Some Papers for the SAMSI course on Algebraic Methods


Madalena Chaves, Reka Albert, and Eduardo Sontag.  Robustness and fragility of Boolean models for genetic regulatory networks.  Journal of Theoretical Biolgoy 235 (2005) 431-449.

Reinhard Laubenbacher and Brandilyn Stigler. Design of experiments and biochemical network inference.

Celine Lefebvre, Wei Keat Lim, Katia Basso, Ricardo Dalla Favera, and Andrea Califano.  A Context-specific network of Protein-DNA and Protein-Protein interactions reveals new regulatory motifs in human B cells. (T. Ideker adn V. Bafna (Eds.) Syst. Biolo. and Comput. Protemics Ws, LNBI 4532, 42--56, 2007.

Kevin Murphy and Saira Mian.  Modeling gene expression data using dynamic Bayesian networks.

Brandilyn Stigler and Alan Veliz-Cruz.  Network topology as a driver of bistability in the LAC operon.  

Yael Berstein, Hugo Maruri-Aguilar, Shmuel Onn, Eva Riccomagno, Henry Wynn.  Minimal average degree aberration and the state polytope for experimental designs.   

Fabrizio Catanese, Serkan Hosten, Amit Khetan, Bernd Sturmfels.  The maximum likelihood degree. 

Mathias Drton.  Likelihood ratio tests and singularities.  

Mathias Drton.  Discrete chain graph models. 

Hisayuki Hara, Akimichi Takemura, Ruriko Yoshida.  Markov bases for two-way subtable sum problem. 

Elizabeth Allman, John Rhodes.  The identifiability of covarion models in phylogenetics.

Niko Beerenwinkel, Lior Pachter, Bernd Sturmfels.  Epistasis and shapes of fitness landscapes. 

Lou Billera, Susan Holmes and Karen Vogtmann, Geometry of the space of phylogenetic trees,  Advances in Applied Math.  27 (2001) 733-767.

Lior Pachter, Bernd Sturmfels.  Parametric inference for biological sequence analysis.