Biomolecular Engineering People

Faculty
Current Students
Alumni
Program Contacts

Principal Biomolecular Engineering Faculty

Mark Akeson

Professor

Phillip Berman

Professor Emeritus

David Bernick

Teaching Professor

Angela N. Brooks

Associate Professor

Russell Corbett-Detig

Assistant Professor

David Deamer

Research Professor

Rebecca M. DuBois

Associate Professor

Camilla Forsberg

Professor

Richard Edward Green

Professor

David Haussler

Distinguished Professor

Dianne Hendricks

Teaching Professor

Kevin Karplus

Professor Emeritus

Daniel H. Kim

Assistant Professor

Todd M. Lowe

Professor

Karen Miga

Assistant Professor

Benedict Paten

Associate Professor

Nader Pourmand

Professor

Shelbi L Russell

Assistant Professor

Ali Shariati

Assistant Professor

Josh Stuart

Professor

Christopher Vollmers

Associate Professor

Collaborating Faculty

Hinrich Boeger Professor, MCD Biology hboeger@ucsc.edu 217 Sinsheimer	Manel Camps Associate Professor, METX mcamps@ucsc.edu PSB 434	Lars Fehren-Schmitz Associate Professor, Anthropology lfehrens@ucsc.edu Soc Sci 1, Room 301	Melissa Jurica Professor, MCD Biology mjurica@ucsc.edu 450 Sinsheimer	Scott Lokey Professor, Chemistry slokey@ucsc.edu PSB 352
Olena Morozova-Vaske Assistant Professor, MCD Biology olena@ucsc.edu 220 Sinsheimer	Beth Shapiro Professor, EEB bashapir@ucsc.edu Biomed 144

