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October 2014, Volume 10, Issue 10
- 1-27 Ensembles of Spiking Neurons with Noise Support Optimal Probabilistic Inference in a Dynamically Changing Environment
by Robert Legenstein & Wolfgang Maass
September 2014, Volume 10, Issue 9
- 1-7 The Time Scale of Evolutionary Innovation
by Krishnendu Chatterjee & Andreas Pavlogiannis & Ben Adlam & Martin A Nowak - 1-9 Multi-state Modeling of Biomolecules
by Melanie I Stefan & Thomas M Bartol & Terrence J Sejnowski & Mary B Kennedy - 1-10 Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis
by Hong Yang & Elias W Krumholz & Evan D Brutinel & Nagendra P Palani & Michael J Sadowsky & Andrew M Odlyzko & Jeffrey A Gralnick & Igor G L Libourel - 1-10 IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform
by N Lance Hepler & Konrad Scheffler & Steven Weaver & Ben Murrell & Douglas D Richman & Dennis R Burton & Pascal Poignard & Davey M Smith & Sergei L Kosakovsky Pond - 1-11 A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing
by Yun-Ching Chen & Christopher Douville & Cheng Wang & Noushin Niknafs & Grace Yeo & Violeta Beleva-Guthrie & Hannah Carter & Peter D Stenson & David N Cooper & Biao Li & Sean Mooney & Rachel Karchin - 1-11 NESmapper: Accurate Prediction of Leucine-Rich Nuclear Export Signals Using Activity-Based Profiles
by Shunichi Kosugi & Hiroshi Yanagawa & Ryohei Terauchi & Satoshi Tabata - 1-12 Environmental Statistics and Optimal Regulation
by David A Sivak & Matt Thomson - 1-13 Pupil-Linked Arousal Determines Variability in Perceptual Decision Making
by Peter R Murphy & Joachim Vandekerckhove & Sander Nieuwenhuis - 1-14 Principal Component Analysis Characterizes Shared Pathogenetics from Genome-Wide Association Studies
by Diana Chang & Alon Keinan - 1-15 eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models
by Michal Brylinski - 1-16 Determining Individual Variation in Growth and Its Implication for Life-History and Population Processes Using the Empirical Bayes Method
by Simone Vincenzi & Marc Mangel & Alain J Crivelli & Stephan Munch & Hans J Skaug - 1-17 Quantifying the Impact and Extent of Undocumented Biomedical Synonymy
by David R Blair & Kanix Wang & Svetlozar Nestorov & James A Evans & Andrey Rzhetsky - 1-19 Inferring on the Intentions of Others by Hierarchical Bayesian Learning
by Andreea O Diaconescu & Christoph Mathys & Lilian A E Weber & Jean Daunizeau & Lars Kasper & Ekaterina I Lomakina & Ernst Fehr & Klaas E Stephan
August 2014, Volume 10, Issue 8
- 1-3 The Upside of Failure: How Regional Student Groups Learn from Their Mistakes
by Tarun Mishra & R Gonzalo Parra & Thomas Abeel - 1-9 Unveiling Time in Dose-Response Models to Infer Host Susceptibility to Pathogens
by Delphine Pessoa & Caetano Souto-Maior & Erida Gjini & Joao S Lopes & Bruno Ceña & Cláudia T Codeço & M Gabriela M Gomes - 1-10 Phenotypic Signatures Arising from Unbalanced Bacterial Growth
by Cheemeng Tan & Robert Phillip Smith & Ming-Chi Tsai & Russell Schwartz & Lingchong You - 1-11 Sparsity and Compressed Coding in Sensory Systems
by Victor J Barranca & Gregor Kovačič & Douglas Zhou & David Cai - 1-11 Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism
by Rui Xia & Selina Vattathil & Paul Scheet - 1-11 Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis
by Shuo Gu & Daniel-Adriano Silva & Luming Meng & Alexander Yue & Xuhui Huang - 1-12 OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis
by Greg Finak & Jacob Frelinger & Wenxin Jiang & Evan W Newell & John Ramey & Mark M Davis & Spyros A Kalams & Stephen C De Rosa & Raphael Gottardo - 1-12 Unsupervised Feature Learning Improves Prediction of Human Brain Activity in Response to Natural Images
by Umut Güçlü & Marcel A J van Gerven - 1-13 Modeling Viral Evolutionary Dynamics after Telaprevir-Based Treatment
by Eric L Haseltine & Sandra De Meyer & Inge Dierynck & Doug J Bartels & Anne Ghys & Andrew Davis & Eileen Z Zhang & Ann M Tigges & Joan Spanks & Gaston Picchio & Tara L Kieffer & James C Sullivan - 1-14 Cost-Effective Control of Plant Disease When Epidemiological Knowledge Is Incomplete: Modelling Bahia Bark Scaling of Citrus
by Nik J Cunniffe & Francisco F Laranjeira & Franco M Neri & R Erik DeSimone & Christopher A Gilligan - 1-14 Mechanical Cell-Matrix Feedback Explains Pairwise and Collective Endothelial Cell Behavior In Vitro
