Applied Bioinformatics Laboratories Featured Publications | NYU Langone Health

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Applied Bioinformatics Laboratories Applied Bioinformatics Laboratories Featured Publications

Applied Bioinformatics Laboratories Featured Publications

Faculty and staff of the Applied Bioinformatics Laboratories publish frequently in peer-reviewed journals. Here is a selection of their recent publications.

Cimmino L, Dolgalev I, Wang Y, Yoshimi A, Martin GH, Wang J, et al. Restoration of TET2 function blocks aberrant self-renewal and leukemia progression. Cell. 2017;170(6):1079-95.

Tetz GV, Ruggles KV, Zhou H, Heguy A, Tsirigos A, Tetz V. Bacteriophages as potential new mammalian pathogens. Sci Rep. 2017;7(1):7043.

Cerrone M, Montnach J, Lin X, Zhao YT, Zhang M, Agullo-Pascual E, et al. Plakophilin-2 is required for transcription of genes that control calcium cycling and cardiac rhythm. Nat Commun. 2017;8(1):106.

Gong Y, Huang HT, Liang Y, Trimarchi T, Aifantis I, Tsirigos A. lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets. BMC Genomics. 2017;18(1):434.

Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, et al. Methods, tools and current perspectives in proteogenomics. Mol Cell Proteomics. 2017;16(6):959-81.

Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, et al. Proteogenomic integration reveals therapeutic targets in breast cancer xenografts. Nat Commun. 2017;8:14864.

Koetz-Ploch L, Hanniford D, Dolgalev I, Sokolova E, Zhong J, Díaz-Martínez M, et al. MicroRNA-125a promotes resistance to BRAF inhibitors through suppression of the intrinsic apoptotic pathway. Pigment Cell Melanoma Res. 2017;30(3):328-38.

Coudray N, L Seyler S, Lasala R, Zhang Z, Clark KM, Dumont ME, et al. Structure of the SLC4 transporter Bor1p in an inward-facing conformation. Protein Sci. 2017;26(1):130-45.

Gutiérrez GD, Bender AS, Cirulli V, Mastracci TL, Kelly SM, Tsirigos A, et al. Pancreatic β cell identity requires continual repression of non-β cell programs. J Clin Invest. 2017;127(1):244-59.

Lazaris C, Kelly S, Ntziachristos P, Aifantis I, Tsirigos A. HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking. BMC Genomics. 2017;18(1):22.

Tissue-resident macrophages promote early dissemination of multiple myeloma via IL-6 and TNFa

Akhmetzyanova, I; Aaron, T; Galbo, P; Tikhonova, A; Dolgalev, I; Tanaka, M; Aifantis, I; Zheng, D; Zang, X; Fooksman, D

Blood advances. 2021 Sep 28; 5:3592-3608

Combined Inhibition of SHP2 and CXCR1/2 Promotes Anti-Tumor T Cell Response in NSCLC

Tang, Kwan Ho; Li, Shuai; Khodadadi-Jamayran, Alireza; Jen, Jayu; Han, Han; Guidry, Kayla; Chen, Ting; Hao, Yuan; Fedele, Carmine; Zebala, John A; Maeda, Dean Y; Christensen, James G; Olson, Peter; Athanas, Argus; Loomis, Cynthia A; Tsirigos, Aristotelis; Wong, Kwok-Kin; Neel, Benjamin G

Cancer discovery. 2021 Aug 05;

Progressive Cellular Senescence Mediates Renal Dysfunction in Ischemic Nephropathy

Kim, Seo Rin; Puranik, Amrutesh; Jiang, Kai; Chen, Xiaojun; Zhu, Xiang-Yang; Taylor, Ian; Khodadadi-Jamayran, Alireza; Lerman, Amir; Hickson, LaTonya; Childs, Bennett; Textor, Stephen; Tchkonia, Tamara; Niewold, Timothy; Kirkland, James; Lerman, Lilach

