RMI Scholars

Kevin Ton

2023 – 2024

Major: MCD Bio 

Faculty/Staff Mentor: TBD

Research Mentor:  TBD

Amy Li

2023 – 2024

 Major: Biotech

Faculty/Staff Mentor: TBD

Research Mentor: TBD

Sky Gomez

2022 – 2024

 Major: Anthropology

Faculty/Staff Mentor: Carol Grider

Research Mentor: Joshua Gardner (Miga) and Ajona Groot (Greider)

Sofia Moreno

2022 – 2023

 Major: Biology

“Application of Long Read Sequencing to Pediatric Cancer”

Faculty/Staff Mentor: Olena Vaske

Research Mentor: Anouk van den Bout (Assistant Specialist)

Ron Barulich

2022 – 2024

Major: MCD Biology

“Investigating the Ribonucleases Responsible for tRNA Fragment Biogenesis in Mus musculus Epididymides”

Faculty/Staff Mentor:  Upasna Sharma

Research Mentor:  Joshua Shaffer

Eduardo Del Rio

2022 – 2024

 Major: Biomolecular Engineering and Bioinformatics

Faculty/Staff Mentor: Russ Corbett-Detig

Research Mentor: Gabriel Penunuri

Kiki Galvez

2021 – 2024

Major: Computer Science and Bioinformatics

“Optimizing the R2C2 protocol for the sequencing of mammalian cDNA”

Faculty/Staff Mentor: Beth Shapiro

Research Mentor:  Megan Supple

Rakshya Sharma

2021 – 2024

Major: Computer Science and Bioinformatics

“Identifying RNA Splicing Patterns in Cancer using MESA”

Faculty/Staff Mentor: Angela Brooks

Research Mentor: Dennis Mulligan and Alexis Thornton

Cristina Vargas Vasquez

2022 – 2023

 Major: Human Biology

“Generating Ribosomal Mutants that Cannot Perform Nonsense-Mediated mRNA Decay in S. cerevisiae“

Faculty Mentor: Joshua Arribere

Jovan Morales Hurtado

2021 – 2023

Major: Cognitive Science

“A Bottom-Up Approach to Identify Inhibitory Glutamate Signal“

Faculty Mentor: Dan Turner-Evans

Randy Cabrera

2021 – 2023

Major: Computer Science

“Trout Conservation and Genetic Transgressions”

Faculty Mentor: Beth Shapiro

Beza Abesha

2021 – 2022

Major: Neuroscience

“Neuronal DNA damage and repair associated with the sleep/wakefulness cycle”

Faculty Mentor:  Yi Zuo

Rosa Sanchez

2021 – 2022

 Major: Molecular Cell and Developmental Biology

TUBI (Treehouse)

Faculty Mentor:  Michael Stone

Lucy Zheng

2021 – 2022

Major: Biomolecular Engineering and Bioinformatics

“Re-Analysis of RNA-Seq Variant Detection Study”

Faculty Mentor: Olena Vaske

Milagros Rivera

2020 – 2022

Major: Marine Biology

“Environmental DNA based bioinventory of Palmyra Atoll”

Faculty Mentor: Beth Shapiro

Diana Reyna

2020 – 2022

Major:  Biochemistry and Molecular Biology

“ Understanding the role of ZNF257, ZNF534, & HERV-H in early human development“

Faculty Mentor:  Sofie Salama

Daniel Lozano

2020 – 2022

 Major:  Biochemistry and Molecular Biology

“Understanding the Role of CPPED1 in Breast Cancer“

Faculty Mentor:  Shaheen Sikandar

Matthew Loven

2021 – 2022

Major: Molecular Cell and Developmental Biology

“Understanding the Role of CPPED1 in Breast Cancer”

Faculty Mentor:  Vicki Auerbuch Stone

Aisha Lakshman

2021 – 2022

Major: Sociology

“Normalizing Slow-Science: RNA-Therapeutics, Research Pace, and Public Trust in Science”

Faculty Mentor: Jenny Reardon

Ruby Guevara

2020 – 2022

Major:  Molecular Cell and Developmental Biology

“The Expression of the Human LL-37 Antimicrobial Peptide Impairs the Detrimental Effect of Beta-amyloid in a Drosophila Model of Alzheimer’s Disease“

Faculty Mentor:  Jeremy Lee

Melica Baboldashtian

2020 – 2022

 Major:  Human Biology

“L-Methionine enhances neuroinflammation and impairs neurogenesis: Implication for Alzheimer’s disease“

Faculty Mentor:  Holly Beale

Laya Ashley

2020 – 2022

Major: Chemistry

“Envelope Stress Response CpxRA regulating Yersinia Pseudotuberculosis Virulence”

Faculty Mentor:  Vicki Auerbuch Stone

Sara Amirkiai

2020 – 2022

Major: Molecular Cell and Developmental Biology

“Identification and characterization of long noncoding RNAs during inflammation.“

Faculty Mentor:  Susan Carpenter 

Darhien Gaddis

2020 – 2022

Major:  Molecular Cell and Developmental Biology

“Developing a scalable assay for identifying cellular identities of cerebral organoids“

Faculty Mentor:  Sofie Salama

Gifti Gemeda

2019 – 2021

 Major:  Biomolecular Engineering and Bioinformatics

“Using a Notch-reporter assay to understand the ability of specific NOTCH2NL alleles to activate Notch signaling“

Faculty Mentor:  Sofie Salama

Juliana Limon

2020 – 2021

Major: Marine Biology/Ecology and Evolutionary Biology

“The Complete mitogenome of Dascyllus trimaculatus“

Faculty Mentor:  Giacomo Bernardi

Linh Thuy Nguyen

2019 – 2021

Major: Molecular, Cellular and Developmental Biology

“Characterization of a Genetic Suppressor of a Histone H3 Mutations That Perturbs Transcription Elongation in Budding Yeast“

