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Items: 19

1.

Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.

Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, Guo T, Favorov AV, Yegnasubramanian S, Fertig EJ, Ha P, Tamayo P, Yamasoba T, Ideker T, Messer K, Califano JA.

Nat Commun. 2019 May 16;10(1):2188. doi: 10.1038/s41467-019-09937-w. Erratum in: Nat Commun. 2019 May 29;10(1):2415.

2.

RNA-sequencing in ophthalmology research: considerations for experimental design and analysis.

Owen N, Moosajee M.

Ther Adv Ophthalmol. 2019 Mar 15;11:2515841419835460. doi: 10.1177/2515841419835460. eCollection 2019 Jan-Dec. Review.

3.

Machine Learning and Integrative Analysis of Biomedical Big Data.

Mirza B, Wang W, Wang J, Choi H, Chung NC, Ping P.

Genes (Basel). 2019 Jan 28;10(2). pii: E87. doi: 10.3390/genes10020087. Review.

4.

RNA based individualized drug selection in breast cancer patients without patient-matched normal tissue.

Forster M, Mark A, Egberts F, Rosati E, Rodriguez E, Stanulla M, Bauerschlag D, Schem C, Maass N, Amallraja A, Murphy KK, Prouse BR, Sulaiman RA, Young BM, Mathiak M, Hemmrich-Stanisak G, Ellinghaus D, Weidinger S, Rosenstiel P, Arnold N, Leyland-Jones B, Williams CB, Franke A, Meißner T.

Oncotarget. 2018 Aug 17;9(64):32362-32372. doi: 10.18632/oncotarget.25981. eCollection 2018 Aug 17.

5.

Cloud computing for genomic data analysis and collaboration.

Langmead B, Nellore A.

Nat Rev Genet. 2018 Apr;19(4):208-219. doi: 10.1038/nrg.2017.113. Epub 2018 Jan 30. Review. Erratum in: Nat Rev Genet. 2018 Feb 12;:.

6.

DGIdb 3.0: a redesign and expansion of the drug-gene interaction database.

Cotto KC, Wagner AH, Feng YY, Kiwala S, Coffman AC, Spies G, Wollam A, Spies NC, Griffith OL, Griffith M.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1068-D1073. doi: 10.1093/nar/gkx1143.

7.

Investigating reproducibility and tracking provenance - A genomic workflow case study.

Kanwal S, Khan FZ, Lonie A, Sinnott RO.

BMC Bioinformatics. 2017 Jul 12;18(1):337. doi: 10.1186/s12859-017-1747-0.

8.

Kronos: a workflow assembler for genome analytics and informatics.

Taghiyar MJ, Rosner J, Grewal D, Grande BM, Aniba R, Grewal J, Boutros PC, Morin RD, Bashashati A, Shah SP.

Gigascience. 2017 Jul 1;6(7):1-10. doi: 10.1093/gigascience/gix042.

9.

Id3 Orchestrates Germinal Center B Cell Development.

Chen S, Miyazaki M, Chandra V, Fisch KM, Chang AN, Murre C.

Mol Cell Biol. 2016 Sep 26;36(20):2543-52. doi: 10.1128/MCB.00150-16. Print 2016 Oct 15.

10.

Reannotation of Yersinia pestis Strain 91001 Based on Omics Data.

Mao Y, Yang X, Liu Y, Yan Y, Du Z, Han Y, Song Y, Zhou L, Cui Y, Yang R.

Am J Trop Med Hyg. 2016 Sep 7;95(3):562-70. doi: 10.4269/ajtmh.16-0215. Epub 2016 Jul 5.

11.

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report.

MetaSUB International Consortium.

Microbiome. 2016 Jun 3;4(1):24. doi: 10.1186/s40168-016-0168-z. Erratum in: Microbiome. 2016;4(1):45.

12.

SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis.

Hatakeyama M, Opitz L, Russo G, Qi W, Schlapbach R, Rehrauer H.

BMC Bioinformatics. 2016 Jun 2;17(1):228. doi: 10.1186/s12859-016-1104-8.

13.

Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions.

Bianchi V, Ceol A, Ogier AG, de Pretis S, Galeota E, Kishore K, Bora P, Croci O, Campaner S, Amati B, Morelli MJ, Pelizzola M.

Front Genet. 2016 May 6;7:75. doi: 10.3389/fgene.2016.00075. eCollection 2016.

14.

miARma-Seq: a comprehensive tool for miRNA, mRNA and circRNA analysis.

Andrés-León E, Núñez-Torres R, Rojas AM.

Sci Rep. 2016 May 11;6:25749. doi: 10.1038/srep25749. Erratum in: Sci Rep. 2018 Jan 08;8:46928.

15.

A review of bioinformatic pipeline frameworks.

Leipzig J.

Brief Bioinform. 2017 May 1;18(3):530-536. doi: 10.1093/bib/bbw020. Review.

16.

DGIdb 2.0: mining clinically relevant drug-gene interactions.

Wagner AH, Coffman AC, Ainscough BJ, Spies NC, Skidmore ZL, Campbell KM, Krysiak K, Pan D, McMichael JF, Eldred JM, Walker JR, Wilson RK, Mardis ER, Griffith M, Griffith OL.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1036-44. doi: 10.1093/nar/gkv1165. Epub 2015 Nov 3.

17.

The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data.

McInerney J, Pisani D, O'Connell MJ.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678):20140323. doi: 10.1098/rstb.2014.0323. Review.

18.

Cpipe: a shared variant detection pipeline designed for diagnostic settings.

Sadedin SP, Dashnow H, James PA, Bahlo M, Bauer DC, Lonie A, Lunke S, Macciocca I, Ross JP, Siemering KR, Stark Z, White SM; Melbourne Genomics Health Alliance, Taylor G, Gaff C, Oshlack A, Thorne NP.

Genome Med. 2015 Jul 10;7(1):68. doi: 10.1186/s13073-015-0191-x. eCollection 2015.

19.

OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing.

Meißner T, Fisch KM, Gioia L, Su AI.

BMC Med Genomics. 2015 May 21;8:24. doi: 10.1186/s12920-015-0095-z.

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