S Hannenhalli - Publications

Affiliations: 
University of Pennsylvania, Philadelphia, PA, United States 
Area:
Bioinformatics Biology, Genetics, Computer Science

99 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Sharmin M, Bravo HC, Hannenhalli S. Heterogeneity of transcription factor binding specificity models within and across cell lines. Genome Research. PMID 27311443 DOI: 10.1101/gr.199166.115  0.36
2015 Sharmin M, Bravo HC, Hannenhalli S. Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer. Bmc Cancer. 16: 88. PMID 26868017 DOI: 10.1186/s12885-016-2128-1  0.6
2015 Kumar MS, Plotkin JB, Hannenhalli S. Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution. Plos Computational Biology. 11: e1004603. PMID 26544847 DOI: 10.1371/journal.pcbi.1004603  0.6
2015 Das A, Morley M, Moravec CS, Tang WH, Hakonarson H, Margulies KB, Cappola TP, Jensen S, Hannenhalli S. Bayesian integration of genetics and epigenetics detects causal regulatory SNPs underlying expression variability. Nature Communications. 6: 8555. PMID 26456756 DOI: 10.1038/ncomms9555  0.6
2015 Sarda S, Hannenhalli S. High-Throughput Identification of Cis-Regulatory Rewiring Events in Yeast. Molecular Biology and Evolution. 32: 3047-63. PMID 26399482 DOI: 10.1093/molbev/msv203  0.6
2015 Kun Wang, Das A, Zheng-Mei Xiong, Kan Cao, Hannenhalli S. Phenotype-Dependent Coexpression Gene Clusters: Application to Normal and Premature Ageing. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 12: 30-9. PMID 26357076 DOI: 10.1109/TCBB.2014.2359446  0.6
2015 Rangarajan N, Kulkarni P, Hannenhalli S. Evolutionarily conserved network properties of intrinsically disordered proteins. Plos One. 10: e0126729. PMID 25974317 DOI: 10.1371/journal.pone.0126729  0.6
2015 Liu Y, Morley M, Brandimarto J, Hannenhalli S, Hu Y, Ashley EA, Tang WH, Moravec CS, Margulies KB, Cappola TP, Li M. RNA-Seq identifies novel myocardial gene expression signatures of heart failure. Genomics. 105: 83-9. PMID 25528681 DOI: 10.1016/j.ygeno.2014.12.002  0.6
2015 Wang K, Cao K, Hannenhalli S. Chromatin and genomic determinants of alternative splicing Bcb 2015 - 6th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. 345-354. DOI: 10.1145/2808719.2808755  0.36
2014 Park SG, Hannenhalli S, Choi SS. Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals. Bmc Genomics. 15: 526. PMID 24964727 DOI: 10.1186/1471-2164-15-526  0.6
2014 Darnell DK, Zhang LS, Hannenhalli S, Yaklichkin SY. Developmental expression of chicken FOXN1 and putative target genes during feather development. The International Journal of Developmental Biology. 58: 57-64. PMID 24860996 DOI: 10.1387/ijdb.130023sy  0.6
2014 Alemu EY, Carl JW, Corrada Bravo H, Hannenhalli S. Determinants of expression variability. Nucleic Acids Research. 42: 3503-14. PMID 24435799 DOI: 10.1093/nar/gkt1364  0.6
2014 Plasschaert RN, Vigneau S, Tempera I, Gupta R, Maksimoska J, Everett L, Davuluri R, Mamorstein R, Lieberman PM, Schultz D, Hannenhalli S, Bartolomei MS. CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation. Nucleic Acids Research. 42: 774-89. PMID 24121688 DOI: 10.1093/nar/gkt910  0.6
2014 Lu Y, Hannenhalli S, Cappola T, Putt M. An evaluation of Monte-Carlo logic and logicFS motivated by a study of the regulation of gene expression in heart failure Journal of Applied Statistics. 41: 1956-1975. DOI: 10.1080/02664763.2014.898133  0.6
2013 Malin J, Aniba MR, Hannenhalli S. Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers. Nucleic Acids Research. 41: 6828-38. PMID 23700312 DOI: 10.1093/nar/gkt374  0.6
2013 Kim R, Kulkarni P, Hannenhalli S. Derepression of Cancer/testis antigens in cancer is associated with distinct patterns of DNA hypomethylation. Bmc Cancer. 13: 144. PMID 23522060 DOI: 10.1186/1471-2407-13-144  0.6
