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Content
July 2014, Volume 10, Issue 7
- 1-11 Stability Curve Prediction of Homologous Proteins Using Temperature-Dependent Statistical Potentials
by Fabrizio Pucci & Marianne Rooman - 1-11 Membrane Interaction of Bound Ligands Contributes to the Negative Binding Cooperativity of the EGF Receptor
by Anton Arkhipov & Yibing Shan & Eric T Kim & David E Shaw - 1-11 LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry
by Jacob D Durrant & Rommie E Amaro - 1-12 CeleST: Computer Vision Software for Quantitative Analysis of C. elegans Swim Behavior Reveals Novel Features of Locomotion
by Christophe Restif & Carolina Ibáñez-Ventoso & Mehul M Vora & Suzhen Guo & Dimitris Metaxas & Monica Driscoll - 1-12 Modeling Higher-Order Correlations within Cortical Microcolumns
by Urs Köster & Jascha Sohl-Dickstein & Charles M Gray & Bruno A Olshausen - 1-12 Rethinking Transcriptional Activation in the Arabidopsis Circadian Clock
by Karl Fogelmark & Carl Troein - 1-12 Analysis of Graph Invariants in Functional Neocortical Circuitry Reveals Generalized Features Common to Three Areas of Sensory Cortex
by Suchin S Gururangan & Alexander J Sadovsky & Jason N MacLean - 1-13 Hydrophobin Film Structure for HFBI and HFBII and Mechanism for Accelerated Film Formation
by Aniket Magarkar & Nawel Mele & Noha Abdel-Rahman & Sarah Butcher & Mika Torkkeli & Ritva Serimaa & Arja Paananen & Markus Linder & Alex Bunker - 1-13 P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape
by Huiyong Sun & Youyong Li & Sheng Tian & Junmei Wang & Tingjun Hou - 1-14 PolyUbiquitin Chain Linkage Topology Selects the Functions from the Underlying Binding Landscape
by Yong Wang & Chun Tang & Erkang Wang & Jin Wang - 1-14 CCAST: A Model-Based Gating Strategy to Isolate Homogeneous Subpopulations in a Heterogeneous Population of Single Cells
by Benedict Anchang & Mary T Do & Xi Zhao & Sylvia K Plevritis - 1-15 On the Use of Human Mobility Proxies for Modeling Epidemics
by Michele Tizzoni & Paolo Bajardi & Adeline Decuyper & Guillaume Kon Kam King & Christian M Schneider & Vincent Blondel & Zbigniew Smoreda & Marta C González & Vittoria Colizza - 1-15 Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features
by Mahmoud Ghandi & Dongwon Lee & Morteza Mohammad-Noori & Michael A Beer - 1-15 Characterizing the Impact of Category Uncertainty on Human Auditory Categorization Behavior
by Adam M Gifford & Yale E Cohen & Alan A Stocker - 1-15 Structure-Function Discrepancy: Inhomogeneity and Delays in Synchronized Neural Networks
by Robert Ton & Gustavo Deco & Andreas Daffertshofer - 1-16 A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes
by Richard Lonsdale & Sarah L Rouse & Mark S P Sansom & Adrian J Mulholland - 1-17 Quantifying the Length and Variance of the Eukaryotic Cell Cycle Phases by a Stochastic Model and Dual Nucleoside Pulse Labelling
by Tom Serge Weber & Irene Jaehnert & Christian Schichor & Michal Or-Guil & Jorge Carneiro - 1-17 ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics
by Jan Hasenauer & Christine Hasenauer & Tim Hucho & Fabian J Theis - 1-19 Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics
by Salim Akhter Chowdhury & Stanley E Shackney & Kerstin Heselmeyer-Haddad & Thomas Ried & Alejandro A Schäffer & Russell Schwartz - 1-19 Computational Modeling and Analysis of Iron Release from Macrophages
by Alka A Potdar & Joydeep Sarkar & Nupur K Das & Paroma Ghosh & Miklos Gratzl & Paul L Fox & Gerald M Saidel - 1-25 Hotspot Mutations in KIT Receptor Differentially Modulate Its Allosterically Coupled Conformational Dynamics: Impact on Activation and Drug Sensitivity
by Isaure Chauvot de Beauchêne & Ariane Allain & Nicolas Panel & Elodie Laine & Alain Trouvé & Patrice Dubreuil & Luba Tchertanov
June 2014, Volume 10, Issue 6
- 1-3 International Society for Computational Biology Honors Dana Pe'er with Top Bioinformatics/Computational Biology Award for 2014
by Christiana N Fogg & Diane E Kovats - 1-3 A New Online Computational Biology Curriculum
by David B Searls - 1-3 Ten Simple Rules for Approaching a New Job
by Philip E Bourne - 1-7 CGBayesNets: Conditional Gaussian Bayesian Network Learning and Inference with Mixed Discrete and Continuous Data
