Journal papers

Please cite the following papers when using GNW in your publication:

• GeneNetWeaver: In silico benchmark generation and performance profiling of network inference methods.
  Schaffter T, Marbach D, and Floreano D.
  Bioinformatics, 27(16):2263-70, 2011. [info] [bibtex] [Featured by Faculty of 1000 as must read]

• Generating realistic in silico gene networks for performance assessment of reverse engineering methods.
  Marbach D, Schaffter T, Mattiussi C, and Floreano D.
  Journal of Computational Biology, 16(2):229-239, 2009. [info] [bibtex]

For the DREAM network inference challenges, please cite:

• Wisdom of crowds for robust gene network inference.
  Marbach D*, Costello JC*, Küffner R*, Vega N, Prill RJ, Camacho DM, Allison KR, the DREAM5 Consortium, Kellis M, Collins JJ, Stolovitzky G.
  Submitted. *Contributed equally

• Revealing strengths and weaknesses of methods for gene network inference.
  Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G.
  PNAS, 107(14):6286-6291, 2010. [PNAS] [info] [bibtex]

Other papers:

• Verification of systems biology research in the age of collaborative competition.
  Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, Rice JJ, Royyuru A, Schacherer F, Sprengel J, Stolle K, Vitkup D, and Stolovitzky G.
  Nature Biotechnology, 29(9):811-5, 2011 [PubMed] [pdf]

• Towards a rigorous assessment of systems biology models: the DREAM3 challenges.
  Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, and Stolovitzky G. PLoS ONE, 5(2):e9202, 2010. [PLoS] [bibtex]

Theses

• Evolutionary reverse engineering of gene networks.
  Daniel Marbach. Ph.D. Thesis, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland, 2009. [info] [bibtex]

Conference presentations

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• Marbach D*, Costello JC*, Küffner R*, Vega N, Prill RJ, Camacho DM, Allison KR, the DREAM5 Consortium, Kellis M, Collins JJ, and Stolovitzky G. Wisdom of crowds for gene network inference. International Conference on Systems Biology of Human Disease, Harvard Medical School, Boston, June 22-24, 2011. [Boehringer Ingelheim Best Poster Award]

• Marbach D*, Costello JC*, Küffner R*, Vega N, Prill RJ, Camacho DM, Allison KR, the DREAM5 Consortium, Kellis M, Collins JJ, and Stolovitzky G. Wisdom of crowds for gene network inference. 9th BC2 Basel Computational Biology Conference, Basel, Switzerland, June 23-24, 2011. [poster]

• Marbach D. Community assessment of methods for gene network inference. Systems Biology Verification Symposium, Zürich, Switzerland, March 23, 2011. [oral presentation]

• Marbach D. Profiling network inference methods - The DREAM5 network inference challenge. DREAM5, Columbia University, New York, November 16, 2010. [oral presentation]

• Marbach D. Revealing strengths and weaknesses of methods for gene network inference. DREAM4, Broad Institute of MIT and Harvard, Cambridge, December 4, 2009. [oral presentation]

• Marbach D. The DREAM4 in silico network challenge. DREAM4, Broad Institute of MIT and Harvard, Cambridge, December 4, 2009. [NYAS eBriefing] [video]

• Marbach D. Generating realistic in silico gene networks for performance assessment of reverse engineering methods. DREAM3, Broad Institute of MIT and Harvard, Cambridge, Oct 31, 2008.
  [NYAS eBriefing] [video]