Volume 8; Issue 12

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PLoS Computational Biology
Volume 8; Issue 12

PLoS Computational Biology

Volume 8; Issue 12

1

Introduction to Translational Bioinformatics Collection

Altman, Russ B., Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 159 KB

english, 2012

2

Soft-bound Synaptic Plasticity Increases Storage Capacity

van Rossum, Mark C. W., Shippi, Maria, Barrett, Adam B., Latham, Peter E.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 602 KB

english, 2012

3

Nucleoid-Associated Proteins Affect Mutation Dynamics in E. coli in a Growth Phase-Specific Manner

Warnecke, Tobias, Supek, Fran, Lehner, Ben, Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 625 KB

english, 2012

4

Chapter 7: Pharmacogenomics

Karczewski, Konrad J., Daneshjou, Roxana, Altman, Russ B., Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.38 MB

english, 2012

5

A Comparison of Computational Models for Eukaryotic Cell Shape and Motility

Holmes, William R., Edelstein-Keshet, Leah, Glazier, James A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.14 MB

english, 2012

6

Modelling Hair Follicle Growth Dynamics as an Excitable Medium

Murray, Philip J., Maini, Philip K., Plikus, Maksim V., Chuong, Cheng-Ming, Baker, Ruth E., Shvartsman, Stanislav

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 4.46 MB

english, 2012

7

Molecular Evolution of Peptide Ligands with Custom-Tailored Characteristics for Targeting of Glycostructures

Röckendorf, Niels, Borschbach, Markus, Frey, Andreas, Ofran, Yanay

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 672 KB

english, 2012

8

Chapter 3: Small Molecules and Disease

Wishart, David S., Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.07 MB

english, 2012

9

Chapter 14: Cancer Genome Analysis

Vazquez, Miguel, de la Torre, Victor, Valencia, Alfonso, Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 665 KB

english, 2012

10

Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities

O'Dwyer, James P., Kembel, Steven W., Green, Jessica L., Guttman, David S.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 868 KB

english, 2012

11

Chapter 8: Biological Knowledge Assembly and Interpretation

Kim, Ju Han, Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 6.49 MB

english, 2012

12

Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking

Kringelum, Jens Vindahl, Lundegaard, Claus, Lund, Ole, Nielsen, Morten, Peters, Bjoern

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.16 MB

english, 2012

13

Chapter 10: Mining Genome-Wide Genetic Markers

Zhang, Xiang, Huang, Shunping, Zhang, Zhaojun, Wang, Wei, Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 392 KB

english, 2012

14

Sensitivity Analysis of Flux Determination in Heart by H218O -provided Labeling Using a Dynamic Isotopologue Model of Energy Transfer Pathways

Schryer, David W., Peterson, Pearu, Illaste, Ardo, Vendelin, Marko, Crampin, Edmund J.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.15 MB

english, 2012

15

Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli

Brewster, Robert C., Jones, Daniel L., Phillips, Rob, van Nimwegen, Erik

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 851 KB

english, 2012

16

Parameter Identifiability and Sensitivity Analysis Predict Targets for Enhancement of STAT1 Activity in Pancreatic Cancer and Stellate Cells

Rateitschak, Katja, Winter, Felix, Lange, Falko, Jaster, Robert, Wolkenhauer, Olaf, Markel, Scott

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.41 MB

english, 2012

17

Quantitative Dynamics of Telomere Bouquet Formation

Richards, David M., Greer, Emma, Martin, Azahara C., Moore, Graham, Shaw, Peter J., Howard, Martin, Noble, William Stafford

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.36 MB

english, 2012

18

Mechanics of Undulatory Swimming in a Frictional Fluid

Ding, Yang, Sharpe, Sarah S., Masse, Andrew, Goldman, Daniel I., Levin, Simon A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.65 MB

english, 2012

19

Chapter 12: Human Microbiome Analysis

Morgan, Xochitl C., Huttenhower, Curtis, Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 541 KB

english, 2012

20

Localizing Genes to Cerebellar Layers by Classifying ISH Images

Kirsch, Lior, Liscovitch, Noa, Chechik, Gal, Ohler, Uwe

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.22 MB

english, 2012

21

Task-Dependent Changes in Cross-Level Coupling between Single Neurons and Oscillatory Activity in Multiscale Networks

Canolty, Ryan T., Ganguly, Karunesh, Carmena, Jose M., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 3.16 MB

english, 2012

22

Climbing Fiber Burst Size and Olivary Sub-threshold Oscillations in a Network Setting

De Gruijl, Jornt R., Bazzigaluppi, Paolo, de Jeu, Marcel T. G., De Zeeuw, Chris I., Behrens, Tim

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.05 MB

english, 2012

23

The Evolution of Cell-to-Cell Communication in a Sporulating Bacterium

van Gestel, Jordi, Nowak, Martin A., Tarnita, Corina E., Doebeli, Michael

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 780 KB

english, 2012

24

Chapter 5: Network Biology Approach to Complex Diseases

Cho, Dong-Yeon, Kim, Yoo-Ah, Przytycka, Teresa M., Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 394 KB

english, 2012

25

Chapter 6: Structural Variation and Medical Genomics

Raphael, Benjamin J., Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.14 MB

english, 2012

26

Chapter 11: Genome-Wide Association Studies

Bush, William S., Moore, Jason H., Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 517 KB

english, 2012

27

Chapter 13: Mining Electronic Health Records in the Genomics Era

Denny, Joshua C., Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 592 KB

english, 2012

28

Chapter 1: Biomedical Knowledge Integration

Payne, Philip R. O., Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 839 KB

english, 2012

29

Chapter 9: Analyses Using Disease Ontologies

Shah, Nigam H., Cole, Tyler, Musen, Mark A., Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 5.57 MB

english, 2012

30

3D Reconstruction and Standardization of the Rat Vibrissal Cortex for Precise Registration of Single Neuron Morphology

