Volume 16; Issue 1

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BMC Bioinformatics
Volume 16; Issue 1

BMC Bioinformatics

Volume 16; Issue 1

1

Fast individual ancestry inference from DNA sequence data leveraging allele frequencies for multiple populations

Bansal, Vikas, Libiger, Ondrej

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 751 KB

english, 2015

2

Pollux: platform independent error correction of single and mixed genomes

Marinier, Eric, Brown, Daniel G, McConkey, Brendan J

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 605 KB

english, 2015

3

Nonparametric Bayesian clustering to detect bipolar methylated genomic loci

Wu, Xiaowei, Sun, Ming-an, Zhu, Hongxiao, Xie, Hehuang

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1009 KB

english, 2015

4

The effect of rare variants on inflation of the test statistics in case–control analyses

Pirie, Ailith, Wood, Angela, Lush, Michael, Tyrer, Jonathan, Pharoah, Paul DP

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.06 MB

english, 2015

5

Semi-supervised adaptive-height snipping of the hierarchical clustering tree

Obulkasim, Askar, Meijer, Gerrit A, van de Wiel, Mark A

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.33 MB

english, 2015

6

Identification of indels in next-generation sequencing data

Ratan, Aakrosh, Olson, Thomas L, Loughran, Thomas P, Miller, Webb

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 879 KB

english, 2015

7

Improving statistical inference on pathogen densities estimated by quantitative molecular methods: malaria gametocytaemia as a case study

Walker, Martin, Basáñez, María-Gloria, Ouédraogo, André Lin, Hermsen, Cornelus, Bousema, Teun, Churcher, Thomas S

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.08 MB

english, 2015

8

OTO: Ontology Term Organizer

Huang, Fengqiong, Macklin, James A, Cui, Hong, Cole, Heather A, Endara, Lorena

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.47 MB

english, 2015

9

Rational selection of experimental readout and intervention sites for reducing uncertainties in computational model predictions

Flassig, Robert J, Migal, Iryna, der Zalm, Esther van, Rihko-Struckmann, Liisa, Sundmacher, Kai

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.05 MB

english, 2015

10

A systematic evaluation of high-dimensional, ensemble-based regression for exploring large model spaces in microbiome analyses

Shankar, Jyoti, Szpakowski, Sebastian, Solis, Norma V, Mounaud, Stephanie, Liu, Hong, Losada, Liliana, Nierman, William C, Filler, Scott G

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.65 MB

english, 2015

11

An evidence-based approach to identify aging-related genes in Caenorhabditis elegans

Callahan, Alison, Cifuentes, Juan José, Dumontier, Michel

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.59 MB

english, 2015

12

HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species

Duchemin, Wandrille, Dupont, Pierre-Yves, Campbell, Matthew A, Ganley, Austen RD, Cox, Murray P

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 748 KB

english, 2015

13

Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains

Zych, Konrad, Li, Yang, van der Velde, Joeri K, Joosen, Ronny VL, Ligterink, Wilco, Jansen, Ritsert C, Arends, Danny

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 764 KB

english, 2015

14

Biomedical question answering using semantic relations

Hristovski, Dimitar, Dinevski, Dejan, Kastrin, Andrej, Rindflesch, Thomas C

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.76 MB

english, 2015

15

Fast and robust group-wise eQTL mapping using sparse graphical models

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

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.04 MB

english, 2015

16

YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia

Tan, Shi Yang, Dutta, Avirup, Jakubovics, Nicholas S, Ang, Mia Yang, Siow, Cheuk Chuen, Mutha, Naresh VR, Heydari, Hamed, Wee, Wei Yee, Wong, Guat Jah, Choo, Siew Woh

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.31 MB

english, 2015

17

SubPatCNV: approximate subspace pattern mining for mapping copy-number variations

Johnson, Nicholas, Zhang, Huanan, Fang, Gang, Kumar, Vipin, Kuang, Rui

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.73 MB

english, 2015

18

Quantitative analysis of differences in copy numbers using read depth obtained from PCR-enriched samples and controls

Reinecke, Frank, Satya, Ravi Vijaya, DiCarlo, John

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 5.50 MB

english, 2015

19

Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data

Greenfeld, Max, van de Meent, Jan-Willem, Pavlichin, Dmitri S, Mabuchi, Hideo, Wiggins, Chris H, Gonzalez, Ruben L, Herschlag, Daniel

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 574 KB

english, 2015

20

Predicting protein functions using incomplete hierarchical labels

Yu, Guoxian, Zhu, Hailong, Domeniconi, Carlotta

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 950 KB

english, 2015

21

Amyloid precursor protein interaction network in human testis: sentinel proteins for male reproduction

Silva, Joana Vieira, Yoon, Sooyeon, Domingues, Sara, Guimarães, Sofia, Goltsev, Alexander V, da Cruz e Silva, Edgar Figueiredo, Mendes, José Fernando F, da Cruz e Silva, Odete Abreu Beirão, Fardilha,

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.08 MB

english, 2015

22

Fast inexact mapping using advanced tree exploration on backward search methods

Salavert, José, Tomás, Andrés, Tárraga, Joaquín, Medina, Ignacio, Dopazo, Joaquín, Blanquer, Ignacio

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 795 KB

english, 2015

23

MDAT- Aligning multiple domain arrangements

Kemena, Carsten, Bitard-Feildel, Tristan, Bornberg-Bauer, Erich

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.44 MB

english, 2015

24

The application of sparse estimation of covariance matrix to quadratic discriminant analysis

Sun, Jiehuan, Zhao, Hongyu

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 749 KB

english, 2015

25

ERD: a fast and reliable tool for RNA design including constraints

Esmaili-Taheri, Ali, Ganjtabesh, Mohammad

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 705 KB

english, 2015

26

Evaluation and improvements of clustering algorithms for detecting remote homologous protein families

Bernardes, Juliana S, Vieira, Fabio RJ, Costa, Lygia MM, Zaverucha, Gerson

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 936 KB

english, 2015

27

MARZ: an algorithm to combinatorially analyze gapped n-mer models of transcription factor binding

Zellers, Rowan G, Drewell, Robert A, Dresch, Jacqueline M

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.30 MB

english, 2015

28

PathwayBooster: a tool to support the curation of metabolic pathways

Liberal, Rodrigo, Lisowska, Beata K, Leak, David J, Pinney, John W

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.18 MB

english, 2015

29

Exploring possible DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data

Sawaya, Sterling, Boocock, James, Black, Michael A, Gemmell, Neil J

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.92 MB

english, 2015

30

Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach

Broin, Pilib Ó, Smith, Terry J, Golden, Aaron AJ

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.32 MB

english, 2015

31

An algorithm to enumerate all possible protein conformations verifying a set of distance constraints

Cassioli, Andrea, Bardiaux, Benjamin, Bouvier, Guillaume, Mucherino, Antonio, Alves, Rafael, Liberti, Leo, Nilges, Michael, Lavor, Carlile, Malliavin, Thérèse E

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.85 MB

english, 2015

32

Data-intensive analysis of HIV mutations

Ozahata, Mina Cintho, Sabino, Ester Cerdeira, Diaz, Ricardo Sobhie, M Cesar-, Roberto, Ferreira, João Eduardo

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.84 MB

english, 2015

33

MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis

Tsuyuzaki, Koki, Morota, Gota, Ishii, Manabu, Nakazato, Takeru, Miyazaki, Satoru, Nikaido, Itoshi

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 4.70 MB

english, 2015

34

TagDust2: a generic method to extract reads from sequencing data

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 792 KB

english, 2015

35

Candidate prioritization for low-abundant differentially expressed proteins in 2D-DIGE datasets

Nandal, Umesh K, Vlietstra, Wytze J, Byrman, Carsten, Jeeninga, Rienk E, Ringrose, Jeffrey H, van Kampen, Antoine HC, Speijer, Dave, Moerland, Perry D

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.37 MB

english, 2015

36

Aber-OWL: a framework for ontology-based data access in biology

Hoehndorf, Robert, Slater, Luke, Schofield, Paul N, Gkoutos, Georgios V

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 799 KB

english, 2015

37

SFMetrics: an analysis tool for scanning force microscopy images of biomolecules

Sánchez, Humberto, Wyman, Claire

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.55 MB

english, 2015

38

ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering

Verbist, Bie, Clement, Lieven, Reumers, Joke, Thys, Kim, Vapirev, Alexander, Talloen, Willem, Wetzels, Yves, Meys, Joris, Aerssens, Jeroen, Bijnens, Luc, Thas, Olivier

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 889 KB

english, 2015

39

BMC Bioinformatics reviewer acknowledgement 2014

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 330 KB

english, 2015

40

Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data

Gong, Wuming, Koyano-Nakagawa, Naoko, Li, Tongbin, Garry, Daniel J

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.74 MB

english, 2015

41

Metabolome searcher: a high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction

Dhanasekaran, A Ranjitha, Pearson, Jon L, Ganesan, Balasubramanian, Weimer, Bart C

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.24 MB

english, 2015

42

Discovery of prognostic biomarkers for predicting lung cancer metastasis using microarray and survival data

Huang, Hui-Ling, Wu, Yu-Chung, Su, Li-Jen, Huang, Yun-Ju, Charoenkwan, Phasit, Chen, Wen-Liang, Lee, Hua-Chin, Chu, William Cheng-Chung, Ho, Shinn-Ying

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.18 MB

english, 2015

43

Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores

Song, Yang, Hua, Lei, Shapiro, Bruce A, Wang, Jason TL

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.93 MB

english, 2015

44

Computational study of β-N-acetylhexosaminidase from Talaromyces flavus, a glycosidase with high substrate flexibility

Kulik, Natallia, Slámová, Kristýna, Ettrich, Rüdiger, Křen, Vladimír

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.39 MB

english, 2015

45

Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling

Diaz-Uriarte, Ramon

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.78 MB

english, 2015

46

The acquisition of novel N-glycosylation sites in conserved proteins during human evolution

Kim, Dong Seon, Hahn, Yoonsoo

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.17 MB

english, 2015

47

Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

Comoglio, Federico, Sievers, Cem, Paro, Renato

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 955 KB

english, 2015

48

MBBC: an efficient approach for metagenomic binning based on clustering

Wang, Ying, Hu, Haiyan, Li, Xiaoman

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.06 MB

english, 2015

49

Measuring semantic similarities by combining gene ontology annotations and gene co-function networks

Peng, Jiajie, Uygun, Sahra, Kim, Taehyong, Wang, Yadong, Rhee, Seung Y, Chen, Jin

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.71 MB

english, 2015

50

Sampling with poling-based flux balance analysis: optimal versus sub-optimal flux space analysis of Actinobacillus succinogenes

Binns, Michael, de Atauri, Pedro, Vlysidis, Anestis, Cascante, Marta, Theodoropoulos, Constantinos

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.24 MB

english, 2015

51

BACA: bubble chArt to compare annotations

Fortino, Vittorio, Alenius, Harri, Greco, Dario

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.77 MB

english, 2015

52

Removing batch effects from purified plasma cell gene expression microarrays with modified ComBat

