PLOS Computational Biology

2005 - 2025

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Volume 15, issue 12, 2019

Regulatory context drives conservation of glycine riboswitch aptamers pp. 1-24

Matt Crum, Nikhil Ram-Mohan and Michelle M Meyer

CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data pp. 1-18

Kai Kang, Qian Meng, Igor Shats, David M Umbach, Melissa Li, Yuanyuan Li, Xiaoling Li and Leping Li

Fine-scale family structure shapes influenza transmission risk in households: Insights from primary schools in Matsumoto city, 2014/15 pp. 1-18

Akira Endo, Mitsuo Uchida, Adam J Kucharski and Sebastian Funk

Nine quick tips for analyzing network data pp. 1-10

Vincent Miele, Catherine Matias, Stéphane Robin and Stéphane Dray

Motion prediction enables simulated MR-imaging of freely moving model organisms pp. 1-16

Markus Reischl, Mazin Jouda, Neil MacKinnon, Erwin Fuhrer, Natalia Bakhtina, Andreas Bartschat, Ralf Mikut and Jan G Korvink

Statistical inference in ensemble modeling of cellular metabolism pp. 1-16

Tuure Hameri, Marc-Olivier Boldi and Vassily Hatzimanikatis

Benchmarking network algorithms for contextualizing genes of interest pp. 1-14

Abby Hill, Scott Gleim, Florian Kiefer, Frederic Sigoillot, Joseph Loureiro, Jeremy Jenkins and Melody K Morris

ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest pp. 1-30

Jiajin Li, Brandon Jew, Lingyu Zhan, Sungoo Hwang, Giovanni Coppola, Nelson B Freimer and Jae Hoon Sul

Representation learning of genomic sequence motifs with convolutional neural networks pp. 1-17

Peter K Koo and Sean R Eddy

Inferring reaction network structure from single-cell, multiplex data, using toric systems theory pp. 1-25

Shu Wang, Jia-Ren Lin, Eduardo D Sontag and Peter K Sorger

Stability of spontaneous, correlated activity in mouse auditory cortex pp. 1-25

Richard F Betzel, Katherine C Wood, Christopher Angeloni, Maria Neimark Geffen and Danielle S Bassett

Incomplete information about the partner affects the development of collaborative strategies in joint action pp. 1-23

Vinil T Chackochan and Vittorio Sanguineti

Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling pp. 1-23

Giacomo Janson, Alessandro Grottesi, Marco Pietrosanto, Gabriele Ausiello, Giulia Guarguaglini and Alessandro Paiardini

From energy to cellular forces in the Cellular Potts Model: An algorithmic approach pp. 1-23

Elisabeth G Rens and Leah Edelstein-Keshet

Stochasticity of replication forks’ speeds plays a key role in the dynamics of DNA replication pp. 1-19

Razie Yousefi and Maga Rowicka

Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models pp. 1-21

Colette Mair, Sema Nickbakhsh, Richard Reeve, Jim McMenamin, Arlene Reynolds, Rory N Gunson, Pablo R Murcia and Louise Matthews

Overlap matrix completion for predicting drug-associated indications pp. 1-21

Mengyun Yang, Huimin Luo, Yaohang Li, Fang-Xiang Wu and Jianxin Wang

The effect of inhibition on rate code efficiency indicators pp. 1-21

Tomas Barta and Lubomir Kostal

Volume 15, issue 11, 2019

Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process pp. 1-17

Jifan Shi, Tiejun Li, Luonan Chen and Kazuyuki Aihara

Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture pp. 1-35

Jilin W J L Wang, Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet and Plamen Ch Ivanov

Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences pp. 1-27

Ilya Plyusnin, Liisa Holm and Petri Törönen

Large-scale cortical travelling waves predict localized future cortical signals pp. 1-34

David M Alexander, Tonio Ball, Andreas Schulze-Bonhage and Cees van Leeuwen

Feasibility of functional magnetic resonance imaging of ocular dominance and orientation preference in primary visual cortex pp. 1-19

Marilia Menezes de Oliveira, James C Pang, Peter A Robinson, Xiaochen Liu and Mark M Schira

Uncovering the subtype-specific temporal order of cancer pathway dysregulation pp. 1-19

Sahand Khakabimamaghani, Dujian Ding, Oliver Snow and Martin Ester

Accuracy of real-time multi-model ensemble forecasts for seasonal influenza in the U.S pp. 1-19

Nicholas G Reich, Craig J McGowan, Teresa K Yamana, Abhinav Tushar, Evan L Ray, Dave Osthus, Sasikiran Kandula, Logan C Brooks, Willow Crawford-Crudell, Graham Casey Gibson, Evan Moore, Rebecca Silva, Matthew Biggerstaff, Michael A Johansson, Roni Rosenfeld and Jeffrey Shaman

Neural field models for latent state inference: Application to large-scale neuronal recordings pp. 1-23

