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Sridhar Hannenhalli

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Oligonucleotide Array Sequence Analysis

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Publications

TOP 3
Sun Shim Choi; Sridhar Hannenhalli
Three independent determinants of protein evolutionary rate.
Robert Kim; PRAKASH KULKARNI; Sridhar Hannenhalli
Derepression of Cancer/testis antigens in cancer is associated with distinct patterns of DNA hypomethylation.
Avinash Das Sahu; Radhouane Aniba; Yen-Pei C Chang; Sridhar Hannenhalli
Epigenomic model of cardiac enhancers with application to genome wide association studies.

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All Publications

2013: Sun Shim Choi; Sridhar Hannenhalli
Three independent determinants of protein evolutionary rate.
Journal of molecular evolution 2013;76(3):98-111.
2013: Robert Kim; PRAKASH KULKARNI; Sridhar Hannenhalli
Derepression of Cancer/testis antigens in cancer is associated with distinct patterns of DNA hypomethylation.
BMC cancer 2013;13():144.
2013: Avinash Das Sahu; Radhouane Aniba; Yen-Pei C Chang; Sridhar Hannenhalli
Epigenomic model of cardiac enhancers with application to genome wide association studies.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2013;():92-102.
2013: Rithun Mukherjee; Larry N Singh; Perry Evans; Sridhar Hannenhalli
Correlated evolution of positions within mammalian cis elements.
PloS one 2013;8(2):e55521.
2013: Joseph W Carl; Joanne Trgovcich; Sridhar Hannenhalli
Widespread evidence of viral miRNAs targeting host pathways.
BMC bioinformatics 2013;14 Suppl 2():S3.
2013: Jia Zeng; Sridhar Hannenhalli
Inferring evolution of gene duplicates using probabilistic models and nonparametric belief propagation.
BMC genomics 2013;14 Suppl 1():S15.
2013: Gita Mahmoudabadi; Krithika Rajagopalan; Govindan Rangarajan; Robert H Getzenberg; Sridhar Hannenhalli; PRAKASH KULKARNI
Intrinsically disordered proteins and conformational noise: implications in cancer.
Cell cycle (Georgetown, Tex.) 2013;12(1):26-31.
2012: Jian Li; Xiaohong Zhu; Nina Bowens; Thomas P Cappola; Mary Chen; Lan Cheng; Sridhar Hannenhalli; Michael S Parmacek
Myocardin-like protein 2 regulates TGFβ signaling in embryonic stem cells and the developing vasculature.
Development (Cambridge, England) 2012;139(19):3531-42.
2012: Mugdha Khaladkar; Sridhar Hannenhalli
Functional divergence of gene duplicates - a domain-centric view.
BMC evolutionary biology 2012;12():126.
2011: Anchal Vishnoi; Joshua B Plotkin; Praveen Sethupathy; Daniel Simola; Sridhar Hannenhalli
Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus.
Molecular biology and evolution 2011;28(9):2615-27.
2011: Logan J Everett; Shane T Jensen; Sridhar Hannenhalli
Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis.
Nucleic acids research 2011;39(12):e78.
2011: Mugdha Khaladkar; Mark Smyda; Sridhar Hannenhalli
Epigenomic and RNA structural correlates of polyadenylation.
RNA biology 2011;8(3):529-37.
2011: Ying Tian; Yuzhen Zhang; Laura Hurd; Sridhar Hannenhalli; Feiyan Liu; Min Min Lu; Edward Morrisey
Regulation of lung endoderm progenitor cell behavior by miR302/367.
Development (Cambridge, England) 2011;138(7):1235-45.
2011: Frederick E Dewey; Marco V Perez; Matthew T Wheeler; Clifton Watt; Joshua Spin; Peter Langfelder; Steve Horvath; Sridhar Hannenhalli; Thomas P Cappola; Euan Ashley
Gene coexpression network topology of cardiac development, hypertrophy, and failure.
Circulation. Cardiovascular genetics 2011;4(1):26-35.
2011: Sergey Yu Yaklichkin; Maricela V Pier; Parker B Antin; Diana K Darnell; Sridhar Hannenhalli
Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1.
