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Page 1
Genome-wide Interaction Study with Smoking for Colorectal Cancer Risk Identifies Novel Genetic Loci Related to Tumor Suppression, Inflammation, and Immune Response.
Carreras-Torres R, Kim AE, Lin Y, Díez-Obrero V, Bien SA, Qu C, Wang J, Dimou N, Aglago EK, Albanes D, Arndt V, Baurley JW, Berndt SI, Bézieau S, Bishop DT, Bouras E, Brenner H, Budiarto A, Campbell PT, Casey G, Chan AT, Chang-Claude J, Chen X, Conti DV, Dampier CH, Devall MAM, Drew DA, Figueiredo JC, Gallinger S, Giles GG, Gruber SB, Gsur A, Gunter MJ, Harrison TA, Hidaka A, Hoffmeister M, Huyghe JR, Jenkins MA, Jordahl KM, Kawaguchi E, Keku TO, Kundaje A, Le Marchand L, Lewinger JP, Li L, Mahesworo B, Morrison JL, Murphy N, Nan H, Nassir R, Newcomb PA, Obón-Santacana M, Ogino S, Ose J, Pai RK, Palmer JR, Papadimitriou N, Pardamean B, Peoples AR, Pharoah PDP, Platz EA, Rennert G, Ruiz-Narvaez E, Sakoda LC, Scacheri PC, Schmit SL, Schoen RE, Shcherbina A, Slattery ML, Stern MC, Su YR, Tangen CM, Thomas DC, Tian Y, Tsilidis KK, Ulrich CM, van Duijnhoven FJB, Van Guelpen B, Visvanathan K, Vodicka P, Cenggoro TW, Weinstein SJ, White E, Wolk A, Woods MO, Hsu L, Peters U, Moreno V, Gauderman WJ. Carreras-Torres R, et al. Among authors: kundaje a. Cancer Epidemiol Biomarkers Prev. 2023 Mar 6;32(3):315-328. doi: 10.1158/1055-9965.EPI-22-0763. Cancer Epidemiol Biomarkers Prev. 2023. PMID: 36576985 Free PMC article.
Architecture of the human regulatory network derived from ENCODE data.
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. Gerstein MB, et al. Among authors: kundaje a. Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245. Nature. 2012. PMID: 22955619 Free PMC article.
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. Landt SG, et al. Among authors: kundaje a. Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111. Genome Res. 2012. PMID: 22955991 Free PMC article.
Integrative annotation of chromatin elements from ENCODE data.
Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS. Hoffman MM, et al. Among authors: kundaje a. Nucleic Acids Res. 2013 Jan;41(2):827-41. doi: 10.1093/nar/gks1284. Epub 2012 Dec 5. Nucleic Acids Res. 2013. PMID: 23221638 Free PMC article.
Extensive variation in chromatin states across humans.
Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M. Kasowski M, et al. Among authors: kundaje a. Science. 2013 Nov 8;342(6159):750-2. doi: 10.1126/science.1242510. Epub 2013 Oct 17. Science. 2013. PMID: 24136358 Free PMC article.
Defining functional DNA elements in the human genome.
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC. Kellis M, et al. Among authors: kundaje a. Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6131-8. doi: 10.1073/pnas.1318948111. Epub 2014 Apr 21. Proc Natl Acad Sci U S A. 2014. PMID: 24753594 Free PMC article. Review.
Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster.
Slattery M, Ma L, Spokony RF, Arthur RK, Kheradpour P, Kundaje A, Nègre N, Crofts A, Ptashkin R, Zieba J, Ostapenko A, Suchy S, Victorsen A, Jameel N, Grundstad AJ, Gao W, Moran JR, Rehm EJ, Grossman RL, Kellis M, White KP. Slattery M, et al. Among authors: kundaje a. Genome Res. 2014 Jul;24(7):1224-35. doi: 10.1101/gr.168807.113. Genome Res. 2014. PMID: 24985916 Free PMC article.
170 results