Volume 18; Issue 1

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BMC Bioinformatics
Volume 18; Issue 1

BMC Bioinformatics

Volume 18; Issue 1

1

JACUSA: site-specific identification of RNA editing events from replicate sequencing data

Piechotta, Michael, Wyler, Emanuel, Ohler, Uwe, Landthaler, Markus, Dieterich, Christoph

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 13.84 MB

english, 2017

2

TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas

Cumbo, Fabio, Fiscon, Giulia, Ceri, Stefano, Masseroli, Marco, Weitschek, Emanuel

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.15 MB

english, 2017

3

Minimum redundancy maximum relevance feature selection approach for temporal gene expression data

Radovic, Milos, Ghalwash, Mohamed, Filipovic, Nenad, Obradovic, Zoran

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.88 MB

english, 2017

4

A mixed-integer linear programming approach to the reduction of genome-scale metabolic networks

Röhl, Annika, Bockmayr, Alexander

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 712 KB

english, 2017

5

T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes

Tsimpidis, Michail, Bachoumis, Georgios, Mimouli, Kalliopi, Kyriakopoulou, Zaharoula, Robertson, David L., Markoulatos, Panayotis, Amoutzias, Grigoris D.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.32 MB

english, 2017

6

Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data

Torkamaneh, Davoud, Laroche, Jérôme, Bastien, Maxime, Abed, Amina, Belzile, François

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 533 KB

english, 2017

7

MicroRNA based Pan-Cancer Diagnosis and Treatment Recommendation

Cheerla, Nikhil, Gevaert, Olivier

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.23 MB

english, 2017

8

SCOPA and META-SCOPA: software for the analysis and aggregation of genome-wide association studies of multiple correlated phenotypes

Mägi, Reedik, Suleimanov, Yury V., Clarke, Geraldine M., Kaakinen, Marika, Fischer, Krista, Prokopenko, Inga, Morris, Andrew P.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 880 KB

english, 2017

9

iGC—an integrated analysis package of gene expression and copy number alteration

Lai, Yi-Pin, Wang, Liang-Bo, Wang, Wei-An, Lai, Liang-Chuan, Tsai, Mong-Hsun, Lu, Tzu-Pin, Chuang, Eric Y.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.49 MB

english, 2017

10

The use of novel selectivity metrics in kinase research

Bosc, Nicolas, Meyer, Christophe, Bonnet, Pascal

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.30 MB

english, 2017

11

GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants

Tebel, Katrin, Boldt, Vivien, Steininger, Anne, Port, Matthias, Ebert, Grit, Ullmann, Reinhard

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.39 MB

english, 2017

12

GSAR: Bioconductor package for Gene Set analysis in R

Rahmatallah, Yasir, Zybailov, Boris, Emmert-Streib, Frank, Glazko, Galina

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.87 MB

english, 2017

13

A systematic comparative evaluation of biclustering techniques

Padilha, Victor A., Campello, Ricardo J. G. B.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.78 MB

english, 2017

14

Eigen-Epistasis for detecting gene-gene interactions

Stanislas, Virginie, Dalmasso, Cyril, Ambroise, Christophe

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.19 MB

english, 2017

15

Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking

Zafrir, Zohar, Tuller, Tamir

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.61 MB

english, 2017

16

Mixture model normalization for non-targeted gas chromatography/mass spectrometry metabolomics data

Reisetter, Anna C., Muehlbauer, Michael J., Bain, James R., Nodzenski, Michael, Stevens, Robert D., Ilkayeva, Olga, Metzger, Boyd E., Newgard, Christopher B., Lowe, William L., Scholtens, Denise M.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.05 MB

english, 2017

17

Predicting probable Alzheimer’s disease using linguistic deficits and biomarkers

Orimaye, Sylvester O., Wong, Jojo S-M., Golden, Karen J., Wong, Chee P., Soyiri, Ireneous N.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 411 KB

english, 2017

18

Nonlinear dimensionality reduction methods for synthetic biology biobricks’ visualization

Yang, Jiaoyun, Wang, Haipeng, Ding, Huitong, An, Ning, Alterovitz, Gil

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.28 MB

english, 2017

19

An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data

Wadsworth, W. Duncan, Argiento, Raffaele, Guindani, Michele, Galloway-Pena, Jessica, Shelburne, Samuel A., Vannucci, Marina

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 929 KB

english, 2017

20

VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology

Rizwan, Muhammad, Naz, Anam, Ahmad, Jamil, Naz, Kanwal, Obaid, Ayesha, Parveen, Tamsila, Ahsan, Muhammad, Ali, Amjad

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 841 KB

english, 2017

21

TipMT: Identification of PCR-based taxon-specific markers

Rodrigues-Luiz, Gabriela F., Cardoso, Mariana S., Valdivia, Hugo O., Ayala, Edward V., Gontijo, Célia M. F., Rodrigues, Thiago de S., Fujiwara, Ricardo T., Lopes, Robson S., Bartholomeu, Daniella C.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 848 KB

english, 2017

22

Negative binomial mixed models for analyzing microbiome count data

Zhang, Xinyan, Mallick, Himel, Tang, Zaixiang, Zhang, Lei, Cui, Xiangqin, Benson, Andrew K., Yi, Nengjun

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.17 MB

english, 2017

23

Exploring the transcriptome of non-model oleaginous microalga Dunaliella tertiolecta through high-throughput sequencing and high performance computing

Yao, Lina, Tan, Kenneth Wei Min, Tan, Tin Wee, Lee, Yuan Kun

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.08 MB

english, 2017

24

BicPAMS: software for biological data analysis with pattern-based biclustering

Henriques, Rui, Ferreira, Francisco L., Madeira, Sara C.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.90 MB

english, 2017

25

A novel statistical approach for identification of the master regulator transcription factor

Sikdar, Sinjini, Datta, Susmita

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 652 KB

english, 2017

26

MVIAeval: a web tool for comprehensively evaluating the performance of a new missing value imputation algorithm

Wu, Wei-Sheng, Jhou, Meng-Jhun

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.22 MB

english, 2017

27

FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples

Paciello, Giulia, Ficarra, Elisa

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.20 MB

english, 2017

28

ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains

Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Ritchie, David W.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 762 KB

english, 2017

29

SEEG assistant: a 3DSlicer extension to support epilepsy surgery

Narizzano, Massimo, Arnulfo, Gabriele, Ricci, Serena, Toselli, Benedetta, Tisdall, Martin, Canessa, Andrea, Fato, Marco Massimo, Cardinale, Francesco

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 4.50 MB

english, 2017

30

Metabolomics variable selection and classification in the presence of observations below the detection limit using an extension of ERp

van Reenen, Mari, Westerhuis, Johan A., Reinecke, Carolus J., Venter, J Hendrik

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 733 KB

english, 2017

31

3D: diversity, dynamics, differential testing – a proposed pipeline for analysis of next-generation sequencing T cell repertoire data

Zhang, Li, Cham, Jason, Paciorek, Alan, Trager, James, Sheikh, Nadeem, Fong, Lawrence

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.55 MB

english, 2017

32

MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms

Rohart, Florian, Eslami, Aida, Matigian, Nicholas, Bougeard, Stéphanie, Lê Cao, Kim-Anh

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.21 MB

english, 2017

33

Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival

Chiu, Yu-Chiao, Wang, Li-Ju, Lu, Tzu-Pin, Hsiao, Tzu-Hung, Chuang, Eric Y., Chen, Yidong

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.23 MB

english, 2017

34

Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers

Hofmann, Ariane L., Behr, Jonas, Singer, Jochen, Kuipers, Jack, Beisel, Christian, Schraml, Peter, Moch, Holger, Beerenwinkel, Niko

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.38 MB

english, 2017

35

Optimal knockout strategies in genome-scale metabolic networks using particle swarm optimization

Nair, Govind, Jungreuthmayer, Christian, Zanghellini, Jürgen

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 680 KB

english, 2017

36

Statistical method to compare massive parallel sequencing pipelines

Elsensohn, MH., Leblay, N., Dimassi, S., Campan-Fournier, A., Labalme, A., Roucher-Boulez, F., Sanlaville, D., Lesca, G., Bardel, C., Roy, P.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 522 KB

english, 2017

37

Comparison of statistical methods for subnetwork detection in the integration of gene expression and protein interaction network

He, Hao, Lin, Dongdong, Zhang, Jigang, Wang, Yu-ping, Deng, Hong-wen

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 383 KB

english, 2017

38

ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data

Gonzalez, Sergio, Clavijo, Bernardo, Rivarola, Máximo, Moreno, Patricio, Fernandez, Paula, Dopazo, Joaquín, Paniego, Norma