Current Students

Name	Contact	Program	Advisor
Aguiar, Gabriel	gaguiar@ucsc.edu	Masters	TBD
Asri, Mobin	masri@ucsc.edu	PhD	Paten
Bagi, Alex	abagi@ucsc.edu	PhD	Haussler & Lowe
Casaletto, James	jcasalet@ucsc.edu	PhD	Paten
Chang, Xian Hui	xhchang@ucsc.edu	PhD	Paten
Chen, Samuel	sacchen@ucsc.edu	Masters	TBD
Cisar, Cecilia	ccsidar@ucsc.edu	PhD	Paten
Clever, Karoli	kclever@ucsc.edu	Masters	TBD
Condon, Chris	cjcondon@ucsc.edu	PhD	Rotations
Davidson, Andy	aedavids@ucsc.edu	PhD	Kim
Elliott, Elliott	melliot1@ucsc.edu	PhD	Haussler & Salama
Felton, Colette	cafelton@ucsc.edu	PhD	Brooks
Genetti, Max	mgenetti@ucsc.edu	PhD	Corbett-Detig
George, Alexander	achoi18@ucsc.edu	PhD	Sanford
Ghasemi, Sarah	sghasem2@ucsc.edu	Masters	TBD
Green, Kassidy	kaangree@ucsc.edu	Masters	DuBois
Haukness, Marina	mhauknes@ucsc.edu	PhD	Paten & Green
Hershauer, Sam	shershau@ucsc.edu	PhD	Shapiro
Hwang, Stephen	sjhwang@ucsc.edu	Masters	TBD
Karim, Lily	lkarim@ucsc.edu	PhD	Rotations
Keener, Nick	nkeener@ucsc.edu	PhD	Paten
Kramer, Alexander	alex.kramer@ucsc.edu	PhD	Corbett-Detig
Leavitt, Jesse	jsleavit@ucsc.edu	PhD	Lowe
Lee, Eunnie	elee111@ucsc.edu	Masters	TBD
Liang, Wenyu	wliang34@ucsc.edu	Masters	TBD
Lohith, Akshar	alohith@ucsc.edu	PhD	Lokey
Lorig-Roach, Nick	nlorigro@ucsc.edu	PhD	DuBois
Lorig-Roach, Ryan	rlorigro@ucsc.edu	PhD	Haussler
Lu, Eloise	hlu73@ucsc.edu	Masters	TBD
Malekos, Eric	emalekos@ucsc.edu	PhD	Carpenter
Manning, Aidan	aimannin@ucsc.edu	PhD	Lowe
Mastoras, Mira	mmastora@ucsc.edu	PhD	Rotations
Maulding, Nathan	nmauldin@ucsc.edu	PhD	Stuart
McBroome, Jakob	jmcbroom@ucsc.edu	PhD	Corbett-Detig & Green
Mendelson, Rachel	rmendels@ucsc.edu	PhD	Corbett-Detig
Meredith, Melissa	mmmeredi@ucsc.edu	PhD	Paten
Mithal, Arushi	armithal@ucsc.edu	Masters	TBD
Mok, Lydia	lymok@ucsc.edu	PhD	Rotations
Mulligan, Dennis	dmulliga@ucsc.edu	PhD	Brooks
Neudorf, Celine	cneudorf@ucsc.edu	PhD	Rotations
Nguyen, Chris	cnguy230@ucsc.edu	Masters	TBD
Nguyen, Remy	rennguye@ucsc.edu	PhD	Green
Oppenheimer, Jonas	jooppenh@ucsc.edu	PhD	Shapiro & Green
Park, Jimin	jpark621@ucsc.edu	Masters	TBD
Parks, David	dfparks@ucsc.edu	PhD	Haussler
Peddu, Vikas	vpeddu@ucsc.edu	PhD	Kim
Reggiardo, Roman	rreggiar@ucsc.edu	PhD	Kim
Rose, Nick	nrrose@ucsc.edu	Masters	TBD
Rounthwaite, Robin	rrounthw@ucsc.edu	PhD	Paten
Saint-John, Brandon	bsaintjo@ucsc.edu	PhD	Brooks
Schimke, Kayla	kschimke@ucsc.edu	PhD	Vollmers
Seiler, Spencer	sseiler@ucsc.edu	PhD	Haussler & Teodorescu
Stephan, Taylorlyn	tastepha@ucsc.edu	PhD	Green & Salama
Sundararaman, Balaji	bsundara@ucsc.edu	PhD	Green
Sung, Jun Mo	jsung8@ucsc.edu	Masters	TBD
Tang, Qiuxia	qtang6@ucsc.edu	PhD	Lowe
Thornton, Alexis	althornt@ucsc.edu	PhD	Brooks
Torres Montoya, Sebastian	storre22@ucsc.edu	PhD	Teodorescu & Haussler
Voitiuk, Kate	kvoitiuk@ucsc.edu	PhD	Haussler & Teodorescu
Weinstein, Alana	asweinst@ucsc.edu	PhD	Stuart
Xu, Dan	yxu267@ucsc.edu	PhD	Rotations
Xue, Bianca	yxue26@ucsc.edu	PhD	Stuart
Zee, Alex	azee@ucsc.edu	PhD	Vollmers