by Michael J McGeachie & Hsun-Hsien Chang & Scott T Weiss - 1-10 Place Cell Rate Remapping by CA3 Recurrent Collaterals
by Trygve Solstad & Hosam N Yousif & Terrence J Sejnowski - 1-11 Variability of Metabolite Levels Is Linked to Differential Metabolic Pathways in Arabidopsis's Responses to Abiotic Stresses
by Nadine Töpfer & Federico Scossa & Alisdair Fernie & Zoran Nikoloski - 1-12 Negative Example Selection for Protein Function Prediction: The NoGO Database
by Noah Youngs & Duncan Penfold-Brown & Richard Bonneau & Dennis Shasha - 1-13 Unsupervised Learning of Cone Spectral Classes from Natural Images
by Noah C Benson & Jeremy R Manning & David H Brainard - 1-13 An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes
by Kevin J Liu & Jingxuan Dai & Kathy Truong & Ying Song & Michael H Kohn & Luay Nakhleh - 1-13 Historical Pedigree Reconstruction from Extant Populations Using PArtitioning of RElatives (PREPARE)
by Doron Shem-Tov & Eran Halperin - 1-13 Optimal Sampling Strategies for Detecting Zoonotic Disease Epidemics
by Jake M Ferguson & Jessica B Langebrake & Vincent L Cannataro & Andres J Garcia & Elizabeth A Hamman & Maia Martcheva & Craig W Osenberg - 1-14 AprioriGWAS, a New Pattern Mining Strategy for Detecting Genetic Variants Associated with Disease through Interaction Effects
by Qingrun Zhang & Quan Long & Jurg Ott - 1-14 Model Selection in Systems Biology Depends on Experimental Design
by Daniel Silk & Paul D W Kirk & Chris P Barnes & Tina Toni & Michael P H Stumpf - 1-14 The Effects of Theta Precession on Spatial Learning and Simplicial Complex Dynamics in a Topological Model of the Hippocampal Spatial Map
by Mamiko Arai & Vicky Brandt & Yuri Dabaghian - 1-15 A Novel Cell Traction Force Microscopy to Study Multi-Cellular System
by Xin Tang & Alireza Tofangchi & Sandeep V Anand & Taher A Saif - 1-16 Understanding the Sub-Cellular Dynamics of Silicon Transportation and Synthesis in Diatoms Using Population-Level Data and Computational Optimization
by Narjes Javaheri & Roland Dries & Jaap Kaandorp - 1-16 A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks
by Ankit Gupta & Corentin Briat & Mustafa Khammash - 1-16 Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference
by Guocai Chen & Michael J Cairelli & Halil Kilicoglu & Dongwook Shin & Thomas C Rindflesch - 1-16 The Self-Limiting Dynamics of TGF-β Signaling In Silico and In Vitro, with Negative Feedback through PPM1A Upregulation
by Junjie Wang & Lisa Tucker-Kellogg & Inn Chuan Ng & Ruirui Jia & P S Thiagarajan & Jacob K White & Hanry Yu - 1-16 A Unifying Mechanistic Model of Selective Attention in Spiking Neurons
by Bruce Bobier & Terrence C Stewart & Chris Eliasmith - 1-21 An Expanded Notch-Delta Model Exhibiting Long-Range Patterning and Incorporating MicroRNA Regulation
by Jerry S Chen & Abygail M Gumbayan & Robert W Zeller & Joseph M Mahaffy - 1-23 Identifying Crucial Parameter Correlations Maintaining Bursting Activity
by Anca Doloc-Mihu & Ronald L Calabrese - 1-23 On the Origins of Suboptimality in Human Probabilistic Inference
by Luigi Acerbi & Sethu Vijayakumar & Daniel M Wolpert
May 2014, Volume 10, Issue 5
- 1-3 Ten Simple Rules for Internship in a Pharmaceutical Company
by Bin Chen - 1-3 Paving the Way Towards a Successful and Fulfilling Career in Computational Biology
by Olugbenga Oluwagbemi & Marion Adebiyi & Segun Fatumo & Geoff Macintyre - 1-3 2014 ISCB Accomplishment by a Senior Scientist Award: Gene Myers
by Christiana N Fogg & Diane E Kovats - 1-3 Learn from the Best
by Virginie Bernard & Sebastian J Schultheiss & Magali Michaut - 1-8 Barriers to Cooperation Aid Ideological Rigidity and Threaten Societal Collapse
by Marko Jusup & Tadasu Matsuo & Yoh Iwasa - 1-8 Spatial Generalization in Operant Learning: Lessons from Professional Basketball
by Tal Neiman & Yonatan Loewenstein - 1-9 Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions
by Daphna Rothschild & Erez Dekel & Jean Hausser & Anat Bren & Guy Aidelberg & Pablo Szekely & Uri Alon - 1-9 Optimism as a Prior Belief about the Probability of Future Reward
by Aistis Stankevicius & Quentin J M Huys & Aditi Kalra & Peggy Seriès - 1-10 The Changing Geometry of a Fitness Landscape Along an Adaptive Walk
by Devin Greene & Kristina Crona - 1-11 Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?
