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The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
Richard Bonneau, David J Reiss, Paul Shannon, Marc Facciotti, Leroy Hood, Nitin S Baliga, Vesteinn Thorsson
Genome Biol. 2006; 7(5): R36. Published online 2006 May 10. doi: 10.1186/gb-2006-7-5-r36
PMCID:
PMC1779511
Abstract Full Text PDF–829K Supplementary Material
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 Is Cited by the Following 53 Articles in this Archive:
Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems
Jason E McDermott, Harish Shankaran, Amie J Eisfeld, Sarah E Belisle, Gabriele Neuman, Chengjun Li, Shannon McWeeney, Carol Sabourin, Yoshihiro Kawaoka, Michael G Katze, Katrina M Waters
BMC Syst Biol. 2011; 5: 190. Published online 2011 November 11. doi: 10.1186/1752-0509-5-190
PMCID:
PMC3229612
Abstract Full Text PDF–2.7M Supplementary Material
Construction of gene regulatory networks using biclustering and bayesian networks
Fadhl M Alakwaa, Nahed H Solouma, Yasser M Kadah
Theor Biol Med Model. 2011; 8: 39. Published online 2011 October 22. doi: 10.1186/1742-4682-8-39
PMCID:
PMC3231811
Abstract Full Text PDF–1.7M
Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states
Sriram Chandrasekaran, Seth A. Ament, James A. Eddy, Sandra L. Rodriguez-Zas, Bruce R. Schatz, Nathan D. Price, Gene E. Robinson
Proc Natl Acad Sci U S A. 2011 November 1; 108(44): 18020–18025. Published online 2011 September 29. doi: 10.1073/pnas.1114093108
PMCID:
PMC3207651
Abstract Full Text PDF–1.3M Supplementary Material
A proof of the DBRF-MEGN method, an algorithm for deducing minimum equivalent gene networks
Koji Kyoda, Kotaro Baba, Hiroaki Kitano, Shuichi Onami
Source Code Biol Med. 2011; 6: 12. Published online 2011 June 24. doi: 10.1186/1751-0473-6-12
PMCID:
PMC3152880
Abstract Full Text PDF–776K Supplementary Material
TREEGL: reverse engineering tree-evolving gene networks underlying developing biological lineages
Ankur P. Parikh, Wei Wu, Ross E. Curtis, Eric P. Xing
Bioinformatics. 2011 July 1; 27(13): i196–i204. Published online 2011 June 14. doi: 10.1093/bioinformatics/btr239
PMCID:
PMC3117339
Abstract Full Text
Controlling the Response: Predictive Modeling of a Highly Central, Pathogen-Targeted Core Response Module in Macrophage Activation
Jason E. McDermott, Michelle Archuleta, Brian D. Thrall, Joshua N. Adkins, Katrina M. Waters
PLoS One. 2011; 6(2): e14673. Published online 2011 February 14. doi: 10.1371/journal.pone.0014673
PMCID:
PMC3038849
Abstract Full Text PDF–1.5M Supplementary Material
DEFINING THE PLAYERS IN HIGHER-ORDER NETWORKS: PREDICTIVE MODELING FOR REVERSE ENGINEERING FUNCTIONAL INFLUENCE NETWORKS
JASON E. MCDERMOTT, MICHELLE ARCHULETA, SUSAN L. STEVENS, MARY P. STENZEL-POORE, ANTONIO SANFILIPPO
Pac Symp Biocomput. Author manuscript; available in PMC 2011 March 10.
Published in final edited form as: Pac Symp Biocomput. 2011: 314–325.
