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Content
February 2018, Volume 14, Issue 2
- 1-21 Control fast or control smart: When should invading pathogens be controlled?
by Robin N Thompson & Christopher A Gilligan & Nik J Cunniffe - 1-22 A multiscale modelling approach to assess the impact of metabolic zonation and microperfusion on the hepatic carbohydrate metabolism
by Nikolaus Berndt & Marius Stefan Horger & Sascha Bulik & Hermann-Georg Holzhütter - 1-23 Prediction of infectious disease epidemics via weighted density ensembles
by Evan L Ray & Nicholas G Reich - 1-26 Interpretation of correlated neural variability from models of feed-forward and recurrent circuits
by Volker Pernice & Rava Azeredo da Silveira - 1-26 Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains
by Sneha Vishwanath & Alexandre G de Brevern & Narayanaswamy Srinivasan - 1-32 Simulation enabled search for explanatory mechanisms of the fracture healing process
by Ryan C Kennedy & Meir Marmor & Ralph Marcucio & C Anthony Hunt - 1-33 Imaging of neural oscillations with embedded inferential and group prevalence statistics
by Peter W Donhauser & Esther Florin & Sylvain Baillet - 1-34 Self-crowding of AMPA receptors in the excitatory postsynaptic density can effectuate anomalous receptor sub-diffusion
by Rahul Gupta - 1-36 Spike and burst coding in thalamocortical relay cells
by Fleur Zeldenrust & Pascal Chameau & Wytse J Wadman
January 2018, Volume 14, Issue 1
- 1-12 The ISCB Student Council Internship Program: Expanding computational biology capacity worldwide
by Jigisha Anupama & Margherita Francescatto & Farzana Rahman & Nazeefa Fatima & Dan DeBlasio & Avinash Kumar Shanmugam & Venkata Satagopam & Alberto Santos & Pandurang Kolekar & Magali Michaut & Emre Guney - 1-14 GSimp: A Gibbs sampler based left-censored missing value imputation approach for metabolomics studies
by Runmin Wei & Jingye Wang & Erik Jia & Tianlu Chen & Yan Ni & Wei Jia - 1-18 The E2.65A mutation disrupts dynamic binding poses of SB269652 at the dopamine D2 and D3 receptors
by Ravi Kumar Verma & Ara M Abramyan & Mayako Michino & R Benjamin Free & David R Sibley & Jonathan A Javitch & J Robert Lane & Lei Shi - 1-18 A model for cooperative gating of L-type Ca2+ channels and its effects on cardiac alternans dynamics
by Daisuke Sato & Rose E Dixon & Luis F Santana & Manuel F Navedo - 1-20 Interactions between species introduce spurious associations in microbiome studies
by Rajita Menon & Vivek Ramanan & Kirill S Korolev - 1-20 The role of spatial heterogeneity in the evolution of local and global infections of viruses
by Koich Saeki & Akira Sasaki - 1-23 Improving pairwise comparison of protein sequences with domain co-occurrence
by Christophe Menichelli & Olivier Gascuel & Laurent Bréhélin - 1-24 A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition
by Talia Zeppelin & Lucy Kate Ladefoged & Steffen Sinning & Xavier Periole & Birgit Schiøtt - 1-26 SozRank: A new approach for localizing the epileptic seizure onset zone
by Yonathan Murin & Jeremy Kim & Josef Parvizi & Andrea Goldsmith - 1-27 Clustering gene expression time series data using an infinite Gaussian process mixture model
by Ian C McDowell & Dinesh Manandhar & Christopher M Vockley & Amy K Schmid & Timothy E Reddy & Barbara E Engelhardt - 1-28 Robust and efficient coding with grid cells
by Lajos Vágó & Balázs B Ujfalussy - 1-29 Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance
by Jacob C Kimmel & Amy Y Chang & Andrew S Brack & Wallace F Marshall - 1-32 Bayesian inference of phylogenetic networks from bi-allelic genetic markers
by Jiafan Zhu & Dingqiao Wen & Yun Yu & Heidi M Meudt & Luay Nakhleh - 1-38 What drives the perceptual change resulting from speech motor adaptation? Evaluation of hypotheses in a Bayesian modeling framework
by Jean-François Patri & Pascal Perrier & Jean-Luc Schwartz & Julien Diard - 1-44 Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening
by Zixuan Cang & Lin Mu & Guo-Wei Wei
December 2017, Volume 13, Issue 12
- 1-5 Ten simple rules for international short-term research stays
by Diego A Forero & Sandra Lopez-Leon & George P Patrinos - 1-6 Ten simple rules for writing a career development award proposal
by Crystal M Botham & Joshua A Arribere & Sky W Brubaker & Kevin T Beier - 1-8 Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP
by Sanjay Sonney & Jeremy Leipzig & Marie T Lott & Shiping Zhang & Vincent Procaccio & Douglas C Wallace & Neal Sondheimer - 1-11 MAGPIE: Simplifying access and execution of computational models in the life sciences
