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Items: 8

1.

Leveraging protein dynamics to identify cancer mutational hotspots using 3D structures.

Kumar S, Clarke D, Gerstein MB.

Proc Natl Acad Sci U S A. 2019 Sep 17;116(38):18962-18970. doi: 10.1073/pnas.1901156116. Epub 2019 Aug 28.

2.

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C.

Nat Commun. 2019 Apr 16;10(1):1784. doi: 10.1038/s41467-018-08148-z.

3.

Insights into genetics, human biology and disease gleaned from family based genomic studies.

Posey JE, O'Donnell-Luria AH, Chong JX, Harel T, Jhangiani SN, Coban Akdemir ZH, Buyske S, Pehlivan D, Carvalho CMB, Baxter S, Sobreira N, Liu P, Wu N, Rosenfeld JA, Kumar S, Avramopoulos D, White JJ, Doheny KF, Witmer PD, Boehm C, Sutton VR, Muzny DM, Boerwinkle E, Günel M, Nickerson DA, Mane S, MacArthur DG, Gibbs RA, Hamosh A, Lifton RP, Matise TC, Rehm HL, Gerstein M, Bamshad MJ, Valle D, Lupski JR; Centers for Mendelian Genomics.

Genet Med. 2019 Apr;21(4):798-812. doi: 10.1038/s41436-018-0408-7. Epub 2019 Jan 18. Review.

PMID:
30655598
4.

Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity.

Shi W, Ng CKY, Lim RS, Jiang T, Kumar S, Li X, Wali VB, Piscuoglio S, Gerstein MB, Chagpar AB, Weigelt B, Pusztai L, Reis-Filho JS, Hatzis C.

Cell Rep. 2018 Nov 6;25(6):1446-1457. doi: 10.1016/j.celrep.2018.10.046.

5.

Cancer genomics: Less is more in the hunt for driver mutations.

Kumar S, Gerstein M.

Nature. 2017 Jul 6;547(7661):40-41. doi: 10.1038/nature23085. Epub 2017 Jun 28. No abstract available.

PMID:
28658210
6.

Localized structural frustration for evaluating the impact of sequence variants.

Kumar S, Clarke D, Gerstein M.

Nucleic Acids Res. 2016 Dec 1;44(21):10062-10073. Epub 2016 Oct 18.

7.

Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation.

Clarke D, Sethi A, Li S, Kumar S, Chang RWF, Chen J, Gerstein M.

Structure. 2016 May 3;24(5):826-837. doi: 10.1016/j.str.2016.03.008. Epub 2016 Apr 7.

8.

Reads meet rotamers: structural biology in the age of deep sequencing.

Sethi A, Clarke D, Chen J, Kumar S, Galeev TR, Regan L, Gerstein M.

Curr Opin Struct Biol. 2015 Dec;35:125-34. doi: 10.1016/j.sbi.2015.11.003. Epub 2015 Dec 1. Review.

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