14. ncbi request reprint A statistical method for alignment-free comparison of regulatory sequences
    Miriam R Kantorovitz
    Department of Computer Science, University of Illinois, Urbana Champaign, Illinois, USA
    Bioinformatics 23:i249-55. 2007
    ..Here we focus on the task of identifying functional relationships between cis-regulatory sequences that are non-orthologous or greatly diverged. 'Alignment-free' measures of sequence similarity are required in this regime...
  15. pmc Simulations of enhancer evolution provide mechanistic insights into gene regulation
    Thyago Duque
    Department of Computer Science, University of Illinois at Urbana Champaign
    Mol Biol Evol 31:184-200. 2014
    ..We thus demonstrate how specific mechanistic details encoded in CRMs can be revealed by modeling their evolution and fitting such models to multispecies data. ..
  16. pmc New meta-analysis tools reveal common transcriptional regulatory basis for multiple determinants of behavior
    Seth A Ament
    Neuroscience Program, Department of Computer Science, and Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 109:E1801-10. 2012
    ..This regulatory code would have been missed by traditional gene coexpression or cis-regulatory analytic methods. We expect that our meta-analysis tools will be useful for a broad array of problems in systems biology and other fields...
  17. ncbi request reprint Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment
    Jaebum Kim
    Department of Computer Science, University of Illinois, Urbana Champaign, Urbana, IL, USA
    Bioinformatics 23:289-97. 2007
    ..Although the former requirement has been extensively addressed, the latter problem has received little attention, especially in a comprehensive probabilistic framework...
  18. pmc Genome Surveyor 2.0: cis-regulatory analysis in Drosophila
    Majid Kazemian
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Nucleic Acids Res 39:W79-85. 2011
    ..The server is free and open to all users, and there is no login requirement. Address: http://veda.cs.uiuc.edu/gs...
  19. pmc The transcription factor ultraspiracle influences honey bee social behavior and behavior-related gene expression
    Seth A Ament
    Neuroscience Program, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
    PLoS Genet 8:e1002596. 2012
    ..Our findings demonstrate how "single gene effects" on behavioral plasticity can involve complex transcriptional networks, in both brain and peripheral tissues...
  20. pmc Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse
    Miriam R Kantorovitz
    Department of Mathematics, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Dev Cell 17:568-79. 2009
    ..Overall, 7/7 predictions were validated successfully in vivo, demonstrating the effectiveness of our approach for insect and mammalian genomes...
  21. doi request reprint Evolution of cis-regulatory sequences in Drosophila
    Xin He
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, IL, USA
    Methods Mol Biol 674:283-96. 2010
    ..We point out common technical challenges, such as reliable sequence alignment and binding site prediction, when doing comparative regulatory sequence analysis and note some potential solutions thereof...
  22. pmc Honey bee aggression supports a link between gene regulation and behavioral evolution
    Cedric Alaux
    Department of Entomology, University of Illinois, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 106:15400-5. 2009
    ..It appears that one element in the evolution of different degrees of aggressive behavior in honey bees involved changes in regulation of genes that mediate the response to alarm pheromone...
  23. pmc Quantitative modeling of a gene's expression from its intergenic sequence
    Md Abul Hassan Samee
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
    PLoS Comput Biol 10:e1003467. 2014
    ..Thus, interference between enhancer activities was a possible factor necessitating enhancer independence in our model. ..
  24. pmc Towards realistic benchmarks for multiple alignments of non-coding sequences
    Jaebum Kim
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    BMC Bioinformatics 11:54. 2010
    ..However, it is not clear if such benchmarks truly represent real sequence data from any given group of species, in terms of the difficulty of alignment tasks...
  25. ncbi request reprint PhyME: a software tool for finding motifs in sets of orthologous sequences
    Saurabh Sinha
    Department of Computer Science, University of Illinois, USA
    Methods Mol Biol 395:309-18. 2007
    ..Here, we describe the usage of this algorithm, publicly available as a Linux-based implementation...
  26. doi request reprint Global parameter estimation for thermodynamic models of transcriptional regulation
    Yerzhan Suleimenov
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Methods 62:99-108. 2013
    ....
  27. pmc Systematic functional characterization of cis-regulatory motifs in human core promoters
    Saurabh Sinha
    Department of Computer Science, University of Illinois Urbana Champaign, Urbana, Illinois 61801, USA
    Genome Res 18:477-88. 2008
    ..Our analysis thus provides a concrete framework for uncovering the biological function of cis-regulatory motifs genome wide...
