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Volume 5; Issue 12
Main
PLoS Computational Biology
Volume 5; Issue 12
PLoS Computational Biology
Volume 5; Issue 12
1
A Quick Guide for Developing Effective Bioinformatics Programming Skills
Dudley, Joel T.
,
Butte, Atul J.
,
Lewitter, Fran
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 137 KB
Your tags:
english, 2009
2
Population Structure Induces a Symmetry Breaking Favoring the Emergence of Cooperation
Pacheco, Jorge M.
,
Pinheiro, Flávio L.
,
Santos, Francisco C.
,
Szabo, Gyorgy
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 378 KB
Your tags:
english, 2009
3
Alu and B1 Repeats Have Been Selectively Retained in the Upstream and Intronic Regions of Genes of Specific Functional Classes
Tsirigos, Aristotelis
,
Rigoutsos, Isidore
,
Stormo, Gary D.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 390 KB
Your tags:
english, 2009
4
Human Cancer Protein-Protein Interaction Network: A Structural Perspective
Kar, Gozde
,
Gursoy, Attila
,
Keskin, Ozlem
,
Nussinov, Ruth
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 1.89 MB
Your tags:
english, 2009
5
Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure
Capra, John A.
,
Laskowski, Roman A.
,
Thornton, Janet M.
,
Singh, Mona
,
Funkhouser, Thomas A.
,
Lengauer, Thomas
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 3.00 MB
Your tags:
english, 2009
6
Cortical Gamma Rhythms Modulate NMDAR-Mediated Spike Timing Dependent Plasticity in a Biophysical Model
Lee, Shane
,
Sen, Kamal
,
Kopell, Nancy
,
Graham, Lyle J.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 1.38 MB
Your tags:
english, 2009
7
Calculating Evolutionary Dynamics in Structured Populations
Nathanson, Charles G.
,
Tarnita, Corina E.
,
Nowak, Martin A.
,
Bergstrom, Carl T.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 242 KB
Your tags:
english, 2009
8
Order and Stochastic Dynamics in Drosophila Planar Cell Polarity
Burak, Yoram
,
Shraiman, Boris I.
,
Asthagiri, Anand R.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 1.55 MB
Your tags:
english, 2009
9
Spike-Based Reinforcement Learning in Continuous State and Action Space: When Policy Gradient Methods Fail
Vasilaki, Eleni
,
Frémaux, Nicolas
,
Urbanczik, Robert
,
Senn, Walter
,
Gerstner, Wulfram
,
Friston, Karl J.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 934 KB
Your tags:
english, 2009
10
Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data
Mitsos, Alexander
,
Melas, Ioannis N.
,
Siminelakis, Paraskeuas
,
Chairakaki, Aikaterini D.
,
Saez-Rodriguez, Julio
,
Alexopoulos, Leonidas G.
,
Bourne, Philip E.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 1.43 MB
Your tags:
english, 2009
11
Emergent Patterns of Social Affiliation in Primates, a Model
Puga-Gonzalez, Ivan
,
Hildenbrandt, Hanno
,
Hemelrijk, Charlotte K.
,
Friston, Karl J.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 250 KB
Your tags:
english, 2009
12
Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins
Fromer, Menachem
,
Shifman, Julia M.
,
Mirny, Leonid A.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 1.59 MB
Your tags:
english, 2009
13
Integrin Clustering Is Driven by Mechanical Resistance from the Glycocalyx and the Substrate
Paszek, Matthew J.
,
Boettiger, David
,
Weaver, Valerie M.
,
Hammer, Daniel A.
,
Lauffenberger, Douglas
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 1.06 MB
Your tags:
english, 2009
14
Effective Reduced Diffusion-Models: A Data Driven Approach to the Analysis of Neuronal Dynamics
Deco, Gustavo
,
Martí, Daniel
,
Ledberg, Anders
,
Reig, Ramon
,
Sanchez Vives, Maria V.
,
Friston, Karl J.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 913 KB
Your tags:
english, 2009
15
What Do Transitive Inference and Class Inclusion Have in Common? Categorical (Co)Products and Cognitive Development
Phillips, Steven
,
Wilson, William H.
,
Halford, Graeme S.
,
Behrens, Tim
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 419 KB
Your tags:
english, 2009
16
Dissecting Early Differentially Expressed Genes in a Mixture of Differentiating Embryonic Stem Cells
Hong, Feng
,
Fang, Fang
,
He, Xuming
,
Cao, Xiaoyi
,
Chipperfield, Hiram
,
Xie, Dan
,
Wong, Wing H.
,
Ng, Huck H.
,
Zhong, Sheng
,
Zhang, Weixiong
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 1.88 MB
Your tags:
english, 2009
17
Nano-motion Dynamics are Determined by Surface-Tethered Selectin Mechanokinetics and Bond Formation
Schmidt, Brian J.
