Table of Contents: April 2012


The algorithmic matrix of patterning information during planarian regeneration.

Image Credit: Image produced by Daniel Lobo and Wendy Beane.
Issue Image

The correct regeneration of complex morphology after amputation in planaria requires precise coordination of global patterning information and individual stem cell activity. This image illustrates the algorithmic information that is processed by cells and tissues to restore missing structures. See Lobo and Beane(e1002281).



Research Articles

Storage of Correlated Patterns in Standard and Bistable Purkinje Cell Models

Claudia Clopath, Jean-Pierre Nadal, Nicolas Brunel

Deconvolution of the Cellular Force-Generating Subsystems that Govern Cytokinesis Furrow Ingression

Christopher C. Poirier, Win Pin Ng, Douglas N. Robinson, Pablo A. Iglesias

Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics

Karen van Eunen, José A. L. Kiewiet, Hans V. Westerhoff, Barbara M. Bakker

Microarray Analysis of LTR Retrotransposon Silencing Identifies Hdac1 as a Regulator of Retrotransposon Expression in Mouse Embryonic Stem Cells

Judith Reichmann, James H. Crichton, Monika J. Madej, Mary Taggart, Philippe Gautier, Jose Luis Garcia-Perez, Richard R. Meehan, Ian R. Adams

Tension and Robustness in Multitasking Cellular Networks

Jeffrey V. Wong, Bochong Li, Lingchong You

Social Interaction, Noise and Antibiotic-Mediated Switches in the Intestinal Microbiota

Vanni Bucci, Serena Bradde, Giulio Biroli, Joao B. Xavier

Are Long-Range Structural Correlations Behind the Aggregration Phenomena of Polyglutamine Diseases?

Mahmoud Moradi, Volodymyr Babin, Christopher Roland, Celeste Sagui

Persisting Viral Sequences Shape Microbial CRISPR-based Immunity

Ariel D. Weinberger, Christine L. Sun, Mateusz M. Pluciński, Vincent J. Denef, Brian C. Thomas, Philippe Horvath, Rodolphe Barrangou, Michael S. Gilmore, Wayne M. Getz, Jillian F. Banfield

Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity

Kyle E. Roberts, Patrick R. Cushing, Prisca Boisguerin, Dean R. Madden, Bruce R. Donald

The Effects of NMDA Subunit Composition on Calcium Influx and Spike Timing-Dependent Plasticity in Striatal Medium Spiny Neurons

Rebekah C. Evans, Teresa Morera-Herreras, Yihui Cui, Kai Du, Tom Sheehan, Jeanette Hellgren Kotaleski, Laurent Venance, Kim T. Blackwell

A New Perceptual Bias Reveals Suboptimal Population Decoding of Sensory Responses

Tom Putzeys, Matthias Bethge, Felix Wichmann, Johan Wagemans, Robbe Goris

Differences in Cell Division Rates Drive the Evolution of Terminal Differentiation in Microbes

João F. Matias Rodrigues, Daniel J. Rankin, Valentina Rossetti, Andreas Wagner, Homayoun C. Bagheri

The Impact of Imitation on Vaccination Behavior in Social Contact Networks

Martial L. Ndeffo Mbah, Jingzhou Liu, Chris T. Bauch, Yonas I. Tekel, Jan Medlock, Lauren Ancel Meyers, Alison P. Galvani

Optimizing Provider Recruitment for Influenza Surveillance Networks

Samuel V. Scarpino, Nedialko B. Dimitrov, Lauren Ancel Meyers

Geometric Theory Predicts Bifurcations in Minimal Wiring Cost Trees in Biology Are Flat

Yihwa Kim, Robert Sinclair, Nol Chindapol, Jaap A. Kaandorp, Erik De Schutter

Impact of Adaptation Currents on Synchronization of Coupled Exponential Integrate-and-Fire Neurons

Josef Ladenbauer, Moritz Augustin, LieJune Shiau, Klaus Obermayer

Establishment and Validation of Computational Model for MT1-MMP Dependent ECM Degradation and Intervention Strategies

Daisuke Hoshino, Naohiko Koshikawa, Takashi Suzuki, Vito Quaranta, Alissa M. Weaver, Motoharu Seiki, Kazuhisa Ichikawa

Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit

Dmitry Nevozhay, Rhys M. Adams, Elizabeth Van Itallie, Matthew R. Bennett, Gábor Balázsi

Replication Fork Polarity Gradients Revealed by Megabase-Sized U-Shaped Replication Timing Domains in Human Cell Lines

Antoine Baker, Benjamin Audit, Chun-Long Chen, Benoit Moindrot, Antoine Leleu, Guillaume Guilbaud, Aurélien Rappailles, Cédric Vaillant, Arach Goldar, Fabien Mongelard, Yves d'Aubenton-Carafa, Olivier Hyrien, Claude Thermes, Alain Arneodo

Molecular Machines in the Synapse: Overlapping Protein Sets Control Distinct Steps in Neurosecretion

L. Niels Cornelisse, Evgeni Tsivtsivadze, Marieke Meijer, Tjeerd M. H. Dijkstra, Tom Heskes, Matthijs Verhage

Automatic Filtering and Substantiation of Drug Safety Signals

Anna Bauer-Mehren, Erik M. van Mullingen, Paul Avillach, María del Carmen Carrascosa, Ricard Garcia-Serna, Janet Piñero, Bharat Singh, Pedro Lopes, José L. Oliveira, Gayo Diallo, Ernst Ahlberg Helgee, Scott Boyer, Jordi Mestres, Ferran Sanz, Jan A. Kors, Laura I. Furlong

What Can Causal Networks Tell Us about Metabolic Pathways?

Rachael Hageman Blair, Daniel J. Kliebenstein, Gary A. Churchill

Parameters in Dynamic Models of Complex Traits are Containers of Missing Heritability

Yunpeng Wang, Arne B. Gjuvsland, Jon Olav Vik, Nicolas P. Smith, Peter J. Hunter, Stig W. Omholt

Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142

Trang T. Vu, Sergey M. Stolyar, Grigoriy E. Pinchuk, Eric A. Hill, Leo A. Kucek, Roslyn N. Brown, Mary S. Lipton, Andrei Osterman, Jim K. Fredrickson, Allan E. Konopka, Alexander S. Beliaev, Jennifer L. Reed

Energetic Selection of Topology in Ferredoxins

J. Dongun Kim, Agustina Rodriguez-Granillo, David A. Case, Vikas Nanda, Paul G. Falkowski

RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm

Onur Sakarya, Heinz Breu, Milan Radovich, Yongzhi Chen, Yulei N. Wang, Catalin Barbacioru, Sowmi Utiramerur, Penn P. Whitley, Joel P. Brockman, Paolo Vatta, Zheng Zhang, Liviu Popescu, Matthew W. Muller, Vidya Kudlingar, Nriti Garg, Chieh-Yuan Li, Benjamin S. Kong, John P. Bodeau, Robert C. Nutter, Jian Gu, Kelli S. Bramlett, Jeffrey K. Ichikawa, Fiona C. Hyland, Asim S. Siddiqui

On Conduction in a Bacterial Sodium Channel

Simone Furini, Carmen Domene