Volume 31; Issue 4

Main
Bioinformatics
Volume 31; Issue 4

Bioinformatics

Volume 31; Issue 4

1

Differential regulation enrichment analysis via the integration of transcriptional regulatory network and gene expression data

Ma, S., Jiang, T., Jiang, R.

Journal:

Year:

2015

Language:

english

File:

PDF, 556 KB

english, 2015

2

miRseqViewer: multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data

Jang, I., Chang, H., Jun, Y., Park, S., Yang, J. O., Lee, B., Kim, W., Kim, V. N., Lee, S.

Journal:

Year:

2015

Language:

english

File:

PDF, 332 KB

english, 2015

3

Accurate estimation of haplotype frequency from pooled sequencing data and cost-effective identification of rare haplotype carriers by overlapping pool sequencing

Cao, C.-C., Sun, X.

Journal:

Year:

2015

Language:

english

File:

PDF, 378 KB

english, 2015

4

FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures

Huang, Y.-F., Golding, G. B.

Journal:

Year:

2015

Language:

english

File:

PDF, 2.59 MB

english, 2015

5

IntSide: a web server for the chemical and biological examination of drug side effects

Juan-Blanco, T., Duran-Frigola, M., Aloy, P.

Journal:

Year:

2015

Language:

english

File:

PDF, 258 KB

english, 2015

6

DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis

Yu, G., Wang, L.-G., Yan, G.-R., He, Q.-Y.

Journal:

Year:

2015

Language:

english

File:

PDF, 294 KB

english, 2015

7

MOST: a software environment for constraint-based metabolic modeling and strain design

Kelley, J. J., Lane, A., Li, X., Mutthoju, B., Maor, S., Egen, D., Lun, D. S.

Journal:

Year:

2015

Language:

english

File:

PDF, 215 KB

english, 2015

8

An efficient algorithm for the blocked pattern matching problem

Deng, F., Wang, L., Liu, X.

Journal:

Year:

2015

Language:

english

File:

PDF, 574 KB

english, 2015

9

Comment on 'protein-protein binding affinity prediction from amino acid sequence'

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

Journal:

Year:

2015

Language:

english

File:

PDF, 119 KB

english, 2015

10

LIGSIFT: an open-source tool for ligand structural alignment and virtual screening

Roy, A., Skolnick, J.

Journal:

Year:

2015

Language:

english

File:

PDF, 211 KB

english, 2015

11

E-MEM: efficient computation of maximal exact matches for very large genomes

Khiste, N., Ilie, L.

Journal:

Year:

2015

Language:

english

File:

PDF, 334 KB

english, 2015

12

flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification

Malek, M., Taghiyar, M. J., Chong, L., Finak, G., Gottardo, R., Brinkman, R. R.

Journal:

Year:

2015

Language:

english

File:

PDF, 321 KB

english, 2015

13

Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus

Karp, P. D., Berger, B., Kovats, D., Lengauer, T., Linial, M., Sabeti, P., Hide, W., Rost, B.

Journal:

Year:

2015

Language:

english

File:

PDF, 69 KB

english, 2015

14

jNMFMA: a joint non-negative matrix factorization meta-analysis of transcriptomics data

Wang, H.-Q., Zheng, C.-H., Zhao, X.-M.

Journal:

Year:

2015

Language:

english

File:

PDF, 433 KB

english, 2015

15

Seed: a user-friendly tool for exploring and visualizing microbial community data

Beck, D., Dennis, C., Foster, J. A.

Journal:

Year:

2015

Language:

english

File:

PDF, 145 KB

english, 2015

16

mimicMe: a web server for prediction and analysis of host-like proteins in microbial pathogens

Petrenko, P., Doxey, A. C.

Journal:

Year:

2015

Language:

english

File:

PDF, 417 KB

english, 2015

17

Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge

Dayarian, A., Romero, R., Wang, Z., Biehl, M., Bilal, E., Hormoz, S., Meyer, P., Norel, R., Rhrissorrakrai, K., Bhanot, G., Luo, F., Tarca, A. L.

