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ORCIDPLoS Computational Biology, Volume 14
Volume 14, Number 1, January 2018
- 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.
- 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.
- 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
- Adam J. Kucharski:
Ten simple rules for writing a popular science book.
- 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.
- Vasundra Touré, Nicolas Le Novère, Dagmar Waltemath, Olaf Wolkenhauer:
Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation.
- 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
- 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.
- 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.
- 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.