S. Hannenhalli

发表

ReversalPiotr Berman, S. Hannenhalli, 1996 .

Whole-genome shotgun assembly and comparison of human genome assemblies

Randall A. Bolanos, Xiangqun H. Zheng, Bjarni V. Halldórsson, 2004, Proceedings of the National Academy of Sciences of the United States of America.

The Sequence of the Human Genome

Timothy B. Stockwell, William H. Majoros, Helen M. Moore, 2001, Science.

Ligand-Receptor Pairing Via Tree Comparison

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

A Note on Efficient Computation of Haplotypes via Perfect Phylogeny

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

Analysis and prediction of functional sub-types from protein sequence alignments.

R. Russell, S. Hannenhalli, R. Russell, 2000, Journal of molecular biology.

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..

Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription

Mary K. Lewinski, F. Bushman, C. Berry, 2005, Journal of Virology.

CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation

S. Hannenhalli, R. Davuluri, Robert N. Plasschaert, 2013, Nucleic acids research.

Analysis and correction of compositional bias in sparse sequencing count data

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

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

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

Heterogeneity of Transcription Factor binding specificity models within and across cell lines

S. Hannenhalli, Héctor Corrada Bravo, Mahfuza Sharmin, 2015, bioRxiv.

Heterogeneity of transcription factor binding specificity models within and across cell lines

H. Bravo, S. Hannenhalli, Mahfuza Sharmin, 2015, bioRxiv.

A path-based analysis of infected cell line and COVID-19 patient transcriptome reveals novel potential targets and drugs against SARS-CoV-2

S. Hannenhalli, P. Agrawal, N. Sambaturu, 2022, Frontiers in Immunology.

PathExt: a general framework for path-based mining of omics-integrated biological networks.

S. Hannenhalli, N. Chandra, N. Sambaturu, 2020, Bioinformatics.

Preliminary Examination Research Proposal Genomics and Computational Biology University of Pennsylvania Post-transcriptional Control in Mammalian Dendrites

M. Bucan, M. Dalva, Lyle Ungar, 2005 .

Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters

S. Hannenhalli, C. Vinson, S. Sarda, 2017, Genome research.

Predicting transcription factor synergism.

S. Levy, S. Hannenhalli, 2002, Nucleic acids research.

Bayesian integration of genetics and epigenetics detects causal regulatory SNPs underlying expression variability

Shane T. Jensen, H. Hakonarson, Mingyao Li, 2015, Nature Communications.

Determinants of expression variability

S. Hannenhalli, Héctor Corrada Bravo, Elfalem Y. Alemu, 2014, Nucleic acids research.

Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals

S. Hannenhalli, S. Choi, Seung Gu Park, 2014, BMC Genomics.

Genome sequence comparison and scenarios for gene rearrangements: a test case.

P A Pevzner, E V Koonin, C Chappey, 1995, Genomics.

A COMMUNITY OVERLAP STRATEGY REVEALS CENTRAL GENES AND NETWORKS IN HEART FAILURE AUTHORS

Kevin S. Smith, Kevin Scott Smith, Mingyao Li, 2016 .

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.

ChIPulate : A comprehensive ChIP-seq simulation pipeline

S. Hannenhalli, R. Siddharthan, V. Datta, 2018 .

Why Transcription Factor Binding Sites Are Ten Nucleotides Long

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

A transcription-centric model of SNP-age interaction

S. Hannenhalli, Kun Wang, Mahashweta Basu, 2020, bioRxiv.

Identification of transcription factor binding sites in the human genome sequence

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

Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation

S. Hannenhalli, S. Vardhanabhuti, Junwen Wang, 2007, Nucleic acids research.

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

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

Transcriptional regulation of protein complexes and biological pathways

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

A mammalian promoter model links cis elements to genetic networks.

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

Regulating the regulators: modulators of transcription factor activity.

