Volume 28; Issue 6

Main
Bioinformatics
Volume 28; Issue 6

Bioinformatics

Volume 28; Issue 6

1

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

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

Journal:

Year:

2012

Language:

english

File:

PDF, 802 KB

english, 2012

2

SOAP3: ultra-fast GPU-based parallel alignment tool for short reads

Liu, C.-M., Wong, T., Wu, E., Luo, R., Yiu, S.-M., Li, Y., Wang, B., Yu, C., Chu, X., Zhao, K.

Journal:

Year:

2012

Language:

english

File:

PDF, 113 KB

english, 2012

3

A Boolean network model of the FA/BRCA pathway

Rodriguez, A., Sosa, D., Torres, L., Molina, B., Frias, S., Mendoza, L.

Journal:

Year:

2012

Language:

english

File:

PDF, 800 KB

english, 2012

4

Functional microRNA targets in protein coding sequences

Reczko, M., Maragkakis, M., Alexiou, P., Grosse, I., Hatzigeorgiou, A. G.

Journal:

Year:

2012

Language:

english

File:

PDF, 288 KB

english, 2012

5

Hadoop-BAM: directly manipulating next generation sequencing data in the cloud

Niemenmaa, M., Kallio, A., Schumacher, A., Klemela, P., Korpelainen, E., Heljanko, K.

Journal:

Year:

2012

Language:

english

File:

PDF, 187 KB

english, 2012

6

Toward community standards in the quest for orthologs

Dessimoz, C., Gabaldon, T., Roos, D. S., Sonnhammer, E. L. L., Herrero, J., Altenhoff, A., Apweiler, R., Ashburner, M., Blake, J., Boeckmann, B., Bridge, A., Bruford, E., Cherry, M., Conte, M., Dannie

Journal:

Year:

2012

Language:

english

File:

PDF, 98 KB

english, 2012

7

Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling

Simonsen, M., Maetschke, S. R., Ragan, M. A.

Journal:

Year:

2012

Language:

english

File:

PDF, 513 KB

english, 2012

8

Assumption weighting for incorporating heterogeneity into meta-analysis of genomic data

Li, Y., Ghosh, D.

Journal:

Year:

2012

Language:

english

File:

PDF, 263 KB

english, 2012

9

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

Leek, J. T., Johnson, W. E., Parker, H. S., Jaffe, A. E., Storey, J. D.

Journal:

Year:

2012

Language:

english

File:

PDF, 81 KB

english, 2012

10

Estimating abundances of retroviral insertion sites from DNA fragment length data

Berry, C. C., Gillet, N. A., Melamed, A., Gormley, N., Bangham, C. R. M., Bushman, F. D.

Journal:

Year:

2012

Language:

english

File:

PDF, 442 KB

english, 2012

11

CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores

Stojmirovic, A., Bliskovsky, A., Yu, Y.-K.

Journal:

Year:

2012

Language:

english

File:

PDF, 291 KB

english, 2012

12

CODEX: exploration of semantic changes between ontology versions

Hartung, M., Gross, A., Rahm, E.

Journal:

Year:

2012

Language:

english

File:

PDF, 278 KB

english, 2012

13

Predicting relapse prior to transplantation in chronic myeloid leukemia by integrating expert knowledge and expression data

Yeung, K. Y., Gooley, T. A., Zhang, A., Raftery, A. E., Radich, J. P., Oehler, V. G.

Journal:

Year:

2012

Language:

english

File:

PDF, 410 KB

english, 2012

14

A method to infer positive selection from marker dynamics in an asexual population

Illingworth, C. J. R., Mustonen, V.

Journal:

Year:

2012

Language:

english

File:

PDF, 391 KB

english, 2012

15

Surrogate variable analysis using partial least squares (SVA-PLS) in gene expression studies

Chakraborty, S., Datta, S., Datta, S.

Journal:

Year:

2012

Language:

english

File:

PDF, 260 KB

english, 2012

16

Gencrypt: one-way cryptographic hashes to detect overlapping individuals across samples

Turchin, M. C., Hirschhorn, J. N.

Journal:

Year:

2012

Language:

english

File:

PDF, 81 KB

english, 2012

17

PathVisio-Validator: a rule-based validation plugin for graphical pathway notations

Chandan, K., van Iersel, M. P., Aladjem, M. I., Kohn, K. W., Luna, A.

Journal:

Year:

2012

Language:

english

File:

PDF, 112 KB

english, 2012

18

CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED

DeJongh, M., Bockstege, B., Frybarger, P., Hazekamp, N., Kammeraad, J., McGeehan, T.

Journal:

Year:

2012

Language:

english

File:

PDF, 272 KB

english, 2012

19

ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites

Gonzalez, S., Montserrat-Sentis, B., Sanchez, F., Puiggros, M., Blanco, E., Ramirez, A., Torrents, D.

Journal:

Year:

2012

Language:

english

File:

PDF, 627 KB

english, 2012

20

Exact coalescent simulation of new haplotype data from existing reference haplotypes

Kang, C. J., Marjoram, P.

Journal:

Year:

2012

Language:

english

File:

PDF, 617 KB

english, 2012

21

Using biologically interrelated experiments to identify pathway genes in Arabidopsis

Kim, K., Jiang, K., Teng, S. L., Feldman, L. J., Huang, H.

Journal:

Year:

2012

Language:

english

File:

PDF, 326 KB

english, 2012

22

SynaptomeDB: an ontology-based knowledgebase for synaptic genes

Pirooznia, M., Wang, T., Avramopoulos, D., Valle, D., Thomas, G., Huganir, R. L., Goes, F. S., Potash, J. B., Zandi, P. P.

Journal:

Year:

2012

Language:

english

File:

PDF, 77 KB

english, 2012

23

Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA)

Schwalb, B., Schulz, D., Sun, M., Zacher, B., Dumcke, S., Martin, D. E., Cramer, P., Tresch, A.

Journal:

Year:

2012

Language:

english

File:

PDF, 207 KB

english, 2012

24

The Transcriptome Analysis and Comparison Explorer--T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms

Philipp, E. E. R., Kraemer, L., Mountfort, D., Schilhabel, M., Schreiber, S., Rosenstiel, P.

Journal:

Year:

2012

Language:

english

File:

PDF, 739 KB

english, 2012

25

A gene-based test of association using canonical correlation analysis

Tang, C. S., Ferreira, M. A. R.

Journal:

Year:

2012

Language:

english

File:

PDF, 321 KB

english, 2012

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