by Christoph Baldow & Sebastian Salentin & Michael Schroeder & Ingo Roeder & Ingmar Glauche - 1-13 A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design
by Rebecca F Alford & Andrew Leaver-Fay & Lynda Gonzales & Erin L Dolan & Jeffrey J Gray - 1-16 Stabilizing patterns in time: Neural network approach
by Nadav Ben-Shushan & Misha Tsodyks - 1-20 MPLasso: Inferring microbial association networks using prior microbial knowledge
by Chieh Lo & Radu Marculescu - 1-20 High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock
by Nawsad Alam & Oriel Goldstein & Bing Xia & Kathryn A Porter & Dima Kozakov & Ora Schueler-Furman - 1-21 Complete hazard ranking to analyze right-censored data: An ALS survival study
by Zhengnan Huang & Hongjiu Zhang & Jonathan Boss & Stephen A Goutman & Bhramar Mukherjee & Ivo D Dinov & Yuanfang Guan & for the Pooled Resource Open-Access ALS Clinical Trials Consortium - 1-28 LRSSLMDA: Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction
by Xing Chen & Li Huang - 1-29 Costs of task allocation with local feedback: Effects of colony size and extra workers in social insects and other multi-agent systems
by Tsvetomira Radeva & Anna Dornhaus & Nancy Lynch & Radhika Nagpal & Hsin-Hao Su - 1-31 Genetic drift and selection in many-allele range expansions
by Bryan T Weinstein & Maxim O Lavrentovich & Wolfram Möbius & Andrew W Murray & David R Nelson - 1-37 Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks
by Ye Henry Li & Dangna Li & Nikolay Samusik & Xiaowei Wang & Leying Guan & Garry P Nolan & Wing Hung Wong
November 2017, Volume 13, Issue 11
- 1-12 fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks
by Edwin van Leeuwen & Petra Klepac & Dominic Thorrington & Richard Pebody & Marc Baguelin - 1-16 Tracking urban human activity from mobile phone calling patterns
by Daniel Monsivais & Asim Ghosh & Kunal Bhattacharya & Robin I M Dunbar & Kimmo Kaski - 1-16 The use of ambient humidity conditions to improve influenza forecast
by Jeffrey Shaman & Sasikiran Kandula & Wan Yang & Alicia Karspeck - 1-17 Individual versus superensemble forecasts of seasonal influenza outbreaks in the United States
by Teresa K Yamana & Sasikiran Kandula & Jeffrey Shaman - 1-18 Are there physicochemical differences between allosteric and competitive ligands?
by Richard D Smith & Jing Lu & Heather A Carlson - 1-18 Choose, rate or squeeze: Comparison of economic value functions elicited by different behavioral tasks
by Alizée Lopez-Persem & Lionel Rigoux & Sacha Bourgeois-Gironde & Jean Daunizeau & Mathias Pessiglione - 1-19 mixOmics: An R package for ‘omics feature selection and multiple data integration
by Florian Rohart & Benoît Gautier & Amrit Singh & Kim-Anh Lê Cao - 1-19 Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems
by Anthony Szedlak & Spencer Sims & Nicholas Smith & Giovanni Paternostro & Carlo Piermarocchi - 1-20 Multivariate pattern dependence
by Stefano Anzellotti & Alfonso Caramazza & Rebecca Saxe - 1-21 A Bayesian method for detecting pairwise associations in compositional data
by Emma Schwager & Himel Mallick & Steffen Ventz & Curtis Huttenhower - 1-22 The effect of spatial randomness on the average fixation time of mutants
by Suzan Farhang-Sardroodi & Amir H Darooneh & Moladad Nikbakht & Natalia L Komarova & Mohammad Kohandel - 1-23 Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs
by Michael F Sloma & David H Mathews - 1-25 Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq
by Ruolin Liu & Julie Dickerson - 1-26 Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil
by Shaima Hashem & Matteo Tiberti & Arianna Fornili - 1-27 An efficient moments-based inference method for within-host bacterial infection dynamics
by David J Price & Alexandre Breuzé & Richard Dybowski & Piero Mastroeni & Olivier Restif - 1-29 Initial-state-dependent, robust, transient neural dynamics encode conscious visual perception
by Alexis T Baria & Brian Maniscalco & Biyu J He - 1-32 Identifying influential neighbors in animal flocking
by Li Jiang & Luca Giuggioli & Andrea Perna & Ramón Escobedo & Valentin Lecheval & Clément Sire & Zhangang Han & Guy Theraulaz - 1-33 Electrical stimulus artifact cancellation and neural spike detection on large multi-electrode arrays
by Gonzalo E Mena & Lauren E Grosberg & Sasidhar Madugula & Paweł Hottowy & Alan Litke & John Cunningham & E J Chichilnisky & Liam Paninski - 1-38 A hierarchical stochastic model for bistable perception
by Stefan Albert & Katharina Schmack & Philipp Sterzer & Gaby Schneider
October 2017, Volume 13, Issue 10