BMC evolutionary biology 2011;11():302.
2010: Anchal Vishnoi; Sergey Kryazhimskiy; Georgii A Bazykin; Sridhar Hannenhalli; Joshua B Plotkin
Young proteins experience more variable selection pressures than old proteins.
Genome research 2010;20(11):1574-81.
2010: Chinmay M Trivedi; Wenting Zhu; Qiaohong Wang; Cheng Jia; Hae Jin Kee; Li Li; Sridhar Hannenhalli; Jonathan A Epstein
Hopx and Hdac2 interact to modulate Gata4 acetylation and embryonic cardiac myocyte proliferation.
Developmental cell 2010;19(3):450-9.
2010: Logan Everett; Matthew Hansen; Sridhar Hannenhalli
Regulating the regulators: modulators of transcription factor activity.
Methods in molecular biology (Clifton, N.J.) 2010;674():297-312.
2010: Anne-Katrin Rohlfing; Yana Miteva; Sridhar Hannenhalli; Todd Lamitina
Genetic and physiological activation of osmosensitive gene expression mimics transcriptional signatures of pathogen infection in C. elegans.
PloS one 2010;5(2):e9010.
2010: Matthew Hansen; Logan Everett; Larry Singh; Sridhar Hannenhalli
Mimosa: mixture model of co-expression to detect modulators of regulatory interaction.
Algorithms for molecular biology : AMB 2010;5():4.
2010: Larry N Singh; Sridhar Hannenhalli
Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families.
Nucleic acids research 2010;38(3):738-49.
2009: Rachana Shah; Yun Lu; Christine C Hinkle; Fiona C McGillicuddy; Roy Kim; Sridhar Hannenhalli; Thomas P Cappola; Sean Heffron; XingMei Wang; Nehal N Mehta; Mary Putt; Muredach P Reilly
Gene profiling of human adipose tissue during evoked inflammation in vivo.
Diabetes 2009;58(10):2211-9.
2009: Mary E Putt; Sridhar Hannenhalli; Yun Lu; Philip Haines; Hareesh R Chandrupatla; Edward E Morrisey; Kenneth B Margulies; Thomas P Cappola
Evidence for coregulation of myocardial gene expression by MEF2 and NFAT in human heart failure.
Circulation. Cardiovascular genetics 2009;2(3):212-9.
2009: Atif N Qasim; Thomas S Metkus; Mahlet G Tadesse; Michael Lehrke; Stephanie Restine; Megan L Wolfe; Sridhar Hannenhalli; Thomas Cappola; Daniel J Rader; Muredach P Reilly
Resistin gene variation is associated with systemic inflammation but not plasma adipokine levels, metabolic syndrome or coronary atherosclerosis in nondiabetic Caucasians.
Clinical endocrinology 2009;70(5):698-705.
2009: Sridhar Hannenhalli; Klaus H Kaestner
The evolution of Fox genes and their role in development and disease.
Nature reviews. Genetics 2009;10(4):233-40.
2009: Kobby Essien; Sébastien Vigneau; Sofia Apreleva; Larry N Singh; Marisa S Bartolomei; Sridhar Hannenhalli
CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.
Genome biology 2009;10(11):R131.
2009: Rui Liu; Sridhar Hannenhalli; Maja Bucan
Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons.
Genome biology 2009;10(7):R72.
2008: David Fermin; Ana Barac; Sangjin Lee; Sean P Polster; Sridhar Hannenhalli; Tracy L Bergemann; Suzanne Grindle; David B Dyke; Francis D Pagani; Leslie W Miller; Sarah Tan; Cris Dos Remedios; Thomas P Cappola; Kenneth B Margulies; Jennifer L Hall
Sex and age dimorphism of myocardial gene expression in nonischemic human heart failure.
Circulation. Cardiovascular genetics 2008;1(2):117-25.
2008: Le-Ben Wan; Hua Pan; Sridhar Hannenhalli; Yong Cheng; Jun Ma; Andrew Fedoriw; Victor Lobanenkov; Keith E Latham; Richard M Schultz; Marisa S Bartolomei
Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development.
Development (Cambridge, England) 2008;135(16):2729-38.
2008: Sridhar Hannenhalli
Eukaryotic transcription factor binding sites--modeling and integrative search methods.
Bioinformatics (Oxford, England) 2008;24(11):1325-31.
2008: Praveen Sethupathy; Sridhar Hannenhalli
A tutorial of the poisson random field model in population genetics.
Advances in bioinformatics 2008;():257864.
2008: Praveen Sethupathy; Hoa Giang; Joshua B Plotkin; Sridhar Hannenhalli
Genome-wide analysis of natural selection on human cis-elements.
PloS one 2008;3(9):e3137.
2008: Kobby Essien; Sridhar Hannenhalli; Christian J Stoeckert
Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity.
PloS one 2008;3(9):e3122.
2008: Larry N Singh; Sridhar Hannenhalli
Functional diversification of paralogous transcription factors via divergence in DNA binding site motif and in expression.
PloS one 2008;3(6):e2345.
2007: Nana Minkah; Young Hwang; Kay Perry; Gregory D Van Duyne; Robert Hendrickson; Elliot J Lefkowitz; Sridhar Hannenhalli; Frederic D Bushman
Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes.
Virology 2007;365(1):60-9.
2007: Shuzhang Yang; Kai Wang; Otto Valladares; Sridhar Hannenhalli; Maja Bucan
Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex.
Genome biology 2007;8(11):R247.
2007: Larry N Singh; Li-San Wang; Sridhar Hannenhalli
TREMOR--a tool for retrieving transcriptional modules by incorporating motif covariance.
Nucleic acids research 2007;35(21):7360-71.
2007: Junwen Wang; Lyle H Ungar; Hung Tseng; Sridhar Hannenhalli
MetaProm: a neural network based meta-predictor for alternative human promoter prediction.
BMC genomics 2007;8():374.
2007: Saran Vardhanabhuti; Junwen Wang; Sridhar Hannenhalli
Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation.
Nucleic acids research 2007;35(10):3203-13.
2007: Yuzhen Zhang; Nibedita Rath; Sridhar Hannenhalli; Zhishan Wang; Thomas P Cappola; Shioko Kimura; Elena N Atochina-Vasserman; Min Min Lu; Michael F Beers; Edward Morrisey
GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivo.
Development (Cambridge, England) 2007;134(1):189-98.
2006: Charles Berry; Sridhar Hannenhalli; Jeremy Leipzig; Frederic D Bushman
Selection of target sites for mobile DNA integration in the human genome.
PLoS computational biology 2006;2(11):e157.
2006: Sridhar Hannenhalli; Mary E Putt; Joan M Gilmore; Junwen Wang; Michael S Parmacek; Jonathan A Epstein; Edward Morrisey; Kenneth B Margulies; Thomas P Cappola
Transcriptional genomics associates FOX transcription factors with human heart failure.
Circulation 2006;114(12):1269-76.
2006: Junwen Wang; Sridhar Hannenhalli
A mammalian promoter model links cis elements to genetic networks.
Biochemical and biophysical research communications 2006;347(1):166-77.
2006: Sridhar Hannenhalli; R P Middleton; S Levy; B Perroud; JA Holzwarth; K McDonald; SS Hannah
Identification and cross-species comparison of canine osteoarthritic gene regulatory cis-elements.
Osteoarthritis and cartilage / OARS, Osteoarthritis Research Society 2006;14(8):830-8.
2006: Logan Everett; Li-San Wang; Sridhar Hannenhalli
Dense subgraph computation via stochastic search: application to detect transcriptional modules.
Bioinformatics (Oxford, England) 2006;22(14):e117-23.
2006: Mary K Lewinski; Masahiro Yamashita; Michael Emerman; Angela Ciuffi; Heather Marshall; Gregory Crawford; Francis Collins; Paul Shinn; Jeremy Leipzig; Sridhar Hannenhalli; Charles C Berry; SD MA; Frederic D Bushman
Retroviral DNA integration: viral and cellular determinants of target-site selection.
