Volume 17; Issue 1

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BMC Bioinformatics
Volume 17; Issue 1

BMC Bioinformatics

Volume 17; Issue 1

1

Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts

Hakenberg, Jörg, Cheng, Wei-Yi, Thomas, Philippe, Wang, Ying-Chih, Uzilov, Andrew V., Chen, Rong

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.39 MB

english, 2016

2

A powerful score-based statistical test for group difference in weighted biological networks

Ji, Jiadong, Yuan, Zhongshang, Zhang, Xiaoshuai, Xue, Fuzhong

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.26 MB

english, 2016

3

Predicting the functions of a protein from its ability to associate with other molecules

Taha, Kamal, Yoo, Paul D.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.30 MB

english, 2016

4

Design, structure prediction and molecular dynamics simulation of a fusion construct containing malaria pre-erythrocytic vaccine candidate, PfCelTOS, and human interleukin 2 as adjuvant

Shamriz, Shabnam, Ofoghi, Hamideh

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.91 MB

english, 2016

5

4Pipe4 – A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information

Pina-Martins, Francisco, Vieira, Bruno M., Seabra, Sofia G., Batista, Dora, Paulo, Octávio S.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 715 KB

english, 2016

6

Detecting false positive sequence homology: a machine learning approach

Fujimoto, M. Stanley, Suvorov, Anton, Jensen, Nicholas O., Clement, Mark J., Bybee, Seth M.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.83 MB

english, 2016

7

Fast and accurate branch lengths estimation for phylogenomic trees

Binet, Manuel, Gascuel, Olivier, Scornavacca, Celine, P. Douzery, Emmanuel J., Pardi, Fabio

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.21 MB

english, 2016

8

GEMINI: a computationally-efficient search engine for large gene expression datasets

DeFreitas, Timothy, Saddiki, Hachem, Flaherty, Patrick

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 767 KB

english, 2016

9

Discrete distributional differential expression (D3E) - a tool for gene expression analysis of single-cell RNA-seq data

Delmans, Mihails, Hemberg, Martin

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.97 MB

english, 2016

10

Consequential considerations when mapping tRNA fragments

Telonis, Aristeidis G., Loher, Phillipe, Kirino, Yohei, Rigoutsos, Isidore

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 369 KB

english, 2016

11

Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis

Dubinkina, Veronika B., Ischenko, Dmitry S., Ulyantsev, Vladimir I., Tyakht, Alexander V., Alexeev, Dmitry G.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.58 MB

english, 2016

12

Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data

Schirmer, Melanie, D’Amore, Rosalinda, Ijaz, Umer Z., Hall, Neil, Quince, Christopher

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.75 MB

english, 2016

13

Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology

Zhao, Zheng, Martin, Che, Fan, Raymond, Bourne, Philip E., Xie, Lei

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.87 MB

english, 2016

14

Measure transcript integrity using RNA-seq data

Wang, Liguo, Nie, Jinfu, Sicotte, Hugues, Li, Ying, Eckel-Passow, Jeanette E., Dasari, Surendra, Vedell, Peter T., Barman, Poulami, Wang, Liewei, Weinshiboum, Richard, Jen, Jin, Huang, Haojie, Kohli,

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.57 MB

english, 2016

15

Testing for association between RNA-Seq and high-dimensional data

Rauschenberger, Armin, Jonker, Marianne A., van de Wiel, Mark A., Menezes, Renée X.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.07 MB

english, 2016

16

GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data

Rue-Albrecht, Kévin, McGettigan, Paul A., Hernández, Belinda, Nalpas, Nicolas C., Magee, David A., Parnell, Andrew C., Gordon, Stephen V., MacHugh, David E.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.81 MB

english, 2016

17

TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation

Wolfien, Markus, Rimmbach, Christian, Schmitz, Ulf, Jung, Julia Jeannine, Krebs, Stefan, Steinhoff, Gustav, David, Robert, Wolkenhauer, Olaf

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.43 MB

english, 2016

18

GenAp: a distributed SQL interface for genomic data

Kozanitis, Christos, Patterson, David A.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 655 KB

english, 2016

19

MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing

Wong, Nicholas C., Pope, Bernard J., Candiloro, Ida L., Korbie, Darren, Trau, Matt, Wong, Stephen Q., Mikeska, Thomas, Zhang, Xinmin, Pitman, Mark, Eggers, Stefanie, Doyle, Stephen R., Dobrovic, Alexa

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.26 MB

english, 2016

20

Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments

Bi, Ran, Liu, Peng

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 816 KB

english, 2016

21

PeTTSy: a computational tool for perturbation analysis of complex systems biology models

Domijan, Mirela, Brown, Paul E., Shulgin, Boris V., Rand, David A.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.98 MB

english, 2016

22

Comparison of module detection algorithms in protein networks and investigation of the biological meaning of predicted modules

Tripathi, Shailesh, Moutari, Salissou, Dehmer, Matthias, Emmert-Streib, Frank

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.24 MB

english, 2016

23

CompNet: a GUI based tool for comparison of multiple biological interaction networks

Kuntal, Bhusan K., Dutta, Anirban, Mande, Sharmila S.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.92 MB

english, 2016

24

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves

Sprouffske, Kathleen, Wagner, Andreas

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.00 MB

english, 2016

25

The systems biology format converter

Rodriguez, Nicolas, Pettit, Jean-Baptiste, Dalle Pezze, Piero, Li, Lu, Henry, Arnaud, van Iersel, Martijn P., Jalowicki, Gael, Kutmon, Martina, Natarajan, Kedar N., Tolnay, David, Stefan, Melanie I.,

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.90 MB

english, 2016

26

SoftPanel: a website for grouping diseases and related disorders for generation of customized panels

Wang, Likun, Zhang, Cong, Watkins, Johnathan, Jin, Yan, McNutt, Michael, Yin, Yuxin

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 897 KB

english, 2016

27

MetICA: independent component analysis for high-resolution mass-spectrometry based non-targeted metabolomics

Liu, Youzhong, Smirnov, Kirill, Lucio, Marianna, Gougeon, Régis D., Alexandre, Hervé, Schmitt-Kopplin, Philippe

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.27 MB

english, 2016

28

SeqPurge: highly-sensitive adapter trimming for paired-end NGS data

Sturm, Marc, Schroeder, Christopher, Bauer, Peter

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 541 KB

english, 2016

29

LimiTT: link miRNAs to targets

Bayer, Julia, Kuenne, Carsten, Preussner, Jens, Looso, Mario

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 720 KB

english, 2016

30

A novel procedure on next generation sequencing data analysis using text mining algorithm

Zhao, Weizhong, Chen, James J., Perkins, Roger, Wang, Yuping, Liu, Zhichao, Hong, Huixiao, Tong, Weida, Zou, Wen

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.33 MB

english, 2016

31

A multiple kernel learning algorithm for drug-target interaction prediction

Nascimento, André C. A., Prudêncio, Ricardo B. C., Costa, Ivan G.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.20 MB

english, 2016

32

A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer)

Berkowitz, Nathan D., Silverman, Ian M., Childress, Daniel M., Kazan, Hilal, Wang, Li-San, Gregory, Brian D.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.89 MB

english, 2016

33

RNA motif search with data-driven element ordering

Rampášek, Ladislav, Jimenez, Randi M., Lupták, Andrej, Vinař, Tomáš, Brejová, Broňa

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 827 KB

english, 2016

34

Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome

Kawaguchi, Risa, Kiryu, Hisanori

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.61 MB

english, 2016

35

BayesFlow: latent modeling of flow cytometry cell populations

Johnsson, Kerstin, Wallin, Jonas, Fontes, Magnus

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.24 MB

english, 2016

36

Erratum to: MetCap: A bioinformatics probe design pipeline for large-scale targeted metagenomics

Kushwaha, Sandeep K., Manoharan, Lokeshwaran, Meerupati, Tejashwari, Hedlund, Katarina, Ahren, Dag

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 361 KB

english, 2016

37

Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks

Landeghem, Sofie Van, Parys, Thomas Van, Dubois, Marieke, Inzé, Dirk, de Peer, Yves Van

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.49 MB

english, 2016

38

ChainRank, a chain prioritisation method for contextualisation of biological networks

Tényi, Ákos, de Atauri, Pedro, Gomez-Cabrero, David, Cano, Isaac, Clarke, Kim, Falciani, Francesco, Cascante, Marta, Roca, Josep, Maier, Dieter

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.46 MB

english, 2016

39

Variable selection for binary classification using error rate p-values applied to metabolomics data

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

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.07 MB

english, 2016

40

An efficient genome-wide association test for multivariate phenotypes based on the Fisher combination function

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

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 972 KB

english, 2016

41

Aligning the unalignable: bacteriophage whole genome alignments

Bérard, Sèverine, Chateau, Annie, Pompidor, Nicolas, Guertin, Paul, Bergeron, Anne, Swenson, Krister M.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.50 MB

english, 2016

42

NOBLE – Flexible concept recognition for large-scale biomedical natural language processing

Tseytlin, Eugene, Mitchell, Kevin, Legowski, Elizabeth, Corrigan, Julia, Chavan, Girish, Jacobson, Rebecca S.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.62 MB

english, 2016

43

MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature

Shivashankar, Nithin, Patil, Sonali, Bhosle, Amrisha, Chandra, Nagasuma, Natarajan, Vijay

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.38 MB

english, 2016

44

IPLaminator: an ImageJ plugin for automated binning and quantification of retinal lamination

Li, Shuai, Woodfin, Michael, Long, Seth S., Fuerst, Peter G.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.64 MB

english, 2016

45

Molecular dynamics simulation and bioinformatics study on chloroplast stromal ridge complex from rice (Oryza sativa L.)