Journal:

Year:

2015

Language:

english

File:

PDF, 452 KB

english, 2015

18

SYSBIONS: nested sampling for systems biology

Johnson, R., Kirk, P., Stumpf, M. P. H.

Journal:

Year:

2015

Language:

english

File:

PDF, 99 KB

english, 2015

19

Introducing dAUTObase: a first step towards the global scale geoepidemiology of autoimmune syndromes and diseases

Gkantouna, V. A., Kambouris, M. E., Viennas, E. S., Ioannou, Z.-M., Paraskevas, M., Lagoumintzis, G., Zagoriti, Z., Patrinos, G. P., Tzimas, G. E., Poulas, K.

Journal:

Year:

2015

Language:

english

File:

PDF, 445 KB

english, 2015

20

Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge

Biehl, M., Sadowski, P., Bhanot, G., Bilal, E., Dayarian, A., Meyer, P., Norel, R., Rhrissorrakrai, K., Zeller, M. D., Hormoz, S.

Journal:

Year:

2015

Language:

english

File:

PDF, 649 KB

english, 2015

21

Statistical significance of variables driving systematic variation in high-dimensional data

Chung, N. C., Storey, J. D.

Journal:

Year:

2015

Language:

english

File:

PDF, 439 KB

english, 2015

22

Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge

Rhrissorrakrai, K., Belcastro, V., Bilal, E., Norel, R., Poussin, C., Mathis, C., Dulize, R. H. J., Ivanov, N. V., Alexopoulos, L., Jeremy Rice, J., Peitsch, M. C., Stolovitzky, G., Meyer, P., Hoeng,

Journal:

Year:

2015

Language:

english

File:

PDF, 966 KB

english, 2015

23

LICRE: unsupervised feature correlation reduction for lipidomics

Wong, G., Chan, J., Kingwell, B. A., Leckie, C., Meikle, P. J.

Journal:

Year:

2015

Language:

english

File:

PDF, 41 KB

english, 2015

24

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing

Han, B. W., Wang, W., Zamore, P. D., Weng, Z.

Journal:

Year:

2015

Language:

english

File:

PDF, 7.12 MB

english, 2015

25

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data

Coil, D., Jospin, G., Darling, A. E.

Journal:

Year:

2015

Language:

english

File:

PDF, 171 KB

english, 2015

26

Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker

Willet, C. E., Haase, B., Charleston, M. A., Wade, C. M.

Journal:

Year:

2015

Language:

english

File:

PDF, 81 KB

english, 2015

27

Where are we at regarding species translation? A review of the sbv IMPROVER challenge

Hoeng, J., Peitsch, M. C., Meyer, P., Jurisica, I.

Journal:

Year:

2015

Language:

english

File:

PDF, 63 KB

english, 2015

28

A crowd-sourcing approach for the construction of species-specific cell signaling networks

Bilal, E., Sakellaropoulos, T., Participants, C., Melas, I. N., Messinis, D. E., Belcastro, V., Rhrissorrakrai, K., Meyer, P., Norel, R., Iskandar, A., Blaese, E., Rice, J. J., Peitsch, M. C., Hoeng,

Journal:

Year:

2015

Language:

english

File:

PDF, 711 KB

english, 2015

29

Inter-species pathway perturbation prediction via data-driven detection of functional homology

Hafemeister, C., Romero, R., Bilal, E., Meyer, P., Norel, R., Rhrissorrakrai, K., Bonneau, R., Tarca, A. L.

Journal:

Year:

2015

Language:

english

File:

PDF, 471 KB

english, 2015

30

Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets

Hormoz, S., Bhanot, G., Biehl, M., Bilal, E., Meyer, P., Norel, R., Rhrissorrakrai, K., Dayarian, A.

Journal:

Year:

2015

Language:

english

File:

PDF, 812 KB

english, 2015

31

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity

Li, Y., Xie, X.

Journal:

Year:

2015

Language:

english

File:

PDF, 44 KB

english, 2015