Stein, Caleb K, Qu, Pingping, Epstein, Joshua, Buros, Amy, Rosenthal, Adam, Crowley, John, Morgan, Gareth, Barlogie, Bart

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.69 MB

english, 2015

53

A hidden Markov approach for ascertaining cSNP genotypes from RNA sequence data in the presence of allelic imbalance by exploiting linkage disequilibrium

Steibel, Juan P, Wang, Heng, Zhong, Ping-Shou

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 737 KB

english, 2015

54

A multiobjective approach to the genetic code adaptability problem

de Oliveira, Lariza Laura, de Oliveira, Paulo SL, Tinós, Renato

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.70 MB

english, 2015

55

Mutations and CpG islands among hepatitis B virus genotypes in Europe

Zhong, Chengyao, Hou, Zhiwei, Huang, Jihua, Xie, Qingdong, Zhong, Ying

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.33 MB

english, 2015

56

Family-based association analysis: a fast and efficient method of multivariate association analysis with multiple variants

Won, Sungho, Kim, Wonji, Lee, Sungyoung, Lee, Young, Sung, Joohon, Park, Taesung

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.37 MB

english, 2015

57

NMF-mGPU: non-negative matrix factorization on multi-GPU systems

Mejía-Roa, Edgardo, Tabas-Madrid, Daniel, Setoain, Javier, García, Carlos, Tirado, Francisco, Pascual-Montano, Alberto

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.57 MB

english, 2015

58

BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology

Moreno, Pablo, Beisken, Stephan, Harsha, Bhavana, Muthukrishnan, Venkatesh, Tudose, Ilinca, Dekker, Adriano, Dornfeldt, Stefanie, Taruttis, Franziska, Grosse, Ivo, Hastings, Janna, Neumann, Steffen, S

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 784 KB

english, 2015

59

Identifying named entities from PubMed® for enriching semantic categories

Kim, Sun, Lu, Zhiyong, Wilbur, W John

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 987 KB

english, 2015

60

Comparing variant calling algorithms for target-exon sequencing in a large sample

Lo, Yancy, Kang, Hyun M, Nelson, Matthew R, Othman, Mohammad I, Chissoe, Stephanie L, Ehm, Margaret G, Abecasis, Gonçalo R, Zöllner, Sebastian

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 456 KB

english, 2015

61

Spectral gene set enrichment (SGSE)

Frost, H Robert, Li, Zhigang, Moore, Jason H

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 922 KB

english, 2015

62

histoneHMM: Differential analysis of histone modifications with broad genomic footprints

Heinig, Matthias, Colomé-Tatché, Maria, Taudt, Aaron, Rintisch, Carola, Schafer, Sebastian, Pravenec, Michal, Hubner, Norbert, Vingron, Martin, Johannes, Frank

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 868 KB

english, 2015

63

A high performance prediction of HPV genotypes by Chaos game representation and singular value decomposition

Tanchotsrinon, Watcharaporn, Lursinsap, Chidchanok, Poovorawan, Yong

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.04 MB

english, 2015

64

Impact of missing data imputation methods on gene expression clustering and classification

de Souto, Marcilio CP, Jaskowiak, Pablo A, Costa, Ivan G

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 381 KB

english, 2015

65

A semi–supervised tensor regression model for siRNA efficacy prediction

Thang, Bui Ngoc, Ho, Tu Bao, Kanda, Tatsuo

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 876 KB

english, 2015

66

GeneDig: a web application for accessing genomic and bioinformatics knowledge

Suciu, Radu M, Aydin, Emir, Chen, Brian E

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.87 MB

english, 2015

67

A model of the regulatory network involved in the control of the cell cycle and cell differentiation in the Caenorhabditis elegans vulva

Weinstein, Nathan, Ortiz-Gutiérrez, Elizabeth, Muñoz, Stalin, Rosenblueth, David A, Álvarez-Buylla, Elena R, Mendoza, Luis

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.74 MB

english, 2015

68

DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe

Wang, Tianmin, Mori, Hiroshi, Zhang, Chong, Kurokawa, Ken, Xing, Xin-Hui, Yamada, Takuji

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.73 MB

english, 2015

69

MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics

Kushwaha, Sandeep K, Manoharan, Lokeshwaran, Meerupati, Tejashwari, Hedlund, Katarina, Ahrén, Dag

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.00 MB

english, 2015

70

SCNVSim: somatic copy number variation and structure variation simulator

Qin, Maochun, Liu, Biao, Conroy, Jeffrey M, Morrison, Carl D, Hu, Qiang, Cheng, Yubo, Murakami, Mitsuko, Odunsi, Adekunle O, Johnson, Candace S, Wei, Lei, Liu, Song, Wang, Jianmin

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.21 MB

english, 2015

71

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets

Scheuch, Matthias, Höper, Dirk, Beer, Martin

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.82 MB

english, 2015

72

Constrained distance transforms for spatial atlas registration

Hill, Bill, Baldock, Richard A

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.74 MB

english, 2015

73

Kernel approaches for differential expression analysis of mass spectrometry-based metabolomics data

Zhan, Xiang, Patterson, Andrew D, Ghosh, Debashis

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 657 KB

english, 2015

74

ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data

Jiang, Chuan, Chen, Chao, Huang, Ziyue, Liu, Renyi, Verdier, Jerome

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 924 KB

english, 2015

75

Classification of bioinformatics workflows using weighted versions of partitioning and hierarchical clustering algorithms

Lord, Etienne, Diallo, Abdoulaye Baniré, Makarenkov, Vladimir

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.79 MB

english, 2015

76

Fully automated pipeline for detection of sex linked genes using RNA-Seq data

Michalovova, Monika, Kubat, Zdenek, Hobza, Roman, Vyskot, Boris, Kejnovsky, Eduard

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.26 MB

english, 2015

77

Automatic segmentation of deep intracerebral electrodes in computed tomography scans

Arnulfo, Gabriele, Narizzano, Massimo, Cardinale, Francesco, Fato, Marco Massimo, Palva, Jaakko Matias

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.83 MB

english, 2015

78

Identification of active miRNA and transcription factor regulatory pathways in human obesity-related inflammation

Zhang, Xi-Mei, Guo, Lin, Chi, Mei-Hua, Sun, Hong-Mei, Chen, Xiao-Wen

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.20 MB

english, 2015

79

USI: a fast and accurate approach for conceptual document annotation

Fiorini, Nicolas, Ranwez, Sylvie, Montmain, Jacky, Ranwez, Vincent

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 797 KB

english, 2015

80

GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments

Herten, Koen, Hestand, Matthew S, Vermeesch, Joris R, Van Houdt, Jeroen KJ

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 434 KB

english, 2015

81

aTRAM - automated target restricted assembly method: a fast method for assembling loci across divergent taxa from next-generation sequencing data

Allen, Julie M, Huang, Daisie I, Cronk, Quentin C, Johnson, Kevin P

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 641 KB

english, 2015

82

Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs

Herman, Joseph L, Novák, Ádám, Lyngsø, Rune, Szabó, Adrienn, Miklós, István, Hein, Jotun

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.33 MB

english, 2015

83

micropan: an R-package for microbial pan-genomics

Snipen, Lars, Liland, Kristian Hovde

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 624 KB

english, 2015

84

Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis

Harigua-Souiai, Emna, Cortes-Ciriano, Isidro, Desdouits, Nathan, Malliavin, Thérèse E, Guizani, Ikram, Nilges, Michael, Blondel, Arnaud, Bouvier, Guillaume

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.83 MB

english, 2015

85

Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity

Zhang, Xindong, Gao, Lin, Liu, Zhi-Ping, Chen, Luonan

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.44 MB

english, 2015

86

NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads

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

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 628 KB

english, 2015

87

Novel genetic matching methods for handling population stratification in genome-wide association studies

Lacour, André, Schüller, Vitalia, Drichel, Dmitriy, Herold, Christine, Jessen, Frank, Leber, Markus, Maier, Wolfgang, Noethen, Markus M, Ramirez, Alfredo, Vaitsiakhovich, Tatsiana, Becker, Tim

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 635 KB

english, 2015

88

EGFR Mutant Structural Database: computationally predicted 3D structures and the corresponding binding free energies with gefitinib and erlotinib

Ma, Lichun, Wang, Debby D, Huang, Yiqing, Yan, Hong, Wong, Maria P, Lee, Victor HF

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.80 MB

english, 2015

89

Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource

Schuette, Scott, Piatkowski, Brian, Corley, Aaron, Lang, Daniel, Geisler, Matt

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.87 MB

english, 2015

90

Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest

Lee, Juyong, Lee, Kiho, Joung, InSuk, Joo, Keehyoung, Brooks, Bernard R, Lee, Jooyoung

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.03 MB

english, 2015

91

Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective

Houseman, E Andres, Kelsey, Karl T, Wiencke, John K, Marsit, Carmen J

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 911 KB

english, 2015

92

Understanding the molecular basis of EGFR kinase domain/MIG-6 peptide recognition complex using computational analyses

Moonrin, Ninnutt, Songtawee, Napat, Rattanabunyong, Siriluk, Chunsrivirot, Surasuk, Mokmak, Wanwimon, Tongsima, Sissades, Choowongkomon, Kiattawee

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.37 MB

english, 2015

93

ProteinVolume: calculating molecular van der Waals and void volumes in proteins

Chen, Calvin R, Makhatadze, George I

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 956 KB

english, 2015

94

FlowClus: efficiently filtering and denoising pyrosequenced amplicons

Gaspar, John M, Thomas, W Kelley

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.25 MB

english, 2015

95

A strategy to build and validate a prognostic biomarker model based on RT-qPCR gene expression and clinical covariates

Tournoud, Maud, Larue, Audrey, Cazalis, Marie-Angelique, Venet, Fabienne, Pachot, Alexandre, Monneret, Guillaume, Lepape, Alain, Veyrieras, Jean-Baptiste

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.95 MB

english, 2015

96

Wide-coverage relation extraction from MEDLINE using deep syntax

Nguyen, Nhung TH, Miwa, Makoto, Tsuruoka, Yoshimasa, Chikayama, Takashi, Tojo, Satoshi

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 752 KB

english, 2015

97

Comparative interactions of withanolides and sterols with two members of sterol glycosyltransferases from Withania somnifera

Pandey, Vibha, Dhar, Yogeshwar Vikram, Gupta, Parul, Bag, Sumit K, Atri, Neelam, Asif, Mehar Hasan, Trivedi, Prabodh Kumar, Misra, Pratibha

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.15 MB

english, 2015

98

PaPI: pseudo amino acid composition to score human protein-coding variants

Limongelli, Ivan, Marini, Simone, Bellazzi, Riccardo

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.91 MB

english, 2015

99

Insertion and deletion correcting DNA barcodes based on watermarks

Kracht, David, Schober, Steffen

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.16 MB

english, 2015

100

Interpolation based consensus clustering for gene expression time series

Chiu, Tai-Yu, Hsu, Ting-Chieh, Yen, Chia-Cheng, Wang, Jia-Shung

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.22 MB

english, 2015

101

Grammar-based compression approach to extraction of common rules among multiple trees of glycans and RNAs

