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PLoS 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. - 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.