PLoS pathogens 2006;2(6):e60.
2006: Michael B Keeley; Marcelo A Wood; Carolina Isiegas; Joel Stein; Kevin Hellman; Sridhar Hannenhalli; Ted Abel
Differential transcriptional response to nonassociative and associative components of classical fear conditioning in the amygdala and hippocampus.
Learning & memory (Cold Spring Harbor, N.Y.) 2006;13(2):135-42.
2006: David A Ross; Sridhar Hannenhalli; John W Tobias; Neil Cooch; Ramin Shiekhattar; Tom Kadesch
Functional analysis of Hes-1 in preadipocytes.
Molecular endocrinology (Baltimore, Md.) 2006;20(3):698-705.
2006: Dexter Hadley; Tara Murphy; Otto Valladares; Sridhar Hannenhalli; Lyle Ungar; Junhyong Kim; Maja Bućan
Patterns of sequence conservation in presynaptic neural genes.
Genome biology 2006;7(11):R105.
2006: Hanno Hinsch; Sridhar Hannenhalli
Recurring genomic breaks in independent lineages support genomic fragility.
BMC evolutionary biology 2006;6():90.
2005: Frederic D Bushman; Mary K Lewinski; Angela Ciuffi; Stephen Barr; Jeremy Leipzig; Sridhar Hannenhalli; Christian Hoffmann
Genome-wide analysis of retroviral DNA integration.
Nature reviews. Microbiology 2005;3(11):848-58.
2005: Sridhar Hannenhalli; Li-San Wang
Enhanced position weight matrices using mixture models.
Bioinformatics (Oxford, England) 2005;21 Suppl 1():i204-12.
2005: Mary K Lewinski; Dwayne Bisgrove; Paul Shinn; Huaming Chen; Christian Hoffmann; Sridhar Hannenhalli; Eric Verdin; Charles C Berry; SD MA; Frederic D Bushman
Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription.
Journal of virology 2005;79(11):6610-9.
2005: Junwen Wang; Sridhar Hannenhalli
Generalizations of Markov model to characterize biological sequences.
BMC bioinformatics 2005;6():219.
2004: Vineet Bafna; Dan Gusfield; Sridhar Hannenhalli; Shibu Yooseph
A note on efficient computation of haplotypes via perfect phylogeny.
Journal of computational biology : a journal of computational molecular cell biology 2004;11(5):858-66.
2003: Sridhar Hannenhalli; Samuel Levy
Transcriptional regulation of protein complexes and biological pathways.
Mammalian genome : official journal of the International Mammalian Genome Society 2003;14(9):611-9.
2002: Sridhar Hannenhalli; Samuel Levy
Predicting transcription factor synergism.
Nucleic acids research 2002;30(19):4278-84.
2002: Samuel Levy; Sridhar Hannenhalli
Identification of transcription factor binding sites in the human genome sequence.
Mammalian genome : official journal of the International Mammalian Genome Society 2002;13(9):510-4.
2002: Sridhar Hannenhalli; Earl Hubell; Robert Lipshutz; Pavel A Pevzner
Combinatorial algorithms for design of DNA arrays.
Advances in biochemical engineering/biotechnology 2002;77():1-19.
2001: Sridhar Hannenhalli; S Levy
Promoter prediction in the human genome.
Bioinformatics (Oxford, England) 2001;17 Suppl 1():S90-6.
2000: Vineet Bafna; Sridhar Hannenhalli; K Rice; L Vawter
Ligand-receptor pairing via tree comparison.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(1-2):59-70.
1997: R Agarwala; S Batzoglou; V Dancík; S E Decatur; Sridhar Hannenhalli; M Farach; S Muthukrishnan; S Skiena
Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model.
Journal of computational biology : a journal of computational molecular cell biology 1997;4(3):275-96.
1997: V Dancík; Sridhar Hannenhalli; S Muthurkrishnan
Hardness of flip-cut problems from optical mapping.
Journal of computational biology : a journal of computational molecular cell biology 1997;4(2):119-25.