Amina Ann Qutub, Principal Investigator


Amina Qutub’s research at Rice University focuses on the development of new computational methods and experimental analyses in order to uncover design principles of human cells during growth and regeneration. A thematic focus of the Qutub Lab is characterizing how cells behave and communicate as a function of hypoxia-inducible proteins – molecules integral to human life and key players in development and in age-related diseases. We are using fundamental knowledge gained by understanding cellular communication to transform the treatment of hematological cancers and neurovascular diseases.
(CV / Resume)
office: (713) 348-8089
department: Department of Bioengineering
program affiliations: Center for Neuroengineering
Systems, Synthetic & Physical Biology Program

Ken Kennedy Institute for Information Technology

Gulf Coast Consortia for Quantitative Biomedical Sciences
videos: Voice of America, AIChE BRAIN workshop, KHOU,
TEDxHouston, DREAM 9, Jeffrey Michel Seminar: Leroy Hood

Byron Long, Research Scientist


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 human cells and how they form tissues, with applications to angiogenesis and cellular differentiation.
project: New models and analysis methods to predict neurovascular cell behaviors
education:PhD, Computer Science, Indiana University, 2009; Postdoc, Bioengineering, Rice University, 2010-2015
videos: DREAM 9 challenge launch panel
awards: Computational Cancer Training Program Scholar; DREAM 8 SubChallenge Winner; Cold Spring Harbor Computational Summer Program Fellowship

David Noren, Post-Doctoral Researcher


Dave Noren’s doctoral research was in computational and experimental studies of endothelial cell behaviors during angiogenesis. Dave has continued his experimental work applying his knowledge to uncover mechanisms of angiogenesis through in vivo zebrafish studies. At the same time, he took a new direction as a fellow to focus on a clinically applied project. Dave’s main research is developing new computational approaches to integrate and interpret high-dimensional clinical and molecular data.
project: Design of new analysis methods to predict patient outcomes from cell and molecular patterns
education: PhD, Biomedical Engineering, Johns Hopkins University, 2012
videos: DREAM 9 challenge launch panel
awards: National Library of Medicine Training Program Scholar; NLM Informatics Conference Best Poster Award 2015; DREAM 8 SubChallenge Winner

George Britton, Graduate Student


George Britton is a PhD student in Rice’s Systems, Synthetic and Physical Biology Program. His project focuses 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.
project: Lineage trajectories and molecular circuitry specifying neural precursor fate
education: MS, Biochemistry, University of Texas-Health Science Center, 2014; BS, Neurobiology, University of Texas, Austin, 2007

YujieChenYujie Chen, Graduate Student

Yujie Chen is a PhD student in the Systems, Synthetic and Physical Biology program. Yujie is developing integrated experimental and computational methods to modulate and test the chemosensitivity of acute myeloid leukemia stem cells based on computationally-predicted proteomic signatures.
project: Modulating proteomic signatures of acute myeloid leukemia
education: BS, Biological Sciences, Zhejiang University, 2015
awards: American Mathematical Society Mathematics in Physiology & Medicine Workshop Fellowship, 2016

Chenyue Wendy Hu, Graduate Student


Wendy Hu is a PhD candidate in bioengineering. Developing a unique computational systems biology approach to high-dimensional proteomics, Wendy works in collaboration with MD Anderson Cancer Center clinicians to uncover the molecular mechanisms of leukemia. She has 4 patent-pending technologies, one of which has been used to design a clinical trial for childhood leukemia.
project: Proteomic landscapes of acute myeloid leukemia
education: BS, Biological Sciences (major), English (minor), Zhejiang University, 2012
videos: Grouping Leukemia Patients using Progeny Clustering
DREAM 9 challenge launch panel
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