2013 Sahu AD, Aniba R, Chang YP, Hannenhalli S. Epigenomic model of cardiac enhancers with application to genome wide association studies. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 92-102. PMID 23424115  0.36
2013 Mukherjee R, Evans P, Singh LN, Hannenhalli S. Correlated evolution of positions within mammalian cis elements. Plos One. 8: e55521. PMID 23408994 DOI: 10.1371/journal.pone.0055521  0.6
2013 Choi SS, Hannenhalli S. Three independent determinants of protein evolutionary rate. Journal of Molecular Evolution. 76: 98-111. PMID 23400388 DOI: 10.1007/s00239-013-9543-6  0.6
2013 Carl JW, Trgovcich J, Hannenhalli S. Widespread evidence of viral miRNAs targeting host pathways. Bmc Bioinformatics. 14: S3. PMID 23369080 DOI: 10.1186/1471-2105-14-S2-S3  0.6
2013 Zeng J, Hannenhalli S. Inferring evolution of gene duplicates using probabilistic models and nonparametric belief propagation. Bmc Genomics. 14: S15. PMID 23368094 DOI: 10.1186/1471-2164-14-S1-S15  0.6
2013 Mahmoudabadi G, Rajagopalan K, Getzenberg RH, Hannenhalli S, Rangarajan G, Kulkarni P. Intrinsically disordered proteins and conformational noise: implications in cancer. Cell Cycle (Georgetown, Tex.). 12: 26-31. PMID 23255110 DOI: 10.4161/cc.23178  0.6
2013 Wang K, Das A, Xiong ZM, Cao K, Hannenhalli S. Identification of gene clusters with phenotype-dependent expression with application to normal and premature ageing 2013 Acm Conference On Bioinformatics, Computational Biology and Biomedical Informatics, Acm-Bcb 2013. 377-383. DOI: 10.1145/2506583.2506652  0.6
2013 Wang H, Duggal G, Patro R, Girvan M, Hannenhalli S, Kingsford C. Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin 2013 Acm Conference On Bioinformatics, Computational Biology and Biomedical Informatics, Acm-Bcb 2013. 306-315. DOI: 10.1145/2506583.2506633  0.6
2013 Wu C, Hannenhalli S. Message from the general chair 2013 Acm Conference On Bioinformatics, Computational Biology and Biomedical Informatics, Acm-Bcb 2013 0.36
2012 Vecsey CG, Peixoto L, Choi JH, Wimmer M, Jaganath D, Hernandez PJ, Blackwell J, Meda K, Park AJ, Hannenhalli S, Abel T. Genomic analysis of sleep deprivation reveals translational regulation in the hippocampus. Physiological Genomics. 44: 981-91. PMID 22930738 DOI: 10.1152/physiolgenomics.00084.2012  0.6
2012 Li J, Bowens N, Cheng L, Zhu X, Chen M, Hannenhalli S, Cappola TP, Parmacek MS. Myocardin-like protein 2 regulates TGFβ signaling in embryonic stem cells and the developing vasculature. Development (Cambridge, England). 139: 3531-42. PMID 22899851 DOI: 10.1242/dev.082222  0.6
2012 Khaladkar M, Hannenhalli S. Functional divergence of gene duplicates - a domain-centric view. Bmc Evolutionary Biology. 12: 126. PMID 22839301 DOI: 10.1186/1471-2148-12-126  0.6
2011 Yaklichkin SY, Darnell DK, Pier MV, Antin PB, Hannenhalli S. Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1. Bmc Evolutionary Biology. 11: 302. PMID 21999483 DOI: 10.1186/1471-2148-11-302  0.6
2011 Khaladkar M, Smyda M, Hannenhalli S. Epigenomic and RNA structural correlates of polyadenylation. Rna Biology. 8: 529-37. PMID 21508683 DOI: 10.4161/rna.8.3.15194  0.6
2011 Vishnoi A, Sethupathy P, Simola D, Plotkin JB, Hannenhalli S. Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus. Molecular Biology and Evolution. 28: 2615-27. PMID 21478372 DOI: 10.1093/molbev/msr085  0.6
2011 Everett LJ, Jensen ST, Hannenhalli S. Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis. Nucleic Acids Research. 39: e78. PMID 21470963 DOI: 10.1093/nar/gkr172  0.6
