PLoS Computational Biology, Volume 14

Volume 14, Number 1, January 2018

Editorials

• 
  Maureen A. Carey, Jason A. Papin:
  Ten simple rules for biologists learning to program.
• 
  Jason E. McDermott, Matthew Partridge, Yana Bromberg:
  Ten simple rules for drawing scientific comics.

Education Articles

• 
  Anupama Jigisha, Margherita Francescatto, Farzana Rahman, Nazeefa Fatima, Dan F. DeBlasio, Avinash Kumar Shanmugam, Venkata P. Satagopam, Alberto Santos, Pandurang Kolekar, Magali Michaut, Emre Guney:
  The ISCB Student Council Internship Program: Expanding computational biology capacity worldwide.
• 
  Andreas Madlung:
  Assessing an effective undergraduate module teaching applied bioinformatics to biology students.

Research Articles

• 
  Runmin Wei, Jingye Wang, Erik Jia, Tianlu Chen, Yan Ni, Wei Jia:
  GSimp: A Gibbs sampler based left-censored missing value imputation approach for metabolomics studies.
• 
  Krzysztof Bartoszek, Marta Majchrzak, Sebastian Sakowski, Anna B. Kubiak-Szeligowska, Ingemar Kaj, Pawel Parniewski:
  Predicting pathogenicity behavior in Escherichia coli population through a state dependent model and TRS profiling.
• 
  Yonathan Murin, Jeremy Kim, Josef Parvizi, Andrea Goldsmith:
  SozRank: A new approach for localizing the epileptic seizure onset zone.
• 
  Francesco Alessandro Massucci, Francesc Sagués, M. Ángeles Serrano:
  Metabolic plasticity in synthetic lethal mutants: Viability at higher cost.
• 
  Antonio Fabregat, Florian Korninger, Guilherme Viteri, Konstantinos Sidiropoulos, Pablo Marín-García, Peipei Ping, Guanming Wu, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob:
  Reactome graph database: Efficient access to complex pathway data.
• 
  Alon Diament, Anna Feldman, Elisheva Schochet, Martin Kupiec, Yoav Arava, Tamir Tuller:
  The extent of ribosome queuing in budding yeast.
• 
  Rahila Rahimova, Simon Fontanel, Corinne Lionne, Lars P. Jordheim, Suzanne Peyrottes, Laurent Chaloin:
  Identification of allosteric inhibitors of the ecto-5'-nucleotidase (CD73) targeting the dimer interface.
• 
  Pablo Martínez-Cañada, Milad Hobbi Mobarhan, Geir Halnes, Marianne Fyhn, Christian A. Morillas, Francisco J. Pelayo, Gaute T. Einevoll:
  Biophysical network modeling of the dLGN circuit: Effects of cortical feedback on spatial response properties of relay cells.
• 
  Guillaume Marçais, Arthur L. Delcher, Adam M. Phillippy, Rachel Coston, Steven L. Salzberg, Aleksey V. Zimin:
  MUMmer4: A fast and versatile genome alignment system.
• 
  Koich Saeki, Akira Sasaki:
  The role of spatial heterogeneity in the evolution of local and global infections of viruses.
• 
  Jagdish Suresh Patel, Celeste J. Brown, F. Marty Ytreberg, Deborah L. Stenkamp:
  Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations.
• 
  Gregory L. Dignon, Wenwei Zheng, Young C. Kim, Robert B. Best, Jeetain Mittal:
  Sequence determinants of protein phase behavior from a coarse-grained model.
• 
  Roman Goulard, Jean-Louis Vercher, Stéphane Viollet:
  Modeling visual-based pitch, lift and speed control strategies in hoverflies.
• 
  Jean-François Patri, Pascal Perrier, Jean-Luc Schwartz, Julien Diard:
  What drives the perceptual change resulting from speech motor adaptation? Evaluation of hypotheses in a Bayesian modeling framework.
• 
  Nikola Ciganovic, Rebecca L. Warren, Batu Keçeli, Stefan Jacob, Anders Fridberger, Tobias Reichenbach:
  Static length changes of cochlear outer hair cells can tune low-frequency hearing.
• 
  Fereshteh Nazari, Alexander T. Pearson, Jacques Eduardo Nör, Trachette L. Jackson:
  A mathematical model for IL-6-mediated, stem cell driven tumor growth and targeted treatment.
• 
  Samhita P. Banavar, Carlos Gomez, Michael Trogdon, Linda R. Petzold, Tau-Mu Yi, Otger Campàs:
  Mechanical feedback coordinates cell wall expansion and assembly in yeast mating morphogenesis.
• 
  Christopher L. Buckley, Taro Toyoizumi:
  A theory of how active behavior stabilises neural activity: Neural gain modulation by closed-loop environmental feedback.
• 
  Giulio Di Minin, Andreas Postlmayr, Anton Wutz:
  HaSAPPy: A tool for candidate identification in pooled forward genetic screens of haploid mammalian cells.
• 
  Ravi Kumar Verma, Ara M. Abramyan, Mayako Michino, R. Benjamin Free, David R. Sibley, Jonathan A. Javitch, Jonathan Robert Lane, Lei Shi:
  The E2.65A mutation disrupts dynamic binding poses of SB269652 at the dopamine D2 and D3 receptors.
• 
  Rajita Menon, Vivek Ramanan, Kirill S. Korolev:
  Interactions between species introduce spurious associations in microbiome studies.
• 
  Takayuki Onojima, Takahiro Goto, Hiroaki Mizuhara, Toshio Aoyagi:
  A dynamical systems approach for estimating phase interactions between rhythms of different frequencies from experimental data.
• 
  Jacob C. Kimmel, Amy Y. Chang, Andrew S. Brack, Wallace F. Marshall:
  Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance.
• 
  Kevin Lloyd, Peter Dayan:
  Interrupting behaviour: Minimizing decision costs via temporal commitment and low-level interrupts.
• 
  Daisuke Sato, Rose E. Dixon, Luis F. Santana, Manuel F. Navedo:
  A model for cooperative gating of L-type Ca2+ channels and its effects on cardiac alternans dynamics.
• 
  Ian C. McDowell, Dinesh Manandhar, Christopher M. Vockley, Amy K. Schmid, Timothy E. Reddy, Barbara E. Engelhardt:
  Clustering gene expression time series data using an infinite Gaussian process mixture model.
• 
  Lenna X. Peterson, Yoichiro Togawa, Juan Esquivel-Rodríguez, Genki Terashi, Charles Christoffer, Amitava Roy, Woong-Hee Shin, Daisuke Kihara:
  Modeling the assembly order of multimeric heteroprotein complexes.
• 
  Talia Zeppelin, Lucy Kate Ladefoged, Steffen Sinning, Xavier Periole, Birgit Schiøtt:
  A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition.
• 
  Cristina Izquierdo, José C. Gómez-Tamayo, Jean-Christophe Nebel, Leonardo Pardo, Angel Gonzalez:
  Identifying human diamine sensors for death related putrescine and cadaverine molecules.
• 
  Daniel S. Calovi, Alexandra Litchinko, Valentin Lecheval, Ugo Lopez, Alfonso Pérez-Escudero, Hugues Chaté, Clément Sire, Guy Theraulaz:
  Disentangling and modeling interactions in fish with burst-and-coast swimming reveal distinct alignment and attraction behaviors.
• 
  Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M. Meudt, Luay Nakhleh:
  Bayesian inference of phylogenetic networks from bi-allelic genetic markers.
• 
  Wesley Wong, Edward A. Wenger, Daniel L. Hartl, Dyann Wirth:
  Modeling the genetic relatedness of Plasmodium falciparum parasites following meiotic recombination and cotransmission.
• 
  Zixuan Cang, Lin Mu, Guo-Wei Wei:
  Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening.
• 
  Lajos Vágó, Balázs Ujfalussy:
  Robust and efficient coding with grid cells.
• 
  Mathias Engel, James Longden, Jesper Ferkinghoff-Borg, Xavier Robin, Gaye Saginc, Rune Linding:
  Bowhead: Bayesian modelling of cell velocity during concerted cell migration.
• 
  Akira Nagamori, Christopher M. Laine, Francisco J. Valero Cuevas:
  Cardinal features of involuntary force variability can arise from the closed-loop control of viscoelastic afferented muscles.
• 
  Zhewei Zhang, Zhenbo Cheng, Zhongqiao Lin, Chechang Nie, Tianming Yang:
  A neural network model for the orbitofrontal cortex and task space acquisition during reinforcement learning.
• 
  Alyaa M. Abdel-Haleem, Hooman Hefzi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori, Bernhard O. Palsson, Nathan E. Lewis, Neema Jamshidi:
  Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.
• 
  Shayna Stein, Rui Zhao, Hiroshi Haeno, Igor Vivanco, Franziska Michor:
  Mathematical modeling identifies optimum lapatinib dosing schedules for the treatment of glioblastoma patients.
• 
  Chloé Bessière, May Taha, Florent Petitprez, Jimmy Vandel, Jean-Michel Marin, Laurent Bréhélin, Sophie Lèbre, Charles-Henri Lecellier:
  Probing instructions for expression regulation in gene nucleotide compositions.
• 
  Igor Marín de Mas, Esther Aguilar, Erika Zodda, Cristina Balcells, Silvia Marin, Guido Dallmann, Timothy M. Thomson, Balázs Papp, Marta Cascante:
  Model-driven discovery of long-chain fatty acid metabolic reprogramming in heterogeneous prostate cancer cells.
• 
  Simon Koplev, Katie Lin, Anders B. Dohlman, Avi Ma'ayan:
  Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition.
• 
  Ali Hadizadeh Esfahani, Angelina Sverchkova, Julio Saez-Rodriguez, Andreas Schuppert, Marc Brehme:
  A systematic atlas of chaperome deregulation topologies across the human cancer landscape.
• 
  Christophe Menichelli, Olivier Gascuel, Laurent Bréhélin:
  Improving pairwise comparison of protein sequences with domain co-occurrence.

Volume 14, Number 2, February 2018

Editorial

• 
  Adam J. Kucharski:
  Ten simple rules for writing a popular science book.

Message from ISCB

• 
  Nicola J. Mulder, Russell Schwartz, Michelle D. Brazas, Cath Brooksbank, Bruno A. Gaëta, Sarah L. Morgan, Mark A. Pauley, Anne G. Rosenwald, Gabriella Rustici, Michael L. Sierk, Tandy J. Warnow, Lonnie R. Welch:
  The development and application of bioinformatics core competencies to improve bioinformatics training and education.

Education

• 
  Vasundra Touré, Nicolas Le Novère, Dagmar Waltemath, Olaf Wolkenhauer:
  Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation.