,
Papin, Jason A.
,
Lawrence, Michael B.
,
Beard, Daniel A.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 1.35 MB
Your tags:
english, 2009
18
Decomposition of Gene Expression State Space Trajectories
Mar, Jessica C.
,
Quackenbush, John
,
Papin, Jason A.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 385 KB
Your tags:
english, 2009
19
Oxidized Calmodulin Kinase II Regulates Conduction Following Myocardial Infarction: A Computational Analysis
Christensen, Matthew D.
,
Dun, Wen
,
Boyden, Penelope A.
,
Anderson, Mark E.
,
Mohler, Peter J.
,
Hund, Thomas J.
,
McCulloch, Andrew D.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 1.50 MB
Your tags:
english, 2009
20
ON/OFF and Beyond - A Boolean Model of Apoptosis
Schlatter, Rebekka
,
Schmich, Kathrin
,
Avalos Vizcarra, Ima
,
Scheurich, Peter
,
Sauter, Thomas
,
Borner, Christoph
,
Ederer, Michael
,
Merfort, Irmgard
,
Sawodny, Oliver
,
Thieffry, Denis
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 550 KB
Your tags:
english, 2009
21
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
Schnoes, Alexandra M.
,
Brown, Shoshana D.
,
Dodevski, Igor
,
Babbitt, Patricia C.
,
Valencia, Alfonso
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 1.35 MB
Your tags:
english, 2009
22
Adaptive Gain Modulation in V1 Explains Contextual Modifications during Bisection Learning
Schäfer, Roland
,
Vasilaki, Eleni
,
Senn, Walter
,
Friston, Karl J.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 958 KB
Your tags:
english, 2009
23
Transcriptome and Proteome Exploration to Model Translation Efficiency and Protein Stability in Lactococcus lactis
Dressaire, Clémentine
,
Gitton, Christophe
,
Loubière, Pascal
,
Monnet, Véronique
,
Queinnec, Isabelle
,
Cocaign-Bousquet, Muriel
,
Stitt, Mark
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 455 KB
Your tags:
english, 2009
24
Burst-Time-Dependent Plasticity Robustly Guides ON/OFF Segregation in the Lateral Geniculate Nucleus
Gjorgjieva, Julijana
,
Toyoizumi, Taro
,
Eglen, Stephen J.
,
Graham, Lyle J.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 1.06 MB
Your tags:
english, 2009
25
Defining an Essence of Structure Determining Residue Contacts in Proteins
Sathyapriya, R.
,
Duarte, Jose M.
,
Stehr, Henning
,
Filippis, Ioannis
,
Lappe, Michael
,
Nussinov, Ruth
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 2.05 MB
Your tags:
english, 2009
26
A Model Analysis of Arterial Oxygen Desaturation during Apnea in Preterm Infants
Sands, Scott A.
,
Edwards, Bradley A.
,
Kelly, Vanessa J.
,
Davidson, Malcolm R.
,
Wilkinson, Malcolm H.
,
Berger, Philip J.
,
Prisk, Kim
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 983 KB
Your tags:
english, 2009
27
The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes
Angly, Florent E.
,
Willner, Dana
,
Prieto-Davó, Alejandra
,
Edwards, Robert A.
,
Schmieder, Robert
,
Vega-Thurber, Rebecca
,
Antonopoulos, Dionysios A.
,
Barott, Katie
,
Cottrell, Matthew T.
,
Desnues, Christ
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 1018 KB
Your tags:
english, 2009
28
Biomedical Text Mining and Its Applications
Rodriguez-Esteban, Raul
,
Lewitter, Fran
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 543 KB
Your tags:
english, 2009
29
An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data
Ramsköld, Daniel
,
Wang, Eric T.
,
Burge, Christopher B.
,
Sandberg, Rickard
,
Jensen, Lars Juhl
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 922 KB
Your tags:
english, 2009
30
Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for Cell-Based Screening
Ljosa, Vebjorn
,
Carpenter, Anne E.
,
Lewitter, Fran
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 803 KB
Your tags:
english, 2009
31
Predicting Functional Alternative Splicing by Measuring RNA Selection Pressure from Multigenome Alignments
Lu, Hongchao
,
Lin, Lan
,
Sato, Seiko
,
Xing, Yi
,
Lee, Christopher J.
,
Li, Wen-Hsiung
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 982 KB
Your tags:
english, 2009
32
Power-Law Scaling in the Brain Surface Electric Potential
Miller, Kai J.
,
Sorensen, Larry B.
,
Ojemann, Jeffrey G.
