Amina’s research focuses on the development of new computational methods and experimental analyses in order to uncover design principles of human cells during growth and regeneration. The Qutub Lab uses fundamental knowledge gained by understanding cellular communication to transform the treatment of hematological cancers and neurovascular diseases
Program Affiliations: UTSA/UT-Health Sciences BME Program (Director), MATRIX AI Consortium (Research Thrust co-Lead), Brain Health, Regenerative Medicine
Byron Long’s doctoral research was in logic for programs that use dynamic memory. Byron built on his training in logic to develop innovative state machine models of endothelial cells and a modeling framework for testing biological hypotheses. He combines these approaches with novel image-analysis programs to study how human cells form tissues, and predictive algorithms to interpret how molecular and cell-level changes influence daily behaviors at a systems level.
Awards: Computational Cancer Biology Training Fellow
Quantu Project Manager
Jennifer (Jenny) Brethen is the Quantu Project manager and a post-bac fellow in UTSA's Department of Biomedical Engineering.
BS: University of Texas, San Antonio
Projects: The Quantu Project
Zacharie Maloney is a PhD student in UTSA's Department of Biomedical Engineering and the Joint UTSA/UTHSC Graduate Group in Biomedical Engineering. Integrating new modeling and experimental methods, Zach's project focuses on characterizing cellular and proteomic processes underlying changes in daily behaviors indicative of brain health. Joining the Qutub Lab in Fall 2019, Zach brings experience in biomedical engineering, systems biology, software engineering and financial modeling.
BS: Biomedical Engineering, Illinois Institute of Technology
Projects: Neural network modeling & experiments, Quantu
Erin Pollet is a PhD student in UTSA's Department of Biomedical Engineering and the Joint UTSA/UTHSC Graduate Group in Biomedical Engineering. Her project focuses on uncovering neural and neurovascular mechanisms underlying changes in sleep and other daily behaviors using integrated modeling and experimental approaches. Joining the Qutub Lab in Fall 2018, Erin brings 10 years of clinical sleep experience as a registered polysomnographic technologist to her research project.
BS: Biomedical Engineering, UTSA
Projects: Quantu, Correlating Behavior to Cellular Changes in Alzheimer's
Awards: Brain Health Consortium Seed Grant 2018
Sean is a senior biomedical engineering undergraduate student and incoming graduate student developing innovative vascularized models of brain regions that regulate sleep, exercise response and circadian rhythm. Sean's co-mentor is Dr. Eric Brey, vascular engineer and Chair of the UTSA Department of Biomedical and Chemical Engineering.
Projects: Vascularized brain-in-a-dish models & experiments, Quantu
Tomisin is a biomedical engineering undergraduate student researching computational and experimental methods to uncover how neural networks form.
Ash is a biomedical engineering undergraduate student applying computational methods to interpret patterns in sensor-based fitness data and identify how changes in daily activity affect the brain.
Elif Ozdemir Kaynak
Visiting Graduate Student
Elif is a PhD candidate in bioengineering at Canakkale Onsekiz Mart University. While visiting in the Qutub lab as part of her thesis work, she is developing a computational model of nanoparticle-encapsulated delivery of bioactive flavanoids (anthocyanins) through the blood-brain barrier and anthocyanin uptake as a potential novel treatment of brain cancer.
BS: Bioengineering, Ege U.
Masters: Bioengineering, Ege U.
Qutub Lab Graduate Profiles & Alumni List
George Britton graduated as a PhD student in Rice’s Systems, Synthetic and Physical Biology Program. His project focused on uncovering the mechanisms underlying human embyronic cell development into neural tissue. George is jointly advised by our collaborator Aryeh Warmflash, a stem cell biologist in Rice’s Biochemistry and Cell Biology Department.