S. Hannenhalli, L. Everett, M. Hansen, 2010, Methods in molecular biology.

Orphan CpG islands as alternative promoters

S. Hannenhalli, S. Sarda, 2017, Transcription.

A pathway-centric view of spatial proximity in the 3D nucleome across cell lines

M. Girvan, S. Hannenhalli, Hiren Karathia, 2015, Scientific Reports.

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

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

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

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

Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development

S. Hannenhalli, Yong Cheng, Jun Ma, 2008, Development.

Epigenomic and RNA structural correlates of polyadenylation

S. Hannenhalli, M. Khaladkar, Mark R. Smyda, 2011, RNA biology.

Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures

David M. Wilson, E. Ruppin, Ronen Levy, 2018, Cell.

Functional Diversification of Paralogous Transcription Factors via Divergence in DNA Binding Site Motif and in Expression

Larry N. Singh, S. Hannenhalli, 2008, PloS one.

Genome‐wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy

Adam A. Friedman, E. Ruppin, K. Flaherty, 2018, bioRxiv.

Genome‐wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy

Adam A. Friedman, E. Ruppin, K. Flaherty, 2018, bioRxiv.

Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers

S. Hannenhalli, M. R. Aniba, Justin Malin, 2013, Nucleic acids research.

1 . 375-Approximation Algorithm forSorting by ReversalsPiotr Berman

M. Karpinski, S. Hannenhalli, 2001 .

Myocardin-like protein 2 regulates TGFβ signaling in embryonic stem cells and the developing vasculature

S. Hannenhalli, Xiaohong Zhu, J. Li, 2012, Development.

Three Independent Determinants of Protein Evolutionary Rate

S. Hannenhalli, S. Choi, 2013, Journal of Molecular Evolution.

Identification and cross-species comparison of canine osteoarthritic gene regulatory cis-elements.

S. Levy, S. Hannenhalli, S. Hannah, 2006, Osteoarthritis and cartilage.

First intron length in mammals is associated with 5’ exon skipping rate

S. Hannenhalli, Seung Gu Park, 2015, bioRxiv.

Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis

Shane T. Jensen, S. Hannenhalli, L. Everett, 2011, Nucleic acids research.

Prediction and Subtyping of Hypertension from Pan-Tissue Transcriptomic and Genetic Analyses

E. Ruppin, S. Hannenhalli, J. Lee, 2017, Genetics.

A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC

Ashutosh Kumar Singh, E. Ruppin, S. Hannenhalli, 2021, Cancer Research.

GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivo

S. Hannenhalli, M. Lu, E. Morrisey, 2007, Development.

Putative functional genes in idiopathic dilated cardiomyopathy

E. Ruppin, S. Hannenhalli, J. Leor, 2018, Scientific Reports.

Intrinsically disordered proteins and conformational noise

G. Rangarajan, K. Rajagopalan, S. Hannenhalli, 2013, Cell cycle.

Resistin gene variation is associated with systemic inflammation but not plasma adipokine levels, metabolic syndrome or coronary atherosclerosis in nondiabetic Caucasians

M. Reilly, D. Rader, S. Hannenhalli, 2009, Clinical endocrinology.

Determinants of expression variability

S. Hannenhalli, Héctor Corrada Bravo, Elfalem Y. Alemu, 2014, Nucleic acids research.

CHAPTER SEVEN Modeling regulatory motifs

S. Hannenhalli, 2018 .

Genome-Wide Analysis of Natural Selection on Human Cis-Elements

J. Plotkin, P. Sethupathy, S. Hannenhalli, 2008, PloS one.

Analysis and prediction of functional sub-types from protein sequence alignments 1 1 Edited by J. Th

R. Russell, S. Hannenhalli, R. Russell, 2000 .

Allele-specific enhancers mediate associations between LCAT and ABCA1 polymorphisms and HDL metabolism

S. Hannenhalli, A. Sahu, Y. C. Chang, 2019, PloS one.

Pathologic gene network rewiring implicates PPP1R3A as a central cardioprotective factor in pressure overload heart failure

Kevin S. Smith, H. Hakonarson, Mingyao Li, 2016, bioRxiv.

