Past BD2K Scholars
The NIH BD2K Summer UP was a summer research program for CSUMB students at the Center for Big Data in Translational Genomics at UC Santa Cruz. The center works to help the biomedical community use genomic information to better understand human health and disease. Visiting CSUMB students spent the summer working side-by-side with UCSC scientists and data specialists, learning research skills to manage and interpret genomic data. Students will participate in professional development, on-campus activities, and seminars throughout the summer in addition to gaining valuable research experience.
The Summer Research Program portion of the BD2K program ended August 2020.
Students completed 8-weeks of research remotely with researchers at both UCSC and CSUMB during the summer of 2020.
Nicholas Vasquez
Major: Statistics
UCSC Mentor: Ash O’Farrell UCSC Computational Genomics Platform, Bioinformatics Systems Analyst
Project: Building Containerized Workflows in Bioinformatics
Scholars completed 8 weeks of research at UCSC during the summer of 2019
Austin Diaz
Major: Mathematics (Statistics)
Minor: Computer Science
UCSC Mentor: Abel Rodriguez Professor of Statistics and Associate Dean for Graduate Affairs, Baskin School of Engineering
Project: Interfacing C++ with R to Build an R Package for Bayesian Spatial Voting Models with Probit and Logit Link Functions
Setsuka Aust
Major: Computer Science
Concentration: Data Science
Minor: Statistics
UCSC Mentor: Joshua Stuart, Professor, Dept. of Biomolecular Engineering, Associate Director, UCSC Genomics Institute
Project: Comparative Analysis of Algorithms to Predict Pathway Activity Levels in Cancer
Vanessa Garcia
Major: Marina Science
Minor: Statistics
UCSC Mentor: Russ Corbett-Detig, Assistant Professor, Department of Biomolecular Engineering
Project: Investigating the parameters responsible for tRNA gene evolution
Joaquin Sanchez
Major: Mathematics (Statistics)
UCSC Mentor: Benedict Paten Director of the BD2K Center for Big Data in Translational Genomics; Director of Comparative Genomics at the UCSC Genomics Institute
Project: Evaluating PEPPER: A Deep Neural Network Polishing Pipeline Based on Long Read Assembly
Isabella McCrory
Major: Marine Science
Minor: Statistics
UCSC Mentor: John Carlos Garza Adjunct Professor, Supervising Research Geneticist, Research Associate; Physical & Biological Sciences Division
Project: Ocean Abundance and Distribution of Chinook Salmon Revealed through Genetic Stock Identification
Gabriel Chavez
Major: Mathematics
UCSC Mentor: Joshua Stuart, Professor, Dept. of Biomolecular Engineering, Associate Director, UCSC Genomics Institute
Project: Generating Interpretable Reports and Visualizations for Cancer Subtype Predictions
Micaela Colmenarez
Major: Biology, Minor: Statistics
UCSC Mentor: Angela Brooks, Assistant Professor, Department of Biomolecular Engineering
Project: Characterizing Complex Splicing Alteration Patterns Across Cancer Types
Diego Quezada-Munoz
Major: Mathematics, Minor: Computer Science
UCSC Mentors: Benedict Paten, Director of the BD2K Center for Big Data in Translational Genomics; Director of Comparative Genomics at the UCSC Genomics Institute & Melissa Cline, Project Scientist, Computational Genomics Lab
Project: Testing the Performance of the MutPred2 Variant Pathogenicity Predictor on a set of BRCA1 and BRCA2 Variants and the Relevance of Solvent Accessibility in Predicting Pathogenicity
Axel Kent
Major: Environmental Science, Technology, & Policy
UCSC Mentor: Russ Corbett-Detig, Assistant Professor, Department of Biomolecular Engineering
Project: Investigation of Double Infection Statuses Within Wolbachia Infected Hosts
Tracey Ramirez
Major: Mathematics
UCSC Mentor: Russ Corbett-Detig, Assistant Professor, Department of Biomolecular Engineering
Project: Accommodating Diploidy in Linkage Disequilibrium Pruning Methods
Jacob Gull
Major: Computer Science
