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.

Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation

Baron, Maayan; Tagore, Mohita; Wall, Patrick; Zheng, Fan; Barkley, Dalia; Yanai, Itai; Yang, Jing; Kiuru, Maija; White, Richard M; Ideker, Trey

Nature genetics. 2025 Apr 16;

scRNA-seq uncovers the transcriptional dynamics of Encephalitozoon intestinalis parasites in human macrophages

Jaroenlak, Pattana; McCarty, Kacie L; Xia, Bo; Lam, Cherry; Zwack, Erin E; Almasri, Nadia L; Sudar, Joseph; Aubry, Maelle; Yanai, Itai; Bhabha, Gira; Ekiert, Damian C

Nature communications. 2025 Apr 05; 16:3269

Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation

Do, Catherine; Jiang, Guimei; Cova, Giulia; Katsifis, Christos C; Narducci, Domenic N; Sakellaropoulos, Theodore; Vidal, Raphael; Lhoumaud, Priscillia; Tsirigos, Aristotelis; Regis, Faye Fara D; Kakabadze, Nata; Nora, Elphege P; Noyes, Marcus; Hansen, Anders S; Skok, Jane A

Cell genomics. 2025 Mar 18; 100813

Self-supervised learning reveals clinically relevant histomorphological patterns for therapeutic strategies in colon cancer

Liu, Bojing; Polack, Meaghan; Coudray, Nicolas; Claudio Quiros, Adalberto; Sakellaropoulos, Theodore; Le, Hortense; Karimkhan, Afreen; Crobach, Augustinus S L P; van Krieken, J Han J M; Yuan, Ke; Tollenaar, Rob A E M; Mesker, Wilma E; Tsirigos, Aristotelis

Nature communications. 2025 Mar 08; 16:2328

Characterization of tumour heterogeneity through segmentation-free representation learning on multiplexed imaging data

Tan, Jimin; Le, Hortense; Deng, Jiehui; Liu, Yingzhuo; Hao, Yuan; Hollenberg, Michelle; Liu, Wenke; Wang, Joshua M; Xia, Bo; Ramaswami, Sitharam; Mezzano, Valeria; Loomis, Cynthia; Murrell, Nina; Moreira, Andre L; Cho, Kyunghyun; Pass, Harvey I; Wong, Kwok-Kin; Ban, Yi; Neel, Benjamin G; Tsirigos, Aristotelis; Fenyö, David

Nature biomedical engineering. 2025 Mar ; 9:405-419

A proinflammatory response and polarized differentiation of stromal elements characterizes the murine myeloma bone marrow niche

Ghamlouch, Hussein; Gagler, Dylan C; Blaney, Patrick; Boyle, Eileen M; Wang, Yubao; Avigan, Jason; Choi, Jinyoung; Landgren, Ola; Tsirigos, Aristotelis; Maura, Francesco; Morgan, Gareth J; Davies, Faith E

Experimental hematology & oncology. 2025 Feb 26; 14:22

Self supervised artificial intelligence predicts poor outcome from primary cutaneous squamous cell carcinoma at diagnosis

Coudray, Nicolas; Juarez, Michelle C; Criscito, Maressa C; Quiros, Adalberto Claudio; Wilken, Reason; Jackson Cullison, Stephanie R; Stevenson, Mary L; Doudican, Nicole A; Yuan, Ke; Aquino, Jamie D; Klufas, Daniel M; North, Jeffrey P; Yu, Siegrid S; Murad, Fadi; Ruiz, Emily; Schmults, Chrysalyne D; Cardona Machado, Cristian D; Cañueto, Javier; Choudhary, Anirudh; Hughes, Alysia N; Stockard, Alyssa; Leibovit-Reiben, Zachary; Mangold, Aaron R; Tsirigos, Aristotelis; Carucci, John A

NPJ digital medicine. 2025 Feb 15; 8:105

AI accurately identifies targetable alterations in lung cancer histological images

Le, Hortense; Tsirigos, Aristotelis

Nature reviews. Clinical oncology. 2025 Feb 10;

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