Click here for M.S. Alumni

Ph.D. Alumni

_{Students are listed by calendar year of graduation, then by last name.}

Name	Year	Dissertation Title	Advisor(s)	Initial Post-Graduation Placement
Jon Akutagawa	2022	Using RNA Sequencing Data to Detect Variants of Interest	Brooks	UCSF
Ioannis Anastopoulos	2022	Leveraging Chemical Structures and Molecular Information with Interpretable Deep Learning	Stuart	UNP
Marina Haukness	2022	Using long reads to improve haplotype phasing, genome assembly, and gene annotation	Paten	TBA
Charles Markello	2022	Improving Sequence Alignment and Variant Calling through the Process of Population and Pedigree-Based Graph Alignment	Paten	Illumina
Trevor Pesout	2022	Methodological Advancements for Genome Reconstruction by Haplotyping Long Read Sequence Data	Paten	TBA
Yohei Rosen	2022	Tools for large and detailed experiments in genomics and tissue development	Haussler & Paten	UC Santa Cruz
Rojin Safavi	2022	Integrative Analysis of Single-Cell RNA and Single-Cell ATAC Profiles to Infer Gene Regulatory Networks	Stuart	GRAIL
Lucas Seninge	2022	Integrating Prior Biological Knowledge and Machine Learning for Single-Cell Transcriptomics Analysis	Stuart & Haussler	NewLimit
Kishwar Shafin	2022	Accurate Genome Analysis with Nanopore Sequencing using Deep Learning Networks	Paten	Google
Alison Tang	2022	Alternative RNA Processing in Cancers	Brooks	Freenome
Andrew Bailey	2021	Modification Detection Using Nanopore Sequencing	Paten	Illumina
Jordan Eizenga	2021	Graph Methods for Computational Pangenomics	Paten	UC Santa Cruz
Verena Friedl	2021	Transcriptional Signatures of the Tumor and the Tumor Microenvironment Predict Cancer Patient Outcomes	Stuart	Bluestar Genomics
Paloma Medina	2021	Bioinformatic Approaches to Admixture and Symbiosis	Corbett-Detig	San Francisco State University
Santrupti Nerli	2021	Structure-based Modeling of Peptide/MHC-I Complexes	Sgourakis & Haussler	Prescient Design/Genentech
Thomas Ng	2021	Probabilistic Graphical Inference of Pedigrees	Anderson	Invitae
Darrin Schultz	2021	Chromosome-Scale Genomes, Resolving the Sister Phylum to Other Animals, and Novel Bioluminescent Systems	Green & Haddock	MBARI
Bryan Thornlow	2021	Evolutionary Genomics of Transfer RNA Genes and SARS-CoV-2	Corbett-Detig & Lowe	ROME Therapeutics
Roger Volden	2021	Single-Cell Nanopore Sequencing	Vollmers	PacBio
Gepoliano dos Santos Chaves	2020	Characterization of Huntington's Disease Cell Model in Gene Expression, Intracellular Glucose Levels and Genetic Variation	Pourmand	University of Chicago
Logan Mulroney	2020	Identification of Full-Length Transcript Isoforms using Nanopore Sequencing of Individual RNA Strands	Akeson	European Molecular Biology Laboratory
Jacob Pfeil	2020	Novel Gene Expression Analyses to Accelerate Precision Pediatric Oncology Research	Haussler	AbbVie
Lauren Sanders	2020	Multi-Omic Analyses and Organoid Models for Identiication of Therapeutic Vulnerabilities and Developmental Origins in Childhood Cancer	Haussler & Vaske	NASA
Nedda Saremi	2020	A Genomic Approach to Studying the Evolutionary Consequences of Population Declines	Green & Shapiro	Agilent Technologies
Robert Shelansky	2020	Specificity in Transcriptional Regulation	Boeger	UC Santa Cruz
Chad Townsend	2020	Empirical determination of the individual permeabilities of thousands of geometrically diverse cyclic hexa- and heptapeptides via multiplex PAMPA and MSMS sequencing	Lokey	TBA
Joel Armstrong	2019	Enabling Comparative Genomics at the Scale of Hundreds of Species	Haussler & Paten	Google
Charles Cole	2019	Antibody Genetics	Vollmers	Sema4
