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ORCIDPLoS Computational Biology, Volume 17
Volume 17, Number 1, January 2021
- Korryn Bodner
, Chris Brimacombe, Emily S. Chenery, Ariel Greiner, Anne M. McLeod, Stephanie R. Penk, Juan S. Vargas Soto:
Ten simple rules for tackling your first mathematical models: A guide for graduate students by graduate students.
- Mehmet Aziz Yirik, Christoph Steinbeck:
Chemical graph generators.
- Graham Casey Gibson, Kelly R. Moran, Nicholas G. Reich, Dave Osthus:
Improving probabilistic infectious disease forecasting through coherence. - Antonino Casile, Rose T. Faghih, Emery N. Brown:
Robust point-process Granger causality analysis in presence of exogenous temporal modulations and trial-by-trial variability in spike trains. - Claudio Tomi-Andrino, Rupert Norman, Thomas Millat, Philippe Soucaille, Klaus Winzer, David A. Barrett, John R. King, Dong-Hyun Kim:
Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions. - Tristan Ursell:
Structured environments foster competitor coexistence by manipulating interspecies interfaces. - Pedro Manuel Martínez García, Miguel García-Torres, Federico Divina, José Terrón-Bautista, Irene Delgado-Sainz, Francisco Gómez-Vela, Felipe Cortés-Ledesma:
Genome-wide prediction of topoisomerase IIβ binding by architectural factors and chromatin accessibility. - Jonas Béal, Lorenzo Pantolini, Vincent Noël, Emmanuel Barillot, Laurence Calzone:
Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers. - Muneki Ikeda, Hirotaka Matsumoto, Eduardo J. Izquierdo:
Persistent thermal input controls steering behavior in Caenorhabditis elegans. - Samhita P. Banavar, Michael Trogdon, Brian Drawert, Tau-Mu Yi, Linda R. Petzold, Otger Campàs:
Coordinating cell polarization and morphogenesis through mechanical feedback. - James Giammona, Otger Campàs:
Physical constraints on early blastomere packings. - Daria Stepanova, Helen M. Byrne, Philip K. Maini, Tomás Alarcón:
A multiscale model of complex endothelial cell dynamics in early angiogenesis. - Evanthia Koukouli, Dennis Wang, Frank Dondelinger, Juhyun Park:
A regularized functional regression model enabling transcriptome-wide dosage-dependent association study of cancer drug response. - Sára Sáray, Christian A. Rössert, Shailesh Appukuttan, Rosanna Migliore, Paola Vitale, Carmen Alina Lupascu, Luca Leonardo Bologna, Werner Van Geit, Armando Romani, Andrew P. Davison, Eilif Müller, Tamás F. Freund, Szabolcs Káli:
HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data. - Satyajit D. Rao, Oleg A. Igoshin:
Overlaid positive and negative feedback loops shape dynamical properties of PhoPQ two-component system. - Hamed Khakzad, Lotta Happonen, Yasaman Karami, Sounak Chowdhury, Gizem Ertürk Bergdahl, Michael Nilges, Guy Tran Van Nhieu, Johan Malmström, Lars Malmström:
Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology. - Zachary B. Haiman, Daniel C. Zielinski, Yuko Koike, James T. Yurkovich, Bernhard O. Palsson:
MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics. - Yohsuke Murase, Seung Ki Baek:
Friendly-rivalry solution to the iterated n-person public-goods game. - Jonathan Lu, Bianca Dumitrascu, Ian C. McDowell, Brian Jo, Alejandro Barrera, Linda K. Hong, Sarah M. Leichter, Timothy E. Reddy, Barbara E. Engelhardt:
Causal network inference from gene transcriptional time-series response to glucocorticoids. - Jan Rombouts, Lendert Gelens:
Dynamic bistable switches enhance robustness and accuracy of cell cycle transitions. - Adil Alsiyabi, Ariadna Gonzalez Solis, Edgar B. Cahoon, Rajib Saha:
Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants. - Marco Aqil, Selen Atasoy, Morten L. Kringelbach, Rikkert Hindriks:
Graph neural fields: A framework for spatiotemporal dynamical models on the human connectome. - Vinícius R. Carvalho, Márcio Flávio Dutra Moraes, Sydney S. Cash, Eduardo Mazoni Andrade Marçal Mendes:
