Volume 6; Issue 1

PLoS Computational Biology

Volume 6; Issue 1

1

Associating Genes and Protein Complexes with Disease via Network Propagation

Vanunu, Oron, Magger, Oded, Ruppin, Eytan, Shlomi, Tomer, Sharan, Roded, Wasserman, Wyeth W.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 406 KB

english, 2010

2

SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models

Sircar, Aroop, Gray, Jeffrey J., Kortemme, Tanja

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 822 KB

english, 2010

3

FluTE, a Publicly Available Stochastic Influenza Epidemic Simulation Model

Chao, Dennis L., Halloran, M. Elizabeth, Obenchain, Valerie J., Longini, Ira M., McLean, Angela R.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 419 KB

english, 2010

4

A Reaction-Diffusion Model of ROS-Induced ROS Release in a Mitochondrial Network

Zhou, Lufang, Aon, Miguel A., Almas, Tabish, Cortassa, Sonia, Winslow, Raimond L., O'Rourke, Brian, Beard, Daniel A.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.25 MB

english, 2010

5

Network-Free Inference of Knockout Effects in Yeast

Peleg, Tal, Yosef, Nir, Ruppin, Eytan, Sharan, Roded, Ouzounis, Christos A.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 444 KB

english, 2010

6

An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer

Nibbe, Rod K., Koyutürk, Mehmet, Chance, Mark R., Price, Nathan D.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.02 MB

english, 2010

7

Identification of Crosstalk between Phosphoprotein Signaling Pathways in RAW 264.7 Macrophage Cells

Gupta, Shakti, Maurya, Mano Ram, Subramaniam, Shankar, Lauffenberger, Douglas

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.13 MB

english, 2010

8

How Synchronization Protects from Noise

Tabareau, Nicolas, Slotine, Jean-Jacques, Pham, Quang-Cuong, Breakspear, Michael

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 685 KB

english, 2010

9

Identification of Networks of Co-Occurring, Tumor-Related DNA Copy Number Changes Using a Genome-Wide Scoring Approach

Klijn, Christiaan, Bot, Jan, Adams, David J., Reinders, Marcel, Wessels, Lodewyk, Jonkers, Jos, Noble, William Stafford

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 3.05 MB

english, 2010

10

Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families

Röttig, Marc, Rausch, Christian, Kohlbacher, Oliver, Ponting, Chris P.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 431 KB

english, 2010

11

A Neurophysiologically Plausible Population Code Model for Feature Integration Explains Visual Crowding

van den Berg, Ronald, Roerdink, Jos B. T. M., Cornelissen, Frans W., Kording, Konrad P.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 907 KB

english, 2010

12

A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology

Durrant, Jacob D., Amaro, Rommie E., Xie, Lei, Urbaniak, Michael D., Ferguson, Michael A. J., Haapalainen, Antti, Chen, Zhijun, Di Guilmi, Anne Marie, Wunder, Frank, Bourne, Philip E., McCammon, J. An

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 152 KB

english, 2010

13

Optimizing Metapopulation Sustainability through a Checkerboard Strategy

Ben Zion, Yossi, Yaari, Gur, Shnerb, Nadav M., McCluskey, Connell

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 762 KB

english, 2010

14

Protein Interaction Networks—More Than Mere Modules

Pinkert, Stefan, Schultz, Jörg, Reichardt, Jörg, Domany, Eytan

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 2.21 MB

english, 2010

15

Live Coverage of Scientific Conferences Using Web Technologies

Lister, Allyson L., Datta, Ruchira S., Hofmann, Oliver, Krause, Roland, Kuhn, Michael, Roth, Bettina, Schneider, Reinhard, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 93 KB

english, 2010

16

Modeling Mitochondrial Bioenergetics with Integrated Volume Dynamics

Bazil, Jason N., Buzzard, Gregery T., Rundell, Ann E., Beard, Daniel A.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 707 KB

english, 2010

17

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

Burger, Lukas, van Nimwegen, Erik, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 748 KB

english, 2010

18

Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations

Seeliger, Daniel, de Groot, Bert L., Lengauer, Thomas

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 2.36 MB

english, 2010

19

Knots: Attractive Places with High Path Tortuosity in Mouse Open Field Exploration

Dvorkin, Anna, Szechtman, Henry, Golani, Ilan, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.70 MB

english, 2010

20

A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules

Zhang, Wei, Zhu, Jun, Schadt, Eric E., Liu, Jun S., Stormo, Gary D.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 673 KB

english, 2010

21

Quantitative Modeling of GRK-Mediated β2AR Regulation

Vayttaden, Sharat J., Friedman, Jacqueline, Tran, Tuan M., Rich, Thomas C., Dessauer, Carmen W., Clark, Richard B., Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 937 KB

english, 2010

22

Modeling Magnification and Anisotropy in the Primate Foveal Confluence

Schira, Mark M., Tyler, Christopher W., Spehar, Branka, Breakspear, Michael, Deco, Gustavo

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 796 KB

english, 2010

23

Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances

Kim, Jaebum, Cunningham, Ryan, James, Brian, Wyder, Stefan, Gibson, Joshua D., Niehuis, Oliver, Zdobnov, Evgeny M., Robertson, Hugh M., Robinson, Gene E., Werren, John H., Sinha, Saurabh, Wasserman, W

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 899 KB

english, 2010

24

Axonal Velocity Distributions in Neural Field Equations

Bojak, Ingo, Liley, David T. J., Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1017 KB

english, 2010

25

Recombination Rate and Selection Strength in HIV Intra-patient Evolution

Neher, Richard A., Leitner, Thomas, Fraser, Christophe

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 331 KB

english, 2010

26

Blurring of High-Resolution Data Shows that the Effect of Intrinsic Nucleosome Occupancy on Transcription Factor Binding is Mostly Regional, Not Local

Goh, Wee Siong, Orlov, Yuriy, Li, Jingmei, Clarke, Neil D., Segal, Eran

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 761 KB

english, 2010

27

Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009

Lister, Allyson L., Datta, Ruchira S., Hofmann, Oliver, Krause, Roland, Kuhn, Michael, Roth, Bettina, Schneider, Reinhard, Troyanskaya, Olga

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 310 KB

english, 2010

28

Acute Effects of Sex Steroid Hormones on Susceptibility to Cardiac Arrhythmias: A Simulation Study

Yang, Pei-Chi, Kurokawa, Junko, Furukawa, Tetsushi, Clancy, Colleen E., McCulloch, Andrew D.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 795 KB

english, 2010

29

Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains

Daidone, Isabella, Neuweiler, Hannes, Doose, Sören, Sauer, Markus, Smith, Jeremy C., Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 879 KB

english, 2010

30

Automatic Assignment of EC Numbers

Egelhofer, Volker, Schomburg, Ida, Schomburg, Dietmar, Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 588 KB

english, 2010

31

Getting Started in Structural Phylogenomics

Sjölander, Kimmen, Troyanskaya, Olga

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 110 KB

english, 2010

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