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

Nair NU, Das A, Rogkoti VM, Fokkelman M, Marcotte R, de Jong CG, Koedoot E, Lee JS, Meilijson I, Hannenhalli S, Neel BG, de Water BV, Le Dévédec SE, Ruppin E.

Sci Rep. 2019 Jul 29;9(1):10989. doi: 10.1038/s41598-019-47440-w.


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

Magen A, Das Sahu A, Lee JS, Sharmin M, Lugo A, Gutkind JS, Schäffer AA, Ruppin E, Hannenhalli S.

Cell Rep. 2019 Jul 23;28(4):938-948.e6. doi: 10.1016/j.celrep.2019.06.067.


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

Cordero P, Parikh VN, Chin ET, Erbilgin A, Gloudemans MJ, Shang C, Huang Y, Chang AC, Smith KS, Dewey F, Zaleta K, Morley M, Brandimarto J, Glazer N, Waggott D, Pavlovic A, Zhao M, Moravec CS, Tang WHW, Skreen J, Malloy C, Hannenhalli S, Li H, Ritter S, Li M, Bernstein D, Connolly A, Hakonarson H, Lusis AJ, Margulies KB, Depaoli-Roach AA, Montgomery SB, Wheeler MT, Cappola T, Ashley EA.

Nat Commun. 2019 Jun 24;10(1):2760. doi: 10.1038/s41467-019-10591-5.


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

Howard AD, Wang X, Prasad M, Sahu AD, Aniba R, Miller M, Hannenhalli S, Chang YC.

PLoS One. 2019 Apr 30;14(4):e0215911. doi: 10.1371/journal.pone.0215911. eCollection 2019.


ChIPulate: A comprehensive ChIP-seq simulation pipeline.

Datta V, Hannenhalli S, Siddharthan R.

PLoS Comput Biol. 2019 Mar 21;15(3):e1006921. doi: 10.1371/journal.pcbi.1006921. eCollection 2019 Mar.


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

Sahu AD, S Lee J, Wang Z, Zhang G, Iglesias-Bartolome R, Tian T, Wei Z, Miao B, Nair NU, Ponomarova O, Friedman AA, Amzallag A, Moll T, Kasumova G, Greninger P, Egan RK, Damon LJ, Frederick DT, Jerby-Arnon L, Wagner A, Cheng K, Park SG, Robinson W, Gardner K, Boland G, Hannenhalli S, Herlyn M, Benes C, Flaherty K, Luo J, Gutkind JS, Ruppin E.

Mol Syst Biol. 2019 Mar 11;15(3):e8323. doi: 10.15252/msb.20188323.


Analysis and correction of compositional bias in sparse sequencing count data.

Kumar MS, Slud EV, Okrah K, Hicks SC, Hannenhalli S, Corrada Bravo H.

BMC Genomics. 2018 Nov 6;19(1):799. doi: 10.1186/s12864-018-5160-5.


Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures.

Lee JS, Adler L, Karathia H, Carmel N, Rabinovich S, Auslander N, Keshet R, Stettner N, Silberman A, Agemy L, Helbling D, Eilam R, Sun Q, Brandis A, Malitsky S, Itkin M, Weiss H, Pinto S, Kalaora S, Levy R, Barnea E, Admon A, Dimmock D, Stern-Ginossar N, Scherz A, Nagamani SCS, Unda M, Wilson DM 3rd, Elhasid R, Carracedo A, Samuels Y, Hannenhalli S, Ruppin E, Erez A.

Cell. 2018 Sep 6;174(6):1559-1570.e22. doi: 10.1016/j.cell.2018.07.019. Epub 2018 Aug 9.


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

Wang K, Wu D, Zhang H, Das A, Basu M, Malin J, Cao K, Hannenhalli S.

Sci Rep. 2018 Jul 19;8(1):10929. doi: 10.1038/s41598-018-29086-2.


Harnessing synthetic lethality to predict the response to cancer treatment.

Lee JS, Das A, Jerby-Arnon L, Arafeh R, Auslander N, Davidson M, McGarry L, James D, Amzallag A, Park SG, Cheng K, Robinson W, Atias D, Stossel C, Buzhor E, Stein G, Waterfall JJ, Meltzer PS, Golan T, Hannenhalli S, Gottlieb E, Benes CH, Samuels Y, Shanks E, Ruppin E.

Nat Commun. 2018 Jun 29;9(1):2546. doi: 10.1038/s41467-018-04647-1.


Genetic Reduction in Left Ventricular Protein Kinase C-α and Adverse Ventricular Remodeling in Human Subjects.

Hu R, Morley MP, Brandimarto J, Tucker NR, Parsons VA, Zhao SD, Meder B, Katus HA, Rühle F, Stoll M, Villard E, Cambien F, Lin H, Smith NL, Felix JF, Vasan RS, van der Harst P, Newton-Cheh C, Li J, Kim CE, Hakonarson H, Hannenhalli S, Ashley EA, Moravec CS, Tang WHW, Maillet M, Molkentin JD, Ellinor PT, Margulies KB, Cappola TP.

