Sridhar Hannenhalli

Summary

Affiliation: University of Pennsylvania
Country: USA

Publications

  1. 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
  2. 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
  3. pmc Genome-wide analysis of natural selection on human cis-elements
    Praveen Sethupathy
    Department of Genetics, School of Medicine, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
    PLoS ONE 3:e3137. 2008
  4. 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
  5. 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
  6. 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
  7. pmc The evolution of Fox genes and their role in development and disease
    Sridhar Hannenhalli
    Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    Nat Rev Genet 10:233-40. 2009
  8. pmc Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction
    Matthew Hansen
    Department of Genetics, Penn Center for Bioinformatics, University of Pennsylvania, Pennsylvania, USA
    Algorithms Mol Biol 5:4. 2010
  9. 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
  10. pmc CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features
    Kobby Essien
    Penn Center for Bioinformatics, Department of Genetics, 415 Curie Boulevard, University of Pennsylvania, Philadelphia, PA 19104, USA
    Genome Biol 10:R131. 2009

Collaborators

Detail Information

Publications51

  1. 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...
  2. 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...
  3. pmc Genome-wide analysis of natural selection on human cis-elements
    Praveen Sethupathy
    Department of Genetics, School of Medicine, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
    PLoS ONE 3:e3137. 2008
    ..Furthermore, the functional regions are comprised of a variety of different types of elements, each under potentially different selection regimes...
  4. 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...
  5. 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...
  6. 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...
  7. pmc The evolution of Fox genes and their role in development and disease
    Sridhar Hannenhalli
    Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    Nat Rev Genet 10:233-40. 2009
    ..We summarize the salient features of the evolution of the Fox gene family and highlight the diverse contribution of various Fox subfamilies to developmental processes, from organogenesis to speech acquisition...
  8. pmc Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction
    Matthew Hansen
    Department of Genetics, Penn Center for Bioinformatics, University of Pennsylvania, Pennsylvania, USA
    Algorithms Mol Biol 5:4. 2010
    ..CONCLUSIONS: While limited in some ways, as discussed, the work represents a novel approach to mine expression data and detect potential modulators of regulatory interactions...
  9. 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
    ....
  10. pmc CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features
    Kobby Essien
    Penn Center for Bioinformatics, Department of Genetics, 415 Curie Boulevard, University of Pennsylvania, Philadelphia, PA 19104, USA
    Genome Biol 10:R131. 2009
    ..It is possible that the differences in CTCF-DNA conformation at different binding sites underlie CTCF's functional diversity. If so, the CTCF binding sites may belong to distinct classes, each compatible with a specific functional role...
  11. pmc Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families
    Larry N Singh
    Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
    Nucleic Acids Res 38:738-49. 2010
    ..Our work presents a novel means of investigating the cis regulatory changes potentially mediating expression divergence in paralogous gene families under specific conditions...
  12. pmc Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons
    Rui Liu
    Department of Genetics and Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Genome Biol 10:R72. 2009
    ..The expression of genes in the pre- and post-synaptic neurons is under stringent spatio-temporal control, but the mechanism underlying the neuronal expression of these genes remains largely unknown...
  13. pmc Regulation of lung endoderm progenitor cell behavior by miR302/367
    Ying Tian
    Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Development 138:1235-45. 2011
    ..Thus, miR302/367 directs lung endoderm development by coordinating multiple aspects of progenitor cell behavior, including proliferation, differentiation and apical-basal polarity...
  14. 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
    ....
  15. 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...
  16. 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...
  17. 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...
  18. pmc Hopx and Hdac2 interact to modulate Gata4 acetylation and embryonic cardiac myocyte proliferation
    Chinmay M Trivedi
    Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
    Dev Cell 19:450-9. 2010
    ..These results suggest that Gata4 is a nonhistone target of Hdac2-mediated deacetylation and that Hdac2, Hopx, and Gata4 coordinately regulate cardiac myocyte proliferation during embryonic development...
  19. 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...
  20. pmc Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity
    Kobby Essien
    Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 3:e3122. 2008
    ..The genetic bases of phenotypic differences between parasites can be understood, in part, by investigating constraints on gene expression and genic sequences, both coding and regulatory...
  21. pmc Why transcription factor binding sites are ten nucleotides long
    Alexander J Stewart
    Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genetics 192:973-85. 2012
    ..Our analysis explains these features as well as the remarkable conservation of binding site characteristics across diverse taxa...
  22. doi request reprint Regulating the regulators: modulators of transcription factor activity
    Logan Everett
    Department of Genetics, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA
    Methods Mol Biol 674:297-312. 2010
    ..PTM-Switchboard is accessible at http://cagr.pcbi.upenn.edu/PTMswitchboard /..
  23. pmc Evidence for coregulation of myocardial gene expression by MEF2 and NFAT in human heart failure
    Mary E Putt
    Department of Biostatistics and Epidemiology, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
    Circ Cardiovasc Genet 2:212-9. 2009
    ..However, interactions among TFs in human heart failure are less understood. Here, we use genomic data to examine the evidence that 5 candidate TF families coregulate gene expression in human heart failure...
  24. pmc Gene profiling of human adipose tissue during evoked inflammation in vivo
    Rachana Shah
    Division of Pediatric Endocrinology, Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
    Diabetes 58:2211-9. 2009
    ..However, few human adipose-secreted proteins are known to mediate these processes. We hypothesized that microarray mRNA profiling of human adipose during evoked inflammation could identify novel adipocytokines...
  25. 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. ..