by Drazen Petrov & Bojan Zagrovic - 1-11 Combined Role of Seizure-Induced Dendritic Morphology Alterations and Spine Loss in Newborn Granule Cells with Mossy Fiber Sprouting on the Hyperexcitability of a Computer Model of the Dentate Gyrus
by Julian Tejada & Norberto Garcia-Cairasco & Antonio C Roque - 1-12 Quantifying and Predicting the Effect of Exogenous Interleukin-7 on CD4+T Cells in HIV-1 Infection
by Rodolphe Thiébaut & Julia Drylewicz & Mélanie Prague & Christine Lacabaratz & Stéphanie Beq & Ana Jarne & Thérèse Croughs & Rafick-Pierre Sekaly & Michael M Lederman & Irini Sereti & Daniel Commenges & Yves Lévy - 1-12 Exploration of the Dynamic Properties of Protein Complexes Predicted from Spatially Constrained Protein-Protein Interaction Networks
by Eric A Yen & Aaron Tsay & Jerome Waldispuhl & Jackie Vogel - 1-13 A Computational Framework for Analyzing Stochasticity in Gene Expression
by Marc S Sherman & Barak A Cohen - 1-13 Slow Feature Analysis on Retinal Waves Leads to V1 Complex Cells
by Sven Dähne & Niko Wilbert & Laurenz Wiskott - 1-13 Modelling Negative Feedback Networks for Activating Transcription Factor 3 Predicts a Dominant Role for miRNAs in Immediate Early Gene Regulation
by Marcus J Tindall & Angela Clerk - 1-14 In-Vivo Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks
by Filippo Menolascina & Gianfranco Fiore & Emanuele Orabona & Luca De Stefano & Mike Ferry & Jeff Hasty & Mario di Bernardo & Diego di Bernardo - 1-15 A Signature of Attractor Dynamics in the CA3 Region of the Hippocampus
by César Rennó-Costa & John E Lisman & Paul F M J Verschure - 1-15 NbIT - A New Information Theory-Based Analysis of Allosteric Mechanisms Reveals Residues that Underlie Function in the Leucine Transporter LeuT
by Michael V LeVine & Harel Weinstein - 1-15 Mathematical Modeling Reveals Kinetics of Lymphocyte Recirculation in the Whole Organism
by Vitaly V Ganusov & Jeremy Auerbach - 1-15 In Silico Screening of the Key Cellular Remodeling Targets in Chronic Atrial Fibrillation
by Jussi T Koivumäki & Gunnar Seemann & Mary M Maleckar & Pasi Tavi - 1-17 Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data
by Ciira wa Maina & Antti Honkela & Filomena Matarese & Korbinian Grote & Hendrik G Stunnenberg & George Reid & Neil D Lawrence & Magnus Rattray - 1-17 Predicting the Responses of Repetitively Firing Neurons to Current Noise
by Charles J Wilson & David Barraza & Todd Troyer & Michael A Farries - 1-17 ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones
by Ignacio J General & Ying Liu & Mandy E Blackburn & Wenzhi Mao & Lila M Gierasch & Ivet Bahar - 1-21 Slow Noise in the Period of a Biological Oscillator Underlies Gradual Trends and Abrupt Transitions in Phasic Relationships in Hybrid Neural Networks
by Umeshkanta S Thounaojam & Jianxia Cui & Sharon E Norman & Robert J Butera & Carmen C Canavier - 1-22 Inferring Host Gene Subnetworks Involved in Viral Replication
by Deborah Chasman & Brandi Gancarz & Linhui Hao & Michael Ferris & Paul Ahlquist & Mark Craven - 1-25 From the Phenomenology to the Mechanisms of Consciousness: Integrated Information Theory 3.0
by Masafumi Oizumi & Larissa Albantakis & Giulio Tononi
April 2014, Volume 10, Issue 4
- 1-1 Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals
by Robert Brown & Bogdan Pasaniuc - 1-2 ISMB 2014—The Premier Conference for the World's Computational Biologists
by Christiana N Fogg & Diane E Kovats - 1-5 Ten Simple Rules for the Care and Feeding of Scientific Data
by Alyssa Goodman & Alberto Pepe & Alexander W Blocker & Christine L Borgman & Kyle Cranmer & Merce Crosas & Rosanne Di Stefano & Yolanda Gil & Paul Groth & Margaret Hedstrom & David W Hogg & Vinay Kashyap & Ashish Mahabal & Aneta Siemiginowska & Aleksandra Slavkovic - 1-6 BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
by Remco Bouckaert & Joseph Heled & Denise Kühnert & Tim Vaughan & Chieh-Hsi Wu & Dong Xie & Marc A Suchard & Andrew Rambaut & Alexei J Drummond - 1-7 rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids
by Sergio Ruiz-Carmona & Daniel Alvarez-Garcia & Nicolas Foloppe & A Beatriz Garmendia-Doval & Szilveszter Juhos & Peter Schmidtke & Xavier Barril & Roderick E Hubbard & S David Morley - 1-9 Feedback Signals in Myelodysplastic Syndromes: Increased Self-Renewal of the Malignant Clone Suppresses Normal Hematopoiesis
by Thomas Walenda & Thomas Stiehl & Hanna Braun & Julia Fröbel & Anthony D Ho & Thomas Schroeder & Tamme W Goecke & Björn Rath & Ulrich Germing & Anna Marciniak-Czochra & Wolfgang Wagner - 1-10 Active Learning to Understand Infectious Disease Models and Improve Policy Making
by Lander Willem & Sean Stijven & Ekaterina Vladislavleva & Jan Broeckhove & Philippe Beutels & Niel Hens - 1-11 Phylogenetic Quantification of Intra-tumour Heterogeneity
by Roland F Schwarz & Anne Trinh & Botond Sipos & James D Brenton & Nick Goldman & Florian Markowetz - 1-11 The Evolution of Multivariate Maternal Effects
by Bram Kuijper & Rufus A Johnstone & Stuart Townley - 1-11 Computational Prediction of Alanine Scanning and Ligand Binding Energetics in G-Protein Coupled Receptors
by Lars Boukharta & Hugo Gutiérrez-de-Terán & Johan Åqvist - 1-11 A Toolbox for Representational Similarity Analysis
by Hamed Nili & Cai Wingfield & Alexander Walther & Li Su & William Marslen-Wilson & Nikolaus Kriegeskorte - 1-12 Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
by Paul J McMurdie & Susan Holmes - 1-12 Prediction and Prioritization of Rare Oncogenic Mutations in the Cancer Kinome Using Novel Features and Multiple Classifiers
by ManChon U & Eric Talevich & Samiksha Katiyar & Khaled Rasheed & Natarajan Kannan - 1-13 Agent-Based Modeling of Oxygen-Responsive Transcription Factors in Escherichia coli
by Hao Bai & Matthew D Rolfe & Wenjing Jia & Simon Coakley & Robert K Poole & Jeffrey Green & Mike Holcombe - 1-13 Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin
by Qing-Miao Nie & Akio Togashi & Takeshi N Sasaki & Mitsunori Takano & Masaki Sasai & Tomoki P Terada - 1-14 Optimal Schedules of Light Exposure for Rapidly Correcting Circadian Misalignment
by Kirill Serkh & Daniel B Forger - 1-15 Comparison of Filtering Methods for the Modeling and Retrospective Forecasting of Influenza Epidemics
by Wan Yang & Alicia Karspeck & Jeffrey Shaman - 1-15 Multiple Model-Informed Open-Loop Control of Uncertain Intracellular Signaling Dynamics
by Jeffrey P Perley & Judith Mikolajczak & Marietta L Harrison & Gregery T Buzzard & Ann E Rundell - 1-16 Bayesian Analysis for Inference of an Emerging Epidemic: Citrus Canker in Urban Landscapes
by Franco M Neri & Alex R Cook & Gavin J Gibson & Tim R Gottwald & Christopher A Gilligan - 1-16 Evolutionary Game Dynamics in Populations with Heterogenous Structures
by Wes Maciejewski & Feng Fu & Christoph Hauert - 1-16 Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method
by Ke Tang & Jinfeng Zhang & Jie Liang - 1-16 Phylodynamic Inference for Structured Epidemiological Models
by David A Rasmussen & Erik M Volz & Katia Koelle - 1-16 Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems
by Justin S Hogg & Leonard A Harris & Lori J Stover & Niketh S Nair & James R Faeder - 1-17 Mechanisms of Zero-Lag Synchronization in Cortical Motifs
by Leonardo L Gollo & Claudio Mirasso & Olaf Sporns & Michael Breakspear - 1-18 Continuous Attractor Network Model for Conjunctive Position-by-Velocity Tuning of Grid Cells
by Bailu Si & Sandro Romani & Misha Tsodyks - 1-21 Glutamate-Bound NMDARs Arising from In Vivo-like Network Activity Extend Spatio-temporal Integration in a L5 Cortical Pyramidal Cell Model
by Matteo Farinella & Daniel T Ruedt & Padraig Gleeson & Frederic Lanore & R Angus Silver - 1-24 Influence of Wiring Cost on the Large-Scale Architecture of Human Cortical Connectivity
by David Samu & Anil K Seth & Thomas Nowotny
March 2014, Volume 10, Issue 3
- 1-3 Crossing Borders for Science
by Sebastian J Schultheiss & Joshua SungWoo Yang & Wataru Iwasaki & Shu-Hsi Lin & Angela Jean & Magali Michaut - 1-3 Ten Simple Rules for Effective Computational Research
