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Results: 1 to 20 of 79

1.

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

Park SG, Hannenhalli S, Choi SS.

BMC Genomics. 2014 Jun 26;15:526. doi: 10.1186/1471-2164-15-526.

PMID:
24964727
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
24860996
[PubMed - in process]
3.

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.

PMID:
24748856
[PubMed]
Free PMC Article
4.

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.

PMID:
24435799
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
24121688
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
23700312
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
23522060
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
23424115
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
23408994
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
23400388
[PubMed - indexed for MEDLINE]
11.

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.

PMID:
23369080
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
23368094
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
23255110
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
22930738
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
22899851
[PubMed - indexed for MEDLINE]
Free PMC Article
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].

PMID:
22887818
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
22839301
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

PMID:
21999483
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
21508683
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
21478372
[PubMed - indexed for MEDLINE]
Free PMC Article

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