Marc A. Schaub

Welcome to my academic webpage. I'm currently a Software Engineer at Google in Mountain View, California.

In June 2012, I completed my Ph.D. in the Computer Science Department at Stanford University under the supervision of Serafim Batzoglou. My broad area of interest throughout my studies has been computational biology and the application of computer science to biomedical problems. My thesis focused on integrative methods that extend Genome Wide Association Studies (GWAS) by developping new methods, asking new questions, and integrating genotype data with other high throughput modalities. Several of my projects were completed in collaboration with the groups of Atul Butte and Mike Snyder, and as a member of the ENCODE consortium. During the Summer of 2011 I participated in the Summer Institute for Entrepreneurship in the Graduate School of Business at Stanford.

Prior to joining Stanford, I was a member of the Models and Theory of Computation group at the Ecole Polytechnique Fédérale de Lausanne (EPFL), where I worked on developping formal methods for the construction and analysis of models of biological systems. I received an MSc in Computer Science with a specialization in bio-computing from EPFL in March 2006. During my undergraduate studies, I was an exchange student in the School of Computer Science at Carnegie Mellon University, where I also took part in the Summer Undergraduate Research Program (SURP) in the Department of Biological Sciences. I'm originally from Switzerland, and grew up in the medieval town of Saillon, and attended the Lycée-Collège des Creusets in Sion.

My hobbies include photography, traveling, and the outdoors, and I volunteer as an Emergency Medical Technician with Stanford EMS.


Email: (replace with my first and last name)

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M.A. Schaub, A.P. Boyle, A. Kundaje, S. Batzoglou, M.P. Snyder.
Linking Disease Associations with Regulatory Information in the Human Genome.
Genome Res. 2012 Sep;22(9):1748-59.
This paper is part of the Nature ENCODE Explorer thread Impact of functional information on understanding variation.
Stanford press release, Results website.

The ENCODE Consortium.
An Integrated Encyclopedia of DNA Elements in the Human Genome.
Nature. 2012 Sep 6;489(7414):57-74.
Interactive Nature ENCODE Explorer, ENCODE website, NIH press release.

A.P. Boyle, E.L. Hong, M. Hariharan, Y. Cheng, M.A. Schaub, M. Kasowski, K.J. Karczewski, J. Park, B.C. Hitz, S. Weng, J.M. Cherry, M.P. Snyder.
Annotation of functional variation in personal genomes using RegulomeDB.
Genome Res. 2012 Sep;22(9):1790-7.
This paper is part of the Nature ENCODE Explorer thread Impact of functional information on understanding variation.
Stanford press release, website.

L.Y. Liu, M.A. Schaub, M. Sirota, A.J. Butte.
Sex Differences in Disease Risk from Reported Genome-Wide Association Study Findings.
Hum Genet. 2012 Mar;131(3):353-64

L.Y. Liu, M.A. Schaub, M. Sirota, A.J. Butte.
Transmission distortion in Crohn’s disease risk gene ATG16L1 leads to sex difference in disease association.
Inflammatory Bowel Diseases 17. doi:10.1002/ibd.21781

M. Sirota, M.A. Schaub, S. Batzoglou, W.H. Robinson, A.J. Butte.
Autoimmune Disease Classification by Inverse Association with SNP Alleles.
PLoS Genet 5(12):e1000792. 2009.
Stanford press release

M.A. Schaub, I.M. Kaplow, M. Sirota, C.B. Do, A.J. Butte, S. Batzoglou.
A Classifier-based Approach to Identify Genetic Similarities Between Diseases.
Bioinformatics 25: i21-29. 2009.
Presentation at the 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB), June 27 - July 2nd, 2009, Stockholm, Sweden.

M.A. Schaub, A.C. Bezdek, T.A. Henzinger, F. Radtke and J. Fisher.
Qualitative Crosstalk Analysis of Wnt and Notch Signaling in Mammalian Skin.
RECOMB Satellite Conferences on Systems Biology - November 30 - December 1st, 2007, San Diego, CA

M.A. Schaub, T.A. Henzinger, and J. Fisher.
Qualitative Networks: A Symbolic Approach to Analyze Biological Signaling Networks.
BMC Systems Biology 2007, 1:4.

J.M. Burnette, E. Miyamoto-Sato, M.A. Schaub, J. Conklin, and A.J. Lopez.
Subdivision of Large Introns in Drosophila by Recursive Splicing at Non-exonic Elements.
Genetics. 2005 Jun;170(2):661-74.

Last modified: September 8, 2012