Applied Bioinformatics Laboratories Featured Publications | NYU Langone Health

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.

Challenges and advances in drug resistance and tolerance in cancer

Bivona, Trever G; Yanai, Itai; Calabrò, Fabio; Mechta-Grigoriou, Fatima; Corleone, Giacomo; Di Martile, Marta; Tocci, Annalisa; Tocci, Piera; Vaccarella, Sebastiano; Ferriero, Marilia Consiglia; Alimonti, Andrea; Ruppin, Eytan; Nisticò, Paola; Bagnato, Anna; Blandino, Giovanni

Journal of experimental & clinical cancer research : CR. 2026 Mar 04; 45:

Epigenetic reactivation of the tumor suppressor ZBTB7A by KDM4 inhibition in human acute myeloid leukemia

Arnuk, Alexander; Han, Cuijuan; Lawal, Abimbola E; Wang, Bofei; Karma, Sadik; Zhang, Zhiping; Yassouf, Mhd Yousuf; Rajendran, Sakthi Harini; Chandok, Harshpreet; Eller, Madeline L; Sajedi, Sogand; McKenna, Meryl; Herman, Eve; Hagen, Louisa; Nadorp, Bettina; Mo, Zengshuo; Orellana, Hector; Tsirigos, Aristotelis; Miura, Pedro; Abbas, Hussein A; Aifantis, Iannis; Wang, Eric

Science translational medicine. 2026 Feb 25; 18:eady2936

Hi-C for genome-wide detection of enhancer-hijacking rearrangements in routine lymphoid cancer biopsies

Wu, Jamin; Chu, Shih-Chun A; Cho, Jang; Movahed-Ezazi, Misha; Galbraith, Kristyn; Fang, Camila S; Yang, Yiying; Schroff, Chanel; Sikkink, Kristin; Perez-Arreola, Michelle; Van Meter, Logan; Gemus, Savanna; Belton, Jon-Matthew; Song, Xue; Gurumurthy, Aishwarya; Xiao, Hong; Nardi, Valentina; Louissant, Abner; Pillai, Raju K; Song, Joo Y; Shasha, Dennis; Tsirigos, Aristotelis; Perry, Anamarija; Brown, Noah; Gindin, Tatyana; Shao, Lina; Cieslik, Marcin P; Kim, Minji; Schmitt, Anthony D; Snuderl, Matija; Ryan, Russell J H

Cell genomics. 2026 Feb 20; 101166

The integrated stress response promotes immune evasion through lipocalin 2

Bossowski, Jozef P; Pillai, Ray; Kilian, John; Wong Lau, Angela; Nakamura, Mari; Rashidfarrokhi, Ali; Hao, Yuan; Li, Ruxuan; Wu, Katherine; Hattori, Takamitsu; Glasser, Eliezra; Koide, Akiko; Wang, Lidong; Moreira, Andre L; Hajdu, Cristina; Rajalingam, Sahith; LeBoeuf, Sarah E; Le, Hortense; Lee, Seungeun; Oh, Jin Woo; Joe, Cheolyong; Kim, Hyemin; Ock, Chan-Young; Lee, Se-Hoon; Wang, Hao; Patel, Angana A H; Sayin, Volkan I; Tsirigos, Aristotelis; Wong, Kwok-Kin; Koralov, Sergei B; Pende, Mario; Sánchez-Rivera, Francisco J; Simeone, Diane M; Zervantonakis, Ioannis K; Koide, Shohei; Papagiannakopoulos, Thales

Nature. 2026 Feb 18;

Transcription factor Etv3 controls the tolerogenic function of dendritic cells

Adams, Nicholas M; Martinez-Krams, Daniel; Esteva, Eduardo; Ra, Ai C; Alexiou, Allegra Iliadi; Jin, Hua; Yun, Tae Jin; Tellaoui, Rayan Sleiman; Mudianto, Tenny; Vollmer, Emily; Novikova, Ekaterina; Tan, Yanjun; Huntley, William; Krichevsky, Oleg; Dolgalev, Igor; Izmirly, Peter; Buyon, Jill P; Moreira, Andre L; Lund, Amanda W; Reizis, Boris

Science (New York, N.Y.). 2026 Feb 12; 391:eads1246

Chromatin-mediated anticipatory control of type I interferon production in plasmacytoid dendritic cells

Adams, Nicholas M; Galitsyna, Aleksandra; Tiniakou, Ioanna; Esteva, Eduardo; Ra, Ai C; Ullrich, Simon; Yeung, Stephen T; Tan, Yanjun; Pucella, Joseph N; Dolgalev, Igor; Levy, David E; Khanna, Kamal M; Solovei, Irina; Mirny, Leonid A; Reizis, Boris

Immunity. 2026 Feb 10; 59:270-287.e11

Cohesin-mediated chromatin organization controls the differentiation and function of dendritic cells

Adams, Nicholas M; Galitsyna, Aleksandra; Tiniakou, Ioanna; Esteva, Eduardo; Ra, Ai C; Martinez-Krams, Daniel; Lau, Colleen M; Reyes, Jojo; Abdennur, Nezar; Shkolikov, Alexey; Yap, George S; Khodadadi-Jamayran, Alireza; Dolgalev, Igor; Mirny, Leonid A; Reizis, Boris

Science immunology. 2026 Feb 06; 11:eadx4622

Duo-nano exosome encapsulating hydrogel boosts wound healing across xenogenic and allogenic models

Subhan, Bibi S; Hanson, Sydney; Almanzar, Dianny; Cortes Troncoso, Juan F; Katyal, Priya; Sun, Jonathan W; Shih, Hao-Wei; Mestvirishvili, Tamara; Meleties, Michael; Arias, Fernando; Wang, Andrew; Ruggles, Kelly; Dolgalev, Igor; Mita, Paolo; Montclare, Jin Kim; Rabbani, Piul S

Biomaterials. 2026 Jan 03; 329:123975

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