Welcome to Oncinfo Lab!

Oncinfo is a research lab in Texas State University. 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 has active collaboration British Columbia Cancer Agency, which has a great research reputation in oncology around the world. Also, several projects are defined in collaboration with the Department of Cell Systems and Anatomy at University of Texas Health Science Center in San Antonio. Oncinfo welcomes further collaborators from related disciplines such as medicine, molecular and cellular biology, pharmacology, computer science, and statistics.We are interested in collaboration with R&D departments of top pharmaceutical companies s such as Novartis and Pfizer.

List of projects

  1. Gene networks inference
  2. Clonal decomposition
  3. Hepatocellular carcinoma
  4. Molecular mechanisms of Alzheimer's disease
  5. Genome evolution

cave2017.jpgCave 2017

Lab members

  1. Dr. Habil Zare (the PI, 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. 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)
  9. Hanie Samimi (graduate student)
  10. Bryan Shaw (graduate student)
  11. Gabriel Hurtado (undergraduate student)
  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 (Visiting undergraduate student from Sharif University in summer 2018)

Open positions

Research assistantship and postdoctoral opportunities are available in Oncinfo Lab. See this advertisement for more details on the postdoctoral position [pdf]. There are also some opportunities to apply for postdoctoral fellowship awards. See this one if you are interested in joining the lab as a graduate student. Also, Research Experiences for Undergraduates (REU) opportunities are available.Taking an R test is essential in the interview process.

Computational resources

To run our in silico experiments, we use Stampede, which is one of the 10 top supercomputers in the world with 10 petaFLOPS dedicated to scientific research [user guide].

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?"

For members