Works matching DE "COMPUTER simulation of biological systems"

Results: 65

Biological hypercomputation: A new research problem in complexity theory.

Published in:

Complexity, 2015, v. 20, n. 4, p. 8, doi. 10.1002/cplx.21535

By:

Maldonado, Carlos E.;
Gómez Cruz, Nelson A.

Publication type:

Article

Developing an online programme in computational biology.

Published in:

Briefings in Bioinformatics, 2013, v. 14, n. 6, p. 775, doi. 10.1093/bib/bbs059

By:

Vincent, Heather M.;
Page, Christopher

Publication type:

Article

Correction: An Integrative Approach for Modeling and Simulation of Heterocyst Pattern Formation in Cyanobacteria Filaments.

Published in:

2015

By:

null, null

Publication type:

Correction Notice

Posterior Probability Matching and Human Perceptual Decision Making.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 6, p. 1, doi. 10.1371/journal.pcbi.1004342

By:

Murray, Richard F.;
Patel, Khushbu;
Yee, Alan

Publication type:

Article

Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 6, p. 1, doi. 10.1371/journal.pcbi.1004332

By:

Ma, Xiaoke;
Gao, Long;
Karamanlidis, Georgios;
Gao, Peng;
Lee, Chi Fung;
Garcia-Menendez, Lorena;
Tian, Rong;
Tan, Kai

Publication type:

Article

Monte Carlo Planning Method Estimates Planning Horizons during Interactive Social Exchange.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 6, p. 1, doi. 10.1371/journal.pcbi.1004254

By:

Hula, Andreas;
Montague, P. Read;
Dayan, Peter

Publication type:

Article

Site-Specific Phosphorylation of VEGFR2 Is Mediated by Receptor Trafficking: Insights from a Computational Model.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 6, p. 1, doi. 10.1371/journal.pcbi.1004158

By:

Clegg, Lindsay Wendel;
Mac Gabhann, Feilim

Publication type:

Article

Is Model Fitting Necessary for Model-Based fMRI?

Published in:

PLoS Computational Biology, 2015, v. 11, n. 6, p. 1, doi. 10.1371/journal.pcbi.1004237

By:

Wilson, Robert C.;
Niv, Yael

Publication type:

Article

Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 6, p. 1, doi. 10.1371/journal.pcbi.1004202

By:

Sun, Jingchun;
Zhao, Min;
Jia, Peilin;
Wang, Lily;
Wu, Yonghui;
Iverson, Carissa;
Zhou, Yubo;
Bowton, Erica;
Roden, Dan M.;
Denny, Joshua C.;
Aldrich, Melinda C.;
Xu, Hua;
Zhao, Zhongming

Publication type:

Article

An Integrative Approach for Modeling and Simulation of Heterocyst Pattern Formation in Cyanobacteria Filaments.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 3, p. 1, doi. 10.1371/journal.pcbi.1004129

By:

Torres-Sánchez, Alejandro;
Gómez-Gardeñes, Jesús;
Falo, Fernando

Publication type:

Article

Predicting Epidemic Risk from Past Temporal Contact Data.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 3, p. 1, doi. 10.1371/journal.pcbi.1004152

By:

Valdano, Eugenio;
Poletto, Chiara;
Giovannini, Armando;
Palma, Diana;
Savini, Lara;
Colizza, Vittoria

Publication type:

Article

Evolving Nutritional Strategies in the Presence of Competition: A Geometric Agent-Based Model.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 3, p. 1, doi. 10.1371/journal.pcbi.1004111

By:

Senior, Alistair M.;
Charleston, Michael A.;
Lihoreau, Mathieu;
Buhl, Jerome;
Raubenheimer, David;
Simpson, Stephen J.

Publication type:

Article

A Neural Mechanism for Background Information-Gated Learning Based on Axonal-Dendritic Overlaps.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 3, p. 1, doi. 10.1371/journal.pcbi.1004155

By:

Mainetti, Matteo;
Ascoli, Giorgio A.

Publication type:

Article

Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 3, p. 1, doi. 10.1371/journal.pcbi.1004186

By:

Albanese, Davide;
De Filippo, Carlotta;
Cavalieri, Duccio;
Donati, Claudio

Publication type:

Article

Integrating Interactive Computational Modeling in Biology Curricula.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 3, p. 1, doi. 10.1371/journal.pcbi.1004131

By:

Helikar, Tomáš;
Cutucache, Christine E.;
Dahlquist, Lauren M.;
Herek, Tyler A.;
Larson, Joshua J.;
Rogers, Jim A.

Publication type:

Article

Evolution of Bow-Tie Architectures in Biology.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 3, p. 1, doi. 10.1371/journal.pcbi.1004055

By:

Friedlander, Tamar;
Mayo, Avraham E.;
Tlusty, Tsvi;
Alon, Uri

Publication type:

Article

Improved Estimation and Interpretation of Correlations in Neural Circuits.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 3, p. 1, doi. 10.1371/journal.pcbi.1004083

By:

Yatsenko, Dimitri;
Josić, Krešimir;
Ecker, Alexander S.;
Froudarakis, Emmanouil;
Cotton, R. James;
Tolias, Andreas S.

