Table of Contents

May 2014

The earliest events in host defense against Candida species fungal pathogens involve the recruitment of anti-fungal receptors to specialized cellular contact sites. Image bioinformatic approaches permit quantitative dissection of spatiotemporal receptor distributions along this complex interface. Human immature dendritic cells (foreground right) recruit DC-SIGN (green) and CD206 (red) to capture C. albicans yeast (yellow), achieving up to two orders of magnitude enrichment of these receptors at the contact site. See Graus et al.

Image Credit: Matthew S. Graus, Aaron K. Neumann


Messages from ISCB

Paving the Way Towards a Successful and Fulfilling Career in Computational Biology

Olugbenga Oluwagbemi, Marion Adebiyi, Segun Fatumo, Geoff Macintyre

2014 ISCB Accomplishment by a Senior Scientist Award: Gene Myers

Christiana N. Fogg, Diane E. Kovats

Learn from the Best

Virginie Bernard, Sebastian J. Schultheiss, Magali Michaut


Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine

Lei Xie, Xiaoxia Ge, Hepan Tan, Li Xie, Yinliang Zhang, Thomas Hart, Xiaowei Yang, Philip E. Bourne

Research Articles

A Computational Model for the Analysis of Lipoprotein Distributions in the Mouse: Translating FPLC Profiles to Lipoprotein Metabolism

Fianne L. P. Sips, Christian A. Tiemann, Maaike H. Oosterveer, Albert K. Groen, Peter A. J. Hilbers, Natal A. W. van Riel

Bistable Dynamics Underlying Excitability of Ion Homeostasis in Neuron Models

Niklas Hübel, Eckehard Schöll, Markus A. Dahlem

Slow Feature Analysis on Retinal Waves Leads to V1 Complex Cells

Sven Dähne, Niko Wilbert, Laurenz Wiskott

From the Phenomenology to the Mechanisms of Consciousness: Integrated Information Theory 3.0

Masafumi Oizumi, Larissa Albantakis, Giulio Tononi

A Computational Framework for Analyzing Stochasticity in Gene Expression

Marc S. Sherman, Barak A. Cohen

Effects of Specular Highlights on Perceived Surface Convexity

Wendy J. Adams, James H. Elder

Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions

Daphna Rothschild, Erez Dekel, Jean Hausser, Anat Bren, Guy Aidelberg, Pablo Szekely, Uri Alon

Synonymous Constraint Elements Show a Tendency to Encode Intrinsically Disordered Protein Segments

Mauricio Macossay-Castillo, Simone Kosol, Peter Tompa, Rita Pancsa

A Simulated Intermediate State for Folding and Aggregation Provides Insights into ΔN6 β2-Microglobulin Amyloidogenic Behavior

Sílvia G. Estácio, Heinrich Krobath, Diogo Vila-Viçosa, Miguel Machuqueiro, Eugene I. Shakhnovich, Patrícia F. N. Faísca

Predicting the Responses of Repetitively Firing Neurons to Current Noise

Charles J. Wilson, David Barraza, Todd Troyer, Michael A. Farries

Axonal Noise as a Source of Synaptic Variability

Ali Neishabouri, A. Aldo Faisal

Myxococcus xanthus Gliding Motors Are Elastically Coupled to the Substrate as Predicted by the Focal Adhesion Model of Gliding Motility

Rajesh Balagam, Douglas B. Litwin, Fabian Czerwinski, Mingzhai Sun, Heidi B. Kaplan, Joshua W. Shaevitz, Oleg A. Igoshin

Barriers to Cooperation Aid Ideological Rigidity and Threaten Societal Collapse

Marko Jusup, Tadasu Matsuo, Yoh Iwasa

Structurally-Constrained Relationships between Cognitive States in the Human Brain

Ann M. Hermundstad, Kevin S. Brown, Danielle S. Bassett, Elissa M. Aminoff, Amy Frithsen, Arianne Johnson, Christine M. Tipper, Michael B. Miller, Scott T. Grafton, Jean M. Carlson

Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data

Ciira wa Maina, Antti Honkela, Filomena Matarese, Korbinian Grote, Hendrik G. Stunnenberg, George Reid, Neil D. Lawrence, Magnus Rattray

Slow Noise in the Period of a Biological Oscillator Underlies Gradual Trends and Abrupt Transitions in Phasic Relationships in Hybrid Neural Networks

Umeshkanta S. Thounaojam, Jianxia Cui, Sharon E. Norman, Robert J. Butera, Carmen C. Canavier

ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones

Ignacio J. General, Ying Liu, Mandy E. Blackburn, Wenzhi Mao, Lila M. Gierasch, Ivet Bahar

Genomic Characterization of Large Heterochromatic Gaps in the Human Genome Assembly

Nicolas Altemose, Karen H. Miga, Mauro Maggioni, Huntington F. Willard

In-Vivo Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks

Filippo Menolascina, Gianfranco Fiore, Emanuele Orabona, Luca De Stefano, Mike Ferry, Jeff Hasty, Mario di Bernardo, Diego di Bernardo

The Changing Geometry of a Fitness Landscape Along an Adaptive Walk

Devin Greene, Kristina Crona

Essential Plasticity and Redundancy of Metabolism Unveiled by Synthetic Lethality Analysis

Oriol Güell, Francesc Sagués, M. Ángeles Serrano

In Silico Screening of the Key Cellular Remodeling Targets in Chronic Atrial Fibrillation

Jussi T. Koivumäki, Gunnar Seemann, Mary M. Maleckar, Pasi Tavi

Evolution of Pathogen Specialisation in a Host Metapopulation: Joint Effects of Host and Pathogen Dispersal

Julien Papaïx, Jeremy J. Burdon, Christian Lannou, Peter H. Thrall

Spatial Generalization in Operant Learning: Lessons from Professional Basketball

Tal Neiman, Yonatan Loewenstein

An Innovative Influenza Vaccination Policy: Targeting Last Season's Patients

Dan Yamin, Arieh Gavious, Eyal Solnik, Nadav Davidovitch, Ran D. Balicer, Alison P. Galvani, Joseph S. Pliskin

A Signature of Attractor Dynamics in the CA3 Region of the Hippocampus

César Rennó-Costa, John E. Lisman, Paul F. M. J. Verschure

Quantifying and Predicting the Effect of Exogenous Interleukin-7 on CD4+T Cells in HIV-1 Infection

Rodolphe Thiébaut, Julia Drylewicz, Mélanie Prague, Christine Lacabaratz, Stéphanie Beq, Ana Jarne, Thérèse Croughs, Rafick-Pierre Sekaly, Michael M. Lederman, Irini Sereti, Daniel Commenges, Yves Lévy

High-Resolution Modeling of Transmembrane Helical Protein Structures from Distant Homologues

Kuang-Yui M. Chen, Jiaming Sun, Jason S. Salvo, David Baker, Patrick Barth

Related Articles

Arterial Stiffening Provides Sufficient Explanation for Primary Hypertension

Klas H. Pettersen, Scott M. Bugenhagen, Javaid Nauman, Daniel A. Beard, Stig W. Omholt

Optimism as a Prior Belief about the Probability of Future Reward

Aistis Stankevicius, Quentin J. M. Huys, Aditi Kalra, Peggy Seriès

The Natural History of Biocatalytic Mechanisms

Neetika Nath, John B. O. Mitchell, Gustavo Caetano-Anollés

Finding Novel Molecular Connections between Developmental Processes and Disease

Jisoo Park, Heather C. Wick, Daniel E. Kee, Keith Noto, Jill L. Maron, Donna K. Slonim

Inferring Host Gene Subnetworks Involved in Viral Replication

Deborah Chasman, Brandi Gancarz, Linhui Hao, Michael Ferris, Paul Ahlquist, Mark Craven

A New Tool to Quantify Receptor Recruitment to Cell Contact Sites during Host-Pathogen Interaction

Matthew S. Graus, Carolyn Pehlke, Michael J. Wester, Lisa B. Davidson, Stanly L. Steinberg, Aaron K. Neumann