Volume 9; Issue 6

PLoS Computational Biology

Volume 9; Issue 6

1

Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress

Petelenz-Kurdziel, Elzbieta, Kuehn, Clemens, Nordlander, Bodil, Klein, Dagmara, Hong, Kuk-Ki, Jacobson, Therese, Dahl, Peter, Schaber, Jörg, Nielsen, Jens, Hohmann, Stefan, Klipp, Edda

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1010 KB

english, 2013

2

How the Dynamics and Structure of Sexual Contact Networks Shape Pathogen Phylogenies

Robinson, Katy, Fyson, Nick, Cohen, Ted, Fraser, Christophe, Colijn, Caroline, Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.18 MB

english, 2013

3

Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus

Nuccitelli, Annalisa, Rinaudo, C. Daniela, Brogioni, Barbara, Cozzi, Roberta, Ferrer-Navarro, Mario, Yero, Daniel, Telford, John L., Grandi, Guido, Daura, Xavier, Zacharias, Martin, Maione, Domenico,

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 7.83 MB

english, 2013

4

Mate Choice and the Origin of Menopause

Morton, Richard A., Stone, Jonathan R., Singh, Rama S., Tanaka, Mark M.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 788 KB

english, 2013

5

The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum

Harcombe, William R., Delaney, Nigel F., Leiby, Nicholas, Klitgord, Niels, Marx, Christopher J., Stelling, Jorg

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 610 KB

english, 2013

6

Constraint and Contingency in Multifunctional Gene Regulatory Circuits

Payne, Joshua L., Wagner, Andreas, Albert, Réka

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 495 KB

english, 2013

7

Exploring Volatile General Anesthetic Binding to a Closed Membrane-Bound Bacterial Voltage-Gated Sodium Channel via Computation

Raju, S. G., Barber, Annika F., LeBard, David N., Klein, Michael L., Carnevale, Vincenzo, Tajkhorshid, Emad

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.54 MB

english, 2013

8

Dual Delayed Feedback Provides Sensitivity and Robustness to the NF-κB Signaling Module

Longo, Diane M., Selimkhanov, Jangir, Kearns, Jeffrey D., Hasty, Jeff, Hoffmann, Alexander, Tsimring, Lev S., Shvartsman, Stanislav

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.12 MB

english, 2013

9

A Design Principle of Group-level Decision Making in Cell Populations

Fujimoto, Koichi, Sawai, Satoshi, Alber, Mark S.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.49 MB

english, 2013

10

Scrutinizing MHC-I Binding Peptides and Their Limits of Variation

Koch, Christian P., Perna, Anna M., Pillong, Max, Todoroff, Nickolay K., Wrede, Paul, Folkers, Gerd, Hiss, Jan A., Schneider, Gisbert, Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.26 MB

english, 2013

11

Modelling Co-Infection with Malaria and Lymphatic Filariasis

Slater, Hannah C., Gambhir, Manoj, Parham, Paul E., Michael, Edwin, Antia, Rustom

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.30 MB

english, 2013

12

A Forced Damped Oscillation Framework for Undulatory Swimming Provides New Insights into How Propulsion Arises in Active and Passive Swimming

Bhalla, Amneet Pal Singh, Griffith, Boyce E., Patankar, Neelesh A., Goldman, Daniel

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.22 MB

english, 2013

13

Dynamic Excitatory and Inhibitory Gain Modulation Can Produce Flexible, Robust and Optimal Decision-making

Niyogi, Ritwik K., Wong-Lin, KongFatt, Behrens, Tim

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.78 MB

english, 2013

14

Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links ATAD3B to Poor Survival in Breast Cancer

Ovaska, Kristian, Matarese, Filomena, Grote, Korbinian, Charapitsa, Iryna, Cervera, Alejandra, Liu, Chengyu, Reid, George, Seifert, Martin, Stunnenberg, Hendrik G., Hautaniemi, Sampsa, Tucker-Kellogg,

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 898 KB

english, 2013

15

Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach

Small, Meagan C., Lopes, Pedro, Andrade, Rodrigo B., MacKerell, Alexander D., Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.85 MB

english, 2013

16

International Society for Computational Biology Honors David Eisenberg with 2013 Accomplishment by a Senior Scientist Award

