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August 2017, Volume 13, Issue 8
- 1-17 Mouth-clicks used by blind expert human echolocators – signal description and model based signal synthesis
by Lore Thaler & Galen M Reich & Xinyu Zhang & Dinghe Wang & Graeme E Smith & Zeng Tao & Raja Syamsul Azmir Bin Raja Abdullah & Mikhail Cherniakov & Christopher J Baker & Daniel Kish & Michail Antoniou - 1-18 Neuron’s eye view: Inferring features of complex stimuli from neural responses
by Xin Chen & Jeffrey M Beck & John M Pearson - 1-19 Robust averaging protects decisions from noise in neural computations
by Vickie Li & Santiago Herce Castañón & Joshua A Solomon & Hildward Vandormael & Christopher Summerfield - 1-19 Host population structure impedes reversion to drug sensitivity after discontinuation of treatment
by Jonas I Liechti & Gabriel E Leventhal & Sebastian Bonhoeffer - 1-21 Rearrangement moves on rooted phylogenetic networks
by Philippe Gambette & Leo van Iersel & Mark Jones & Manuel Lafond & Fabio Pardi & Celine Scornavacca - 1-22 Confirmation bias in human reinforcement learning: Evidence from counterfactual feedback processing
by Stefano Palminteri & Germain Lefebvre & Emma J Kilford & Sarah-Jayne Blakemore - 1-22 Polymodal allosteric regulation of Type 1 Serine/Threonine Kinase Receptors via a conserved electrostatic lock
by Wesley M Botello-Smith & Abdelaziz Alsamarah & Payal Chatterjee & Chen Xie & Jerome J Lacroix & Jijun Hao & Yun Luo - 1-22 Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate
by David Amar & Ron Shamir & Daniel Yekutieli - 1-23 Noise correlations in the human brain and their impact on pattern classification
by Vikranth R Bejjanki & Rava Azeredo da Silveira & Jonathan D Cohen & Nicholas B Turk-Browne - 1-24 Multi-scale approaches for high-speed imaging and analysis of large neural populations
by Johannes Friedrich & Weijian Yang & Daniel Soudry & Yu Mu & Misha B Ahrens & Rafael Yuste & Darcy S Peterka & Liam Paninski - 1-25 Stabilization of diastolic calcium signal via calcium pump regulation of complex local calcium releases and transient decay in a computational model of cardiac pacemaker cell with individual release channels
by Alexander V Maltsev & Victor A Maltsev & Michael D Stern - 1-26 Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data
by Lingfei Wang & Tom Michoel - 1-28 Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors
by Anna Cichonska & Balaguru Ravikumar & Elina Parri & Sanna Timonen & Tapio Pahikkala & Antti Airola & Krister Wennerberg & Juho Rousu & Tero Aittokallio - 1-34 A stochastic-field description of finite-size spiking neural networks
by Grégory Dumont & Alexandre Payeur & André Longtin - 1-34 A computational model of spatio-temporal cardiac intracellular calcium handling with realistic structure and spatial flux distribution from sarcoplasmic reticulum and t-tubule reconstructions
by Michael A Colman & Christian Pinali & Andrew W Trafford & Henggui Zhang & Ashraf Kitmitto - 1-36 The Stochastic Early Reaction, Inhibition, and late Action (SERIA) model for antisaccades
by Eduardo A Aponte & Dario Schöbi & Klaas E Stephan & Jakob Heinzle
July 2017, Volume 13, Issue 7
- 1-7 PCSF: An R-package for network-based interpretation of high-throughput data
by Murodzhon Akhmedov & Amanda Kedaigle & Renan Escalante Chong & Roberto Montemanni & Francesco Bertoni & Ernest Fraenkel & Ivo Kwee - 1-14 Combination therapeutics of Nilotinib and radiation in acute lymphoblastic leukemia as an effective method against drug-resistance
by Kamran Kaveh & Yutaka Takahashi & Michael A Farrar & Guy Storme & Marcucci Guido & Jamie Piepenburg & Jackson Penning & Jasmine Foo & Kevin Z Leder & Susanta K Hui - 1-15 Speciation trajectories in recombining bacterial species
by Pekka Marttinen & William P Hanage - 1-15 Inherent limitations of probabilistic models for protein-DNA binding specificity
by Shuxiang Ruan & Gary D Stormo - 1-16 mRNA/protein sequence complementarity and its determinants: The impact of affinity scales
by Lukas Bartonek & Bojan Zagrovic - 1-17 OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
by Peter Eastman & Jason Swails & John D Chodera & Robert T McGibbon & Yutong Zhao & Kyle A Beauchamp & Lee-Ping Wang & Andrew C Simmonett & Matthew P Harrigan & Chaya D Stern & Rafal P Wiewiora & Bernard R Brooks & Vijay S Pande - 1-18 Effect of depth information on multiple-object tracking in three dimensions: A probabilistic perspective
by James R H Cooke & Arjan C ter Horst & Robert J van Beers & W Pieter Medendorp - 1-19 Growth of bacteria in 3-d colonies
