Bioinformatics and Data Science
in Life & Health Science

  • Professor Jane Grande-Allen’s research applies engineering analysis to understand and fight heart valve disease. This involves mechanical testing, biochemical measurements, and microstructural analysis of critical components found in the extracellular matrix (ECM) that makes up cardiac tissue. Her studies into the basic and applied physiology of heart valve tissue have shown that the ECM – collagen, elastin, glycosaminoglycans and proteoglycans – forms an intricate network of connective tissue that is influenced by valvular function, growth, and abnormalities. Her investigations of the chemical and mechanical conditions in both diseased and healthy valves are designed to reveal why structural defects occur and how to develop alternatives to conventional open-heart surgery to repair/replace diseased heart valves. These alternatives include drug therapies and engineered heart valves for patients of different age groups.
  • Professor Oleg Igoshin specializes in computational systems biology with emphasis on dynamical properties and evolutionary design principles of biochemical networks, pattern formation in bacterial biofilms, and genetic networks in bacterial and stem cell development. Research in Igoshin’s Cellular Systems Dynamics Laboratory uses methods of nonlinear dynamics, biophysics, statistics and bioinformatics to expose emergent properties of biological systems on intercellular and intracellular scales. Professor Igoshin’s computational and theoretical methods complement the experimental approaches of collaborators with leading academic and medical researchers across the U.S., Europe and Australia.
  • Professor Rob Raphael applies engineering principles to understand the auditory system and develop strategies to fight hearing loss and deafness. Through basic research into the intricate workings of inner ear hair cells and the auditory nerve, his overall goal is to bridge the gap between biophysical knowledge to engineering the next generation of auditory implants. The Raphael lab has studied the structure and function of biological membranes for two decades. This research includes using cultured cells, 3D culture models, optical imaging, micromechanical manipulation, and computational modeling to study the cellular and molecular basis of auditory function. Ultimately, the lab seeks to use the research knowledge to derive novel therapies for hearing loss and inspire new ideas for the design of biosensors and microscale biomedical devices.
  • Professor Gang Bao is a pioneer in nanomedicine, molecular imaging, and the emerging area of genome editing. The nanoscale structures and devices engineered in his lab have broad-based applications in basic research to understand the underlying causes of disease, as well as in the translation of nano-scale tools for disease diagnostics and treatment, such as targeted drug/gene and cell-based therapies. Current methodology development includes the superparamagnetic nanoparticle probes, quantum dot bioconjugates, activatable molecular probes and molecular beacons for cellular and in vivo imaging, with applications in disease detection and mechanistic studies. The Bao lab also develops novel strategies for drug/gene delivery using targeted nanoparticles, gene targeting approaches for treating single-gene disorders and other diseases using engineered nucleases, as well as bioinformatics tools and engineered nanodevices driven by biomolecular motors.
  • Professor Antonios Mikos is a member of the National Academy of Engineering and the National Academy of Medicine. His research focuses on the synthesis, processing, and evaluation of new biomaterials for use as scaffolds for tissue engineering, as carriers for controlled drug delivery, as non-viral vectors for gene therapy, and as platforms for disease modeling. His work has led to the development of novel orthopaedic, dental, cardiovascular, neurologic, and ophthalmologic biomaterials. Ongoing projects in the Mikos Research Group include: Investigating novel 3D printing and bioprinting strategies for manufacturing biodegradable polymer scaffolds with precise geometries, physiologically relevant tissue architecture, and controlled release of biochemical signals to direct stem cell differentiation and tissue formation for bone and cartilage regeneration and repair; Synthesizing novel extracellular matrix-derived and nanomaterial-based bioinks for 3D printing; Fabricating injectable, in situ polymerizable, biodegradable composite scaffolds as carriers for stem cells for osteochondral tissue engineering; and many others.
  • Professor Jeffrey Tabor programs living cells to sense and respond to stimuli in the environment with applications in medicine, biotechnology, environmental monitoring, and fundamental science. A particular focus of his lab is developing new technologies to study bacterial two-component systems (TCSs) and repurpose them for biomedical applications. Recently, the Tabor lab has expanded their focus to TCSs that regulate virulence and antimicrobial resistance in human pathogens. In particular, they are developing new synthetic biology technologies to discover antimicrobial peptides sensed by these systems, and to develop new molecular inhibitors that could be developed into next-generation antimicrobial drugs.
