Volume 28; Issue 20

Main
Bioinformatics
Volume 28; Issue 20

Bioinformatics

Volume 28; Issue 20

1

Quantifying uniformity of mapped reads

Hower, V., Starfield, R., Roberts, A., Pachter, L.

Journal:

Year:

2012

Language:

english

File:

PDF, 113 KB

english, 2012

2

SimRare: a program to generate and analyze sequence-based data for association studies of quantitative and qualitative traits

Li, B., Wang, G., Leal, S. M.

Journal:

Year:

2012

Language:

english

File:

PDF, 78 KB

english, 2012

3

EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes

Kumar, N., Skolnick, J.

Journal:

Year:

2012

Language:

english

File:

PDF, 162 KB

english, 2012

4

RazerS 3: Faster, fully sensitive read mapping

Weese, D., Holtgrewe, M., Reinert, K.

Journal:

Year:

2012

Language:

english

File:

PDF, 334 KB

english, 2012

5

EuGene: maximizing synthetic gene design for heterologous expression

Gaspar, P., Oliveira, J. L., Frommlet, J., Santos, M. A. S., Moura, G.

Journal:

Year:

2012

Language:

english

File:

PDF, 197 KB

english, 2012

6

PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data

Sukosd, Z., Knudsen, B., Kjems, J., Pedersen, C. N. S.

Journal:

Year:

2012

Language:

english

File:

PDF, 81 KB

english, 2012

7

A robust approach to extract biomedical events from literature

Bui, Q.-C., Sloot, P. M. A.

Journal:

Year:

2012

Language:

english

File:

PDF, 276 KB

english, 2012

8

FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment

Ma, H., Zhao, H.

Journal:

Year:

2012

Language:

english

File:

PDF, 486 KB

english, 2012

9

treePL: divergence time estimation using penalized likelihood for large phylogenies

Smith, S. A., O'Meara, B. C.

Journal:

Year:

2012

Language:

english

File:

PDF, 94 KB

english, 2012

10

Systematic comparison of RNA-Seq normalization methods using measurement error models

Sun, Z., Zhu, Y.

Journal:

Year:

2012

Language:

english

File:

PDF, 366 KB

english, 2012

11

COMPADRE: an R and web resource for pathway activity analysis by component decompositions

Ramos-Rodriguez, R.-R., Cuevas-Diaz-Duran, R., Falciani, F., Tamez-Pena, J.-G., Trevino, V.

Journal:

Year:

2012

Language:

english

File:

PDF, 166 KB

english, 2012

12

An empirical Bayes mixture model for SNP detection in pooled sequencing data

Journal:

Year:

2012

Language:

english

File:

PDF, 300 KB

english, 2012

13

MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis

Kumar, S., Stecher, G., Peterson, D., Tamura, K.

Journal:

Year:

2012

Language:

english

File:

PDF, 143 KB

english, 2012

14

TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes

Zhang, D., Xue, X., Malmberg, R. L., Cai, L.

Journal:

Year:

2012

Language:

english

File:

PDF, 75 KB

english, 2012

15

PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants

Jiang, Y., Wang, Y., Brudno, M.

Journal:

Year:

2012

Language:

english

File:

PDF, 454 KB

english, 2012

16

BioJava: an open-source framework for bioinformatics in 2012

Prlic, A., Yates, A., Bliven, S. E., Rose, P. W., Jacobsen, J., Troshin, P. V., Chapman, M., Gao, J., Koh, C. H., Foisy, S., Holland, R., Rimsa, G., Heuer, M. L., Brandstatter-Muller, H., Bourne, P. E

Journal:

Year:

2012

Language:

english

File:

PDF, 213 KB

english, 2012

17

Application of asymmetric statistical potentials to antibody-protein docking

Brenke, R., Hall, D. R., Chuang, G.-Y., Comeau, S. R., Bohnuud, T., Beglov, D., Schueler-Furman, O., Vajda, S., Kozakov, D.

Journal:

Year:

2012

Language:

english

File:

PDF, 250 KB

english, 2012

18

Qualimap: evaluating next-generation sequencing alignment data

Garcia-Alcalde, F., Okonechnikov, K., Carbonell, J., Cruz, L. M., Gotz, S., Tarazona, S., Dopazo, J., Meyer, T. F., Conesa, A.

Journal:

Year:

2012

Language:

english

File:

PDF, 157 KB

english, 2012

19

Impact of ontology evolution on functional analyses

Gross, A., Hartung, M., Prufer, K., Kelso, J., Rahm, E.

Journal:

Year:

2012

Language:

english

File:

PDF, 730 KB

english, 2012

20

Identification of trans-acting siRNAs and their regulatory cascades in grapevine

Zhang, C., Li, G., Wang, J., Fang, J.

Journal:

Year:

2012

Language:

english

File:

PDF, 567 KB

english, 2012

21

Intensity quantile estimation and mapping--a novel algorithm for the correction of image non-uniformity bias in HCS data

Lo, E., Soleilhac, E., Martinez, A., Lafanechere, L., Nadon, R.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.07 MB

english, 2012

22

BasyLiCA: a tool for automatic processing of a Bacterial Live Cell Array

Aichaoui, L., Jules, M., Le Chat, L., Aymerich, S., Fromion, V., Goelzer, A.

Journal:

Year:

2012

Language:

english

File:

PDF, 161 KB

english, 2012

23

Positive-unlabeled learning for disease gene identification

Yang, P., Li, X.-L., Mei, J.-P., Kwoh, C.-K., Ng, S.-K.

Journal:

Year:

2012

Language:

english

File:

PDF, 257 KB

english, 2012

24

MetiTree: a web application to organize and process high-resolution multi-stage mass spectrometry metabolomics data

Rojas-Cherto, M., van Vliet, M., Peironcely, J. E., van Doorn, R., Kooyman, M., te Beek, T., van Driel, M. A., Hankemeier, T., Reijmers, T.

Journal:

Year:

2012

Language:

english

File:

PDF, 276 KB

english, 2012

25

SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

Moal, I. H., Fernandez-Recio, J.

Journal:

Year:

2012

Language:

english

File:

PDF, 397 KB

english, 2012

26

Qualitative translation of relations from BioPAX to SBML qual

Buchel, F., Wrzodek, C., Mittag, F., Drager, A., Eichner, J., Rodriguez, N., Le Novere, N., Zell, A.

Journal:

Year:

2012

Language:

english

File:

PDF, 367 KB

english, 2012

27

shortran: a pipeline for small RNA-seq data analysis

Gupta, V., Markmann, K., Pedersen, C. N. S., Stougaard, J., Andersen, S. U.

Journal:

Year:

2012

Language:

english

File:

PDF, 173 KB

english, 2012

28

FACETS: multi-faceted functional decomposition of protein interaction networks

Seah, B.-S., Bhowmick, S. S., Forbes Dewey, C.

Journal:

Year:

2012

Language:

english

File:

PDF, 596 KB

english, 2012

29

An integrated approach to reduce the impact of minor allele frequency and linkage disequilibrium on variable importance measures for genome-wide data

Walters, R., Laurin, C., Lubke, G. H.

Journal:

Year:

2012

Language:

english

File:

PDF, 410 KB

english, 2012