Volume 28; Issue 5

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Bioinformatics
Volume 28; Issue 5

Bioinformatics

Volume 28; Issue 5

1

Predicting folding free energy changes upon single point mutations

Zhang, Z., Wang, L., Gao, Y., Zhang, J., Zhenirovskyy, M., Alexov, E.

Journal:

Year:

2012

Language:

english

File:

PDF, 263 KB

english, 2012

2

GROMACS molecule & liquid database

van der Spoel, D., van Maaren, P. J., Caleman, C.

Journal:

Year:

2012

Language:

english

File:

PDF, 164 KB

english, 2012

3

SNP calling using genotype model selection on high-throughput sequencing data

You, N., Murillo, G., Su, X., Zeng, X., Xu, J., Ning, K., Zhang, S., Zhu, J., Cui, X.

Journal:

Year:

2012

Language:

english

File:

PDF, 211 KB

english, 2012

4

FX: an RNA-Seq analysis tool on the cloud

Hong, D., Rhie, A., Park, S.-S., Lee, J., Ju, Y. S., Kim, S., Yu, S.-B., Bleazard, T., Park, H.-S., Rhee, H., Chong, H., Yang, K.-S., Lee, Y.-S., Kim, I.-H., Lee, J. S., Kim, J.-I., Seo, J.-S.

Journal:

Year:

2012

Language:

english

File:

PDF, 233 KB

english, 2012

5

IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data

Wang, D., Yan, L., Hu, Q., Sucheston, L. E., Higgins, M. J., Ambrosone, C. B., Johnson, C. S., Smiraglia, D. J., Liu, S.

Journal:

Year:

2012

Language:

english

File:

PDF, 98 KB

english, 2012

6

COPICAT: a software system for predicting interactions between proteins and chemical compounds

Sakakibara, Y., Hachiya, T., Uchida, M., Nagamine, N., Sugawara, Y., Yokota, M., Nakamura, M., Popendorf, K., Komori, T., Sato, K.

Journal:

Year:

2012

Language:

english

File:

PDF, 148 KB

english, 2012

7

An effective statistical evaluation of ChIPseq dataset similarity

D. Chikina, M., G. Troyanskaya, O.

Journal:

Year:

2012

Language:

english

File:

PDF, 791 KB

english, 2012

8

nEASE: a method for gene ontology subclassification of high-throughput gene expression data

Chittenden, T. W., Howe, E. A., Taylor, J. M., Mar, J. C., Aryee, M. J., Gomez, H., Sultana, R., Braisted, J., Nair, S. J., Quackenbush, J., Holmes, C.

Journal:

Year:

2012

Language:

english

File:

PDF, 133 KB

english, 2012

9

AnnTools: a comprehensive and versatile annotation toolkit for genomic variants

Makarov, V., O'Grady, T., Cai, G., Lihm, J., Buxbaum, J. D., Yoon, S.

Journal:

Year:

2012

Language:

english

File:

PDF, 68 KB

english, 2012

10

StochSens--matlab package for sensitivity analysis of stochastic chemical systems

Komorowski, M., Zurauskiene, J., Stumpf, M. P. H.

Journal:

Year:

2012

Language:

english

File:

PDF, 142 KB

english, 2012

11

MetExtract: a new software tool for the automated comprehensive extraction of metabolite-derived LC/MS signals in metabolomics research

Bueschl, C., Kluger, B., Berthiller, F., Lirk, G., Winkler, S., Krska, R., Schuhmacher, R.

Journal:

Year:

2012

Language:

english

File:

PDF, 80 KB

english, 2012

12

Mining and evaluation of molecular relationships in literature

Senger, C., Gruning, B. A., Erxleben, A., Doring, K., Patel, H., Flemming, S., Merfort, I., Gunther, S.

Journal:

Year:

2012

Language:

english

File:

PDF, 704 KB

english, 2012

13

medpie: an information extraction package for medical message board posts

Benton, A., Holmes, J. H., Hill, S., Chung, A., Ungar, L.