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 6.11 MB

english, 2017

39

SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data

Chen, Yong, Zhao, Li, Wang, Yi, Cao, Ming, Gelowani, Violet, Xu, Mingchu, Agrawal, Smriti A., Li, Yumei, Daiger, Stephen P., Gibbs, Richard, Wang, Fei, Chen, Rui

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.12 MB

english, 2017

40

SAG-QC: quality control of single amplified genome information by subtracting non-target sequences based on sequence compositions

Maruyama, Toru, Mori, Tetsushi, Yamagishi, Keisuke, Takeyama, Haruko

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.57 MB

english, 2017

41

Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions

Zhang, Aidi, He, Libo, Wang, Yaping

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.57 MB

english, 2017

42

Not all predicted CRISPR–Cas systems are equal: isolated cas genes and classes of CRISPR like elements

Zhang, Quan, Ye, Yuzhen

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.66 MB

english, 2017

43

Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy

Penas, David R., González, Patricia, Egea, Jose A., Doallo, Ramón, Banga, Julio R.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.92 MB

english, 2017

44

ProteoModlR for functional proteomic analysis

Cifani, Paolo, Shakiba, Mojdeh, Chhangawala, Sagar, Kentsis, Alex

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1020 KB

english, 2017

45

A practical exact maximum compatibility algorithm for reconstruction of recent evolutionary history

Cherry, Joshua L.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.01 MB

english, 2017

46

ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface

Fähnrich, Anke, Krebbel, Moritz, Decker, Normann, Leucker, Martin, Lange, Felix D., Kalies, Kathrin, Möller, Steffen

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.22 MB

english, 2017

47

MOST: most-similar ligand based approach to target prediction

Huang, Tao, Mi, Hong, Lin, Cheng-yuan, Zhao, Ling, Zhong, Linda L. D., Liu, Feng-bin, Zhang, Ge, Lu, Ai-ping, Bian, Zhao-xiang

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.59 MB

english, 2017

48

DMDtoolkit: a tool for visualizing the mutated dystrophin protein and predicting the clinical severity in DMD

Zhou, Jiapeng, Xin, Jing, Niu, Yayun, Wu, Shiwen

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 998 KB

english, 2017

49

Sparse kernel canonical correlation analysis for discovery of nonlinear interactions in high-dimensional data

Yoshida, Kosuke, Yoshimoto, Junichiro, Doya, Kenji

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.34 MB

english, 2017

50

Sparse Proteomics Analysis – a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data

Conrad, Tim O. F., Genzel, Martin, Cvetkovic, Nada, Wulkow, Niklas, Leichtle, Alexander, Vybiral, Jan, Kutyniok, Gitta, Schütte, Christof

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.54 MB

english, 2017

51

TTCA: an R package for the identification of differentially expressed genes in time course microarray data

Albrecht, Marco, Stichel, Damian, Müller, Benedikt, Merkle, Ruth, Sticht, Carsten, Gretz, Norbert, Klingmüller, Ursula, Breuhahn, Kai, Matthäus, Franziska

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.35 MB

english, 2017

52

MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration

Hernandez-Ferrer, Carles, Ruiz-Arenas, Carlos, Beltran-Gomila, Alba, González, Juan R.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 614 KB

english, 2017

53

The prediction of a pathogenesis-related secretome of Puccinia helianthi through high-throughput transcriptome analysis

Jing, Lan, Guo, Dandan, Hu, Wenjie, Niu, Xiaofan

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 979 KB

english, 2017

54

Guide Picker is a comprehensive design tool for visualizing and selecting guides for CRISPR experiments

Hough, Soren H., Kancleris, Kris, Brody, Leigh, Humphryes-Kirilov, Neil, Wolanski, Joseph, Dunaway, Keith, Ajetunmobi, Ayokunmi, Dillard, Victor

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.85 MB

english, 2017

55

Bacterial protein meta-interactomes predict cross-species interactions and protein function

Caufield, J. Harry, Wimble, Christopher, Shary, Semarjit, Wuchty, Stefan, Uetz, Peter

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.98 MB

english, 2017

56

Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat

Tchagang, Alain B., Fauteux, François, Tulpan, Dan, Pan, Youlian

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.57 MB

english, 2017

57

MicroRNA categorization using sequence motifs and k-mers

Yousef, Malik, Khalifa, Waleed, Acar, İlhan Erkin, Allmer, Jens

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 811 KB

english, 2017

58

Disorder recognition in clinical texts using multi-label structured SVM

Lin, Wutao, Ji, Donghong, Lu, Yanan

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.53 MB

english, 2017

59

metaX: a flexible and comprehensive software for processing metabolomics data

Wen, Bo, Mei, Zhanlong, Zeng, Chunwei, Liu, Siqi

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.78 MB

english, 2017

60

PCM-SABRE: a platform for benchmarking and comparing outcome prediction methods in precision cancer medicine

Eyal-Altman, Noah, Last, Mark, Rubin, Eitan

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 863 KB

english, 2017

61

rNAV 2.0: a visualization tool for bacterial sRNA-mediated regulatory networks mining

Bourqui, Romain, Dutour, Isabelle, Dubois, Jonathan, Benchimol, William, Thébault, Patricia

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.61 MB

english, 2017

62

Identification of long non-coding transcripts with feature selection: a comparative study

Ventola, Giovanna M. M., Noviello, Teresa M. R., D’Aniello, Salvatore, Spagnuolo, Antonietta, Ceccarelli, Michele, Cerulo, Luigi

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.51 MB

english, 2017

63

Prediction of virus-host protein-protein interactions mediated by short linear motifs

Becerra, Andrés, Bucheli, Victor A., Moreno, Pedro A.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.60 MB

english, 2017

64

M-AMST: an automatic 3D neuron tracing method based on mean shift and adapted minimum spanning tree

Wan, Zhijiang, He, Yishan, Hao, Ming, Yang, Jian, Zhong, Ning

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.28 MB

english, 2017

65

Link prediction in drug-target interactions network using similarity indices

Lu, Yiding, Guo, Yufan, Korhonen, Anna

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 720 KB

english, 2017

66

Preservation affinity in consensus modules among stages of HIV-1 progression

Mosaddek Hossain, Sk Md, Ray, Sumanta, Mukhopadhyay, Anirban

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 8.84 MB

english, 2017

67

SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases

Chiba, Hirokazu, Uchiyama, Ikuo

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.36 MB

english, 2017

68

Drug voyager: a computational platform for exploring unintended drug action

Oh, Min, Ahn, Jaegyoon, Lee, Taekeon, Jang, Giup, Park, Chihyun, Yoon, Youngmi

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.34 MB

english, 2017

69

CURE-SMOTE algorithm and hybrid algorithm for feature selection and parameter optimization based on random forests

Ma, Li, Fan, Suohai

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.61 MB

english, 2017

70

MC-GenomeKey: a multicloud system for the detection and annotation of genomic variants

Elshazly, Hatem, Souilmi, Yassine, Tonellato, Peter J., Wall, Dennis P., Abouelhoda, Mohamed

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.48 MB

english, 2017

71

Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis

Mahajan, Gaurang, Mande, Shekhar C.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.32 MB

english, 2017

72

Ultra-high dimensional variable selection with application to normative aging study: DNA methylation and metabolic syndrome

Yoon, Grace, Zheng, Yinan, Zhang, Zhou, Zhang, Haixiang, Gao, Tao, Joyce, Brian, Zhang, Wei, Guan, Weihua, Baccarelli, Andrea A., Jiang, Wenxin, Schwartz, Joel, Vokonas, Pantel S., Hou, Lifang, Liu, L

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 403 KB

english, 2017

73

Model based heritability scores for high-throughput sequencing data

Rudra, Pratyaydipta, Shi, W. Jenny, Vestal, Brian, Russell, Pamela H., Odell, Aaron, Dowell, Robin D., Radcliffe, Richard A., Saba, Laura M., Kechris, Katerina

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.71 MB

english, 2017

74

Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance

Jabłoński, Michał, Starčuková, Jana, Starčuk, Zenon

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.47 MB

english, 2017

75

Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE)

Martini, Johannes W. R., Gao, Ning, Cardoso, Diercles F., Wimmer, Valentin, Erbe, Malena, Cantet, Rodolfo J. C., Simianer, Henner

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 618 KB

english, 2017

76

De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline

Lin, You-Yu, Hsieh, Chia-Hung, Chen, Jiun-Hong, Lu, Xuemei, Kao, Jia-Horng, Chen, Pei-Jer, Chen, Ding-Shinn, Wang, Hurng-Yi

