Table of Contents: May 2010

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

Making Informed Choices about Microarray Data Analysis

Mark Reimers


What Do I Want from the Publisher of the Future?

Philip E. Bourne

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

Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)

James A. Eddy, Leroy Hood, Nathan D. Price, Donald Geman

Game Theory of Social Distancing in Response to an Epidemic

Timothy C. Reluga

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

Analysis and Computational Dissection of Molecular Signature Multiplicity

Alexander Statnikov, Constantin F. Aliferis

Influence of Low-Level Stimulus Features, Task Dependent Factors, and Spatial Biases on Overt Visual Attention

Sepp Kollmorgen, Nora Nortmann, Sylvia Schröder, Peter König

Quantifying the Effects of Elastic Collisions and Non-Covalent Binding on Glutamate Receptor Trafficking in the Post-Synaptic Density

Fidel Santamaria, Jossina Gonzalez, George J. Augustine, Sridhar Raghavachari

Impact of Dendritic Size and Dendritic Topology on Burst Firing in Pyramidal Cells

Ronald A. J. van Elburg, Arjen van Ooyen

Inductive Game Theory and the Dynamics of Animal Conflict

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

Mathematical Modelling of DNA Replication Reveals a Trade-off between Coherence of Origin Activation and Robustness against Rereplication

Anneke Brümmer, Carlos Salazar, Vittoria Zinzalla, Lilia Alberghina, Thomas Höfer

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

Modeling Reveals Bistability and Low-Pass Filtering in the Network Module Determining Blood Stem Cell Fate

Jatin Narula, Aileen M. Smith, Berthold Gottgens, Oleg A. Igoshin

Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation

Jochen S. Hub, Marcus B. Kubitzki, Bert L. de Groot

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