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.

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

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

Subhan, Bibi S; Hanson, Sydney E; 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. 2025 Dec 27; 329:123953

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

Barzaghi, Guido; Tsirigos, Aristotelis

Nature genetics. 2025 Dec ; 57:2948-2949

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 Dec ; 145:2964-2972

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. 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

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 Nov ; 647:517-527

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