Volume 5; Issue 7

PLoS Computational Biology

Volume 5; Issue 7

1

Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis

Kinnings, Sarah L., Liu, Nina, Buchmeier, Nancy, Tonge, Peter J., Xie, Lei, Bourne, Philip E., Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 264 KB

english, 2009

2

Getting Started in Text Mining: Part Two

Rzhetsky, Andrey, Seringhaus, Michael, Gerstein, Mark B., Troyanskaya, Olga G.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 205 KB

english, 2009

3

Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations

Allen, Lucy R., Krivov, Sergei V., Paci, Emanuele, Dokholyan, Nikolay V.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 691 KB

english, 2009

4

A Compact Representation of Drawing Movements with Sequences of Parabolic Primitives

Polyakov, Felix, Drori, Rotem, Ben-Shaul, Yoram, Abeles, Moshe, Flash, Tamar, Aertsen, Ad

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.91 MB

english, 2009

5

Power Efficiency of Outer Hair Cell Somatic Electromotility

Rabbitt, Richard D., Clifford, Sarah, Breneman, Kathryn D., Farrell, Brenda, Brownell, William E., Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 608 KB

english, 2009

6

PoreWalker: A Novel Tool for the Identification and Characterization of Channels in Transmembrane Proteins from Their Three-Dimensional Structure

Pellegrini-Calace, Marialuisa, Maiwald, Tim, Thornton, Janet M., Lengauer, Thomas

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.70 MB

english, 2009

7

Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants

Du, Jiang, Bjornson, Robert D., Zhang, Zhengdong D., Kong, Yong, Snyder, Michael, Gerstein, Mark B., Noble, William Stafford

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.16 MB

english, 2009

8

Predicting the Distribution of Spiral Waves from Cell Properties in a Developmental-Path Model of Dictyostelium Pattern Formation

Geberth, Daniel, Hütt, Marc-Thorsten, Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 744 KB

english, 2009

9

Small RNAs Originated from Pseudogenes: cis- or trans-Acting?

Guo, Xingyi, Zhang, Zhaolei, Gerstein, Mark B., Zheng, Deyou, Zhang, Weixiong

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.06 MB

english, 2009

10

Dynamic Modeling of Vaccinating Behavior as a Function of Individual Beliefs

Coelho, Flávio Codeço, Codeço, Claudia T., Antia, Rustom

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 853 KB

english, 2009

11

Movement Timing and Invariance Arise from Several Geometries

Bennequin, Daniel, Fuchs, Ronit, Berthoz, Alain, Flash, Tamar, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.72 MB

english, 2009

12

What a Plant Sounds Like: The Statistics of Vegetation Echoes as Received by Echolocating Bats

Yovel, Yossi, Stilz, Peter, Franz, Matthias O., Boonman, Arjan, Schnitzler, Hans-Ulrich, Friston, Karl J.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 842 KB

english, 2009

13

Bistable Perception Modeled as Competing Stochastic Integrations at Two Levels

Gigante, Guido, Mattia, Maurizio, Braun, Jochen, Del Giudice, Paolo, Friston, Karl J.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 673 KB

english, 2009

14

The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species

Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 408 KB

english, 2009

15

An Experimental and Computational Study of the Effect of ActA Polarity on the Speed of Listeria monocytogenes Actin-based Motility

Rafelski, Susanne M., Alberts, Jonathan B., Odell, Garrett M., Goodson, Holly

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 973 KB

english, 2009

16

The Natural Statistics of Audiovisual Speech

Chandrasekaran, Chandramouli, Trubanova, Andrea, Stillittano, Sébastien, Caplier, Alice, Ghazanfar, Asif A., Friston, Karl J.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.91 MB

english, 2009

17

A Neural Computational Model of Incentive Salience

Zhang, Jun, Berridge, Kent C., Tindell, Amy J., Smith, Kyle S., Aldridge, J. Wayne, Friston, Karl J.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 558 KB

english, 2009

18

Harvesting Candidate Genes Responsible for Serious Adverse Drug Reactions from a Chemical-Protein Interactome

Yang, Lun, Chen, Jian, He, Lin, Altman, Russ B.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.25 MB

english, 2009

19

Semantic Similarity in Biomedical Ontologies

Pesquita, Catia, Faria, Daniel, Falcão, André O., Lord, Phillip, Couto, Francisco M., Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 278 KB

english, 2009

20

Identification of a Kinase Profile that Predicts Chromosome Damage Induced by Small Molecule Kinase Inhibitors

Olaharski, Andrew J., Gonzaludo, Nina, Bitter, Hans, Goldstein, David, Kirchner, Stephan, Uppal, Hirdesh, Kolaja, Kyle, Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 500 KB

english, 2009

21

Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation

Guvench, Olgun, MacKerell, Alexander D., Jacobson, Matthew P.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 428 KB

english, 2009

22

Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts

Li, Jiao, Zhu, Xiaoyan, Chen, Jake Yue, Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 757 KB

english, 2009

23

Computational Analysis of Viscoelastic Properties of Crosslinked Actin Networks

Kim, Taeyoon, Hwang, Wonmuk, Lee, Hyungsuk, Kamm, Roger D., Fletcher, Daniel A.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 994 KB

english, 2009

24

Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View

Pan, Yongping, Nussinov, Ruth, Ohler, Uwe

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 694 KB

english, 2009

25

A Three Species Model to Simulate Application of Hyperbaric Oxygen Therapy to Chronic Wounds

Flegg, Jennifer A., McElwain, Donald L. S., Byrne, Helen M., Turner, Ian W., Gaffney, Eamonn

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 351 KB

english, 2009

26

Investigating the Conformational Stability of Prion Strains through a Kinetic Replication Model

Zampieri, Mattia, Legname, Giuseppe, Altafini, Claudio, Shakhnovich, Eugene I.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 459 KB

english, 2009

27

Relating Neuronal Firing Patterns to Functional Differentiation of Cerebral Cortex

Shinomoto, Shigeru, Kim, Hideaki, Shimokawa, Takeaki, Matsuno, Nanae, Funahashi, Shintaro, Shima, Keisetsu, Fujita, Ichiro, Tamura, Hiroshi, Doi, Taijiro, Kawano, Kenji, Inaba, Naoko, Fukushima, Kikur

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 855 KB

english, 2009

28

Topography of Extracellular Matrix Mediates Vascular Morphogenesis and Migration Speeds in Angiogenesis

Bauer, Amy L., Jackson, Trachette L., Jiang, Yi, Czirók, András

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.27 MB

english, 2009

29

Stem Cell Proliferation and Quiescence—Two Sides of the Same Coin

Glauche, Ingmar, Moore, Kateri, Thielecke, Lars, Horn, Katrin, Loeffler, Markus, Roeder, Ingo, Crampin, Edmund J.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 396 KB

english, 2009

30

A Quick Guide to Organizing Computational Biology Projects

Noble, William Stafford, Lewitter, Fran

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 131 KB

english, 2009

31

Identification of a Topological Characteristic Responsible for the Biological Robustness of Regulatory Networks

Wu, Yangle, Zhang, Xiaomeng, Yu, Jianglei, Ouyang, Qi, Zhang, Weixiong

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 457 KB

english, 2009

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