Table of Contents | May 2010

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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).

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A Quick Guide to Large-Scale Genomic Data Mining

Curtis Huttenhower, Oliver Hofmann

Making Informed Choices about Microarray Data Analysis

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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

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

Ronald A. J. van Elburg, Arjen van Ooyen

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Inductive Game Theory and the Dynamics of Animal Conflict

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

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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

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A Model for Genetic and Epigenetic Regulatory Networks Identifies Rare Pathways for Transcription Factor Induced Pluripotency

Maxim N. Artyomov, Alexander Meissner, Arup K. Chakraborty

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

Raul Mendez, Miriam Fritsche, Markus Porto, Ugo Bastolla

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Energy-Information Trade-Offs between Movement and Sensing

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

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A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

Oliver Stegle, Leopold Parts, Richard Durbin, John Winn

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Table of Contents | May 2010

About This Image

Education Articles

A Quick Guide to Large-Scale Genomic Data Mining

Making Informed Choices about Microarray Data Analysis

Perspective

What Do I Want from the Publisher of the Future?

Research Articles

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

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

Game Theory of Social Distancing in Response to an Epidemic

Weak Noise in Neurons May Powerfully Inhibit the Generation of Repetitive Spiking but Not Its Propagation

Chemotactic Response and Adaptation Dynamics in Escherichia coli

Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks

Novel Peptide-Mediated Interactions Derived from High-Resolution 3-Dimensional Structures

Analysis and Computational Dissection of Molecular Signature Multiplicity

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

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

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

Inductive Game Theory and the Dynamics of Animal Conflict

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

A Model for Genetic and Epigenetic Regulatory Networks Identifies Rare Pathways for Transcription Factor Induced Pluripotency

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

Energy-Information Trade-Offs between Movement and Sensing

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

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

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

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

Assimilating Seizure Dynamics

A Differentiation-Based Phylogeny of Cancer Subtypes

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