David Haan	2019	Classifying Cancer Genomic Alterations using Machine Learning and Multi-Omic Data	Stuart	Bluestar Genomics
Jennie Hutchinson	2019	Novel Vaccine Immunogens from Rare HIV-1 Controllers that Possess Broadly Neutralizing Antibodies	Berman	Color
Jay Kim	2019	Computational Genomics Studies of Genetic Adaptation in Different Environmental and Organismal Contexts	Camps	UC Santa Cruz
Thomas Matthew	2019	Inferring Genetic Co-Dependencies to Identify New Vulnerabilities in Cancer	Stuart	IGM Biosciences
Nathan Schaefer	2019	New Tools for Localizing Ancestry Across Genomes of Hybrid Individuals Provide Insight into the Genetics of Speciation	Green	UC Santa Cruz
Vlado Uzunangelov	2019	Prediction of Cancer Phenotypes through the Integration of Multi-Omic Data and Prior Information	Stuart	Bristol-Myers Squibb
John Vivian	2019	Tools for Large-Scale Genomic Analysis and Gene Expression Outlier Modeling for Precision Therapeutics	Haussler	Atreca, Inc.
Gabriel Byrne	2018	Overcoming Challenges of HIV Vaccine Antigen Production	Berman	JUST
Kenneth Durbin	2018	Improving Clinically Relevant Classification of Gene Expression Datasets Using Attribute Classifiers as Features	Stuart	SamplePsychic
Andrew Holmes	2018	Analyzing Regulation of tRNAs, tRNA Fragments, and mRNAs in Whole Genomes	Lowe	UC Santa Cruz
Brian Lin	2018	Practical Tools for Exploring tRNA Conservation	Lowe	Insight Fellow
Arjun Rao	2018	Prediction of T-Cell Epitopes for Cancer Therapy	Haussler	UC San Francisco
Edward Rice	2018	Long-Range Assembly and Transcriptomics Elucidate the Regulatory Architecture of Three Vertebrate Genomes	Green	University of Nebraska-Lincoln
Ian Fiddes	2017	Comparative Annotation Toolkit (CAT) - Simultaneous Clade and Personal Genome Annotation	Haussler	10X Genomics
Miten Jain	2017	High-Coverage Long Read DNA Sequencing with the Oxford Nanopore MinION	Akeson	UC Santa Cruz
Adam Novak	2017	Infrastructure for Scalable Analysis of Genomic Variation	Haussler	UC Santa Cruz
Brendan O'Connell	2017	Developing and Applying Chromatin Proximity Ligation Methods	Green	Oregon Health and Science University
Kiley Graim	2016	Using Sparse Data and Multiple Views to Predict Cancer Progression and Treatment	Stuart	Simons Foundation
Jonathan Magasin	2016	Bioinformatic Approaches for New Insights into Old Marine Metagenomic Data Sets	Gerloff	UC Santa Cruz
Yulia Newton	2016	Discovering Molecular Patterns with Therapeutic Implications in Large-Cohort Heterogeneous Cross-Cancer Data	Stuart	NantOmics
Evan Paull	2016	Sample-Specific Cancer Pathway Prediction from Genomic, Transcriptomic and Phosphoproteomic Data	Stuart	Columbia University
Samuel Vohr	2016	Identification and Mixture Deconvolution of Ancient and Forensic DNA Using Population Genomic Data	Green	Embark
Tracy Ballinger	2015	Analysis of Genomic Rearrangements in Cancer from High-Throughput Sequencing Data	Haussler	University of Edinburgh
Daniel Carlin	2015	Computational Evaluation and Derivation of Biological Networks in Cancer and Stem Cells	Stuart	UC San Diego
Lauren Lui	2015	Evolution of Structure and Function of Kink-turn Containing RNAs in the Domain Archaea	Lowe	Lawrence Berkeley National Lab
Sam Ng	2015	Identifying Key Pathways in Multiple Cancers with Multi-Omics Pathway Analysis	Stuart	Illumina
Amie Radenbaugh	2015	The Identification and Characterization of Alterations to DNA and RNA in Cancer Using Next-Generation Sequencing Data	Haussler	NantOmics
Marcos Woehrmann	2015	Predicting the Mode of Action fo Bioactive Compounds via High-Throughput Screening and Computational Algorithms	Stuart	Thermo Fisher