2011 Tian Y, Zhang Y, Hurd L, Hannenhalli S, Liu F, Lu MM, Morrisey EE. Regulation of lung endoderm progenitor cell behavior by miR302/367. Development (Cambridge, England). 138: 1235-45. PMID 21350014 DOI: 10.1242/dev.061762  0.6
2011 Dewey FE, Perez MV, Wheeler MT, Watt C, Spin J, Langfelder P, Horvath S, Hannenhalli S, Cappola TP, Ashley EA. Gene coexpression network topology of cardiac development, hypertrophy, and failure. Circulation. Cardiovascular Genetics. 4: 26-35. PMID 21127201 DOI: 10.1161/CIRCGENETICS.110.941757  0.6
2010 Vishnoi A, Kryazhimskiy S, Bazykin GA, Hannenhalli S, Plotkin JB. Young proteins experience more variable selection pressures than old proteins. Genome Research. 20: 1574-81. PMID 20921233 DOI: 10.1101/gr.109595.110  0.36
2010 Trivedi CM, Zhu W, Wang Q, Jia C, Kee HJ, Li L, Hannenhalli S, Epstein JA. Hopx and Hdac2 interact to modulate Gata4 acetylation and embryonic cardiac myocyte proliferation. Developmental Cell. 19: 450-9. PMID 20833366 DOI: 10.1016/j.devcel.2010.08.012  0.36
2010 Everett L, Hansen M, Hannenhalli S. Regulating the regulators: modulators of transcription factor activity. Methods in Molecular Biology (Clifton, N.J.). 674: 297-312. PMID 20827600 DOI: 10.1007/978-1-60761-854-6_19  0.6
2010 Rohlfing AK, Miteva Y, Hannenhalli S, Lamitina T. Genetic and physiological activation of osmosensitive gene expression mimics transcriptional signatures of pathogen infection in C. elegans. Plos One. 5: e9010. PMID 20126308 DOI: 10.1371/journal.pone.0009010  0.36
2010 Hansen M, Everett L, Singh L, Hannenhalli S. Mimosa: mixture model of co-expression to detect modulators of regulatory interaction. Algorithms For Molecular Biology : Amb. 5: 4. PMID 20047660 DOI: 10.1186/1748-7188-5-4  0.36
2010 Singh LN, Hannenhalli S. Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families. Nucleic Acids Research. 38: 738-49. PMID 19933262 DOI: 10.1093/nar/gkp989  0.36
2009 Putt ME, Hannenhalli S, Lu Y, Haines P, Chandrupatla HR, Morrisey EE, Margulies KB, Cappola TP. Evidence for coregulation of myocardial gene expression by MEF2 and NFAT in human heart failure. Circulation. Cardiovascular Genetics. 2: 212-9. PMID 20031589 DOI: 10.1161/CIRCGENETICS.108.816686  0.36
2009 Essien K, Vigneau S, Apreleva S, Singh LN, Bartolomei MS, Hannenhalli S. CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features. Genome Biology. 10: R131. PMID 19922652 DOI: 10.1186/gb-2009-10-11-r131  0.36
2009 Shah R, Lu Y, Hinkle CC, McGillicuddy FC, Kim R, Hannenhalli S, Cappola TP, Heffron S, Wang X, Mehta NN, Putt M, Reilly MP. Gene profiling of human adipose tissue during evoked inflammation in vivo. Diabetes. 58: 2211-9. PMID 19581417 DOI: 10.2337/db09-0256  0.36
2009 Liu R, Hannenhalli S, Bucan M. Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons. Genome Biology. 10: R72. PMID 19570198 DOI: 10.1186/gb-2009-10-7-r72  0.36
2009 Hannenhalli S, Kaestner KH. The evolution of Fox genes and their role in development and disease. Nature Reviews. Genetics. 10: 233-40. PMID 19274050 DOI: 10.1038/nrg2523  0.36
2009 Everett L, Vo A, Hannenhalli S. PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. Nucleic Acids Research. 37: D66-71. PMID 18927104 DOI: 10.1093/nar/gkn731  0.36
2009 Qasim AN, Metkus TS, Tadesse M, Lehrke M, Restine S, Wolfe ML, Hannenhalli S, Cappola T, Rader DJ, Reilly MP. Resistin gene variation is associated with systemic inflammation but not plasma adipokine levels, metabolic syndrome or coronary atherosclerosis in nondiabetic Caucasians. Clinical Endocrinology. 70: 698-705. PMID 18710472 DOI: 10.1111/j.1365-2265.2008.03375.x  0.36
2009 Hansen M, Everett L, Singh L, Hannenhalli S. Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5724: 133-144. DOI: 10.1007/978-3-642-04241-6_12  0.36