Egger, Robert, Narayanan, Rajeevan T., Helmstaedter, Moritz, de Kock, Christiaan P. J., Oberlaender, Marcel, Briggman, Kevin

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.48 MB

english, 2012

31

The Two Sides of Complement C3d: Evolution of Electrostatics in a Link between Innate and Adaptive Immunity

Kieslich, Chris A., Morikis, Dimitrios, Gilson, Michael

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 731 KB

english, 2012

32

Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations

Chiappori, Federica, Merelli, Ivan, Colombo, Giorgio, Milanesi, Luciano, Morra, Giulia, Cui, Qiang

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.77 MB

english, 2012

33

Interconnected Cavernous Structure of Bacterial Fruiting Bodies

Harvey, Cameron W., Du, Huijing, Xu, Zhiliang, Kaiser, Dale, Aranson, Igor, Alber, Mark, Shvartsman, Stanislav

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.67 MB

english, 2012

34

What Is the Role of Motif D in the Nucleotide Incorporation Catalyzed by the RNA-dependent RNA Polymerase from Poliovirus?

Shen, Hujun, Sun, Hui, Li, Guohui, MacKerell, Alexander D.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 4.60 MB

english, 2012

35

Genomic Hallmarks of Genes Involved in Chromosomal Translocations in Hematological Cancer

Shugay, Mikhail, Ortiz de Mendíbil, Iñigo, Vizmanos, José L., Novo, Francisco J., Wasserman, Wyeth W.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.28 MB

english, 2012

36

Teaching the Fundamentals of Biological Data Integration Using Classroom Games

Schneider, Maria Victoria, Jimenez, Rafael C., Lewitter, Fran

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 793 KB

english, 2012

37

Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin State

Wilczynski, Bartek, Liu, Ya-Hsin, Yeo, Zhen Xuan, Furlong, Eileen E. M., Segal, Eran

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 930 KB

english, 2012

38

Ten Simple Rules for the Open Development of Scientific Software

Prlić, Andreas, Procter, James B.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 133 KB

english, 2012

39

SnIPRE: Selection Inference Using a Poisson Random Effects Model

Eilertson, Kirsten E., Booth, James G., Bustamante, Carlos D., Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.22 MB

english, 2012

40

Chapter 4: Protein Interactions and Disease

Gonzalez, Mileidy W., Kann, Maricel G., Lewitter, Fran

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 978 KB

english, 2012

41

Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density

Coronnello, Claudia, Hartmaier, Ryan, Arora, Arshi, Huleihel, Luai, Pandit, Kusum V., Bais, Abha S., Butterworth, Michael, Kaminski, Naftali, Stormo, Gary D., Oesterreich, Steffi, Benos, Panayiotis V.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.02 MB

english, 2012

42

Phylodynamic Inference and Model Assessment with Approximate Bayesian Computation: Influenza as a Case Study

Ratmann, Oliver, Donker, Gé, Meijer, Adam, Fraser, Christophe, Koelle, Katia, Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.77 MB

english, 2012

43

PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions

Qiao, Wenlian, Quon, Gerald, Csaszar, Elizabeth, Yu, Mei, Morris, Quaid, Zandstra, Peter W., Bonneau, Richard

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.45 MB

english, 2012

44

Computational Phenotyping of Two-Person Interactions Reveals Differential Neural Response to Depth-of-Thought

Xiang, Ting, Ray, Debajyoti, Lohrenz, Terry, Dayan, Peter, Montague, P. Read, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 561 KB

english, 2012

45

Electron Transfer Interactome of Cytochrome c

Volkov, Alexander N., van Nuland, Nico A. J., Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 919 KB

english, 2012

46

ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes

Mosaliganti, Kishore R., Noche, Ramil R., Xiong, Fengzhu, Swinburne, Ian A., Megason, Sean G., Murphy, Robert F.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 5.64 MB

english, 2012

47

Chapter 2: Data-Driven View of Disease Biology

Greene, Casey S., Troyanskaya, Olga G., Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.14 MB

english, 2012

48

Using Molecular Mechanics to Predict Bulk Material Properties of Fibronectin Fibers

Bradshaw, Mark J., Cheung, Man C., Ehrlich, Daniel J., Smith, Michael L., Mac Gabhann, Feilim

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 947 KB

english, 2012

49

Calcium Wave Propagation in Networks of Endothelial Cells: Model-based Theoretical and Experimental Study

Long, Juexuan, Junkin, Michael, Wong, Pak Kin, Hoying, James, Deymier, Pierre, Ho, Dean

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.36 MB

english, 2012

50

A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor

Mannige, Ranjan V., Brooks, Charles L., Shakhnovich, Eugene I., Grishin, Nick

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 716 KB

english, 2012

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