  • Professor Rebekah Drezek develops optical molecular imaging technologies for the in vivo assessment of tissue pathology and for the quantitative analysis of nanoparticle uptake and interaction within cellular environments. This basic, applied, and translational research emphasizes the design, prototyping, and clinical testing of optical tools and nanomaterials that detect, diagnose, and treat cancer. Her work has included the translation of nanoscale tools, such as gold nanoparticles and quantum dot probes, for targeted molecular imaging and tumor margin assessment as well as the development of photothermal nanoparticles that target and eliminate cancer.
  • Professor Rebecca Richards-Kortum is a member of the National Academy of Sciences, the National Academy of Engineering, the American Academy of Arts and Sciences, and the American Philosophical Society. She holds the rank of University Professor, Rice’s highest academic title awarded to only seven individuals in the university’s history. Guided by the belief that all of the world’s people deserve access to health innovation, Rebecca Richards-Kortum’s research and teaching focus is on the development of low-cost, high-performance technologies for remote and low-resource settings. She is known for providing vulnerable populations with access to life-saving health technologies that address diseases and conditions that cause high morbidity and mortality, such as cervical and oral cancer, premature birth, sickle cell disease and malaria. Ongoing projects in Richards-Kortum's Optical Spectroscopy and Imaging Laboratory include the development cost-effective optical imaging and spectroscopy tools to reduce the incidence and mortality of cancer and infectious disease through early detection at the point-of-care.
  • Professor Sibani Lisa Biswal’s research program focuses on using chemical, biological, and engineering approaches to study soft materials such as colloids, polymers, lipids, and surfactants. One of her main research area has been in developing new materials using colloidal particles. These synthetic materials are chains of patterned magnetic colloids that have rigidity and length specificity, and are able to demonstrate capability for folding, self-assembly, and specific chemical and biorecognition. Another area of interest is the use of microcantilever beams to investigate the lipid-dependent mechanisms responsible for vesicle rupture and bilayer fusion to form supported lipid bilayers and monolayers. A new area of research her group has moved into is use new assembly methods to develop novel materials for batteries and solar technology.
  • Professor Walter Chapman's research into properties and interfacial structure of complex fluids has applications in the energy and high performance materials industries. His research group uses tools such as molecular simulation, computer visualization, statistical mechanics, and NMR to discover how material properties and structure depend on molecular forces. Professor Chapman’s present research program focuses polymer solutions and blends, associating fluids, confined fluids, natural gas hydrates and asphaltenes.
  • Professor Xue Gao’s research program lies at the interface of chemical biology and biomolecular engineering with primary focus on small- and macro-molecule discovery and their applications to human health, agriculture, and energy. One of her main research is microbiome-based natural product discovery and engineering, and moreover, to develop enzymes involved in the natural product biosynthesis as powerful biocatalysts for difficult chemical reactions in the pharmaceutical and biotechnology industries. Another main research interest of her group is to discover and develop advanced genome-editing agents and delivery systems and apply these genome-editing tools as next-generation therapeutics to clinical treatment of human genetic diseases.
  • Professor Kyriacos Zygourakis’ research interests span several important areas of chemical reaction engineering and tissue engineering. Applied mathematics, computer simulations, digital video microscopy, thermal analysis and chemical reactor design are integral parts of his research methodology. Currently, his research group is focusing on elucidating the fundamental mechanisms controlling the transport and reaction of nitrogen fertilizers in biochar-amended soils, and on developing hybrid multi-scale models that describe the growth of heterogeneous cell populations in the presence of mass transfer limitations. His research group is also working on designing processes for sustainable production of biochar for carbon sequestration and soil amendment, and for thermal remediation of soils contaminated with heavy hydrocarbons.