Circ Genom Precis Med. 2018 Mar;11(3):e001901. doi: 10.1161/CIRCGEN.117.001901.


Putative functional genes in idiopathic dilated cardiomyopathy.

Nair NU, Das A, Amit U, Robinson W, Park SG, Basu M, Lugo A, Leor J, Ruppin E, Hannenhalli S.

Sci Rep. 2018 Jan 8;8(1):66. doi: 10.1038/s41598-017-18524-2.


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

Patkar S, Magen A, Sharan R, Hannenhalli S.

PLoS Comput Biol. 2017 Nov 30;13(11):e1005793. doi: 10.1371/journal.pcbi.1005793. eCollection 2017 Nov.


Orphan CpG islands as alternative promoters.

Sarda S, Hannenhalli S.

Transcription. 2018;9(3):171-176. doi: 10.1080/21541264.2017.1373209. Epub 2017 Nov 28.


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

Basu M, Sharmin M, Das A, Nair NU, Wang K, Lee JS, Chang YC, Ruppin E, Hannenhalli S.

Genetics. 2017 Nov;207(3):1121-1134. doi: 10.1534/genetics.117.300280. Epub 2017 Sep 12.


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

Amit U, Kain D, Wagner A, Sahu A, Nevo-Caspi Y, Gonen N, Molotski N, Konfino T, Landa N, Naftali-Shani N, Blum G, Merquiol E, Karo-Atar D, Kanfi Y, Paret G, Munitz A, Cohen HY, Ruppin E, Hannenhalli S, Leor J.

J Am Heart Assoc. 2017 May 20;6(5). pii: e005108. doi: 10.1161/JAHA.116.005108.


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

Sarda S, Das A, Vinson C, Hannenhalli S.

Genome Res. 2017 Apr;27(4):553-566. doi: 10.1101/gr.212050.116. Epub 2017 Feb 21.


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

Karathia H, Kingsford C, Girvan M, Hannenhalli S.

Sci Rep. 2016 Dec 15;6:39279. doi: 10.1038/srep39279.


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

Sharmin M, Bravo HC, Hannenhalli S.

Genome Res. 2016 Aug;26(8):1110-23. doi: 10.1101/gr.199166.115. Epub 2016 Jun 16.


Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer.

Sharmin M, Bravo HC, Hannenhalli S.

BMC Cancer. 2016 Feb 11;16:88. doi: 10.1186/s12885-016-2128-1.


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

Kumar MS, Plotkin JB, Hannenhalli S.

PLoS Comput Biol. 2015 Nov 6;11(11):e1004603. doi: 10.1371/journal.pcbi.1004603. eCollection 2015 Nov.


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

Das A, Morley M, Moravec CS, Tang WH, Hakonarson H; MAGNet Consortium, Margulies KB, Cappola TP, Jensen S, Hannenhalli S.

Nat Commun. 2015 Oct 12;6:8555. doi: 10.1038/ncomms9555.


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

Sarda S, Hannenhalli S.

Mol Biol Evol. 2015 Dec;32(12):3047-63. doi: 10.1093/molbev/msv203. Epub 2015 Sep 23.


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

Wang K, Das A, Xiong ZM, Cao K, Hannenhalli S.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Jan-Feb;12(1):30-9. doi: 10.1109/TCBB.2014.2359446.


Chromatin and Genomic determinants of alternative splicing.

Wang K, Cao K, Hannenhalli S.

ACM BCB. 2015 Sep;2015:345-354. doi: 10.1145/2808719.2808755.


Evolutionarily conserved network properties of intrinsically disordered proteins.

Rangarajan N, Kulkarni P, Hannenhalli S.

PLoS One. 2015 May 14;10(5):e0126729. doi: 10.1371/journal.pone.0126729. eCollection 2015.


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

Liu Y, Morley M, Brandimarto J, Hannenhalli S, Hu Y, Ashley EA, Tang WH, Moravec CS, Margulies KB, Cappola TP, Li M; MAGNet consortium.

Genomics. 2015 Feb;105(2):83-9. doi: 10.1016/j.ygeno.2014.12.002. Epub 2014 Dec 17.


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

Darnell DK, Zhang LS, Hannenhalli S, Yaklichkin SY.

Int J Dev Biol. 2014;58(1):57-64. doi: 10.1387/ijdb.130023sy.


Next-generation sequencing and epigenomics research: a hammer in search of nails.

Sarda S, Hannenhalli S.

Genomics Inform. 2014 Mar;12(1):2-11. doi: 10.5808/GI.2014.12.1.2. Epub 2014 Mar 31. Review.


Determinants of expression variability.

Alemu EY, Carl JW Jr, Corrada Bravo H, Hannenhalli S.

Nucleic Acids Res. 2014 Apr;42(6):3503-14. doi: 10.1093/nar/gkt1364. Epub 2014 Jan 15.