by Xinxian Shao & Andrew Mugler & Justin Kim & Ha Jun Jeong & Bruce R Levin & Ilya Nemenman - 1-20 Hybrid modeling and prediction of dynamical systems
by Franz Hamilton & Alun L Lloyd & Kevin B Flores - 1-22 MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions
by Koon-Kiu Yan & Shaoke Lou & Mark Gerstein - 1-22 Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors
by Saeed Omidi & Mihaela Zavolan & Mikhail Pachkov & Jeremie Breda & Severin Berger & Erik van Nimwegen - 1-23 Long-time analytic approximation of large stochastic oscillators: Simulation, analysis and inference
by Giorgos Minas & David A Rand - 1-23 A hierarchical Bayesian model for understanding the spatiotemporal dynamics of the intestinal epithelium
by Oliver J Maclaren & Aimée Parker & Carmen Pin & Simon R Carding & Alastair J M Watson & Alexander G Fletcher & Helen M Byrne & Philip K Maini - 1-23 Learning and executing goal-directed choices by internally generated sequences in spiking neural circuits
by John Palmer & Adam Keane & Pulin Gong - 1-24 Cooperative stochastic binding and unbinding explain synaptic size dynamics and statistics
by Aseel Shomar & Lukas Geyrhofer & Noam E Ziv & Naama Brenner - 1-27 Deciphering the regulation of P2X4 receptor channel gating by ivermectin using Markov models
by Laurent Mackay & Hana Zemkova & Stanko S Stojilkovic & Arthur Sherman & Anmar Khadra - 1-28 Dissociating error-based and reinforcement-based loss functions during sensorimotor learning
by Joshua G A Cashaback & Heather R McGregor & Ayman Mohatarem & Paul L Gribble - 1-29 CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets
by Yang Li & Alexis A Jourdain & Sarah E Calvo & Jun S Liu & Vamsi K Mootha
June 2017, Volume 13, Issue 6
- 1-4 2017 ISCB Overton Prize awarded to Christoph Bock
by Christiana N Fogg & Diane E Kovats & Bonnie Berger - 1-12 High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE
by Stefano Castellana & Caterina Fusilli & Gianluigi Mazzoccoli & Tommaso Biagini & Daniele Capocefalo & Massimo Carella & Angelo Luigi Vescovi & Tommaso Mazza - 1-16 GINOM: A statistical framework for assessing interval overlap of multiple genomic features
by Darshan Bryner & Stephen Criscione & Andrew Leith & Quyen Huynh & Fred Huffer & Nicola Neretti - 1-16 Leveraging functional annotations in genetic risk prediction for human complex diseases
by Yiming Hu & Qiongshi Lu & Ryan Powles & Xinwei Yao & Can Yang & Fang Fang & Xinran Xu & Hongyu Zhao - 1-19 An efficient coding theory for a dynamic trajectory predicts non-uniform allocation of entorhinal grid cells to modules
by Noga Mosheiff & Haggai Agmon & Avraham Moriel & Yoram Burak - 1-19 Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle
by David L Gibbs & Ilya Shmulevich - 1-22 Optimal structure of metaplasticity for adaptive learning
by Peyman Khorsand & Alireza Soltani - 1-23 A novel algorithm identifies stress-induced alterations in mitochondrial connectivity and inner membrane structure from confocal images
by Mathieu Ouellet & Gérald Guillebaud & Valerie Gervais & David Lupien St-Pierre & Marc Germain - 1-23 Comorbidities in the diseasome are more apparent than real: What Bayesian filtering reveals about the comorbidities of depression
by Peter Marx & Peter Antal & Bence Bolgar & Gyorgy Bagdy & Bill Deakin & Gabriella Juhasz - 1-24 Reduction of multiscale stochastic biochemical reaction networks using exact moment derivation
by Jae Kyoung Kim & Eduardo D Sontag - 1-24 MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory
by Aliza B Rubenstein & Manasi A Pethe & Sagar D Khare - 1-24 Rosetta:MSF: a modular framework for multi-state computational protein design
by Patrick Löffler & Samuel Schmitz & Enrico Hupfeld & Reinhard Sterner & Rainer Merkl - 1-25 Robust transmission of rate coding in the inhibitory Purkinje cell to cerebellar nuclei pathway in awake mice
by Samira Abbasi & Amber E Hudson & Selva K Maran & Ying Cao & Ataollah Abbasi & Detlef H Heck & Dieter Jaeger - 1-25 Epidemiological and economic impact of pandemic influenza in Chicago: Priorities for vaccine interventions
by Nargesalsadat Dorratoltaj & Achla Marathe & Bryan L Lewis & Samarth Swarup & Stephen G Eubank & Kaja M Abbas - 1-29 Fast and general tests of genetic interaction for genome-wide association studies
by Mattias Frånberg & Rona J Strawbridge & Anders Hamsten & PROCARDIS consortium & Ulf de Faire & Jens Lagergren & Bengt Sennblad - 1-29 A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data
