Gene co-expression analysis for functional classification and gene–disease predictions

S Van Dam, U Vosa, A van der Graaf… - Briefings in …, 2018 - academic.oup.com
Gene co-expression networks can be used to associate genes of unknown function with
biological processes, to prioritize candidate disease genes or to discern transcriptional …

CellBox: interpretable machine learning for perturbation biology with application to the design of cancer combination therapy

B Yuan, C Shen, A Luna, A Korkut, DS Marks… - Cell systems, 2021 - cell.com
Systematic perturbation of cells followed by comprehensive measurements of molecular and
phenotypic responses provides informative data resources for constructing computational …

Germline genetic contribution to the immune landscape of cancer

RW Sayaman, M Saad, V Thorsson, D Hu, W Hendrickx… - Immunity, 2021 - cell.com
Understanding the contribution of the host's genetic background to cancer immunity may
lead to improved stratification for immunotherapy and to the identification of novel …

Insulin-like growth factor 1-induced enolase 2 deacetylation by HDAC3 promotes metastasis of pancreatic cancer

Y Zheng, C Wu, J Yang, Y Zhao, H Jia, M Xue… - Signal transduction and …, 2020 - nature.com
Abstract Enolase 2 (ENO2) is a key glycolytic enzyme in the metabolic process of glycolysis,
but its potential function in pancreatic ductal adenocarcinoma (PDAC) is unclear. In this …

From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies

A Mukherjee, S Abraham, A Singh, S Balaji… - Molecular …, 2024 - Springer
In the dynamic landscape of targeted therapeutics, drug discovery has pivoted towards
understanding underlying disease mechanisms, placing a strong emphasis on molecular …

Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses

ME MacGilvray, E Shishkova, M Place… - Journal of proteome …, 2020 - ACS Publications
To cope with sudden changes in the external environment, the budding yeast
Saccharomyces cerevisiae orchestrates a multifaceted response that spans many levels of …

Integrating networks and proteomics: moving forward

WWB Goh, L Wong - Trends in biotechnology, 2016 - cell.com
Networks can resolve many analytical problems in proteomics, including incomplete
coverage and inconsistency. Despite high expectations, network-related research in …

Integrating network reconstruction with mechanistic modeling to predict cancer therapies

M Halasz, BN Kholodenko, W Kolch, T Santra - Science signaling, 2016 - science.org
Signal transduction networks are often rewired in cancer cells. Identifying these alterations
will enable more effective cancer treatment. We developed a computational framework that …

[HTML][HTML] SLFN11 captures cancer-immunity interactions associated with platinum sensitivity in high-grade serous ovarian cancer

C Winkler, M King, J Berthe, D Ferraioli, A Garuti… - JCI insight, 2021 - ncbi.nlm.nih.gov
Large independent analyses on cancer cell lines followed by functional studies have
identified Schlafen 11 (SLFN11), a putative helicase, as the strongest predictor of sensitivity …

Master regulators connectivity map: a transcription factors-centered approach to drug repositioning

MA De Bastiani, B Pfaffenseller, F Klamt - Frontiers in Pharmacology, 2018 - frontiersin.org
Drug discovery is a very expensive and time-consuming endeavor. Fortunately, recent omics
technologies and Systems Biology approaches introduced interesting new tools to achieve …