Lab members

 

 

Gabi Fragiadakis, PhD

Gabi is an Assistant Professor in the Division of Rheumatology, and faculty member of ImmunoX, Benioff Center for Microbiome Medicine (BCMM), and the Bakar Computational Health Sciences Institute (BCHSI). She has expertise in computational immunology, single-cell analysis, and the microbiome. Her lab's research focus is understanding human immune states using single-cell methods across disease contexts including viral infection and autoimmunity. She's a firm believer in the power of team science and leads the UCSF Data Library project. 

 

 

Chris Andersen, BS

Chris is a biological data scientist in the CoLabs postbac program. He graduated from the University of Puget Sound in 2020 where he studied Molecular & Cellular Biology and Mathematics. Currently, he is working with the Roose lab to analyze singele-cell RNA sequencing data of human organoids spanning several cancer indications. The aims of this project are to assess the robustness of organoids as a model system and to improve immunotherapeutic approaches for cancer patients.

 

 

 

Saurabh Asthana, PhD

Saurabh is a data scientist and software engineer. He initiated the Data Library project and continues to participate in its design and development. He received his PhD in Biomedical Sciences from Harvard Medical School, focusing on evolutionary biology and genetics. His current research interests include cancer, immunology and their intersection, often studied through the lens of the human transcriptome.

 

 

 

 

Dan Bunis, PhD

Dan is a Data Scientist in the lab who also works with the UCSF Data Library development team. He did his PhD in Biomedical Sciences at UCSF, in which he gained experience with transcritomics data, and with developing tools to help visualize and analyze these data. His current research projects involve using various single cell-resolution assays to study immune correlates of in-utero infection and pre-term birth, while his Data Library development work focuses on improving data analysis and data exploration capabilities of the library.

 

 

 

Nicholas Carey, BA

Nicholas is a Biomedical Sciences graduate student in Dr. Fragiadakis and Dr. Jody Baron's labs. He graduated from the University of California, Berkeley in 2020 where he studied Molecular & Cell Biology and Statistics. He has experience in computational immunology and single cell analysis utlizing technologies including single cell RNA sequencing and spectral flow cytometry. His research is focused on using animal models to understand immune-mediated mechanisms underlying control versus persistence of hepatitis B virus infection.

 

 

 

Zach Collins, BS

Zach is a software engineer in the Data Science Colab. He has been programming professionally for approaching 20 years in numerous fields, including OCR and image processing, secure networking, payments processing and finance, gaming, hospitality, sales engineering, and SaaS technologies. He is working hard to build out robust technological tooling that helps enable large audiences of data scientists to explore, organize, transform, and store biological data in the Data Library project.

 

 

 

Emily Flynn, PhD

Emily is a Data Scientist in the Data Science CoLab. Emily has a PhD in Biomedical Informatics from Stanford, with expertise in analyzing genetic and transcriptomic data. Now, Emily's research focuses on using transcriptomic (both bulk and single-cell) and epigenomic analysis to better understand autoimmune disease. Emily also has a particular interest in public data and integrative analysis.

 

 

Rebecca Jaszczak, PhD

Rebecca is a Data Scientist in the Data Science Colab. She did her PhD in Biomedical Sciences at UCSF, with experience in transcriptomic data. Her current research includes using computational immunology and single cell approaches to characterize similarities and differences between mouse and human tumor immunology.

 

 

 

 

 

Ravi Patel, PhD

Ravi is a Data Scientist in the Data Science CoLab. He has a background in computational biology and molecular biology and a PhD in Genetics from Cornell University. He has expertise in single-omic and multi-omics analysis of single-cell genomic, proteomic, metabolomic, metagenomic and survey datasets. His current research focuses on interogating cross-talk between the healthy immune system and the gut microbiome, and on studing COVID-19 severity. He also enjoys teaching.

 

 

 

 

Arjun Rao, PhD

Arjun is a senior Computational Immunologist in the Data Science Colab. He graduated from UCSC with a PhD in Bioinformatics and Computational Biology, with a thesis describing a novel end-to-end pipeline for the prediction of T-Cell epitopes in human tumors from clinical sequencing. He has over a decade of experience handling all types of sequencing data across multiple platforms. His research interests lie in the development of new algorithms to analyze complex, large-scale immunological datasets. He is currently researching the genetic basis for viral clearance or persistence in patients with chronic Hepatits B who have been withdrawn from long-term antiviral therapeutics.

 

 

Bushra Samad, MS

Bushra is a Data Scientist and the Data Librarian for the UCSF Data Library. She has experience in computational biology, cancer genomics and acquisition and curation of clinical data. Her current research focuses on understanding the role of the tumor microenvironment and defining tumor immune archetypes in cancer. As Data librarian she has laid the foundation and articulated the vision of the Data Library and manages the priorities and goals of the Data Library Engineers

 

 

 

Cole Shaw, MS

Cole is a Senior Software Engineer working on the UCSF Data Library project. He has experience building research software and data warehousing applications in a variety of environments. At UCSF, Cole builds tools that automate data processing and that enable researchers to query and analyze data.

 

 

 

Urmila Venkataramani, BS

Urmila is a data scientist in the CoLab postbac program. She graduated from USC in 2020 with a degree in biological sciences and a focus on computer programming. She is currently collaborating on several different projects mainly involving the analysis of single cell RNA sequencing data.