Table of Contents: December 2012

The sandfish lizard uses body undulation to swim within sand (x-ray image, left), a granular medium in which frictional forces dominate the dynamics. Numerical simulation (right) consisting of a multibody simulation of the animal coupled to a multiparticle model of the granular medium (several hundred thousand 3 mm–diameter glass spheres) allows investigation of the mechanics of swimming, including resistance forces and power consumption. In the right panel, a localized region of grains around the simulated sandfish is fluidized (brighter color indicates faster motion), while the grains only a body width away remain in a solid state. See Ding et al.

Image Credit: Yang Ding, Sarah S. Sharpe, and Andrew Masse, Georgia Institute of Technology.


Ten Simple Rules for the Open Development of Scientific Software

Andreas Prlić, James B. Procter

Education Articles

Introduction to Translational Bioinformatics Collection

Russ B. Altman

Chapter 1: Biomedical Knowledge Integration

Philip R. O. Payne

Chapter 2: Data-Driven View of Disease Biology

Casey S. Greene, Olga G. Troyanskaya

Chapter 3: Small Molecules and Disease

David S. Wishart

Chapter 4: Protein Interactions and Disease

Mileidy W. Gonzalez, Maricel G. Kann

Chapter 5: Network Biology Approach to Complex Diseases

Dong-Yeon Cho, Yoo-Ah Kim, Teresa M. Przytycka

Chapter 6: Structural Variation and Medical Genomics

Benjamin J. Raphael

Chapter 7: Pharmacogenomics

Konrad J. Karczewski, Roxana Daneshjou, Russ B. Altman

Chapter 9: Analyses Using Disease Ontologies

Nigam H. Shah, Tyler Cole, Mark A. Musen

Chapter 10: Mining Genome-Wide Genetic Markers

Xiang Zhang, Shunping Huang, Zhaojun Zhang, Wei Wang

Chapter 11: Genome-Wide Association Studies

William S. Bush, Jason H. Moore

Chapter 12: Human Microbiome Analysis

Xochitl C. Morgan, Curtis Huttenhower

Chapter 13: Mining Electronic Health Records in the Genomics Era

Joshua C. Denny

Chapter 14: Cancer Genome Analysis

Miguel Vazquez, Victor de la Torre, Alfonso Valencia

Teaching the Fundamentals of Biological Data Integration Using Classroom Games

Maria Victoria Schneider, Rafael C. Jimenez


A Comparison of Computational Models for Eukaryotic Cell Shape and Motility

William R. Holmes, Leah Edelstein-Keshet

Research Articles

ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes

Kishore R. Mosaliganti, Ramil R. Noche, Fengzhu Xiong, Ian A. Swinburne, Sean G. Megason

Localizing Genes to Cerebellar Layers by Classifying ISH Images

Lior Kirsch, Noa Liscovitch, Gal Chechik

Genomic Hallmarks of Genes Involved in Chromosomal Translocations in Hematological Cancer

Mikhail Shugay, Iñigo Ortiz de Mendíbil, José L. Vizmanos, Francisco J. Novo

Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin State

Bartek Wilczynski, Ya-Hsin Liu, Zhen Xuan Yeo, Eileen E. M. Furlong

Molecular Evolution of Peptide Ligands with Custom-Tailored Characteristics for Targeting of Glycostructures

Niels Röckendorf, Markus Borschbach, Andreas Frey

Modelling Hair Follicle Growth Dynamics as an Excitable Medium

Philip J. Murray, Philip K. Maini, Maksim V. Plikus, Cheng-Ming Chuong, Ruth E. Baker

SnIPRE: Selection Inference Using a Poisson Random Effects Model

Kirsten E. Eilertson, James G. Booth, Carlos D. Bustamante

Electron Transfer Interactome of Cytochrome c

Alexander N. Volkov, Nico A. J. van Nuland

Task-Dependent Changes in Cross-Level Coupling between Single Neurons and Oscillatory Activity in Multiscale Networks

Ryan T. Canolty, Karunesh Ganguly, Jose M. Carmena

Mechanics of Undulatory Swimming in a Frictional Fluid

Yang Ding, Sarah S. Sharpe, Andrew Masse, Daniel I. Goldman

Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli

Robert C. Brewster, Daniel L. Jones, Rob Phillips

Quantitative Dynamics of Telomere Bouquet Formation

David M. Richards, Emma Greer, Azahara C. Martin, Graham Moore, Peter J. Shaw, Martin Howard

Climbing Fiber Burst Size and Olivary Sub-threshold Oscillations in a Network Setting

Jornt R. De Gruijl, Paolo Bazzigaluppi, Marcel T. G. de Jeu, Chris I. De Zeeuw

Parameter Identifiability and Sensitivity Analysis Predict Targets for Enhancement of STAT1 Activity in Pancreatic Cancer and Stellate Cells

Katja Rateitschak, Felix Winter, Falko Lange, Robert Jaster, Olaf Wolkenhauer

The Evolution of Cell-to-Cell Communication in a Sporulating Bacterium

Jordi van Gestel, Martin A. Nowak, Corina E. Tarnita

Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking

Jens Vindahl Kringelum, Claus Lundegaard, Ole Lund, Morten Nielsen

Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density

Claudia Coronnello, Ryan Hartmaier, Arshi Arora, Luai Huleihel, Kusum V. Pandit, Abha S. Bais, Michael Butterworth, Naftali Kaminski, Gary D. Stormo, Steffi Oesterreich, Panayiotis V. Benos

Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities

James P. O'Dwyer, Steven W. Kembel, Jessica L. Green

Phylodynamic Inference and Model Assessment with Approximate Bayesian Computation: Influenza as a Case Study

Oliver Ratmann, Gé Donker, Adam Meijer, Christophe Fraser, Katia Koelle

Soft-bound Synaptic Plasticity Increases Storage Capacity

Mark C. W. van Rossum, Maria Shippi, Adam B. Barrett

3D Reconstruction and Standardization of the Rat Vibrissal Cortex for Precise Registration of Single Neuron Morphology

Robert Egger, Rajeevan T. Narayanan, Moritz Helmstaedter, Christiaan P. J. de Kock, Marcel Oberlaender

PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions

Wenlian Qiao, Gerald Quon, Elizabeth Csaszar, Mei Yu, Quaid Morris, Peter W. Zandstra

A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor

Ranjan V. Mannige, Charles L. Brooks, Eugene I. Shakhnovich

Computational Phenotyping of Two-Person Interactions Reveals Differential Neural Response to Depth-of-Thought

Ting Xiang, Debajyoti Ray, Terry Lohrenz, Peter Dayan, P. Read Montague

Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations

Federica Chiappori, Ivan Merelli, Giorgio Colombo, Luciano Milanesi, Giulia Morra

Using Molecular Mechanics to Predict Bulk Material Properties of Fibronectin Fibers

Mark J. Bradshaw, Man C. Cheung, Daniel J. Ehrlich, Michael L. Smith

Nucleoid-Associated Proteins Affect Mutation Dynamics in E. coli in a Growth Phase-Specific Manner

Tobias Warnecke, Fran Supek, Ben Lehner

Calcium Wave Propagation in Networks of Endothelial Cells: Model-based Theoretical and Experimental Study

Juexuan Long, Michael Junkin, Pak Kin Wong, James Hoying, Pierre Deymier

Interconnected Cavernous Structure of Bacterial Fruiting Bodies

Cameron W. Harvey, Huijing Du, Zhiliang Xu, Dale Kaiser, Igor Aranson, Mark Alber