Sridhar Hannenhalli

发表

Epigenomic Model of Cardiac Enhancers with Application to Genome Wide Association Studies

Avinash Das Sahu, Radhouane Aniba, Yen-Pei Christy Chang, 2012, Pacific Symposium on Biocomputing.

A SIMD solution to the sequence comparison problem on the MGAP

Mary Jane Irwin, Sridhar Hannenhalli, Manjit Borah, 1994, Proceedings of IEEE International Conference on Application Specific Array Processors (ASSAP'94).

Enrichment of regulatory signals in conserved non-coding genomic sequence

Sridhar Hannenhalli, Christopher T. Workman, Samuel Levy, 2001, Bioinform..

Hardness of flip-cut problems from optical mapping [DNA molecules application]

S. Muthukrishnan, Sridhar Hannenhalli, Vlado Dancík, 1997, Proceedings. Compression and Complexity of SEQUENCES 1997 (Cat. No.97TB100171).

Proceedings of the 7th international conference on Algorithms in Bioinformatics

Raffaele Giancarlo, Sridhar Hannenhalli, 2007 .

Hardness of Flip-Cut Problems from Optical Mapping

S. Muthukrishnan, Sridhar Hannenhalli, Vlado Dancík, 1997, J. Comput. Biol..

A Tutorial of the Poisson Random Field Model in Population Genetics

Praveen Sethupathy, Sridhar Hannenhalli, P. Sethupathy, 2008, Adv. Bioinformatics.

Mimosa: Mixture Model of Co-expression to Detect Modulators of Regulatory Interaction

Sridhar Hannenhalli, Matthew Hansen, Logan Everett, 2009, WABI.

Polynomial-time Algorithm for Computing Translocation Distance Between Genomes

Sridhar Hannenhalli, S. Hannenhalli, 1995, Discret. Appl. Math..

Generalizations of Markov model to characterize biological sequences

Junwen Wang, Sridhar Hannenhalli, 2005, BMC Bioinformatics.

Conservation Patterns in cis-Elements Reveal Compensatory Mutations

Sridhar Hannenhalli, Perry Evans, Greg Donahue, 2006, Comparative Genomics.

Dense subgraph computation via stochastic search: application to detect transcriptional modules

Sridhar Hannenhalli, Li-San Wang, Logan Everett, 2006, ISMB.

Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction

Sridhar Hannenhalli, Larry N. Singh, Matthew Hansen, 2009, Algorithms for Molecular Biology.

Proceedings of the 7th international workshop on Algorithms in Bioinformatics

Raffaele Giancarlo, Sridhar Hannenhalli, 2007 .

A Note on Efficient Computation of Haplotypes via Perfect Phylogeny

Shibu Yooseph, Vineet Bafna, Dan Gusfield, 2004, J. Comput. Biol..

Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals

Pavel A. Pevzner, Sridhar Hannenhalli, P. Pevzner, 1995, JACM.

Fast Sorting by Reversal

Piotr Berman, Sridhar Hannenhalli, P. Berman, 1996, CPM.

Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin

Michelle Girvan, Robert Patro, Geet Duggal, 2013, BCB.

Transforming Cabbage into Turnip: Polynomial Algorithm for Sorting Signed Permutations by Reversals

Pavel A. Pevzner, Sridhar Hannenhalli, 1999, J. ACM.

1.375-Approximation Algorithm for Sorting by Reversals

Marek Karpinski, Piotr Berman, Sridhar Hannenhalli, 2002, ESA.

ChIPulate: A comprehensive ChIP-seq simulation pipeline

Sridhar Hannenhalli, Rahul Siddharthan, Vishaka Datta, 2018, bioRxiv.

Abstract A023: Cell migration is a stronger predictor of patient survival in breast cancer than cell proliferation

Eytan Ruppin, Sridhar Hannenhalli, Nishanth Ulhas Nair, 2018 .

An Interaction-Dependent Model for Transcription Factor Binding

Sridhar Hannenhalli, Shane T. Jensen, Li-San Wang, 2005, Systems Biology and Regulatory Genomics.

Enhanced position weight matrices using mixture models

Sridhar Hannenhalli, Li-San Wang, S. Hannenhalli, 2005, ISMB.

Phenotype-Dependent Coexpression Gene Clusters: Application to Normal and Premature Ageing

Kun Wang, Avinash Das Sahu, Sridhar Hannenhalli, 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Widespread evidence of viral miRNAs targeting host pathways

Joseph W. Carl, Sridhar Hannenhalli, Joanne Trgovcich, 2013, BMC Bioinformatics.

Guest Editors' Introduction to the Special Section on Algorithms in Bioinformatics

Raffaele Giancarlo, Sridhar Hannenhalli, 2008, IEEE ACM Trans. Comput. Biol. Bioinform..

Polynomial-time Algorithm for Computing Translocation Distance between Genomes

Sridhar Hannenhalli, 1995, CPM.

Selection of Target Sites for Mobile DNA Integration in the Human Genome

Sridhar Hannenhalli, Frederic D. Bushman, Jeremy Leipzig, 2006, PLoS Comput. Biol..

Eukaryotic transcription factor binding sites - modeling and integrative search methods

Sridhar Hannenhalli, S. Hannenhalli, 2008, Bioinform..

Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution

Joshua B. Plotkin, M. Senthil Kumar, Sridhar Hannenhalli, 2015, PLoS Comput. Biol..

Towards a Computational Theory of Genome Rearrangements

Pavel A. Pevzner, Sridhar Hannenhalli, P. Pevzner, 1995, Computer Science Today.

Identification of gene clusters with phenotype-dependent expression with application to normal and premature ageing

Kun Wang, Avinash Das Sahu, Sridhar Hannenhalli, 2013, BCB.

Efficient algorithms for computing matching and chromatic polynomials on series-parallel graphs

Sridhar Hannenhalli, N. Chandrasekharan, 1992, Proceedings ICCI `92: Fourth International Conference on Computing and Information.

Positional sequencing by hybridization

Steven Skiena, Pavel A. Pevzner, Sridhar Hannenhalli, 1996, Comput. Appl. Biosci..

Chromatin and genomic determinants of alternative splicing

Kun Wang, Sridhar Hannenhalli, Kan Cao, 2015, BCB.

Proceedings of the Sixth Annual International Conference on Computational Biology, RECOMB 2002, Washington, DC, USA, April 18-21, 2002

David Sankoff, Sorin Istrail, Pavel A. Pevzner, 2002, RECOMB.

To cut…or not to cut (applications of comparative physical maps in molecular evolution)

Pavel A. Pevzner, Sridhar Hannenhalli, P. Pevzner, 1996, SODA '96.

Algorithms in Bioinformatics, 7th International Workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007, Proceedings

Raffaele Giancarlo, Sridhar Hannenhalli, 2007, WABI.

Ligand-Receptor Pairing Via Tree Comparison

Vineet Bafna, Sridhar Hannenhalli, Ken Rice, 2000, J. Comput. Biol..

Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model

Steven Skiena, S. Muthukrishnan, Martin Farach-Colton, 1997, J. Comput. Biol..

Inferring evolution of gene duplicates using probabilistic models and nonparametric belief propagation

Jia Zeng, Sridhar Hannenhalli, 2013, BMC Genomics.

A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer

Roded Sharan, Sridhar Hannenhalli, Sushant Patkar, 2017, PLoS Comput. Biol..

A distributed algorithm for ear decomposition

R. Sridhar, Kalyan S. Perumalla, Sridhar Hannenhalli, 1993, Proceedings of ICCI'93: 5th International Conference on Computing and Information.

Promoter prediction in the human genome

Sridhar Hannenhalli, Samuel Levy, S. Levy, 2001, ISMB.

Transforming men into mice (polynomial algorithm for genomic distance problem)

Pavel A. Pevzner, Sridhar Hannenhalli, P. Pevzner, 1995, Proceedings of IEEE 36th Annual Foundations of Computer Science.

PTM-Switchboard—a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes

Sridhar Hannenhalli, Logan Everett, Antony Vo, 2008, Nucleic Acids Res..

Prioritizing and characterizing functionally relevant genes across human tissues

Sridhar Hannenhalli, Gowthami Somepalli, Arashdeep Singh, 2021, PLoS Comput. Biol..

Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure

Sridhar Hannenhalli, Thomas P Cappola, Mary E Putt, 2006, Circulation.

