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Daniel Marbach - Publications

Affiliations: 
Massachusetts Institute of Technology, Cambridge, MA, United States 
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20 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  0.456
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  0.531
2019 Delaneau O, Zazhytska M, Borel C, Giannuzzi G, Rey G, Howald C, Kumar S, Ongen H, Popadin K, Marbach D, Ambrosini G, Bielser D, Hacker D, Romano L, Ribaux P, et al. Chromatin three-dimensional interactions mediate genetic effects on gene expression. Science (New York, N.Y.). 364. PMID 31048460 DOI: 10.1126/Science.Aat8266  0.462
2017 Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, et al. A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. Cell Systems. PMID 28988802 DOI: 10.1016/J.Cels.2017.09.004  0.428
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  0.449
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  0.746
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  0.365
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  0.735
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  0.752
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  0.68
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  0.736
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  0.555
2011 Mattiussi C, Dürr P, Marbach D, Floreano D. Beyond graphs: A new synthesis Journal of Computational Science. 2: 165-177. DOI: 10.1016/J.Jocs.2011.01.007  0.455
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  0.512
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  0.566
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  0.43
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  0.509
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  0.544
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  0.539
2008 Mattiussi C, Marbach D, Dürr P, Floreano D. The age of analog networks Ai Magazine. 29: 63-76. DOI: 10.1609/Aimag.V29I3.2156  0.484
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