Works in PLoS Computational Biology, 2014, Vol 10, Issue 7

Results: 63

Dendritic Nonlinearities Reduce Network Size Requirements and Mediate ON and OFF States of Persistent Activity in a PFC Microcircuit Model.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003764

By:

Papoutsi, Athanasia;
Sidiropoulou, Kyriaki;
Poirazi, Panayiota

Publication type:

Article

Robustness and Evolvability of the Human Signaling Network.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003763

By:

Kim, Junil;
Vandamme, Drieke;
Kim, Jeong-Rae;
Munoz, Amaya Garcia;
Kolch, Walter;
Cho, Kwang-Hyun

Publication type:

Article

Apoptotic Lymphocytes of H. sapiens Lose Nucleosomes in GC-Rich Promoters.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003760

By:

Hosid, Sergey;
Ioshikhes, Ilya

Publication type:

Article

Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication".

Published in:

2014

By:

Chen, Wei-Hua;
Zhao, Xing-Ming;
van Noort, Vera;
Bork, Peer

Publication type:

Opinion

Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003757

By:

Rausell, Antonio;
Mohammadi, Pejman;
McLaren, Paul J.;
Bartha, Istvan;
Xenarios, Ioannis;
Fellay, Jacques;
Telenti, Amalio

Publication type:

Article

Identifying Selection in the Within-Host Evolution of Influenza Using Viral Sequence Data.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003755

By:

Illingworth, Christopher J. R.;
Fischer, Andrej;
Mustonen, Ville

Publication type:

Article

Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication.

Published in:

2014

By:

Singh, Param Priya;
Affeldt, Séverine;
Malaguti, Giulia;
Isambert, Hervé

Publication type:

Opinion

Membrane Interaction of Bound Ligands Contributes to the Negative Binding Cooperativity of the EGF Receptor.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003742

By:

Arkhipov, Anton;
Shan, Yibing;
Kim, Eric T.;
Shaw, David E.

Publication type:

Article

Structure-Based Druggability Assessment of the Mammalian Structural Proteome with Inclusion of Light Protein Flexibility.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003741

By:

Loving, Kathryn A.;
Lin, Andy;
Cheng, Alan C.

Publication type:

Article

A Real-Time All-Atom Structural Search Engine for Proteins.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003750

By:

Gonzalez, Gabriel;
Hannigan, Brett;
DeGrado, William F.

Publication type:

Article

Different Inward and Outward Conduction Mechanisms in NaVMs Suggested by Molecular Dynamics Simulations.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003746

By:

Ke, Song;
Timin, E. N.;
Stary-Weinzinger, Anna

Publication type:

Article

Hydrophobin Film Structure for HFBI and HFBII and Mechanism for Accelerated Film Formation.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003745

By:

Magarkar, Aniket;
Mele, Nawel;
Abdel-Rahman, Noha;
Butcher, Sarah;
Torkkeli, Mika;
Serimaa, Ritva;
Paananen, Arja;
Linder, Markus;
Bunker, Alex

Publication type:

Article

No, There Is No 150 ms Lead of Visual Speech on Auditory Speech, but a Range of Audiovisual Asynchronies Varying from Small Audio Lead to Large Audio Lag.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003743

By:

Schwartz, Jean-Luc;
Savariaux, Christophe

Publication type:

Article

Hotspot Mutations in KIT Receptor Differentially Modulate Its Allosterically Coupled Conformational Dynamics: Impact on Activation and Drug Sensitivity.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003749

By:

Chauvot de Beauchêne, Isaure;
Allain, Ariane;
Panel, Nicolas;
Laine, Elodie;
Trouvé, Alain;
Dubreuil, Patrice;
Tchertanov, Luba

Publication type:

Article

Propagating Waves of Directionality and Coordination Orchestrate Collective Cell Migration.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003747

By:

Zaritsky, Assaf;
Kaplan, Doron;
Hecht, Inbal;
Natan, Sari;
Wolf, Lior;
Gov, Nir S.;
Ben-Jacob, Eshel;
Tsarfaty, Ilan

Publication type:

Article

Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003739

By:

Perrin Jr, B. Scott;
Miller, Benjamin T.;
Schalk, Vinushka;
Woodcock, H. Lee;
Brooks, Bernard R.;
Ichiye, Toshiko

Publication type:

Article

Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003740

By:

Chowdhury, Salim Akhter;
Shackney, Stanley E.;
Heselmeyer-Haddad, Kerstin;
Ried, Thomas;
Schäffer, Alejandro A.;
Schwartz, Russell

Publication type:

Article

Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003738

By:

Pickard IV, Frank C.;
Miller, Benjamin T.;
Schalk, Vinushka;
Lerner, Michael G.;
Woodcock III, H. Lee;
Brooks, Bernard R.

