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Volume 9; Issue 10
Main
PLoS Computational Biology
Volume 9; Issue 10
PLoS Computational Biology
Volume 9; Issue 10
1
On the Role of Aggregation Prone Regions in Protein Evolution, Stability, and Enzymatic Catalysis: Insights from Diverse Analyses
Buck, Patrick M.
,
Kumar, Sandeep
,
Singh, Satish K.
,
Iakoucheva, Lilia M.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.75 MB
Your tags:
english, 2013
2
Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis
MartÃnez-Jiménez, Francisco
,
Papadatos, George
,
Yang, Lun
,
Wallace, Iain M.
,
Kumar, Vinod
,
Pieper, Ursula
,
Sali, Andrej
,
Brown, James R.
,
Overington, John P.
,
Marti-Renom, Marc A.
,
MacKerell, Alexan
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 4.55 MB
Your tags:
english, 2013
3
Ligand Clouds around Protein Clouds: A Scenario of Ligand Binding with Intrinsically Disordered Proteins
Jin, Fan
,
Yu, Chen
,
Lai, Luhua
,
Liu, Zhirong
,
van der Spoel, David
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 2.42 MB
Your tags:
english, 2013
4
Synaptic Scaling Enables Dynamically Distinct Short- and Long-Term Memory Formation
Tetzlaff, Christian
,
Kolodziejski, Christoph
,
Timme, Marc
,
Tsodyks, Misha
,
Wörgötter, Florentin
,
Beck, Jeff
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.03 MB
Your tags:
english, 2013
5
A Complex-Valued Firing-Rate Model That Approximates the Dynamics of Spiking Networks
Schaffer, Evan S.
,
Ostojic, Srdjan
,
Abbott, L. F.
,
Ermentrout, Bard
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.09 MB
Your tags:
english, 2013
6
How Can PLOS Computational Biology Help the Biological Sciences?
Nussinov, Ruth
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 111 KB
Your tags:
english, 2013
7
Balanced Excitatory and Inhibitory Synaptic Currents Promote Efficient Coding and Metabolic Efficiency
Sengupta, Biswa
,
Laughlin, Simon B.
,
Niven, Jeremy E.
,
McCulloch, Andrew D.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.62 MB
Your tags:
english, 2013
8
A Genome-Scale Integration and Analysis of Lactococcus lactis Translation Data
Racle, Julien
,
Picard, Flora
,
Girbal, Laurence
,
Cocaign-Bousquet, Muriel
,
Hatzimanikatis, Vassily
,
Shvartsman, Stanislav
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 868 KB
Your tags:
english, 2013
9
Virus Encoded MHC-Like Decoys Diversify the Inhibitory KIR Repertoire
Carrillo-Bustamante, Paola
,
KeÅŸmir, Can
,
de Boer, Rob J.
,
Asquith, Becca
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.04 MB
Your tags:
english, 2013
10
CAPE: An R Package for Combined Analysis of Pleiotropy and Epistasis
Tyler, Anna L.
,
Lu, Wei
,
Hendrick, Justin J.
,
Philip, Vivek M.
,
Carter, Gregory W.
,
Gardner, Paul P.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 632 KB
Your tags:
english, 2013
11
Analysis of Initial Cell Spreading Using Mechanistic Contact Formulations for a Deformable Cell Model
Odenthal, Tim
,
Smeets, Bart
,
Van Liedekerke, Paul
,
Tijskens, Engelbert
,
Van Oosterwyck, Hans
,
Ramon, Herman
,
McCulloch, Andrew D.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 2.41 MB
Your tags:
english, 2013
12
Natural, Persistent Oscillations in a Spatial Multi-Strain Disease System with Application to Dengue
Lourenço, José
,
Recker, Mario
,
Pascual, Mercedes
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.13 MB
Your tags:
english, 2013
13
Keeping up with the Joneses: Interpersonal Prediction Errors and the Correlation of Behavior in a Tandem Sequential Choice Task
Lohrenz, Terry
,
Bhatt, Meghana
,
Apple, Nathan
,
Montague, P. Read
,
Behrens, Tim
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 596 KB
Your tags:
english, 2013
14
A Brain-Machine Interface for Control of Medically-Induced Coma
Shanechi, Maryam M.