- 1-5 Ten simple rules in considering a career in academia versus government
by Philip E Bourne - 1-9 Network propagation in the cytoscape cyberinfrastructure
by Daniel E Carlin & Barry Demchak & Dexter Pratt & Eric Sage & Trey Ideker - 1-14 Identification of immune signatures predictive of clinical protection from malaria
by John Joseph Valletta & Mario Recker - 1-15 Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing
by Yaron Orenstein & David Pellow & Guillaume Marçais & Ron Shamir & Carl Kingsford - 1-18 Vicus: Exploiting local structures to improve network-based analysis of biological data
by Bo Wang & Lin Huang & Yuke Zhu & Anshul Kundaje & Serafim Batzoglou & Anna Goldenberg - 1-18 A mechanistic spatio-temporal framework for modelling individual-to-individual transmission—With an application to the 2014-2015 West Africa Ebola outbreak
by Max S Y Lau & Gavin J Gibson & Hola Adrakey & Amanda McClelland & Steven Riley & Jon Zelner & George Streftaris & Sebastian Funk & Jessica Metcalf & Benjamin D Dalziel & Bryan T Grenfell - 1-21 Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization
by Claire N Bedbrook & Kevin K Yang & Austin J Rice & Viviana Gradinaru & Frances H Arnold - 1-21 Modeling the adenosine system as a modulator of cognitive performance and sleep patterns during sleep restriction and recovery
by Andrew J K Phillips & Elizabeth B Klerman & James P Butler - 1-22 Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster
by Cen Wan & Jonathan G Lees & Federico Minneci & Christine A Orengo & David T Jones - 1-23 Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time
by Anna Hake & Nico Pfeifer - 1-24 A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action
by Shiran Abadi & Winston X Yan & David Amar & Itay Mayrose - 1-24 Decoding brain activity using a large-scale probabilistic functional-anatomical atlas of human cognition
by Timothy N Rubin & Oluwasanmi Koyejo & Krzysztof J Gorgolewski & Michael N Jones & Russell A Poldrack & Tal Yarkoni - 1-25 Learning causal networks with latent variables from multivariate information in genomic data
by Louis Verny & Nadir Sella & Séverine Affeldt & Param Priya Singh & Hervé Isambert - 1-25 Point process analysis of noise in early invertebrate vision
by Kris V Parag & Glenn Vinnicombe - 1-25 A Bayesian approach to modelling heterogeneous calcium responses in cell populations
by Agne Tilūnaitė & Wayne Croft & Noah Russell & Tomas C Bellamy & Rüdiger Thul - 1-27 Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics
by Roman Shevchuk & Jochen S Hub - 1-27 A deep convolutional neural network for classification of red blood cells in sickle cell anemia
by Mengjia Xu & Dimitrios P Papageorgiou & Sabia Z Abidi & Ming Dao & Hong Zhao & George Em Karniadakis - 1-28 A unifying Bayesian account of contextual effects in value-based choice
by Francesco Rigoli & Christoph Mathys & Karl J Friston & Raymond J Dolan - 1-28 Object detection through search with a foveated visual system
by Emre Akbas & Miguel P Eckstein - 1-29 Clusternomics: Integrative context-dependent clustering for heterogeneous datasets
by Evelina Gabasova & John Reid & Lorenz Wernisch - 1-30 Neural field model to reconcile structure with function in primary visual cortex
by James Rankin & Frédéric Chavane - 1-31 The structured ‘low temperature’ phase of the retinal population code
by Mark L Ioffe & Michael J Berry II - 1-31 The evolutionary origins of Lévy walk foraging
by Marina E Wosniack & Marcos C Santos & Ernesto P Raposo & Gandhi M Viswanathan & Marcos G E da Luz - 1-31 Inferring oscillatory modulation in neural spike trains
by Kensuke Arai & Robert E Kass - 1-32 Distinct prediction errors in mesostriatal circuits of the human brain mediate learning about the values of both states and actions: evidence from high-resolution fMRI
by Jaron T Colas & Wolfgang M Pauli & Tobias Larsen & J Michael Tyszka & John P O’Doherty - 1-33 A quadratically regularized functional canonical correlation analysis for identifying the global structure of pleiotropy with NGS data
by Nan Lin & Yun Zhu & Ruzong Fan & Momiao Xiong - 1-37 A theoretical framework for analyzing coupled neuronal networks: Application to the olfactory system
by Andrea K Barreiro & Shree Hari Gautam & Woodrow L Shew & Cheng Ly - 1-41 A single-cell spiking model for the origin of grid-cell patterns
by Tiziano D’Albis & Richard Kempter - 1-44 Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models
by Vahid Rostami & PierGianLuca Porta Mana & Sonja Grün & Moritz Helias
September 2017, Volume 13, Issue 9
- 1-3 How can computation advance microbiome research?
