GATK Development Team
The Genome Sequencing and Analysis Group @ Broad

The Genome Sequencing and Analysis Group (GSA) in Medical and Population Genetics at the Broad Institute is a team of computational biologists, software engineers, and hosted students and researchers developing algorithms for next generation DNA sequencers for medical and population genetics and cancer applications, as well as applying these algorithms to answer fundamental scientific questions.

GSA has extensive experience with processing of next-generation DNA sequencer data as well as genotyping and validation data along with downstream analysis of this data for medical and population genetics studies. The method development arm of GSA has created a powerful framework in the The Genome Analysis Toolkit for analysis of next-generation sequencing data and analysis of variation discovered by NGS. These tools are now widely used in many NGS projects, including the 1000 Genomes Project, The Cancer Genome Atlas, the Broad's production sequencing pipeline, as well as at many other sequencing centers and individual labs with sequencing machines.

Eric Banks, PhD, is the Group Leader of the Methods Development Team in the Genome Sequencing and Analysis Group at the Broad Institute. His team develops many of the highly used analysis tools that make the GATK so powerful.

Before working at the Broad, Eric completed his PhD in Computational Biology under Professor Mona Singh at Princeton University, where he held Gordon Wu and PICASso fellowships. The title of his thesis was Algorithms for Analyzing and Interrogating Protein Interaction Networks. Eric worked both as an undergraduate and for his Masters in Engineering at MIT with Professor Bonnie Berger.

Check out Eric's contributions on the forum

Ryan Poplin joined the Broad Institute in October of 2009 and has developed several methods such as Base Quality Score Recalibration and Variant Quality Score Recalibration. Previously, Ryan was a graduate student in the laboratory of Tai Sing Lee studying how brains perform Bayesian inference during visual perception. And before that, Ryan worked at MIT Lincoln Laboratory where he attached lasers to airplanes and made beautiful 3D maps of cities and forests.

Ryan holds a Master of Science in Neural Computation from Carnegie Mellon University (2009) and a Bachelor of Science in Computer Science and Mathematics from Rose-Hulman Institute of Technology (2004).

Check out Ryan's contributions on the forum

Ami needs to sign up on the forum and fill in his profile.

Check out Ami's contributions on the forum

Valentín Ruano-Rubio joined in April 2013 as a Computational Biologist in the methods development team.

Valentín completed a degree in Computer Science at Universitat Politècnica de Catalunya, Barcelona (2000). After working in industry for a few years he came back to academia completing a PhD in Evolutionary Bionformatics at University of Dublin Trinity College Ireland (2008). He did a postdoctoral stay at IGBMC Strasbourg France and them moved to a Senior Bioinformatician position working in the Malaria Program at the Wellcome Trust Sanger Institute. He continue on that role at the Wellcome Trust Centre for Human Genetics University of Oxford before becoming a Broadie.

Check out Valentin's contributions on the forum

At the Broad, Mauricio Carneiro, PhD, leads the technology development team of the Genome Sequence and Analysis group. His team's role includes developing and evaluating new sequencing technologies, development operations, infrastructure and analytics as well as reaching out to the GATK user community.

"I can't remember the last time someone walked into my office and asked me, 'Could you do something real easy for me, please?' " he says. "It is always something no one has tried before, something we have no idea whether or not it is feasible, or something that we would be able to do easily if we had 3 million times more computing capacity."

When Mauricio isn't in the office, you'll find him playing soccer, climbing either ice or rock, surfing, or snowboarding, depending on the season. A native of Rio de Janeiro, Brazil, he relishes New England weather.

"Having lived all my life in a place with only one season - the extremely hot one ­- I learned to love each season in its own special way."

To balance indoors with the outdoors, he is a passionate video game player. He played Quake and Starcraft professionally from 1997 through 2001 and counts as a career highlight leading the production of Alien Revolt in 2004, the first massive multiplayer role-playing game using one's real location.

You can visit his personal webpage for curriculum vitae and publications and more information.

Check out Mauricio's contributions on the forum

Bertrand needs to edit his profile.

Check out Bertrand's contributions on the forum

Builder Monkey

Géraldine Van der Auwera joined the Broad Institute in April of 2012 and is in charge of outreach to the GATK user community, which includes developing this website and the documentation it hosts, as well as responding to user questions on this forum and organizing user workshops.

Before becoming a tech support webmonkey, Géraldine was most notably a postdoctoral fellow at Harvard Medical School, where she studied not human genomes but microbial ones (Bacillus for the win!).

She can be plied to answer USER ERROR questions with liberal amounts of beer and chocolate from her native land of Belgium.

Géraldine holds a PhD in Biological Engineering (sp. Microbial Genetics) from the University of Louvain (UCL) in Louvain-la-Neuve, Belgium (2007).

Check out Geraldine's contributions on the forum

Joel needs to fill in his profile.

Check out Joel's contributions on the forum

Laura Doyle Gauthier joined the Broad in February 2014 as a Computational Biologist with the methods development team.

Laura began her research career in the lab of Raimond Winslow at Johns Hopkins University. There she worked on various cardiac imaging projects on the way to earning her BS in biomedical engineering. She decided she just couldn't get enough of Baltimore and stayed on in the Winslow lab to do her PhD research in mathematical modeling of reactive oxygen species in the heart. This work led to NSF and NDSEG fellowships, a penchant for all things computational and biological, and a fond appreciation of mitochondria.

Check out Laura's contributions on the forum

Sheila has a BA in English from the University of Florida and a MS in Computational Biology from Carnegie Mellon University. Her role is to document the tools of the GATK in a way all types of users can understand.

In her spare time, Sheila likes to play tennis and play the violin. She is looking forward to answering all of your questions about the GATK!

Check out Sheila's contributions on the forum