Volume 30; Issue 12

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Bioinformatics
Volume 30; Issue 12

Bioinformatics

Volume 30; Issue 12

1

Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis

Carrella, D., Napolitano, F., Rispoli, R., Miglietta, M., Carissimo, A., Cutillo, L., Sirci, F., Gregoretti, F., Di Bernardo, D.

Journal:

Year:

2014

Language:

english

File:

PDF, 194 KB

english, 2014

2

TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes

Anvar, S. Y., van der Gaag, K. J., van der Heijden, J. W. F., Veltrop, M. H. A. M., Vossen, R. H. A. M., de Leeuw, R. H., Breukel, C., Buermans, H. P. J., Verbeek, J. S., de Knijff, P., den Dunnen, J.

Journal:

Year:

2014

Language:

english

File:

PDF, 886 KB

english, 2014

3

BioPlat: a software for human cancer biomarker discovery

Butti, M. D., Chanfreau, H., Martinez, D., Garcia, D., Lacunza, E., Abba, M. C.

Journal:

Year:

2014

Language:

english

File:

PDF, 234 KB

english, 2014

4

Improved protein-ligand binding affinity prediction by using a curvature-dependent surface-area model

Cao, Y., Li, L.

Journal:

Year:

2014

Language:

english

File:

PDF, 516 KB

english, 2014

5

Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals

Cheng, A. Y., Teo, Y.-Y., Ong, R. T.-H.

Journal:

Year:

2014

Language:

english

File:

PDF, 461 KB

english, 2014

6

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

Pierce, B. G., Wiehe, K., Hwang, H., Kim, B.-H., Vreven, T., Weng, Z.

Journal:

Year:

2014

Language:

english

File:

PDF, 359 KB

english, 2014

7

Dynamic networks reveal key players in aging

Faisal, F. E., Milenkovi , T.

Journal:

Year:

2014

Language:

english

File:

PDF, 412 KB

english, 2014

8

GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database

Leslie, R., O'Donnell, C. J., Johnson, A. D.

Journal:

Year:

2014

Language:

english

File:

PDF, 663 KB

english, 2014

9

SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing

Wang, X., Cairns, M. J.

Journal:

Year:

2014

Language:

english

File:

PDF, 90 KB

english, 2014

10

Condition-specific target prediction from motifs and expression

Meng, G., Vingron, M.

Journal:

Year:

2014

Language:

english

File:

PDF, 677 KB

english, 2014

11

GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms

Guney, E., Garcia-Garcia, J., Oliva, B.

Journal:

Year:

2014

Language:

english

File:

PDF, 248 KB

english, 2014

12

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

Xie, Y., Wu, G., Tang, J., Luo, R., Patterson, J., Liu, S., Huang, W., He, G., Gu, S., Li, S., Zhou, X., Lam, T.-W., Li, Y., Xu, X., Wong, G. K.-S., Wang, J.

Journal:

Year:

2014

Language:

english

File:

PDF, 521 KB

english, 2014

13

CanSNPer: a hierarchical genotype classifier of clonal pathogens

Larkeryd, A., Myrtennas, K., Karlsson, E., Dwibedi, C. K., Forsman, M., Larsson, P., Johansson, A., Sjodin, A.

Journal:

Year:

2014

Language:

english

File:

PDF, 125 KB

english, 2014

14

Automated analysis of giant unilamellar vesicles using circular Hough transformation

Hermann, E., Bleicken, S., Subburaj, Y., Garcia-Saez, A. J.

Journal:

Year:

2014

Language:

english

File:

PDF, 1021 KB

english, 2014

15

SBARS: fast creation of dotplots for DNA sequences on different scales using GA-,GC-content

Pyatkov, M. I., Pankratov, A. N.

Journal:

Year:

2014

Language:

english

File:

PDF, 148 KB

english, 2014

16

Using association rule mining to determine promising secondary phenotyping hypotheses

Oellrich, A., Jacobsen, J., Papatheodorou, I., Smedley, D.

Journal:

Year:

2014

Language:

english

File:

PDF, 448 KB

english, 2014

17

EXTREME: an online EM algorithm for motif discovery

Quang, D., Xie, X.

Journal:

Year:

2014

Language:

english

File:

PDF, 821 KB

english, 2014

18

MRHMMs: Multivariate Regression Hidden Markov Models and the variantS

Lee, Y., Ghosh, D., Hardison, R. C., Zhang, Y.

Journal:

Year:

2014

Language:

english

File:

PDF, 143 KB

english, 2014

19

BicOverlapper 2.0: visual analysis for gene expression

Santamaria, R., Theron, R., Quintales, L.

Journal:

Year:

2014

Language:

english

File:

PDF, 227 KB

english, 2014

20

Inductive matrix completion for predicting gene-disease associations

Natarajan, N., Dhillon, I. S.

Journal:

Year:

2014

Language:

english

File:

PDF, 500 KB

english, 2014

21

A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data

Hajirasouliha, I., Mahmoody, A., Raphael, B. J.

Journal:

Year:

2014

Language:

english

File:

PDF, 889 KB

english, 2014

22

Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach

Kotera, M., Tabei, Y., Yamanishi, Y., Muto, A., Moriya, Y., Tokimatsu, T., Goto, S.

Journal:

Year:

2014

Language:

english

File:

PDF, 769 KB

english, 2014

23

Pareto-optimal phylogenetic tree reconciliation

Libeskind-Hadas, R., Wu, Y.-C., Bansal, M. S., Kellis, M.

Journal:

Year:

2014

Language:

english

File:

PDF, 620 KB

english, 2014

24

MIRA: mutual information-based reporter algorithm for metabolic networks

Cicek, A. E., Roeder, K., Ozsoyoglu, G.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.77 MB

english, 2014

25

Privacy preserving protocol for detecting genetic relatives using rare variants

Hormozdiari, F., Joo, J. W. J., Wadia, A., Guan, F., Ostrosky, R., Sahai, A., Eskin, E.

Journal:

Year:

2014

Language:

english

File:

PDF, 572 KB

english, 2014

26

Metabolite identification through multiple kernel learning on fragmentation trees

Shen, H., Duhrkop, K., Bocker, S., Rousu, J.

Journal:

Year:

2014

Language:

english

File:

PDF, 473 KB

english, 2014

27

A statistical approach for inferring the 3D structure of the genome

Varoquaux, N., Ay, F., Noble, W. S., Vert, J.-P.

Journal:

Year:

2014

Language:

english

File:

PDF, 683 KB

english, 2014

28

Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing

Rampa ek, L., Arbabi, A., Brudno, M.

Journal:

Year:

2014

Language:

english

File:

PDF, 3.04 MB

english, 2014

29

Discrete mixture modeling to address genetic heterogeneity in time-to-event regression

Eng, K. H., Hanlon, B. M.

Journal:

Year:

2014

Language:

english

File:

PDF, 688 KB

english, 2014

30

New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence

Cao, M., Pietras, C. M., Feng, X., Doroschak, K. J., Schaffner, T., Park, J., Zhang, H., Cowen, L. J., Hescott, B. J.

Journal:

Year:

2014

Language:

english

File:

PDF, 622 KB

english, 2014

31

BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles

Videm, P., Rose, D., Costa, F., Backofen, R.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.02 MB

english, 2014

32

jHeatmap: an interactive heatmap viewer for the web

Deu-Pons, J., Schroeder, M. P., Lopez-Bigas, N.

Journal:

Year:

2014

Language:

english

File:

PDF, 257 KB

english, 2014

33

Evaluating synteny for improved comparative studies

Ghiurcuta, C. G., Moret, B. M. E.

Journal:

Year:

2014

Language:

english

File:

PDF, 692 KB

english, 2014

34

Ragout--a reference-assisted assembly tool for bacterial genomes

Kolmogorov, M., Raney, B., Paten, B., Pham, S.

Journal:

Year:

2014

Language:

english

File:

PDF, 661 KB

english, 2014

35

RNA-Skim: a rapid method for RNA-Seq quantification at transcript level

Zhang, Z., Wang, W.

Journal:

Year:

2014

Language:

english

File:

PDF, 2.46 MB

english, 2014

36

Tertiary structure-based prediction of conformational B-cell epitopes through B factors

Ren, J., Liu, Q., Ellis, J., Li, J.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.04 MB

english, 2014

37

Stochastic EM-based TFBS motif discovery with MITSU

Kilpatrick, A. M., Ward, B., Aitken, S.

Journal:

Year:

2014

Language:

english

File:

PDF, 412 KB

english, 2014

38

Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics

Penzlin, A., Lindner, M. S., Doellinger, J., Dabrowski, P. W., Nitsche, A., Renard, B. Y.

Journal:

Year:

2014

Language:

english

File:

PDF, 495 KB

english, 2014

39

Cross-study validation for the assessment of prediction algorithms

Bernau, C., Riester, M., Boulesteix, A.-L., Parmigiani, G., Huttenhower, C., Waldron, L., Trippa, L.

Journal:

Year:

2014

Language:

english

File:

PDF, 501 KB

english, 2014

40

Inferring gene ontologies from pairwise similarity data

Kramer, M., Dutkowski, J., Yu, M., Bafna, V., Ideker, T.

Journal:

Year:

2014

Language:

english

File:

PDF, 685 KB

english, 2014

41

DrugComboRanker: drug combination discovery based on target network analysis

Huang, L., Li, F., Sheng, J., Xia, X., Ma, J., Zhan, M., Wong, S. T. C.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.78 MB

english, 2014

42

An efficient parallel algorithm for accelerating computational protein design

Zhou, Y., Xu, W., Donald, B. R., Zeng, J.

Journal:

Year:

2014

Language:

english

File:

PDF, 335 KB

english, 2014

43

ExSPAnder: a universal repeat resolver for DNA fragment assembly

Prjibelski, A. D., Vasilinetc, I., Bankevich, A., Gurevich, A., Krivosheeva, T., Nurk, S., Pham, S., Korobeynikov, A., Lapidus, A., Pevzner, P. A.

Journal:

Year:

2014

Language:

english

File:

PDF, 602 KB

english, 2014

44

Canto: an online tool for community literature curation

Rutherford, K. M., Harris, M. A., Lock, A., Oliver, S. G., Wood, V.

Journal:

Year:

2014

Language:

english

File:

PDF, 80 KB

english, 2014

45

Editorial

Batzoglou, S., Schwartz, R.

Journal:

Year:

2014

Language:

english

File:

PDF, 49 KB

english, 2014

46

Deep learning of the tissue-regulated splicing code

Leung, M. K. K., Xiong, H. Y., Lee, L. J., Frey, B. J.

Journal:

Year:

2014

Language:

english

File:

PDF, 559 KB

english, 2014

47

iCall: a genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array

Zhou, J., Tantoso, E., Wong, L.-P., Ong, R. T.-H., Bei, J.-X., Li, Y., Liu, J., Khor, C.-C., Teo, Y.-Y.

Journal:

Year:

2014

Language:

english

File:

PDF, 248 KB

english, 2014

48

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation

Aijo, T., Butty, V., Chen, Z., Salo, V., Tripathi, S., Burge, C. B., Lahesmaa, R., Lahdesmaki, H.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.49 MB

english, 2014

49

Graph-regularized dual Lasso for robust eQTL mapping

Cheng, W., Zhang, X., Guo, Z., Shi, Y., Wang, W.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.26 MB

english, 2014

50

Large scale analysis of signal reachability

Todor, A., Gabr, H., Dobra, A., Kahveci, T.

Journal:

Year:

2014

Language:

english

File:

PDF, 492 KB

english, 2014

51

SKINK: a web server for string kernel based kink prediction in -helices

Seifert, T., Lund, A., Kneissl, B., Mueller, S. C., Tautermann, C. S., Hildebrandt, A.

Journal:

Year:

2014

Language:

english

File:

PDF, 134 KB

english, 2014

52

EPIQ--efficient detection of SNP-SNP epistatic interactions for quantitative traits

Arkin, Y., Rahmani, E., Kleber, M. E., Laaksonen, R., Marz, W., Halperin, E.

Journal:

Year:

2014

Language:

english

File:

PDF, 567 KB

english, 2014

53

Accurate viral population assembly from ultra-deep sequencing data

Mangul, S., Wu, N. C., Mancuso, N., Zelikovsky, A., Sun, R., Eskin, E.

Journal:

Year:

2014

Language:

english

File:

PDF, 783 KB

english, 2014

54

fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data

Hung, L.-H., Samudrala, R.

Journal:

Year:

2014

Language:

english

File:

PDF, 175 KB

english, 2014

55

Optimization of gene set annotations via entropy minimization over variable clusters (EMVC)

Frost, H. R., Moore, J. H.

Journal:

Year:

2014

Language:

english

File:

PDF, 777 KB

english, 2014

56

Functional association networks as priors for gene regulatory network inference

Studham, M. E., Tjarnberg, A., Nordling, T. E. M., Nelander, S., Sonnhammer, E. L. L.

Journal:

Year:

2014

Language:

english

File:

PDF, 591 KB

english, 2014

57

AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references

Bao, E., Jiang, T., Girke, T.

Journal:

Year:

2014

Language:

english

File:

PDF, 659 KB

english, 2014

58

Deciphering kinase-substrate relationships by analysis of domain-specific phosphorylation network

Damle, N. P., Mohanty, D.

Journal:

Year:

2014

Language:

english

File:

PDF, 680 KB

english, 2014

59

AUTHOR INDEX

Journal:

Year:

2014

Language:

english

File:

PDF, 37 KB

english, 2014

60

Detecting independent and recurrent copy number aberrations using interval graphs

Wu, H.-T., Hajirasouliha, I., Raphael, B. J.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.04 MB

english, 2014

61

Automated detection and tracking of many cells by using 4D live-cell imaging data

Tokunaga, T., Hirose, O., Kawaguchi, S., Toyoshima, Y., Teramoto, T., Ikebata, H., Kuge, S., Ishihara, T., Iino, Y., Yoshida, R.

Journal:

Year:

2014

Language:

english

File:

PDF, 925 KB

english, 2014

62

Scale-space measures for graph topology link protein network architecture to function

Hulsman, M., Dimitrakopoulos, C., de Ridder, J.

Journal:

Year:

2014

Language:

english

File:

PDF, 989 KB

english, 2014

63

ISMB 2014 Proceedings Papers Committee

Journal:

Year:

2014

Language:

english

File:

PDF, 89 KB

english, 2014

64

ADaCGH2: parallelized analysis of (big) CNA data

Diaz-Uriarte, R.

Journal:

Year:

2014

Language:

english

File:

PDF, 403 KB

english, 2014