Zhao, Yang, Hayashida, Morihiro, Cao, Yue, Hwang, Jaewook, Akutsu, Tatsuya

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.64 MB

english, 2015

102

ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins

Ruiz-Blanco, Yasser B, Paz, Waldo, Green, James, Marrero-Ponce, Yovani

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.14 MB

english, 2015

103

MAESTRO - multi agent stability prediction upon point mutations

Laimer, Josef, Hofer, Heidi, Fritz, Marko, Wegenkittl, Stefan, Lackner, Peter

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.02 MB

english, 2015

104

dbVOR: a database system for importing pedigree, phenotype and genotype data and exporting selected subsets

Baron, Robert V, Conley, Yvette P, Gorin, Michael B, Weeks, Daniel E

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.78 MB

english, 2015

105

Deep convolutional neural networks for annotating gene expression patterns in the mouse brain

Zeng, Tao, Li, Rongjian, Mukkamala, Ravi, Ye, Jieping, Ji, Shuiwang

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.75 MB

english, 2015

106

PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis

Benavente, Ernest D, Coll, Francesc, Furnham, Nick, McNerney, Ruth, Glynn, Judith R, Campino, Susana, Pain, Arnab, Mohareb, Fady R, Clark, Taane G

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.09 MB

english, 2015

107

Elviz – exploration of metagenome assemblies with an interactive visualization tool

Cantor, Michael, Nordberg, Henrik, Smirnova, Tatyana, Hess, Matthias, Tringe, Susannah, Dubchak, Inna

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.87 MB

english, 2015

108

In-vitro diagnosis of single and poly microbial species targeted for diabetic foot infection using e-nose technology

Yusuf, Nurlisa, Zakaria, Ammar, Omar, Mohammad Iqbal, Shakaff, Ali Yeon Md, Masnan, Maz Jamilah, Kamarudin, Latifah Munirah, Abdul Rahim, Norasmadi, Zakaria, Nur Zawatil Isqi, Abdullah, Azian Azamimi,

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.18 MB

english, 2015

109

ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles

Anghel, Catalina V, Quon, Gerald, Haider, Syed, Nguyen, Francis, Deshwar, Amit G, Morris, Quaid D, Boutros, Paul C

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.31 MB

english, 2015

110

GENLIB: an R package for the analysis of genealogical data

Gauvin, Héloïse, Lefebvre, Jean-François, Moreau, Claudia, Lavoie, Eve-Marie, Labuda, Damian, Vézina, Hélène, Roy-Gagnon, Marie-Hélène

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.11 MB

english, 2015

111

DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder

Varadi, Mihaly, Guharoy, Mainak, Zsolyomi, Fruzsina, Tompa, Peter

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.70 MB

english, 2015

112

Performance of a blockwise approach in variable selection using linkage disequilibrium information

Dehman, Alia, Ambroise, Christophe, Neuvial, Pierre

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.28 MB

english, 2015

113

Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions

Natarajan, Padmaja, Punta, Marco, Kumar, Abhinav, Yeh, Andrew P, Godzik, Adam, Aravind, L

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.00 MB

english, 2015

114

Decomposing the space of protein quaternary structures with the interface fragment pair library

Xie, Zhong-Ru, Chen, Jiawen, Zhao, Yilin, Wu, Yinghao

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.10 MB

english, 2015

115

PCalign: a method to quantify physicochemical similarity of protein-protein interfaces

Cheng, Shanshan, Zhang, Yang, Brooks, Charles L

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.85 MB

english, 2015

116

Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms

Mbandi, Stanley Kimbung, Hesse, Uljana, van Heusden, Peter, Christoffels, Alan

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 668 KB

english, 2015

117

Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia

Yang, Xinan Holly, Li, Meiyi, Wang, Bin, Zhu, Wanqi, Desgardin, Aurelie, Onel, Kenan, de Jong, Jill, Chen, Jianjun, Chen, Luonan, Cunningham, John M

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.11 MB

english, 2015

118

SimBA: simulation algorithm to fit extant-population distributions

Parida, Laxmi, Haiminen, Niina

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1020 KB

english, 2015

119

Feature engineering for MEDLINE citation categorization with MeSH

Jimeno Yepes, Antonio Jose, Plaza, Laura, Carrillo-de-Albornoz, Jorge, Mork, James G, Aronson, Alan R

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 708 KB

english, 2015

120

OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction

Wang, Yaojun, Yang, Fei, Wu, Peng, Bu, Dongbo, Sun, Shiwei

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.47 MB

english, 2015

121

Differential co-expression and regulation analyses reveal different mechanisms underlying major depressive disorder and subsyndromal symptomatic depression

Xu, Fan, Yang, Jing, Chen, Jin, Wu, Qingyuan, Gong, Wei, Zhang, Jianguo, Shao, Weihua, Mu, Jun, Yang, Deyu, Yang, Yongtao, Li, Zhiwei, Xie, Peng

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.41 MB

english, 2015

122

plethy: management of whole body plethysmography data in R

Bottomly, Daniel, Wilmot, Beth, McWeeney, Shannon K

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 522 KB

english, 2015

123

A network model for angiogenesis in ovarian cancer

Glass, Kimberly, Quackenbush, John, Spentzos, Dimitrios, Haibe-Kains, Benjamin, Yuan, Guo-Cheng

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.67 MB

english, 2015

124

SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering

Van den Eynden, Jimmy, Fierro, Ana Carolina, Verbeke, Lieven PC, Marchal, Kathleen

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.64 MB

english, 2015

125

IPO: a tool for automated optimization of XCMS parameters

Libiseller, Gunnar, Dvorzak, Michaela, Kleb, Ulrike, Gander, Edgar, Eisenberg, Tobias, Madeo, Frank, Neumann, Steffen, Trausinger, Gert, Sinner, Frank, Pieber, Thomas, Magnes, Christoph

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.10 MB

english, 2015

126

Quantifying conformational changes in GPCRs: glimpse of a common functional mechanism

Dalton, James AR, Lans, Isaias, Giraldo, Jesús

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.58 MB

english, 2015

127

coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns

Martin, Tiphaine C, Yet, Idil, Tsai, Pei-Chien, Bell, Jordana T

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 408 KB

english, 2015

128

Moment based gene set tests

Larson, Jessica L, Owen, Art B

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.25 MB

english, 2015

129

Customised fragments libraries for protein structure prediction based on structural class annotations

Abbass, Jad, Nebel, Jean-Christophe

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.10 MB

english, 2015

130

PathRings: a web-based tool for exploration of ortholog and expression data in biological pathways

Zhu, Yongnan, Sun, Liang, Garbarino, Alexander, Schmidt, Carl, Fang, Jinglong, Chen, Jian

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.96 MB

english, 2015

131

Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation

de Hijas-Liste, Gundián M, Balsa-Canto, Eva, Ewald, Jan, Bartl, Martin, Li, Pu, Banga, Julio R, Kaleta, Christoph

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 867 KB

english, 2015

132

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation

Levy, Roie, Carr, Rogan, Kreimer, Anat, Freilich, Shiri, Borenstein, Elhanan

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.94 MB

english, 2015

133

Determining minimum set of driver nodes in protein-protein interaction networks

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

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.31 MB

english, 2015

134

Estimation of the methylation pattern distribution from deep sequencing data

Lin, Peijie, Forêt, Sylvain, Wilson, Susan R, Burden, Conrad J

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 926 KB

english, 2015

135

WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration

Santella, Anthony, Catena, Raúl, Kovacevic, Ismar, Shah, Pavak, Yu, Zidong, Marquina-Solis, Javier, Kumar, Abhishek, Wu, Yicong, Schaff, James, Colón-Ramos, Daniel, Shroff, Hari, Mohler, William A., B

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.59 MB

english, 2015

136

Simulated unbound structures for benchmarking of protein docking in the Dockground resource

Kirys, Tatsiana, Ruvinsky, Anatoly M., Singla, Deepak, Tuzikov, Alexander V., Kundrotas, Petras J., Vakser, Ilya A.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.93 MB

english, 2015

137

Odintifier - A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing

Samaniego Castruita, Jose Alfredo, Zepeda Mendoza, Marie Lisandra, Barnett, Ross, Wales, Nathan, Gilbert, M Thomas P.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.14 MB

english, 2015

138

KnowLife: a versatile approach for constructing a large knowledge graph for biomedical sciences

Ernst, Patrick, Siu, Amy, Weikum, Gerhard

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 757 KB

english, 2015

139

VISA - Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing

Hocum, Jonah D., Battrell, Logan R., Maynard, Ryan, Adair, Jennifer E., Beard, Brian C., Rawlings, David J., Kiem, Hans-Peter, Miller, Daniel G., Trobridge, Grant D.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 538 KB

english, 2015

140

Reliable scaling of position weight matrices for binding strength comparisons between transcription factors

Ma, Xiaoyan, Ezer, Daphne, Navarro, Carmen, Adryan, Boris

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.45 MB

english, 2015

141

Software for the analysis and visualization of deep mutational scanning data

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.64 MB

english, 2015

142

Topological characterization of neuronal arbor morphology via sequence representation: I - motif analysis

Gillette, Todd A, Ascoli, Giorgio A

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.31 MB

english, 2015

143

Evaluation of variant detection software for pooled next-generation sequence data

Huang, Howard W., Mullikin, James C., Hansen, Nancy F.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.20 MB

english, 2015

144

Alignment of time course gene expression data and the classification of developmentally driven genes with hidden Markov models

Robinson, Sean, Glonek, Garique, Koch, Inge, Thomas, Mark, Davies, Christopher

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 759 KB

english, 2015

145

GPCRtm: An amino acid substitution matrix for the transmembrane region of class A G Protein-Coupled Receptors

Rios, Santiago, Fernandez, Marta F., Caltabiano, Gianluigi, Campillo, Mercedes, Pardo, Leonardo, Gonzalez, Angel

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.10 MB

english, 2015

146

SW1PerS: Sliding windows and 1-persistence scoring; discovering periodicity in gene expression time series data

Perea, Jose A., Deckard, Anastasia, Haase, Steve B., Harer, John

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.40 MB

english, 2015

147

YOC, A new strategy for pairwise alignment of collinear genomes

Uricaru, Raluca, Michotey, Célia, Chiapello, Hélène, Rivals, Eric

Journal:

BMC Bioinformatics

Année:

2015

Fichier:

PDF, 1.66 MB

2015

148

Structured learning for spatial information extraction from biomedical text: bacteria biotopes

Kordjamshidi, Parisa, Roth, Dan, Moens, Marie-Francine

Journal:

BMC Bioinformatics

Année:

2015

Fichier:

PDF, 1.04 MB

2015

149

Amplitude spectrum distance: measuring the global shape divergence of protein fragments

Galiez, Clovis, Coste, François

Journal:

BMC Bioinformatics

Année:

2015

Fichier:

PDF, 3.53 MB

2015

150

MSCA: a spectral comparison algorithm between time series to identify protein-protein interactions

Arenas, Ailan F, Salcedo, Gladys E, Montoya, Andrey M, Gomez-Marin, Jorge E

Journal:

BMC Bioinformatics

Année:

2015

Fichier:

PDF, 454 KB

2015

151

NetworkPainter: dynamic intracellular pathway animation in Cytobank

Karr, Jonathan R, Guturu, Harendra, Chen, Edward Y, Blair, Stuart L, Irish, Jonathan M, Kotecha, Nikesh, Covert, Markus W

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.76 MB

english, 2015

152

Multiobjective triclustering of time-series transcriptome data reveals key genes of biological processes

Bhar, Anirban, Haubrock, Martin, Mukhopadhyay, Anirban, Wingender, Edgar

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.72 MB

english, 2015

153

Erratum to: Improving protein order-disorder classification using charge-hydropathy plots

Huang, Fei, Oldfield, Christopher J., Xue, Bin, Hsu, Wei-Lun, Meng, Jingwei, Liu, Xiaowen, Shen, Li, Romero, Pedro, Uversky, Vladimir N., Dunker, A. Keith

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 647 KB

english, 2015

154

Object-based representation and analysis of light and electron microscopic volume data using Blender

Asadulina, Albina, Conzelmann, Markus, Williams, Elizabeth A., Panzera, Aurora, Jékely, Gáspár

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.81 MB

english, 2015

155

REGULATOR: a database of metazoan transcription factors and maternal factors for developmental studies

Wang, Kai, Nishida, Hiroki

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.23 MB

english, 2015

156

GESPA: classifying nsSNPs to predict disease association

Khurana, Jay K., Reeder, Jay E., Shrimpton, Antony E., Thakar, Juilee

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.03 MB

english, 2015

157

Erratum to: Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm

Gibbons, Theodore R., Mount, Stephen M., Cooper, Endymion D., Delwiche, Charles F.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 382 KB

english, 2015

158

Hierarchical decomposition of dynamically evolving regulatory networks

Ay, Ahmet, Gong, Dihong, Kahveci, Tamer

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 4.77 MB

english, 2015

159

Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data

Dabrowski, Michal, Dojer, Norbert, Krystkowiak, Izabella, Kaminska, Bozena, Wilczynski, Bartek

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.41 MB

english, 2015

160

Controlling false discoveries in high-dimensional situations: boosting with stability selection

Hofner, Benjamin, Boccuto, Luigi, Göker, Markus

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.53 MB

english, 2015

161

Optimizing agent-based transmission models for infectious diseases

Willem, Lander, Stijven, Sean, Tijskens, Engelbert, Beutels, Philippe, Hens, Niel, Broeckhove, Jan

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1022 KB

english, 2015

162

Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition

Mathew, B., Schmitz, A., Muñoz-Descalzo, S., Ansari, N., Pampaloni, F., Stelzer, E.H.K., Fischer, S.C.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.83 MB

english, 2015

163

Comparing K-mer based methods for improved classification of 16S sequences

Vinje, Hilde, Liland, Kristian Hovde, Almøy, Trygve, Snipen, Lars

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 804 KB

english, 2015

164

Mapping side chain interactions at protein helix termini

Newell, Nicholas E

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.64 MB

english, 2015

165

MultiSETTER: web server for multiple RNA structure comparison

Čech, Petr, Hoksza, David, Svozil, Daniel

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.76 MB

english, 2015

166

Prior knowledge driven Granger causality analysis on gene regulatory network discovery

Yao, Shun, Yoo, Shinjae, Yu, Dantong

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.18 MB

english, 2015

167

ContextMap 2: fast and accurate context-based RNA-seq mapping

Bonfert, Thomas, Kirner, Evelyn, Csaba, Gergely, Zimmer, Ralf, Friedel, Caroline C

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.77 MB

english, 2015

168

Learning-guided automatic three dimensional synapse quantification for drosophila neurons

Sanders, Jonathan, Singh, Anil, Sterne, Gabriella, Ye, Bing, Zhou, Jie

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.72 MB

english, 2015

169

AllelicImbalance: an R/ bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing

Gådin, Jesper R., van’t Hooft, Ferdinand M., Eriksson, Per, Folkersen, Lasse

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.50 MB

english, 2015

170

Optimal combination of feature selection and classification via local hyperplane based learning strategy

Cheng, Xiaoping, Cai, Hongmin, Zhang, Yue, Xu, Bo, Su, Weifeng

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 975 KB

english, 2015

171

RDML-Ninja and RDMLdb for standardized exchange of qPCR data

Ruijter, Jan M., Lefever, Steve, Anckaert, Jasper, Hellemans, Jan, Pfaffl, Michael W., Benes, Vladimir, Bustin, Stephen A., Vandesompele, Jo, Untergasser, Andreas

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.09 MB

english, 2015

172

Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data

Ogoe, Henry A., Visweswaran, Shyam, Lu, Xinghua, Gopalakrishnan, Vanathi

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.09 MB

english, 2015

173

Comparison of phosphorylation patterns across eukaryotes by discriminative N-gram analysis

Frades, Itziar, Resjö, Svante, Andreasson, Erik

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.93 MB

english, 2015

174

InteMAP: Integrated metagenomic assembly pipeline for NGS short reads

Lai, Binbin, Wang, Fumeng, Wang, Xiaoqi, Duan, Liping, Zhu, Huaiqiu

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.83 MB

english, 2015

175

YOC, A new strategy for pairwise alignment of collinear genomes

Uricaru, Raluca, Michotey, Célia, Chiapello, Hélène, Rivals, Eric

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.66 MB

english, 2015

176

Structured learning for spatial information extraction from biomedical text: bacteria biotopes

Kordjamshidi, Parisa, Roth, Dan, Moens, Marie-Francine

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.04 MB

english, 2015

177

Amplitude spectrum distance: measuring the global shape divergence of protein fragments

Galiez, Clovis, Coste, François

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.53 MB

english, 2015

178

MSCA: a spectral comparison algorithm between time series to identify protein-protein interactions

Arenas, Ailan F, Salcedo, Gladys E, Montoya, Andrey M, Gomez-Marin, Jorge E

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 454 KB

english, 2015

179

Topological characterization of neuronal arbor morphology via sequence representation: II - global alignment

Gillette, Todd A, Hosseini, Parsa, Ascoli, Giorgio A

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.98 MB

english, 2015

180

BitMapper: an efficient all-mapper based on bit-vector computing

Cheng, Haoyu, Jiang, Huaipan, Yang, Jiaoyun, Xu, Yun, Shang, Yi

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 706 KB

english, 2015

181

Clotho: addressing the scalability of forward time population genetic simulation

Putnam, Patrick P., Wilsey, Philip A., Zhang, Ge

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 6.23 MB

english, 2015

182

Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications

Yu, Fang, Chen, Ming-Hui, Kuo, Lynn, Talbott, Heather, Davis, John S.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 717 KB

english, 2015

183

Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species

Avila-Herrera, Aram, Pollard, Katherine S.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.57 MB

english, 2015

184

A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples

Bernard, Elsa, Jacob, Laurent, Mairal, Julien, Viara, Eric, Vert, Jean-Philippe

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 986 KB

english, 2015

185

MONALISA for stochastic simulations of Petri net models of biochemical systems

Balazki, Pavel, Lindauer, Klaus, Einloft, Jens, Ackermann, Jörg, Koch, Ina

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.36 MB

english, 2015

186

Sealer: a scalable gap-closing application for finishing draft genomes

Paulino, Daniel, Warren, René L., Vandervalk, Benjamin P., Raymond, Anthony, Jackman, Shaun D., Birol, Inanç

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 695 KB

english, 2015

187

Automated interpretation of 3D laserscanned point clouds for plant organ segmentation

Wahabzada, Mirwaes, Paulus, Stefan, Kersting, Kristian, Mahlein, Anne-Katrin

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.06 MB

english, 2015

188

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS

Fosso, Bruno, Santamaria, Monica, Marzano, Marinella, Alonso-Alemany, Daniel, Valiente, Gabriel, Donvito, Giacinto, Monaco, Alfonso, Notarangelo, Pasquale, Pesole, Graziano

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.42 MB

english, 2015

189

Field phenotyping of grapevine growth using dense stereo reconstruction

Klodt, Maria, Herzog, Katja, Töpfer, Reinhard, Cremers, Daniel

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.51 MB

english, 2015

190

Probing long-range interactions by extracting free energies from genome-wide chromosome conformation capture data

Saberi, Saeed, Farré, Pau, Cuvier, Olivier, Emberly, Eldon

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.80 MB

english, 2015

191

Machine learning approach for pooled DNA sample calibration

Hellicar, Andrew D, Rahman, Ashfaqur, Smith, Daniel V, Henshall, John M

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.48 MB

english, 2015

192

BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data

Hu, Ke, Ting, Angela H., Li, Jing

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.87 MB

english, 2015

193

A multi-view genomic data simulator

Fratello, Michele, Serra, Angela, Fortino, Vittorio, Raiconi, Giancarlo, Tagliaferri, Roberto, Greco, Dario

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 893 KB

english, 2015

194

Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm

Gibbons, Theodore R., Mount, Stephen M., Cooper, Endymion D., Delwiche, Charles F.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 4.46 MB

english, 2015

195

A composite genome approach to identify phylogenetically informative data from next-generation sequencing

Schwartz, Rachel S., Harkins, Kelly M., Stone, Anne C., Cartwright, Reed A.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 624 KB

english, 2015

196

Is this the right normalization? A diagnostic tool for ChIP-seq normalization

Angelini, Claudia, Heller, Ruth, Volkinshtein, Rita, Yekutieli, Daniel

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.96 MB

english, 2015

197

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale

Girgis, Hani Z.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 670 KB

english, 2015

198

Visual analysis of biological data-knowledge networks

Vehlow, Corinna, Kao, David P, Bristow, Michael R, Hunter, Lawrence E, Weiskopf, Daniel, Görg, Carsten

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.08 MB

english, 2015

199

DOCKSCORE: a webserver for ranking protein-protein docked poses

Malhotra, Sony, Mathew, Oommen K, Sowdhamini, Ramanathan

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.52 MB

english, 2015

200

Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism

Patel, Sejal, Roncaglia, Paola, Lovering, Ruth C.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.86 MB

english, 2015

201

TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool

Kozma, Dániel, Tusnády, Gábor E.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.21 MB

english, 2015

202

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, PhD, Hongfang Liu

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 4.08 MB

english, 2015

203

KaBOB: ontology-based semantic integration of biomedical databases

Livingston, Kevin M, Bada, Michael, Baumgartner, William A, Hunter, Lawrence E

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.41 MB

english, 2015

204

Integrated web visualizations for protein-protein interaction databases

Jeanquartier, Fleur, Jean-Quartier, Claire, Holzinger, Andreas

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.74 MB

english, 2015

205

groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data

Chae, Minho, Danko, Charles G., Kraus, W. Lee

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.79 MB

english, 2015

206

Secondary structural entropy in RNA switch (Riboswitch) identification

Manzourolajdad, Amirhossein, Arnold, Jonathan

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.67 MB

english, 2015

207

MetaDiff: differential isoform expression analysis using random-effects meta-regression

