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Content
September 2013, Volume 9, Issue 9
- 1-20 Limited Agreement of Independent RNAi Screens for Virus-Required Host Genes Owes More to False-Negative than False-Positive Factors
by Linhui Hao & Qiuling He & Zhishi Wang & Mark Craven & Michael A Newton & Paul Ahlquist - 1-27 Characterizing Changes in the Rate of Protein-Protein Dissociation upon Interface Mutation Using Hotspot Energy and Organization
by Rudi Agius & Mieczyslaw Torchala & Iain H Moal & Juan Fernández-Recio & Paul A Bates
August 2013, Volume 9, Issue 8
- 1-10 Predicting Disease Risk Using Bootstrap Ranking and Classification Algorithms
by Ohad Manor & Eran Segal - 1-10 Software for Computing and Annotating Genomic Ranges
by Michael Lawrence & Wolfgang Huber & Hervé Pagès & Patrick Aboyoun & Marc Carlson & Robert Gentleman & Martin T Morgan & Vincent J Carey - 1-11 Sensory Information and Encounter Rates of Interacting Species
by Andrew M Hein & Scott A McKinley - 1-11 Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization
by Guillermo Rodrigo & Thomas E Landrain & Eszter Majer & José-Antonio Daròs & Alfonso Jaramillo - 1-12 A Self-Directed Method for Cell-Type Identification and Separation of Gene Expression Microarrays
by Neta S Zuckerman & Yair Noam & Andrea J Goldsmith & Peter P Lee - 1-14 Determinants of Beat-to-Beat Variability of Repolarization Duration in the Canine Ventricular Myocyte: A Computational Analysis
by Jordi Heijman & Antonio Zaza & Daniel M Johnson & Yoram Rudy & Ralf L M Peeters & Paul G A Volders & Ronald L Westra - 1-14 Quantifying Cell Fate Decisions for Differentiation and Reprogramming of a Human Stem Cell Network: Landscape and Biological Paths
by Chunhe Li & Jin Wang - 1-14 Priors Engaged in Long-Latency Responses to Mechanical Perturbations Suggest a Rapid Update in State Estimation
by Frédéric Crevecoeur & Stephen H Scott - 1-15 Model-Based Analysis of HER Activation in Cells Co-Expressing EGFR, HER2 and HER3
by Harish Shankaran & Yi Zhang & Yunbing Tan & Haluk Resat - 1-15 Parameter Trajectory Analysis to Identify Treatment Effects of Pharmacological Interventions
by Christian A Tiemann & Joep Vanlier & Maaike H Oosterveer & Albert K Groen & Peter A J Hilbers & Natal A W van Riel - 1-16 Characteristic Effects of Stochastic Oscillatory Forcing on Neural Firing: Analytical Theory and Comparison to Paddlefish Electroreceptor Data
by Christoph Bauermeister & Tilo Schwalger & David F Russell & Alexander B Neiman & Benjamin Lindner - 1-17 From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction
by Simona Cocco & Remi Monasson & Martin Weigt - 1-20 Shape Similarity, Better than Semantic Membership, Accounts for the Structure of Visual Object Representations in a Population of Monkey Inferotemporal Neurons
by Carlo Baldassi & Alireza Alemi-Neissi & Marino Pagan & James J DiCarlo & Riccardo Zecchina & Davide Zoccolan
July 2013, Volume 9, Issue 7
- 1-10 Co-expression Profiling of Autism Genes in the Mouse Brain
by Idan Menashe & Pascal Grange & Eric C Larsen & Sharmila Banerjee-Basu & Partha P Mitra - 1-11 Consistent Estimation of Gibbs Energy Using Component Contributions
by Elad Noor & Hulda S Haraldsdóttir & Ron Milo & Ronan M T Fleming - 1-14 Statistical Analysis of Molecular Signal Recording
by Joshua I Glaser & Bradley M Zamft & Adam H Marblestone & Jeffrey R Moffitt & Keith Tyo & Edward S Boyden & George Church & Konrad P Kording - 1-14 Hierarchical Modeling for Rare Event Detection and Cell Subset Alignment across Flow Cytometry Samples
by Andrew Cron & Cécile Gouttefangeas & Jacob Frelinger & Lin Lin & Satwinder K Singh & Cedrik M Britten & Marij J P Welters & Sjoerd H van der Burg & Mike West & Cliburn Chan - 1-17 A Family of Algorithms for Computing Consensus about Node State from Network Data
by Eleanor R Brush & David C Krakauer & Jessica C Flack - 1-18 A Mixture of Delta-Rules Approximation to Bayesian Inference in Change-Point Problems
by Robert C Wilson & Matthew R Nassar & Joshua I Gold - 1-18 Inferring Nonlinear Neuronal Computation Based on Physiologically Plausible Inputs