Dent Earl	2014	Evaluation and Application of the Three A's of Genomics: Assembly, Alignment, Annotation	Haussler	Google
Mia Grifford (Bosinger)	2014	Using High-Throughput Sequencing to Study the Progression of Cancer	Haussler	Worcester Polytechnic Institute
Philip Heller	2014	Bioinformatic Investigations in Marine Microbial Ecology	Zehr	San Jose State University
Hyunsung Kim	2014	Applications of High-Throughput Sequencing for Immunology and Clinical Diagnostics	Pourmand	GRAIL, Inc.
Wendy Lee	2014	Single-Cell Analyses of Transcriptional Heterogeneity During Drug Tolerance Transition in Cancer Cells by RNA Sequencing	Pourmand	San Jose State University
Ngan Nguyen	2014	Addressing the OMICS Data Explosion: A Comprehensive Reference Genome Representation and the Democratization of Comparative Genomics and Immunogenomics	Haussler	Atreca, Inc.
Ted Goldstein	2013	Tools for Extracting Actionable Medical Knowledge from Genomic Big Data	Haussler	UC San Francisco
Andrew Nguyen	2013	Molecular Mechanisms of Hematopoietic Stem Cell Migration and Engraftment	Forsberg	NantOmics
Timothy Sterne-Weiler	2013	Integrated Analysis of cis-Acting RNA Elements in Posttranscriptional Gene Regulation and Human Inherited Disease	Sanford	University of Toronto
Christopher Szeto	2013	Discovery of Clinically Relevant Molecular Signatures in Cancer	Haussler	NantCell
Andrew Uzilov	2013	Novel Applications of High-Throughput RNA Sequencing: Mapping RNA Structure Discovering Circular RNAs	Lowe	Sema4
Stephen Benz	2012	Sample-Specific Cancer Pathway Analysis Using Paradigm	Haussler	NantOmics
Alastair Fyfe	2012	Hydration of r(UGGGGU) Quadruplexes	Scott	UC Santa Cruz
Zack Sanborn	2012	Tumor vs Matched-Normal Sequencing: Analysis and Data Integration	Haussler	NantOmics
Courtney Onodera	2011	Characterization of Transcriptional Enhancers in the Human and Mouse Genome	Haussler	UC San Francisco
Robert Baertsch	2010	Improving Gene Annotation and Understanding of Mammalian Evolution by Identifying Retrocopies of mRNA Transcripts	Haussler	SkyTran
David Bernick	2010	Sequential Discovery--from Small RNA to Genomes, an Investigation of the Hyperthermophilic Genus Pyrobaculum	Lowe	UC Santa Cruz
Patricia Chan	2010	Characterization of Archaeal Species through RNASE P and Transfer RNAs	Lowe	Maverix Biomics
Jenny Draper	2010	Chemoreceptors and the Genome Sequence of Helicobacter Pylori Strain SSI	Ottemann	Institute of Environmental Science & Research, New Zealand
Sol Katzmann	2010	Evolutionary Forces at Work in the Human Genome	Haussler	UC Santa Cruz
Craig Lowe	2010	The Contribution of Mobile Elements to Gene Regulatory Innovations on the Human Lineage	Haussler	Duke University School of Medicine
Brian Raney	2010	Reconstructing Ancestral Genomes: A Case Study of Small Inversions on the Human Lineage Since the Eutherian Explosion	Haussler	UC Santa Cruz
George Shackelford	2010	Residue-residue Contact Predictions Using Neural Networks and Selected Statistics	Karplus	Shackelford Labs
Grant Thiltgen	2010	Creating New Local Structure Alphabets for Protein Structure Prediction	Karplus	Metis
Martina Koeva	2009	Stemness Revisited: a Meta Analysis of Stem Cell Signatures Using High-Throughput Data Integration	Stuart	Merck
Josue Samayoa	2009	A Bioinformatic Analysis of Simple Repeats and Small Proteins in Prokaryotic Genome	Karplus	AbbVie
Charles Vaske	2009	Prediction and Expansion of Biological Pathways from Perturbation Effects	Stuart	UC Santa Cruz
Matthew Weirauch	2009	Data Integration Methods for Systems-Level Investigation of Gene Functional Association Networks	Stuart	University of Cincinnati