Recurring genomic breaks in independent lineages support genomic fragility

Sridhar Hannenhalli, Hanno Hinsch, S. Hannenhalli, 2006, BMC Evolutionary Biology.

Identification of transcription factor binding sites in the human genome sequence

Sridhar Hannenhalli, Samuel Levy, S. Levy, 2002, Mammalian Genome.

Why Transcription Factor Binding Sites Are Ten Nucleotides Long

Alexander J. Stewart, Sridhar Hannenhalli, Joshua B Plotkin, 2012, Genetics.

Young Proteins Experience More Variable Selection Pressures than Material Supplemental P

Joshua B. Plotkin, Georgii A. Bazykin, Sridhar Hannenhalli, 2022 .

Retroviral DNA Integration: Viral and Cellular Determinants of Target-Site Selection

Paul Shinn, Sridhar Hannenhalli, Francis Collins, 2006, PLoS pathogens.

High-Throughput Identification of Cis-Regulatory Rewiring Events in Yeast.

Sridhar Hannenhalli, Shrutii Sarda, S. Hannenhalli, 2015, Molecular biology and evolution.

TREMOR—a tool for retrieving transcriptional modules by incorporating motif covariance

Sridhar Hannenhalli, Larry N. Singh, Li-San Wang, 2007, Nucleic acids research.

A mammalian promoter model links cis elements to genetic networks.

Sridhar Hannenhalli, S. Hannenhalli, Junwen Wang, 2006, Biochemical and biophysical research communications.

Young proteins experience more variable selection pressures than old proteins.

Sridhar Hannenhalli, Sergey Kryazhimskiy, Anchal Vishnoi, 2010, Genome research.

RNA-Seq identifies novel myocardial gene expression signatures of heart failure.

Euan A Ashley, Sridhar Hannenhalli, Thomas P Cappola, 2015, Genomics.

Harnessing synthetic lethality to predict the response to cancer treatment

Eytan Ruppin, Sridhar Hannenhalli, Paul S. Meltzer, 2018, Nature Communications.

Analysis and correction of compositional bias in sparse sequencing count data

Stephanie C. Hicks, Sridhar Hannenhalli, Eric V. Slud, 2017, BMC Genomics.

Next-Generation Sequencing and Epigenomics Research: A Hammer in Search of Nails

Sridhar Hannenhalli, Shrutii Sarda, S. Hannenhalli, 2014, Genomics & informatics.

MetaProm: a neural network based meta-predictor for alternative human promoter prediction

Sridhar Hannenhalli, Hung Tseng, Lyle H Ungar, 2007, BMC Genomics.

Genome-wide analysis of retroviral DNA integration

Sridhar Hannenhalli, Jeremy Leipzig, Christian Hoffmann, 2005, Nature Reviews Microbiology.

The evolution of Fox genes and their role in development and disease

Sridhar Hannenhalli, Klaus H. Kaestner, K. Kaestner, 2009, Nature Reviews Genetics.

New Role for Interleukin‐13 Receptor α1 in Myocardial Homeostasis and Heart Failure

Eytan Ruppin, Sridhar Hannenhalli, Allon Wagner, 2017, Journal of the American Heart Association.

Computational Analysis of Constraints on Noncoding Regions, Coding Regions and Gene Expression in Relation to Plasmodium Phenotypic Diversity

Christian J. Stoeckert, Sridhar Hannenhalli, Kobby Essien, 2008, PloS one.

Gene Coexpression Network Topology of Cardiac Development, Hypertrophy, and Failure

Euan A. Ashley, Sridhar Hannenhalli, Frederick E. Dewey, 2011, Circulation. Cardiovascular genetics.

.375-approximation Algorithm for Sorting by Reversals

Marek Karpinski, Sridhar Hannenhalli, 2011 .

Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons

Sridhar Hannenhalli, Rui Liu, Maja Bucan, 2009, Genome Biology.

CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features

Sridhar Hannenhalli, Larry N. Singh, Sofia Apreleva, 2009, Genome Biology.

Transcriptional regulation of protein complexes and biological pathways

Sridhar Hannenhalli, Samuel Levy, S. Levy, 2003, Mammalian Genome.