Zhang, Yubo, Ding, Yi

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.52 MB

english, 2016

46

Algorithms for reconstruction of chromosomal structures

Lyubetsky, Vassily, Gershgorin, Roman, Seliverstov, Alexander, Gorbunov, Konstantin

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.67 MB

english, 2016

47

GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data

Melo, Arthur T. O., Bartaula, Radhika, Hale, Iago

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.19 MB

english, 2016

48

EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms

Janies, Daniel A., Witter, Zach, Linchangco, Gregorio V., Foltz, David W., Miller, Allison K., Kerr, Alexander M., Jay, Jeremy, Reid, Robert W., Wray, Gregory A.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 599 KB

english, 2016

49

Deciphering transcriptional regulations coordinating the response to environmental changes

Acuña, Vicente, Aravena, Andrés, Guziolowski, Carito, Eveillard, Damien, Siegel, Anne, Maass, Alejandro

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.03 MB

english, 2016

50

An integrative analysis of gene expression and molecular interaction data to identify dys-regulated sub-networks in inflammatory bowel disease

Muraro, Daniele, Simmons, Alison

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 925 KB

english, 2016

51

Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations

Leung, Elo, Huang, Amy, Cadag, Eithon, Montana, Aldrin, Soliman, Jan Lorenz, Zhou, Carol L. Ecale

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 868 KB

english, 2016

52

An individualized predictor of health and disease using paired reference and target samples

Liu, Tzu-Yu, Burke, Thomas, Park, Lawrence P., Woods, Christopher W., Zaas, Aimee K., Ginsburg, Geoffrey S., Hero, Alfred O.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.85 MB

english, 2016

53

Impact of data resolution on three-dimensional structure inference methods

Park, Jincheol, Lin, Shili

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 860 KB

english, 2016

54

Arabidopsis Motif Scanner

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 595 KB

english, 2016

55

The role of structural parameters in DNA cyclization

Alexandrov, Ludmil B., Bishop, Alan R., Rasmussen, Kim Ø., Alexandrov, Boian S.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 725 KB

english, 2016

56

Impact of imputation methods on the amount of genetic variation captured by a single-nucleotide polymorphism panel in soybeans

Xavier, A., Muir, William M., Rainey, Katy M.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 744 KB

english, 2016

57

Broadwick: a framework for computational epidemiology

O’Hare, Anthony, Lycett, Samantha J., Doherty, Thomas, M. Salvador, Liliana C., Kao, Rowland R.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 615 KB

english, 2016

58

The exceptional genomic word symmetry along DNA sequences

Afreixo, Vera, Rodrigues, João M. O. S., Bastos, Carlos A. C., Silva, Raquel M.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 847 KB

english, 2016

59

Method to represent the distribution of QTL additive and dominance effects associated with quantitative traits in computer simulation

Sun, Xiaochun, Mumm, Rita H.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.62 MB

english, 2016

60

Netter: re-ranking gene network inference predictions using structural network properties

Ruyssinck, Joeri, Demeester, Piet, Dhaene, Tom, Saeys, Yvan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 954 KB

english, 2016

61

CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks

Paroni, Andrea, Graudenzi, Alex, Caravagna, Giulio, Damiani, Chiara, Mauri, Giancarlo, Antoniotti, Marco

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.41 MB

english, 2016

62

Web-TCGA: an online platform for integrated analysis of molecular cancer data sets

Deng, Mario, Brägelmann, Johannes, Schultze, Joachim L., Perner, Sven

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 616 KB

english, 2016

63

An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom

Vujaklija, Ivan, Bielen, Ana, Paradžik, Tina, Biđin, Siniša, Goldstein, Pavle, Vujaklija, Dušica

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.85 MB

english, 2016

64

SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis

Johnson, Benjamin K., Scholz, Matthew B., Teal, Tracy K., Abramovitch, Robert B.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 951 KB

english, 2016

65

Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data

Dellicour, Simon, Rose, Rebecca, Pybus, Oliver G.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.55 MB

english, 2016

66

CellECT: cell evolution capturing tool

Delibaltov, Diana L., Gaur, Utkarsh, Kim, Jennifer, Kourakis, Matthew, Newman-Smith, Erin, Smith, William, Belteton, Samuel A., Szymanski, Daniel B., Manjunath, B. S.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.30 MB

english, 2016

67

Gene set analysis using sufficient dimension reduction

Hsueh, Huey-Miin, Tsai, Chen-An

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.50 MB

english, 2016

68

ksRepo: a generalized platform for computational drug repositioning

Brown, Adam S., Kong, Sek Won, Kohane, Isaac S., Patel, Chirag J.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 815 KB

english, 2016

69

MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression

Kim, Minji, Zhang, Xiejia, Ligo, Jonathan G., Farnoud, Farzad, Veeravalli, Venugopal V., Milenkovic, Olgica

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.19 MB

english, 2016

70

BMC Bioinformatics reviewer acknowledgement 2015

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 354 KB

english, 2016

71

A two-layer integration framework for protein complex detection

Ou-Yang, Le, Wu, Min, Zhang, Xiao-Fei, Dai, Dao-Qing, Li, Xiao-Li, Yan, Hong

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.77 MB

english, 2016

72

Intra- and interspecies gene expression models for predicting drug response in canine osteosarcoma

Fowles, Jared S., Brown, Kristen C., Hess, Ann M., Duval, Dawn L., Gustafson, Daniel L.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.64 MB

english, 2016

73

Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.34 MB

english, 2016

74

CUDAMPF: a multi-tiered parallel framework for accelerating protein sequence search in HMMER on CUDA-enabled GPU

Jiang, Hanyu, Ganesan, Narayan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.32 MB

english, 2016

75

Structure-based Markov random field model for representing evolutionary constraints on functional sites

Jeong, Chan-Seok, Kim, Dongsup

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.21 MB

english, 2016

76

Erratum to: PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events

Izuogu, Osagie G., Alhasan, Abd A., Alafghani, Hani M., Santibanez-Koref, Mauro, Elliott, David J., Jackson, Michael S.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 295 KB

english, 2016

77

Regularized logistic regression with network-based pairwise interaction for biomarker identification in breast cancer

Wu, Meng-Yun, Zhang, Xiao-Fei, Dai, Dao-Qing, Ou-Yang, Le, Zhu, Yuan, Yan, Hong

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.96 MB

english, 2016

78

A NMF based approach for integrating multiple data sources to predict HIV-1–human PPIs

Ray, Sumanta, Bandyopadhyay, Sanghamitra

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.06 MB

english, 2016

79

Structured feature selection using coordinate descent optimization

Ghalwash, Mohamed F., Cao, Xi Hang, Stojkovic, Ivan, Obradovic, Zoran

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.69 MB

english, 2016

80

Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection

Zhang, Qi, Zeng, Xin, Younkin, Sam, Kawli, Trupti, Snyder, Michael P., Keleş, Sündüz

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 936 KB

english, 2016

81

isomiR-SEA: an RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation

Urgese, Gianvito, Paciello, Giulia, Acquaviva, Andrea, Ficarra, Elisa

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.37 MB

english, 2016

82

Computational methods for ubiquitination site prediction using physicochemical properties of protein sequences

Cai, Binghuang, Jiang, Xia

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.16 MB

english, 2016

83

Analysis of secondary structural elements in human microRNA hairpin precursors

Liu, Biao, Childs-Disney, Jessica L., Znosko, Brent M., Wang, Dan, Fallahi, Mohammad, Gallo, Steven M., Disney, Matthew D.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.83 MB

english, 2016

84

Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order

Jindalertudomdee, Jira, Hayashida, Morihiro, Zhao, Yang, Akutsu, Tatsuya

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.38 MB

english, 2016

85

HPG pore: an efficient and scalable framework for nanopore sequencing data

Tarraga, Joaquin, Gallego, Asunción, Arnau, Vicente, Medina, Ignacio, Dopazo, Joaquin

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.03 MB

english, 2016

86

ADEPT, a dynamic next generation sequencing data error-detection program with trimming

Feng, Shihai, Lo, Chien-Chi, Li, Po-E, Chain, Patrick S. G.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.63 MB

english, 2016

87

Stepwise approach for combining many sources of evidence for site-recognition in genomic sequences

Pérez-Rodríguez, Javier, García-Pedrajas, Nicolás

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 818 KB

english, 2016

88

Erratum to: BayesFlow: latent modeling of flow cytometry cell populations

Johnsson, Kerstin, Wallin, Jonas, Fontes, Magnus

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 336 KB

english, 2016

89

Erratum to: Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature

Ravikumar, Komandur Elayavilli, Wagholikar, Kavishwar B., Li, Dingcheng, Kocher, Jean-Pierre, Liu, Hongfang

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 333 KB

english, 2016

90

CoeViz: a web-based tool for coevolution analysis of protein residues

Baker, Frazier N., Porollo, Aleksey

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.24 MB

english, 2016

91

A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction

Öztürk, Hakime, Ozkirimli, Elif, Özgür, Arzucan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 462 KB

english, 2016

92

From the desktop to the grid: scalable bioinformatics via workflow conversion

de la Garza, Luis, Veit, Johannes, Szolek, Andras, Röttig, Marc, Aiche, Stephan, Gesing, Sandra, Reinert, Knut, Kohlbacher, Oliver

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.31 MB

english, 2016

93

Bottom-up GGM algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways or processes

Kumari, Sapna, Deng, Wenping, Gunasekara, Chathura, Chiang, Vincent, Chen, Huann-sheng, Ma, Hao, Davis, Xin, Wei, Hairong

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.83 MB

english, 2016

94

Modeling the integration of bacterial rRNA fragments into the human cancer genome

Sieber, Karsten B., Gajer, Pawel, Dunning Hotopp, Julie C.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 884 KB

english, 2016

95

Three-dimensional protein model similarity analysis based on salient shape index

Yao, Bo, Li, Zhong, Ding, Meng, Chen, Minhong

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.76 MB

english, 2016

96

pcaReduce: hierarchical clustering of single cell transcriptional profiles

žurauskienė, Justina, Yau, Christopher

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.48 MB

english, 2016

97

Does the choice of nucleotide substitution models matter topologically?

