Each month Levy Library showcases the achievements of Mount Sinai faculty and researchers by highlighting an article and its altmetrics. Altmetrics are alternative measures of impact that capture non-traditional data like abstract views, article downloads, and social media activity.
This month we highlight Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. This study was written by a team of researchers including Mount Sinai’s John A. Martignetti (Genetics and Genomic Sciences), Robert Korst (Thoracic Surgery) and Peter Dottino (Gynecologic Oncology).
Citation: The Cancer Genome Atlas Research Network (2018). Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Reports, 23(1), 172-180.e3. DOI: 10.1016/j.celrep.2018.03.046
Summary
Precision oncology uses genomic evidence to match patients with treatment but often fails to identify all patients who may respond. The transcriptome of these “hidden responders” may reveal responsive molecular states. We describe and evaluate a machine-learning approach to classify aberrant pathway activity in tumors, which may aid in hidden responder identification. The algorithm integrates RNA-seq, copy number, and mutations from 33 different cancer types across The Cancer Genome Atlas (TCGA) PanCanAtlas project to predict aberrant molecular states in tumors. Applied to the Ras pathway, the method detects Ras activation across cancer types and identifies phenocopying variants. The model, trained on human tumors, can predict response to MEK inhibitors in wild-type Ras cell lines. We also present data that suggest that multiple hits in the Ras pathway confer increased Ras activity. The transcriptome is underused in precision oncology and, combined with machine learning, can aid in the identification of hidden responders.
View this article's profile on PLUMX
Interested in exploring the world of open access publishing or eager to dive deeper into the subject?
Join us on Wednesday, October 24th for a mini-conference celebrating Open Access Week 2018. We will hear from experts in the field and learn about the impact and future of open access publishing within the health sciences field. We will also discuss how to navigate through the journal selection process so you can confidently publish your own research in an open access journal.
Our Presenters:
Brian Hole is the Founder and CEO of Ubiquity Press. He started the company in order to help drive open access forward by supporting university-led publishing, and they currently support over 30 university presses and 500 journals. Prior to this he worked at the British Library and Elsevier, and he has a PhD in archaeology from University College London.
Brooke LaFlamme joined the editorial team at Nature Genetics in 2013 and is currently Chief Editor of Communications Biology. Her duties at the journal include development of the journal’s editorial strategy, choosing manuscripts for peer review and overseeing the peer review process. She received her PhD from Cornell University where she studied Drosophila seminal fluid proteins with Prof. Mariana Wolfner. Brooke conducted her postdoctoral work in stem cell biology with Dr. Shuibing Chen at Weill Cornell Medical College.
Gali Halevi is the Associate Dean of Libraries and Information Sciences at the Icahn School of Medicine at Mount Sinai and an assistant professor at the department of medicine and medical education. Before joining Mount Sinai Gali Halevi was responsible for the development of research evaluation and metrics tools for Elsevier’s leading products and was the director of research evaluation metrics development programs. Gali received her Master’s degree in Library & Information Science from the Hebrew University of Jerusalem and her PhD in Information Science from Long Island University in New York.
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