Volume 28; Issue 14

Main
Bioinformatics
Volume 28; Issue 14

Bioinformatics

Volume 28; Issue 14

1

Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs

Saunders, C. T., Wong, W. S. W., Swamy, S., Becq, J., Murray, L. J., Cheetham, R. K.

Journal:

Year:

2012

Language:

english

File:

PDF, 182 KB

english, 2012

2

Efficient RNA pairwise structure comparison by SETTER method

Hoksza, D., Svozil, D.

Journal:

Year:

2012

Language:

english

File:

PDF, 734 KB

english, 2012

3

Exhaustive database searching for amino acid mutations in proteomes

Hyatt, D., Pan, C.

Journal:

Year:

2012

Language:

english

File:

PDF, 270 KB

english, 2012

4

Identifying mechanistic similarities in drug responses

Zhao, C., Hua, J., Bittner, M. L., Ivanov, I., Dougherty, a. E. R.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.35 MB

english, 2012

5

Genome-scale analysis of interaction dynamics reveals organization of biological networks

Das, J., Mohammed, J., Yu, H.

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Year:

2012

Language:

english

File:

PDF, 2.69 MB

english, 2012

6

HCS-Analyzer: open source software for high-content screening data correction and analysis

Ogier, A., Dorval, T.

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Year:

2012

Language:

english

File:

PDF, 310 KB

english, 2012

7

OSA: a fast and accurate alignment tool for RNA-Seq

Hu, J., Ge, H., Newman, M., Liu, K.

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Year:

2012

Language:

english

File:

PDF, 136 KB

english, 2012

8

CPSS: a computational platform for the analysis of small RNA deep sequencing data

Zhang, Y., Xu, B., Yang, Y., Ban, R., Zhang, H., Jiang, X., Cooke, H. J., Xue, Y., Shi, Q.

Journal:

Year:

2012

Language:

english

File:

PDF, 206 KB

english, 2012

9

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform

Liu, Y., Schmidt, B., Maskell, D. L.

Journal:

Year:

2012

Language:

english

File:

PDF, 992 KB

english, 2012

10

BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data

Chen, K., Wallis, J. W., Kandoth, C., Kalicki-Veizer, J. M., Mungall, K. L., Mungall, A. J., Jones, S. J., Marra, M. A., Ley, T. J., Mardis, E. R., Wilson, R. K., Weinstein, J. N., Ding, L.

Journal:

Year:

2012

Language:

english

File:

PDF, 209 KB

english, 2012

11

Fast computation for genome-wide association studies using boosted one-step statistics

Voorman, A., Rice, K., Lumley, T.

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Year:

2012

Language:

english

File:

PDF, 318 KB

english, 2012

12

BEDOPS: high-performance genomic feature operations

Neph, S., Kuehn, M. S., Reynolds, A. P., Haugen, E., Thurman, R. E., Johnson, A. K., Rynes, E., Maurano, M. T., Vierstra, J., Thomas, S., Sandstrom, R., Humbert, R., Stamatoyannopoulos, J. A.

Journal:

Year:

2012

Language:

english

File:

PDF, 255 KB

english, 2012

13

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

Pruesse, E., Peplies, J., Glockner, F. O.

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Year:

2012

Language:

english

File:

PDF, 378 KB

english, 2012

14

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

Journal:

Year:

2012

Language:

english

File:

PDF, 177 KB

english, 2012

15

Robustness and accuracy of functional modules in integrated network analysis

Beisser, D., Brunkhorst, S., Dandekar, T., Klau, G. W., Dittrich, M. T., Muller, T.

Journal:

Year:

2012

Language:

english

File:

PDF, 943 KB

english, 2012

16

MicrobeDB: a locally maintainable database of microbial genomic sequences

Langille, M. G. I., Laird, M. R., Hsiao, W. W. L., Chiu, T. A., Eisen, J. A., Brinkman, F. S. L.