Faculty Mentor:  Grant Hartzog

Carlos Arevalo

2019 – 2021

Major:  Molecular, Cell, and Developmental Biology and Bioinformatics

“Pan-cancer analysis of driver mutations and modules.“

Faculty Mentor:  Angela Brooks

Pablo Alvarez

2019 – 2020 

 Major:  Human Biology, Chemistry Minor

“Unraveling mechanisms of type III secretion in pathogenic yersinia”

Faculty Mentor:  Vicki Stone

Ikenna Anigbogu

2019 – 2020 

Major: Biomolecular Engineering and Bioinformatics

“Exploring single-stranded nicks in the Nanopore to better understand a Pediatric Case”

Faculty Mentor:   Doug Kellogg

Kavya Aswadhati

2019 – 2020

Major: Bioinformatics and Critical Race, Ethnic Studies

“Data-mining and Phylogenetic Approaches to Characterize the Stability of Wolbachia Infections in Malarial Mosquitoes”

Faculty Mentor:  Russ Corbett-Detig

Sydney Renee Fregoso

2019 – 2020

Major:  Human Biology

“The influence of parental environment on future generational phenotypes”

Faculty Mentor:   Upasna Sharma

Patrick Fuller

2018 – 2020

 Major:  Human Biology

“Characterizing Genetic Suppressors of SPT5 Cs”

Faculty Mentor: Grant Hartzog

Alinne Gonzalez Armenta

2019 – 2020 

Major: Biomolecular Engineering and Bioinformatics

“Exploring the mechanisms of intron transposition”

Faculty Mentor: Manny Ares

Azuah Gonzalez

2018 – 2020

Major: Biochemistry and Molecular Biology

“The Monitoring Yersinia Type III Secretion System in vitro”

Faculty Mentor: Vicki Stone 

Alexander Hoefler

2019 – 2020

Major:  Biomolecular Engineering, Bioinformatics Mino

“Quality assessment of cerebral cortex organoids using immunofluorescence and RNA expression measurements”

Faculty Mentor: David Haussler

Vanessa Howland

2019 – 2020

 Major:  Biology

“Investigating whether maternal choline supplementation protects against alterations in epigenetically regulated gene expression caused by developmental Manganese exposure”

Faculty Mentor:  Donald Smith

Preet Kaur

2019 – 2020 

Major: Biomolecular Engineering and Bioinformatics

“Investigating Functional Genomics and Inferring Distribution of Fitness Effects of Intron Gain in the pelagic tunicate species Oikopleura dioica”

Faculty Mentor: Russ Corbett-Detig

Began Nguy

2019 – 2020

Major: Computer Science

“The Human Cell Atlas Initiative” 

Faculty Mentor: Jim Kent 

Taylor Real

2018 – 2020

Major:  Molecular, Cell, and Developmental Biology

“Optimizing Molecular Inversion Probes to Characterize Human Specific Neurodevelopmental Genes”

Faculty Mentor: David Haussler

Stefanie Brizuela

2017- 2020

 Major:  Biomolecular Engineering and Bioinformatics

“Determining the effects of mutations in SMARCA4 on alternative splicing in lung adenocarcinoma”

Faculty Mentor:   Angela Brooks

Jackie Roger

2017 – 2019

Major: Bioinformatics, Statistics Minor

“Wolbachia Host-Switching”

Faculty Mentor: Russ Corbett-Detig

Jessica Pierce

2018 – 2019

Major: Biomolecular Engineering and Bioinformatics

“Recognition and Binding of Individual Zinc Finger Domains in Zinc Finger 649 to Primate Transposable Element, L1PA4.”

Faculty Mentor: Sofie Salama/David Haussler 

Paola Angulo

2018 – 2019

Major:  Biomolecular Engineering, Bioinformatics

“Observation of the Evolutionary Race Between L1 Retrotransposon and KRAB Zinc-Finger ZNF649 Repression in the Human Genome.”

Faculty Mentor: David Haussler/Sofie Salama

Lourdes Gomez

2018 – 2019

 Major:  Biomolecular Engineering and Bioinformatics

“Using genomics to infer the consequences of pathogen exposure.”

Faculty Mentor:  Beth Shapiro

Dante Moreno

2018-2019

Major: Ocean Sciences

“Comparative analysis of the genes involved in the domoic acid biosynthetic pathway of Pseudo-nitzschia species.”

Faculty Mentor: Marilou Sison-Mangus

Manuel Varela

2018 – 2019

Major: Paleogenomics/ Bioinformatics

“Building a bioinformatic pipeline to detect rare species in complex sequencing libraries.”

Faculty Mentor: Beth Shapiro

Sascha Zepeda

2018 – 2019

Major:  Biomolecular Engineering and Bioinformatics

“Admixture and epistatic interactions between cosmopolitan and ancestral populations of Drosophila populations from Ethiopia and France.”

Faculty Mentor: Russell Corbett-Detig

Adrian Salguero

2017 – 2018

 Major:  Computer Science

“Development of a parallel workflow to find structural variations and the phasing of these variants from a large cohort of human whole genome sequences.”

Faculty Mentor: Benedict Paten

Maelia Uy-Gomez

2017- 2018

Faculty Mentor: Angela Brooks

Selam Gebremedhin

2017 – 2018

Major: Molecular, Cell, and Developmental Biology

“Identifying functional links between transcription and splicing of mRNAs.”

Faculty Mentor:  Grant Hartzog

Yulia Zybina

2017 – 2018

Major:  Chemistry and Biology (Neuroscience)

“Characterizing NOTCH2NL CRISPR mutants/determining CNV of NOTCH2NL paralogs in autism patients.”