Draft Genome Assembly and Annotation of Red Raspberry Rubus Idaeus

Stephen M. Mount, S. Hannenhalli, S. Mount, 2019, bioRxiv.

Big data in basic and translational cancer research

E. Ruppin, S. Hannenhalli, C. Sahinalp, 2022, Nature Reviews Cancer.

Cross-species identification of cancer resistance–associated genes that may mediate human cancer risk

Lipika R. Pal, Y. Tabach, E. Ruppin, 2022, Science advances.

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

P. Pevzner, S. Hannenhalli, 1995, STOC '95.

miRSCAPE - inferring miRNA expression from scRNA-seq data

S. Hannenhalli, Gulden Olgun, Vishaka Gopalan, 2022, iScience.

Single-cell sequencing reveals activation of core transcription factors in PRC2-deficient malignant peripheral nerve sheath tumor

S. Hannenhalli, M. Yohe, C. Thiele, 2022, Cell reports.

Larry N. Singh, S. Hannenhalli, Perry Evans, 2013, PloS one.

Comprehensive single-cell transcriptomic analysis of embryonic melanoblasts uncovers lineage-specific mechanisms of melanoma metastasis and therapy resistance

Maxwell P. Lee, Howard H. Yang, S. Hannenhalli, 2022, bioRxiv.

ischemiaexpression profile in mouse myocardium after

S. Horvath, E. Ashley, M. Perez, 2015 .

Three Independent Determinants of Protein Evolutionary Rate

S. Hannenhalli, S. Choi, 2013, Journal of Molecular Evolution.

Cross-species identification of PIP5K1-, splicing- and ubiquitin-related pathways as potential targets for RB1-deficient cells.

N. Perrimon, Yanhui Hu, Colm J. Ryan, 2021, PLoS genetics.

Genomic analysis of sleep deprivation reveals translational regulation in the hippocampus.

T. Abel, P. Hernandez, S. Hannenhalli, 2012, Physiological genomics.

Bacterial start site prediction.

J W Fickett, J. Fickett, A. Hatzigeorgiou, 1999, Nucleic acids research.

Positional sequencing by hybridization

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

ChIPulate: A comprehensive ChIP-seq simulation pipeline

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

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

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

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

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

Eukaryotic transcription factor binding sites - modeling and integrative search methods

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

Genetically engineered myeloid cells rebalance the core immune suppression program in metastasis

S. Hannenhalli, R. Kaplan, J. Drake, 2021, Cell.

Genome-wide analysis of retroviral DNA integration

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

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

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

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.

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

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

Putative functional genes in idiopathic dilated cardiomyopathy

E. Ruppin, S. Hannenhalli, J. Leor, 2018, Scientific Reports.

Immune cell gene expression signatures in diffuse glioma are associated with IDH mutation status, patient outcome and malignant cell state, and highlight the importance of specific cell subsets in glioma biology

Ashutosh Kumar Singh, K. Aldape, S. Hannenhalli, 2022, Acta neuropathologica communications.

Analysis and correction of compositional bias in sparse sequencing count data

E. Slud, S. Hannenhalli, M. S. Kumar, 2017, bioRxiv.

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

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

Crowdsourcing: Spatial clustering of low-affinity binding sites amplifies in vivo transcription factor occupancy

S. Hannenhalli, B. Adryan, Daphne Ezer, 2015, bioRxiv.

Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure

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

Ligand dependent gene regulation by transient ERα clustered enhancers

S. Hannenhalli, D. Notani, R. Jayani, 2019, bioRxiv.

Young proteins experience more variable selection pressures than old proteins.

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

Broad misappropriation of developmental splicing profile by cancer in multiple organs

Ashutosh Kumar Singh, S. Hannenhalli, Chi-Ping Day, 2021, bioRxiv.

