Daniel Marbach

Daniel Marbach

Short bio

• Since 2013: Senior Researcher at Sven Bergmann's group, University of Lausanne
• 2009 - 2013: Postdoctoral Fellow at Manolis Kellis' group, Broad Institute of MIT and Harvard
• 2005 - 2009: PhD Student at Dario Floreano's group, EPFL

Research

The overarching aim of my work is to:

• (1) Develop computational methods to unravel molecular networks from large-scale data
• (2) Leverage these networks to improve our understanding of genetic variants and disease mechanisms

I have a strong interest in open, collaborative approaches to tackle these problems. As part of the DREAM Challenges, I develop and lead crowdsourced competitions addressing key challenges in systems biology and translational medicine. By bringing together teams of researchers working on the same problem, I leverage the wisdom of crowds to accelerate biological and biomedical discoveries.

Publications

Complete list of publications: Google Scholar

Selected publications:

• Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases. (PDF)
  Marbach D, Lamparter D, Quon G, Kellis M, Kutalik Z, and Bergmann S.
  Nature Methods, 13, 366-370, 2016.
  • Nature Reviews Genetics highlight, SIB news, UNIL news
  • regulatorycircuits.org
• Fast and rigorous computation of gene and pathway scores from SNP-based summary statistics. (PDF)
  Lamparter D*, Marbach D*, Rueedi R, Kutalik Z, and Bergmann S.
  PLoS Computational Biology 12, e1004714, 2016.
  • Project website
• 
  Wisdom of crowds for robust gene network inference. (PDF)
  Marbach D*, Costello JC*, Küffner R*, Vega NM, Prill RJ, Camacho DM, Allison KR, The DREAM5 Consortium, Kellis M, Collins JJ, Stolovitzky G.
  Nature Methods, 9, 796-804, 2012.
  • From the cover, MIT news
  • dream.broadinstitute.org
• Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. (PDF)
  Marbach D*, Roy S*, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M.
  Genome Research, 22, 1334-49, 2012.
• Revealing strengths and weaknesses of methods for gene network inference. (PDF)
  Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G.
  PNAS, 107, 6286-6291, 2010.

Web sites

• Disease Module Identification DREAM Challenge
• regulatorycircuits.org
• compbio.mit.edu/marbach

Contact

• Address: Rue du Bugnon 27 - CH-1011 Lausanne - Switzerland
• Cell phone: +41-78-966-3168
• e-mail: daniel.marb...@gmail.com (fill in the blank)