Volume 6; Issue 2

PLoS Computational Biology

Volume 6; Issue 2

1

Design of a Trichromatic Cone Array

Garrigan, Patrick, Ratliff, Charles P., Klein, Jennifer M., Sterling, Peter, Brainard, David H., Balasubramanian, Vijay, Latham, Peter E.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.36 MB

english, 2010

2

Self versus Environment Motion in Postural Control

Dokka, Kalpana, Kenyon, Robert V., Keshner, Emily A., Kording, Konrad P., Diedrichsen, Jörn

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 265 KB

english, 2010

3

A Review of 2009 for PLoS Computational Biology

Dickin, Rosemary, Marden, Cecy, Nancarrow, Catherine, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 65 KB

english, 2010

4

A Bayesian Approach to Quantifying the Effects of Mass Poultry Vaccination upon the Spatial and Temporal Dynamics of H5N1 in Northern Vietnam

Walker, Patrick G. T., Cauchemez, Simon, Métras, Raphaëlle, Dung, Do Huu, Pfeiffer, Dirk, Ghani, Azra C., Meyers, Lauren Ancel

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.34 MB

english, 2010

5

A Primer on Metagenomics

Wooley, John C., Godzik, Adam, Friedberg, Iddo, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 362 KB

english, 2010

6

Explicit Kinetic Heterogeneity: Mathematical Models for Interpretation of Deuterium Labeling of Heterogeneous Cell Populations

Ganusov, Vitaly V., Borghans, José A. M., De Boer, Rob J., McLean, Angela R.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 539 KB

english, 2010

7

Interpreting Metabolomic Profiles using Unbiased Pathway Models

Deo, Rahul C., Hunter, Luke, Lewis, Gregory D., Pare, Guillaume, Vasan, Ramachandran S., Chasman, Daniel, Wang, Thomas J., Gerszten, Robert E., Roth, Frederick P., Ideker, Trey

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.02 MB

english, 2010

8

Numerical Modelling Of The V-J Combinations Of The T Cell Receptor TRA/TRD Locus

Thuderoz, Florence, Simonet, Maria-Ana, Hansen, Olivier, Pasqual, Nicolas, Dariz, Aurélie, Baum, Thierry Pascal, Hierle, Vivien, Demongeot, Jacques, Marche, Patrice Noël, Jouvin-Marche, Evelyne, De Bo

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.34 MB

english, 2010

9

Identifying the Rules of Engagement Enabling Leukocyte Rolling, Activation, and Adhesion

Tang, Jonathan, Hunt, C. Anthony, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 823 KB

english, 2010

10

Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable α-Lytic Protease

Salimi, Neema L., Ho, Bosco, Agard, David A., Pettitt, B. Montgomery

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 2.89 MB

english, 2010

11

In Silico Analysis of the Apolipoprotein E and the Amyloid β Peptide Interaction: Misfolding Induced by Frustration of the Salt Bridge Network

Luo, Jinghui, Maréchal, Jean-Didier, Wärmländer, Sebastian, Gräslund, Astrid, Perálvarez-Marín, Alex, Shakhnovich, Eugene I.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.11 MB

english, 2010

12

How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens

Markowetz, Florian, Lewitter, Fran

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 324 KB

english, 2010

13

Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets

Suthram, Silpa, Dudley, Joel T., Chiang, Annie P., Chen, Rong, Hastie, Trevor J., Butte, Atul J., Ofran, Yanay

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 803 KB

english, 2010

14

A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes

Gu, Wanjun, Zhou, Tong, Wilke, Claus O., Snel, Berend

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 358 KB

english, 2010

15

A Kinetic Model of Dopamine- and Calcium-Dependent Striatal Synaptic Plasticity

Nakano, Takashi, Doi, Tomokazu, Yoshimoto, Junichiro, Doya, Kenji, Gutkin, Boris S.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 946 KB

english, 2010

16

Adaptable Functionality of Transcriptional Feedback in Bacterial Two-Component Systems

Ray, J. Christian J., Igoshin, Oleg A., Goulian, Mark

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 919 KB

english, 2010

17

Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture

Han, Ju, Chang, Hang, Giricz, Orsi, Lee, Genee Y., Baehner, Frederick L., Gray, Joe W., Bissell, Mina J., Kenny, Paraic A., Parvin, Bahram, Ohler, Uwe

