Full List

2018

Creating a scalable deep learning based Named Entity Recognition Model for biomedical textual data by repurposing BioSample free-text annotations
Tsui B, Mollah S, Skola D, Dow M, Hsu C, Carter H
Biorxiv (2018)

Evolutionary pressure against MHC class II binding cancer mutations
Marty R, Thompson W, Salem R, Zanetti M, Carter H
Cell. In Press (2018)

Integrative genomic analysis of mouse and human hepatocellular carcinoma
Dow M, Marty R, Tsui B, Alexandrov LB, Nakagawa H, Taniguchi K, Seki E, Harismendy O, Shalapour S, Karin M, Carter H, Font-Burgada J
PNAS. In Press (2018)

Extracting allelic read counts from 250,000 human sequencing runs in Sequence Read Archive
Tsui BDow MSkola DCarter H
Biorxiv (2018)

The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine
Ozturk K, Dow M, Carlin DE, Bejar R, Carter H
Journal of Molecular Biology Sep 14;(18 Pt A):2865-2899 (2018)

2017

MHC-I genotype restricts the oncogenic mutational landscape
Marty R, Kaabinejadian S, Rossell D, Slifker MJ, van de Haar J, Engin HB, de Prisco N, Ideker T, Hildebrand WH, Font-Burgada J, Carter H 
Cell Nov 30;171(6):1272-1283 (2017)

Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Wang T, Tsui B, Kreisberg, J, Robertson N, Gross Andrew, Yu M, Carter H, Brown-Borg H, Adam H, Adam P, Ideker T.
Genome Biology; 2017; 18: 57.

3D collagen architecture induces vascular mimicry through an integrin b1 mediated migratory and transcriptional response
Ortiz D, Tsui B, Goshia T, Chute-Ricker C, Han A, Carter H, Fraley SI 
Nature Communications Nov 21(8):1651 (2017)

Circulating tumour DNA methylation markers for diagnosis and prognosis of hepatocellular carcinoma
Xu R, Wei W,Krawczyk M, Wang W, Luo H, Flagg K, Yi S, Shi W, Li K, Zheng L, Zhang H, Caughey BA, Zhao Q, Hou J, Zhang R, Xu Y, Cai H, Li G, Hou R, Zhong Z, Lin D, Fu X, Zhu J, Duan Y, Zhang E, Zhang C, Li O, Carter H, Zhu J, Hao X, Zhang K 
Nature Materials Nov;16(11):1155-1161(2017)

Modeling of RAS Complexes Supports Roles in Cancer for Less Studied Partners
Engin B, Carlin D, Pratt D, Carter H 
BMC Biophysics Aug 11;10(1):5 (2017)

Pan-Cancer Analysis Reveals Technical Artifacts in The Cancer Genome Atlas (TCGA) Germline Variant Call
Buckley AR, Standish KA, Bhutani K, Ideker T, Harismendy O, Carter H, Schork NJ. 
BMC Genomics Jun 12;18(1):458 (2017)

Interaction landscape of inherited polymorphisms with somatic events in cancer
Carter H, Marty R, Hofree M, Gross A, Jensen J, Fisch K, Wu X, DeBoever C, Van Nostrand E, Song Y, Wheeler E, Kreisberg J, Lippman S, Yeo G, Gutkind S, Ideker T 
Cancer Discovery Apr 1;7(4):410-23 (2017)

2016

Immune DNA signature of T-Cell infiltration in breast tumor exomes
Levy E, Marty R, Garate-Calderon V, Woo B, Dow M, Armisen R, Carter H, Harismendy O 
Scientific Reports (2016)

Challenges in identifying cancer genes by analysis of exome sequencing data
Hofree M, Carter H, Kreisberg J, Bandyopadhyay S, Mischel P, Friend S, Ideker T 
Nature Communications Jul 15;7:12096 (2016)

Structure-based Analysis Reveals Cancer Missense Mutations Target Protein Interaction Interfaces
Engin B, Kreisberg J, Carter H 
PLoS One Apr 4;11(4):e0152929 (2016)

2015

Periportal Hybrid Hepatocytes Regenerate the Injured Liver without Giving Rise to Cancer
Font-Burgada J, Shalapour S, Ramaswamy S, Hsueh B, Rossell D, Umemura A, Taniguchi K, Nakagawa H, Valasek M, Ye L, Kopp JL, Sander M, Carter H, Deisseroth K, Verma I and Karin M 
Cell, 162(4), 766-779 (2015)

Identifying Mutation-Specific Cancer Pathways Using a Structurally Resolved Protein Interaction Network
Engin B, Hofree M, Carter H 
Pac Symp Biocomput. 84-95 (2015)

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