Journal: PLoS Computational Biology

Volume 5, Issue 9

0 -- 0Jasmine Foo, Mark W. Drummond, Bayard Clarkson, Tessa Holyoake, Franziska Michor. Eradication of Chronic Myeloid Leukemia Stem Cells: A Novel Mathematical Model Predicts No Therapeutic Benefit of Adding G-CSF to Imatinib
0 -- 0Juen Guo, Kevin D. Hall. Estimating the Continuous-Time Dynamics of Energy and Fat Metabolism in Mice
0 -- 0Julie Baussand, Alessandra Carbone. A Combinatorial Approach to Detect Coevolved Amino Acid Networks in Protein Families of Variable Divergence
0 -- 0Jiguang Wang, Shi-Hua Zhang, Yong Wang, Luonan Chen, Xiang-Sun Zhang. Disease-Aging Network Reveals Significant Roles of Aging Genes in Connecting Genetic Diseases
0 -- 0Xueping Yu, Joseph Ivanic, Anders Wallqvist, Jaques Reifman. A Novel Scoring Approach for Protein Co-Purification Data Reveals High Interaction Specificity
0 -- 0Sami El Boustani, Olivier Marre, Sébastien Béhuret, Pierre Baudot, Pierre Yger, Thierry Bal, Alain Destexhe, Yves Frégnac. Network-State Modulation of Power-Law Frequency-Scaling in Visual Cortical Neurons
0 -- 0Santhosh Palani, Casim A. Sarkar. Integrating Extrinsic and Intrinsic Cues into a Minimal Model of Lineage Commitment for Hematopoietic Progenitors
0 -- 0Pietro Berkes, Richard E. Turner, Maneesh Sahani. A Structured Model of Video Reproduces Primary Visual Cortical Organisation
0 -- 0Alex Bateman, Philip E. Bourne. Ten Simple Rules for Chairing a Scientific Session
0 -- 0Steve Hoffmann, Christian Otto, Stefan Kurtz, Cynthia M. Sharma, Philipp Khaitovich, Jörg Vogel, Peter F. Stadler, Jörg Hackermüller. Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures
0 -- 0Stefano Allesina, Mercedes Pascual. Googling Food Webs: Can an Eigenvector Measure Species' Importance for Coextinctions?
0 -- 0Balázs Ujfalussy, Tamás Kiss, Péter Érdi. Parallel Computational Subunits in Dentate Granule Cells Generate Multiple Place Fields
0 -- 0Rui-Ru Ji, Heshani de Silva, Yisheng Jin, Robert E. Bruccoleri, Jian Cao, Aiqing He, Wenjun Huang, Paul S. Kayne, Isaac Neuhaus, Karl-Heinz Ott, Becky Penhallow, Mark I. Cockett, Michael G. Neubauer, Nathan O. Siemers, Petra Ross-MacDonald. Transcriptional Profiling of the Dose Response: A More Powerful Approach for Characterizing Drug Activities
0 -- 0Yemin Shi, Hanbin Liu, Dahai Gai, Jianpeng Ma, Xiaojiang S. Chen. A Computational Analysis of ATP Binding of SV40 Large Tumor Antigen Helicase Motor
0 -- 0Dusan Misevic, Roger D. Kouyos, Sebastian Bonhoeffer. Predicting the Evolution of Sex on Complex Fitness Landscapes
0 -- 0Samuel A. Danziger, Roberta Baronio, Lydia Ho, Linda Hall, Kirsty Salmon, G. Wesley Hatfield, Peter Kaiser, Richard H. Lathrop. Predicting Positive p53 Cancer Rescue Regions Using Most Informative Positive (MIP) Active Learning
0 -- 0Amrita Mohan, Vladimir N. Uversky, Predrag Radivojac. Influence of Sequence Changes and Environment on Intrinsically Disordered Proteins
0 -- 0Deborah A. Striegel, Monica K. Hurdal. Chemically Based Mathematical Model for Development of Cerebral Cortical Folding Patterns
0 -- 0Cuong Than, Luay Nakhleh. Species Tree Inference by Minimizing Deep Coalescences
0 -- 0Michiel W. H. Remme, Máté Lengyel, Boris S. Gutkin. The Role of Ongoing Dendritic Oscillations in Single-Neuron Dynamics
0 -- 0Jiyong Park, Byungnam Kahng, Wonmuk Hwang. β Spine
0 -- 0Jennifer L. Lahti, Adam P. Silverman, Jennifer R. Cochran. E. elaterium Trypsin Inhibitor-II Cystine-Knot Miniprotein
0 -- 0Philippe Lemey, Andrew Rambaut, Alexei J. Drummond, Marc A. Suchard. Bayesian Phylogeography Finds Its Roots
0 -- 0William Ritchie, Megha Rajasekhar, Stephane Flamant, John E. J. Rasko. Conserved Expression Patterns Predict microRNA Targets
0 -- 0Steven H. Wu, Michael A. Black, Robyn A. North, Kelly R. Atkinson, Allen G. Rodrigo. A Statistical Model to Identify Differentially Expressed Proteins in 2D PAGE Gels
0 -- 0Frank J. Bruggeman, Nils Blüthgen, Hans V. Westerhoff. Noise Management by Molecular Networks
0 -- 0Timothy R. Lezon, Andrej Sali, Ivet Bahar. Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models
0 -- 0Frank Eisenhaber, Chee Keong Kwoh, See-Kiong Ng, Wing-Kin Sung, Limsoon Wong. Brief Overview of Bioinformatics Activities in Singapore
0 -- 0Michelle S. Scott, Fabio Avolio, Motoharu Ono, Angus I. Lamond, Geoffrey J. Barton. Human miRNA Precursors with Box H/ACA snoRNA Features
0 -- 0Simon Barthelmé, Pascal Mamassian. Evaluation of Objective Uncertainty in the Visual System
0 -- 0Stephen A. Stanhope, Srikumar Sengupta, Johan den Boon, Paul Ahlquist, Michael A. Newton. Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification

Volume 5, Issue 8

0 -- 0Pu Liu, Fangqiang Zhu, Dmitrii N. Rassokhin, Dimitris K. Agrafiotis. A Self-Organizing Algorithm for Modeling Protein Loops
0 -- 0Yurie Okabe-Oho, Hiroki Murakami, Suguru Oho, Masaki Sasai. Drosophila Embryo
0 -- 0Virginia Castillo, Salvador Ventura. Amyloidogenic Regions and Interaction Surfaces Overlap in Globular Proteins Related to Conformational Diseases
0 -- 0Leighton Pritchard, Hui Liu, Clare Booth, Emma Douglas, Patrice François, Jacques Schrenzel, Peter E. Hedley, Paul R. J. Birch, Ian K. Toth. Microarray Comparative Genomic Hybridisation Analysis Incorporating Genomic Organisation, and Application to Enterobacterial Plant Pathogens
0 -- 0Yuzhen Ye, Thomas G. Doak. A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes
0 -- 0Goedele Roos, Nicolas Foloppe, Koen Van Laer, Lode Wyns, Lennart Nilsson, Paul Geerlings, Joris Messens. How Thioredoxin Dissociates Its Mixed Disulfide
0 -- 0Frederik Graw, Roland R. Regoes. Investigating CTL Mediated Killing with a 3D Cellular Automaton
0 -- 0Jochen S. Hub, Bert L. de Groot. Detection of Functional Modes in Protein Dynamics
0 -- 0Paola Causin, Giuseppe Facchetti. Autocatalytic Loop, Amplification and Diffusion: A Mathematical and Computational Model of Cell Polarization in Neural Chemotaxis
0 -- 0Stefan J. Kiebel, Katharina von Kriegstein, Jean Daunizeau, Karl J. Friston. Recognizing Sequences of Sequences
0 -- 0Jing Tang, William P. Hanage, Christophe Fraser, Jukka Corander. Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach
0 -- 0Daniel A. Beard, Martin J. Kushmerick. Strong Inference for Systems Biology
0 -- 0Oleksii Kuchaiev, Marija Rasajski, Desmond J. Higham, Natasa Przulj. Geometric De-noising of Protein-Protein Interaction Networks
0 -- 0Yuval Itan, Adam Powell, Mark A. Beaumont, Joachim Burger, Mark G. Thomas. The Origins of Lactase Persistence in Europe
0 -- 0Naaman Kam, Yitzhak Pilpel, Mike Fainzilber. Can Molecular Motors Drive Distance Measurements in Injured Neurons?
0 -- 0David Balduzzi, Giulio Tononi. Qualia: The Geometry of Integrated Information
0 -- 0Daniel A. Braun, Pedro A. Ortega, Daniel M. Wolpert. Nash Equilibria in Multi-Agent Motor Interactions
0 -- 0Jan Engelstädter, Sebastian Bonhoeffer. Red Queen Dynamics with Non-Standard Fitness Interactions
0 -- 0Eilen Nordlie, Marc-Oliver Gewaltig, Hans Ekkehard Plesser. Towards Reproducible Descriptions of Neuronal Network Models
0 -- 0Robert K. Bradley, Ian Holmes. Evolutionary Triplet Models of Structured RNA
0 -- 0Stefan Auer, Antonio Trovato, Michele Vendruscolo. A Condensation-Ordering Mechanism in Nanoparticle-Catalyzed Peptide Aggregation
0 -- 0Steven Lemm, Klaus-Robert Müller, Gabriel Curio. A Generalized Framework for Quantifying the Dynamics of EEG Event-Related Desynchronization
0 -- 0James Corey Adams, Michael J. Keiser, Li Basuino, Henry F. Chambers, Deok-Sun Lee, Olaf G. Wiest, Patricia C. Babbitt. A Mapping of Drug Space from the Viewpoint of Small Molecule Metabolism
0 -- 0Brian A. Kidd, David Baker, Wendy E. Thomas. Computation of Conformational Coupling in Allosteric Proteins
0 -- 0Anne Cori, Pierre-Yves Boëlle, Guy Thomas, Gabriel M. Leung, Alain-Jacques Valleron. Temporal Variability and Social Heterogeneity in Disease Transmission: The Case of SARS in Hong Kong
0 -- 0Oliver Redfern, Benoit H. Dessailly, Timothy Dallman, Ian Sillitoe, Christine A. Orengo. FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies
0 -- 0Caroline Colijn, Aaron Brandes, Jeremy Zucker, Desmond S. Lun, Brian Weiner, Maha R. Farhat, Tan-Yun Cheng, D. Branch Moody, Megan Murray, James E. Galagan. Mycobacterium tuberculosis Mycolic Acid Production
0 -- 0Fabrizio Marinelli, Fabio Pietrucci, Alessandro Laio, Stefano Piana. A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations
0 -- 0Regina Samaga, Julio Saez-Rodriguez, Leonidas G. Alexopoulos, Peter K. Sorger, Steffen Klamt. The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data
0 -- 0Wilfred Ndifon, Joshua B. Plotkin, Jonathan Dushoff. On the Accessibility of Adaptive Phenotypes of a Bacterial Metabolic Network
0 -- 0Azura M. H. Zeti, Mohd Shahir Shamsir, Khairina Tajul-Arifin, Amir F. Merican, Rahmah Mohamed, Sheila Nathan, Nor Muhammad Mahadi, Suhaimi Napis, Tin Wee Tan. Bioinformatics in Malaysia: Hope, Initiative, Effort, Reality, and Challenges
0 -- 0Mati Cohen, Vladimir Potapov, Gideon Schreiber. Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction
0 -- 0Dan Siegal-Gaskins, Joshua N. Ash, Sean Crosson. Model-Based Deconvolution of Cell Cycle Time-Series Data Reveals Gene Expression Details at High Resolution
0 -- 0Roberto Mosca, Carles Pons, Juan Fernández-Recio, Patrick Aloy. Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments
0 -- 0Stephen J. Eglen. A Quick Guide to Teaching R Programming to Computational Biology Students
0 -- 0Anshuman Dixit, Gennady Verkhivker. Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations
0 -- 0Joost J. J. van Durme, Sebastian Maurer-Stroh, Rodrigo Gallardo, Hannah Wilkinson, Frederic Rousseau, Joost Schymkowitz. Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data
0 -- 0Shenghua Li, Paul Brazhnik, Bruno W. S. Sobral, John J. Tyson. Caulobacter crescentus

Volume 5, Issue 7

0 -- 0Susanne M. Rafelski, Jonathan B. Alberts, Garrett M. Odell. Listeria monocytogenes Actin-based Motility
0 -- 0. The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species
0 -- 0Flávio Codeço Coelho, Cláudia T. Codeço. Dynamic Modeling of Vaccinating Behavior as a Function of Individual Beliefs
0 -- 0Ingmar Glauche, Kateri Moore, Lars Thielecke, Katrin Horn, Markus Loeffler, Ingo Roeder. Stem Cell Proliferation and Quiescence - Two Sides of the Same Coin
0 -- 0Chandramouli Chandrasekaran, Andrea Trubanova, Sébastien Stillittano, Alice Caplier, Asif A. Ghazanfar. The Natural Statistics of Audiovisual Speech
0 -- 0Guido Gigante, Maurizio Mattia, Jochen Braun, Paolo Del Giudice. Bistable Perception Modeled as Competing Stochastic Integrations at Two Levels
0 -- 0Richard D. Rabbitt, Sarah Clifford, Kathryn D. Breneman, Brenda Farrell, William E. Brownell. Power Efficiency of Outer Hair Cell Somatic Electromotility
0 -- 0Jiang Du, Robert D. Bjornson, Zhengdong D. Zhang, Yong Kong, Michael Snyder, Mark B. Gerstein. Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants
0 -- 0Yossi Yovel, Peter Stilz, Matthias O. Franz, Arjan Boonman, Hans-Ulrich Schnitzler. What a Plant Sounds Like: The Statistics of Vegetation Echoes as Received by Echolocating Bats
0 -- 0Felix Polyakov, Rotem Drori, Yoram Ben-Shaul, Moshe Abeles, Tamar Flash. A Compact Representation of Drawing Movements with Sequences of Parabolic Primitives
0 -- 0Lucy R. Allen, Sergei V. Krivov, Emanuele Paci. Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations
0 -- 0Taeyoon Kim, Wonmuk Hwang, Hyungsuk Lee, Roger D. Kamm. Computational Analysis of Viscoelastic Properties of Crosslinked Actin Networks
0 -- 0Andrew J. Olaharski, Nina Gonzaludo, Hans Bitter, David Goldstein, Stephan Kirchner, Hirdesh Uppal, Kyle Kolaja. Identification of a Kinase Profile that Predicts Chromosome Damage Induced by Small Molecule Kinase Inhibitors
0 -- 0Amy L. Bauer, Trachette L. Jackson, Yi Jiang. Topography of Extracellular Matrix Mediates Vascular Morphogenesis and Migration Speeds in Angiogenesis
0 -- 0Xingyi Guo, Zhaolei Zhang, Mark B. Gerstein, Deyou Zheng. trans-Acting?
0 -- 0Mattia Zampieri, Giuseppe Legname, Claudio Altafini. Investigating the Conformational Stability of Prion Strains through a Kinetic Replication Model
0 -- 0Andrey Rzhetsky, Michael R. Seringhaus, Mark B. Gerstein. Getting Started in Text Mining: Part Two
0 -- 0Yongping Pan, Ruth Nussinov. Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View
0 -- 0Yangle Wu, Xiaomeng Zhang, Jianglei Yu, Qi Ouyang. Identification of a Topological Characteristic Responsible for the Biological Robustness of Regulatory Networks
0 -- 0Lun Yang, Jian Chen, Lin He. Harvesting Candidate Genes Responsible for Serious Adverse Drug Reactions from a Chemical-Protein Interactome
0 -- 0Jun Zhang, Kent C. Berridge, Amy J. Tindell, Kyle S. Smith, J. Wayne Aldridge. A Neural Computational Model of Incentive Salience
0 -- 0Catia Pesquita, Daniel Faria, André O. Falcão, Phillip Lord, Francisco M. Couto. Semantic Similarity in Biomedical Ontologies
0 -- 0Daniel Bennequin, Ronit Fuchs, Alain Berthoz, Tamar Flash. Movement Timing and Invariance Arise from Several Geometries
0 -- 0Sarah L. Kinnings, Nina Liu, Nancy Buchmeier, Peter J. Tonge, Lei Xie, Philip E. Bourne. Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis
0 -- 0Jiao Li, Xiaoyan Zhu, Jake Yue Chen. Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts
0 -- 0Marialuisa Pellegrini-Calace, Tim Maiwald, Janet M. Thornton. PoreWalker: A Novel Tool for the Identification and Characterization of Channels in Transmembrane Proteins from Their Three-Dimensional Structure
0 -- 0William Stafford Noble. A Quick Guide to Organizing Computational Biology Projects
0 -- 0Jennifer A. Flegg, Donald L. S. McElwain, Helen M. Byrne, Ian W. Turner. A Three Species Model to Simulate Application of Hyperbaric Oxygen Therapy to Chronic Wounds
0 -- 0Daniel Geberth, Marc-Thorsten Hütt. Dictyostelium Pattern Formation
0 -- 0Shigeru Shinomoto, Hideaki Kim, Takeaki Shimokawa, Nanae Matsuno, Shintaro Funahashi, Keisetsu Shima, Ichiro Fujita, Hiroshi Tamura, Taijiro Doi, Kenji Kawano, Naoko Inaba, Kikuro Fukushima, Sergei Kurkin, Kiyoshi Kurata, Masato Taira, Ken-Ichiro Tsutsui, Hidehiko Komatsu, Tadashi Ogawa, Kowa Koida, Jun Tanji, Keisuke Toyama. Relating Neuronal Firing Patterns to Functional Differentiation of Cerebral Cortex
0 -- 0Olgun Guvench, Alexander D. MacKerell Jr.. Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation

Volume 5, Issue 6

0 -- 0Anu Chakicherla, Carol L. Ecale Zhou, Martha Ligon Dang, Virginia Rodriguez, J. Norman Hansen, Adam Zemla. in Vitro Phosphorylation Studies
0 -- 0Yuanyuan Xiao, Mark R. Segal. Identification of Yeast Transcriptional Regulation Networks Using Multivariate Random Forests
0 -- 0Dennis A. Dean II, Daniel B. Forger, Elizabeth B. Klerman. Taking the Lag out of Jet Lag through Model-Based Schedule Design
0 -- 0Leonardo L. Gollo, Osame Kinouchi, Mauro Copelli. Active Dendrites Enhance Neuronal Dynamic Range
0 -- 0Ankit Patel, William T. Gibson, Matthew C. Gibson, Radhika Nagpal. Modeling and Inferring Cleavage Patterns in Proliferating Epithelia
0 -- 0Yossi Yovel, Mariana Laura Melcon, Matthias O. Franz, Annette Denzinger, Hans-Ulrich Schnitzler. The Voice of Bats: How Greater Mouse-eared Bats Recognize Individuals Based on Their Echolocation Calls
0 -- 0Fran Lewitter, Michael Rebhan, Brent Richter, David Sexton. The Need for Centralization of Computational Biology Resources
0 -- 0David B. Searls. Ten Simple Rules for Choosing between Industry and Academia
0 -- 0Fran Lewitter, Michael Rebhan. Establishing a Successful Bioinformatics Core Facility Team
0 -- 0Hiroshi Okamoto, Tomoki Fukai. Recurrent Network Models for Perfect Temporal Integration of Fluctuating Correlated Inputs
0 -- 0Nicholas J. Savill, William Chadwick, Sarah E. Reece. Quantitative Analysis of Mechanisms That Govern Red Blood Cell Age Structure and Dynamics during Anaemia
0 -- 0Arne J. Nagengast, Daniel A. Braun, Daniel M. Wolpert. Optimal Control Predicts Human Performance on Objects with Internal Degrees of Freedom
0 -- 0Stanca M. Ciupe, Blythe H. Devlin, M. Louise Markert, Thomas B. Kepler. The Dynamics of T-Cell Receptor Repertoire Diversity Following Thymus Transplantation for DiGeorge Anomaly
0 -- 0Diego Prada-Gracia, Jesús Gómez-Gardeñes, Pablo Echenique, Fernando Falo. Exploring the Free Energy Landscape: From Dynamics to Networks and Back
0 -- 0Maria D. Chikina, Curtis Huttenhower, Coleen T. Murphy, Olga G. Troyanskaya. Caenorhabditis elegans
0 -- 0Brent G. Richter, David P. Sexton. Managing and Analyzing Next-Generation Sequence Data
0 -- 0Zhang Zhang, Jeffrey P. Townsend. Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences
0 -- 0Nobuyoshi Nagamine, Takayuki Shirakawa, Yusuke Minato, Kentaro Torii, Hiroki Kobayashi, Masaya Imoto, Yasubumi Sakakibara. Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening
0 -- 0Erwin P. Gianchandani, Andrew R. Joyce, Bernhard O. Palsson, Jason A. Papin. Escherichia Coli Transcriptional Regulatory System
0 -- 0Yu Xia, Eric A. Franzosa, Mark B. Gerstein. Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate
0 -- 0Jeffrey Alstott, Michael Breakspear, Patric Hagmann, Leila Cammoun, Olaf Sporns. Modeling the Impact of Lesions in the Human Brain
0 -- 0Sangtae Ahn, Richard T. Wang, Christopher C. Park, Andy Lin, Richard M. Leahy, Kenneth Lange, Desmond J. Smith. Directed Mammalian Gene Regulatory Networks Using Expression and Comparative Genomic Hybridization Microarray Data from Radiation Hybrids
0 -- 0Michal Brylinski, Jeffrey Skolnick. LHM: A Threading-Based Approach to Ligand Homology Modeling
0 -- 0Jes Frellsen, Ida Moltke, Martin Thiim, Kanti V. Mardia, Jesper Ferkinghoff-Borg, Thomas Hamelryck. A Probabilistic Model of RNA Conformational Space
0 -- 0Josep M. Pujol, Joseph E. Eisenberg, Charles N. Haas, James S. Koopman. The Effect of Ongoing Exposure Dynamics in Dose Response Relationships
0 -- 0Gaëlle Lelandais, Yann Saint-Georges, Colette Geneix, Liza Al-Shikhley, Geneviève Dujardin, Claude Jacq. Spatio-Temporal Dynamics of Yeast Mitochondrial Biogenesis: Transcriptional and Post-Transcriptional mRNA Oscillatory Modules
0 -- 0Bas Teusink, Anne Wiersma, Leo Jacobs, Richard A. Notebaart, Eddy J. Smid. In Silico Optimisation

Volume 5, Issue 5

0 -- 0Christian I. Hong, Judit Zámborszky, Attila Csikasz-Nagy. Minimum Criteria for DNA Damage-Induced Phase Advances in Circadian Rhythms
0 -- 0Nicholas J. Hudson, Antonio Reverter, Brian P. Dalrymple. A Differential Wiring Analysis of Expression Data Correctly Identifies the Gene Containing the Causal Mutation
0 -- 0Siebe B. van Albada, Pieter Rein ten Wolde. E. coli Chemotaxis
0 -- 0Gregory D. Friedland, Nils-Alexander Lakomek, Christian Griesinger, Jens Meiler, Tanja Kortemme. A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family
0 -- 0Yasser Roudi, Sheila Nirenberg, Peter E. Latham. Pairwise Maximum Entropy Models for Studying Large Biological Systems: When They Can Work and When They Can't
0 -- 0Mark D. McDonnell, Derek Abbott. What Is Stochastic Resonance? Definitions, Misconceptions, Debates, and Its Relevance to Biology
0 -- 0Stefano M. Marino, Vadim N. Gladyshev. A Structure-Based Approach for Detection of Thiol Oxidoreductases and Their Catalytic Redox-Active Cysteine Residues
0 -- 0Scott Markel. BioLINK Special Interest Group Session on the Future of Scientific Publishing
0 -- 0Damien A. Fair, Alexander L. Cohen, Jonathan D. Power, Nico U. F. Dosenbach, Jessica A. Church, Francis M. Miezin, Bradley L. Schlaggar, Steven E. Petersen. Functional Brain Networks Develop from a "Local to Distributed" Organization
0 -- 0Janneke F. M. Jehee, Dana H. Ballard. Predictive Feedback Can Account for Biphasic Responses in the Lateral Geniculate Nucleus
0 -- 0Olga Vitek. Getting Started in Computational Mass Spectrometry-Based Proteomics
0 -- 0Maoz Shamir, Oded Ghitza, Steven Epstein, Nancy Kopell. Representation of Time-Varying Stimuli by a Network Exhibiting Oscillations on a Faster Time Scale
0 -- 0Bálint Mészáros, István Simon, Zsuzsanna Dosztányi. Prediction of Protein Binding Regions in Disordered Proteins
0 -- 0Li Xie, Jerry Li, Lei Xie, Philip E. Bourne. Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors
0 -- 0Javad Golji, Robert Collins, Mohammad R. K. Mofrad. Molecular Mechanics of the α-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior
0 -- 0Andrey Rzhetsky, Hagit Shatkay, W. John Wilbur. How to Get the Most out of Your Curation Effort
0 -- 0Axel R. Pries, Annemiek J. M. Cornelissen, Anoek A. Sloot, Marlene Hinkeldey, Matthew R. Dreher, Michael Höpfner, Mark W. Dewhirst, Timothy W. Secomb. Structural Adaptation and Heterogeneity of Normal and Tumor Microvascular Networks
0 -- 0Yonghui Li, Yong Liu, Jun Li, Wen Qin, Kuncheng Li, Chunshui Yu, Tianzi Jiang. Brain Anatomical Network and Intelligence
0 -- 0Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend Sidow, Michael Brudno. SHRiMP: Accurate Mapping of Short Color-space Reads
0 -- 0Quentin J. M. Huys, Liam Paninski. Smoothing of, and Parameter Estimation from, Noisy Biophysical Recordings
0 -- 0Smita Agrawal, Colin Archer, David V. Schaffer. Computational Models of the Notch Network Elucidate Mechanisms of Context-dependent Signaling
0 -- 0Steffen Klamt, Utz-Uwe Haus, Fabian J. Theis. Hypergraphs and Cellular Networks
0 -- 0Robert K. Bradley, Adam Roberts, Michael Smoot, Sudeep Juvekar, Jaeyoung Do, Colin N. Dewey, Ian Holmes, Lior Pachter. Fast Statistical Alignment
0 -- 0Joel O. Wertheim, Michael Worobey. Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2