PMCID:
PMC3052927
Abstract Full Text PDF–1002K
Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate
Gabriel Krouk, Piotr Mirowski, Yann LeCun, Dennis E Shasha, Gloria M Coruzzi
Genome Biol. 2010; 11(12): R123. Published online 2010 December 23. doi: 10.1186/gb-2010-11-12-r123
PMCID:
PMC3046483
Abstract Full Text PDF–2.1M Supplementary Material
Predicting DNA-Binding Specificities of Eukaryotic Transcription Factors
Adrian Schröder, Johannes Eichner, Jochen Supper, Jonas Eichner, Dierk Wanke, Carsten Henneges, Andreas Zell
PLoS One. 2010; 5(11): e13876. Published online 2010 November 30. doi: 10.1371/journal.pone.0013876
PMCID:
PMC2994704
Abstract Full Text PDF–1.3M Supplementary Material
Inferring Regulatory Networks from Expression Data Using Tree-Based Methods
Vân Anh Huynh-Thu, Alexandre Irrthum, Louis Wehenkel, Pierre Geurts
PLoS One. 2010; 5(9): e12776. Published online 2010 September 28. doi: 10.1371/journal.pone.0012776
PMCID:
PMC2946910
Abstract Full Text PDF–696K Supplementary Material
Nonparametric identification of regulatory interactions from spatial and temporal gene expression data
Anil Aswani, Soile VE Keränen, James Brown, Charless C Fowlkes, David W Knowles, Mark D Biggin, Peter Bickel, Claire J Tomlin
BMC Bioinformatics. 2010; 11: 413. Published online 2010 August 4. doi: 10.1186/1471-2105-11-413
PMCID:
PMC2933715
Abstract Full Text PDF–4.0M Supplementary Material
Coordination of frontline defense mechanisms under severe oxidative stress
Amardeep Kaur, Phu T Van, Courtney R Busch, Courtney K Robinson, Min Pan, Wyming Lee Pang, David J Reiss, Jocelyne DiRuggiero, Nitin S Baliga
Mol Syst Biol. 2010; 6: 393. Published online 2010 July 27. doi: 10.1038/msb.2010.50
PMCID:
PMC2925529
Abstract Full Text PDF–2.6M Supplementary Material
In silico models of cancer
Lucas B. Edelman, James A. Eddy, Nathan D. Price
Wiley Interdiscip Rev Syst Biol Med. Author manuscript; available in PMC 2011 August 17.
Published in final edited form as: Wiley Interdiscip Rev Syst Biol Med. 2010 Jul-Aug; 2(4): 438–459. doi: 10.1002/wsbm.75
PMCID:
PMC3157287
Abstract Full Text PDF–2.2M
Learning transcriptional networks from the integration of ChIP–chip and expression data in a non-parametric model
Ahrim Youn, David J. Reiss, Werner Stuetzle
Bioinformatics. 2010 August 1; 26(15): 1879–1886. Published online 2010 June 4. doi: 10.1093/bioinformatics/btq289
PMCID:
PMC2913654
Abstract Full Text PDF–424K Supplementary Material
Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis
Marc T Facciotti, Wyming L Pang, Fang-yin Lo, Kenia Whitehead, Tie Koide, Ken-ichi Masumura, Min Pan, Amardeep Kaur, David J Larsen, David J Reiss, Linh Hoang, Ewa Kalisiak, Trent Northen, Sunia A Trauger, Gary Siuzdak, Nitin S Baliga
BMC Syst Biol. 2010; 4: 64. Published online 2010 May 14. doi: 10.1186/1752-0509-4-64
PMCID:
PMC2880973
Abstract Full Text PDF–1.2M Supplementary Material
Adapting functional genomic tools to metagenomic analyses: investigating the role of gut bacteria in relation to obesity
Yuanhua Liu, Chenhong Zhang, Liping Zhao, Christine Nardini
Brief Funct Genomics. 2010 December; 9(5-6): 355–361. Published online 2010 May 6. doi: 10.1093/bfgp/elq011
PMCID:
PMC3080776
Abstract Full Text PDF–306K
Learning “graph-mer” Motifs that Predict Gene Expression Trajectories in Development
Xuejing Li, Casandra Panea, Chris H. Wiggins, Valerie Reinke, Christina Leslie
PLoS Comput Biol. 2010 April; 6(4): e1000761. Published online 2010 April 29. doi: 10.1371/journal.pcbi.1000761
PMCID:
PMC2861633
Abstract Full Text PDF–1004K Supplementary Material
Inference of Cancer-specific Gene Regulatory Networks Using Soft Computing Rules
Xiaosheng Wang, Osamu Gotoh
Gene Regul Syst Bio. 2010; 4: 19–34. Published online 2010 March 24.