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.41 MB

english, 2010

18

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species

Freilich, Shiri, Kreimer, Anat, Borenstein, Elhanan, Gophna, Uri, Sharan, Roded, Ruppin, Eytan, Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 630 KB

english, 2010

19

Amplification of Asynchronous Inhibition-Mediated Synchronization by Feedback in Recurrent Networks

Marella, Sashi, Ermentrout, Bard, Gutkin, Boris S.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.45 MB

english, 2010

20

Conditions for the Evolution of Gene Clusters in Bacterial Genomes

Ballouz, Sara, Francis, Andrew R., Lan, Ruiting, Tanaka, Mark M., Eisen, Jonathan A.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 592 KB

english, 2010

21

Ten Simple Rules for Organizing a Virtual Conference—Anywhere

Gichora, Nelson N., Fatumo, Segun A., Ngara, Mtakai V., Chelbat, Noura, Ramdayal, Kavisha, Opap, Kenneth B., Siwo, Geoffrey H., Adebiyi, Marion O., El Gonnouni, Amina, Zofou, Denis, Maurady, Amal A. M

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 82 KB

english, 2010

22

A Variant of TNFR2-Fc Fusion Protein Exhibits Improved Efficacy in Treating Experimental Rheumatoid Arthritis

Yang, Tong, Wang, Zheng, Wu, Fang, Tan, Jingwei, Shen, Yijun, Li, Erguang, Dai, Jingzhi, Shen, Ronghai, Li, Gang, Wu, Jinsong, Wang, Luochun, Wang, Haibo, Liu, Yanjun, Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 3.21 MB

english, 2010

23

Will Widgets and Semantic Tagging Change Computational Biology?

Bourne, Philip E., Beran, Bojan, Bi, Chunxiao, Bluhm, Wolfgang, Dunbrack, Roland, Prlić, Andreas, Quinn, Greg, Rose, Peter, Shah, Raship, Tao, Wendy, Weitzner, Brian, Yukich, Ben, Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 432 KB

english, 2010

24

Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization

Junier, Ivan, Martin, Olivier, Képès, François, Margalit, Hanah

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 986 KB

english, 2010

25

Stochastic Model of Integrin-Mediated Signaling and Adhesion Dynamics at the Leading Edges of Migrating Cells

Cirit, Murat, Krajcovic, Matej, Choi, Colin K., Welf, Erik S., Horwitz, Alan F., Haugh, Jason M., Asthagiri, Anand R.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.60 MB

english, 2010

26

Predicted Functions of MdmX in Fine-Tuning the Response of p53 to DNA Damage

Kim, Sohyoung, Aladjem, Mirit I., McFadden, Geoffrey B., Kohn, Kurt W., Kitano, Hiroaki

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 2.28 MB

english, 2010

27

The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures

Davis, Fred P., Sali, Andrej, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 850 KB

english, 2010

28

Minimization of Biosynthetic Costs in Adaptive Gene Expression Responses of Yeast to Environmental Changes

Vilaprinyo, Ester, Alves, Rui, Sorribas, Albert, Price, Nathan D.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.27 MB

english, 2010

29

Temporal Sensitivity of Protein Kinase A Activation in Late-Phase Long Term Potentiation

Kim, MyungSook, Huang, Ted, Abel, Ted, Blackwell, Kim T., Nowotny, Thomas

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.03 MB

english, 2010

30

Characterizing Dynamic Changes in the Human Blood Transcriptional Network

Zhu, Jun, Chen, Yanqing, Leonardson, Amy S., Wang, Kai, Lamb, John R., Emilsson, Valur, Schadt, Eric E., Miyano, Satoru

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 758 KB

english, 2010

31

Computational Complementation: A Modelling Approach to Study Signalling Mechanisms during Legume Autoregulation of Nodulation

Han, Liqi, Hanan, Jim, Gresshoff, Peter M., Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 631 KB

english, 2010

32

Spatial Simulations of Myxobacterial Development

Holmes, Antony B., Kalvala, Sara, Whitworth, David E., Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.15 MB

english, 2010

33

A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II

Pepke, Shirley, Kinzer-Ursem, Tamara, Mihalas, Stefan, Kennedy, Mary B., Ranganathan, Rama

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.31 MB

english, 2010

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