Volume 5; Issue 3

PLoS Computational Biology

Volume 5; Issue 3

1

Broadband Criticality of Human Brain Network Synchronization

Kitzbichler, Manfred G., Smith, Marie L., Christensen, Søren R., Bullmore, Ed, Behrens, Tim

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.83 MB

english, 2009

2

The Modulation Transfer Function for Speech Intelligibility

Elliott, Taffeta M., Theunissen, Frédéric E., Friston, Karl J.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 810 KB

english, 2009

3

Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics

Grant, Barry J., Gorfe, Alemayehu A., McCammon, J. Andrew, Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 744 KB

english, 2009

4

Steady-State Kinetic Modeling Constrains Cellular Resting States and Dynamic Behavior

Purvis, Jeremy E., Radhakrishnan, Ravi, Diamond, Scott L., Rao, Christopher

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 950 KB

english, 2009

5

Estimation of Thalamocortical and Intracortical Network Models from Joint Thalamic Single-Electrode and Cortical Laminar-Electrode Recordings in the Rat Barrel System

Blomquist, Patrick, Devor, Anna, Indahl, Ulf G., Ulbert, Istvan, Einevoll, Gaute T., Dale, Anders M., Friston, Karl J.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.47 MB

english, 2009

6

Cortical Factor Feedback Model for Cellular Locomotion and Cytofission

Nishimura, Shin I., Ueda, Masahiro, Sasai, Masaki, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 732 KB

english, 2009

7

Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors

Manu,, Surkova, Svetlana, Spirov, Alexander V., Gursky, Vitaly V., Janssens, Hilde, Kim, Ah-Ram, Radulescu, Ovidiu, Vanario-Alonso, Carlos E., Sharp, David H., Samsonova, Maria, Reinitz, John, Shvart

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.30 MB

english, 2009

8

Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis

Hibbs, Matthew A., Myers, Chad L., Huttenhower, Curtis, Hess, David C., Li, Kai, Caudy, Amy A., Troyanskaya, Olga G., Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 991 KB

english, 2009

9

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

Kumar, Vinay Satish, Maranas, Costas D., Ouzounis, Christos A.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 489 KB

english, 2009

10

Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors in Yeast

Ye, Chun, Galbraith, Simon J., Liao, James C., Eskin, Eleazar, Crampin, Edmund J.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 846 KB

english, 2009

11

A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale

Bohland, Jason W., Wu, Caizhi, Barbas, Helen, Bokil, Hemant, Bota, Mihail, Breiter, Hans C., Cline, Hollis T., Doyle, John C., Freed, Peter J., Greenspan, Ralph J., Haber, Suzanne N., Hawrylycz, Micha

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 638 KB

english, 2009

12

Robust Detection and Genotyping of Single Feature Polymorphisms from Gene Expression Data

Wang, Minghui, Hu, Xiaohua, Li, Gang, Leach, Lindsey J., Potokina, Elena, Druka, Arnis, Waugh, Robbie, Kearsey, Michael J., Luo, Zewei, Stormo, Gary D.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 695 KB

english, 2009

13

Mechanical Network in Titin Immunoglobulin from Force Distribution Analysis

Stacklies, Wolfram, Vega, M. Cristina, Wilmanns, Matthias, Gräter, Frauke, Ranganathan, Rama

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 538 KB

english, 2009

14

“I Look in Your Eyes, Honey”: Internal Face Features Induce Spatial Frequency Preference for Human Face Processing

Keil, Matthias S., Friston, Karl J.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 2.66 MB

english, 2009

15

Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery

Schwartz, Schraga, Gal-Mark, Nurit, Kfir, Nir, Oren, Ram, Kim, Eddo, Ast, Gil, Guigó, Roderic

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 848 KB

english, 2009

16

Intrinsic Disorder in Protein Interactions: Insights From a Comprehensive Structural Analysis

Fong, Jessica H., Shoemaker, Benjamin A., Garbuzynskiy, Sergiy O., Lobanov, Michail Y., Galzitskaya, Oxana V., Panchenko, Anna R., Dunker, Keith

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.18 MB

english, 2009

17

Understanding Pitch Perception as a Hierarchical Process with Top-Down Modulation

Balaguer-Ballester, Emili, Clark, Nicholas R., Coath, Martin, Krumbholz, Katrin, Denham, Susan L., Friston, Karl J.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.03 MB

english, 2009

18

Robustness in Glyoxylate Bypass Regulation

Shinar, Guy, Rabinowitz, Joshua D., Alon, Uri, Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 163 KB

english, 2009

19

Detection of Alpha-Rod Protein Repeats Using a Neural Network and Application to Huntingtin

Palidwor, Gareth A., Shcherbinin, Sergey, Huska, Matthew R., Rasko, Tamas, Stelzl, Ulrich, Arumughan, Anup, Foulle, Raphaele, Porras, Pablo, Sanchez-Pulido, Luis, Wanker, Erich E., Andrade-Navarro, Mi