Michael E Rule, David Schnoerr, Matthias H Hennig and Guido Sanguinetti

Forecasting dengue and influenza incidences using a sparse representation of Google trends, electronic health records, and time series data pp. 1-24

Prashant Rangarajan, Sandeep K Mody and Madhav Marathe

Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps pp. 1-32

Yichen Zheng and Thomas Wiehe

Tonic exploration governs both flexibility and lapses pp. 1-37

R Becket Ebitz, Brianna J Sleezer, Hank P Jedema, Charles W Bradberry and Benjamin Y Hayden

Volume 15, issue 10, 2019

Hypergraph-based connectivity measures for signaling pathway topologies pp. 1-26

Nicholas Franzese, Adam Groce, T M Murali and Anna Ritz

Phylogenetic correlations can suffice to infer protein partners from sequences pp. 1-24

Guillaume Marmier, Martin Weigt and Anne-Florence Bitbol

Categorical encoding of decision variables in orbitofrontal cortex pp. 1-27

Arno Onken, Jue Xie, Stefano Panzeri and Camillo Padoa-Schioppa

Color improves edge classification in human vision pp. 1-15

Camille Breuil, Ben J Jennings, Simon Barthelmé, Nathalie Guyader and Frederick A A Kingdom

The folded X-pattern is not necessarily a statistical signature of decision confidence pp. 1-18

Manuel Rausch and Michael Zehetleitner

Sequence specificity despite intrinsic disorder: How a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein pp. 1-29

Ruchi Lohia, Reza Salari and Grace Brannigan

Ten simple rules for providing optimal administrative support to research teams pp. 1-9

Romina Garrido, Casandra A Trowbridge and Nana Tamura

Combinations of low-level and high-level neural processes account for distinct patterns of context-dependent choice pp. 1-31

Mehran Spitmaan, Oihane Horno, Emily Chu and Alireza Soltani

Estimating influenza incidence using search query deceptiveness and generalized ridge regression pp. 1-23

Reid Priedhorsky, Ashlynn R Daughton, Martha Barnard, Fiona O’Connell and Dave Osthus

A computational account of threat-related attentional bias pp. 1-21

Toby Wise, Jochen Michely, Peter Dayan and Raymond J Dolan

Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature pp. 1-22

Qiao Liu, Di He and Lei Xie

A simulation of the random and directed motion of dendritic cells in chemokine fields pp. 1-16

Avery Parr, Nicholas R Anderson and Daniel A Hammer

Uncovering and characterizing splice variants associated with survival in lung cancer patients pp. 1-16

Sean West, Sushil Kumar, Surinder K Batra, Hesham Ali and Dario Ghersi

Ten simple rules to aid in achieving a vision pp. 1-5

Philip E Bourne

Evaluation of linear and non-linear activation dynamics models for insect muscle pp. 1-30

Nalin Harischandra, Anthony J Clare, Jure Zakotnik, Laura M L Blackburn, Tom Matheson and Volker Dürr

Fungal feature tracker (FFT): A tool for quantitatively characterizing the morphology and growth of filamentous fungi pp. 1-20

Guillermo Vidal-Diez de Ulzurrun, Tsung-Yu Huang, Ching-Wen Chang, Hung-Che Lin and Yen-Ping Hsueh

SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways pp. 1-28

Elisa Salviato, Vera Djordjilović, Monica Chiogna and Chiara Romualdi

Volume 15, issue 9, 2019

A flexible and generalizable model of online latent-state learning pp. 1-31

Amy L Cochran and Josh M Cisler

Network trade-offs and homeostasis in Arabidopsis shoot architectures pp. 1-19

Adam Conn, Arjun Chandrasekhar, Martin van Rongen, Ottoline Leyser, Joanne Chory and Saket Navlakha

Executable pathway analysis using ensemble discrete-state modeling for large-scale data pp. 1-21

Rohith Palli, Mukta G Palshikar and Juilee Thakar

Multi-cell ECM compaction is predictable via superposition of nonlinear cell dynamics linearized in augmented state space pp. 1-22

Michaëlle N Mayalu, Min-Cheol Kim and H Harry Asada

Learning the structure of the world: The adaptive nature of state-space and action representations in multi-stage decision-making pp. 1-22

Amir Dezfouli and Bernard W Balleine

Time scales and wave formation in non-linear spatial public goods games pp. 1-22

Gregory J Kimmel, Philip Gerlee and Philipp M Altrock

Prepaid parameter estimation without likelihoods pp. 1-42

Merijn Mestdagh, Stijn Verdonck, Kristof Meers, Tim Loossens and Francis Tuerlinckx

Estimating information in time-varying signals pp. 1-33

Sarah Anhala Cepeda-Humerez, Jakob Ruess and Gašper Tkačik

Characterizing and dissociating multiple time-varying modulatory computations influencing neuronal activity pp. 1-38

Kaiser Niknam, Amir Akbarian, Kelsey Clark, Yasin Zamani, Behrad Noudoost and Neda Nategh

