Volume 30; Issue 23

Main
Bioinformatics
Volume 30; Issue 23

Bioinformatics

Volume 30; Issue 23

1

READemption--a tool for the computational analysis of deep-sequencing-based transcriptome data

Forstner, K. U., Vogel, J., Sharma, C. M.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.13 MB

english, 2014

2

MR_predictor: a simulation engine for Mendelian Randomization studies

Journal:

Year:

2014

Language:

english

File:

PDF, 79 KB

english, 2014

3

SUBAcon: a consensus algorithm for unifying the subcellular localization data of the Arabidopsis proteome

Hooper, C. M., Tanz, S. K., Castleden, I. R., Vacher, M. A., Small, I. D., Millar, A. H.

Journal:

Year:

2014

Language:

english

File:

PDF, 732 KB

english, 2014

4

Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation

Zhu, F., Shi, L., Li, H., Eksi, R., Engel, J. D., Guan, Y.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.20 MB

english, 2014

5

PyBamView: a browser-based application for viewing short read alignments

Journal:

Year:

2014

Language:

english

File:

PDF, 217 KB

english, 2014

6

MethylAid: visual and interactive quality control of large Illumina 450k datasets

van Iterson, M., Tobi, E. W., Slieker, R. C., den Hollander, W., Luijk, R., Slagboom, P. E., Heijmans, B. T.

Journal:

Year:

2014

Language:

english

File:

PDF, 165 KB

english, 2014

7

Visualization of protein sequence features using JavaScript and SVG with pViz.js

Mukhyala, K., Masselot, A.

Journal:

Year:

2014

Language:

english

File:

PDF, 314 KB

english, 2014

8

GlycoPattern: a web platform for glycan array mining

Agravat, S. B., Saltz, J. H., Cummings, R. D., Smith, D. F.

Journal:

Year:

2014

Language:

english

File:

PDF, 172 KB

english, 2014

9

Cordova: Web-based management of genetic variation data

Ephraim, S. S., Anand, N., DeLuca, A. P., Taylor, K. R., Kolbe, D. L., Simpson, A. C., Azaiez, H., Sloan, C. M., Shearer, A. E., Hallier, A. R., Casavant, T. L., Scheetz, T. E., Smith, R. J. H., Braun

Journal:

Year:

2014

Language:

english

File:

PDF, 153 KB

english, 2014

10

Comparative assembly hubs: Web-accessible browsers for comparative genomics

Nguyen, N., Hickey, G., Raney, B. J., Armstrong, J., Clawson, H., Zweig, A., Karolchik, D., Kent, W. J., Haussler, D., Paten, B.

Journal:

Year:

2014

Language:

english

File:

PDF, 881 KB

english, 2014

11

NetComm: a network analysis tool based on communicability

Campbell, I. M., James, R. A., Chen, E. S., Shaw, C. A.

Journal:

Year:

2014

Language:

english

File:

PDF, 205 KB

english, 2014

12

Cross-validation under separate sampling: strong bias and how to correct it

Braga-Neto, U. M., Zollanvari, A., Dougherty, E. R.

Journal:

Year:

2014

Language:

english

File:

PDF, 600 KB

english, 2014

13

Cosi2: an efficient simulator of exact and approximate coalescent with selection

Shlyakhter, I., Sabeti, P. C., Schaffner, S. F.

Journal:

Year:

2014

Language:

english

File:

PDF, 95 KB

english, 2014

14

A novel feature-based approach to extract drug-drug interactions from biomedical text

Bui, Q.-C., Sloot, P. M. A., van Mulligen, E. M., Kors, J. A.

Journal:

Year:

2014

Language:

english

File:

PDF, 159 KB

english, 2014

15

FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution

Newman, A. M., Bratman, S. V., Stehr, H., Lee, L. J., Liu, C. L., Diehn, M., Alizadeh, A. A.

Journal:

Year:

2014

Language:

english

File:

PDF, 218 KB

english, 2014

16

Cell population identification using fluorescence-minus-one controls with a one-class classifying algorithm

Feher, K., Kirsch, J., Radbruch, A., Chang, H.-D., Kaiser, T.

Journal:

Year:

2014

Language:

english

File:

PDF, 351 KB

english, 2014

17

PHOXTRACK-a tool for interpreting comprehensive datasets of post-translational modifications of proteins

Weidner, C., Fischer, C., Sauer, S.