Journal:

Year:

2012

Language:

english

File:

PDF, 66 KB

english, 2012

14

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts

Goke, J., Schulz, M. H., Lasserre, J., Vingron, M.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.95 MB

english, 2012

15

BESC knowledgebase public portal

Syed, M. H., Karpinets, T. V., Parang, M., Leuze, M. R., Park, B. H., Hyatt, D., Brown, S. D., Moulton, S., Galloway, M. D., Uberbacher, E. C.

Journal:

Year:

2012

Language:

english

File:

PDF, 67 KB

english, 2012

16

De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae

Chen, M.-J. M., Chou, L.-C., Hsieh, T.-T., Lee, D.-D., Liu, K.-W., Yu, C.-Y., Oyang, Y.-J., Tsai, H.-K., Chen, C.-Y.

Journal:

Year:

2012

Language:

english

File:

PDF, 555 KB

english, 2012

17

NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment

Carr, R., Borenstein, E.

Journal:

Year:

2012

Language:

english

File:

PDF, 128 KB

english, 2012

18

Interactome-transcriptome integration for predicting distant metastasis in breast cancer

Garcia, M., Millat-Carus, R., Bertucci, F., Finetti, P., Birnbaum, D., Bidaut, G.

Journal:

Year:

2012

Language:

english

File:

PDF, 333 KB

english, 2012

19

influx_s: increasing numerical stability and precision for metabolic flux analysis in isotope labelling experiments

Sokol, S., Millard, P., Portais, J.-C.

Journal:

Year:

2012

Language:

english

File:

PDF, 256 KB

english, 2012

20

IMID: integrated molecular interaction database

Balaji, S., Mcclendon, C., Chowdhary, R., Liu, J. S., Zhang, J.

Journal:

Year:

2012

Language:

english

File:

PDF, 192 KB

english, 2012

21

A scalable and portable framework for massively parallel variable selection in genetic association studies

Journal:

Year:

2012

Language:

english

File:

PDF, 101 KB

english, 2012

22

Roundup 2.0: enabling comparative genomics for over 1800 genomes

DeLuca, T. F., Cui, J., Jung, J.-Y., St. Gabriel, K. C., Wall, D. P.

Journal:

Year:

2012

Language:

english

File:

PDF, 71 KB

english, 2012

23

Application of canonical correlation analysis for identifying viral integration preferences

Gumus, E., Kursun, O., Sertbas, A., Ustek, D.

Journal:

Year:

2012

Language:

english

File:

PDF, 356 KB

english, 2012

24

Mining and integration of pathway diagrams from imaging data

Kozhenkov, S., Baitaluk, M.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.05 MB

english, 2012

25

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS

Emde, A.-K., Schulz, M. H., Weese, D., Sun, R., Vingron, M., Kalscheuer, V. M., Haas, S. A., Reinert, K.

Journal:

Year:

2012

Language:

english

File:

PDF, 562 KB

english, 2012

26

PHACTS, a computational approach to classifying the lifestyle of phages

McNair, K., Bailey, B. A., Edwards, R. A.

Journal:

Year:

2012

Language:

english

File:

PDF, 208 KB

english, 2012

27

Transformations for the compression of FASTQ quality scores of next-generation sequencing data

Wan, R., Anh, V. N., Asai, K.

Journal:

Year:

2012

Language:

english

File:

PDF, 628 KB

english, 2012

28

CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signatures

Hentrich, T., Schulze, J. M., Emberly, E., Kobor, M. S.

Journal:

Year:

2012

Language:

english

File:

PDF, 164 KB

english, 2012

29

The evolution of nitrogen fixation in cyanobacteria

Latysheva, N., Junker, V. L., Palmer, W. J., Codd, G. A., Barker, D.

Journal:

Year:

2012

Language:

english

File:

PDF, 479 KB

english, 2012

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