Optimizing spatial allocation of seasonal influenza vaccine under temporal constraints pp. 1-17

Srinivasan Venkatramanan, Jiangzhuo Chen, Arindam Fadikar, Sandeep Gupta, Dave Higdon, Bryan Lewis, Madhav Marathe, Henning Mortveit and Anil Vullikanti

MHC binding affects the dynamics of different T-cell receptors in different ways pp. 1-17

Bernhard Knapp, P Anton van der Merwe, Omer Dushek and Charlotte M Deane

Cost-benefit trade-offs in decision-making and learning pp. 1-28

Nura Sidarus, Stefano Palminteri and Valérian Chambon

Close spatial arrangement of mutants favors and disfavors fixation pp. 1-20

Yunming Xiao and Bin Wu

Benchmarking network propagation methods for disease gene identification pp. 1-24

Sergio Picart-Armada, Steven J Barrett, David R Willé, Alexandre Perera-Lluna, Alex Gutteridge and Benoit H Dessailly

Deconvolving multiplexed protease signatures with substrate reduction and activity clustering pp. 1-18

Qinwei Zhuang, Brandon Alexander Holt, Gabriel A Kwong and Peng Qiu

Ten simple rules for helping newcomers become contributors to open projects pp. 1-10

Dan Sholler, Igor Steinmacher, Denae Ford, Mara Averick, Mike Hoye and Greg Wilson

Generation of Binary Tree-Child phylogenetic networks pp. 1-29

Gabriel Cardona, Joan Carles Pons and Celine Scornavacca

Volume 15, issue 8, 2019

The formation of preference in risky choice pp. 1-25

Moshe Glickman, Orian Sharoni, Dino J Levy, Ernst Niebur, Veit Stuphorn and Marius Usher

Machine learning-based microarray analyses indicate low-expression genes might collectively influence PAH disease pp. 1-25

Song Cui, Qiang Wu, James West and Jiangping Bai

Mechanical properties of tubulin intra- and inter-dimer interfaces and their implications for microtubule dynamic instability pp. 1-25

Vladimir A Fedorov, Philipp S Orekhov, Ekaterina G Kholina, Artem A Zhmurov, Fazoil I Ataullakhanov, Ilya B Kovalenko and Nikita B Gudimchuk

PanoView: An iterative clustering method for single-cell RNA sequencing data pp. 1-17

Ming-Wen Hu, Dong Won Kim, Sheng Liu, Donald J Zack, Seth Blackshaw and Jiang Qian

Predicting the effects of deep brain stimulation using a reduced coupled oscillator model pp. 1-28

Gihan Weerasinghe, Benoit Duchet, Hayriye Cagnan, Peter Brown, Christian Bick and Rafal Bogacz

Transient crosslinking kinetics optimize gene cluster interactions pp. 1-28

Benjamin Walker, Dane Taylor, Josh Lawrimore, Caitlin Hult, David Adalsteinsson, Kerry Bloom and M Gregory Forest

A generative learning model for saccade adaptation pp. 1-35

Carlos R Cassanello, Florian Ostendorf and Martin Rolfs

Identifying nonlinear dynamical systems via generative recurrent neural networks with applications to fMRI pp. 1-35

Georgia Koppe, Hazem Toutounji, Peter Kirsch, Stefanie Lis and Daniel Durstewitz

Fast uncertainty quantification for dynamic flux balance analysis using non-smooth polynomial chaos expansions pp. 1-35

Joel A Paulson, Marc Martin-Casas and Ali Mesbah

Directed migration shapes cooperation in spatial ecological public goods games pp. 1-14

Felix Funk and Christoph Hauert

Reappraising the utility of Google Flu Trends pp. 1-16

Sasikiran Kandula and Jeffrey Shaman

FAMoS: A Flexible and dynamic Algorithm for Model Selection to analyse complex systems dynamics pp. 1-23

Michael Gabel, Tobias Hohl, Andrea Imle, Oliver T Fackler and Frederik Graw

Twelve quick tips for designing sound dynamical models for bioprocesses pp. 1-8

Francis Mairet and Olivier Bernard

Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties pp. 1-29

Ljubisa Miskovic, Jonas Béal, Michael Moret and Vassily Hatzimanikatis

Bayesian hypothesis testing and experimental design for two-photon imaging data pp. 1-27

Luke E Rogerson, Zhijian Zhao, Katrin Franke, Thomas Euler and Philipp Berens

Arrhythmia mechanisms and spontaneous calcium release: Bi-directional coupling between re-entrant and focal excitation pp. 1-34

Michael A Colman

Tracking Pseudomonas aeruginosa transmissions due to environmental contamination after discharge in ICUs using mathematical models pp. 1-26

Thi Mui Pham, Mirjam Kretzschmar, Xavier Bertrand, Martin Bootsma and on behalf of COMBACTE-MAGNET Consortium