Active probing to highlight approaching transitions to ictal states in coupled neural mass models. - Linda K. Sundermann, Jeff Wintersinger, Gunnar Rätsch, Jens Stoye, Quaid Morris:
Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine. - Rachael L. Sumner, Meg J. Spriggs, Alexander D. Shaw:
Modelling thalamocortical circuitry shows that visually induced LTP changes laminar connectivity in human visual cortex. - David W. Eyre, Mirjam Laager, A. Sarah Walker, Ben S. Cooper, Daniel J. Wilson:
Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission. - Viacheslav N. Kachalov, Huyen Nguyen, Suraj Balakrishna, Luisa Salazar-Vizcaya, Rami Sommerstein, Stefan P. Kuster, Anthony Hauser, Pia Abel zur Wiesch, Eili Y. Klein, Roger D. Kouyos:
Identifying the drivers of multidrug-resistant Klebsiella pneumoniae at a European level. - Bruce Y. Lee, Sarah M. Bartsch, Marie C. Ferguson, Patrick T. Wedlock, Kelly J. O'Shea, Sheryl S. Siegmund, Sarah N. Cox, James A. McKinnell:
The value of decreasing the duration of the infectious period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. - N. Suhas Jagannathan, Christopher W. V. Hogue, Lisa Tucker-Kellogg:
Computational modeling suggests binding-induced expansion of Epsin disordered regions upon association with AP2. - Miri Gordin, Hagit Philip, Alona Zilberberg, Moriah Gidoni, Raanan Margalit, Christopher Clouser, Kristofor Adams, Francois Vigneault, Irun R. Cohen, Gur Yaari, Sol Efroni:
Breast cancer is marked by specific, Public T-cell receptor CDR3 regions shared by mice and humans. - Preecha Patumcharoenpol, Massalin Nakphaichit, Gianni Panagiotou, Anchalee Senavonge, Narissara Suratannon, Wanwipa Vongsangnak:
MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome. - Maral Budak, Karl Grosh, Aritra Sasmal, Gabriel Corfas, Michal Zochowski, Victoria Booth:
Contrasting mechanisms for hidden hearing loss: Synaptopathy vs myelin defects. - Oleksandr Sorochynskyi, Stéphane Deny, Olivier Marre, Ulisse Ferrari:
Predicting synchronous firing of large neural populations from sequential recordings. - Marzia Antonella Scelsi, Valerio Napolioni, Michael D. Greicius, André Altmann, Alzheimer's Disease Neuroimaging Initiative, Alzheimer's Disease Sequencing Project:
Network propagation of rare variants in Alzheimer's disease reveals tissue-specific hub genes and communities. - Bor Kavcic, Gasper Tkacik, Tobias Bollenbach:
Minimal biophysical model of combined antibiotic action. - Ronald E. Crump, Ching-I Huang, Edward S. Knock, Simon E. F. Spencer, Paul E. Brown, Erick Mwamba Miaka, Chansy Shampa, Matt J. Keeling, Kat S. Rock:
Quantifying epidemiological drivers of gambiense human African Trypanosomiasis across the Democratic Republic of Congo. - Guillaume Lingas, Kyle Rosenke, David Safronetz, Jérémie Guedj:
Lassa viral dynamics in non-human primates treated with favipiravir or ribavirin. - Jun Li, Juliane Manitz, Enrico Bertuzzo, Eric D. Kolaczyk:
Sensor-based localization of epidemic sources on human mobility networks. - Beatriz Seoane, Alessandra Carbone:
The complexity of protein interactions unravelled from structural disorder. - Albertas Janulevicius, G. Sander van Doorn:
Selection for rapid uptake of scarce or fluctuating resource explains vulnerability of glycolysis to imbalance. - Lillian R. Thistlethwaite, Varduhi Petrosyan, Xiqi Li, Marcus J. Miller, Sarah H. Elsea, Aleksandar Milosavljevic:
CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models. - Giulio Tesei, João M. Martins, Micha B. A. Kunze, Yong Wang, Ramon Crehuet, Kresten Lindorff-Larsen:
DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles. - Rani Moran, Mehdi Keramati, Raymond J. Dolan:
Model based planners reflect on their model-free propensities. - Vikki Neville, Peter Dayan, Iain D. Gilchrist, Elizabeth S. Paul, Michael Mendl:
Dissecting the links between reward and loss, decision-making, and self-reported affect using a computational approach. - Zhongling Jiang, Bin Zhang:
On the role of transcription in positioning nucleosomes. - Hungyo Kharerin, Lu Bai:
Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast. - Antanas Kalkauskas, Umberto Perron, Yuxuan Sun, Nick Goldman, Guy Baele, Stéphane Guindon, Nicola De Maio:
Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk. - Katharine Best, Dan H. Barouch, Jérémie Guedj, Ruy M. Ribeiro, Alan S. Perelson:
Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference. - Johannes Friedrich, Andrea Giovannucci, Eftychios A. Pnevmatikakis:
Online analysis of microendoscopic 1-photon calcium imaging data streams. - Michael C. Tackenberg, Jacob J. Hughey:
The risks of using the chi-square periodogram to estimate the period of biological rhythms. - Samuel Schmitz, Moritz Ertelt, Rainer Merkl, Jens Meiler:
Rosetta design with co-evolutionary information retains protein function. - Andreas Tjärnberg, Omar Mahmood, Christopher A. Jackson, Giuseppe-Antonio Saldi, Kyunghyun Cho, Lionel A. Christiaen, Richard A. Bonneau:
Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data. - Muir Morrison, Manuel Razo-Mejia, Rob Phillips:
Reconciling kinetic and thermodynamic models of bacterial transcription. - Aniello Lombardi, Peter Jedlicka, Heiko J. Luhmann, Werner Kilb:
Coincident glutamatergic depolarizations enhance GABAA receptor-dependent Cl- influx in mature and suppress Cl- efflux in immature neurons. - Grant Hartung, Shoale Badr, Mohammad Moeini, Frédéric Lesage, David Kleinfeld, Ali Alaraj, Andreas A. Linninger:
Voxelized simulation of cerebral oxygen perfusion elucidates hypoxia in aged mouse cortex. - Charlotte Soneson, Avi Srivastava, Rob Patro, Michael B. Stadler:
Preprocessing choices affect RNA velocity results for droplet scRNA-seq data. - Son Hoang Nguyen, Minh Duc Cao, Lachlan J. M. Coin:
Real-time resolution of short-read assembly graph using ONT long reads. - Filipe Tostevin, Manon Wigbers, Lotte Søgaard-Andersen, Ulrich Gerland:
Four different mechanisms for switching cell polarity. - Ke Chen, Amitesh Anand, Connor A. Olson, Troy E. Sandberg, Ye Gao, Nathan Mih, Bernhard O. Palsson:
Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types. - Bansho Masutani, Shin-ichi Arimura, Shinichi Morishita:
Investigating the mitochondrial genomic landscape of Arabidopsis thaliana by long-read sequencing. - Samuel Planton, Timo van Kerkoerle, Leïla Abbih, Maxime Maheu, Florent Meyniel, Mariano Sigman, Liping Wang, Santiago Figueira, Sergio Romano, Stanislas Dehaene:
A theory of memory for binary sequences: Evidence for a mental compression algorithm in humans. - Yushuf Sharker, Eben Kenah:
Estimating and interpreting secondary attack risk: Binomial considered biased. - Sara Ibrahim Omar, Meng Zhao, Rohith Vedhthaanth Sekar, Sahar Arbabi Moghadam, Jack A. Tuszynski, Michael T. Woodside:
Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers. - Michelangelo Bin, Peter Y. K. Cheung, Emanuele Crisostomi, Pietro Ferraro, Hugo Lhachemi, Roderick Murray-Smith, Connor Myant, Thomas Parisini, Robert Shorten, Sebastian Stein, Lewi Stone:
Post-lockdown abatement of COVID-19 by fast periodic switching. - Wilson Louie, Max W. Shen, Zakir Tahiry, Sophia Zhang, Daniel Worstell, Christopher A. Cassa, Richard I. Sherwood, David K. Gifford:
Machine learning based CRISPR gRNA design for therapeutic exon skipping. - Oren Avram, Aya Kigel, Anna Vaisman-Mentesh, Sharon Kligsberg, Shai Rosenstein, Yael Dror, Tal Pupko, Yariv Wine:
PASA: Proteomic analysis of serum antibodies web server. - Burcu Tepekule, Anthony Hauser, Viacheslav N. Kachalov, Sara Andresen, Thomas Scheier, Peter W. Schreiber, Huldrych F. Günthard, Roger D. Kouyos:
Assessing the potential impact of transmission during prolonged viral shedding on the effect of lockdown relaxation on COVID-19. - Leonardo Miele, Silvia De Monte:
Aggregative cycles evolve as a solution to conflicts in social investment. - Matt J. Keeling, Edward M. Hill, Erin E. Gorsich, Bridget S. Penman, Glen Guyver-Fletcher, Alex Holmes, Trystan Leng, Hector McKimm, Massimiliano Tamborrino, Louise Dyson, Michael J. Tildesley:
Predictions of COVID-19 dynamics in the UK: Short-term forecasting and analysis of potential exit strategies. - Seth Talyansky, Braden A. W. Brinkman:
Dysregulation of excitatory neural firing replicates physiological and functional changes in aging visual cortex. - Vikas Pandey, Lai-Hua Xie, Zhilin Qu, Zhen Song:
Mitochondrial depolarization promotes calcium alternans: Mechanistic insights from a ventricular myocyte model. - Stephanie C. Hicks, Ruoxi Liu, Yuwei Ni, Elizabeth Purdom, Davide Risso:
mbkmeans: Fast clustering for single cell data using mini-batch k-means. - Kathryn L. Schaber, T. Alex Perkins, Alun L. Lloyd, Lance A. Waller, Uriel Kitron, Valerie A. Paz-Soldan, John P. Elder, Alan L. Rothman, David J. Civitello, William H. Elson, Amy C. Morrison, Thomas W. Scott, Gonzalo M. Vazquez-Prokopec:
Disease-driven reduction in human mobility influences human-mosquito contacts and dengue transmission dynamics. - Victor Boutin, Angelo Franciosini, Frédéric Chavane, Franck Ruffier, Laurent Perrinet:
Sparse deep predictive coding captures contour integration capabilities of the early visual system. - Martina Conte, Sergio Casas-Tintò, Juan Soler:
Modeling invasion patterns in the glioblastoma battlefield. - Dániel Vörös, Balázs Könnyü, Tamás Czárán:
Catalytic promiscuity in the RNA World may have aided the evolution of prebiotic metabolism. - Steven Phillips:
A reconstruction theory of relational schema induction. - Helen M. Kurkjian, M. Javad Akbari, Babak Momeni:
The impact of interactions on invasion and colonization resistance in microbial communities. - Daniel A. Burbano L., Maurizio Porfiri:
Modeling multi-sensory feedback control of zebrafish in a flow. - Leonard Schmiester, Yannik Schälte, Frank T. Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina A. Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang Müller, Dilan Pathirana, Elba Raimúndez-Álvarez, Lukas Refisch, Marcus Rosenblatt, Paul Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl:
PEtab - Interoperable specification of parameter estimation problems in systems biology. - Gabriel Studer, Gerardo Tauriello, Stefan Bienert, Marco Biasini, Niklaus Johner, Torsten Schwede:
ProMod3 - A versatile homology modelling toolbox. - Alessandro Toso, Arash Fassihi, Luciano Paz, Francesca Pulecchi, Mathew E. Diamond:
A sensory integration account for time perception. - Carlos Valiente-Mullor, Beatriz Beamud, Iván Ansari, Carlos Francés-Cuesta, Neris García-González, Lorena Mejía, Paula Ruiz-Hueso, Fernando González-Candelas:
One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads. - Shinsuke Koyama, Taiki Horie, Shigeru Shinomoto:
Estimating the time-varying reproduction number of COVID-19 with a state-space method.
Volume 17, Number 2, February 2021
- Avni Malik, Paranjay Patel, Lubaina Ehsan, Shan Guleria, Thomas Hartka, Sodiq Adewole, Sana Syed:
Ten simple rules for engaging with artificial intelligence in biomedicine. - Sabrina Islam, Christine A. Wells:
Ten simple rules for navigating the computational aspect of an interdisciplinary PhD. - Johannes Werner, Debora Jeske:
Ten simple rules for running and managing virtual internships. - Micaela S. Parker, Arlyn E. Burgess, Philip E. Bourne:
Ten simple rules for starting (and sustaining) an academic data science initiative. - Parice A. Brandies, Carolyn J. Hogg:
Ten simple rules for getting started with command-line bioinformatics. - Jennifer H. Kong, Latishya J. Steele, Crystal M. Botham:
Ten simple rules for writing compelling recommendation letters. - Matthias C. Rillig, Karine Bonneval, Christian de Lutz, Johannes Lehmann, India Mansour, Regine Rapp, Sasa Spacal, Vera Meyer:
Ten simple rules for hosting artists in a scientific lab. - Mathieu Boudreau, Jean-Baptiste Poline, Pierre Bellec, Nikola Stikov:
On the open-source landscape of PLOS Computational Biology.