  • Professor Laura Segatori develops innovative, system-level strategies based on the integration of synthetic biology, protein engineering, and bionanotechnology to reprogram the cellular quality control system in mammalian cells. The approaches allow for a broader understanding and control over the molecular mechanisms that regulate protein processing for applications ranging from development of cell-based therapies to the production of biologics. Significant research has involved the development of protein engineering toolkits designed to unlock, probe, and manipulate the chaperone and degradation processes. Recently, she won the award of Rice Covid-19 research grant, and currently works on engineering cell lines for the rapid development of clinically translatable neutralizing antibodies for infection control.
  • Professor Lydia Beaudrot combines observational data with statistical modeling approaches to investigate questions at the interface of ecological theory and conservation biology. The primary goals of her research are to: (1) Identify mechanisms that structure tropical vertebrate communities across spatial scales, (2) Understand how tropical mammals and birds respond to global change, and (3) Apply results to biodiversity conservation.
  • Professor Amy Dunham’s research program is broadly concerned with tropical community ecology with a focus on identifying mechanisms important for structuring forest communities and dynamics and how such mechanisms can be used to guide conservation management actions. She is particularly interested in the impacts of anthropogenic pressures including defaunation, invasion and habitat fragmentation on species interactions, communities, and ecosystem processes. The goal of her work is to provide novel insights for our understanding of how complex communities and ecosystems work and how they might respond to anthropogenic pressures.
  • Professor Scott Egan is interested in the processes that promote or constrain the evolution of new biological species. This includes (1) understanding the role of adaptation via natural selection in the speciation process and (2) exploring the genomic architecture associated with and mediating the evolution of new species. This work integrates natural history, manipulative field experiments, behavioral observations, population genetics, and genomics. He also collaborates in a large interdisciplinary research group that combines principles of population genetics, ecology, engineering, biogeochemistry, and nanoparticle physics to address important societal challenges, such as the rapid environmental detection of disease or their vectors or invasive species, or quantifying biodiversity.
  • Professor Michael Kohn’s lab employs molecular and bioinformatics tools to study the evolutionary dynamics of genes and genomes in populations and species. Some of his research projects have implications for conservation biology or medicine. Much of his work is concerned with the evolutionary dynamics and medical effects of mutations in the vitamin K cycle genes, foremost vkorc1, in rats and mice that have developed a resistance to anticoagulant rodenticides such as warfarin.
  • Professor Tom Miller’s research addresses fundamental questions regarding population dynamics and the population-level consequences of inter-specific interactions, mostly in plant and insect systems. His work spans population, community, and evolutionary ecology, including the spread of biological invasions, the dynamics of consumer-resource and host-symbiont interactions, and the evolution of life histories.  His interests are broad but united by an emphasis on demography and demographic structure. He addresses research questions using both empirical and theoretical methods, and he is particularly excited about the integration of data and theory.
  • Professor Volker Rudolf’s interests are broad but mainly focus on the ecological and evolutionary factors that determine the structure and dynamics of communities and ecosystem functioning. He combines theoretical and empirical work to develop predictive frameworks for understanding how species interactions and abiotic environmental factors determine the structure and dynamics of communities and how they drive population dynamics and the evolution of complex life histories. Most of his current research focuses on the impact of population size structure, cannibalism and seasonal variation (including climate change) on the structure and dynamics of communities and their evolutionary consequences.
  • Professor Jolf Silberg’s research is focused on understanding the organizing principles of life through bottom-up synthetic biology. His team is developing strategies to reliably design cellular programs with robust characteristics that allow for applications in agriculture, biogeochemical cycling, ecology, electronics, energy, information storage, and medicine. His research falls into three major areas: (1) Environmental Synthetic Biology, (2) Redox Synthetic Biology, and (3) Overcoming Component Limitations in Biology.
  • Professor George Bennett’s laboratory focuses on genetic engineering of metabolic pathways of microbes for production of biofuels and chemicals. His team studies the responses of bacteria to stresses either encountered in nature or in an industrial fermentor, such as pH, oxygen limitation or salt concentration. These fundamental studies have developed their approaches to metabolic engineering: cofactor engineering-the modification of the availability of redox factors such as NADH; the “cellular refinery” approach of producing multiple compatible products during a process; and the modeling and use of available genetic resources from the large genomic and biochemical databases for optimal metabolic performance.