  26. pmc Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis
    Logan J Everett
    Genomics and Computational Biology Program, 700 Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104, USA
    Nucleic Acids Res 39:e78. 2011
    ..We validated our tool on a well-studied stress response network in yeast and on a STAT1-mediated regulatory network in human B cells. Our work represents a significant step toward a comprehensive model of gene transcription...
  27. pmc Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus
    Anchal Vishnoi
    Department of Biology, University of Pennsylvania, USA
    Mol Biol Evol 28:2615-27. 2011
    ..The population genetic-based analysis of selection operating within a single lineage ameliorates these limitations...
  28. pmc Genetic and physiological activation of osmosensitive gene expression mimics transcriptional signatures of pathogen infection in C. elegans
    Anne Katrin Rohlfing
    Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 5:e9010. 2010
    ..Together, our data suggest infection and osmotic adaptation share previously unappreciated transcriptional similarities which might be controlled via regulation of tissue-specific GATA transcription factors...
  29. 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...
  30. 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...
  31. pmc Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1
    Sergey Yu Yaklichkin
    Penn Center for Bioinformatics, 1424 Blockley Hall, 423 Guardian Drive, University of Pennsylvania, Philadelphia, PA 19104 USA
    BMC Evol Biol 11:302. 2011
    ..However, avian FOXE1 genes have not been characterized and as such, codon evolution of FOXE1 orthologs in a broader evolutionary context of mammals and birds is not known...
  32. pmc Myocardin-like protein 2 regulates TGFβ signaling in embryonic stem cells and the developing vasculature
    Jian Li
    University of Pennsylvania Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104 4283, USA
    Development 139:3531-42. 2012
    ..Taken together, these data demonstrate that MKL2 regulates a conserved TGF-β signaling pathway that is required for angiogenesis and ultimately embryonic survival...
  33. pmc Epigenomic and RNA structural correlates of polyadenylation
    Mugdha Khaladkar
    Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
    RNA Biol 8:529-37. 2011
    ..Additionally we report hitherto unknown epigenomic correlates for poly(A) site usage...
  34. pmc PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes
    Logan Everett
    Penn Center for Bioinformatics, Department of Genetics and Department of Computer Science, University of Pennsylvania, Philadelphia, PA, USA
    Nucleic Acids Res 37:D66-71. 2009
    ..In the future, the database will be expanded to mammalian organisms, and will also include triplets predicted from computational approaches. The database can be accessed at http://cagr.pcbi.upenn.edu/PTMswitchboard...
  35. pmc Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development
    Le Ben Wan
    Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Development 135:2729-38. 2008
    ..This is the first study detailing a global and essential role for CTCF in mouse oocytes and preimplantation embryos...
  36. pmc Young proteins experience more variable selection pressures than old proteins
    Anchal Vishnoi
    Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Res 20:1574-81. 2010
    ..We discuss, via specific examples, the consequences of these findings for understanding of the sources of evolutionary novelty...
  37. 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...
  38. pmc Resistin gene variation is associated with systemic inflammation but not plasma adipokine levels, metabolic syndrome or coronary atherosclerosis in nondiabetic Caucasians
    Atif N Qasim
    Cardiovascular Institute, Institute for Translational Medicine and Therapeutics, and Department of Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 6160, USA
    Clin Endocrinol (Oxf) 70:698-705. 2009
    ..We hypothesized that the -420C>G putative gain-of-function resistin variant would be associated with inflammatory markers and atherosclerosis but not with metabolic syndrome or adipokines in humans...
  39. pmc Functional divergence of gene duplicates - a domain-centric view
    Mugdha Khaladkar
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
    BMC Evol Biol 12:126. 2012
    ..Here we further investigate the mechanism and functional underpinning of this phenomenon by assessing asymmetric evolution specifically within functional domains of gene duplicates...
  40. 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...
  41. pmc Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes
    Nana Minkah
    Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 6076, USA
    Virology 365:60-9. 2007
    ..These data define the full variola virus topoisomerase recognition site and provide a new window on topoisomerase function in vivo...
  42. 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...
  43. pmc Recurring genomic breaks in independent lineages support genomic fragility
    Hanno Hinsch
    Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA
    BMC Evol Biol 6:90. 2006
    ..In contrast, we investigate whether this regional fragility is an inherent genomic characteristic and is thus conserved over multiple independent lineages...
  44. pmc Differential transcriptional response to nonassociative and associative components of classical fear conditioning in the amygdala and hippocampus
    Michael B Keeley
    Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Learn Mem 13:135-42. 2006
    ....
  45. 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
    ....
  46. 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...
  47. 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...
  48. 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
    ....
  49. ncbi request reprint A note on efficient computation of haplotypes via perfect phylogeny
    Vineet Bafna
    Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
    J Comput Biol 11:858-66. 2004
    ..For the second problem of computing a PPH solution that minimizes the number of distinct haplotypes, we show that the problem is NP-hard using a reduction from Vertex Cover (Garey and Johnson, 1979)...
  50. 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...
  51. 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...

Research Grants4

  1. Algorithms to investigate transcriptional networks
    Sridhar Hannenhalli; Fiscal Year: 2007
    ....
  2. Methods for evolutionary analysis of eukaryotic transcriptional regulation
    Sridhar Hannenhalli; Fiscal Year: 2009
    ..We proposed to develop computational algorithms and statistical analysis methods to address some of these questions concerning the evolution of gene families and transcriptional regulation. ..
  3. Methods for evolutionary analysis of eukaryotic transcriptional regulation
    Sridhar Hannenhalli; Fiscal Year: 2009
    ..We proposed to develop computational algorithms and statistical analysis methods to address some of these questions concerning the evolution of gene families and transcriptional regulation. ..