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March 2014, Volume 10, Issue 3
- 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 - 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 - 1-14 Comprehensive Repertoire of Foldable Regions within Whole Genomes
by Guilhem Faure & Isabelle Callebaut - 1-15 GINI: From ISH Images to Gene Interaction Networks
by Kriti Puniyani & Eric P Xing - 1-15 Attention-Dependent Modulation of Cortical Taste Circuits Revealed by Granger Causality with Signal-Dependent Noise
by Qiang Luo & Tian Ge & Fabian Grabenhorst & Jianfeng Feng & Edmund T Rolls - 1-15 Deciding Not to Decide: Computational and Neural Evidence for Hidden Behavior in Sequential Choice
by Sebastian Gluth & Jörg Rieskamp & Christian Büchel - 1-16 The Influence of Synaptic Weight Distribution on Neuronal Population Dynamics
by Ramakrishnan Iyer & Vilas Menon & Michael Buice & Christof Koch & Stefan Mihalas - 1-16 The Convallis Rule for Unsupervised Learning in Cortical Networks
by Pierre Yger & Kenneth D Harris - 1-16 Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster
by Kolja Becker & Eva Balsa-Canto & Damjan Cicin-Sain & Astrid Hoermann & Hilde Janssens & Julio R Banga & Johannes Jaeger - 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 - 1-18 An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis
by Pralay Mitra & David Shultis & Jeffrey R Brender & Jeff Czajka & David Marsh & Felicia Gray & Tomasz Cierpicki & Yang Zhang
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 - 1-4 Ten Simple Rules for Cultivating Open Science and Collaborative R&D
by Hassan Masum & Aarthi Rao & Benjamin M Good & Matthew H Todd & Aled M Edwards & Leslie Chan & Barry A Bunin & Andrew I Su & Zakir Thomas & Philip E Bourne - 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 - 1-9 Predictive Modeling of In Vivo Response to Gemcitabine in Pancreatic Cancer
by James J Lee & Justin Huang & Christopher G England & Lacey R McNally & Hermann B Frieboes - 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 - 1-15 Frequency Response of a Protein to Local Conformational Perturbations
by Dilek Eren & Burak Alakent - 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 - 1-20 Limited Agreement of Independent RNAi Screens for Virus-Required Host Genes Owes More to False-Negative than False-Positive Factors
by Linhui Hao & Qiuling He & Zhishi Wang & Mark Craven & Michael A Newton & Paul Ahlquist - 1-27 Characterizing Changes in the Rate of Protein-Protein Dissociation upon Interface Mutation Using Hotspot Energy and Organization
by Rudi Agius & Mieczyslaw Torchala & Iain H Moal & Juan Fernández-Recio & Paul A Bates
August 2013, Volume 9, Issue 8
- 1-10 Predicting Disease Risk Using Bootstrap Ranking and Classification Algorithms
by Ohad Manor & Eran Segal - 1-10 Software for Computing and Annotating Genomic Ranges
by Michael Lawrence & Wolfgang Huber & Hervé Pagès & Patrick Aboyoun & Marc Carlson & Robert Gentleman & Martin T Morgan & Vincent J Carey - 1-11 Sensory Information and Encounter Rates of Interacting Species
by Andrew M Hein & Scott A McKinley - 1-11 Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization
by Guillermo Rodrigo & Thomas E Landrain & Eszter Majer & José-Antonio Daròs & Alfonso Jaramillo - 1-12 A Self-Directed Method for Cell-Type Identification and Separation of Gene Expression Microarrays
by Neta S Zuckerman & Yair Noam & Andrea J Goldsmith & Peter P Lee - 1-14 Determinants of Beat-to-Beat Variability of Repolarization Duration in the Canine Ventricular Myocyte: A Computational Analysis
by Jordi Heijman & Antonio Zaza & Daniel M Johnson & Yoram Rudy & Ralf L M Peeters & Paul G A Volders & Ronald L Westra - 1-14 Quantifying Cell Fate Decisions for Differentiation and Reprogramming of a Human Stem Cell Network: Landscape and Biological Paths
