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Items: 14

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.

Comprehensive functional genomic resource and integrative model for the human brain.

Wang D, Liu S, Warrell J, Won H, Shi X, Navarro FCP, Clarke D, Gu M, Emani P, Yang YT, Xu M, Gandal MJ, Lou S, Zhang J, Park JJ, Yan C, Rhie SK, Manakongtreecheep K, Zhou H, Nathan A, Peters M, Mattei E, Fitzgerald D, Brunetti T, Moore J, Jiang Y, Girdhar K, Hoffman GE, Kalayci S, Gümüş ZH, Crawford GE; PsychENCODE Consortium, Roussos P, Akbarian S, Jaffe AE, White KP, Weng Z, Sestan N, Geschwind DH, Knowles JA, Gerstein MB.

Science. 2018 Dec 14;362(6420). pii: eaat8464. doi: 10.1126/science.aat8464.

3.

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder.

Gandal MJ, Zhang P, Hadjimichael E, Walker RL, Chen C, Liu S, Won H, van Bakel H, Varghese M, Wang Y, Shieh AW, Haney J, Parhami S, Belmont J, Kim M, Moran Losada P, Khan Z, Mleczko J, Xia Y, Dai R, Wang D, Yang YT, Xu M, Fish K, Hof PR, Warrell J, Fitzgerald D, White K, Jaffe AE; PsychENCODE Consortium, Peters MA, Gerstein M, Liu C, Iakoucheva LM, Pinto D, Geschwind DH.

Science. 2018 Dec 14;362(6420). pii: eaat8127. doi: 10.1126/science.aat8127.

4.

Integrative functional genomic analysis of human brain development and neuropsychiatric risks.

Li M, Santpere G, Imamura Kawasawa Y, Evgrafov OV, Gulden FO, Pochareddy S, Sunkin SM, Li Z, Shin Y, Zhu Y, Sousa AMM, Werling DM, Kitchen RR, Kang HJ, Pletikos M, Choi J, Muchnik S, Xu X, Wang D, Lorente-Galdos B, Liu S, Giusti-Rodríguez P, Won H, de Leeuw CA, Pardiñas AF; BrainSpan Consortium; PsychENCODE Consortium; PsychENCODE Developmental Subgroup, Hu M, Jin F, Li Y, Owen MJ, O'Donovan MC, Walters JTR, Posthuma D, Reimers MA, Levitt P, Weinberger DR, Hyde TM, Kleinman JE, Geschwind DH, Hawrylycz MJ, State MW, Sanders SJ, Sullivan PF, Gerstein MB, Lein ES, Knowles JA, Sestan N.

Science. 2018 Dec 14;362(6420). pii: eaat7615. doi: 10.1126/science.aat7615.

5.

Transcriptome and epigenome landscape of human cortical development modeled in organoids.

Amiri A, Coppola G, Scuderi S, Wu F, Roychowdhury T, Liu F, Pochareddy S, Shin Y, Safi A, Song L, Zhu Y, Sousa AMM; PsychENCODE Consortium, Gerstein M, Crawford GE, Sestan N, Abyzov A, Vaccarino FM.

Science. 2018 Dec 14;362(6420). pii: eaat6720. doi: 10.1126/science.aat6720.

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.

9.

Integrative annotation of variants from 1092 humans: application to cancer genomics.

Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M.

Science. 2013 Oct 4;342(6154):1235587. doi: 10.1126/science.1235587.

10.

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.

Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.

11.

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.

Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M.

Bioinformatics. 2012 Sep 1;28(17):2267-9. Epub 2012 Jun 28.

12.

Novel insights through the integration of structural and functional genomics data with protein networks.

Clarke D, Bhardwaj N, Gerstein MB.

J Struct Biol. 2012 Sep;179(3):320-6. doi: 10.1016/j.jsb.2012.02.001. Epub 2012 Feb 11.

13.

Systematic control of protein interactions for systems biology.

Bhardwaj N, Clarke D, Gerstein M.

Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20279-80. doi: 10.1073/pnas.1118084109. Epub 2011 Dec 12. No abstract available.

14.

Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions.

Bhardwaj N, Abyzov A, Clarke D, Shou C, Gerstein MB.

Protein Sci. 2011 Oct;20(10):1745-54. doi: 10.1002/pro.710. Epub 2011 Sep 15.

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