Hoff, Michael, Orf, Stefan, Riehm, Benedikt, Darriba, Diego, Stamatakis, Alexandros

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 954 KB

english, 2016

98

Sparse regression models for unraveling group and individual associations in eQTL mapping

Cheng, Wei, Shi, Yu, Zhang, Xiang, Wang, Wei

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.56 MB

english, 2016

99

A benchmark for microRNA quantification algorithms using the OpenArray platform

McCall, Matthew N., Baras, Alexander S., Crits-Christoph, Alexander, Ingersoll, Roxann, McAlexander, Melissa A., Witwer, Kenneth W., Halushka, Marc K.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.36 MB

english, 2016

100

Common molecular mechanism of the hepatic lesion and the cardiac parasympathetic regulation in chronic hepatitis C infection: a critical role for the muscarinic receptor type 3

Glišić, Sanja, Cavanaugh, David P., Chittur, Krishnan K., Sencanski, Milan, Perovic, Vladimir, Bojić, Tijana

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.20 MB

english, 2016

101

Mutanalyst, an online tool for assessing the mutational spectrum of epPCR libraries with poor sampling

Ferla, Matteo Paolo

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 438 KB

english, 2016

102

Unaccounted uncertainty from qPCR efficiency estimates entails uncontrolled false positive rates

Bilgrau, Anders E., Falgreen, Steffen, Petersen, Anders, Kjeldsen, Malene K., Bødker, Julie S., Johnsen, Hans E., Dybkær, Karen, Bøgsted, Martin

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 729 KB

english, 2016

103

Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells

Beltman, Joost B., Urbanus, Jos, Velds, Arno, van Rooij, Nienke, Rohr, Jan C., Naik, Shalin H., Schumacher, Ton N.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.77 MB

english, 2016

104

ChemiRs: a web application for microRNAs and chemicals

Su, Emily Chia-Yu, Chen, Yu-Sing, Tien, Yun-Cheng, Liu, Jeff, Ho, Bing-Ching, Yu, Sung-Liang, Singh, Sher

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.73 MB

english, 2016

105

eSTGt: a programming and simulation environment for population dynamics

Spiro, Adam, Shapiro, Ehud

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.09 MB

english, 2016

106

CollapsABEL: an R library for detecting compound heterozygote alleles in genome-wide association studies

Zhong, Kaiyin, Karssen, Lennart C., Kayser, Manfred, Liu, Fan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.59 MB

english, 2016

107

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin

Patro, Rob, Norel, Raquel, Prill, Robert J., Saez-Rodriguez, Julio, Lorenz, Peter, Steinbeck, Felix, Ziems, Bjoern, Luštrek, Mitja, Barbarini, Nicola, Tiengo, Alessandra, Bellazzi, Riccardo, Thiesen,

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.78 MB

english, 2016

108

Gene signature-based mapping of immunological systems and diseases

Liu, Hong, Liu, Jessica, Toups, Michelle, Soos, Timothy, Arendt, Christopher

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.06 MB

english, 2016

109

BAGEL: a computational framework for identifying essential genes from pooled library screens

Hart, Traver, Moffat, Jason

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.34 MB

english, 2016

110

Detection and tracking of overlapping cell nuclei for large scale mitosis analyses

Li, Yingbo, Rose, France, di Pietro, Florencia, Morin, Xavier, Genovesio, Auguste

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.53 MB

english, 2016

111

Sequence-based prediction of protein-protein interactions using weighted sparse representation model combined with global encoding

Huang, Yu-An, You, Zhu-Hong, Chen, Xing, Chan, Keith, Luo, Xin

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.33 MB

english, 2016

112

Erratum to: ‘CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments’

Waardenberg, Ashley J., Bassett, Samuel D., Bouveret, Romaric, Harvey, Richard P.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 337 KB

english, 2016

113

Erratum to: ‘Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images’

Wu, Allison Chia-Yi, Rifkin, Scott A.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 393 KB

english, 2016

114

gtrellis: an R/Bioconductor package for making genome-level Trellis graphics

Gu, Zuguang, Eils, Roland, Schlesner, Matthias

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 8.42 MB

english, 2016

115

Empirical estimation of sequencing error rates using smoothing splines

Zhu, Xuan, Wang, Jian, Peng, Bo, Shete, Sanjay

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 466 KB

english, 2016

116

Hierarchical classification strategy for Phenotype extraction from epidermal growth factor receptor endocytosis screening

Cao, Lu, Graauw, Marjo de, Yan, Kuan, Winkel, Leah, Verbeek, Fons J.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.66 MB

english, 2016

117

DensityMap: a genome viewer for illustrating the densities of features

Guizard, Sébastien, Piégu, Benoît, Bigot, Yves

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.04 MB

english, 2016

118

Stochastic epigenetic outliers can define field defects in cancer

Teschendorff, Andrew E., Jones, Allison, Widschwendter, Martin

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.46 MB

english, 2016

119

TopHat-Recondition: a post-processor for TopHat unmapped reads

Brueffer, Christian, Saal, Lao H.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 390 KB

english, 2016

120

A principal components method constrained by elementary flux modes: analysis of flux data sets

von Stosch, Moritz, Rodrigues de Azevedo, Cristiana, Luis, Mauro, Feyo de Azevedo, Sebastiao, Oliveira, Rui

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.14 MB

english, 2016

121

DrugGenEx-Net: a novel computational platform for systems pharmacology and gene expression-based drug repurposing

Issa, Naiem T., Kruger, Jordan, Wathieu, Henri, Raja, Rajarajan, Byers, Stephen W., Dakshanamurthy, Sivanesan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.77 MB

english, 2016

122

A gene-signature progression approach to identifying candidate small-molecule cancer therapeutics with connectivity mapping

Wen, Qing, Kim, Chang-Sik, Hamilton, Peter W., Zhang, Shu-Dong

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.04 MB

english, 2016

123

Joint analysis of histopathology image features and gene expression in breast cancer

Popovici, Vlad, Budinská, Eva, Čápková, Lenka, Schwarz, Daniel, Dušek, Ladislav, Feit, Josef, Jaggi, Rolf

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.06 MB

english, 2016

124

Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis

Cloete, Ruben, Oppon, Ekow, Murungi, Edwin, Schubert, Wolf-Dieter, Christoffels, Alan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.33 MB

english, 2016

125

sciReptor: analysis of single-cell level immunoglobulin repertoires

Imkeller, Katharina, Arndt, Peter F., Wardemann, Hedda, Busse, Christian E.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.19 MB

english, 2016

126

Erratum to: MINE: Module Identification in Networks

Rhrissorrakrai, Kahn, Gunsalus, Kristin C.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 515 KB

english, 2016

127

A new method to measure complexity in binary or weighted networks and applications to functional connectivity in the human brain

Hahn, Klaus, Massopust, Peter R., Prigarin, Sergei

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.83 MB

english, 2016

128

FastPop: a rapid principal component derived method to infer intercontinental ancestry using genetic data

Li, Yafang, Byun, Jinyoung, Cai, Guoshuai, Xiao, Xiangjun, Han, Younghun, Cornelis, Olivier, Dinulos, James E., Dennis, Joe, Easton, Douglas, Gorlov, Ivan, Seldin, Michael F., Amos, Christopher I.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 959 KB

english, 2016

129

MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data

Madoui, Mohammed-Amin, Dossat, Carole, d’Agata, Léo, van Oeveren, Jan, van der Vossen, Edwin, Aury, Jean-Marc

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.17 MB

english, 2016

130

Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis

Yang, Bo, Wang, Yong, Qian, Pei-Yuan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.61 MB

english, 2016

131

The effect of noise-induced variance on parameter recovery from reaction times

Vadillo, Miguel A., Garaizar, Pablo

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.89 MB

english, 2016

132

Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data

Rask, Thomas S., Petersen, Bent, Chen, Donald S., Day, Karen P., Pedersen, Anders Gorm

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 765 KB

english, 2016

133

Addressing inaccuracies in BLOSUM computation improves homology search performance

Hess, Martin, Keul, Frank, Goesele, Michael, Hamacher, Kay

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 925 KB

english, 2016

134

QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics

O’Reilly, Paul G., Wen, Qing, Bankhead, Peter, Dunne, Philip D., McArt, Darragh G., McPherson, Suzanne, Hamilton, Peter W., Mills, Ken I., Zhang, Shu-Dong

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.82 MB

english, 2016

135

A novel semi-supervised algorithm for the taxonomic assignment of metagenomic reads

Le, Vinh Van, Tran, Lang Van, Tran, Hoai Van

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 737 KB

english, 2016

136

A computational method for genotype calling in family-based sequencing data

Chang, Lun-Ching, Li, Bingshan, Fang, Zhou, Vrieze, Scott, McGue, Matt, Iacono, William G., Tseng, George C., Chen, Wei

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.49 MB

english, 2016

137

PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events

Izuogu, Osagie G., Alhasan, Abd A., Alafghani, Hani M., Santibanez-Koref, Mauro, Elliott, David J., Jackson, Michael S.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.94 MB

english, 2016

138

Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis

Geistlinger, Ludwig, Csaba, Gergely, Zimmer, Ralf

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.57 MB

english, 2016

139

DNAism: exploring genomic datasets on the web with Horizon Charts

Rio Deiros, David, Gibbs, Richard A., Rogers, Jeffrey

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.57 MB

english, 2016

140

CP-CHARM: segmentation-free image classification made accessible

Uhlmann, Virginie, Singh, Shantanu, Carpenter, Anne E.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.00 MB

english, 2016

141

ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research

Pandey, Ram Vinay, Pabinger, Stephan, Kriegner, Albert, Weinhäusel, Andreas

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.50 MB

english, 2016

142

Erratum to: Weakly supervised learning of biomedical information extraction from curated data