by Chunhe Li & Jin Wang - 1-14 Priors Engaged in Long-Latency Responses to Mechanical Perturbations Suggest a Rapid Update in State Estimation
by Frédéric Crevecoeur & Stephen H Scott - 1-15 Model-Based Analysis of HER Activation in Cells Co-Expressing EGFR, HER2 and HER3
by Harish Shankaran & Yi Zhang & Yunbing Tan & Haluk Resat - 1-15 Parameter Trajectory Analysis to Identify Treatment Effects of Pharmacological Interventions
by Christian A Tiemann & Joep Vanlier & Maaike H Oosterveer & Albert K Groen & Peter A J Hilbers & Natal A W van Riel - 1-16 Characteristic Effects of Stochastic Oscillatory Forcing on Neural Firing: Analytical Theory and Comparison to Paddlefish Electroreceptor Data
by Christoph Bauermeister & Tilo Schwalger & David F Russell & Alexander B Neiman & Benjamin Lindner - 1-17 From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction
by Simona Cocco & Remi Monasson & Martin Weigt - 1-20 Shape Similarity, Better than Semantic Membership, Accounts for the Structure of Visual Object Representations in a Population of Monkey Inferotemporal Neurons
by Carlo Baldassi & Alireza Alemi-Neissi & Marino Pagan & James J DiCarlo & Riccardo Zecchina & Davide Zoccolan
July 2013, Volume 9, Issue 7
- 1-10 Co-expression Profiling of Autism Genes in the Mouse Brain
by Idan Menashe & Pascal Grange & Eric C Larsen & Sharmila Banerjee-Basu & Partha P Mitra - 1-11 Consistent Estimation of Gibbs Energy Using Component Contributions
by Elad Noor & Hulda S Haraldsdóttir & Ron Milo & Ronan M T Fleming - 1-14 Statistical Analysis of Molecular Signal Recording
by Joshua I Glaser & Bradley M Zamft & Adam H Marblestone & Jeffrey R Moffitt & Keith Tyo & Edward S Boyden & George Church & Konrad P Kording - 1-14 Hierarchical Modeling for Rare Event Detection and Cell Subset Alignment across Flow Cytometry Samples
by Andrew Cron & Cécile Gouttefangeas & Jacob Frelinger & Lin Lin & Satwinder K Singh & Cedrik M Britten & Marij J P Welters & Sjoerd H van der Burg & Mike West & Cliburn Chan - 1-17 A Family of Algorithms for Computing Consensus about Node State from Network Data
by Eleanor R Brush & David C Krakauer & Jessica C Flack - 1-18 A Mixture of Delta-Rules Approximation to Bayesian Inference in Change-Point Problems
by Robert C Wilson & Matthew R Nassar & Joshua I Gold - 1-18 Inferring Nonlinear Neuronal Computation Based on Physiologically Plausible Inputs
by James M McFarland & Yuwei Cui & Daniel A Butts
June 2013, Volume 9, Issue 6
- 1-9 Scrutinizing MHC-I Binding Peptides and Their Limits of Variation
by Christian P Koch & Anna M Perna & Max Pillong & Nickolay K Todoroff & Paul Wrede & Gerd Folkers & Jan A Hiss & Gisbert Schneider - 1-11 Leveraging Prior Information to Detect Causal Variants via Multi-Variant Regression
by Nanye Long & Samuel P Dickson & Jessica M Maia & Hee Shin Kim & Qianqian Zhu & Andrew S Allen - 1-11 The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum
by William R Harcombe & Nigel F Delaney & Nicholas Leiby & Niels Klitgord & Christopher J Marx - 1-13 Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links ATAD3B to Poor Survival in Breast Cancer
by Kristian Ovaska & Filomena Matarese & Korbinian Grote & Iryna Charapitsa & Alejandra Cervera & Chengyu Liu & George Reid & Martin Seifert & Hendrik G Stunnenberg & Sampsa Hautaniemi - 1-14 Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach
by Meagan C Small & Pedro Lopes & Rodrigo B Andrade & Alexander D MacKerell Jr - 1-15 Patterns of Proliferative Activity in the Colonic Crypt Determine Crypt Stability and Rates of Somatic Evolution
by Rui Zhao & Franziska Michor - 1-16 Are V1 Simple Cells Optimized for Visual Occlusions? A Comparative Study
by Jörg Bornschein & Marc Henniges & Jörg Lücke - 1-19 Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins
by Louis-François Handfield & Yolanda T Chong & Jibril Simmons & Brenda J Andrews & Alan M Moses - 1-19 PUMA: A Unified Framework for Penalized Multiple Regression Analysis of GWAS Data
