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Items: 1 to 20 of 90


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.


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.

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