  • Professor Matthew Bennett’s research spans the boundary between theoretical and experimental synthetic biology. He is particularly interested in the dynamics of gene regulation – from small-scale interactions such as transcription and translation, to the large-scale dynamics of gene networks and synthetic microbial consortia. I use an interdisciplinary approach to (1) uncover the underlying design principles governing gene networks and microbial consortia, (2) engineer novel synthetic gene circuits for practical applications, and (3) develop new mathematical tools to better describe gene networks. The ultimate goal of my research is to develop synthetic multicellular systems for biomedical and environmental applications
  • Professor James Chappell’s lab aims to forward their ability to understand and engineer the bacteria domain of life. Central to this is their ability to control how cells express their genetic code. The Chappell Lab focuses on understanding how the biomolecule RNA can be designed to create synthetic regulators of gene expression—allowing for the manipulation of natural cellular processes to elicit deeper biological understanding and for the engineering of new synthetic cellular functions. As such his lab focuses both on the creation of new gene regulatory tools and their application. The main areas of research focus are currently: (1) Creation of synthetic RNA regulators of gene expression. (2) Deciphering the portability of RNA regulators across the bacteria domain of life. (3) Creation of synthetic genetic circuits capable of performing signal processing. (4) Applying RNA-based tools for functional genomics
  • Professor Natasha Kirienko uses the model organism Caenorhabditis elegans to study the conserved mechanisms (immune and otherwise) that are used by the organism to defend itself against abiotic (i.e., environmental) and biological (i.e., pathogenic) stresses. Research in her lab currently focuses on two interrelated topics. The first of these goals is to identify novel treatments for bacterial infections that exhibit resistance to antimicrobials. She has recently begun to study the importance of mitophagy (autophagic destruction of mitochondria) in cancer as well. This research effort will harness the particularly deep knowledge base of C. elegans cell cycle events that has been amassed by researchers across the globe over the past thirty years and leverage the high-throughput capabilities of C. elegans assays to identify novel therapies that may help cancer patients.
  • Professor Yousif Shamoo’s research lab studies the dangerous rise of multi-drug resistant bacteria. With multi-drug resistant bacteria becoming increasingly common in hospitals, antibiotic resistance has threatened to return us to a pre-antibiotic era that would completely undermine modern medicine. His work seeks to elucidate the underlying biophysical principles of adaptation within bacterial populations during protein evolution. His group uses a combination of experimental evolution and biophysical approaches including X-ray crystallography, enzyme kinetics, protein folding, calorimetry and genomics to link changes in protein structure and function to their resulting phenotypes within evolving populations. His lab extends these physicochemical principles to predict the success or failure of specific adaptive alleles undergoing selection. By combining approaches from biophysics, genomics and experimental evolution, his group is able to identify and characterize successful evolutionary trajectories and then link those intermediates to the overall evolutionary trajectory of the bacterial populations.
  • Professor Yizhi Tao’s lab is interested in the catalytic mechanisms of viral RNA polymerases and in how RNA viruses exert regulation over RNA synthesis through polymerase interactions with viral and cellular factors. Her research currently focuses on the following two virus systems: (1) Birnaviruses (dsRNA), and (2) Influenza viruses (-ssRNA). Recently, she has won a National Science Foundation (NSF) RAPID grant with Professor Pedro Alvarez to develop a "novel approach for selective adsorption and photocatalytic disinfection" of SARS-CoV-2. They plan to reconfigure their "trap and zap" wastewater-treatment technology to capture and deactivate the virus that causes COVID-19.
  • Professor Aryeh Warmflash’s research focuses on quantitative studies of signaling dynamics and spatial pattern formation during embryonic development and in the cancer microenvironment. His previous work has used live-cell signaling assays to show that the dynamics of the TGF-beta signaling pathway are adaptive and to explore the consequences of this discovery for the function of TGFbeta as a patterning signal. He has also used micropatterning technology to develop in vitro systems for studying pattern formation. In particular, he has demonstrated that human embryonic stem cells (hESCs) confined to micropatterns during differentiation form self-organized patterns containing all three germ layers and reminiscent of those in mammalian embryos.