by En-Yu Lai & Yi-Hau Chen & Kun-Pin Wu - 1-32 Locking of correlated neural activity to ongoing oscillations
by Tobias Kühn & Moritz Helias - 1-33 A state space approach for piecewise-linear recurrent neural networks for identifying computational dynamics from neural measurements
by Daniel Durstewitz - 1-46 Low-dimensional spike rate models derived from networks of adaptive integrate-and-fire neurons: Comparison and implementation
by Moritz Augustin & Josef Ladenbauer & Fabian Baumann & Klaus Obermayer - 1-47 Linking structure and activity in nonlinear spiking networks
by Gabriel Koch Ocker & Krešimir Josić & Eric Shea-Brown & Michael A Buice
May 2017, Volume 13, Issue 5
- 1-7 Ten simple rules to make the most out of your undergraduate research career
by Megan Yu & Yu-Min Kuo - 1-7 Ten simple rules for surviving an interdisciplinary PhD
by Samuel Demharter & Nicholas Pearce & Kylie Beattie & Isabel Frost & Jinwoo Leem & Alistair Martin & Robert Oppenheimer & Cristian Regep & Tammo Rukat & Alexander Skates & Nicola Trendel & David J Gavaghan & Charlotte M Deane & Bernhard Knapp - 1-10 ROTS: An R package for reproducibility-optimized statistical testing
by Tomi Suomi & Fatemeh Seyednasrollah & Maria K Jaakkola & Thomas Faux & Laura L Elo - 1-15 Predicting cryptic links in host-parasite networks
by Tad Dallas & Andrew W Park & John M Drake - 1-19 Automatically tracking neurons in a moving and deforming brain
by Jeffrey P Nguyen & Ashley N Linder & George S Plummer & Joshua W Shaevitz & Andrew M Leifer - 1-22 Nucleotide-time alignment for molecular recorders
by Thaddeus R Cybulski & Edward S Boyden & George M Church & Keith E J Tyo & Konrad P Kording - 1-23 Co-occurring protein phosphorylation are functionally associated
by Ying Li & Xueya Zhou & Zichao Zhai & Tingting Li - 1-25 Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates
by Andreas Tuerk & Gregor Wiktorin & Serhat Güler - 1-26 An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci
by Jin Hyun Ju & Sushila A Shenoy & Ronald G Crystal & Jason G Mezey - 1-30 Chemomechanical regulation of myosin Ic cross-bridges: Deducing the elastic properties of an ensemble from single-molecule mechanisms
by Florian Berger & A J Hudspeth - 1-30 Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes
by Nick E Phillips & Cerys Manning & Nancy Papalopulu & Magnus Rattray - 1-37 Dynamic decomposition of spatiotemporal neural signals
by Luca Ambrogioni & Marcel A J van Gerven & Eric Maris
April 2017, Volume 13, Issue 4
- 1-16 ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time
by Yunpeng Cai & Wei Zheng & Jin Yao & Yujie Yang & Volker Mai & Qi Mao & Yijun Sun - 1-16 Dynamics of adaptive immunity against phage in bacterial populations
by Serena Bradde & Marija Vucelja & Tiberiu Teşileanu & Vijay Balasubramanian - 1-17 Computation and measurement of cell decision making errors using single cell data
by Iman Habibi & Raymond Cheong & Tomasz Lipniacki & Andre Levchenko & Effat S Emamian & Ali Abdi - 1-18 Variable habitat conditions drive species covariation in the human microbiota
by Charles K Fisher & Thierry Mora & Aleksandra M Walczak - 1-20 Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data
by Ofir Shukron & David Holcman - 1-21 Geospatial characteristics of measles transmission in China during 2005−2014
by Wan Yang & Liang Wen & Shen-Long Li & Kai Chen & Wen-Yi Zhang & Jeffrey Shaman - 1-22 From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints
by Steffen Klamt & Georg Regensburger & Matthias P Gerstl & Christian Jungreuthmayer & Stefan Schuster & Radhakrishnan Mahadevan & Jürgen Zanghellini & Stefan Müller - 1-24 Probabilistic fluorescence-based synapse detection
by Anish K Simhal & Cecilia Aguerrebere & Forrest Collman & Joshua T Vogelstein & Kristina D Micheva & Richard J Weinberg & Stephen J Smith & Guillermo Sapiro - 1-27 Heterogeneous firing responses predict diverse couplings to presynaptic activity in mice layer V pyramidal neurons
by Yann Zerlaut & Alain Destexhe - 1-27 Cheminformatics-aided discovery of small-molecule Protein-Protein Interaction (PPI) dual inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL)
by Georgia Melagraki & Evangelos Ntougkos & Vagelis Rinotas & Christos Papaneophytou & Georgios Leonis & Thomas Mavromoustakos & George Kontopidis & Eleni Douni & Antreas Afantitis & George Kollias - 1-28 Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling
by Irene Otero-Muras & Pencho Yordanov & Joerg Stelling - 1-30 When do correlations increase with firing rates in recurrent networks?