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 812 KB

english, 2017

77

An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids

Barrero, Roberto A., Napier, Kathryn R., Cunnington, James, Liefting, Lia, Keenan, Sandi, Frampton, Rebekah A., Szabo, Tamas, Bulman, Simon, Hunter, Adam, Ward, Lisa, Whattam, Mark, Bellgard, Matthew

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.29 MB

english, 2017

78

Dynamic substrate preferences predict metabolic properties of a simple microbial consortium

Erbilgin, Onur, Bowen, Benjamin P., Kosina, Suzanne M., Jenkins, Stefan, Lau, Rebecca K., Northen, Trent R.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.07 MB

english, 2017

79

MIDcor, an R-program for deciphering mass interferences in mass spectra of metabolites enriched in stable isotopes

Selivanov, Vitaly A., Benito, Adrián, Miranda, Anibal, Aguilar, Esther, Polat, Ibrahim Halil, Centelles, Josep J., Jayaraman, Anusha, Lee, Paul W. N., Marin, Silvia, Cascante, Marta

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 482 KB

english, 2017

80

A neural joint model for entity and relation extraction from biomedical text

Li, Fei, Zhang, Meishan, Fu, Guohong, Ji, Donghong

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 724 KB

english, 2017

81

Combining phylogenetic footprinting with motif models incorporating intra-motif dependencies

Nettling, Martin, Treutler, Hendrik, Cerquides, Jesus, Grosse, Ivo

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 935 KB

english, 2017

82

Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization

Nikumbh, Sarvesh, Pfeifer, Nico

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.00 MB

english, 2017

83

Incorporating prior biological knowledge for network-based differential gene expression analysis using differentially weighted graphical LASSO

Zuo, Yiming, Cui, Yi, Yu, Guoqiang, Li, Ruijiang, Ressom, Habtom W.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.64 MB

english, 2017

84

HALC: High throughput algorithm for long read error correction

Bao, Ergude, Lan, Lingxiao

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 538 KB

english, 2017

85

AHCODA-DB: a data repository with web-based mining tools for the analysis of automated high-content mouse phenomics data

Koopmans, Bastijn, Smit, August B., Verhage, Matthijs, Loos, Maarten

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 604 KB

english, 2017

86

Geminivirus data warehouse: a database enriched with machine learning approaches

Silva, Jose Cleydson F., Carvalho, Thales F. M., Basso, Marcos F., Deguchi, Michihito, Pereira, Welison A., Sobrinho, Roberto R., Vidigal, Pedro M. P., Brustolini, Otávio J. B., Silva, Fabyano F., Dal

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.26 MB

english, 2017

87

ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana

Hazarika, Rashmi R., De Coninck, Barbara, Yamamoto, Lidia R., Martin, Laura R., Cammue, Bruno P. A., van Noort, Vera

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1020 KB

english, 2017

88

A vascular image registration method based on network structure and circuit simulation

Chen, Li, Lian, Yuxi, Guo, Yi, Wang, Yuanyuan, Hatsukami, Thomas S., Pimentel, Kristi, Balu, Niranjan, Yuan, Chun

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 3.70 MB

english, 2017

89

Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer

Zhang, Junpeng, Le, Thuc Duy, Liu, Lin, Li, Jiuyong

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.13 MB

english, 2017

90

Identification of the sequence determinants of proteinN-terminal acetylation through a decision tree approach

Yamada, Kazunori D., Omori, Satoshi, Nishi, Hafumi, Miyagi, Masaru

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 498 KB

english, 2017

91

Sequence-based prediction of protein protein interaction using a deep-learning algorithm

Sun, Tanlin, Zhou, Bo, Lai, Luhua, Pei, Jianfeng

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 567 KB

english, 2017

92

Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

Birkel, Garrett W., Ghosh, Amit, Kumar, Vinay S., Weaver, Daniel, Ando, David, Backman, Tyler W. H., Arkin, Adam P., Keasling, Jay D., Martín, Héctor García

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 330 KB

english, 2017

93

A systematic evaluation of nucleotide properties for CRISPR sgRNA design

Kuan, Pei Fen, Powers, Scott, He, Shuyao, Li, Kaiqiao, Zhao, Xiaoyu, Huang, Bo

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 687 KB

english, 2017

94

Biomarker correlation network in colorectal carcinoma by tumor anatomic location

Reiko Nishihara,Kimberly Glass,Kosuke Mima,Tsuyoshi Hamada…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 859 KB

english, 2017

95

DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data

Zhuo Wang,Shuilin Jin,Guiyou Liu,Xiurui Zhang,Nan Wang…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.63 MB

english, 2017

96

“gnparser”: a powerful parser for scientific names based on Parsing Expression Grammar

Dmitry Y. Mozzherin,Alexander A. Myltsev,David J. Patterson

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.41 MB

english, 2017

97

In silico approach to designing rational metagenomic libraries for functional studies

Anna Kusnezowa,Lars I. Leichert

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.49 MB

english, 2017

98

Meta-analysis of cell- specific transcriptomic data using fuzzy c-means clustering discovers versatile viral responsive genes

Atif Khan,Dejan Katanic,Juilee Thakar

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 12.72 MB

english, 2017

99

JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories

Charles C. David,Ettayapuram Ramaprasad Azhagiya Singam…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.83 MB

english, 2017

100

Coordinates and intervals in graph-based reference genomes

Knut D. Rand,Ivar Grytten,Alexander J. Nederbragt,Geir O. Storvik…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 767 KB

english, 2017

101

The rainfall plot: its motivation, characteristics and pitfalls

Diana Domanska,Daniel Vodák,Christin Lund-Andersen…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.62 MB

english, 2017

102

CircularLogo: A lightweight web application to visualize intra-motif dependencies

Zhenqing Ye,Tao Ma,Michael T. Kalmbach,Surendra Dasari…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.77 MB

english, 2017

103

An unsupervised learning approach for tracking mice in an enclosed area

Jakob Unger,Mike Mansour,Marcin Kopaczka,Nina Gronloh,Marc Spehr…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 5.24 MB

english, 2017

104

Numerical integration methods and layout improvements in the context of dynamic RNA visualization

Boris Shabash,Kay C. Wiese

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.70 MB

english, 2017

105

SurvivalGWAS_SV: software for the analysis of genome-wide association studies of imputed genotypes with “time-to-event” outcomes

Hamzah Syed,Andrea L. Jorgensen,Andrew P. Morris

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 811 KB

english, 2017

106

An integrated enhancement and reconstruction strategy for the quantitative extraction of actin stress fibers from fluorescence micrographs

Zhen Zhang,Shumin Xia,Pakorn Kanchanawong

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.92 MB

english, 2017

107

Large scale tissue histopathology image classification, segmentation, and visualization via deep convolutional activation features

Yan Xu,Zhipeng Jia,Liang-Bo Wang,Yuqing Ai,Fang Zhang,Maode Lai…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 3.79 MB

english, 2017

108

Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance

Toshiyuki Oda,Kyungtaek Lim,Kentaro Tomii

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.89 MB

english, 2017

109

A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays

Marijke Van Moerbeke,Adetayo Kasim,Willem Talloen,Joke Reumers…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.12 MB

english, 2017

110

AGeNNT: annotation of enzyme families by means of refined neighborhood networks

Florian Kandlinger,Maximilian G. Plach,Rainer Merkl

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.82 MB

english, 2017

111

MQAPRank: improved global protein model quality assessment by learning-to-rank

Xiaoyang Jing,Qiwen Dong

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 583 KB

english, 2017

112

Hapl-o-Mat: open-source software for HLA haplotype frequency estimation from ambiguous and heterogeneous data

Christian Schäfer,Alexander H. Schmidt,Jürgen Sauter

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.40 MB

english, 2017

113

FluoRender: joint freehand segmentation and visualization for many-channel fluorescence data analysis

Yong Wan,Hideo Otsuna,Holly A. Holman,Brig Bagley,Masayoshi Ito…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 10.48 MB

english, 2017

114

Limitations of a metabolic network-based reverse ecology method for inferring host–pathogen interactions

Kazuhiro Takemoto,Kazuki Aie

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 516 KB

english, 2017

115

NaviSE: superenhancer navigator integrating epigenomics signal algebra

Alex M. Ascensión,Mikel Arrospide-Elgarresta,Ander Izeta…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 5.69 MB

english, 2017

116

Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species

Jennifer Rogers,Andrew Fishberg,Nora Youngs,Yi-Chieh Wu

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 795 KB

english, 2017

117

3D deep convolutional neural networks for amino acid environment similarity analysis

Wen Torng,Russ B. Altman

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 5.29 MB

english, 2017

118

PFASUM: a substitution matrix from Pfam structural alignments

Frank Keul,Martin Hess,Michael Goesele,Kay Hamacher

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 756 KB

english, 2017

119

Recognizing RNA structural motifs in HT-SELEX data for ribosomal protein S15

Shermin Pei,Betty L. Slinger,Michelle M. Meyer

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.10 MB

english, 2017

120

An evaluation of copy number variation detection tools for cancer using whole exome sequencing data

Fatima Zare,Michelle Dow,Nicholas Monteleone,Abdelrahman Hosny…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.41 MB

english, 2017

121

dictyExpress: a web-based platform for sequence data management and analytics inDictyosteliumand beyond

Miha Stajdohar,Rafael D. Rosengarten,Janez Kokosar,Luka Jeran…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.05 MB

english, 2017

122

Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing

Marek Palkowski,Wlodzimierz Bielecki

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 645 KB

english, 2017

123

Intervene: a tool for intersection and visualization of multiple gene or genomic region sets

Aziz Khan,Anthony Mathelier

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.59 MB

english, 2017

124

Prediction of bioluminescent proteins by using sequence-derived features and lineage-specific scheme

Jian Zhang,Haiting Chai,Guifu Yang,Zhiqiang Ma

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.56 MB

english, 2017

125

Variable-order sequence modeling improves bacterial strain discrimination for Ion Torrent DNA reads

Thomas M. Poulsen,Martin Frith

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 963 KB

english, 2017

126

Early response index: a statistic to discover potential early stage disease biomarkers

Sirajul Salekin,Mehrab Ghanat Bari,Itay Raphael…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 895 KB

english, 2017

127

EPSILON-CP: using deep learning to combine information from multiple sources for protein contact prediction

Kolja Stahl,Michael Schneider,Oliver Brock

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 697 KB

english, 2017

128

Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries

Stephen J. Bush,Mary E. B. McCulloch,Kim M. Summers,David A. Hume…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1003 KB

english, 2017

129

Analysis and prediction of single-stranded and double-stranded DNA binding proteins based on protein sequences

Wei Wang,Lin Sun,Shiguang Zhang,Hongjun Zhang,Jinling Shi…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 976 KB

english, 2017

130

A multiplex primer design algorithm for target amplification of continuous genomic regions

Ahmet Rasit Ozturk,Tolga Can

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.41 MB

english, 2017

131

Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data

Atul Kamboj,Claus V. Hallwirth,Ian E. Alexander…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 897 KB

english, 2017

132

SBMLmod: a Python-based web application and web service for efficient data integration and model simulation

Sascha Schäuble,Anne-Kristin Stavrum,Mathias Bockwoldt…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 730 KB

english, 2017

133

CMSA: a heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment

Xi Chen,Chen Wang,Shanjiang Tang,Ce Yu,Quan Zou

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 839 KB

english, 2017

134

OrthoReD: a rapid and accurate orthology prediction tool with low computational requirement

Kai Battenberg,Ernest K. Lee,Joanna C. Chiu,Alison M. Berry…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.34 MB

english, 2017

135

A novel pathway-based distance score enhances assessment of disease heterogeneity in gene expression

Xiting Yan,Anqi Liang,Jose Gomez,Lauren Cohn,Hongyu Zhao…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 3.81 MB

english, 2017

136

Optimal alpha reduces error rates in gene expression studies: a meta-analysis approach

J. F. Mudge,C. J. Martyniuk,J. E. Houlahan

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 542 KB

english, 2017

137

Bioinformatics: indispensable, yet hidden in plain sight?

Andrew Bartlett,Bart Penders,Jamie Lewis

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 356 KB

english, 2017

138

ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data

Giorgos Minas,Hiroshi Momiji,Dafyd J. Jenkins,Maria J. Costa…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.04 MB

english, 2017

139

GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles

Michael I. Klein,David F. Stern,Hongyu Zhao

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.97 MB

english, 2017

140

Biologically constrained optimization based cell membrane segmentation inC. elegansembryos

Yusuke Azuma,Shuichi Onami

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.76 MB

english, 2017

141

Semi-automated quantitative Drosophila wings measurements

Sheng Yang Michael Loh,Yoshitaka Ogawa,Sara Kawana,Koichiro Tamura…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.97 MB

english, 2017

142

Quasi-linear score for capturing heterogeneous structure in biomarkers

Katsuhiro Omae,Osamu Komori,Shinto Eguchi

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.16 MB

english, 2017

143

SparkBLAST: scalable BLAST processing using in-memory operations

Marcelo Rodrigo de Castro,Catherine dos Santos Tostes…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.46 MB

english, 2017

144

RGIFE: a ranked guided iterative feature elimination heuristic for the identification of biomarkers

Nicola Lazzarini,Jaume Bacardit

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.30 MB

english, 2017

145

ISVASE: identification of sequence variant associated with splicing event using RNA-seq data

Hasan Awad Aljohi,Wanfei Liu,Qiang Lin,Jun Yu,Songnian Hu

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1002 KB

english, 2017

146

SLMSuite: a suite of algorithms for segmenting genomic profiles

Valerio Orlandini,Aldesia Provenzano,Sabrina Giglio,Alberto Magi

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 584 KB

english, 2017

147

BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data

Yuxuan Yuan,Philipp E. Bayer,Armin Scheben,Chon-Kit Kenneth Chan…

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.42 MB

english, 2017

148

Learning rule sets from survival data

Łukasz Wróbel,Adam Gudyś,Marek Sikora

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.30 MB

english, 2017

149

VB-MK-LMF: fusion of drugs, targets and interactions using variational Bayesian multiple kernel logistic matrix factorization

Bolgár, Bence, Antal, Péter

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.71 MB

english, 2017

150

chngpt: threshold regression model estimation and inference

Fong, Youyi, Huang, Ying, Gilbert, Peter B., Permar, Sallie R.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 560 KB

english, 2017

151

dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder

Zhang, Shuyun, Deng, Libin, Jia, Qiyue, Huang, Shaoting, Gu, Junwang, Zhou, Fankun, Gao, Meng, Sun, Xinyi, Feng, Chang, Fan, Guangqin

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 856 KB

english, 2017

152

Explorative visual analytics on interval-based genomic data and their metadata

Jalili, Vahid, Matteucci, Matteo, Masseroli, Marco, Ceri, Stefano

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.59 MB

english, 2017

153

Long short-term memory RNN for biomedical named entity recognition

Lyu, Chen, Chen, Bo, Ren, Yafeng, Ji, Donghong

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1018 KB

english, 2017

154

Decontaminating eukaryotic genome assemblies with machine learning

Fierst, Janna L., Murdock, Duncan A.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.57 MB

english, 2017

155

SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines

Audoux, Jérôme, Salson, Mikaël, Grosset, Christophe F., Beaumeunier, Sacha, Holder, Jean-Marc, Commes, Thérèse, Philippe, Nicolas

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.45 MB

english, 2017

156

pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms

Molnos, Sophie, Baumbach, Clemens, Wahl, Simone, Müller-Nurasyid, Martina, Strauch, Konstantin, Wang-Sattler, Rui, Waldenberger, Melanie, Meitinger, Thomas, Adamski, Jerzy, Kastenmüller, Gabi, Suhre,

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.00 MB

english, 2017

157

VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences

Xu, Duo, Jaber, Yousef, Pavlidis, Pavlos, Gokcumen, Omer

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.48 MB

english, 2017

158

pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing data

Beyens, Matthias, Boeckx, Nele, Van Camp, Guy, Op de Beeck, Ken, Vandeweyer, Geert

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 609 KB

english, 2017

159

eccCL: parallelized GPU implementation of Ensemble Classifier Chains

Riemenschneider, Mona, Herbst, Alexander, Rasch, Ari, Gorlatch, Sergei, Heider, Dominik

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 398 KB

english, 2017

160

DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data

Gaspar, John M., Hart, Ronald P.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.05 MB

english, 2017

161

A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support

Connolly, Brian, Cohen, K. Bretonnel, Santel, Daniel, Bayram, Ulya, Pestian, John

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.40 MB

english, 2017

162

Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles

Cohen, K. Bretonnel, Lanfranchi, Arrick, Choi, Miji Joo-young, Bada, Michael, Baumgartner, William A., Panteleyeva, Natalya, Verspoor, Karin, Palmer, Martha, Hunter, Lawrence E.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 510 KB

english, 2017

163

Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family

Song, Jia, Zheng, Sisi, Nguyen, Nhung, Wang, Youjun, Zhou, Yubin, Lin, Kui

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 600 KB

english, 2017

164

LiverWiki: a wiki-based database for human liver

Chen, Tao, Li, Mansheng, He, Qiang, Zou, Lei, Li, Youhuan, Chang, Cheng, Zhao, Dongyan, Zhu, Yunping

