Amina  Byron  Cecilia
 George  Wendy  Arun
 Tien  Natalie  Quentin
 Cole  Andrew  Sanket

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

CeciliaLantosCecilia Lantos, Postdoctoral Fellow

Cecilia Lantos’s doctoral work focused on model-based imaging approaches to quantify tissue structural properties from optical coherence topography. Joining the lab in 2017, Cecilia is building on her background in image analysis to develop new methods that enable the rapid assessment of patient molecular signatures from common histology images in leukemia. Applications of Cecilia’s work are to inform personalized medicine for patients with acute myeloid leukemia, and more broadly, to build a rule-based modeling platform that enables low-resolution biological images to uncover unique proteomic and genomic information.
project: Deep learning methods and models to map biological images and histology slides to proteomic signatures
education: PhD, Biomedical Engineering, Paris Diderot University, 2014; MS in Mechanical Engineering, Superior Engineering Institute of Paris and Budapest University of Technology and Economics, 2007
awards: Computational Cancer Training Program Scholar, 2017-2018; Fulbright Scholar, 2011

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

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; Screech People’s Choice Award, 2017; Bioengineering Innovation Day Research Pitch Award Winner, 2017

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: HHMI Med-Into-Grad Fellowship; Rice University Graduate Student Travel Award, 2015; Radiation Research Meeting Award, 2016; Smalley-Curl Institute’s Transdisciplinary Award for Best Student Talk, 2016; IBB Travel Award, 2018

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 senior bioengineering student at Rice University. He has been working together with Dr. Chenyue Wendy Hu and Dr. Byron Long to build tools to rapidly analyze complex data on human cells and their protein expression patterns.
project: Design of image-based and machine learning methods for multicellular and intracellular analysis

AndrewLigeralde.pngAndrew Ligeralde, Undergraduate

Andrew is a senior 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; and recently started working with Arun Mahadevan to develop three-dimensional in vitro models of neural stem cell development.
project: Tools to interpret protein signatures in cancer and model neural stem cell development

SanketMehta2.pngSanket Mehta, Undergraduate

Sanket is a junior bioengineering student at Rice University. He has been 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


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.
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; Bioinformatics Peer Prize, 2017
education: BS, Bioengineering, Rice University, 2015

Cole Grandel

ColeGrandelCole Grandel is a bioengineering undergraduate student at Stanford University, and a 2016-2017 intern and 2018 visiting scholar 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 Mahadevan and Dr. Byron Long, Cole has been developing and optimizing image analysis tools and quantitative models that assess neuronal communication through Ca2+ signaling, while mapping this communication to predictive algorithms of human behaviors.
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


Dr. Chenyue Wendy Hu


Wendy Hu graduated in December 2017 with a PhD in Bioengineering. Developing a unique computational systems biology approach to high-dimensional proteomics, Wendy worked in collaboration with MD Anderson Cancer Center clinicians to uncover the molecular mechanisms of leukemia. She is first or co-author on eighteen manuscripts (2015-2018), and co-inventor of four analysis technologies from the lab, one of which has been used to design a clinical trial for childhood leukemia. Wendy started as a data scientist at Uber Technologies in San Francisco in 2018. Wendy is also co-founder of the data visualization and learning startup DiBS, and founder of the Texas Medical Center Data Workshops.
project: Proteomic landscapes of acute myeloid leukemia
education: BS, Biological Sciences (major), English (minor), Zhejiang University, 2012; PhD, Bioengineering, Rice University, 2018
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; Bioinformatics Peer Prize Award, 2017

Dr. Andre Schultz


Andre Schultz graduated in Summer 2017 with a PhD in Bioengineering. Through his thesis work, Andre has developed a suite of new computational tools and methods to characterize metabolic changes in tissues as a function of genetic perturbations resulting from whole body hypoxic adaptation, disease, and exercise. Andre is first or co-author on six manuscripts (2015-2018), including one that was designed a top paper of the year for BMC Systems Biology. Andre started a postdoctoral fellowship in the Department of Computational Biology at MD Anderson Cancer Center in Fall 2017.
project: Models of metabolic adaptation
education: BS, Mathematics, University of Michigan, 2012; PhD, Bioengineering, Rice University, 2017
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

KylieBalotin1.jpg.pngKylie Balotin

Kylie graduated in Spring 2017. She worked together with Dr. Byron Long to build models of neurovascular growth and tools to computationally analyze neurons. Kylie starts a PhD program in bioengineering at Vanderbilt University in Fall 2017.
project: Design of analysis tools to track neural cell properties
education: BS, Bioengineering, Rice University, 2017

JenniferDawkins1.pngJennifer Dawkins

Jennifer graduated in Spring 2017. She worked together with Dr. Dave Noren to develop and validate new computational models predicting clinical outcomes for leukemia. She also helped to perform experiments to validate predictions of leukemia proteomic signatures and control the cancer cells’ chemosensitivity. In summer of 2017 she was a Computational Cancer Biology fellow continuing her work in the lab to develop algorithms informed by the knowledge of a ‘clinical crowd’ of oncologists. She also interned with an image-analysis start-up in Irvine. Jennifer starts a PhD program in Bioengineering at UCSD in Fall 2017, as a National Science Foundation graduate fellow.
project: Design and experimental testing of methods to predict leukemia patient outcomes
education: BS, Bioengineering, Rice University, 2017
awards: Computational Cancer Biology Summer Research Fellowship, 2017; National Science Foundation Graduate Fellowship, 2017

Sanjana Ranganathan


Sanjana graduated in Spring 2017. Through in vitro experiments and analysis, she helped to uncover how crosstalk between insulin and hypoxic response signaling alters brain cancer cell behaviors and accelerates tumor progression. Sanjana graduated with a Distinction in Research, and started Rice’s Global Medical Innovations masters program in summer 2017.
project: Crosstalk between insulin and hypoxic response pathways in glioma progression
education: BS, Bioengineering, Rice University, 2017
awards: Computational Cancer Biology Summer Research Fellowship, 2016

Dr. David Noren


Dave Noren’s doctoral research was in computational and experimental studies of endothelial cell behaviors during angiogenesis. As a postdoc in the Qutub Lab, Dave 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. Dave currently works at Philips Research, North America in Cambridge, MA.
project: Design of new analysis methods to predict patient outcomes from cell and molecular patterns
education: PhD, Biomedical Engineering, Johns Hopkins University, 2012; Postdoctoral Fellow, Department of Bioengineering, Rice University, 2013-2016
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

Qutub Lab Alumni

Current Position

Chenyue Wendy Hu, Ph.D. Data Scientist, Uber; Founder, DiBS
Andre Schultz, Ph.D. Postdoctoral Fellow, MD Anderson Cancer Center
Sanjana Ranganathan, B.S. Graduate Student, Rice University
Kylie Balotin, B.S. Graduate Student, Vanderbilt University
Jennifer Dawkins, B.S. Graduate Student, University of California, San Diego
David Noren, Ph.D. Scientist, Phillips Research
Amada Abrego, M.B.E. Graduate Student, Rice University (ECE, Neuro)
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 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, B.S. Graduate Student, University of Washington
Rahul Rekhi, B.S. Financial and Healthcare Advisor, Lazard
Holley Love, Ph.D. Engineer, JBL Technologies
Taylor Birk, B.S. Software Engineer, Hewlett Packard
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