Jain, Suvir, Tumkur, Kashyap R., Kuo, Tsung-Ting, Bhargava, Shitij, Lin, Gordon, Hsu, Chun-Nan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 283 KB

english, 2016

143

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.84 MB

english, 2016

144

LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer

Melloni, Giorgio E. M., de Pretis, Stefano, Riva, Laura, Pelizzola, Mattia, Céol, Arnaud, Costanza, Jole, Müller, Heiko, Zammataro, Luca

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.42 MB

english, 2016

145

Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators

Piechota, Marcin, Korostynski, Michal, Ficek, Joanna, Tomski, Andrzej, Przewlocki, Ryszard

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.71 MB

english, 2016

146

Trimming of sequence reads alters RNA-Seq gene expression estimates

Williams, Claire R., Baccarella, Alyssa, Parrish, Jay Z., Kim, Charles C.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.35 MB

english, 2016

147

CyTRANSFINDER: a Cytoscape 3.3 plugin for three-component (TF, gene, miRNA) signal transduction pathway construction

Politano, Gianfranco, Orso, Francesca, Raimo, Monica, Benso, Alfredo, Savino, Alessandro, Taverna, Daniela, Di Carlo, Stefano

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.48 MB

english, 2016

148

On the comparison of regulatory sequences with multiple resolution Entropic Profiles

Comin, Matteo, Antonello, Morris

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.25 MB

english, 2016

149

McTwo: a two-step feature selection algorithm based on maximal information coefficient

Ge, Ruiquan, Zhou, Manli, Luo, Youxi, Meng, Qinghan, Mai, Guoqin, Ma, Dongli, Wang, Guoqing, Zhou, Fengfeng

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.94 MB

english, 2016

150

Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains

Starmer, Joshua, Magnuson, Terry

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.23 MB

english, 2016

151

PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies

Jeon, Jouhyun, Arnold, Roland, Singh, Fateh, Teyra, Joan, Braun, Tatjana, Kim, Philip M.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.34 MB

english, 2016

152

Predicting drug target interactions using meta-path-based semantic network analysis

Fu, Gang, Ding, Ying, Seal, Abhik, Chen, Bin, Sun, Yizhou, Bolton, Evan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.00 MB

english, 2016

153

readat: An R package for reading and working with SomaLogic ADAT files

Cotton, Richard J., Graumann, Johannes

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 432 KB

english, 2016

154

Sortal anaphora resolution to enhance relation extraction from biomedical literature

Kilicoglu, Halil, Rosemblat, Graciela, Fiszman, Marcelo, Rindflesch, Thomas C.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.04 MB

english, 2016

155

MutSpec: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes

Ardin, Maude, Cahais, Vincent, Castells, Xavier, Bouaoun, Liacine, Byrnes, Graham, Herceg, Zdenko, Zavadil, Jiri, Olivier, Magali

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.63 MB

english, 2016

156

UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing

Park, Daniel J., Li, Roger, Lau, Edmund, Georgeson, Peter, Nguyen-Dumont, Tú, Pope, Bernard J.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.29 MB

english, 2016

157

Analysis of significant factors for dengue fever incidence prediction

Siriyasatien, Padet, Phumee, Atchara, Ongruk, Phatsavee, Jampachaisri, Katechan, Kesorn, Kraisak

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 967 KB

english, 2016

158

Construction of dynamic probabilistic protein interaction networks for protein complex identification

Zhang, Yijia, Lin, Hongfei, Yang, Zhihao, Wang, Jian

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 985 KB

english, 2016

159

ImiRP: a computational approach to microRNA target site mutation

Ryan, Bridget C., Werner, Torben S., Howard, Perry L., Chow, Robert L.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.80 MB

english, 2016

160

Automatic detection of diffusion modes within biological membranes using back-propagation neural network

Dosset, Patrice, Rassam, Patrice, Fernandez, Laurent, Espenel, Cedric, Rubinstein, Eric, Margeat, Emmanuel, Milhiet, Pierre-Emmanuel

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.94 MB

english, 2016

161

Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner

Gutiérrez, Fernando I., Rodriguez-Valenzuela, Felipe, Ibarra, Ignacio L., Devos, Damien P., Melo, Francisco

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.84 MB

english, 2016

162

Combining location-and-scale batch effect adjustment with data cleaning by latent factor adjustment

Hornung, Roman, Boulesteix, Anne-Laure, Causeur, David

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 832 KB

english, 2016

163

A two-phase procedure for non-normal quantitative trait genetic association study

Zhang, Wei, Li, Huiyun, Li, Zhaohai, Li, Qizhai

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 841 KB

english, 2016

164

Informative gene selection and the direct classification of tumors based on relative simplicity

Chen, Yuan, Wang, Lifeng, Li, Lanzhi, Zhang, Hongyan, Yuan, Zheming

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 725 KB

english, 2016

165

An experimental study of the intrinsic stability of random forest variable importance measures

Wang, Huazhen, Yang, Fan, Luo, Zhiyuan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.29 MB

english, 2016

166

NEAT: a framework for building fully automated NGS pipelines and analyses

Schorderet, Patrick

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.76 MB

english, 2016

167

Sparse regressions for predicting and interpreting subcellular localization of multi-label proteins

Wan, Shibiao, Mak, Man-Wai, Kung, Sun-Yuan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.61 MB

english, 2016

168

Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL)

Koestler, Devin C., Jones, Meaghan J., Usset, Joseph, Christensen, Brock C., Butler, Rondi A., Kobor, Michael S., Wiencke, John K., Kelsey, Karl T.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.89 MB

english, 2016

169

Computational modeling of phagocyte transmigration for foreign body responses to subcutaneous biomaterial implants in mice

Kang, Mingon, Tang, Liping, Gao, Jean

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.61 MB

english, 2016

170

Erratum to: Predicting the functions of a protein from its ability to associate with other molecules

Taha, Kamal, Yoo, Paul D.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 296 KB

english, 2016

171

Leveraging protein quaternary structure to identify oncogenic driver mutations

Ryslik, Gregory A., Cheng, Yuwei, Modis, Yorgo, Zhao, Hongyu

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.05 MB

english, 2016

172

G-DOC Plus – an integrative bioinformatics platform for precision medicine

Bhuvaneshwar, Krithika, Belouali, Anas, Singh, Varun, Johnson, Robert M., Song, Lei, Alaoui, Adil, Harris, Michael A., Clarke, Robert, Weiner, Louis M., Gusev, Yuriy, Madhavan, Subha

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.54 MB

english, 2016

173

ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data

Rustagi, Navin, Hampton, Oliver A, Li, Jie, Xi, Liu, Gibbs, Richard A., Plon, Sharon E., Kimmel, Marek, Wheeler, David A.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 852 KB

english, 2016

174

IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data

Mysara, Mohamed, Leys, Natalie, Raes, Jeroen, Monsieurs, Pieter

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.59 MB

english, 2016

175

Brain Radiation Information Data Exchange (BRIDE): integration of experimental data from low-dose ionising radiation research for pathway discovery

Karapiperis, Christos, Kempf, Stefan J., Quintens, Roel, Azimzadeh, Omid, Vidal, Victoria Linares, Pazzaglia, Simonetta, Bazyka, Dimitry, Mastroberardino, Pier G., Scouras, Zacharias G., Tapio, Soile,

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.45 MB

english, 2016

176

PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq

Wen, Bo, Xu, Shaohang, Zhou, Ruo, Zhang, Bing, Wang, Xiaojing, Liu, Xin, Xu, Xun, Liu, Siqi

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 700 KB

english, 2016

177

CerealsDB 3.0: expansion of resources and data integration

Wilkinson, Paul A., Winfield, Mark O., Barker, Gary L. A., Tyrrell, Simon, Bian, Xingdong, Allen, Alexandra M., Burridge, Amanda, Coghill, Jane A., Waterfall, Christy, Caccamo, Mario, Davey, Robert P.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.46 MB

english, 2016

178

PhytoCRISP-Ex: a web-based and stand-alone application to find specific target sequences for CRISPR/CAS editing

Rastogi, Achal, Murik, Omer, Bowler, Chris, Tirichine, Leila

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 720 KB

english, 2016

179

Exploiting expression patterns across multiple tissues to map expression quantitative trait loci

Acharya, Chaitanya R., McCarthy, Janice M., Owzar, Kouros, Allen, Andrew S.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 849 KB

english, 2016

180

Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server

Abriata, Luciano A., Bovigny, Christophe, Dal Peraro, Matteo

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.69 MB

english, 2016

181

Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis

Cormier, Nathan, Kolisnik, Tyler, Bieda, Mark

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.22 MB

english, 2016

182

multiDE: a dimension reduced model based statistical method for differential expression analysis using RNA-sequencing data with multiple treatment conditions

Kang, Guangliang, Du, Li, Zhang, Hong

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.74 MB

english, 2016

183

SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis

Hatakeyama, Masaomi, Opitz, Lennart, Russo, Giancarlo, Qi, Weihong, Schlapbach, Ralph, Rehrauer, Hubert

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.45 MB

english, 2016

184

Bagging survival tree procedure for variable selection and prediction in the presence of nonsusceptible patients