Volume 15, issue 7, 2019

DART-ID increases single-cell proteome coverage pp. 1-30

Albert Tian Chen, Alexander Franks and Nikolai Slavov

Think: Theory for Africa pp. 1-5

Christopher B Currin, Phumlani N Khoza, Alexander D Antrobus, Peter E Latham, Tim P Vogels and Joseph V Raimondo

Disease gene prediction for molecularly uncharacterized diseases pp. 1-14

Juan J Cáceres and Alberto Paccanaro

A computational framework for the morpho-elastic development of molluskan shells by surface and volume growth pp. 1-28

Shiva Rudraraju, Derek E Moulton, Régis Chirat, Alain Goriely and Krishna Garikipati

Ten simple rules for giving an effective academic job talk pp. 1-8

Shayna A Sura, Lauren L Smith, Monique R Ambrose, C Eduardo Guerra Amorim, Annabel C Beichman, Ana C R Gomez, Mark Juhn, Gaurav S Kandlikar, Julie S Miller, Jazlyn Mooney, Riley O Mummah, Kirk E Lohmueller and James O Lloyd-Smith

Foraging as an evidence accumulation process pp. 1-25

Jacob D Davidson and Ahmed El Hady

Human online adaptation to changes in prior probability pp. 1-26

Elyse H Norton, Luigi Acerbi, Wei Ji Ma and Michael S Landy

Predictions of time to HIV viral rebound following ART suspension that incorporate personal biomarkers pp. 1-26

Jessica M Conway, Alan S Perelson and Jonathan Z Li

With an eye on uncertainty: Modelling pupillary responses to environmental volatility pp. 1-22

Peter Vincent, Thomas Parr, David Benrimoh and Karl J Friston

Primacy coding facilitates effective odor discrimination when receptor sensitivities are tuned pp. 1-22

David Zwicker

Depressive symptoms are associated with blunted reward learning in social contexts pp. 1-22

Lou Safra, Coralie Chevallier and Stefano Palminteri

Volume 15, issue 6, 2019

Ten simple rules for successfully hosting an intern at a scientific software company pp. 1-4

Kristine Briedis, Yi-Shiou Chen and Scott Markel

Telling ecological networks apart by their structure: A computational challenge pp. 1-13

Matthew J Michalska-Smith and Stefano Allesina

From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training pp. 1-12

Annette McGrath, Katherine Champ, Catherine A Shang, Ellen van Dam, Cath Brooksbank and Sarah L Morgan

Mathematical model studies of the comprehensive generation of major and minor phyllotactic patterns in plants with a predominant focus on orixate phyllotaxis pp. 1-27

Takaaki Yonekura, Akitoshi Iwamoto, Hironori Fujita and Munetaka Sugiyama

Evolution of interface binding strengths in simplified model of protein quaternary structure pp. 1-15

Alexander S Leonard and Sebastian E Ahnert

Evidence accumulation is biased by motivation: A computational account pp. 1-15

Filip Gesiarz, Donal Cahill and Tali Sharot

How single neuron properties shape chaotic dynamics and signal transmission in random neural networks pp. 1-35

Samuel P Muscinelli, Wulfram Gerstner and Tilo Schwalger

Learning to use past evidence in a sophisticated world model pp. 1-20

Sanjeevan Ahilan, Rebecca B Solomon, Yannick-André Breton, Kent Conover, Ritwik K Niyogi, Peter Shizgal and Peter Dayan

Drosophila melanogaster grooming possesses syntax with distinct rules at different temporal scales pp. 1-25

Joshua M Mueller, Primoz Ravbar, Julie H Simpson and Jean M Carlson

Ten quick tips for effective dimensionality reduction pp. 1-19

Lan Huong Nguyen and Susan Holmes

Modeling the temporal dynamics of the gut microbial community in adults and infants pp. 1-21

Liat Shenhav, Ori Furman, Leah Briscoe, Mike Thompson, Justin D Silverman, Itzhak Mizrahi and Eran Halperin

DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences pp. 1-21

Ingoo Lee, Jongsoo Keum and Hojung Nam

Volume 15, issue 5, 2019

Beyond Bouma's window: How to explain global aspects of crowding? pp. 1-28

Adrien Doerig, Alban Bornet, Ruth Rosenholtz, Gregory Francis, Aaron M Clarke and Michael H Herzog

DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images pp. 1-20

Victor Kulikov, Syuan-Ming Guo, Matthew Stone, Allen Goodman, Anne Carpenter, Mark Bathe and Victor Lempitsky

Forecasting national and regional influenza-like illness for the USA pp. 1-20

Michal Ben-Nun, Pete Riley, James Turtle, David P Bacon and Steven Riley

An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis pp. 1-25

Niki Karagianni, Ksanthi Kranidioti, Nikolaos Fikas, Maria Tsochatzidou, Panagiotis Chouvardas, Maria C Denis, George Kollias and Christoforos Nikolaou