Faculty Mentor: David Haussler

Victoria Serrano

2017- 2018

 Major:  Bio Chemistry

“Meiotic recombination and the effects of inversions on chromosome pairing.”

Faculty Mentor:  Russ Corbett-Detig

Vanessa Veneer

2017- 2018

Major: Chemistry/Biology

“Characterizing NOTCH2NL CRISPR mutants/determining CNV of NOTCH2NL paralogs in autism patients.”

Faculty Mentor: Russ Corbett-Detig

Jessica Arozqueta

2017-2018

 Major:  Neurobiology and Neurosciences

Melawit Tekeste

2017 – 2017

Major: Molecular, Cell, and Developmental Biology

“Phenotypic analysis of mutant mouse mammary glands (Prickle2 gene: knock- out, heterozygote, and wild- type tissue).”

Faculty Mentor: Lindsay Hinck & Prestina Smith

Chelsea Stewart

2016 – 2017

Major:  Molecular, Cell, and Developmental Biology

Faculty Mentor:  Bin Chen

Thao O

2015 – 2016

Major: Molecular, Cell, and Developmental Biology

Worked on pre-RNA splicing and human disease.

Faculty Mentor: Jeremy Sanford

Kevyn Hart

2015-2016

Major:  Molecular, Cell, Developmental Biology

“Assessment of spliced- alignment methods for nanopore sequencing reads.”

Faculty Mentor: Angela Brooks

Du Linh Lam

2015 – 2016

Major:  Biomolecular Engineering

“Modeling Gliomas using human ES cells.”

Faculty Mentor: David Haussler, Olena Morozova

Parisa Nejad 

2014 – 2015

Major: Molecular, Cell, and Developmental Biology

Worked on the analysis, visualization, and curation of stem cell genomics.

Faculty Mentor: Jim Kent

Natalia Herrera

2014 – 2015

Major: Biochemistry and Molecular Biology with a minor in Bioinformatics

Faculty Mentor: Victoria Auerbuch Stone

Layla Cervantes

2013 – 2015

Major:  Molecular, Cell, and Developmental Biology & Department of Microbiology and Environmental Toxicology

“System for Continuous Mutagenesis of a Target Gene” and studied TEM-1 Beta-lactamase evolution in E.coli.”

Faculty Mentor: Manel Camps

Read More

Layla Cervantes studied how the beta-lactamase protein evolves in E. coli cells under antibiotic (cefotaxmine) selection. She identified how starting mutations condition subsequent mutational trajectories and more generally how individual mutations interact with each other phenotypically. She then subjects the bacteria to cefotaxmine to cause another mutation that increases resistance to this antibiotic. This will allow her to obtain combinations of mutations contributing positively to cefotaxmine resistance. Cervantes also studied how modulating the fidelity of replication affects beta-lactamase’s ability to evolve cefotaxmine-resistant mutants. She will be comparing side-by-side libraries generated by polymerases having different mutation frequency and spectrum, and she will compare the frequency and type of cefotaxmine-resistant mutants after parallel selection of the two libraries. Her work will elucidate how new biochemical activities evolve and provide the tools to anticipate the outcome of complex mutations. December 8, 2014: CONGRATULATIONS Layla who has received a $1500 Undergraduate Research Award from the Sciences Awards Division of UCSC. Layla plans to use the award to present her work at the 2015 Emerging Researchers National (ERN) Conference in STEM in Washington, D.C.

Sandrine Kyane

2014 – 2015

Major:  Biochemistry

“Introduction of NOTCH2NL Mutations into Human Cells.”

Faculty Mentor: David Haussler, Sofie Salama, and Olena Morozova

Read More

Gliomas are the most common malignant brain tumors diagnosed in the United States, and they are often incurable using available treatment options. While grade 2 and grade 3 gliomas are known to be associated with mutations in genes IDH1 and ATRX, the exact tumorigenic mechanisms of these mutations are unknown. Sandrine’s project will involve using the recently described CRISPR-Cas9 system to introduce IDH1 and ATRX mutations into human embryonic stem cells. In particular, she will work on constructing and testing special guide RNAs that will ensure the mutations are introduced at the sites of interest. Successful generation of embryonic stem cell lines carrying glioma mutations would provide an invaluable model system to study glioma development in the laboratory and develop new therapies for the disease.

Eric Curiel Lares

2013 – 2014

Major: Ecology & Evolutionary Biology

“The evolution and diversification of innate immunity genes in sea urchins.”

Read More

He uses the UCSC Genome Browser to compare the complete genomes of nine sea urchins and search for patterns of duplication (paralogs) in innate immunity genes. Lares found that the majority of innate immunity genes contained paralogs in all species, suggesting a rapid rate of new gene formation. He then used a phylogenetic analysis by maximum likelihood (PAML) program to test for signs of positive natural selection in single-copy innate immunity genes. Tests for positive selection were significant at roughly a third of the genes examined. Lares’s results are consistent with those of earlier studies in drosophila where innate immunity genes demonstrated rapid diversification and evolution through antagonistic host-parasite co-evolutionary interactions.

Jordan Hughey

2013 – 2014

Major: Bioinformatics

“Site directed mutagenesis and pore formation testing of nanopores.”

Faculty Mentor: Mark Akeson

Gerardo Perez

2013 – 2014

Major:  Biomolecular Engineering

“The goal of HIV research is to produce a vaccine that offers complete protection from the virus.”

Read More

To date, no vaccine has shown this. Broadly neutralizing antibodies are antibodies capable of blocking infection from a wide variety of clinical isolates. PG9 is a broadly neutralizing antibody that targets the V1/V2 region of the HIV gp120. Gerardo’s project involves Structure-focused vaccine design of the V1/V2 region of gp120. The goal is to engineer a scaffold to fold like the native structure in the gp120 and stabilizing the β -hairpin leading to Mannose 5 at N160. This involves making mutations to V1/V2 scaffolds in variety of clades to optimize PG9 binding. Ultimately, these scaffolds could possibly be used in immunizations.