Volume 5, Issue 4

0 -- 0Srinivas Ramachandran, Adrian W. R. Serohijos, Le Xu, Gerhard Meissner, Nikolay V. Dokholyan. A Structural Model of the Pore-Forming Region of the Skeletal Muscle Ryanodine Receptor (RyR1)
0 -- 0Patrycja Vasilyev Missiuro, Kesheng Liu, Lihua Zou, Brian C. Ross, Guoyan Zhao, Jun S. Liu, Hui Ge. Information Flow Analysis of Interactome Networks
0 -- 0David M. Shotton, Katie Portwin, Graham Klyne, Alistair Miles. Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article
0 -- 0Xing Xu, Yongmei Ji, Gary D. Stormo. Shewanella Genomes by Support Vector Machines
0 -- 0Dipak Barua, James R. Faeder, Jason M. Haugh. A Bipolar Clamp Mechanism for Activation of Jak-Family Protein Tyrosine Kinases
0 -- 0Cheng Ly, Brent Doiron. Divisive Gain Modulation with Dynamic Stimuli in Integrate-and-Fire Neurons
0 -- 0Ping Jiang, Weixin Xu, Yuguang Mu. Amyloidogenesis Abolished by Proline Substitutions but Enhanced by Lipid Binding
0 -- 0Judith Legrand, Joseph R. Egan, Ian M. Hall, Simon Cauchemez, Steve Leach, Neil M. Ferguson. Estimating the Location and Spatial Extent of a Covert Anthrax Release
0 -- 0Se-Bum Paik, Tribhawan Kumar, Donald A. Glaser. Spontaneous Local Gamma Oscillation Selectively Enhances Neural Network Responsiveness
0 -- 0Mu Gao, Jeffrey Skolnick. From Nonspecific DNA-Protein Encounter Complexes to the Prediction of DNA-Protein Interactions
0 -- 0B. J. Morrison McKay, Clare Sansom. Webb Miller and Trey Ideker To Receive Top International Bioinformatics Awards for 2009 from the International Society for Computational Biology
0 -- 0Jesse D. Bloom, Matthew J. Glassman. Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin
0 -- 0Bree B. Aldridge, Julio Saez-Rodriguez, Jeremy Muhlich, Peter K. Sorger, Douglas A. Lauffenburger. Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling
0 -- 0Cesar A. Hidalgo R., Nicholas Blumm, Albert-László Barabási, Nicholas A. Christakis. A Dynamic Network Approach for the Study of Human Phenotypes
0 -- 0Christina Toft, Tom A. Williams, Mario A. Fares. Genome-Wide Functional Divergence after the Symbiosis of Proteobacteria with Insects Unraveled through a Novel Computational Approach
0 -- 0Jan Eichhorn, Fabian H. Sinz, Matthias Bethge. Natural Image Coding in V1: How Much Use Is Orientation Selectivity?
0 -- 0Ian O'Sullivan, Etienne Burdet, Jörn Diedrichsen. Dissociating Variability and Effort as Determinants of Coordination
0 -- 0Claudiu A. Giurumescu, Paul W. Sternberg, Anand R. Asthagiri. Predicting Phenotypic Diversity and the Underlying Quantitative Molecular Transitions
0 -- 0Curt Scharfe, Henry Horng-Shing Lu, Jutta K. Neuenburg, Edward A. Allen, Guan-Cheng Li, Thomas Klopstock, Tina M. Cowan, Gregory M. Enns, Ronald W. Davis. Mapping Gene Associations in Human Mitochondria using Clinical Disease Phenotypes
0 -- 0Steven Niederer, Nicolas Smith. The Role of the Frank-Starling Law in the Transduction of Cellular Work to Whole Organ Pump Function: A Computational Modeling Analysis
0 -- 0Orland R. Gonzalez, Susanne Gronau, Friedhelm Pfeiffer, Eduardo Mendoza, Ralf Zimmer, Dieter Oesterhelt. Halobacterium salinarum
0 -- 0Gregory W. Carter, David J. Galas, Timothy Galitski. Maximal Extraction of Biological Information from Genetic Interaction Data
0 -- 0Steffen Eikenberry, Craig J. Thalhauser, Yang Kuang. Tumor-Immune Interaction, Surgical Treatment, and Cancer Recurrence in a Mathematical Model of Melanoma
0 -- 0Gitanjali Yadav, Rajesh S. Gokhale, Debasisa Mohanty. In Silico Analysis
0 -- 0Zheng Yang, Peter Májek, Ivet Bahar. Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL
0 -- 0Romulus Breban, John M. Drake, David E. Stallknecht, Pejman Rohani. The Role of Environmental Transmission in Recurrent Avian Influenza Epidemics
0 -- 0Chase L. Beisel, Christina D. Smolke. Design Principles for Riboswitch Function
0 -- 0Nadav Kashtan, Avi E. Mayo, Tomer Kalisky, Uri Alon. An Analytically Solvable Model for Rapid Evolution of Modular Structure
0 -- 0Quentin Vicens, Philip E. Bourne. Ten Simple Rules To Combine Teaching and Research
0 -- 0Yosef E. Maruvka, Nadav M. Shnerb. Polymorphism Data Can Reveal the Origin of Species Abundance Statistics
0 -- 0James Robert White, Niranjan Nagarajan, Mihai Pop. Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
0 -- 0Florence Débarre, Thomas Lenormand, Sylvain Gandon. Evolutionary Epidemiology of Drug-Resistance in Space
0 -- 0Bosco K. Ho, David A. Agard. Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations
0 -- 0Jakob M. A. Mauritz, Alessandro Esposito, Hagai Ginsburg, Clemens F. Kaminski, Teresa Tiffert, Virgilio L. Lew. Plasmodium falciparum-Infected Red Blood Cells

