Volume 8; Issue 2

PLoS Computational Biology

Volume 8; Issue 2

1

Structural Consensus among Antibodies Defines the Antigen Binding Site

Kunik, Vered, Peters, Bjoern, Ofran, Yanay, Baker, Brian

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.89 MB

english, 2012

2

Stochastic De-repression of Rhodopsins in Single Photoreceptors of the Fly Retina

Sood, Pranidhi, Johnston, Robert J., Kussell, Edo, Shvartsman, Stanislav

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.50 MB

english, 2012

3

Using Functional Signatures to Identify Repositioned Drugs for Breast, Myelogenous Leukemia and Prostate Cancer

Shigemizu, Daichi, Hu, Zhenjun, Hung, Jui-Hung, Huang, Chia-Ling, Wang, Yajie, DeLisi, Charles, Altman, Russ B.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 307 KB

english, 2012

4

In silico Experimentation of Glioma Microenvironment Development and Anti-tumor Therapy

Wu, Yu, Lu, Yao, Chen, Weiqiang, Fu, Jianping, Fan, Rong, Tucker-Kellogg, Greg

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.42 MB

english, 2012

5

DOGS: Reaction-Driven de novo Design of Bioactive Compounds

Hartenfeller, Markus, Zettl, Heiko, Walter, Miriam, Rupp, Matthias, Reisen, Felix, Proschak, Ewgenij, Weggen, Sascha, Stark, Holger, Schneider, Gisbert, Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 832 KB

english, 2012

6

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

Zomorrodi, Ali R., Maranas, Costas D., Rao, Christopher V.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 760 KB

english, 2012

7

Joint Analysis of Multiple Metagenomic Samples

Baran, Yael, Halperin, Eran, Ponting, Chris P.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 512 KB

english, 2012

8

Minimal Size of Cell Assemblies Coordinated by Gamma Oscillations

Börgers, Christoph, Talei Franzesi, Giovanni, LeBeau, Fiona E. N., Boyden, Edward S., Kopell, Nancy J., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.03 MB

english, 2012

9

A Cell-based Computational Modeling Approach for Developing Site-Directed Molecular Probes

Yu, Jing-yu, Zheng, Nan, Mane, Gerta, Min, Kyoung Ah, Hinestroza, Juan P., Zhu, Huaning, Stringer, Kathleen A., Rosania, Gus R., Mac Gabhann, Feilim

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.01 MB

english, 2012

10

Use It and Improve It or Lose It: Interactions between Arm Function and Use in Humans Post-stroke

Hidaka, Yukikazu, Han, Cheol E., Wolf, Steven L., Winstein, Carolee J., Schweighofer, Nicolas, Diedrichsen, Jörn

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 574 KB

english, 2012

11

A Race between Tumor Immunoescape and Genome Maintenance Selects for Optimum Levels of (epi)genetic Instability

Iwami, Shingo, Haeno, Hiroshi, Michor, Franziska, Byrne, Helen M.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.57 MB

english, 2012

12

Subcellular Location of PKA Controls Striatal Plasticity: Stochastic Simulations in Spiny Dendrites

Oliveira, Rodrigo F., Kim, MyungSook, Blackwell, Kim T., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.11 MB

english, 2012

13

Comparison of Insertional RNA Editing in Myxomycetes

Chen, Cai, Frankhouser, David, Bundschuh, Ralf, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 670 KB

english, 2012

14

Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function

Quarta, Giulio, Sin, Ken, Schlick, Tamar, Gonzalez, Ruben

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.24 MB

english, 2012

15

Noise and Robustness in Phyllotaxis

Mirabet, Vincent, Besnard, Fabrice, Vernoux, Teva, Boudaoud, Arezki, Levine, Herbert

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.73 MB

english, 2012

16

Early Warning Signals for Critical Transitions: A Generalized Modeling Approach

Lade, Steven J., Gross, Thilo, Pascual, Mercedes

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 338 KB

english, 2012

17

Human Visual Search Does Not Maximize the Post-Saccadic Probability of Identifying Targets