  28. pmc Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs
    Andra Ivan
    Department of Computer Science and Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Genome Biol 9:R22. 2008
    ..We find that the challenge of predicting cis-regulatory modules ab initio, without any input of relevant motifs, is a realizable goal...
  29. pmc Big Data: Astronomical or Genomical?
    Zachary D Stephens
    Coordinated Science Laboratory and Department of Electrical and Computer Engineering, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
    PLoS Biol 13:e1002195. 2015
    ..Now is the time for concerted, community-wide planning for the "genomical" challenges of the next decade...
  30. pmc Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism
    Charles Blatti
    Department of Computer Science, University of Illinois, Urbana, IL 61801, USA
    Nucleic Acids Res 43:3998-4012. 2015
    ....
  31. pmc Transcriptional regulation of brain gene expression in response to a territorial intrusion
    Yibayiri O Sanogo
    Integrative Biology, University of Illinois, Urbana Champaign, IL, USA
    Proc Biol Sci 279:4929-38. 2012
    ..Finally, we found a remarkably close association between gene expression and aggressive behaviour at the individual level. This study sheds light on the molecular mechanisms in the brain that underlie the response to social challenges...
  32. pmc Quantitative modeling of gene expression using DNA shape features of binding sites
    Pei Chen Peng
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Nucleic Acids Res 44:e120. 2016
    ..It also provides a framework for future studies to predict gene expression better than with PWM models alone. ..
  33. pmc Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks
    Charles Blatti
    Department of Computer Science, University of Illinois, Urbana, IL 61801, USA
    Bioinformatics 32:2167-75. 2016
    ..Most existing network-based approaches for recognizing genes or annotations relevant to a given gene set collapse information about different properties to simplify (homogenize) the networks...
  34. pmc Redeployment of a conserved gene regulatory network during Aedes aegypti development
    Kushal Suryamohan
    Department of Biochemistry, University at Buffalo State University of New York, Buffalo, NY, United States NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, United States
    Dev Biol 416:402-13. 2016
    ....
  35. pmc What does it take to evolve an enhancer? A simulation-based study of factors influencing the emergence of combinatorial regulation
    Thyago Duque
    Department of Computer Science, University of Illinois at Urbana Champaign
    Genome Biol Evol 7:1415-31. 2015
    ..Our simulations also revealed that certain features of an enhancer might evolve not due to their biological function but as aids to the evolutionary process itself. ..
  36. pmc Motif enrichment tool
    Charles Blatti
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Nucleic Acids Res 42:W20-5. 2014
    ..The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. ADDRESS: http://veda.cs.uiuc.edu/MET/...
  37. 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...
  38. pmc A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system
    Marcus B Noyes
    Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Nucleic Acids Res 36:2547-60. 2008
    ....
  39. 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...
  40. 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...
  41. ncbi request reprint A probabilistic method to detect regulatory modules
    Saurabh Sinha
    Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 0021, USA
    Bioinformatics 19:i292-301. 2003
    ..The discovery of cis-regulatory modules in metazoan genomes is crucial for understanding the connection between genes and organism diversity...
  42. pmc Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila
    Saurabh Sinha
    Center for Studies in Physics and Biology, Rockefeller University, 1230 York Ave, New York, NY10021, USA
    BMC Bioinformatics 5:129. 2004
    ..It is important to quantify how comparative genomics can improve computational detection of such modules...
  43. 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...
  44. ncbi request reprint Sequence turnover and tandem repeats in cis-regulatory modules in drosophila
    Saurabh Sinha
    Center for Studies in Physics and Biology, The Rockefeller University, USA
    Mol Biol Evol 22:874-85. 2005
    ....
  45. ncbi request reprint Discriminative motifs
    Saurabh Sinha
    Center for Studies in Physics and Biology, Box 25, The Rockefeller University, New York, NY 10021, USA
    J Comput Biol 10:599-615. 2003
    ..We apply our framework to two popular motif models and are able to detect several known binding sites in sets of co-regulated genes in yeast...
  46. pmc Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
    Long Li
    Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14214, USA
    Genome Biol 8:R101. 2007
    ..Transcriptional cis-regulatory modules (for example, enhancers) play a critical role in regulating gene expression. While many individual regulatory elements have been characterized, they have never been analyzed as a class...
  47. pmc Motif module map reveals enforcement of aging by continual NF-kappaB activity
    Adam S Adler
    Program in Epithelial Biology and Cancer Biology Program, Stanford University School of Medicine, Stanford, California 94305, USA
    Genes Dev 21:3244-57. 2007
    ..These results identify a conserved network of regulatory pathways underlying mammalian aging and show that NF-kappaB is continually required to enforce many features of aging in a tissue-specific manner...