by Ruth Nussinov & Jason A Papin - 1-4 Ten simple rules for developing a mentor–mentee expectations document
by Kristyn S Masters & Pamela K Kreeger - 1-8 Ten simple rules for successfully completing a graduate degree in Latin America
by Ernesto Ruelas Inzunza & Gabriela I Salazar-Rivera & Magdiel Láinez & María Guadalupe Ruiz-Gómez & Carlo A Domínguez-Eusebio & Griselda Cristóbal-Sánchez & Issaac A Teodosio Faustino & Edel Pérez-López & Meagan L Campbell & Marcus Vinicius Merfa & Ivonne Tatiana Latorre Beltrán & Fernanda Armas & Claudio Mota-Vargas - 1-9 Ten simple rules for structuring papers
by Brett Mensh & Konrad Kording - 1-13 Reconstructing promoter activity from Lux bioluminescent reporters
by Mudassar Iqbal & Neil Doherty & Anna M L Page & Saara N A Qazi & Ishan Ajmera & Peter A Lund & Theodore Kypraios & David J Scott & Philip J Hill & Dov J Stekel - 1-15 Flexibility to contingency changes distinguishes habitual and goal-directed strategies in humans
by Julie J Lee & Mehdi Keramati - 1-17 DeepPep: Deep proteome inference from peptide profiles
by Minseung Kim & Ameen Eetemadi & Ilias Tagkopoulos - 1-17 Exploiting ecology in drug pulse sequences in favour of population reduction
by Marianne Bauer & Isabella R Graf & Vudtiwat Ngampruetikorn & Greg J Stephens & Erwin Frey - 1-18 Cost-efficient vaccination protocols for network epidemiology
by Petter Holme & Nelly Litvak - 1-20 Stochastic principles governing alternative splicing of RNA
by Jianfei Hu & Eli Boritz & William Wylie & Daniel C Douek - 1-20 C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis
by Kaido Lepik & Tarmo Annilo & Viktorija Kukuškina & eQTLGen Consortium & Kai Kisand & Zoltán Kutalik & Pärt Peterson & Hedi Peterson - 1-22 Modeling antibiotic treatment in hospitals: A systematic approach shows benefits of combination therapy over cycling, mixing, and mono-drug therapies
by Burcu Tepekule & Hildegard Uecker & Isabel Derungs & Antoine Frenoy & Sebastian Bonhoeffer - 1-25 Relating dynamic brain states to dynamic machine states: Human and machine solutions to the speech recognition problem
by Cai Wingfield & Li Su & Xunying Liu & Chao Zhang & Phil Woodland & Andrew Thwaites & Elisabeth Fonteneau & William D Marslen-Wilson - 1-26 Probabilistic models for neural populations that naturally capture global coupling and criticality
by Jan Humplik & Gašper Tkačik - 1-29 A single Markov-type kinetic model accounting for the macroscopic currents of all human voltage-gated sodium channel isoforms
by Pietro Balbi & Paolo Massobrio & Jeanette Hellgren Kotaleski - 1-35 Predictive representations can link model-based reinforcement learning to model-free mechanisms
by Evan M Russek & Ida Momennejad & Matthew M Botvinick & Samuel J Gershman & Nathaniel D Daw - 1-37 Features of spatial and functional segregation and integration of the primate connectome revealed by trade-off between wiring cost and efficiency
by Yuhan Chen & Shengjun Wang & Claus C Hilgetag & Changsong Zhou
August 2017, Volume 13, Issue 8
- 1-7 Ten simple rules for getting the most out of a summer laboratory internship
by Toby P Aicher & Dániel L Barabási & Benjamin D Harris & Ajay Nadig & Kaitlin L Williams - 1-7 Ten simple rules to initiate and run a postdoctoral association
by Chiara Bruckmann & Endre Sebestyén - 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