Sridhar Hannenhalli

Summary

Affiliation: Celera Genomics
Country: USA

Publications

  1. ncbi request reprint Promoter prediction in the human genome
    S Hannenhalli
    Informatics Research, Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Bioinformatics 17:S90-6. 2001
  2. pmc Predicting transcription factor synergism
    Sridhar Hannenhalli
    Informatics Research, Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 30:4278-84. 2002
  3. ncbi request reprint Transcriptional regulation of protein complexes and biological pathways
    Sridhar Hannenhalli
    Informatics Research, Celera Genomics, 45 West Gude Drive, Rockville, Maryland 20850, USA
    Mamm Genome 14:611-9. 2003
  4. ncbi request reprint Identification of transcription factor binding sites in the human genome sequence
    Samuel Levy
    Informatics Research, Celera Corporation, Rockville, Maryland 20850, USA
    Mamm Genome 13:510-4. 2002
  5. pmc CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation
    Robert N Plasschaert
    Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA, Program of Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA, Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA and Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
    Nucleic Acids Res 42:774-89. 2014
  6. pmc Whole-genome shotgun assembly and comparison of human genome assemblies
    Sorin Istrail
    Applied Biosystems, 45 West Gude Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 101:1916-21. 2004
  7. pmc Functional diversification of paralogous transcription factors via divergence in DNA binding site motif and in expression
    Larry N Singh
    Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania, Philadephia, Pennsylvania, United States of America
    PLoS ONE 3:e2345. 2008
  8. doi request reprint Eukaryotic transcription factor binding sites--modeling and integrative search methods
    Sridhar Hannenhalli
    Penn Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, USA
    Bioinformatics 24:1325-31. 2008
  9. pmc Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex
    Shuzhang Yang
    Department of Genetics and Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Genome Biol 8:R247. 2007
  10. pmc Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation
    Saran Vardhanabhuti
    Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104 6021, USA
    Nucleic Acids Res 35:3203-13. 2007