M.S. Alumni

Name	Year	Capstone Project Title	Chair	Initial Post-Graduation Placement
Deanna Fedash	2021	Golden Slug: Towards an All-in-One Software Suite for Golden Gate Assembly	Bernick	RealSeq Biosciences
Nick Kreusser	2021	Golden Slug: Towards an All-in-One Software Suite for Golden Gate Assembly	Bernick	Cepheid
Victoria Le	2021	Golden Slug: Towards an All-in-One Software Suite for Golden Gate Assembly	Bernick	Cepheid
Letitia Mueller	2021	Mutational signatures in breast cancer patients: Evidence of an aberrant Homologous Recombination Repair Pathway	Cline	UCSD School of Medicine
Zeal Panchal	2021	Developing Nanopore Devices to Detect Biomarkers in Extreme Environments	Oye	SnapDNA
Danilo Dubocanin	2020	Comparative Analysis of Long-Read Transcriptome Assembly Pipelines	Vollmers	University of Washington
Erik Hanson	2020	Developing Methods for Construction of Population Pedigrees From Low Coverage Sequencing Data	Corbett-Detig	TBA
Jim Zheng	2020	A Minimal-Feature Classifier for Pan-Cancer Subtyping	Stuart	TBA
Andrew Blair	2019	Single-Cell Transcriptomic Profiling of the Human Fetal Heart	Stuart	Gladstone Institutes
Beth DeVogeleare	2019	Identifying Open Reading Frames in 5' Untranslated Regions	Brooks	Takeda Oncology
Benjamin McCreath	2019	Improving the Accuracy of Nanopore Reads via Computational Methods	Corbett-Detig	10X Genomics
Vinay Poodari	2019	Direct RNA Sequencing of E. coli Initiator tRNA Using the MinION Sequencing Platform	Bernick	UC Santa Cruz
Naveed Ziari	2019	Feature Extraction from Brain Organoids	Haussler	PhD, UC Berkeley
Allysia Mak	2018	Comparative Analysis of Variant Callers for Somatic Mutations in RNA-Seq	Brooks	Guardant Health
Joseph Olivier	2018	Development of a Nanosensor for Molecular Detection and Quantification using the Nanopipette	Pourmand	Margeta
Lori Siao	2018	Exploration of Tumor Versus Normal Gene Expression Analysis Methods to Identify Therapeutic Targets in Pediatric Cancer	Haussler	Zymergen
Audrey Lyman	2017	Thermodynamic Landscape of Pairwise Mutations in TEM-1 Suggests a Pervasive Role of Global Suppressors During ESBL Evolution	Camps	Dovetail Genomics
Audrey Musselman-Brown	2017	Identifying BRACA Variants in Published Literature using PubMunch	Haussler	Color Genomics
Paul Sanghera	2017	Capstone Project		Park University
Sean Blum	2016	A Community Evaluation of Reference Genome Graphs	Haussler	Stealth Start-Up
Sumedha Dharmadhikari	2016	Using RNA Spike-In Control for Quantification of Immune Repertoire Sequencing Data	Vollmers	Arc Bio
Joshua Espinoza	2016	Fluxomic Analysis-Based Approach for Engineering an Ethanologenic Strain of Haloferax Volcanii	Bernick	J. Craig Venter Institute
Jessica Kost	2016	Targeting Wolbachia Inside the Host: A Computational Study of Wolbachia-Host Interactions	Sullivan	Nirmidas Biotech
Baldandorj Baatar	2015	A Method to Assess Epigenetic Cytosine Modifications in Synthetic Oligonucleotides Using Liquid Chromatography-Tandem Mass Spectrometry	Akeson	Sensor-Kinesis
Peter Ryabinin	2015	Computational Analysis of tRNA Identity Elements in Bacterial and Eukaryote Genomes	Lowe	Oregon Health and Science University
Thomas Busch	2014	Bioinformatics Prediction of Cancer Drug Targets	Berman	Western Connecticut Health Network
John Collins	2014	Manipulation of Gene Expression in Breast Cancer Cells to Recapitulate a Taxol-Resistant Phenotype	Pourmand	Brain Corp
Andrea Corredor	2014	Target Prediction of Archaeal C/D Box RNA	Lowe	Square
Thomas Konneker	2013	Capstone Project		Apex
Olga Botvinnik	2012	Capstone Project	Pourmand	Chan Zuckerberg Biohub
Paola Castro	2012	Capstone Project		Bugcrowd Inc
Nicholas Hahner	2012	Capstone Project		Sema4
Edward Liaw	2012	Capstone Project		Human Longevity, Inc
Daniel Sam	2012	Capstone Project	Stuart	TBA
Kaleem Khwaja	2011	Capstone Project	Lowe	Children's Hospital, Oakland
Alexander Atkins	2010	Capstone Project	Hughey	TBA
Samuel Boyarsky	2010	Capstone Project	Stuart	A Big Company
Shyamini Vasili	2010	Analysis of Alternative Splicing Events Across Human and Mouse	Lowe	cPacket Networks
Alexander Williams	2010	Capstone Project	Karplus	UCLA
Christopher Wong	2010	Capstone Project	Stuart	UC Santa Cruz
Miriam Bellows	2009	Analysis of Additional Cystenines in HIV-1 Subtype E Envelope Glycoprotein gp 120 V4 Domain	Berman	Azul Ancora
Pinal Kanabar	2009	Joint Intervention Networks: Multi-Perturbation Probabilistic Epstasis Analysis for Predicting Pathways	Stuart	University of Illinois at Chicago

Program Contacts

Chris Vollmers
Graduate Director

vollmers@ucsc.edu

Sinsheimer Laboratories - Room 121

René Marchington
Graduate Advisor

bme-gradadvising@ucsc.edu

Engineering 2, Suite 595 (T/TH)

Westside Research Park (W)

(831) 459-2332

**Schedule Appointment**

Walk-in hours: Tuesday, Wednesday, & Thursday
from 1:00-3:00pm.