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 4.81 MB

english, 2017

165

Sequence-based information-theoretic features for gene essentiality prediction

Nigatu, Dawit, Sobetzko, Patrick, Yousef, Malik, Henkel, Werner

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 845 KB

english, 2017

166

Unsupervised gene selection using biological knowledge : application in sample clustering

Acharya, Sudipta, Saha, Sriparna, Nikhil, N.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.34 MB

english, 2017

167

Repliscan: a tool for classifying replication timing regions

Zynda, Gregory J., Song, Jawon, Concia, Lorenzo, Wear, Emily E., Hanley-Bowdoin, Linda, Thompson, William F., Vaughn, Matthew W.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.42 MB

english, 2017

168

A machine learning approach for predicting methionine oxidation sites

Aledo, Juan C., Cantón, Francisco R., Veredas, Francisco J.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 660 KB

english, 2017

169

Identification of gene pairs through penalized regression subject to constraints

Shen, Rex, Luo, Lan, Jiang, Hui

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 540 KB

english, 2017

170

K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity

Kim, Chang Sik, Winn, Martyn D., Sachdeva, Vipin, Jordan, Kirk E.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 885 KB

english, 2017

171

RNA inverse folding using Monte Carlo tree search

Yang, Xiufeng, Yoshizoe, Kazuki, Taneda, Akito, Tsuda, Koji

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.41 MB

english, 2017

172

An improved filtering algorithm for big read datasets and its application to single-cell assembly

Wedemeyer, Axel, Kliemann, Lasse, Srivastav, Anand, Schielke, Christian, Reusch, Thorsten B., Rosenstiel, Philip

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 827 KB

english, 2017

173

sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters

Tripathi, Shailesh, Lloyd-Price, Jason, Ribeiro, Andre, Yli-Harja, Olli, Dehmer, Matthias, Emmert-Streib, Frank

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 725 KB

english, 2017

174

Estimating Phred scores of Illumina base calls by logistic regression and sparse modeling

Zhang, Sheng, Wang, Bo, Wan, Lin, Li, Lei M.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 997 KB

english, 2017

175

TnseqDiff: identification of conditionally essential genes in transposon sequencing studies

Zhao, Lili, Anderson, Mark T., Wu, Weisheng, T. Mobley, Harry L., Bachman, Michael A.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 877 KB

english, 2017

176

HLA-check: evaluating HLA data from SNP information

Jeanmougin, Marc, Noirel, Josselin, Coulonges, Cédric, Zagury, Jean-François

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 590 KB

english, 2017

177

Investigating reproducibility and tracking provenance – A genomic workflow case study

Kanwal, Sehrish, Khan, Farah Zaib, Lonie, Andrew, Sinnott, Richard O.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.76 MB

english, 2017

178

CRISPulator: a discrete simulation tool for pooled genetic screens

Nagy, Tamas, Kampmann, Martin

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.28 MB

english, 2017

179

EL_PSSM-RT: DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation

Zhou, Jiyun, Lu, Qin, Xu, Ruifeng, He, Yulan, Wang, Hongpeng

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.01 MB

english, 2017

180

A weighted string kernel for protein fold recognition

Nojoomi, Saghi, Koehl, Patrice

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.13 MB

english, 2017

181

SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees

Beccati, Alan, Gerken, Jan, Quast, Christian, Yilmaz, Pelin, Glöckner, Frank Oliver

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.11 MB

english, 2017

182

RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement

Sandhu, Maninder, Sureshkumar, V., Prakash, Chandra, Dixit, Rekha, Solanke, Amolkumar U., Sharma, Tilak Raj, Mohapatra, Trilochan, S. V., Amitha Mithra

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.99 MB

english, 2017

183

Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies

Needhamsen, Maria, Ewing, Ewoud, Lund, Harald, Gomez-Cabrero, David, Harris, Robert Adam, Kular, Lara, Jagodic, Maja

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.30 MB

english, 2017

184

SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome

Li, Yiwei, Ilie, Lucian

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.40 MB

english, 2017

185

BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness

Mazariegos-Canellas, Oriol, Do, Trien, Peto, Tim, Eyre, David W., Underwood, Anthony, Crook, Derrick, Wyllie, David H.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.47 MB

english, 2017

186

Reference-guided de novo assembly approach improves genome reconstruction for related species

Lischer, Heidi E. L., Shimizu, Kentaro K.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.24 MB

english, 2017

187

Reconstructing cancer karyotypes from short read data: the half empty and half full glass

Eitan, Rami, Shamir, Ron

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.45 MB

english, 2017

188

Structural prediction of the interaction of the tumor suppressor p27KIP1 with cyclin A/CDK2 identifies a novel catalytically relevant determinant

Li, Jinyu, Vervoorts, Jörg, Carloni, Paolo, Rossetti, Giulia, Lüscher, Bernhard

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.02 MB

english, 2017

189

Predicting potential drug-drug interactions by integrating chemical, biological, phenotypic and network data

Zhang, Wen, Chen, Yanlin, Liu, Feng, Luo, Fei, Tian, Gang, Li, Xiaohong

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 637 KB

english, 2017

190

KinMap: a web-based tool for interactive navigation through human kinome data

Eid, Sameh, Turk, Samo, Volkamer, Andrea, Rippmann, Friedrich, Fulle, Simone

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.72 MB

english, 2017

191

MPD: multiplex primer design for next-generation targeted sequencing

Wingo, Thomas S., Kotlar, Alex, Cutler, David J.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 500 KB

english, 2017

192

Power analysis for RNA-Seq differential expression studies

Yu, Lianbo, Fernandez, Soledad, Brock, Guy

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.26 MB

english, 2017

193

Using the multi-objective optimization replica exchange Monte Carlo enhanced sampling method for protein–small molecule docking

Wang, Hongrui, Liu, Hongwei, Cai, Leixin, Wang, Caixia, Lv, Qiang

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 8.90 MB

english, 2017

194

Integrated genomic analysis of biological gene sets with applications in lung cancer prognosis

Chu, Su Hee, Huang, Yen-Tsung

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.40 MB

english, 2017

195

Reliable Biomarker discovery from Metagenomic data via RegLRSD algorithm

Alshawaqfeh, Mustafa, Bashaireh, Ahmad, Serpedin, Erchin, Suchodolski, Jan

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.22 MB

english, 2017

196

Spatial pattern analysis of nuclear migration in remodelled muscles during Drosophila metamorphosis

Kuleesha,, Feng, Lin, Wasser, Martin

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 4.17 MB

english, 2017

197

Incorporating biological information in sparse principal component analysis with application to genomic data

Li, Ziyi, Safo, Sandra E., Long, Qi

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 593 KB

english, 2017

198

ACE: an efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data

Guo, Dianhao, Luo, Jiapeng, Zhou, Yuenan, Xiao, Huamei, He, Kang, Yin, Chuanlin, Xu, Jianhua, Li, Fei

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.78 MB

english, 2017

199

SegCorr a statistical procedure for the detection of genomic regions of correlated expression

Delatola, Eleni Ioanna, Lebarbier, Emilie, Mary-Huard, Tristan, Radvanyi, François, Robin, Stéphane, Wong, Jennifer

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.16 MB

english, 2017

200

LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data

Koelmel, Jeremy P., Kroeger, Nicholas M., Ulmer, Candice Z., Bowden, John A., Patterson, Rainey E., Cochran, Jason A., Beecher, Christopher W. W., Garrett, Timothy J., Yost, Richard A.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 990 KB

english, 2017

201

NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences

Khelik, Ksenia, Lagesen, Karin, Sandve, Geir Kjetil, Rognes, Torbjørn, Nederbragt, Alexander Johan

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.43 MB

english, 2017

202

Examining the role of unmeasured confounding in mediation analysis with genetic and genomic applications

Lutz, Sharon M., Thwing, Annie, Schmiege, Sarah, Kroehl, Miranda, Baker, Christopher D., Starling, Anne P., Hokanson, John E., Ghosh, Debashis

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 537 KB

english, 2017

203

Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints

Liu, Jie, Su, Minyi, Liu, Zhihai, Li, Jie, Li, Yan, Wang, Renxiao

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 4.02 MB

english, 2017

204

Quantiprot - a Python package for quantitative analysis of protein sequences

Konopka, Bogumił M., Marciniak, Marta, Dyrka, Witold

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 684 KB

english, 2017

205

Variant Ranker: a web-tool to rank genomic data according to functional significance

Alexander, John, Mantzaris, Dimitris, Georgitsi, Marianthi, Drineas, Petros, Paschou, Peristera

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.67 MB

english, 2017

206

Quantification of tumour evolution and heterogeneity via Bayesian epiallele detection

Barrett, James E., Feber, Andrew, Herrero, Javier, Tanic, Miljana, Wilson, Gareth A., Swanton, Charles, Beck, Stephan

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.09 MB

english, 2017

207

Factors affecting interactome-based prediction of human genes associated with clinical signs

González-Pérez, Sara, Pazos, Florencio, Chagoyen, Mónica

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.23 MB

english, 2017

208

An efficient algorithm for improving structure-based prediction of transcription factor binding sites

Farrel, Alvin, Guo, Jun-tao

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.72 MB

english, 2017

209

Identifying and mitigating batch effects in whole genome sequencing data

Tom, Jennifer A., Reeder, Jens, Forrest, William F., Graham, Robert R., Hunkapiller, Julie, Behrens, Timothy W., Bhangale, Tushar R.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.02 MB

english, 2017

210

A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy

Zhu, Yanan, Ouyang, Qi, Mao, Youdong

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.62 MB

english, 2017

211

Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone

Ruiz-Blanco, Yasser B., Agüero-Chapin, Guillermin, García-Hernández, Enrique, Álvarez, Orlando, Antunes, Agostinho, Green, James

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 891 KB

english, 2017

212

CLOVE: classification of genomic fusions into structural variation events

Schröder, Jan, Wirawan, Adrianto, Schmidt, Bertil, Papenfuss, Anthony T.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 564 KB

english, 2017

213

Assessment of genome annotation using gene function similarity within the gene neighborhood

Jun, Se-Ran, Nookaew, Intawat, Hauser, Loren, Gorin, Andrey

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.31 MB

english, 2017

214

Variable selection for disease progression models: methods for oncogenetic trees and application to cancer and HIV

Hainke, Katrin, Szugat, Sebastian, Fried, Roland, Rahnenführer, Jörg

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.14 MB

english, 2017

215

Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture

Azman, Syafiq Kamarul, Anwar, Muhammad Zohaib, Henschel, Andreas

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.06 MB

english, 2017

216

NoGOA: predicting noisy GO annotations using evidences and sparse representation

Yu, Guoxian, Lu, Chang, Wang, Jun

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 717 KB

english, 2017

217

An extended model of vesicle fusion at the plasma membrane to estimate protein lateral diffusion from TIRF microscopy images

Basset, Antoine, Bouthemy, Patrick, Boulanger, Jérôme, Waharte, François, Salamero, Jean, Kervrann, Charles

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.25 MB

english, 2017

218

l1kdeconv: an R package for peak calling analysis with LINCS L1000 data

Li, Zhao, Li, Jin, Yu, Peng

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.27 MB

english, 2017

219

Parallel multiple instance learning for extremely large histopathology image analysis

Xu, Yan, Li, Yeshu, Shen, Zhengyang, Wu, Ziwei, Gao, Teng, Fan, Yubo, Lai, Maode, Chang, Eric I-Chao

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.25 MB

english, 2017

220

Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility

Liu, Sheng, Zibetti, Cristina, Wan, Jun, Wang, Guohua, Blackshaw, Seth, Qian, Jiang

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.12 MB

english, 2017

221

CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction

Guzman, Carlos, D’Orso, Iván

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 3.12 MB

english, 2017

222

Full L1-regularized Traction Force Microscopy over whole cells

Suñé-Auñón, Alejandro, Jorge-Peñas, Alvaro, Aguilar-Cuenca, Rocío, Vicente-Manzanares, Miguel, Van Oosterwyck, Hans, Muñoz-Barrutia, Arrate

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 4.27 MB

english, 2017

223

Evaluation of high-throughput isomiR identification tools: illuminating the early isomiRome of Tribolium castaneum

Amsel, Daniel, Vilcinskas, Andreas, Billion, André

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.57 MB

english, 2017

224

Network design and analysis for multi-enzyme biocatalysis

Blaß, Lisa Katharina, Weyler, Christian, Heinzle, Elmar

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.47 MB

english, 2017

225

A neural network multi-task learning approach to biomedical named entity recognition

Crichton, Gamal, Pyysalo, Sampo, Chiu, Billy, Korhonen, Anna

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 942 KB

english, 2017

226

ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding

Guhlin, Joseph, Silverstein, Kevin A. T., Zhou, Peng, Tiffin, Peter, Young, Nevin D.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.63 MB

english, 2017

227

SG-ADVISER mtDNA: a web server for mitochondrial DNA annotation with data from 200 samples of a healthy aging cohort

Rueda, Manuel, Torkamani, Ali

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1018 KB

english, 2017

228

Cancerouspdomains: comprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains

Hashemi, Seirana, Nowzari Dalini, Abbas, Jalali, Adrin, Banaei-Moghaddam, Ali Mohammad, Razaghi-Moghadam, Zahra

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.90 MB

english, 2017

229

Local sequence and sequencing depth dependent accuracy of RNA-seq reads

Cai, Guoshuai, Liang, Shoudan, Zheng, Xiaofeng, Xiao, Feifei

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.57 MB

english, 2017

230

Improving fold resistance prediction of HIV-1 against protease and reverse transcriptase inhibitors using artificial neural networks

Sheik Amamuddy, Olivier, Bishop, Nigel T., Tastan Bishop, Özlem

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 589 KB

english, 2017

231

Evaluation of the impact of Illumina error correction tools on de novo genome assembly

Heydari, Mahdi, Miclotte, Giles, Demeester, Piet, Van de Peer, Yves, Fostier, Jan

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 863 KB

english, 2017

232

Identifying pleiotropic genes in genome-wide association studies from related subjects using the linear mixed model and Fisher combination function

Yang, James J., Williams, L Keoki, Buu, Anne

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.01 MB

english, 2017

233

A new and updated resource for codon usage tables

Athey, John, Alexaki, Aikaterini, Osipova, Ekaterina, Rostovtsev, Alexandre, Santana-Quintero, Luis V., Katneni, Upendra, Simonyan, Vahan, Kimchi-Sarfaty, Chava

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.74 MB

english, 2017

234

A regulation probability model-based meta-analysis of multiple transcriptomics data sets for cancer biomarker identification

Xie, Xin-Ping, Xie, Yu-Feng, Wang, Hong-Qiang

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.19 MB

english, 2017

235

Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer

Wang, Hao, Luo, Jiamao, Liu, Chun, Niu, Huilin, Wang, Jing, Liu, Qi, Zhao, Zhongming, Xu, Hua, Ding, Yanqing, Sun, Jingchun, Zhang, Qingling

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.65 MB

english, 2017

236

Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts

Adhikari, Badri, Cheng, Jianlin

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.25 MB

english, 2017

237

QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model

Liu, Lian, Zhang, Shao-Wu, Huang, Yufei, Meng, Jia

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.26 MB

english, 2017

238

High-throughput PCR assay design for targeted resequencing using primerXL

Lefever, Steve, Pattyn, Filip, De Wilde, Bram, Coppieters, Frauke, De Keulenaer, Sarah, Hellemans, Jan, Vandesompele, Jo

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 900 KB

english, 2017

239

Robust gene selection methods using weighting schemes for microarray data analysis

Kang, Suyeon, Song, Jongwoo

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.58 MB

english, 2017

240

RRCRank: a fusion method using rank strategy for residue-residue contact prediction

Jing, Xiaoyang, Dong, Qiwen, Lu, Ruqian

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 778 KB

english, 2017

241

BUFET: boosting the unbiased miRNA functional enrichment analysis using bitsets

Zagganas, Konstantinos, Vergoulis, Thanasis, Paraskevopoulou, Maria D., Vlachos, Ioannis S., Skiadopoulos, Spiros, Dalamagas, Theodore

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 976 KB

english, 2017

242

Interactive visual exploration and refinement of cluster assignments

Kern, Michael, Lex, Alexander, Gehlenborg, Nils, Johnson, Chris R.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 3.53 MB

english, 2017

243

Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis

Ostmeyer, Jared, Christley, Scott, Rounds, William H., Toby, Inimary, Greenberg, Benjamin M., Monson, Nancy L., Cowell, Lindsay G.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.64 MB

english, 2017

244

Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling

Sferra, Gabriella, Fratini, Federica, Ponzi, Marta, Pizzi, Elisabetta

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 735 KB

english, 2017

245

mmquant: how to count multi-mapping reads?

Zytnicki, Matthias

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 448 KB

english, 2017

246

Segmentation and classification of two-channel C. elegans nucleus-labeled fluorescence images

Zhao, Mengdi, An, Jie, Li, Haiwen, Zhang, Jiazhi, Li, Shang-Tong, Li, Xue-Mei, Dong, Meng-Qiu, Mao, Heng, Tao, Louis

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 4.28 MB

english, 2017

247

Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata

Hu, Wei, Zaveri, Amrapali, Qiu, Honglei, Dumontier, Michel

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.24 MB

english, 2017

248

Anaconda: AN automated pipeline for somatic COpy Number variation Detection and Annotation from tumor exome sequencing data

Gao, Jianing, Wan, Changlin, Zhang, Huan, Li, Ao, Zang, Qiguang, Ban, Rongjun, Ali, Asim, Yu, Zhenghua, Shi, Qinghua, Jiang, Xiaohua, Zhang, Yuanwei

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.82 MB

english, 2017

249

Deep learning methods for protein torsion angle prediction

Li, Haiou, Hou, Jie, Adhikari, Badri, Lyu, Qiang, Cheng, Jianlin

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.59 MB

english, 2017

250

Improving contig binning of metagenomic data using d 2 S $$ {d}_2^S $$ oligonucleotide frequency dissimilarity

Wang, Ying, Wang, Kun, Lu, Yang Young, Sun, Fengzhu

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.24 MB

english, 2017

251

Methods for discovering genomic loci exhibiting complex patterns of differential methylation

Hardcastle, Thomas J.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.78 MB

english, 2017

252

VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy

Juanes, José M., Gallego, Asunción, Tárraga, Joaquín, Chaves, Felipe J., Marín-Garcia, Pablo, Medina, Ignacio, Arnau, Vicente, Dopazo, Joaquín

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 771 KB

english, 2017

253

Fangorn Forest (F2): a machine learning approach to classify genes and genera in the family Geminiviridae

Silva, José Cleydson F., Carvalho, Thales F. M., Fontes, Elizabeth P. B., Cerqueira, Fabio R.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.61 MB

english, 2017

254

BioCarian: search engine for exploratory searches in heterogeneous biological databases

Zaki, Nazar, Tennakoon, Chandana

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.03 MB

english, 2017

255

Protein remote homology detection based on bidirectional long short-term memory

Li, Shumin, Chen, Junjie, Liu, Bin

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 848 KB

english, 2017

256

Interpretation of microbiota-based diagnostics by explaining individual classifier decisions

Eck, A., Zintgraf, L. M., de Groot, E. F. J., de Meij, T. G. J., Cohen, T. S., Savelkoul, P. H. M., Welling, M., Budding, A. E.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.73 MB

english, 2017

257

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data

Paulson, Joseph N., Chen, Cho-Yi, Lopes-Ramos, Camila M., Kuijjer, Marieke L., Platig, John, Sonawane, Abhijeet R., Fagny, Maud, Glass, Kimberly, Quackenbush, John

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.14 MB

english, 2017

258

MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics

Zhai, Peng, Yang, Longshu, Guo, Xiao, Wang, Zhe, Guo, Jiangtao, Wang, Xiaoqi, Zhu, Huaiqiu

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.47 MB

english, 2017

259

Block-based characterization of protease specificity from substrate sequence profile

Qi, Enfeng, Wang, Dongyu, Gao, Bo, Li, Yang, Li, Guojun

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1006 KB

english, 2017

260

VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data

Christley, Scott, Levin, Mikhail K., Toby, Inimary T., Fonner, John M., Monson, Nancy L., Rounds, William H., Rubelt, Florian, Scarborough, Walter, Scheuermann, Richard H., Cowell, Lindsay G.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 378 KB

english, 2017

261

Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods

Notaro, Marco, Schubach, Max, Robinson, Peter N., Valentini, Giorgio

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.71 MB

english, 2017

262

An attention-based effective neural model for drug-drug interactions extraction

Zheng, Wei, Lin, Hongfei, Luo, Ling, Zhao, Zhehuan, Li, Zhengguang, Zhang, Yijia, Yang, Zhihao, Wang, Jian

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 863 KB

english, 2017

263

Mapping eQTL by leveraging multiple tissues and DNA methylation

Acharya, Chaitanya R., Owzar, Kouros, Allen, Andrew S.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 678 KB

english, 2017

264

A method for named entity normalization in biomedical articles: application to diseases and plants

Cho, Hyejin, Choi, Wonjun, Lee, Hyunju

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.58 MB

english, 2017

265

A new synonym-substitution method to enrich the human phenotype ontology

Taboada, Maria, Rodriguez, Hadriana, Gudivada, Ranga C., Martinez, Diego

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.85 MB

english, 2017

266

Identify Huntington’s disease associated genes based on restricted Boltzmann machine with RNA-seq data

Jiang, Xue, Zhang, Han, Duan, Feng, Quan, Xiongwen

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.41 MB

english, 2017

267

Partitioning of functional gene expression data using principal points

Kim, Jaehee, Kim, Haseong

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.56 MB

english, 2017

268

LSTrAP: efficiently combining RNA sequencing data into co-expression networks

Proost, Sebastian, Krawczyk, Agnieszka, Mutwil, Marek

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.34 MB

english, 2017

269

An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome

Ferlaino, Michael, Rogers, Mark F., Shihab, Hashem A., Mort, Matthew, Cooper, David N., Gaunt, Tom R., Campbell, Colin

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 711 KB

english, 2017

270

A heuristic model for computational prediction of human branch point sequence

Wen, Jia, Wang, Jue, Zhang, Qing, Guo, Dianjing

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 3.32 MB

english, 2017

271

A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE)

Stacey, R. Greg, Skinnider, Michael A., Scott, Nichollas E., Foster, Leonard J.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 3.17 MB

english, 2017

272

A strategy for evaluating pathway analysis methods

Yu, Chenggang, Woo, Hyung Jun, Yu, Xueping, Oyama, Tatsuya, Wallqvist, Anders, Reifman, Jaques

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.11 MB

english, 2017

273

LCS-TA to identify similar fragments in RNA 3D structures

Wiedemann, Jakub, Zok, Tomasz, Milostan, Maciej, Szachniuk, Marta

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 3.39 MB

english, 2017

274

QuaDMutEx: quadratic driver mutation explorer

Bokhari, Yahya, Arodz, Tomasz

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.91 MB

english, 2017

275

riboviz: analysis and visualization of ribosome profiling datasets

Carja, Oana, Xing, Tongji, Wallace, Edward W. J., Plotkin, Joshua B., Shah, Premal

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 722 KB

english, 2017

276

An optimized approach for annotation of large eukaryotic genomic sequences using genetic algorithm

Chowdhury, Biswanath, Garai, Arnav, Garai, Gautam

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.23 MB

english, 2017

277

Correction to: Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2017: bioinformatics

Rouchka, Eric C., Chariker, Julia L., Tieri, David, Park, Juw W.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 240 KB

english, 2017

278

JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals

Rosen, Jebediah, Handy, Kyle, Gillan, André, Smith, Rob

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.32 MB

english, 2017

279

TRAVeLer: a tool for template-based RNA secondary structure visualization

Elias, Richard, Hoksza, David

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.70 MB

english, 2017

280

BoolFilter: an R package for estimation and identification of partially-observed Boolean dynamical systems

Mcclenny, Levi D., Imani, Mahdi, Braga-Neto, Ulisses M.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 894 KB

english, 2017

281

Brain medical image diagnosis based on corners with importance-values

Gao, Linlin, Pan, Haiwei, Li, Qing, Xie, Xiaoqin, Zhang, Zhiqiang, Han, Jinming, Zhai, Xiao

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.19 MB

english, 2017

282

A fragment based method for modeling of protein segments into cryo-EM density maps

Ismer, Jochen, Rose, Alexander S., Tiemann, Johanna K. S., Hildebrand, Peter W.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.57 MB

english, 2017

283

ADAGE signature analysis: differential expression analysis with data-defined gene sets

Tan, Jie, Huyck, Matthew, Hu, Dongbo, Zelaya, René A., Hogan, Deborah A., Greene, Casey S.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 4.07 MB

english, 2017

284

fLPS: Fast discovery of compositional biases for the protein universe

Harrison, Paul M.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.79 MB

english, 2017

285

MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F1 population of outbred species

Liu, Fenxiang, Tong, Chunfa, Tao, Shentong, Wu, Jiyan, Chen, Yuhua, Yao, Dan, Li, Huogen, Shi, Jisen

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 705 KB

english, 2017

286

Swellix: a computational tool to explore RNA conformational space

Sloat, Nathan, Liu, Jui-Wen, Schroeder, Susan J.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 959 KB

english, 2017

287

DBNorm: normalizing high-density oligonucleotide microarray data based on distributions

Meng, Qinxue, Catchpoole, Daniel, Skillicorn, David, Kennedy, Paul J.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.66 MB

english, 2017

288

GPU-based detection of protein cavities using Gaussian surfaces

Dias, Sérgio E. D., Martins, Ana Mafalda, Nguyen, Quoc T., Gomes, Abel J. P.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.37 MB

english, 2017

289

bcROCsurface: an R package for correcting verification bias in estimation of the ROC surface and its volume for continuous diagnostic tests

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 834 KB

english, 2017

290

HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data

Beccuti, Marco, Genuardi, Elisa, Romano, Greta, Monitillo, Luigia, Barbero, Daniela, Boccadoro, Mario, Ladetto, Marco, Calogero, Raffaele, Ferrero, Simone, Cordero, Francesca

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 855 KB

english, 2017

291

Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs

Le, Duc-Hau, Verbeke, Lieven, Son, Le Hoang, Chu, Dinh-Toi, Pham, Van-Huy

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.35 MB

english, 2017

292

Integration of RNA-Seq data with heterogeneous microarray data for breast cancer profiling

Castillo, Daniel, Gálvez, Juan Manuel, Herrera, Luis Javier, Román, Belén San, Rojas, Fernando, Rojas, Ignacio

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 3.01 MB

english, 2017

293

Analysis of breast cancer subtypes by AP-ISA biclustering

Yang, Liying, Shen, Yunyan, Yuan, Xiguo, Zhang, Junying, Wei, Jianhua

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.20 MB

english, 2017

294

Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data

Al-Nakeeb, Kosai, Petersen, Thomas Nordahl, Sicheritz-Pontén, Thomas

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 501 KB

english, 2017

295

Modeling, validation and verification of three-dimensional cell-scaffold contacts from terabyte-sized images

Bajcsy, Peter, Yoon, Soweon, Florczyk, Stephen J., Hotaling, Nathan A., Simon, Mylene, Szczypinski, Piotr M., Schaub, Nicholas J., Simon, Carl G., Brady, Mary, Sriram, Ram D.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 6.88 MB

english, 2017

296

GFF3sort: a novel tool to sort GFF3 files for tabix indexing

Zhu, Tao, Liang, Chengzhen, Meng, Zhigang, Guo, Sandui, Zhang, Rui

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 893 KB

english, 2017

297

ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data

Oluwadare, Oluwatosin, Cheng, Jianlin

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 3.68 MB

english, 2017

298

ANAT 2.0: reconstructing functional protein subnetworks

Almozlino, Yomtov, Atias, Nir, Silverbush, Dana, Sharan, Roded

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 919 KB

english, 2017

299

ImageJ2: ImageJ for the next generation of scientific image data

Rueden, Curtis T., Schindelin, Johannes, Hiner, Mark C., DeZonia, Barry E., Walter, Alison E., Arena, Ellen T., Eliceiri, Kevin W.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 4.55 MB

english, 2017

300

A proximity-based graph clustering method for the identification and application of transcription factor clusters

Spadafore, Maxwell, Najarian, Kayvan, Boyle, Alan P.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.59 MB

english, 2017

301

Software for rapid time dependent ChIP-sequencing analysis (TDCA)

Myschyshyn, Mike, Farren-Dai, Marco, Chuang, Tien-Jui, Vocadlo, David

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.06 MB

english, 2017

302

VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites

Spinozzi, Giulio, Calabria, Andrea, Brasca, Stefano, Beretta, Stefano, Merelli, Ivan, Milanesi, Luciano, Montini, Eugenio

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.44 MB

english, 2017

303

Fast batch searching for protein homology based on compression and clustering

Ge, Hongwei, Sun, Liang, Yu, Jinghong

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.36 MB

english, 2017

304

Synima: a Synteny imaging tool for annotated genome assemblies

Farrer, Rhys A.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.49 MB

english, 2017

305

An efficient error correction algorithm using FM-index

Huang, Yao-Ting, Huang, Yu-Wen

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 786 KB

english, 2017

306

A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa

Bowman, Megan J., Pulman, Jane A., Liu, Tiffany L., Childs, Kevin L.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.33 MB

english, 2017

307

Detecting transitions in protein dynamics using a recurrence quantification analysis based bootstrap method

Karain, Wael I.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.62 MB

english, 2017

308

Chromosome structures: reduction of certain problems with unequal gene content and gene paralogs to integer linear programming

Lyubetsky, Vassily, Gershgorin, Roman, Gorbunov, Konstantin

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 708 KB

english, 2017

309

A comprehensive analysis on preservation patterns of gene co-expression networks during Alzheimer’s disease progression

Ray, Sumanta, Hossain, Sk Md Mosaddek, Khatun, Lutfunnesa, Mukhopadhyay, Anirban

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.75 MB

english, 2017

310

PON-SC – program for identifying steric clashes caused by amino acid substitutions

Čalyševa, Jelena, Vihinen, Mauno

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 669 KB

english, 2017

311

Bayesian estimation of scaled mutation rate under the coalescent: a sequential Monte Carlo approach

Ogundijo, Oyetunji E., Wang, Xiaodong

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.52 MB

english, 2017

312

A common base method for analysis of qPCR data and the application of simple blocking in qPCR experiments

Ganger, Michael T., Dietz, Geoffrey D., Ewing, Sarah J.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 675 KB

english, 2017

313

Canary: an atomic pipeline for clinical amplicon assays

Doig, Kenneth D., Ellul, Jason, Fellowes, Andrew, Thompson, Ella R., Ryland, Georgina, Blombery, Piers, Papenfuss, Anthony T., Fox, Stephen B.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 966 KB

english, 2017

314

Using variant databases for variant prioritization and to detect erroneous genotype-phenotype associations

Broeckx, Bart J. G., Peelman, Luc, Saunders, Jimmy H., Deforce, Dieter, Clement, Lieven

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 693 KB

english, 2017

315

CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences

Gdanetz, Kristi, Benucci, Gian Maria Niccolò, Vande Pol, Natalie, Bonito, Gregory

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 618 KB

english, 2017

316

HISEA: HIerarchical SEed Aligner for PacBio data

Khiste, Nilesh, Ilie, Lucian

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.21 MB

english, 2017

317

A comparison of graph- and kernel-based –omics data integration algorithms for classifying complex traits

Yan, Kang K., Zhao, Hongyu, Pang, Herbert

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.22 MB

english, 2017

318

Diverse effects of distance cutoff and residue interval on the performance of distance-dependent atom-pair potential in protein structure prediction

Yao, Yuangen, Gui, Rong, Liu, Quan, Yi, Ming, Deng, Haiyou

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 3.04 MB

english, 2017

319

A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data

Kang, Tianyu, Ding, Wei, Zhang, Luoyan, Ziemek, Daniel, Zarringhalam, Kourosh

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 951 KB

english, 2017

320

Redundancy analysis allows improved detection of methylation changes in large genomic regions

Ruiz-Arenas, Carlos, González, Juan R.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.41 MB

english, 2017

321

CSmetaPred: a consensus method for prediction of catalytic residues

Choudhary, Preeti, Kumar, Shailesh, Bachhawat, Anand Kumar, Pandit, Shashi Bhushan

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 2.03 MB

english, 2017

322

An Eigenvalue test for spatial principal component analysis

Montano, V., Jombart, T.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 987 KB

english, 2017

323

An integrated meta-analysis approach to identifying medications with potential to alter breast cancer risk through connectivity mapping

Thillaiyampalam, Gayathri, Liberante, Fabio, Murray, Liam, Cardwell, Chris, Mills, Ken, Zhang, Shu-Dong

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.77 MB

english, 2017

324

MetaGenyo: a web tool for meta-analysis of genetic association studies

Martorell-Marugan, Jordi, Toro-Dominguez, Daniel, Alarcon-Riquelme, Marta E., Carmona-Saez, Pedro

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 610 KB

english, 2017

325

Super-delta: a new differential gene expression analysis procedure with robust data normalization

Liu, Yuhang, Zhang, Jinfeng, Qiu, Xing

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 901 KB

english, 2017

326

Improved high-dimensional prediction with Random Forests by the use of co-data

te Beest, Dennis E., Mes, Steven W., Wilting, Saskia M., Brakenhoff, Ruud H., van de Wiel, Mark A.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.27 MB

english, 2017

327

fDETECT webserver: fast predictor of propensity for protein production, purification, and crystallization

Meng, Fanchi, Wang, Chen, Kurgan, Lukasz

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.41 MB

english, 2017

328

Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction

Han, Youngmahn, Kim, Dongsup

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.38 MB

english, 2017

329

A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy

Wickland, Daniel P., Battu, Gopal, Hudson, Karen A., Diers, Brian W., Hudson, Matthew E.

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 3.76 MB

english, 2017