PhD: SSPB, Rice University
BS: Neurobiology, UT-Austin
Masters: Biochemistry, UT-Health Sciences
Projects: Ectoderm modeling, analysis of neural lineage
Thesis: Network Analysis of Developing Neural Progenitor Cells
Awards: NSF Neuroengineering IGERT Fellow; Ideas that Go Viral Speaker; Bioengineering Department Travel Award, 2015; Outstanding Student Poster Award GEM4 Mechanobiology of the Brain Workshop, 2015; IBB Travel Award, 2017; Screech People’s Choice Award, 2017; Bioengineering Innovation Day Research Pitch Award Winner, 2017; 3-Min Thesis Overall Winner & Alumni Choice Winner, 2018
Project: Design of image-based and machine learning methods for multicellular and intracellular analysis
Awards: Distinction in Research & Creative Works, 2018
email: BS: Bioengineering, 2018
Carnegie Mellon University
Chenyue Wendy Hu
Thesis: Data-Driven Discovery of Proteomic Hallmarks in Acute Myeloid Leukemia
Awards: NHGRI Travel Award for Genomics & Personalized Medicine 2016; HHMI Med-Into-Grad Fellowship; Texas Life Science Forum Presenter; DREAM 8 SubChallenge Winner; Texata Big Data Semi-Finalist; IGNITE Entrepreneurship Conference, Invited Participant; OwlSpark Summer Accelerator; IBB Travel Award (2014, 2016); Bioengineering Department Travel Award, 2015; Gold Medal, iGEM; 1st Prize, China’s National Undergraduate Mathematical Contest in Modeling; Bioinformatics Peer Prize Award, 2017; Best Thesis in Bioinformatics, 2018
email: PhD: Bioengineering, 2018
Data Scientist, Uber Technologies
Project: Tools to interpret protein signatures in cancer and model neural stem cell development
Awards: National Science Foundation summer fellowship, National Science Foundation Graduate Fellowship, 2019
email: BS: Chemistry, 2018
University of California, Berkeley
Thesis: Improved Methods for Constraint Based Modeling of Mammalian Systems
Awards:BMC Systems Biology Top 5 paper, 2015; NSF Travel Award, Pan American Advanced Studies Institute; Outstanding Bioengineering Graduate Teaching Assistant; Duke TIP Teaching Summer Internship; Jeffrey Michel Innovations in Systems Biology Dissertation Award, 2016
email: PhD: Bioengineering, 2017
Stanford University, School of Medicine
Project: Design and experimental testing of methods to predict leukemia patient outcomes
Awards: Computational Cancer Biology Summer Research Fellowship, 2017; National Science Foundation Graduate Fellowship, 2017
email: BS: Bioengineering, 2017
Harvard / MIT HST Program
Project: Crosstalk between insulin and hypoxic response pathways in glioma progression
Awards: Computational Cancer Biology Summer Research Fellowship, 2016
email: BS: Bioengineering, 2017
Global Medical Innovation, 2018
Graduate Student / TA
Qutub Lab Alumni
Undergraduate Student, University of Texas at San Antonio
Undergraduate Student, Trinity University
Kelsey Phelan, B.S.
Graduate Student, University of Texas at San Antonio
Arun Mahadevan, PhD
Postdoctoral Fellow, University of Pennsylvania
Tien Tang, PhD
Postdoctoral Fellow, Texas Children's Hospital
Undergraduate Student, Rice University
Undergraduate Student, Rice University
Andrew Ligeralde, B.S.
Graduate Student, University of California, Berkeley
Quentin (Hanyang) Li, B.S.
Graduate Student, Carnegie Mellon
Chenyue Wendy Hu, PhD
Data Scientist, Uber
Andre Schultz, PhD
Bioinformaticist, Stanford University, School of Medicine
Sanjana Ranganathan, M.B.E., B.S.
Clinical Consultant, GE Healthcare
Kylie Balotin, B.S.
Graduate Student, Vanderbilt University
Nicholas (Cole) E. Grandel, B.S.
Graduate Student, Rice University (SSPB)
Jennifer Dawkins, B.S.
Graduate Student, MIT & Harvard University (HST)
David Noren, PhD
Scientist, Phillips Research
Amada Abrego, M.B.E.
Graduate Student, Rice University (ECE, Neuro)
Alex Bisberg, B.S.
Graduate Student, University of Utah
Ka Wai Lin, PhD
Data Scientist, Allstate
Angela Liao, B.S.
Graduate Student, University of California, San Diego
Jiwon Jung, B.S.
Graduate Student, University of Texas, Austin
Medical Student, UT-Health San Antonio
David Gabriel Mora-Boellstorff
Graduate Student, UT-Health Sciences, Houston
David Ryan, M.B.E.
Product Development Engineer, EKOS Corporation
Becky Zaunbrecher, PhD
Allen Institute for Cell Science
Rahul Rekhi, M.S.
Financial and Healthcare Advisor, Lazard
Holley Love, PhD
Engineer, JBL Technologies
Instructional Assistant Professor of Mechanical Engineering, University of Houston
Taylor Birk, B.S.
Software Engineer, Hewlett Packard
Head of Biomedical Engineering, San Jorge Hospital
Shun-Ming Ting, M.B.E.
Research Associate, Baylor
Heather York Brisendine, B.S.
Engineering Consultant, Alliantgroup Houston
Tyler Young, B.S.
Medical Student, Baylor College of Medicine
Grace Ching, B.S.
Medical Student, Texas A&M
Norman Truong, PhD
Clinical Data Consultant, Ritual
NAVWAR Test Manager, United States Air Force
Joanna Nathan, B.S., M.B.E.
Venture Fellow, Mercury Fund
Duncan Eddy, M.S.
Capella Space Corporation
Abir Khan, M.D.
Clinician, Baylor College of Medicine
Alex Arevalos, PhD
Chief Technology Officer & Co-Founder, Alleviant Medical