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.

Single-cell 3D architecture maps the drivers of lung adenocarcinoma

Barzaghi, Guido; Tsirigos, Aristotelis

Nature genetics. 2025 Nov 27;

DNA Methylation Profiling Classifies and Reveals Origin of Gynecologic Central Nervous System-like Tumors

Wang, Lucy; Vasudevaraja, Varshini; Serrano, Jonathan; Kerkhof, Jennifer; Rzasa, Jessica; Kelly, Stephen; Oliva, Esther; Young, Robert H; Christian-Horn, Lars; Park, Kay J; Momeni-Boroujeni, Amir; Antonescu, Cristina R; Abu-Rustum, Nadeem R; Zhang, Yanming; Wang, Lu; Jungbluth, Achim; Rosenblum, Marc K; Sadikovic, Bekim; Dolgalev, Igor; Snuderl, Matija; Chiang, Sarah

Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc. 2025 Nov 22; 100941

Dicer is essential for proper maturation, composition, and function in the postnatal retina

Kang, Seoyoung; Larbi, Daniel; Bruns, Eik; Hahne, Konstantin; Khodadadi-Jamayran, Alireza; Sreenivasaiah, Chaitra; Carneiro, Mariana Lima; Andrade, Monica; Batsuuri, Khulan; Chen, Shaoheng; Jager, Julia; Viswanathan, Suresh; Clark, Brian Stewart; Wohl, Stefanie Gabriele

iScience. 2025 Nov 21; 28:113794

Tonic type I interferon signaling optimizes the antiviral function of plasmacytoid dendritic cells

Pucella, Joseph N; Maqueda-Alfaro, Raul A; Ni, Hai; Bandeira Sulczewski, Fernando; Eichinger, Anna; Esteva, Eduardo; Ra, Ai C; Das, Annesa; Perez, Oriana A; Feng, Jue; Stoeckius, Marlon; Smibert, Peter; Khodadadi-Jamayran, Alireza; Dolgalev, Igor; Ivanova, Ellie; Sota, Stela; Cadwell, Ken; Koralov, Sergei B; Zhong, Judy; Soni, Chetna; Stetson, Daniel B; Weisberg, Stuart P; Farber, Donna L; Idoyaga, Juliana; Reizis, Boris

Nature immunology. 2025 Nov ; 26:1946-1961

Regulating white blood cell activity through the novel universal receptive system

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

Scientific reports. 2025 Oct 30; 15:37988

The Polygenic Architecture of Human Diseases Affecting the Hair Follicle

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

Journal of investigative dermatology. 2025 Oct 24;

Unbiased self supervised learning of kidney histology reveals phenotypic and prognostic insights

Pandit, Krutika; Coudray, Nicolas; Quiros, Adalberto Claudio; Surapaneni, Aditya; Upadhyay, Dhairya; Vanguri, Rami Sesha; Hirohama, Daigoro; Mohandes, Samer; Schlosser, Pascal; Thiessen-Philbrook, Heather; Wen, Yumeng; Parikh, Chirag R; Rhee, Eugene P; Waikar, Sushrut S; Schmidt, Insa; Rosenberg, Avi Z; Palmer, Matthew B; Susztak, Katalin; Grams, Morgan E; Tsirigos, Aristotelis; ,

Scientific reports. 2025 Oct 08; 15:35131

Peritumoral macrophages recruit eosinophils to promote antitumor immune responses in breast cancer

Saglimbeni, Joseph; Esteva, Eduardo; Canales, Josue; Perez, Oriana A; Eichinger, Anna; Huntley, William; Khanna, Kamal M; Dolgalev, Igor; Klar, Natalie; Adams, Sylvia; Reizis, Boris

Proceedings of the National Academy of Sciences of the United States of America (PNAS). 2025 Sep 23; 122:e2504645122

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