Difference between revisions of "Daniel Marbach"
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I have a strong interest in open, collaborative approaches to tackle these problems. As part of the [http://dreamchallenges.org/ 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 [http://web.mit.edu/newsoffice/2012/the-wisdom-of-crowds-nature-methods-paper.html wisdom of crowds] to accelerate biological and biomedical discoveries. | I have a strong interest in open, collaborative approaches to tackle these problems. As part of the [http://dreamchallenges.org/ 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 [http://web.mit.edu/newsoffice/2012/the-wisdom-of-crowds-nature-methods-paper.html wisdom of crowds] to accelerate biological and biomedical discoveries. | ||
| − | + | == Publications == | |
| + | [[File:nature_methods_cover2.png|130px|thumb|right|]] | ||
Selected publications: | Selected publications: | ||
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* '''Fast and rigorous computation of gene and pathway scores from SNP-based summary statistics'''. ('''[http://regulatorycircuits.org/data/papers/LamparterMarbach2016.pdf PDF]''')<br> Lamparter D*, Marbach D*, Rico R, Kutalik Z, and Bergmann S. <br> [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004714 ''PLoS Computational Biology'' 12, e1004714, 2016]. | * '''Fast and rigorous computation of gene and pathway scores from SNP-based summary statistics'''. ('''[http://regulatorycircuits.org/data/papers/LamparterMarbach2016.pdf PDF]''')<br> Lamparter D*, Marbach D*, Rico R, Kutalik Z, and Bergmann S. <br> [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004714 ''PLoS Computational Biology'' 12, e1004714, 2016]. | ||
** [http://www2.unil.ch/cbg/index.php?title=Pascal Project website] | ** [http://www2.unil.ch/cbg/index.php?title=Pascal Project website] | ||
| − | * '''Wisdom of crowds for robust gene network inference'''. ('''[http://compbio.mit.edu/marbach/papers/Marbach2012b.pdf PDF]''')<br> Marbach D*, Costello JC*, Küffner R*, Vega NM, Prill RJ, Camacho DM, Allison KR, The DREAM5 Consortium, Kellis M, Collins JJ, Stolovitzky G. <br> [http://dx.doi.org/10.1038/nmeth.2016 ''Nature Methods'', 9, 796-804, 2012]. | + | * [[File:nature_methods_cover1.gif|130px|thumb|right|]] '''Wisdom of crowds for robust gene network inference'''. ('''[http://compbio.mit.edu/marbach/papers/Marbach2012b.pdf PDF]''')<br> Marbach D*, Costello JC*, Küffner R*, Vega NM, Prill RJ, Camacho DM, Allison KR, The DREAM5 Consortium, Kellis M, Collins JJ, Stolovitzky G. <br> [http://dx.doi.org/10.1038/nmeth.2016 ''Nature Methods'', 9, 796-804, 2012]. |
** [http://www.nature.com/nmeth/journal/v9/n8/covers/index.html From the cover], [http://web.mit.edu/newsoffice/2012/the-wisdom-of-crowds-nature-methods-paper.html MIT news] | ** [http://www.nature.com/nmeth/journal/v9/n8/covers/index.html From the cover], [http://web.mit.edu/newsoffice/2012/the-wisdom-of-crowds-nature-methods-paper.html MIT news] | ||
** [http://dream.broadinstitute.org dream.broadinstitute.org] | ** [http://dream.broadinstitute.org dream.broadinstitute.org] | ||
* '''Predictive regulatory models in ''Drosophila melanogaster'' by integrative inference of transcriptional networks'''. ('''[http://compbio.mit.edu/marbach/papers/Marbach2012a.pdf PDF]''') <br> Marbach D*, Roy S*, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M. <br>[http://genome.cshlp.org/content/22/7/1334.short ''Genome Research'', 22, 1334-49, 2012]. | * '''Predictive regulatory models in ''Drosophila melanogaster'' by integrative inference of transcriptional networks'''. ('''[http://compbio.mit.edu/marbach/papers/Marbach2012a.pdf PDF]''') <br> Marbach D*, Roy S*, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M. <br>[http://genome.cshlp.org/content/22/7/1334.short ''Genome Research'', 22, 1334-49, 2012]. | ||
* '''Revealing strengths and weaknesses of methods for gene network inference'''. ('''[http://infoscience.epfl.ch/record/148228/files/Marbach2010.pdf PDF]''')<br> Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G.<br> [http://www.pnas.org/content/107/14/6286.abstract ''PNAS'', 107, 6286-6291, 2010.] | * '''Revealing strengths and weaknesses of methods for gene network inference'''. ('''[http://infoscience.epfl.ch/record/148228/files/Marbach2010.pdf PDF]''')<br> Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G.<br> [http://www.pnas.org/content/107/14/6286.abstract ''PNAS'', 107, 6286-6291, 2010.] | ||
| + | |||
| + | Complete list of publications: '''[https://scholar.google.com/citations?user=UxH51HkAAAAJ&hl=en Google Scholar]''' | ||
== Web sites == | == Web sites == | ||
Revision as of 01:39, 4 April 2016
File:Daniel Marbach.png
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
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. - Fast and rigorous computation of gene and pathway scores from SNP-based summary statistics. (PDF)
Lamparter D*, Marbach D*, Rico R, Kutalik Z, and Bergmann S.
PLoS Computational Biology 12, e1004714, 2016. - 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. - 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.
Complete list of publications: Google Scholar
Web sites
Contact
- Address: Rue du Bugnon 27 - DGM 023 - CH-1005 Lausanne - Switzerland
- Phone at work: +41-21-692-5378
- Cell phone: +41-78-966-3168
- e-mail: daniel.marb...@unil.ch (fill in the blank)