Research Articles

• 
  Stefano Motta, Claudia Minici, Dario Corrada, Laura Bonati, Alessandro Pandini:
  Ligand-induced perturbation of the HIF-2α: ARNT dimer dynamics.
• 
  Meenu R. Mridula, Ashalatha S. Nair, K. Satheesh Kumar:
  Genetic programming based models in plant tissue culture: An addendum to traditional statistical approach.
• 
  Chloe Spalding, Emma Keen, David J. Smith, Anne-Marie Krachler, Sara Jabbari:
  Mathematical modelling of the antibiotic-induced morphological transition of Pseudomonas aeruginosa.
• 
  Huijing Du, Yangyang Wang, Daniel Haensel, Briana Lee, Xing Dai, Qing Nie:
  Multiscale modeling of layer formation in epidermis.
• 
  Miquel Marin-Riera, Jacqueline Moustakas-Verho, Yoland Savriama, Jukka Jernvall, Isaac Salazar-Ciudad:
  Differential tissue growth and cell adhesion alone drive early tooth morphogenesis: An ex vivo and in silico study.
• 
  Romesh G. Abeysuriya, Jonathan Hadida, Stamatios N. Sotiropoulos, Saâd Jbabdi, Robert Becker, Benjamin A. E. Hunt, Matthew J. Brookes, Mark W. Woolrich:
  A biophysical model of dynamic balancing of excitation and inhibition in fast oscillatory large-scale networks.
• 
  Ahmadreza Ghaffarizadeh, Randy W. Heiland, Samuel H. Friedman, Shannon M. Mumenthaler, Paul Macklin:
  PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems.
• 
  Michael A. Moxley, Kalyan C. Vinnakota, Jason N. Bazil, Nathan R. Qi, Daniel A. Beard:
  Systems-level computational modeling demonstrates fuel selection switching in high capacity running and low capacity running rats.
• 
  Yishai Shimoni:
  Association between expression of random gene sets and survival is evident in multiple cancer types and may be explained by sub-classification.
• 
  Edgar Herrera-Delgado, Ruben Perez-Carrasco, James Briscoe, Peter Sollich:
  Memory functions reveal structural properties of gene regulatory networks.
• 
  Zhaoran Zhang, Dena Guo, Meghan E. Huber, Se-Woong Park, Dagmar Sternad:
  Exploiting the geometry of the solution space to reduce sensitivity to neuromotor noise.
• 
  Vincent Mirabet, Pawel Krupinski, Olivier Hamant, Elliot M. Meyerowitz, Henrik Jönsson, Arezki Boudaoud:
  The self-organization of plant microtubules inside the cell volume yields their cortical localization, stable alignment, and sensitivity to external cues.
• 
  Evan L. Ray, Nicholas G. Reich:
  Prediction of infectious disease epidemics via weighted density ensembles.
• 
  Robin N. Thompson, Christopher A. Gilligan, Nik J. Cunniffe:
  Control fast or control smart: When should invading pathogens be controlled?
• 
  Meike T. Wortel, Elad Noor, Michael Ferris, Frank J. Bruggeman, Wolfram Liebermeister:
  Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield.
• 
  Vipul Gupta, Narendra M. Dixit:
  Trade-off between synergy and efficacy in combinations of HIV-1 latency-reversing agents.
• 
  Eric W. Jones, Jean M. Carlson:
  In silico analysis of antibiotic-induced Clostridium difficile infection: Remediation techniques and biological adaptations.
• 
  Yen-Ting Lin, Peter G. Hufton, Esther J. Lee, Davit A. Potoyan:
  A stochastic and dynamical view of pluripotency in mouse embryonic stem cells.
• 
  Alexander M. Sevy, Swetasudha Panda, James E. Crowe Jr., Jens Meiler, Yevgeniy Vorobeychik:
  Integrating linear optimization with structural modeling to increase HIV neutralization breadth.
• 
  Nikolaus Berndt, Marius Stefan Horger, Sascha Bulik, Hermann-Georg Holzhütter:
  A multiscale modelling approach to assess the impact of metabolic zonation and microperfusion on the hepatic carbohydrate metabolism.
• 
  Cesar Alvarado, Nicole A. Fider, Helen J. Wearing, Natalia L. Komarova:
  Optimizing homeostatic cell renewal in hierarchical tissues.
• 
  David Westergaard, Hans Henrik Stærfeldt, Christian Tønsberg, Lars Juhl Jensen, Søren Brunak:
  A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts.
• 
  Dorjsuren Battogtokh, Shihoko Kojima, John J. Tyson:
  Modeling the interactions of sense and antisense Period transcripts in the mammalian circadian clock network.
• 
  Iulia A. Neagu, Jason Olejarz, Mark Freeman, Daniel I. S. Rosenbloom, Martin A. Nowak, Alison L. Hill:
  Life cycle synchronization is a viral drug resistance mechanism.
• 
  Andreas Hula, Iris Vilares, Terry Lohrenz, Peter Dayan, P. Read Montague:
  A model of risk and mental state shifts during social interaction.
• 
  Chase Cockrell, Gary An:
  Examining the controllability of sepsis using genetic algorithms on an agent-based model of systemic inflammation.
• 
  Rahul Gupta:
  Self-crowding of AMPA receptors in the excitatory postsynaptic density can effectuate anomalous receptor sub-diffusion.
• 
  Raju Kalaivani, Raju Reema, Narayanaswamy Srinivasan:
  Recognition of sites of functional specialisation in all known eukaryotic protein kinase families.
• 
  Sneha Vishwanath, Alexandre G. de Brevern, Narayanaswamy Srinivasan:
  Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains.
• 
  Matias I. Maturana, Nicholas V. Apollo, David J. Garrett, Tatiana Kameneva, Shaun L. Cloherty, David B. Grayden, Anthony N. Burkitt, Michael R. Ibbotson, Hamish Meffin:
  Electrical receptive fields of retinal ganglion cells: Influence of presynaptic neurons.
• 
  Aurina Arnatkeviciute, Ben D. Fulcher, Roger Pocock, Alex Fornito:
  Hub connectivity, neuronal diversity, and gene expression in the Caenorhabditis elegans connectome.
• 
  Richard Pang, Floris van Breugel, Michael Dickinson, Jeffrey A. Riffell, Adrienne L. Fairhall:
  History dependence in insect flight decisions during odor tracking.
• 
  Fleur Zeldenrust, Pascal J. P. Chameau, Wytse J. Wadman:
  Spike and burst coding in thalamocortical relay cells.
• 
  Margriet M. Palm, Marjet Elemans, Joost B. Beltman:
  Heritable tumor cell division rate heterogeneity induces clonal dominance.
• 
  Michaël Dougoud, Laura Vinckenbosch, Rudolf P. Rohr, Louis-Félix Bersier, Christian Mazza:
  The feasibility of equilibria in large ecosystems: A primary but neglected concept in the complexity-stability debate.
• 
  James X. Sun, Yuting He, Eric Sanford, Meagan Montesion, Garrett M. Frampton, Stéphane Vignot, Jean-Charles Soria, Jeffrey S. Ross, Vincent A. Miller, Philip J. Stephens, Doron Lipson, Roman Yelensky:
  A computational approach to distinguish somatic vs. germline origin of genomic alterations from deep sequencing of cancer specimens without a matched normal.
• 
  Peter W. Donhauser, Esther Florin, Sylvain Baillet:
  Imaging of neural oscillations with embedded inferential and group prevalence statistics.
• 
  Volker Pernice, Rava Azeredo da Silveira:
  Interpretation of correlated neural variability from models of feed-forward and recurrent circuits.
• 
  Cesar A. López, Clifford J. Unkefer, Basil I. Swanson, Jessica M. J. Swanson, S. Gnanakaran:
  Membrane perturbing properties of toxin mycolactone from Mycobacterium ulcerans.
• 
  Caitlin Collins, Xavier Didelot:
  A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination.
• 
  Pau Farré, Eldon Emberly:
  A maximum-entropy model for predicting chromatin contacts.
• 
  Ximing Li, William R. Holmes:
  Biophysical attributes that affect CaMKII activation deduced with a novel spatial stochastic simulation approach.
• 
  Ryan C. Kennedy, Meir Marmor, Ralph Marcucio, C. Anthony Hunt:
  Simulation enabled search for explanatory mechanisms of the fracture healing process.
• 
  Bandan Chakrabortty, Ikram Blilou, Ben Scheres, Bela M. Mulder:
  A computational framework for cortical microtubule dynamics in realistically shaped plant cells.
• 
  Fei Qi, Magdalena Motz, Kirsten Jung, Jürgen Lassak, Dmitrij Frishman:
  Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation.

Volume 14, Number 3, March 2018

Editorials

• 
  Marc Baaden, Olivier Delalande, Nicolas Férey, Samuela Pasquali, Jérôme Waldispühl, Antoine Taly:
  Ten simple rules to create a serious game, illustrated with examples from structural biology.
• 
  Gabriel A. Devenyi, Rémi Emonet, Rayna M. Harris, Kate L. Hertweck, Damien Irving, Ian Milligan, Greg Wilson:
  Ten simple rules for collaborative lesson development.

Education Articles

• 
  Timothy E. Saunders, Cynthia Y. He, Patrice Koehl, Lee-Ling Sharon Ong, Peter T. C. So:
  Eleven quick tips for running an interdisciplinary short course for new graduate students.
• 
  Brian S. Cole, Jason H. Moore:
  Eleven quick tips for architecting biomedical informatics workflows with cloud computing.
• 
  Nika Abdollahi, Alexandre Albani, Éric Anthony, Agnes Baud, Mélissa Cardon, Robert Clerc, Dariusz Czernecki, Romain Conte, Laurent David, Agathe Delaune, Samia Djerroud, Pauline Fourgoux, Nadège Guiglielmoni, Jeanne Laurentie, Nathalie Lehmann, Camille Lochard, Rémi Montagne, Vasiliki Myrodia, Vaitea Opuu, Elise Parey, Lélia Polit, Sylvain Privé, Chloé Quignot, Maria Ruiz-Cuevas, Mariam Sissoko, Nicolas Sompairac, Audrey Vallerix, Violaine Verrecchia, Marc Delarue, Raphaël Guérois, Yann Ponty, Sophie Sacquin-Mora, Alessandra Carbone, Christine Froidevaux, Stéphane Le Crom, Olivier Lespinet, Martin Weigt, Samer Abboud, Juliana S. Bernardes, Guillaume Bouvier, Chloé Dequeker, Arnaud Ferré, Patrick Fuchs, Gaëlle Lelandais, Pierre Poulain, Hugues Richard, Hugo Schweke, Elodie Laine, Anne Lopes:
  Meet-U: Educating through research immersion.
• 
  Manuel Corpas, Nadezda Kovalevskaya, Amanda McMurray, Fiona G. G. Nielsen:
  A FAIR guide for data providers to maximise sharing of human genomic data.

Research Articles

• 
  Juan Prada, Manju Sasi, Corinna Martin, Sibylle Jablonka, Thomas Dandekar, Robert Blum:
  An open source tool for automatic spatiotemporal assessment of calcium transients and local 'signal-close-to-noise' activity in calcium imaging data.
• 
  Iván Dotú, Scott I. Adamson, Benjamin Coleman, Cyril Fournier, Emma Ricart-Altimiras, Eduardo Eyras, Jeffrey H. Chuang:
  SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data.
• 
  Soroush Samadian, Jeff P. Bruce, Trevor J. Pugh:
  Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.
• 
  Aloys Dufour, Emilie Gontran, Christophe Deroulers, Pascale Varlet, Johan Pallud, Basile Grammaticos, Mathilde Badoual:
  Modeling the dynamics of oligodendrocyte precursor cells and the genesis of gliomas.
• 
  Mengmeng Du, Jiajia Li, Liang Chen, Yuguo Yu, Ying Wu:
  Astrocytic Kir4.1 channels and gap junctions account for spontaneous epileptic seizure.
• 
  Shiva Farashahi, Chih-Chung Ting, Chang-Hao Kao, Shih-Wei Wu, Alireza Soltani:
  Dynamic combination of sensory and reward information under time pressure.
• 
  Roman Vaxenburg, Isis Wyche, Karel Svoboda, Alexander L. Efros, Samuel Andrew Hires:
  Dynamic cues for whisker-based object localization: An analytical solution to vibration during active whisker touch.
• 
  Jonathan Schiefer, Alexander Niederbühl, Volker Pernice, Carolin Lennartz, Jürgen Hennig, Pierre LeVan, Stefan Rotter:
  From correlation to causation: Estimating effective connectivity from zero-lag covariances of brain signals.
• 
  Timothy M. Kinyanjui, Jo Middleton, Stefan Güttel, Jackie Cassell, Joshua V. Ross, Thomas A. House:
  Scabies in residential care homes: Modelling, inference and interventions for well-connected population sub-units.
• 
  Mehdi Bouhaddou, Anne Marie Barrette, Alan D. Stern, Rick J. Koch, Matthew S. DiStefano, Eric A. Riesel, Luis C. Santos, Annie L. Tan, Alex E. Mertz, Marc R. Birtwistle:
  A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens.
• 
  Matthew P. Edgington, Luke S. Alphey:
  Population dynamics of engineered underdominance and killer-rescue gene drives in the control of disease vectors.
• 
  Albert Solernou, Benjamin S. Hanson, Robin A. Richardson, Robert Welch, Daniel J. Read, Oliver G. Harlen, Sarah A. Harris:
  Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules.
• 
  Hyun Jung Park, Soyeon Kim, Wei Li:
  Model-based analysis of competing-endogenous pathways (MACPath) in human cancers.
• 
  Sabine Hummert, Susanne Thon, Thomas Eick, Ralf Schmauder, Eckhard Schulz, Klaus Benndorf:
  Activation gating in HCN2 channels.
• 
  Guillaume Viejo, Thomas Cortier, Adrien Peyrache:
  Brain-state invariant thalamo-cortical coordination revealed by non-linear encoders.
• 
  Atsushi Takagi, Francesco Usai, Ganesh Gowrishankar, Vittorio Sanguineti, Etienne Burdet:
  Haptic communication between humans is tuned by the hard or soft mechanics of interaction.
• 
  Narmada Sambaturu, Sumanta Mukherjee, Martín López-García, Carmen Molina-París, Gautam I. Menon, Nagasuma Chandra:
  Role of genetic heterogeneity in determining the epidemiological severity of H1N1 influenza.
• 
  Yanting Luo, Jianlin He, Xiguang Xu, Ming-an Sun, Xiaowei Wu, Xuemei Lu, Hehuang Xie:
  Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells.
• 
  Yered Pita-Juárez, Gabriel M. Altschuler, Sokratis Kariotis, Wenbin Wei, Katjusa Koler, Claire Green, Rudolph E. Tanzi, Winston Hide:
  The Pathway Coexpression Network: Revealing pathway relationships.
• 
  Yani Zhao, Pawel Dabrowski-Tumanski, Szymon Niewieczerzal, Joanna I. Sulkowska:
  The exclusive effects of chaperonin on the behavior of proteins with 52 knot.
• 
  Núria Folguera-Blasco, Elisabet Cuyàs, Javier A. Menéndez, Tomás Alarcón:
  Epigenetic regulation of cell fate reprogramming in aging and disease: A predictive computational model.
• 
  Christopher Ebsch, Robert Rosenbaum:
  Imbalanced amplification: A mechanism of amplification and suppression from local imbalance of excitation and inhibition in cortical circuits.
• 
  Jun Ding, James S. Hagood, Namasivayam Ambalavanan, Naftali Kaminski, Ziv Bar-Joseph:
  iDREM: Interactive visualization of dynamic regulatory networks.
• 
  Stefan Gahbauer, Kristyna Pluhackova, Rainer A. Böckmann:
  Closely related, yet unique: Distinct homo- and heterodimerization patterns of G protein coupled chemokine receptors and their fine-tuning by cholesterol.
• 
  Jinbo Chen, Uwe Scholz, Ruonan Zhou, Matthias Lange:
  LAILAPS-QSM: A RESTful API and JAVA library for semantic query suggestions.
• 
  Hao Ge, Pingping Wu, Hong Qian, X. Sunney Xie:
  Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stabilizing the uninduced phenotypic state.
• 
  Guillaume Pernelle, Wilten Nicola, Claudia Clopath:
  Gap junction plasticity as a mechanism to regulate network-wide oscillations.
• 
  Michael Pablo, Samuel A. Ramirez, Timothy C. Elston:
  Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation.
• 
  James Elber Duverger, Vincent Jacquemet, Alain Vinet, Philippe Comtois:
  In silico study of multicellular automaticity of heterogeneous cardiac cell monolayers: Effects of automaticity strength and structural linear anisotropy.
• 
  Britta U. Westner, Sarang S. Dalal, Simon Hanslmayr, Tobias Staudigl:
  Across-subjects classification of stimulus modality from human MEG high frequency activity.
• 
  James A. Grogan, Anthony J. Connor, Joe Pitt-Francis, Philip K. Maini, Helen M. Byrne:
  The importance of geometry in the corneal micropocket angiogenesis assay.
• 
  Nicholas B. DeFelice, Zachary D. Schneider, Eliza Little, Christopher Barker, Kevin A. Caillouët, Scott R. Campbell, Dan Damian, Patrick Irwin, Herff M. P. Jones, John Townsend, Jeffrey Shaman:
  Use of temperature to improve West Nile virus forecasts.
• 
  Ibai Irastorza-Azcarate, Rafael D. Acemel, Juan J. Tena, Ignacio Maeso, José Luis Gómez-Skarmeta, Damien P. Devos:
  4Cin: A computational pipeline for 3D genome modeling and virtual Hi-C analyses from 4C data.
• 
  Sarah Jarvis, Konstantin Nikolic, Simon R. Schultz:
  Neuronal gain modulability is determined by dendritic morphology: A computational optogenetic study.
• 
  Carl Barton, Sandro Morganella, Øyvind Ødegård-Fougner, Stephanie Alexander, Jonas Ries, Tomas W. Fitzgerald, Jan Ellenberg, Ewan Birney:
  ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy.
• 
  David O. Holland, Margaret E. Johnson:
  Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis.
• 
  Oisin Mac Aodha, Rory Gibb, Kate E. Barlow, Ella Browning, Michael Firman, Robin Freeman, Briana Harder, Libby Kinsey, Gary R. Mead, Stuart E. Newson, Ivan Pandourski, Stuart Parsons, Jon Russ, Abigel Szodoray-Paradi, Farkas Szodoray-Paradi, Elena Tilova, Mark A. Girolami, Gabriel J. Brostow, Kate E. Jones:
  Bat detective - Deep learning tools for bat acoustic signal detection.
• 
  Alexander E. Moskalensky, Maxim A. Yurkin, Artem R. Muliukov, Alena L. Litvinenko, Vyacheslav M. Nekrasov, Andrei V. Chernyshev, Valeri P. Maltsev:
  Method for the simulation of blood platelet shape and its evolution during activation.
• 
  Elizabeth C. Lee, Ali Arab, Sandra M. Goldlust, Cécile Viboud, Bryan T. Grenfell, Shweta Bansal:
  Deploying digital health data to optimize influenza surveillance at national and local scales.
• 
  Osman N. Yogurtçu, Margaret E. Johnson:
  Cytosolic proteins can exploit membrane localization to trigger functional assembly.
• 
  Hidetoshi Kono, Shun Sakuraba, Hisashi Ishida:
  Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA.
• 
  Laura Martinez-Mateu, Lucía Romero, Ana Ferrer-Albero, Rafael Sebastián, José F. Rodríguez Matas, José Jalife, Omer Berenfeld, Javier Saiz:
  Factors affecting basket catheter detection of real and phantom rotors in the atria: A computational study.
• 
  Rui Zhen Tan, Keng-Hwee Chiam:
  A computational model for how cells choose temporal or spatial sensing during chemotaxis.
• 
  Helen R. Fryer, Steven M. Wolinsky, Angela R. McLean:
  Increased T cell trafficking as adjunct therapy for HIV-1.
• 
  Lauric A. Ferrat, Marc Goodfellow, John R. Terry:
  Classifying dynamic transitions in high dimensional neural mass models: A random forest approach.
• 
  Benjamin Schubert, Charlotta Schärfe, Pierre Dönnes, Thomas A. Hopf, Debora S. Marks, Oliver Kohlbacher:
  Population-specific design of de-immunized protein biotherapeutics.
• 
  Diego Fernández Slezak, Mariano Sigman, Guillermo A. Cecchi:
  An entropic barriers diffusion theory of decision-making in multiple alternative tasks.
• 
  Yohei Kondo, Kazuhiro Aoki, Shin Ishii:
  Inverse tissue mechanics of cell monolayer expansion.
• 
  Charlie Beirnaert, Pieter Meysman, Trung-Nghia Vu, Nina Hermans, Sandra Apers, Luc Pieters, Adrian Covaci, Kris Laukens:
  speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification.
• 
  Gregory Handy, Sean D. Lawley, Alla Borisyuk:
  Receptor recharge time drastically reduces the number of captured particles.
• 
  Ting Hu, Karoliina Oksanen, Weidong Zhang, Edward Randell, Andrew Furey, Guang Sun, Guangju Zhai:
  An evolutionary learning and network approach to identifying key metabolites for osteoarthritis.
• 
  J. Kenneth Baillie, Andrew Bretherick, Christopher S. Haley, Sara Clohisey, Alan Gray, Lucile P. A. Neyton, Jeffrey Barrett, Eli A. Stahl, Albert Tenesa, Robin Andersson, J. Ben Brown, Geoffrey J. Faulkner, Marina Lizio, Ulf Schaefer, Carsten O. Daub, Masayoshi Itoh, Naoto Kondo, Timo Lassmann, Jun Kawai, IIBDGC Consortium, Damian Mole, Vladimir B. Bajic, Peter Heutink, Michael Rehli, Hideya Kawaji, Albin Sandelin, Harukazu Suzuki, Jack Satsangi, Christine A. Wells, Nir Hacohen, Tom C. Freeman, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, David A. Hume:
  Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

