Talk:Biological network inference

Untitled

I'd love to see this expanded upon. As a neurobiologist with no real programming experience, I've been struggling with how to turn tons of microarray expression data I have acquired into bonafide depictions of gene regulatory networks. I've tried several of the off-the-shelf programs with little luck. Reading the primary literature isn't getting me anywhere. 68.46.183.96 (talk) 20:22, 11 July 2008 (UTC)

move refs here

This is just a dump of articles with unclear relation to what's written in the article. Moving them here. Headbomb {^ταλκ_{κοντριβς} – WP Physics} 20:21, 25 August 2009 (UTC)

• Bansal, M; et al. (2007). "How to infer gene networks from expression profiles". Molecular Systems Biology. 3 (78). {{cite journal}}: Explicit use of et al. in: |author= (help)
• Bansal, M; Gatta, GD; di Bernardo, D (2006). "Inference of gene regulatory networks and compound mode of action from time course gene expression profiles". Bioinformatics. 22 (7): 815–822. doi:10.1093/bioinformatics/btl003. PMID 16418235.{{cite journal}}: CS1 maint: multiple names: authors list (link)
• Faith, JJ; et al. (2007). "Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles". PLoS Biology. 5 (1): 54–66. doi:10.1371/journal.pbio.0050008. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: unflagged free DOI (link)
• Barrett, Christian L. (2006). "Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach". PLoS Comput. Biol. 2 (5): e52. doi:10.1371/journal.pcbi.0020052.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• Basso, Katia (2005). "Reverse engineering of regulatory networks in human B cells". Nat. Genet. 37 (4): 382–390. doi:10.1038/ng1532.
• Bonneau, Richard (2006). "The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo". Genome Biology. 7 (5): R36. doi:10.1186/gb-2006-7-5-r36.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• "Context Likelihood or Relatedness (CLR) algorithm". Gardner Lab. 2006.
• Chen, X.-w. (2006). "An effective structure learning method for constructing gene networks". Bioinformatics. 22 (11): 1367–1374. doi:10.1093/bioinformatics/btl090. PMID 16543279.
• Chu, T. (2003). "A statistical problem for inference to regulatory structure from associations of gene expression measurements with microarrays". Bioinformatics. 19 (9): 1147–1152. doi:10.1093/bioinformatics/btg011. PMID 12801876.
• Cover, TM; Thomas, JA (1991). Elements of Information Theory. John Wiley & Sons.{{cite book}}: CS1 maint: multiple names: authors list (link)
• Daub, Carsten O (2004). BMC Bioinformatics. 5: 118. doi:10.1186/1471-2105-5-118. {{cite journal}}: Missing or empty |title= (help)CS1 maint: unflagged free DOI (link)
• de Jong, H (2002). "Modeling and simulation of genetic regulatory systems: a literature review". J Comput Biol. 9 (1): 67–103. doi:10.1089/10665270252833208.
• de la Fuente, A; et al. (2004). "Discovery of meaningful associations in genomic data using partial correlation coefficients". Bioinformatics. 20 (18): 3565-3574. {{cite journal}}: Explicit use of et al. in: |author= (help)
• Filkov, V (2005). "Identifying Gene Regulatory Networks from Gene Expression Data". Handbook of Computational Molecular Biology. Chapman & Hall / CRC Press.
• Hartemink, AJ (2005). "Bayesian Network Inference with Java Objects (BANJO)". Duke University.
• Hartemink, AJ (2005). "Reverse engineering gene regulatory networks". Nat. Biotech. 23 (5): 554–555. doi:10.1038/nbt0505-554.
• Hecker, M; Lambeck, S; Toepfer, S; van Someren, E; Guthke, R (2009). "Gene Regulatory Network Inference - Data Integration in Dynamic Models - A Review". BioSystems. 96: 86–103. doi:10.1016/j.biosystems.2008.12.004.{{cite journal}}: CS1 maint: multiple names: authors list (link)
• Husmeier, D (2003). "Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks". Bioinformatics. 19 (17): 2271–2282. doi:10.1093/bioinformatics/btg313. PMID 14630656.