,
Chemali, Jessica J.
,
Liberman, Max
,
Solt, Ken
,
Brown, Emery N.
,
Sporns, Olaf
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.19 MB
Your tags:
english, 2013
15
Comprehensive Repertoire of Foldable Regions within Whole Genomes
Faure, Guilhem
,
Callebaut, Isabelle
,
Radivojac, Predrag
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.12 MB
Your tags:
english, 2013
16
The Lazy Visual Word Form Area: Computational Insights into Location-Sensitivity
Hannagan, Thomas
,
Grainger, Jonathan
,
Daunizeau, Jean
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.34 MB
Your tags:
english, 2013
17
Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster
Becker, Kolja
,
Balsa-Canto, Eva
,
Cicin-Sain, Damjan
,
Hoermann, Astrid
,
Janssens, Hilde
,
Banga, Julio R.
,
Jaeger, Johannes
,
Shvartsman, Stanislav
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.66 MB
Your tags:
english, 2013
18
Feature Selection Methods for Identifying Genetic Determinants of Host Species in RNA Viruses
Aguas, Ricardo
,
Ferguson, Neil M.
,
Kosakovsky Pond, Sergei L.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 4.82 MB
Your tags:
english, 2013
19
Human Genome Replication Proceeds through Four Chromatin States
Julienne, Hanna
,
Zoufir, Azedine
,
Audit, Benjamin
,
Arneodo, Alain
,
Ouzounis, Christos A.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 2.80 MB
Your tags:
english, 2013
20
dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data
Chung, Dongjun
,
Park, Dan
,
Myers, Kevin
,
Grass, Jeffrey
,
Kiley, Patricia
,
Landick, Robert
,
Keleş, Sündüz
,
Guigo, Roderic
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 2.70 MB
Your tags:
english, 2013
21
Reassessing Google Flu Trends Data for Detection of Seasonal and Pandemic Influenza: A Comparative Epidemiological Study at Three Geographic Scales
Olson, Donald R.
,
Konty, Kevin J.
,
Paladini, Marc
,
Viboud, Cecile
,
Simonsen, Lone
,
Ferguson, Neil
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 626 KB
Your tags:
english, 2013
22
Properties of MHC Class I Presented Peptides That Enhance Immunogenicity
Calis, Jorg J. A.
,
Maybeno, Matt
,
Greenbaum, Jason A.
,
Weiskopf, Daniela
,
De Silva, Aruna D.
,
Sette, Alessandro
,
KeÅŸmir, Can
,
Peters, Bjoern
,
Asquith, Becca
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 686 KB
Your tags:
english, 2013
23
Ten Simple Rules for Reproducible Computational Research
Sandve, Geir Kjetil
,
Nekrutenko, Anton
,
Taylor, James
,
Hovig, Eivind
,
Bourne, Philip E.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 131 KB
Your tags:
english, 2013
24
Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution
Carr, Rogan
,
Shen-Orr, Shai S.
,
Borenstein, Elhanan
,
Ouzounis, Christos A.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 664 KB
Your tags:
english, 2013
25
Deciding Not to Decide: Computational and Neural Evidence for Hidden Behavior in Sequential Choice
Gluth, Sebastian
,
Rieskamp, Jörg
,
Büchel, Christian
,
Behrens, Tim
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.10 MB
Your tags:
english, 2013
26
Sensitive Detection of Viral Transcripts in Human Tumor Transcriptomes
Schelhorn, Sven-Eric
,
Fischer, Matthias
,
Tolosi, Laura
,
Altmüller, Janine
,
Nürnberg, Peter
,
Pfister, Herbert
,
Lengauer, Thomas
,
Berthold, Frank
,
Wilke, Claus O.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.59 MB
Your tags:
english, 2013
27
Prediction of the P. falciparum Target Space Relevant to Malaria Drug Discovery
Spitzmüller, Andreas
,
Mestres, Jordi
,
Russell, Robert B.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 953 KB
Your tags:
english, 2013
28
Cellular Adaptation Facilitates Sparse and Reliable Coding in Sensory Pathways
Farkhooi, Farzad
,
Froese, Anja
,
Muller, Eilif
,
Menzel, Randolf
,
Nawrot, Martin P.