Volume 14, Number 4, April 2018

Editorials

• 
  Bart Penders:
  Ten simple rules for responsible referencing.
• 
  Jacquelyn S. Fetrow, Patricia C. Babbitt:
  New computational approaches to understanding molecular protein function.

Education Articles

• 
  Kathleen Gregory, Siri Jodha S. Khalsa, William K. Michener, Fotis E. Psomopoulos, Anita de Waard, Mingfang Wu:
  Eleven quick tips for finding research data.
• 
  Neil C. C. Brown, Greg Wilson:
  Ten quick tips for teaching programming.

Review

• 
  Jana Wäldchen, Michael Rzanny, Marco Seeland, Patrick Mäder:
  Automated plant species identification - Trends and future directions.

Research Articles

• 
  Malgorzata Kardynska, Anna Paszek, Jaroslaw Smieja, David G. Spiller, Wieslawa Widlak, Michael R. H. White, Pawel Paszek, Marek Kimmel:
  Quantitative analysis reveals crosstalk mechanisms of heat shock-induced attenuation of NF-κB signaling at the single cell level.
• 
  Spencer Bliven, Aleix Lafita, Althea Parker, Guido Capitani, Jose M. Duarte:
  Automated evaluation of quaternary structures from protein crystals.
• 
  Wilberforce Zachary Ouma, Katja Pogacar, Erich Grotewold:
  Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties.
• 
  David R. J. Pleydell, Samuel Soubeyrand, Sylvie Dallot, Gérard Labonne, Joël Chadoeuf, Emmanuel Jacquot, Gaël Thébaud:
  Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape.
• 
  Kevin J. Flynn, David O. F. Skibinski, Christian Lindemann:
  Effects of growth rate, cell size, motion, and elemental stoichiometry on nutrient transport kinetics.
• 
  Jared Adolf-Bryfogle, Oleksandr Kalyuzhniy, Michael Kubitz, Brian D. Weitzner, Xiaozhen Hu, Yumiko Adachi, William R. Schief, Roland L. Dunbrack Jr.:
  RosettaAntibodyDesign (RAbD): A general framework for computational antibody design.
• 
  Masataka Sawayama, Shin'ya Nishida:
  Material and shape perception based on two types of intensity gradient information.
• 
  Jessica Ausborn, Hidehiko Koizumi, William H. Barnett, Tibin T. John, Ruli Zhang, Yaroslav I. Molkov, Jeffrey C. Smith, Ilya A. Rybak:
  Organization of the core respiratory network: Insights from optogenetic and modeling studies.
• 
  Catherine M. Byrne, Soren Gantt, Daniel Coombs:
  Effects of spatiotemporal HSV-2 lesion dynamics and antiviral treatment on the risk of HIV-1 acquisition.
• 
  Vasyl V. Mykuliak, Alexander William M. Haining, Magdaléna von Essen, Armando del Río Hernández, Vesa P. Hytönen:
  Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin.
• 
  Ji-Sung Kim, Xin Gao, Andrey Rzhetsky:
  RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning.
• 
  Maria Concetta Palumbo, Micaela Morettini, Paolo Tieri, Fasma Diele, Massimo Sacchetti, Filippo Castiglione:
  Personalizing physical exercise in a computational model of fuel homeostasis.
• 
  Falk Lieder, Amitai Shenhav, Sebastian Musslick, Thomas L. Griffiths:
  Rational metareasoning and the plasticity of cognitive control.
• 
  Guillaume Drion, Julie Dethier, Alessio Franci, Rodolphe Sepulchre:
  Switchable slow cellular conductances determine robustness and tunability of network states.
• 
  Tomás Gedeon, Bree Cummins, Shaun Harker, Konstantin Mischaikow:
  Identifying robust hysteresis in networks.
• 
  William Marshall, Larissa Albantakis, Giulio Tononi:
  Black-boxing and cause-effect power.
• 
  Michael F. Bonner, Russell A. Epstein:
  Computational mechanisms underlying cortical responses to the affordance properties of visual scenes.
• 
  Sean M. Gibbons, Claire Duvallet, Eric J. Alm:
  Correcting for batch effects in case-control microbiome studies.
• 
  Leander Schietgat, Celine Vens, Ricardo Cerri, Carlos N. Fischer, Eduardo P. Costa, Jan Ramon, Claudia M. A. Carareto, Hendrik Blockeel:
  A machine learning based framework to identify and classify long terminal repeat retrotransposons.
• 
  Sneha Mitra, Anushua Biswas, Leelavati Narlikar:
  DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP.
• 
  Wen-Han Yu, Peng Zhao, Monia Draghi, Claudia Arevalo, Christina B. Karsten, Todd J. Suscovich, Bronwyn Gunn, Hendrik Streeck, Abraham L. Brass, Michael Tiemeyer, Michael S. Seaman, John R. Mascola, Lance Wells, Douglas A. Lauffenburger, Galit Alter:
  Exploiting glycan topography for computational design of Env glycoprotein antigenicity.
• 
  Reuben M. Buckley, R. Daniel Kortschak, David L. Adelson:
  Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse.
• 
  Benjamin Schott, Manuel Traub, Cornelia Schlagenhauf, Masanari Takamiya, Thomas Antritter, Andreas Bartschat, Katharina Löffler, Denis Blessing, Jens C. Otte, Andrei Kobitski, G. Ulrich Nienhaus, Uwe Strähle, Ralf Mikut, Johannes Stegmaier:
  EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos.
• 
  Nicholas T. Franklin, Michael Joshua Frank:
  Compositional clustering in task structure learning.
• 
  Justus A. Kromer, Steffen Märcker, Steffen Lange, Christel Baier, Benjamin M. Friedrich:
  Decision making improves sperm chemotaxis in the presence of noise.
• 
  Itziar Irurzun-Arana, Alvaro Janda, Sergio Ardanza-Trevijano, Iñaki F. Trocóniz:
  Optimal dynamic control approach in a multi-objective therapeutic scenario: Application to drug delivery in the treatment of prostate cancer.
• 
  Nicola De Maio, Colin J. Worby, Daniel J. Wilson, Nicole Stoesser:
  Bayesian reconstruction of transmission within outbreaks using genomic variants.
• 
  Geoffrey D. Hannigan, Melissa Beth Duhaime, Danai Koutra, Patrick D. Schloss:
  Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome.
• 
  Ricardo Roberto da Silva, Mingxun Wang, Louis-Félix Nothias, Justin J. J. van der Hooft, Andrés Mauricio Caraballo-Rodríguez, Evan Fox, Marcy J. Balunas, Jonathan L. Klassen, Norberto Peporine Lopes, Pieter C. Dorrestein:
  Propagating annotations of molecular networks using in silico fragmentation.
• 
  J. Swaroop Guntupalli, Feilong Ma, James V. Haxby:
  A computational model of shared fine-scale structure in the human connectome.
• 
  Marco Del Giudice, Stefano Bo, Silvia Grigolon, Carla Bosia:
  On the role of extrinsic noise in microRNA-mediated bimodal gene expression.
• 
  Stephanie A. Ross, Nilima Nigam, James M. Wakeling:
  A modelling approach for exploring muscle dynamics during cyclic contractions.
• 
  Russell B. Davidson, Josie Hendrix, Brian J. Geiss, Martin McCullagh:
  Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations.
• 
  Florian Kaiser, Sebastian Bittrich, Sebastian Salentin, Christoph Leberecht, V. Joachim Haupt, Sarah Krautwurst, Michael Schroeder, Dirk Labudde:
  Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases.
• 
  Mark Reppell, John Novembre:
  Using pseudoalignment and base quality to accurately quantify microbial community composition.
• 
  Ricardo Martínez-García, Carey D. Nadell, Raimo Hartmann, Knut Drescher, Juan A. Bonachela:
  Cell adhesion and fluid flow jointly initiate genotype spatial distribution in biofilms.
• 
  Juan Francisco Viso, Patricia Belelli, Matías R. Machado, Humberto González, Sergio Pantano, María Julia Amundarain, Fernando Zamarreño, Maria Marta Branda, Diego M. A. Guérin, Marcelo D. Costabel:
  Multiscale modelization in a small virus: Mechanism of proton channeling and its role in triggering capsid disassembly.
• 
  Joydeep Sarkar, Alka A. Potdar, Gerald M. Saidel:
  Whole-body iron transport and metabolism: Mechanistic, multi-scale model to improve treatment of anemia in chronic kidney disease.
• 
  Bronac Flanagan, Liam McDaid, John J. Wade, KongFatt Wong-Lin, Jim Harkin:
  A computational study of astrocytic glutamate influence on post-synaptic neuronal excitability.
• 
  Fatemeh Khatami, Markus Wöhr, Heather L. Read, Monty A. Escabí:
  Origins of scale invariance in vocalization sequences and speech.
• 
  Martin Weigert, Kaushikaram Subramanian, Sebastian T. Bundschuh, Eugene W. Myers, Moritz Kreysing:
  Biobeam - Multiplexed wave-optical simulations of light-sheet microscopy.
• 
  Jian-Geng Chiou, Samuel A. Ramirez, Timothy C. Elston, Thomas P. Witelski, David G. Schaeffer, Daniel J. Lew:
  Principles that govern competition or co-existence in Rho-GTPase driven polarization.
• 
  Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G. Barrett, Peter H. Thrall:
  Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens.
• 
  Robin Mills, Hanno Hildenbrandt, Graham K. Taylor, Charlotte K. Hemelrijk:
  Physics-based simulations of aerial attacks by peregrine falcons reveal that stooping at high speed maximizes catch success against agile prey.
• 
  Travers Ching, Xun Zhu, Lana X. Garmire:
  Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data.
• 
  Laurent Dollé, Ricardo Chavarriaga, Agnès Guillot, Mehdi Khamassi:
  Interactions of spatial strategies producing generalization gradient and blocking: A computational approach.
• 
  Arnaud Messé, Marc-Thorsten Hütt, Claus C. Hilgetag:
  Toward a theory of coactivation patterns in excitable neural networks.
• 
  Wolfgang Giese, Gregor Milicic, Andreas Schröder, Edda Klipp:
  Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction.
• 
  Huanan Zhang, Catherine A. A. Lee, Zhuliu Li, John R. Garbe, Cindy R. Eide, Raphael Petegrosso, Rui Kuang, Jakub Tolar:
  A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa.
• 
  Stefan Sellman, Kimberly Tsao, Michael J. Tildesley, Peter Brommesson, Colleen Webb, Uno Wennergren, Matt J. Keeling, Tom Lindström:
  Need for speed: An optimized gridding approach for spatially explicit disease simulations.
• 
  Annie M. Westerlund, Lucie Delemotte:
  Effect of Ca2+ on the promiscuous target-protein binding of calmodulin.
• 
  Hironori Fujita, Masayoshi Kawaguchi:
  Spatial regularity control of phyllotaxis pattern generated by the mutual interaction between auxin and PIN1.
• 
  Yoram Zarai, Tamir Tuller:
  Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources.
• 
  Javier A. Caballero, Mark D. Humphries, Kevin N. Gurney:
  A probabilistic, distributed, recursive mechanism for decision-making in the brain.