by Andrea K Barreiro & Cheng Ly - 1-33 Predicting explorative motor learning using decision-making and motor noise
by Xiuli Chen & Kieran Mohr & Joseph M Galea - 1-33 Representational models: A common framework for understanding encoding, pattern-component, and representational-similarity analysis
by Jörn Diedrichsen & Nikolaus Kriegeskorte - 1-35 Robust information propagation through noisy neural circuits
by Joel Zylberberg & Alexandre Pouget & Peter E Latham & Eric Shea-Brown - 1-38 Personalized glucose forecasting for type 2 diabetes using data assimilation
by David J Albers & Matthew Levine & Bruce Gluckman & Henry Ginsberg & George Hripcsak & Lena Mamykina - 1-40 Intrinsically-generated fluctuating activity in excitatory-inhibitory networks
by Francesca Mastrogiuseppe & Srdjan Ostojic
March 2017, Volume 13, Issue 3
- 1-8 Ten simple rules for forming a scientific professional society
by Bruno A Gaëta & Javier De Las Rivas & Paul Horton & Pieter Meysman & Nicola Mulder & Paolo Romano & Lonnie Welch - 1-9 Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells
by James T Yurkovich & Laurence Yang & Bernhard O Palsson - 1-16 Fidelity of the representation of value in decision-making
by Paul M Bays & Ben A Dowding - 1-16 Novel non-invasive algorithm to identify the origins of re-entry and ectopic foci in the atria from 64-lead ECGs: A computational study
by Erick A Perez Alday & Michael A Colman & Philip Langley & Henggui Zhang - 1-18 Parameter estimation for multistage clonal expansion models from cancer incidence data: A practical identifiability analysis
by Andrew F Brouwer & Rafael Meza & Marisa C Eisenberg - 1-19 A human judgment approach to epidemiological forecasting
by David C Farrow & Logan C Brooks & Sangwon Hyun & Ryan J Tibshirani & Donald S Burke & Roni Rosenfeld - 1-19 Bistable front dynamics in a contractile medium: Travelling wave fronts and cortical advection define stable zones of RhoA signaling at epithelial adherens junctions
by Rashmi Priya & Guillermo A Gomez & Srikanth Budnar & Bipul R Acharya & Andras Czirok & Alpha S Yap & Zoltan Neufeld - 1-20 Systematic identification of phosphorylation-mediated protein interaction switches
by Matthew J Betts & Oliver Wichmann & Mathias Utz & Timon Andre & Evangelia Petsalaki & Pablo Minguez & Luca Parca & Frederick P Roth & Anne-Claude Gavin & Peer Bork & Robert B Russell - 1-20 Multiregional integration in the brain during resting-state fMRI activity
by Etay Hay & Petra Ritter & Nancy J Lobaugh & Anthony R McIntosh - 1-22 Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N
by Polydefkis Diamantis & Oliver T Unke & Markus Meuwly - 1-25 Feedback between motion and sensation provides nonlinear boost in run-and-tumble navigation
by Junjiajia Long & Steven W Zucker & Thierry Emonet - 1-26 Fast online deconvolution of calcium imaging data
by Johannes Friedrich & Pengcheng Zhou & Liam Paninski - 1-27 Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells
by Aurélien Naldi & Romain M Larive & Urszula Czerwinska & Serge Urbach & Philippe Montcourrier & Christian Roy & Jérôme Solassol & Gilles Freiss & Peter J Coopman & Ovidiu Radulescu - 1-28 Learning about and from others' prudence, impatience or laziness: The computational bases of attitude alignment
by Marie Devaine & Jean Daunizeau - 1-28 A model for brain life history evolution
by Mauricio González-Forero & Timm Faulwasser & Laurent Lehmann - 1-30 A critical analysis of computational protein design with sparse residue interaction graphs
by Swati Jain & Jonathan D Jou & Ivelin S Georgiev & Bruce R Donald - 1-31 Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study
by Emma Saulnier & Olivier Gascuel & Samuel Alizon
February 2017, Volume 13, Issue 2
- 1-6 Ten Simple Rules for Developing a Successful Research Proposal in Brazil
