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Items: 28

1.

Detecting the impact of subject characteristics on machine learning-based diagnostic applications.

Chaibub Neto E, Pratap A, Perumal TM, Tummalacherla M, Snyder P, Bot BM, Trister AD, Friend SH, Mangravite L, Omberg L.

NPJ Digit Med. 2019 Oct 11;2:99. doi: 10.1038/s41746-019-0178-x. eCollection 2019.

2.

Identifying and ranking potential driver genes of Alzheimer's disease using multiview evidence aggregation.

Mukherjee S, Perumal TM, Daily K, Sieberts SK, Omberg L, Preuss C, Carter GW, Mangravite LM, Logsdon BA.

Bioinformatics. 2019 Jul 15;35(14):i568-i576. doi: 10.1093/bioinformatics/btz365.

3.

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics.

Liu J, Lichtenberg T, Hoadley KA, Poisson LM, Lazar AJ, Cherniack AD, Kovatich AJ, Benz CC, Levine DA, Lee AV, Omberg L, Wolf DM, Shriver CD, Thorsson V; Cancer Genome Atlas Research Network, Hu H.

Cell. 2018 Apr 5;173(2):400-416.e11. doi: 10.1016/j.cell.2018.02.052.

4.

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.

Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kamińska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwińska P, Mazurek S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ; Cancer Genome Atlas Research Network, Stuart JM, Hoadley KA, Laird PW, Noushmehr H, Wiznerowicz M.

Cell. 2018 Apr 5;173(2):338-354.e15. doi: 10.1016/j.cell.2018.03.034.

5.

Unsupervised Analysis of Transcriptomics in Bacterial Sepsis Across Multiple Datasets Reveals Three Robust Clusters.

Sweeney TE, Azad TD, Donato M, Haynes WA, Perumal TM, Henao R, Bermejo-Martin JF, Almansa R, Tamayo E, Howrylak JA, Choi A, Parnell GP, Tang B, Nichols M, Woods CW, Ginsburg GS, Kingsmore SF, Omberg L, Mangravite LM, Wong HR, Tsalik EL, Langley RJ, Khatri P.

Crit Care Med. 2018 Jun;46(6):915-925. doi: 10.1097/CCM.0000000000003084.

6.

A community approach to mortality prediction in sepsis via gene expression analysis.

Sweeney TE, Perumal TM, Henao R, Nichols M, Howrylak JA, Choi AM, Bermejo-Martin JF, Almansa R, Tamayo E, Davenport EE, Burnham KL, Hinds CJ, Knight JC, Woods CW, Kingsmore SF, Ginsburg GS, Wong HR, Parnell GP, Tang B, Moldawer LL, Moore FE, Omberg L, Khatri P, Tsalik EL, Mangravite LM, Langley RJ.

Nat Commun. 2018 Feb 15;9(1):694. doi: 10.1038/s41467-018-03078-2.

7.

Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives.

Daily K, Ho Sui SJ, Schriml LM, Dexheimer PJ, Salomonis N, Schroll R, Bush S, Keddache M, Mayhew C, Lotia S, Perumal TM, Dang K, Pantano L, Pico AR, Grassman E, Nordling D, Hide W, Hatzopoulos AK, Malik P, Cancelas JA, Lutzko C, Aronow BJ, Omberg L.

Sci Data. 2017 Mar 28;4:170030. doi: 10.1038/sdata.2017.30.

8.

Spatiotemporal Reconstruction of the Human Blastocyst by Single-Cell Gene-Expression Analysis Informs Induction of Naive Pluripotency.

Durruthy-Durruthy J, Wossidlo M, Pai S, Takahashi Y, Kang G, Omberg L, Chen B, Nakauchi H, Reijo Pera R, Sebastiano V.

Dev Cell. 2016 Jul 11;38(1):100-15. doi: 10.1016/j.devcel.2016.06.014.

9.

Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium.

Salomonis N, Dexheimer PJ, Omberg L, Schroll R, Bush S, Huo J, Schriml L, Ho Sui S, Keddache M, Mayhew C, Shanmukhappa SK, Wells J, Daily K, Hubler S, Wang Y, Zambidis E, Margolin A, Hide W, Hatzopoulos AK, Malik P, Cancelas JA, Aronow BJ, Lutzko C.

Stem Cell Reports. 2016 Jul 12;7(1):110-25. doi: 10.1016/j.stemcr.2016.05.006. Epub 2016 Jun 9.

10.

Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases.

Chen R, Shi L, Hakenberg J, Naughton B, Sklar P, Zhang J, Zhou H, Tian L, Prakash O, Lemire M, Sleiman P, Cheng WY, Chen W, Shah H, Shen Y, Fromer M, Omberg L, Deardorff MA, Zackai E, Bobe JR, Levin E, Hudson TJ, Groop L, Wang J, Hakonarson H, Wojcicki A, Diaz GA, Edelmann L, Schadt EE, Friend SH.

Nat Biotechnol. 2016 May;34(5):531-8. doi: 10.1038/nbt.3514. Epub 2016 Apr 11.

PMID:
27065010
11.

PERSONALIZED HYPOTHESIS TESTS FOR DETECTING MEDICATION RESPONSE IN PARKINSON DISEASE PATIENTS USING iPHONE SENSOR DATA.

Chaibub Neto E, Bot BM, Perumal T, Omberg L, Guinney J, Kellen M, Klein A, Friend SH, Trister AD.

Pac Symp Biocomput. 2016;21:273-84.

12.

The PsychENCODE project.

PsychENCODE Consortium, Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N.

Nat Neurosci. 2015 Dec;18(12):1707-12. doi: 10.1038/nn.4156. Review. No abstract available.

13.

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin.

Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MDM, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin AA, Van't Veer LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA; Cancer Genome Atlas Research Network, Benz CC, Perou CM, Stuart JM.

Cell. 2014 Aug 14;158(4):929-944. doi: 10.1016/j.cell.2014.06.049. Epub 2014 Aug 7.

14.

Assessing the clinical utility of cancer genomic and proteomic data across tumor types.

Yuan Y, Van Allen EM, Omberg L, Wagle N, Amin-Mansour A, Sokolov A, Byers LA, Xu Y, Hess KR, Diao L, Han L, Huang X, Lawrence MS, Weinstein JN, Stuart JM, Mills GB, Garraway LA, Margolin AA, Getz G, Liang H.

Nat Biotechnol. 2014 Jul;32(7):644-52. doi: 10.1038/nbt.2940. Epub 2014 Jun 22.

15.

Feed premix: a difficult matrix for the accurate determination of trace elements - the outcome of IMEP-114 and IMEP-36.

Fiamegos Y, Cordeiro F, Robouch P, Emteborg H, Charoud-Got J, Omberg LG, Rodushkin I, de la Calle B.

Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2014;31(1):63-72. doi: 10.1080/19440049.2013.861083. Epub 2014 Jan 10.

PMID:
24195486
16.

Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas.

Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA.

Nat Genet. 2013 Oct;45(10):1121-6. doi: 10.1038/ng.2761.

17.

PCAdmix: principal components-based assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations.

Brisbin A, Bryc K, Byrnes J, Zakharia F, Omberg L, Degenhardt J, Reynolds A, Ostrer H, Mezey JG, Bustamante CD.

Hum Biol. 2012 Aug;84(4):343-64. doi: 10.3378/027.084.0401.

18.

Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.

Kidd JM, Gravel S, Byrnes J, Moreno-Estrada A, Musharoff S, Bryc K, Degenhardt JD, Brisbin A, Sheth V, Chen R, McLaughlin SF, Peckham HE, Omberg L, Bormann Chung CA, Stanley S, Pearlstein K, Levandowsky E, Acevedo-Acevedo S, Auton A, Keinan A, Acuña-Alonzo V, Barquera-Lozano R, Canizales-Quinteros S, Eng C, Burchard EG, Russell A, Reynolds A, Clark AG, Reese MG, Lincoln SE, Butte AJ, De La Vega FM, Bustamante CD.

Am J Hum Genet. 2012 Oct 5;91(4):660-71. doi: 10.1016/j.ajhg.2012.08.025.

19.

Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations.

Omberg L, Salit J, Hackett N, Fuller J, Matthew R, Chouchane L, Rodriguez-Flores JL, Bustamante C, Crystal RG, Mezey JG.

BMC Genet. 2012 Jun 26;13:49. doi: 10.1186/1471-2156-13-49.

20.

Patterns of ancestry, signatures of natural selection, and genetic association with stature in Western African pygmies.

Jarvis JP, Scheinfeldt LB, Soi S, Lambert C, Omberg L, Ferwerda B, Froment A, Bodo JM, Beggs W, Hoffman G, Mezey J, Tishkoff SA.

PLoS Genet. 2012;8(4):e1002641. doi: 10.1371/journal.pgen.1002641. Epub 2012 Apr 26.

21.

RNA-Seq quantification of the human small airway epithelium transcriptome.

Hackett NR, Butler MW, Shaykhiev R, Salit J, Omberg L, Rodriguez-Flores JL, Mezey JG, Strulovici-Barel Y, Wang G, Didon L, Crystal RG.

BMC Genomics. 2012 Feb 29;13:82. doi: 10.1186/1471-2164-13-82.

22.

Biologic phenotyping of the human small airway epithelial response to cigarette smoking.

Tilley AE, O'Connor TP, Hackett NR, Strulovici-Barel Y, Salit J, Amoroso N, Zhou XK, Raman T, Omberg L, Clark A, Mezey J, Crystal RG.

PLoS One. 2011;6(7):e22798. doi: 10.1371/journal.pone.0022798. Epub 2011 Jul 28.

23.

Glutathione S-transferase copy number variation alters lung gene expression.

Butler MW, Hackett NR, Salit J, Strulovici-Barel Y, Omberg L, Mezey J, Crystal RG.

Eur Respir J. 2011 Jul;38(1):15-28. doi: 10.1183/09031936.00029210. Epub 2011 Feb 24.

24.

Threshold of biologic responses of the small airway epithelium to low levels of tobacco smoke.

Strulovici-Barel Y, Omberg L, O'Mahony M, Gordon C, Hollmann C, Tilley AE, Salit J, Mezey J, Harvey BG, Crystal RG.

Am J Respir Crit Care Med. 2010 Dec 15;182(12):1524-32. doi: 10.1164/rccm.201002-0294OC. Epub 2010 Aug 6.

25.

Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression.

Omberg L, Meyerson JR, Kobayashi K, Drury LS, Diffley JF, Alter O.

Mol Syst Biol. 2009;5:312. doi: 10.1038/msb.2009.70. Epub 2009 Oct 13.

26.

Coordinate control of expression of Nrf2-modulated genes in the human small airway epithelium is highly responsive to cigarette smoking.

Hübner RH, Schwartz JD, De Bishnu P, Ferris B, Omberg L, Mezey JG, Hackett NR, Crystal RG.

Mol Med. 2009 Jul-Aug;15(7-8):203-19. doi: 10.2119/molmed.2008.00130. Epub 2009 Mar 20.

27.

A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies.

Omberg L, Golub GH, Alter O.

Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18371-6. Epub 2007 Nov 14.

28.

Detecting the onset of bifurcations and their precursors from noisy data

Omberg L, Dolan K, Neiman A, Moss F.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 May;61(5A):4848-53.

PMID:
11031525

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