Ten simple rules for carrying out and writing meta-analyses pp. 1-7

Diego A Forero, Sandra Lopez-Leon, Yeimy González-Giraldo and Pantelis G Bagos

Representational structure or task structure? Bias in neural representational similarity analysis and a Bayesian method for reducing bias pp. 1-30

Ming Bo Cai, Nicolas W Schuck, Jonathan W Pillow and Yael Niv

The statistics of epidemic transitions pp. 1-14

John M Drake, Tobias S Brett, Shiyang Chen, Bogdan I Epureanu, Matthew J Ferrari, Éric Marty, Paige B Miller, Eamon B O’Dea, Suzanne M O’Regan, Andrew W Park and Pejman Rohani

Identification of avian flapping motion from non-volant winged dinosaurs based on modal effective mass analysis pp. 1-16

Yaser Saffar Talori, Jing-Shan Zhao, Yun-Fei Liu, Wen-Xiu Lu, Zhi-Heng Li and Jingmai Kathleen O'Connor

Interacting cells driving the evolution of multicellular life cycles pp. 1-16

Yuanxiao Gao, Arne Traulsen and Yuriy Pichugin

Spatial neuronal synchronization and the waveform of oscillations: Implications for EEG and MEG pp. 1-22

Natalie Schaworonkow and Vadim V Nikulin

Amplitude cancellation influences the association between frequency components in the neural drive to muscle and the rectified EMG signal pp. 1-19

Jakob Lund Dideriksen and Dario Farina

Modeling enamel matrix secretion in mammalian teeth pp. 1-12

Teemu J Häkkinen, S Susanna Sova, Ian J Corfe, Leo Tjäderhane, Antti Hannukainen and Jukka Jernvall

Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features pp. 1-18

David A Knowles, Gina Bouchard and Sylvia Plevritis

Parameter estimation and identifiability in a neural population model for electro-cortical activity pp. 1-27

Agus Hartoyo, Peter J Cadusch, David T J Liley and Damien G Hicks

State-aware detection of sensory stimuli in the cortex of the awake mouse pp. 1-24

Audrey J Sederberg, Aurélie Pala, He J V Zheng, Biyu J He and Garrett B Stanley

Efficient algorithms to discover alterations with complementary functional association in cancer pp. 1-24

Rebecca Sarto Basso, Dorit S Hochbaum and Fabio Vandin

Volume 15, issue 4, 2019

A Bayesian framework for the analysis of systems biology models of the brain pp. 1-29

Joshua Russell-Buckland, Christopher P Barnes and Ilias Tachtsidis

A benchmark-driven approach to reconstruct metabolic networks for studying cancer metabolism pp. 1-29

Oveis Jamialahmadi, Sameereh Hashemi-Najafabadi, Ehsan Motamedian, Stefano Romeo and Fatemeh Bagheri

Ten simple rules towards healthier research labs pp. 1-8

Fernando T Maestre

Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size pp. 1-24

Daniel I S Rosenbloom, Peter Bacchetti, Mars Stone, Xutao Deng, Ronald J Bosch, Douglas D Richman, Janet D Siliciano, John W Mellors, Steven G Deeks, Roger G Ptak, Rebecca Hoh, Sheila M Keating, Melanie Dimapasoc, Marta Massanella, Jun Lai, Michele D Sobolewski, Deanna A Kulpa, Michael P Busch and for the Reservoir Assay Validation and Evaluation Network (RAVEN) Study Group

Confidence resets reveal hierarchical adaptive learning in humans pp. 1-24

Micha Heilbron and Florent Meyniel

Rich-club connectivity, diverse population coupling, and dynamical activity patterns emerging from local cortical circuits pp. 1-34

Yifan Gu, Yang Qi and Pulin Gong

Imperfect Bayesian inference in visual perception pp. 1-27

Elina Stengård and Ronald van den Berg

The relative contribution of color and material in object selection pp. 1-27

Ana Radonjić, Nicolas P Cottaris and David H Brainard

Contextual influence on confidence judgments in human reinforcement learning pp. 1-27

Mael Lebreton, Karin Bacily, Stefano Palminteri and Jan Engelmann

Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE) pp. 1-10

Hailong Meng, Gur Yaari, Christopher R Bolen, Stefan Avey and Steven H Kleinstein

Adaptive multi-view multi-label learning for identifying disease-associated candidate miRNAs pp. 1-18

Cheng Liang, Shengpeng Yu and Jiawei Luo

The intrinsic dimension of protein sequence evolution pp. 1-16

Elena Facco, Andrea Pagnani, Elena Tea Russo and Alessandro Laio

Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features pp. 1-35

Craig A Magaret, David C Benkeser, Brian D Williamson, Bhavesh R Borate, Lindsay N Carpp, Ivelin S Georgiev, Ian Setliff, Adam S Dingens, Noah Simon, Marco Carone, Christopher Simpkins, David Montefiori, Galit Alter, Wen-Han Yu, Michal Juraska, Paul T Edlefsen, Shelly Karuna, Nyaradzo M Mgodi, Srilatha Edugupanti and Peter B Gilbert

