Works matching IS 1553734X AND DT 2013 AND VI 9 AND IP 3

Results: 73

Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002961

By:

Mann, Richard P.;
Perna, Andrea;
Strömbom, Daniel;
Garnett, Roman;
Herbert-Read, James E.;
Sumpter, David J. T.;
Ward, Ashley J. W.

Publication type:

Article

A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002958

By:

Stegmaier, Philip;
Kel, Alexander;
Wingender, Edgar;
Borlak, Jürgen

Publication type:

Article

Computational Predictions Provide Insights into the Biology of TAL Effector Target Sites.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002962

By:

Grau, Jan;
Wolf, Annett;
Reschke, Maik;
Bonas, Ulla;
Posch, Stefan;
Boch, Jens

Publication type:

Article

Revealing a Two-Loop Transcriptional Feedback Mechanism in the Cyanobacterial Circadian Clock.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002966

By:

Hertel, Stefanie;
Brettschneider, Christian;
Axmann, Ilka M.

Publication type:

Article

Trade-off between Multiple Constraints Enables Simultaneous Formation of Modules and Hubs in Neural Systems.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002937

By:

Yuhan Chen;
Shengjun Wang;
Hilgetag, Claus C.;
Changsong Zhou

Publication type:

Article

Dual Coordination of Post Translational Modifications in Human Protein Networks.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002933

By:

Woodsmith, Jonathan;
Kamburov, Atanas;
Stelzl, Ulrich

Publication type:

Article

Interpretation of Genomic Variants Using a Unified Biological Network Approach.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002886

By:

Khurana, Ekta;
Yao Fu;
Jieming Chen;
Gerstein, Mark

Publication type:

Article

Split Histidine Kinases Enable Ultrasensitivity and Bistability in Two-Component Signaling Networks.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002949

By:

Amin, Munia;
Porter, Steven L.;
Soyer, Orkun S.

Publication type:

Article

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002968

By:

Rajagopal, Nisha;
Xie, Wei;
Li, Yan;
Wagner, Uli;
Wang, Wei;
Stamatoyannopoulos, John;
Ernst, Jason;
Kellis, Manolis;
Ren, Bing

Publication type:

Article

Processing of Multi-dimensional Sensorimotor Information in the Spinal and Cerebellar Neuronal Circuitry: A New Hypothesis.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002979

By:

Spanne, Anton;
Jörntell, Henrik

Publication type:

Article

Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002929

By:

Dasmeh, Pouria;
Serohijos, Adrian W. R.;
Kepp, Kasper P.;
Shakhnovich, Eugene I.

Publication type:

Article

Noise-invariant Neurons in the Avian Auditory Cortex: Hearing the Song in Noise.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002942

By:

Moore, R. Channing;
Lee, Tyler;
Theunissen, Frédéric E.

Publication type:

Article

Measurements of the Impact of 3' End Sequences on Gene Expression Reveal Wide Range and Sequence Dependent Effects.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002934

By:

Shalem, Ophir;
Carey, Lucas;
Zeevi, Danny;
Sharon, Eilon;
Keren, Leeat;
Weinberger, Adina;
Dahan, Orna;
Pilpel, Yitzhak;
Segal, Eran

Publication type:

Article

Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002950

By:

Larsson, Per;
Kasson, Peter M.

Publication type:

Article

High Prevalence of Multistability of Rest States and Bursting in a Database of a Model Neuron.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002930

By:

Marin, Bóris;
Barnett, William H.;
Doloc-Mihu, Anca;
Calabrese, Ronald L.;
Cymbalyuk, Gennady S.

Publication type:

Article

Directional Summation in Non-direction Selective Retinal Ganglion Cells.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002969

By:

Abbas, Syed Y.;
Hamade, Khaldoun C.;
Yang, Ellen J.;
Nawy, Scott;
Smith, Robert G.;
Pettit, Diana L.