Publication type:

Article

Evolution and Phenotypic Selection of Cancer Stem Cells.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 3, p. 1, doi. 10.1371/journal.pcbi.1004025

By:

Poleszczuk, Jan;
Hahnfeldt, Philip;
Enderling, Heiko

Publication type:

Article

150 Years of the Mass Action Law.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 1, p. 1, doi. 10.1371/journal.pcbi.1004012

By:

Voit, Eberhard O.;
Martens, Harald A.;
Omholt, Stig W.

Publication type:

Article

Developmental Self-Construction and -Configuration of Functional Neocortical Neuronal Networks.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 12, p. 1, doi. 10.1371/journal.pcbi.1003994

By:

Bauer, Roman;
Zubler, Frédéric;
Pfister, Sabina;
Hauri, Andreas;
Pfeiffer, Michael;
Muir, Dylan R.;
Douglas, Rodney J.

Publication type:

Article

Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 12, p. 1, doi. 10.1371/journal.pcbi.1003990

By:

Ando, Tadashi;
Skolnick, Jeffrey

Publication type:

Article

Protein-Protein Docking with Dynamic Residue Protonation States.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 12, p. 1, doi. 10.1371/journal.pcbi.1004018

By:

Kilambi, Krishna Praneeth;
Reddy, Kavan;
Gray, Jeffrey J.

Publication type:

Article

Correction: Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model.

Published in:: 2014
Publication type:: Correction Notice

Automated Discovery of Tissue-Targeting Enhancers and Transcription Factors from Binding Motif and Gene Function Data.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 1, p. 1, doi. 10.1371/journal.pcbi.1003449

By:

Tuteja, Geetu;
Moreira, Karen Betancourt;
Chung, Tisha;
Chen, Jenny;
Wenger, Aaron M.;
Bejerano, Gill

Publication type:

Article

Segregation and Crosstalk of D1 Receptor-Mediated Activation of ERK in Striatal Medium Spiny Neurons upon Acute Administration of Psychostimulants.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 1, p. 1, doi. 10.1371/journal.pcbi.1003445

By:

Gutierrez-Arenas, Omar;
Eriksson, Olivia;
Hellgren Kotaleski, Jeanette

Publication type:

Article

<i>De Novo</i> Prediction of PTBP1 Binding and Splicing Targets Reveals Unexpected Features of Its RNA Recognition and Function.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 1, p. 1, doi. 10.1371/journal.pcbi.1003442

By:

Han, Areum;
Stoilov, Peter;
Linares, Anthony J.;
Zhou, Yu;
Fu, Xiang-Dong;
Black, Douglas L.

Publication type:

Article

Consequences of Converting Graded to Action Potentials upon Neural Information Coding and Energy Efficiency.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 1, p. 1, doi. 10.1371/journal.pcbi.1003439

By:

Sengupta, Biswa;
Laughlin, Simon Barry;
Niven, Jeremy Edward

Publication type:

Article

Robustness of DNA Repair through Collective Rate Control.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 1, p. 1, doi. 10.1371/journal.pcbi.1003438

By:

Verbruggen, Paul;
Heinemann, Tim;
Manders, Erik;
von Bornstaedt, Gesa;
van Driel, Roel;
Höfer, Thomas

Publication type:

Article

Coarse-Grained Molecular Simulation of Epidermal Growth Factor Receptor Protein Tyrosine Kinase Multi-Site Self-Phosphorylation.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 1, p. 1, doi. 10.1371/journal.pcbi.1003435

By:

Koland, John G.

Publication type:

Article

Microenvironmental Variables Must Influence Intrinsic Phenotypic Parameters of Cancer Stem Cells to Affect Tumourigenicity.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 1, p. 1, doi. 10.1371/journal.pcbi.1003433

By:

Scott, Jacob G.;
Hjelmeland, Anita B.;
Chinnaiyan, Prakash;
Anderson, Alexander R. A.;
Basanta, David

Publication type:

Article

The Correlation Structure of Local Neuronal Networks Intrinsically Results from Recurrent Dynamics.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 1, p. 1, doi. 10.1371/journal.pcbi.1003428

By:

Helias, Moritz;
Tetzlaff, Tom;
Diesmann, Markus

Publication type:

Article

PEX5 and Ubiquitin Dynamics on Mammalian Peroxisome Membranes.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 1, p. 1, doi. 10.1371/journal.pcbi.1003426

By:

Brown, Aidan I.;
Kim, Peter K.;
Rutenberg, Andrew D.

Publication type:

Article

Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 1, p. 1, doi. 10.1371/journal.pcbi.1003378

By:

von Kamp, Axel;
Klamt, Steffen

Publication type:

Article

Interference and Shaping in Sensorimotor Adaptations with Rewards.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 1, p. 1, doi. 10.1371/journal.pcbi.1003377

By:

Darshan, Ran;
Leblois, Arthur;
Hansel, David

Publication type:

Article

Current Practice in Software Development for Computational Neuroscience and How to Improve It.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 1, p. 1, doi. 10.1371/journal.pcbi.1003376

By:

Gewaltig, Marc-Oliver;
Cannon, Robert

Publication type:

Article

Ten Quick Tips for Using the Gene Ontology.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 11, p. 1, doi. 10.1371/journal.pcbi.1003343

By:

Blake, Judith A.

