Faculty / Leadership

Benedict Patten Team Photo
Benedict Paten Director; Assistant Professor, Computational Genomics Laboratory (CGL)

I am a principal investigator, director of the Computational Genomics Lab and an associate research scientist within the UC Santa Cruz Genomics Institute. I have a PhD from Cambridge University and the European Molecular Biology Laboratory. I am trying to contribute to answering some big questions, e.g. how we became human?, how we relate genetically to each other and other species?, and how genomes relate to the states of health and disease? To attack these questions I love algorithms, computers and coffee.

Brian O'Connor
Brian O’Connor Director of the Computational Genomics Platform

Dr. Brian O’Connor is the Director of the UCSC Genomics Institute Computational Genomics Platform, a sister project to the Computational Genomics Lab. There he focuses on the development and deployment of large-scale, cloud-based systems for analyzing genomics data. This includes the Toil workflow execution platform, which is designed to run genomic pipelines on a wide range of cloud environments including AWS, Azure, Google and OpenStack, and ADAM, a distributed genomics platform developed in collaboration with UC Berkeley. He is also the co-chair of the Containers and Workflows task team of the Global Alliance for Genomics and Health (GA4GH) where he works on tool and workflow container standards. Brian joined UCSC from the Ontario Institute for Cancer Research (OICR) where his previous projects included leading the technical implementation of cloud-based analysis systems for the PanCancer Analysis of Whole Genomes (PCAWG, https://dcc.icgc.org/pcawg) effort, acting as the project manager for the International Cancer Genome Consortium’s Data Portal (https://dcc.icgc.org), and creating the Dockstore project (https://dockstore.org), a platform for tool and workflow sharing.”

 

Program Managers

Trevor Heathorn
Trevor Heathorn Program Manager, Computational Genomics Platform (CGP)

My background is in software development and managing development teams in the computer storage industry. I have helped develop NAS (network attached storage) products such as SnapServer, which delivers easy-to-use network storage for SMBs (small and medium businesses) as well as clustered Enterprise Storage systems (BlueArc Titan and Overland Storage SnapScale) offering such features as High Availability, Clustered File System, Snapshots and Data Replication. I joined the Genomics Institute to help make a positive contribution to the development of treatments for genetically related diseases. My LinkedIn profile.

Kevin Osborne Team
Kevin Osborn Technical Director of Software Development, Computational Genomics Platform (CGP)

I spent 20 years working as an engineering manager in the file server storage industry starting with CDROM, moving to network attached storage and finally to clustered file servers and distributed computing before coming to UCSC to work in genomics. I have a patent on network security abstraction and another on distributed server synchronization (in process). My current work is with the GA4GH team to produce industry standard genomics APIs. I have bachelor degrees in Computer Science from UCSC and another in Natural Resources from Humboldt State, as well as an MFA from Brooks Institute in Photography. In my spare time I teach photography workshops and work on my own fine art business. I am also a long time fencing club operator in Santa Cruz who is certified as a Prevot level instructor.


Cricket Sloan Program Manager , Computational Genomics Platform (CGP)

Scientists

 
 
 

Software Engineers


Michael Baumann Senior Software Engineer, Computational Genomics Platform (CGP)
Benedict Patten Team Photo
Louise Cabansay Junior Software Engineer, Computational Genomics Platform (CGP)

Michael Krause Software Engineer, Computational Genomics Platform (CGP)

Natalie Perez Junior Software Engineer, Computational Genomics Platform (CGP)

Walt Shands Software Engineer, Computational Genomics Platform (CGP)

Walt develops software for the Computational Genomics Platform (CGP) where his focus is on integration of bioinformatics pipelines such as RNA-Seq, ProTECT, and BCBio into the software infrastructure, running those pipelines on genomic data and developing new features. In addition he contributes to HMMER, a homology search application, most recently implementing translated search. Walt has a wealth of industry experience which includes significant contributions at Intel, Fujitsu and AT&T Bell Laboratories. Walt has both an M.S. and B.S from the School of Engineering at Columbia University in New York, and a black belt in Aikido.

Lon Blauvelt
Lon Blauvelt Junior Software Engineer (BP2), Computational Genomics Platform (CGP)

I currently work on Toil development, UCSC’s workflow execution engine for large biological compute jobs. I have a B.S. in Bioengineering from UC Santa Cruz, and have a strong interest in pursuing bioinformatic approaches to research questions in biology using big data.


Abraham ChavezJunior Software Engineer, Computational Genomics Platform (CGP)

Geryl Pelayo Software Engineer, Computational Genomics Platform (CGP)

Charles Overbeck Senior Software Engineer, Computational Genomics Platform (CGP)

Daniel Sotirhos Software Engineer, Computational Genomics Platform (CGP)

Jesse Brennan Junior Software Engineer, Computational Genomics Platform (CGP)

I’m a recent graduate of UCSC, and started at CGL as an undergraduate student researcher. I work on full-time on projects including Toil.

Benedict Patten Team Photo
Amar Jandu Junior Software Engineer, Computational Genomics Platformv (CGP)

Brian Hannafious Software Engineer, Computational Genomics Platform (CGP)
Hannes Schmidt Team Pic
Hannes Schmidt Senior Software Engineer, Computational Genomics Platform (CGP)

Hannes re-joined the Genomics Institute in November, 2017 as a Senior Software Engineer working under Kevin Osborn as part of the Computational Genomics Platform (CGP), directed by Brian O’Connor.

Hannes holds a Dipl.Ing. (M.Eng) in computer science from Technische Universität Berlin. During his previous stint at UCSC he contributed to CGHub, the TCGA data repository, and CGL projects like Toil, CGCloud, Apache Spark, S3AM and Conductor. His interests are in cloud computing, big data, systems programming, and programming language design. He re-joined the Genomics Institute in November, 2017 as a Senior Software Engineer working under Kevin Osborn as part of the Computational Genomics Platform (CGP), directed by Brian O’Connor.

David Steinberg Team
David Steinberg Software Engineer, Computational Genomics Platform (CGP)

As a software developer with the Genomics Institute I have worked on enabling software systems for genomic analysis. My background is in software design for the web, visual analytics, and systems integration. I hold a BA in Philosophy from UCSC and am interested in how technology can be used to reduce human suffering.

Undergraduate Student Researchers


Ryan Bautista Undergraduate Student Researcher

Natan Lao Undergraduate Student Researcher

I’m an undergraduate studying computer engineering with a concentration in networking. I work on Toil and sometimes on other things that aren’t as cool as Toil.


Benjamin Van de Brooke Undergraduate Student Researcher

Justin Krupp Undergraduate Student Researcher

Shreya Radesh Undergraduate Student Researcher
Melaina Legaspi Undergraduate Student Researcher

Emily Soth Undergraduate Student Researcher

Administrative Staff

Nadine Gassner
Nadine Gassner Associate Director Research Development

In partnership with principal investigators, I lead development of a portfolio of Computational Genomics Lab programs.