Publication type:

Article

Differential Expression Analysis for Pathways.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002967

By:

Haynes, Winston A.;
Higdon, Roger;
Stanberry, Larissa;
Collins, Dwayne;
Kolker, Eugene

Publication type:

Article

Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002936

By:

Stewart, Ron;
Rascón, Cynthia Alexander;
Shulan Tian;
Nie, Jeff;
Barry, Chris;
Li-Fang Chu;
Ardalani, Hamisha;
Wagner, Ryan J.;
Probasco, Mitchell D.;
Bolin, Jennifer M.;
Ning Leng;
Sengupta, Srikumar;
Volkmer, Michael;
Habermann, Bianca;
Tanaka, Elly M.;
Thomson, James A.;
Dewey, Colin N.

Publication type:

Article

Analysis of Hepatitis C Virus Decline during Treatment with the Protease Inhibitor Danoprevir Using a Multiscale Model.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002959

By:

Rong, Libin;
Guedj, Jeremie;
Dahari, Harel;
Coffield, Jr., Daniel J.;
Levi, Micha;
Smith, Patrick;
Perelson, Alan S.

Publication type:

Article

A Simple Iterative Model Accurately Captures Complex Trapline Formation by Bumblebees Across Spatial Scales and Flower Arrangements.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002938

By:

Reynolds, Andrew M.;
Lihoreau, Mathieu;
Chittka, Lars

Publication type:

Article

Chaste: An Open Source C++ Library for Computational Physiology and Biology.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002970

By:

Mirams, Gary R.;
Arthurs, Christopher J.;
Bernabeu, Miguel O.;
Bordas, Rafel;
Cooper, Jonathan;
Corrias, Alberto;
Davit, Yohan;
Dunn, Sara-Jane;
Fletcher, Alexander G.;
Harvey, Daniel G.;
Marsh, Megan E.;
Osborne, James M.;
Pathmanathan, Pras;
Pitt-Francis, Joe;
Southern, James;
Zemzemi, Nejib;
Gavaghan, David J.

Publication type:

Article

Optimal Vaccine Allocation for the Early Mitigation of Pandemic Influenza.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002964

By:

Matrajt, Laura;
Halloran, M. Elizabeth;
Longini Jr., Ira M.

Publication type:

Article

Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1003019

By:

Di Stefano, Marco;
Rosa, Angelo;
Belcastro, Vincenzo;
di Bernardo, Diego;
Micheletti, Cristian

Publication type:

Article

Sparse Distributed Representation of Odors in a Largescale Olfactory Bulb Circuit.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1003014

By:

Yu, Yuguo;
McTavish, Thomas S.;
Hines, Michael L.;
Shepherd, Gordon M.;
Valenti, Cesare;
Migliore, Michele

Publication type:

Article

Origin and Evolution of Protein Fold Designs Inferred from Phylogenomic Analysis of CATH Domain Structures in Proteomes.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1003009

By:

Bukhari, Syed Abbas;
Caetano-Anollés, Gustavo

Publication type:

Article

An Integrated Computational/Experimental Model of Lymphoma Growth.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1003008

By:

Frieboes, Hermann B.;
Smith, Bryan R.;
Chuang, Yao-Li;
Ito, Ken;
Roettgers, Allison M.;
Gambhir, Sanjiv S.;
Cristini, Vittorio

Publication type:

Article

Systems Model of T Cell Receptor Proximal Signaling Reveals Emergent Ultrasensitivity.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1003004

By:

Mukhopadhyay, Himadri;
Cordoba, Shaun-Paul;
Maini, Philip K.;
van der Merwe, P. Anton;
Dushek, Omer

Publication type:

Article

Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1003003

By:

Whitford, Paul C.;
Blanchard, Scott C.;
Cate, Jamie H. D.;
Sanbonmatsu, Karissa Y.

Publication type:

Article

Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1003002

By:

a Beccara, Silvio;
Škrbić, Tatjana;
Covino, Roberto;
Micheletti, Cristian;
Faccioli, Pietro

Publication type:

Article

Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1003000

By:

Franzén, Oscar;
Jerlström-Hultqvist, Jon;
Einarsson, Elin;
Ankarklev, Johan;
Ferella, Marcela;
Andersson, Björn;
Svärd, Staffan G.