,
Gutkin, Boris S.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 796 KB
Your tags:
english, 2013
29
GINI: From ISH Images to Gene Interaction Networks
Puniyani, Kriti
,
Xing, Eric P.
,
Chechik, Gal
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 2.26 MB
Your tags:
english, 2013
30
The Convallis Rule for Unsupervised Learning in Cortical Networks
Yger, Pierre
,
Harris, Kenneth D.
,
Behrens, Tim
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.84 MB
Your tags:
english, 2013
31
Inferring Evolutionary Histories of Pathway Regulation from Transcriptional Profiling Data
Schraiber, Joshua G.
,
Mostovoy, Yulia
,
Hsu, Tiffany Y.
,
Brem, Rachel B.
,
Teichmann, Sarah A.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 776 KB
Your tags:
english, 2013
32
ToPS: A Framework to Manipulate Probabilistic Models of Sequence Data
Kashiwabara, André Yoshiaki
,
Bonadio, �gor
,
Onuchic, Vitor
,
Amado, Felipe
,
Mathias, Rafael
,
Durham, Alan Mitchell
,
Lapp, Hilmar
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 787 KB
Your tags:
english, 2013
33
Dynamic Change of Global and Local Information Processing in Propofol-Induced Loss and Recovery of Consciousness
Monti, Martin M.
,
Lutkenhoff, Evan S.
,
Rubinov, Mikail
,
Boveroux, Pierre
,
Vanhaudenhuyse, Audrey
,
Gosseries, Olivia
,
Bruno, Marie-Aurélie
,
Noirhomme, Quentin
,
Boly, Mélanie
,
Laureys, Steven
,
Daunize
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 6.87 MB
Your tags:
english, 2013
34
Attention-Dependent Modulation of Cortical Taste Circuits Revealed by Granger Causality with Signal-Dependent Noise
Luo, Qiang
,
Ge, Tian
,
Grabenhorst, Fabian
,
Feng, Jianfeng
,
Rolls, Edmund T.
,
Sporns, Olaf
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.69 MB
Your tags:
english, 2013
35
The Influence of Synaptic Weight Distribution on Neuronal Population Dynamics
Iyer, Ramakrishnan
,
Menon, Vilas
,
Buice, Michael
,
Koch, Christof
,
Mihalas, Stefan
,
Sporns, Olaf
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.77 MB
Your tags:
english, 2013
36
Lipid Receptor S1P1 Activation Scheme Concluded from Microsecond All-Atom Molecular Dynamics Simulations
Yuan, Shuguang
,
Wu, Rongliang
,
Latek, Dorota
,
Trzaskowski, Bartosz
,
Filipek, Slawomir
,
Grubmüller, Helmut
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 3.27 MB
Your tags:
english, 2013
37
Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening
Bhattacherjee, Arnab
,
Wallin, Stefan
,
Iakoucheva, Lilia M.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 796 KB
Your tags:
english, 2013
38
Machines vs. Ensembles: Effective MAPK Signaling through Heterogeneous Sets of Protein Complexes
Suderman, Ryan
,
Deeds, Eric J.
,
Dunbrack, Roland L.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 906 KB
Your tags:
english, 2013
39
An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis
Mitra, Pralay
,
Shultis, David
,
Brender, Jeffrey R.
,
Czajka, Jeff
,
Marsh, David
,
Gray, Felicia
,
Cierpicki, Tomasz
,
Zhang, Yang
,
Shakhnovich, Eugene I.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.38 MB
Your tags:
english, 2013
40
Emergence of Metastable State Dynamics in Interconnected Cortical Networks with Propagation Delays
Kutchko, Katrina M.
,
Fröhlich, Flavio
,
Jirsa, Viktor K.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 2.01 MB
Your tags:
english, 2013
41
Explain Bioinformatics to Your Grandmother!
Bernard, Virginie
,
Michaut, Magali
,
Troyanskaya, Olga G.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 140 KB
Your tags:
english, 2013
42
APBioNet—Transforming Bioinformatics in the Asia-Pacific Region
Khan, Asif M.
,
Tan, Tin Wee
,
Schönbach, Christian
,
Ranganathan, Shoba
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 148 KB
Your tags:
english, 2013
43
The Molecular Mechanism of Ion-Dependent Gating in Secondary Transporters
Zhao, Chunfeng
,
Noskov, Sergei Yu.
