People

Principal Investigator

EDWARD MARCOTTE

Office: MBB 3.148BA Phone: (512)471-5435 Fax: (512)232-3472

Affiliations
Center for Systems and Synthetic Biology
Department of Molecular Biosciences
Institute for Cellular & Molecular Biology (ICMB)

Zack (in a category by himself!)

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ZACK BOOTH SIMPSON Office: occasionally MBB 3.148 Fellow, Artist in residence; Center for Systems and Synthetic Biology Personal Pages: http://www.mine-control.com/zack/ and http://www.mine-control.com/ Hear about Zack on the Studio360 radio show (full link) or read about him in Science magazine. Zack's latest project is Appsoma, an open environment for scientific cloud computing.

Research scientists, associates, and fellows

ANGELA M. BARDO Office: MBB 3.128B Postdoc Microscopy Core Facility Director, University of Texas at Austin Postdoc Optical Technology Div. NIST Ph.D. (Analytical Chemistry) Kansas State University B.S. (Chemistry) Truman State University

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ANNA BATTENHOUSE Office: MBB 3.106 Commercial Software Developer B.S. Biochemistry, University of Texas B.A. English Literature, Carleton College My Roles: Associate Research Scientist, Edward Marcotte lab Manager, Biomedical Research Support Facility (BRCF) - https://cloud.wikis.utexas.edu/wiki/spaces/RCTFusers Member, Bioinformatics Consulting Group (BCG) - https://site.research.utexas.edu/cbrs/cores/cbb/bioinformatics-services/ Workshop instructor, Center for Biomedical Research Support (CBRS) - https://site.research.utexas.edu/cbrs/classes/ After a long career in professional software development at Texas Instruments, Motorola, and other companies, Anna began her “retirement career” at UT Austin in 2007 in the Functional Genomics lab of Vishwanath Iyer, co-inventor of Microarray technology. At that time Dr. Iyer was one of the first UT researchers to experiment with high-throughput Next-Generation Sequencing (NGS). Anna was fortunate to be part of the first wave in this then-new technology and has acquired extensive experience in NGS over the years. Today she assists Marcotte lab members with NGS analysis, performs fee-based bioinformatics analyses for UT researchers in UT’s Bioinformatics Consulting Group, and teaches a number of workshops on NGS and other topics for training offerings in the Center for Biomedical Research Support. Anna also helped found, and now manages, the Biomedical Research Support Facility (BRCF), which provisions small compute clusters that provide a standard hardware, software and storage architecture suitable for small-scale, interactive research computing, that can be efficiently managed; where her role requires a unique combination of skills in systems administration, programming, project management, problem troubleshooting, and customer communication, as well as bioinformatics/biology knowledge. In her (limited) free time, Anna loves to read widely, travel with her husband John Kolts, play contract bridge, and take walks with their beloved Shih Tzu, Lola.

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OPHELIA PAPOULAS Office: MBB 3.148B Postdoc Stanford University Postdoc University of California at Santa Cruz Ph.D. (Cell and Developmental Biology) Harvard University, Division of Medical Sciences B.A. Wesleyan University I love proteins. Trained in protein purification and transcriptional biochemistry (with Robert E. Kingston), studied chromatin remodeling complexes in Drosophila with Welcome Bender, Matthew P. Scott, and John Tamkun, and the role of Golgi and membrane dynamics in the mid blastula transition with John C. Sisson. Currently I’m using mass-spectrometry based methods to characterize proteins in diverse organisms to understand commonalities and reveal functions. Fun methods include Co-fractionation Mass Spectrometry to identify novel protein complexes, and Crosslinking Mass Spectrometry to characterize protein and protein complex structures.

