Table of Contents: May 2010


Image Credit:
Issue Image
Multiplicity of molecular signatures.

Molecular signatures constitute one of the most important translational and basic science developments enabled by recent high-throughput molecular assays. A perplexing phenomenon that characterizes high-throughput data analysis is the ubiquitous multiplicity of molecular signatures. This phenomenon has far-reaching implications for biological discovery and development of next generation patient diagnostics and personalized treatments. Currently, the causes and interpretation of signature multiplicity are unknown, and several—often contradictory—conjectures have been made to explain it. The authors shed light on the causes of signature multiplicity and provide a method for extracting all equivalently accurate signatures from high-throughput data. (See Statnikov and Aliferis, e1000790).

Image Credit: William Sommer (New York University Langone Medical Center).

Education Articles

A Quick Guide to Large-Scale Genomic Data Mining

Curtis Huttenhower, Oliver Hofmann


Research Articles

Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets

Nitin Bhardwaj, Matthew B. Carson, Alexej Abyzov, Koon-Kiu Yan, Hui Lu, Mark B. Gerstein

Chemotactic Response and Adaptation Dynamics in Escherichia coli

Diana Clausznitzer, Olga Oleksiuk, Linda Løvdok, Victor Sourjik, Robert G. Endres

Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks

Karine Audouze, Agnieszka Sierakowska Juncker, Francisco J. S. S. A. Roque, Konrad Krysiak-Baltyn, Nils Weinhold, Olivier Taboureau, Thomas Skøt Jensen, Søren Brunak

Inductive Game Theory and the Dynamics of Animal Conflict

Simon DeDeo, David C. Krakauer, Jessica C. Flack

Mutation Bias Favors Protein Folding Stability in the Evolution of Small Populations

Raul Mendez, Miriam Fritsche, Markus Porto, Ugo Bastolla

Energy-Information Trade-Offs between Movement and Sensing

Malcolm A. MacIver, Neelesh A. Patankar, Anup A. Shirgaonkar

On the Zwitterionic Nature of Gas-Phase Peptides and Protein Ions

Roberto Marchese, Rita Grandori, Paolo Carloni, Simone Raugei

Assimilating Seizure Dynamics

Ghanim Ullah, Steven J. Schiff

A Differentiation-Based Phylogeny of Cancer Subtypes

Markus Riester, Camille Stephan-Otto Attolini, Robert J. Downey, Samuel Singer, Franziska Michor

Identification of Key Processes that Control Tumor Necrosis Factor Availability in a Tuberculosis Granuloma

Mohammad Fallahi-Sichani, Matthew A. Schaller, Denise E. Kirschner, Steven L. Kunkel, Jennifer J. Linderman