Journal Club Archive

We are meeting in CE214 every Monday at 11:00 am

Date	Paper	Host	Theme
09/24/2012	Sergi is here	Joshua Weitz	Networks
10/01/2012	Research Ethics	Joshua Weitz
10/08/2012	TBA	Joshua Weitz
10/15/2012	Papers on PCA	Lauren Childs	Microbial Ecology
10/22/2012	Papers on PCA	Lauren Childs	Microbial Ecology
10/29/2012	Papers on Multi-scale modeling	Mike Cortez	Epidemiology, Microbial Ecology
11/05/2012	Papers on Multi-scale modeling	Mike Cortez	Epidemiology, Microbial Ecology
11/12/2012	Papers on BLAST	Abhiram Das
11/19/2012	Papers on BLAST	Abhiram Das
11/26/2012	Papers on Virology	Gabriel Mitchell	Epidemiology, Microbial Ecology
12/03/2012	Papers on Virology	Gabriel Mitchell	Epidemiology, Microbial Ecology
12/10/2012	Papers on Virology	Gabriel Mitchell	Epidemiology, Microbial Ecology

We are meeting in CE214 every Monday from 1:00pm-2:00pm.

Date	Paper	Host	Theme
01/30/2012	The mystery of missing heritability: Genetic interactions create phantom heritability	Lauren Childs
02/04/2012	TBA	Bradford Taylor	Microbial Ecology
02/06/2012	Second-Order Selection for Evolvability in a Large Escherichia coli population	Abhiram Das
02/13/2012	Specialization and evolutionary branching within migratory populations	Gabriel Mitchell
02/20/2012	Bacteria-phage coevolution and the emergence of generalist pathogens	Mike Cortez
02/27/2012	TBA	Alexander Bucksch
03/05/2012	TBA	Bradford Taylor

We are meeting in CE214 from 10:00am to 11:00am every Friday.

Date	Paper	Host	Theme
09/14/2011	Are There Laws of Genome Evolution?	Abhiram Das
09/23/2011	Inducible defenses - continuous reaction norms or threshold traits?	Mike Cortez
10/07/2011	Minimal Gene Regulatory Circuits that Can Count like Bacteriophage Lambda	Bradford Taylor	Systems Biology
10/14/2011	Ethics	Joshua Weitz
10/21/2011	Transcriptional Coupling of Neighboring Genes and Gene Expression Noise: Evidence that Gene Orientation and Noncoding Transcripts Are Modulators of Noise	Tae Lee
10/28/2011	Strong contributors to network persistence are the most vulnerable to extinction	Luis Jover
11/04/2011	Having a BLAST with bioinformatics (and avoiding BLASTphemy)
11/11/2011	Ethics	Lauren Childs
11/18/2011	TBA	Alexander Bucksch
12/02/2011	TBA	Cesar Flores
12/09/2011	Ethics	Joshua Weitz
12/16/2011	TBA	Gabriel Mitchell
12/23/2011	Party

We are meeting in CE214 from 02:00PM to 03:00PM every Thursday.

Date	Paper	Host	Theme
01/27/2011	Control of Transcription by Cell Size
02/03/2011	A unified model for the coevolution of resistance, tolerance, and virulence	Mike Cortez
02/10/2011	Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains	Gabriel Mitchell
02/17/2011	Gene duplication and the adaptive evolution of a classic genetic switch	Tae Lee
02/24/2011	Presentation - Challenges in Bioinformatics	Abhiram Das
03/03/2011	On nestedness analyses: rethinking matrix temperature and anti-nestedness	Cesar Flores	Networks
03/10/2011	Distributed biological computation with multicellular engineered networks	Joshua Weitz	Networks, Systems Biology
03/17/2011	A model for the evolutionary diversification of religions	Lauren Childs
03/31/2011	Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems	Luis Jover
04/07/2011	Evolution of Evolvability in Gene Regulatory Networks	Bradford Taylor
04/14/2011	Quantitative Models of In Vitro Bacteriophage-Host Dynamics and Their Application to Phage Therapy
04/21/2011	Genomic Analysis of Uncultured Marine Viral Communities - By Nicholas and Ryan

We are meeting in CE214 at 10:00am-11:00pm.

