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.

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

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

Dissecting microbial communities with single-cell transcriptome analysis

Pountain, Andrew W; Yanai, Itai

Science. 2025 Sep 04; 389:eadp6252

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

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. 2025 Aug 14; 31:3526-3536

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