Program in Molecular and Computational Biology
Department of Biological Sciences
University of Southern California
1050 Childs Way, RRI 201B
Los Angeles, CA 90089-2910
Phone: 213 740 8766
FAX: 213 740 2437
Email: stavare at usc dot edu
I have been at USC since 1989, where I am now a Research Professor and hold the George and Louise Kawamoto Chair in Biological Sciences. My research has focused on statistical problems arising in molecular biology, human genetics, population genetics, molecular evolution and bioinformatics. I am PI of the USC NIH Center of Excellence in Genomic Science, focusing on a Genomic approach to the genotype-phenotype map.
I am on Advisory Boards for a number of Institutes and Consortia:
I am a member of the Advisory Board of Science Translational Medicine, an associate editor of Journal of Computational Biology and Statistics Surveys, on the Editorial Board of Cancer Prevention Research, MathematicS In Action, Human Genomics, and Evolutionary Bioinformatics Online. and past Associate Editor for 13 other journals in probability, statistics and biology.
Since 2003, I have been a professor in the Department of Applied Mathematics and Theoretical Physics at the University of Cambridge, UK. Further details may be found here. I am Director of the Cancer Research UK Cambridge Institute (CRI) and also Professor of Cancer Research (Bioinformatics) in the Oncology Department. Our research focusses on cancer genomics. For further details see here. In 2009 I was elected as a Fellow of the Academy of Medical Sciences (FMedSci), and I am serving on its Council 2011-2014. In 2011 I was elected as a Fellow of the Royal Society (FRS).
CV and Publications
Current Research Interests in the Group
- Stochastic computation (MCMC without likelihoods, approximate Bayesian computation)
- Population genetics (inference for coalescent processes)
- Stem cell modeling, cellular Potts models (including methods for using methylation patterns to study stem cell evolution and mitotic division).
- Statistical genomics (microarrays and next generation sequencing particularly in D. melanogaster, genome evolution and motif detection in E. coli, origins of replication in S. cerevisiae.)
- Tracking algorithms (particularly for following behavior of multiple flies in real time)
- Probabilistic combinatorics
Current Research Funding
We are supported by grants from the National Institutes of Health and the National Science Foundation.
Current Research Students
- Mary Sara McPeek (1994-1995) Professor, Departments of Statistics and Human Genetics, University of Chicago
- Paul Marjoram (1995-1998) Research Associate Professor, USC Keck School of Medicine
- Jae K. Lee (1995-1997) Professor and Director, Division of Biostatistics, University of Virginia
- Sophie Schbath (1996) INRA, France
- Anna Pluzhnikov (1996-1998) Research Associate, Cox Lab, University of Chicago
- Semyon Kruglyak (1998-2000) Illumina, Inc.
- Daniela Golinelli (2000-2002) Statistician, RAND Corporation
- Pierre Nicolas (2004-2005) INRA, France
- Noah Rosenberg (2001-2004) Department of Biology, Stanford University
- Peter Calabrese (2001-2004) CMB, USC
- Claudia Rangel (2003-2006) INMEGEN, Mexico City
- Andrew E. Teschendorff (2005-2006) Heller Research Fellow, UCL Cancer Institute
- Natalie P. Thorne (2004-2008) Senior Postdoc, WEHI, Melbourne.
- Irene Tiemann-Boege (2007-2008) University Assistant, Institute of Biophysics, Johannes Kepler University, Linz, Austria.
- Matthew E. Ritchie (2006-2008) Senior Research Officier, WEHI, Melbourne.
- Nuno Barbosa-Morais (2005-2010) Senior Postdoctoral Fellow, Blencowe Lab, University of Toronto.
- Christina Curtis (2007-2010) Assistant Professor, USC Keck School of Medicine.
- Audrey Fu (2008-2011) Postdoc, Stephens Lab, University of Chicago.
- Nick Marko (AANS Van Wagenen Fellow, 2011-2012) M D Anderson, Houston.
- Ernest Turro (2011-2012) Senior Research Associate, Ouwehand lab, Department
of Haematology, University of Cambridge
- Benilton Carvalho (Cambridge, 2010--2012) Senior Research Associate, Department of Medical Genetics, Universidade Estadual de Campinas, Brazil
- Nick Shannon (Cambridge, 2011--2013; ICGC oesophagus project) Medical Student, National University of Singapore.
Former Research Assistant
Former Research Students
- P. J. Joyce (PhD 1988) Professor, Department of Mathematics and Statistics, University of Idaho
- R. S. Lundstrom (PhD 1990) Director of Software Engineering, Idaho Technology Inc., Salt lake City
- L. Markovtsova (PhD 2000) Bioinformatician, Roche Pharmaceuticals
- O. Will (PhD 2001) Ipsos, Los Angeles
- J. Wu (PhD 2001) Model validation analyst, PNC Bank
- K. Millman (PhD 2005) The Millman Clinic, San Jose
- D. Abdueva (PhD 2006) Affymetrix Inc.
- D. Skvortsov (PhD 2006) Illumina Inc.
- R. Jiang (PhD 2006) Illumina, Inc.
- V. Plagnol (PhD 2006) Lecturer, UCL Genetics Institute
- O. Sargsyan (PhD 2006) Leitner Lab, Los Alamos National Labs
- W. Xu (PhD 2006) Statistician, Genome Technology Center, Stanford
- R. Alaghband (PhD 2007)
- C. Curtis (PhD 2007) Assistant Professor, USC Keck School of Medicine
- J. C. Marioni (PhD 2007) Group Leader, EBI
- R. D. Wilkinson (PhD 2007) Lecturer, Mathematics Department, University of Nottingham
- M. J. Dunning (PhD 2008) Bioinformatics Core, Cancer Research UK CRI
- I. Manolopoulou (PhD 2009) Visiting Assistant Professor, Department of Statistical Science, Duke University
- T. Hardcastle (PhD 2009) [joint with JD Brenton] Postdoc, Baulcombe Lab, Cambridge
- D. Grover (PhD 2009) Associate, Reiser Lab, HHMI Janelia Farm
- L. D. Goldstein (PhD 2010) Postdoc, Gentleman Lab, Genentech
- C. Spyrou (PhD 2010) Head of Biostatistics and Regulatory Affairs, NIPD Genetics Ltd, Cyprus
- S. Ivakhno (PhD 2011) Illumina UK
- S. Knott (PhD 2011) [joint with O. Aparicio] Postdoc, Hannon lab, CSHL
- D. C. Speed (PhD 2011) Postdoc, Balding Lab, UCL Genetics Institute
- J. Woolford (PhD 2011) [joint with EA Miska]
- A. Sottoriva (PhD 2012) Postdoc, Curtis Lab, USC Keck School of Medicine
- R. Ardekani (PhD 2013) Postdoc, Fraser Lab, USC
- M. L. Smith (PhD 2013) Postdoc, Tavaré lab, Cancer Research UK Cambridge Institute
- T. Nellimoottil (PhD 2013) [Joint with O. Aparicio] EventForte, Los Angeles.
- J. Cairns (PhD submitted 2013)
USC Computational Biology Home Page
December 3 2013