2008 Fermin DR, Barac A, Lee S, Polster SP, Hannenhalli S, Bergemann TL, Grindle S, Dyke DB, Pagani F, Miller LW, Tan S, Dos Remedios C, Cappola TP, Margulies KB, Hall JL. Sex and age dimorphism of myocardial gene expression in nonischemic human heart failure. Circulation. Cardiovascular Genetics. 1: 117-25. PMID 20031553 DOI: 10.1161/CIRCGENETICS.108.802652  0.36
2008 Sethupathy P, Hannenhalli S. A tutorial of the poisson random field model in population genetics. Advances in Bioinformatics. 257864. PMID 19920987 DOI: 10.1155/2008/257864  1
2008 Sethupathy P, Giang H, Plotkin JB, Hannenhalli S. Genome-wide analysis of natural selection on human cis-elements. Plos One. 3: e3137. PMID 18781197 DOI: 10.1371/journal.pone.0003137  0.36
2008 Essien K, Hannenhalli S, Stoeckert CJ. Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity. Plos One. 3: e3122. PMID 18769675 DOI: 10.1371/journal.pone.0003122  0.36
2008 Wan LB, Pan H, Hannenhalli S, Cheng Y, Ma J, Fedoriw A, Lobanenkov V, Latham KE, Schultz RM, Bartolomei MS. Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development Development. 135: 2729-2738. PMID 18614575 DOI: 10.1242/dev.024539  0.36
2008 Singh LN, Hannenhalli S. Functional diversification of paralogous transcription factors via divergence in DNA binding site motif and in expression. Plos One. 3: e2345. PMID 18523562 DOI: 10.1371/journal.pone.0002345  0.36
2008 Hannenhalli S. Eukaryotic transcription factor binding sites--modeling and integrative search methods. Bioinformatics (Oxford, England). 24: 1325-31. PMID 18426806 DOI: 10.1093/bioinformatics/btn198  0.36
2008 Giancarlo R, Hannenhalli S. Guest editors' introduction to the special section on algorithms in bioinformatics (WABI '07) Ieee/Acm Transactions On Computational Biology and Bioinformatics. 5: 482-483. DOI: 10.1109/TCBB.2008.116  0.36
2007 Yang S, Wang K, Valladares O, Hannenhalli S, Bucan M. Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex. Genome Biology. 8: R247. PMID 18028544 DOI: 10.1186/gb-2007-8-11-r247  0.36
2007 Singh LN, Wang LS, Hannenhalli S. TREMOR--a tool for retrieving transcriptional modules by incorporating motif covariance. Nucleic Acids Research. 35: 7360-71. PMID 17962303 DOI: 10.1093/nar/gkm885  0.36
2007 Wang J, Ungar LH, Tseng H, Hannenhalli S. MetaProm: a neural network based meta-predictor for alternative human promoter prediction. Bmc Genomics. 8: 374. PMID 17941982 DOI: 10.1186/1471-2164-8-374  0.36
2007 Minkah N, Hwang Y, Perry K, Van Duyne GD, Hendrickson R, Lefkowitz EJ, Hannenhalli S, Bushman FD. Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes. Virology. 365: 60-9. PMID 17462694 DOI: 10.1016/j.virol.2007.02.037  0.36
2007 Vardhanabhuti S, Wang J, Hannenhalli S. Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucleic Acids Research. 35: 3203-13. PMID 17452354 DOI: 10.1093/nar/gkm201  0.36
2007 Zhang Y, Rath N, Hannenhalli S, Wang Z, Cappola T, Kimura S, Atochina-Vasserman E, Lu MM, Beers MF, Morrisey EE. GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivo. Development (Cambridge, England). 134: 189-98. PMID 17164424 DOI: 10.1242/dev.02720  0.36
2007 Giancarlo R, Hannenhalli S. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4645.  0.36
2007 Wang LS, Jensen ST, Hannenhalli S. An interaction-dependent model for transcription factor binding Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4023: 225-234.  0.36
2006 Berry C, Hannenhalli S, Leipzig J, Bushman FD. Selection of target sites for mobile DNA integration in the human genome. Plos Computational Biology. 2: e157. PMID 17166054 DOI: 10.1371/journal.pcbi.0020157  0.36