Volume 5, Issue 3

0 -- 0Taffeta M. Elliott, Frédéric E. Theunissen. The Modulation Transfer Function for Speech Intelligibility
0 -- 0Junghyo Jo, Oksana Gavrilova, Stephanie Pack, William Jou, Shawn Mullen, Anne E. Sumner, Samuel W. Cushman, Vipul Periwal. Hypertrophy and/or Hyperplasia: Dynamics of Adipose Tissue Growth
0 -- 0Evangelia Petsalaki, Alexander Stark, Eduardo Garcia Urdiales, Robert B. Russell. Accurate Prediction of Peptide Binding Sites on Protein Surfaces
0 -- 0Jessica H. Fong, Benjamin A. Shoemaker, Sergiy O. Garbuzynskiy, Michail Yu. Lobanov, Oxana V. Galzitskaya, Anna R. Panchenko. Intrinsic Disorder in Protein Interactions: Insights From a Comprehensive Structural Analysis
0 -- 0Allen W. Bryan Jr., Matthew Menke, Lenore J. Cowen, Susan Lindquist, Bonnie Berger. BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis
0 -- 0Gabriel Krouk, Daniel Tranchina, Laurence Lejay, Alexis A. Cruikshank, Dennis Shasha, Gloria M. Coruzzi, Rodrigo A. Gutiérrez. A Systems Approach Uncovers Restrictions for Signal Interactions Regulating Genome-wide Responses to Nutritional Cues in Arabidopsis
0 -- 0Vinay Satish Kumar, Costas D. Maranas. In Vivo Growth Predictions
0 -- 0Arash Bahrami, Amir H. Assadi, John L. Markley, Hamid Eghbalnia. Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy
0 -- 0Yuqiao Gu, Philippe Lucas, Jean-Pierre Rospars. Computational Model of the Insect Pheromone Transduction Cascade
0 -- 0Matthias S. Keil. "I Look in Your Eyes, Honey": Internal Face Features Induce Spatial Frequency Preference for Human Face Processing
0 -- 0Guy Shinar, Joshua D. Rabinowitz, Uri Alon. Robustness in Glyoxylate Bypass Regulation
0 -- 0Sonia M. Leach, Hannah J. Tipney, Weiguo Feng, William A. Baumgartner Jr., Priyanka Kasliwal, Ronald P. Schuyler, Trevor Williams, Richard A. Spritz, Lawrence Hunter. Biomedical Discovery Acceleration, with Applications to Craniofacial Development
0 -- 0Wolfram Stacklies, M. Cristina Vega, Matthias Wilmanns, Frauke Gräter. Mechanical Network in Titin Immunoglobulin from Force Distribution Analysis
0 -- 0Shin I. Nishimura, Masahiro Ueda, Masaki Sasai. Cortical Factor Feedback Model for Cellular Locomotion and Cytofission
0 -- 0Manfred G. Kitzbichler, Marie L. Smith, Søren R. Christensen, Ed Bullmore. Broadband Criticality of Human Brain Network Synchronization
0 -- 0Javier Muñoz-García, Zoltan Neufeld, Boris N. Kholodenko. Positional Information Generated by Spatially Distributed Signaling Cascades
0 -- 0Jason W. Bohland, Caizhi Wu, Helen Barbas, Hemant Bokil, Mihail Bota, Hans C. Breiter, Hollis T. Cline, John C. Doyle, Peter J. Freed, Ralph J. Greenspan, Suzanne N. Haber, Michael Hawrylycz, Daniel G. Herrera, Claus C. Hilgetag, Z. Josh Huang, Allan Jones, Edward G. Jones, Harvey J. Karten, David Kleinfeld, Rolf Kötter, Henry A. Lester, John M. Lin, Brett D. Mensh, Shawn Mikula, Jaak Panksepp, Joseph L. Price, Joseph Safdieh, Clifford B. Saper, Nicholas D. Schiff, Jeremy D. Schmahmann, Bruce W. Stillman, Karel Svoboda, Larry W. Swanson, Arthur W. Toga, David C. Van Essen, James D. Watson, Partha P. Mitra. A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale
0 -- 0Vanessa Leone, Gianluca Lattanzi, Carla Molteni, Paolo Carloni. Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations
0 -- 0Giulia Morra, Gennady Verkhivker, Giorgio Colombo. Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer
0 -- 0Jeremy E. Purvis, Ravi Radhakrishnan, Scott L. Diamond. Steady-State Kinetic Modeling Constrains Cellular Resting States and Dynamic Behavior
0 -- 0Pedro M. B. M. Coelho, Armindo Salvador, Michael A. Savageau. Quantifying Global Tolerance of Biochemical Systems: Design Implications for Moiety-Transfer Cycles
0 -- 0Aidan MacNamara, Ulrich D. Kadolsky, Charles R. M. Bangham, Becca Asquith. T-Cell Epitope Prediction: Rescaling Can Mask Biological Variation between MHC Molecules
0 -- 0Xionglei He, Jianzhi Zhang. On the Growth of Scientific Knowledge: Yeast Biology as a Case Study
0 -- 0Schraga Schwartz, Nurit Gal-Mark, Nir Kfir, Ram Oren, Eddo Kim, Gil Ast. Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery
0 -- 0Boian S. Alexandrov, Vladimir Gelev, Sang Wook Yoo, Alan R. Bishop, Kim Ø. Rasmussen, Anny Usheva. Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter
0 -- 0Patrick Blomquist, Anna Devor, Ulf G. Indahl, Istvan Ulbert, Gaute T. Einevoll, Anders M. Dale. Estimation of Thalamocortical and Intracortical Network Models from Joint Thalamic Single-Electrode and Cortical Laminar-Electrode Recordings in the Rat Barrel System
0 -- 0Stella Veretnik, Christopher Wills, Philippe Youkharibache, Ruben E. Valas, Philip E. Bourne. Sm/Lsm Genes Provide a Glimpse into the Early Evolution of the Spliceosome
0 -- 0Alberto Pascual-García, David Abia, Angel R. Ortiz, Ugo Bastolla. Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures
0 -- 0Xin He, Xu Ling, Saurabh Sinha. cis-Regulatory Modules Based on a Probabilistic Model of Evolution
0 -- 0Ines Thiele, Neema Jamshidi, Ronan M. T. Fleming, Bernhard O. Palsson. Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization
0 -- 0Manu, Svetlana Surkova, Alexander V. Spirov, Vitaly V. Gursky, Hilde Janssens, Ah-Ram Kim, Ovidiu Radulescu, Carlos E. Vanario-Alonso, David H. Sharp, Maria Samsonova, John Reinitz. Drosophila Blastoderm by Dynamical Attractors
0 -- 0Matthew A. Hibbs, Chad L. Myers, Curtis Huttenhower, David C. Hess, Kai Li, Amy A. Caudy, Olga G. Troyanskaya. Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis
0 -- 0Emili Balaguer-Ballester, Nicholas R. Clark, Martin Coath, Katrin Krumbholz, Susan L. Denham. Understanding Pitch Perception as a Hierarchical Process with Top-Down Modulation
0 -- 0Gareth A. Palidwor, Sergey Shcherbinin, Matthew R. Huska, Tamas Rasko, Ulrich Stelzl, Anup Arumughan, Raphaele Foulle, Pablo Porras, Luis Sánchez-Pulido, Erich E. Wanker, Miguel A. Andrade-Navarro. Detection of Alpha-Rod Protein Repeats Using a Neural Network and Application to Huntingtin
0 -- 0Chun Ye, Simon J. Galbraith, James C. Liao, Eleazar Eskin. Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors in Yeast
0 -- 0Oscar Westesson, Ian Holmes. Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments
0 -- 0Barry J. Grant, Alemayehu A. Gorfe, James Andrew McCammon. Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics
0 -- 0Pankhuri Arora, Narendra M. Dixit. Timing the Emergence of Resistance to Anti-HIV Drugs with Large Genetic Barriers
0 -- 0Minghui Wang, Xiaohua Hu, Gang Li, Lindsey J. Leach, Elena Potokina, Arnis Druka, Robbie Waugh, Michael J. Kearsey, Zewei Luo. Robust Detection and Genotyping of Single Feature Polymorphisms from Gene Expression Data

Volume 5, Issue 2

0 -- 0Ana Perisic, Chris T. Bauch. Social Contact Networks and Disease Eradicability under Voluntary Vaccination
0 -- 0Maoz Shamir. The Temporal Winner-Take-All Readout
0 -- 0Yoram Burak, Ila R. Fiete. Accurate Path Integration in Continuous Attractor Network Models of Grid Cells
0 -- 0Joshua T. Dudman, Matthew F. Nolan. Stochastically Gating Ion Channels Enable Patterned Spike Firing through Activity-Dependent Modulation of Spike Probability
0 -- 0Barak Raveh, Angela Enosh, Ora Schueler-Furman, Dan Halperin. Rapid Sampling of Molecular Motions with Prior Information Constraints
0 -- 0Kwang-il Lim, John Yin. Computational Fitness Landscape for All Gene-Order Permutations of an RNA Virus
0 -- 0Fan Li, Ines Thiele, Neema Jamshidi, Bernhard O. Palsson. Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling
0 -- 0Michael D. Daily, Jeffrey J. Gray. Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins
0 -- 0Kerry J. Kim, Vilaiwan M. Fernandes. Effects of Ploidy and Recombination on Evolution of Robustness in a Model of the Segment Polarity Network
0 -- 0Alexander M. Bailey, Michael B. Lawrence, Hulan Shang, Adam J. Katz, Shayn M. Peirce. Agent-Based Model of Therapeutic Adipose-Derived Stromal Cell Trafficking during Ischemia Predicts Ability To Roll on P-Selectin
0 -- 0Vincent A. Voelz, M. Scott Shell, Ken A. Dill. Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments
0 -- 0Irit Gat-Viks, Martin Vingron. Evidence for Gene-Specific Rather Than Transcription Rate-Dependent Histone H3 Exchange in Yeast Coding Regions
0 -- 0Pär Bjelkmar, Perttu S. Niemelä, Ilpo Vattulainen, Erik Lindahl. Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel
0 -- 0John M. Higgins, David T. Eddington, Sangeeta N. Bhatia, L. Mahadevan. Statistical Dynamics of Flowing Red Blood Cells by Morphological Image Processing
0 -- 0Samuel Feng, Philip Holmes, Alan Rorie, William T. Newsome. Can Monkeys Choose Optimally When Faced with Noisy Stimuli and Unequal Rewards?
0 -- 0Patrick F. Suthers, Madhukar S. Dasika, Vinay Satish Kumar, Gennady Denisov, John I. Glass, Costas D. Maranas. iPS189
0 -- 0Pragati Jain, Upinder S. Bhalla. Signaling Logic of Activity-Triggered Dendritic Protein Synthesis: An mTOR Gate But Not a Feedback Switch

