Applied Bioinformatics Laboratories Featured Publications | NYU Langone Health

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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.

The tempo and mode of gene regulatory programs during bacterial infection

Avital, Gal; Kuperwaser, Felicia; Pountain, Andrew W; Lacey, Keenan A; Zwack, Erin E; Podkowik, Magdalena; Shopsin, Bo; Torres, Victor J; Yanai, Itai

Cell reports. 2022 10 11; 41:111477

Lineage-coupled clonal capture identifies clonal evolution mechanisms and vulnerabilities of BRAFV600E inhibition resistance in melanoma

Zhang, Ze-Yan; Ding, Yingwen; Ezhilarasan, Ravesanker; Lhakhang, Tenzin; Wang, Qianghu; Yang, Jie; Modrek, Aram S; Zhang, Hua; Tsirigos, Aristotelis; Futreal, Andrew; Draetta, Giulio F; Verhaak, Roel G W; Sulman, Erik P

Cell discovery. 2022 Oct 06; 8:102

The impact of inflammation-induced tumor plasticity during myeloid transformation

Yeaton, Anna; Cayanan, Geraldine; Loghavi, Sanam; Dolgalev, Igor; Leddin, Emmett M; Loo, Christian E; Torabifard, Hedieh; Nicolet, Deedra; Wang, Jingjing; Corrigan, Kate; Paraskevopoulou, Varvara; Starczynowski, Daniel T; Wang, Eric; Abdel-Wahab, Omar; Viny, Aaron D; Stone, Richard M; Byrd, John C; Guryanova, Olga A; Kohli, Rahul M; Cisneros, G Andres; Tsirigos, Aristotelis; Eisfeld, Ann-Kathrin; Aifantis, Iannis; Guillamot, Maria

Cancer discovery. 2022 Oct 05; 12:2392-2413

Publisher Correction: Gene expression levels modulate germline mutation rates through the compound effects of transcription-coupled repair and damage

Xia, Bo; Yanai, Itai

Human genetics. 2022 Oct ; 141:1695

DNA methylation profiling identifies subgroups of lung adenocarcinoma with distinct immune cell composition, DNA methylation age, and clinical outcome

Guidry, Kayla; Vasudevaraja, Varshini; Labbe, Kristen; Mohamed, Hussein; Serrano, Jonathan; Guidry, Brett W; DeLorenzo, Michael; Zhang, Hua; Deng, Jiehui; Sahu, Soumyadip; Almonte, Christina; Moreira, Andre L; Tsirigos, Aristotelis; Papagiannakopoulos, Thales; Pass, Harvey; Snuderl, Matija; Wong, Kwok-Kin

Clinical cancer research. 2022 Sep 01; 28:3824-3835

ACE2-containing defensosomes serve as decoys to inhibit SARS-CoV-2 infection

Ching, Krystal L; de Vries, Maren; Gago, Juan; Dancel-Manning, Kristen; Sall, Joseph; Rice, William J; Barnett, Clea; Khodadadi-Jamayran, Alireza; Tsirigos, Aristotelis; Liang, Feng-Xia; Thorpe, Lorna E; Shopsin, Bo; Segal, Leopoldo N; Dittmann, Meike; Torres, Victor J; Cadwell, Ken

PLoS biology. 2022 Sep ; 20:e3001754

Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment

Barkley, Dalia; Moncada, Reuben; Pour, Maayan; Liberman, Deborah A; Dryg, Ian; Werba, Gregor; Wang, Wei; Baron, Maayan; Rao, Anjali; Xia, Bo; França, Gustavo S; Weil, Alejandro; Delair, Deborah F; Hajdu, Cristina; Lund, Amanda W; Osman, Iman; Yanai, Itai

Nature genetics. 2022 Aug ; 54:1192-1201

DNA methylation-based epigenetic signatures predict somatic genomic alterations in gliomas

Yang, Jie; Wang, Qianghu; Zhang, Ze-Yan; Long, Lihong; Ezhilarasan, Ravesanker; Karp, Jerome M; Tsirigos, Aristotelis; Snuderl, Matija; Wiestler, Benedikt; Wick, Wolfgang; Miao, Yinsen; Huse, Jason T; Sulman, Erik P

Nature communications. 2022 Jul 29; 13:4410