Elvira Contreras

2012 – 2013

Major:  Molecular, Cell, and Developmental Biology

“Analysis of a family of genes predicted to encode calcium/proton transporter.”

Faculty Mentor: Barry Bowman

Geoffrey Slaughter

2012 – 2013

Major: Molecular, Cell, and Developmental Biology

“Regulation of lifespan by the MES complex in c.elegans.” Read Geoff’s award-wining senior thesis, based on his research in the Strome lab.”

Faculty Mentor: Susan Strome

Britney Martinez 

2012 – 2013

Major: Molecular, Cell, and Developmental Biology

“Genomics of the RNA binding splicing factor Mer1.”

Faculty Mentor: Manny Ares

Cynthia Smith

2012-2013

Major:  Microbiology and Environmental Toxicology

“Role of antiretroviral-selected mutations in HIV-reverse transcriptase in shaping the HIV genome.”

Faculty Mentor: Manel Camps

Read More

Drug resistance limits use of antiretroviral drug treatment for patients infected with HIV, primarily drugs that inhibit reverse transcriptase (RT). Cynthia’s project focused on the mechanisms by which RT functions in HIV to understand how replication fidelity impacts viral fitness and determine the frequency of selected mutations generated by HIV wild-type and variant polymerases. She used an E. coli in vivo model and direct sequencing to generate a distinct replication and mutation footprint for each polymerase. Determining distinct replication mechanisms and patterns will help predict the risk for developing resistance to additional drugs and understand how these mutations increase persistence.

Alex Salazar

2012 – 2013

Major:  Biomolecular Engineering

“Semi automated MagArray chip fictionalization.”

Faculty Mentor: Alan Zahler

Read More

Alex is currently designing and engineering a device that will simplify the immobilization of specific receptor molecules on a magnetic chip. The magnetic chip’s system is based on GMR (Giant Magnetic Sensor), and with the help of paramagnetic nanobeads, one can detect the presence of a specific protein/molecule. Ideally, we would test and detect multiplex proteins on a single chip by transferring a solution to a specific region on the sensor array. However, the current method is rather challenging and inefficient. With the help of this device, researchers will be able to detect multiplex proteins more efficiently and accurately. Read about Alex’s project at the Harvard-MIT Broad Institute Summer Research Program in Genomics. View Alex’s ISMB 2014 Poster presentation Investigating large sequence variants in drug resistant Mycobacterium tuberculosis

Rocio Ramos

2011 – 2012

Major: Molecular, Cell, and Developmental Biology

“Investigating the relationship between VANGL2 and cilia in the mammary gland.”

Faculty Mentor: Lindsay Hinck

Laci Hampton 

2010 – 2011

Major: Biomolecular Engineering

“Improving next-generation sequencing flow.”

Faculty Mentor:  Nader Pourmand

Santiago Salazar

2010 – 2011

Major:  Microbiology & Environmental Toxicology

“The role of SLIT signals in the regulation of  breast stem cell growth and cancer initiation.”

Faculty Mentor:  Lindsay  Hinck

Rene Moreno

2010 – 2011

Major:  Microbiology & Environmental Toxicology

“Green fluorescence protein based biosensor for arsenic contamination detection.”

Faculty Mentor: Chad Saltikov

Read More

Rene worked on two projects. The first focused on creating a bio-sensor for arsenic in collaboration with UCSC adjunct professor Dr. Dominik Rabus (Electrical Engineering and Computer Science). The bio-sensor will serve as a microbial sensor in which arsenic in found in-front of a green fluorescence protein, which can be used to detect arsenic more efficiently using fluorescence. Rene’s contribution to the  project was to help determine how robust the bio-sensor strain is at detecting different arsenic concentrations and how accurately it can be read by fluorescence and optical density. The second project consisted of engineering a more proficient strain that contains the arsenic genome, by inserting a green fluorescent protein element into a region of the genome that regulates arsenic. The approach was to develop a molecular approach such as polymerase chain reaction and genome sequencing to determine where the green fluorescence protein is inserted. Once the arsenic bio-sensor is successful, the Saltikov Lab plans to develop bio-sensors for other metals. Moreno graduated in June 2011 and is currently working as a program coordinator at the SACNAS main office, in Santa Cruz, CA, and applying to graduate programs.

Katrina Luna

2009 – 2010

Major: Ecology & Evolutionary Biology

“Genetic diversity arising from bacteria-bacteriophage interactions driven by different genetic mechanisms.”

Faculty Mentor: Samantha Forde

Jose Loza

2009 – 2010

Major: Computer Engineering

“Analyzing the effectiveness of the IZON resizable nanopore device.”

Faculty Mentor: William Dunbar

Claudia Mariella
Lavarreda-Pearce

2009 – 2010

Major:  Microbiology & Environmental Toxicology

“Transposon mutanogenesis of Shewanella sp. ANA-3.”

Faculty Mentor: Chad Saltikov

Christopher Robles

2008 – 2009

Major:  Biomolecular Engineering

Faculty Mentor:  Nader Pourmand

Regina Chavez

2008 – 2009

Major:  Community Studies

“Obesity and genetic research: What are we really learning?”

Faculty Mentor: Claudia Chaufan

Christine Sinclair

2008 – 2009

Major: Molecular, Cell, and Developmental Biology

“Molecular paternity analysis of the side-blotched lizard, Uta stansburiana.”

Faculty Mentor: Barry Sinervo

Nicole Milner

2008 – 2009

Major:  Ecology & Evolutionary Biology

“Determining the presence of T3 and Lambda in communities of coevolving bacteria and bacteriophage.”

