Daniel Marbach - Publications

Affiliations: 
Massachusetts Institute of Technology, Cambridge, MA, United States 

17 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Tomasoni M, Gómez S, Crawford J, Zhang W, Choobdar S, Marbach D, Bergmann S. MONET: a toolbox integrating top-performing methods for network modularisation. Bioinformatics (Oxford, England). PMID 32271874 DOI: 10.1093/bioinformatics/btaa236  0.32
2019 Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R, Subramanian A, Zhang JD, ... ... Marbach D, et al. Assessment of network module identification across complex diseases. Nature Methods. 16: 843-852. PMID 31471613 DOI: 10.1038/s41592-019-0509-5  0.32
2017 Lamparter D, Marbach D, Rueedi R, Bergmann S, Kutalik Z. Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility. Plos Computational Biology. 13: e1005311. PMID 28118358 DOI: 10.1371/journal.pcbi.1005311  0.32
2016 Marbach D, Lamparter D, Quon G, Kellis M, Kutalik Z, Bergmann S. Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases. Nature Methods. PMID 26950747 DOI: 10.1038/nmeth.3799  0.56
2016 Lamparter D, Marbach D, Rueedi R, Kutalik Z, Bergmann S. Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics. Plos Computational Biology. 12: e1004714. PMID 26808494 DOI: 10.1371/journal.pcbi.1004714  0.32
2015 Feizi S, Marbach D, Médard M, Kellis M. Corrigendum: Network deconvolution as a general method to distinguish direct dependencies in networks. Nature Biotechnology. 33: 424. PMID 25850062 DOI: 10.1038/nbt0415-424  0.56
2013 Feizi S, Marbach D, Médard M, Kellis M. Network deconvolution as a general method to distinguish direct dependencies in networks. Nature Biotechnology. 31: 726-33. PMID 23851448 DOI: 10.1038/nbt.2635  0.56
2012 Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR, Kellis M, Collins JJ, Stolovitzky G. Wisdom of crowds for robust gene network inference. Nature Methods. 9: 796-804. PMID 22796662 DOI: 10.1038/nmeth.2016  0.56
2012 Marbach D, Roy S, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M. Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. Genome Research. 22: 1334-49. PMID 22456606 DOI: 10.1101/gr.127191.111  0.56
2011 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, et al. Verification of systems biology research in the age of collaborative competition. Nature Biotechnology. 29: 811-5. PMID 21904331 DOI: 10.1038/nbt.1968  0.56
2011 Schaffter T, Marbach D, Floreano D. GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods. Bioinformatics (Oxford, England). 27: 2263-70. PMID 21697125 DOI: 10.1093/bioinformatics/btr373  0.56
2010 Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, ... ... Marbach D, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/science.1198374  0.56
2010 Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G. Revealing strengths and weaknesses of methods for gene network inference. Proceedings of the National Academy of Sciences of the United States of America. 107: 6286-91. PMID 20308593 DOI: 10.1073/pnas.0913357107  0.56
2010 Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, Stolovitzky G. Towards a rigorous assessment of systems biology models: the DREAM3 challenges. Plos One. 5: e9202. PMID 20186320 DOI: 10.1371/journal.pone.0009202  0.56
2009 Marbach D, Mattiussi C, Floreano D. Replaying the evolutionary tape: biomimetic reverse engineering of gene networks. Annals of the New York Academy of Sciences. 1158: 234-45. PMID 19348645 DOI: 10.1111/j.1749-6632.2008.03944.x  0.56
2009 Marbach D, Mattiussi C, Floreano D. Combining multiple results of a reverse-engineering algorithm: application to the DREAM five-gene network challenge. Annals of the New York Academy of Sciences. 1158: 102-13. PMID 19348636 DOI: 10.1111/j.1749-6632.2008.03945.x  0.56
2009 Marbach D, Schaffter T, Mattiussi C, Floreano D. Generating realistic in silico gene networks for performance assessment of reverse engineering methods. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 229-39. PMID 19183003 DOI: 10.1089/cmb.2008.09TT  0.56
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