fellows

Hal Alper

The Alper lab focuses on engineering biology to produce organic molecules of interest such as biofuels, commodity and specialty chemicals, and protein pharmaceuticals.  To accomplish these tasks, traditional pathway engineering approaches are merged with novel synthetic biology tools, protein engineering strategies, systems biology paradigms and applied genetic engineering capabilities.  The group utilizes a variety of host systems including microbial (eg. Escherichia coli), fungal (eg. the yeasts Saccharomyces cerevisiae and Yarrowia lipolytica), and mammalian cells (eg. Chinese Hamster Ovary (CHO) cells and Human HEK293) to produce a diverse array of products.  In each case, the goal is to “rewire” cellular systems into industrially-relevant biochemical factories.

Marcelo Behar

Professor Marcelo Behar’s research focuses on understanding the functional principles underlying how biological networks collect, process, and use different types of information available in their environment. Professor Behar specializes in the dynamical properties of the intracellular information highways that allow cells to adapt to changing conditions. His research addresses the fundamental problem of signal transduction as well as applied instances in the context of the immune response and cancer.

Matt Cowperthwaite

CSSB Research Fellow

I use computationally-predicted RNA secondary structure as a model system to study many aspects evolutionary dynamics. In my models, I consider the primary nucleotide sequence as a genotype and the estimated repertoire of lowest free energy secondary structures as the phenotype. Therefore, RNA encompases a compact, biologically grounded genotype-to-phenotype model that is also computationally tractable. I am currently using this system to study several areas of evolutionary dynamics: (1) adaptation, (2) evolution in a fluctuating environment, and (3) evolution of robustness in RNA secondary structures.

Lauren Ehrlich

The overarching goal of the Ehrlich lab is to understand the cellular and molecular interactions between thymocytes and heterogeneous stromal cells in the thymic microenvironment that promote development of a healthy, non-autoreactive, and non-malignant T cell repertoire.

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George Georgiou

The Georgiou Lab is currently working primarily on the discovery and development of protein therapeutics and applied immunology by capitalizing on state of the art protein engineering, directed evolution and systems biology technologies. Areas of interest include i) the engineering of human therapeutic enzymes for the treatment of a variety of malignancies; ii) the deconvolution of antibody responses and signatures in disease states; iii) the engineering and optimization of therapeutic antibodies; and iv) the design of proteolytic enzymes that cleave and irreversibly inactivate disease targets.

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Ryan S Gray

Single nucleotide genetics changes can act alone or in concert to affect the development or homeostasis of tissues and organ systems. The Gray lab takes an integrated approach to understanding this process combining Human genomic data with experimental modeling in zebrafish and mouse model organisms.

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Jenny Jiang

Professor Jiang’s research is focused on systems immunology. A dysfunctional or dysregulated immune system not only fails to offer protection, it can also introduce unnecessary immune responses such as allergies or autoimmune diseases. The key to immune modulation and engineering and regenerative medicine is to understand how the normal immune system works. However, a full understanding of the complex interactions among immune cells and between immune cells and cytokines and chemokines requires a quantitative and systems approach. Using high-throughput sequencing and single-cell analysis in combination with quantitative analysis, Professor Jiang is interested in answering the following questions: How does the immune system develop and age? What are the molecular signatures of autoimmune diseases? Why does the immune system tolerate tumors?

Jonghwan Kim

The Kim Laboratory studies transcriptional and epigenetic regulation of pluripotent stem cells such as embryonic stem cells (ES) and induced pluripotent stem cells (iPS). Pluripotent stem cells are of great interest as a model system for studying early developmental processes and as a tool for therapeutic applications in regenerative medicine. Obtaining a systematic understanding of the mechanisms controlling the stemness (self-renewal and pluripotency) of these cells relies on high-throughput tools to define regulatory networks consisting of various DNA binding proteins and their chromosomal targets at the genome level. The Kim Lab is interested in elucidating how these trans- and cis-regulators are tightly intertwined and influence the pluripotent status of stem cells. The lab uses a broad panel of techniques, including genetics, molecular biology, and high-throughput genomic approaches, in combination with computational analysis. Research focuses include 1) the construction of novel regulatory networks modeling the stemness of ES cells and iPS cells, 2) identifying transcriptional and epigenetic regulators involved in early embryonic development and lineage specification, and 3) understanding common gene expression signatures between pluripotent stem cell and cancer cells.