by James M Osborne & Miguel O Bernabeu & Maria Bruna & Ben Calderhead & Jonathan Cooper & Neil Dalchau & Sara-Jane Dunn & Alexander G Fletcher & Robin Freeman & Derek Groen & Bernhard Knapp & Greg J McInerny & Gary R Mirams & Joe Pitt-Francis & Biswa Sengupta & David W Wright & Christian A Yates & David J Gavaghan & Stephen Emmott & Charlotte Deane - 1-4 If You Can't Measure It, You Can't Manage It
by Jean Peccoud - 1-9 Relating Structure and Function in the Human Brain: Relative Contributions of Anatomy, Stationary Dynamics, and Non-stationarities
by Arnaud Messé & David Rudrauf & Habib Benali & Guillaume Marrelec - 1-9 Correction of Distortion in Flattened Representations of the Cortical Surface Allows Prediction of V1-V3 Functional Organization from Anatomy
by Noah C Benson & Omar H Butt & David H Brainard & Geoffrey K Aguirre - 1-10 Probabilistic Approach to Predicting Substrate Specificity of Methyltransferases
by Teresa Szczepińska & Jan Kutner & Michał Kopczyński & Krzysztof Pawłowski & Andrzej Dziembowski & Andrzej Kudlicki & Krzysztof Ginalski & Maga Rowicka - 1-10 Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies
by Lonnie Welch & Fran Lewitter & Russell Schwartz & Cath Brooksbank & Predrag Radivojac & Bruno Gaeta & Maria Victoria Schneider - 1-11 Slowness and Sparseness Have Diverging Effects on Complex Cell Learning
by Jörn-Philipp Lies & Ralf M Häfner & Matthias Bethge - 1-11 Universal Count Correction for High-Throughput Sequencing
by Tatsunori B Hashimoto & Matthew D Edwards & David K Gifford - 1-12 MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
by Jianzhu Ma & Sheng Wang & Zhiyong Wang & Jinbo Xu - 1-12 Modeling Mutual Exclusivity of Cancer Mutations
by Ewa Szczurek & Niko Beerenwinkel - 1-13 Global Quantitative Modeling of Chromatin Factor Interactions
by Jian Zhou & Olga G Troyanskaya - 1-13 Comprehensive Analyses of Ventricular Myocyte Models Identify Targets Exhibiting Favorable Rate Dependence
by Megan A Cummins & Pavan J Dalal & Marco Bugana & Stefano Severi & Eric A Sobie - 1-13 Behavioral Lateralization and Optimal Route Choice in Flying Budgerigars
by Partha S Bhagavatula & Charles Claudianos & Michael R Ibbotson & Mandyam V Srinivasan - 1-14 Identification of New IκBα Complexes by an Iterative Experimental and Mathematical Modeling Approach
by Fabian Konrath & Johannes Witt & Thomas Sauter & Dagmar Kulms - 1-14 An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding
by Shaun Mahony & Matthew D Edwards & Esteban O Mazzoni & Richard I Sherwood & Akshay Kakumanu & Carolyn A Morrison & Hynek Wichterle & David K Gifford - 1-14 Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating
by Ramya Gamini & Wei Han & John E Stone & Klaus Schulten - 1-14 Neuronal Spike Timing Adaptation Described with a Fractional Leaky Integrate-and-Fire Model
by Wondimu Teka & Toma M Marinov & Fidel Santamaria - 1-16 Computational Analyses of Synergism in Small Molecular Network Motifs
by Yili Zhang & Paul Smolen & Douglas A Baxter & John H Byrne - 1-16 Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems
by Samanthe M Lyons & Wenlong Xu & June Medford & Ashok Prasad - 1-17 Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins
by Lit-Hsin Loo & Danai Laksameethanasan & Yi-Ling Tung - 1-18 Spatio-Temporal Simulation of First Pass Drug Perfusion in the Liver
by Lars Ole Schwen & Markus Krauss & Christoph Niederalt & Felix Gremse & Fabian Kiessling & Andrea Schenk & Tobias Preusser & Lars Kuepfer - 1-18 Model-Based Analysis for Qualitative Data: An Application in Drosophila Germline Stem Cell Regulation
by Michael Pargett & Ann E Rundell & Gregery T Buzzard & David M Umulis - 1-19 Dynamic Alignment Models for Neural Coding
by Sepp Kollmorgen & Richard H R Hahnloser - 1-19 Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains
by Vladimir Kazeev & Mustafa Khammash & Michael Nip & Christoph Schwab - 1-20 Spatiotemporal Computations of an Excitable and Plastic Brain: Neuronal Plasticity Leads to Noise-Robust and Noise-Constructive Computations
