Volume 27; Issue 8

Main
Bioinformatics
Volume 27; Issue 8

Bioinformatics

Volume 27; Issue 8

1

Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets

Brown, M., Wedge, D. C., Goodacre, R., Kell, D. B., Baker, P. N., Kenny, L. C., Mamas, M. A., Neyses, L., Dunn, W. B.

Journal:

Year:

2011

Language:

english

File:

PDF, 99 KB

english, 2011

2

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software

Kamentsky, L., Jones, T. R., Fraser, A., Bray, M.-A., Logan, D. J., Madden, K. L., Ljosa, V., Rueden, C., Eliceiri, K. W., Carpenter, A. E.

Journal:

Year:

2011

Language:

english

File:

PDF, 121 KB

english, 2011

3

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs

Kinsella, M., Harismendy, O., Nakano, M., Frazer, K. A., Bafna, V.

Journal:

Year:

2011

Language:

english

File:

PDF, 369 KB

english, 2011

4

Assigning spectrum-specific P-values to protein identifications by mass spectrometry

Spirin, V., Shpunt, A., Seebacher, J., Gentzel, M., Shevchenko, A., Gygi, S., Sunyaev, S.

Journal:

Year:

2011

Language:

english

File:

PDF, 370 KB

english, 2011

5

Human variation database: an open-source database template for genomic discovery

Fejes, A. P., Khodabakhshi, A. H., Birol, I., Jones, S. J. M.

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Year:

2011

Language:

english

File:

PDF, 61 KB

english, 2011

6

ACT: aggregation and correlation toolbox for analyses of genome tracks

Jee, J., Rozowsky, J., Yip, K. Y., Lochovsky, L., Bjornson, R., Zhong, G., Zhang, Z., Fu, Y., Wang, J., Weng, Z., Gerstein, M.

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Year:

2011

Language:

english

File:

PDF, 160 KB

english, 2011

7

Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows

Specht, M., Kuhlgert, S., Fufezan, C., Hippler, M.

Journal:

Year:

2011

Language:

english

File:

PDF, 165 KB

english, 2011

8

Topology and prediction of RNA pseudoknots

Reidys, C. M., Huang, F. W. D., Andersen, J. E., Penner, R. C., Stadler, P. F., Nebel, M. E.

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Year:

2011

Language:

english

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PDF, 884 KB

english, 2011

9

eGOB: eukaryotic Gene Order Browser

Lopez, M. D., Samuelsson, T.

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Year:

2011

Language:

english

File:

PDF, 227 KB

english, 2011

10

FNV: light-weight flash-based network and pathway viewer

Dannenfelser, R., Lachmann, A., Szenk, M., Ma'ayan, A.

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Year:

2011

Language:

english

File:

PDF, 111 KB

english, 2011

11

Gene List significance at-a-glance with GeneValorization

Brancotte, B., Biton, A., Bernard-Pierrot, I., Radvanyi, F., Reyal, F., Cohen-Boulakia, S.

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Year:

2011

Language:

english

File:

PDF, 229 KB

english, 2011

12

ProtTest 3: fast selection of best-fit models of protein evolution

Darriba, D., Taboada, G. L., Doallo, R., Posada, D.

Journal:

Year:

2011

Language:

english

File:

PDF, 258 KB

english, 2011

13

Condensing biomedical journal texts through paragraph ranking

Chiang, J.-H., Liu, H.-H., Huang, Y.-T.

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Year:

2011

Language:

english

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PDF, 386 KB

english, 2011

14

eCEO: an efficient Cloud Epistasis cOmputing model in genome-wide association study

Wang, Z., Wang, Y., Tan, K.-L., Wong, L., Agrawal, D.

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Year:

2011

Language:

english

File:

PDF, 673 KB

english, 2011

15

A comprehensive protein-centric ID mapping service for molecular data integration

Huang, H., McGarvey, P. B., Suzek, B. E., Mazumder, R., Zhang, J., Chen, Y., Wu, C. H.

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Year:

2011

Language:

english

File:

PDF, 200 KB

english, 2011

16

All-atom knowledge-based potential for RNA structure prediction and assessment

Capriotti, E., Norambuena, T., Marti-Renom, M. A., Melo, F.