Fogg, Christiana N., Kovats, Diane E.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 944 KB

english, 2013

17

Emotional Valence and the Free-Energy Principle

Joffily, Mateus, Coricelli, Giorgio, Behrens, Tim

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.30 MB

english, 2013

18

Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins

Handfield, Louis-François, Chong, Yolanda T., Simmons, Jibril, Andrews, Brenda J., Moses, Alan M., Murphy, Robert F.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 6.84 MB

english, 2013

19

Theta Coordinated Error-Driven Learning in the Hippocampus

Ketz, Nicholas, Morkonda, Srinimisha G., O'Reilly, Randall C., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 911 KB

english, 2013

20

Towards Systematic Discovery of Signaling Networks in Budding Yeast Filamentous Growth Stress Response Using Interventional Phosphorylation Data

Zhang, Yan, Kweon, Hye Kyong, Shively, Christian, Kumar, Anuj, Andrews, Philip C., Orengo, Christine A.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.58 MB

english, 2013

21

Patterns of Proliferative Activity in the Colonic Crypt Determine Crypt Stability and Rates of Somatic Evolution

Zhao, Rui, Michor, Franziska, Beerenwinkel, Niko

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.77 MB

english, 2013

22

PUMA: A Unified Framework for Penalized Multiple Regression Analysis of GWAS Data

Hoffman, Gabriel E., Logsdon, Benjamin A., Mezey, Jason G., Brem, Rachel B.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 770 KB

english, 2013

23

Gag-Pol Processing during HIV-1 Virion Maturation: A Systems Biology Approach

Könnyű, Balázs, Sadiq, S. Kashif, Turányi, Tamás, Hírmondó, Rita, Müller, Barbara, Kräusslich, Hans-Georg, Coveney, Peter V., Müller, Viktor, Wilke, Claus O.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.28 MB

english, 2013

24

Neuronal Functional Connection Graphs among Multiple Areas of the Rat Somatosensory System during Spontaneous and Evoked Activities

Zippo, Antonio G., Storchi, Riccardo, Nencini, Sara, Caramenti, Gian Carlo, Valente, Maurizio, Biella, Gabriele Eliseo M., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.77 MB

english, 2013

25

Are V1 Simple Cells Optimized for Visual Occlusions? A Comparative Study

Bornschein, Jörg, Henniges, Marc, Lücke, Jörg, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.96 MB

english, 2013

26

Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803

Knoop, Henning, Gründel, Marianne, Zilliges, Yvonne, Lehmann, Robert, Hoffmann, Sabrina, Lockau, Wolfgang, Steuer, Ralf, Rao, Christopher V.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.34 MB

english, 2013

27

Combinatorial Clustering of Residue Position Subsets Predicts Inhibitor Affinity across the Human Kinome

Bryant, Drew H., Moll, Mark, Finn, Paul W., Kavraki, Lydia E., Singh, Mona

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 5.24 MB

english, 2013

28

Molecular Mechanisms in the Activation of Abscisic Acid Receptor PYR1

Dorosh, Lyudmyla, Kharenko, Olesya A., Rajagopalan, Nandhakishore, Loewen, Michele C., Stepanova, Maria, Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 7.39 MB

english, 2013

29

Leveraging Prior Information to Detect Causal Variants via Multi-Variant Regression

Long, Nanye, Dickson, Samuel P., Maia, Jessica M., Kim, Hee Shin, Zhu, Qianqian, Allen, Andrew S., Wasserman, Wyeth W.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 962 KB

english, 2013

30

Fibrin Networks Regulate Protein Transport during Thrombus Development

Kim, Oleg V., Xu, Zhiliang, Rosen, Elliot D., Alber, Mark S., McCulloch, Andrew D.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.08 MB

english, 2013

31

Cooperative Binding

Stefan, Melanie I., Le Novère, Nicolas, Wodak, Shoshana

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 631 KB

english, 2013

32

Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples

Riley, David R., Sieber, Karsten B., Robinson, Kelly M., White, James Robert, Ganesan, Ashwinkumar, Nourbakhsh, Syrus, Dunning Hotopp, Julie C., Eisen, Jonathan A.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.07 MB

english, 2013

33

Bioinformatics Goes to School—New Avenues for Teaching Contemporary Biology

Wood, Louisa, Gebhardt, Philipp, Lewitter, Fran

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 588 KB

english, 2013

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