Mbogning, Cyprien, Broët, Philippe

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.94 MB

english, 2016

185

SHIVA - a web application for drug resistance and tropism testing in HIV

Riemenschneider, Mona, Hummel, Thomas, Heider, Dominik

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 936 KB

english, 2016

186

An ensemble framework for identifying essential proteins

Zhang, Xue, Xiao, Wangxin, Acencio, Marcio Luis, Lemke, Ney, Wang, Xujing

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.99 MB

english, 2016

187

The tumor as an organ: comprehensive spatial and temporal modeling of the tumor and its microenvironment

Bloch, Naamah, Harel, David

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.18 MB

english, 2016

188

The parameter sensitivity of random forests

Huang, Barbara F.F., Boutros, Paul C.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.20 MB

english, 2016

189

FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data

DeTomaso, David, Yosef, Nir

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.57 MB

english, 2016

190

NEAT: an efficient network enrichment analysis test

Signorelli, Mirko, Vinciotti, Veronica, Wit, Ernst C.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 825 KB

english, 2016

191

LMAP: Lightweight Multigene Analyses in PAML

Maldonado, Emanuel, Almeida, Daniela, Escalona, Tibisay, Khan, Imran, Vasconcelos, Vitor, Antunes, Agostinho

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.48 MB

english, 2016

192

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data

duVerle, David A., Yotsukura, Sohiya, Nomura, Seitaro, Aburatani, Hiroyuki, Tsuda, Koji

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 5.01 MB

english, 2016

193

Comparative analysis of housekeeping and tissue-specific driver nodes in human protein interaction networks

Zhang, Xiao-Fei, Ou-Yang, Le, Dai, Dao-Qing, Wu, Meng-Yun, Zhu, Yuan, Yan, Hong

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.04 MB

english, 2016

194

A genetic algorithm-based weighted ensemble method for predicting transposon-derived piRNAs

Li, Dingfang, Luo, Longqiang, Zhang, Wen, Liu, Feng, Luo, Fei

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 947 KB

english, 2016

195

Tissue enrichment analysis for C. elegans genomics

Angeles-Albores, David, N. Lee, Raymond Y., Chan, Juancarlos, Sternberg, Paul W.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.32 MB

english, 2016

196

CryGetter: a tool to automate retrieval and analysis of Cry protein data

Buzatto, David, de Castro França, Suzelei, Zingaretti, Sônia Marli

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.94 MB

english, 2016

197

Erratum to: A comparative evaluation of data-merging and meta-analysis methods for reconstructing gene-gene interactions

Lagani, Vincenzo, Karozou, Argyro D., Gomez-Cabrero, David, Silberberg, Gilad, Tsamardinos, Ioannis

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 337 KB

english, 2016

198

BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori

Zhou, Qiu-Zhong, Zhang, Bindan, Yu, Quan-You, Zhang, Ze

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.17 MB

english, 2016

199

CloneCNA: detecting subclonal somatic copy number alterations in heterogeneous tumor samples from whole-exome sequencing data

Yu, Zhenhua, Li, Ao, Wang, Minghui

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.60 MB

english, 2016

200

Automatic classification of registered clinical trials towards the Global Burden of Diseases taxonomy of diseases and injuries

Atal, Ignacio, Zeitoun, Jean-David, Névéol, Aurélie, Ravaud, Philippe, Porcher, Raphaël, Trinquart, Ludovic

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 704 KB

english, 2016

201

SAMSA: a comprehensive metatranscriptome analysis pipeline

Westreich, Samuel T., Korf, Ian, Mills, David A., Lemay, Danielle G.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.20 MB

english, 2016

202

Impact of post-alignment processing in variant discovery from whole exome data

Tian, Shulan, Yan, Huihuang, Kalmbach, Michael, Slager, Susan L.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.39 MB

english, 2016

203

Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers

Girardot, Charles, Scholtalbers, Jelle, Sauer, Sajoscha, Su, Shu-Yi, Furlong, Eileen E.M.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 632 KB

english, 2016

204

PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics

Fernandez-Ricaud, Luciano, Kourtchenko, Olga, Zackrisson, Martin, Warringer, Jonas, Blomberg, Anders

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.95 MB

english, 2016

205

Identification of gene-drug interactions that impact patient survival in TCGA

Spainhour, John Christian Givhan, Qiu, Peng

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 737 KB

english, 2016

206

In-silico discovery of cancer-specific peptide-HLA complexes for targeted therapy

Dhanik, Ankur, R. Kirshner, Jessica, MacDonald, Douglas, Thurston, Gavin, C. Lin, Hsin, J. Murphy, Andrew, Zhang, Wen

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.01 MB

english, 2016

207

VennDiagramWeb: a web application for the generation of highly customizable Venn and Euler diagrams

Lam, Felix, Lalansingh, Christopher M., Babaran, Holly E., Wang, Zhiyuan, Prokopec, Stephenie D., Fox, Natalie S., Boutros, Paul C.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.48 MB

english, 2016

208

Reduction strategies for hierarchical multi-label classification in protein function prediction

Cerri, Ricardo, Barros, Rodrigo C., P. L. F. de Carvalho, André C., Jin, Yaochu

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.83 MB

english, 2016

209

Combinatorial identification of DNA methylation patterns over age in the human brain

Torabi Moghadam, Behrooz, Dabrowski, Michal, Kaminska, Bozena, Grabherr, Manfred G., Komorowski, Jan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 21.25 MB

english, 2016

210

Stepwise iterative maximum likelihood clustering approach

Sharma, Alok, Shigemizu, Daichi, Boroevich, Keith A., López, Yosvany, Kamatani, Yoichiro, Kubo, Michiaki, Tsunoda, Tatsuhiko

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.74 MB

english, 2016

211

SCOUP: a probabilistic model based on the Ornstein–Uhlenbeck process to analyze single-cell expression data during differentiation

Matsumoto, Hirotaka, Kiryu, Hisanori

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.98 MB

english, 2016

212

An integrative imputation method based on multi-omics datasets

Lin, Dongdong, Zhang, Jigang, Li, Jingyao, Xu, Chao, Deng, Hong-Wen, Wang, Yu-Ping

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.55 MB

english, 2016

213

DISMISS: detection of stranded methylation in MeDIP-Seq data

Niazi, Umar, Geyer, Kathrin K., Vickers, Martin J., Hoffmann, Karl F., Swain, Martin T.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 858 KB

english, 2016

214

SGFSC: speeding the gene functional similarity calculation based on hash tables

Tian, Zhen, Wang, Chunyu, Guo, Maozu, Liu, Xiaoyan, Teng, Zhixia

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.45 MB

english, 2016

215

Structural alignment of protein descriptors – a combinatorial model

Antczak, Maciej, Kasprzak, Marta, Lukasiak, Piotr, Blazewicz, Jacek

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 588 KB

english, 2016

216

A statistical approach to detection of copy number variations in PCR-enriched targeted sequencing data

Demidov, German, Simakova, Tamara, Vnuchkova, Julia, Bragin, Anton

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.34 MB

english, 2016

217

AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments

Shafee, Thomas, Cooke, Ira

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.19 MB

english, 2016

218

Predicting protein-protein interactions via multivariate mutual information of protein sequences

Ding, Yijie, Tang, Jijun, Guo, Fei

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.51 MB

english, 2016

219

Large scale analysis of amino acid substitutions in bacterial proteomics

Ischenko, Dmitry, Alexeev, Dmitry, Shitikov, Egor, Kanygina, Alexandra, Malakhova, Maja, Kostryukova, Elena, Larin, Andrey, Kovalchuk, Sergey, Pobeguts, Olga, Butenko, Ivan, Anikanov, Nikolay, Altukho

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 914 KB

english, 2016

220

LSCplus: a fast solution for improving long read accuracy by short read alignment

Hu, Ruifeng, Sun, Guibo, Sun, Xiaobo

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 827 KB

english, 2016

221

Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs?

Prabh, Neel, Rödelsperger, Christian

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1014 KB

english, 2016

222

Disease gene prioritization by integrating tissue-specific molecular networks using a robust multi-network model

Ni, Jingchao, Koyuturk, Mehmet, Tong, Hanghang, Haines, Jonathan, Xu, Rong, Zhang, Xiang

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 959 KB

english, 2016

223

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies

Kim, Jiwoong, Kim, Min Soo, Koh, Andrew Y., Xie, Yang, Zhan, Xiaowei

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.45 MB

english, 2016

224

RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory

Garcia-Martin, Juan Antonio, Bayegan, Amir H., Dotu, Ivan, Clote, Peter

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.03 MB

english, 2016

225

GEN3VA: aggregation and analysis of gene expression signatures from related studies

Gundersen, Gregory W., Jagodnik, Kathleen M., Woodland, Holly, Fernandez, Nicholas F., Sani, Kevin, Dohlman, Anders B., Ung, Peter Man-Un, Monteiro, Caroline D., Schlessinger, Avner, Ma’ayan, Avi

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.55 MB

english, 2016

226

Protein ligand-specific binding residue predictions by an ensemble classifier

Hu, Xiuzhen, Wang, Kai, Dong, Qiwen

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.14 MB

english, 2016

227

A robust data scaling algorithm to improve classification accuracies in biomedical data

Cao, Xi Hang, Stojkovic, Ivan, Obradovic, Zoran

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 706 KB

english, 2016

228

LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length

Bao, Yu, Hayashida, Morihiro, Akutsu, Tatsuya

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.44 MB

english, 2016

229

Erratum to: Practical impacts of genomic data “cleaning” on biological discovery using surrogate variable analysis

Jaffe, Andrew E., Hyde, Thomas, Kleinman, Joel, Weinberger, Daniel R., Chenoweth, Joshua G., McKay, Ronald D., Leek, Jeffrey T., Colantuoni, Carlo

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 338 KB

english, 2016

230

Comparison of different statistical approaches for urinary peptide biomarker detection in the context of coronary artery disease

Stanley, Eleanor, Delatola, Eleni Ioanna, Nkuipou-Kenfack, Esther, Spooner, William, Kolch, Walter, Schanstra, Joost P., Mischak, Harald, Koeck, Thomas

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.19 MB

english, 2016

231

ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database

Yu, Fengchao, Li, Ning, Yu, Weichuan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 681 KB

english, 2016

232

Handling missing rows in multi-omics data integration: multiple imputation in multiple factor analysis framework

Voillet, Valentin, Besse, Philippe, Liaubet, Laurence, San Cristobal, Magali, González, Ignacio

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.48 MB

english, 2016

233

Scalable metagenomics alignment research tool (SMART): a scalable, rapid, and complete search heuristic for the classification of metagenomic sequences from complex sequence populations

Lee, Aaron Y., Lee, Cecilia S., Van Gelder, Russell N.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.75 MB

english, 2016

234

acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data

Lux, Markus, Krüger, Jan, Rinke, Christian, Maus, Irena, Schlüter, Andreas, Woyke, Tanja, Sczyrba, Alexander, Hammer, Barbara

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.29 MB

english, 2016

235

EnsCat: clustering of categorical data via ensembling

Clarke, Bertrand S., Amiri, Saeid, Clarke, Jennifer L.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.74 MB

english, 2016

236

Erratum to: A novel procedure on next generation sequencing data analysis using text mining algorithm

Zhao, Weizhong, Chen, James J., Perkins, Roger, Wang, Yuping, Liu, Zhichao, Hong, Huixiao, Tong, Weida, Zou, Wen

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 353 KB

english, 2016

237

TopoICSim: a new semantic similarity measure based on gene ontology

Ehsani, Rezvan, Drabløs, Finn

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.43 MB

english, 2016

238

Robust differential expression analysis by learning discriminant boundary in multi-dimensional space of statistical attributes

Bei, Yuanzhe, Hong, Pengyu

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 5.41 MB

english, 2016

239

TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments

Ud-Dean, S.M. Minhaz, Heise, Sandra, Klamt, Steffen, Gunawan, Rudiyanto

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.80 MB

english, 2016

240

UQlust: combining profile hashing with linear-time ranking for efficient clustering and analysis of big macromolecular data

Adamczak, Rafal, Meller, Jarek

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 641 KB

english, 2016

241

MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing

Parikh, Hardik I., Koparde, Vishal N., Bradley, Steven P., Buck, Gregory A., Sheth, Nihar U.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 481 KB

english, 2016

242

Gene regulatory network inference using PLS-based methods

Guo, Shun, Jiang, Qingshan, Chen, Lifei, Guo, Donghui

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 938 KB

english, 2016

243

Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs

Le, Nguyen-Quoc-Khanh, Ou, Yu-Yen

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.79 MB

english, 2016

244

Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sources

Mao, Jin, Moore, Lisa R., Blank, Carrine E., Wu, Elvis Hsin-Hui, Ackerman, Marcia, Ranade, Sonali, Cui, Hong

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.82 MB

english, 2016

245

Profiling networks of distinct immune-cells in tumors

Clancy, Trevor, Hovig, Eivind

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.44 MB

english, 2016

246

Reference-free deconvolution of DNA methylation data and mediation by cell composition effects

Houseman, E. Andres, Kile, Molly L., Christiani, David C., Ince, Tan A., Kelsey, Karl T., Marsit, Carmen J.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.69 MB

english, 2016

247

MetaMIS: a metagenomic microbial interaction simulator based on microbial community profiles

Shaw, Grace Tzun-Wen, Pao, Yueh-Yang, Wang, Daryi

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.20 MB

english, 2016

248

DeepQA: improving the estimation of single protein model quality with deep belief networks

Cao, Renzhi, Bhattacharya, Debswapna, Hou, Jie, Cheng, Jianlin

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 510 KB

english, 2016

249

Identification of DNA-binding proteins using multi-features fusion and binary firefly optimization algorithm

Zhang, Jian, Gao, Bo, Chai, Haiting, Ma, Zhiqiang, Yang, Guifu

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.91 MB

english, 2016

250

libFLASM: a software library for fixed-length approximate string matching

Ayad, Lorraine A. K., Pissis, Solon P., Retha, Ahmad

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 688 KB

english, 2016

251

Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries

Grassi, Elena, Mariella, Elisa, Lembo, Antonio, Molineris, Ivan, Provero, Paolo

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 824 KB

english, 2016

252

Improving feature selection performance using pairwise pre-evaluation

Li, Songlu, Oh, Sejong

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.46 MB

english, 2016

253

Evaluating the accuracy of protein design using native secondary sub-structures

Movahedi, Marziyeh, Zare-Mirakabad, Fatemeh, Arab, Seyed Shahriar

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 614 KB

english, 2016

254

Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approach

Rashid, Shamima, Saraswathi, Saras, Kloczkowski, Andrzej, Sundaram, Suresh, Kolinski, Andrzej

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.34 MB

english, 2016

255

Topology-aware illumination design for volume rendering

Zhou, Jianlong, Wang, Xiuying, Cui, Hui, Gong, Peng, Miao, Xianglin, Miao, Yalin, Xiao, Chun, Chen, Fang, Feng, Dagan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.83 MB

english, 2016

256

WUFlux: an open-source platform for13C metabolic flux analysis of bacterial metabolism

He, Lian, Wu, Stephen G., Zhang, Muhan, Chen, Yixin, Tang, Yinjie J.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.59 MB

english, 2016

257

Bioimage classification with subcategory discriminant transform of high dimensional visual descriptors

Song, Yang, Cai, Weidong, Huang, Heng, Feng, Dagan, Wang, Yue, Chen, Mei

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.10 MB

english, 2016

258

Gene expression prediction using low-rank matrix completion

Kapur, Arnav, Marwah, Kshitij, Alterovitz, Gil

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.10 MB

english, 2016

259

A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes

Gkanogiannis, Anestis, Gazut, Stéphane, Salanoubat, Marcel, Kanj, Sawsan, Brüls, Thomas

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.76 MB

english, 2016

260

TRIg: a robust alignment pipeline for non-regular T-cell receptor and immunoglobulin sequences

Hung, Sheng-Jou, Chen, Yi-Lin, Chu, Chia-Hung, Lee, Chuan-Chun, Chen, Wan-Li, Lin, Ya-Lan, Lin, Ming-Ching, Ho, Chung-Liang, Liu, Tsunglin

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.13 MB

english, 2016

261

STON: exploring biological pathways using the SBGN standard and graph databases

Touré, Vasundra, Mazein, Alexander, Waltemath, Dagmar, Balaur, Irina, Saqi, Mansoor, Henkel, Ron, Pellet, Johann, Auffray, Charles

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.32 MB

english, 2016

262

Protein complex detection based on partially shared multi-view clustering

Ou-Yang, Le, Zhang, Xiao-Fei, Dai, Dao-Qing, Wu, Meng-Yun, Zhu, Yuan, Liu, Zhiyong, Yan, Hong

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.55 MB

english, 2016

263

MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps

Khomtchouk, Bohdan B., Hennessy, James R., Wahlestedt, Claes

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.59 MB

english, 2016

264

Read mapping on de Bruijn graphs

Limasset, Antoine, Cazaux, Bastien, Rivals, Eric, Peterlongo, Pierre

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.16 MB

english, 2016

265

Accurate prediction of RNA-binding protein residues with two discriminative structural descriptors

Sun, Meijian, Wang, Xia, Zou, Chuanxin, He, Zenghui, Liu, Wei, Li, Honglin

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.21 MB

english, 2016

266

DASP3: identification of protein sequences belonging to functionally relevant groups

Leuthaeuser, Janelle B., Morris, John H., Harper, Angela F., Ferrin, Thomas E., Babbitt, Patricia C., Fetrow, Jacquelyn S.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.82 MB

english, 2016

267

Automated prostate tissue referencing for cancer detection and diagnosis

Kwak, Jin Tae, Hewitt, Stephen M., Kajdacsy-Balla, André Alexander, Sinha, Saurabh, Bhargava, Rohit

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.75 MB

english, 2016

268

An effective and robust method for tracking multiple fish in video image based on fish head detection

Qian, Zhi-Ming, Wang, Shuo Hong, Cheng, Xi En, Chen, Yan Qiu

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.64 MB

english, 2016

269

The role of nucleotide composition in premature termination codon recognition

Fouad Zahdeh,Liran Carmel

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.13 MB

english, 2016

270

Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations

Mora Osorio, Camilo Andrés, González Barrios, Andrés Fernando

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 981 KB

english, 2016

271

systemPipeR: NGS workflow and report generation environment

Backman, Tyler W. H., Girke, Thomas

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 857 KB

english, 2016

272

Fine-grained parallelization of fitness functions in bioinformatics optimization problems: gene selection for cancer classification and biclustering of gene expression data

Gomez-Pulido, Juan A., Cerrada-Barrios, Jose L., Trinidad-Amado, Sebastian, Lanza-Gutierrez, Jose M., Fernandez-Diaz, Ramon A., Crawford, Broderick, Soto, Ricardo

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.66 MB

english, 2016

273

Erratum to: General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable?

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 417 KB

english, 2016

274

Block network mapping approach to quantitative trait locus analysis

Zeina Z. Shreif,Daniel M. Gatti,Vipul Periwal

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.27 MB

english, 2016

275

SPECtre: a spectral coherence-based classifier of actively translated transcripts from ribosome profiling sequence data

Sang Y. Chun,Caitlin M. Rodriguez,Peter K. Todd,Ryan E. Mills

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.45 MB

english, 2016

276

The Lair: a resource for exploratory analysis of published RNA-Seq data

Harold Pimentel,Pascal Sturmfels,Nicolas Bray,Páll Melsted…

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 772 KB

english, 2016

277

Pathway collages: personalized multi-pathway diagrams

Suzanne Paley,Paul E. O’Maille,Daniel Weaver,Peter D. Karp

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.72 MB

english, 2016

278

SCIFIO: an extensible framework to support scientific image formats

Mark C. Hiner,Curtis T. Rueden,Kevin W. Eliceiri

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 744 KB

english, 2016

279

Predicting the recurrence of noncoding regulatory mutations in cancer

Woojin Yang,Hyoeun Bang,Kiwon Jang,Min Kyung Sung,Jung Kyoon Choi

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.20 MB

english, 2016

280

Prior knowledge guided eQTL mapping for identifying candidate genes

Yunli Wang,Rene Richard,Youlian Pan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.00 MB

english, 2016

281

New tools to analyze overlapping coding regions

Amir H. Bayegan,Juan Antonio Garcia-Martin,Peter Clote

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.87 MB

english, 2016

282

SwitchFinder – a novel method and query facility for discovering dynamic gene expression patterns

Svetlana Bulashevska,Colin Priest,Daniel Speicher,Jörg Zimmermann…

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.66 MB

english, 2016

283

Finding an appropriate equation to measure similarity between binary vectors: case studies on Indonesian and Japanese herbal medicines

Sony Hartono Wijaya,Farit Mochamad Afendi,Irmanida Batubara…

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.44 MB

english, 2016

284

Integrating mean and variance heterogeneities to identify differentially expressed genes

Weiwei Ouyang,Qiang An,Jinying Zhao,Huaizhen Qin

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.50 MB

english, 2016

285

PROPER: global protein interaction network alignment through percolation matching

Ehsan Kazemi,Hamed Hassani,Matthias Grossglauser…

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 6.82 MB

english, 2016

286

COUSCOus: improved protein contact prediction using an empirical Bayes covariance estimator

Reda Rawi,Raghvendra Mall,Khalid Kunji,Mohammed El Anbari…

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 856 KB

english, 2016

287

PCAN: phenotype consensus analysis to support disease-gene association

Patrice Godard,Matthew Page

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 907 KB

english, 2016

288

Efficient randomization of biological networks while preserving functional characterization of individual nodes

Francesco Iorio,Marti Bernardo-Faura,Andrea Gobbi,Thomas Cokelaer…

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.63 MB

english, 2016

289

Robust multi-group gene set analysis with few replicates

Pashupati P. Mishra,Alan Medlar,Liisa Holm,Petri Törönen

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.78 MB

english, 2016

290

ConEVA: a toolbox for comprehensive assessment of protein contacts

Badri Adhikari,Jackson Nowotny,Debswapna Bhattacharya,Jie Hou…

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.54 MB

english, 2016

291

Combining independentde novoassemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms

Nicolas Cerveau,Daniel J. Jackson

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 792 KB

english, 2016

292

SurvivalGWAS_Power: a user friendly tool for power calculations in pharmacogenetic studies with “time to event” outcomes

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

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.65 MB

english, 2016

293

variancePartition: interpreting drivers of variation in complex gene expression studies

Gabriel E. Hoffman,Eric E. Schadt

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 6.87 MB

english, 2016

294

A statistical model for the analysis of beta values in DNA methylation studies

Leonie Weinhold,Simone Wahl,Sonali Pechlivanis,Per Hoffmann…

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.42 MB

english, 2016

295

Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23

David T. Barkan,Xiao-li Cheng,Herodion Celino,Tran T. Tran…

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.14 MB

english, 2016

296

Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building

Hong Cui,Dongfang Xu,Steven S. Chong,Martin Ramirez…

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.96 MB

english, 2016

297

Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules

Natalia Acevedo-Luna,Leonardo Mariño-Ramírez,Armand Halbert…

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.29 MB

english, 2016

298

A new method of finding groups of coexpressed genes and conditions of coexpression

Rajat Anand,Srikanth Ravichandran,Samrat Chatterjee

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.21 MB

english, 2016

299

FluxFix: automatic isotopologue normalization for metabolic tracer analysis

Sophie Trefely,Peter Ashwell,Nathaniel W. Snyder

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 600 KB

english, 2016

300

ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons

Giovanni Scala,Ornella Affinito,Domenico Palumbo,Ermanno Florio…

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.80 MB

english, 2016

301

Evolutionary relationships between heme-binding ferredoxin α + β barrels

Acharya, Giriraj, Kaur, Gurmeet, Subramanian, Srikrishna

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.82 MB

english, 2016

302

General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.00 MB

english, 2016

303

Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs

Zerbino, Daniel R., Ballinger, Tracy, Paten, Benedict, Hickey, Glenn, Haussler, David

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.04 MB

english, 2016

304

BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly

Lam, Ka-Kit, Hall, Richard, Clum, Alicia, Rao, Satish

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 762 KB

english, 2016

305

CINOEDV: a co-information based method for detecting and visualizing n-order epistatic interactions

Shang, Junliang, Sun, Yingxia, Liu, Jin-Xing, Xia, Junfeng, Zhang, Junying, Zheng, Chun-Hou

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.15 MB

english, 2016

306

Erratum to: eSTGt: a programming and simulation environment for population dynamics

Spiro, Adam, Shapiro, Ehud

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 336 KB

english, 2016

307

BAMQL: a query language for extracting reads from BAM files

Masella, Andre P., Lalansingh, Christopher M., Sivasundaram, Pragash, Fraser, Michael, Bristow, Robert G., Boutros, Paul C.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 401 KB

english, 2016

308

Fold-specific sequence scoring improves protein sequence matching

Leelananda, Sumudu P., Kloczkowski, Andrzej, Jernigan, Robert L.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.03 MB

english, 2016

309

DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems

Memišević, Vesna, Kumar, Kamal, Zavaljevski, Nela, DeShazer, David, Wallqvist, Anders, Reifman, Jaques

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 778 KB

english, 2016

310

A covert authentication and security solution for GMOs

Mueller, Siguna, Jafari, Farhad, Roth, Don

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 907 KB

english, 2016

311

A method for identification of highly conserved elements and evolutionary analysis of superphylum Alveolata

Rubanov, Lev I., Seliverstov, Alexandr V., Zverkov, Oleg A., Lyubetsky, Vassily A.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 823 KB

english, 2016

312

A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions

Saethang, Thammakorn, Payne, D. Michael, Avihingsanon, Yingyos, Pisitkun, Trairak

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.80 MB

english, 2016

313

Replica exchange molecular dynamics simulations reveal the structural and molecular properties of levan-type fructo-oligosaccharides of various chain lengths

Kanjanatanin, Pongsakorn, Pichyangkura, Rath, Chunsrivirot, Surasak

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.89 MB

english, 2016

314

Prediction of redox-sensitive cysteines using sequential distance and other sequence-based features

Sun, Ming-an, Zhang, Qing, Wang, Yejun, Ge, Wei, Guo, Dianjing

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1017 KB

english, 2016

315

A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation

Hejase, Hussein A., Liu, Kevin J.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 610 KB

english, 2016

316

Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks

Fakhry, Carl Tony, Choudhary, Parul, Gutteridge, Alex, Sidders, Ben, Chen, Ping, Ziemek, Daniel, Zarringhalam, Kourosh

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.58 MB

english, 2016

317

Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack

X. Menezes, Renée, Mohammadi, Leila, J. Goeman, Jelle, M. Boer, Judith

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.76 MB

english, 2016

318

Automatic learning of pre-miRNAs from different species

O. N. Lopes, Ivani de, Schliep, Alexander, de L. F. de Carvalho, André P.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.21 MB

english, 2016

319

Erratum to: ‘NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology’

Romano, Paolo, Cordero, Francesca

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 344 KB

english, 2016

320

Reduction, alignment and visualisation of large diverse sequence families

Taylor, William R.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.76 MB

english, 2016

321

Evaluation of properties over phylogenetic trees using stochastic logics

Requeno, José Ignacio, Colom, José Manuel

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.50 MB

english, 2016

322

Generalized enrichment analysis improves the detection of adverse drug events from the biomedical literature

Winnenburg, Rainer, Shah, Nigam H.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.44 MB

english, 2016

323

Efficient analysis of large datasets and sex bias with ADMIXTURE

Shringarpure, Suyash S., Bustamante, Carlos D., Lange, Kenneth, Alexander, David H.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 586 KB

english, 2016

324

flowVS: channel-specific variance stabilization in flow cytometry

Azad, Ariful, Rajwa, Bartek, Pothen, Alex

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.94 MB

english, 2016

325

Discovering causal interactions using Bayesian network scoring and information gain

Zeng, Zexian, Jiang, Xia, Neapolitan, Richard

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.60 MB

english, 2016

326

Identification of recurrent focal copy number variations and their putative targeted driver genes in ovarian cancer

Zhang, Liangcai, Yuan, Ying, Lu, Karen H., Zhang, Li

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.59 MB

english, 2016

327

Prediction of aptamer-protein interacting pairs using an ensemble classifier in combination with various protein sequence attributes

Zhang, Lina, Zhang, Chengjin, Gao, Rui, Yang, Runtao, Song, Qing

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.31 MB

english, 2016

328

RevEcoR: an R package for the reverse ecology analysis of microbiomes

Cao, Yang, Wang, Yuanyuan, Zheng, Xiaofei, Li, Fei, Bo, Xiaochen

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.89 MB

english, 2016

329

Crowdsourcing the nodulation gene network discovery environment

Li, Yupeng, Jackson, Scott A.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 806 KB

english, 2016

330

Erratum to: Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations

Johner, Niklaus, Harries, Daniel, Khelashvili, George

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 746 KB

english, 2016

331

General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable?

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.25 MB

english, 2016

332

Classification of polyhedral shapes from individual anisotropically resolved cryo-electron tomography reconstructions

Bag, Sukantadev, Prentice, Michael B, Liang, Mingzhi, Warren, Martin J, Roy Choudhury, Kingshuk

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.78 MB

english, 2016

333

tarSVM: Improving the accuracy of variant calls derived from microfluidic PCR-based targeted next generation sequencing using a support vector machine

Gillies, Christopher E., Otto, Edgar A., Vega-Warner, Virginia, Robertson, Catherine C., Sanna-Cherchi, Simone, Gharavi, Ali, Crawford, Brendan, Bhimma, Rajendra, Winkler, Cheryl, Kang, Hyun Min, Samp

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.29 MB

english, 2016

334

A model of the spatial tumour heterogeneity in colorectal adenocarcinoma tissue

Kovacheva, Violeta N., Snead, David, Rajpoot, Nasir M.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.87 MB

english, 2016

335

EmpPrior: using outside empirical data to inform branch-length priors for Bayesian phylogenetics

Andersen, John J., Nelson, Bradley J., Brown, Jeremy M.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 868 KB

english, 2016

336

Non-Markovian effects on protein sequence evolution due to site dependent substitution rates

Rizzato, Francesca, Rodriguez, Alex, Laio, Alessandro

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 840 KB

english, 2016

337

Consistency of biological networks inferred from microarray and sequencing data

Vinciotti, Veronica, Wit, Ernst C., Jansen, Rick, de Geus, Eco J. C. N., Penninx, Brenda W. J. H., Boomsma, Dorret I., ’t Hoen, Peter A. C.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.05 MB

english, 2016

338

MethPed: an R package for the identification of pediatric brain tumor subtypes

Ahamed, Mohammad Tanvir, Danielsson, Anna, Nemes, Szilárd, Carén, Helena

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 431 KB

english, 2016

339

GCORE-sib: An efficient gene-gene interaction tool for genome-wide association studies based on discordant sib pairs

Sung, Pei-Yuan, Wang, Yi-Ting, Hsiung, Chao A., Chung, Ren-Hua

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 800 KB

english, 2016

340

LEON-BIS: multiple alignment evaluation of sequence neighbours using a Bayesian inference system

Vanhoutreve, Renaud, Kress, Arnaud, Legrand, Baptiste, Gass, Hélène, Poch, Olivier, Thompson, Julie D.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.21 MB

english, 2016

341

Model-based clustering with certainty estimation: implication for clade assignment of influenza viruses

Zhang, Shunpu, Li, Zhong, Beland, Kevin, Lu, Guoqing

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 915 KB

english, 2016

342

IGDD: a database of intronless genes in dicots

Yan, Hanwei, Dai, Xiaogang, Feng, Kai, Ma, Qiuyue, Yin, Tongming

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.09 MB

english, 2016

343

Boosting the discriminatory power of sparse survival models via optimization of the concordance index and stability selection

Mayr, Andreas, Hofner, Benjamin, Schmid, Matthias

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 676 KB

english, 2016

344

Additive methods for genomic signatures

Karamichalis, Rallis, Kari, Lila, Konstantinidis, Stavros, Kopecki, Steffen, Solis-Reyes, Stephen

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.44 MB

english, 2016

345

Gene, Environment and Methylation (GEM): a tool suite to efficiently navigate large scale epigenome wide association studies and integrate genotype and interaction between genotype and environment

Pan, Hong, Holbrook, Joanna D., Karnani, Neerja, Kwoh, Chee Keong

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.37 MB

english, 2016

346

Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model

Sun, Xiaoxiao, Dalpiaz, David, Wu, Di, S. Liu, Jun, Zhong, Wenxuan, Ma, Ping

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.01 MB

english, 2016

347

Integrating multiple molecular sources into a clinical risk prediction signature by extracting complementary information

Hieke, Stefanie, Benner, Axel, Schlenl, Richard F., Schumacher, Martin, Bullinger, Lars, Binder, Harald

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.20 MB

english, 2016

348

Development of a prediction system for tail-anchored proteins

Shigemitsu, Shunsuke, Cao, Wei, Terada, Tohru, Shimizu, Kentaro

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.92 MB

english, 2016

349

Fusing literature and full network data improves disease similarity computation

Li, Ping, Nie, Yaling, Yu, Jingkai

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.59 MB

english, 2016

350

NBLDA: negative binomial linear discriminant analysis for RNA-Seq data

Dong, Kai, Zhao, Hongyu, Tong, Tiejun, Wan, Xiang

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1012 KB

english, 2016

351

Tilting the lasso by knowledge-based post-processing

Tharmaratnam, Kukatharmini, Sperrin, Matthew, Jaki, Thomas, Reppe, Sjur, Frigessi, Arnoldo

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 466 KB

english, 2016

352

A hybrid computational strategy to address WGS variant analysis in >5000 samples

Huang, Zhuoyi, Rustagi, Navin, Veeraraghavan, Narayanan, Carroll, Andrew, Gibbs, Richard, Boerwinkle, Eric, Venkata, Manjunath Gorentla, Yu, Fuli

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.17 MB

english, 2016

353

Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets

Oytam, Yalchin, Sobhanmanesh, Fariborz, Duesing, Konsta, Bowden, Joshua C., Osmond-McLeod, Megan, Ross, Jason

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 733 KB

english, 2016

354

MMinte: an application for predicting metabolic interactions among the microbial species in a community

Mendes-Soares, Helena, Mundy, Michael, Soares, Luis Mendes, Chia, Nicholas

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.07 MB

english, 2016

355

Pathogen metadata platform: software for accessing and analyzing pathogen strain information

Chang, Wenling E., Peterson, Matthew W., Garay, Christopher D., Korves, Tonia

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.57 MB

english, 2016

356

Interactive knowledge discovery and data mining on genomic expression data with numeric formal concept analysis

González-Calabozo, Jose M, Valverde-Albacete, Francisco J, Peláez-Moreno, Carmen

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.57 MB

english, 2016

357

A haplotype-based normalization technique for the analysis and detection of allele specific expression

Hodgkinson, Alan, Grenier, Jean-Christophe, Gbeha, Elias, Awadalla, Philip

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.11 MB

english, 2016

358

nbCNV: a multi-constrained optimization model for discovering copy number variants in single-cell sequencing data

Zhang, Changsheng, Cai, Hongmin, Huang, Jingying, Song, Yan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.67 MB

english, 2016

359

solveME: fast and reliable solution of nonlinear ME models

Yang, Laurence, Ma, Ding, Ebrahim, Ali, Lloyd, Colton J., Saunders, Michael A., Palsson, Bernhard O.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 999 KB

english, 2016

360

Subcellular protein expression models for microsatellite instability in colorectal adenocarcinoma tissue images

Kovacheva, Violeta N., Rajpoot, Nasir M.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 8.45 MB

english, 2016

361

rapidGSEA: Speeding up gene set enrichment analysis on multi-core CPUs and CUDA-enabled GPUs

Hundt, Christian, Hildebrandt, Andreas, Schmidt, Bertil

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.66 MB

english, 2016

362

Parametric bootstrapping for biological sequence motifs

O’Neill, Patrick K., Erill, Ivan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.20 MB

english, 2016

363

Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering

Müller, Lydia, Gerighausen, Daniel, Farman, Mariam, Zeckzer, Dirk

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.28 MB

english, 2016

364

GeneSCF: a real-time based functional enrichment tool with support for multiple organisms

Subhash, Santhilal, Kanduri, Chandrasekhar

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 909 KB

english, 2016

365

Large-scale localization of touching somas from 3D images using density-peak clustering

Cheng, Shenghua, Quan, Tingwei, Liu, Xiaomao, Zeng, Shaoqun

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.44 MB

english, 2016

366

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline

Qin, Qian, Mei, Shenglin, Wu, Qiu, Sun, Hanfei, Li, Lewyn, Taing, Len, Chen, Sujun, Li, Fugen, Liu, Tao, Zang, Chongzhi, Xu, Han, Chen, Yiwen, Meyer, Clifford A., Zhang, Yong, Brown, Myles, Long, Henr

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.58 MB

english, 2016

367

Extending digital PCR analysis by modelling quantification cycle data

Wilson, Philip J., Ellison, Stephen L. R.

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.29 MB

english, 2016

368

dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data

Sayols, Sergi, Scherzinger, Denise, Klein, Holger

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 745 KB

english, 2016

369

Simulating cryo electron tomograms of crowded cell cytoplasm for assessment of automated particle picking

Pei, Long, Xu, Min, Frazier, Zachary, Alber, Frank

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.02 MB

english, 2016

370

A decision analysis model for KEGG pathway analysis

Du, Junli, Li, Manlin, Yuan, Zhifa, Guo, Mancai, Song, Jiuzhou, Xie, Xiaozhen, Chen, Yulin

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 683 KB

english, 2016

371

Convert your favorite protein modeling program into a mutation predictor: “MODICT”

Tanyalcin, Ibrahim, Stouffs, Katrien, Daneels, Dorien, Al Assaf, Carla, Lissens, Willy, Jansen, Anna, Gheldof, Alexander

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 4.53 MB

english, 2016

372

Boolean regulatory network reconstruction using literature based knowledge with a genetic algorithm optimization method

Dorier, Julien, Crespo, Isaac, Niknejad, Anne, Liechti, Robin, Ebeling, Martin, Xenarios, Ioannis

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 3.10 MB

english, 2016

373

RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information

Ghosh, Pritha, Mathew, Oommen K., Sowdhamini, Ramanathan

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 2.58 MB

english, 2016