Journal of the American Society of Nephrology. 2021 Aug ; 32:1987-2004

A pan-cancer organoid platform for precision medicine

Larsen, Brian M; Kannan, Madhavi; Langer, Lee F; Leibowitz, Benjamin D; Bentaieb, Aicha; Cancino, Andrea; Dolgalev, Igor; Drummond, Bridgette E; Dry, Jonathan R; Ho, Chi-Sing; Khullar, Gaurav; Krantz, Benjamin A; Mapes, Brandon; McKinnon, Kelly E; Metti, Jessica; Perera, Jason F; Rand, Tim A; Sanchez-Freire, Veronica; Shaxted, Jenna M; Stein, Michelle M; Streit, Michael A; Tan, Yi-Hung Carol; Zhang, Yilin; Zhao, Ende; Venkataraman, Jagadish; Stumpe, Martin C; Borgia, Jeffrey A; Masood, Ashiq; Catenacci, Daniel V T; Mathews, Jeremy V; Gursel, Demirkan B; Wei, Jian-Jun; Welling, Theodore H; Simeone, Diane M; White, Kevin P; Khan, Aly A; Igartua, Catherine; Salahudeen, Ameen A

Cell reports. 2021 Jul 27; 36:109429

Regulatory T cell transcriptomic reprogramming characterizes adverse events by checkpoint inhibitors in solid tumors

Grigoriou, Maria; Banos, Aggelos; Hatzioannou, Aikaterini; Kloetgen, Andreas; Kouzis, Panagiotis; Aggouraki, Despoina; Zakopoulou, Roubini; Bamias, Giorgos; Kassi, Eva; Mavroudis, Dimitris; Bamias, Aristotelis; Boumpas, Dimitrios T; Tsirigos, Aristotelis; Gogas, Helen J; Alissafi, Themis; Verginis, Panagiotis

Cancer immunology research. 2021 Jul ; 9:726-734

HEAL: an automated deep learning framework for cancer histopathology image analysis

Wang, Yanan; Coudray, Nicolas; Zhao, Yun; Li, Fuyi; Hu, Changyuan; Zhang, Yao-Zhong; Imoto, Seiya; Tsirigos, Aristotelis; Webb, Geoffrey I; Daly, Roger J; Song, Jiangning

Bioinformatics. 2021 May 19;

Autoantibody-mediated impairment of DNASE1L3 activity in sporadic systemic lupus erythematosus

Hartl, Johannes; Serpas, Lee; Wang, Yueyang; Rashidfarrokhi, Ali; Perez, Oriana A; Sally, Benjamin; Sisirak, Vanja; Soni, Chetna; Khodadadi-Jamayran, Alireza; Tsirigos, Aristotelis; Caiello, Ivan; Bracaglia, Claudia; Volpi, Stefano; Ghiggeri, Gian Marco; Chida, Asiya Seema; Sanz, Ignacio; Kim, Mimi Y; Belmont, H Michael; Silverman, Gregg J; Clancy, Robert M; Izmirly, Peter M; Buyon, Jill P; Reizis, Boris

Journal of experimental medicine. 2021 05 03; 218:

ULK1 inhibition overcomes compromised antigen presentation and restores antitumor immunity in LKB1 mutant lung cancer

Deng, Jiehui; Thennavan, Aatish; Dolgalev, Igor; Chen, Ting; Li, Jie; Marzio, Antonio; Poirier, John T; Peng, David; Bulatovic, Mirna; Mukhopadhyay, Subhadip; Silver, Heather; Papadopoulos, Eleni; Pyon, Val; Thakurdin, Cassandra; Han, Han; Li, Fei; Li, Shuai; Ding, Hailin; Hu, Hai; Pan, Yuanwang; Weerasekara, Vajira; Jiang, Baishan; Wang, Eric S; Ahearn, Ian; Philips, Mark; Papagiannakopoulos, Thales; Tsirigos, Aristotelis; Rothenberg, Eli; Gainor, Justin; Freeman, Gordon J; Rudin, Charles M; Gray, Nathanael S; Hammerman, Peter S; Pagano, Michele; Heymach, John V; Perou, Charles M; Bardeesy, Nabeel; Wong, Kwok-Kin

Nature cancer. 2021 May ; 2:503-514