Volume 14, Number 5, May 2018

Editorials

• 
  Daniel Mietchen, Shoshana J. Wodak, Szymon Wasik, Natalia Szostak, Christophe Dessimoz:
  Submit a Topic Page to PLOS Computational Biology and Wikipedia.
• 
  Lubomir Tomaska, Jozef Nosek:
  Ten simple rules for writing a cover letter to accompany a job application for an academic position.

Messages from ISCB

• 
  Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
  2018 outstanding contributions to ISCB award: Russ Altman.
• 
  Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
  2018 ISCB accomplishments by a senior scientist award.
• 
  Milana Frenkel-Morgenstern, Lonnie R. Welch, Bruno A. Gaëta, Diane E. Kovats:
  Art in Science Competition invites artworks to the annual exhibition on ISMB 2018 in Chicago.

Research Articles

• 
  Anton V. Chizhov, Artyom V. Zefirov, Dmitry V. Amakhin, Elena Yu. Smirnova, Aleksey V. Zaitsev:
  Minimal model of interictal and ictal discharges "Epileptor-2".
• 
  Eli J. Müller, Peter A. Robinson:
  Quantitative theory of deep brain stimulation of the subthalamic nucleus for the suppression of pathological rhythms in Parkinson's disease.
• 
  William Hedley Thompson, Craig G. Richter, Pontus Plavén-Sigray, Peter Fransson:
  Simulations to benchmark time-varying connectivity methods for fMRI.
• 
  Marissa Renardy, Tau-Mu Yi, Dongbin Xiu, Ching-Shan Chou:
  Parameter uncertainty quantification using surrogate models applied to a spatial model of yeast mating polarization.
• 
  Han-Lin Hsieh, Maryam M. Shanechi:
  Optimizing the learning rate for adaptive estimation of neural encoding models.
• 
  Benjamin Skerritt-Davis, Mounya Elhilali:
  Detecting change in stochastic sound sequences.
• 
  Surya K. Ghosh, Daniel Jost:
  How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes.
• 
  Rui Ma, Julien Berro:
  Structural organization and energy storage in crosslinked actin assemblies.
• 
  Peter Helfer, Thomas R. Shultz:
  Coupled feedback loops maintain synaptic long-term potentiation: A computational model of PKMzeta synthesis and AMPA receptor trafficking.
• 
  Viola Priesemann, Oren Shriki:
  Can a time varying external drive give rise to apparent criticality in neural systems?
• 
  Caroline H. Roney, Jason D. Bayer, Hubert Cochet, Marianna Meo, Rémi Dubois, Pierre Jaïs, Edward J. Vigmond:
  Variability in pulmonary vein electrophysiology and fibrosis determines arrhythmia susceptibility and dynamics.
• 
  Lazaro M. Sanchez-Rodriguez, Yasser Iturria-Medina, Erica A. Baines, Sabela C. Mallo, Mehdy Dousty, Roberto C. Sotero:
  Design of optimal nonlinear network controllers for Alzheimer's disease.
• 
  Seth Haney, Jessica Konen, Adam I. Marcus, Maxim Bazhenov:
  The complex ecosystem in non small cell lung cancer invasion.
• 
  Yun Tao, Katriona Shea, Matthew J. Ferrari:
  Logistical constraints lead to an intermediate optimum in outbreak response vaccination.
• 
  Méziane Aite, Marie Chevallier, Clémence Frioux, Camille Trottier, Jeanne Got, María Paz Cortés, Sebastián N. Mendoza, Grégory Carrier, Olivier Dameron, Nicolas Guillaudeux, Mauricio Latorre, Nicolás Loira, Gabriel V. Markov, Alejandro Maass, Anne Siegel:
  Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models.
• 
  Linda Dib, Nicolas Salamin, David Gfeller:
  Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins.
• 
  Ji Hyun Bak, Seogjoo J. Jang, Chang-hyeon Lim:
  Implications for human odor sensing revealed from the statistics of odorant-receptor interactions.
• 
  Philipp Berens, Jeremy Freeman, Thomas Deneux, Nicolay Chenkov, Thomas McColgan, Artur Speiser, Jakob H. Macke, Srinivas C. Turaga, Patrick J. Mineault, Peter Rupprecht, Stephan Gerhard, Rainer W. Friedrich, Johannes Friedrich, Liam Paninski, Marius Pachitariu, Kenneth D. Harris, Ben Bolte, Timothy A. Machado, Dario Ringach, Jasmine Stone, Luke E. Rogerson, Nicolas J. Sofroniew, Jacob Reimer, Emmanouil Froudarakis, Thomas Euler, Miroslav Román Rosón, Lucas Theis, Andreas S. Tolias, Matthias Bethge:
  Community-based benchmarking improves spike rate inference from two-photon calcium imaging data.
• 
  Andrew D. Rouillard, Mark Hurle, Pankaj Agarwal:
  Systematic interrogation of diverse Omic data reveals interpretable, robust, and generalizable transcriptomic features of clinically successful therapeutic targets.
• 
  Jagannath Mondal, Navjeet Ahalawat, Subhendu Pandit, Lewis E. Kay, Pramodh Vallurupalli:
  Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme.
• 
  Carlos Espinosa-Soto:
  On the role of sparseness in the evolution of modularity in gene regulatory networks.
• 
  Kevin Breslin, John Joseph Wade, KongFatt Wong-Lin, Jim Harkin, Bronac Flanagan, Harm Van Zalinge, Steve Hall, Matthew C. Walker, Alexei Verkhratsky, Liam McDaid:
  Potassium and sodium microdomains in thin astroglial processes: A computational model study.
• 
  Milad Hobbi Mobarhan, Geir Halnes, Pablo Martínez-Cañada, Torkel Hafting, Marianne Fyhn, Gaute T. Einevoll:
  Firing-rate based network modeling of the dLGN circuit: Effects of cortical feedback on spatiotemporal response properties of relay cells.
• 
  Andreas Petrides, Glenn Vinnicombe:
  Enzyme sequestration by the substrate: An analysis in the deterministic and stochastic domains.
• 
  Damiano Pasetto, Flavio Finger, Anton Camacho, Francesco Grandesso, Sandra Cohuet, Joseph Chadi Lemaitre, Andrew S. Azman, Francisco J. Luquero, Enrico Bertuzzo, Andrea Rinaldo:
  Near real-time forecasting for cholera decision making in Haiti after Hurricane Matthew.
• 
  Aaditya V. Rangan, Caroline C. McGrouther, John Kelsoe, Nicholas J. Schork, Eli Stahl, Qian Zhu, Arjun Krishnan, Vicky Yao, Olga G. Troyanskaya, Seda Bilaloglu, Preeti Raghavan, Sarah Bergen, Anders Juréus, Mikael Landen:
  A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data.
• 
  Thanos Manos, Magteld Zeitler, Peter A. Tass:
  How stimulation frequency and intensity impact on the long-lasting effects of coordinated reset stimulation.
• 
  Jonathan E. Ron, Itai Pinkoviezky, Ehud Fonio, Ofer Feinerman, Nir S. Gov:
  Bi-stability in cooperative transport by ants in the presence of obstacles.
• 
  Tim van Mourik, Lukas Snoek, Tomas Knapen, David G. Norris:
  Porcupine: A visual pipeline tool for neuroimaging analysis.
• 
  Vicente Botella-Soler, Stéphane Deny, Georg Martius, Olivier Marre, Gasper Tkacik:
  Nonlinear decoding of a complex movie from the mammalian retina.
• 
  Arturo Blazquez-Navarro, Thomas Schachtner, Ulrik Stervbo, Anett Sefrin, Maik Stein, Timm H. Westhoff, Petra Reinke, Edda Klipp, Nina Babel, Avidan U. Neumann, Michal Or-Guil:
  Differential T cell response against BK virus regulatory and structural antigens: A viral dynamics modelling approach.
• 
  Gonçalo M. Marques, Starrlight Augustine, Konstadia Lika, Laure Pecquerie, Tiago Domingos, Sebastiaan A. L. M. Kooijman:
  The AmP project: Comparing species on the basis of dynamic energy budget parameters.
• 
  Matthew E. MacGilvray, Evgenia Shishkova, Deborah Chasman, Michael Place, Anthony Gitter, Joshua J. Coon, Audrey P. Gasch:
  Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response.
• 
  Joseph B. Dechery, Jason N. MacLean:
  Functional triplet motifs underlie accurate predictions of single-trial responses in populations of tuned and untuned V1 neurons.
• 
  Florian Aspart, Michiel W. H. Remme, Klaus Obermayer:
  Differential polarization of cortical pyramidal neuron dendrites through weak extracellular fields.
• 
  Nathanaël Hozé, Sebastian Bonhoeffer, Roland R. Regoes:
  Assessing the public health impact of tolerance-based therapies with mathematical models.
• 
  Aaron T. L. Lun, Hervé Pagès, Mike L. Smith:
  beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types.
• 
  Paul A. Roberts, Ryan M. Huebinger, Emma Keen, Anne-Marie Krachler, Sara Jabbari:
  Predictive modelling of a novel anti-adhesion therapy to combat bacterial colonisation of burn wounds.
• 
  Shoichiro Yamaguchi, Honda Naoki, Muneki Ikeda, Yuki Tsukada, Shunji Nakano, Ikue Mori, Shin Ishii:
  Identification of animal behavioral strategies by inverse reinforcement learning.

Volume 14, Number 6, June 2018

Messages from ISCB

• 
  Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
  2018 ISCB Innovator Award recognizes M. Madan Babu.
• 
  Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
  2018 ISCB Overton Prize awarded to Cole Trapnell.

Education

• 
  Vivek Navale, Philip E. Bourne:
  Cloud computing applications for biomedical science: A perspective.

