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Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs
Amin V, Harris RA, Onuchic V, Jackson A, Charnecki T, Paithankar S, Subramanian S, Riehle K, Coarfa C, Milosavljevic A.
Nat. Commun. 6:6370 doi: 10.1038/ncomms7370 (2015)
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Integrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium et. al.
Nature doi: 10.1038/nature14248 (2015)
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Analysis of interactions between the epigenome and structural mutability of the genome using Genboree Workbench tools
Coarfa C, Pichot C, Jackson A, Tandon A, Amin V, Raghuraman S, Paithankar S, Lee AV, McGuire SE, Milosavljevic A.
BMC Bioinformatics. 2014;15 Suppl 7:S2. doi: 10.1186/1471-2105-15-S7-S2. Epub 2014 May 28.
PMID: 25080362
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Nasopharyngeal Proteobacteria are associated with viral etiology and acute wheezing in children with severe bronchiolitis
Hyde ER, Petrosino JF, Piedra PA, Camargo CA, Espinola JA, Mansbach JM.
J Allergy Clin Immunol. 2014 Apr;133(4):1220-2. doi: 10.1016/j.jaci.2013.10.049. Epub 2013 Dec 22.
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Microbiota modulate behavorial and physiological abnormalities associated with neurodevelopmental disorders
Hsiao EY, McBride SW, Sharon G, Hyde ER, McCue T, Codelli JA, Chow J, Reisman SE, Petrosino JF, Patterson PH, Mazamanian SK.
Cell. 2013 Dec 19;155(7):1451-63. doi: 10.1016/j.cell.2013.11.024. Epub 2013 Dec 5.
PMID: 24315484
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Cellulose supplementation early in life ameliorates colitis in adult mice
Nagy-Szakal D, Hollister EB, Luna RA, Sziget R, Tatevian N, smith CW, Versalovic J, Kellermayer R.
PLoS One. 2013;8(2):e56685. doi: 10.1371/journal.pone.0056685. Epub 2013 Feb 20.
PMID: 23437211
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Atlas2 Cloud: a framework for personal genome analysis in the cloud
Evani US, Challis D, Yu J,, Jackson AR,, Paithankar S, Bainbridge MN, Jakkamsetti A, Pham P, Coarfa C, Milosavljevic A, Yu F.
BMC Genomics. 2012;13 Suppl 6:S19. doi: 10.1186/1471-2164-13-S6-S19. Epub 2012 Oct 26.
PMID: 23134663
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The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences
Riehle K, Coarfa C, Jackson A, Ma J, Tandon A, Paithankar S, Raghuraman S, Mistretta TA, Saulnier D, Raza S, Diaz MA, Shulman R, Aagaard K, Versalovic J, Milosavljevic A.
BMC Bioinformatics. 2012;13 Suppl 13:S11. doi: 10.1186/1471-2105-13-S13-S11. Epub 2012 Aug 24.
PMID: 23320832
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Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood
Davies MN, Volta M, Pidsley R, Lunnon K, Dixit A, Lovestone S, Coarfa C, Harris RA, Milosavljevic A, Troakes C, Al-Saraj S, Dobson R, Schalkwyk LC, Mill J.
Genome Biol. 2012 Jun 15;13(6):R43. doi: 10.1186/gb-2012-13-6-r43.
PMID: 22703893
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A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy
Aagaard K, Riehle K, Ma J, Segata N, Mistretta TA, Coarfa C, Raza S, Rosenbaum S, Van den Veyver I, Milosavljevic A, Gevers D, Huttenhower C, Petrosino J, Versalovic J.
PLoS One. 2012;7(6):e36466. doi: 10.1371/journal.pone.0036466. Epub 2012 Jun 13.
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An integrative variant analysis suite for whole exome next-generation sequencing data
Challis D, Yu J, Evani US, Jackson AR, Paithankar S, Coarfa C, Milosavljevic A, Gibbs RA, Yu F.
BMC Bioinformatics. 2012 Jan 12;13:8. doi: 10.1186/1471-2105-13-8.
PMID: 22239737
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Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE
Celestino-Soper PB, Shaw CA, Sanders SJ, Li J, Murtha MT, Ercan-Sencicek AG, Davis L, Thomson S, Gambin T, Chinault AC, Ou Z, German JR, Milosavljevic A, Sutcliffe JS, Cook EH Jr, Stankiewicz P, State MW, Beaudet AL.
Hum Mol Genet. 2011 Nov 15;20(22):4360-70. doi: 10.1093/hmg/ddr363. Epub 2011 Aug 24.
PMID: 21865298