,
Livesay, Dennis R.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 2.79 MB
Your tags:
english, 2013
44
Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks
Pritykin, Yuri
,
Singh, Mona
,
Rzhetsky, Andrey
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.06 MB
Your tags:
english, 2013
45
Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks
Roy, Sushmita
,
Lagree, Stephen
,
Hou, Zhonggang
,
Thomson, James A.
,
Stewart, Ron
,
Gasch, Audrey P.
,
Przytycka, Teresa M.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 3.25 MB
Your tags:
english, 2013
46
A Dendritic Mechanism for Decoding Traveling Waves: Principles and Applications to Motor Cortex
Heitmann, Stewart
,
Boonstra, Tjeerd
,
Breakspear, Michael
,
Miller, Kai
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.85 MB
Your tags:
english, 2013
47
A Network Approach to Analyzing Highly Recombinant Malaria Parasite Genes
Larremore, Daniel B.
,
Clauset, Aaron
,
Buckee, Caroline O.
,
Antia, Rustom
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.44 MB
Your tags:
english, 2013
48
Novel Methods for Analysing Bacterial Tracks Reveal Persistence in Rhodobacter sphaeroides
Rosser, Gabriel
,
Fletcher, Alexander G.
,
Wilkinson, David A.
,
de Beyer, Jennifer A.
,
Yates, Christian A.
,
Armitage, Judith P.
,
Maini, Philip K.
,
Baker, Ruth E.
,
Coombs, Daniel
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.24 MB
Your tags:
english, 2013
49
Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision
Grieco, Luca
,
Calzone, Laurence
,
Bernard-Pierrot, Isabelle
,
Radvanyi, François
,
Kahn-Perlès, Brigitte
,
Thieffry, Denis
,
Miyano, Satoru
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.38 MB
Your tags:
english, 2013
50
Model of Fission Yeast Cell Shape Driven by Membrane-Bound Growth Factors and the Cytoskeleton
Drake, Tyler
,
Vavylonis, Dimitrios
,
Haugh, Jason M.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.27 MB
Your tags:
english, 2013
51
Dynamic Rendering of the Heterogeneous Cell Response to Anticancer Treatments
Falcetta, Francesca
,
Lupi, Monica
,
Colombo, Valentina
,
Ubezio, Paolo
,
Tucker-Kellogg, Greg
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 2.68 MB
Your tags:
english, 2013
52
Unraveling Adaptation in Eukaryotic Pathways: Lessons from Protocells
De Palo, Giovanna
,
Endres, Robert G.
,
Wingreen, Ned S.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 2.41 MB
Your tags:
english, 2013
53
A Simple Rule for Dendritic Spine and Axonal Bouton Formation Can Account for Cortical Reorganization after Focal Retinal Lesions
Butz, Markus
,
van Ooyen, Arjen
,
Graham, Lyle J.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 19.90 MB
Your tags:
english, 2013
54
A Horizontal Alignment Tool for Numerical Trend Discovery in Sequence Data: Application to Protein Hydropathy
Hadzipasic, Omar
,
Wrabl, James O.
,
Hilser, Vincent J.
,
Fetrow, Jacquelyn S.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 3.58 MB
Your tags:
english, 2013
55
Molecular Mechanical Differences between Isoforms of Contractile Actin in the Presence of Isoforms of Smooth Muscle Tropomyosin
Hilbert, Lennart
,
Bates, Genevieve
,
Roman, Horia N.
,
Blumenthal, Jenna L.
,
Zitouni, Nedjma B.
,
Sobieszek, Apolinary
,
Mackey, Michael C.
,
Lauzon, Anne-Marie
,
McCulloch, Andrew D.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 908 KB
Your tags:
english, 2013
56
Conformational Changes in Talin on Binding to Anionic Phospholipid Membranes Facilitate Signaling by Integrin Transmembrane Helices
Kalli, Antreas C.
,
Campbell, Iain D.
,
Sansom, Mark S. P.
,
Ben-Tal, Nir
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 4.78 MB
Your tags:
english, 2013
57
A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins
Gao, Mu
,
Skolnick, Jeffrey
,
Singh, Mona
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 6.69 MB
Your tags:
english, 2013
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