Bioinformatics

Department Milestones

2023

  • Our faculty body grows with the promotion of Bo-Jui Chang, Tadamoto Isogai, and Benjamin Nanes to Assistant Professor positions. To the ultimate end goal of probing the role of morphology in cancer metastasis, Dr. Chang brings expertise in bio-imaging with specialization in light-sheet microscopy (LSM) and super-resolution structured illumination microscopy (SIM), Dr. Isogai brings expertise in molecular signal amplifications within cellular organelles in 3D microenvironments, and Dr. Nanes brings his expertise in molecular circuits controlling the critical stability/plasticity balance and how disruption of these signaling networks contributes to disease.
  • The June 2023 Discovery Engine Program grant is awarded to James McCormick, PhD (Reynolds Lab) for his proposal A Bright Future: introducing light-based allosteric control to cytochrome p450.
  • Four of our faculty, Dr. Reynolds, Dr. Lin, Dr. Kim, and Dr. Saunders launch a Biosynthetic Pathway Design Collaborative. Moving beyond the creation of a few bespoke pathways by a handful of well-resourced laboratories requires new approaches for accelerated programmatic engineering of biosynthesis. Together, this collaborative aims to develop predictive computational tools and “design rules” that can limit the space of possible variants that must be explored. By coupling advances in the basic science of bacterial physiology with new tools in deep learning, cell simulation, and bacterial genetics, the end goal is to transform the process of cellular engineering.
  • Kevin Dean awarded the Distinguished Researcher Award from the President's Research Council at UT Southwestern at a dinner reception held on May 2, 2023.
  • The departmental Discovery Engine Program inaugural grant for March 2023 is awarded to Muhammed Sadik Yildiz, PhD (Toprak Lab) for his proposal Developing platelet profiling-based diagnosis tools for Alzheimer's Disease.

2022

  • In collaboration with the Peter O'Donnell Jr. Brain Institute, the Department launches a virtual global Journal Club to highlight the first authors of cutting edge publications in neuroinformatics. Visit our website U-Hack Med NeuroChats. 
  • The UTSW-UNC Center for Cell Signaling Analyses is established from an NIH RM1 grant to Gaudenz Danuser, Kevin Dean, and Klaus Hahn (UNC Chapel Hill). The goal of the center is to comprehensively develop and disseminate imaging technology and computational pipelines for the study of cellular signal transduction.
  • The Green Center for Systems Biology is featured at the Biophysical Society annual meeting. Watch the video here.
  • Scott Saunders is recruited from Caltech as our second UTSW Distinguished Fellow. Scott develops innovative CRISPR-based technology to probe with high efficiency genetic interactions in bacterial circuits.

2021

  • Wenhao Zhang is recruited as the first tenure track Assistant Professor with a joint appointment between Bioinformatics and the O'Donnell Brain Institute. He is a recipient of an UTSW Endowed Scholars award. Zhang completed his Ph.D. in Theoretical and Computational Neuroscience from the Institute of Neuroscience, Chinese Academic of Sciences and then received his postdoctoral training in the labs of Drs Tai Sing Lee and Brent Doiron at Carnegie Mellon University and University of Chicago, respectively. Zhang's research is in the mathematical modeling of brain circuitry. We are particularly excited about his plans of marrying human brain circuit models with designs of artificial neural networks.
  • A Center for Metastasis Tumor Imaging is established from an NIH NCI CCBIR grant to Gaudenz Danuser, Kevin Dean, and Reto Fiolka with Sean Morrison (CRI-UTSW), Peter Sorger (HMS), and James Amatruda (CHLA/USC). The goal of the center is to develop and disseminate innovative technology for the quantitative analysis cellular processes that enable metastatic colonization.
  • Jian Zhou, tenure track Assistant Professor in the Department since November 2019 (recruited with a CPRIT Scholar and an Endowed Scholar package), receives a New Innovator Award from NIH Director's Office. The goal of the project is to develop deep learning models that can translate genomic sequences into 3D chromatin structure. Ability to do so will be transformative for our understanding of the effects genomic variation on the gene transcription regulation.
  • After six years of providing data science services to UTSW's community, the Bioinformatics Core Facility closes its doors. Our rich interactions with the campus are more efficiently channeled through bidirectional collaborations rather than service. The most popular elements of the former Core's outreach programs, i.e. help desk consultations and Nanocourses, continue under the CTSA Informatics Coordination Office and as a departmental education initiative, respectively.
  • Bo Li becomes the co-founder of Serum Inc. The company is dedicated to scaling up Bo's early cancer detection pipeline described in an article in Science Translational Medicine. This is the first direct spin-off by the Department.
  • The former Cecil H. and Ida Green Comprehensive Center for Molecular, Computational, and Systems Biology, now Cecil H. and Ida Green Center for Systems Biology joins the Department as a 'little c' center. The joining of forces between bioinformatics and systems biology faculty provides exciting opportunities for synergizing computational and experimental approaches for the study of complex biological systems. The goal of the center remains to develop a 'circuit theory' of biology. However, we narrow this broader agenda on two specific areas in need of advanced circuit theories: non-genetic mechanisms of cancer metastasis and bacterial regulation and resistance. The existing faculty members, Kim Reynolds, Milo Lin and Erdal Toprak are joined by Reto Fiolka, Kevin Dean, and Gaudenz Danuser, who are developing a cancer cell imaging program; and by Daehwan Kim, who is developing L++ as a programming language that will eventually translate biological circuitry into genetic programs for engineering organisms. The new center will be housed in the old space on ND11, renovated for the needs of the new labs.

