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Computational Systems Biology |
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Mini-Review Topics
Below are suggested topics. You are encouraged to fashion your own. Pick at least 2 articles to present during your mini-review.
Data Integration
- Integration of Protein-Protein Interaction Networks with Gene Coexpression
- Integration of PPI or coexpression networks with Genetic Interaction
- Integrating promoter sequence with gene expression analysis
- Learning Joint Models
Connecting expression to sequence
- Periodicity in Bacteria: Wright et al. 2007 [2M pdf]
- Connecting cis-regulatory motifs to expression: Bussemaker et al. 2001 [87K pdf]
- Chromosomal patterns: Roy et al. 2002 [458K pdf]
- Connecting expression to sequence.
- Coregulation to sequence.
- Sequence to coregulation.
- Chromosomal patterns.
- Periodicity in bacteria.
Advanced Computational Methods in Systems Biology
- Bayesian Biclustering [Dhollander et al. 2007]
- Bayesian Hierarchical Modeling [Gerber et al. 2007]
- Dynamic Networks.
- Metabolic Networks. Covert et al 2004. [pubmed html], Segre et al 2002 [pubmed html]
- Flux Balance Analysis.
- Iterative wet-dry refinement of molecular models.
- Drew Endy, MIT. BioBricks.
Kelley and Ideker 2003. [html]
Bandyopadhyay 2006 [pdf]
Huang et al. 2007 [428K pdf]
- Ala et al PLoS Comp Bio 2008 [html] - mouse/human conserved nets for disease
- Hong et al Bioinformatics 2008 [html] - compare meta-analysis methods across arrays
- Edelman et al PLoS Comp Bio 2008 [html] - cancer nets
- Kaleav et al '08 [pubmed] - Network BLAST
- Ideker et al '02 [pubmed] - Explain gene expression data with PPI and protein-DNA networks. Use that Z-score transformation.
- Sharan et al '05 [pubmed] - PPI across species
- Tan et al '07 [pubmed] - Integration of transcription and PPI across species.
High-throughput experimental techniques
- HT expression analysis
- ChIP on chip.
- HT sequencing. ChIP/seq.
- PPI mapping.
- Synthetic lethal mapping.
- mass-spectroscopy - SELDI-TOF-MS
- perturbation/observation methods: RNAi->phenotype, drug->phenotype
- proteomics, protein modification
- SNP (Hapmap)
Drug-Target Identification
- Using DNA microarrays as a signature: Marton and Brown [html], Hughes 2000
Semi-supervised Learning
- Scoring pre-computed classes: PSB paper by Pavlidis.
- Recommender systems. E.g. ClueGene.
- Ihmels '04. Hashimoto '04. Hergaard '03. Dhollander '07.
Function Prediction with Integration
- BN approach. Friedman, Science '04.
- PPI with expression. Chen-Hsiang
- PRMs by Pfeffer and Koller.
- Promoter and expression. Segal '03.
- Combining evidence to predict interactions. Troyanskaya's MAGIC.
- CREAM - community-wide competition in mouse to predict gene function (~100 attendees this year). Califano, Roth, Troyanskaya
- Lee and Marcotte, Science '04 [pubmed]
- AVID from Amy Keating, MIT, BMC Bioinformatics '05 [pubmed]
- MAGIC from Olga, PNAS '03 [pubmed]
- Jansen and Gerstein for PPI, Science '03 [pubmed]
- Tanay and Shamir, PNAS '04 [pubmed]
- STRING: Peer Bork's group, NAR 2000 [pubmed]
- Toward reference networks: Srinivasan et al 2007 [html]
Cross-species
- Orthology prediction: Inparanoid. Sonhammer
- Network alignment: Pathblast. Ideker. PPI across (Tan & Ideker)
- Projecting across species: Ihmels and Barkai.
- Meta-analysis of correlation. Stuart '03.
- Search-engine for gene module expansion. MSGR: Chen '07.
- Aging experiments by Bargman and McCaroll.
Reverse Engineering
- State Space Models - Beal and Wild 2005 [url]
- Probabilistic Graphical Models
- Gene-gene networks from observations and interventions.
- Boolean net approach (REVEAL algorithm)
- Using mutual information. Butte and Kohane.
- Alternative approach - ARACHNE by A Califano.
- Nested Effects models, learning from secondary effects. - Markowetz and Spang, 2004.
- Hughes et al 2000.
- Pe'er et al. 2000.
- Hartemink et al 2001 [245K pdf]
- Jaimovich et al 2006.
- Joint models that incorporate expression and additional information. Segal et al 2003 [1.6M pdf]
Databases, exchange languages, resources, societies
- GO/KEGG/BioCarta/Reactome/BioPAX
- Interactions: BioGRID, DIP, INTACT, BIND, YPD, SGD
- Species databases: SGD, MGD, RatDB, etc,
- Data methodology databases: GEO, ArrayExpress
- Minimum Information About a Microarray Experiment (MIAME) and MGED society
- NCIBI at Univ Michigan
Software Tools for Systems Biology
- GenePattern
- geWorkbench - Andrea Califano, MAGnet
- BioPixie
- Recommenders: ClueGene/GeneRecommender/ISA
- Cytoscape
- TreeView / Java TreeView / MeV
- DAVID - Gene set analysis (url)
- Microsoft's Bayes Nets [url]
- SGI's ML library in C++ [url]
- NASA's AutoClass (unsupervised BNs) in C [url]
- WEKA Java data mining software [url]
Applied Network Analysis to Focused Questions
- Telomere length maintenance network. Unger and Roded Sharan's group. (MSB url)
- Viral Detection: Yves Lussier, Univ Chicago; Joe Derisi, UCSF
- Host-pathogen interactions
- Fraser and Marcotte, Jan 08, Nat Genet - Aging and cancer networks in C. elegans.
- Sayan Mukherjee at Duke, Net analysis of colon cancer
- B cell lymphoma using ARACHNe - Andreas Califano
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- Sea Urchin development, Oliveri et al 2008 [pubmed html]
- Investigating DNA damage response pathways, Workman et al 2006 [Science html]
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