SPINDLE: End-to-end learning from EEG/EMG to extrapolate animal sleep scoring across experimental settings, labs and species pp. 1-30

Đorđe Miladinović, Christine Muheim, Stefan Bauer, Andrea Spinnler, Daniela Noain, Mojtaba Bandarabadi, Benjamin Gallusser, Gabriel Krummenacher, Christian Baumann, Antoine Adamantidis, Steven A Brown and Joachim M Buhmann

Inferring neural circuit structure from datasets of heterogeneous tuning curves pp. 1-38

Takafumi Arakaki, G Barello and Yashar Ahmadian

Bet-hedging strategies in expanding populations pp. 1-17

Paula Villa Martín, Miguel A Muñoz and Simone Pigolotti

Model diagnostics and refinement for phylodynamic models pp. 1-17

Max S Y Lau, Bryan T Grenfell, Colin J Worby and Gavin J Gibson

A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation pp. 1-25

Marko Järvenpää, Mohamad R Abdul Sater, Georgia K Lagoudas, Paul C Blainey, Loren G Miller, James A McKinnell, Susan S Huang, Yonatan H Grad and Pekka Marttinen

Competing evolutionary paths in growing populations with applications to multidrug resistance pp. 1-25

Michael D Nicholson and Tibor Antal

Exon level machine learning analyses elucidate novel candidate miRNA targets in an avian model of fetal alcohol spectrum disorder pp. 1-25

Abrar E Al-Shaer, George R Flentke, Mark E Berres, Ana Garic and Susan M Smith

GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity pp. 1-25

Lex E Flagel, Benjamin K Blackman, Lila Fishman, Patrick J Monnahan, Andrea Sweigart and John K Kelly

Ten simple rules for organizing a webinar series pp. 1-7

Faisal M Fadlelmola, Sumir Panji, Azza E Ahmed, Amel Ghouila, Wisdom A Akurugu, Jean-Baka Domelevo Entfellner, Oussema Souiai, Nicola Mulder and H3ABioNet Research working group as members of the H3Africa Consortium

Ten simple rules for providing a meaningful research experience to high school students pp. 1-7

Emily A Lescak, Kate M O’Neill, Giovanna M Collu and Subhamoy Das

TASmania: A bacterial Toxin-Antitoxin Systems database pp. 1-28

Hatice Akarsu, Patricia Bordes, Moise Mansour, Donna-Joe Bigot, Pierre Genevaux and Laurent Falquet

I_MDS: an inflammatory bowel disease molecular activity score to classify patients with differing disease-driving pathways and therapeutic response to anti-TNF treatment pp. 1-23

Stelios Pavlidis, Calixte Monast, Matthew J Loza, Patrick Branigan, Kiang F Chung, Ian M Adcock, Yike Guo, Anthony Rowe and Frédéric Baribaud

Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions pp. 1-19

Anne Richelle, Austin W T Chiang, Chih-Chung Kuo and Nathan E Lewis

Evolutionary multiplayer games on graphs with edge diversity pp. 1-22

Qi Su, Lei Zhou and Long Wang

Unsupervised extraction of epidemic syndromes from participatory influenza surveillance self-reported symptoms pp. 1-21

Kyriaki Kalimeri, Matteo Delfino, Ciro Cattuto, Daniela Perrotta, Vittoria Colizza, Caroline Guerrisi, Clement Turbelin, Jim Duggan, John Edmunds, Chinelo Obi, Richard Pebody, Ana O Franco, Yamir Moreno, Sandro Meloni, Carl Koppeschaar, Charlotte Kjelsø, Ricardo Mexia and Daniela Paolotti

Hydrodynamics of transient cell-cell contact: The role of membrane permeability and active protrusion length pp. 1-21

Kai Liu, Brian Chu, Jay Newby, Elizabeth L Read, John Lowengrub and Jun Allard

Chemical features mining provides new descriptive structure-odor relationships pp. 1-21

Carmen C Licon, Guillaume Bosc, Mohammed Sabri, Marylou Mantel, Arnaud Fournel, Caroline Bushdid, Jerome Golebiowski, Celine Robardet, Marc Plantevit, Mehdi Kaytoue and Moustafa Bensafi

Neural crest streaming as an emergent property of tissue interactions during morphogenesis pp. 1-21

András Szabó, Eric Theveneau, Melissa Turan and Roberto Mayor

Learning and forgetting using reinforced Bayesian change detection pp. 1-41

Vincent Moens and Alexandre Zénon

Volume 15, issue 3, 2019

Scalable nonlinear programming framework for parameter estimation in dynamic biological system models pp. 1-29

Sungho Shin, Ophelia S Venturelli and Victor M Zavala

A spectrum of routing strategies for brain networks pp. 1-24

Andrea Avena-Koenigsberger, Xiaoran Yan, Artemy Kolchinsky, Martijn P van den Heuvel, Patric Hagmann and Olaf Sporns