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

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

Predicting tumor immune microenvironment and checkpoint therapy response of head & neck cancer patients from blood immune single-cell transcriptomics

E. Ruppin, S. Hannenhalli, Kun Wang, 2023, bioRxiv.

Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals

S. Hannenhalli, S. Choi, Seung Gu Park, 2014, BMC Genomics.

Development and Stem Cells Research Article

S. Hannenhalli, M. Lu, E. Morrisey, 2022 .

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

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

Young Proteins Experience More Variable Selection Pressures than Material Supplemental P

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

Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin

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

Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus.

J. Plotkin, D. Simola, P. Sethupathy, 2011, Molecular biology and evolution.

A Tutorial of the Poisson Random Field Model in Population Genetics

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

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

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

Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer

H. Bravo, S. Hannenhalli, Mahfuza Sharmin, 2015, BMC Cancer.

Pathologic gene network rewiring implicates PPP1R3A as a central regulator in pressure overload heart failure

Michael J. Gloudemans, Kevin S. Smith, H. Hakonarson, 2019, Nature Communications.

De novo human brain enhancers created by single-nucleotide mutations

I. Ovcharenko, S. Hannenhalli, Shan Li, 2021, bioRxiv.

An Integrated Epigenomic and Transcriptomic Map of Mouse and Human αβ T Cell Development.

S. Hannenhalli, M. Bosticardo, R. Bosselut, 2020, Immunity.

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

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

Patterns of sequence conservation in presynaptic neural genes

D. Hadley, M. Bucan, L. Ungar, 2006, Genome Biology.

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..

Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells

S. Hannenhalli, M. Mehta, Bao Tran, 2019, Cell reports.

Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes.

F. Bushman, S. Hannenhalli, E. Lefkowitz, 2007, Virology.

Single-cell profiling of tumor-reactive CD4+ T-cells reveals unexpected transcriptomic diversity

S. Hannenhalli, M. Mehta, Bao Tran, 2019, bioRxiv.

Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1

S. Hannenhalli, P. Antin, D. Darnell, 2011, BMC Evolutionary Biology.

Sex and Age Dimorphism of Myocardial Gene Expression in Nonischemic Human Heart Failure

S. Hannenhalli, C. D. dos Remedios, F. Pagani, 2008, Circulation. Cardiovascular genetics.

Widespread evidence of viral miRNAs targeting host pathways

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

Synthetic lethality-mediated precision oncology via the tumor transcriptome

E. Ruppin, M. Gilbert, R. Berger, 2021, Cell.

Whole exome precision oncology targeting synthetic lethal vulnerabilities across the tumor transcriptome

Lesley M. Chapman, E. Ruppin, K. Aldape, 2020, bioRxiv.

Differential transcriptional response to nonassociative and associative components of classical fear conditioning in the amygdala and hippocampus.

T. Abel, S. Hannenhalli, K. Hellman, 2006, Learning & memory.

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.

Harnessing synthetic lethality to predict the response to cancer treatment

E. Ruppin, P. Meltzer, C. Benes, 2018, Nature Communications.

Beyond Synthetic Lethality: Charting the Landscape of Pairwise Gene Expression States Associated with Survival in Cancer.

A. Schäffer, E. Ruppin, S. Hannenhalli, 2019, Cell reports.

Beyond Synthetic Lethality: Charting the Landscape of Clinically Relevant Genetic Interactions in Cancer

A. Schäffer, E. Ruppin, S. Hannenhalli, 2019, SSRN Electronic Journal.

Beyond synthetic lethality: multiple gene interaction types play a key functional role in cancer

E. Ruppin, S. Hannenhalli, J. Lee, 2018 .

Hopx and Hdac2 interact to modulate Gata4 acetylation and embryonic cardiac myocyte proliferation.

