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Welcome to the Oncinfo Lab!


Oncinfo is a research lab at the University of Texas Health Science Center at San Antonio . The focus of our projects is on bioinformatics and computational biology. We develop and apply sophisticated machine learning algorithms to analyze large biological, or clinical, data sets. From these complex data, our goal is to infer useful information which provides insight into biology, or leads to clinical applications. Oncinfo contributes to neuroscience through collaboration with The Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases. Also, several cancer research projects are defined in collaboration with the Department of Cell Systems and Anatomy. Our external collaboration include the British Columbia Cancer Agency, which has a great research reputation in oncology around the world. Oncinfo welcomes further collaborators from related disciplines such as medicine, molecular and cellular biology, pharmacology, computer science, and statistics. We are particularly interested in collaboration with R&D departments of top pharmaceutical companies.


List of projects

Current and former lab members

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Photos: Lost Maples 2019, Cave 2017

  1. Dr. Habil Zare (the PI, CV, lab notebook)
  2. Shuvabrata Saha (graduate student, left in 2014)
  3. Rupesh Agrahari (graduate student, graduated in 2016, Update: Software Developer at Crossvale Inc in Dallas)
  4. Dr. Amir Foroushani (Postdoctoral Associate until 2016, Update: Computer Scientist at Laboratory of Immunology, NIAID, NIH)
  5. Vignesh Kuppa (volunteer graduate student, left in 2015)
  6. Jessica Zavadil (MD/PhD student in Dr. Christi Walter's lab at UTHSCSA, graduated in 2016)
  7. Aamir Zainulabadeen (Visiting undergraduate student in summers 2016 and 2017 from Princeton University)
  8. Philip Yao (Visiting undergraduate student in summer 2016 from the University of Michigan, software engineer at Amazon)
  9. Hanie Samimi (graduate student, graduated in 2018. Update: PhD student at Texas State University)
  10. Bryan Shaw (graduate student, left in 2017)
  11. Gabriel Hurtado (undergraduate student 2016-2017)
  12. Allison Yang (2017 Summer Camp high school student)
  13. Angela Zhang (2017 Summer Camp high school student)
  14. Shilpita Mitra-Behura (2017 Summer Camp high school student)
  15. Ghazal Ebrahimi (Volunteer undergraduate student from Sharif University since 2018)
  16. Dr. Isha Mehta (Postdoctoral Associate, since 2019)
  17. Dr. Meghan Short (Postdoc Associate since 2019)
  18. Shiva Kazempour (Visiting Scientist since 2019).
  19. Dr. Raheleh Roudi (Visiting Scientist since 2020).
skype-20200721-085353.jpegTo help flatten the COVID-19 curve, we have been working from home since mid March 2020. This is the full list of the things we do to increase efficiency and to maintain mental health when working from home.

skype-20200721-085353.jpegTo help flatten the COVID-19 curve, we have been working from home since mid March 2020. This is the full list of the things we do to increase efficiency and to maintain mental health when working from home..



Open positions

Research assistantship and postdoctoral opportunities are available in the Oncinfo Lab. See the 2018 [pdf] and 2019 [pdf ] advertisements for more details on the postdoctoral position, and also if you are interested in joining the lab as a graduate student. PhD applicants must be strong in machine learning and knowledgeable in molecular biology to be successful in multidisciplinary research as illustrated in our exemplar papers. Even if the application deadline is passed, strong applicants with a masters degree may start immediately as a visiting scientist with possibility of joining the PhD program within a year. There are also some opportunities to apply for postdoctoral fellowship awards. Taking an R test is essential in the interview process.


Computational resources

To run our in silico experiments, we use several resources provided by The Texas Advanced Computing Center (TACC) e.g., Lonestar , which is a computing system with over 30,00 cores, and Stampede, which is one of the 10 top supercomputers in the world with 10 petaFLOPS dedicated to scientific research. Secure HEPA compliant resources at TACC include Hikari, which has 10K cores and is connected to Corral with a capacity of 15 PBs. We have also access to NSF-supported ​XSEDE recourses including Jetstream.


Educational services

- The “Bioinformatics for biologist workshop” is a practical introduction to some basic bioinformatics tools for audience with little computational skills. Slides are available from the workshop page. Additional resources are listed at “How to begin learning bioinformatics?”

- The Slides for Habil's hands-on workshop in the 2019 Neurepiomics Course.

How to

Please feel free to use and contribute to our How to page, which is a list of miscellaneous solutions for data analysis and other challenges in computational biology.

For members


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