,
den Nijs, Marcel
,
Sporns, Olaf
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 812 KB
Your tags:
english, 2009
33
Distributed Dynamical Computation in Neural Circuits with Propagating Coherent Activity Patterns
Gong, Pulin
,
van Leeuwen, Cees
,
Friston, Karl J.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 496 KB
Your tags:
english, 2009
34
Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks
Matias Rodrigues, João F.
,
Wagner, Andreas
,
Price, Nathan D.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 781 KB
Your tags:
english, 2009
35
Meta-analysis of Inter-species Liver Co-expression Networks Elucidates Traits Associated with Common Human Diseases
Wang, Kai
,
Narayanan, Manikandan
,
Zhong, Hua
,
Tompa, Martin
,
Schadt, Eric E.
,
Zhu, Jun
,
Ohler, Uwe
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 1.16 MB
Your tags:
english, 2009
36
Design Principles for Ligand-Sensing, Conformation-Switching Ribozymes
Chen, Xi
,
Ellington, Andrew D.
,
Walter, Nils
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 881 KB
Your tags:
english, 2009
37
A Stochastic Model for Microtubule Motors Describes the In Vivo Cytoplasmic Transport of Human Adenovirus
Gazzola, Mattia
,
Burckhardt, Christoph J.
,
Bayati, Basil
,
Engelke, Martin
,
Greber, Urs F.
,
Koumoutsakos, Petros
,
Sauro, Herbert M.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 290 KB
Your tags:
english, 2009
38
Rational Mutational Analysis of a Multidrug MFS Transporter CaMdr1p of Candida albicans by Employing a Membrane Environment Based Computational Approach
Kapoor, Khyati
,
Rehan, Mohd
,
Kaushiki, Ajeeta
,
Pasrija, Ritu
,
Lynn, Andrew M.
,
Prasad, Rajendra
,
Dunbrack, Roland
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 2.72 MB
Your tags:
english, 2009
39
Bayesian Integration and Non-Linear Feedback Control in a Full-Body Motor Task
Stevenson, Ian H.
,
Fernandes, Hugo L.
,
Vilares, Iris
,
Wei, Kunlin
,
Körding, Konrad P.
,
Friston, Karl J.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 696 KB
Your tags:
english, 2009
40
Bistability of Mitochondrial Respiration Underlies Paradoxical Reactive Oxygen Species Generation Induced by Anoxia
Selivanov, Vitaly A.
,
Votyakova, Tatyana V.
,
Zeak, Jennifer A.
,
Trucco, Massimo
,
Roca, Josep
,
Cascante, Marta
,
Budinger, G. R. Scott
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 578 KB
Your tags:
english, 2009
41
Model of Transcriptional Activation by MarA in Escherichia coli
Wall, Michael E.
,
Markowitz, David A.
,
Rosner, Judah L.
,
Martin, Robert G.
,
Stormo, Gary D.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 1.04 MB
Your tags:
english, 2009
42
Trade-off between Positive and Negative Design of Protein Stability: From Lattice Models to Real Proteins
Noivirt-Brik, Orly
,
Horovitz, Amnon
,
Unger, Ron
,
Onuchic, Jose
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 307 KB
Your tags:
english, 2009
43
Challenges Predicting Ligand-Receptor Interactions of Promiscuous Proteins: The Nuclear Receptor PXR
Ekins, Sean
,
Kortagere, Sandhya
,
Iyer, Manisha
,
Reschly, Erica J.
,
Lill, Markus A.
,
Redinbo, Matthew R.
,
Krasowski, Matthew D.
,
Briggs, James M.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 3.15 MB
Your tags:
english, 2009
44
Inferring Binding Energies from Selected Binding Sites
Zhao, Yue
,
Granas, David
,
Stormo, Gary D.
,
Workman, Christopher
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 328 KB
Your tags:
english, 2009
45
The Presence of VEGF Receptors on the Luminal Surface of Endothelial Cells Affects VEGF Distribution and VEGF Signaling
Stefanini, Marianne O.
,
Wu, Florence T. H.
,
Mac Gabhann, Feilim
,
Popel, Aleksander S.
,
Pries, Axel R.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 1.51 MB
Your tags:
english, 2009
46
Hyperbolic Planforms in Relation to Visual Edges and Textures Perception
Chossat, Pascal
,
Faugeras, Olivier
,
Friston, Karl J.
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 967 KB
Your tags:
english, 2009
47
A Multi-Component Model of the Developing Retinocollicular Pathway Incorporating Axonal and Synaptic Growth
Godfrey, Keith B.
,
Eglen, Stephen J.
,
Swindale, Nicholas V.
,
Sporns, Olaf
Journal:
PLoS Computational Biology
Year:
2009
Language:
english
File:
PDF, 1.34 MB
Your tags:
english, 2009
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