JAGANNATH SWAMINATHAN Office: MBB 3.128B Postdoc The University of Texas at Austin Ph.D. The University of Texas at Austin

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MADELYN SZILAGYI Office: MBB 3.128B B.S. Biology, Case Western Reserve University Madelyn is part of the Army Research Laboratory’s southern outpost at UT Austin and studies microbial communities, primarily through next-generation sequencing and bioinformatics. She is excited to be back in the Marcotte lab, having worked here one summer as an undergraduate. When not in the lab, she enjoys sewing, playing video and board games, reading, and spending time with friends and family.

Postdoctoral fellows

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NAYELI G. REYES-NAVA Office: PAT 216 Ph.D. Biosciences, University of Texas at El Paso B.S. Biology, Universidad Autónoma de Ciudad Juárez, México Nayeli is a joint postdoctoral fellow in the Marcotte and Wallingford labs. As a graduate student, she developed a deep interest in developmental biology and proteomics, which led her to UT. Her current research focuses on investigating rare genetic disorders that disrupt cilia—tiny hair-like cellular structures essential for development and health. She combines cell and molecular biology with proteomics to uncover the mechanisms underlying ciliopathies. Outside the lab, she enjoys tending to her plants and exploring Austin with her 4-pound Yorkie sidekick, Chewbacca.

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BIJUN TANG Office: MBB 3.128AB Ph.D. Department of Biochemistry, Sainsbury Laboratory, University of Cambridge, UK M.Phil. Biochemistry, University of Cambridge, UK B.A. Natural Science, University of Cambridge, UK Bijun is a postdoctoral fellow co-advised in the Ellington Lab. She is passionate about leveraging computational tools for the de novo design of protein structures and functions. Her research focuses on integrating computational modeling with cell biology techniques to explore innovative approaches for therapeutic development. Previously, Bijun worked on developing biosensors for plant phytohormones, enhancing spatiotemporal resolution to study host responses to biotic stress in vivo. Outside the lab, she can be found swinging a racket in any sport, getting lost in deep philosophical musings, or playing music just for the joy of it.

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VY DANG Office: MBB 3.128AB Ph.D. Biochemistry, University of Texas at Austin B.S. Biochemistry & Microbiology, University of Washington, Seattle Vy embarked on her journey of joining the dark side of proteomics since 2019. Her passion for comparative genomics significantly shapes her research focus, particularly her major thesis project—constructing a comprehensive protein-protein interaction map in the vertebrate brain. Vy is actively investigating innovative methodologies and techniques to enhance the study of protein-protein interactions in general. Outside the lab, Vy is a full-time procrastinating baker and a part-time collector of things.

Graduate students

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BRITTNEY VOIGT Office: MBB 3.128A B.S.A. Biology, University of Texas at Austin B.S. Nutritional Sciences, University of Texas at Austin Co-advised in the Gray Lab, Brittney is interested in musculoskeletal development and disorders. She uses zebrafish genetics, quantitative image analysis, and molecular biology to understand the role of inppl1a in notochord, spine, and endochondral bone development, with the hopes of better understanding scoliosis and short stature disorders. When she’s not in the lab, she enjoys baking sourdough bread, spending time with her family, and taking her dog, Banjo, on walks around Austin with her husband.

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MUYOUNG LEE Office: MBB 3.128A M.S. Biotechnology, Yonsei University B.S. Biochemistry, Yonsei University Co-advised by Dr. Jonghwan Kim. Muyoung is interested in applying bioinformatics approaches to answer interesting biological questions. At UT, he’s been working on some projects, including ‘Finding new modes of gene regulation using protein domains’ and ‘Mapping of TF-mediated cell fate changes.’ Outside the lab, he enjoys taking a stroll while listening to music/pod decasts and being absorbed in good stories from books, movies, video games, etc.

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TYNAN GARDNER Office: MBB 3.128B B.A. Molecular Biology, Princeton University Co-advised in the Wallingford Lab, Tynan uses proteomic, computational, and cell biological techniques to study protein complexes and genetic diseases. Before grad school, he studied synthetic biology in yeast and stem cell niche development in Drosophila. Outside the lab, he enjoys backpacking, cooking, and making music. Check out his lab assistant @mochi.pbp on Instagram.