  • Professor Janet Braam is interested in understanding how plants perceive environmental conditions and respond in ways that may make them better able to withstand abiotic and biotic environmental stress. The roles of the jasmonate phytohormone, the circadian clock, autophagy, chlorophyll biosynthetic pathways, and calmodulin and calmodulin-like proteins in plant biology are specific areas of ongoing research. Her research areas include abiotic stress responses, the circadian clock, plant defense, autophagy regulation, fungal perception, genetic control of seed development, and nanoparticle-plant interactions.
  • Professor Daniel Carson’s lab is examining the expression and function of cell surface components that participate in and regulate cellular interactions in developing embryos and various tumor cell models. He is interested in identifying the molecular controls over MUC1 gene and protein expression in both normal and tumor cell contexts. Additionally, he is exploring therapeutic avenues to reduce MUC1 expression.
  • Professor Kathleen Matthews’ research focuses on the examination of protein-DNA interactions involved in regulating gene expression. Genetic regulation is an essential function in all organisms and provides the ability to respond to signals that reflect environmental conditions, determine developmental processes, and communicate other information within an organism. The lactose repressor (LacI) controls expression of the enzymes that metabolize lactose in E. coli. Her long-term goal is detailed insight into mechanisms by which both LacI recognition and regulation occur, and experiments with collaborators extend the applications of this protein.
  • Professor George Phillips’ overall goal is to relate the three-dimensional structure and dynamics of proteins to their biological functions. They use techniques of X-ray crystallography and other biophysical methods to elucidate the molecular structures, dynamics, and functions of proteins. Extensive use is made of modern computational methods to analyze the structures and their dynamics. One project they have underway is directed towards obtaining an atomic description of the basis for binding of oxygen and other ligands to heme proteins. Members of his laboratory are also involved in the field of structural genomics, the solving of structures whose function may not yet be known. Another longstanding interest in the laboratory is computational biology. This activity entails the development and application of modern algorithms from computer science and applied mathematics to solve interesting biological problems.
  • Professor Rosa Uribe’s research focuses on deciphering the genetic, cellular and signaling level mechanisms of neural crest stem cell proliferation, migration and cell -type differentiation during embryogenesis. Currently, among various derivatives of the neural crest, her lab study how the largest division of the peripheral nervous system, the Enteric Nervous System (ENS), develops from the neural crest. Ultimately, her overarching goal is to enhance basic knowledge on the mechanisms that direct neural crest stem cell development and diversification in a tissue-specific context, leading to treatments for neural crest-derived diseases and cancers, affecting both children and adults world-wide.
  • Professor Kirsten Ostherr is the Gladys Louise Fox Professor of English at Rice University, where she is a media scholar, health researcher, and technology analyst. Her research on trust and privacy in digital health ecosystems has been featured in Slate, The Washington Post, Big Data & Society, and Catalyst. She has recently published research on medical humanities and artificial intelligence in The Journal of Medical Humanities, and her writing on COVID-19 has been featured in Inside Higher Ed and in American Literature. She is currently leading a multidisciplinary project called "Translational Humanities for Public Health" that will identify humanities-based (and humanities-inspired) responses to the COVID-19 pandemic, to document and help others build upon these creative efforts.
  • Professor Caroline Levander is the Vice President for Global and Digital Strategy at Rice University. In this capacity, she is responsible for expanding the university's global impact through the development of new degrees, academic programs, partnerships, and research collaborations that increase the university’s global impact and innovate Rice's educational enterprise with new technologies. In her current administrative role she oversees Rice’s international strategies, program development, and the coordination of international activities across the university. The university’s global presence and international partnerships increasingly depend upon strategic use of digital education technologies, which also fall under Levander’s leadership. Levander oversees all university online curricula as well as K-20 initiatives, through Rice Online Learning and other university collaborations such as OpenStax College.