Jia, Cheng, Guan, Weihua, Yang, Amy, Xiao, Rui, Tang, W. H. Wilson, Moravec, Christine S., Margulies, Kenneth B., Cappola, Thomas P., Li, Chun, Li, Mingyao

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.72 MB

english, 2015

208

A cascade computer model for mocrobicide diffusivity from mucoadhesive formulations

Lee, Yugyung, Khemka, Alok, Acharya, Gayathri, Giri, Namita, Lee, Chi H.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 972 KB

english, 2015

209

ImmunExplorer (IMEX): a software framework for diversity and clonality analyses of immunoglobulins and T cell receptors on the basis of IMGT/HighV-QUEST preprocessed NGS data

Schaller, Susanne, Weinberger, Johannes, Jimenez-Heredia, Raul, Danzer, Martin, Oberbauer, Rainer, Gabriel, Christian, Winkler, Stephan M.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.52 MB

english, 2015

210

Factors affecting the accuracy of a class prediction model in gene expression data

Novianti, Putri W., Jong, Victor L., Roes, Kit C. B., Eijkemans, Marinus J. C.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 889 KB

english, 2015

211

Equalizer reduces SNP bias in Affymetrix microarrays

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.35 MB

english, 2015

212

TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins

Perea, Marc, Lugtenburg, Ivar, Mayol, Eduardo, Cordomí, Arnau, Deupí, Xavier, Pardo, Leonardo, Olivella, Mireia

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.40 MB

english, 2015

213

Capturing coevolutionary signals inrepeat proteins

Espada, Rocío, Parra, R Gonzalo, Mora, Thierry, Walczak, Aleksandra M, Ferreiro, Diego U

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.63 MB

english, 2015

214

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment

Bohler, Anwesha, Eijssen, Lars M. T., van Iersel, Martijn P., Leemans, Christ, Willighagen, Egon L., Kutmon, Martina, Jaillard, Magali, Evelo, Chris T.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.03 MB

english, 2015

215

Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs

Huo, Tong, Liu, Wei, Guo, Yu, Yang, Cheng, Lin, Jianping, Rao, Zihe

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.98 MB

english, 2015

216

UrQt: an efficient software for the Unsupervised Quality trimming of NGS data

Modolo, Laurent, Lerat, Emmanuelle

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 780 KB

english, 2015

217

Domain similarity based orthology detection

Bitard-Feildel, Tristan, Kemena, Carsten, Greenwood, Jenny M, Bornberg-Bauer, Erich

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.02 MB

english, 2015

218

Principal component analysis-based unsupervised feature extraction applied to in silico drug discovery for posttraumatic stress disorder-mediated heart disease

Taguchi, Y-h, Iwadate, Mitsuo, Umeyama, Hideaki

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 4.33 MB

english, 2015

219

DECODE: an integrated differential co-expression and differential expression analysis of gene expression data

Lui, Thomas WH, Tsui, Nancy BY, Chan, Lawrence WC, Wong, Cesar SC, Siu, Parco MF, Yung, Benjamin YM

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.55 MB

english, 2015

220

Weighted protein residue networks based on joint recurrences between residues

Karain, Wael I., Qaraeen, Nael I.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 837 KB

english, 2015

221

An evaluation of statistical methods for DNA methylation microarray data analysis

Li, Dongmei, Xie, Zidian, Pape, Marc Le, Dye, Timothy

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.40 MB

english, 2015

222

YBYRÁ facilitates comparison of large phylogenetic trees

Machado, Denis Jacob

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 648 KB

english, 2015

223

SIMAT: GC-SIM-MS data analysis tool

Nezami Ranjbar, Mohammad R., Poto, Cristina Di, Wang, Yue, Ressom, Habtom W.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.58 MB

english, 2015

224

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:

2015

Langue:

english

Fichier:

PDF, 1.35 MB

english, 2015

225

A density-based clustering approach for identifying overlapping protein complexes with functional preferences

Hu, Lun, Chan, Keith CC

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.86 MB

english, 2015

226

Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data

Higashi, Susan, Fournier, Cyril, Gautier, Christian, Gaspin, Christine, Sagot, Marie-France

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.87 MB

english, 2015

227

Bilingual term alignment from comparable corpora in English discharge summary and Chinese discharge summary

Xu, Yan, Chen, Luoxin, Wei, Junsheng, Ananiadou, Sophia, Fan, Yubo, Qian, Yi, Chang, Eric I-Chao, Tsujii, Junichi

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.12 MB

english, 2015

228

Discrimination of cell cycle phases in PCNA-immunolabeled cells

Schönenberger, Felix, Deutzmann, Anja, Ferrando-May, Elisa, Merhof, Dorit

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.74 MB

english, 2015

229

Deciding when to stop: efficient experimentation to learn to predict drug-target interactions

Temerinac-Ott, Maja, Naik, Armaghan W, Murphy, Robert F

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.09 MB

english, 2015

230

Inferring 3D chromatin structure using a multiscale approach based on quaternions

Caudai, Claudia, Salerno, Emanuele, Zoppè, Monica, Tonazzini, Anna

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.93 MB

english, 2015

231

Predicting protein function via downward random walks on a gene ontology

Yu, Guoxian, Zhu, Hailong, Domeniconi, Carlotta, Liu, Jiming

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 702 KB

english, 2015

232

MANTIS: an R package that simulates multilocus models of pathogen evolution

Lourenço, José, Wikramaratna, Paul S, Gupta, Sunetra

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.17 MB

english, 2015

233

RNA-binding residues prediction using structural features

Ren, Huizhu, Shen, Ying

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.28 MB

english, 2015

234

Pydna: a simulation and documentation tool for DNA assembly strategies using python

Pereira, Filipa, Azevedo, Flávio, Carvalho, Ângela, Ribeiro, Gabriela F, Budde, Mark W, Johansson, Björn

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.98 MB

english, 2015

235

CHEXVIS: a tool for molecular channel extraction and visualization

Masood, Talha Bin, Sandhya, Sankaran, Chandra, Nagasuma, Natarajan, Vijay

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.02 MB

english, 2015

236

tcR: an R package for T cell receptor repertoire advanced data analysis

Nazarov, Vadim, Pogorelyy, Mikhail, Komech, Ekaterina, Zvyagin, Ivan, Bolotin, Dmitry, Shugay, Mikhail, Chudakov, Dmitry, Lebedev, Yury, Mamedov, Ilgar

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 740 KB

english, 2015

237

PredSTP: a highly accurate SVM based model to predict sequential cystine stabilized peptides

Islam, S. M. Ashiqul, Sajed, Tanvir, Kearney, Christopher Michel, Baker, Erich J

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.89 MB

english, 2015

238

POPE: post optimization posterior evaluation of likelihood free models

Meeds, Edward, Chiang, Michael, Lee, Mary, Cinquin, Olivier, Lowengrub, John, Welling, Max

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 4.45 MB

english, 2015

239

Epitopemap: a web application for integrated whole proteome epitope prediction

Farrell, Damien, Gordon, Stephen V

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 622 KB

english, 2015

240

Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix

Ndhlovu, Andrew, Hazelhurst, Scott, Durand, Pierre M.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.21 MB

english, 2015

241

Navigating 3D electron microscopy maps with EM-SURFER

Esquivel-Rodríguez, Juan, Xiong, Yi, Han, Xusi, Guang, Shuomeng, Christoffer, Charles, Kihara, Daisuke

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.31 MB

english, 2015

242

UNCLES: method for the identification of genes differentially consistently co-expressed in a specific subset of datasets

Abu-Jamous, Basel, Fa, Rui, Roberts, David J, Nandi, Asoke K

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.42 MB

english, 2015

243

Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off

Dutheil, Julien Y, Figuet, Emeric

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 907 KB

english, 2015

244

Computing all hybridization networks for multiple binary phylogenetic input trees

Albrecht, Benjamin

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.19 MB

english, 2015

245

A unified framework for estimating parameters of kinetic biological models

Baker, Syed Murtuza, Poskar, C Hart, Schreiber, Falk, Junker, Björn H

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.43 MB

english, 2015

246

A Long Fragment Aligner called ALFALFA

Vyverman, Michaël, Baets, Bernard De, Fack, Veerle, Dawyndt, Peter

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.08 MB

english, 2015

247

Ambivalent covariance models

Janssen, Stefan, Giegerich, Robert

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.90 MB

english, 2015

248

VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery

Nim, Hieu T, Furtado, Milena B, Costa, Mauro W, Rosenthal, Nadia A, Kitano, Hiroaki, Boyd, Sarah E

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.81 MB

english, 2015

249

Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data

Liu, Yang, Chiaromonte, Francesca, Ross, Howard, Malhotra, Raunaq, Elleder, Daniel, Poss, Mary

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.07 MB

english, 2015

250

affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling

Hernandez-Ferrer, Carles, Quintela Garcia, Ines, Danielski, Katharina, Carracedo, Ángel, Pérez-Jurado, Luis A., González, Juan R.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.51 MB

english, 2015

251

Light-weight reference-based compression of FASTQ data

Zhang, Yongpeng, Li, Linsen, Yang, Yanli, Yang, Xiao, He, Shan, Zhu, Zexuan

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 963 KB

english, 2015

252

Ferret: a sentence-based literature scanning system

Srinivasan, Padmini, Zhang, Xiao-Ning, Bouten, Roxane, Chang, Caren

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 982 KB

english, 2015

253

Distribution Analyzer, a methodology for identifying and clustering outlier conditions from single-cell distributions, and its application to a Nanog reporter RNAi screen

Gingold, Julian A., Coakley, Ed S., Su, Jie, Lee, Dung-Fang, Lau, Zerlina, Zhou, Hongwei, Felsenfeld, Dan P., Schaniel, Christoph, Lemischka, Ihor R.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 4.68 MB

english, 2015

254

SuRankCo: supervised ranking of contigs in de novo assemblies

Kuhring, Mathias, Dabrowski, Piotr Wojtek, Piro, Vitor C., Nitsche, Andreas, Renard, Bernhard Y.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 926 KB

english, 2015

255

Joint haplotype assembly and genotype calling via sequential Monte Carlo algorithm

Ahn, Soyeon, Vikalo, Haris

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 741 KB

english, 2015

256

An investigation into inter- and intragenomic variations of graphic genomic signatures

Karamichalis, Rallis, Kari, Lila, Konstantinidis, Stavros, Kopecki, Steffen

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.59 MB

english, 2015

257

QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments

Hartley, Stephen W., Mullikin, James C.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.53 MB

english, 2015

258

Breaking the computational barriers of pairwise genome comparison

Torreno, Oscar, Trelles, Oswaldo

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.26 MB

english, 2015

259

MVDA: a multi-view genomic data integration methodology

Serra, Angela, Fratello, Michele, Fortino, Vittorio, Raiconi, Giancarlo, Tagliaferri, Roberto, Greco, Dario

