Sridhar Hannenhalli - researchr alias

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Viewing Publication 1 - 48 from 48

2021

PathExt: a general framework for path-based mining of omics-integrated biological networksNarmada Sambaturu, Vaidehi Pusadkar, Sridhar Hannenhalli, Nagasuma Chandra. bioinformatics, 37(9):1254-1262, 2021. [doi]

Prioritizing and characterizing functionally relevant genes across human tissuesGowthami Somepalli, Sarthak Sahoo, Arashdeep Singh, Sridhar Hannenhalli. ploscb, 17(7), 2021. [doi]

2019

ChIPulate: A comprehensive ChIP-seq simulation pipelineVishaka Datta, Sridhar Hannenhalli, Rahul Siddharthan. ploscb, 15(3), 2019. [doi]

2017

A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancerSushant Patkar, Assaf Magen, Roded Sharan, Sridhar Hannenhalli. ploscb, 13(11), 2017. [doi]

2015

2013

Widespread evidence of viral miRNAs targeting host pathwaysJoseph W. Carl, Joanne Trgovcich, Sridhar Hannenhalli. bmcbi, 14(S-2), 2013. [doi]

Epigenomic Model of Cardiac Enhancers with Application to Genome Wide Association StudiesAvinash Das Sahu, Radhouane Aniba, Yen-Pei Christy Chang, Sridhar Hannenhalli. psb 2013: 92-102 [doi]

Identification of gene clusters with phenotype-dependent expression with application to normal and premature ageingKun Wang, Avinash Das, Zheng-Mei Xiong, Kan Cao, Sridhar Hannenhalli. bcb 2013: 377 [doi]

Topological properties of chromosome conformation graphs reflect spatial proximities within chromatinHao Wang, Geet Duggal, Robert Patro, Michelle Girvan, Sridhar Hannenhalli, Carl Kingsford. bcb 2013: 306 [doi]

Inferring evolution of gene duplicates using probabilistic models and nonparametric belief propagationJia Zeng, Sridhar Hannenhalli. bmcgenomics, 14(S-1), 2013. [doi]

2010

Mimosa: Mixture model of co-expression to detect modulators of regulatory interactionMatthew Hansen, Logan Everett, Larry Singh, Sridhar Hannenhalli. almob, 5:4, 2010. [doi]

2009

PTM-Switchboard - a database of posttranslational modifications of transcription factors, the mediating enzymes and target genesLogan Everett, Antony Vo, Sridhar Hannenhalli. nar, 37(Database-Issue):66-71, 2009. [doi]

Mimosa: Mixture Model of Co-expression to Detect Modulators of Regulatory InteractionMatthew Hansen, Logan Everett, Larry Singh, Sridhar Hannenhalli. wabi 2009: 133-144 [doi]

2008

Guest Editors Introduction to the Special Section on Algorithms in BioinformaticsRaffaele Giancarlo, Sridhar Hannenhalli. tcbb, 5(4):482-483, 2008. [doi]

Eukaryotic transcription factor binding sites - modeling and integrative search methodsSridhar Hannenhalli. bioinformatics, 24(11):1325-1331, 2008. [doi]

A Tutorial of the Poisson Random Field Model in Population GeneticsPraveen Sethupathy, Sridhar Hannenhalli. abi, 2008, 2008. [doi]

2006

Selection of Target Sites for Mobile DNA Integration in the Human GenomeCharles C. Berry, Sridhar Hannenhalli, Jeremy Leipzig, Frederic D. Bushman. ploscb, 2(11), 2006. [doi]

Conservation Patterns in ::::cis::::-Elements Reveal Compensatory MutationsPerry Evans, Greg Donahue, Sridhar Hannenhalli. recomb 2006: 186-199 [doi]

Dense subgraph computation via stochastic search: application to detect transcriptional modulesLogan Everett, Li-San Wang, Sridhar Hannenhalli. ismb 2006: 117-123 [doi]

2005

Enhanced position weight matrices using mixture modelsSridhar Hannenhalli, Li-San Wang. ismb 2005: 204-212 [doi]

An Interaction-Dependent Model for Transcription Factor BindingLi-San Wang, Shane T. Jensen, Sridhar Hannenhalli. recomb 2006: 225-234 [doi]

Generalizations of Markov model to characterize biological sequencesJunwen Wang, Sridhar Hannenhalli. bmcbi, 6:219, 2005. [doi]

