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.

Mechanical confinement governs phenotypic plasticity in melanoma

Hunter, Miranda V; Joshi, Eshita; Bowker, Sydney; Montal, Emily; Ma, Yilun; Kim, Young Hun; Yang, Zhifan; Tuffery, Laura; Li, Zhuoning; Rosiek, Eric; Browning, Alexander; Moncada, Reuben; Yanai, Itai; Byrne, Helen; Monetti, Mara; de Stanchina, Elisa; Hamard, Pierre-Jacques; Koche, Richard P; White, Richard M

Nature. 2025 Aug 27;

A Comprehensive Review of GWASs of Human Hair Traits

Needle, Carli D; Brinks, Anna L; Perez, Olivia D; Shapiro, Jerry; Lo Sicco, Kristen I; Tsirigos, Aristotelis; Petukhova, Lynn

The Journal of investigative dermatology. 2025 Aug 19;

Artificial Intelligence Algorithm Predicts Response to Immune Checkpoint Inhibitors

Fa'ak, Faisal; Coudray, Nicolas; Jour, George; Ibrahim, Milad; Illa-Bochaca, Irineu; Qiu, Shi; Claudio Quiros, Adalberto; Yuan, Ke; Johnson, Douglas B; Rimm, David L; Weber, Jeffrey S; Tsirigos, Aristotelis; Osman, Iman

Clinical cancer research : an official journal of the American Association for Cancer Research. 2025 Aug 14; 31:3526-3536

Damaging effects and altered gene expression from temperature stress in early life-stages of Atlantic tomcod from the Hudson River

Adenekan, Adedamola; Terez, Kristin; Khodadadi-Jamayran, Alireza; Wirgin, Isaac

The Science of the total environment. 2025 Aug 02; 996:180129

A Phase I Dose-Escalation Clinical Trial of Bronchoscopic Cryoimmunotherapy in Advanced-Stage NSCLC

Tsay, Jun-Chieh J; Velez, Antonio; Collazo, Destiny; Laniado, Isaac; Bessich, Jamie; Murthy, Vivek; DeMaio, Andrew; Rafeq, Samaan; Kwok, Benjamin; Darawshy, Fares; Pillai, Ray; Wong, Kendrew; Li, Yonghua; Schluger, Rosemary; Lukovnikova, Alena; Roldan, Sofia; Blaisdell, Matt; Paz, Fernanda; Krolikowski, Kelsey; Gershner, Katherine; Liu, Yong; Gong, Judy; Borghi, Sara; Zhou, Fang; Tsirigos, Aristotelis; Pass, Harvey; Segal, Leopoldo N; Sterman, Daniel H

JTO clinical & research reports. 2025 Aug ; 6:100849

Uncovering Novel lncRNAs Linked to Melanoma Growth and Migration with CRISPR Inhibition Screening

Petroulia, Stavroula; Hockemeyer, Kathryn; Tiwari, Shashank; Berico, Pietro; Shamloo, Sama; Banijamali, Seyedeh Elnaz; Vega-Saenz de Miera, Eleazar; Gong, Yixiao; Thandapani, Palaniraja; Wang, Eric; Schloßhauer, Jeffrey L; Tsirigos, Aristotelis; Osman, Iman; Aifantis, Ioannis; Imig, Jochen

Cancer research communications. 2025 Jul 01; 5:1102-1118

Inherited mitochondrial genetics as a predictor of immune checkpoint inhibition efficacy in melanoma

Monson, Kelsey R; Ferguson, Robert; Handzlik, Joanna E; Morales, Leah; Xiong, Jiahan; Chat, Vylyny; Dagayev, Sasha; Khodadadi-Jamayran, Alireza; Simpson, Danny; Kazlow, Esther; Bunis, Anabelle; Sreenivasaiah, Chaitra; Ibrahim, Milad; Voloshyna, Iryna; Ouwerkerk, Wouter; Luiten, Rosalie M; Capone, Mariaelena; Madonna, Gabriele; Lu, Yuting; Shao, Yongzhao; Pavlick, Anna; Krogsgaard, Michelle; Mehnert, Janice; Tang, Hao; Dolfi, Sonia; Tenney, Daniel; Haanen, John B A G; Gajewski, Thomas F; Hodi, F Stephen; Flaherty, Keith T; Couts, Kasey; Robinson, William; Puzanov, Igor; Ernstoff, Marc S; Rahma, Osama; Postow, Michael; Sullivan, Ryan J; Luke, Jason J; Ascierto, Paolo A; ,; Osman, Iman; Kirchhoff, Tomas

Nature medicine. 2025 Jun 05;

The universal receptive system: a novel regulator of antimicrobial and anticancer compound production by white blood cells

Tetz, Victor; Kardava, Kristina; Vecherkovskaya, Maria; Khodadadi-Jamayran, Alireza; Tsirigos, Aristotelis; Tetz, George

Journal of leukocyte biology. 2025 Jun 04; 117:

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