Research Articles

• 
  Gregory J. Gerling, Lingtian Wan, Benjamin U. Hoffman, Yuxiang Wang, Ellen A. Lumpkin:
  Computation predicts rapidly adapting mechanotransduction currents cannot account for tactile encoding in Merkel cell-neurite complexes.
• 
  Daniel Munro, Dario Ghersi, Mona Singh:
  Two critical positions in zinc finger domains are heavily mutated in three human cancer types.
• 
  Giri P. Krishnan, Burke Q. Rosen, Jen-Yung Chen, Lyle Muller, Terrence J. Sejnowski, Sydney S. Cash, Eric Halgren, Maxim Bazhenov:
  Thalamocortical and intracortical laminar connectivity determines sleep spindle properties.
• 
  Fahad Alhasoun, Faisal Aleissa, May Alhazzani, Luis Gregorio Moyano, Claudio S. Pinhanez, Marta C. González:
  Age density patterns in patients medical conditions: A clustering approach.
• 
  Jennifer Lu, Steven L. Salzberg:
  Removing contaminants from databases of draft genomes.
• 
  Luke Zappia, Belinda Phipson, Alicia Oshlack:
  Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database.
• 
  Jonathan U. Harrison, Ruth E. Baker:
  The impact of temporal sampling resolution on parameter inference for biological transport models.
• 
  Alexander D. Bird, Magnus J. E. Richardson:
  Transmission of temporally correlated spike trains through synapses with short-term depression.
• 
  Nicolas Henry, Eva-Maria Krammer, Florian Stengel, Quentin Adams, François Van Liefferinge, Ellen Hubin, Rui Chaves, Rouslan Efremov, Ruedi Aebersold, Guy Vandenbussche, Martine Prévost, Vincent Raussens, Stéphanie Deroo:
  Lipidated apolipoprotein E4 structure and its receptor binding mechanism determined by a combined cross-linking coupled to mass spectrometry and molecular dynamics approach.
• 
  Brendan A. Bicknell, Zac Pujic, Peter Dayan, Geoffrey J. Goodhill:
  Control of neurite growth and guidance by an inhibitory cell-body signal.
• 
  Sylvie Estrela, Sam P. Brown:
  Community interactions and spatial structure shape selection on antibiotic resistant lineages.
• 
  Peter K. Eastman, Jade Shi, Bharath Ramsundar, Vijay S. Pande:
  Solving the RNA design problem with reinforcement learning.
• 
  Sung-Young Shin, Anna-Katharina Müller, Nandini Verma, Sima Lev, Lan K. Nguyen:
  Systems modelling of the EGFR-PYK2-c-Met interaction network predicts and prioritizes synergistic drug combinations for triple-negative breast cancer.
• 
  Wei-Ven Tee, Enrico Guarnera, Igor N. Berezovsky:
  Reversing allosteric communication: From detecting allosteric sites to inducing and tuning targeted allosteric response.
• 
  Bruck Taddese, Madeline Deniaud, Antoine Garnier, Asma Tiss, Hajer Guissouma, Hervé Abdi, Daniel Henrion, Marie Chabbert:
  Evolution of chemokine receptors is driven by mutations in the sodium binding site.
• 
  Deena R. Schmidt, Roberto F. Galán, Peter J. Thomas:
  Stochastic shielding and edge importance for Markov chains with timescale separation.
• 
  Yuji Sakai, Atsushi Mochizuki, Kazuhisa Kinoshita, Tatsuya Hirano, Masashi Tachikawa:
  Modeling the functions of condensin in chromosome shaping and segregation.
• 
  Nathaniel Mon Père, Tom Lenaerts, Jorge M. Pacheco, David Dingli:
  Evolutionary dynamics of paroxysmal nocturnal hemoglobinuria.
• 
  Alexander Kihm, Lars Kaestner, Christian Wagner, Stephan Quint:
  Classification of red blood cell shapes in flow using outlier tolerant machine learning.
• 
  J. Kyle Medley, Kiri Choi, Matthias König, Lucian P. Smith, Stanley Gu, Joseph L. Hellerstein, Stuart C. Sealfon, Herbert M. Sauro:
  Tellurium notebooks - An environment for reproducible dynamical modeling in systems biology.
• 
  Logan C. Brooks, David C. Farrow, Sangwon Hyun, Ryan J. Tibshirani, Roni Rosenfeld:
  Nonmechanistic forecasts of seasonal influenza with iterative one-week-ahead distributions.
• 
  Fabrizio Cleri, Fabio Landuzzi, Ralf Blossey:
  Mechanical evolution of DNA double-strand breaks in the nucleosome.
• 
  Sulav Duwal, Laura Dickinson, Saye Khoo, Max von Kleist:
  Hybrid stochastic framework predicts efficacy of prophylaxis against HIV: An example with different dolutegravir prophylaxis schemes.
• 
  Alexander Borst:
  A biophysical mechanism for preferred direction enhancement in fly motion vision.
• 
  Sergio Luengo-Sanchez, Isabel Fernaud, Concha Bielza, Ruth Benavides-Piccione, Pedro Larrañaga, Javier DeFelipe:
  3D morphology-based clustering and simulation of human pyramidal cell dendritic spines.
• 
  Mary M. Rorick, Edward B. Baskerville, Thomas S. Rask, Karen P. Day, Mercedes Pascual:
  Identifying functional groups among the diverse, recombining antigenic var genes of the malaria parasite Plasmodium falciparum from a local community in Ghana.
• 
  Adrien Henry, Mathieu Hemery, Paul François:
  φ-evo: A program to evolve phenotypic models of biological networks.
• 
  Michael Trogdon, Brian Drawert, Carlos Gomez, Samhita P. Banavar, Tau-Mu Yi, Otger Campàs, Linda R. Petzold:
  The effect of cell geometry on polarization in budding yeast.
• 
  Angelika Manhart, Stefanie Windner, Mary Baylies, Alex Mogilner:
  Mechanical positioning of multiple nuclei in muscle cells.
• 
  Suma Ghosh, Matthew J. Ferrari, Ashutosh K. Pathak, Isabella M. Cattadori:
  Changes in parasite traits, rather than intensity, affect the dynamics of infection under external perturbation.
• 
  Tobias S. Brett, Eamon B. O'Dea, Éric Marty, Paige B. Miller, Andrew W. Park, John M. Drake, Pejman Rohani:
  Anticipating epidemic transitions with imperfect data.
• 
  Benjamin Werner, Andrea Sottoriva:
  Variation of mutational burden in healthy human tissues suggests non-random strand segregation and allows measuring somatic mutation rates.
• 
  Ya-Zhou Shi, Lei Jin, Chen-Jie Feng, Ya-Lan Tan, Zhi-Jie Tan:
  Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions.
• 
  Shivam Gupta, Julien Varennes, Hendrik C. Korswagen, Andrew Mugler:
  Temporal precision of regulated gene expression.
• 
  Yvonne J. W. Rozendaal, Yanan Wang, Yared Paalvast, Lauren L. Tambyrajah, Zhuang Li, Ko Willems van Dijk, Patrick C. N. Rensen, Jan A. Kuivenhoven, Albert K. Groen, Peter A. J. Hilbers, Natal A. W. van Riel:
  In vivo and in silico dynamics of the development of Metabolic Syndrome.
• 
  Kumaresan Jayaraman, Alex N. Morley, Dániel Szöllosi, Tsjerk A. Wassenaar, Harald H. Sitte, Thomas Stockner:
  Dopamine transporter oligomerization involves the scaffold domain, but spares the bundle domain.
• 
  Lucas Boczkowski, Emanuele Natale, Ofer Feinerman, Amos Korman:
  Limits on reliable information flows through stochastic populations.
• 
  Koichi Higashi, Shinya Suzuki, Shin Kurosawa, Hiroshi Mori, Ken Kurokawa:
  Latent environment allocation of microbial community data.
• 
  Christian Klos, Daniel Miner, Jochen Triesch:
  Bridging structure and function: A model of sequence learning and prediction in primary visual cortex.
• 
  Philipp Schustek, Rubén Moreno-Bote:
  Instance-based generalization for human judgments about uncertainty.
• 
  Filip Radom, Andreas Plückthun, Emanuele Paci:
  Assessment of ab initio models of protein complexes by molecular dynamics.
• 
  Xiaoru Xue, Chuan Xue, Min Tang:
  The role of intracellular signaling in the stripe formation in engineered Escherichia coli populations.

Volume 14, Number 7, July 2018

Research Articles

• 
  Farzaneh Mohajerani, Michael F. Hagan:
  The role of the encapsulated cargo in microcompartment assembly.
• 
  Naihui Zhou, Zachary D. Siegel, Scott Zarecor, Nigel Lee, Darwin A. Campbell, Carson M. Andorf, Dan Nettleton, Carolyn J. Lawrence-Dill, Baskar Ganapathysubramanian, Jonathan W. Kelly, Iddo Friedberg:
  Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning.
• 
  Fredrik Allenmark, Hermann J. Müller, Zhuanghua Shi:
  Inter-trial effects in visual pop-out search: Factorial comparison of Bayesian updating models.
• 
  Ida Friis, Ilia A. Solov'yov:
  Activation of the DNA-repair mechanism through NBS1 and MRE11 diffusion.
• 
  Luigi Acerbi, Kalpana Dokka, Dora E. Angelaki, Wei Ji Ma:
  Bayesian comparison of explicit and implicit causal inference strategies in multisensory heading perception.
• 
  William G. P. Mayner, William Marshall, Larissa Albantakis, Graham Findlay, Robert Marchman, Giulio Tononi:
  PyPhi: A toolbox for integrated information theory.
• 
  Edvin Fuglebakk, Nathalie Reuter:
  A model for hydrophobic protrusions on peripheral membrane proteins.
• 
  Ajay Seth, Jennifer L. Hicks, Thomas K. Uchida, Ayman Habib, Christopher L. Dembia, James J. Dunne, Carmichael F. Ong, Matthew S. DeMers, Apoorva Rajagopal, Matthew Millard, Samuel R. Hamner, Edith M. Arnold, Jennifer R. Yong, Shrinidhi K. Lakshmikanth, Michael A. Sherman, Joy P. Ku, Scott L. Delp:
  OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement.
• 
  Magdalena San Román, Andreas Wagner:
  An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment.
• 
  Michelle R. Greene, Bruce C. Hansen:
  Shared spatiotemporal category representations in biological and artificial deep neural networks.
• 
  Chia-Chin Wu, Hannah C. Beird, Jianhua Zhang, P. Andrew Futreal:
  FusionPathway: Prediction of pathways and therapeutic targets associated with gene fusions in cancer.
• 
  William J. M. Probert, Chris P. Jewell, Marleen Werkman, Christopher Fonnesbeck, Yoshitaka Goto, Michael C. Runge, Satoshi Sekiguchi, Katriona Shea, Matt J. Keeling, Matthew J. Ferrari, Michael J. Tildesley:
  Real-time decision-making during emergency disease outbreaks.
• 
  Haitao Chai, Hongmei Jiang, Lu Lin, Lei Liu:
  A marginalized two-part Beta regression model for microbiome compositional data.
• 
  Xiaojie Chen, Attila Szolnoki:
  Punishment and inspection for governing the commons in a feedback-evolving game.
• 
  Bita Khalili, Laura Merlini, Vincent Vincenzetti, Sophie G. Martin, Dimitrios Vavylonis:
  Exploration and stabilization of Ras1 mating zone: A mechanism with positive and negative feedbacks.
• 
  Ximo Pechuan, Raymond Puzio, Aviv Bergman:
  The evolutionary dynamics of metabolic protocells.
• 
  Malbor Asllani, Paul Expert, Timoteo Carletti:
  A minimally invasive neurostimulation method for controlling abnormal synchronisation in the neuronal activity.
• 
  Antoine de Weck, Javad Golji, Michael D. Jones, Joshua M. Korn, Eric Billy, E. Robert McDonald III, Tobias Schmelzle, Hans Bitter, Audrey Kauffmann:
  Correction of copy number induced false positives in CRISPR screens.
• 
  Onno van der Groen, Matthew F. Tang, Nicole Wenderoth, Jason B. Mattingley:
  Stochastic resonance enhances the rate of evidence accumulation during combined brain stimulation and perceptual decision-making.
• 
  Darshan Mandge, Rohit Manchanda:
  A biophysically detailed computational model of urinary bladder small DRG neuron soma.
• 
  Dominik Freche, Jodie Naim-Feil, Avi Peled, Nava Levit-Binnun, Elisha Moses:
  A quantitative physical model of the TMS-induced discharge artifacts in EEG.
• 
  Duc Do, Serdar Bozdag:
  Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks.
• 
  Antreas C. Kalli, Reinhart A. F. Reithmeier:
  Interaction of the human erythrocyte Band 3 anion exchanger 1 (AE1, SLC4A1) with lipids and glycophorin A: Molecular organization of the Wright (Wr) blood group antigen.
• 
  Tanmay A. Gokhale, Huda Asfour, Shravan Verma, Nenad Bursac, Craig S. Henriquez:
  Microheterogeneity-induced conduction slowing and wavefront collisions govern macroscopic conduction behavior: A computational and experimental study.
• 
  Albert Pla, Xiangfu Zhong, Simon Rayner:
  miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts.
• 
  Vishnu Venugopal, Pranesh Padmanabhan, Rubesh Raja, Narendra M. Dixit:
  Modelling how responsiveness to interferon improves interferon-free treatment of hepatitis C virus infection.
• 
  Sebastian D. Boie, Erin G. Connor, Margaret McHugh, Katherine I. Nagel, G. Bard Ermentrout, John P. Crimaldi, Jonathan D. Victor:
  Information-theoretic analysis of realistic odor plumes: What cues are useful for determining location?
• 
  Spase Petkoski, J. Matias Palva, Viktor K. Jirsa:
  Phase-lags in large scale brain synchronization: Methodological considerations and in-silico analysis.
• 
  Yina Wei, Giri P. Krishnan, Maxim Komarov, Maxim Bazhenov:
  Differential roles of sleep spindles and sleep slow oscillations in memory consolidation.
• 
  Betül Senay Aras, Y. C. Zhou, Adriana T. Dawes, Ching-Shan Chou:
  The importance of mechanical constraints for proper polarization and psuedo-cleavage furrow generation in the early Caenorhabditis elegans embryo.
• 
  Joshua H. Goldwyn, Bradley R. Slabe, Joseph B. Travers, David H. Terman:
  Gain control with A-type potassium current: IA as a switch between divisive and subtractive inhibition.
• 
  Xiuli Chen, Robb B. Rutledge, Harriet R. Brown, Raymond J. Dolan, Sven Bestmann, Joseph M. Galea:
  Age-dependent Pavlovian biases influence motor decision-making.
• 
  Lukas Großberger, Francesco P. Battaglia, Martin A. Vinck:
  Unsupervised clustering of temporal patterns in high-dimensional neuronal ensembles using a novel dissimilarity measure.
• 
  Sonja E. M. Boas, Joao Carvalho, Marloes van den Broek, Ester M. Weijers, Marie-José Goumans, Pieter Koolwijk, Roeland M. H. Merks:
  A local uPAR-plasmin-TGFβ1 positive feedback loop in a qualitative computational model of angiogenic sprouting explains the in vitro effect of fibrinogen variants.
• 
  Ankit N. Khambhati, John D. Medaglia, Elisabeth A. Karuza, Sharon L. Thompson-Schill, Danielle S. Bassett:
  Subgraphs of functional brain networks identify dynamical constraints of cognitive control.
• 
  Hesam Setareh, Moritz Deger, Wulfram Gerstner:
  Excitable neuronal assemblies with adaptation as a building block of brain circuits for velocity-controlled signal propagation.
• 
  Kaixi Tang, Colton G. Boudreau, Claire M. Brown, Anmar Khadra:
  Paxillin phosphorylation at serine 273 and its effects on Rac, Rho and adhesion dynamics.
• 
  Colton J. Lloyd, Ali Ebrahim, Laurence Yang, Zachary A. King, Edward Catoiu, Edward J. O'Brien, Joanne K. Liu, Bernhard O. Palsson:
  COBRAme: A computational framework for genome-scale models of metabolism and gene expression.
• 
  Felix Brinkmann, Moritz Mercker, Thomas Richter, Anna K. Marciniak-Czochra:
  Post-Turing tissue pattern formation: Advent of mechanochemistry.
• 
  Bernardo A. Mello, Wenlin Pan, Gerald L. Hazelbauer, Yuhai Tu:
  A dual regulation mechanism of histidine kinase CheA identified by combining network-dynamics modeling and system-level input-output data.