Publication type:

Article

Outlier Responses Reflect Sensitivity to Statistical Structure in the Human Brain.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002999

By:

Garrido, Marta I.;
Sahani, Maneesh;
Dolan, Raymond J.

Publication type:

Article

Systematic Prediction of Pharmacodynamic Drug-Drug Interactions through Protein-Protein-Interaction Network.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002998

By:

Jialiang Huang;
Chaoqun Niu;
Green, Christopher D.;
Yang, Lun;
Hongkang Mei;
Jing-Dong, J. Han

Publication type:

Article

Rampant Exchange of the Structure and Function of Extramembrane Domains between Membrane and Water Soluble Proteins.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002997

By:

Nam, Hyun-Jun;
Han, Seong Kyu;
Bowie, James U.;
Kim, Sanguk

Publication type:

Article

The Fate of Cooperation during Range Expansions.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002994

By:

Korolev, Kirill S.

Publication type:

Article

Under-Dominance Constrains the Evolution of Negative Autoregulation in Diploids.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002992

By:

Stewart, Alexander J.;
Seymour, Robert M.;
Pomiankowski, Andrew;
Reuter, Max

Publication type:

Article

A Model of Binocular Rivalry and Cross-orientation Suppression.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002991

By:

Said, Christopher P.;
Heeger, David J.

Publication type:

Article

In-silico Assessment of Protein-Protein Electron Transfer. A Case Study: Cytochrome c Peroxidase - Cytochrome c.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002990

By:

Wallrapp, Frank H.;
Voityuk, Alexander A.;
Guallar, Victor

Publication type:

Article

A Multi-scale Analysis of Influenza A Virus Fitness Tradeoffs due to Temperature-dependent Virus Persistence.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002989

By:

Handel, Andreas;
Brown, Justin;
Stallknecht, David;
Rohani, Pejman

Publication type:

Article

Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002988

By:

Rossell, Sergio;
Huynen, Martijn A.;
Notebaart, Richard A.

Publication type:

Article

A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002986

By:

Schmal, Christoph;
Reimann, Peter;
Staiger, Dorothee

Publication type:

Article

Neuronal Avalanches Differ from Wakefulness to Deep Sleep - Evidence from Intracranial Depth Recordings in Humans.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002985

By:

Priesemann, Viola;
Valderrama, Mario;
Wibral, Michael;
Van Quyen, Michel Le

Publication type:

Article

Stability and Responsiveness in a Self-Organized Living Architecture.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002984

By:

Garnier, Simon;
Murphy, Tucker;
Lutz, Matthew;
Hurme, Edward;
Leblanc, Simon;
Couzin, Iain D.

Publication type:

Article

Angiogenesis: An Adaptive Dynamic Biological Patterning Problem.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002983

By:

Secomb, Timothy W.;
Alberding, Jonathan P.;
Hsu, Richard;
Dewhirst, Mark W.;
Pries, Axel R.

Publication type:

Article

Sustained Firing of Model Central Auditory Neurons Yields a Discriminative Spectro-temporal Representation for Natural Sounds.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002982

By:

Carlin, Michael A.;
Elhilali, Mounya

Publication type:

Article

Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002981

By:

Jiao, Dazhi;
Ye, Yuzhen;
Tang, Haixu

Publication type:

Article

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002980

By:

Agren, Rasmus;
Liu, Liming;
Shoaie, Saeed;
Vongsangnak, Wanwipa;
Nookaew, Intawat;
Nielsen, Jens

Publication type:

Article

Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002977

By:

Bozek, Katarzyna;
Lengauer, Thomas;
Sierra, Saleta;
Kaiser, Rolf

Publication type:

Article

Automated Analysis of a Diverse Synapse Population.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002976

By:

Busse, Brad;
Smith, Stephen

Publication type:

Article

Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002975

By:

Zhang, Wei;
Ota, Takayo;
Shridhar, Viji;
Chien, Jeremy;
Wu, Baolin;
Kuang, Rui

Publication type:

Article

Bursts of Vertex Activation and Epidemics in Evolving Networks.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002974

By:

Rocha, Luis E. C.;
Blondel, Vincent D.

Publication type:

Article