by Hazem Toutounji & Gordon Pipa - 1-22 STDP Installs in Winner-Take-All Circuits an Online Approximation to Hidden Markov Model Learning
by David Kappel & Bernhard Nessler & Wolfgang Maass - 1-26 An In-Silico Model of Lipoprotein Metabolism and Kinetics for the Evaluation of Targets and Biomarkers in the Reverse Cholesterol Transport Pathway
by James Lu & Katrin Hübner & M Nazeem Nanjee & Eliot A Brinton & Norman A Mazer
February 2014, Volume 10, Issue 2
- 1-3 Workshops: A Great Way to Enhance and Supplement a Degree
by Segun Fatumo & Sayane Shome & Geoff Macintyre - 1-9 Combining Experiments and Simulations Using the Maximum Entropy Principle
by Wouter Boomsma & Jesper Ferkinghoff-Borg & Kresten Lindorff-Larsen - 1-10 Mathematical Modeling of the Phoenix Rising Pathway
by Chad Liu & Chuan-Yuan Li & Fan Yuan - 1-10 Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations
by James C Gumbart & Morgan Beeby & Grant J Jensen & Benoît Roux - 1-11 GAGA: A New Algorithm for Genomic Inference of Geographic Ancestry Reveals Fine Level Population Substructure in Europeans
by Oscar Lao & Fan Liu & Andreas Wollstein & Manfred Kayser - 1-12 A Combination of Transcriptional and MicroRNA Regulation Improves the Stability of the Relative Concentrations of Target Genes
by Andrea Riba & Carla Bosia & Mariama El Baroudi & Laura Ollino & Michele Caselle - 1-12 A Unified View of “How Allostery Works”
by Chung-Jung Tsai & Ruth Nussinov - 1-12 Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species
by Esa Pitkänen & Paula Jouhten & Jian Hou & Muhammad Fahad Syed & Peter Blomberg & Jana Kludas & Merja Oja & Liisa Holm & Merja Penttilä & Juho Rousu & Mikko Arvas - 1-12 Compact Modeling of Allosteric Multisite Proteins: Application to a Cell Size Checkpoint
by Germán Enciso & Douglas R Kellogg & Arturo Vargas - 1-13 In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics
by Pascal Carrivain & Maria Barbi & Jean-Marc Victor - 1-14 Overexpression of Heat Shock Protein 72 Attenuates NF-κB Activation Using a Combination of Regulatory Mechanisms in Microglia
by Patrick W Sheppard & Xiaoyun Sun & Mustafa Khammash & Rona G Giffard - 1-14 A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses
by Frederick A Matsen IV & Christopher T Small & Khanh Soliven & Gregory A Engel & Mostafa M Feeroz & Xiaoxing Wang & Karen L Craig & M Kamrul Hasan & Michael Emerman & Maxine L Linial & Lisa Jones-Engel - 1-15 A Virtual Infection Model Quantifies Innate Effector Mechanisms and Candida albicans Immune Escape in Human Blood
by Kerstin Hünniger & Teresa Lehnert & Kristin Bieber & Ronny Martin & Marc Thilo Figge & Oliver Kurzai - 1-18 Modelling Individual Differences in the Form of Pavlovian Conditioned Approach Responses: A Dual Learning Systems Approach with Factored Representations
by Florian Lesaint & Olivier Sigaud & Shelly B Flagel & Terry E Robinson & Mehdi Khamassi - 1-20 A Unified Model of Heading and Path Perception in Primate MSTd
by Oliver W Layton & N Andrew Browning - 1-20 Learning Gene Networks under SNP Perturbations Using eQTL Datasets
by Lingxue Zhang & Seyoung Kim - 1-22 The Sign Rule and Beyond: Boundary Effects, Flexibility, and Noise Correlations in Neural Population Codes
by Yu Hu & Joel Zylberberg & Eric Shea-Brown - 1-23 A Network Characteristic That Correlates Environmental and Genetic Robustness
by Zeina Shreif & Vipul Periwal
January 2014, Volume 10, Issue 1
- 1-2 The Making of the Women in Biology Forum (WiB) at Bioclues
by Reeta Rani Singhania & Dhatri Madduru & Pranathi Pappu & Sameera Panchangam & Renuka Suravajhala & Mohanalatha Chandrasekharan - 1-3 Ten Simple Rules for Writing Research Papers
by Weixiong Zhang - 1-6 Bioinformatics Projects Supporting Life-Sciences Learning in High Schools
by Isabel Marques & Paulo Almeida & Renato Alves & Maria João Dias & Ana Godinho & José B Pereira-Leal - 1-8 Machine Learning Estimates of Natural Product Conformational Energies