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Year:

2011

Language:

english

File:

PDF, 288 KB

english, 2011

17

STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

Klingbeil, G., Erban, R., Giles, M., Maini, P. K.

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Year:

2011

Language:

english

File:

PDF, 142 KB

english, 2011

18

Automatically identifying and annotating mouse embryo gene expression patterns

Han, L., van Hemert, J. I., Baldock, R. A.

Journal:

Year:

2011

Language:

english

File:

PDF, 472 KB

english, 2011

19

SiGN-SSM: open source parallel software for estimating gene networks with state space models

Tamada, Y., Yamaguchi, R., Imoto, S., Hirose, O., Yoshida, R., Nagasaki, M., Miyano, S.

Journal:

Year:

2011

Language:

english

File:

PDF, 219 KB

english, 2011

20

BiC: a web server for calculating bimodality of coexpression between gene and protein networks

Linderman, G. C., Patel, V. N., Chance, M. R., Bebek, G.

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Year:

2011

Language:

english

File:

PDF, 212 KB

english, 2011

21

Comments on 'Bayesian variable selection for disease classification using gene expression data'

Baragatti, M. C., Pommeret, D.

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Year:

2011

Language:

english

File:

PDF, 57 KB

english, 2011

22

A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data

Ahmad, I., Suits, F., Hoekman, B., Swertz, M. A., Byelas, H., Dijkstra, M., Hooft, R., Katsubo, D., van Breukelen, B., Bischoff, R., Horvatovich, P.

Journal:

Year:

2011

Language:

english

File:

PDF, 346 KB

english, 2011

23

Interactive, multiscale navigation of large and complicated biological networks

Praneenararat, T., Takagi, T., Iwasaki, W.

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Year:

2011

Language:

english

File:

PDF, 587 KB

english, 2011

24

The effects of feedback loops on disease comorbidity in human signaling networks

Le, D.-H., Kwon, Y.-K.

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Year:

2011

Language:

english

File:

PDF, 599 KB

english, 2011

25

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

Walters, W. A., Caporaso, J. G., Lauber, C. L., Berg-Lyons, D., Fierer, N., Knight, R.

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Year:

2011

Language:

english

File:

PDF, 562 KB

english, 2011

26

R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data

Klein, H.-U., Bartenhagen, C., Kohlmann, A., Grossmann, V., Ruckert, C., Haferlach, T., Dugas, M.

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Year:

2011

Language:

english

File:

PDF, 141 KB

english, 2011

27

Improving SNP discovery by base alignment quality

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Year:

2011

Language:

english

File:

PDF, 136 KB

english, 2011

28

Topological entropy of DNA sequences

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Year:

2011

Language:

english

File:

PDF, 260 KB

english, 2011

29

MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures

Khan, J. M., Cheruku, H. R., Tong, J. C., Ranganathan, S.

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Year:

2011

Language:

english

File:

PDF, 67 KB

english, 2011

30

Defining an informativeness metric for clustering gene expression data

Mar, J. C., Wells, C. A., Quackenbush, J.

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Year:

2011

Language:

english

File:

PDF, 366 KB

english, 2011

31

AGRA: analysis of gene ranking algorithms

Kocbek, S., Saetre, R., Stiglic, G., Kim, J.-D., Pernek, I., Tsuruoka, Y., Kokol, P., Ananiadou, S., Tsujii, J.

Journal:

Year:

2011

Language:

english

File:

PDF, 128 KB

english, 2011

32

SurvJamda: an R package to predict patients' survival and risk assessment using joint analysis of microarray gene expression data

Journal:

Year:

2011

Language:

english

File:

PDF, 61 KB

english, 2011

33

Performance assessment of copy number microarray platforms using a spike-in experiment

Halper-Stromberg, E., Frelin, L., Ruczinski, I., Scharpf, R., Jie, C., Carvalho, B., Hao, H., Hetrick, K., Jedlicka, A., Dziedzic, A., Doheny, K., Scott, A. F., Baylin, S., Pevsner, J., Spencer, F., I

Journal:

Year:

2011

Language:

english

File:

PDF, 2.16 MB

english, 2011