Sean Maden

  • Biomedical Engineering Graduate Program, School of Medicine

Biography

Sean is a Ph.D. Computational Biology candidate, mentored by Prof. Abhi Nellore in the Biomedical Engineering Department at OHSU. His affiliations include PDXgx (Nellore/Thomopson joint lab group) at OHSU and the recount team at Johns Hopkins. He has over 5 years of experience with bioinformatics analysis in biomedical research. He is interested in problems with data access and large-scale reanalysis, or meta-analysis, of samples across studies. Prior to enrolling at OHSU, Sean obtained his B.A. Biology from Reed College and studied cancer epigenetics with Grady Lab at Fred Hutch.

Education

  • B.A., 2011, Reed College
  • Internship:

    • Bioinformatics Research Intern, April – September 2015
  • Fellowship:

    • 2016 SAS-BWF Fellow, May 2016 – 2017
    • Fischer Memorial Fellow, Summer 2010

Honors and awards

  • Grad Student Travel Stipend, MOMACS Modeling the World’s Systems Conference 2019, Washington, DC
  • Undergraduate Research Grant, Reed College, Portland, OR, Winter 2010

Memberships and associations

  • Affiliate Member, Fred Hutch, Seattle, WA, June 2018 – September 2019
  • American Association for the Advancement of Science (AAAS) Member, June 2018 – September 2019
  • Association for Cancer Research (AACR) Associate Member, Fred Hutch, Seattle, WA, January 2016 – 2017

Areas of interest

  • bioinformatics
  • computational biology
  • epigenetics and epigenomics
  • biostatistics
  • data science
  • machine learning
  • software development

Publications

Selected publications

  • Sean K. Maden, Reid F. Thompson, Kasper D. Hansen, Abhi Nellore. Human methylome variation across Infinium 450K raw data on the Gene Expression Omnibus. 2019 (preprint in preparation).
  • Jenny Smith*, Sean K. Maden*, David Lee*, Ronald Buie, Vikas Peddu, Ryan Shean, Ben Busby. Consensus Machine Learning for Gene Target Selection in Pediatric AML Risk. 2019 BioRxiv, 632166. *first authors (preprint).
  • Julianne K. David, Sean K. Maden, Benjamin R. Weeder, Reid F. Thompson, Abhi Nellore. “Cancer-specific” exon-exon junctions appear in embryological and other normal cells. 2019 (under review).
  • Ting Wang, Sean K. Maden, Georg Luebeck, Chris Li, Polly Newcomb, Cornelia Ulrich, Kelly Carter, Michael Luo, Ming Yu, William M. Grady. Dysfunctional epigenetic aging of the normal colon in association with colorectal adenoma and cancer risk. 2019 (under review).
  • Yuna Guo, Kelly Carter, Ming Yu, Sean K. Maden, Darwin Edmonds, Polly Newcomb P, Christopher Li, Neli Ulrich, William M. Grady. Senescence-associated tissue microenvironment promotes colon cancer formation through the secretory factor GDF15. 2019 Aging Cell.
  • Georg E. Luebeck, William D. Hazelton, Kit Curtius, Sean K. Maden, Ming Yu, Kelly T. Carter, Wynn Burke, Paul D. Lampe, Christopher I. Li, Cornelia M. Ulrich, Polly A. Newcomb, Maria Westerhoff11, Andrew M. Kaz, Yanxin Luo, John M. Inadomi, William M. Grady. Implications of epigenetic drift in colorectal neoplasia. 2019 Cancer Res. 1;79(3):495-504
  • Ming Yu*, Sean K. Maden*, Matthew Stachler*, Andrew M. Kaz, Tai J. Heinzerling, Rachele M O’Leary, Xinsen Xu, Adam Bass, Amitabh Chak, Joseph E. Willis, Sanford D. Markowitz, William M. Grady. Subtypes of Barrett’s Esophagus and Esophageal Adenocarcinoma Based on Genome-wide Methylation Analysis. 2019 Gut 68:389-399 *first authors.
  • Georg E. Luebeck, Kit Curtius, William D Hazelton, Sean Maden, Ming Yu, Prashanthi N Thota, Deepa T Patil, Amitabh Chak, Joseph E Willis, William M Grady. Identification of a key role of widespread epigenetic drift in Barrett’s esophagus and esophageal adenocarcinoma. 2017 Clinical Epigenetics; PMCID: PMC5644061.