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November 2014, Volume 10, Issue 11
- 1-16 Global Disease Monitoring and Forecasting with Wikipedia
by Nicholas Generous & Geoffrey Fairchild & Alina Deshpande & Sara Y Del Valle & Reid Priedhorsky
October 2014, Volume 10, Issue 10
- 1-6 FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units
by Gang Peng & Yu Fan & Wenyi Wang - 1-10 Confidence Sharing: An Economic Strategy for Efficient Information Flows in Animal Groups
by Amos Korman & Efrat Greenwald & Ofer Feinerman - 1-14 Predicting Chemical Environments of Bacteria from Receptor Signaling
by Diana Clausznitzer & Gabriele Micali & Silke Neumann & Victor Sourjik & Robert G Endres - 1-17 Synaptic Size Dynamics as an Effectively Stochastic Process
by Adiel Statman & Maya Kaufman & Amir Minerbi & Noam E Ziv & Naama Brenner - 1-17 Deducing the Kinetics of Protein Synthesis In Vivo from the Transition Rates Measured In Vitro
by Sophia Rudorf & Michael Thommen & Marina V Rodnina & Reinhard Lipowsky - 1-19 Tracking the Sleep Onset Process: An Empirical Model of Behavioral and Physiological Dynamics
by Michael J Prerau & Katie E Hartnack & Gabriel Obregon-Henao & Aaron Sampson & Margaret Merlino & Karen Gannon & Matt T Bianchi & Jeffrey M Ellenbogen & Patrick L Purdon - 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 - 1-11 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 - 1-12 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 - 1-15 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
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 - 1-11 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 - 1-14 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 - 1-19 Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque
by Fang-Chieh Chou & Jan Lipfert & Rhiju Das
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 - 1-12 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 - 1-14 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 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
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 - 1-12 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 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 - 1-15 A Novel Cell Traction Force Microscopy to Study Multi-Cellular System
by Xin Tang & Alireza Tofangchi & Sandeep V Anand & Taher A Saif - 1-16 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
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 - 1-17 Predicting the Responses of Repetitively Firing Neurons to Current Noise
by Charles J Wilson & David Barraza & Todd Troyer & Michael A Farries - 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 - 1-11 The Evolution of Multivariate Maternal Effects
by Bram Kuijper & Rufus A Johnstone & Stuart Townley - 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 - 1-15 Comparison of Filtering Methods for the Modeling and Retrospective Forecasting of Influenza Epidemics
by Wan Yang & Alicia Karspeck & Jeffrey Shaman - 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
March 2014, Volume 10, Issue 3
- 1-4 If You Can't Measure It, You Can't Manage It
by Jean Peccoud - 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 - 1-12 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 - 1-14 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 - 1-17 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 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 - 1-12 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 - 1-20 Learning Gene Networks under SNP Perturbations Using eQTL Datasets
by Lingxue Zhang & Seyoung Kim - 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 - 1-10 Fast Reconstruction of Compact Context-Specific Metabolic Network Models
by Nikos Vlassis & Maria Pires Pacheco & Thomas Sauter - 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 - 1-16 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 - 1-18 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 - 1-23 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
- 1-9 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 - 1-22 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 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 - 1-8 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 - 1-10 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 - 1-15 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
October 2013, Volume 9, Issue 10
- 1-3 Explain Bioinformatics to Your Grandmother!