by Dyoni M de Oliveira & Marcos S Buckeridge & Wanderley D dos Santos - 1-8 Ten Simple Rules on How to Organize a Scientific Retreat
by Julia Ponomarenko & Romina Garrido & Roderic Guigó - 1-17 Predicting Structure-Function Relations and Survival following Surgical and Bronchoscopic Lung Volume Reduction Treatment of Emphysema
by Jarred R Mondoñedo & Béla Suki - 1-20 Two dynamic regimes in the human gut microbiome
by Sean M Gibbons & Sean M Kearney & Chris S Smillie & Eric J Alm - 1-20 The genotype-phenotype map of an evolving digital organism
by Miguel A Fortuna & Luis Zaman & Charles Ofria & Andreas Wagner - 1-20 graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture
by Dongjun Chung & Hang J Kim & Hongyu Zhao - 1-25 A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons
by Yen-Fu Chen & Hsiu-Chuan Lin & Kai-Neng Chuang & Chih-Hsu Lin & Hsueh-Chi S Yen & Chen-Hsiang Yeang - 1-28 The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt
by Sophie K Kay & Heather A Harrington & Sarah Shepherd & Keith Brennan & Trevor Dale & James M Osborne & David J Gavaghan & Helen M Byrne - 1-31 On the stability and dynamics of stochastic spiking neuron models: Nonlinear Hawkes process and point process GLMs
by Felipe Gerhard & Moritz Deger & Wilson Truccolo - 1-32 Accuracy Maximization Analysis for Sensory-Perceptual Tasks: Computational Improvements, Filter Robustness, and Coding Advantages for Scaled Additive Noise
by Johannes Burge & Priyank Jaini - 1-34 Elucidation of molecular kinetic schemes from macroscopic traces using system identification
by Miguel Fribourg & Diomedes E Logothetis & Javier González-Maeso & Stuart C Sealfon & Belén Galocha-Iragüen & Fernando Las-Heras Andrés & Vladimir Brezina - 1-40 Mindboggling morphometry of human brains
by Arno Klein & Satrajit S Ghosh & Forrest S Bao & Joachim Giard & Yrjö Häme & Eliezer Stavsky & Noah Lee & Brian Rossa & Martin Reuter & Elias Chaibub Neto & Anisha Keshavan
January 2017, Volume 13, Issue 1
- 1-15 The Power of Malaria Vaccine Trials Using Controlled Human Malaria Infection
by Luc E Coffeng & Cornelus C Hermsen & Robert W Sauerwein & Sake J de Vlas - 1-16 Efficient Switches in Biology and Computer Science
by Luca Cardelli & Rosa D Hernansaiz-Ballesteros & Neil Dalchau & Attila Csikász-Nagy - 1-16 Coevolutionary dynamics of phenotypic diversity and contingent cooperation
by Te Wu & Long Wang & Feng Fu - 1-18 Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
by Fabian Fröhlich & Barbara Kaltenbacher & Fabian J Theis & Jan Hasenauer - 1-19 Structure-Function Network Mapping and Its Assessment via Persistent Homology
by Hualou Liang & Hongbin Wang - 1-19 Complex Dynamics of Virus Spread from Low Infection Multiplicities: Implications for the Spread of Oncolytic Viruses
by Ignacio A Rodriguez-Brenes & Andrew Hofacre & Hung Fan & Dominik Wodarz - 1-19 Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility
by David Lamparter & Daniel Marbach & Rico Rueedi & Sven Bergmann & Zoltán Kutalik - 1-20 Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome
by Erik Andrews & Yue Wang & Tian Xia & Wenqing Cheng & Chao Cheng - 1-20 Iterative sure independence screening EM-Bayesian LASSO algorithm for multi-locus genome-wide association studies
by Cox Lwaka Tamba & Yuan-Li Ni & Yuan-Ming Zhang - 1-21 A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models
by Christoph Zimmer & Reza Yaesoubi & Ted Cohen - 1-24 Inferring the Chemotactic Strategy of P. putida and E. coli Using Modified Kramers-Moyal Coefficients
by Oliver Pohl & Marius Hintsche & Zahra Alirezaeizanjani & Maximilian Seyrich & Carsten Beta & Holger Stark - 1-25 Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing
by Edward S Lee & Paul G Thomas & Jeff E Mold & Andrew J Yates - 1-26 Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans
by Ho-Yon Hwang & Jiou Wang - 1-26 Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies
by Tanmay A Gokhale & Jong M Kim & Robert D Kirkton & Nenad Bursac & Craig S Henriquez - 1-27 Approximate Inference for Time-Varying Interactions and Macroscopic Dynamics of Neural Populations
by Christian Donner & Klaus Obermayer & Hideaki Shimazaki - 1-28 Suboptimal Criterion Learning in Static and Dynamic Environments
by Elyse H Norton & Stephen M Fleming & Nathaniel D Daw & Michael S Landy - 1-29 Multiple Choice Neurodynamical Model of the Uncertain Option Task
by Andrea Insabato & Mario Pannunzi & Gustavo Deco - 1-31 Real Time Multiplicative Memory Amplification Mediated by Whole-Cell Scaling of Synaptic Response in Key Neurons
by Iris Reuveni & Sourav Ghosh & Edi Barkai - 1-31 The Flash-Lag Effect as a Motion-Based Predictive Shift
by Mina A Khoei & Guillaume S Masson & Laurent U Perrinet - 1-34 Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
by Sheng Wang & Siqi Sun & Zhen Li & Renyu Zhang & Jinbo Xu - 1-36 A New Approach to Model Pitch Perception Using Sparse Coding
by Oded Barzelay & Miriam Furst & Omri Barak
December 2016, Volume 12, Issue 12
- 1-13 Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs
by Nadezda Kryuchkova-Mostacci & Marc Robinson-Rechavi - 1-15 Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist
by Brian Drawert & Andreas Hellander & Ben Bales & Debjani Banerjee & Giovanni Bellesia & Bernie J Daigle Jr. & Geoffrey Douglas & Mengyuan Gu & Anand Gupta & Stefan Hellander & Chris Horuk & Dibyendu Nath & Aviral Takkar & Sheng Wu & Per Lötstedt & Chandra Krintz & Linda R Petzold - 1-17 Stability of Cross-Feeding Polymorphisms in Microbial Communities
by Ivana Gudelj & Margie Kinnersley & Peter Rashkov & Karen Schmidt & Frank Rosenzweig - 1-18 Systematic Approximations to Susceptible-Infectious-Susceptible Dynamics on Networks
by Matt J Keeling & Thomas House & Alison J Cooper & Lorenzo Pellis - 1-22 When Optimal Feedback Control Is Not Enough: Feedforward Strategies Are Required for Optimal Control with Active Sensing
by Sang-Hoon Yeo & David W Franklin & Daniel M Wolpert - 1-23 Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology
by James C Schaff & Fei Gao & Ye Li & Igor L Novak & Boris M Slepchenko - 1-24 Competing Mechanistic Hypotheses of Acetaminophen-Induced Hepatotoxicity Challenged by Virtual Experiments
by Andrew K Smith & Brenden K Petersen & Glen E P Ropella & Ryan C Kennedy & Neil Kaplowitz & Murad Ookhtens & C Anthony Hunt - 1-24 The Hamiltonian Brain: Efficient Probabilistic Inference with Excitatory-Inhibitory Neural Circuit Dynamics
by Laurence Aitchison & Máté Lengyel - 1-25 Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites
by Angela Re & Levi Waldron & Alessandro Quattrone - 1-26 Human Inferences about Sequences: A Minimal Transition Probability Model
by Florent Meyniel & Maxime Maheu & Stanislas Dehaene - 1-26 The Limitations of Model-Based Experimental Design and Parameter Estimation in Sloppy Systems
by Andrew White & Malachi Tolman & Howard D Thames & Hubert Rodney Withers & Kathy A Mason & Mark K Transtrum - 1-27 Scaling Properties of Dimensionality Reduction for Neural Populations and Network Models
by Ryan C Williamson & Benjamin R Cowley & Ashok Litwin-Kumar & Brent Doiron & Adam Kohn & Matthew A Smith & Byron M Yu - 1-27 Utility and Limitations of Using Gene Expression Data to Identify Functional Associations
by Sahra Uygun & Cheng Peng & Melissa D Lehti-Shiu & Robert L Last & Shin-Han Shiu - 1-29 Decoding Single Molecule Time Traces with Dynamic Disorder
by Wonseok Hwang & Il-Buem Lee & Seok-Cheol Hong & Changbong Hyeon - 1-29 Temporal Dynamics and Developmental Maturation of Salience, Default and Central-Executive Network Interactions Revealed by Variational Bayes Hidden Markov Modeling
by Srikanth Ryali & Kaustubh Supekar & Tianwen Chen & John Kochalka & Weidong Cai & Jonathan Nicholas & Aarthi Padmanabhan & Vinod Menon - 1-30 Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations
by Andrew F Neuwald & Stephen F Altschul - 1-31 m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks
by Song-Yao Zhang & Shao-Wu Zhang & Lian Liu & Jia Meng & Yufei Huang - 1-31 Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos
by Jonathan Desponds & Huy Tran & Teresa Ferraro & Tanguy Lucas & Carmina Perez Romero & Aurelien Guillou & Cecile Fradin & Mathieu Coppey & Nathalie Dostatni & Aleksandra M Walczak - 1-31 Stimulus-Driven Population Activity Patterns in Macaque Primary Visual Cortex
by Benjamin R Cowley & Matthew A Smith & Adam Kohn & Byron M Yu - 1-32 Zipf’s Law Arises Naturally When There Are Underlying, Unobserved Variables
by Laurence Aitchison & Nicola Corradi & Peter E Latham - 1-33 Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data
by Simeon Carstens & Michael Nilges & Michael Habeck
November 2016, Volume 12, Issue 11
- 1-12 NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents
by Sophia S Liu & Adam J Hockenberry & Andrea Lancichinetti & Michael C Jewett & Luís A N Amaral - 1-14 Machine Learning for Characterization of Insect Vector Feeding
by Denis S Willett & Justin George & Nora S Willett & Lukasz L Stelinski & Stephen L Lapointe - 1-15 Kinase Inhibition Leads to Hormesis in a Dual Phosphorylation-Dephosphorylation Cycle
by Peter Rashkov & Ian P Barrett & Robert E Beardmore & Claus Bendtsen & Ivana Gudelj - 1-18 Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway
by Kazunari Iwamoto & Yuki Shindo & Koichi Takahashi - 1-20 Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference
by Kieran R Campbell & Christopher Yau - 1-22 Neural Population Dynamics during Reaching Are Better Explained by a Dynamical System than Representational Tuning
by Jonathan A Michaels & Benjamin Dann & Hansjörg Scherberger - 1-26 Drivers of Inter-individual Variation in Dengue Viral Load Dynamics
by Rotem Ben-Shachar & Scott Schmidler & Katia Koelle - 1-28 Do Vascular Networks Branch Optimally or Randomly across Spatial Scales?
by Elif Tekin & David Hunt & Mitchell G Newberry & Van M Savage - 1-29 Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan
by Elizabeth N Davison & Benjamin O Turner & Kimberly J Schlesinger & Michael B Miller & Scott T Grafton & Danielle S Bassett & Jean M Carlson - 1-30 Interrogating Emergent Transport Properties for Molecular Motor Ensembles: A Semi-analytical Approach
by Shreyas Bhaban & Donatello Materassi & Mingang Li & Thomas Hays & Murti Salapaka - 1-30 Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks
by Hulda S Haraldsdóttir & Ronan M T Fleming - 1-32 Error-Robust Modes of the Retinal Population Code
by Jason S Prentice & Olivier Marre & Mark L Ioffe & Adrianna R Loback & Gašper Tkačik & Michael J Berry II - 1-34 Improved Measures of Integrated Information
by Max Tegmark - 1-35 WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning
by George L Sutphin & J Matthew Mahoney & Keith Sheppard & David O Walton & Ron Korstanje - 1-35 Kinetic Modeling of ABCG2 Transporter Heterogeneity: A Quantitative, Single-Cell Analysis of the Side Population Assay
by Adam F Prasanphanich & Douglas E White & Margaret A Gran & Melissa L Kemp
October 2016, Volume 12, Issue 10
- 1-4 Ten Simple Rules for Developing a MOOC
by David T Manallack & Elizabeth Yuriev - 1-18 Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements
by Samuel M D Oliveira & Antti Häkkinen & Jason Lloyd-Price & Huy Tran & Vinodh Kandavalli & Andre S Ribeiro - 1-18 rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison
by Lars Hahn & Chris-André Leimeister & Rachid Ounit & Stefano Lonardi & Burkhard Morgenstern - 1-20 Mechano-chemical Interactions in Cardiac Sarcomere Contraction: A Computational Modeling Study