Journal:

Year:

2012

Language:

english

File:

PDF, 70 KB

english, 2012

17

Mosaic: making biological sense of complex networks

Zhang, C., Hanspers, K., Kuchinsky, A., Salomonis, N., Xu, D., Pico, A. R.

Journal:

Year:

2012

Language:

english

File:

PDF, 361 KB

english, 2012

18

MotifSuite: workflow for probabilistic motif detection and assessment

Claeys, M., Storms, V., Sun, H., Michoel, T., Marchal, K.

Journal:

Year:

2012

Language:

english

File:

PDF, 120 KB

english, 2012

19

Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human

Piasecka, B., Robinson-Rechavi, M., Bergmann, S.

Journal:

Year:

2012

Language:

english

File:

PDF, 406 KB

english, 2012

20

Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure

Koes, D. R., Camacho, C. J.

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Year:

2012

File:

PDF, 36 KB

2012

21

CodonLogo: a sequence logo-based viewer for codon patterns

Sharma, V., Murphy, D. P., Provan, G., Baranov, P. V.

Journal:

Year:

2012

Language:

english

File:

PDF, 233 KB

english, 2012

22

iFad: an integrative factor analysis model for drug-pathway association inference

Ma, H., Zhao, H.

Journal:

Year:

2012

Language:

english

File:

PDF, 609 KB

english, 2012

23

SRMA: an R package for resequencing array data analysis

Zhang, N., Xu, Y., O'Hely, M., Speed, T. P., Scharfe, C., Wang, W.

Journal:

Year:

2012

Language:

english

File:

PDF, 293 KB

english, 2012

24

Gossamer -- a resource-efficient de novo assembler

Conway, T., Wazny, J., Bromage, A., Zobel, J., Beresford-Smith, B.

Journal:

Year:

2012

Language:

english

File:

PDF, 78 KB

english, 2012

25

IRView: a database and viewer for protein interacting regions

Fujimori, S., Hirai, N., Masuoka, K., Oshikubo, T., Yamashita, T., Washio, T., Saito, A., Nagasaki, M., Miyano, S., Miyamoto-Sato, E.

Journal:

Year:

2012

Language:

english

File:

PDF, 71 KB

english, 2012

26

R/EBcoexpress: an empirical Bayesian framework for discovering differential co-expression

Dawson, J. A., Ye, S., Kendziorski, C.

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Year:

2012

Language:

english

File:

PDF, 115 KB

english, 2012

27

Anonymous nuclear loci in non-model organisms: making the most of high-throughput genome surveys

Bertozzi, T., Sanders, K. L., Sistrom, M. J., Gardner, M. G.

Journal:

Year:

2012

Language:

english

File:

PDF, 90 KB

english, 2012

28

Marker2sequence, mine your QTL regions for candidate genes

Chibon, P.-Y., Schoof, H., Visser, R. G. F., Finkers, R.

Journal:

Year:

2012

Language:

english

File:

PDF, 69 KB

english, 2012

29

A holistic in silico approach to predict functional sites in protein structures

Segura, J., Jones, P. F., Fernandez-Fuentes, N.

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Year:

2012

Language:

english

File:

PDF, 550 KB

english, 2012

30

Improvement of 3D protein models using multiple templates guided by single-template model quality assessment

Buenavista, M. T., Roche, D. B., McGuffin, L. J.

Journal:

Year:

2012

Language:

english

File:

PDF, 303 KB

english, 2012

31

The Hematopoietic Expression Viewer: expanding mobile apps as a scientific tool

James, R. A., Rao, M. M., Chen, E. S., Goodell, M. A., Shaw, C. A.

Journal:

Year:

2012

Language:

english

File:

PDF, 195 KB

english, 2012

32

regSNPs: a strategy for prioritizing regulatory single nucleotide substitutions

Teng, M., Ichikawa, S., Padgett, L. R., Wang, Y., Mort, M., Cooper, D. N., Koller, D. L., Foroud, T., Edenberg, H. J., Econs, M. J., Liu, Y.

Journal:

Year:

2012

Language:

english

File:

PDF, 546 KB

english, 2012