UCSC Mentor: Benedict Paten, Director of the BD2K Center for Big Data in Translational Genomics; Director of Comparative Genomics at the UCSC Genomics Institute
Project: Aligning and Encoding Base Called Signals Using Nanopore Raw Signal and Dimensionality Reduction in Variant Detection Models
Armando Zamudio-Hurtado
Major: Molecular Biology
UCSC Mentor: Sofie Salama, Director of the Haussler Lab, Research Scientist in Biomolecular Engineering, HHMI Senior Scientist
Project: Examining the Evolutionary Paths Taken by Transposable Elements to Avoid Repression in Primate and Human Genomes
Nicholas Heyer
Majors: Biology & Mathematics
UCSC Mentor: Sofie Salama, Director of the Haussler Lab, Research Scientist in Biomolecular Engineering, HHMI Senior Scientist
Project: Establishing Genotiypic Variation of the Human Population at NOTCH2NL
Iason Myttas
Major: Computer Science, Minor: Mathematics
UCSC Mentor: Joshua Stuart, Professor, Dept. of Biomolecular Engineering, Associate Director, UCSC Genomics Institute
Project: Deep Learning for Predicting Gene Essentiality in Cancer Cell Lines
Melissa Meredith
Major: Molecular Biology
UCSC Mentor: Melissa Cline, Project Scientist, Computational Genomics Lab
Project: Predicting Pathogenic Nonsense Mutations in BRCA Gene Variants
Tiffany Thisner
Major: Molecular Biology
UCSC Mentor: Sofie Salama, Director of the Haussler Lab, Research Scientist in Biomolecular Engineering, HHMI Senior Scientist
Project: Evidence for Co-evolution of KRAB Zinc Finger Protein ZNF649 and L1PA Elements
Maria Teresa "MT" Hernandez
Major: Mathematics, Minor: Global Studies
UCSC Mentor: Russ Corbett-Detig, Assistant Professor, Department of Biomolecular Engineering
Project: Wolbachia Genome Sequence Assemply Using DNA Sequences of Infected Arthropods
Adolfo Huerta
Major: Mathematics
UCSC Mentor: Benedict Paten, Director of the BD2K Center for Big Data in Translational Genomics
Project: Implementation of Workflow Description Language into UCSC's Toil
Skylar Kensinger
Major: Molecular Biology
UCSC Mentor: Russ Corbett-Detig, Assistant Professor, Department of Biomolecular Engineering
Project: Investigating Somatic Mutations in tRNAs and Flanking Regions
Julian Quilatan
Major: Biology, Statistics Minor
UCSC Mentor(s): Benedict Paten, Director of the BD2K Center for Big Data in Translational Genomics
Project: Extracting openSNP Data for BRCA Exchange
Daniel Meza
Major: Mathematics (Statistics Concentration)
UCSC Mentor(s): Richard Green, Associate Professor, Biomolecular Engineering, Co-director of the UCSC Paleogenomics lab
Project: Determining the Best Parameters for Mapping Ancient DNA
Raquel Figueroa
Major: Computer Science
UCSC Mentor: Richard Green, Associate Professor, Biomolecular Engineering, Co-director of the UCSC Paleogenomics lab
Project: Computational Analysis of Age Related Mouse DNA Mutations to Determine Chromatin Structure Alterations
Charlie Farber
Major: Biology
UCSC Mentor: Mark Akeson, Professor, Dept. of Biomolecular Engineering
Project: Development of Generative Adversarial Networks for Creation of Novel Protein Sequences
Kara Spencer
Major: Computer Science
UCSC Mentor: Benedict Paten, Director of the BD2K Center for Big Data in Translational Genomics
Project: VCF to GA4GH
Juan Cerda
Major: Biology
UCSC Mentor: Joshua Stuart, Professor, Dept. of Biomolecular Engineering, Associate Director, UCSC Genomics Institute
Project: De novo inference of brain cell types from single-cell transcriptomes via principled master regulatory analysis
Blake Hansen
Major: Mathematics (Statistics), Biology Minor
UCSC Mentor: Joshua Stuart, Professor, Dept. of Biomolecular Engineering, Associate Director, UCSC Genomics Institute
Project: Do Cancer Cells have Achilles Heels?
Alexander Doria
Major: Computer Science
UCSC Mentor: Benedict Paten, Director of the BD2K Center for Big Data in Translational Genomics
Project: Building a Genomics Web Application Using GA4GH APIs