Date	Paper	Host	Theme
09/08/2010	Richard, Gabriel and Cesar will present their work for up-coming biology retreat		Microbial Ecology, Networks, Systems Biology
09/15/2010	Mean mass-specific metabolic rates are strikingly similar across life’s major domains: Evidence for life’s metabolic optimum
09/22/2010	Experimental evolution of bet hedging
09/29/2010	Hypergraphs and Cellular Networks	Gabriel Mitchell
10/06/2010	Principles and challenges of genomewide DNA methylation analysis	Abhiram Das
10/13/2010	Error bars in experimental biology	Cesar Flores
10/20/2010	Social interactions, information use, and the evolution of collective migration	Lauren Childs
10/27/2010	No Talk	Joshua Weitz
11/03/2010	Identification of MicroRNAs Associated with Ileal and Colonic Crohn’s Disease (Bradford & Kristen)
11/10/2010	TBA	Mike Cortez
11/17/2010	Principles and challenges of genomewide DNA methylation analysis	Abhiram Das
11/29/2010	TBA	Tae Lee

We are meeting in CE214 at 11:00am-12:00pm.

Date	Paper	Host	Theme
06/16/2010	Reprogramming bacteria to seek and destroy an herbicide		Systems Biology
06/23/2010	Hierarchical group dynamics in pigeon flocks	Gabriel Mitchell	Systems Biology
06/30/2010	A SOFTWARE ARCHITECTURE FOR DEVELOPMENTAL MODELING IN PLANTS: THE COMPUTABLE PLANT PROJECT		Microbial Ecology, Networks
07/07/2010	The Small-World Problem	Cesar Flores
07/14/2010	Scale-free correlations in starling ﬂocks		Systems Biology
07/28/2010	Problem-Based Learning Modifying Medical School Model for Teaching High School Econ
08/04/2010	TBA

We are meeting in CE214 at 11:00am-12:00pm.

Date	Paper	Host	Theme
01/26/2010	TBA
02/02/2010	Dimensionality and dynamics in the behavior of C. elegans		Systems Biology
02/09/2010	Pivoting approaches for bulk extraction of Entity–Attribute–Value data	Abhiram Das
02/16/2010	Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets
02/23/2010	TBA
03/02/2010	TBA
03/09/2010	Multiple native states reveal persistent ruggedness of an RNA folding landscape	Gabriel Mitchell
03/19/2010	Oscillation in a quorum	Joshua Weitz
03/30/2010	TBA
04/06/2010	Listening to the noise: random fluctuations reveal gene network parameters		Systems Biology
04/13/2010	Metagenomics and the Units of Biological Organization	Abhiram Das
04/20/2010	TBA
04/27/2010	TBA

We are meeting in CE214 at 12:00-1:00pm. Bring your lunch.

Date	Paper	Host	Theme
09/14/2009	Mathematics Is Biology’s Next Microscope, Only Better
09/21/2009	The implications of human metabolic network topology for disease comorbidity		Networks
09/28/2009	The genetics of geometry
10/12/2009	Metagenomics binning - Phymm paper		Systems Biology
10/19/2009	The Gaggle: An open-source software system for integrating bioinformatics software and data sources.	Abhiram Das
10/26/2009	Multiscale complex network of protein conformational fluctuations in single-molecule time series	Gabriel Mitchell
11/09/2009	TBA
11/16/2009	TBA	Joshua Weitz
11/23/2009	Cytoplasmic diffusion: molecular motors mix it up
11/23/2009	TBA
11/30/2009	TBA

We are meeting in CE214 at 11:00am-12:00pm.

Date	Paper	Host	Theme
06/16/2010	Reprogramming bacteria to seek and destroy an herbicide		Systems Biology
06/23/2010	Hierarchical group dynamics in pigeon flocks	Gabriel Mitchell	Systems Biology
06/30/2010	A SOFTWARE ARCHITECTURE FOR DEVELOPMENTAL MODELING IN PLANTS: THE COMPUTABLE PLANT PROJECT		Microbial Ecology, Networks
07/07/2010	The Small-World Problem	Cesar Flores
07/14/2010	Scale-free correlations in starling ﬂocks		Systems Biology
07/28/2010	Problem-Based Learning Modifying Medical School Model for Teaching High School Econ
08/04/2010	TBA

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