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October 2017, Volume 13, Issue 10
- 1-12 Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology
by Kevin S Bonham & Melanie I Stefan - 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 - 1-19 General principles of binding between cell surface receptors and multi-specific ligands: A computational study
by Jiawen Chen & Steven C Almo & Yinghao Wu - 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 Systematic, network-based characterization of therapeutic target inhibitors
by Yao Shen & Mariano J Alvarez & Brygida Bisikirska & Alexander Lachmann & Ronald Realubit & Sergey Pampou & Jorida Coku & Charles Karan & Andrea Califano - 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 Signatures of criticality arise from random subsampling in simple population models
by Marcel Nonnenmacher & Christian Behrens & Philipp Berens & Matthias Bethge & Jakob H Macke - 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 A continuum-mechanical skeletal muscle model including actin-titin interaction predicts stable contractions on the descending limb of the force-length relation
by Thomas Heidlauf & Thomas Klotz & Christian Rode & Tobias Siebert & Oliver Röhrle - 1-25 Image-based model of the spectrin cytoskeleton for red blood cell simulation
by Thomas G Fai & Alejandra Leo-Macias & David L Stokes & Charles S Peskin - 1-25 Point process analysis of noise in early invertebrate vision
by Kris V Parag & Glenn Vinnicombe - 1-25 Identifying parameter regions for multistationarity
by Carsten Conradi & Elisenda Feliu & Maya Mincheva & Carsten Wiuf - 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 - 1-26 Dynamics and heterogeneity of brain damage in multiple sclerosis
by Ekaterina Kotelnikova & Narsis A Kiani & Elena Abad & Elena H Martinez-Lapiscina & Magi Andorra & Irati Zubizarreta & Irene Pulido-Valdeolivas & Inna Pertsovskaya & Leonidas G Alexopoulos & Tomas Olsson & Roland Martin & Friedemann Paul & Jesper Tegnér & Jordi Garcia-Ojalvo & Pablo Villoslada - 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
- 1-1 Correction: Multiscale Approach to the Determination of the Photoactive Yellow Protein Signaling State Ensemble
by The PLOS Computational Biology Staff - 1-1 Correction: lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites
by The PLOS Computational Biology Staff - 1-1 Correction: Dose-response relationships for environmentally mediated infectious disease transmission models
by The PLOS Computational Biology Staff - 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 - 1-19 Mobility can promote the evolution of cooperation via emergent self-assortment dynamics
by Jaideep Joshi & Iain D Couzin & Simon A Levin & Vishwesha Guttal - 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 - 1-22 Probing eukaryotic cell mechanics via mesoscopic simulations
by Kirill Lykov & Yasaman Nematbakhsh & Menglin Shang & Chwee Teck Lim & Igor V Pivkin - 1-23 Limited synapse overproduction can speed development but sometimes with long-term energy and discrimination penalties
by Harang Ju & Costa M Colbert & William B Levy - 1-24 A conceptual and computational framework for modelling and understanding the non-equilibrium gene regulatory networks of mouse embryonic stem cells
by Richard B Greaves & Sabine Dietmann & Austin Smith & Susan Stepney & Julianne D Halley - 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 - 1-27 Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations
by Shintaroh Kubo & Wenfei Li & Shoji Takada - 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 - 1-31 Funneled potential and flux landscapes dictate the stabilities of both the states and the flow: Fission yeast cell cycle
by Xiaosheng Luo & Liufang Xu & Bo Han & Jin Wang - 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 - 1-8 The application of project-based learning in bioinformatics training
by Laura R Emery & Sarah L Morgan - 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 Measuring distance through dense weighted networks: The case of hospital-associated pathogens
by Tjibbe Donker & Timo Smieszek & Katherine L Henderson & Alan P Johnson & A Sarah Walker & Julie V Robotham - 1-19 Host population structure impedes reversion to drug sensitivity after discontinuation of treatment
by Jonas I Liechti & Gabriel E Leventhal & Sebastian Bonhoeffer - 1-20 Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing
by Mohamed Ali Ghadie & Luke Lambourne & Marc Vidal & Yu Xia - 1-21 Rearrangement moves on rooted phylogenetic networks
by Philippe Gambette & Leo van Iersel & Mark Jones & Manuel Lafond & Fabio Pardi & Celine Scornavacca - 1-22 Spatial dynamics of synthetic microbial mutualists and their parasites
by Daniel R Amor & Raúl Montañez & Salva Duran-Nebreda & Ricard Solé - 1-22 Histologic and biochemical alterations predict pulmonary mechanical dysfunction in aging mice with chronic lung inflammation