Journal:

Year:

2014

Language:

english

File:

PDF, 190 KB

english, 2014

18

ExpTreeDB: Web-based query and visualization of manually annotated gene expression profiling experiments of human and mouse from GEO

Ni, M., Ye, F., Zhu, J., Li, Z., Yang, S., Yang, B., Han, L., Wu, Y., Chen, Y., Li, F., Wang, S., Bo, X.

Journal:

Year:

2014

Language:

english

File:

PDF, 567 KB

english, 2014

19

ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments

Khan, I. A., Fraser, A., Bray, M.-A., Smith, P. J., White, N. S., Carpenter, A. E., Errington, R. J.

Journal:

Year:

2014

Language:

english

File:

PDF, 108 KB

english, 2014

20

SecureMA: protecting participant privacy in genetic association meta-analysis

Xie, W., Kantarcioglu, M., Bush, W. S., Crawford, D., Denny, J. C., Heatherly, R., Malin, B. A.

Journal:

Year:

2014

Language:

english

File:

PDF, 608 KB

english, 2014

21

Quartet Inference from SNP Data Under the Coalescent Model

Chifman, J., Kubatko, L.

Journal:

Year:

2014

Language:

english

File:

PDF, 811 KB

english, 2014

22

subSeq: Determining Appropriate Sequencing Depth Through Efficient Read Subsampling

Robinson, D. G., Storey, J. D.

Journal:

Year:

2014

Language:

english

File:

PDF, 135 KB

english, 2014

23

OptiType: precision HLA typing from next-generation sequencing data

Szolek, A., Schubert, B., Mohr, C., Sturm, M., Feldhahn, M., Kohlbacher, O.

Journal:

Year:

2014

Language:

english

File:

PDF, 750 KB

english, 2014

24

Poretools: a toolkit for analyzing nanopore sequence data

Loman, N. J., Quinlan, A. R.

Journal:

Year:

2014

Language:

english

File:

PDF, 139 KB

english, 2014

25

RVboost: RNA-seq variants prioritization using a boosting method

Wang, C., Davila, J. I., Baheti, S., Bhagwate, A. V., Wang, X., Kocher, J.-P. A., Slager, S. L., Feldman, A. L., Novak, A. J., Cerhan, J. R., Thompson, E. A., Asmann, Y. W.

Journal:

Year:

2014

Language:

english

File:

PDF, 172 KB

english, 2014

26

diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals

Tataru, P., Nirody, J. A., Song, Y. S.

Journal:

Year:

2014

Language:

english

File:

PDF, 125 KB

english, 2014

27

MIRPIPE: quantification of microRNAs in niche model organisms

Kuenne, C., Preussner, J., Herzog, M., Braun, T., Looso, M.

Journal:

Year:

2014

Language:

english

File:

PDF, 128 KB

english, 2014

28

VSEAMS: a pipeline for variant set enrichment analysis using summary GWAS data identifies IKZF3, BATF and ESRRA as key transcription factors in type 1 diabetes

Burren, O. S., Guo, H., Wallace, C.

Journal:

Year:

2014

Language:

english

File:

PDF, 456 KB

english, 2014

29

Acceleration of short and long DNA read mapping without loss of accuracy using suffix array

Tarraga, J., Arnau, V., Martinez, H., Moreno, R., Cazorla, D., Salavert-Torres, J., Blanquer-Espert, I., Dopazo, J., Medina, I.

Journal:

Year:

2014

Language:

english

File:

PDF, 111 KB

english, 2014

30

PEPPER: cytoscape app for protein complex expansion using protein-protein interaction networks

Winterhalter, C., Nicolle, R., Louis, A., To, C., Radvanyi, F., Elati, M.

Journal:

Year:

2014

Language:

english

File:

PDF, 196 KB

english, 2014

31

SCDFinder, a Web-based tool for the identification of putative novel ATM and ATR targets

Cara, L., Baitemirova, M., Duong, F., Larios-Sanz, M., Ribes-Zamora, A.

Journal:

Year:

2014

Language:

english

File:

PDF, 140 KB

english, 2014

32

HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations

Usuyama, N., Shiraishi, Y., Sato, Y., Kume, H., Homma, Y., Ogawa, S., Miyano, S., Imoto, S.

Journal:

Year:

2014

Language:

english

File:

PDF, 531 KB

english, 2014

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