by James M McFarland & Yuwei Cui & Daniel A Butts
June 2013, Volume 9, Issue 6
- 1-9 Scrutinizing MHC-I Binding Peptides and Their Limits of Variation
by Christian P Koch & Anna M Perna & Max Pillong & Nickolay K Todoroff & Paul Wrede & Gerd Folkers & Jan A Hiss & Gisbert Schneider - 1-11 Leveraging Prior Information to Detect Causal Variants via Multi-Variant Regression
by Nanye Long & Samuel P Dickson & Jessica M Maia & Hee Shin Kim & Qianqian Zhu & Andrew S Allen - 1-11 The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum
by William R Harcombe & Nigel F Delaney & Nicholas Leiby & Niels Klitgord & Christopher J Marx - 1-13 Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links ATAD3B to Poor Survival in Breast Cancer
by Kristian Ovaska & Filomena Matarese & Korbinian Grote & Iryna Charapitsa & Alejandra Cervera & Chengyu Liu & George Reid & Martin Seifert & Hendrik G Stunnenberg & Sampsa Hautaniemi - 1-14 Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach
by Meagan C Small & Pedro Lopes & Rodrigo B Andrade & Alexander D MacKerell Jr - 1-15 Patterns of Proliferative Activity in the Colonic Crypt Determine Crypt Stability and Rates of Somatic Evolution
by Rui Zhao & Franziska Michor - 1-16 Are V1 Simple Cells Optimized for Visual Occlusions? A Comparative Study
by Jörg Bornschein & Marc Henniges & Jörg Lücke - 1-19 Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins
by Louis-François Handfield & Yolanda T Chong & Jibril Simmons & Brenda J Andrews & Alan M Moses - 1-19 PUMA: A Unified Framework for Penalized Multiple Regression Analysis of GWAS Data
by Gabriel E Hoffman & Benjamin A Logsdon & Jason G Mezey
May 2013, Volume 9, Issue 5
- 1-1 A Kinetic Platform to Determine the Fate of Nitric Oxide in Escherichia coli
by Jonathan L Robinson & Mark P Brynildsen - 1-9 Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA
by Tobias Linder & Bert L de Groot & Anna Stary-Weinzinger - 1-11 Polymorphisms in the F8 Gene and MHC-II Variants as Risk Factors for the Development of Inhibitory Anti-Factor VIII Antibodies during the Treatment of Hemophilia A: A Computational Assessment
by Gouri Shankar Pandey & Chen Yanover & Tom E Howard & Zuben E Sauna - 1-11 Testing Whether Humans Have an Accurate Model of Their Own Motor Uncertainty in a Speeded Reaching Task
by Hang Zhang & Nathaniel D Daw & Laurence T Maloney - 1-12 Effect of Regulatory Architecture on Broad versus Narrow Sense Heritability
by Yunpeng Wang & Jon Olav Vik & Stig W Omholt & Arne B Gjuvsland - 1-13 Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations
by Xiaodong Cai & Juan Andrés Bazerque & Georgios B Giannakis - 1-13 Modeling and Measuring Signal Relay in Noisy Directed Migration of Cell Groups
by Can Guven & Erin Rericha & Edward Ott & Wolfgang Losert - 1-14 Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation
by Haipeng Li & Thomas Wiehe - 1-14 STL-based Analysis of TRAIL-induced Apoptosis Challenges the Notion of Type I/Type II Cell Line Classification
by Szymon Stoma & Alexandre Donzé & François Bertaux & Oded Maler & Gregory Batt - 1-16 Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling
by Erhan Bilal & Janusz Dutkowski & Justin Guinney & In Sock Jang & Benjamin A Logsdon & Gaurav Pandey & Benjamin A Sauerwine & Yishai Shimoni & Hans Kristian Moen Vollan & Brigham H Mecham & Oscar M Rueda & Jorg Tost & Christina Curtis & Mariano J Alvarez & Vessela N Kristensen & Samuel Aparicio & Anne-Lise Børresen-Dale & Carlos Caldas & Andrea Califano & Stephen H Friend & Trey Ideker & Eric E Schadt & Gustavo A Stolovitzky & Adam A Margolin - 1-17 Inference of R0 and Transmission Heterogeneity from the Size Distribution of Stuttering Chains
by Seth Blumberg & James O Lloyd-Smith - 1-17 Sparse Coding Can Predict Primary Visual Cortex Receptive Field Changes Induced by Abnormal Visual Input
by Jonathan J Hunt & Peter Dayan & Geoffrey J Goodhill
April 2013, Volume 9, Issue 4
- 1-6 A Healthy Fear of the Unknown: Perspectives on the Interpretation of Parameter Fits from Computational Models in Neuroscience
by Matthew R Nassar & Joshua I Gold - 1-9 A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase
by Lin-Tai Da & Fátima Pardo Avila & Dong Wang & Xuhui Huang - 1-14 Localization of Protein Aggregation in Escherichia coli Is Governed by Diffusion and Nucleoid Macromolecular Crowding Effect
by Anne-Sophie Coquel & Jean-Pascal Jacob & Mael Primet & Alice Demarez & Mariella Dimiccoli & Thomas Julou & Lionel Moisan & Ariel B Lindner & Hugues Berry - 1-14 Human Germline Antibody Gene Segments Encode Polyspecific Antibodies
by Jordan R Willis & Bryan S Briney & Samuel L DeLuca & James E Crowe Jr & Jens Meiler - 1-15 Data-Driven Modeling of Src Control on the Mitochondrial Pathway of Apoptosis: Implication for Anticancer Therapy Optimization
by Annabelle Ballesta & Jonathan Lopez & Nikolay Popgeorgiev & Philippe Gonzalo & Marie Doumic & Germain Gillet - 1-15 Computational Biomarker Pipeline from Discovery to Clinical Implementation: Plasma Proteomic Biomarkers for Cardiac Transplantation
by Gabriela V Cohen Freue & Anna Meredith & Derek Smith & Axel Bergman & Mayu Sasaki & Karen K Y Lam & Zsuzsanna Hollander & Nina Opushneva & Mandeep Takhar & David Lin & Janet Wilson-McManus & Robert Balshaw & Paul A Keown & Christoph H Borchers & Bruce McManus & Raymond T Ng & W Robert McMaster & for the Biomarkers in Transplantation and the NCE CECR Prevention of Organ Failure Centre of Excellence Teams - 1-15 Lifespan Differences in Hematopoietic Stem Cells are Due to Imperfect Repair and Unstable Mean-Reversion
by Hans B Sieburg & Giulio Cattarossi & Christa E Muller-Sieburg - 1-15 Noise Suppression and Surplus Synchrony by Coincidence Detection
by Matthias Schultze-Kraft & Markus Diesmann & Sonja Grün & Moritz Helias - 1-17 Learning Multisensory Integration and Coordinate Transformation via Density Estimation
by Joseph G Makin & Matthew R Fellows & Philip N Sabes - 1-30 Bayesian Computation Emerges in Generic Cortical Microcircuits through Spike-Timing-Dependent Plasticity
by Bernhard Nessler & Michael Pfeiffer & Lars Buesing & Wolfgang Maass
March 2013, Volume 9, Issue 3
- 1-9 Bursts of Vertex Activation and Epidemics in Evolving Networks
by Luis E C Rocha & Vincent D Blondel - 1-9 The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks
by Clive G Bowsher & Margaritis Voliotis & Peter S Swain - 1-9 Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field
by Silvio a Beccara & Tatjana Škrbić & Roberto Covino & Cristian Micheletti & Pietro Faccioli - 1-11 Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences
by Dazhi Jiao & Yuzhen Ye & Haixu Tang - 1-12 Explaining the Determinants of First Phase HIV Decay Dynamics through the Effects of Stage-dependent Drug Action
by James B Gilmore & Anthony D Kelleher & David A Cooper & John M Murray - 1-12 Collective Cell Motion in an Epithelial Sheet Can Be Quantitatively Described by a Stochastic Interacting Particle Model
by Néstor Sepúlveda & Laurence Petitjean & Olivier Cochet & Erwan Grasland-Mongrain & Pascal Silberzan & Vincent Hakim - 1-12 Analysis of Hepatitis C Virus Decline during Treatment with the Protease Inhibitor Danoprevir Using a Multiscale Model
by Libin Rong & Jeremie Guedj & Harel Dahari & Daniel J Coffield Jr & Micha Levi & Patrick Smith & Alan S Perelson - 1-13 Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage
by Katarzyna Bozek & Thomas Lengauer & Saleta Sierra & Rolf Kaiser & Francisco S Domingues - 1-13 Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection
by Richard P Mann & Andrea Perna & Daniel Strömbom & Roman Garnett & James E Herbert-Read & David J T Sumpter & Ashley J W Ward - 1-14 Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes
by Christopher Y Park & Aaron K Wong & Casey S Greene & Jessica Rowland & Yuanfang Guan & Lars A Bongo & Rebecca D Burdine & Olga G Troyanskaya - 1-14 Noise-invariant Neurons in the Avian Auditory Cortex: Hearing the Song in Noise
by R Channing Moore & Tyler Lee & Frédéric E Theunissen - 1-14 Automated Analysis of a Diverse Synapse Population
by Brad Busse & Stephen Smith - 1-14 Stimulus-dependent Maximum Entropy Models of Neural Population Codes
by Einat Granot-Atedgi & Gašper Tkačik & Ronen Segev & Elad Schneidman - 1-15 Optimal Vaccine Allocation for the Early Mitigation of Pandemic Influenza