2006 Hadley D, Murphy T, Valladares O, Hannenhalli S, Ungar L, Kim J, Bućan M. Patterns of sequence conservation in presynaptic neural genes. Genome Biology. 7: R105. PMID 17096848 DOI: 10.1186/gb-2006-7-11-r105  0.36
2006 Hinsch H, Hannenhalli S. Recurring genomic breaks in independent lineages support genomic fragility. Bmc Evolutionary Biology. 6: 90. PMID 17090315 DOI: 10.1186/1471-2148-6-90  0.36
2006 Hannenhalli S, Putt ME, Gilmore JM, Wang J, Parmacek MS, Epstein JA, Morrisey EE, Margulies KB, Cappola TP. Transcriptional genomics associates FOX transcription factors with human heart failure. Circulation. 114: 1269-76. PMID 16952980 DOI: 10.1161/CIRCULATIONAHA.106.632430  0.36
2006 Everett L, Wang LS, Hannenhalli S. Dense subgraph computation via stochastic search: application to detect transcriptional modules. Bioinformatics (Oxford, England). 22: e117-23. PMID 16873461 DOI: 10.1093/bioinformatics/btl260  0.36
2006 Wang J, Hannenhalli S. A mammalian promoter model links cis elements to genetic networks. Biochemical and Biophysical Research Communications. 347: 166-77. PMID 16806065 DOI: 10.1016/j.bbrc.2006.06.062  0.36
2006 Lewinski MK, Yamashita M, Emerman M, Ciuffi A, Marshall H, Crawford G, Collins F, Shinn P, Leipzig J, Hannenhalli S, Berry CC, Ecker JR, Bushman FD. Retroviral DNA integration: viral and cellular determinants of target-site selection. Plos Pathogens. 2: e60. PMID 16789841 DOI: 10.1371/journal.ppat.0020060  0.36
2006 Hannenhalli SS, Middleton RP, Levy S, Perroud B, Holzwarth JA, McDonald K, Hannah SS. Identification and cross-species comparison of canine osteoarthritic gene regulatory cis-elements Osteoarthritis and Cartilage. 14: 830-838. PMID 16580849 DOI: 10.1016/j.joca.2006.02.007  0.36
2006 Keeley MB, Wood MA, Isiegas C, Stein J, Hellman K, Hannenhalli S, Abel T. Differential transcriptional response to nonassociative and associative components of classical fear conditioning in the amygdala and hippocampus. Learning & Memory (Cold Spring Harbor, N.Y.). 13: 135-42. PMID 16547164 DOI: 10.1101/lm.86906  0.36
2006 Ross DA, Hannenhalli S, Tobias JW, Cooch N, Shiekhattar R, Kadesch T. Functional analysis of Hes-1 in preadipocytes. Molecular Endocrinology (Baltimore, Md.). 20: 698-705. PMID 16282371 DOI: 10.1210/me.2005-0325  0.36
2006 Evans P, Donahue G, Hannenhalli S. Conservation patterns in cis-elements reveal compensatory mutations Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4205: 186-199.  0.36
2006 Hannenhalli SS, Middleton RP, Levy S, Perroud B, Holzwarth JA, McDonald K, Hannah SS. Identification and cross-species comparison of canine osteoarthritic gene regulatory cis elements Compendium On Continuing Education For the Practicing Veterinarian. 28: 60.  0.36
2005 Bushman F, Lewinski M, Ciuffi A, Barr S, Leipzig J, Hannenhalli S, Hoffmann C. Genome-wide analysis of retroviral DNA integration. Nature Reviews. Microbiology. 3: 848-58. PMID 16175173 DOI: 10.1038/nrmicro1263  0.36
2005 Wang J, Hannenhalli S. Generalizations of Markov model to characterize biological sequences. Bmc Bioinformatics. 6: 219. PMID 16144548 DOI: 10.1186/1471-2105-6-219  0.36
2005 Hannenhalli S, Wang LS. Enhanced position weight matrices using mixture models. Bioinformatics (Oxford, England). 21: i204-12. PMID 15961459 DOI: 10.1093/bioinformatics/bti1001  0.36
2005 Lewinski MK, Bisgrove D, Shinn P, Chen H, Hoffmann C, Hannenhalli S, Verdin E, Berry CC, Ecker JR, Bushman FD. Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription. Journal of Virology. 79: 6610-9. PMID 15890899 DOI: 10.1128/JVI.79.11.6610-6619.2005  0.36
