Applied Bioinformatics Laboratories Featured Publications | NYU Langone Health

Skip to Main Content
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.

Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation

Tiniakou, Ioanna; Hsu, Pei-Feng; Lopez-Zepeda, Lorena S; Garipler, Görkem; Esteva, Eduardo; Adams, Nicholas M; Jang, Geunhyo; Soni, Chetna; Lau, Colleen M; Liu, Fan; Khodadadi-Jamayran, Alireza; Rodrick, Tori C; Jones, Drew; Tsirigos, Aristotelis; Ohler, Uwe; Bedford, Mark T; Nimer, Stephen D; Kaartinen, Vesa; Mazzoni, Esteban O; Reizis, Boris

Science immunology. 2024 Apr 12; 9:eadi1023

Glutamine antagonist DRP-104 suppresses tumor growth and enhances response to checkpoint blockade in KEAP1 mutant lung cancer

Pillai, Ray; LeBoeuf, Sarah E; Hao, Yuan; New, Connie; Blum, Jenna L E; Rashidfarrokhi, Ali; Huang, Shih Ming; Bahamon, Christian; Wu, Warren L; Karadal-Ferrena, Burcu; Herrera, Alberto; Ivanova, Ellie; Cross, Michael; Bossowski, Jozef P; Ding, Hongyu; Hayashi, Makiko; Rajalingam, Sahith; Karakousi, Triantafyllia; Sayin, Volkan I; Khanna, Kamal M; Wong, Kwok-Kin; Wild, Robert; Tsirigos, Aristotelis; Poirier, John T; Rudin, Charles M; Davidson, Shawn M; Koralov, Sergei B; Papagiannakopoulos, Thales

Science advances. 2024 Mar 29; 10:eadm9859

Self-Supervised Learning Reveals Clinically Relevant Histomorphological Patterns for Therapeutic Strategies in Colon Cancer

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

bioRxiv : the preprint server for biology. 2024 Mar 21;

Transcription-replication interactions reveal bacterial genome regulation

Pountain, Andrew W; Jiang, Peien; Yao, Tianyou; Homaee, Ehsan; Guan, Yichao; McDonald, Kevin J C; Podkowik, Magdalena; Shopsin, Bo; Torres, Victor J; Golding, Ido; Yanai, Itai

Nature. 2024 Feb ; 626:661-669

Gene regulatory patterning codes in early cell fate specification of the C. elegans embryo

Cole, Alison G; Hashimshony, Tamar; Du, Zhuo; Yanai, Itai

eLife. 2024 Jan 29; 12:

Transcription"“replication interactions reveal bacterial genome regulation

Pountain, Andrew W.; Jiang, Peien; Yao, Tianyou; Homaee, Ehsan; Guan, Yichao; McDonald, Kevin J.C.; Podkowik, Magdalena; Shopsin, Bo; Torres, Victor J.; Golding, Ido; Yanai, Itai

Nature. 2024 Jan 01; ?-?

SETD2 mutations do not contribute to clonal fitness in response to chemotherapy in childhood B cell acute lymphoblastic leukemia

Contreras Yametti, Gloria P; Robbins, Gabriel; Chowdhury, Ashfiyah; Narang, Sonali; Ostrow, Talia H; Kilberg, Harrison; Greenberg, Joshua; Kramer, Lindsay; Raetz, Elizabeth; Tsirigos, Aristotelis; Evensen, Nikki A; Carroll, William L

Leukemia & lymphoma. 2024 Jan ; 65:78-90

3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages

Murphy, Dylan; Salataj, Eralda; Di Giammartino, Dafne Campigli; Rodriguez-Hernaez, Javier; Kloetgen, Andreas; Garg, Vidur; Char, Erin; Uyehara, Christopher M; Ee, Ly-Sha; Lee, UkJin; Stadtfeld, Matthias; Hadjantonakis, Anna-Katerina; Tsirigos, Aristotelis; Polyzos, Alexander; Apostolou, Effie

Nature structural & molecular biology. 2024 Jan ; 31:125-140

See All Publications
Thank you for printing content from NYU Langone Health. © 2024 NYU Grossman School of Medicine.