Volume 14, Number 8, August 2018

Research Articles

• 
  Nathan Insel, Jordan Guerguiev, Blake A. Richards:
  Irrelevance by inhibition: Learning, computation, and implications for schizophrenia.
• 
  Valentina Marziano, Piero Poletti, Guillaume Béraud, Pierre-Yves Boëlle, Stefano Merler, Vittoria Colizza:
  Modeling the impact of changes in day-care contact patterns on the dynamics of varicella transmission in France between 1991 and 2015.
• 
  Luisa M. R. Napolitano, Arin Marchesi, Alex Rodriguez, Matteo De March, Silvia Onesti, Alessandro Laio, Vincent Torre:
  The permeation mechanism of organic cations through a CNG mimic channel.
• 
  Xiao Ma, Onur Dagliyan, Klaus M. Hahn, Gaudenz Danuser:
  Profiling cellular morphodynamics by spatiotemporal spectrum decomposition.
• 
  Margaret J. Tse, Brian K. Chu, Cameron P. Gallivan, Elizabeth L. Read:
  Rare-event sampling of epigenetic landscapes and phenotype transitions.
• 
  Andrew G. McDonald, Keith F. Tipton, Gavin P. Davey:
  A mechanism for bistability in glycosylation.
• 
  Tianwei Yu:
  A new dynamic correlation algorithm reveals novel functional aspects in single cell and bulk RNA-seq data.
• 
  Cesar A. O. Coelho, Tatiana L. Ferreira, Juliana C. Kramer-Soares, João R. Sato, Maria Gabriela M. Oliveira:
  Network supporting contextual fear learning after dorsal hippocampal damage has increased dependence on retrosplenial cortex.
• 
  James T. Yurkovich, Miguel A. Alcantar, Zachary B. Haiman, Bernhard O. Palsson:
  Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials.
• 
  Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard:
  Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.
• 
  Jason S. Sherfey, Salva Ardid, Joachim Hass, Michael E. Hasselmo, Nancy J. Kopell:
  Flexible resonance in prefrontal networks with strong feedback inhibition.
• 
  Teresa Katthagen, Christoph Mathys, Lorenz Deserno, Henrik Walter, Norbert Kathmann, Andreas Heinz, Florian Schlagenhauf:
  Modeling subjective relevance in schizophrenia and its relation to aberrant salience.
• 
  Mohanalakshmi Narasumani, Paul M. Harrison:
  Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins.
• 
  Luyi Tian, Shian Su, Xueyi Dong, Daniela Amann-Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J. Hilton, Shalin H. Naik, Matthew E. Ritchie:
  scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data.
• 
  Fabio Lauria, Toma Tebaldi, Paola Bernabò, Ewout J. N. Groen, Thomas H. Gillingwater, Gabriella Viero:
  riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data.
• 
  Silke Bergeler, Erwin Frey:
  Regulation of Pom cluster dynamics in Myxococcus xanthus.
• 
  Rong Zhang, Zhao Ren, Wei Chen:
  SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks.
• 
  Kyubum Lee, Maria Livia Famiglietti, Aoife McMahon, Chih-Hsuan Wei, Jacqueline A. L. MacArthur, Sylvain Poux, Lionel Breuza, Alan J. Bridge, Fiona Cunningham, Ioannis Xenarios, Zhiyong Lu:
  Scaling up data curation using deep learning: An application to literature triage in genomic variation resources.
• 
  Gaëtan Vignoud, Laurent Venance, Jonathan D. Touboul:
  Interplay of multiple pathways and activity-dependent rules in STDP.
• 
  Lorenzo Posani, Simona Cocco, Rémi Monasson:
  Integration and multiplexing of positional and contextual information by the hippocampal network.
• 
  Bernard Cazelles, Clara Champagne, Joseph Dureau:
  Accounting for non-stationarity in epidemiology by embedding time-varying parameters in stochastic models.
• 
  Robert Cope, Joshua V. Ross, Monique Chilver, Nigel P. Stocks, Lewis Mitchell:
  Characterising seasonal influenza epidemiology using primary care surveillance data.
• 
  Christos Vlachos, Robert Kofler:
  MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies.
• 
  Gert Peters, Jo Maertens, Jeroen Lammertyn, Marjan De Mey:
  Exploring of the feature space of de novo developed post-transcriptional riboregulators.
• 
  Christina L. Hamlet, Kathleen A. Hoffman, Eric D. Tytell, Lisa J. Fauci:
  The role of curvature feedback in the energetics and dynamics of lamprey swimming: A closed-loop model.
• 
  Diego Garrido-Martín, Emilio Palumbo, Roderic Guigó, Alessandra Breschi:
  ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization.
• 
  Kirsten Henderson, Michel Loreau:
  How ecological feedbacks between human population and land cover influence sustainability.
• 
  Shishir Adhikari, Jacob Moran, Christopher Weddle, Michael Hinczewski:
  Unraveling the mechanism of the cadherin-catenin-actin catch bond.
• 
  Jaime Agudo-Canalejo, Reinhard Lipowsky:
  Domes and cones: Adhesion-induced fission of membranes by ESCRT proteins.
• 
  Arnab Bandyopadhyay, Huijing Wang, J. Christian J. Ray:
  Lineage space and the propensity of bacterial cells to undergo growth transitions.
• 
  Paula Sanz-Leon, Peter A. Robinson, Stuart A. Knock, Peter M. Drysdale, Romesh G. Abeysuriya, Felix K. Fung, Christopher J. Rennie, Xuelong Zhao:
  NFTsim: Theory and Simulation of Multiscale Neural Field Dynamics.
• 
  Niru Maheswaranathan, David B. Kastner, Stephen A. Baccus, Surya Ganguli:
  Inferring hidden structure in multilayered neural circuits.
• 
  Richard Rosch, Paul R. Hunter, Torsten Baldeweg, Karl J. Friston, Martin P. Meyer:
  Calcium imaging and dynamic causal modelling reveal brain-wide changes in effective connectivity and synaptic dynamics during epileptic seizures.
• 
  Massimo Silvetti, Eliana Vassena, Elger L. Abrahamse, Tom Verguts:
  Dorsal anterior cingulate-brainstem ensemble as a reinforcement meta-learner.
• 
  Alena van Bömmel, Michael I. Love, Ho-Ryun Chung, Martin Vingron:
  coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers.
• 
  Xing Chen, Jun Yin, Jia Qu, Li Huang:
  MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction.
• 
  Vito Paolo Pastore, Paolo Massobrio, Aleksandar Godjoski, Sergio Martinoia:
  Identification of excitatory-inhibitory links and network topology in large-scale neuronal assemblies from multi-electrode recordings.
• 
  Stefano Zappacosta, Francesco Mannella, Marco Mirolli, Gianluca Baldassarre:
  General differential Hebbian learning: Capturing temporal relations between events in neural networks and the brain.
• 
  Ilya Patrushev, Christina James-Zorn, Aldo Ciau-Uitz, Roger Patient, Michael J. Gilchrist:
  New methods for computational decomposition of whole-mount in situ images enable effective curation of a large, highly redundant collection of Xenopus images.

Corrections

• 
  Correction: Limits on reliable information flows through stochastic populations.
• 
  Ankit N. Khambhati, John D. Medaglia, Elisabeth A. Karuza, Sharon L. Thompson-Schill, Danielle S. Bassett:
  Correction: Subgraphs of functional brain networks identify dynamical constraints of cognitive control.

Volume 14, Number 9, September 2018

Research Articles

• 
  Zeynep Ertem, Dorrie Raymond, Lauren Ancel Meyers:
  Optimal multi-source forecasting of seasonal influenza.
• 
  Davide Risso, Liam Purvis, Russell B. Fletcher, Diya Das, John Ngai, Sandrine Dudoit, Elizabeth Purdom:
  clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets.
• 
  Alexander J. Titus, Audrey Flower, Patrick Hagerty, Paul Gamble, Charlie Lewis, Todd Stavish, Kevin P. OConnell, Greg Shipley, Stephanie M. Rogers:
  SIG-DB: Leveraging homomorphic encryption to securely interrogate privately held genomic databases.
• 
  Itamar Eliakim, Zahi Cohen, Gabor Kosa, Yossi Yovel:
  A fully autonomous terrestrial bat-like acoustic robot.
• 
  Weizhong Chen, Yi Liu, Shanshan Zhu, Guoyu Chen, Jing-Dong J. Han:
  Inter-nucleosomal communication between histone modifications for nucleosome phasing.
• 
  Helmut Schmidt, Daniele Avitabile, Ernest Montbrió, Alex Roxin:
  Network mechanisms underlying the role of oscillations in cognitive tasks.
• 
  Ahmed Abdul Quadeer, David Morales-Jiménez, Matthew R. McKay:
  Co-evolution networks of HIV/HCV are modular with direct association to structure and function.
• 
  Lia Papadopoulos, Pablo Blinder, Henrik Ronellenfitsch, Florian Klimm, Eleni Katifori, David Kleinfeld, Danielle S. Bassett:
  Comparing two classes of biological distribution systems using network analysis.
• 
  Fridolin Gross, Paolo Bonaiuti, Silke Hauf, Andrea Ciliberto:
  Implications of alternative routes to APC/C inhibition by the mitotic checkpoint complex.
• 
  Tatu Pantsar, Sami Rissanen, Daniel Dauch, Tuomo Laitinen, Ilpo Vattulainen, Antti Poso:
  Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling.
• 
  Sergi Elizalde, Ashley M. Laughney, Samuel F. Bakhoum:
  A Markov chain for numerical chromosomal instability in clonally expanding populations.
• 
  Emelie Flood, Céline Boiteux, Toby W. Allen:
  Selective ion permeation involves complexation with carboxylates and lysine in a model human sodium channel.
• 
  Francisco José Esteban, Javier A. Galadí, José A. Langa, José Ramón Portillo, Fernando Soler-Toscano:
  Informational structures: A dynamical system approach for integrated information.
• 
  Edward M. Hill, Thomas A. House, Madhur S. Dhingra, Wantanee Kalpravidh, Subhash Morzaria, Muzaffar G. Osmani, Eric Brum, Mat Yamage, Md. A. Kalam, Diann J. Prosser, John Y. Takekawa, Xiangming Xiao, Marius Gilbert, Michael J. Tildesley:
  The impact of surveillance and control on highly pathogenic avian influenza outbreaks in poultry in Dhaka division, Bangladesh.
• 
  Nikhil Bhagwat, Joseph D. Viviano, Aristotle N. Voineskos, M. Mallar Chakravarty, Alzheimer's Disease Neuroimaging Initiative:
  Modeling and prediction of clinical symptom trajectories in Alzheimer's disease using longitudinal data.
• 
  Jan Poleszczuk, Malgorzata Debowska, Wojciech Dabrowski, Alicja Wojcik-Zaluska, Wojciech Zaluska, Jacek Waniewski:
  Patient-specific pulse wave propagation model identifies cardiovascular risk characteristics in hemodialysis patients.
• 
  Ivilin Peev Stoianov, Cyriel M. A. Pennartz, Carien Lansink, Giovanni Pezzulo:
  Model-based spatial navigation in the hippocampus-ventral striatum circuit: A computational analysis.
• 
  Callie J. Miller, Demetrius Harris, Robert Weaver, G. Bard Ermentrout, Lance A. Davidson:
  Emergent mechanics of actomyosin drive punctuated contractions and shape network morphology in the cell cortex.
• 
  Rosanna Migliore, Carmen Alina Lupascu, Luca Leonardo Bologna, Armando Romani, Jean-Denis Courcol, Stefano Antonel, Werner Van Geit, Alex M. Thomson, Audrey Mercer, Sigrun Lange, Joanne Falck, Christian Rössert, Ying Shi, Olivier Hagens, Maurizio Pezzoli, Tamás F. Freund, Szabolcs Káli, Eilif B. Müller, Felix Schürmann, Henry Markram, Michele Migliore:
  The physiological variability of channel density in hippocampal CA1 pyramidal cells and interneurons explored using a unified data-driven modeling workflow.
• 
  Gabriele Pedruzzi, Ayuna Barlukova, Igor M. Rouzine:
  Evolutionary footprint of epistasis.
• 
  Alex J. Cope, Eleni Vasilaki, Dorian Minors, Chelsea Sabo, James A. R. Marshall, Andrew B. Barron:
  Abstract concept learning in a simple neural network inspired by the insect brain.
• 
  Andrey Babichev, Dmitriy Morozov, Yuri Dabaghian:
  Robust spatial memory maps encoded by networks with transient connections.
• 
  Hyuntae Na, Guang Song:
  All-atom normal mode dynamics of HIV-1 capsid.
• 
  Rowan D. Brackston, Eszter Lakatos, Michael P. H. Stumpf:
  Transition state characteristics during cell differentiation.
• 
  Robert Planqué, Josephus Hulshof, Bas Teusink, Johannes C. Hendriks, Frank J. Bruggeman:
  Maintaining maximal metabolic flux by gene expression control.
• 
  Yafei Lyu, Lingzhou Xue, Feipeng Zhang, Hillary Koch, Laura M. Saba, Katerina J. Kechris, Qunhua Li:
  Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network.
• 
  Sean M. Cascarina, Eric D. Ross:
  Proteome-scale relationships between local amino acid composition and protein fates and functions.
• 
  Kaushik J. Lakshminarasimhan, Alexandre Pouget, Gregory C. DeAngelis, Dora E. Angelaki, Xaq Pitkow:
  Inferring decoding strategies for multiple correlated neural populations.
• 
  Oliver Hädicke, Axel von Kamp, Timur Aydogan, Steffen Klamt:
  OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli.
• 
  Bin Wu, Lei Zhou:
  Individualised aspiration dynamics: Calculation by proofs.
• 
  Makoto Fukushima, Olaf Sporns:
  Comparison of fluctuations in global network topology of modeled and empirical brain functional connectivity.
• 
  Jörn H. Buchbinder, Dennis Pischel, Kai Sundmacher, Robert J. Flassig, Inna N. Lavrik:
  Quantitative single cell analysis uncovers the life/death decision in CD95 network.
• 
  Farzaneh Khajouei, Saurabh Sinha:
  An information theoretic treatment of sequence-to-expression modeling.
• 
  Kristopher A. Hunt, Ryan M. Jennings, William P. Inskeep, Ross P. Carlson:
  Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community.
• 
  Hamidreza Jamalabadi, Sarah Alizadeh, Monika Schönauer, Christian Leibold, Steffen Gais:
  Multivariate classification of neuroimaging data with nested subclasses: Biased accuracy and implications for hypothesis testing.
• 
  Marcus Anthony Triplett, Lilach Avitan, Geoffrey J. Goodhill:
  Emergence of spontaneous assembly activity in developing neural networks without afferent input.

Correction

• 
  Vijay Vedula, Juhyun Lee, Hao Xu, C.-C. Jay Kuo, Tzung K. Hsiai, Alison L. Marsden:
  Correction: A method to quantify mechanobiologic forces during zebrafish cardiac development using 4-D light sheet imaging and computational modeling.

Volume 14, Number 10, October 2018

Editorials

• 
  Todd C. Peterson, Sofie R. Kleppner, Crystal M. Botham:
  Ten simple rules for scientists: Improving your writing productivity.
• 
  Philip E. Bourne:
  Ten simple rules when considering retirement.
• 
  Marcos Méndez:
  Ten simple rules for developing good reading habits during graduate school and beyond.

Education Articles

• 
  Richard A. Erickson, Michael N. Fienen, S. Grace McCalla, Emily L. Weiser, Melvin L. Bower, Jonathan M. Knudson, Greg Thain:
  Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor.
• 
  Lars Ole Schwen, Sabrina Rueschenbaum:
  Ten quick tips for getting the most scientific value out of numerical data.

Perspective

• 
  Prithwish Chakraborty, Bryan L. Lewis, Stephen G. Eubank, John S. Brownstein, Madhav V. Marathe, Naren Ramakrishnan:
  What to know before forecasting the flu.

