Table of Contents

February 2008

Moving sinusoidal electrosensory gratings elicit direction-selective responses in the brains of Eigenmannia virescens (see Carver et al., e32).

Image Credit: Photograph of Eigenmannia by Will Kirk. Composite image composed and edited by Eric Fortune and Eatai Roth.

Message from ISCB

Getting Started in Biological Pathway Construction and Analysis

Ganesh A Viswanathan, Jeremy Seto, Sonali Patil, German Nudelman, Stuart C Sealfon


Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductor

Michał J Okoniewski, Crispin J Miller


Computational Methods for Protein Identification from Mass Spectrometry Data

Leo McHugh, Jonathan W Arthur

Research Articles

Serotonin, Inhibition, and Negative Mood

Peter Dayan, Quentin J. M Huys

Predicting the Receptive Range of Olfactory Receptors

Rafi Haddad, Liran Carmel, Noam Sobel, David Harel

Evolution of Complex Modular Biological Networks

Arend Hintze, Christoph Adami

Modeling Cancer Progression via Pathway Dependencies

Elena J Edelman, Justin Guinney, Jen-Tsan Chi, Phillip G Febbo, Sayan Mukherjee

Selective Adaptation in Networks of Heterogeneous Populations: Model, Simulation, and Experiment

Avner Wallach, Danny Eytan, Shimon Marom, Ron Meir

Stimulus Design for Model Selection and Validation in Cell Signaling

Joshua F Apgar, Jared E Toettcher, Drew Endy, Forest M White, Bruce Tidor

The Peri-Saccadic Perception of Objects and Space

Fred H Hamker, Marc Zirnsak, Dirk Calow, Markus Lappe

Synaptic Plasticity Can Produce and Enhance Direction Selectivity

Sean Carver, Eatai Roth, Noah J Cowan, Eric S Fortune

Modeling an Evolutionary Conserved Circadian Cis-Element

Eric R Paquet, Guillaume Rey, Felix Naef

Control of Cation Permeation through the Nicotinic Receptor Channel

Hai-Long Wang, Xiaolin Cheng, Palmer Taylor, J. Andrew McCammon, Steven M Sine

Accurate Structural Correlations from Maximum Likelihood Superpositions

Douglas L Theobald, Deborah S Wuttke

Genome Landscapes and Bacteriophage Codon Usage

Julius B. Lucks, David R. Nelson, Grzegorz R. Kudla, Joshua B. Plotkin

How Protein Stability and New Functions Trade Off

Nobuhiko Tokuriki, Francois Stricher, Luis Serrano, Dan S. Tawfik

Systematic Analysis of Pleiotropy in C. elegans Early Embryogenesis

Lihua Zou, Sira Sriswasdi, Brian Ross, Patrycja V. Missiuro, Jun Liu, Hui Ge

Stochastic Differential Equation Model for Cerebellar Granule Cell Excitability

Antti Saarinen, Marja-Leena Linne, Olli Yli-Harja

The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks

Derek Ruths, Melissa Muller, Jen-Te Tseng, Luay Nakhleh, Prahlad T. Ram

Multi-Scale Simulations Provide Supporting Evidence for the Hypothesis of Intramolecular Protein Translocation in GroEL/GroES Complexes

Ivan Coluzza, Alfonso De Simone, Franca Fraternali, Daan Frenkel

Diminished Self-Chaperoning Activity of the ΔF508 Mutant of CFTR Results in Protein Misfolding

Adrian W. R. Serohijos, Tamás Hegedűs, John R. Riordan, Nikolay V. Dokholyan

Computer-Based Screening of Functional Conformers of Proteins

Héctor Marlosti Montiel Molina, César Millán-Pacheco, Nina Pastor, Gabriel del Rio

Sensing and Integration of Erk and PI3K Signals by Myc

Tae Lee, Guang Yao, Joseph Nevins, Lingchong You

Mutations of Different Molecular Origins Exhibit Contrasting Patterns of Regional Substitution Rate Variation

Navin Elango, Seong-Ho Kim, NISC Comparative Sequencing Program, Eric Vigoda, Soojin V. Yi

Statistical Resolution of Ambiguous HLA Typing Data

Jennifer Listgarten, Zabrina Brumme, Carl Kadie, Gao Xiaojiang, Bruce Walker, Mary Carrington, Philip Goulder, David Heckerman

Identification of Synaptic Targets of Drosophila Pumilio

Gengxin Chen, Wanhe Li, Qing-Shuo Zhang, Michael Regulski, Nishi Sinha, Jody Barditch, Tim Tully, Adrian R. Krainer, Michael Q. Zhang, Josh Dubnau

Mouse Cognition-Related Behavior in the Open-Field: Emergence of Places of Attraction

Anna Dvorkin, Yoav Benjamini, Ilan Golani


On the Process of Becoming a Great Scientist

Morgan C Giddings