Journal: PLoS Computational Biology

Volume 13, Issue 10

0 -- 0Kensuke Arai, Robert E. Kass. Inferring oscillatory modulation in neural spike trains
0 -- 0Tiziano D'albis, Richard Kempter. A single-cell spiking model for the origin of grid-cell patterns
0 -- 0Bo Wang, Lin Huang, Yuke Zhu, Anshul Kundaje, Serafim Batzoglou, Anna Goldenberg. Vicus: Exploiting local structures to improve network-based analysis of biological data
0 -- 0Cen Wan, Jonathan G. Lees, Federico Minneci, Christine A. Orengo, David T. Jones. Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster
0 -- 0Jiawen Chen, Steven C. Almo, Yinghao Wu. General principles of binding between cell surface receptors and multi-specific ligands: A computational study
0 -- 0Phuong Dao, Yoo Ah Kim, Damian Wójtowicz, Sanna Madan, Roded Sharan, Teresa M. Przytycka. BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions
0 -- 0Claire N. Bedbrook, Kevin K. Yang, Austin J. Rice, Viviana Gradinaru, Frances H. Arnold. Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization
0 -- 0Carsten Conradi, Elisenda Feliu, Maya Mincheva, Carsten Wiuf. Identifying parameter regions for multistationarity
0 -- 0Gudrun Gygli, Maria Fátima Lucas, Victor Guallar, Willem J. H. van Berkel. The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths
0 -- 0Shiran Abadi, Winston X. Yan, David Amar, Itay Mayrose. A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action
0 -- 0Guoshi Li, Craig S. Henriquez, Flavio Fröhlich. Unified thalamic model generates multiple distinct oscillations with state-dependent entrainment by stimulation
0 -- 0Lindsay Barone, Jason Williams, David Micklos. Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators
0 -- 0Kim T. Gurwitz, Shaun Aron, Sumir Panji, Suresh Maslamoney, Pedro L. Fernandes, David P. Judge, Amel Ghouila, Jean-Baka Domelevo Entfellner, Fatma Z. Guerfali, Colleen Saunders, Ahmed Mansour Alzohairy, Samson P. Salifu, Rehab Ahmed, Ruben Cloete, Jonathan Kayondo, Deogratius Ssemwanga, Nicola J. Mulder, H3ABioNet Consortium. Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience
0 -- 0Emine Guven-Maiorov, Chung-Jung Tsai, Ruth Nussinov. Structural host-microbiota interaction networks
0 -- 0Ekaterina Kotelnikova, Narsis A. Kiani, Elena Abad, Elena H. Martinez-Lapiscina, Magí Andorrà, Irati Zubizarreta, Irene Pulido-Valdeolivas, Inna Pertsovskaya, Leonidas G. Alexopoulos, Tomas Olsson, Roland Martin, Friedemann Paul, Jesper Tegnér, Jordi García-Ojalvo, Pablo Villoslada. Dynamics and heterogeneity of brain damage in multiple sclerosis
0 -- 0Akshay Kakumanu, Silvia Velasco, Esteban O. Mazzoni, Shaun Mahony. Deconvolving sequence features that discriminate between overlapping regulatory annotations
0 -- 0Thomas Heidlauf, Thomas Klotz, Christian Rode, Tobias Siebert, Oliver Röhrle. A continuum-mechanical skeletal muscle model including actin-titin interaction predicts stable contractions on the descending limb of the force-length relation
0 -- 0Spencer J. Fox, Joel C. Miller, Lauren Ancel Meyers. Seasonality in risk of pandemic influenza emergence
0 -- 0Vijay Vedula, Juhyun Lee, Hao Xu, C. C. Jay Kuo, Tzung K. Hsiai, Alison L. Marsden. A method to quantify mechanobiologic forces during zebrafish cardiac development using 4-D light sheet imaging and computational modeling
0 -- 0Trey Ideker, Ruth Nussinov. Network approaches and applications in biology
0 -- 0Daniel E. Carlin, Barry Demchak, Dexter Pratt, Eric Sage, Trey Ideker. Network propagation in the cytoscape cyberinfrastructure