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

Plasschaert RN, Vigneau S, Tempera I, Gupta R, Maksimoska J, Everett L, Davuluri R, Mamorstein R, Lieberman PM, Schultz D, Hannenhalli S, Bartolomei MS.

Nucleic Acids Res. 2014 Jan;42(2):774-89. doi: 10.1093/nar/gkt910. Epub 2013 Oct 10.


Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers.

Malin J, Aniba MR, Hannenhalli S.

Nucleic Acids Res. 2013 Aug;41(14):6828-38. doi: 10.1093/nar/gkt374. Epub 2013 May 21.


Derepression of Cancer/testis antigens in cancer is associated with distinct patterns of DNA hypomethylation.

Kim R, Kulkarni P, Hannenhalli S.

BMC Cancer. 2013 Mar 22;13:144. doi: 10.1186/1471-2407-13-144.


Epigenomic model of cardiac enhancers with application to genome wide association studies.

Sahu AD, Aniba R, Chang YP, Hannenhalli S.

Pac Symp Biocomput. 2013:92-102.


Correlated evolution of positions within mammalian cis elements.

Mukherjee R, Evans P, Singh LN, Hannenhalli S.

PLoS One. 2013;8(2):e55521. doi: 10.1371/journal.pone.0055521. Epub 2013 Feb 8.


Three independent determinants of protein evolutionary rate.

Choi SS, Hannenhalli S.

J Mol Evol. 2013 Mar;76(3):98-111. doi: 10.1007/s00239-013-9543-6. Epub 2013 Feb 12. Review.


Widespread evidence of viral miRNAs targeting host pathways.

Carl JW Jr, Trgovcich J, Hannenhalli S.

BMC Bioinformatics. 2013;14 Suppl 2:S3. doi: 10.1186/1471-2105-14-S2-S3. Epub 2013 Jan 21.


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

Zeng J, Hannenhalli S.

BMC Genomics. 2013;14 Suppl 1:S15. doi: 10.1186/1471-2164-14-S1-S15. Epub 2013 Jan 21.


Intrinsically disordered proteins and conformational noise: implications in cancer.

Mahmoudabadi G, Rajagopalan K, Getzenberg RH, Hannenhalli S, Rangarajan G, Kulkarni P.

Cell Cycle. 2013 Jan 1;12(1):26-31. doi: 10.4161/cc.23178. Epub 2012 Dec 19.


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

Vecsey CG, Peixoto L, Choi JH, Wimmer M, Jaganath D, Hernandez PJ, Blackwell J, Meda K, Park AJ, Hannenhalli S, Abel T.

Physiol Genomics. 2012 Oct 17;44(20):981-91. doi: 10.1152/physiolgenomics.00084.2012. Epub 2012 Aug 28.


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

Li J, Bowens N, Cheng L, Zhu X, Chen M, Hannenhalli S, Cappola TP, Parmacek MS.

Development. 2012 Oct;139(19):3531-42. doi: 10.1242/dev.082222. Epub 2012 Aug 16.


Why transcription factor binding sites are ten nucleotides long.

Stewart AJ, Hannenhalli S, Plotkin JB.

Genetics. 2012 Nov;192(3):973-85. doi: 10.1534/genetics.112.143370. Epub 2012 Aug 10. Erratum in: Genetics. 2013 Apr;193(4):1311. Hannenhalli, Sridhar [added].


Functional divergence of gene duplicates - a domain-centric view.

Khaladkar M, Hannenhalli S.

BMC Evol Biol. 2012 Jul 27;12:126. doi: 10.1186/1471-2148-12-126.


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

Yaklichkin SY, Darnell DK, Pier MV, Antin PB, Hannenhalli S.

BMC Evol Biol. 2011 Oct 15;11:302. doi: 10.1186/1471-2148-11-302.


Epigenomic and RNA structural correlates of polyadenylation.

Khaladkar M, Smyda M, Hannenhalli S.

RNA Biol. 2011 May-Jun;8(3):529-37. Epub 2011 May 1.


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

Vishnoi A, Sethupathy P, Simola D, Plotkin JB, Hannenhalli S.

Mol Biol Evol. 2011 Sep;28(9):2615-27. doi: 10.1093/molbev/msr085. Epub 2011 Apr 3.


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

Everett LJ, Jensen ST, Hannenhalli S.

Nucleic Acids Res. 2011 Jul;39(12):e78. doi: 10.1093/nar/gkr172. Epub 2011 Apr 5.


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

Tian Y, Zhang Y, Hurd L, Hannenhalli S, Liu F, Lu MM, Morrisey EE.

Development. 2011 Apr;138(7):1235-45. doi: 10.1242/dev.061762. Epub 2011 Feb 24.


Gene coexpression network topology of cardiac development, hypertrophy, and failure.

Dewey FE, Perez MV, Wheeler MT, Watt C, Spin J, Langfelder P, Horvath S, Hannenhalli S, Cappola TP, Ashley EA.

Circ Cardiovasc Genet. 2011 Feb;4(1):26-35. doi: 10.1161/CIRCGENETICS.110.941757. Epub 2010 Dec 2.

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