by Gabriel E Hoffman & Benjamin A Logsdon & Jason G Mezey
May 2013, Volume 9, Issue 5
- 1-1 A Kinetic Platform to Determine the Fate of Nitric Oxide in Escherichia coli
by Jonathan L Robinson & Mark P Brynildsen - 1-9 Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA
by Tobias Linder & Bert L de Groot & Anna Stary-Weinzinger - 1-11 Polymorphisms in the F8 Gene and MHC-II Variants as Risk Factors for the Development of Inhibitory Anti-Factor VIII Antibodies during the Treatment of Hemophilia A: A Computational Assessment
by Gouri Shankar Pandey & Chen Yanover & Tom E Howard & Zuben E Sauna - 1-11 Testing Whether Humans Have an Accurate Model of Their Own Motor Uncertainty in a Speeded Reaching Task
by Hang Zhang & Nathaniel D Daw & Laurence T Maloney - 1-12 Effect of Regulatory Architecture on Broad versus Narrow Sense Heritability
by Yunpeng Wang & Jon Olav Vik & Stig W Omholt & Arne B Gjuvsland - 1-13 Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations
by Xiaodong Cai & Juan Andrés Bazerque & Georgios B Giannakis - 1-13 Modeling and Measuring Signal Relay in Noisy Directed Migration of Cell Groups
by Can Guven & Erin Rericha & Edward Ott & Wolfgang Losert - 1-14 Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation
by Haipeng Li & Thomas Wiehe - 1-14 STL-based Analysis of TRAIL-induced Apoptosis Challenges the Notion of Type I/Type II Cell Line Classification
by Szymon Stoma & Alexandre Donzé & François Bertaux & Oded Maler & Gregory Batt - 1-16 Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling
by Erhan Bilal & Janusz Dutkowski & Justin Guinney & In Sock Jang & Benjamin A Logsdon & Gaurav Pandey & Benjamin A Sauerwine & Yishai Shimoni & Hans Kristian Moen Vollan & Brigham H Mecham & Oscar M Rueda & Jorg Tost & Christina Curtis & Mariano J Alvarez & Vessela N Kristensen & Samuel Aparicio & Anne-Lise Børresen-Dale & Carlos Caldas & Andrea Califano & Stephen H Friend & Trey Ideker & Eric E Schadt & Gustavo A Stolovitzky & Adam A Margolin - 1-17 Inference of R0 and Transmission Heterogeneity from the Size Distribution of Stuttering Chains
by Seth Blumberg & James O Lloyd-Smith - 1-17 Sparse Coding Can Predict Primary Visual Cortex Receptive Field Changes Induced by Abnormal Visual Input
by Jonathan J Hunt & Peter Dayan & Geoffrey J Goodhill
April 2013, Volume 9, Issue 4
- 1-6 A Healthy Fear of the Unknown: Perspectives on the Interpretation of Parameter Fits from Computational Models in Neuroscience
by Matthew R Nassar & Joshua I Gold - 1-9 A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase
by Lin-Tai Da & Fátima Pardo Avila & Dong Wang & Xuhui Huang - 1-14 Localization of Protein Aggregation in Escherichia coli Is Governed by Diffusion and Nucleoid Macromolecular Crowding Effect
by Anne-Sophie Coquel & Jean-Pascal Jacob & Mael Primet & Alice Demarez & Mariella Dimiccoli & Thomas Julou & Lionel Moisan & Ariel B Lindner & Hugues Berry - 1-14 Human Germline Antibody Gene Segments Encode Polyspecific Antibodies
by Jordan R Willis & Bryan S Briney & Samuel L DeLuca & James E Crowe Jr & Jens Meiler - 1-15 Data-Driven Modeling of Src Control on the Mitochondrial Pathway of Apoptosis: Implication for Anticancer Therapy Optimization
by Annabelle Ballesta & Jonathan Lopez & Nikolay Popgeorgiev & Philippe Gonzalo & Marie Doumic & Germain Gillet - 1-15 Computational Biomarker Pipeline from Discovery to Clinical Implementation: Plasma Proteomic Biomarkers for Cardiac Transplantation
by Gabriela V Cohen Freue & Anna Meredith & Derek Smith & Axel Bergman & Mayu Sasaki & Karen K Y Lam & Zsuzsanna Hollander & Nina Opushneva & Mandeep Takhar & David Lin & Janet Wilson-McManus & Robert Balshaw & Paul A Keown & Christoph H Borchers & Bruce McManus & Raymond T Ng & W Robert McMaster & for the Biomarkers in Transplantation and the NCE CECR Prevention of Organ Failure Centre of Excellence Teams - 1-15 Lifespan Differences in Hematopoietic Stem Cells are Due to Imperfect Repair and Unstable Mean-Reversion