by Christopher B Massa & Angela M Groves & Smita U Jaggernauth & Debra L Laskin & Andrew J Gow - 1-22 Spread of hospital-acquired infections: A comparison of healthcare networks
by Narimane Nekkab & Pascal Astagneau & Laura Temime & Pascal Crépey - 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 - 1-23 A method of determining where to target surveillance efforts in heterogeneous epidemiological systems
by Alexander J Mastin & Frank van den Bosch & Timothy R Gottwald & Vasthi Alonso Chavez & Stephen R Parnell - 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 Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity
by Michal Bassani-Sternberg & Chloé Chong & Philippe Guillaume & Marthe Solleder & HuiSong Pak & Philippe O Gannon & Lana E Kandalaft & George Coukos & David Gfeller - 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 - 1-7 Correction: Parameter estimation for multistage clonal expansion models from cancer incidence data: A practical identifiability analysis
by Andrew F Brouwer & Rafael Meza & Marisa C Eisenberg - 1-14 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 - 1-18 Temporal specificity of the initial adaptive response in motor adaptation
by Wilsaan M Joiner & Gary C Sing & Maurice A Smith - 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 - 1-20 A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape
by William Gilpin & Marcus W Feldman - 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 A mixture of sparse coding models explaining properties of face neurons related to holistic and parts-based processing
by Haruo Hosoya & Aapo Hyvärinen - 1-27 TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions
by Zixuan Cang & Guo-Wei Wei - 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 - 1-27 Recurrently connected and localized neuronal communities initiate coordinated spontaneous activity in neuronal networks
by Davide Lonardoni & Hayder Amin & Stefano Di Marco & Alessandro Maccione & Luca Berdondini & Thierry Nieus - 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 - 1-10 Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network
by C Victor Jongeneel & Ovokeraye Achinike-Oduaran & Ezekiel Adebiyi & Marion Adebiyi & Seun Adeyemi & Bola Akanle & Shaun Aron & Efejiro Ashano & Hocine Bendou & Gerrit Botha & Emile Chimusa & Ananyo Choudhury & Ravikiran Donthu & Jenny Drnevich & Oluwadamila Falola & Christopher J Fields & Scott Hazelhurst & Liesl Hendry & Itunuoluwa Isewon & Radhika S Khetani & Judit Kumuthini & Magambo Phillip Kimuda & Lerato Magosi & Liudmila Sergeevna Mainzer & Suresh Maslamoney & Mamana Mbiyavanga & Ayton Meintjes & Danny Mugutso & Phelelani Mpangase & Richard Munthali & Victoria Nembaware & Andrew Ndhlovu & Trust Odia & Adaobi Okafor & Olaleye Oladipo & Sumir Panji & Venesa Pillay & Gloria Rendon & Dhriti Sengupta & Nicola Mulder - 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 - 1-18 Detecting similar binding pockets to enable systems polypharmacology
by Miquel Duran-Frigola & Lydia Siragusa & Eytan Ruppin & Xavier Barril & Gabriele Cruciani & Patrick Aloy - 1-19 LASSIM—A network inference toolbox for genome-wide mechanistic modeling
by Rasmus Magnusson & Guido Pio Mariotti & Mattias Köpsén & William Lövfors & Danuta R Gawel & Rebecka Jörnsten & Jörg Linde & Torbjörn E M Nordling & Elin Nyman & Sylvie Schulze & Colm E Nestor & Huan Zhang & Gunnar Cedersund & Mikael Benson & Andreas Tjärnberg & Mika Gustafsson - 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 - 1-20 Good enough practices in scientific computing
by Greg Wilson & Jennifer Bryan & Karen Cranston & Justin Kitzes & Lex Nederbragt & Tracy K Teal - 1-21 Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome
by Jens Christian Claussen & Jurgita Skiecevičienė & Jun Wang & Philipp Rausch & Tom H Karlsen & Wolfgang Lieb & John F Baines & Andre Franke & Marc-Thorsten Hütt - 1-22 Optimal structure of metaplasticity for adaptive learning
by Peyman Khorsand & Alireza Soltani - 1-23 Mitochondrial respiration and ROS emission during β-oxidation in the heart: An experimental-computational study
by Sonia Cortassa & Steven J Sollott & Miguel A Aon - 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 - 1-26 A review of active learning approaches to experimental design for uncovering biological networks
by Yuriy Sverchkov & Mark Craven - 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 - 1-30 A motor unit-based model of muscle fatigue
by Jim R Potvin & Andrew J Fuglevand - 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 - 1-34 Active Vertex Model for cell-resolution description of epithelial tissue mechanics
by Daniel L Barton & Silke Henkes & Cornelis J Weijer & Rastko Sknepnek - 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
- 1-1 Correction: Intrinsic Noise Profoundly Alters the Dynamics and Steady State of Morphogen-Controlled Bistable Genetic Switches