J. Epstein, S. Hannenhalli, Cheng Jia, 2010, Developmental cell.

Derepression of Cancer/Testis Antigens in cancer is associated with distinct patterns of DNA Hypomethylation

S. Hannenhalli, Prakash Kulkarni, R. Kim, 2013, BMC Cancer.

Promoter prediction in the human genome

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

Gene Profiling of Human Adipose Tissue During Evoked Inflammation In Vivo

M. Reilly, S. Hannenhalli, M. Putt, 2009, Diabetes.

Migration rather than proliferation transcriptomic signatures are strongly associated with breast cancer patient survival

Sylvia E. Le Dévédec, E. Ruppin, I. Meilijson, 2018, Scientific Reports.

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

S. Hannenhalli, J. Zeng, 2013, BMC Genomics.

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.

Functional divergence of gene duplicates – a domain-centric view

S. Hannenhalli, M. Khaladkar, 2012, BMC Evolutionary Biology.

Chromatin and genomic determinants of alternative splicing

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

Cross-species identification of cancer-resistance associated genes uncovers their relevance to human cancer risk

Lipika R. Pal, Y. Tabach, E. Ruppin, 2021, bioRxiv.

miRSCAPE - Inferring miRNA expression in single-cell clusters

S. Hannenhalli, Gulden Olgun, Vishaka Gopalan, 2021, bioRxiv.

Evolutionarily Conserved Network Properties of Intrinsically Disordered Proteins

S. Hannenhalli, Prakash Kulkarni, Nivedita Rangarajan, 2015, PloS one.

Combinatorial algorithms for design of DNA arrays.

Pavel A Pevzner, Sridhar Hannenhalli, Earl Hubell, 2002, Advances in biochemical engineering/biotechnology.

PathExt: a general framework for path-based mining of omics-integrated biological networks

Nagasuma Chandra, Narmada Sambaturu, Vaidehi Pusadkar, 2020, bioRxiv.

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.

Comprehensive map of age-associated splicing changes across human tissues and their contributions to age-associated diseases

S. Hannenhalli, Avinash Das, Kun Wang, 2018, Scientific Reports.

Towards a Computational Theory of Genome Rearrangements

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

Enrichment of regulatory signals in conserved non-coding genomic sequence

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

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

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

Polynomial-time Algorithm for Computing Translocation Distance Between Genomes

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

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..

Prioritizing and characterizing functionally relevant genes across human tissues

Ashutosh Kumar Singh, S. Hannenhalli, Sarthak Sahoo, 2021, bioRxiv.

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.

Transcriptomes of the tumor-adjacent normal tissues are more informative than tumors in predicting recurrence in colorectal cancer patients

Yeon Jeong Kim, Y. Cho, S. Yun, 2023, Journal of Translational Medicine.

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

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

Comprehensive map of age-associated splicing changes across human tissues and their contributions to age-associated diseases

S. Hannenhalli, Avinash Das, Kun Wang, 2018, Scientific Reports.

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.

Towards a Synthesis of the Non-Genetic and Genetic Views of Cancer in Understanding Pancreatic Ductal Adenocarcinoma Initiation and Prevention

S. Hannenhalli, Vishaka Gopalan, 2023, Cancers.

Larry N. Singh, S. Hannenhalli, 2009, Nucleic acids research.

Melanoma clonal subline analysis uncovers heterogeneity-driven immunotherapy resistance mechanisms

Howard H. Yang, S. Hannenhalli, C. Sahinalp, 2023, bioRxiv.

Genetic and Physiological Activation of Osmosensitive Gene Expression Mimics Transcriptional Signatures of Pathogen Infection in C. elegans

S. Hannenhalli, T. Lamitina, Y. Miteva, 2010, PloS one.

Genetic Reduction in Left Ventricular Protein Kinase C-&agr; and Adverse Ventricular Remodeling in Human Subjects

H. Hakonarson, Cecilia Kim, E. Ashley, 2018, Circulation. Genomic and precision medicine.

Predicting tissue-specific gene expression from whole blood transcriptome

E. Ruppin, S. Hannenhalli, Kun Wang, 2020, Science Advances.

Transcriptomes of the tumor-adjacent normal tissues are more informative than tumors in predicting recurrence in colorectal cancer patients

Yeon Jeong Kim, Y. Cho, S. Yun, 2023, Journal of Translational Medicine.

Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in Triple Negative Breast Cancer

Ashutosh Kumar Singh, S. Hannenhalli, P. Rajagopal, 2023, bioRxiv.

Evidence for Coregulation of Myocardial Gene Expression by MEF2 and NFAT in Human Heart Failure

S. Hannenhalli, E. Morrisey, M. Putt, 2009, Circulation. Cardiovascular genetics.

Noncoding RNA circuitry in melanoma onset, plasticity, and therapeutic response.

S. Hannenhalli, C. Stathopoulos, G. Merlino, 2023, Pharmacology & therapeutics.

1.375-Approximation Algorithm for Sorting by Reversals

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

Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex

Kai Wang, M. Bucan, S. Hannenhalli, 2007, Genome Biology.

Predicting gene expression changes upon epigenomic drug treatment

S. Hannenhalli, P. Agrawal, Vishaka Gopalan, 2023, bioRxiv.

Recurring genomic breaks in independent lineages support genomic fragility

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

Protocol for using single-cell sequencing to study the heterogeneity of NF1 nerve sheath tumors from clinical biospecimens

S. Hannenhalli, Xiyuan Zhang, J. Shern, 2023, STAR Protocols.

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

Larry N. Singh, S. Hannenhalli, S. Vigneau, 2009, Genome Biology.

Transcription factors organize into functional groups on the linear genome and in 3D chromatin

S. Hannenhalli, R. Siddharthan, Rakesh Netha Vadnala, 2022, bioRxiv.

Intrinsically disordered proteins and conformational noise Implications in cancer

K. Rajagopalan, S. Hannenhalli, Prakash Kulkarni, 2013 .

Harnessing synthetic lethality to predict the response to cancer treatment

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

Beyond synthetic lethality: charting the landscape of clinically relevant genetic interactions in cancer

A. Schäffer, E. Ruppin, S. Hannenhalli, 2018, bioRxiv.

Pathologic gene network rewiring implicates PPP1R3A as a central cardioprotective factor in pressure overload heart failure

Kevin S. Smith, H. Hakonarson, Mingyao Li, 2016, bioRxiv.

Fast Sorting by Reversal

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

Functional analysis of Hes-1 in preadipocytes.

R. Shiekhattar, J. Tobias, Neil Cooch, 2006, Molecular endocrinology.

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

E. Ruppin, Allon Wagner, S. Hannenhalli, 2017, Journal of the American Heart Association.

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

M. Bucan, S. Hannenhalli, Rui Liu, 2009, Genome Biology.

Developmental expression of chicken FOXN1 and putative target genes during feather development.

S. Hannenhalli, D. Darnell, S. Yaklichkin, 2014, The International journal of developmental biology.

Myocardin-like protein 2 regulates TGFβ signaling in embryonic stem cells and the developing vasculature

S. Hannenhalli, Xiaohong Zhu, J. Li, 2012, Development.

Pacific symposium on biocomputing 2006

Lawrence Hunter, Russ B. Altman, Teri E. Klein, 2005, PSB 2016.

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

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

Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model

Scott E. Decatur, S. Batzoglou, R. Agarwala, 1997, SODA '97.

Genome‐wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy

Adam A. Friedman, E. Ruppin, K. Flaherty, 2018, bioRxiv.

Regulation of lung endoderm progenitor cell behavior by miR302/367.

S. Hannenhalli, M. Lu, E. Morrisey, 2011, Development.

Determinants of expression variability

S. Hannenhalli, Héctor Corrada Bravo, Elfalem Y. Alemu, 2014, Nucleic acids research.