Research Articles

• 
  Francisco Y. Cai, Thomas Fussell, Sarah Cobey, Marc Lipsitch:
  Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine.
• 
  Fabian A. Soto, Lauren Vucovich, F. Gregory Ashby:
  Linking signal detection theory and encoding models to reveal independent neural representations from neuroimaging data.
• 
  Michael F. Staddon, Dapeng Bi, A. Pasha Tabatabai, Visar Ajeti, Michael P. Murrell, Shiladitya Banerjee:
  Cooperation of dual modes of cell motility promotes epithelial stress relaxation to accelerate wound healing.
• 
  Andreas Handel, Yan Li, Brian McKay, Kasia A. Pawelek, Veronika Zarnitsyna, Rustom Antia:
  Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine design.
• 
  Sahar Gelfman, Quanli Wang, Yi-Fan Lu, Diana Hall, Christopher D. Bostick, Ryan Dhindsa, Matt Halvorsen, K. Melodi McSweeney, Ellese Cotterill, Tom Edinburgh, Michael A. Beaumont, Wayne N. Frankel, Slavé Petrovski, Andrew S. Allen, Michael J. Boland, David B. Goldstein, Stephen J. Eglen:
  meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays.
• 
  Ling Chen, Alexandra E. Fish, John A. Capra:
  Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties.
• 
  Andreas Solbrå, Aslak Wigdahl Bergersen, Jonas van den Brink, Anders Malthe-Sørenssen, Gaute T. Einevoll, Geir Halnes:
  A Kirchhoff-Nernst-Planck framework for modeling large scale extracellular electrodiffusion surrounding morphologically detailed neurons.
• 
  Istvan T. Kleijn, Laurens H. J. Krah, Rutger Hermsen:
  Noise propagation in an integrated model of bacterial gene expression and growth.
• 
  Ik-Soo Huh, Isabel Mendizabal, Taesung Park, Soojin V. Yi:
  Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals.
• 
  Toshitake Asabuki, Naoki Hiratani, Tomoki Fukai:
  Interactive reservoir computing for chunking information streams.
• 
  Vasileios Vavourakis, Triantafyllos Stylianopoulos, Peter A. Wijeratne:
  In-silico dynamic analysis of cytotoxic drug administration to solid tumours: Effect of binding affinity and vessel permeability.
• 
  Robin Moss, Frank B. Sachse, Eloy G. Moreno-Galindo, Ricardo A. Navarro-Polanco, Martin Tristani-Firouzi, Gunnar Seemann:
  Modeling effects of voltage dependent properties of the cardiac muscarinic receptor on human sinus node function.
• 
  Ernest C. Y. Ho, Juan Nicolas Malagón, Abha Ahuja, Rama Singh, Ellen Larsen:
  Rotation of sex combs in Drosophila melanogaster requires precise and coordinated spatio-temporal dynamics from forces generated by epithelial cells.
• 
  Philippa J. Karoly, Levin Kuhlmann, Daniel Soudry, David B. Grayden, Mark J. Cook, Dean R. Freestone:
  Seizure pathways: A model-based investigation.
• 
  Huy Tran, Jonathan Desponds, Carmina Perez Romero, Mathieu Coppey, Cecile Fradin, Nathalie Dostatni, Aleksandra M. Walczak:
  Precision in a rush: Trade-offs between reproducibility and steepness of the hunchback expression pattern.
• 
  Daniel Strömbom, Audrey Dussutour:
  Self-organized traffic via priority rules in leaf-cutting ants.
• 
  Joseph A. Lombardo, Matthew V. Macellaio, Bing Liu, Stephanie E. Palmer, Leslie C. Osborne:
  State dependence of stimulus-induced variability tuning in macaque MT.
• 
  Ivan Tomic, Paul M. Bays:
  Internal but not external noise frees working memory resources.
• 
  Amrit Dhar, Kristian Davidsen, Frederick A. Matsen IV, Vladimir N. Minin:
  Predicting B cell receptor substitution profiles using public repertoire data.
• 
  Michael A. Skinnider, R. Greg Stacey, Leonard J. Foster:
  Genomic data integration systematically biases interactome mapping.
• 
  Kanika Bansal, John D. Medaglia, Danielle S. Bassett, Jean M. Vettel, Sarah Feldt Muldoon:
  Data-driven brain network models differentiate variability across language tasks.
• 
  Maximilian Schmidt, Rembrandt Bakker, Kelly Shen, Gleb Bezgin, Markus Diesmann, Sacha Jennifer van Albada:
  A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas.
• 
  Dominik Wodarz, Pamela J. Skinner, David N. Levy, Elizabeth Connick:
  Virus and CTL dynamics in the extrafollicular and follicular tissue compartments in SIV-infected macaques.
• 
  Song Xu, Sanggu Kim, Irvin S. Y. Chen, Tom Chou:
  Modeling large fluctuations of thousands of clones during hematopoiesis: The role of stem cell self-renewal and bursty progenitor dynamics in rhesus macaque.
• 
  Hao Wang, Simonas Marcisauskas, Benjamín J. Sánchez, Iván Domenzain, Daniel Hermansson, Rasmus Agren, Jens Nielsen, Eduard J. Kerkhoven:
  RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor.
• 
  Erki Aun, Age Brauer, Veljo Kisand, Tanel Tenson, Maido Remm:
  A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria.
• 
  Braden A. W. Brinkman, Fred Rieke, Eric Shea-Brown, Michael A. Buice:
  Predicting how and when hidden neurons skew measured synaptic interactions.
• 
  Sandra Giuliani, Arthur C. Silva, Joyce V. V. B. Borba, Pablo I. P. Ramos, Ross A. Paveley, Eugene N. Muratov, Carolina Horta Andrade, Nicholas Furnham:
  Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents.
• 
  Xinjian Mao, Sarah McManaway, Jagdish K. Jaiswal, Priyanka B. Patel, William R. Wilson, Kevin O. Hicks, Gib Bogle:
  An agent-based model for drug-radiation interactions in the tumour microenvironment: Hypoxia-activated prodrug SN30000 in multicellular tumour spheroids.
• 
  Adrian Jinich, Avi I. Flamholz, Haniu Ren, Sungjin Kim, Benjamín Sánchez-Lengeling, Charles A. R. Cotton, Elad Noor, Alán Aspuru-Guzik, Arren Bar-Even:
  Quantum chemistry reveals thermodynamic principles of redox biochemistry.
• 
  Frank S. Heldt, Reece Lunstone, John J. Tyson, Béla Novák:
  Dilution and titration of cell-cycle regulators may control cell size in budding yeast.
• 
  Ruohan Zhang, Shun Zhang, Matthew H. Tong, Yuchen Cui, Constantin A. Rothkopf, Dana H. Ballard, Mary M. Hayhoe:
  Modeling sensory-motor decisions in natural behavior.
• 
  Ying-Chih Chiang, Olesya Levsh, Chun Kei Lam, Jing-Ke Weng, Yi Wang:
  Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT).
• 
  Ioannis Kalfas, Kasper Vinken, Rufin Vogels:
  Representations of regular and irregular shapes by deep Convolutional Neural Networks, monkey inferotemporal neurons and human judgments.
• 
  Misbah Razzaq, Loïc Paulevé, Anne Siegel, Julio Saez-Rodriguez, Jérémie Bourdon, Carito Guziolowski:
  Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data.
• 
  Scott W. Simpkins, Justin Nelson, Raamesh Deshpande, Sheena C. Li, Jeff S. Piotrowski, Erin H. Wilson, Abraham A. Gebre, Hamid Safizadeh, Reika Okamoto, Mami Yoshimura, Michael Costanzo, Yoko Yashiroda, Yoshikazu Ohya, Hiroyuki Osada, Minoru Yoshida, Charles Boone, Chad L. Myers:
  Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions.
• 
  Eduardo Garrido, Juan Lázaro, Montserrat Jaumot, Neus Agell, Jaime Rubio-Martinez:
  Modeling and subtleties of K-Ras and Calmodulin interaction.
• 
  Michael A. Henson, Poonam Phalak:
  Suboptimal community growth mediated through metabolite crossfeeding promotes species diversity in the gut microbiota.
• 
  Tycho Bismeijer, Sander Canisius, Lodewyk F. A. Wessels:
  Molecular characterization of breast and lung tumors by integration of multiple data types with functional sparse-factor analysis.
• 
  Daniel S. Moore, Conor Brines, Heather Jewhurst, John P. Dalton, Irina G. Tikhonova:
  Steered molecular dynamics simulations reveal critical residues for (un)binding of substrates, inhibitors and a product to the malarial M1 aminopeptidase.
• 
  Katharina Nöh, Sebastian Niedenführ, Martin Beyß, Wolfgang Wiechert:
  A Pareto approach to resolve the conflict between information gain and experimental costs: Multiple-criteria design of carbon labeling experiments.

Correction

• 
  Miguel Fribourg, Diomedes E. Logothetis, Javier González-Maeso, Stuart C. Sealfon, Belén Galocha-Iragüen, Fernando Las-Heras Andrés, Vladimir Brezina:
  Correction: Elucidation of molecular kinetic schemes from macroscopic traces using system identification.

Volume 14, Number 11, November 2018

Editorials

• 
  Bjoern Peters, Steven E. Brenner, Edwin Wang, Donna K. Slonim, Maricel G. Kann:
  Putting benchmarks in their rightful place: The heart of computational biology.
• 
  Denise Carvalho-Silva, Leyla J. García, Sarah L. Morgan, Cath Brooksbank, Ian Dunham:
  Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars.
• 
  Marieke A. Frassl, David P. Hamilton, Blaize A. Denfeld, Elvira de Eyto, Stephanie E. Hampton, Philipp S. Keller, Sapna Sharma, Abigail S. L. Lewis, Gesa A. Weyhenmeyer, Catherine M. O'Reilly, Mary E. Lofton, Núria Catalán:
  Ten simple rules for collaboratively writing a multi-authored paper.

Perspective

• 
  Ryman Shoko, Justen Manasa, Mcebisi Maphosa, Joshua Mbanga, Reagan Mudziwapasi, Victoria Nembaware, Walter T. Sanyika, Tawanda Tinago, Zedias Chikwambi, Cephas Mawere, Alice Matimba, Grace Mugumbate, Jonathan Mufandaedza, Nicola J. Mulder, Hugh Patterton:
  Strategies and opportunities for promoting bioinformatics in Zimbabwe.