by Hans B Sieburg & Giulio Cattarossi & Christa E Muller-Sieburg - 1-15 Noise Suppression and Surplus Synchrony by Coincidence Detection
by Matthias Schultze-Kraft & Markus Diesmann & Sonja Grün & Moritz Helias - 1-17 Learning Multisensory Integration and Coordinate Transformation via Density Estimation
by Joseph G Makin & Matthew R Fellows & Philip N Sabes - 1-30 Bayesian Computation Emerges in Generic Cortical Microcircuits through Spike-Timing-Dependent Plasticity
by Bernhard Nessler & Michael Pfeiffer & Lars Buesing & Wolfgang Maass
March 2013, Volume 9, Issue 3
- 1-9 Bursts of Vertex Activation and Epidemics in Evolving Networks
by Luis E C Rocha & Vincent D Blondel - 1-9 The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks
by Clive G Bowsher & Margaritis Voliotis & Peter S Swain - 1-9 Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field
by Silvio a Beccara & Tatjana Škrbić & Roberto Covino & Cristian Micheletti & Pietro Faccioli - 1-11 Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences
by Dazhi Jiao & Yuzhen Ye & Haixu Tang - 1-12 Explaining the Determinants of First Phase HIV Decay Dynamics through the Effects of Stage-dependent Drug Action
by James B Gilmore & Anthony D Kelleher & David A Cooper & John M Murray - 1-12 Collective Cell Motion in an Epithelial Sheet Can Be Quantitatively Described by a Stochastic Interacting Particle Model
by Néstor Sepúlveda & Laurence Petitjean & Olivier Cochet & Erwan Grasland-Mongrain & Pascal Silberzan & Vincent Hakim - 1-12 Analysis of Hepatitis C Virus Decline during Treatment with the Protease Inhibitor Danoprevir Using a Multiscale Model
by Libin Rong & Jeremie Guedj & Harel Dahari & Daniel J Coffield Jr & Micha Levi & Patrick Smith & Alan S Perelson - 1-13 Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage
by Katarzyna Bozek & Thomas Lengauer & Saleta Sierra & Rolf Kaiser & Francisco S Domingues - 1-13 Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection
by Richard P Mann & Andrea Perna & Daniel Strömbom & Roman Garnett & James E Herbert-Read & David J T Sumpter & Ashley J W Ward - 1-14 Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes
by Christopher Y Park & Aaron K Wong & Casey S Greene & Jessica Rowland & Yuanfang Guan & Lars A Bongo & Rebecca D Burdine & Olga G Troyanskaya - 1-14 Noise-invariant Neurons in the Avian Auditory Cortex: Hearing the Song in Noise
by R Channing Moore & Tyler Lee & Frédéric E Theunissen - 1-14 Automated Analysis of a Diverse Synapse Population
by Brad Busse & Stephen Smith - 1-14 Stimulus-dependent Maximum Entropy Models of Neural Population Codes
by Einat Granot-Atedgi & Gašper Tkačik & Ronen Segev & Elad Schneidman - 1-15 Optimal Vaccine Allocation for the Early Mitigation of Pandemic Influenza
by Laura Matrajt & M Elizabeth Halloran & Ira M Longini Jr - 1-16 A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana
by Christoph Schmal & Peter Reimann & Dorothee Staiger - 1-16 Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment
by Wei Zhang & Takayo Ota & Viji Shridhar & Jeremy Chien & Baolin Wu & Rui Kuang - 1-17 Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology
by Tina Toni & Bruce Tidor - 1-18 Sustained Firing of Model Central Auditory Neurons Yields a Discriminative Spectro-temporal Representation for Natural Sounds
by Michael A Carlin & Mounya Elhilali
February 2013, Volume 9, Issue 2
- 1-6 Optimal Properties of Analog Perceptrons with Excitatory Weights
by Claudia Clopath & Nicolas Brunel - 1-9 No Evidence for an Item Limit in Change Detection
by Shaiyan Keshvari & Ronald van den Berg & Wei Ji Ma - 1-9 Spartan : A Comprehensive Tool for Understanding Uncertainty in Simulations of Biological Systems
