Journal: PLoS Computational Biology

Volume 14, Issue 3

0 -- 0Juan 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
0 -- 0Alexander 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
0 -- 0Soroush Samadian, Jeff P. Bruce, Trevor J. Pugh. Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
0 -- 0Carl Barton, Sandro Morganella, Øyvind Ødegård-Fougner, Stephanie Alexander, Jonas Ries, Tomas Fitzgerald, Jan Ellenberg, Ewan Birney. ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy
0 -- 0Nicholas B. DeFelice, Zachary D. Schneider, Eliza Little, Christopher Barker, Kevin A. Caillouet, Scott R. Campbell, Dan Damian, Patrick Irwin, Herff M. P. Jones, John Townsend, Jeffrey Shaman. Use of temperature to improve West Nile virus forecasts
0 -- 0Yohei Kondo, Kazuhiro Aoki, Shin Ishii. Inverse tissue mechanics of cell monolayer expansion
0 -- 0Helen R. Fryer, Steven M. Wolinsky, Angela R. McLean. Increased T cell trafficking as adjunct therapy for HIV-1
0 -- 0Atsushi Takagi, Francesco Usai, Ganesh Gowrishankar, Vittorio Sanguineti, Etienne Burdet. Haptic communication between humans is tuned by the hard or soft mechanics of interaction
0 -- 0Timothy Kinyanjui, Jo Middleton, Stefan Güttel, Jackie Cassell, Joshua V. Ross, Thomas House. Scabies in residential care homes: Modelling, inference and interventions for well-connected population sub-units
0 -- 0Osman N. Yogurtçu, Margaret E. Johnson. Cytosolic proteins can exploit membrane localization to trigger functional assembly
0 -- 0Christopher Ebsch, Robert Rosenbaum. Imbalanced amplification: A mechanism of amplification and suppression from local imbalance of excitation and inhibition in cortical circuits
0 -- 0Mehdi 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
0 -- 0Marc 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
0 -- 0Aloys 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
0 -- 0Yanting 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
0 -- 0Brian S. Cole, Jason H. Moore. Eleven quick tips for architecting biomedical informatics workflows with cloud computing
0 -- 0Guillaume Pernelle, Wilten Nicola, Claudia Clopath. Gap junction plasticity as a mechanism to regulate network-wide oscillations
0 -- 0Charlie 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
0 -- 0Hao 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
0 -- 0Manuel Corpas, Nadezda Kovalevskaya, Amanda McMurray, Fiona G. G. Nielsen. A FAIR guide for data providers to maximise sharing of human genomic data
0 -- 0Matthew P. Edgington, Luke S. Alphey. Population dynamics of engineered underdominance and killer-rescue gene drives in the control of disease vectors
0 -- 0Laura 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
0 -- 0Nika Abdollahi, Alexandre Albani, Eric 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
0 -- 0Narmada 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
0 -- 0Britta U. Westner, Sarang S. Dalal, Simon Hanslmayr, Tobias Staudigl. Across-subjects classification of stimulus modality from human MEG high frequency activity
0 -- 0Sabine Hummert, Susanne Thon, Thomas Eick, Ralf Schmauder, Eckhard Schulz, Klaus Benndorf. Activation gating in HCN2 channels
0 -- 0Roman 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
0 -- 0Albert 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
0 -- 0Manuel Corpas, Nadezda Kovalevskaya, Amanda McMurray, Fiona G. G. Nielsen. A FAIR guide for data providers to maximise sharing of human genomic data
0 -- 0Michael Pablo, Samuel A. Ramirez, Timothy C. Elston. Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation
0 -- 0Rui Zhen Tan, Keng-Hwee Chiam. A computational model for how cells choose temporal or spatial sensing during chemotaxis
0 -- 0Jinbo Chen, Uwe Scholz, Ruonan Zhou, Matthias Lange 0001. LAILAPS-QSM: A RESTful API and JAVA library for semantic query suggestions
0 -- 0Diego Fernández Slezak, Mariano Sigman, Guillermo A. Cecchi. An entropic barriers diffusion theory of decision-making in multiple alternative tasks
0 -- 0Ting 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
0 -- 0Ibai 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
0 -- 0Timothy 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
0 -- 0Sarah Jarvis, Konstantin Nikolic, Simon R. Schultz. Neuronal gain modulability is determined by dendritic morphology: A computational optogenetic study
0 -- 0Elizabeth 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
0 -- 0Hidetoshi Kono, Shun Sakuraba, Hisashi Ishida. Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA
0 -- 0Gabriel A. Devenyi, Rémi Emonet, Rayna M. Harris, Kate L. Hertweck, Damien Irving, Ian Milligan, Greg Wilson. Ten simple rules for collaborative lesson development
0 -- 0Mengmeng Du, Jia-Jia Li, Liang Chen, Yuguo Yu, Ying Wu. Astrocytic Kir4.1 channels and gap junctions account for spontaneous epileptic seizure
0 -- 0Núria Folguera-Blasco, Elisabet Cuyàs, Javier A. Menéndez, Tomás Alarcón. Epigenetic regulation of cell fate reprogramming in aging and disease: A predictive computational model
0 -- 0Stefan 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
0 -- 0James A. Grogan, Anthony J. Connor, Joe Pitt-Francis, Philip K. Maini, Helen M. Byrne. The importance of geometry in the corneal micropocket angiogenesis assay
0 -- 0Yered 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
0 -- 0Hyun Jung Park, Soyeon Kim, Wei Li. Model-based analysis of competing-endogenous pathways (MACPath) in human cancers
0 -- 0Oisin 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
0 -- 0James 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
0 -- 0Yani Zhao, Pawel Dabrowski-Tumanski, Szymon Niewieczerzal, Joanna I. Sulkowska. The exclusive effects of chaperonin on the behavior of proteins with 52 knot
0 -- 0David 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
0 -- 0Shiva Farashahi, Chih-Chung Ting, Chang-Hao Kao, Shih-Wei Wu, Alireza Soltani. Dynamic combination of sensory and reward information under time pressure
0 -- 0Gregory Handy, Sean D. Lawley, Alla Borisyuk. Receptor recharge time drastically reduces the number of captured particles
0 -- 0Iván 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
0 -- 0Jun Ding, James S. Hagood, Namasivayam Ambalavanan, Naftali Kaminski, Ziv Bar-Joseph. iDREM: Interactive visualization of dynamic regulatory networks
0 -- 0Guillaume Viejo, Thomas Cortier, Adrien Peyrache. Brain-state invariant thalamo-cortical coordination revealed by non-linear encoders
0 -- 0Jonathan 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
0 -- 0Lauric A. Ferrat, Marc Goodfellow, John R. Terry. Classifying dynamic transitions in high dimensional neural mass models: A random forest approach
0 -- 0Benjamin Schubert, Charlotta Schärfe, Pierre Dönnes, Thomas A. Hopf, Debora S. Marks, Oliver Kohlbacher. Population-specific design of de-immunized protein biotherapeutics
0 -- 0J. 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