Faculty Mentor:  Samantha Forde

Nicole Coppage

2008 – 2009

Major: Microbiology & Environmental Toxicology

“Creation and phenotypic characterization of a cheZHP mutant.”

Faculty Mentor:  Karen Ottemann

Tiffany Lopes

2007 – 2008

Major:  Molecular, Cell, and Developmental Biology

“Can stalling of RNA polymerase influence alternative splicing?”

Faculty Mentor: Manny Ares

Christine Sinclair

2007 – 2008

Major: Chemistry and Biochemistry

“Biochemical mechanisms that control the cell cycle.” Ouwole worked to deepen understanding of the process involved in regulating retinoblastoma protein, which is implicated in a childhood cancer of the eye.”

Faculty Mentor: Seth Rubin

Shewit Tekeste

2007 – 2008

Major:  Molecular, Cell, and Developmental Biology

“Splicosome structural analysis.”

Faculty Mentor:  Melissa Jurica

Read More

Tekeste worked to understand a critical step in the process where information in DNA is read and then used in cells. The step is called pre-mRNA splicing, and errors in this process are responsible for a large number of human genetic diseases. Shewit focused on the structural analysis of an early phase of the spliceosome, called E complex.

Israel Murguia

2006 – 2007

Major: Politics/Community Studies

“Combating health disparities.” Murguia researched minority access to healthcare, the disparities minorities face in receiving equitable medical care, and how genomic information may help to improve health outcomes. Read the paper“

Faculty Mentor:  Mike Rotkin

Sonia Arevalo

2005 – 2006

Major:  Environmental Toxicology

“Rho-independent termination in Helicobacter pylori.”

Faculty Mentor: Karen Ottemann

Emily Berry

2005 – 2006

Major: Molecular, Cell, and Developmental Biology

“Role of the Caenorhabditis elegans extracellular matrix protein F-spondin/SPON-1 in neural development.” Read the paper

Faculty Mentor: Andrew Chisholm 

Alexander John Yambao 

2005 – 2006

Major:  Molecular, Cell, Developmental Biology

“Using immunoliposomes in combination with the immune system to treat cancer.” The project was conducted in Doug Kellogg‘s laboratory.”

Faculty Mentor: Melissa Jurica

Edward Cabral

2005 – 2006

Major: Environmental Toxicology

“Quantitative real time PCR detection of Helicobacter pylori.”

Faculty Mentor:   Karen Ottemann

Matt Riese 

2004 – 2005

Major:  Philosophy

“The biological meaning of ‘race.’” Read the paper

Read More

Riese outlined the debate now raging in academic circles as to whether race is a scientifically valid descriptor of humans or simply an arbitrary social label. He described a range of issues related to understanding race from both ethno-cultural and scientific vantage points. He laid out the dangers of relying on race to categorize people for medical and social purposes and argues that while humans may fall into “races” that are at least somewhat biologically dissimilar, we must make sure this information is used only to benefit people.

Daphne Ochoa

2004 – 2005

Major: Molecular, Cell, and Developmental Biology

“Interactions between the 17-beta-estrodiol/estrogen receptor-alpha and the mitogen-activated proten kinase (MAPK) cascade in regulating mammary gland development; the effect of antiestrogen and MAPK inhibitor.”

Faculty Mentor: John Tamkun

Oscar Hernandez 

2004 – 2005

Major:  Molecular, Cell, Developmental Biology

“Gene expression. Hernandez worked on a project that involved solving the structures of 150 proteins that make up the spliceosome, a critical macromolecular complex in gene expression.”

Faculty Mentor: Melissa Jurica

Lucy Silva

2003 – 2004

Major: Computer Science

“The possibility of a DNA database society.” Silva examined the practices of genetic profiling by police and collecting DNA samples from prisoners in California and the related legal and social implications. Read the paper.

Emilia Lopez

2003 – 2004

Major:  Philosophy & Education

Genetic modification/Cloning

Read the genetic modification and egalitarianism paper

Read the cloning and regulation paper

Read More

In her first paper, “Genetic modification and  egalitarianism: distinguish and distribute,” Lopez illustrated the difference between “preventative” gene therapy and “enhancement” gene therapy. She described the threat genetic engineering poses in a society with an unequal distribution of health care. In her second paper, “Three types of cloning and the necessity to regulate,” Lopez defined and evaluated DNA cloning, reproductive cloning, and therapeutic cloning. She referred to current legislation in the US and examines the results of the California Advisory Committee of Human Cloning.

Alexis Rojas

2003-2004

Major: Philosophy and Biology

“Moral issues of genetic engineering” and “Somatic cell gene therapy.”

Read the germline engineering paper

Read the somatic cell gene therapy paper

Marcia Soriano

2003-2004

Major:  Biomolecular Engineering

“Protein structure prediction.” Soriano worked on developing a program to evaluate the output of various computer algorithms for predicting local protein structure.

Faculty Mentor: Kevin Karplus

Terrill Yazzie

2016 -2017

Major:  Ocean Sciences

“The role of phytoplankton- associated bacteria in degrading polycyclic aromatic hydrocarbons via host lipids with concomitant transcriptomics.”

Faculty Mentor: Marilou Sison-Mangus

Jessica Morgan

2016 – 2017

Major: Microbiology and Environmental Toxicology

“Identifying molecular targets of the Yersinia pseudo tuberculosis type three secretion system inhibitor piercidin A1.”

Faculty Mentor: Victoria Auebuch-Stone

Martha Arciniega

2010 – 2011,
2015 – 2016

Major: Ocean Sciences

“Genetic diversity of the toxin mediating aryl hydrocarbon (AhR) genes in resident Oncorhyncus mykiss.”

