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.

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:

CNS-CLIP: Transforming a Neurosurgical Journal Into a Multimodal Medical Model

Alyakin, Anton; Kurland, David; Alber, Daniel Alexander; Sangwon, Karl L; Li, Danxun; Tsirigos, Aristotelis; Leuthardt, Eric; Kondziolka, Douglas; Oermann, Eric Karl

Neurosurgery. 2025 Jun 01; 96:1227-1235

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 May ; 57:1179-1188

Detection of Gene Fusions and Rearrangements in Formalin-Fixed, Paraffin-Embedded Solid Tumor Specimens Using High-Throughput Chromosome Conformation Capture

Galbraith, Kristyn; Wu, Jamin; Sikkink, Kristin; Mohamed, Hussein; Reid, Derek; Perez-Arreola, Michelle; Belton, Jon-Matthew; Nomikou, Sofia; Melnyk, Shadi; Yang, Yiying; Liechty, Benjamin L; Jour, George; Tsirigos, Aristotelis; Hermel, David J; Beck, Alyssa; Sigal, Darren; Dahl, Nathan A; Vibhakar, Rajeev; Schmitt, Anthony; Snuderl, Matija

Journal of molecular diagnostics. 2025 May ; 27:346-359

Native stem cell transcriptional circuits define cardinal features of high-risk leukemia

Wang, Qing; Boccalatte, Francesco; Xu, Jason; Gambi, Giovanni; Nadorp, Bettina; Akter, Fatema; Mullin, Carea; Melnick, Ashley F; Choe, Elizabeth; McCarter, Anna C; Jerome, Nicole A; Chen, Siyi; Lin, Karena; Khan, Sarah; Kodgule, Rohan; Sussman, Jonathan H; Pölönen, Petri; Rodriguez-Hernaez, Javier; Narang, Sonali; Avrampou, Kleopatra; King, Bryan; Tsirigos, Aristotelis; Ryan, Russell J H; Mullighan, Charles G; Teachey, David T; Tan, Kai; Aifantis, Iannis; Chiang, Mark Y

Journal of experimental medicine. 2025 Apr 07; 222:

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