Publication type:

Article

Ten Simple Rules for Reproducible Computational Research.

Published in:

2013

By:

Sandve, Geir Kjetil;
Nekrutenko, Anton;
Taylor, James;
Hovig, Eivind

Publication type:

Editorial

The hidden models of model checking.

Published in:

Software & Systems Modeling, 2012, v. 11, n. 4, p. 541, doi. 10.1007/s10270-012-0281-9

By:

Visser, Willem;
Dwyer, Matthew;
Whalen, Michael

Publication type:

Article

Open problems in Petri net modeling and simulation of biological systems.

Published in:

IT: Information Technology, 2014, v. 56, n. 2, p. 76, doi. 10.1515/itit-2013-1021

By:

Chen, Ming;
Hofestädt, Ralf

Publication type:

Article

THE EVOLUTION OF LANDSCAPE GENETICS.

Published in:

Evolution, 2013, v. 67, n. 12, p. 3383, doi. 10.1111/evo.12278

By:

Petren, K.

Publication type:

Article

INTEGRATING LANDSCAPE GENOMICS AND SPATIALLY EXPLICIT APPROACHES TO DETECT LOCI UNDER SELECTION IN CLINAL POPULATIONS.

Published in:

Evolution, 2013, v. 67, n. 12, p. 3455, doi. 10.1111/evo.12237

By:

Jones, Matthew R.;
Forester, Brenna R.;
Teufel, Ashley I.;
Adams, Rachael V.;
Anstett, Daniel N.;
Goodrich, Betsy A.;
Landguth, Erin L.;
Joost, Stéphane;
Manel, Stéphanie

Publication type:

Article

EXAMINING THE FULL EFFECTS OF LANDSCAPE HETEROGENEITY ON SPATIAL GENETIC VARIATION: A MULTIPLE MATRIX REGRESSION APPROACH FOR QUANTIFYING GEOGRAPHIC AND ECOLOGICAL ISOLATION.

Published in:

Evolution, 2013, v. 67, n. 12, p. 3403, doi. 10.1111/evo.12134

By:

Wang, Ian J.

Publication type:

Article

The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study.

Published in:

PLoS ONE, 2016, v. 11, n. 3, p. 1, doi. 10.1371/journal.pone.0152002

By:

Sun, Lili;
Tabaka, Marcin;
Hou, Sen;
Li, Lin;
Burdzy, Krzysztof;
Aksimentiev, Aleksei;
Maffeo, Christopher;
Zhang, Xuzhu;
Holyst, Robert

Publication type:

Article

Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 3, p. 1, doi. 10.1371/journal.pcbi.1005424

By:

Yurkovich, James T.;
Yang, Laurence;
Palsson, Bernhard O.

Publication type:

Article

A Topological Criterion for Filtering Information in Complex Brain Networks.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 1, p. 1, doi. 10.1371/journal.pcbi.1005305

By:

De Vico Fallani, Fabrizio;
Latora, Vito;
Chavez, Mario

Publication type:

Article

Efficient Switches in Biology and Computer Science.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 1, p. 1, doi. 10.1371/journal.pcbi.1005100

By:

Cardelli, Luca;
Hernansaiz-Ballesteros, Rosa D.;
Dalchau, Neil;
Csikász-Nagy, Attila

Publication type:

Article

QSAR-BASED VIRTUAL SCREENING FOR COMPUTATIONAL PREDICTION OF WEST NILE VIRUS NS3 PROTEASE INHIBITORS.

Published in:

Pharmacophore, 2014, v. 5, n. 1, p. 84

By:

Khedr, Mohammed Abdou

Publication type:

Article

In-silico design of computational nucleic acids for molecular information processing.

Published in:

Journal of Cheminformatics, 2013, v. 5, n. 1, p. 1, doi. 10.1186/1758-2946-5-22

By:

Ramlan, Effirul Ikhwan;
Zauner, Klaus-Peter

Publication type:

Article

Rapid, optimized interactomic screening.

Published in:

Nature Methods, 2015, v. 12, n. 6, p. 553, doi. 10.1038/nmeth.3395

By:

Hakhverdyan, Zhanna;
Domanski, Michal;
Hough, Loren E;
Oroskar, Asha A;
Oroskar, Anil R;
Keegan, Sarah;
Dilworth, David J;
Molloy, Kelly R;
Sherman, Vadim;
Aitchison, John D;
Fenyö, David;
Chait, Brian T;
Jensen, Torben Heick;
Rout, Michael P;
LaCava, John

Publication type:

Article

Mitochondrial genomes gleaned from human whole-exome sequencing.

Published in:

Nature Methods, 2012, v. 9, n. 6, p. 523, doi. 10.1038/nmeth.2029

By:

Picardi, Ernesto;
Pesole, Graziano

Publication type:

Article