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 602 KB

english, 2009

20

Timing the Emergence of Resistance to Anti-HIV Drugs with Large Genetic Barriers

Arora, Pankhuri, Dixit, Narendra M., Fraser, Christophe

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 432 KB

english, 2009

21

Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations

Leone, Vanessa, Lattanzi, Gianluca, Molteni, Carla, Carloni, Paolo, Pettitt, B. Montgomery

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.59 MB

english, 2009

22

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization

Thiele, Ines, Jamshidi, Neema, Fleming, Ronan M. T., Palsson, Bernhard Ø., Ouzounis, Christos A.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.59 MB

english, 2009

23

Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter

Alexandrov, Boian S., Gelev, Vladimir, Yoo, Sang Wook, Bishop, Alan R., Rasmussen, Kim Ø., Usheva, Anny, Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.92 MB

english, 2009

24

Sm/Lsm Genes Provide a Glimpse into the Early Evolution of the Spliceosome

Veretnik, Stella, Wills, Christopher, Youkharibache, Philippe, Valas, Ruben E., Bourne, Philip E., Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.40 MB

english, 2009

25

Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments

Westesson, Oscar, Holmes, Ian, Regev, Aviv

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.12 MB

english, 2009

26

On the Growth of Scientific Knowledge: Yeast Biology as a Case Study

He, Xionglei, Zhang, Jianzhi, Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 870 KB

english, 2009

27

Computational Model of the Insect Pheromone Transduction Cascade

Gu, Yuqiao, Lucas, Philippe, Rospars, Jean-Pierre, Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.55 MB

english, 2009

28

A Systems Approach Uncovers Restrictions for Signal Interactions Regulating Genome-wide Responses to Nutritional Cues in Arabidopsis

Krouk, Gabriel, Tranchina, Daniel, Lejay, Laurence, Cruikshank, Alexis A., Shasha, Dennis, Coruzzi, Gloria M., Gutiérrez, Rodrigo A., Ranganathan, Rama

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 724 KB

english, 2009

29

T-Cell Epitope Prediction: Rescaling Can Mask Biological Variation between MHC Molecules

MacNamara, Aidan, Kadolsky, Ulrich, Bangham, Charles R. M., Asquith, Becca, De Boer, Rob J.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 308 KB

english, 2009

30

Positional Information Generated by Spatially Distributed Signaling Cascades

Muñoz-García, Javier, Neufeld, Zoltan, Kholodenko, Boris N., Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.02 MB

english, 2009

31

BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis

Bryan, Allen W., Menke, Matthew, Cowen, Lenore J., Lindquist, Susan L., Berger, Bonnie, Dunbrack, Roland

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 981 KB

english, 2009

32

Accurate Prediction of Peptide Binding Sites on Protein Surfaces

Petsalaki, Evangelia, Stark, Alexander, García-Urdiales, Eduardo, Russell, Robert B., Rost, Burkhard

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 467 KB

english, 2009

33

From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions

Gao, Mu, Skolnick, Jeffrey, Vakser, Ilya

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 906 KB

english, 2009

34

Biomedical Discovery Acceleration, with Applications to Craniofacial Development

Leach, Sonia M., Tipney, Hannah, Feng, Weiguo, Baumgartner, William A., Kasliwal, Priyanka, Schuyler, Ronald P., Williams, Trevor, Spritz, Richard A., Hunter, Lawrence, Miyano, Satoru

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.67 MB

english, 2009

35

Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy

Bahrami, Arash, Assadi, Amir H., Markley, John L., Eghbalnia, Hamid R., Cowburn, David

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.06 MB

english, 2009

36

Quantifying Global Tolerance of Biochemical Systems: Design Implications for Moiety-Transfer Cycles

Coelho, Pedro M. B. M., Salvador, Armindo, Savageau, Michael A., Stormo, Gary D.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 299 KB

english, 2009

37

Hypertrophy and/or Hyperplasia: Dynamics of Adipose Tissue Growth

Jo, Junghyo, Gavrilova, Oksana, Pack, Stephanie, Jou, William, Mullen, Shawn, Sumner, Anne E., Cushman, Samuel W., Periwal, Vipul, Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 502 KB

english, 2009

38

Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures

Pascual-García, Alberto, Abia, David, Ortiz, Ángel R., Bastolla, Ugo, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.26 MB

english, 2009

39

Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution

He, Xin, Ling, Xu, Sinha, Saurabh, Wasserman, Wyeth W.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 661 KB

english, 2009

40

Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer

Morra, Giulia, Verkhivker, Gennady, Colombo, Giorgio, Jacobson, Matthew P.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.93 MB

english, 2009

41

Spontaneous Local Gamma Oscillation Selectively Enhances Neural Network Responsiveness

Paik, Se-Bum, Kumar, Tribhawan, Glaser, Donald A., Friston, Karl J.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 708 KB

english, 2009

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