People

 

Principal Investigator - Josh Stuart

JoshStuart

Josh Stuart
My passion is to develop computational approaches that aid in the discovery of new fundamental biology to enlighten our understanding of evolution, cell fate decisions, and disease mechanisms. I have a particular interest in probablistic approaches that infer and leverage genetic pathway information to ground our analysis in intuition. 

Postdoc Scholar - Hongxu Ding

HongxuDing

Hongxu Ding
My research focuses on developing computational and experimental tools for the analysis of single cells. These interests have led to projects addressing questions ranging from the development of novel algorithm for single cell transcriptional profile analysis to application of these algorithms to explore specific biological questions in cancer, development, and complex diseases, such as diabetes.

Staff

ChrisWong Chris Wong - Staff
I am working on various data visualizations in support of various projects in the lab, including Observation Deck and circle map network graphs for the WCDT prostate cancer team and BMEG project. I also help with the UCSC Genomics Core project developing tools for their genomics data storage and pipelining system.
   
   
RosalynHuffman Rosalyn Huffman - Staff
Executive Assistant to Josh Stuart and Stuart Laboratory Executive Coordinator

Students

Alana Weinstein

Alana Weinstein - PhD Student                                                                   

 

verena2017 Verena Friedl - PhD Candidate                                                                    
I am generally interested in applying and developing machine learning methods and prediction algorithms to improve tumor sample analysis and cancer treatment decisions by using patient sample similarities, multi-omics data, and prior knowledge integration.           
Rojin Safavi- PhD Student                                                                                         
       

henry2017

Henry Gong - Graduate Student                                                                    
I study the genetics of human disease and development, the mid/brain, and evolution using machine learning and genomics approaches.           

IoannisAnastopoulos

Ioannis (Yianni) Anastopoulos - Graduate Student Researcher                                                                   

Lucas Seninge

Lucas Seninge - PhD Student                                                                   

Bianca Xue

Bianca Xue - PhD Student                                                                   

 

Nathan Maulding

Nathan Maulding - PhD Student 
I am interested in building computational tools to capture and model the developmental histories, spatial positions, and environmental interactions of single cells and how they influence the biology of the system as a whole.
                                                                 

 

Alex Pearson

Alex Pearson - MS Student
 I am interested in creating robust and interpretable machine learning models to analyze genomic data, particularly single cell sequencing data.  I am currently developing probabilistic models for annotating single cell ontologies and identifying biomarkers that specify different cell types.
 

                                                                  

 

Alumni

Corey Powell - MS - Statistical Consultant at Center for Statistical Consultation and Research, University of Michigan,                               Ann Arbor, Michigan 

Alex Williams - MS 2009 - currently at Gladstone Institute

Matt Weirauch - PhD - Associate Professor at Cincinnati Childrens Hospital Medical Center, Toronto, Ontario, Canada

Charlie Vaske - PhD - VP Bioinformatics at Claret Bioscience, Santa Cruz, CA 

Martina Koeva - PhD - Associate Principal Scientist, Merck, Cambridge, MA

Pinal Kanabar - MS - Bioinformatics Scientist at Waksman Genomics Core Facility

Sam Boyarsky - MS - Working as a naturalist at Exploring New Horizons Outdoor Schools in Loma Mar.

Chris Wong - MS - Working as staff in the Stuart lab, UCSC, Biomolecular Engineering.

Shyamini Vasili - MS - Software Quality Assurance & Test Engineer, Sunnyvale, California

Cath Penfold - Summer Student from UK

Daniel Sam - graduate student

Robert Shelansky - undergrad - currently PhD candidate at UCSC

Kevin Lam - PhD from UT at Dallas -Advanced Imaging Specialist, Dallas-Fort Worth Metroplex, TX 

Evan Paull - PhD - Senior Bioinformatics Data Scientist at BenevolentAI, Brooklyn, NY

Peter Harris Waltman - Postdoc - Associate Research Scientist at Columbia University Medical Center

Adrian Bivol - MS - Staff Scientist, Bioinformatics at Thermo Fisher Scientific, San Francisco Bay Area

Marcos Woehrmann - PhD - Senior Staff Bioinformatics Scientist, ThermoFisher, San Francisco Bay Area 

Artem Sokolov - PhD - Research Associate, Harvard Medical School, Boston, MA

Daniel Carlin - PhD - Postdoctoral Scholar in the Ideker Lab, Depart of Medicine, University of California, San Diego

Sam Ng - PhD - Working as a Bioinformatics Scientist, Illumina, Inc., Menlo Park, CA

Kiley Graim - PhD - Flatiron Research Fellow, Simons Foundation, NYC, New York.  Effective January 2021, Assistant Professor, Department of Computer Information Science & Engineering (CISE), University of Florida

Yulia Newton - PhD - Bioinformatics Data Scientist at ImmunityBio, LLC, Aptos, CA 

Pablo Sanchez Cordero Gonzalez - Scientist - Hexagon Bio, Menlo Park, CA

Naveed Ziari - PhD Student - UC Berkeley, CA

Duncan McColl - BS - Software Engineer, Unnatural Products, Santa Cruz, CA

Andrew Blair - MS  -  Computational Researcher II at Gladstone Institutes, San Francisco, CA

David Haan - PhD - Bioinformatics Engineer - Bluestar Genomics, San Diego, CA

Vlado Uzunangelov - PhD - Translational Bioinformatics at Bristol-Myers Squibb, Redwood City, CA

Thomas Matthew - PhD - Bioinformatics Scientist, IGM Biosciences, San Jose, CA