by Laura Matrajt & M Elizabeth Halloran & Ira M Longini Jr - 1-16 A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana
by Christoph Schmal & Peter Reimann & Dorothee Staiger - 1-16 Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment
by Wei Zhang & Takayo Ota & Viji Shridhar & Jeremy Chien & Baolin Wu & Rui Kuang - 1-17 Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology
by Tina Toni & Bruce Tidor - 1-18 Sustained Firing of Model Central Auditory Neurons Yields a Discriminative Spectro-temporal Representation for Natural Sounds
by Michael A Carlin & Mounya Elhilali
February 2013, Volume 9, Issue 2
- 1-6 Optimal Properties of Analog Perceptrons with Excitatory Weights
by Claudia Clopath & Nicolas Brunel - 1-9 No Evidence for an Item Limit in Change Detection
by Shaiyan Keshvari & Ronald van den Berg & Wei Ji Ma - 1-9 Spartan : A Comprehensive Tool for Understanding Uncertainty in Simulations of Biological Systems
by Kieran Alden & Mark Read & Jon Timmis & Paul S Andrews & Henrique Veiga-Fernandes & Mark Coles - 1-10 Standard Anatomical and Visual Space for the Mouse Retina: Computational Reconstruction and Transformation of Flattened Retinae with the Retistruct Package
by David C Sterratt & Daniel Lyngholm & David J Willshaw & Ian D Thompson - 1-11 Virus Neutralisation: New Insights from Kinetic Neutralisation Curves
by Carsten Magnus - 1-13 Evidence for Model-based Computations in the Human Amygdala during Pavlovian Conditioning
by Charlotte Prévost & Daniel McNamee & Ryan K Jessup & Peter Bossaerts & John P O'Doherty - 1-13 Multi-Population Classical HLA Type Imputation
by Alexander Dilthey & Stephen Leslie & Loukas Moutsianas & Judong Shen & Charles Cox & Matthew R Nelson & Gil McVean - 1-14 Biomolecular Events in Cancer Revealed by Attractor Metagenes
by Wei-Yi Cheng & Tai-Hsien Ou Yang & Dimitris Anastassiou - 1-14 Discriminating External and Internal Causes for Heading Changes in Freely Flying Drosophila
by Andrea Censi & Andrew D Straw & Rosalyn W Sayaman & Richard M Murray & Michael H Dickinson - 1-15 Passive Dendrites Enable Single Neurons to Compute Linearly Non-separable Functions
by Romain Daniel Cazé & Mark Humphries & Boris Gutkin - 1-18 Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data
by Gerard J P van Westen & Alwin Hendriks & Jörg K Wegner & Adriaan P IJzerman & Herman W T van Vlijmen & Andreas Bender - 1-19 Delay Selection by Spike-Timing-Dependent Plasticity in Recurrent Networks of Spiking Neurons Receiving Oscillatory Inputs
by Robert R Kerr & Anthony N Burkitt & Doreen A Thomas & Matthieu Gilson & David B Grayden
January 2013, Volume 9, Issue 1
- 1-3 Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator
by Jeroen de Ridder & Thomas Abeel & Magali Michaut & Venkata P Satagopam & Nils Gehlenborg - 1-6 Reward from Punishment Does Not Emerge at All Costs
by Jeromos Vukov & Flávio L Pinheiro & Francisco C Santos & Jorge M Pacheco - 1-9 The Effects of City Streets on an Urban Disease Vector
by Corentin M Barbu & Andrew Hong & Jennifer M Manne & Dylan S Small & Javier E Quintanilla Calderón & Karthik Sethuraman & Víctor Quispe-Machaca & Jenny Ancca-Juárez & Juan G Cornejo del Carpio & Fernando S Málaga Chavez & César Náquira & Michael Z Levy - 1-10 Approximate Bayesian Computation
by Mikael Sunnåker & Alberto Giovanni Busetto & Elina Numminen & Jukka Corander & Matthieu Foll & Christophe Dessimoz - 1-13 Temporal Adaptation Enhances Efficient Contrast Gain Control on Natural Images
by Fabian Sinz & Matthias Bethge - 1-13 Saccadic Momentum and Facilitation of Return Saccades Contribute to an Optimal Foraging Strategy
by Niklas Wilming & Simon Harst & Nico Schmidt & Peter König - 1-13 Maximizing the Information Content of Experiments in Systems Biology
by Juliane Liepe & Sarah Filippi & Michał Komorowski & Michael P H Stumpf - 1-14 How Evolving Heterogeneity Distributions of Resource Allocation Strategies Shape Mortality Patterns
by Yann Le Cunff & Annette Baudisch & Khashayar Pakdaman - 1-14 Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships
by Nives Škunca & Matko Bošnjak & Anita Kriško & Panče Panov & Sašo Džeroski & Tomislav Šmuc & Fran Supek - 1-15 Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective
by Graham Rockwell & Nicholas J Guido & George M Church - 1-17 Significance Analysis of Prognostic Signatures
by Andrew H Beck & Nicholas W Knoblauch & Marco M Hefti & Jennifer Kaplan & Stuart J Schnitt & Aedin C Culhane & Markus S Schroeder & Thomas Risch & John Quackenbush & Benjamin Haibe-Kains - 1-21 Dynamic Finite Size Effects in Spiking Neural Networks
by Michael A Buice & Carson C Chow
December 2012, Volume 8, Issue 12
- 1-8 Chapter 2: Data-Driven View of Disease Biology
by Casey S Greene & Olga G Troyanskaya - 1-9 Chapter 10: Mining Genome-Wide Genetic Markers
by Xiang Zhang & Shunping Huang & Zhaojun Zhang & Wei Wang - 1-9 Computational Phenotyping of Two-Person Interactions Reveals Differential Neural Response to Depth-of-Thought
by Ting Xiang & Debajyoti Ray & Terry Lohrenz & Peter Dayan & P Read Montague - 1-10 Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking
by Jens Vindahl Kringelum & Claus Lundegaard & Ole Lund & Morten Nielsen - 1-10 Molecular Evolution of Peptide Ligands with Custom-Tailored Characteristics for Targeting of Glycostructures
by Niels Röckendorf & Markus Borschbach & Andreas Frey - 1-12 Chapter 9: Analyses Using Disease Ontologies
by Nigam H Shah & Tyler Cole & Mark A Musen - 1-12 Chapter 8: Biological Knowledge Assembly and Interpretation
by Ju Han Kim - 1-13 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density
by 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 - 1-14 SnIPRE: Selection Inference Using a Poisson Random Effects Model
by Kirsten E Eilertson & James G Booth & Carlos D Bustamante - 1-14 ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes
by Kishore R Mosaliganti & Ramil R Noche & Fengzhu Xiong & Ian A Swinburne & Sean G Megason - 1-14 Parameter Identifiability and Sensitivity Analysis Predict Targets for Enhancement of STAT1 Activity in Pancreatic Cancer and Stellate Cells
by Katja Rateitschak & Felix Winter & Falko Lange & Robert Jaster & Olaf Wolkenhauer - 1-15 Chapter 13: Mining Electronic Health Records in the Genomics Era
by Joshua C Denny - 1-17 A Comparison of Computational Models for Eukaryotic Cell Shape and Motility
by William R Holmes & Leah Edelstein-Keshet
November 2012, Volume 8, Issue 11
- 1-4 Ten Simple Rules to Protect Your Intellectual Property
by Mark Jolly & Anthony C Fletcher & Philip E Bourne - 1-11 How Random Is Social Behaviour? Disentangling Social Complexity through the Study of a Wild House Mouse Population
by Nicolas Perony & Claudio J Tessone & Barbara König & Frank Schweitzer - 1-12 Mesoscopic Model of Actin-Based Propulsion
by Jie Zhu & Alex Mogilner - 1-13 Chemotactic Migration of T Cells towards Dendritic Cells Promotes the Detection of Rare Antigens
by Renske M A Vroomans & Athanasius F M Marée & Rob J de Boer & Joost B Beltman - 1-13 A Graphical Modelling Approach to the Dissection of Highly Correlated Transcription Factor Binding Site Profiles
by Robert Stojnic & Audrey Qiuyan Fu & Boris Adryan - 1-14 Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay
by Filippo Cacace & Paola Paci & Valerio Cusimano & Alfredo Germani & Lorenzo Farina - 1-14 A Bayesian Inference Framework to Reconstruct Transmission Trees Using Epidemiological and Genetic Data
by Marco J Morelli & Gaël Thébaud & Joël Chadœuf & Donald P King & Daniel T Haydon & Samuel Soubeyrand - 1-14 Strategy Diversity Stabilizes Mutualism through Investment Cycles, Phase Polymorphism, and Spatial Bubbles
by Gergely Boza & Ádám Kun & István Scheuring & Ulf Dieckmann - 1-15 Reconstructing Mammalian Sleep Dynamics with Data Assimilation
by Madineh Sedigh-Sarvestani & Steven J Schiff & Bruce J Gluckman - 1-17 Functional Inference of Complex Anatomical Tendinous Networks at a Macroscopic Scale via Sparse Experimentation
by Anupam Saxena & Hod Lipson & Francisco J Valero-Cuevas - 1-19 Internal Representations of Temporal Statistics and Feedback Calibrate Motor-Sensory Interval Timing
by Luigi Acerbi & Daniel M Wolpert & Sethu Vijayakumar - 1-24 Coordinated Optimization of Visual Cortical Maps (I) Symmetry-based Analysis