2020

  • Because of the COVID-19 pandemic, the department hosts a U-Hack Med Gap year for the U-Hack Med Hackathon Series where students from across the nation worked on computational solutions to Biomedical problems virtually.
  • Jun Suk Park receives the Nominata Award, the highest honor for academic and research accomplishment bestowed by the graduate school to an advanced graduate student. Read more: https://www.utsouthwestern.edu/labs/danuser/news/may2020-news.html.
  • Andrew Jamieson and Mike Holcomb join a team under the direction of Dr. Trish Perl to develop a COVID-19 forecast model. In the following months and years the model is used by the institutional leadership for strategic decisions and to inform the public on the state of the pandemic in North Texas.
  • The COVID-19 pandemic closes our labs. For more than 2 years our teams work at least partially remote.

2019

  • The second U-Hack Med was focused on computational solutions for clinical medicine and genomics and brought together developers, engineers and researchers at all career levels. Read about the outcomes and details in this UTSW News article and video.

2018

  • In the First Biomedical Hackathon at UT Southwestern, the Lyda Hill Department of Bioinformatics, together with community partners including the NIH's National Center for Biotechnology Information, Mark III Systems and the Cancer Prevention and Research Institute of Texas, brought together local and national computer science talent with the UT Southwestern community to produce prototype solutions for complex data analytical problems. Over two days, clinicians and biomedical researchers joined software developers, data analysts, and mathematicians to tackle projects ranging from artificial intelligence for predicting genetic changes in tumors to ways to crunch through large data sets to identify the risk of pediatric critical care therapy to induce long-term neurological injury. Other investigators took on the challenges of creating tools to identify variations in genetic codes and molecular structures, and a natural language processing tool to determine variations in genes for inclusion in clinical trials. Read our Outcomes Report and our Article.

 2017

  • The Department's First four tenure-track faculty recruits:
    • Satwik Rajaram joins the Department as the first of three tenure track Assistant Professors we recruit as our inaugural faculty cluster. He has a joint appointment between the Departments of Bioinformatics and Pathology. Rajaram received his Ph.D. from the University of Illinois at Urbana-Champaign in statistical physics and then worked in the joint research program of Drs. Steven Altschuler and Lani Wu at the University of California, San Francisco. Rajaram seeks to understand the origins and impact of cellular heterogeneity on tissue organization in cancer through machine learning and quantitative molecular biology.
    • Daehwan Kim joins the Department as the second of three tenure track Assistant Professors we recruit as our inaugural faculty cluster. He is appointed as a CPRIT Scholar and as a recipient of a UTSW Endowed Scholars award. After receiving his Ph.D. in Computer Science at the University of Maryland, Kim served as a postdoctoral research fellow at the Johns Hopkins University Center for Computational Biology. Both trainings were with Steven Salzberg. Kim's research is focused on development of algorithms and software to rapidly and accurately analyze data generated by high-throughput next generation sequencers.
    • Bo Li joins the Department as the third of three tenure track Assistant Professors we recruit as our inaugural faculty cluster. He is the recipient of a CPRIT Scholar award and has secondary appointment in the Department of Immunology. Li received his Ph.D. in Bioinformatics at the University of Michigan at Ann Arbor, then completed a postdoctoral research fellowship with joint training in the labs of Dr. Xiaole Shirley Liu at Dana-Farber Cancer Institute and Dr. Jun S. Liu at the Harvard School of Public Health. Li's research is in cancer genomics and immunology with a focus on understanding immune evasive pathways and developing prognostic biomarkers for cancer immunotherapies..  
    • The Department welcomes Albert Montillo as the fourth tenure track Assistant Professor with secondary appointments in the Department of Radiology and the Advanced Imaging Research Center. Montillo received his Ph.D. in Computer Science from the University of Pennsylvania. Prior to joining UTSW, Montillo led neuroimaging research efforts at the General Electric Research Center in New York. The focus of Montillo's research is advancing the theory and application of deep learning and developing de novo machine learning algorithms that have both clinical and neuroscience applications.
  • staff listening to lecture in new bioinformatics department facility 
    The Department moves into a newly constructed facility on south campus. With the Library's progression to a digital-only resource center, space became available for a new academic department. The E4 area was transformed using an innovative concept in work space design for UT Southwestern. The overall design is inspired by Piet Mondrian's works, with bright color blocks, open workspaces to promote collaboration, and smaller "huddle rooms" for more focused team discussions. The space also features lithograph prints of minerals from the Lyda Hill Gems and Minerals collection at the Perot Museum of Nature and Science.

 2016

  • The Department broadly announces targeted faculty searches in the areas of single-cell genomics and tissue morphogenesis, and an open search in all areas of applied and foundational computer science. 
  • Recruitment of Murat Can Cobanoglu from Carnegie Mellon University as the first UT Southwestern Distinguished Fellow, a new type of faculty position created to accelerate the path to independence for fresh Ph.D. graduates.

 2015

  • Integration of BioHPC (biomedical high performance computing) infrastructure with the Department, to serve the scientific computing needs of UT Southwestern departments and centers. 
  • Official opening of the Lyda Hill Department of Bioinformatics with the Danuser lab as the first research unit.
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    In the News 
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  • Danuser accepts offer to serve as the founding chairman.
  • Danuser receives a $5.6 Million grant from the Cancer Prevention Research Institute of Texas to launch the Bioinformatics Core Facility as a campus-wide service infrastructure for bioinformatics.

2014

Deans Fitz and Russell agree with Danuser on the vision and implementation plan for a Department of Bioinformatics that is in essence structured as a computer science department in an academic medical center.