by Lauren J Dupuis & Joost Lumens & Theo Arts & Tammo Delhaas - 1-21 Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections
by Jason Karslake & Jeff Maltas & Peter Brumm & Kevin B Wood - 1-22 PreTIS: A Tool to Predict Non-canonical 5’ UTR Translational Initiation Sites in Human and Mouse
by Kerstin Reuter & Alexander Biehl & Laurena Koch & Volkhard Helms - 1-22 The Spatial Dynamics of Predators and the Benefits and Costs of Sharing Information
by Matthieu Barbier & James R Watson - 1-22 Structural Identifiability of Dynamic Systems Biology Models
by Alejandro F Villaverde & Antonio Barreiro & Antonis Papachristodoulou - 1-26 Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing
by Hansaim Lim & Aleksandar Poleksic & Yuan Yao & Hanghang Tong & Di He & Luke Zhuang & Patrick Meng & Lei Xie - 1-28 Likelihood-Based Inference of B Cell Clonal Families
by Duncan K Ralph & Frederick A Matsen IV - 1-34 Identifying Anatomical Origins of Coexisting Oscillations in the Cortical Microcircuit
by Hannah Bos & Markus Diesmann & Moritz Helias - 1-34 How Do Efficient Coding Strategies Depend on Origins of Noise in Neural Circuits?
by Braden A W Brinkman & Alison I Weber & Fred Rieke & Eric Shea-Brown - 1-41 Forgetting in Reinforcement Learning Links Sustained Dopamine Signals to Motivation
by Ayaka Kato & Kenji Morita
September 2016, Volume 12, Issue 9
- 1-11 A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains
by Florian C Rieger & Peter Virnau - 1-13 The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community
by Xiaokan Guo & James Q Boedicker - 1-14 Novel Covariance-Based Neutrality Test of Time-Series Data Reveals Asymmetries in Ecological and Economic Systems
by Alex D Washburne & Joshua W Burby & Daniel Lacker - 1-17 How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates
by Fabian Paul & Thomas R Weikl - 1-17 Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline
by Hao Chen & Mai Chan Lau & Michael Thomas Wong & Evan W Newell & Michael Poidinger & Jinmiao Chen - 1-17 Bipartite Community Structure of eQTLs
by John Platig & Peter J Castaldi & Dawn DeMeo & John Quackenbush - 1-18 The Computational Properties of a Simplified Cortical Column Model
by Nicholas Cain & Ramakrishnan Iyer & Christof Koch & Stefan Mihalas - 1-20 The Statistical Determinants of the Speed of Motor Learning
by Kang He & You Liang & Farnaz Abdollahi & Moria Fisher Bittmann & Konrad Kording & Kunlin Wei - 1-20 Including Thermal Fluctuations in Actomyosin Stable States Increases the Predicted Force per Motor and Macroscopic Efficiency in Muscle Modelling
by Lorenzo Marcucci & Takumi Washio & Toshio Yanagida - 1-22 Statistical Analysis of Tract-Tracing Experiments Demonstrates a Dense, Complex Cortical Network in the Mouse
by Rolf J F Ypma & Edward T Bullmore - 1-23 Forecasting Human African Trypanosomiasis Prevalences from Population Screening Data Using Continuous Time Models
by Harwin de Vries & Albert P M Wagelmans & Epco Hasker & Crispin Lumbala & Pascal Lutumba & Sake J de Vlas & Joris van de Klundert - 1-25 Direct Correlation between Motile Behavior and Protein Abundance in Single Cells
by Yann S Dufour & Sébastien Gillet & Nicholas W Frankel & Douglas B Weibel & Thierry Emonet - 1-27 Separating Timing, Movement Conditions and Individual Differences in the Analysis of Human Movement
by Lars Lau Raket & Britta Grimme & Gregor Schöner & Christian Igel & Bo Markussen - 1-30 Error Correction and the Structure of Inter-Trial Fluctuations in a Redundant Movement Task
by Joby John & Jonathan B Dingwell & Joseph P Cusumano - 1-30 A Computational Model of Hepatic Energy Metabolism: Understanding Zonated Damage and Steatosis in NAFLD
by William B Ashworth & Nathan A Davies & I David L Bogle - 1-34 Leukocyte Motility Models Assessed through Simulation and Multi-objective Optimization-Based Model Selection
by Mark N Read & Jacqueline Bailey & Jon Timmis & Tatyana Chtanova