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.37 MB

english, 2015

260

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data

Lun, Aaron T.L., Smyth, Gordon K.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.49 MB

english, 2015

261

leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences

Flandrois, Jean-Pierre, Perrière, Guy, Gouy, Manolo

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.07 MB

english, 2015

262

A simplicial complex-based approach to unmixing tumor progression data

Roman, Theodore, Nayyeri, Amir, Fasy, Brittany Terese, Schwartz, Russell

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.51 MB

english, 2015

263

Efficient test for nonlinear dependence of two continuous variables

Wang, Yi, Li, Yi, Cao, Hongbao, Xiong, Momiao, Shugart, Yin Yao, Jin, Li

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 848 KB

english, 2015

264

OD-seq: outlier detection in multiple sequence alignments

Jehl, Peter, Sievers, Fabian, Higgins, Desmond G.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.59 MB

english, 2015

265

GelJ – a tool for analyzing DNA fingerprint gel images

Heras, Jónathan, Domínguez, César, Mata, Eloy, Pascual, Vico, Lozano, Carmen, Torres, Carmen, Zarazaga, Myriam

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.58 MB

english, 2015

266

MSAIndelFR: a scheme for multiple protein sequence alignment using information on indel flanking regions

Al-Shatnawi, Mufleh, Ahmad, M. Omair, S. Swamy, M. N.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.16 MB

english, 2015

267

Comparative proteomics: assessment of biological variability and dataset comparability

Kim, Sa Rang, Nguyen, Tuong Vi, Seo, Na Ri, Jung, Seunghup, An, Hyun Joo, Mills, David A, Kim, Jae Han

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 726 KB

english, 2015

268

SpirPro: A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1

Senachak, Jittisak, Cheevadhanarak, Supapon, Hongsthong, Apiradee

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.77 MB

english, 2015

269

A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea

Kristensen, David M., Saeed, Usman, Frishman, Dmitrij, Koonin, Eugene V.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.82 MB

english, 2015

270

2D and 3D similarity landscape analysis identifies PARP as a novel off-target for the drug Vatalanib

Gohlke, Bjoern-Oliver, Overkamp, Tim, Richter, Anja, Richter, Antje, Daniel, Peter T., Gillissen, Bernd, Preissner, Robert

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.00 MB

english, 2015

271

DiSNPindel: improved intra-individual SNP and InDel detection in direct amplicon sequencing of a diploid

Deng, Jizhong, Huang, Huasheng, Yu, Xiaoli, Jin, Ji, Lin, Weisen, Li, Fagen, Song, Zhijiao, Li, Mei, Gan, Siming

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.15 MB

english, 2015

272

QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles

Van der Borght, Koen, Thys, Kim, Wetzels, Yves, Clement, Lieven, Verbist, Bie, Reumers, Joke, van Vlijmen, Herman, Aerssens, Jeroen

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 714 KB

english, 2015

273

Boosting for high-dimensional two-class prediction

Blagus, Rok, Lusa, Lara

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.85 MB

english, 2015

274

Fully automated registration of vibrational microspectroscopic images in histologically stained tissue sections

Yang, Chen, Niedieker, Daniel, Großerüschkamp, Frederik, Horn, Melanie, Tannapfel, Andrea, Kallenbach-Thieltges, Angela, Gerwert, Klaus, Mosig, Axel

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.02 MB

english, 2015

275

Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform

Kilianski, Andy, Carcel, Patrick, Yao, Shijie, Roth, Pierce, Schulte, Josh, Donarum, Greg B., Fochler, Ed T., Hill, Jessica M., Liem, Alvin T., Wiley, Michael R., Ladner, Jason T., Pfeffer, Bradley P.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 814 KB

english, 2015

276

A Lattice-Boltzmann scheme for the simulation of diffusion in intracellular crowded systems

Angeles-Martinez, Liliana, Theodoropoulos, Constantinos

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.51 MB

english, 2015

277

Survey statistics of automated segmentations applied to optical imaging of mammalian cells

Bajcsy, Peter, Cardone, Antonio, Chalfoun, Joe, Halter, Michael, Juba, Derek, Kociolek, Marcin, Majurski, Michael, Peskin, Adele, Simon, Carl, Simon, Mylene, Vandecreme, Antoine, Brady, Mary

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.72 MB

english, 2015

278

CATCHing putative causative variants in consanguineous families

Santoni, Federico Andrea, Makrythanasis, Periklis, Antonarakis, Stylianos E.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 656 KB

english, 2015

279

antaRNA – Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization

Kleinkauf, Robert, Houwaart, Torsten, Backofen, Rolf, Mann, Martin

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 761 KB

english, 2015

280

High-order dynamic Bayesian Network learning with hidden common causes for causal gene regulatory network

Lo, Leung-Yau, Wong, Man-Leung, Lee, Kin-Hong, Leung, Kwong-Sak

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.07 MB

english, 2015

281

Use and mis-use of supplementary material in science publications

Pop, Mihai, Salzberg, Steven L.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 353 KB

english, 2015

282

Phylogenetic network analysis as a parsimony optimization problem

Wheeler, Ward C

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.85 MB

english, 2015

283

HiCdat: a fast and easy-to-use Hi-C data analysis tool

Schmid, Marc W., Grob, Stefan, Grossniklaus, Ueli

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.03 MB

english, 2015

284

Reconstruction of novel transcription factor regulons through inference of their binding sites

Elmas, Abdulkadir, Wang, Xiaodong, Samoilov, Michael S.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.48 MB

english, 2015

285

Finite mixture clustering of human tissues with different levels of IGF-1 splice variants mRNA transcripts

Pelosi, Michele, Alfò, Marco, Martella, Francesca, Pappalardo, Elisa, Musarò, Antonio

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 968 KB

english, 2015

286

A reverse-engineering approach to dissect post-translational modulators of transcription factor’s activity from transcriptional data

Gambardella, Gennaro, Peluso, Ivana, Montefusco, Sandro, Bansal, Mukesh, Medina, Diego L., Lawrence, Neil, di Bernardo, Diego

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 888 KB

english, 2015

287

EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering

Lee, Soohyun, Seo, Chae Hwa, Alver, Burak Han, Lee, Sanghyuk, Park, Peter J.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 5.97 MB

english, 2015

288

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data

Farrant, Gregory K., Hoebeke, Mark, Partensky, Frédéric, Andres, Gwendoline, Corre, Erwan, Garczarek, Laurence

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.25 MB

english, 2015

289

Multi-objective optimization for RNA design with multiple target secondary structures

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.54 MB

english, 2015

290

Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph

Benoit, Gaëtan, Lemaitre, Claire, Lavenier, Dominique, Drezen, Erwan, Dayris, Thibault, Uricaru, Raluca, Rizk, Guillaume

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.64 MB

english, 2015

291

Seq-ing improved gene expression estimates from microarrays using machine learning

Korir, Paul K., Geeleher, Paul, Seoighe, Cathal

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.62 MB

english, 2015

292

Scientific workflow optimization for improved peptide and protein identification

Holl, Sonja, Mohammed, Yassene, Zimmermann, Olav, Palmblad, Magnus

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.55 MB

english, 2015

293

A weighting approach for judging the effect of patient strata on high-dimensional risk prediction signatures

Weyer, Veronika, Binder, Harald

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.53 MB

english, 2015

294

mAPKL: R/ Bioconductor package for detecting gene exemplars and revealing their characteristics

Sakellariou, Argiris, Spyrou, George

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.80 MB

english, 2015

295

PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli

Esmaeili, Afshin, Davison, Timothy, Wu, Andrew, Alcantara, Joenel, Jacob, Christian

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 4.87 MB

english, 2015

296

Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees

Zhu, Sha, Degnan, James H., Goldstien, Sharyn J., Eldon, Bjarki

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 732 KB

english, 2015

297

Development and validation of an epitope prediction tool for swine (PigMatrix) based on the pocket profile method

Gutiérrez, Andres H., Martin, William D., Bailey-Kellogg, Chris, Terry, Frances, Moise, Leonard, De Groot, Anne S.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.23 MB

english, 2015

298

Erratum to: MONALISA for stochastic simulations of Petri net models of biochemical systems

Balazki, Pavel, Lindauer, Klaus, Einloft, Jens, Ackermann, Jörg, Koch, Ina

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 302 KB

english, 2015

299

SMRT sequencing only de novo assembly of the sugar beet (Beta vulgaris) chloroplast genome

Stadermann, Kai Bernd, Weisshaar, Bernd, Holtgräwe, Daniela

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.18 MB

english, 2015

300

NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference

Bellot, Pau, Olsen, Catharina, Salembier, Philippe, Oliveras-Vergés, Albert, Meyer, Patrick E.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 851 KB

english, 2015

301

htsint: a Python library for sequencing pipelines that combines data through gene set generation

Richards, Adam J., Herrel, Anthony, Bonneaud, Camille

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 874 KB

english, 2015

302

Label noise in subtype discrimination of class C G protein-coupled receptors: A systematic approach to the analysis of classification errors

König, Caroline, Cárdenas, Martha I, Giraldo, Jesús, Alquézar, René, Vellido, Alfredo

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.89 MB

english, 2015

303

Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains

Xia, Li C., Ai, Dongmei, Cram, Jacob A., Liang, Xiaoyi, Fuhrman, Jed A., Sun, Fengzhu

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.76 MB

english, 2015

304

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies

Thiele, Sven, Cerone, Luca, Saez-Rodriguez, Julio, Siegel, Anne, Guziołowski, Carito, Klamt, Steffen

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.44 MB

english, 2015

305

Inference of regulatory networks with a convergence improved MCMC sampler

Agostinho, Nilzair B., Machado, Karina S., Werhli, Adriano V.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.27 MB

english, 2015

306

Differential analysis of biological networks

Ruan, Da, Young, Alastair, Montana, Giovanni

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.37 MB

english, 2015

307

Subtype prediction in pediatric acute myeloid leukemia: classification using differential network rank conservation revisited

Obulkasim, Askar, Fornerod, Maarten, Zwaan, Michel C., Reinhardt, Dirk, van den Heuvel-Eibrink, Marry M.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.91 MB

english, 2015

308

Segmental HOG: new descriptor for glomerulus detection in kidney microscopy image

Kato, Tsuyoshi, Relator, Raissa, Ngouv, Hayliang, Hirohashi, Yoshihiro, Takaki, Osamu, Kakimoto, Tetsuhiro, Okada, Kinya

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.79 MB

english, 2015

309

Lab Retriever: a software tool for calculating likelihood ratios incorporating a probability of drop-out for forensic DNA profiles

Inman, Keith, Rudin, Norah, Cheng, Ken, Robinson, Chris, Kirschner, Adam, Inman-Semerau, Luke, Lohmueller, Kirk E.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 985 KB

english, 2015

310

Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor

Kara, Altan, Vickers, Martin, Swain, Martin, Whitworth, David E., Fernandez-Fuentes, Narcis