A spatio-temporal individual-based network framework for West Nile virus in the USA: Spreading pattern of West Nile virus pp. 1-24

Sifat A Moon, Lee W Cohnstaedt, D Scott McVey and Caterina M Scoglio

A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory pp. 1-26

Rodoniki Athanasiadou, Benjamin Neymotin, Nathan Brandt, Wei Wang, Lionel Christiaen, David Gresham and Daniel Tranchina

Building a mechanistic mathematical model of hepatitis C virus entry pp. 1-26

Mphatso Kalemera, Dilyana Mincheva, Joe Grove and Christopher J R Illingworth

LMTRDA: Using logistic model tree to predict MiRNA-disease associations by fusing multi-source information of sequences and similarities pp. 1-18

Lei Wang, Zhu-Hong You, Xing Chen, Yang-Ming Li, Ya-Nan Dong, Li-Ping Li and Kai Zheng

Goal-related feedback guides motor exploration and redundancy resolution in human motor skill acquisition pp. 1-27

Marieke Rohde, Kenichi Narioka, Jochen J Steil, Lina K Klein and Marc O Ernst

The gradient of the reinforcement landscape influences sensorimotor learning pp. 1-27

Joshua G A Cashaback, Christopher K Lao, Dimitrios J Palidis, Susan K Coltman, Heather R McGregor and Paul L Gribble

Spatial clustering and common regulatory elements correlate with coordinated gene expression pp. 1-16

Jingyu Zhang, Hengyu Chen, Ruoyan Li, David A Taft, Guang Yao, Fan Bai and Jianhua Xing

A dynamic power-law sexual network model of gonorrhoea outbreaks pp. 1-20

Lilith K Whittles, Peter J White and Xavier Didelot

Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data pp. 1-20

Finlay Campbell, Anne Cori, Neil Ferguson and Thibaut Jombart

Evolutionary model for the unequal segregation of high copy plasmids pp. 1-17

Karin Münch, Richard Münch, Rebekka Biedendieck, Dieter Jahn and Johannes Müller

Bayes-optimal estimation of overlap between populations of fixed size pp. 1-17

Daniel B Larremore

Methods for computing the maximum performance of computational models of fMRI responses pp. 1-25

Agustin Lage-Castellanos, Giancarlo Valente, Elia Formisano and Federico De Martino

Synchrony is more than its top-down and climatic parts: interacting Moran effects on phytoplankton in British seas pp. 1-25

Lawrence W Sheppard, Emma J Defriez, Philip C Reid and Daniel C Reuman

Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome pp. 1-31

Bernardo P de Almeida, André F Vieira, Joana Paredes, Mónica Bettencourt-Dias and Nuno L Barbosa-Morais

ChIPulate: A comprehensive ChIP-seq simulation pipeline pp. 1-32

Vishaka Datta, Sridhar Hannenhalli and Rahul Siddharthan

Contrasting the effects of adaptation and synaptic filtering on the timescales of dynamics in recurrent networks pp. 1-33

Manuel Beiran and Srdjan Ostojic

Understanding narwhal diving behaviour using Hidden Markov Models with dependent state distributions and long range dependence pp. 1-21

Manh Cuong Ngô, Mads Peter Heide-Jørgensen and Susanne Ditlevsen

A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations pp. 1-21

Weiling Li, Lin Lin, Raunaq Malhotra, Lei Yang, Raj Acharya and Mary Poss

Optimizing the depth and the direction of prospective planning using information values pp. 1-21

Can Eren Sezener, Amir Dezfouli and Mehdi Keramati

Latent goal models for dynamic strategic interaction pp. 1-21

Shariq N Iqbal, Lun Yin, Caroline B Drucker, Qian Kuang, Jean-François Gariépy, Michael L Platt and John M Pearson

Volume 15, issue 2, 2019

Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks pp. 1-16

Ahmed A Metwally, Philip S Yu, Derek Reiman, Yang Dai, Patricia W Finn and David L Perkins

Development and validation of influenza forecasting for 64 temperate and tropical countries pp. 1-20

Sarah C Kramer and Jeffrey Shaman

Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis pp. 1-28

Hongyu Zhou, Zheng Dong, Gennady Verkhivker, Brian D Zoltowski and Peng Tao

16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses pp. 1-25

Stephen Woloszynek, Zhengqiao Zhao, Jian Chen and Gail L Rosen

Changes in morphogen kinetics and pollen grain size are potential mechanisms of aberrant pollen aperture patterning in previously observed and novel mutants of Arabidopsis thaliana pp. 1-25

Shayne M Plourde, Prativa Amom, Michelle Tan, Adriana T Dawes and Anna A Dobritsa

How good are pathogenicity predictors in detecting benign variants? pp. 1-17

Abhishek Niroula and Mauno Vihinen

A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications pp. 1-17

He Peng, Xiangxiang Zeng, Yadi Zhou, Defu Zhang, Ruth Nussinov and Feixiong Cheng

Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15 pp. 1-17

Sebastian Funk, Anton Camacho, Adam J Kucharski, Rachel Lowe, Rosalind M Eggo and W John Edmunds

Structure and variability of delay activity in premotor cortex pp. 1-17

Nir Even-Chen, Blue Sheffer, Saurabh Vyas, Stephen I Ryu and Krishna V Shenoy

Even a good influenza forecasting model can benefit from internet-based nowcasts, but those benefits are limited pp. 1-19

Dave Osthus, Ashlynn R Daughton and Reid Priedhorsky

CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis pp. 1-19

Marzieh Ayati, Danica Wiredja, Daniela Schlatzer, Sean Maxwell, Ming Li, Mehmet Koyutürk and Mark R Chance

Maps of variability in cell lineage trees pp. 1-32

Damien G Hicks, Terence P Speed, Mohammed Yassin and Sarah M Russell

A data-driven interactome of synergistic genes improves network-based cancer outcome prediction pp. 1-21

Amin Allahyar, Joske Ubels and Jeroen de Ridder

Phylogenies from dynamic networks pp. 1-21

Cornelia Metzig, Oliver Ratmann, Daniela Bezemer and Caroline Colijn

Correlation Structure in Micro-ECoG Recordings is Described by Spatially Coherent Components pp. 1-21

Nicholas Rogers, John Hermiz, Mehran Ganji, Erik Kaestner, Kıvılcım Kılıç, Lorraine Hossain, Martin Thunemann, Daniel R Cleary, Bob S Carter, David Barba, Anna Devor, Eric Halgren, Shadi A Dayeh and Vikash Gilja

A local measure of symmetry and orientation for individual spikes of grid cells pp. 1-21

Simon N Weber and Henning Sprekeler

Social evolution under demographic stochasticity pp. 1-13

David V McLeod and Troy Day

Population dynamics and entrainment of basal ganglia pacemakers are shaped by their dendritic arbors pp. 1-29

Lior Tiroshi and Joshua A Goldberg

Identifying individual risk rare variants using protein structure guided local tests (POINT) pp. 1-24

Rachel Marceau West, Wenbin Lu, Daniel M Rotroff, Melaine A Kuenemann, Sheng-Mao Chang, Michael C Wu, Michael J Wagner, John B Buse, Alison A Motsinger-Reif, Denis Fourches and Jung-Ying Tzeng

Information integration in large brain networks pp. 1-26

Daniel Toker and Friedrich T Sommer

Identifying the mechanism for superdiffusivity in mouse fibroblast motility pp. 1-15

Giuseppe Passucci, Megan E Brasch, James H Henderson, Vasily Zaburdaev and M Lisa Manning

Volume 15, issue 1, 2019

Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization pp. 1-20

Timothy D Majarian, Robert F Murphy and Seema S Lakdawala

A low-threshold potassium current enhances sparseness and reliability in a model of avian auditory cortex pp. 1-20

Margot C Bjoring and C Daniel Meliza

Protein—protein binding supersites pp. 1-17

Raji Viswanathan, Eduardo Fajardo, Gabriel Steinberg, Matthew Haller and Andras Fiser

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems pp. 1-4

Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel and Anders Wallqvist

Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures pp. 1-21

Jordan J Clark, Mark L Benson, Richard D Smith and Heather A Carlson

The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments pp. 1-23

Zachary R Fox and Brian Munsky

STRFs in primary auditory cortex emerge from masking-based statistics of natural sounds pp. 1-23

Abdul-Saboor Sheikh, Nicol S Harper, Jakob Drefs, Yosef Singer, Zhenwen Dai, Richard E Turner and Jörg Lücke

Deep image reconstruction from human brain activity pp. 1-23

Guohua Shen, Tomoyasu Horikawa, Kei Majima and Yukiyasu Kamitani

Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis pp. 1-19

Xiaohu Hu, Yibo Wang, Amanda Hunkele, Davide Provasi, Gavril W Pasternak and Marta Filizola

Predicting change: Approximate inference under explicit representation of temporal structure in changing environments pp. 1-31

Dimitrije Marković, Andrea M F Reiter and Stefan J Kiebel

PAIRUP-MS: Pathway analysis and imputation to relate unknowns in profiles from mass spectrometry-based metabolite data pp. 1-26

Yu-Han H Hsu, Claire Churchhouse, Tune H Pers, Josep M Mercader, Andres Metspalu, Krista Fischer, Kristen Fortney, Eric K Morgen, Clicerio Gonzalez, Maria E Gonzalez, Tonu Esko and Joel N Hirschhorn

Sour grapes and sweet victories: How actions shape preferences pp. 1-24

Fabien Vinckier, Lionel Rigoux, Irma T Kurniawan, Chen Hu, Sacha Bourgeois-Gironde, Jean Daunizeau and Mathias Pessiglione