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Items: 16

1.

Longitudinal multi-omics of host-microbe dynamics in prediabetes.

Zhou W, Sailani MR, Contrepois K, Zhou Y, Ahadi S, Leopold SR, Zhang MJ, Rao V, Avina M, Mishra T, Johnson J, Lee-McMullen B, Chen S, Metwally AA, Tran TDB, Nguyen H, Zhou X, Albright B, Hong BY, Petersen L, Bautista E, Hanson B, Chen L, Spakowicz D, Bahmani A, Salins D, Leopold B, Ashland M, Dagan-Rosenfeld O, Rego S, Limcaoco P, Colbert E, Allister C, Perelman D, Craig C, Wei E, Chaib H, Hornburg D, Dunn J, Liang L, Rose SMS, Kukurba K, Piening B, Rost H, Tse D, McLaughlin T, Sodergren E, Weinstock GM, Snyder M.

Nature. 2019 May;569(7758):663-671. doi: 10.1038/s41586-019-1236-x. Epub 2019 May 29.

PMID:
31142858
2.

Longitudinal personal DNA methylome dynamics in a human with a chronic condition.

Chen R, Xia L, Tu K, Duan M, Kukurba K, Li-Pook-Than J, Xie D, Snyder M.

Nat Med. 2018 Dec;24(12):1930-1939. doi: 10.1038/s41591-018-0237-x. Epub 2018 Nov 5.

PMID:
30397358
3.

Integrative Personal Omics Profiles during Periods of Weight Gain and Loss.

Piening BD, Zhou W, Contrepois K, Röst H, Gu Urban GJ, Mishra T, Hanson BM, Bautista EJ, Leopold S, Yeh CY, Spakowicz D, Banerjee I, Chen C, Kukurba K, Perelman D, Craig C, Colbert E, Salins D, Rego S, Lee S, Zhang C, Wheeler J, Sailani MR, Liang L, Abbott C, Gerstein M, Mardinoglu A, Smith U, Rubin DL, Pitteri S, Sodergren E, McLaughlin TL, Weinstock GM, Snyder MP.

Cell Syst. 2018 Feb 28;6(2):157-170.e8. doi: 10.1016/j.cels.2017.12.013. Epub 2018 Jan 17.

4.

Population- and individual-specific regulatory variation in Sardinia.

Pala M, Zappala Z, Marongiu M, Li X, Davis JR, Cusano R, Crobu F, Kukurba KR, Gloudemans MJ, Reinier F, Berutti R, Piras MG, Mulas A, Zoledziewska M, Marongiu M, Sorokin EP, Hess GT, Smith KS, Busonero F, Maschio A, Steri M, Sidore C, Sanna S, Fiorillo E, Bassik MC, Sawcer SJ, Battle A, Novembre J, Jones C, Angius A, Abecasis GR, Schlessinger D, Cucca F, Montgomery SB.

Nat Genet. 2017 May;49(5):700-707. doi: 10.1038/ng.3840. Epub 2017 Apr 10.

5.

PML nuclear bodies contribute to the basal expression of the mTOR inhibitor DDIT4.

Salsman J, Stathakis A, Parker E, Chung D, Anthes LE, Koskowich KL, Lahsaee S, Gaston D, Kukurba KR, Smith KS, Chute IC, Léger D, Frost LD, Montgomery SB, Lewis SM, Eskiw C, Dellaire G.

Sci Rep. 2017 Mar 23;7:45038. doi: 10.1038/srep45038.

6.

Impact of the X Chromosome and sex on regulatory variation.

Kukurba KR, Parsana P, Balliu B, Smith KS, Zappala Z, Knowles DA, Favé MJ, Davis JR, Li X, Zhu X, Potash JB, Weissman MM, Shi J, Kundaje A, Levinson DF, Awadalla P, Mostafavi S, Battle A, Montgomery SB.

Genome Res. 2016 Jun;26(6):768-77. doi: 10.1101/gr.197897.115. Epub 2016 Apr 21.

7.

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.

Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J; GTEx Consortium; Geuvadis Consortium, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG.

Science. 2015 May 8;348(6235):666-9. doi: 10.1126/science.1261877.

8.

The landscape of genomic imprinting across diverse adult human tissues.

Baran Y, Subramaniam M, Biton A, Tukiainen T, Tsang EK, Rivas MA, Pirinen M, Gutierrez-Arcelus M, Smith KS, Kukurba KR, Zhang R, Eng C, Torgerson DG, Urbanek C; GTEx Consortium, Li JB, Rodriguez-Santana JR, Burchard EG, Seibold MA, MacArthur DG, Montgomery SB, Zaitlen NA, Lappalainen T.

Genome Res. 2015 Jul;25(7):927-36. doi: 10.1101/gr.192278.115. Epub 2015 May 7.

9.

RNA Sequencing and Analysis.

Kukurba KR, Montgomery SB.

Cold Spring Harb Protoc. 2015 Apr 13;2015(11):951-69. doi: 10.1101/pdb.top084970.

10.

Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse.

Babak T, DeVeale B, Tsang EK, Zhou Y, Li X, Smith KS, Kukurba KR, Zhang R, Li JB, van der Kooy D, Montgomery SB, Fraser HB.

Nat Genet. 2015 May;47(5):544-9. doi: 10.1038/ng.3274. Epub 2015 Apr 13.

11.

Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants.

Li X, Battle A, Karczewski KJ, Zappala Z, Knowles DA, Smith KS, Kukurba KR, Wu E, Simon N, Montgomery SB.

Am J Hum Genet. 2014 Sep 4;95(3):245-56. doi: 10.1016/j.ajhg.2014.08.004.

12.

Allelic expression of deleterious protein-coding variants across human tissues.

Kukurba KR, Zhang R, Li X, Smith KS, Knowles DA, How Tan M, Piskol R, Lek M, Snyder M, Macarthur DG, Li JB, Montgomery SB.

PLoS Genet. 2014 May 1;10(5):e1004304. doi: 10.1371/journal.pgen.1004304. eCollection 2014 May.

13.

PATH-SCAN: a reporting tool for identifying clinically actionable variants.

Daneshjou R, Zappala Z, Kukurba K, Boyle SM, Ormond KE, Klein TE, Snyder M, Bustamante CD, Altman RB, Montgomery SB.

Pac Symp Biocomput. 2014:229-40.

14.

Genome-wide profiling of human cap-independent translation-enhancing elements.

Wellensiek BP, Larsen AC, Stephens B, Kukurba K, Waern K, Briones N, Liu L, Snyder M, Jacobs BL, Kumar S, Chaput JC.

Nat Methods. 2013 Aug;10(8):747-50. doi: 10.1038/nmeth.2522. Epub 2013 Jun 16.

15.

Systematic functional regulatory assessment of disease-associated variants.

Karczewski KJ, Dudley JT, Kukurba KR, Chen R, Butte AJ, Montgomery SB, Snyder M.

Proc Natl Acad Sci U S A. 2013 Jun 4;110(23):9607-12. doi: 10.1073/pnas.1219099110. Epub 2013 May 20.

16.

Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations.

Gray VE, Kukurba KR, Kumar S.

Bioinformatics. 2012 Aug 15;28(16):2093-6. doi: 10.1093/bioinformatics/bts336. Epub 2012 Jun 8.

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