Publication type:

Article

Structure-Function Discrepancy: Inhomogeneity and Delays in Synchronized Neural Networks.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003736

By:

Ton, Robert;
Deco, Gustavo;
Daffertshofer, Andreas

Publication type:

Article

Analysis of the Protein Domain and Domain Architecture Content in Fungi and Its Application in the Search of New Antifungal Targets.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003733

By:

Barrera, Alejandro;
Alastruey-Izquierdo, Ana;
Martín, María J.;
Cuesta, Isabel;
Vizcaíno, Juan Antonio

Publication type:

Article

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003731

By:

Janky, Rekin's;
Verfaillie, Annelien;
Imrichová, Hana;
Van de Sande, Bram;
Standaert, Laura;
Christiaens, Valerie;
Hulselmans, Gert;
Herten, Koen;
Naval Sanchez, Marina;
Potier, Delphine;
Svetlichnyy, Dmitry;
Kalender Atak, Zeynep;
Fiers, Mark;
Marine, Jean-Christophe;
Aerts, Stein

Publication type:

Article

Antibody Responses during Hepatitis B Viral Infection.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003730

By:

Ciupe, Stanca M.;
Ribeiro, Ruy M.;
Perelson, Alan S.

Publication type:

Article

P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003729

By:

Sun, Huiyong;
Li, Youyong;
Tian, Sheng;
Wang, Junmei;
Hou, Tingjun

Publication type:

Article

A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003726

By:

Zarecki, Raphy;
Oberhardt, Matthew A.;
Reshef, Leah;
Gophna, Uri;
Ruppin, Eytan

Publication type:

Article

The Long and Viscous Road: Uncovering Nuclear Diffusion Barriers in Closed Mitosis.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003725

By:

Zavala, Eder;
Marquez-Lago, Tatiana T.

Publication type:

Article

Phase-Coherence Transitions and Communication in the Gamma Range between Delay-Coupled Neuronal Populations.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003723

By:

Barardi, Alessandro;
Sancristóbal, Belen;
Garcia-Ojalvo, Jordi

Publication type:

Article

Electric Imaging through Evolution, a Modeling Study of Commonalities and Differences.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003722

By:

Pedraja, Federico;
Aguilera, Pedro;
Caputi, Angel A.;
Budelli, Ruben

Publication type:

Article

Correlated Inter-Domain Motions in Adenylate Kinase.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003721

By:

Esteban-Martín, Santiago;
Fenwick, Robert Bryn;
Ådén, Jörgen;
Cossins, Benjamin;
Bertoncini, Carlos W.;
Guallar, Victor;
Wolf-Watz, Magnus;
Salvatella, Xavier

Publication type:

Article

LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003720

By:

Durrant, Jacob D.;
Amaro, Rommie E.

Publication type:

Article

Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003719

By:

Miller, Benjamin T.;
Singh, Rishi P.;
Schalk, Vinushka;
Pevzner, Yuri;
Sun, Jingjun;
Miller, Carrie S.;
Boresch, Stefan;
Ichiye, Toshiko;
Brooks, Bernard R.;
Woodcock III, H. Lee

Publication type:

Article

De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003718

By:

Smadbeck, James;
Chan, Kiat Hwa;
Khoury, George A.;
Xue, Bo;
Robinson, Robert C.;
Hauser, Charlotte A. E.;
Floudas, Christodoulos A.

Publication type:

Article

On the Use of Human Mobility Proxies for Modeling Epidemics.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003716

By:

Tizzoni, Michele;
Bajardi, Paolo;
Decuyper, Adeline;
Kon Kam King, Guillaume;
Schneider, Christian M.;
Blondel, Vincent;
Smoreda, Zbigniew;
González, Marta C.;
Colizza, Vittoria

Publication type:

Article

Characterizing the Impact of Category Uncertainty on Human Auditory Categorization Behavior.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003715

By:

Gifford, Adam M.;
Cohen, Yale E.;
Stocker, Alan A.

Publication type:

Article

A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003714

By:

Lonsdale, Richard;
Rouse, Sarah L.;
Sansom, Mark S. P.;
Mulholland, Adrian J.