2004

A Note on Efficient Computation of Haplotypes via Perfect PhylogenyVineet Bafna, Dan Gusfield, Sridhar Hannenhalli, Shibu Yooseph. jcb, 11(5):858-866, 2004. [doi]

2002

1.375-Approximation Algorithm for Sorting by ReversalsPiotr Berman, Sridhar Hannenhalli, Marek Karpinski. esa 2002: 200-210 [doi]

2001

1.375-Approximation Algorithm for Sorting by ReversalsPiotr Berman, Sridhar Hannenhalli, Marek Karpinski. eccc, 8(47), 2001. [doi]

Promoter prediction in the human genomeSridhar Hannenhalli, Samuel Levy. ismb 2001: 90-96

Enrichment of regulatory signals in conserved non-coding genomic sequenceSamuel Levy, Sridhar Hannenhalli, Christopher T. Workman. bioinformatics, 17(10):871-877, 2001.

2000

Ligand-Receptor Pairing Via Tree ComparisonVineet Bafna, Sridhar Hannenhalli, Ken Rice, Lisa Vawter. jcb, 7(1-2):59-70, 2000.

1999

Transforming Cabbage into Turnip: Polynomial Algorithm for Sorting Signed Permutations by ReversalsSridhar Hannenhalli, Pavel A. Pevzner. JACM, 46(1):1-27, 1999. [doi]

1997

Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP modelRicha Agarwala, Serafim Batzoglou, Vlado Dancík, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, S. Muthukrishnan, Steven Skiena. recomb 1997: 1-2 [doi]

Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP ModelRicha Agarwala, Serafim Batzoglou, Vlado Dancík, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, Steven Skiena. soda 1997: 390-399

Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP ModelRicha Agarwala, Serafim Batzoglou, Vlado Dancík, Scott E. Decatur, Sridhar Hannenhalli, Martin Farach, S. Muthukrishnan, Steven Skiena. jcb, 4(3):275-296, 1997.

Hardness of Flip-Cut Problems from Optical MappingVlado Dancík, Sridhar Hannenhalli, S. Muthukrishnan. jcb, 4(2):119-126, 1997.

Hardness of flip-cut problems from optical mapping [DNA molecules application]Vlado Dancík, Sridhar Hannenhalli, S. Muthukrishnan. sequences 1997: 275-284 [doi]

1996

Fast Sorting by ReversalPiotr Berman, Sridhar Hannenhalli. cpm 1996: 168-185

Polynomial-time Algorithm for Computing Translocation Distance Between GenomesSridhar Hannenhalli. DAM, 71(1-3):137-151, 1996. [doi]

To Cut... or Not to Cut (Applications of Comparative Physical Maps in Molecular Evolution)Sridhar Hannenhalli, Pavel A. Pevzner. soda 1996: 304-313

Positional sequencing by hybridizationSridhar Hannenhalli, W. Feldman, H. F. Lewis, Steven Skiena, Pavel A. Pevzner. bioinformatics, 12(1):19-24, 1996.

1995

Polynomial-time Algorithm for Computing Translocation Distance between GenomesSridhar Hannenhalli. cpm 1995: 162-176

Towards a Computational Theory of Genome RearrangementsSridhar Hannenhalli, Pavel A. Pevzner. In Jan van Leeuwen, editor, Computer Science Today: Recent Trends and Developments. Volume 1000 of Lecture Notes in Computer Science, pages 184-202, Springer, 1995.

Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversalsSridhar Hannenhalli, Pavel A. Pevzner. stoc 1995: 178-189 [doi]

Transforming Men into Mice (Polynomial Algorithm for Genomic Distance Problem)Sridhar Hannenhalli, Pavel A. Pevzner. focs 1995: 581-592

1994

A SIMD solution to the sequence comparison problem on the MGAPManjit Borah, Raminder Singh Bajwa, Sridhar Hannenhalli, Mary Jane Irwin. asap 1994: 336-345 [doi]

1993

A Distributed Algorithm for Ear DecompositionSridhar Hannenhalli, Kalyan S. Perumalla, N. Chandrasekharan, R. Sridhar. icci 1993: 180-184

1992

Efficient Algorithms for Computing Matching and Chromatic Polynominals on Series-Parallel GraphsN. Chandrasekharan, Sridhar Hannenhalli. icci 1992: 42-45

1991

Parallel Transitive Closure Computations Using Topological SortKien A. Hua, Sridhar Hannenhalli. pdis 1991: 122-129 [doi]

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