Research Topics
Genomes and Genes
| Sridhar HannenhalliSummaryAffiliation: University of Pennsylvania Country: USA Publications
Research Grants
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Detail Information
Publications
Generalizations of Markov model to characterize biological sequencesJunwen 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...
Eukaryotic transcription factor binding sites--modeling and integrative search methodsSridhar 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...
Enhanced position weight matrices using mixture modelsSridhar 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...- Mimosa: Mixture model of co-expression to detect modulators of regulatory interactionMatthew 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... - The evolution of Fox genes and their role in development and diseaseSridhar 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... - CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic featuresKobby 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... - Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neuronsRui 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... - Regulation of lung endoderm progenitor cell behavior by miR302/367Ying 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... - Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene familiesLarry 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... - Patterns of sequence conservation in presynaptic neural genesDexter Hadley
Penn Center for Bioinformatics, 423 Guardian Drive, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Genome Biol 7:R105. 2006..Furthermore, comparative sequence analysis will facilitate selection of genes and noncoding sequences for future functional studies and analysis of variation studies in neurodevelopmental and psychiatric disorders... - Genome-wide analysis of natural selection on human cis-elementsPraveen Sethupathy
Department of Genetics, School of Medicine, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
PLoS ONE 3:e3137. 2008..Thus our genome-scale investigation provides evidence for positive selection on putative transcription factor binding sites in human proximal promoters... - Dense subgraph computation via stochastic search: application to detect transcriptional modulesLogan Everett
Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
Bioinformatics 22:e117-23. 2006..Finally, our combined analysis of Cardiac, Skeletal, and Smooth muscle data recapitulates the evolutionary relationship among the three tissues... - Hopx and Hdac2 interact to modulate Gata4 acetylation and embryonic cardiac myocyte proliferationChinmay 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... - GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivoYuzhen Zhang
Department of Medicine and University of Pennsylvania, Philadelphia, PA 19104, USA
Development 134:189-98. 2007.... - Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortexShuzhang 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... - Evidence for coregulation of myocardial gene expression by MEF2 and NFAT in human heart failureMary 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... - Regulating the regulators: modulators of transcription factor activityLogan 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 /.. - Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservationSaran 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... - Gene profiling of human adipose tissue during evoked inflammation in vivoRachana 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... - A mammalian promoter model links cis elements to genetic networksJunwen 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... - Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysisLogan 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... - TREMOR--a tool for retrieving transcriptional modules by incorporating motif covarianceLarry 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... - Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxusAnchal 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... - Genetic and physiological activation of osmosensitive gene expression mimics transcriptional signatures of pathogen infection in C. elegansAnne 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... - Functional diversification of paralogous transcription factors via divergence in DNA binding site motif and in expressionLarry 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... - Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversityKobby 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... - Transcriptional genomics associates FOX transcription factors with human heart failureSridhar 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... - Genome-wide analysis of retroviral DNA integrationFrederic 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... - Myocardin-like protein 2 regulates TGFβ signaling in embryonic stem cells and the developing vasculatureJian 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... - Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1Sergey 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... - Epigenomic and RNA structural correlates of polyadenylationMugdha 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... - PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genesLogan 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... - Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo developmentLe 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... - Young proteins experience more variable selection pressures than old proteinsAnchal 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... - Functional divergence of gene duplicates - a domain-centric viewMugdha 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... - MetaProm: a neural network based meta-predictor for alternative human promoter predictionJunwen 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... - Recurring genomic breaks in independent lineages support genomic fragilityHanno 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... - Functional analysis of Hes-1 in preadipocytesDavid 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... - Differential transcriptional response to nonassociative and associative components of classical fear conditioning in the amygdala and hippocampusMichael B Keeley
Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Learn Mem 13:135-42. 2006.... - Resistin gene variation is associated with systemic inflammation but not plasma adipokine levels, metabolic syndrome or coronary atherosclerosis in nondiabetic CaucasiansAtif 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... - Predicting transcription factor synergismSridhar 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... - Transcriptional regulation of protein complexes and biological pathwaysSridhar 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... - Identification of transcription factor binding sites in the human genome sequenceSamuel Levy
Informatics Research, Celera Corporation, Rockville, Maryland 20850, USA
Mamm Genome 13:510-4. 2002.... - Retroviral DNA integration: viral and cellular determinants of target-site selectionMary K Lewinski
Infectious Disease Laboratory, The Salk Institute, La Jolla, California, USA
PLoS Pathog 2:e60. 2006.... - Selection of target sites for mobile DNA integration in the human genomeCharles 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.... - Combinatorial algorithms for design of DNA arraysSridhar 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... - Whole-genome shotgun assembly and comparison of human genome assembliesSorin 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... - A note on efficient computation of haplotypes via perfect phylogenyVineet 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)...
Research Grants
- Algorithms to investigate transcriptional networksSridhar Hannenhalli; Fiscal Year: 2007....
- Methods for evolutionary analysis of eukaryotic transcriptional regulationSridhar 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. ..