Volume 5, Issue 12

0 -- 0Gozde Kar, Attila Gürsoy, Ozlem Keskin. Human Cancer Protein-Protein Interaction Network: A Structural Perspective
0 -- 0Clémentine Dressaire, Christophe Gitton, Pascal Loubière, Véronique Monnet, Isabelle Queinnec, Muriel Cocaign-Bousquet. Lactococcus lactis
0 -- 0Raul Rodriguez-Esteban. Biomedical Text Mining and Its Applications
0 -- 0Michael E. Wall, David A. Markowitz, Judah L. Rosner, Robert G. Martin. Escherichia coli
0 -- 0Julijana Gjorgjieva, Taro Toyoizumi, Stephen J. Eglen. Burst-Time-Dependent Plasticity Robustly Guides ON/OFF Segregation in the Lateral Geniculate Nucleus
0 -- 0Pascal Chossat, Olivier P. Faugeras. Hyperbolic Planforms in Relation to Visual Edges and Textures Perception
0 -- 0Shane Lee, Kamal Sen, Nancy Kopell. Cortical Gamma Rhythms Modulate NMDAR-Mediated Spike Timing Dependent Plasticity in a Biophysical Model
0 -- 0Orly Noivirt-Brik, Amnon Horovitz, Ron Unger. Trade-off between Positive and Negative Design of Protein Stability: From Lattice Models to Real Proteins
0 -- 0Joel Dudley, Atul J. Butte. A Quick Guide for Developing Effective Bioinformatics Programming Skills
0 -- 0Pulin Gong, Cees van Leeuwen. Distributed Dynamical Computation in Neural Circuits with Propagating Coherent Activity Patterns
0 -- 0Marianne O. Stefanini, Florence T. H. Wu, Feilim Mac Gabhann, Aleksander S. Popel. The Presence of VEGF Receptors on the Luminal Surface of Endothelial Cells Affects VEGF Distribution and VEGF Signaling
0 -- 0Feng Hong, Fang Fang, Xuming He, Xiaoyi Cao, Hiram Chipperfield, Dan Xie, Wing H. Wong, Huck H. Ng, Sheng Zhong. Dissecting Early Differentially Expressed Genes in a Mixture of Differentiating Embryonic Stem Cells
0 -- 0Scott A. Sands, Bradley A. Edwards, Vanessa J. Kelly, Malcolm R. Davidson, Malcolm H. Wilkinson, Philip J. Berger. A Model Analysis of Arterial Oxygen Desaturation during Apnea in Preterm Infants
0 -- 0Rajagopal Sathyapriya, Jose M. Duarte, Henning Stehr, Ioannis Filippis, Michael Lappe. Defining an Essence of Structure Determining Residue Contacts in Proteins
0 -- 0Yue Zhao, David Granas, Gary D. Stormo. Inferring Binding Energies from Selected Binding Sites
0 -- 0Matthew J. Paszek, David Boettiger, Valerie M. Weaver, Daniel A. Hammer. Integrin Clustering Is Driven by Mechanical Resistance from the Glycocalyx and the Substrate
0 -- 0Steven Phillips, William H. Wilson, Graeme S. Halford. What Do Transitive Inference and Class Inclusion Have in Common? Categorical (Co)Products and Cognitive Development
0 -- 0Vebjorn Ljosa, Anne E. Carpenter. Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for Cell-Based Screening
0 -- 0Jessica C. Mar, John Quackenbush. Decomposition of Gene Expression State Space Trajectories
0 -- 0Kai J. Miller, Larry B. Sorensen, Jeffrey G. Ojemann, Marcel den Nijs. Power-Law Scaling in the Brain Surface Electric Potential
0 -- 0Roland Schäfer, Eleni Vasilaki, Walter Senn. Adaptive Gain Modulation in V1 Explains Contextual Modifications during Bisection Learning
0 -- 0Hongchao Lu, Lan Lin, Seiko Sato, Yi Xing, Christopher J. Lee. Predicting Functional Alternative Splicing by Measuring RNA Selection Pressure from Multigenome Alignments
0 -- 0Brian J. Schmidt, Jason A. Papin, Michael B. Lawrence. Nano-motion Dynamics are Determined by Surface-Tethered Selectin Mechanokinetics and Bond Formation
0 -- 0Eleni Vasilaki, Nicolas Frémaux, Robert Urbanczik, Walter Senn, Wulfram Gerstner. Spike-Based Reinforcement Learning in Continuous State and Action Space: When Policy Gradient Methods Fail
0 -- 0Xi Chen, Andrew D. Ellington. Design Principles for Ligand-Sensing, Conformation-Switching Ribozymes
0 -- 0Florent E. Angly, Dana Willner, Alejandra Prieto-Davó, Robert A. Edwards, Robert Schmieder, Rebecca Vega-Thurber, Dionysios A. Antonopoulos, Katie Barott, Matthew T. Cottrell, Christelle Desnues, Elizabeth A. Dinsdale, Mike Furlan, Matthew Haynes, Matthew R. Henn, Yongfei Hu, David L. Kirchman, Tracey McDole, John D. McPherson, Folker Meyer, R. Michael Miller, Egbert Mundt, Robert K. Naviaux, Beltran Rodriguez-Mueller, Rick Stevens, Linda Wegley, Lixin Zhang, Baoli Zhu, Forest Rohwer. The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes
0 -- 0Gustavo Deco, Daniel Martí, Anders Ledberg, Ramon Reig, Maria V. Sanchez-Vives. Effective Reduced Diffusion-Models: A Data Driven Approach to the Analysis of Neuronal Dynamics
0 -- 0Yoram Burak, Boris I. Shraiman. Order and Stochastic Dynamics in Drosophila Planar Cell Polarity
0 -- 0Charles G. Nathanson, Corina E. Tarnita, Martin A. Nowak. Calculating Evolutionary Dynamics in Structured Populations
0 -- 0Khyati Kapoor, Mohd Rehan, Ajeeta Kaushiki, Ritu Pasrija, Andrew M. Lynn, Rajendra Prasad. Candida albicans by Employing a Membrane Environment Based Computational Approach
0 -- 0Rebekka Schlatter, Kathrin Schmich, Ima Avalos Vizcarra, Peter Scheurich, Thomas Sauter, Christoph Borner, Michael Ederer, Irmgard Merfort, Oliver Sawodny. ON/OFF and Beyond - A Boolean Model of Apoptosis
0 -- 0Sean Ekins, Sandhya Kortagere, Manisha Iyer, Erica J. Reschly, Markus A. Lill, Matthew R. Redinbo, Matthew D. Krasowski. Challenges Predicting Ligand-Receptor Interactions of Promiscuous Proteins: The Nuclear Receptor PXR
0 -- 0Vitaly A. Selivanov, Tatyana V. Votyakova, Jennifer Zeak, Massimo Trucco, Josep Roca, Marta Cascante. Bistability of Mitochondrial Respiration Underlies Paradoxical Reactive Oxygen Species Generation Induced by Anoxia
0 -- 0Aristotelis Tsirigos, Isidore Rigoutsos. Alu and B1 Repeats Have Been Selectively Retained in the Upstream and Intronic Regions of Genes of Specific Functional Classes
0 -- 0Menachem Fromer, Julia M. Shifman. Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins
0 -- 0John A. Capra, Roman A. Laskowski, Janet M. Thornton, Mona Singh, Thomas A. Funkhouser. Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure
0 -- 0Ivan Puga-Gonzalez, Hanno Hildenbrandt, Charlotte K. Hemelrijk. Emergent Patterns of Social Affiliation in Primates, a Model
0 -- 0Matthew D. Christensen, Wen Dun, Penelope A. Boyden, Mark E. Anderson, Peter J. Mohler, Thomas J. Hund. Oxidized Calmodulin Kinase II Regulates Conduction Following Myocardial Infarction: A Computational Analysis
0 -- 0Keith B. Godfrey, Stephen J. Eglen, Nicholas V. Swindale. A Multi-Component Model of the Developing Retinocollicular Pathway Incorporating Axonal and Synaptic Growth
0 -- 0João F. Matias Rodrigues, Andreas Wagner. Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks
0 -- 0Alexandra M. Schnoes, Shoshana D. Brown, Igor Dodevski, Patricia C. Babbitt. Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
0 -- 0Daniel Ramsköld, Eric T. Wang, Christopher B. Burge, Rickard Sandberg. An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data
0 -- 0Alexander Mitsos, Ioannis N. Melas, Paraskeuas Siminelakis, Aikaterini D. Chairakaki, Julio Saez-Rodriguez, Leonidas G. Alexopoulos. Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data
0 -- 0Kai Wang, Manikandan Narayanan, Hua Zhong, Martin Tompa, Eric E. Schadt, Jun Zhu. Meta-analysis of Inter-species Liver Co-expression Networks Elucidates Traits Associated with Common Human Diseases
0 -- 0Ian H. Stevenson, Hugo L. Fernandes, Iris Vilares, Kunlin Wei, Konrad P. Körding. Bayesian Integration and Non-Linear Feedback Control in a Full-Body Motor Task
0 -- 0Jorge M. Pacheco, Flávio L. Pinheiro, Francisco C. Santos. Population Structure Induces a Symmetry Breaking Favoring the Emergence of Cooperation
0 -- 0Mattia Gazzola, Christoph J. Burckhardt, Basil Bayati, Martin Engelke, Urs F. Greber, Petros Koumoutsakos. In Vivo Cytoplasmic Transport of Human Adenovirus