• Ideker, T; Thorsson, V; Karp, RM (2000). "Discovery of regulatory interactions through perturbation: inference and experimental design". Pacific Symposium on Biocomputing.{{cite journal}}: CS1 maint: multiple names: authors list (link)
• Liang, S; Fuhrman, S; Somogyi, R (1998). "REVEAL: a general reverse engineering algorithm for inference of genetic network architectures". Pac. Symp. Biocomput. 3: 18–29.{{cite journal}}: CS1 maint: multiple names: authors list (link)
• Margolin, A.A., et al., Reverse engineering cellular networks. Nature Protocols, 2006. 1(2): p. 663-672. (full description of ARACNE algorithm)
• Margolin, A.A., et al., ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics, 2006. 7(Suppl1): p. S1-7.
• Markowetz, F. A bibliography on learning causal networks of gene interactions (July 31, 2006).[available from: http://www.molgen.mpg.de/~markowet/doc/network-bib.pdf; http://genomics.princeton.edu/~florian/docs/network-bib.pdf]
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• Papin, J.A., et al., Reconstruction of cellular signalling networks and analysis of their properties. Nat. Rev. Mol. Cell Biol., 2005. 6(2): p. 99-111.
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• Pe'er, D. Bayesian Network Analysis of Signaling Networks: A Primer. Science STKE 2005 [on-line primer]. Available from: www.stke.org/content/full/sigtrans.
• Perrin, B.E., et al., Gene networks inference using dynamic Bayesian networks. Bioinformatics, 2003. 19(S2): p. ii138-ii148.
• Sachs, K., et al., Causal protein-signaling networks derived from multiparameter single-cell data. Science, 2005. 308: p. 523-529.
• Schadt, E.E., et al., An integrative genomics approach to infer causal associations between gene expressiona and disease. Nat. Genet., 2005. 37(7): p. 710-717.
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• Shannon, P., et al., Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 2003. 13(11): p. 2498-504.
• Singhal, M. and K. Domico, CABIN: Collective Analysis of Biological Interaction Networks. Journal of Computational Biology and Chemistry, (accepted for publication in 2007)
• Taylor, R.C., et al., SEBINI: Software Environment for BIological Network Inference. Bioinformatics, 2006. 21: p. 2706-2708.
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• van Someren, E.P., et al., Genetic network modeling. Pharmacogenomics, 2002. 3(4): p. 507-25.
• Weaver, D.C., C.T. Workman, and G.D. Stromo, Modeling regulatory networks with weight matrices. Pac. Symp. Biocomput., 1999.
• Werhli, A.V., M. Grezegorczyk, and D. Husmeier, Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks. Bioinformatics, 2006. 22(20): p. 2523-2531.
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• Zhou, X., et al., A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks. Bioinformatics, 2004. 20(17): p. 2918-27.
• Zou, M. and S.D. Conzen, A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course data. Bioinformatics, 2005. 21(1): p. 71-79.

Co-relation-based inference algorithms

{{cleanup-jargon|date = January 2008}}

1) from classical statistics - STUB

• baseline: Pearson correlation

2) from information theory - STUB

• Concept of mutual information
• ARACNE algorithm
• CLR algorithm
• MRNET algorithm

3) from graphical probabilistic models - STUB

• Bayesian network structure learning
• K2 alg - needs a node ordering
• BANJO toolkit

DREAM project - stub

Platforms for network inference - STUB

• geWorkbench, Columbia
• SEBINI

Visualization of inferred network - STUB

• Cytoscape tool

Expansion of inferred network using public databases - data integration - STUB

• CABIN tool

Changes 5/5/2022

This expansion is for CS4364. Please refrain from any changes until 5/13/2022 for grading purposes, thank you. — Preceding unsigned comment added by ErgoFoxy (talk • contribs) 19:47, 5 May 2022 (UTC)