by Matthias Rupp & Matthias R Bauer & Rainer Wilcken & Andreas Lange & Michael Reutlinger & Frank M Boeckler & Gisbert Schneider - 1-9 Current Practice in Software Development for Computational Neuroscience and How to Improve It
by Marc-Oliver Gewaltig & Robert Cannon - 1-9 Leadership and Path Characteristics during Walks Are Linked to Dominance Order and Individual Traits in Dogs
by Zsuzsa Ákos & Róbert Beck & Máté Nagy & Tamás Vicsek & Enikő Kubinyi - 1-10 Fast Reconstruction of Compact Context-Specific Metabolic Network Models
by Nikos Vlassis & Maria Pires Pacheco & Thomas Sauter - 1-11 Optimal Screening Strategies for Healthcare Associated Infections in a Multi-Institutional Setting
by Aaron C Miller & Linnea A Polgreen & Philip M Polgreen - 1-11 PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations
by Jaroslav Bendl & Jan Stourac & Ondrej Salanda & Antonin Pavelka & Eric D Wieben & Jaroslav Zendulka & Jan Brezovsky & Jiri Damborsky - 1-12 Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures
by Yi-Fei Huang & G Brian Golding - 1-13 Competition for Antigen between Th1 and Th2 Responses Determines the Timing of the Immune Response Switch during Mycobaterium avium Subspecies paratuberulosis Infection in Ruminants
by Gesham Magombedze & Shigetoshi Eda & Vitaly V Ganusov - 1-13 Stress and Strain Provide Positional and Directional Cues in Development
by Behruz Bozorg & Pawel Krupinski & Henrik Jönsson - 1-13 Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks
by Axel von Kamp & Steffen Klamt - 1-13 The Role of Thalamic Population Synchrony in the Emergence of Cortical Feature Selectivity
by Sean T Kelly & Jens Kremkow & Jianzhong Jin & Yushi Wang & Qi Wang & Jose-Manuel Alonso & Garrett B Stanley - 1-14 Population Decoding in Rat Barrel Cortex: Optimizing the Linear Readout of Correlated Population Responses
by Mehdi Adibi & James S McDonald & Colin W G Clifford & Ehsan Arabzadeh - 1-15 Intrinsic Noise Induces Critical Behavior in Leaky Markovian Networks Leading to Avalanching
by Garrett Jenkinson & John Goutsias - 1-16 Linkage of Viral Sequences among HIV-Infected Village Residents in Botswana: Estimation of Linkage Rates in the Presence of Missing Data
by Nicole Bohme Carnegie & Rui Wang & Vladimir Novitsky & Victor De Gruttola - 1-16 Task-Specific Response Strategy Selection on the Basis of Recent Training Experience
by Jacqueline M Fulvio & C Shawn Green & Paul R Schrater - 1-16 VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data
by Jean Daunizeau & Vincent Adam & Lionel Rigoux - 1-17 Environmental Influence on the Evolution of Morphological Complexity in Machines
by Joshua E Auerbach & Josh C Bongard - 1-18 Consequences of Converting Graded to Action Potentials upon Neural Information Coding and Energy Efficiency
by Biswa Sengupta & Simon Barry Laughlin & Jeremy Edward Niven - 1-18 De Novo Prediction of PTBP1 Binding and Splicing Targets Reveals Unexpected Features of Its RNA Recognition and Function
by Areum Han & Peter Stoilov & Anthony J Linares & Yu Zhou & Xiang-Dong Fu & Douglas L Black - 1-20 Coarse-Grained Molecular Simulation of Epidermal Growth Factor Receptor Protein Tyrosine Kinase Multi-Site Self-Phosphorylation
by John G Koland - 1-20 Interference and Shaping in Sensorimotor Adaptations with Rewards
by Ran Darshan & Arthur Leblois & David Hansel - 1-21 The Correlation Structure of Local Neuronal Networks Intrinsically Results from Recurrent Dynamics
by Moritz Helias & Tom Tetzlaff & Markus Diesmann - 1-23 Searching for Collective Behavior in a Large Network of Sensory Neurons
by Gašper Tkačik & Olivier Marre & Dario Amodei & Elad Schneidman & William Bialek & Michael J Berry II
December 2013, Volume 9, Issue 12
- 1-2 Education in Computational Biology Today and Tomorrow
by Joanne A Fox & B F Francis Ouellette - 1-7 Extrapolating Weak Selection in Evolutionary Games
by Bin Wu & Julián García & Christoph Hauert & Arne Traulsen - 1-9 A Network Inference Method for Large-Scale Unsupervised Identification of Novel Drug-Drug Interactions