Volume 5, Issue 11

0 -- 0Gary Hon, Wei Wang, Bing Ren. Discovery and Annotation of Functional Chromatin Signatures in the Human Genome
0 -- 0Fabio Luciani, Samuel Alizon. The Evolutionary Dynamics of a Rapidly Mutating Virus within and between Hosts: The Case of Hepatitis C Virus
0 -- 0Nicola J. van Rijsbergen, Philippe G. Schyns. Dynamics of Trimming the Content of Face Representations for Categorization in the Brain
0 -- 0Russell S. A. Brinkworth, David C. O'Carroll. Robust Models for Optic Flow Coding in Natural Scenes Inspired by Insect Biology
0 -- 0Mu Gao, Jeffrey Skolnick. A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome
0 -- 0Dominik M. Wittmann, Florian Blöchl, Dietrich Trümbach, Wolfgang Wurst, Nilima Prakash, Fabian J. Theis. Spatial Analysis of Expression Patterns Predicts Genetic Interactions at the Mid-Hindbrain Boundary
0 -- 0Allyson L. Lister, Ruchira S. Datta, Oliver Hofmann, Roland Krause, Michael Kuhn 0004, Bettina Roth, Reinhard Schneider 0002. Live Coverage of Scientific Conferences Using Web Technologies
0 -- 0Tian Ge, Keith M. Kendrick, Jianfeng Feng. A Novel Extended Granger Causal Model Approach Demonstrates Brain Hemispheric Differences during Face Recognition Learning
0 -- 0Nathan Salomonis, Brandon Nelson, Karen Vranizan, Alexander R. Pico, Kristina Hanspers, Allan Kuchinsky, Linda Ta, Mark Mercola, Bruce R. Conklin. Alternative Splicing in the Differentiation of Human Embryonic Stem Cells into Cardiac Precursors
0 -- 0Nicolas Pinto, David Doukhan, James J. DiCarlo, David D. Cox. A High-Throughput Screening Approach to Discovering Good Forms of Biologically Inspired Visual Representation
0 -- 0Eivind Valen, Albin Sandelin, Ole Winther, Anders Krogh. Discovery of Regulatory Elements is Improved by a Discriminatory Approach
0 -- 0Ivan Iossifov, Raul Rodriguez-Esteban, Ilya Mayzus, Kathleen J. Millen, Andrey Rzhetsky. Looking at Cerebellar Malformations through Text-Mined Interactomes of Mice and Humans
0 -- 0Asif U. Tamuri, Mario dos Reis, Alan J. Hay, Richard A. Goldstein. Identifying Changes in Selective Constraints: Host Shifts in Influenza
0 -- 0Wolfram Stacklies, Fei Xia, Frauke Gräter. Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis
0 -- 0Srivas Chennu, Patrick Craston, Bradley P. Wyble, Howard Bowman. 2 Model
0 -- 0Sergei L. Kosakovsky Pond, David Posada, Eric Stawiski, Colombe Chappey, Art F. Y. Poon, Gareth Hughes, Esther Fearnhill, Mike B. Gravenor, Andrew J. Leigh Brown, Simon D. W. Frost. An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1
0 -- 0Mary Shimoyama, G. Thomas Hayman, Stanley J. F. Laulederkind, Rajni Nigam, Timothy Lowry, Victoria Petri, Jennifer R. Smith, Shur-Jen Wang, Diane H. Munzenmaier, Melinda R. Dwinell, Simon N. Twigger, Howard J. Jacob. The Rat Genome Database Curators: Who, What, Where, Why
0 -- 0Arno Onken, Steffen Grünewälder, Matthias H. J. Munk, Klaus Obermayer. Analyzing Short-Term Noise Dependencies of Spike-Counts in Macaque Prefrontal Cortex Using Copulas and the Flashlight Transformation
0 -- 0Raibatak Das, Christopher W. Cairo, Daniel Coombs. A Hidden Markov Model for Single Particle Tracks Quantifies Dynamic Interactions between LFA-1 and the Actin Cytoskeleton
0 -- 0Albert A. de Graaf, Andreas P. Freidig, Baukje De Roos, Neema Jamshidi, Matthias Heinemann, Johan A. C. Rullmann, Kevin D. Hall, Martin Adiels, Ben van Ommen. Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology
0 -- 0Samuel Bandara, Johannes P. Schlöder, Roland Eils, Hans Georg Bock, Tobias Meyer. Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model
0 -- 0Kenneth S. Campbell. Interactions between Connected Half-Sarcomeres Produce Emergent Mechanical Behavior in a Mathematical Model of Muscle
0 -- 0Omer Dushek, Raibatak Das, Daniel Coombs. A Role for Rebinding in Rapid and Reliable T Cell Responses to Antigen
0 -- 0Eric A. Zilli, Motoharu Yoshida, Babak Tahvildari, Lisa M. Giocomo, Michael E. Hasselmo. Evaluation of the Oscillatory Interference Model of Grid Cell Firing through Analysis and Measured Period Variance of Some Biological Oscillators
0 -- 0Gur Fabrikant, Suman Lata, James D. Riches, John A. G. Briggs, Winfried Weissenhorn, Michael M. Kozlov. Computational Model of Membrane Fission Catalyzed by ESCRT-III
0 -- 0Jasmine Foo, Franziska Michor. Evolution of Resistance to Targeted Anti-Cancer Therapies during Continuous and Pulsed Administration Strategies
0 -- 0Congxin Li, Xiaofang Chen, Pengye Wang, Weichi Wang. Circadian KaiC Phosphorylation: A Multi-Layer Network
0 -- 0Suresh Kumar Poovathingal, Jan Gruber, Barry Halliwell, Rudiyanto Gunawan. Ex Silico
0 -- 0Carla S. Möller-Levet, Guy N. J. Betts, Adrian L. Harris, Jarrod J. Homer, Catharine M. West, Crispin J. Miller. LAMA3 Associated with a Poor Prognosis
0 -- 0Pål O. Westermark, David K. Welsh, Hitoshi Okamura, Hanspeter Herzel. Quantification of Circadian Rhythms in Single Cells

