Difference between revisions of "Daniel Marbach"
| (7 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| − | [[File:Daniel_Marbach. | + | [[File:Daniel_Marbach.jpg|160px|thumb|left|Daniel Marbach]] |
== Short bio == | == Short bio == | ||
| Line 6: | Line 6: | ||
* 2009 - 2013: Postdoctoral Fellow at [http://compbio.mit.edu Manolis Kellis' group], '''Broad Institute of MIT and Harvard''' | * 2009 - 2013: Postdoctoral Fellow at [http://compbio.mit.edu Manolis Kellis' group], '''Broad Institute of MIT and Harvard''' | ||
* 2005 - 2009: PhD Student at [http://lis.epfl.ch Dario Floreano's group], '''EPFL''' | * 2005 - 2009: PhD Student at [http://lis.epfl.ch Dario Floreano's group], '''EPFL''' | ||
| − | + | <br> | |
== Research == | == Research == | ||
| − | The overarching aim of my | + | The overarching aim of my research is to advance the impact of large-scale biomedical data on human health. Having a background in computer science and machine learning, I am developing novel tools that leverage heterogeneous, high-dimensional data to identify context- and patient-specific disease mechanisms. For example, in recent work I introduced integrative models bridging the current gap between genetic risk factors and disease outcomes by layering in tissue-specific molecular circuits that are disrupted by variants occurring in our genome. Mapping these context-specific disease circuits will be key to develop better biomarkers and personalized therapeutics. |
| − | |||
| − | |||
| − | 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 | + | 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 personalized medicine. By bringing together hundreds of researchers and citizens with diverse backgrounds working on the same problem, these open data challenges 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. |
| − | == | + | == Selected publications == |
| − | [ | + | |
| + | Complete list of publications: '''[https://scholar.google.com/citations?user=UxH51HkAAAAJ&hl=en Google Scholar]''' | ||
Selected publications: | Selected publications: | ||
| Line 26: | Line 25: | ||
* '''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*, Rueedi 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*, Rueedi 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] | ||
| − | * [[File: | + | * [[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.] | ||
| − | |||
| − | |||
== Web sites == | == Web sites == | ||
| + | * [https://synapse.org/modulechallenge Disease Module Identification DREAM Challenge] | ||
* [http://regulatorycircuits.org regulatorycircuits.org] | * [http://regulatorycircuits.org regulatorycircuits.org] | ||
* [http://compbio.mit.edu/marbach/ compbio.mit.edu/marbach] | * [http://compbio.mit.edu/marbach/ compbio.mit.edu/marbach] | ||
| Line 41: | Line 39: | ||
== Contact == | == Contact == | ||
| − | * Address: Rue du Bugnon 27 | + | * Address: Rue du Bugnon 27 - CH-1011 Lausanne - Switzerland |
| − | |||
* Cell phone: +41-78-966-3168 | * Cell phone: +41-78-966-3168 | ||
| − | * e-mail: daniel.marb...@ | + | * e-mail: daniel.marb...@gmail.com (fill in the blank) |
Latest revision as of 15:49, 15 March 2017
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 research is to advance the impact of large-scale biomedical data on human health. Having a background in computer science and machine learning, I am developing novel tools that leverage heterogeneous, high-dimensional data to identify context- and patient-specific disease mechanisms. For example, in recent work I introduced integrative models bridging the current gap between genetic risk factors and disease outcomes by layering in tissue-specific molecular circuits that are disrupted by variants occurring in our genome. Mapping these context-specific disease circuits will be key to develop better biomarkers and personalized therapeutics.
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 personalized medicine. By bringing together hundreds of researchers and citizens with diverse backgrounds working on the same problem, these open data challenges leverage the wisdom of crowds to accelerate biological and biomedical discoveries.
Selected 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. - 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. - 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.
Web sites
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)