  • Professor Ashutosh Sabharwal is the Sheafor-Lindsay Professor and depart chair of Electrical and Computer Engineering. He currently works in two research areas, wireless and health. His wireless research spans fundamental theory and experimental systems. He is the founder of WARP project (warp.rice.edu), an open-source project which is now in use at more than 125 research groups worldwide, and have been used by more than 500 research articles. His health research is at the intersection of engineering, behavioral sciences and medicine, and he established Scalable Health Labs (sh.rice.edu). Scalable Health Labs’ mission to develop methods to uncover behavior-biology causal pathways, with a specific focus in three areas: bio-behavioral sensing, mobile bio-imaging, and data science methodologies.
  • Professor Ashok Veeraraghavan’s research areas include Computational Imaging, compressive sensing for imaging, signal processing and computer vision. Data Science, and Neuroengineering. He is co-developer of FlatCam, a thin sensor chip with a mask that replaces lenses in a traditional camera. Making it practical are the sophisticated computer algorithms that process what the sensor detects and converts the sensor measurements into images and videos. FlatCams may find use in security or disaster-relief applications and as flexible, foldable, wearable cameras, and even disposable cameras. His team has also developed FlatScope, a flat microscope and software system that can decode and trigger neurons on the surface of the brain.
  • Professor Akane Sano’s research includes data science, machine learning, and human-centered intelligent systems for health and wellbeing and spans in the field of affective computing, ubiquitous and wearable computing, and biobehavioral sensing and analysis/modeling. Her research targets (1) the analysis and modeling of human ambulatory multimodal time series data including physiological, biological and behavioral data and surveys for measuring, predicting, improving, and understanding human physiology and behavior and human factors such as health, wellbeing, and performance and (2) development of human-centered computing technologies for health, wellbeing, and performance. She has been working on developing tools, algorithms, and systems to measure, forecast, understand, and improve health and wellbeing using multimodal data from mobile and wearable sensors, devices in daily life settings, and clinical assessment especially for measuring, predicting, and intervening/improving clinical outcomes, stress, mental health, sleep, and performance.
  • Professor Lydia Kavraki is the director of the Ken Kennedy Institute at Rice University. She is a member of the National Academy of Medicine. Her research interests span robotics, AI, and biomedicine. In robotics and AI, she is interested in enabling robots to work with people and in support of people. Her research develops the underlying methodologies for achieving this goal: algorithms for motion planning for high-dimensional systems with kinematic and dynamic constraints, integrated frameworks for reasoning under sensing and control uncertainty, novel methods for learning and for using experiences, and ways to instruct robots at a high level and collaborate with them. Kavraki’s lab is inspired by a variety of applications: from robots that will assist people in their homes, to robots that would build space habitats. In biomedicine she develops computational methods and tools to model protein structure and function, understand biomolecular interactions, aid the process of medicinal drug discovery, analyze the molecular machinery of the cell, and help integrate biological and biomedical data for improving human health.
  • Professor Luay Nakhleh is the William and Stephanie Sick Dean for the George R. Brown School of Engineering at Rice University. He leads research at the intersection of computing and biology, particularly computational research on topics related to evolution. His research areas include combinatorial optimization, statistical inference, and their applications to biological problems; phylogenomics and population genomics; Evolution of biological networks (protein interaction networks and regulatory networks); and modeling and analysis of biological networks (metabolic and regulatory networks).
  • Professor Todd Treangen's research interests lie at the intersection of computer science and genomics, and is focused on the development of novel algorithms, methods, and software for the analysis of genomes and metagenomes. Given the computational challenges presented by the metagenomic data deluge, coupled with the time-sensitive nature of problems specific to tracking pandemics and synthetic DNA screening, the Treangen lab strives to develop efficient and accurate computational solutions to emerging problems in these fields. Specifically, his research group focuses on the design, development, and implementation of novel algorithms, heuristics, and data structures to solve emerging computational research questions specific to biosecurity, infectious disease monitoring, and host-associated microbiome characterization.
  • Professor Vicky Yao’s research focus is in computational biology, where she develops machine learning and statistical methods to improve our understanding of the biological circuitry that underlies living organisms and how its dysregulation may lead to disease. More specifically, she has worked on modeling tissue and cell type specificity as well as disease progression, both by developing general methods (such as semi-supervised network integration) and in applying them to decipher the molecular underpinnings of diseases such as Alzheimer’s, Parkinson’s, and rheumatoid arthritis.