by Virginie Bernard & Magali Michaut - 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 Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening
by Arnab Bhattacherjee & Stefan Wallin - 1-13 dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data
by Dongjun Chung & Dan Park & Kevin Myers & Jeffrey Grass & Patricia Kiley & Robert Landick & Sündüz Keleş - 1-13 Inferring Evolutionary Histories of Pathway Regulation from Transcriptional Profiling Data
by Joshua G Schraiber & Yulia Mostovoy & Tiffany Y Hsu & Rachel B Brem - 1-15 GINI: From ISH Images to Gene Interaction Networks
by Kriti Puniyani & Eric P Xing - 1-17 A Brain-Machine Interface for Control of Medically-Induced Coma
by Maryam M Shanechi & Jessica J Chemali & Max Liberman & Ken Solt & Emery N Brown - 1-18 Novel Methods for Analysing Bacterial Tracks Reveal Persistence in Rhodobacter sphaeroides
by Gabriel Rosser & Alexander G Fletcher & David A Wilkinson & Jennifer A de Beyer & Christian A Yates & Judith P Armitage & Philip K Maini & Ruth E Baker
September 2013, Volume 9, Issue 9
- 1-4 The Regional Student Group Program of the ISCB Student Council: Stories from the Road
by Geoff Macintyre & Magali Michaut & Thomas Abeel - 1-5 Using Biological Pathway Data with Paxtools
by Emek Demir & Özgün Babur & Igor Rodchenkov & Bülent Arman Aksoy & Ken I Fukuda & Benjamin Gross & Onur Selçuk Sümer & Gary D Bader & Chris Sander - 1-10 From Cellular Characteristics to Disease Diagnosis: Uncovering Phenotypes with Supercells
by Julián Candia & Ryan Maunu & Meghan Driscoll & Angélique Biancotto & Pradeep Dagur & J Philip McCoy Jr & H Nida Sen & Lai Wei & Amos Maritan & Kan Cao & Robert B Nussenblatt & Jayanth R Banavar & Wolfgang Losert - 1-12 Genome-Wide Signatures of Transcription Factor Activity: Connecting Transcription Factors, Disease, and Small Molecules
by Jing Chen & Zhen Hu & Mukta Phatak & John Reichard & Johannes M Freudenberg & Siva Sivaganesan & Mario Medvedovic - 1-12 Spike Triggered Covariance in Strongly Correlated Gaussian Stimuli
by Johnatan Aljadeff & Ronen Segev & Michael J Berry II & Tatyana O Sharpee - 1-12 Predicting Odor Perceptual Similarity from Odor Structure
by Kobi Snitz & Adi Yablonka & Tali Weiss & Idan Frumin & Rehan M Khan & Noam Sobel - 1-12 Antimicrobial Peptides Design by Evolutionary Multiobjective Optimization
by Giuseppe Maccari & Mariagrazia Di Luca & Riccardo Nifosí & Francesco Cardarelli & Giovanni Signore & Claudia Boccardi & Angelo Bifone - 1-16 Task-Based Core-Periphery Organization of Human Brain Dynamics
by Danielle S Bassett & Nicholas F Wymbs & M Puck Rombach & Mason A Porter & Peter J Mucha & Scott T Grafton - 1-16 Target Inhibition Networks: Predicting Selective Combinations of Druggable Targets to Block Cancer Survival Pathways
by Jing Tang & Leena Karhinen & Tao Xu & Agnieszka Szwajda & Bhagwan Yadav & Krister Wennerberg & Tero Aittokallio - 1-18 The Next Generation of Transcription Factor Binding Site Prediction
by Anthony Mathelier & Wyeth W Wasserman - 1-19 Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs
by Ioannis N Melas & Regina Samaga & Leonidas G Alexopoulos & Steffen Klamt
August 2013, Volume 9, Issue 8
- 1-10 Predicting Disease Risk Using Bootstrap Ranking and Classification Algorithms
by Ohad Manor & Eran Segal - 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 - 1-14 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 - 1-16 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
July 2013, Volume 9, Issue 7
- 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 Inferring Nonlinear Neuronal Computation Based on Physiologically Plausible Inputs
by James M McFarland & Yuwei Cui & Daniel A Butts
June 2013, Volume 9, Issue 6
- 1-11 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 - 1-19 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
- 1-11 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 - 1-13 Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations
by Xiaodong Cai & Juan Andrés Bazerque & Georgios B Giannakis - 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
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 - 1-15 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 - 1-17 Learning Multisensory Integration and Coordinate Transformation via Density Estimation
by Joseph G Makin & Matthew R Fellows & Philip N Sabes
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 - 1-12 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 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 Automated Analysis of a Diverse Synapse Population
by Brad Busse & Stephen Smith - 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 - 1-17 Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology
by Tina Toni & Bruce Tidor
February 2013, Volume 9, Issue 2
- 1-6 Optimal Properties of Analog Perceptrons with Excitatory Weights
by Claudia Clopath & Nicolas Brunel - 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 - 1-15 Passive Dendrites Enable Single Neurons to Compute Linearly Non-separable Functions
by Romain Daniel Cazé & Mark Humphries & Boris Gutkin
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 - 1-10 Approximate Bayesian Computation
by Mikael Sunnåker & Alberto Giovanni Busetto & Elina Numminen & Jukka Corander & Matthieu Foll & Christophe Dessimoz - 1-13 Saccadic Momentum and Facilitation of Return Saccades Contribute to an Optimal Foraging Strategy
by Niklas Wilming & Simon Harst & Nico Schmidt & Peter König - 1-14 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
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 - 1-12 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 - 1-15 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
- 1-11 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 - 1-14 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 Strategy Diversity Stabilizes Mutualism through Investment Cycles, Phase Polymorphism, and Spatial Bubbles
by Gergely Boza & Ádám Kun & István Scheuring & Ulf Dieckmann - 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 - 1-13 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
September 2012, Volume 8, Issue 9
- 1-3 Ten Simple Rules To Commercialize Scientific Research
by Anthony C Fletcher & Philip E Bourne - 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 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 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
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 - 1-10 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