Schonna R. Manning

Research Associate

Dr. Schonna R. Manning began her career in phycology more than a decade ago investigating harmful blooms and toxic polyketide metabolites from golden algae (Prymnesium parvum, Haptophyta). She earned a Ph.D. in Plant Biology and was presented the Research Excellence Award for her dissertation, “Molecular and phytochemical investigations of the harmful, bloom-forming alga, Prymnesium parvum Carter (Haptophyta)”. Learn more

Nancy Moran

Moran obtained her bachelor’s degree from The University of Texas at Austin and her doctoral degree from the University of Michigan. She is an evolutionary biologist whose research intersects the fields of genetics and genomics, microbiology, entomology, and ecology. Moran’s focus is on genome evolution in host-associated microorganisms, especially bacterial symbionts of insects, and on the consequences of symbiotic associations for biological diversity and ecological relationships. She has authored 200 research papers. Moran was elected as a Member of the National Academy of Science in 2004 and of the American Academy of Arts and Sciences in 2005. She was awarded the International Prize for Biology in 2010. Before coming to The University of Texas at Austin, she was Regent’s Professor at the University of Arizona (1986-2010) and the William Fleming Professor of Biology at Yale University (2010-2013).

Hong Qiao

Qiao received her Ph.D. degree from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (IGDB). She subsequently moved Salk Institute for Biological studies at San Diego, CA. Qiao’s research focuses on chromatin remodeling and the establishment of the specificity of gene expression in response to hormones and stressors.

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Max Shpak

Max Shpak’s research has focuses on evolutionary genetics and computational biology. Learn more

Zack Simpson

Marvin Whiteley

The Whiteley Lab uses a multifaceted approach to study two important aspects of infectious disease: chronic infections and polymicrobial infections. By combining gene expression analysis and whole-genome shotgun sequencing, Dr. Whitely is identifying traits that promote chronic infection and common bacterial mutations that promote long-term host colonization. Ongoing studies in Dr. Whiteley’s lab are identifying genes and secreted molecules that enhance polymicrobial synergy, and virulence traits that could be exploited as novel drug targets.

Claus Wilke

The Wilke Lab uses computational biology. Bioinformatical and statistical methods are employed to analyze biological data sets, in particular whole-genome and high-throughput data sets; The Wilke Lab also develops mathematical models and computer simulations of biological systems. While the lab is purely computational, they frequently collaborate with experimental groups. Current research covers three broad but interconnected areas: 1. biophysical mechanisms of molecular evolution; 2. microbial adaptation and experimental evolution; 3. disease dynamics. A recurring theme in the research is evolution; modern biomedical research is deeply connected to evolutionary biology. For example, evolutionary methods are used to track and study infectious diseases such as inuenza or HIV/AIDS. Many vaccines are developed through experimental evolution. Cancer progression is governed by evolutionary dynamics. Patterns of genome evolution can reveal costs and constraints under which cells operate.

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Blerta Xhemalce

Dr. Xhemalce received her Ph.D. at the Pasteur Institute in Paris, France and performed her postdoctoral training at the Gurdon Institute at the University of Cambridge in the United Kingdom. The focus of her research is to unravel how gene expression is regulated by epigenetic modifications of chromatin and RNAs. The ultimate goal of her lab is to discover novel enzymes, writers, or erasers of such modifications that are potential targets for therapeutic drugs that could alleviate human diseases including cancer. To achieve this goal the Xhemalce lab uses a diverse array of approaches, including cellular and molecular biology, biochemistry, next generation sequencing and mass spectrometry.

Christopher Yellman

Research Associate