Discovery of synthetic lethal interactions from large-scale pan-cancer perturbation screens

Autor: Sumana Srivatsa, Hesam Montazeri, Gaia Bianco, Mairene Coto-Llerena, Mattia Marinucci, Charlotte K. Y. Ng, Salvatore Piscuoglio, Niko Beerenwinkel

Publikováno v: Nature Communications, Vol 13, Iss 1, Pp 1-15 (2022)

Synthetic lethality can be used to identify potential drug targets in cancer based on simultaneous inactivation of two genes through genetic aberrations and gene silencing. Here, the authors develop a statistical framework to identify synthetic letha

Externí odkaz: https://doaj.org/article/1e9e77d5338c4f05aac121e0023b2907

Author Correction: GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers

Autor: Gaia Bianco, Mairene Coto-Llerena, John Gallon, Venkatesh Kancherla, Stephanie Taha-Mehlitz, Mattia Marinucci, Martina Konantz, Sumana Srivatsa, Hesam Montazeri, Federica Panebianco, Vijaya G. Tirunagaru, Marta De Menna, Viola Paradiso, Caner Ercan, Ahmed Dahmani, Elodie Montaudon, Niko Beerenwinkel, Marianna Kruithof-de Julio, Luigi M. Terracciano, Claudia Lengerke, Rinath M. Jeselsohn, Robert C. Doebele, François-Clément Bidard, Elisabetta Marangoni, Charlotte K. Y. Ng, Salvatore Piscuoglio

Publikováno v: Communications Biology, Vol 5, Iss 1, Pp 1-1 (2022)

Externí odkaz: https://doaj.org/article/37ccb3e2ab0647d9b2d4b5fb70da5a42

Context-dependent deposition and regulation of mRNAs in P-bodies

Autor: Congwei Wang, Fabian Schmich, Sumana Srivatsa, Julie Weidner, Niko Beerenwinkel, Anne Spang

Publikováno v: eLife, Vol 7 (2018)

Cells respond to stress by remodeling their transcriptome through transcription and degradation. Xrn1p-dependent degradation in P-bodies is the most prevalent decay pathway, yet, P-bodies may facilitate not only decay, but also act as a storage compa

Externí odkaz: https://doaj.org/article/f774038236ce4bc7a6a3668106ace87d

Systematic identification of novel cancer genes through analysis of deep shRNA perturbation screens

Autor: Salvatore Piscuoglio, Stephanie Taha-Mehlitz, Antoine de Weck, Hesam Montazeri, Manuela Lanzafame, Sumana Srivatsa, Viola Paradiso, Guglielmo Roma, Charlotte K.Y. Ng, Ehsan Zangene, Niko Beerenwinkel, Gaia Bianco, Luigi Terracciano, Mairene Coto-Llerena, Markus von Flüe, Martin Bolli

Publikováno v: Nucleic Acids Research, 49 (15)
Montazeri, Hesam; Coto-Llerena, Mairene; Bianco, Gaia; Zangene, Ehsan; Taha-Mehlitz, Stephanie; Paradiso, Viola; Srivatsa, Sumana; de Weck, Antoine; Roma, Guglielmo; Lanzafame, Manuela; Bolli, Martin; Beerenwinkel, Niko; von Flüe, Markus; Terracciano, Luigi M; Piscuoglio, Salvatore; Ng, Charlotte K Y (2021). Systematic identification of novel cancer genes through analysis of deep shRNA perturbation screens. Nucleic acids research, 49(15), pp. 8488-8504. Oxford University Press 10.1093/nar/gkab627
Nucleic Acids Research

BackgroundSystematic perturbation screens provide comprehensive resources for the elucidation of cancer driver genes, including rarely mutated genes that are missed by approaches focused on frequently mutated genes and driver genes for which the basi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9ea8828b498526269a1316bc3a3ec366

Improved pathway reconstruction from RNA interference screens by exploiting off-target effects

Autor: Sumana Srivatsa, Jack Kuipers, Niko Beerenwinkel, Fabian Schmich, Christoph Dehio, Simone Eicher, Mario Emmenlauer

Publikováno v: Bioinformatics
Bioinformatics, 34 (13)

Motivation Pathway reconstruction has proven to be an indispensable tool for analyzing the molecular mechanisms of signal transduction underlying cell function. Nested effects models (NEMs) are a class of probabilistic graphical models designed to re

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2152384e5a7a6c44776fd4194b154a7e
https://doi.org/10.1093/bioinformatics/bty240