Laurent Jacob

Presentation

I am a currently a postdoctoral researcher in the department of statistics of UC Berkeley.

I recently finished my Ph.D. at the École des Mines de Paris, in the Center for Computational Biology lead by Jean-Philippe Vert. The final manuscript is available here.

My research deals with statistical learning, and its application to biological and therapeutic problems, in particular cancer outcome prediction, molecular data analysis and drug discovery.

Education

• 2009 - Ph.D. at the École des Mines de Paris.
• 2006 - Master MVA (Mathematics, Vision, Learning) at the École Normale Supérieure de Cachan.
• Fall 2004 - One semester at Universidad Politécnica de Valencia.
• 2000-2005 - Université de Technologie de Compiègne ("Grande École"). Major: Computer Sciences, Minor: Philosophy, Technology and Cognition.

A more complete resume can be downloaded here.

Publications

• Short research summary (2009)
• BibTeX

Submitted

• Group Lasso with Overlaps: the Latent Group Lasso approach. G. Obozinski*, L. Jacob*, J.-P. Vert.
  [Techreport]
• A More Powerful Two-Sample Test in High Dimensions using Random Projection. M. Lopes, L. Jacob, M. Wainwright.
  [Techreport (journal version)]

2012

• Search for a gene-expression signature of breast cancer local recurrence in young women. N. Servant, M. A. Bollet, H. Halfwerk, K. Bleakley, B. Kreike, L. Jacob, D. Sie, R. Kerkhoven, P. Hupe, R. Hadhri, A. Fourquet, H. Bartelink, E. Barillot, B. Sigal-Zafrani, M. J. van de Vijver. Clinical Cancer Research, to appear.

2011

• A More Powerful Two-Sample Test in High Dimensions using Random Projection. M. Lopes, L. Jacob, M. Wainwright. Advances in Neural Information Processing Systems (NIPS 24), 2011.
  [Link]
• More Power via Graph-Structured Tests for Differential Expression of Gene Networks. L. Jacob, P. Neuvial, S. Dudoit. The Annals of Applied Statistics, 2011.
  [Link] [Video] [Bioconductor package DEGraph] [Bioconductor package NCIgraph]
• Regularized learning in bioinformatics. L. Jacob. Journal de la Société Francaise de Statistiques Vol. 152, No 2, 2011.
  [Link]

2010

• Gains in Power from Structured Two-Sample Tests of Means on Graphs. L. Jacob, P. Neuvial, S. Dudoit. Techreport, 2010.
  [Techreport] [Video] [Bioconductor package DEGraph] [Bioconductor package NCIgraph]
• Increasing stability and interpretability of gene expression signatures. A.-C. Haury, L. Jacob, J.-P. Vert. Techreport, 2010.
  [arXiv]

2009

• Structured priors for supervised learning in computational biology. L. Jacob. Ph.D. dissertation, 2009.
  [Manuscript][Defense slides]
• Group Lasso with Overlap and Graph Lasso. L. Jacob, G. Obozinski, J.-P. Vert. International Conference on Machine Learning (ICML 26), 2009.
  [Link][Slides][Video][Code and data]
• Clustered Multi-Task Learning: A Convex Formulation. L. Jacob, F. Bach, J.-P. Vert. Advances in Neural Information Processing Systems (NIPS 21), 2009.
  [Link][Old techreport (arXiv)] [Code and data]

2008

• Virtual screening of GPCRs: an in silico chemogenomics approach. L. Jacob, B. Hoffmann, V. Stoven, J.-P. Vert. BMC Bioinformatics, 9:363, 2008.
  [Link] [Old techreport (arXiv)] [Code and data]
• Protein-ligand interaction prediction: an improved chemogenomics approach, L. Jacob and J.-P. Vert. Bioinformatics, 24(19):2149-2156, 2008.
  [Link] [Old techreport (arXiv)] [NIPS 2007 MLCB workshop slides] [CAp 2008 conference slides]
• Machine learning for in silico virtual screening and chemical genomics: new strategies, J.-P. Vert and L. Jacob. Combinatorial Chemistry & High Throughput Screening, 11(8):677-685, 2008.
  [Link] [Old techreport]
• Efficient peptide-MHC-I binding prediction for alleles with few known binders, L. Jacob and J.-P. Vert. Bioinformatics, 24(3):358-366, 2008.
  [Link] [Application (KISS)] [Old techreport (arXiv)] [Code and data]

Before 2008

• Master report, Multitask learning for epitope prediction.
  [Report] [Defense slides]
• Final project for Université de Technologie de Compiègne, Développement d'outils de clustering pour l'analyse de données en génomique fonctionnelle (in french).
  [Report] [Poster]

Teaching

• Fall 2010, Teaching assistant for the "PB HLTH C240C/STAT C245C: Biostatistical Methods: Computational Statistics with Applications in Biology and Medicine" class, UC Berkeley. [Website (password protected)]
• Fall 2010, "Using networks in machine learning and statistics", 1-hour class at BioInfoSummer 2010 summer school, Melbourne, Australia.
  [Slides]
• Fall 2010, "Statistical Methods and Software for mRNA-Seq and ChIP-Seq", 3-day class at Centro de Investigacion Principe Felipe, Valencia, Spain.
  [Course website]
• Spring 2009, "Apprentissage en bioinformatique et noyaux pour structures" for the machine learning module of École des Mines de Paris (in french).
  Lecture slides, material and questions for the practical session.
• Spring 2008, "Apprentissage en bioinformatique et noyaux pour structures" for the machine learning module of École des Mines de Paris (in french).
  Lecture slides, material and questions for the practical session.
• Spring 2007, "Apprentissage en bioinformatique et noyaux pour structures" for the machine learning module of École des Mines de Paris (in french).
  Lecture slides (inspired by Jean-Philippe Vert's slides and Pierre Mahé's PhD defense slides), material for the practical session.