by The PLOS Computational Biology Staff - 1-6 Ten simple rules to consider regarding preprint submission
by Philip E Bourne & Jessica K Polka & Ronald D Vale & Robert Kiley - 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 - 1-10 Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers
by Björn A Grüning & Eric Rasche & Boris Rebolledo-Jaramillo & Carl Eberhard & Torsten Houwaart & John Chilton & Nate Coraor & Rolf Backofen & James Taylor & Anton Nekrutenko - 1-15 FIMTrack: An open source tracking and locomotion analysis software for small animals
by Benjamin Risse & Dimitri Berh & Nils Otto & Christian Klämbt & Xiaoyi Jiang - 1-15 Predicting cryptic links in host-parasite networks
by Tad Dallas & Andrew W Park & John M Drake - 1-17 phyC: Clustering cancer evolutionary trees
by Yusuke Matsui & Atsushi Niida & Ryutaro Uchi & Koshi Mimori & Satoru Miyano & Teppei Shimamura - 1-17 Short-term activity cycles impede information transmission in ant colonies
by Thomas O Richardson & Jonas I Liechti & Nathalie Stroeymeyt & Sebastian Bonhoeffer & Laurent Keller - 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 - 1-20 Post-transcriptional regulation across human tissues
by Alexander Franks & Edoardo Airoldi & Nikolai Slavov - 1-21 A predictive coding account of bistable perception - a model-based fMRI study
by Veith Weilnhammer & Heiner Stuke & Guido Hesselmann & Philipp Sterzer & Katharina Schmack - 1-21 Epidemiological modeling of Trypanosoma cruzi: Low stercorarian transmission and failure of host adaptive immunity explain the frequency of mixed infections in humans
by Nicolás Tomasini & Paula Gabriela Ragone & Sébastien Gourbière & Juan Pablo Aparicio & Patricio Diosque - 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 - 1-22 Mechanisms underlying different onset patterns of focal seizures
by Yujiang Wang & Andrew J Trevelyan & Antonio Valentin & Gonzalo Alarcon & Peter N Taylor & Marcus Kaiser - 1-22 Multi-scale computational study of the mechanical regulation of cell mitotic rounding in epithelia
by Ali Nematbakhsh & Wenzhao Sun & Pavel A Brodskiy & Aboutaleb Amiri & Cody Narciso & Zhiliang Xu & Jeremiah J Zartman & Mark Alber - 1-22 BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
by Eugen Bauer & Johannes Zimmermann & Federico Baldini & Ines Thiele & Christoph Kaleta - 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 - 1-29 The decay of motor adaptation to novel movement dynamics reveals an asymmetry in the stability of motion state-dependent learning
by Eghbal A Hosseini & Katrina P Nguyen & Wilsaan M Joiner - 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 - 1-32 Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks
by Don Klinkenberg & Jantien A Backer & Xavier Didelot & Caroline Colijn & Jacco Wallinga - 1-37 Dynamic decomposition of spatiotemporal neural signals
by Luca Ambrogioni & Marcel A J van Gerven & Eric Maris
April 2017, Volume 13, Issue 4
- 1-1 Correction: Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression
by The PLOS Computational Biology Staff - 1-1 Correction: The missing link: Predicting connectomes from noisy and partially observed tract tracing data
by Max Hinne & Annet Meijers & Rembrandt Bakker & Paul H E Tiesinga & Morten Mørup & Marcel A J van Gerven - 1-10 Ten simple rules for making research software more robust
by Morgan Taschuk & Greg Wilson - 1-14 Human behavioral complexity peaks at age 25
by Nicolas Gauvrit & Hector Zenil & Fernando Soler-Toscano & Jean-Paul Delahaye & Peter Brugger - 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 - 1-17 Dynamic compensation, parameter identifiability, and equivariances
by Eduardo D Sontag - 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 - 1-22 Sequence dependency of canonical base pair opening in the DNA double helix
by Viveca Lindahl & Alessandra Villa & Berk Hess - 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 - 1-26 Polarization and migration in the zebrafish posterior lateral line system
by Hildur Knutsdottir & Cole Zmurchok & Dhananjay Bhaskar & Eirikur Palsson & Damian Dalle Nogare & Ajay B Chitnis & Leah Edelstein-Keshet - 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
- 1-1 Correction: A Molecular Clock Infers Heterogeneous Tissue Age Among Patients with Barrett's Esophagus
by The PLOS Computational Biology Staff - 1-6 Ten simple rules for short and swift presentations
by Christopher J Lortie - 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 - 1-10 Ten simple rules for responsible big data research
by Matthew Zook & Solon Barocas & danah boyd & Kate Crawford & Emily Keller & Seeta Peña Gangadharan & Alyssa Goodman & Rachelle Hollander & Barbara A Koenig & Jacob Metcalf & Arvind Narayanan & Alondra Nelson & Frank Pasquale - 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 - 1-17 Dynamics robustness of cascading systems
by Jonathan T Young & Tetsuhiro S Hatakeyama & Kunihiko Kaneko