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

Amina Ann Qutub, Principal Investigator

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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)
email: amina@rice.edu
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

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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.
email: byron.long@rice.edu
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.
email: cecilia.lantos@rice.edu
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; Fulbright Scholar, 2011

George Britton, Graduate Student

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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.
email: glb3@rice.edu
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.
email: yujie.chen@rice.edu
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

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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.
email: chenyue.hu@rice.edu
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

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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.
email: asm7@rice.edu
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

Tien Tang, Graduate Student

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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.
email: tien.t.tang@rice.edu
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

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.
email: nnd2@rice.edu
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.
email: hl43@rice.edu
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.
email: adl4@rice.edu
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.
email: sm96@rice.edu
project: Analysis of tissue-specific metabolic changes


VISITING SCHOLARS


Alex Bisberg

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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.
email: alex.bisberg@rice.edu
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.
email: cole.grandel@rice.edu
project: Quantitative analysis of neural cell communication

Elif Ozdemir Kaynak, Graduate Student

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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.
email: elifozdemir89@gmail.com
project: Modeling brain delivery of bioactive anthocyanins
education: BS, Bioengineering, 2012; MS, Bioengineering, Ege University, 2014



RECENT GRADUATES & ALUMNI


Andre Schultz, Graduate Student

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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 starts a postdoctoral fellowship in the Department of Computational Biology at MD Anderson Cancer Center in Fall 2017.
email: as86@rice.edu
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, Undergraduate

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.
email: kylie.m.balotin@rice.edu
project: Design of analysis tools to track neural cell properties
education: BS, Bioengineering, Rice University

JenniferDawkins1.pngJennifer Dawkins, Undergraduate

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.
email: jjd4@rice.edu
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, Undergraduate

SanjanaRanganathan

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.
email: sr38@rice.edu
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

David Noren, Post-Doctoral Researcher

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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.
email: david.noren@rice.edu
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

Qutub Lab Alumni

Current Position

Andre Schultz, Ph.D. Postdoctoral Fellow, MD Anderson Cancer Center
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 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