Volume 5, Issue 10

0 -- 0Wesley C. Van Voorhis, Wim G. J. Hol, Peter J. Myler, Lance J. Stewart. The Role of Medical Structural Genomics in Discovering New Drugs for Infectious Diseases
0 -- 0Donna K. Slonim, Itai Yanai. Getting Started in Gene Expression Microarray Analysis
0 -- 0Mark P. Little, Anna Gola, Ioanna Tzoulaki. A Model of Cardiovascular Disease Giving a Plausible Mechanism for the Effect of Fractionated Low-Dose Ionizing Radiation Exposure
0 -- 0Nobuto Takeuchi, Paulien Hogeweg. Multilevel Selection in Models of Prebiotic Evolution II: A Direct Comparison of Compartmentalization and Spatial Self-Organization
0 -- 0Jin Liu, Ruth Nussinov. The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation
0 -- 0Jouhyun Jeon, Jae-Seong Yang, Sanguk Kim. Integration of Evolutionary Features for the Identification of Functionally Important Residues in Major Facilitator Superfamily Transporters
0 -- 0Edward C. Holmes, Bryan T. Grenfell. Discovering the Phylodynamics of RNA Viruses
0 -- 0José M. Peregrin-Alvarez, Xuejian Xiong, Chong Su, John Parkinson. Escherichia coli
0 -- 0Alon Zaslaver, Shai Kaplan, Anat Bren, Adrian Jinich, Avi E. Mayo, Erez Dekel, Uri Alon, Shalev Itzkovitz. Escherichia coli
0 -- 0Takeshi Hase, Hiroshi Tanaka, Yasuhiro Suzuki, So Nakagawa, Hiroaki Kitano. Structure of Protein Interaction Networks and Their Implications on Drug Design
0 -- 0Libin Rong, Alan S. Perelson. Modeling Latently Infected Cell Activation: Viral and Latent Reservoir Persistence, and Viral Blips in HIV-infected Patients on Potent Therapy
0 -- 0Silvia Restrepo, Andrés Pinzón, Luis Miguel Rodriguez-Rojas, Roberto Sierra, Alejandro Grajales, Adriana Bernal, Emiliano Barreto, Pedro Moreno, Maria Mercedes Zambrano, Marco Cristancho, Andrés González, Harold Castro. Computational Biology in Colombia
0 -- 0Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji, Atsushi Suenaga, Gentaro Morimoto, Ryoko Yanai, Yousuke Ohno, Tetsu Narumi, Makoto Taiji. High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations
0 -- 0Hédi Hegyi, László Buday, Peter Tompa. Intrinsic Structural Disorder Confers Cellular Viability on Oncogenic Fusion Proteins
0 -- 0Hsiao-Mei Lu, Jie Liang. Perturbation-based Markovian Transmission Model for Probing Allosteric Dynamics of Large Macromolecular Assembling: A Study of GroEL-GroES
0 -- 0Maksat Ashyraliyev, Ken Siggens, Hilde Janssens, Joke Blom, Michael Akam, Johannes Jaeger. huckebein
0 -- 0Bard Ermentrout, Daniel J. Simons, Peter W. Land. Subbarrel Patterns in Somatosensory Cortical Barrels Can Emerge from Local Dynamic Instabilities
0 -- 0Holly J. Atkinson, Patricia C. Babbitt. An Atlas of the Thioredoxin Fold Class Reveals the Complexity of Function-Enabling Adaptations
0 -- 0Thierry Mora, Howard Yu, Yoshiyuki Sowa, Ned S. Wingreen. Steps in the Bacterial Flagellar Motor
0 -- 0François O. David, Etienne Hugues, Tristan Cenier, Nicolas Fourcaud-Trocmé, Nathalie Buonviso. Specific Entrainment of Mitral Cells during Gamma Oscillation in the Rat Olfactory Bulb
0 -- 0Eva C. Berglund, Björn Nystedt, Siv G. E. Andersson. Computational Resources in Infectious Disease: Limitations and Challenges
0 -- 0Yizhi Cai, Matthew W. Lux, Laura Adam, Jean Peccoud. Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars
0 -- 0Canan Atilgan, Ali Rana Atilgan. Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein
0 -- 0Mateusz Sikora, Joanna I. Sulkowska, Marek Cieplak. Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots
0 -- 0Marc Hafner, Heinz Koeppl, Martin Hasler, Andreas Wagner. 'Glocal' Robustness Analysis and Model Discrimination for Circadian Oscillators
0 -- 0Ibrahim Baris, Aytug Tuncel, Natali Ozber, Ozlem Keskin, I. Halil Kavakli. Investigation of the Interaction between the Large and Small Subunits of Potato ADP-Glucose Pyrophosphorylase
0 -- 0Katie Bentley, Giovanni Mariggi, Holger Gerhardt, Paul A. Bates. Tipping the Balance: Robustness of Tip Cell Selection, Migration and Fusion in Angiogenesis
0 -- 0Dileep George, Jeff Hawkins. Towards a Mathematical Theory of Cortical Micro-circuits
0 -- 0Omar N. A. Demerdash, Michael D. Daily, Julie C. Mitchell. Structure-Based Predictive Models for Allosteric Hot Spots
0 -- 0Penelope A. Hancock. Combining Fungal Biopesticides and Insecticide-Treated Bednets to Enhance Malaria Control
0 -- 0Vassilios N. Christopoulos, Paul R. Schrater. Grasping Objects with Environmentally Induced Position Uncertainty
0 -- 0Alexander Lange, Neil M. Ferguson. Antigenic Diversity, Transmission Mechanisms, and the Evolution of Pathogens

Volume 5, Issue 1

0 -- 0Adrian M. Altenhoff, Christophe Dessimoz. Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods
0 -- 0Alain Mechulam, Konstantin G. Chernov, Elodie Mucher, Loic Hamon, Patrick A. Curmi, David Pastré. Polyamine Sharing between Tubulin Dimers Favours Microtubule Nucleation and Elongation via Facilitated Diffusion
0 -- 0Lucy J. Colwell, Michael P. Brenner. Action Potential Initiation in the Hodgkin-Huxley Model
0 -- 0Edoardo M. Airoldi, Curtis Huttenhower, David Gresham, Charles Lu, Amy A. Caudy, Maitreya J. Dunham, James R. Broach, David Botstein, Olga G. Troyanskaya. Predicting Cellular Growth from Gene Expression Signatures
0 -- 0M. Kemal Sönmez, Naunihal T. Zaveri, Ilan A. Kerman, Sharon Burke, Charles R. Neal, Xinmin Xie, Stanley J. Watson, Lawrence Toll. Evolutionary Sequence Modeling for Discovery of Peptide Hormones
0 -- 0Amos Ben-Zvi, Suzanne D. Vernon, Gordon Broderick. Model-Based Therapeutic Correction of Hypothalamic-Pituitary-Adrenal Axis Dysfunction
0 -- 0Patrick H. Bradley, Matthew J. Brauer, Joshua D. Rabinowitz, Olga G. Troyanskaya. Saccharomyces cerevisiae
0 -- 0Charles J. Vaske, Carrie House, Truong Luu, Bryan Frank, Chen-Hsiang Yeang, Norman H. Lee, Joshua M. Stuart. A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations
0 -- 0Wenxu Tong, Ying Wei, Leonel F. Murga, Mary Jo Ondrechen, Ronald J. Williams. Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties
0 -- 0Todd A. Gibson, Debra Goldberg. Questioning the Ubiquity of Neofunctionalization
0 -- 0Thorsten Lenser, Günter Theißen, Peter Dittrich. Developmental Robustness by Obligate Interaction of Class B Floral Homeotic Genes and Proteins
0 -- 0Debopriya Das, Matteo Pellegrini, Joe W. Gray. cis-Regulatory Logic
0 -- 0Evie Browne, Rosemary Dickin, Philip E. Bourne. PLoS Computational Biology
0 -- 0Katherine V. Wendelsdorf, Zhuo Song, Yang Cao, David C. Samuels. An Analysis of Enzyme Kinetics Data for Mitochondrial DNA Strand Termination by Nucleoside Reverse Transcription Inhibitors
0 -- 0Dan S. Bolintineanu, Abdallah Sayyed-Ahmad, H. Ted Davis, Yiannis N. Kaznessis. Poisson-Nernst-Planck Models of Nonequilibrium Ion Electrodiffusion through a Protegrin Transmembrane Pore
0 -- 0Adel Dayarian, Madalena Chaves, Eduardo D. Sontag, Anirvan M. Sengupta. Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks
0 -- 0Dirk Müller, Jörg Stelling. Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures
0 -- 0Adam B. Barrett, Guy O. Billings, Richard G. M. Morris, Mark C. W. van Rossum. State Based Model of Long-Term Potentiation and Synaptic Tagging and Capture
0 -- 0Mile Sikic, Sanja Tomic, Kristian Vlahovicek. Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests
0 -- 0Sinisa Pajevic, Dietmar Plenz. Efficient Network Reconstruction from Dynamical Cascades Identifies Small-World Topology of Neuronal Avalanches
0 -- 0Neil F. W. Saunders, Pedro Beltrão, Lars Juhl Jensen, Daniel Jurczak, Roland Krause, Michael Kuhn 0004, Shirley Wu. Microblogging the ISMB: A New Approach to Conference Reporting
0 -- 0Vijay Chickarmane, Tariq Enver, Carsten Peterson. Computational Modeling of the Hematopoietic Erythroid-Myeloid Switch Reveals Insights into Cooperativity, Priming, and Irreversibility
0 -- 0Mun Ju Kim, Ivan V. Maly. Deterministic Mechanical Model of T-Killer Cell Polarization Reproduces the Wandering of Aim between Simultaneously Engaged Targets
0 -- 0Like Fokkens, Berend Snel. Cohesive versus Flexible Evolution of Functional Modules in Eukaryotes
0 -- 0Stefan Engelen, Ladislas A. Trojan, Sophie Sacquin-Mora, Richard Lavery, Alessandra Carbone. Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling
0 -- 0Ivar Østby, Leiv Øyehaug, Gaute T. Einevoll, Erlend A. Nagelhus, Erik Plahte, Thomas Zeuthen, Catherine M. Lloyd, Ole P. Ottersen, Stig W. Omholt. Astrocytic Mechanisms Explaining Neural-Activity-Induced Shrinkage of Extraneuronal Space