Publication type:

Article

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003711

By:

Ghandi, Mahmoud;
Lee, Dongwon;
Mohammad-Noori, Morteza;
Beer, Michael A.

Publication type:

Article

Network Analysis of Breast Cancer Progression and Reversal Using a Tree-Evolving Network Algorithm.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003713

By:

Parikh, Ankur P.;
Curtis, Ross E.;
Kuhn, Irene;
Becker-Weimann, Sabine;
Bissell, Mina;
Xing, Eric P.;
Wu, Wei

Publication type:

Article

Analysis of Graph Invariants in Functional Neocortical Circuitry Reveals Generalized Features Common to Three Areas of Sensory Cortex.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003710

By:

Gururangan, Suchin S.;
Sadovsky, Alexander J.;
MacLean, Jason N.

Publication type:

Article

The Dynamics of DNA Methylation Covariation Patterns in Carcinogenesis.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003709

By:

Teschendorff, Andrew E.;
Liu, Xiaoping;
Caren, Helena;
Pollard, Steve M.;
Beck, Stephan;
Widschwendter, Martin;
Chen, Luonan

Publication type:

Article

Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003708

By:

de Ridder, Jeroen;
Meysman, Pieter;
Oluwagbemi, Olugbenga;
Abeel, Thomas

Publication type:

Article

Signaling Domain of Sonic Hedgehog as Cannibalistic Calcium-Regulated Zinc-Peptidase.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003707

By:

Rebollido-Rios, Rocio;
Bandari, Shyam;
Wilms, Christoph;
Jakuschev, Stanislav;
Vortkamp, Andrea;
Grobe, Kay;
Hoffmann, Daniel

Publication type:

Article

Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003706

By:

Karlsson, Fredrik H.;
Nookaew, Intawat;
Nielsen, Jens

Publication type:

Article

Rethinking Transcriptional Activation in the Arabidopsis Circadian Clock.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003705

By:

Fogelmark, Karl;
Troein, Carl

Publication type:

Article

Alkylpurine Glycosylase D Employs DNA Sculpting as a Strategy to Extrude and Excise Damaged Bases.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003704

By:

Kossmann, Bradley;
Ivanov, Ivaylo

Publication type:

Article

Inferring Clonal Composition from Multiple Sections of a Breast Cancer.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003703

By:

Zare, Habil;
Wang, Junfeng;
Hu, Alex;
Weber, Kris;
Smith, Josh;
Nickerson, Debbie;
Song, ChaoZhong;
Witten, Daniela;
Blau, C. Anthony;
Noble, William Stafford

Publication type:

Article

CeleST: Computer Vision Software for Quantitative Analysis of C. elegans Swim Behavior Reveals Novel Features of Locomotion.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003702

By:

Restif, Christophe;
Ibáñez-Ventoso, Carolina;
Vora, Mehul M.;
Guo, Suzhen;
Metaxas, Dimitris;
Driscoll, Monica

Publication type:

Article

Computational Modeling and Analysis of Iron Release from Macrophages.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003701

By:

Potdar, Alka A.;
Sarkar, Joydeep;
Das, Nupur K.;
Ghosh, Paroma;
Gratzl, Miklos;
Fox, Paul L.;
Saidel, Gerald M.

Publication type:

Article

Brain and Behavior in Decision-Making.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003700

By:

Cassey, Peter;
Heathcote, Andrew;
Brown, Scott D.

Publication type:

Article

Regulation of the Nucleosome Repeat Length In Vivo by the DNA Sequence, Protein Concentrations and Long-Range Interactions.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003698

By:

Beshnova, Daria A.;
Cherstvy, Andrey G.;
Vainshtein, Yevhen;
Teif, Vladimir B.

Publication type:

Article

Collective Behaviour without Collective Order in Wild Swarms of Midges.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003697

By:

Attanasi, Alessandro;
Cavagna, Andrea;
Del Castello, Lorenzo;
Giardina, Irene;
Melillo, Stefania;
Parisi, Leonardo;
Pohl, Oliver;
Rossaro, Bruno;
Shen, Edward;
Silvestri, Edmondo;
Viale, Massimiliano

Publication type:

Article

Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003696

By:

McDavid, Andrew;
Dennis, Lucas;
Danaher, Patrick;
Finak, Greg;
Krouse, Michael;
Wang, Alice;
Webster, Philippa;
Beechem, Joseph;
Gottardo, Raphael

Publication type:

Article