Arun Mahadevan, Graduate Student


Arun Mahadevan is a PhD candidate in bioengineering, and a Neuroengineering fellow. Arun focuses on understanding how neural progenitor cells communicate as they differentiate into functional neuronal networks, through integrated experimental and computational analyses. Arun is co-advised by our collaborator Jacob Robinson, a neuroengineer in Rice’s Department of Electrical Engineering.
project: Identifying how human progenitor cells form electrically active neural networks
education: BS, Chemical Engineering, National Institute of Technology – Karnataka, 2011
videos: Ideas that Go Viral: Neural Progenitor Network Dynamics
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

Andre Schultz, Graduate Student


Andre Schultz is a PhD candidate in bioengineering. Andre is developing computational methods to characterize metabolic changes in tissues as a function of genetic perturbations resulting from whole body hypoxic adaptation, disease, and exercise.
project: Models of metabolic adaptation
education: BS, Mathematics, University of Michigan, 2012
webpage: Andre’s site
videos: Studying how mammals adapt to hypoxia
DREAM 9 challenge launch – Hackathon
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

Tien Tang, Graduate Student


Tien Tang is a PhD student in bioengineering in the Gaber Lab at Texas Children’s Hospital, and co-advised by Amina Qutub. Tien’s research focuses on understanding how metabolism governs brain tumor growth and radiation response using translational imaging.
project: Translational imaging and modeling of metabolic adaptation in brain cancer
education: BS, Biomedical Engineering, University of Minnesota, 2012; MBE, Bioengineering, Rice University 2013
awards: Smalley-Curl Institute’s Transdisciplinary Travel Award for Best Student Talk, 2016

KylieBalotin1.jpg.pngKylie Balotin, Undergraduate

Kylie is a senior bioengineering student at Rice University. She is working together with Dr. Byron Long to build models of neurovascular growth and tools to computationally analyze neurons.
project: Design of analysis tools to track neural cell properties

JenniferDawkins1.pngJennifer Dawkins, Undergraduate

Jennifer is a senior bioengineering student at Rice University. She has worked together with Dr. Dave Noren to develop and validate new computational models predicting clinical outcomes for leukemia. She currently is performing experiments to validate predictions of leukemia proteomic signatures and control the cancer cells’ chemosensitivity.
project: Design and experimental testing of methods to predict leukemia patient outcomes

NatalieDickman.pngNatalie Dickman, Undergraduate

Natalie is a sophomore bioengineering student at Rice University. She is working on a new computational framework and experiments to uncover the protein signaling of leukemia cells, in collaboration with Chenyue Wendy Hu and Dr. Qutub.
project: Methods to interpret the protein signatures of leukemia patient cells

HanyangQuentinLI.pngQuentin Li, Undergraduate

Quentin is a junior bioengineering student at Rice University. He is working together with Dr. Byron Long to build tools to rapidly computationally analyze neural progenitor cells and neurons.
project: Design of image-based tools for neural cell and intracellular analysis

AndrewLigeralde.pngAndrew Ligeralde, Undergraduate

Andrew is a junior biochemistry student at Rice University. He is working together with Chenyue Wendy Hu and Dr. Qutub to build web tools to computationally study protein signatures in cancer cells, and test the response of the cells to in vitro chemotherapy.
project: Tools to interpret protein signatures in cancer

SanketMehta2.pngSanket Mehta, Undergraduate

Sanket is a sophomore bioengineering student at Rice University. He is working together with Andre Schultz to optimize models of tissue metabolism as a function of protein and gene signaling.
project: Analysis of tissue-specific metabolic changes

Sanjana Ranganathan, Undergraduate


Sanjana is a senior bioengineering student at Rice University. Through in vitro experiments and analysis, she is working to uncover how crosstalk between insulin and hypoxic response signaling alters brain cancer cell behaviors and accelerates tumor progression.
project: Crosstalk between insulin and hypoxic response pathways in glioma progression
awards: Computational Cancer Biology Summer Research Fellowship, 2016