by Kieran Alden & Mark Read & Jon Timmis & Paul S Andrews & Henrique Veiga-Fernandes & Mark Coles - 1-10 Standard Anatomical and Visual Space for the Mouse Retina: Computational Reconstruction and Transformation of Flattened Retinae with the Retistruct Package
by David C Sterratt & Daniel Lyngholm & David J Willshaw & Ian D Thompson - 1-11 Virus Neutralisation: New Insights from Kinetic Neutralisation Curves
by Carsten Magnus - 1-13 Evidence for Model-based Computations in the Human Amygdala during Pavlovian Conditioning
by Charlotte Prévost & Daniel McNamee & Ryan K Jessup & Peter Bossaerts & John P O'Doherty - 1-13 Multi-Population Classical HLA Type Imputation
by Alexander Dilthey & Stephen Leslie & Loukas Moutsianas & Judong Shen & Charles Cox & Matthew R Nelson & Gil McVean - 1-14 Biomolecular Events in Cancer Revealed by Attractor Metagenes
by Wei-Yi Cheng & Tai-Hsien Ou Yang & Dimitris Anastassiou - 1-14 Discriminating External and Internal Causes for Heading Changes in Freely Flying Drosophila
by Andrea Censi & Andrew D Straw & Rosalyn W Sayaman & Richard M Murray & Michael H Dickinson - 1-15 Passive Dendrites Enable Single Neurons to Compute Linearly Non-separable Functions
by Romain Daniel Cazé & Mark Humphries & Boris Gutkin - 1-18 Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data
by Gerard J P van Westen & Alwin Hendriks & Jörg K Wegner & Adriaan P IJzerman & Herman W T van Vlijmen & Andreas Bender - 1-19 Delay Selection by Spike-Timing-Dependent Plasticity in Recurrent Networks of Spiking Neurons Receiving Oscillatory Inputs
by Robert R Kerr & Anthony N Burkitt & Doreen A Thomas & Matthieu Gilson & David B Grayden
January 2013, Volume 9, Issue 1
- 1-3 Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator
by Jeroen de Ridder & Thomas Abeel & Magali Michaut & Venkata P Satagopam & Nils Gehlenborg - 1-6 Reward from Punishment Does Not Emerge at All Costs
by Jeromos Vukov & Flávio L Pinheiro & Francisco C Santos & Jorge M Pacheco - 1-9 The Effects of City Streets on an Urban Disease Vector
by Corentin M Barbu & Andrew Hong & Jennifer M Manne & Dylan S Small & Javier E Quintanilla Calderón & Karthik Sethuraman & Víctor Quispe-Machaca & Jenny Ancca-Juárez & Juan G Cornejo del Carpio & Fernando S Málaga Chavez & César Náquira & Michael Z Levy - 1-10 Approximate Bayesian Computation
by Mikael Sunnåker & Alberto Giovanni Busetto & Elina Numminen & Jukka Corander & Matthieu Foll & Christophe Dessimoz - 1-13 Temporal Adaptation Enhances Efficient Contrast Gain Control on Natural Images
by Fabian Sinz & Matthias Bethge - 1-13 Saccadic Momentum and Facilitation of Return Saccades Contribute to an Optimal Foraging Strategy
by Niklas Wilming & Simon Harst & Nico Schmidt & Peter König - 1-13 Maximizing the Information Content of Experiments in Systems Biology
by Juliane Liepe & Sarah Filippi & Michał Komorowski & Michael P H Stumpf - 1-14 How Evolving Heterogeneity Distributions of Resource Allocation Strategies Shape Mortality Patterns
by Yann Le Cunff & Annette Baudisch & Khashayar Pakdaman - 1-14 Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships
by Nives Škunca & Matko Bošnjak & Anita Kriško & Panče Panov & Sašo Džeroski & Tomislav Šmuc & Fran Supek - 1-15 Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective
by Graham Rockwell & Nicholas J Guido & George M Church - 1-17 Significance Analysis of Prognostic Signatures
by Andrew H Beck & Nicholas W Knoblauch & Marco M Hefti & Jennifer Kaplan & Stuart J Schnitt & Aedin C Culhane & Markus S Schroeder & Thomas Risch & John Quackenbush & Benjamin Haibe-Kains - 1-21 Dynamic Finite Size Effects in Spiking Neural Networks
by Michael A Buice & Carson C Chow
December 2012, Volume 8, Issue 12
- 1-8 Chapter 2: Data-Driven View of Disease Biology
by Casey S Greene & Olga G Troyanskaya