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 572 KB

english, 2015

311

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data

Kishore, Kamal, de Pretis, Stefano, Lister, Ryan, Morelli, Marco J., Bianchi, Valerio, Amati, Bruno, Ecker, Joseph R., Pelizzola, Mattia

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.25 MB

english, 2015

312

ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization

Daniel, Edward, Onwukwe, Goodluck U., Wierenga, Rik K., Quaggin, Susan E., Vainio, Seppo J., Krause, Mirja

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.97 MB

english, 2015

313

Accelerating the Smith-Waterman algorithm with interpair pruning and band optimization for the all-pairs comparison of base sequences

Okada, Daiki, Ino, Fumihiko, Hagihara, Kenichi

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.60 MB

english, 2015

314

Systematic noise degrades gene co-expression signals but can be corrected

Freytag, Saskia, Gagnon-Bartsch, Johann, Speed, Terence P., Bahlo, Melanie

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.16 MB

english, 2015

315

A computer simulation model of Wolbachia invasion for disease vector population modification

Guevara-Souza, Mauricio, Vallejo, Edgar E.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.90 MB

english, 2015

316

SPINGO: a rapid species-classifier for microbial amplicon sequences

Allard, Guy, Ryan, Feargal J., Jeffery, Ian B., Claesson, Marcus J.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.02 MB

english, 2015

317

VEGAWES: variational segmentation on whole exome sequencing for copy number detection

Anjum, Samreen, Morganella, Sandro, D’Angelo, Fulvio, Iavarone, Antonio, Ceccarelli, Michele

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.44 MB

english, 2015

318

DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment

Wright, Erik S.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.35 MB

english, 2015

319

Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate

Liu, Xuejun, Shi, Xinxin, Chen, Chunlin, Zhang, Li

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.90 MB

english, 2015

320

Comparative study on gene set and pathway topology-based enrichment methods

Bayerlová, Michaela, Jung, Klaus, Kramer, Frank, Klemm, Florian, Bleckmann, Annalen, Beißbarth, Tim

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.91 MB

english, 2015

321

Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery

López-Fernández, H., Santos, H. M., Capelo, J. L., Fdez-Riverola, F., Glez-Peña, D., Reboiro-Jato, M.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.67 MB

english, 2015

322

DectICO: an alignment-free supervised metagenomic classification method based on feature extraction and dynamic selection

Ding, Xiao, Cheng, Fudong, Cao, Changchang, Sun, Xiao

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 943 KB

english, 2015

323

Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms

Jafari, Mohieddin, Mirzaie, Mehdi, Sadeghi, Mehdi

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.04 MB

english, 2015

324

Indexing a protein-protein interaction network expedites network alignment

Hasan, Md Mahmudul, Kahveci, Tamer

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.20 MB

english, 2015

325

SCExV: a webtool for the analysis and visualisation of single cell qRT-PCR data

Lang, Stefan, Ugale, Amol, Erlandsson, Eva, Karlsson, Göran, Bryder, David, Soneji, Shamit

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.80 MB

english, 2015

326

Estimating cumulative pathway effects on risk for age-related macular degeneration using mixed linear models

Hall, Jacob B., Cooke Bailey, Jessica N., Hoffman, Joshua D., Pericak-Vance, Margaret A., Scott, William K., Kovach, Jaclyn L., Schwartz, Stephen G., Agarwal, Anita, Brantley, Milam A., Haines, Jonath

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 637 KB

english, 2015

327

ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data

Ihnatova, Ivana, Budinska, Eva

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 775 KB

english, 2015

328

ODTbrain: a Python library for full-view, dense diffraction tomography

Müller, Paul, Schürmann, Mirjam, Guck, Jochen

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.99 MB

english, 2015

329

DiffLogo: a comparative visualization of sequence motifs

Nettling, Martin, Treutler, Hendrik, Grau, Jan, Keilwagen, Jens, Posch, Stefan, Grosse, Ivo

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.85 MB

english, 2015

330

Iterative sub-network component analysis enables reconstruction of large scale genetic networks

Jayavelu, Naresh Doni, Aasgaard, Lasse S., Bar, Nadav

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 789 KB

english, 2015

331

Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data

Nowotny, Jackson, Ahmed, Sharif, Xu, Lingfei, Oluwadare, Oluwatosin, Chen, Hannah, Hensley, Noelan, Trieu, Tuan, Cao, Renzhi, Cheng, Jianlin

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.79 MB

english, 2015

332

Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes

Machnicka, Magdalena A., Kaminska, Katarzyna H., Dunin-Horkawicz, Stanislaw, Bujnicki, Janusz M.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 6.46 MB

english, 2015

333

Predicting drug side effects by multi-label learning and ensemble learning

Zhang, Wen, Liu, Feng, Luo, Longqiang, Zhang, Jingxia

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 894 KB

english, 2015

334

PDB-Explorer: a web-based interactive map of the protein data bank in shape space

Jin, Xian, Awale, Mahendra, Zasso, Michaël, Kostro, Daniel, Patiny, Luc, Reymond, Jean-Louis

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.80 MB

english, 2015

335

GOTA: GO term annotation of biomedical literature

Lena, Pietro Di, Domeniconi, Giacomo, Margara, Luciano, Moro, Gianluca

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 642 KB

english, 2015

336

Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data

Li, Peipei, Piao, Yongjun, Shon, Ho Sun, Ryu, Keun Ho

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 419 KB

english, 2015

337

BitTorious volunteer: server-side extensions for centrally-managed volunteer storage in BitTorrent swarms

Lee, Preston V., Dinu, Valentin

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.11 MB

english, 2015

338

Neuron anatomy structure reconstruction based on a sliding filter

Luo, Gongning, Sui, Dong, Wang, Kuanquan, Chae, Jinseok

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.41 MB

english, 2015

339

HMMvar-func: a new method for predicting the functional outcome of genetic variants

Liu, Mingming, Watson, Layne T., Zhang, Liqing

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.56 MB

english, 2015

340

CytoSpectre: a tool for spectral analysis of oriented structures on cellular and subcellular levels

Kartasalo, Kimmo, Pölönen, Risto-Pekka, Ojala, Marisa, Rasku, Jyrki, Lekkala, Jukka, Aalto-Setälä, Katriina, Kallio, Pasi

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.65 MB

english, 2015

341

Joint use of over- and under-sampling techniques and cross-validation for the development and assessment of prediction models

Blagus, Rok, Lusa, Lara

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 879 KB

english, 2015

342

Novel gene sets improve set-level classification of prokaryotic gene expression data

Holec, Matěj, Kuželka, Ondřej, železný, Filip

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 539 KB

english, 2015

343

Peak shape clustering reveals biological insights

Cremona, Marzia A., Sangalli, Laura M., Vantini, Simone, Dellino, Gaetano I., Pelicci, Pier Giuseppe, Secchi, Piercesare, Riva, Laura

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 11.13 MB

english, 2015

344

Evaluation of shotgun metagenomics sequence classification methods usingin silicoandin vitrosimulated communities

Peabody, Michael A., Van Rossum, Thea, Lo, Raymond, Brinkman, Fiona S. L.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.40 MB

english, 2015

345

Inferring plant microRNA functional similarity using a weighted protein-protein interaction network

Meng, Jun, Liu, Dong, Luan, Yushi

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.46 MB

english, 2015

346

The Gap Procedure: for the identification of phylogenetic clusters in HIV-1 sequence data

Vrbik, Irene, Stephens, David A., Roger, Michel, Brenner, Bluma G.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.30 MB

english, 2015

347

Fizzy: feature subset selection for metagenomics

Ditzler, Gregory, Morrison, J. Calvin, Lan, Yemin, Rosen, Gail L.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 625 KB

english, 2015

348

Evaluation of methods for differential expression analysis on multi-group RNA-seq count data

Tang, Min, Sun, Jianqiang, Shimizu, Kentaro, Kadota, Koji

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 929 KB

english, 2015

349

TOGGLE: toolbox for generic NGS analyses

Monat, Cécile, Tranchant-Dubreuil, Christine, Kougbeadjo, Ayité, Farcy, Cédric, Ortega-Abboud, Enrique, Amanzougarene, Souhila, Ravel, Sébastien, Agbessi, Mawussé, Orjuela-Bouniol, Julie, Summo, Maryl

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.12 MB

english, 2015

350

From raw data to data-analysis for magnetic resonance spectroscopy – the missing link: jMRUI2XML

Mocioiu, Victor, Ortega-Martorell, Sandra, Olier, Iván, Jablonski, Michal, Starcukova, Jana, Lisboa, Paulo, Arús, Carles, Julià-Sapé, Margarida

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.36 MB

english, 2015

351

miRA: adaptable novel miRNA identification in plants using small RNA sequencing data

Evers, Maurits, Huttner, Michael, Dueck, Anne, Meister, Gunter, Engelmann, Julia C.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 730 KB

english, 2015

352

Reconstruction of 3D genome architecture via a two-stage algorithm

Segal, Mark R., Bengtsson, Henrik L.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.17 MB

english, 2015

353

tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data

Selitsky, Sara R., Sethupathy, Praveen

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.69 MB

english, 2015

354

An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome

Ribeiro, Antonio, Golicz, Agnieszka, Hackett, Christine Anne, Milne, Iain, Stephen, Gordon, Marshall, David, Flavell, Andrew J., Bayer, Micha

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.71 MB

english, 2015

355

A fast method for calculating reliable event supports in tree reconciliations via Pareto optimality

To, Thu-Hien, Jacox, Edwin, Ranwez, Vincent, Scornavacca, Celine

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 919 KB

english, 2015

356

Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data

Aflitos, Saulo Alves, Severing, Edouard, Sanchez-Perez, Gabino, Peters, Sander, de Jong, Hans, de Ridder, Dick

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.37 MB

english, 2015

357

An assessment of catalytic residue 3D ensembles for the prediction of enzyme function

Žváček, Clemens, Friedrichs, Gerald, Heizinger, Leonhard, Merkl, Rainer

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 497 KB

english, 2015

358

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

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

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.63 MB

english, 2015

359

Estimation of evolutionary parameters using short, random and partial sequences from mixed samples of anonymous individuals

Wu, Steven H., Rodrigo, Allen G.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 963 KB

english, 2015

360

Analysis of in vivo single cell behavior by high throughput, human-in-the-loop segmentation of three-dimensional images

Chiang, Michael, Hallman, Sam, Cinquin, Amanda, de Mochel, Nabora Reyes, Paz, Adrian, Kawauchi, Shimako, Calof, Anne L., Cho, Ken W., Fowlkes, Charless C., Cinquin, Olivier

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.25 MB

english, 2015

361

FoCo: a simple and robust quantification algorithm of nuclear foci

Lapytsko, Anastasiya, Kollarovic, Gabriel, Ivanova, Lyubomira, Studencka, Maja, Schaber, Jörg

