Journal: PLoS Computational Biology

Volume 14, Issue 1

0 -- 0Mathias Engel, James Longden, Jesper Ferkinghoff-Borg, Xavier Robin, Gaye Saginc, Rune Linding. Bowhead: Bayesian modelling of cell velocity during concerted cell migration
0 -- 0Guillaume Marçais, Arthur L. Delcher, Adam M. Phillippy, Rachel Coston, Steven L. Salzberg, Aleksey V. Zimin. MUMmer4: A fast and versatile genome alignment system
0 -- 0Alon Diament, Anna Feldman, Elisheva Schochet, Martin Kupiec, Yoav Arava, Tamir Tuller. The extent of ribosome queuing in budding yeast
0 -- 0Lenna 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
0 -- 0Ravi Kumar Verma, Ara M. Abramyan, Mayako Michino, R. Benjamin Free, David R. Sibley, Jonathan A. Javitch, J. Robert Lane, Lei Shi. The E2.65A mutation disrupts dynamic binding poses of SB269652 at the dopamine D2 and D3 receptors
0 -- 0Nikola 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
0 -- 0Rajita Menon, Vivek Ramanan, Kirill S. Korolev. Interactions between species introduce spurious associations in microbiome studies
0 -- 0Maureen A. Carey, Jason A. Papin. Ten simple rules for biologists learning to program
0 -- 0Cristina Izquierdo, José C. Gómez-Tamayo, Jean-Christophe Nebel, Leonardo Pardo, Angel Gonzalez. Identifying human diamine sensors for death related putrescine and cadaverine molecules
0 -- 0Ali Hadizadeh Esfahani, Angelina Sverchkova, Julio Saez-Rodriguez, Andreas Schuppert, Marc Brehme. A systematic atlas of chaperome deregulation topologies across the human cancer landscape
0 -- 0Roman Goulard, Jean-Louis Vercher, Stéphane Viollet. Modeling visual-based pitch, lift and speed control strategies in hoverflies
0 -- 0Talia 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
0 -- 0Igor 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
0 -- 0Alyaa 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
0 -- 0Andreas Madlung. Assessing an effective undergraduate module teaching applied bioinformatics to biology students
0 -- 0Shayna Stein, Rui Zhao, Hiroshi Haeno, Igor Vivanco, Franziska Michor. Mathematical modeling identifies optimum lapatinib dosing schedules for the treatment of glioblastoma patients
0 -- 0Daniel 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
0 -- 0Jacob 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
0 -- 0Zhewei Zhang, ZhenBo Cheng, Zhongqiao Lin, Chechang Nie, Tianming Yang. A neural network model for the orbitofrontal cortex and task space acquisition during reinforcement learning
0 -- 0Jason E. McDermott, Matthew Partridge, Yana Bromberg. Ten simple rules for drawing scientific comics
0 -- 0Christophe Menichelli, Olivier Gascuel, Laurent Bréhélin. Improving pairwise comparison of protein sequences with domain co-occurrence
0 -- 0Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M. Meudt, Luay Nakhleh. Bayesian inference of phylogenetic networks from bi-allelic genetic markers
0 -- 0Simon Koplev, Katie Lin, Anders B. Dohlman, Avi Ma'ayan. Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition
0 -- 0Takayuki Onojima, Takahiro Goto, Hiroaki Mizuhara, Toshio Aoyagi. A dynamical systems approach for estimating phase interactions between rhythms of different frequencies from experimental data
0 -- 0Kevin Lloyd, Peter Dayan. Interrupting behaviour: Minimizing decision costs via temporal commitment and low-level interrupts
0 -- 0Daisuke 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
0 -- 0Ian 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
0 -- 0Runmin 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
0 -- 0Lajos Vágó, Balázs Ujfalussy. Robust and efficient coding with grid cells
0 -- 0Rahila 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
0 -- 0Samhita 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
0 -- 0Akira 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
0 -- 0Gregory L. Dignon, Wenwei Zheng, Young C. Kim, Robert B. Best, Jeetain Mittal. Sequence determinants of protein phase behavior from a coarse-grained model
0 -- 0Yonathan Murin, Jeremy Kim, Josef Parvizi, Andrea Goldsmith. SozRank: A new approach for localizing the epileptic seizure onset zone
0 -- 0Chloé 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
0 -- 0Christopher L. Buckley, Taro Toyoizumi. A theory of how active behavior stabilises neural activity: Neural gain modulation by closed-loop environmental feedback
0 -- 0Koich Saeki, Akira Sasaki. The role of spatial heterogeneity in the evolution of local and global infections of viruses
0 -- 0Krzysztof 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
0 -- 0Anupama 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
0 -- 0Francesco Alessandro Massucci, Francesc Sagués, M. Ángeles Serrano. Metabolic plasticity in synthetic lethal mutants: Viability at higher cost
0 -- 0Jagdish Suresh Patel, Celeste J. Brown, F. Marty Ytreberg, Deborah L. Stenkamp. Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations
0 -- 0Antonio 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
0 -- 0Fereshteh 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
0 -- 0Pablo 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
0 -- 0Giulio Di Minin, Andreas Postlmayr, Anton Wutz. HaSAPPy: A tool for candidate identification in pooled forward genetic screens of haploid mammalian cells
0 -- 0Wesley Wong, Edward A. Wenger, Daniel L. Hartl, Dyann Wirth. Modeling the genetic relatedness of Plasmodium falciparum parasites following meiotic recombination and cotransmission
0 -- 0Jean-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
0 -- 0Zixuan Cang, Lin Mu, Guo-Wei Wei. Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening