Volume 30; Issue 17

Main
Bioinformatics
Volume 30; Issue 17

Bioinformatics

Volume 30; Issue 17

1

GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms

Wang, J.-H., Zhao, L.-F., Lin, P., Su, X.-R., Chen, S.-J., Huang, L.-Q., Wang, H.-F., Zhang, H., Hu, Z.-F., Yao, K.-T., Huang, Z.-X.

Journal:

Year:

2014

Language:

english

File:

PDF, 87 KB

english, 2014

2

Mirin: identifying microRNA regulatory modules in protein-protein interaction networks

Yang, K.-C., Hsu, C.-L., Lin, C.-C., Juan, H.-F., Huang, H.-C.

Journal:

Year:

2014

Language:

english

File:

PDF, 250 KB

english, 2014

3

unifiedWMWqPCR: the unified Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data in R

De Neve, J., Meys, J., Ottoy, J.-P., Clement, L., Thas, O.

Journal:

Year:

2014

Language:

english

File:

PDF, 78 KB

english, 2014

4

Ceiba: scalable visualization of phylogenies and 2D/3D image collections

Sanderson, M. J.

Journal:

Year:

2014

Language:

english

File:

PDF, 197 KB

english, 2014

5

PhenoNet: identification of key networks associated with disease phenotype

Ben-Hamo, R., Gidoni, M., Efroni, S.

Journal:

Year:

2014

Language:

english

File:

PDF, 638 KB

english, 2014

6

lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs

Park, C., Yu, N., Choi, I., Kim, W., Lee, S.

Journal:

Year:

2014

Language:

english

File:

PDF, 855 KB

english, 2014

7

MethylSig: a whole genome DNA methylation analysis pipeline

Park, Y., Figueroa, M. E., Rozek, L. S., Sartor, M. A.

Journal:

Year:

2014

Language:

english

File:

PDF, 746 KB

english, 2014

8

RNASeqExpressionBrowser--a web interface to browse and visualize high-throughput expression data

Nussbaumer, T., Kugler, K. G., Bader, K. C., Sharma, S., Seidel, M., Mayer, K. F. X.

Journal:

Year:

2014

Language:

english

File:

PDF, 852 KB

english, 2014

9

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments

Choi, M., Chang, C.-Y., Clough, T., Broudy, D., Killeen, T., MacLean, B., Vitek, O.

Journal:

Year:

2014

Language:

english

File:

PDF, 6.42 MB

english, 2014

10

A framework for installable external tools in Skyline

Broudy, D., Killeen, T., Choi, M., Shulman, N., Mani, D. R., Abbatiello, S. E., Mani, D., Ahmad, R., Sahu, A. K., Schilling, B., Tamura, K., Boss, Y., Sharma, V., Gibson, B. W., Carr, S. A., Vitek, O.

Journal:

Year:

2014

Language:

english

File:

PDF, 211 KB

english, 2014

11

Inferring the paths of somatic evolution in cancer

Misra, N., Szczurek, E., Vingron, M.

Journal:

Year:

2014

Language:

english

File:

PDF, 916 KB

english, 2014

12

compcodeR--an R package for benchmarking differential expression methods for RNA-seq data

Journal:

Year:

2014

Language:

english

File:

PDF, 252 KB

english, 2014

13

FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data

Wang, W., Wang, P., Xu, F., Luo, R., Wong, M. P., Lam, T.-W., Wang, J.

Journal:

Year:

2014

Language:

english

File:

PDF, 209 KB

english, 2014

14

PeakLink: a new peptide peak linking method in LC-MS/MS using wavelet and SVM

Ghanat Bari, M., Ma, X., Zhang, J.

Journal:

Year:

2014

Language:

english

File:

PDF, 437 KB

english, 2014

15

RiboMaker: computational design of conformation-based riboregulation

Rodrigo, G., Jaramillo, A.

Journal:

Year:

2014

Language:

english

File:

PDF, 232 KB

english, 2014

16

Exploring protein domain organization by recognition of secondary structure packing interfaces

Deng, L., Wu, A., Dai, W., Song, T., Cui, Y., Jiang, T.

Journal:

Year:

2014

Language:

english

File:

PDF, 750 KB

english, 2014

17

Probabilistic partitioning methods to find significant patterns in ChIP-Seq data

Nair, N. U., Kumar, S., Moret, B. M. E., Bucher, P.

Journal:

Year:

2014

Language:

english

File:

PDF, 836 KB

english, 2014

18

Universal dynamical properties preclude standard clustering in a large class of biochemical data

Gomez, F., Stoop, R. L., Stoop, R.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.40 MB

english, 2014

19

Broad-Enrich: functional interpretation of large sets of broad genomic regions

Cavalcante, R. G., Lee, C., Welch, R. P., Patil, S., Weymouth, T., Scott, L. J., Sartor, M. A.

Journal:

Year:

2014

Language:

english

File:

PDF, 579 KB

english, 2014

20

Exploration and retrieval of whole-metagenome sequencing samples

Seth, S., Valimaki, N., Kaski, S., Honkela, A.

Journal:

Year:

2014

Language:

english

File:

PDF, 694 KB

english, 2014

21

A new statistical framework to assess structural alignment quality using information compression

Collier, J. H., Allison, L., Lesk, A. M., Garcia de la Banda, M., Konagurthu, A. S.

Journal:

Year:

2014

Language:

english

File:

PDF, 440 KB

english, 2014

22

SIBIS: a Bayesian model for inconsistent protein sequence estimation

Khenoussi, W., Vanhoutreve, R., Poch, O., Thompson, J. D.

Journal:

Year:

2014

Language:

english

File:

PDF, 510 KB

english, 2014

23

RNASeqGUI: a GUI for analysing RNA-Seq data

Russo, F., Angelini, C.

Journal:

Year:

2014

Language:

english

File:

PDF, 169 KB

english, 2014

24

Bioinformatics-driven discovery of rational combination for overcoming EGFR-mutant lung cancer resistance to EGFR therapy

Kim, J., Vasu, V. T., Mishra, R., Singleton, K. R., Yoo, M., Leach, S. M., Farias-Hesson, E., Mason, R. J., Kang, J., Ramamoorthy, P., Kern, J. A., Heasley, L. E., Finigan, J. H., Tan, A. C.

Journal:

Year:

2014

Language:

english

File:

PDF, 428 KB

english, 2014

25

SEK: sparsity exploiting k-mer-based estimation of bacterial community composition

Chatterjee, S., Koslicki, D., Dong, S., Innocenti, N., Cheng, L., Lan, Y., Vehkapera, M., Skoglund, M., Rasmussen, L. K., Aurell, E., Corander, J.

Journal:

Year:

2014

Language:

english

File:

PDF, 527 KB

english, 2014

26

Point estimates in phylogenetic reconstructions

Benner, P., Ba ak, M., Bourguignon, P.-Y.

Journal:

Year:

2014

Language:

english

File:

PDF, 365 KB

english, 2014

27

Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images

Frasconi, P., Silvestri, L., Soda, P., Cortini, R., Pavone, F. S., Iannello, G.

Journal:

Year:

2014

Language:

english

File:

PDF, 418 KB

english, 2014

28

cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data

Bellos, E., Coin, L. J. M.

Journal:

Year:

2014

Language:

english

File:

PDF, 633 KB

english, 2014

29

ASTRAL: genome-scale coalescent-based species tree estimation

Mirarab, S., Reaz, R., Bayzid, M. S., Zimmermann, T., Swenson, M. S., Warnow, T.

Journal:

Year:

2014

Language:

english

File:

PDF, 482 KB

english, 2014

30

PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition

Lancaster, A. K., Nutter-Upham, A., Lindquist, S., King, O. D.

Journal:

Year:

2014

Language:

english

File:

PDF, 256 KB

english, 2014

31

PconsFold: improved contact predictions improve protein models

Michel, M., Hayat, S., Skwark, M. J., Sander, C., Marks, D. S., Elofsson, A.

Journal:

Year:

2014

Language:

english

File:

PDF, 799 KB

english, 2014

32

Integration of molecular network data reconstructs Gene Ontology

Gligorijevi , V., Janji , V., Pr ulj, N.

Journal:

Year:

2014

Language:

english

File:

PDF, 390 KB

english, 2014

33

Effects of small particle numbers on long-term behaviour in discrete biochemical systems

Kreyssig, P., Wozar, C., Peter, S., Veloz, T., Ibrahim, B., Dittrich, P.

Journal:

Year:

2014

Language:

english

File:

PDF, 558 KB

english, 2014

34

FastHap: fast and accurate single individual haplotype reconstruction using fuzzy conflict graphs

Mazrouee, S., Wang, W.

Journal:

Year:

2014

Language:

english

File:

PDF, 402 KB

english, 2014

35

SNPsea: an algorithm to identify cell types, tissues and pathways affected by risk loci

Slowikowski, K., Hu, X., Raychaudhuri, S.

Journal:

Year:

2014

Language:

english

File:

PDF, 169 KB

english, 2014

36

Transcriptome-guided amyloid imaging genetic analysis via a novel structured sparse learning algorithm

Yan, J., Du, L., Kim, S., Risacher, S. L., Huang, H., Moore, J. H., Saykin, A. J., Shen, L.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.19 MB

english, 2014

37

Fast randomization of large genomic datasets while preserving alteration counts

Gobbi, A., Iorio, F., Dawson, K. J., Wedge, D. C., Tamborero, D., Alexandrov, L. B., Lopez-Bigas, N., Garnett, M. J., Jurman, G., Saez-Rodriguez, J.

Journal:

Year:

2014

Language:

english

File:

PDF, 419 KB

english, 2014

38

Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis

Khan, S. A., Virtanen, S., Kallioniemi, O. P., Wennerberg, K., Poso, A., Kaski, S.

Journal:

Year:

2014

Language:

english

File:

PDF, 852 KB

english, 2014

39

ECCB 2014 Organization

Journal:

Year:

2014

Language:

english

File:

PDF, 68 KB

english, 2014

40

Extracting patterns of database and software usage from the bioinformatics literature

Duck, G., Nenadic, G., Brass, A., Robertson, D. L., Stevens, R.

Journal:

Year:

2014

Language:

english

File:

PDF, 904 KB

english, 2014

41

Modeling DNA methylation dynamics with approaches from phylogenetics

Capra, J. A., Kostka, D.

Journal:

Year:

2014

Language:

english

File:

PDF, 770 KB

english, 2014

42

Fiona: a parallel and automatic strategy for read error correction

Schulz, M. H., Weese, D., Holtgrewe, M., Dimitrova, V., Niu, S., Reinert, K., Richard, H.

Journal:

Year:

2014

Language:

english

File:

PDF, 450 KB

english, 2014

43

Two-dimensional segmentation for analyzing Hi-C data

Levy-Leduc, C., Delattre, M., Mary-Huard, T., Robin, S.

Journal:

Year:

2014

Language:

english

File:

PDF, 460 KB

english, 2014

44

HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks

Hashemifar, S., Xu, J.

Journal:

Year:

2014

Language:

english

File:

PDF, 339 KB

english, 2014

45

Identifying transcription factor complexes and their roles

Will, T., Helms, V.

Journal:

Year:

2014

Language:

english

File:

PDF, 505 KB

english, 2014

46

Entropy-driven partitioning of the hierarchical protein space

Rappoport, N., Stern, A., Linial, N., Linial, M.

Journal:

Year:

2014

Language:

english

File:

PDF, 554 KB

english, 2014

47

Polytomy refinement for the correction of dubious duplications in gene trees

Lafond, M., Chauve, C., Dondi, R., El-Mabrouk, N.

Journal:

Year:

2014

Language:

english

File:

PDF, 588 KB

english, 2014

48

Personalized identification of altered pathways in cancer using accumulated normal tissue data

Ahn, T., Lee, E., Huh, N., Park, T.

Journal:

Year:

2014

Language:

english

File:

PDF, 592 KB

english, 2014

49

Causal network inference using biochemical kinetics

Oates, C. J., Dondelinger, F., Bayani, N., Korkola, J., Gray, J. W., Mukherjee, S.

Journal:

Year:

2014

Language:

english

File:

PDF, 739 KB

english, 2014

50

GEPdb: a database for investigating the ternary association of genotype, gene expression and phenotype

Ryu, D., Cho, S., Kim, H., Lee, S., Kim, W.

Journal:

Year:

2014

Language:

english

File:

PDF, 250 KB

english, 2014

51

Microarray R-based analysis of complex lysate experiments with MIRACLE

List, M., Block, I., Pedersen, M. L., Christiansen, H., Schmidt, S., Thomassen, M., Tan, Q., Baumbach, J., Mollenhauer, J.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.11 MB

english, 2014

52

CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci

Alkhnbashi, O. S., Costa, F., Shah, S. A., Garrett, R. A., Saunders, S. J., Backofen, R.

Journal:

Year:

2014

Language:

english

File:

PDF, 550 KB

english, 2014

53

Alignment-free protein interaction network comparison

Ali, W., Rito, T., Reinert, G., Sun, F., Deane, C. M.

Journal:

Year:

2014

Language:

english

File:

PDF, 322 KB

english, 2014

54

Experimental design schemes for learning Boolean network models

Atias, N., Gershenzon, M., Labazin, K., Sharan, R.

Journal:

Year:

2014

Language:

english

File:

PDF, 385 KB

english, 2014

55

Efficient RNA isoform identification and quantification from RNA-Seq data with network flows

Bernard, E., Jacob, L., Mairal, J., Vert, J.-P.

Journal:

Year:

2014

Language:

english

File:

PDF, 618 KB

english, 2014

56

Bioclojure: a functional library for the manipulation of biological sequences

Plieskatt, J., Rinaldi, G., Brindley, P. J., Jia, X., Potriquet, J., Bethony, J., Mulvenna, J.

Journal:

Year:

2014

Language:

english

File:

PDF, 95 KB

english, 2014

57

SAMBLASTER: fast duplicate marking and structural variant read extraction

Faust, G. G., Hall, I. M.

Journal:

Year:

2014

Language:

english

File:

PDF, 105 KB

english, 2014

58

Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations

Suvitaival, T., Rogers, S., Kaski, S.

Journal:

Year:

2014

Language:

english

File:

PDF, 267 KB

english, 2014

59

Probabilistic single-individual haplotyping

Journal:

Year:

2014

Language:

english

File:

PDF, 355 KB

english, 2014

60

ECCB 2014: The 13th European Conference on Computational Biology

Devignes, M.-D., Moreau, Y.

Journal:

Year:

2014

Language:

english

File:

PDF, 84 KB

english, 2014

61

Towards a piRNA prediction using multiple kernel fusion and support vector machine

Brayet, J., Zehraoui, F., Jeanson-Leh, L., Israeli, D., Tahi, F.

Journal:

Year:

2014

Language:

english

File:

PDF, 273 KB

english, 2014

62

Estimating the activity of transcription factors by the effect on their target genes

Schacht, T., Oswald, M., Eils, R., Eichmuller, S. B., Konig, R.

Journal:

Year:

2014

Language:

english

File:

PDF, 255 KB

english, 2014

63

ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples

Tian, R., Basu, M. K., Capriotti, E.

Journal:

Year:

2014

Language:

english

File:

PDF, 277 KB

english, 2014

64

RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees

Kratsch, C., McHardy, A. C.

Journal:

Year:

2014

Language:

english

File:

PDF, 471 KB

english, 2014

65

Lambda: the local aligner for massive biological data

Hauswedell, H., Singer, J., Reinert, K.

Journal:

Year:

2014

Language:

english

File:

PDF, 309 KB

english, 2014

66

Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning

Gonen, M., Margolin, A. A.

Journal:

Year:

2014

Language:

english

File:

PDF, 348 KB

english, 2014

67

FASTGAPFILL: efficient gap filling in metabolic networks

Thiele, I., Vlassis, N., Fleming, R. M. T.

Journal:

Year:

2014

Language:

english

File:

PDF, 101 KB

english, 2014

68

Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane)

Studer, G., Biasini, M., Schwede, T.

Journal:

Year:

2014

Language:

english

File:

PDF, 481 KB

english, 2014

69

OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action

Schroeder, M. P., Rubio-Perez, C., Tamborero, D., Gonzalez-Perez, A., Lopez-Bigas, N.

Journal:

Year:

2014

Language:

english

File:

PDF, 345 KB

english, 2014

70

TEMPI: probabilistic modeling time-evolving differential PPI networks with multiPle information

Kim, Y., Jang, J.-H., Choi, S., Hwang, D.

Journal:

Year:

2014

Language:

english

File:

PDF, 745 KB

english, 2014

71

The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective

Jiang, Y., Clark, W. T., Friedberg, I., Radivojac, P.

Journal:

Year:

2014

Language:

english

File:

PDF, 682 KB

english, 2014

72

PyCorrFit--generic data evaluation for fluorescence correlation spectroscopy

Muller, P., Schwille, P., Weidemann, T.

Journal:

Year:

2014

Language:

english

File:

PDF, 149 KB

english, 2014

73

Unveiling new biological relationships using shared hits of chemical screening assay pairs

Liu, X., Campillos, M.

Journal:

Year:

2014

Language:

english

File:

PDF, 762 KB

english, 2014