by Lars Reichl & Dominik Heide & Siegrid Löwel & Justin C Crowley & Matthias Kaschube & Fred Wolf - 1-26 Coordinated Optimization of Visual Cortical Maps (II) Numerical Studies
by Lars Reichl & Dominik Heide & Siegrid Löwel & Justin C Crowley & Matthias Kaschube & Fred Wolf
October 2012, Volume 8, Issue 10
- 1-2 Seven Years; It's Time for a Change
by Philip E Bourne - 1-10 Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations
by Noah S Bieler & Tuomas P J Knowles & Daan Frenkel & Robert Vácha - 1-10 Ubiquitin Dynamics in Complexes Reveal Molecular Recognition Mechanisms Beyond Induced Fit and Conformational Selection
by Jan H Peters & Bert L de Groot - 1-10 Probability Fluxes and Transition Paths in a Markovian Model Describing Complex Subunit Cooperativity in HCN2 Channels
by Klaus Benndorf & Jana Kusch & Eckhard Schulz - 1-10 How Recent History Affects Perception: The Normative Approach and Its Heuristic Approximation
by Ofri Raviv & Merav Ahissar & Yonatan Loewenstein - 1-12 CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
by Eva Chovancova & Antonin Pavelka & Petr Benes & Ondrej Strnad & Jan Brezovsky & Barbora Kozlikova & Artur Gora & Vilem Sustr & Martin Klvana & Petr Medek & Lada Biedermannova & Jiri Sochor & Jiri Damborsky - 1-12 Predictive Dynamics of Human Pain Perception
by Guillermo A Cecchi & Lejian Huang & Javeria Ali Hashmi & Marwan Baliki & María V Centeno & Irina Rish & A Vania Apkarian - 1-12 Very Slow Search and Reach: Failure to Maximize Expected Gain in an Eye-Hand Coordination Task
by Hang Zhang & Camille Morvan & Louis-Alexandre Etezad-Heydari & Laurence T Maloney - 1-12 Evaluating the Adequacy of Gravity Models as a Description of Human Mobility for Epidemic Modelling
by James Truscott & Neil M Ferguson - 1-13 A Model of Reward- and Effort-Based Optimal Decision Making and Motor Control
by Lionel Rigoux & Emmanuel Guigon - 1-13 Analysis of Slow (Theta) Oscillations as a Potential Temporal Reference Frame for Information Coding in Sensory Cortices
by Christoph Kayser & Robin A A Ince & Stefano Panzeri - 1-14 Estimating the Hidden Burden of Bovine Tuberculosis in Great Britain
by Andrew J K Conlan & Trevelyan J McKinley & Katerina Karolemeas & Ellen Brooks Pollock & Anthony V Goodchild & Andrew P Mitchell & Colin P D Birch & Richard S Clifton-Hadley & James L N Wood - 1-14 Coding and Decoding with Adapting Neurons: A Population Approach to the Peri-Stimulus Time Histogram
by Richard Naud & Wulfram Gerstner - 1-16 Spatially Pooled Contrast Responses Predict Neural and Perceptual Similarity of Naturalistic Image Categories
by Iris I A Groen & Sennay Ghebreab & Victor A F Lamme & H Steven Scholte
September 2012, Volume 8, Issue 9
- 1-3 Ten Simple Rules To Commercialize Scientific Research
by Anthony C Fletcher & Philip E Bourne - 1-3 Why Open Drug Discovery Needs Four Simple Rules for Licensing Data and Models
by Antony J Williams & John Wilbanks & Sean Ekins - 1-7 Risk-Sensitivity in Bayesian Sensorimotor Integration
by Jordi Grau-Moya & Pedro A Ortega & Daniel A Braun - 1-8 Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function
by Michael A Jamros & Leandro C Oliveira & Paul C Whitford & José N Onuchic & Joseph A Adams & Patricia A Jennings - 1-9 Speeded Reaching Movements around Invisible Obstacles
by Todd E Hudson & Uta Wolfe & Laurence T Maloney - 1-9 Binding of Two Intrinsically Disordered Peptides to a Multi-Specific Protein: A Combined Monte Carlo and Molecular Dynamics Study
by Iskra Staneva & Yongqi Huang & Zhirong Liu & Stefan Wallin - 1-10 Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease
by Omar Haq & Michael Andrec & Alexandre V Morozov & Ronald M Levy - 1-12 Spike-based Decision Learning of Nash Equilibria in Two-Player Games
by Johannes Friedrich & Walter Senn - 1-12 High-throughput Computer Method for 3D Neuronal Structure Reconstruction from the Image Stack of the Drosophila Brain and Its Applications
by Ping-Chang Lee & Chao-Chun Chuang & Ann-Shyn Chiang & Yu-Tai Ching - 1-13 Spike-Timing Dependence of Structural Plasticity Explains Cooperative Synapse Formation in the Neocortex