Morvan, Camille, Maloney, Laurence T., Kording, Konrad P.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 762 KB

english, 2012

18

Novel Approach to Meta-Analysis of Microarray Datasets Reveals Muscle Remodeling-related Drug Targets and Biomarkers in Duchenne Muscular Dystrophy

Kotelnikova, Ekaterina, Shkrob, Maria A., Pyatnitskiy, Mikhail A., Ferlini, Alessandra, Daraselia, Nikolai, Altman, Russ B.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.15 MB

english, 2012

19

Control of Whole Heart Geometry by Intramyocardial Mechano-Feedback: A Model Study

Arts, Theo, Lumens, Joost, Kroon, Wilco, Delhaas, Tammo, McCulloch, Andrew D.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 908 KB

english, 2012

20

Developmental Maturation of Dynamic Causal Control Signals in Higher-Order Cognition: A Neurocognitive Network Model

Supekar, Kaustubh, Menon, Vinod, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.23 MB

english, 2012

21

Integrating Flux Balance Analysis into Kinetic Models to Decipher the Dynamic Metabolism of Shewanella oneidensis MR-1

Feng, Xueyang, Xu, You, Chen, Yixin, Tang, Yinjie J., Reed, Jennifer L.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.23 MB

english, 2012

22

Modeling Cortisol Dynamics in the Neuro-endocrine Axis Distinguishes Normal, Depression, and Post-traumatic Stress Disorder (PTSD) in Humans

Sriram, K., Rodriguez-Fernandez, Maria, Doyle, Francis J., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.11 MB

english, 2012

23

The Efficiency of the Human CD8+ T Cell Response: How Should We Quantify It, What Determines It, and Does It Matter?

Elemans, Marjet, Seich al Basatena, Nafisa-Katrin, Asquith, Becca, Antia, Rustom

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 368 KB

english, 2012

24

Paradoxical Evidence Integration in Rapid Decision Processes

Rüter, Johannes, Marcille, Nicolas, Sprekeler, Henning, Gerstner, Wulfram, Herzog, Michael H., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 482 KB

english, 2012

25

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

Thomas, Paul D., Wood, Valerie, Mungall, Christopher J., Lewis, Suzanna E., Blake, Judith A., Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 100 KB

english, 2012

26

Effects of Electrical and Structural Remodeling on Atrial Fibrillation Maintenance: A Simulation Study

Krogh-Madsen, Trine, Abbott, Geoffrey W., Christini, David J., McCulloch, Andrew D.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.18 MB

english, 2012

27

Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data

Treviño, Santiago, Sun, Yudong, Cooper, Tim F., Bassler, Kevin E., Miyano, Satoru

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.18 MB

english, 2012

28

The Role of Conserved Waters in Conformational Transitions of Q61H K-ras

Prakash, Priyanka, Sayyed-Ahmad, Abdallah, Gorfe, Alemayehu A., Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.18 MB

english, 2012

29

Positive Evolutionary Selection of an HD Motif on Alzheimer Precursor Protein Orthologues Suggests a Functional Role

Miklós, István, Zádori, Zoltán, Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 825 KB

english, 2012

30

Viral Proteins Acquired from a Host Converge to Simplified Domain Architectures

Rappoport, Nadav, Linial, Michal, Rost, Burkhard

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.48 MB

english, 2012

31

On the Effect of Thermodynamic Equilibrium on the Assembly Efficiency of Complex Multi-Layered Virus-Like Particles (VLP): the Case of Rotavirus VLP

Roldão, António, Mellado, Maria Candida M., Lima, J. C., Carrondo, Manuel J. T., Alves, Paula M., Oliveira, R., Jernigan, Robert L.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.21 MB

english, 2012

32

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

Khatri, Purvesh, Sirota, Marina, Butte, Atul J., Ouzounis, Christos A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 644 KB

english, 2012

33

Branch Mode Selection during Early Lung Development

Menshykau, Denis, Kraemer, Conradin, Iber, Dagmar, Crampin, Edmund J.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 3.22 MB

english, 2012

34

Multi-Scale Modeling of HIV Infection in vitro and APOBEC3G-Based Anti-Retroviral Therapy

Hosseini, Iraj, Mac Gabhann, Feilim, Müller, Viktor

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 3.39 MB

english, 2012