PMCID:
PMC2865768
Abstract Full Text PDF–1.8M Supplementary Material
DREAM3: Network Inference Using Dynamic Context Likelihood of Relatedness and the Inferelator
Aviv Madar, Alex Greenfield, Eric Vanden-Eijnden, Richard Bonneau
PLoS One. 2010; 5(3): e9803. Published online 2010 March 22. doi: 10.1371/journal.pone.0009803
PMCID:
PMC2842436
Abstract Full Text PDF–544K
Revealing strengths and weaknesses of methods for gene network inference
Daniel Marbach, Robert J. Prill, Thomas Schaffter, Claudio Mattiussi, Dario Floreano, Gustavo Stolovitzky
Proc Natl Acad Sci U S A. 2010 April 6; 107(14): 6286–6291. Published online 2010 March 22. doi: 10.1073/pnas.0913357107
PMCID:
PMC2851985
Abstract Full Text PDF–453K Supplementary Material
MiDReG: A method of mining developmentally regulated genes using Boolean implications
Debashis Sahoo, Jun Seita, Deepta Bhattacharya, Matthew A. Inlay, Irving L. Weissman, Sylvia K. Plevritis, David L. Dill
Proc Natl Acad Sci U S A. 2010 March 30; 107(13): 5732–5737. Published online 2010 March 15. doi: 10.1073/pnas.0913635107
PMCID:
PMC2851930
Abstract Full Text PDF–2.1M Supplementary Material
Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges
Robert J. Prill, Daniel Marbach, Julio Saez-Rodriguez, Peter K. Sorger, Leonidas G. Alexopoulos, Xiaowei Xue, Neil D. Clarke, Gregoire Altan-Bonnet, Gustavo Stolovitzky
PLoS One. 2010; 5(2): e9202. Published online 2010 February 23. doi: 10.1371/journal.pone.0009202
Correction in:
PLoS One. 2010; 5(3): 10.1371/annotation/f633213a-dc4f-4bee-b6c5-72d50e7073b8.
PMCID:
PMC2826397
Abstract Full Text PDF–1021K Correction
Identification of Crosstalk between Phosphoprotein Signaling Pathways in RAW 264.7 Macrophage Cells
Shakti Gupta, Mano Ram Maurya, Shankar Subramaniam
PLoS Comput Biol. 2010 January; 6(1): e1000654. Published online 2010 January 29. doi: 10.1371/journal.pcbi.1000654
PMCID:
PMC2813256
Abstract Full Text PDF–1.1M Supplementary Material
Toward the dynamic interactome: it's about time
Teresa M. Przytycka, Mona Singh, Donna K. Slonim
Brief Bioinform. 2010 January; 11(1): 15–29. Published online 2010 January 8. doi: 10.1093/bib/bbp057
PMCID:
PMC2810115
Abstract Full Text PDF–151K
Network inference and network response identification: moving genome-scale data to the next level of biological discovery
Diogo F. T. Veiga, Bhaskar Dutta, Gábor Balaźsi
Mol Biosyst. Author manuscript; available in PMC 2011 May 4.
Published in final edited form as: Mol Biosyst. 2010 March; 6(3): 469–480. Published online 2009 December 11. doi: 10.1039/b916989j
PMCID:
PMC3087299
Abstract Full Text PDF–1.1M
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction
Julio Saez-Rodriguez, Leonidas G Alexopoulos, Jonathan Epperlein, Regina Samaga, Douglas A Lauffenburger, Steffen Klamt, Peter K Sorger
Mol Syst Biol. 2009; 5: 331. Published online 2009 December 1. doi: 10.1038/msb.2009.87
PMCID:
PMC2824489
Abstract Full Text PDF–1.8M Supplementary Material
Classification and biomarker identification using gene network modules and support vector machines
Malik Yousef, Mohamed Ketany, Larry Manevitz, Louise C Showe, Michael K Showe
BMC Bioinformatics. 2009; 10: 337. Published online 2009 October 15. doi: 10.1186/1471-2105-10-337
PMCID:
PMC2774324
Abstract Full Text PDF–285K
Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data
Yong Wang, Xiang-Sun Zhang, Yu Xia
Nucleic Acids Res. 2009 October; 37(18): 5943–5958. Published online 2009 October. doi: 10.1093/nar/gkp625
PMCID:
PMC2764433
Abstract Full Text PDF–3.1M Supplementary Material
Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions
Javier Carrera, Guillermo Rodrigo, Alfonso Jaramillo, Santiago F Elena
Genome Biol. 2009; 10(9): R96. Published online 2009 September 15. doi: 10.1186/gb-2009-10-9-r96
PMCID:
PMC2768985
Abstract Full Text PDF–2.6M Supplementary Material
Incorporating Existing Network Information into Gene Network Inference
Scott Christley, Qing Nie, Xiaohui Xie
PLoS One. 2009; 4(8): e6799. Published online 2009 August 27. doi: 10.1371/journal.pone.0006799
PMCID:
PMC2729382
Abstract Full Text PDF–744K Supplementary Material
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