by René F M van Oers & Elisabeth G Rens & Danielle J LaValley & Cynthia A Reinhart-King & Roeland M H Merks - 1-14 Logarithmic and Power Law Input-Output Relations in Sensory Systems with Fold-Change Detection
by Miri Adler & Avi Mayo & Uri Alon - 1-15 A Deterministic Model Predicts the Properties of Stochastic Calcium Oscillations in Airway Smooth Muscle Cells
by Pengxing Cao & Xiahui Tan & Graham Donovan & Michael J Sanderson & James Sneyd - 1-15 Memory Capacity of Networks with Stochastic Binary Synapses
by Alexis M Dubreuil & Yali Amit & Nicolas Brunel - 1-15 Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes
by Anne-Florence Bitbol & David J Schwab - 1-16 A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data
by Yuan Zhang & Yanni Sun & James R Cole - 1-16 Random Migration and Signal Integration Promote Rapid and Robust T Cell Recruitment
by Johannes Textor & Sarah E Henrickson & Judith N Mandl & Ulrich H von Andrian & Jürgen Westermann & Rob J de Boer & Joost B Beltman - 1-19 Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque
by Fang-Chieh Chou & Jan Lipfert & Rhiju Das - 1-19 Classical Mathematical Models for Description and Prediction of Experimental Tumor Growth
by Sébastien Benzekry & Clare Lamont & Afshin Beheshti & Amanda Tracz & John M L Ebos & Lynn Hlatky & Philip Hahnfeldt
July 2014, Volume 10, Issue 7
- 1-2 Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication"
by Wei-Hua Chen & Xing-Ming Zhao & Vera van Noort & Peer Bork - 1-3 Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities
by Jeroen de Ridder & Pieter Meysman & Olugbenga Oluwagbemi & Thomas Abeel - 1-7 Correlated Inter-Domain Motions in Adenylate Kinase
by Santiago Esteban-Martín & Robert Bryn Fenwick & Jörgen Ådén & Benjamin Cossins & Carlos W Bertoncini & Victor Guallar & Magnus Wolf-Watz & Xavier Salvatella - 1-8 Brain and Behavior in Decision-Making
by Peter Cassey & Andrew Heathcote & Scott D Brown - 1-10 A Likelihood-Based Approach to Identifying Contaminated Food Products Using Sales Data: Performance and Challenges
by James Kaufman & Justin Lessler & April Harry & Stefan Edlund & Kun Hu & Judith Douglas & Christian Thoens & Bernd Appel & Annemarie Käsbohrer & Matthias Filter - 1-10 Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells
by Andrew McDavid & Lucas Dennis & Patrick Danaher & Greg Finak & Michael Krouse & Alice Wang & Philippa Webster & Joseph Beechem & Raphael Gottardo - 1-11 Stability Curve Prediction of Homologous Proteins Using Temperature-Dependent Statistical Potentials
by Fabrizio Pucci & Marianne Rooman - 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 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 - 1-14 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 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 - 1-17 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 - 1-25 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 - 1-14 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 - 1-21 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 - 1-12 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 Mathematical Modeling Reveals Kinetics of Lymphocyte Recirculation in the Whole Organism
by Vitaly V Ganusov & Jeremy Auerbach - 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
- 1-2 ISMB 2014—The Premier Conference for the World's Computational Biologists
by Christiana N Fogg & Diane E Kovats - 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 - 1-11 The Evolution of Multivariate Maternal Effects
by Bram Kuijper & Rufus A Johnstone & Stuart Townley - 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 - 1-13 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 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 - 1-18 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 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 - 1-10 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 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 - 1-16 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 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 - 1-22 STDP Installs in Winner-Take-All Circuits an Online Approximation to Hidden Markov Model Learning
by David Kappel & Bernhard Nessler & Wolfgang Maass
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 - 1-11 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 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 - 1-20 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
- 1-3 Ten Simple Rules for Writing Research Papers
