Candidate papers for the Systems Biology Lab journal club
Please state
- your name,
- a few words why you like the paper, and why it is interesting for the group, and
a hyperlink to the paper file (local), the PubMed Web page, or the Web page for the paper.
Papers organized by journal club topic
Please feel free to add papers and comment.
1. Regulation of the cell cycle
2. New omic experimental technologies
3. Metabolic network modeling and applications
4. Module finding (from combined interaction and expression data)
Discovering regulatory and signalling circuits in molecular interaction networks [Tero] Identification of active subnetworks by scoring differential expression over particular subset of conditions.
Functional modules by relating protein interaction networks and gene expression [Tero] Evaluating the concordance between sets of genes from different types of networks by multi-body correlation function.
Discovering molecular pathways from protein interaction and gene expression data [Tero] Probabilistic models for learning sets of genes that are co-expressed and whose products interact.
Graph-based iterative Group Analysis enhances microarray interpretation [Tero] Graph-driven identification of subgraphs that show the most significant differential expression.
Identifying active transcription factors and kinases from expression data using pathway queries [Tero] User-specified pathway queries to search for more flexible subnetworks relevant for the given experiment.
Inferring pathways from gene lists using a literature-derived network of biological relationships [Tero] Scoring subnetworks according to a query set of interesting genes with a method modified from Ideker et al. (2002).
Differential network expression during drug and stress response [Tero] Identification of response subnetworks by scoring differential expression as in Ideker et al. (2002).
Identifying Regulatory Subnetworks for a Set of Genes [Tero] Finding subnetworks responsible for regulating a given list of significant genes or proteins with Steiner trees.
Detecting functional modules in the yeast protein–protein interaction network [Tero] Network clustering by microarray-weighted Girvan and Newman partitioning algorithm.
Identification of functional modules using network topology and high-throughput data [Tero] Functional modules by identifying connected subnetworks in the interaction data that exhibit high average internal similarity.
5. Immune systems biology
Other interesting papers
Genetic basis of proteome variation in yeast[Benno] A new type of interaction data (protein expression QTLs) generated using large-scale alignment. Our collaborator David Goodlett in Seattle was involved into this one.
Integrating molecular and network biology to decode endocytosis [Benno] A paper that demonstrates the integration of network biology with molecular biology, and might inspire new and advanced network biology.
A geometric approach for the alignment of liquid chromatography—mass spectrometry data [Benno] A technically interesting July 2007 paper on MS1 alignment from an OpenMS group.
Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis [Melissa] A very cool accomplishment - predictive network modeling on a moderately-complex eukaryote, not a single-cell organism! The authors have some interesting methods based on expression, network, and phenotypic data taken together, and somewhere in the process they use Cytoscape.
Plasticity of the cis-regulatory input function of a gene [Benno] A study from the Uri Alon lab on the question: "What is the mathematical function that translates the concentrations of transcription factors into the concentration of the regulated mRNA, and how is that function affected by mutations?". I find this a central question for regulatory networks and their evolution.
Systematic interpretation of genetic interactions using protein networks. [Benno] Work by our collaborators at UCSD that seems to be closely related to our project with the Jacquier lab.
A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis [Benno] A global approach to link a signaling pathway to its phenotype in a formal way -- with interesting ideas on including biological knowledge and limited experimental resources.
Optimality and evolutionary tuning of the expression level of a protein [Benno] One paper in a series of papers by Uri Alon (and others) that introduces a "top-down" organizational principle as the logic by which gene expression is controlled.
An evolutionary and functional assessment of regulatory network motifs [Benno] A throught-provoking paper from Massimo Vergassola, a colleague here on campus claiming that "motifs don't exist". I think this is an interesting question, and we might discuss with him in person!
http://bioinformatics.oupjournals.org/cgi/content/full/21/7/1189 [Andrea] An average interest paper, maybe not suited for a journal club... but did not know where to post it!
http://genomebiology.com/2004/5/5/R35 [Victoria]
A Map of the Interactome Network of the Metazoan C. elegans (Andrea? [Benno])