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Items: 19

1.

Assessment of network module identification across complex diseases.

Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R; DREAM Module Identification Challenge Consortium, Subramanian A, Zhang JD, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D.

Nat Methods. 2019 Sep;16(9):843-852. doi: 10.1038/s41592-019-0509-5. Epub 2019 Aug 30.

2.

Chromatin three-dimensional interactions mediate genetic effects on gene expression.

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, Wiederkehr M, Falconnet E, Bucher P, Bergmann S, Antonarakis SE, Reymond A, Dermitzakis ET.

Science. 2019 May 3;364(6439). pii: eaat8266. doi: 10.1126/science.aat8266.

PMID:
31048460
3.

Eliminating contraction during culture maintains global and local Ca2+ dynamics in cultured rabbit pacemaker cells.

Segal S, Kirschner Peretz N, Arbel-Ganon L, Liang J, Li L, Marbach D, Yang D, Wang SQ, Yaniv Y.

Cell Calcium. 2019 Mar;78:35-47. doi: 10.1016/j.ceca.2018.12.008. Epub 2018 Dec 18.

4.

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.

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, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA, Newton Y, Ng S, Pahikkala T, Paull E, Sokolov A, Tang H, Tang J, Wennerberg K, Xie Y, Zhan X, Zhu F; Broad-DREAM Community, Aittokallio T, Mamitsuka H, Stuart JM, Boehm JS, Root DE, Xiao G, Stolovitzky G, Hahn WC, Margolin AA.

Cell Syst. 2017 Nov 22;5(5):485-497.e3. doi: 10.1016/j.cels.2017.09.004. Epub 2017 Oct 4.

5.

Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility.

Lamparter D, Marbach D, Rueedi R, Bergmann S, Kutalik Z.

PLoS Comput Biol. 2017 Jan 24;13(1):e1005311. doi: 10.1371/journal.pcbi.1005311. eCollection 2017 Jan.

6.

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases.

Marbach D, Lamparter D, Quon G, Kellis M, Kutalik Z, Bergmann S.

Nat Methods. 2016 Apr;13(4):366-70. doi: 10.1038/nmeth.3799. Epub 2016 Mar 7.

7.

Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics.

Lamparter D, Marbach D, Rueedi R, Kutalik Z, Bergmann S.

PLoS Comput Biol. 2016 Jan 25;12(1):e1004714. doi: 10.1371/journal.pcbi.1004714. eCollection 2016 Jan.

8.

Corrigendum: Network deconvolution as a general method to distinguish direct dependencies in networks.

Feizi S, Marbach D, Médard M, Kellis M.

Nat Biotechnol. 2015 Apr;33(4):424. doi: 10.1038/nbt0415-424. No abstract available.

PMID:
25850062
9.

Network deconvolution as a general method to distinguish direct dependencies in networks.

Feizi S, Marbach D, Médard M, Kellis M.

Nat Biotechnol. 2013 Aug;31(8):726-33. doi: 10.1038/nbt.2635. Epub 2013 Jul 14. Erratum in: Nat Biotechnol. 2015 Apr;33(4):424.

10.

Wisdom of crowds for robust gene network inference.

Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR; DREAM5 Consortium, Kellis M, Collins JJ, Stolovitzky G.

Nat Methods. 2012 Jul 15;9(8):796-804. doi: 10.1038/nmeth.2016.

11.

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks.

Marbach D, Roy S, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M.

Genome Res. 2012 Jul;22(7):1334-49. doi: 10.1101/gr.127191.111. Epub 2012 Mar 28.

12.

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, Stolovitzky G.

Nat Biotechnol. 2011 Sep 8;29(9):811-5. doi: 10.1038/nbt.1968. No abstract available.

PMID:
21904331
13.

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods.

Schaffter T, Marbach D, Floreano D.

Bioinformatics. 2011 Aug 15;27(16):2263-70. doi: 10.1093/bioinformatics/btr373. Epub 2011 Jun 22.

PMID:
21697125
14.

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

modENCODE Consortium, 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, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M.

Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.

15.

Revealing strengths and weaknesses of methods for gene network inference.

Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G.

Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6286-91. doi: 10.1073/pnas.0913357107. Epub 2010 Mar 22.

16.

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, Stolovitzky G.

PLoS One. 2010 Feb 23;5(2):e9202. doi: 10.1371/journal.pone.0009202. Erratum in: PLoS One. 2010;5(3). doi: 10.1371/annotation/f633213a-dc4f-4bee-b6c5-72d50e7073b8.

17.

Replaying the evolutionary tape: biomimetic reverse engineering of gene networks.

Marbach D, Mattiussi C, Floreano D.

Ann N Y Acad Sci. 2009 Mar;1158:234-45. doi: 10.1111/j.1749-6632.2008.03944.x.

PMID:
19348645
18.

Combining multiple results of a reverse-engineering algorithm: application to the DREAM five-gene network challenge.

Marbach D, Mattiussi C, Floreano D.

Ann N Y Acad Sci. 2009 Mar;1158:102-13. doi: 10.1111/j.1749-6632.2008.03945.x.

PMID:
19348636
19.

Generating realistic in silico gene networks for performance assessment of reverse engineering methods.

Marbach D, Schaffter T, Mattiussi C, Floreano D.

J Comput Biol. 2009 Feb;16(2):229-39. doi: 10.1089/cmb.2008.09TT.

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