Collaborators

Detail Information

Publications24

  1. ncbi request reprint Promoter prediction in the human genome
    S Hannenhalli
    Informatics Research, Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Bioinformatics 17:S90-6. 2001
    ..We suggest some biological experiments and studies to better understand the biology of transcription...
  2. pmc Predicting transcription factor synergism
    Sridhar Hannenhalli
    Informatics Research, Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 30:4278-84. 2002
    ..Further investigation of 50 pairs randomly selected from each of these two sets using PubMed queries provided additional supporting evidence from the existing biological literature suggesting TF synergism for these novel pairs...
  3. ncbi request reprint Transcriptional regulation of protein complexes and biological pathways
    Sridhar Hannenhalli
    Informatics Research, Celera Genomics, 45 West Gude Drive, Rockville, Maryland 20850, USA
    Mamm Genome 14:611-9. 2003
    ..This suggests a novel computational methodology for constructing high-order gene regulatory models and detecting co-regulated gene products...
  4. ncbi request reprint Identification of transcription factor binding sites in the human genome sequence
    Samuel Levy
    Informatics Research, Celera Corporation, Rockville, Maryland 20850, USA
    Mamm Genome 13:510-4. 2002
    ....
  5. pmc CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation
    Robert N Plasschaert
    Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA, Program of Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA, Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA and Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
    Nucleic Acids Res 42:774-89. 2014
    ..Our results suggest that the regulatory control of CTCF is dependent in part on specific motifs within its binding site. ..
  6. pmc Whole-genome shotgun assembly and comparison of human genome assemblies
    Sorin Istrail
    Applied Biosystems, 45 West Gude Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 101:1916-21. 2004
    ..The Celera results provide more order and orientation, and the consortium sequence provides better coverage of exact and nearly exact repeats...
  7. pmc Functional diversification of paralogous transcription factors via divergence in DNA binding site motif and in expression
    Larry N Singh
    Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania, Philadephia, Pennsylvania, United States of America
    PLoS ONE 3:e2345. 2008
    ..The relationship between these two modes of functional diversification of transcription factor paralogs has not been previously investigated, and is essential for understanding adaptive evolution of transcription factor gene families...
  8. doi request reprint Eukaryotic transcription factor binding sites--modeling and integrative search methods
    Sridhar Hannenhalli
    Penn Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, USA
    Bioinformatics 24:1325-31. 2008
    ..In this review we will discuss recent attempts to improve computational identification of TFBS through these two types of approaches and conclude with thoughts on future development...
  9. pmc Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex
    Shuzhang Yang
    Department of Genetics and Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Genome Biol 8:R247. 2007
    ..Bioinformatics analysis of these genes will provide insights into a wide-range of pathways that are involved in the pathophysiology of sleep disorders and psychiatric disorders with sleep disturbances...
  10. pmc Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation
    Saran Vardhanabhuti
    Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104 6021, USA
    Nucleic Acids Res 35:3203-13. 2007
    ..We then use the position and distance specificity to discover novel motifs. Our work highlights the importance of distance and position specificity, in addition to the evolutionary conservation, in discovering cis-regulatory motifs...
  11. pmc Selection of target sites for mobile DNA integration in the human genome
    Charles Berry
    Department of Family and Preventive Medicine, School of Medicine, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 2:e157. 2006
    ....
  12. pmc Patterns of sequence conservation in presynaptic neural genes
    Dexter Hadley
    Penn Center for Bioinformatics, 423 Guardian Drive, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Biol 7:R105. 2006
    ..Because synaptic function is evolutionarily conserved, we reasoned that functional sequences of genes and related genomic elements known to play important roles in neurotransmitter release would also be conserved...
  13. ncbi request reprint Transcriptional genomics associates FOX transcription factors with human heart failure
    Sridhar Hannenhalli
    Department of Genetics and Penn Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
    Circulation 114:1269-76. 2006
    ..We developed and applied a computational approach called transcriptional genomics to test the hypothesis that a discrete set of cardiac TFs is associated with human heart failure...
  14. ncbi request reprint Dense subgraph computation via stochastic search: application to detect transcriptional modules
    Logan Everett
    Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Bioinformatics 22:e117-23. 2006
    ..This is just one context in which an efficient computation of dense subgraphs in a multi-partite graph is needed...
  15. ncbi request reprint A mammalian promoter model links cis elements to genetic networks
    Junwen Wang
    Penn Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, 19104 6021, USA
    Biochem Biophys Res Commun 347:166-77. 2006
    ..The discovered links between promoter elements and gene function allows us to infer genetic networks from promoter elements. The web server for the PSPA promoter predictor is available at /PSPA...
  16. ncbi request reprint Enhanced position weight matrices using mixture models
    Sridhar Hannenhalli
    Department of Genetics, University of Pennsylvania Philadelphia, PA 19104, USA
    Bioinformatics 21:i204-12. 2005
    ..Intuitively, the subclasses correspond to either distinct binding preference of the same transcription factor in different contexts or distinct subtypes of the transcription factor...
  17. pmc Generalizations of Markov model to characterize biological sequences
    Junwen Wang
    Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104 6021, USA
    BMC Bioinformatics 6:219. 2005
    ..However, this neither takes into account the joint dependency of multiple neighboring nucleotides, nor does it consider the long range dependency with gap > 0...
  18. ncbi request reprint Genome-wide analysis of retroviral DNA integration
    Frederic Bushman
    University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104 6076, USA
    Nat Rev Microbiol 3:848-58. 2005
    ..Here, we review retroviral DNA integration, with emphasis on recent genome-wide studies of targeting and on the status of efforts to modulate target-site selection...
  19. pmc TREMOR--a tool for retrieving transcriptional modules by incorporating motif covariance
    Larry N Singh
    Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Nucleic Acids Res 35:7360-71. 2007
    ..The application of TREMOR on human muscle-specific, liver-specific and cell-cycle-related genes reveals TFs and TMs that were validated from literature and also reveals additional related genes...
  20. pmc MetaProm: a neural network based meta-predictor for alternative human promoter prediction
    Junwen Wang
    Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    BMC Genomics 8:374. 2007
    ..Furthermore, most PPPs are trained and tested on the most-upstream promoters; their performances on alternative promoters have not been assessed...
  21. ncbi request reprint Functional analysis of Hes-1 in preadipocytes
    David A Ross
    Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    Mol Endocrinol 20:698-705. 2006
    ..We conclude that Notch most likely blocks adipogenesis through the induction of Hes-1 homodimers, which repress transcription of key target genes...
  22. pmc Retroviral DNA integration: viral and cellular determinants of target-site selection
    Mary K Lewinski
    Infectious Disease Laboratory, The Salk Institute, La Jolla, California, USA
    PLoS Pathog 2:e60. 2006
    ....
  23. ncbi request reprint GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivo
    Yuzhen Zhang
    Department of Medicine and University of Pennsylvania, Philadelphia, PA 19104, USA
    Development 134:189-98. 2007
    ....
  24. ncbi request reprint Combinatorial algorithms for design of DNA arrays
    Sridhar Hannenhalli
    Department of Mathematics, University of Southern California, Los Angeles 90089 1113, USA
    Adv Biochem Eng Biotechnol 77:1-19. 2002
    ..We also address the difficult problem of finding an arrangement which minimizes the border length and come up with a new idea of threading that significantly reduces the border length as compared to standard designs...