by Weixiong Zhang - 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 - 1-10 Fast Reconstruction of Compact Context-Specific Metabolic Network Models
by Nikos Vlassis & Maria Pires Pacheco & Thomas Sauter - 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 - 1-15 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 - 1-18 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 - 1-21 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
- 1-7 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 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 - 1-13 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 - 1-14 Actions, Action Sequences and Habits: Evidence That Goal-Directed and Habitual Action Control Are Hierarchically Organized
by Amir Dezfouli & Bernard W Balleine - 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 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 - 1-4 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 - 1-9 Prediction of Drug-Target Interactions for Drug Repositioning Only Based on Genomic Expression Similarity
by Kejian Wang & Jiazhi Sun & Shufeng Zhou & Chunling Wan & Shengying Qin & Can Li & Lin He & Lun Yang - 1-9 Beyond GLMs: A Generative Mixture Modeling Approach to Neural System Identification
by Lucas Theis & Andrè Maia Chagas & Daniel Arnstein & Cornelius Schwarz & Matthias Bethge - 1-10 Distribution of the Fittest Individuals and the Rate of Muller's Ratchet in a Model with Overlapping Generations
by Jakob J Metzger & Stephan Eule - 1-11 Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data
by Weronika Sikora-Wohlfeld & Marit Ackermann & Eleni G Christodoulou & Kalaimathy Singaravelu & Andreas Beyer - 1-13 Mapping the Structural and Dynamical Features of Kinesin Motor Domains
by Guido Scarabelli & Barry J Grant - 1-13 A Data-Driven Mathematical Model of CA-MRSA Transmission among Age Groups: Evaluating the Effect of Control Interventions
by Xiaoxia Wang & Sarada Panchanathan & Gerardo Chowell - 1-14 A Neurocomputational Model of the Mismatch Negativity
by Falk Lieder & Klaas E Stephan & Jean Daunizeau & Marta I Garrido & Karl J Friston - 1-14 Average Is Optimal: An Inverted-U Relationship between Trial-to-Trial Brain Activity and Behavioral Performance
by Biyu J He & John M Zempel - 1-15 Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos
by Julian E Fuchs & Susanne von Grafenstein & Roland G Huber & Christian Kramer & Klaus R Liedl - 1-15 Optimality Conditions for Cell-Fate Heterogeneity That Maximize the Effects of Growth Factors in PC12 Cells
by Kazunari Mouri & Yasushi Sako - 1-16 Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks
by Takeshi Hase & Samik Ghosh & Ryota Yamanaka & Hiroaki Kitano - 1-16 Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data
by Ridvan Eksi & Hong-Dong Li & Rajasree Menon & Yuchen Wen & Gilbert S Omenn & Matthias Kretzler & Yuanfang Guan - 1-17 Comparing Algorithms That Reconstruct Cell Lineage Trees Utilizing Information on Microsatellite Mutations
by Noa Chapal-Ilani & Yosef E Maruvka & Adam Spiro & Yitzhak Reizel & Rivka Adar & Liran I Shlush & Ehud Shapiro - 1-18 Dread and the Disvalue of Future Pain
by Giles W Story & Ivaylo Vlaev & Ben Seymour & Joel S Winston & Ara Darzi & Raymond J Dolan - 1-28 Stochastic Computations in Cortical Microcircuit Models
by Stefan Habenschuss & Zeno Jonke & Wolfgang Maass
October 2013, Volume 9, Issue 10
- 1-3 Explain Bioinformatics to Your Grandmother!
by Virginie Bernard & Magali Michaut - 1-3 APBioNet—Transforming Bioinformatics in the Asia-Pacific Region
by Asif M Khan & Tin Wee Tan & Christian Schönbach & Shoba Ranganathan - 1-9 Molecular Mechanical Differences between Isoforms of Contractile Actin in the Presence of Isoforms of Smooth Muscle Tropomyosin
by Lennart Hilbert & Genevieve Bates & Horia N Roman & Jenna L Blumenthal & Nedjma B Zitouni & Apolinary Sobieszek & Michael C Mackey & Anne-Marie Lauzon - 1-10 ToPS: A Framework to Manipulate Probabilistic Models of Sequence Data
by André Yoshiaki Kashiwabara & Ígor Bonadio & Vitor Onuchic & Felipe Amado & Rafael Mathias & Alan Mitchell Durham - 1-10 Feature Selection Methods for Identifying Genetic Determinants of Host Species in RNA Viruses
by Ricardo Aguas & Neil M Ferguson - 1-10 Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening
by Arnab Bhattacherjee & Stefan Wallin - 1-11 A Complex-Valued Firing-Rate Model That Approximates the Dynamics of Spiking Networks
by Evan S Schaffer & Srdjan Ostojic & L F Abbott