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Items: 7

1.

GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner.

Lou S, Cotter KA, Li T, Liang J, Mohsen H, Liu J, Zhang J, Cohen S, Xu J, Yu H, Rubin MA, Gerstein M.

PLoS Genet. 2019 Aug 30;15(8):e1007860. doi: 10.1371/journal.pgen.1007860. eCollection 2019 Aug.

2.

Building a Hybrid Physical-Statistical Classifier for Predicting the Effect of Variants Related to Protein-Drug Interactions.

Wang B, Yan C, Lou S, Emani P, Li B, Xu M, Kong X, Meyerson W, Yang YT, Lee D, Gerstein M.

Structure. 2019 Sep 3;27(9):1469-1481.e3. doi: 10.1016/j.str.2019.06.001. Epub 2019 Jul 3.

PMID:
31279629
3.

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.

4.

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.

Yan KK, Lou S, Gerstein M.

PLoS Comput Biol. 2017 Jul 24;13(7):e1005647. doi: 10.1371/journal.pcbi.1005647. eCollection 2017 Jul.

5.

Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation.

Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M.

Genome Biol. 2016 Apr 28;17:78. doi: 10.1186/s13059-016-0961-9. No abstract available.

6.

The real cost of sequencing: scaling computation to keep pace with data generation.

Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M.

Genome Biol. 2016 Mar 23;17:53. doi: 10.1186/s13059-016-0917-0. Erratum in: Genome Biol. 2016;17:78.

7.

FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.

Fu Y, Liu Z, Lou S, Bedford J, Mu XJ, Yip KY, Khurana E, Gerstein M.

Genome Biol. 2014;15(10):480.

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