Pathway-level information extractor (PLIER): a new tool to quantify pathway level effects in gene expression data
A major challenge in gene expression analysis is to accurately infer relevant biological insights, such as variation in cell-type proportion or pathway activity, from global gene expression studies. We present pathway-level information extractor (PLIER), a broadly applicable solution for this problem that outperforms available cell proportion inference algorithms and can automatically identify specific pathways that regulate gene expression. Our method improves interstudy replicability and reveals biological insights when applied to trans-eQTL (expression quantitative trait loci) identification.
Mao W, Zaslavsky E, Hartmann BM, Sealfon SC, Chikina M. Pathway-level information extractor (PLIER) for gene expression data. Nature Methods; 16, 607–610 (2019)
||Maria Chikina, PhD
George Oster (1940-2018), professor of Cell and Developmental Biology at the University of California, Berkeley, is a pioneer and world leader in biophysics, mathematical biology, and applied mathematics. He is also a great mentor who guided numerous young researchers along their career paths.
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Photo: Informal group meetings almost every morning in a local cafe (taken in year 2005).
A team of University of Pittsburgh neuroscientists and computational biologists have moved another step toward preventing brain cell death after an acute stroke event. In a paper published this week in the Proceedings of the National Academy of Sciences, they describe how first-in-class molecules discovered by student Zhaofeng Ye and Professor Carlos J. Camacho stops a key protein-protein interaction from opening the door to stroke-triggered damage to neurons.
Dr. Carlos Camacho
Yeh CY, Ye Z, Moutal A, Gaur S, Henton AM, Kouvaros S, Saloman J Hartnett-Scott KA, Tzounopoulos T, Khanna R, Aizenman E, Camacho C. Defining the Kv2.1-syntaxin molecular interaction identifies a first-in-class small molecule neuroprotectant. Proc Natl Acad Sci USA. 2019 Jul 15. pii: 201903401. doi: 10.1073/pnas.1903401116.
Dr. Joeseph Ayoob was named as the National Research Mentoring Network Mentor of the Month for July 2019, where he is also one of only four NRMN’s Master Mentors. Dr. Ayoob is an Associate Professor in the Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh. Additionally, he is the Founding Program Director of our NSF-funded Training and Experimentation in Computational Biology (TECBio) Research Experience for Undergraduates (REU) Program and the UPMC Hillman Cancer Center and University of Pittsburgh’s Computational Biology Research Academy (CoBRA) for outstanding high-school scholars. Dr. Ayoob is also the Co-Founding Program Director for our CPCB MetaSchool Graduate Student Professional Development Series and the Course Director for Laboratory Methods for Computational Biologists, part of our Joint Carnegie Mellon/Pitt, Ph.D. Program in Computational Biology (CPCB), as well as the Co-Founding Director for the Computational Biomedicine & Biotechnology Masters Program (COBB). Click here to read more about his story as a scientist and mentor.
About the program:
Despite several decades of efforts to increase diversity in the U.S. biomedical workforce, the issue of the under-representation of many populations remains. Scholars from non-majority backgrounds–whether by race, ethnicity, socioeconomic status, sexual orientation, or disability–have overcome many barriers yet still carry the burdens of disadvantaged and discrimination. NRMN is funded by NIH and is a part of the NIH Diversity Program Consortium (DPC), which is a national collaborative that develops, implements, and determines the effectiveness of innovative approaches to strengthen institutional capacity to sustain mentor-mentee relationships. The NRMN is a nationwide consortium of biomedical professionals and institutions collaborating to provide enhanced networking and mentorship experiences in support of the training and career development of individuals from under represented backgrounds who are pursuing biomedical, behavioral, clinical, and social science research careers (collectively termed biomedical research careers). The NRMN is intended to enable mentees across career stages to find effective mentors who will engage in productive, supportive, and culturally responsive mentoring relationships. The NRMN monthly newsletter serves over 15,000 researchers around the country across all career stages in the biomedical sciences.