Alex Bisberg


Alex Bisberg graduated from Rice University (BS, Bioengineering) in 2015. As a visiting scholar in the lab, he is continuing his research developing tools to visualize and characterize protein networks in acute myeloid leukemia patients. Alex is co-inventor on several technologies from the lab, and co-founder of the startup DiBS, located at TMCx in the Texas Medical Center.
project: Visual analytics to interpret biomedical data
videos: DREAM 8 challenge visualization – BioWheel
DREAM 9 challenge launch panel
DREAM 9 challenge visualization demo
awards: Distinction in Research & Creative Works; DREAM 8 SubChallenge Winner; OwlSpark Summer Accelerator; MD Anderson Cancer Prevention Research Training Fellowship
education: BS, Bioengineering, Rice University, 2015

Cole Grandel

ColeGrandelCole Grandel is a bioengineering undergraduate student at Stanford University, and a 2016 intern in the Qutub lab. Cole’s research in the lab focuses on methods to automatically analyze the functional activity of developing neuronal networks. As a visiting scholar working with Arun, Cole is developing and optimizing image analysis tools and quantitative models that assess neuronal communication through Ca2+ signaling.
project: Quantitative analysis of neural cell communication

Elif Ozdemir Kaynak, 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.
project: Modeling brain delivery of bioactive anthocyanins
education: BS, Bioengineering, 2012; MS, Bioengineering, Ege University, 2014


Amada Abrego, Graduate Student


Amada Abrego is a recent MBE graduate in bioengineering and research associate at Baylor College of Medicine, Department of Neuroscience. Amada’s work in the lab focused on experimental studies of neuron-endothelial cell interactions and the neurovasculature, with applications to treatment of Alzheimer’s disease.
project: Behavior patterns of neural and endothelial cells as a function of hypoxic response signaling
education: BS, Bioengineering, Tecnológico de Monterrey, 2013; MBE, Bioengineering, Rice University, 2015

Ka Wai Lin, Graduate Student


Ka Wai Lin graduated with his doctorate in bioengineering in Dec 2015. Ka Wai’s thesis project combined modeling & in vitro assays to characterize how the crosstalk between insulin signaling and hypoxic response changes the behaviors of brain tumor cells. Current work in the lab is following-up on Ka Wai’s finding on the role of the protein IGFBP2 and its coregulators experimentally, with the goals of targeting this pathway therapeutically and mapping the intracellular molecular signaling with metrics obtainable through non-invasive imaging of glioma in vivo.
project: Crosstalk between insulin and hypoxic response pathways in glioma progression
education: BS, Bioengineering, University of California, San Diego, 2011
videos: Studying insulin-hypoxic pathway interactions in brain cancer
awards: HHMI Med-Into-Grad Fellowship; IGNITE Entrepreneurship Conference, Invited Participant; IBB Travel Award; Frontiers in Systems & Synthetic Biology Travel Award & Talk

Qutub Lab Alumni

Current Position

Amada Abrego, M.B.E. Research Associate, Department of Neuroscience, Baylor College of Medicine
Alex Bisberg, B.S. Data Scientist, Harvest Exchange; Founder, DiBS
Ka Wai Lin, Ph.D. Data Scientist, Allstate
Angela Liao, B.S. Graduate Student, University of California, San Diego
Jiwon Jung, B.S. Graduate Student, University of Texas, Austin
Nikhil Gupte Undergraduate, Georgia Tech
David Gabriel Mora-Boellstroff Undergraduate, University of Texas, Austin
David Ryan, M.B.E. Data Scientist, Elder Research
Becky Zaunbrecher, B.S. Graduate Student, University of Washington
Rahul Rekhi, B.S. Economic Adviser, The White House
Holley Love, Ph.D. Engineer, JBL Technologies
Taylor Birk, B.S. Engineer, National Instruments
Rocio Nava 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, B.S. Graduate Student, University of California, Los Angeles
Ashley Kelsey NAVWAR Test Manager, United States Air Force
Joanna Nathan, B.S., M.B.E. Director of Business Development, Saranas; Founder, Enventure
Duncan Eddy Graduate Student, Stanford University
Abir Khan, B.S. Medical Student
Alex Arevalos, B.S. Chief Technology Officer & Co-Founder, Saranas