2005 Hannenhalli S, Wang LS. Enhanced position weight matrices using mixture models Ismb 2005 Proceedings - 13th International Conference On Intelligent Systems For Molecular Biology 0.6
2004 Bafna V, Gusfield D, Hannenhalli S, Yooseph S. A note on efficient computation of haplotypes via perfect phylogeny. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 858-66. PMID 15700406 DOI: 10.1089/cmb.2004.11.858  0.36
2004 Istrail S, Sutton GG, Florea L, Halpern AL, Mobarry CM, Lippert R, Walenz B, Shatkay H, Dew I, Miller JR, Flanigan MJ, Edwards NJ, Bolanos R, Fasulo D, Halldorsson BV, ... Hannenhalli S, et al. Whole-genome shotgun assembly and comparison of human genome assemblies. Proceedings of the National Academy of Sciences of the United States of America. 101: 1916-21. PMID 14769938 DOI: 10.1073/pnas.0307971100  0.36
2003 Hannenhalli S, Levy S. Transcriptional regulation of protein complexes and biological pathways. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 14: 611-9. PMID 14629111 DOI: 10.1007/s00335-002-2260-x  0.36
2002 Levy S, Hannenhalli S. Identification of transcription factor binding sites in the human genome sequence. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 13: 510-4. PMID 12370781 DOI: 10.1007/s00335-002-2175-6  0.36
2002 Hannenhalli S, Levy S. Predicting transcription factor synergism. Nucleic Acids Research. 30: 4278-84. PMID 12364607  0.36
2002 Hannenhalli S, Hubell E, Lipshutz R, Pevzner PA. Combinatorial algorithms for design of DNA arrays. Advances in Biochemical Engineering/Biotechnology. 77: 1-19. PMID 12227732  0.36
2002 Berman P, Hannenhalli S, Karpinski M. 1.375-Approximation algorithm for sorting by Reversals Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2461: 200-210.  0.36
2001 Levy S, Hannenhalli S, Workman C. Enrichment of regulatory signals in conserved non-coding genomic sequence Bioinformatics. 17: 871-877. PMID 11673231  0.36
2001 Hannenhalli S, Levy S. Promoter prediction in the human genome Bioinformatics. 17. PMID 11472997  0.36
2001 Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, ... ... Hannenhalli S, et al. The sequence of the human genome. Science (New York, N.Y.). 291: 1304-51. PMID 11181995 DOI: 10.1126/science.1058040  0.36
2000 Hannenhalli SS, Russell RB. Analysis and prediction of functional sub-types from protein sequence alignments. Journal of Molecular Biology. 303: 61-76. PMID 11021970 DOI: 10.1006/jmbi.2000.4036  0.36
2000 Bafna V, Hannenhalli S, Rice K, Vawter L. Ligand-receptor pairing via tree comparison Journal of Computational Biology. 7: 59-70. PMID 10890388 DOI: 10.1089/10665270050081388  0.36
1999 Hannenhalli SS, Hayes WS, Hatzigeorgiou AG, Fickett JW. Bacterial start site prediction. Nucleic Acids Research. 27: 3577-82. PMID 10446249 DOI: 10.1093/nar/27.17.3577  0.36
1999 Hannenhalli S, Pevzner PA. Transforming Cabbage into Turnip: Polynomial Algorithm for Sorting Signed Permutations by Reversals Journal of the Acm. 46: 1-22.  0.36
1996 Hannenhalli S, Feldman W, Lewis HF, Skiena SS, Pevzner PA. Positional sequencing by hybridization. Computer Applications in the Biosciences : Cabios. 12: 19-24. PMID 8670615  0.36
1996 Berman P, Hannenhalli S. Fast sorting by reversal Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1075: 168-185. DOI: 10.1007/3-540-61258-0_14  0.36
1996 Hannenhalli S. Polynomial-time algorithm for computing translocation distance between genomes Discrete Applied Mathematics. 71: 137-151. DOI: 10.1007/3-540-60044-2_41  0.36
1995 Hannenhalli S, Chappey C, Koonin EV, Pevzner PA. Genome sequence comparison and scenarios for gene rearrangements: a test case. Genomics. 30: 299-311. PMID 8586431 DOI: 10.1006/geno.1995.9873  0.36
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