Research Articles

• 
  Reshma Basak, Rishikesh Narayanan:
  Active dendrites regulate the spatiotemporal spread of signaling microdomains.
• 
  Maurits J. J. Dijkstra, Punto Bawono, Sanne Abeln, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa:
  Motif-Aware PRALINE: Improving the alignment of motif regions.
• 
  Jerome Kelleher, Kevin R. Thornton, Jaime Ashander, Peter L. Ralph:
  Efficient pedigree recording for fast population genetics simulation.
• 
  Yarden Golan, Raphael Alhadeff, Fabian Glaser, Assaf Ganoth, Arieh Warshel, Yehuda G. Assaraf:
  Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter.
• 
  Stefano Luccioli, David Angulo-Garcia, Rosa Cossart, Arnaud Malvache, Laura Módol, Vitor Hugo Sousa, Paolo Bonifazi, Alessandro Torcini:
  Modeling driver cells in developing neuronal networks.
• 
  Giovanni B. Brandani, Shoji Takada:
  Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA.
• 
  Susann Vorberg, Stefan Seemayer, Johannes Söding:
  Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction.
• 
  Keisuke Fujii, Takeshi Kawasaki, Yuki Inaba, Yoshinobu Kawahara:
  Prediction and classification in equation-free collective motion dynamics.
• 
  Francisco J. H. Heras, Mikko Vähäsöyrinki, Jeremy E. Niven:
  Modulation of voltage-dependent K+ conductances in photoreceptors trades off investment in contrast gain for bandwidth.
• 
  Ruben Zamora, Sebastian Korff, Qi Mi, Derek Barclay, Lukas Schimunek, Riccardo Zucca, Xerxes D. Arsiwalla, Richard L. Simmons, Paul F. M. J. Verschure, Timothy R. Billiar, Yoram Vodovotz:
  A computational analysis of dynamic, multi-organ inflammatory crosstalk induced by endotoxin in mice.
• 
  Weilong Zhao, Xinwei Sher:
  Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes.
• 
  Christiane Ehrt, Tobias Brinkjost, Oliver Koch:
  A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs).
• 
  Michael Muthukrishna, Michael Doebeli, Maciej Chudek, Joseph Henrich:
  The Cultural Brain Hypothesis: How culture drives brain expansion, sociality, and life history.
• 
  Hongyang Li, Xin-Qiu Yao, Barry J. Grant:
  Comparative structural dynamic analysis of GTPases.
• 
  Jason E. Pina, Mark Bodner, Bard Ermentrout:
  Oscillations in working memory and neural binding: A mechanism for multiple memories and their interactions.
• 
  Anton Arkhipov, Nathan W. Gouwens, Yazan N. Billeh, Sergey L. Gratiy, Ramakrishnan Iyer, Ziqiang Wei, Zihao Xu, Reza Abbasi-Asl, Jim Berg, Michael A. Buice, Nicholas Cain, Nuno daCosta, Saskia C. J. De Vries, Daniel Denman, Severine Durand, David Feng, Tim Jarsky, Jérôme A. Lecoq, Brian Lee, Lu Li, Stefan Mihalas, Gabriel Koch Ocker, Shawn R. Olsen, R. Clay Reid, Gilberto Soler-Llavina, Staci A. Sorensen, Quanxin Wang, Jack Waters, Massimo Scanziani, Christof Koch:
  Visual physiology of the layer 4 cortical circuit in silico.
• 
  Stefano Giaimo, Jordi Arranz, Arne Traulsen:
  Invasion and effective size of graph-structured populations.
• 
  James A. Henderson, Pulin Gong:
  Functional mechanisms underlie the emergence of a diverse range of plasticity phenomena.
• 
  Laura Anton-Sanchez, Felix Effenberger, Concha Bielza, Pedro Larrañaga, Hermann Cuntz:
  A regularity index for dendrites - local statistics of a neuron's input space.
• 
  Anne-Florence Bitbol:
  Inferring interaction partners from protein sequences using mutual information.
• 
  Erik M. Volz, Igor Siveroni:
  Bayesian phylodynamic inference with complex models.
• 
  William T. Adler, Wei Ji Ma:
  Comparing Bayesian and non-Bayesian accounts of human confidence reports.
• 
  Marie Levakova, Lubomir Kostal, Christelle Monsempès, Vincent Jacob, Philippe Lucas:
  Moth olfactory receptor neurons adjust their encoding efficiency to temporal statistics of pheromone fluctuations.
• 
  Haleh Ebadi, Michael Perry, Keith Short, Konstantin Klemm, Claude Desplan, Peter F. Stadler, Anita Mehta:
  Patterning the insect eye: From stochastic to deterministic mechanisms.
• 
  Nils Klughammer, Johanna Bischof, Nikolas Schnellbächer, Andrea Callegari, Péter Lénárt, Ulrich S. Schwarz:
  Cytoplasmic flows in starfish oocytes are fully determined by cortical contractions.
• 
  Joana C. Xavier, Kiran Raosaheb Patil, Isabel Rocha:
  Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes.
• 
  Andrej Berg, Oleksandra Kukharenko, Martin Scheffner, Christine Peter:
  Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers.
• 
  Grant Hartung, Claudia Vesel, Ryan Morley, Ali Alaraj, John G. Sled, David Kleinfeld, Andreas A. Linninger:
  Simulations of blood as a suspension predicts a depth dependent hematocrit in the circulation throughout the cerebral cortex.
• 
  Jaume Bonet, Sarah Wehrle, Karen Schriever, Che Yang, Anne Billet, Fabian Sesterhenn, Andreas Scheck, Freyr Sverrisson, Barbora Veselkova, Sabrina Vollers, Roxanne Lourman, Mélanie Villard, Stéphane Rosset, Thomas Krey, Bruno E. Correia:
  Rosetta FunFolDes - A general framework for the computational design of functional proteins.
• 
  Yusuf Ozuysal, David B. Kastner, Stephen A. Baccus:
  Adaptive feature detection from differential processing in parallel retinal pathways.
• 
  Ryan R. Wick, Louise M. Judd, Kathryn E. Holt:
  Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks.
• 
  Xiaodong Huang, Zhen Song, Zhilin Qu:
  Determinants of early afterdepolarization properties in ventricular myocyte models.
• 
  Sarah F. Beul, Alexandros Goulas, Claus C. Hilgetag:
  Comprehensive computational modelling of the development of mammalian cortical connectivity underlying an architectonic type principle.
• 
  Letícia Stock, Juliana Hosoume, Leonardo Cirqueira, Werner Treptow:
  Binding of the general anesthetic sevoflurane to ion channels.
• 
  Jun Li, Wei Zhu, Jun Wang, Wenfei Li, Sheng Gong, Jian Zhang, Wei Wang:
  RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks.
• 
  Oliver M. Crook, Claire M. Mulvey, Paul D. W. Kirk, Kathryn S. Lilley, Laurent Gatto:
  A Bayesian mixture modelling approach for spatial proteomics.
• 
  Lina Meinecke, Praveer P. Sharma, Huijing Du, Lei Zhang, Qing Nie, Thomas F. Schilling:
  Modeling craniofacial development reveals spatiotemporal constraints on robust patterning of the mandibular arch.
• 
  Hillary Koch, Dmytro Starenki, Sara J. Cooper, Richard M. Myers, Qunhua Li:
  powerTCR: A model-based approach to comparative analysis of the clone size distribution of the T cell receptor repertoire.
• 
  Gaël Varoquaux, Yannick Schwartz, Russell A. Poldrack, Baptiste Gauthier, Danilo Bzdok, Jean-Baptiste Poline, Bertrand Thirion:
  Atlases of cognition with large-scale human brain mapping.
• 
  Holger Mohr, Katharina Zwosta, Dimitrije Markovic, Sebastian Bitzer, Uta Wolfensteller, Hannes Ruge:
  Deterministic response strategies in a trial-and-error learning task.
• 
  Brandon M. Butler, I. Can Kazan, Avishek Kumar, S. Banu Ozkan:
  Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs.
• 
  Daniel Jimenez-Carretero, Vahid Abrishami, Laura Fernandez-de-Manuel, Irene Palacios, Antonio Quílez-Álvarez, Alberto Díez-Sánchez, Miguel A. del Pozo, María C. Montoya:
  Tox_(R)CNN: Deep learning-based nuclei profiling tool for drug toxicity screening.
• 
  Wei Wang, Shanzhuo Zhang, Haibo Ni, Clifford J. Garratt, Mark R. Boyett, Jules C. Hancox, Henggui Zhang:
  Mechanistic insight into spontaneous transition from cellular alternans to arrhythmia - A simulation study.
• 
  Joanne C. Van Slooten, Sara Jahfari, Tomas Knapen, Jan Theeuwes:
  How pupil responses track value-based decision-making during and after reinforcement learning.

Correction

• 
  Correction: Assessment of ab initio models of protein complexes by molecular dynamics.

Volume 14, Number 12, December 2018

Editorials

• 
  Benjamin D. Lee:
  Ten simple rules for documenting scientific software.
• 
  Philip E. Bourne, Fran Lewitter, Scott Markel, Jason A. Papin:
  One thousand simple rules.

Education Articles

• 
  Aleksandra Tarkowska, Denise Carvalho-Silva, Charles E. Cook, Edd Turner, Robert D. Finn, Andrew D. Yates:
  Eleven quick tips to build a usable REST API for life sciences.
• 
  Anne V. Brown, Jacqueline D. Campbell, Teshale Assefa, David M. Grant, Rex T. Nelson, Nathan T. Weeks, Steven B. Cannon:
  Ten quick tips for sharing open genomic data.

Perspectives

• 
  Wang Xi, Michael A. Beer:
  Local epigenomic state cannot discriminate interacting and non-interacting enhancer-promoter pairs with high accuracy.
• 
  Lindley Darden, Kunal Kundu, Lipika R. Pal, John Moult:
  Harnessing formal concepts of biological mechanism to analyze human disease.

Research Articles

• 
  Luhao Zhang, Maodong Li, Zhirong Liu:
  A comprehensive ensemble model for comparing the allosteric effect of ordered and disordered proteins.
• 
  Lei Liu, Guang Shi, D. Thirumalai, Changbong Hyeon:
  Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci.
• 
  Agustina Razetti, Caroline Medioni, Grégoire Malandain, Florence Besse, Xavier Descombes:
  A stochastic framework to model axon interactions within growing neuronal populations.
• 
  Edouard A. Hay, Raghuveer Parthasarathy:
  Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets.
• 
  Hayden Tronnolone, Jennifer M. Gardner, Joanna F. Sundstrom, Vladimir Jiranek, Stephen G. Oliver, Benjamin J. Binder:
  TAMMiCol: Tool for analysis of the morphology of microbial colonies.
• 
  Rory G. Townsend, Pulin Gong:
  Detection and analysis of spatiotemporal patterns in brain activity.
• 
  Renato Pagliara, Deborah M. Gordon, Naomi Ehrich Leonard:
  Regulation of harvester ant foraging as a closed-loop excitable system.
• 
  Peter Neri:
  The empirical characteristics of human pattern vision defy theoretically-driven expectations.
• 
  Shouryadipta Ghosh, Kenneth Tran, Lea M. D. Delbridge, Anthony Hickey, Eric Hanssen, Edmund J. Crampin, Vijay Rajagopal:
  Insights on the impact of mitochondrial organisation on bioenergetics in high-resolution computational models of cardiac cell architecture.
• 
  Logan L. Grado, Matthew D. Johnson, Theoden I. Netoff:
  Bayesian adaptive dual control of deep brain stimulation in a computational model of Parkinson's disease.
• 
  Michiel W. H. Remme, John Rinzel, Susanne Schreiber:
  Function and energy consumption constrain neuronal biophysics in a canonical computation: Coincidence detection.
• 
  Anna Bochicchio, Miroslav Krepl, Fan Yang, Gabriele Varani, Jirí Sponer, Paolo Carloni:
  Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.
• 
  Mengrou Shan, David Dai, Arunodai Vudem, Jeffrey D. Varner, Abraham Duncan Stroock:
  Multi-scale computational study of the Warburg effect, reverse Warburg effect and glutamine addiction in solid tumors.
• 
  Nicholas Baker, Hongjing Lu, Gennady Erlikhman, Philip J. Kellman:
  Deep convolutional networks do not classify based on global object shape.
• 
  Jennifer L. Wilson, Rebecca Racz, Tianyun Liu, Oluseyi Adeniyi, Jielin Sun, Anuradha Ramamoorthy, Michael Pacanowski, Russ B. Altman:
  PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development.
• 
  Sergio Arregui, Alberto Aleta, Joaquín Sanz, Yamir Moreno:
  Projecting social contact matrices to different demographic structures.
• 
  Nicolas A. Pabon, Yan Xia, Samuel K. Estabrooks, Zhaofeng Ye, Amanda K. Herbrand, Evelyn Süß, Ricardo M. Biondi, Victoria A. Assimon, Jason E. Gestwicki, Jeffrey L. Brodsky, Carlos J. Camacho, Ziv Bar-Joseph:
  Predicting protein targets for drug-like compounds using transcriptomics.
• 
  Ho Ka Chan, Fabian Hersperger, Emiliano Marachlian, Brian H. Smith, Fernando Locatelli, Paul Szyszka, Thomas Nowotny:
  Odorant mixtures elicit less variable and faster responses than pure odorants.
• 
  Isao T. Tokuda, Daisuke Ono, Sato Honma, Ken-ichi Honma, Hanspeter Herzel:
  Coherency of circadian rhythms in the SCN is governed by the interplay of two coupling factors.
• 
  Jordan C. Rozum, Réka Albert:
  Identifying (un)controllable dynamical behavior in complex networks.
• 
  Aleksandr V. Zhuravlev, Oleg V. Vetrovoy, Elena V. Savvateeva-Popova:
  Enzymatic and non-enzymatic pathways of kynurenines' dimerization: the molecular factors for oxidative stress development.
• 
  Ning Zhang, Yuting Chen, Feiyang Zhao, Qing Yang, Franco L. Simonetti, Minghui Li:
  PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions.
• 
  Wen Zhang, Xiang Yue, Guifeng Tang, Wenjian Wu, Feng Huang, Xining Zhang:
  SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions.
• 
  Itamar Daniel Landau, Haim Sompolinsky:
  Coherent chaos in a recurrent neural network with structured connectivity.
• 
  Kemal Eren, Steven Weaver, Robert Ketteringham, Morné Valentyn, Melissa Laird Smith, Venkatesh Kumar, Sanjay Mohan, Sergei L. Kosakovsky Pond, Ben Murrell:
  Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons.
• 
  Enrico Lavezzo, Michele Berselli, Ilaria Frasson, Rosalba Perrone, Giorgio Palù, Alessandra R. Brazzale, Sara N. Richter, Stefano Toppo:
  G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide.
• 
  Danesh Moradigaravand, Martin Palm, Anne Farewell, Ville Mustonen, Jonas Warringer, Leopold Parts:
  Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data.
• 
  Kellen Chen, Xiao Hu, Silvia S. Blemker, Jeffrey W. Holmes:
  Multiscale computational model of Achilles tendon wound healing: Untangling the effects of repair and loading.
• 
  Anne Cori, Pierre Nouvellet, Tini Garske, Hervé Bourhy, Emmanuel Nakouné, Thibaut Jombart:
  A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies.
• 
  Wojciech Potrzebowski, Jill Trewhella, Ingemar André:
  Bayesian inference of protein conformational ensembles from limited structural data.
• 
  Vlad Elgart, Jia-Ren Lin, Joseph Loscalzo:
  Determinants of drug-target interactions at the single cell level.
• 
  Nele Vandersickel, Masaya Watanabe, Qian Tao, Jan Fostier, Katja Zeppenfeld, Alexander V. Panfilov:
  Dynamical anchoring of distant arrhythmia sources by fibrotic regions via restructuring of the activation pattern.
• 
  Marius Somveille, Josh A. Firth, Lucy M. Aplin, Damien Farine, Ben C. Sheldon, Robin N. Thompson:
  Movement and conformity interact to establish local behavioural traditions in animal populations.
• 
  Daniel H. Blustein, Ahmed W. Shehata, Kevin B. Englehart, Jonathon W. Sensinger:
  Conventional analysis of trial-by-trial adaptation is biased: Empirical and theoretical support using a Bayesian estimator.
• 
  Brian C. Lee, Daniel Jacob Tward, Partha P. Mitra, Michael I. Miller:
  On variational solutions for whole brain serial-section histology using a Sobolev prior in the computational anatomy random orbit model.
• 
  Gina Polo, Carlos Mera Acosta, Marcelo B. Labruna, Fernando Ferreira, Dirk Brockmann:
  Hosts mobility and spatial spread of Rickettsia rickettsii.
• 
  Jia Lu, Xiaoyi Cao, Sheng Zhong:
  A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome.
• 
  John M. Jumper, Nabil F. Faruk, Karl F. Freed, Tobin R. Sosnick:
  Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics.
• 
  John M. Jumper, Nabil F. Faruk, Karl F. Freed, Tobin R. Sosnick:
  Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours.
• 
  Nicholas A. Rossi, Thierry Mora, Aleksandra M. Walczak, Mary J. Dunlop:
  Active degradation of MarA controls coordination of its downstream targets.
• 
  Ashish B. George, Kirill S. Korolev:
  Chirality provides a direct fitness advantage and facilitates intermixing in cellular aggregates.
• 
  Andrew F. Neuwald, Stephen F. Altschul:
  Statistical investigations of protein residue direct couplings.
• 
  Murat Cokol, Chen Li, Sriram Chandrasekaran:
  Chemogenomic model identifies synergistic drug combinations robust to the pathogen microenvironment.
• 
  Michael Moutoussis, Edward T. Bullmore, Ian M. Goodyer, Peter Fonagy, Peter B. Jones, Raymond J. Dolan, Peter Dayan:
  Change, stability, and instability in the Pavlovian guidance of behaviour from adolescence to young adulthood.
• 
  Zhen Wah Tan, Enrico Guarnera, Igor N. Berezovsky:
  Exploring chromatin hierarchical organization via Markov State Modelling.
• 
  Iris I. A. Groen, Sara Jahfari, Noor Seijdel, Sennay Ghebreab, Victor A. F. Lamme, H. Steven Scholte:
  Scene complexity modulates degree of feedback activity during object detection in natural scenes.