by Moritz Deger & Moritz Helias & Stefan Rotter & Markus Diesmann - 1-13 Dependencies among Editing Sites in Serotonin 2C Receptor mRNA
by Liran Carmel & Eugene V Koonin & Stella Dracheva - 1-16 Predicting the Extension of Biomedical Ontologies
by Catia Pesquita & Francisco M Couto - 1-17 Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts
by Tobias Sikosek & Erich Bornberg-Bauer & Hue Sun Chan
August 2012, Volume 8, Issue 8
- 1-1 Design and Implementation of a Genomics Field Trip Program Aimed at Secondary School Students
by Jennifer McQueen & Jody J Wright & Joanne A Fox - 1-1 Unifying Time to Contact Estimation and Collision Avoidance across Species
by Matthias S Keil & Joan López-Moliner - 1-7 Evolutionary Dynamics of Strategic Behavior in a Collective-Risk Dilemma
by Maria Abou Chakra & Arne Traulsen - 1-8 Hybrid Models and Biological Model Reduction with PyDSTool
by Robert Clewley - 1-10 The Roots of Bioinformatics in ISMB
by Todd A Gibson - 1-11 Locust Dynamics: Behavioral Phase Change and Swarming
by Chad M Topaz & Maria R D'Orsogna & Leah Edelstein-Keshet & Andrew J Bernoff - 1-13 A Network-based Approach for Predicting Missing Pathway Interactions
by Saket Navlakha & Anthony Gitter & Ziv Bar-Joseph - 1-14 The Landscape of the Prion Protein's Structural Response to Mutation Revealed by Principal Component Analysis of Multiple NMR Ensembles
by Deena M A Gendoo & Paul M Harrison - 1-14 A Topological Paradigm for Hippocampal Spatial Map Formation Using Persistent Homology
by Y Dabaghian & F Mémoli & L Frank & G Carlsson - 1-15 Combining the Finite Element Method with Structural Connectome-based Analysis for Modeling Neurotrauma: Connectome Neurotrauma Mechanics
by Reuben H Kraft & Phillip Justin Mckee & Amy M Dagro & Scott T Grafton - 1-29 Decorrelation of Neural-Network Activity by Inhibitory Feedback
by Tom Tetzlaff & Moritz Helias & Gaute T Einevoll & Markus Diesmann
July 2012, Volume 8, Issue 7
- 1-5 Which of Our Modeling Predictions Are Robust?
by Rob J De Boer - 1-8 Automated Tracking of Whiskers in Videos of Head Fixed Rodents
by Nathan G Clack & Daniel H O'Connor & Daniel Huber & Leopoldo Petreanu & Andrew Hires & Simon Peron & Karel Svoboda & Eugene W Myers - 1-10 A Preformed Binding Interface in the Unbound Ensemble of an Intrinsically Disordered Protein: Evidence from Molecular Simulations
by Michael Knott & Robert B Best - 1-10 Assessing Drug Target Association Using Semantic Linked Data
by Bin Chen & Ying Ding & David J Wild - 1-11 Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia
by Peilin Jia & Lily Wang & Ayman H Fanous & Carlos N Pato & Todd L Edwards & The International Schizophrenia Consortium & Zhongming Zhao - 1-11 Why SIT Works: Normal Function Despite Typical Myofiber Pattern in Situs Inversus Totalis (SIT) Hearts Derived by Shear-induced Myofiber Reorientation
by Marieke Pluijmert & Wilco Kroon & Alessandro C Rossi & Peter H M Bovendeerd & Tammo Delhaas - 1-12 Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data
by Haipeng Xing & Yifan Mo & Will Liao & Michael Q Zhang - 1-13 Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation
by Jason Flannick & Joshua M Korn & Pierre Fontanillas & George B Grant & Eric Banks & Mark A Depristo & David Altshuler - 1-16 Coding Conspecific Identity and Motion in the Electric Sense
by Na Yu & Ginette Hupé & Charles Garfinkle & John E Lewis & André Longtin - 1-18 Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity
by Miles Miller & Marc Hafner & Eduardo Sontag & Noah Davidsohn & Sairam Subramanian & Priscilla E M Purnick & Douglas Lauffenburger & Ron Weiss - 1-22 Spectral Analysis of Input Spike Trains by Spike-Timing-Dependent Plasticity
by Matthieu Gilson & Tomoki Fukai & Anthony N Burkitt
June 2012, Volume 8, Issue 6
- 1-2 A Report of the Curriculum Task Force of the ISCB Education Committee
by Lonnie R Welch & Russell Schwartz & Fran Lewitter - 1-9 Protein Scaffolds Can Enhance the Bistability of Multisite Phosphorylation Systems
by Carlo Chan & Xinfeng Liu & Liming Wang & Lee Bardwell & Qing Nie & Germán Enciso - 1-9 A Model-Based Bayesian Estimation of the Rate of Evolution of VNTR Loci in Mycobacterium tuberculosis