Faculty Mentor: John Carlos Garza

Read More

Arciniega studied sea otters, Enhydra lutris ssp, known as a “keystone species” because they have a strong influence on diversity of near-shore marine communities. Unfortunately, sea otters were hunted almost to extinction and population sizes have dramatically decreased in the past 50 years. Information about the amount and distribution of genetic variation is vital for implementing effective conservation efforts. Martha’s project involves adding variable markers to the microsatellites already in use for sea otters. Microsatellites–DNA sequences that include tandem-repeated base pairs–are used to determine the relatedness between individuals and among populations. Microsatellites can provide information about population history, genetic drift, mate choice and migration. This project will provide enough statistical power to reconstruct pedigrees and investigate levels of differentiation between otter populations in California, Alaska and Russia. The pedigrees will show the lineages of sea otters that are closely related or part of the same family. A more complete knowledge regarding otter pedigrees will help marine scientists understand patterns of dispersal as well as past historical demography. 

In Fall 2015 and Winter 2016, she worked on a project, “Parallel  evolution & adaptive genomics of the steelhead summer ‘ecotype’ in multiple populations in Oregon and California.

Javier Morales

2015 – 2014

Major: Biomolecular Engineering

“Engineering V1/V2 scaffolds to bind the broadly neutralizing antibody PG9 produced in normal cell lines.”

Faculty Mentor: Phillip Berman

Rigo Dicochea

2010 – 2012,
2013

Major:  Computer Engineering

“Enhancing performance of genome sequencing processors.”

Faculty Mentor: Jose Renau and Mark Diekhans

Read More

Dicochea examined how architectural modifications to a general purpose processor design can increase the computational performance of current genome sequencing algorithms. Scientific applications such as those necessary in the genomic sciences are heavily data parallel. Thus, the issues addressed in the design of a CPU for scientific applications must take into account additional parameters above what is specified for a general purpose processor. Rigo’s research project seeks to explore those parameters. His goal is the design and fabrication of a microprocessor architecture aimed at providing very high computational performance on very large genomic data sets. He also hopes to introduce a new suite of benchmarks to the computer architecture community that will enable researchers to quantify the performance of genomic applications on their processor designs.

In Fall 2015 and Winter 2016, she worked on a project, “Parallel  evolution & adaptive genomics of the steelhead summer ‘ecotype’ in multiple populations in Oregon and California.

Pamela Ruth Tilus Watson

2012 – 2013

Major: Microbiology and Environmental Toxicology

“Molecular mechanism for arsenic reduction.”

Faculty Mentor: Chad Saltikov

Read More

Pamela studies a key component of the molecular mechanism whereby arsenic, a naturally occurring toxic metal, leaches into drinking water aquifers. Arsenic contaminated drinking water is tasteless and odorless, and therefore hard to detect. Arsenic gets into the natural water system because in natural sediments low in oxygen and rich in arsenic and carbon, microbes generate energy by reducing arsenic instead of oxygen during cellular respiration. The reduced form of arsenic is water soluble, and thus can seep into drinking water aquifers. Pamela’s research aims at understanding exactly which aspects of microbial respiration impact the mobilization of this toxin.

In Fall 2015 and Winter 2016, she worked on a project, “Parallel  evolution & adaptive genomics of the steelhead summer ‘ecotype’ in multiple populations in Oregon and California.

Walter Adams

2010 – 2012

Major: Microbiology and Environmental Toxicology

“The role of the central region of YopD in Yersinia pseudotuberculosis virulence.”

Faculty Mentor: Victoria Auerbuch Stone

Janine Llagan

2007 – 2009

Major: Molecular, Cell, and Developmental Biology

“Structural changes in spliceosomes created by pre-mRNA trimming as visualized by electron microscopy.”

Faculty Mentor: Melissa Jurica

Iligan aimed to better characterize the structure of the human spliceosome, an important catalyst for gene expression.

Daniel Garalde

2007 – 2009

Major:  Computer Engineering

“Electrical, structural, and biological refinement of a nanopore sensor for sequencing DNA and RNA.”

Faculty Mentor: William Dunbar and David Deamer

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Through his unique, interdisciplinary research, Geralde developed new nanopore-based technology for sequencing DNA and RNA. He focused on addressing weaknesses in current alpha-hemolysin-based sensor technology developed at UCSC to improve its effectiveness. You can read about his research in a 2011 paper that he co-authored with other members of his research team: “Distinct complexes of DNA polymerase I (Klenow fragment) for base and sugar discrimination during nucleotide substrate selection”. Garalde received his Ph.D. in 2011 and now works as a research scientist at Oxford Nanopore Technologies in Oxford, UK.

In Fall 2015 and Winter 2016, she worked on a project, “Parallel  evolution & adaptive genomics of the steelhead summer ‘ecotype’ in multiple populations in Oregon and California.

Monica Lares

2005 – 2007

Major: Chemistry and Biochemistry

“Towards the structure and function of a novel RNA gene/determining the structure and fragile X syndrome of CGG RNA repeats.”

Faculty Mentor: William Scott

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Lares studied a novel RNA gene occurring in a segment of the human genome that has evolved with surprising rapidity between the chimpanzee and the human genomes. She used x-ray crystallography to investigate the structure and possible function of this RNA gene.

In Fall 2015 and Winter 2016, she worked on a project, “Parallel  evolution & adaptive genomics of the steelhead summer ‘ecotype’ in multiple populations in Oregon and California.

MaryAnn Dassah

2004 – 2006

Major: Molecular, Cellular, and Developmental Biology

“Refining the rules of 5′ splice site selection and suppression of +1G mutations of pre-MRNA.”

Faculty Mentor: Al Zahler

Gabirel Roybal

2006 – 2007,
2009 – 2010

Major: Molecular, Cell, and Developmental Biology

“Capture and characterization of catalytic complex spliceosomes: understanding how genomes are used, maintained, and regulated.”

