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
Cell reports. 2022 10 11; 41:111477
Lineage-coupled clonal capture identifies clonal evolution mechanisms and vulnerabilities of BRAFV600E inhibition resistance in melanoma
Cell discovery. 2022 Oct 06; 8:102
The impact of inflammation-induced tumor plasticity during myeloid transformation
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
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
Clinical cancer research. 2022 Sep 01; 28:3824-3835
ACE2-containing defensosomes serve as decoys to inhibit SARS-CoV-2 infection
PLoS biology. 2022 Sep ; 20:e3001754
Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment
Nature genetics. 2022 Aug ; 54:1192-1201
DNA methylation-based epigenetic signatures predict somatic genomic alterations in gliomas
Nature communications. 2022 Jul 29; 13:4410