Volume 7; Issue 1

PLoS Computational Biology

Volume 7; Issue 1

1

From Spiking Neuron Models to Linear-Nonlinear Models

Ostojic, Srdjan, Brunel, Nicolas, Latham, Peter E.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.77 MB

english, 2011

2

Practical Measures of Integrated Information for Time-Series Data

Barrett, Adam B., Seth, Anil K., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 613 KB

english, 2011

3

Measuring the Evolutionary Rewiring of Biological Networks

Shou, Chong, Bhardwaj, Nitin, Lam, Hugo Y. K., Yan, Koon-Kiu, Kim, Philip M., Snyder, Michael, Gerstein, Mark B., Snel, Berend

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 682 KB

english, 2011

4

Relationships between Gene Expression and Brain Wiring in the Adult Rodent Brain

French, Leon, Pavlidis, Paul, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.87 MB

english, 2011

5

Theoretical Analysis of the Stress Induced B-Z Transition in Superhelical DNA

Zhabinskaya, Dina, Benham, Craig J., Dokholyan, Nikolay V.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 713 KB

english, 2011

6

A Computational and Experimental Study of the Regulatory Mechanisms of the Complement System

Liu, Bing, Zhang, Jing, Tan, Pei Yi, Hsu, David, Blom, Anna M., Leong, Benjamin, Sethi, Sunil, Ho, Bow, Ding, Jeak Ling, Thiagarajan, P. S., Antia, Rustom

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 899 KB

english, 2011

7

Integrative Features of the Yeast Phosphoproteome and Protein–Protein Interaction Map

Yachie, Nozomu, Saito, Rintaro, Sugiyama, Naoyuki, Tomita, Masaru, Ishihama, Yasushi, Ofran, Yanay

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 513 KB

english, 2011

8

A Novel Approach to Pharmacodynamic Assessment of Antimicrobial Agents: New Insights to Dosing Regimen Design

Tam, Vincent H., Nikolaou, Michael, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 378 KB

english, 2011

9

A Comprehensive Model of the Spatio-Temporal Stem Cell and Tissue Organisation in the Intestinal Crypt

Buske, Peter, Galle, Jörg, Barker, Nick, Aust, Gabriela, Clevers, Hans, Loeffler, Markus, Lauffenburger, Douglas

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.02 MB

english, 2011

10

Using Transcription Modules to Identify Expression Clusters Perturbed in Williams-Beuren Syndrome

Henrichsen, Charlotte N., Csárdi, Gábor, Zabot, Marie-Thérèse, Fusco, Carmela, Bergmann, Sven, Merla, Giuseppe, Reymond, Alexandre, Shamir, Ron

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.16 MB

english, 2011

11

Risk, Unexpected Uncertainty, and Estimation Uncertainty: Bayesian Learning in Unstable Settings

Payzan-LeNestour, Elise, Bossaerts, Peter, Behrens, Tim

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 773 KB

english, 2011

12

Thermodynamic Stability of Histone H3 Is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation

Ramachandran, Srinivas, Vogel, Lisa, Strahl, Brian D., Dokholyan, Nikolay V., Shakhnovich, Eugene I.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 431 KB

english, 2011

13

Decrypting the Sequence of Structural Events during the Gating Transition of Pentameric Ligand-Gated Ion Channels Based on an Interpolated Elastic Network Model

Zheng, Wenjun, Auerbach, Anthony, Bonneau, Richard

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 567 KB

english, 2011

14

Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding

Melvin, Iain, Weston, Jason, Noble, William Stafford, Leslie, Christina, Levitt, Michael

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.04 MB

english, 2011

15

Predicting Novel Binding Modes of Agonists to β Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations

Vanni, Stefano, Neri, Marilisa, Tavernelli, Ivano, Rothlisberger, Ursula, Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.64 MB

english, 2011

16

PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data

Sharpton, Thomas J., Riesenfeld, Samantha J., Kembel, Steven W., Ladau, Joshua, O'Dwyer, James P., Green, Jessica L., Eisen, Jonathan A., Pollard, Katherine S., Béjà, Oded

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 779 KB

english, 2011

17

Impact of Sarcoplasmic Reticulum Calcium Release on Calcium Dynamics and Action Potential Morphology in Human Atrial Myocytes: A Computational Study

Koivumäki, Jussi T., Korhonen, Topi, Tavi, Pasi, McCulloch, Andrew D.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.32 MB

english, 2011

18

A Review of 2010 for PLoS Computational Biology

Dickin, Rosemary, Marden, Cecy, Collings, Andrew M., Nussinov, Ruth, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 70 KB

english, 2011

19

Neural Development Features: Spatio-Temporal Development of the Caenorhabditis elegans Neuronal Network

Varier, Sreedevi, Kaiser, Marcus, Friston, Karl J.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 497 KB

english, 2011

20

Is My Network Module Preserved and Reproducible?

Langfelder, Peter, Luo, Rui, Oldham, Michael C., Horvath, Steve, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.20 MB

english, 2011

21

Estimation of Parent Specific DNA Copy Number in Tumors using High-Density Genotyping Arrays

Chen, Hao, Xing, Haipeng, Zhang, Nancy R., Markel, Scott

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.62 MB

english, 2011

22

Erratic Flu Vaccination Emerges from Short-Sighted Behavior in Contact Networks

Cornforth, Daniel M., Reluga, Timothy C., Shim, Eunha, Bauch, Chris T., Galvani, Alison P., Meyers, Lauren Ancel, Salathé, Marcel

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 574 KB

english, 2011

23

The Role of Additive Neurogenesis and Synaptic Plasticity in a Hippocampal Memory Model with Grid-Cell Like Input

Appleby, Peter A., Kempermann, Gerd, Wiskott, Laurenz, Morrison, Abigail

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.31 MB

english, 2011

24

Protrusive Push versus Enveloping Embrace: Computational Model of Phagocytosis Predicts Key Regulatory Role of Cytoskeletal Membrane Anchors

Herant, Marc, Lee, Cheng-Yuk, Dembo, Micah, Heinrich, Volkmar, McCulloch, Andrew D.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 275 KB

english, 2011

25

Benchmarking Ontologies: Bigger or Better?

Yao, Lixia, Divoli, Anna, Mayzus, Ilya, Evans, James A., Rzhetsky, Andrey, Cohen, K. Bretonnel

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.32 MB

english, 2011

26

Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia

Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 68 KB

english, 2011