Faculty Mentor: Melissa Jurica

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Gabriel’s project focused on investigating how our cells process genetic information. He used small molecule inhibitors of pre-mRNA splicing as tools to isolate and study the human spliceosome.  In particular, he worked with the small molecule known as Spliceostatin A to investigate the role of SF3b protein during the later stages of spliceosome assembly.  This work will be crucial to understand the mechanism and structure of the spliceosome.

Update: Gabe received his PhD in 2010, and is currently a post doctoral researcher UC San Francisco in the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research Center. His research focuses on studying the mechanisms that regulate the epigenetic landscape of adult neural stem cells. Congratulations, Dr. Roybal!

Brandon Saint-John 

2017 – 2018

Major:  Biomolecular Engineering

“Determining the effects of SMARCA4 mutation on alternative splicing in lung adenocarcinoma.”

Faculty Mentor: Angela Brooks

Prestina Smith

2012 – 2017

Major: Molecular, Cell, and Developmental Biology

“Vangl2 and planar cell polarity genes in mammary gland morphogenesis.”

Faculty Mentor: Lindsay Hinck

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Tissues are distinctly engineered to carry out a given function. The breast (or murine mammary gland) is an example of this, forming a network of bi-layered ducts that terminate in alveoli formed during pregnancy. These specialized structures have an outer layer of myoepithelial cells that will contract during lactation to squeeze milk from an inner layer of polarized epithelial cells. In order to generate this system of ducts, the mammary gland undergoes growth by branching; therefore, mechanisms involved in branch formation define mammary architecture. Diseases, such as breast cancer, often result in highly unorganized tissues; therefore, understanding the genes that regulate the overall architecture of the mammary gland could aid in understanding breast cancer pathology and identify potential therapeutic targets. Recent studies have identified genes involved in establishing proximal-distal (planar) polarity in epithelial cells as regulators of branching morphogenesis, however the mechanism of their action is currently unknown. Prestina’s project aims to understand how the core planar cell polarity (PCP) gene Vangl2 regulates branching in the mammary gland by investigating changes in mammary morphology in Vangl2 mutant mice, identifying regulators of Vangl2 and determining how VANGL2 cooperates with other PCP proteins to promote mammary development. Smith’s studies will provide insight into the mechanisms that function to establish the architecture of the mammary gland and elucidate a novel role for planar cell polarity in tissue morphogenesis.

Richard Cathey

2012 – 2014

Major: Microbiology and Environmental Toxicology

“How early life manganese exposure disrupts dopamine function and leads to attention deficits.”

Faculty Mentor: Donald Smith

Joseph Parks

2012 – 2013

Major: Biochemistry

“Understanding telomerase activity through single-molecule methods.”

Faculty Mentor: Michael Stone

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In the fall of 2012 Joe received the prestigious NSF Graduate Research Fellowship Award. Congratulations, Joe!
Telomerase is an essential eukaryotic enzyme that extends the ends of chromosomes. This enzyme is of particularly interest to the cancer field as telomerase hyperactivity is associated with over 90% of all cancers. Similarly, telomerase over-expression in normal cells has been shown to increase the lifespan of yeast and rats by up to 20% without an increase in cancer occurrence. Although many researchers have studied telomerase at a biochemical level, the detailed telomerase mechanism and structural features of the enzyme remains unclear due to the lack of a complete crystal structure. In order to dissect the structure and function of telomerase components, Joe will study individual molecules and their structural dynamics using single molecule FRET. Through real-time observation of telomerase internal dynamics, he hopes to gain direct insight into the function of telomerase sub-domains.

Publications:
Nucleic Acids Res. 2013 Feb 1;41(4):2746-55. doi: 10.1093/nar/gks1341. Epub 2013 Jan 8.
Mechanical unfolding of human telomere G-quadruplex DNA probed by integrated fluorescence and magnetic tweezers spectroscopy. Long X, Parks JW, Bagshaw CR, Stone MD.
PMID: 23303789 Free PMC Article
2. Plast Reconstr Surg. 2012 Oct;130(4):739-46. PMID: 23018685
Human acellular dermis versus no acellular dermis in tissue expansion breast reconstruction.
Parks JW, Hammond SE, Walsh WA, Adams RL, Chandler RG, Luce EA.

Margarita Gonzalez  

2009 – 2012

Major:  Chemistry and Biochemistry

“Investigations on DNA sequence vulnerability to NO-mediated DNA damage.”

Faculty Mentor: Pradip Mascharak

Hector Macias

2009 – 2010

Major: Molecular, Cell, and Developmental Biology

“Uncovering the mechanism behind SLIT2/ROBO 1 mediated mammary gland branch inhibition.” Read the paper

Faculty Mentor: Lindsay Hinck

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Hector’s research focused on developing therapeutic strategies for diagnosing and treating breast cancer.

Update: Hector received his Ph.D. in 2010 and is currently a post doctoral researcher in the Michael German lab at the University of California, San Francisco. The German lab is interested in identifying genetic factors that influence diabetes by identifyingthe genes that regulate the transition of stem cells to mature pancreatic beta-cells. Pancreatic beta-cells are the body’s sole provider of insulin. By understanding the role of these factors inbeta-cell production the German research team is developing novel strategies for curing diabetes. Congratulations, Dr. Macias! We look forward to your future contributions to biomedical science.

Josue Samayoa

2004 – 2006,
2008

Major: Biomolecular Engineering

“Protein structure prediction.”

Faculty Mentor: Carol Rohl, Kevin Karplus, and Fitnat Yildiz

Mark Rivero

2005 – 2006

Major: Computer Engineering

“Data visualization of genomic information.”

Faculty Mentor: Pat Mantey

Rivero looked for ways to improve the UCSC Genome Browser by allowing 3-dimensional visualization of any given data.