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.17 MB

english, 2015

362

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads

Zhu, Xiao, Leung, Henry C. M., Wang, Rongjie, Chin, Francis Y. L., Yiu, Siu Ming, Quan, Guangri, Li, Yajie, Zhang, Rui, Jiang, Qinghua, Liu, Bo, Dong, Yucui, Zhou, Guohui, Wang, Yadong

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.67 MB

english, 2015

363

Proposal of supervised data analysis strategy of plasma miRNAs from hybridisation array data with an application to assess hemolysis-related deregulation

Landoni, Elena, Miceli, Rosalba, Callari, Maurizio, Tiberio, Paola, Appierto, Valentina, Angeloni, Valentina, Mariani, Luigi, Daidone, Maria Grazia

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.23 MB

english, 2015

364

M3-S: a genotype calling method incorporating information from samples with known genotypes

Li, Gengxin, Zhao, Hongyu

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.51 MB

english, 2015

365

Accurate prediction of nuclear receptors with conjoint triad feature

Wang, Hongchu, Hu, Xuehai

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.07 MB

english, 2015

366

Reads2Type: a web application for rapid microbial taxonomy identification

Saputra, Dhany, Rasmussen, Simon, Larsen, Mette V., Haddad, Nizar, Sperotto, Maria Maddalena, Aarestrup, Frank M., Lund, Ole, Sicheritz-Pontén, Thomas

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.60 MB

english, 2015

367

Scalable analysis of Big pathology image data cohorts using efficient methods and high-performance computing strategies

Kurc, Tahsin, Qi, Xin, Wang, Daihou, Wang, Fusheng, Teodoro, George, Cooper, Lee, Nalisnik, Michael, Yang, Lin, Saltz, Joel, Foran, David J.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.88 MB

english, 2015

368

Parameterizing sequence alignment with an explicit evolutionary model

Rivas, Elena, Eddy, Sean R.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.36 MB

english, 2015

369

GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oysterCrassostrea gigas

Riviere, Guillaume, Klopp, Christophe, Ibouniyamine, Nabihoudine, Huvet, Arnaud, Boudry, Pierre, Favrel, Pascal

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.09 MB

english, 2015

370

Penalized weighted low-rank approximation for robust recovery of recurrent copy number variations

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.27 MB

english, 2015

371

Bioinformatics approach to predict target genes for dysregulated microRNAs in hepatocellular carcinoma: study on a chemically-induced HCC mouse model

Del Vecchio, Filippo, Gallo, Francesco, Di Marco, Antinisca, Mastroiaco, Valentina, Caianiello, Pasquale, Zazzeroni, Francesca, Alesse, Edoardo, Tessitore, Alessandra

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.96 MB

english, 2015

372

MIA: Mutual Information Analyzer, a graphic user interface program that calculates entropy, vertical and horizontal mutual information of molecular sequence sets

Lichtenstein, Flavio, Antoneli, Fernando, Briones, Marcelo R. S.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.95 MB

english, 2015

373

Erratum to: Efficient experimental design for uncertainty reduction in gene regulatory networks

Dehghannasiri, Roozbeh, Yoon, Byung-Jun, Dougherty, Edward R.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 337 KB

english, 2015

374

Multi-label multi-instance transfer learning for simultaneous reconstruction and cross-talk modeling of multiple human signaling pathways

Mei, Suyu, Zhu, Hao

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 6.69 MB

english, 2015

375

Unsupervised image segmentation for microarray spots with irregular contours and inner holes

Belean, Bogdan, Borda, Monica, Ackermann, Jörg, Koch, Ina, Balacescu, Ovidiu

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.11 MB

english, 2015

376

Treelink: data integration, clustering and visualization of phylogenetic trees

Allende, Christian, Sohn, Erik, Little, Cedric

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.56 MB

english, 2015

377

Statistical analysis of a Bayesian classifier based on the expression of miRNAs

Ricci, Leonardo, Vescovo, Valerio Del, Cantaloni, Chiara, Grasso, Margherita, Barbareschi, Mattia, Denti, Michela Alessandra

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.59 MB

english, 2015

378

Enabling network inference methods to handle missing data and outliers

Folch-Fortuny, Abel, Villaverde, Alejandro F., Ferrer, Alberto, Banga, Julio R.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 853 KB

english, 2015

379

New in silico approach to assessing RNA secondary structures with non-canonical base pairs

Rybarczyk, Agnieszka, Szostak, Natalia, Antczak, Maciej, Zok, Tomasz, Popenda, Mariusz, Adamiak, Ryszard, Blazewicz, Jacek, Szachniuk, Marta

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.50 MB

english, 2015

380

Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies

Standish, Kristopher A., Carland, Tristan M., Lockwood, Glenn K., Pfeiffer, Wayne, Tatineni, Mahidhar, Huang, C Chris, Lamberth, Sarah, Cherkas, Yauheniya, Brodmerkel, Carrie, Jaeger, Ed, Smith, Lance

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.27 MB

english, 2015

381

cnvCurator: an interactive visualization and editing tool for somatic copy number variations

Ma, Lingnan, Qin, Maochun, Liu, Biao, Hu, Qiang, Wei, Lei, Wang, Jianmin, Liu, Song

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.41 MB

english, 2015

382

Whole genome SNP genotype piecemeal imputation

Wang, Yining, Wylie, Tim, Stothard, Paul, Lin, Guohui

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 690 KB

english, 2015

383

Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree

Dib, Linda, Meyer, Xavier, Artimo, Panu, Ioannidis, Vassilios, Stockinger, Heinz, Salamin, Nicolas

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.22 MB

english, 2015

384

AlignWise: a tool for identifying protein-coding sequence and correcting frame-shifts

Evans, Teri, Loose, Matthew

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.98 MB

english, 2015

385

MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development

Aiyetan, Paul, Thomas, Stefani N., Zhang, Zhen, Zhang, Hui

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.08 MB

english, 2015

386

CoSREM: a graph mining algorithm for the discovery of combinatorial splicing regulatory elements

Badr, Eman, Heath, Lenwood S.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.65 MB

english, 2015

387

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:

2015

Langue:

english

Fichier:

PDF, 2.83 MB

english, 2015

388

SFESA: a web server for pairwise alignment refinement by secondary structure shifts

Tong, Jing, Pei, Jimin, Grishin, Nick V.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.76 MB

english, 2015

389

A methodology for exploring biomarker – phenotype associations: application to flow cytometry data and systemic sclerosis clinical manifestations

Huang, Hongtai, Fava, Andrea, Guhr, Tara, Cimbro, Raffaello, Rosen, Antony, Boin, Francesco, Ellis, Hugh

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.55 MB

english, 2015

390

Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2

Huang, Hui-Wen, Chen, Yao-Shen, Chen, Jeff Yi-Fu, Lu, Po-Liang, Lin, Yung-Cheng, Chen, Bao-Chen, Chou, Li-Chiu, Wang, Chu-Feng, Su, Hui-Ju, Huang, Yi-Chien, Shi, Yong-Ying, Chen, Hsiu-Lin, Sanno-Duand

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.68 MB

english, 2015

391

BRANE Cut: biologically-related a priori network enhancement with graph cuts for gene regulatory network inference

Pirayre, Aurélie, Couprie, Camille, Bidard, Frédérique, Duval, Laurent, Pesquet, Jean-Christophe

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 999 KB

english, 2015

392

Sequence specificity between interacting and non-interacting homologs identifies interface residues – a homodimer and monomer use case

Hou, Qingzhen, Dutilh, Bas E., Huynen, Martijn A., Heringa, Jaap, Feenstra, K. Anton

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.19 MB

english, 2015

393

CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data

Bray, Mark-Anthony, Carpenter, Anne E.

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.39 MB

english, 2015

394

An automated real-time integration and interoperability framework for bioinformatics

Lopes, Pedro, Oliveira, José Luís

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.07 MB

english, 2015

395

AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis

Greener, Joe G, Sternberg, Michael JE

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 971 KB

english, 2015

396

A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11

Li, Jilong, Cao, Renzhi, Cheng, Jianlin

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.46 MB

english, 2015

397

QCScreen: a software tool for data quality control in LC-HRMS based metabolomics

Simader, Alexandra Maria, Kluger, Bernhard, Neumann, Nora Katharina Nicole, Bueschl, Christoph, Lemmens, Marc, Lirk, Gerald, Krska, Rudolf, Schuhmacher, Rainer

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.58 MB

english, 2015

398

A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins

Morton, James T., Freed, Stefan D., Lee, Shaun W., Friedberg, Iddo

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.94 MB

english, 2015

399

Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data

Eggeling, Ralf, Roos, Teemu, Myllymäki, Petri, Grosse, Ivo

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.22 MB

english, 2015

400

Two molecular measures of relatedness based on haplotype sharing

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.11 MB

english, 2015

401

A new network representation of the metabolism to detect chemical transformation modules

Sorokina, Maria, Medigue, Claudine, Vallenet, David

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1016 KB

english, 2015

402

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

AlQuraishi, Mohammed, Tang, Shengdong, Xia, Xide

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.21 MB

english, 2015

403

An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors

Broeckx, Bart J. G., Coopman, Frank, Verhoeven, Geert, Bosmans, Tim, Gielen, Ingrid, Dingemanse, Walter, Saunders, Jimmy H., Deforce, Dieter, Van Nieuwerburgh, Filip

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.02 MB

english, 2015

404

Rare variants analysis using penalization methods for whole genome sequence data

Yazdani, Akram, Yazdani, Azam, Boerwinkle, Eric

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.20 MB

english, 2015

405

PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information

Meckbach, Cornelia, Tacke, Rebecca, Hua, Xu, Waack, Stephan, Wingender, Edgar, Gültas, Mehmet

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.67 MB

english, 2015

406

DHOEM: a statistical simulation software for simulating new markers in real SNP marker data

Jacquin, Laval, Cao, Tuong-Vi, Grenier, Cécile, Ahmadi, Nourollah

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 831 KB

english, 2015

407

BigQ: a NoSQL based framework to handle genomic variants in i2b2

Gabetta, Matteo, Limongelli, Ivan, Rizzo, Ettore, Riva, Alberto, Segagni, Daniele, Bellazzi, Riccardo

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.75 MB

english, 2015

408

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

Heberle, Henry, Meirelles, Gabriela Vaz, da Silva, Felipe R, Telles, Guilherme P, Minghim, Rosane

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1022 KB

english, 2015

409

A straightforward method to compute average stochastic oscillations from data samples

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 15.92 MB

english, 2015

410

Revisiting operons: an analysis of the landscape of transcriptional units in E. coli

Mao, Xizeng, Ma, Qin, Liu, Bingqiang, Chen, Xin, Zhang, Hanyuan, Xu, Ying

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 968 KB

english, 2015

411

Sequence information gain based motif analysis

Maynou, Joan, Pairó, Erola, Marco, Santiago, Perera, Alexandre

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.43 MB

english, 2015

412

MixChIP: a probabilistic method for cell type specific protein-DNA binding analysis

Rautio, Sini, Lähdesmäki, Harri

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 1.35 MB

english, 2015