by Roger Guimerà & Marta Sales-Pardo - 1-10 Epidemic Spread on Weighted Networks
by Christel Kamp & Mathieu Moslonka-Lefebvre & Samuel Alizon - 1-10 Flow Cytometry Bioinformatics
by Kieran O'Neill & Nima Aghaeepour & Josef Špidlen & Ryan Brinkman - 1-10 A Latent Markov Modelling Approach to the Evaluation of Circulating Cathodic Antigen Strips for Schistosomiasis Diagnosis Pre- and Post-Praziquantel Treatment in Uganda
by Artemis Koukounari & Christl A Donnelly & Irini Moustaki & Edridah M Tukahebwa & Narcis B Kabatereine & Shona Wilson & Joanne P Webster & André M Deelder & Birgitte J Vennervald & Govert J van Dam - 1-10 Sharpness of Spike Initiation in Neurons Explained by Compartmentalization
by Romain Brette - 1-13 Utilizing a Dynamical Description of IspH to Aid in the Development of Novel Antimicrobial Drugs
by Patrick G Blachly & César A F de Oliveira & Sarah L Williams & J Andrew McCammon - 1-13 Inferring the Source of Transmission with Phylogenetic Data
by Erik M Volz & Simon D W Frost - 1-14 Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei
by Eduard J Kerkhoven & Fiona Achcar & Vincent P Alibu & Richard J Burchmore & Ian H Gilbert & Maciej Trybiło & Nicole N Driessen & David Gilbert & Rainer Breitling & Barbara M Bakker & Michael P Barrett - 1-14 Actions, Action Sequences and Habits: Evidence That Goal-Directed and Habitual Action Control Are Hierarchically Organized
by Amir Dezfouli & Bernard W Balleine - 1-15 A Sequential Vesicle Pool Model with a Single Release Sensor and a Ca2+-Dependent Priming Catalyst Effectively Explains Ca2+-Dependent Properties of Neurosecretion
by Alexander M Walter & Paulo S Pinheiro & Matthijs Verhage & Jakob B Sørensen - 1-16 Heterogeneity, Mixing, and the Spatial Scales of Mosquito-Borne Pathogen Transmission
by T Alex Perkins & Thomas W Scott & Arnaud Le Menach & David L Smith - 1-18 Modeling the Afferent Dynamics of the Baroreflex Control System
by Adam Mahdi & Jacob Sturdy & Johnny T Ottesen & Mette S Olufsen - 1-18 Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information
by Anne Lopes & Sophie Sacquin-Mora & Viktoriya Dimitrova & Elodie Laine & Yann Ponty & Alessandra Carbone - 1-22 Forward and Backward Inference in Spatial Cognition
by Will D Penny & Peter Zeidman & Neil Burgess - 1-23 Perturbation Biology: Inferring Signaling Networks in Cellular Systems
by Evan J Molinelli & Anil Korkut & Weiqing Wang & Martin L Miller & Nicholas P Gauthier & Xiaohong Jing & Poorvi Kaushik & Qin He & Gordon Mills & David B Solit & Christine A Pratilas & Martin Weigt & Alfredo Braunstein & Andrea Pagnani & Riccardo Zecchina & Chris Sander
November 2013, Volume 9, Issue 11
- 1-2 Learning How to Run a Lab: Interviews with Principal Investigators
by Theodore Alexandrov & Philip E Bourne - 1-3 Breaking the Ice and Forging Links: The Importance of Socializing in Research
by Miranda Stobbe & Tarun Mishra & Geoff Macintyre - 1-3 About Dice, Bouldering, and Team Empowerment: Running the CompOmics Group at VIB and Ghent University, Belgium
by Lennart Martens - 1-3 Leading a Statistical Bioinformatics Lab: It's All About Finding Balance
by Olga Vitek - 1-4 Ten Simple Rules for Starting a Regional Student Group
by Avinash Kumar Shanmugam & Geoff Macintyre & Magali Michaut & Thomas Abeel - 1-4 The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013
by Jeroen de Ridder & Yana Bromberg & Magali Michaut & Venkata P Satagopam & Manuel Corpas & Geoff Macintyre & Theodore Alexandrov - 1-6 Communication and Common Interest
by Peter Godfrey-Smith & Manolo Martínez - 1-7 Auditory Frequency and Intensity Discrimination Explained Using a Cortical Population Rate Code
by Christophe Micheyl & Paul R Schrater & Andrew J Oxenham - 1-8 Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
by Timothy Bailey & Pawel Krajewski & Istvan Ladunga & Celine Lefebvre & Qunhua Li & Tao Liu & Pedro Madrigal & Cenny Taslim & Jie Zhang - 1-8 A Tunable Coarse-Grained Model for Ligand-Receptor Interaction
by Teresa Ruiz-Herrero & Javier Estrada & Raúl Guantes & David G Miguez