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JUJU DESSERT Office: MBB 3.128B B.S. Entomology, University of Wisconsin, Madison Hi, I'm Juju. I discovered my love for bugs in the Amazon rainforest at the Tiputini Biodiversity Reserve in Ecuador. After graduating, I spent some time exploring RNA biology, which led me to pursue a PhD in Molecular Biology. I'm thrilled that my current research has brought me back to my entomological roots. I currently study proteomics in the leafcutter ant-fungus symbiosis, investigating the enzymes responsible for plant biomass degradation. If I'm not in the lab, I'm probably playing tennis.

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VICKI DENG Office: MBB 3.128AB B.A. Biochemistry and Molecular Biology, Reed College Inspired by the diverse coastal ecosystems of San Francisco that first sparked her love for biology, Vicki is a scientist driven by the wonders of the natural world. Her research journey has spanned studying cytoskeletal dynamics in Drosophila, toxin-antitoxin systems in Caulobacter crescentus, and the origins of multicellularity and cell-state switching in choanoflagellates. For her PhD, she is exploring the molecular mechanisms behind the bizarre biology of an algae considered the world’s largest single-celled organism. Outside the lab, Vicki enjoys biking, climbing, and painting. Every so often, she trades pipettes for paintbrushes, setting up her art booth at local Austin markets.

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CLAYTON KOSONOCKY Office: MBB 3.128B B.S. Chemical & Biological Engineering, The University of Colorado Clay’s thesis project focuses on developing AI models that use words to discover drugs. Clay is the co-founder of the BioML Society at UT Austin, through which he ran a world-wide protein design competition (featured in Nature) and a seminar series on Biology & Machine Learning that has become an official UT course. Outside of research Clay enjoys bouldering, surfing or skiing when near the various phases of water, and reading books. His favorites include The Brothers Karamazov, The Beginning of Infinity, and The Lord of the Rings.

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ZOYA ANSARI Office: MBB 3.128B BS Biochemistry, University of California, San Diego Zoya is interested in the role of evolution in protein structure and function. Her research is split into a mix of computation and molecular biology, with projects consisting of characterizing novel proteins found from the bottom of the ocean and elucidating gene-phenotype relationships between diverse organisms. In her free time she enjoys reading fiction, swimming, and exploring the Austin music scene.

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ALIA CLARK-ELSAYED Office: MBB 3.128B BA Molecular, Cellular and Developmental Biology, University of Colorado Alia is passionate about protein engineering, specifically in designing transcription factors for detecting steroid hormones. She enjoys integrating computational tools into her engineering projects, combining data-driven modeling with experimental validation. She is particularly interested in engineering proteins with novel functions to address real-world challenges. Through her research, she aims to expand the capabilities of synthetic biology for applications in health and environmental monitoring.

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UJWAL PUNYAMURTULA Office: MBB 3.128AB B.Sc. Biology, Brown University M.Sc. Biotechnology, Brown University Ujwal is interested in all things proteomics and mass spectrometry, especially applied in the context of cell biology and human disease. Currently, he is using quantitative mass spectrometry to characterize the regulatory proteome governing trophoblast differentiation, a critical event in placental development. When he’s not in the lab, Ujwal is either reading science fiction/fantasy series such as The Stormlight Archive, spending time with family and friends, or playing video games (his current obsession is Final Fantasy).

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BAHAR KASGARI Office: MBB 3.128B B.S. Biotechnology, University of Tehran Co-advised in the Wilke Lab, Bahar is interested in using protein language models to study the evolution of proteins, such as antimicrobial peptides and microcins to find long lost cousins of their family. Outside of school she is a newbie standup comedian, improviser and performer.

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ISA MADRIGAL HARRISON Office: MBB 3.128A isa!

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GABRIEL HOOGERBRUGGE Office: MBB 3.128AB gabe!