- Michael Jackson, Kostas Kavoussanakis, Edward W. J. Wallace:
Using prototyping to choose a bioinformatics workflow management system. - Verena Ras, Gerrit Botha, Shaun Aron, Katie Lennard, Imane Allali, Shantelle Claassen-Weitz, Kilaza Samson Mwaikono, Dane Kennedy, Jessica R. Holmes, Gloria Rendon, Sumir Panji, Christopher J. Fields, Nicola J. Mulder:
Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa. - Kimberly A. Dill-McFarland, Stephan G. König, Florent Mazel, David C. Oliver, Lisa M. McEwen, Kris Y. Hong, Steven J. Hallam:
An integrated, modular approach to data science education in microbiology.
- Johannes Bracher, Evan L. Ray, Tilmann Gneiting, Nicholas G. Reich:
Evaluating epidemic forecasts in an interval format.
- Lowell T. Edgar, Claudio A. Franco, Holger Gerhardt, Miguel O. Bernabeu:
On the preservation of vessel bifurcations during flow-mediated angiogenic remodelling. - Hana Susak, Laura Serra-Saurina, German Demidov, Raquel Rabionet, Laura Domènech, Mattia Bosio, Francesc Muyas, Xavier Estivill, Geòrgia Escaramís, Stephan Ossowski:
Efficient and flexible Integration of variant characteristics in rare variant association studies using integrated nested Laplace approximation. - Mathew Titus, George Hagstrom, James R. Watson:
Unsupervised manifold learning of collective behavior. - Davide Bernardi, Guy Doron, Michael Brecht, Benjamin Lindner:
A network model of the barrel cortex combined with a differentiator detector reproduces features of the behavioral response to single-neuron stimulation. - Marc A. Dämgen, Philip C. Biggin:
State-dependent protein-lipid interactions of a pentameric ligand-gated ion channel in a neuronal membrane. - Helmut Schmidt, Gerald Hahn, Gustavo Deco, Thomas R. Knösche:
Ephaptic coupling in white matter fibre bundles modulates axonal transmission delays. - George G. Vega Yon, Duncan C. Thomas, John Morrison, Huaiyu Mi, Paul D. Thomas, Paul Marjoram:
Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees. - Casey A. Cole, Nourhan S. Daigham, Gaohua Liu, Gaetano T. Montelione, Homayoun Valafar:
REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution. - Sam Gijsen, Miro Grundei, Robert T. Lange, Dirk Ostwald, Felix Blankenburg:
Neural surprise in somatosensory Bayesian learning. - Karoline Horgmo Jæger, Samuel Wall, Aslak Tveito:
Computational prediction of drug response in short QT syndrome type 1 based on measurements of compound effect in stem cell-derived cardiomyocytes. - Boris I. Ratnikov, Piotr Cieplak, Albert G. Remacle, Elise Nguyen, Jeffrey W. Smith:
Quantitative profiling of protease specificity. - Guillaume P. Dehaene, Ruben Coen Cagli, Alexandre Pouget:
Investigating the representation of uncertainty in neuronal circuits. - Satyabrata Parida, Hari M. Bharadwaj, Michael G. Heinz:
Spectrally specific temporal analyses of spike-train responses to complex sounds: A unifying framework. - Junho Lee, Donggu Lee, Sean Lawler, Yangjin Kim:
Role of neutrophil extracellular traps in regulation of lung cancer invasion and metastasis: Structural insights from a computational model. - Juan Jiménez-Sánchez, Álvaro Martínez-Rubio, Anton Popov, Julián Pérez-Beteta, Youness Azimzade, David Molina-García, Juan Belmonte-Beitia, Gabriel Fernández Calvo, Víctor M. Pérez-García:
A mesoscopic simulator to uncover heterogeneity and evolutionary dynamics in tumors. - Wei Lu, Carlos Bueno, Nicholas P. Schafer, Joshua Moller, Shikai Jin, Xun Chen, Mingchen Chen, Xinyu Gu, Aram Davtyan, Juan J. de Pablo, Peter G. Wolynes:
OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations. - Filip Stefaniak, Janusz M. Bujnicki:
AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses. - Jordan Douglas, Rong Zhang, Remco R. Bouckaert:
Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model.