by R Zachariah Aandahl & Josephine F Reyes & Scott A Sisson & Mark M Tanaka - 1-10 MC EMiNEM Maps the Interaction Landscape of the Mediator
by Theresa Niederberger & Stefanie Etzold & Michael Lidschreiber & Kerstin C Maier & Dietmar E Martin & Holger Fröhlich & Patrick Cramer & Achim Tresch - 1-11 Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation
by Crina-Maria Ionescu & Radka Svobodová Vařeková & Jochen H M Prehn & Heinrich J Huber & Jaroslav Koča - 1-12 A Maximum Entropy Test for Evaluating Higher-Order Correlations in Spike Counts
by Arno Onken & Valentin Dragoi & Klaus Obermayer - 1-12 A Scalable Algorithm to Explore the Gibbs Energy Landscape of Genome-Scale Metabolic Networks
by Daniele De Martino & Matteo Figliuzzi & Andrea De Martino & Enzo Marinari - 1-12 Structural Drift: The Population Dynamics of Sequential Learning
by James P Crutchfield & Sean Whalen - 1-12 The Role of Non-Native Interactions in the Folding of Knotted Proteins
by Tatjana Škrbić & Cristian Micheletti & Pietro Faccioli - 1-16 Posterior Association Networks and Functional Modules Inferred from Rich Phenotypes of Gene Perturbations
by Xin Wang & Mauro A Castro & Klaas W Mulder & Florian Markowetz - 1-16 Fast Coding of Orientation in Primary Visual Cortex
by Oren Shriki & Adam Kohn & Maoz Shamir - 1-17 Fast Spatiotemporal Smoothing of Calcium Measurements in Dendritic Trees
by Eftychios A Pnevmatikakis & Keith Kelleher & Rebecca Chen & Petter Saggau & Krešimir Josić & Liam Paninski - 1-17 Modeling Boundary Vector Cell Firing Given Optic Flow as a Cue
by Florian Raudies & Michael E Hasselmo - 1-18 Short Term Synaptic Depression Imposes a Frequency Dependent Filter on Synaptic Information Transfer
by Robert Rosenbaum & Jonathan Rubin & Brent Doiron - 1-18 Deceleration of Fusion–Fission Cycles Improves Mitochondrial Quality Control during Aging
by Marc Thilo Figge & Andreas S Reichert & Michael Meyer-Hermann & Heinz D Osiewacz
May 2012, Volume 8, Issue 5
- 1-10 Intermittent Motion in Desert Locusts: Behavioural Complexity in Simple Environments
by Sepideh Bazazi & Frederic Bartumeus & Joseph J Hale & Iain D Couzin - 1-10 Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs
by Adrian M Altenhoff & Romain A Studer & Marc Robinson-Rechavi & Christophe Dessimoz - 1-12 Exploring Massive, Genome Scale Datasets with the GenometriCorr Package
by Alexander Favorov & Loris Mularoni & Leslie M Cope & Yulia Medvedeva & Andrey A Mironov & Vsevolod J Makeev & Sarah J Wheelan - 1-12 Crossing Over…Markov Meets Mendel
by Saad Mneimneh - 1-13 A Spatial Model of Mosquito Host-Seeking Behavior
by Bree Cummins & Ricardo Cortez & Ivo M Foppa & Justin Walbeck & James M Hyman - 1-14 Measuring Granger Causality between Cortical Regions from Voxelwise fMRI BOLD Signals with LASSO
by Wei Tang & Steven L Bressler & Chad M Sylvester & Gordon L Shulman & Maurizio Corbetta - 1-17 Optimality of Human Contour Integration
by Udo A Ernst & Sunita Mandon & Nadja Schinkel–Bielefeld & Simon D Neitzel & Andreas K Kreiter & Klaus R Pawelzik - 1-18 Optimal Control of Saccades by Spatial-Temporal Activity Patterns in the Monkey Superior Colliculus
by H H L M Goossens & A J van Opstal
April 2012, Volume 8, Issue 4
- 1-1 Are Long-Range Structural Correlations Behind the Aggregration Phenomena of Polyglutamine Diseases?
by Mahmoud Moradi & Volodymyr Babin & Christopher Roland & Celeste Sagui - 1-7 Geometric Theory Predicts Bifurcations in Minimal Wiring Cost Trees in Biology Are Flat
by Yihwa Kim & Robert Sinclair & Nol Chindapol & Jaap A Kaandorp & Erik De Schutter - 1-9 Parameters in Dynamic Models of Complex Traits are Containers of Missing Heritability
by Yunpeng Wang & Arne B Gjuvsland & Jon Olav Vik & Nicolas P Smith & Peter J Hunter & Stig W Omholt - 1-10 Storage of Correlated Patterns in Standard and Bistable Purkinje Cell Models
by Claudia Clopath & Jean-Pierre Nadal & Nicolas Brunel - 1-11 Power-Law Inter-Spike Interval Distributions Infer a Conditional Maximization of Entropy in Cortical Neurons
by Yasuhiro Tsubo & Yoshikazu Isomura & Tomoki Fukai