SBCP

Systems Biology and Computational Pathology

Departments of Neurosurgery and Translational Molecular Pathology
UT MD Anderson Cancer Center

Striving to be the world leader developing state of the art next-generation digital pathology analytical tools using computational and statistical approaches

The CPP Family

We are a family of students, scientists and programmers at MD Anderson Cancer Center pioneering spatial stochastic processes and its application to high throughput multiplexed immunofluorescence images.

Afrooz Jahedi, Post-Doctoral Researcher

I am a computational pathology postdoctoral fellow at the University of Texas MD Anderson Cancer Center. I received my doctorate in Computational Statistics from the joint doctoral program at San Diego State University and Claremont Graduate University. My dissertation work focused on designing and implementing multiple Random Forest-based algorithms to solve computational challenges in autism research. I also received my first Masters degree in Mathematical Statistics from Shiraz University in Iran and my second Masters in Biostatistics from San Diego State University. My research interests include Machine Learning, Data Mining, and Spatial Analysis. Currently, I am working on developing a spatial pipeline to analyze CODEX images on Glioblastoma.
Anthony Kang, Undergraduate, Rice University

Anthony is a Rice undergraduate currently studying Computational and Applied Mathematics with minors in Biochemistry & Cell Biology and in Data Science. He aspires to become a physician scientist in the future. He is currently creating spatial analysis pipelines that automate the process of generating useful spatial information from data. In his free time, he likes to play golf, sing Italian opera, and hold Zoom calls with his friends.
Prachi Shah, Summer Student, UT Austin

Prachi is a fourth year undergraduate studying Neuroscience at UT Austin. This summer, she is working with Dr. Kannan and Dr. Jahedi to use spatial analysis to study Myelodysplastic Syndrome. Outside of research, Prachi enjoys drawing, dancing, and spending time with her friends.

Prahlad Bhat, High School Intern

My name is Prahlad Bhat and I am a high school intern at MD Anderson Cancer center. I am a rising senior at Carnegie Vanguard High School. My research focus involves utilizing spatial models and spatial functions to quantify dynamic cell behavior and answer a variety of questions about the Tumor Microenvironments of Clear Cell Renal Cell Carcinomas. On my free time, I love playing basketball, coding and playing video games.
Anvi Garyali, High School Summer Student

Hi, I am Anvi Garyali. Currently, I am a rising junior at Dulles High School’s Math and Science Academy. I am interested in precision medicine platforms powered by computational modelling to predict tumor patterns. I plan to use Spatial analysis and R- programming with special references to Myelodysplastic syndrome (MDS) to better prognosticate tumors.

Scope

A major goal of this program is applying statistical and computational principles to high-throughput multiplexed immunofluorescence images. We perform data analysis and analytics for elucidating and predicting biological and clinical variables that underlie different cancer types and mechanisms. Click here for several examples. Our specific mission is as follows.

Discover

physiological, pathological and immunological patterns obtained through statistical and computational analyses of digital images

Integrate

image analysis with cancer relevant clinical, biological, radiological and drug response features with the goal of redefining cancer from personalized and precision medicine perspectives

Ensure

best practices including standardized reports, visualization, data interpretation and data privacy in delivering results to CPP project initiators

Educate

and consult on available analysis options. Identify new projects and research opportunities with direct clinical utility

Train

future research pathologists for data-driven decision-making

Identify

funding opportunities for long term scientific success of the CPP

Opportunities

We have an open Research Scientist position in Computational Pathology Program at MD Anderson Cancer Center. Here is the summary. If you feel you meet the qualifications and would like to apply, feel free to contact me at kskannan at mdanderson dot org. Or please pass it to your friends whom you think might be interested.

Position Summary

The newly established Computational Pathology Program at Translational Molecular Pathology at the University of Texas MD Anderson Cancer Center is seeking a Research Scientist programmer to join the team. The primary purpose of the Research Scientist will be to help perform cutting-edge research and development interfacing with our scientists and clinicians by developing computational pathology solutions. We invite a highly motivated and independent-thinking individual who will work on spatial image analysis of immunohistochemistry (IHC) assays and develops research projects using multiplexed technologies.

Preferred Experience

4+ years of research and programming experience (preferred)
Experience in biostatistics and/or computational modeling (preferred)
Knowledge of high-performance computing (preferred)
Experience in web application, data visualization, and modeling
Knowledge of geospatial tools and algorithms, such as spatstat (preferred)

job application

Manuscripts

Clinton Yam, Er-Yen Yen, Jeffrey Chang, Roland Bassett, Gheath Al-Atrash, Haven Garber, Lei Huo, Fei Yang, Anne Philips, Qingqing Ding, Bora Lim, Naoto Ueno, Kasthuri Kannan, Xiangjie Sun, Baohua Sun, Edwin Parra, W. Fraser Symmans, Jason White, Elizabeth Ravenberg, Sahil Seth, Jennifer Guerriero, Gaiane Rauch, Senthilkumar Damodaran, Jennifer Litton, Jennifer Wargo, Gabriel Hortobagyi, Andrew Futreal, Ignacio Wistuba, Ryan Sun, Stacy Moulder-Thompson, and Elizabeth Mittendorf. Immune Phenotype and Response to Neoadjuvant Therapy in Triple-Negative Breast Cancer. Clinical Cancer Research, July 2021.

Xiangjie Sun, Jie Zhai, Baohua Sun, Edwin Roger Parra, Mei Jiang, Wencai Ma, Jing (2) Wang, Anthony Kang, Kasthuri Kannan, Renganayaki Pandurengan, Shanyu Zhang, Luisa Maren Solis Soto, Cara Haymaker, Maria Gabriela Raso, Julia Mendoza Perze, Aysegul Sahin, Ignacio Wistuba, Clinton Yam, Jennifer Litton, and Fei Yang. Effector Memory Cytotoxic T cell CD3+/CD8+/CD45RO+ predicts good survival with less risk to recurrence in Triple Negative Breast Cancer. Modern Pathology (provisionally accepted).