0 -- 0Francesco Rigoli, Christoph Mathys, Karl J. Friston, Raymond J. Dolan. A unifying Bayesian account of contextual effects in value-based choice
0 -- 0Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford. Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing
0 -- 0Yao Shen, Mariano J. Alvarez, Brygida C. Bisikirska, Alexander Lachmann, Ronald Realubit, Sergey Pampou, Jorida Coku, Charles Karan, Andrea Califano. Systematic, network-based characterization of therapeutic target inhibitors
0 -- 0Kris Parag, Glenn Vinnicombe. Point process analysis of noise in early invertebrate vision
0 -- 0Evelina Gabasova, John E. Reid, Lorenz Wernisch. Clusternomics: Integrative context-dependent clustering for heterogeneous datasets
0 -- 0Andrea K. Barreiro, Shree Hari Gautam, Woodrow L. Shew, Cheng Ly. A theoretical framework for analyzing coupled neuronal networks: Application to the olfactory system
0 -- 0James Rankin, Frédéric Chavane. Neural field model to reconcile structure with function in primary visual cortex
0 -- 0John Joseph Valletta, Mario Recker. Identification of immune signatures predictive of clinical protection from malaria
0 -- 0Thomas G. Fai, Alejandra Leo-Macias, David L. Stokes, Charles S. Peskin. Image-based model of the spectrin cytoskeleton for red blood cell simulation
0 -- 0Niklas Hübel, Mahshid S. Hosseini-Zare, Jokubas Ziburkus, Ghanim Ullah. The role of glutamate in neuronal ion homeostasis: A case study of spreading depolarization
0 -- 0Marcel Nonnenmacher, Christian Behrens, Philipp Berens, Matthias Bethge, Jakob H. Macke. Signatures of criticality arise from random subsampling in simple population models
0 -- 0Cynthia Sandor, Nicola L. Beer, Caleb Webber. Diverse type 2 diabetes genetic risk factors functionally converge in a phenotype-focused gene network
0 -- 0Andrew J. K. Phillips, Elizabeth B. Klerman, James P. Butler. Modeling the adenosine system as a modulator of cognitive performance and sleep patterns during sleep restriction and recovery
0 -- 0Mark L. Ioffe, Michael J. Berry II. The structured 'low temperature' phase of the retinal population code
0 -- 0Mengjia Xu, Dimitrios P. Papageorgiou, Sabia Z. Abidi, Ming Dao, Hong Zhao, George E. Karniadakis. A deep convolutional neural network for classification of red blood cells in sickle cell anemia
0 -- 0Louis Verny, Nadir Sella, Séverine Affeldt, Param Priya Singh, Hervé Isambert. Learning causal networks with latent variables from multivariate information in genomic data
0 -- 0Nicolas E. Martin, Siddharth Malik, Nicolas Calimet, Jean-Pierre Changeux, Marco Cecchini. Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics
0 -- 0Amir Houshang Bahrami, Mary G. Lin, Xuefeng Ren, James H. Hurley, Gerhard Hummer. Scaffolding the cup-shaped double membrane in autophagy
0 -- 0William Stafford Noble. Ten simple rules for writing a response to reviewers
0 -- 0Shreejoy J. Tripathy, Lilah Toker, Brenna Li, Cindy-Lee Crichlow, Dmitry Tebaykin, B. Ogan Mancarci, Paul Pavlidis. Transcriptomic correlates of neuron electrophysiological diversity
0 -- 0Emre Akbas, Miguel P. Eckstein. Object detection through search with a foveated visual system
0 -- 0Alex Finnegan, Jun S. Song. Maximum entropy methods for extracting the learned features of deep neural networks
0 -- 0Kevin S. Bonham, Melanie I. Stefan. Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology
0 -- 0Andreas Handel. Learning infectious disease epidemiology in a modern framework
0 -- 0Jaymar Soriano, Takatomi Kubo, Takao Inoue, Hiroyuki Kida, Toshitaka Yamakawa, Michiyasu Suzuki, Kazushi Ikeda. Differential temperature sensitivity of synaptic and firing processes in a neural mass model of epileptic discharges explains heterogeneous response of experimental epilepsy to focal brain cooling
0 -- 0Giray Enkavi, Heikki Mikkolainen, Burçin Güngör, Elina Ikonen, Ilpo Vattulainen. Concerted regulation of npc2 binding to endosomal/lysosomal membranes by bis(monoacylglycero)phosphate and sphingomyelin
0 -- 0Kevin Drew, Christian L. Müller, Richard Bonneau, Edward M. Marcotte. Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets
0 -- 0Jaron T. Colas, Wolfgang M. Pauli, Tobias Larsen, J. Michael Tyszka, John P. O'Doherty. Distinct prediction errors in mesostriatal circuits of the human brain mediate learning about the values of both states and actions: evidence from high-resolution fMRI
0 -- 0Kalinga Pavan T. Silva, Prithiviraj Chellamuthu, James Q. Boedicker. Quantifying the strength of quorum sensing crosstalk within microbial communities
0 -- 0Alex D. M. Dewar, Antoine Wystrach, Andrew Philippides, Paul Graham. Neural coding in the visual system of Drosophila melanogaster: How do small neural populations support visually guided behaviours?
0 -- 0Max S. Y. Lau, Gavin J. Gibson, Hola Adrakey, Amanda McClelland, Steven Riley, Jon Zelner, George Streftaris, Sebastian Funk, C. Jessica E. Metcalf, Benjamin D. Dalziel, Bryan T. Grenfell. A mechanistic spatio-temporal framework for modelling individual-to-individual transmission - With an application to the 2014-2015 West Africa Ebola outbreak
0 -- 0Vahid Rostami, PierGianLuca Porta Mana, Sonja Grün, Moritz Helias. Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models
0 -- 0Philip E. Bourne. Ten simple rules in considering a career in academia versus government
0 -- 0Aziz M. Mezlini, Anna Goldenberg. Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases
0 -- 0Marina E. Wosniack, Marcos C. Santos, Ernesto P. Raposo, Gandhi M. Viswanathan, Marcos G. E. da Luz. The evolutionary origins of Lévy walk foraging
0 -- 0Theodore Roman, Lu Xie, Russell Schwartz. Automated deconvolution of structured mixtures from heterogeneous tumor genomic data
0 -- 0Roman Shevchuk, Jochen S. Hub. Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics
0 -- 0Anna Hake, Nico Pfeifer. Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time
0 -- 0Agne Tilunaite, Wayne Croft, Noah Russell, Tomas C. Bellamy, Rüdiger Thul. A Bayesian approach to modelling heterogeneous calcium responses in cell populations
0 -- 0Vadim Puller, Richard Neher, Jan Albert. Estimating time of HIV-1 infection from next-generation sequence diversity
0 -- 0Timothy N. Rubin, Oluwasanmi Koyejo, Krzysztof J. Gorgolewski, Michael N. Jones, Russell A. Poldrack, Tal Yarkoni. Decoding brain activity using a large-scale probabilistic functional-anatomical atlas of human cognition
0 -- 0Peter Ashcroft, Markus G. Manz, Sebastian Bonhoeffer. Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments
0 -- 0Ryan Thomas Philips, Mriganka Sur, V. Srinivasa Chakravarthy. The influence of astrocytes on the width of orientation hypercolumns in visual cortex: A computational perspective
0 -- 0Nan Lin, Yun Zhu, Ruzong Fan, Momiao Xiong. A quadratically regularized functional canonical correlation analysis for identifying the global structure of pleiotropy with NGS data