Edward Olano   

2004 – 2005

Major:  Chemistry

“Developing assays for prostate-specific antigen and early detection of ovarian cancer.”

Faculty Mentor: Jin Zhang

Veronica De Guzman

2003 – 2005

Major: Chemistry

“Nanopore devices.” De Guzman studied a nanopore device, which is an artificial membrane that has a single ion channel through it.

Faculty Mentor: Mark Akeson, UCSC Nanopore Project.

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The ion channel is used to capture and examine one molecule of DNA at a time. The interaction of double-stranded DNA or single-stranded DNA with the channel can readily be observed via changes in an electrical current through the channel. De Guzman observes and studies double-stranded-DNA ends fraying and reforming in a channel—an important step in biological processes. In HIV infection, for example, DNA fraying is necessary for HIV DNA to be spliced into human host DNA.

LEARN MORE about the Nanopore Project at UC Santa Cruz

David Balderas

2016- 2017

Major: Microbiology and Environmental Toxicology

“Regulon of the Iron-sulfur cluster transcription factor IscR in Yersinia”

Faculty Mentor: Victoria Auerbuch-Stone

Jamie Hernandez

2015 – 2016

Major: Microbiology and Environmental Toxicology

“System biology of anoxygenic photosynthetic arsenite oxidation in Ectothiorhodospira  BSL-9.”

Faculty Mentor: Chad Saltikov

Angel Resendez  

2014 – 2015

Major:  Chemistry

“Development of a chemical tool for measuring gut permeability.”

Faculty Mentor: Bakthan Singaram

Tara deBoer

2014 – 2015

Major: Chemistry and Biochemistry

“Investigation into the potential epigenetic nature of peroxynitrite.”

Faculty Mentor: Pradip Mascharak

Andrew Knutson

2012 – 2014

Major: Molecular, Cell, and Developmental Biology

“The role of SUMOxylation in preventing expression of germline proteins in somatic cells of Caenorhabditis elegant.”

Faculty Mentor: Susan Strome

Josh Parks

2015 – 2016

Major: Electrical Engineering

“Single molecule detection on an optofluidic platform.”

Faculty Mentor: Holger Schmidt

Daniel Sam  

2007 – 2009,
2010 – 2011

Major:  Biomolecular Engineering

“Computational approaches for predicting gene function.” Sam developed computational tools to predict and elucidate functional relationships between biological data collected from a variety of sources.

Faculty Mentor:  Josh Stuart

Carolina Reyes

2010 – 2011

Major: Microbiology and Environmental Toxicology

“Microbial genetics underlying iron geochemistry in anaerobic microorganisms.”

Faculty Mentor: Chad Saltikov

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How bacteria metabolize a solid mineral externally is of interest to microbiologists and geologists. Reyes investigated how bacteria metabolize iron minerals using the model bacterium Shewanella sp. strain ANA-3. The precise steps involved in bacterial metabolism of the iron mineral are not known, however, several hypotheses have been proposed. One hypothesis is that the bacterium metabolizes the iron using proteins inside the cell and sitting on the cell surface. These cytochrome proteins are thought to pass electrons from inside the cell to the iron mineral outside the cell. All organisms possess cytochrome proteins, and animals and plants use them in oxygen metabolism. In certain bacteria, these cytochrome proteins are composed of multiple residues that allow for the passage of electrons, a feature not common in animals and plants. The goal of her project is to determine why these bacterial cytochromes require multiple residues to pass electrons from inside the cell to iron minerals outside the cell. By altering the genetic material of ANA-3, she has eliminated specific regions of a cytochrome involved in iron metabolism in hopes of discovering which components enable this protein to pass electrons to the mineral outside the cell.

Reyes received her doctorate in 2011 and is  currently a research fellow at the Hanse-Wissenschaftskolleg Institute for Advanced Study in Bremen, Germany. Her research is supported in part by a fellowship from the J. William Fulbright Foundation, and an International Research Fellowship from the National Science Foundation.

Sachiko Reed

2007 – 2008

Major: Sociology

“Considering implications of mixed race identity and genomics.”

Faculty Mentor: Jenny Reardon

Genevieve Halpenny

2004 – 2007

Major: Chemistry

“DNA damage via light-activited nitric oxide release.” Halpenny delivered nitric oxide (NO) to living cells such as E. coli and ultimately cancer cells and then used microscopy to observe NO-induced DNA damage.

Faculty Mentor: Pradip Mascharak

Blake Riggs  

2004 – 2005

Major:  Molecular, Cellular, and Developmental Biology

“The centrosome-associated protein, nuclear fallout, and its role in metaphase furrow formation.”

Faculty Mentor:  Bill Sullivan

Loni Townsley-Montoya 

2012 – 2013

Major: Microbiology and Environmental Toxicology

“Construction and characterization of regulatory networks controlling cold shock adaptation in Vibrio cholerae.”

Faculty Mentor: Fitnat Yildiz 

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Bacterial pathogens are a major cause of mortality worldwide, yet we know little about how these organisms adapt to habitats outside of the human host. Vibrio cholerae, the causative agent of the severe diarrheal disease cholera, is an excellent model system to study environmental adaptation because it must survive in aquatic habitats for prolonged periods between outbreaks. Temperature is a critical environmental signal governing the occurrence of V. cholerae, and cholera outbreaks are highly correlated with sea surface temperature.  However, it is unknown how V. cholerae senses and responds to temperature change or how this response impacts environmental survival and infectivity of this pathogen.  Loni’s research aims to identify the regulatory networks responsible for temperature adaptation in V. cholerae and determine their impact on the environmental survival of this pathogen.     

Marc Hanson

2003 – 2004

Major: Computer Engineering

“Visualizing database queries.”