Works in BMC Bioinformatics, 2018, Vol 19

Results: 537

Detecting gene-gene interactions for complex quantitative traits using generalized fuzzy classification.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2361-5

By:

Zhou, Xiangdong;
Chan, Keith C. C.

Publication type:

Article

Data-driven human transcriptomic modules determined by independent component analysis.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2338-4

By:

Zhou, Weizhuang;
Altman, Russ B.

Publication type:

Article

A document level neural model integrated domain knowledge for chemical-induced disease relations.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2316-x

By:

Zheng, Wei;
Lin, Hongfei;
Liu, Xiaoxia;
Xu, Bo

Publication type:

Article

Phage spanins: diversity, topological dynamics and gene convergence.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2342-8

By:

Kongari, Rohit;
Rajaure, Manoj;
Cahill, Jesse;
Rasche, Eric;
Mijalis, Eleni;
Berry, Joel;
Young, Ry

Publication type:

Article

Using controls to limit false discovery in the era of big data.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2356-2

By:

Parks, Matthew M.;
Raphael, Benjamin J.;
Lawrence, Charles E.

Publication type:

Article

Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2352-6

By:

Tamura, Takeyuki

Publication type:

Article

DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2347-3

By:

Villandré, Luc;
Labbe, Aurélie;
Brenner, Bluma;
Roger, Michel;
Stephens, David A

Publication type:

Article

Searching for 3D structural models from a library of biological shapes using a few 2D experimental images.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2358-0

By:

Tiwari, Sandhya P.;
Tama, Florence;
Miyashita, Osamu

Publication type:

Article

GeFaST: An improved method for OTU assignment by generalising Swarm’s fastidious clustering approach.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2349-1

By:

Müller, Robert;
Nebel, Markus E.

Publication type:

Article

Priority-Lasso: a simple hierarchical approach to the prediction of clinical outcome using multi-omics data.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2344-6

By:

Klau, Simon;
Jurinovic, Vindi;
Hornung, Roman;
Herold, Tobias;
Boulesteix, Anne-Laure

Publication type:

Article

SuperNoder: a tool to discover over-represented modular structures in networks.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2350-8

By:

Dessì, Danilo;
Cirrone, Jacopo;
Recupero, Diego Reforgiato;
Shasha, Dennis

Publication type:

Article

Enhancer reprogramming in mammalian genomes.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2343-7

By:

Flores, Mario A.;
Ovcharenko, Ivan

Publication type:

Article

Linked open data-based framework for automatic biomedical ontology generation.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2339-3

By:

Alobaidi, Mazen;
Malik, Khalid Mahmood;
Sabra, Susan

Publication type:

Article

Identification of differentially expressed genes by means of outlier detection.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2318-8

By:

Irigoien, Itziar;
Arenas, Concepción

Publication type:

Article

An integrated strategy for identifying new targets and inferring the mechanism of action: taking rhein as an example.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2346-4

By:

Sun, Hao;
Shen, Yiting;
Luo, Guangwen;
Cai, Yuepiao;
Xiang, Zheng

Publication type:

Article

Classification based on extensions of LS-PLS using logistic regression: application to clinical and multiple genomic data.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2311-2

By:

Bazzoli, Caroline;
Lambert-Lacroix, Sophie

Publication type:

Article

Effective normalization for copy number variation in Hi-C data.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2256-5

By:

Servant, Nicolas;
Varoquaux, Nelle;
Heard, Edith;
Barillot, Emmanuel;
Vert, Jean-Philippe

Publication type:

Article

BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2319-7

By:

Heydari, Mahdi;
Miclotte, Giles;
Van de Peer, Yves;
Fostier, Jan

Publication type:

Article

Application of whole genome data for in silico evaluation of primers and probes routinely employed for the detection of viral species by RT-qPCR using dengue virus as a case study.

Published in:

2018

By:

Vanneste, Kevin;
Garlant, Linda;
Broeders, Sylvia;
Van Gucht, Steven;
Roosens, Nancy H.

Publication type:

Case Study

HebbPlot: an intelligent tool for learning and visualizing chromatin mark signatures.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2312-1

By:

Girgis, Hani Z.;
Velasco II, Alfredo;
Reyes, Zachary E.

Publication type:

Article

Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2320-1

By:

Rotimi, Adeola M.;
Pierneef, Rian;
Reva, Oleg N.

Publication type:

Article

Rapid and precise alignment of raw reads against redundant databases with KMA.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2336-6

By:

Clausen, Philip T. L. C.;
Aarestrup, Frank M.;
Lund, Ole

Publication type:

Article

PseUI: Pseudouridine sites identification based on RNA sequence information.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2321-0

By:

He, Jingjing;
Fang, Ting;
Zhang, Zizheng;
Huang, Bei;
Zhu, Xiaolei;
Xiong, Yi

Publication type:

Article

Clustering approaches for visual knowledge exploration in molecular interaction networks.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2314-z

By:

Ostaszewski, Marek;
Kieffer, Emmanuel;
Danoy, Grégoire;
Schneider, Reinhard;
Bouvry, Pascal

Publication type:

Article

RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2317-9

By:

Antczak, Maciej;
Zok, Tomasz;
Osowiecki, Maciej;
Popenda, Mariusz;
Adamiak, Ryszard W.;
Szachniuk, Marta

Publication type:

Article

bioSyntax: syntax highlighting for computational biology.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2315-y

By:

Babaian, Artem;
Ebou, Anicet;
Fegen, Alyssa;
Kam, Ho Yin;
Novakovsky, German E.;
Wong, Jasper;
Aïssi, Dylan;
Yao, Li

Publication type:

Article

Predicting overlapping protein complexes based on core-attachment and a local modularity structure.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2309-9

By:

Wang, Rongquan;
Liu, Guixia;
Wang, Caixia;
Su, Lingtao;
Sun, Liyan

Publication type:

Article

Rscreenorm: normalization of CRISPR and siRNA screen data for more reproducible hit selection.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2306-z

By:

Bachas, Costa;
Hodzic, Jasmina;
van der Mijn, Johannes C.;
Stoepker, Chantal;
Verheul, Henk M. W.;
Wolthuis, Rob M. F.;
Felley-Bosco, Emanuela;
van Wieringen, Wessel N.;
van Beusechem, Victor W.;
Brakenhoff, Ruud H.;
de Menezes, Renée X.

Publication type:

Article

Clustering of circular consensus sequences: accurate error correction and assembly of single molecule real-time reads from multiplexed amplicon libraries.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2293-0

By:

Francis, Felix;
Dumas, Michael D.;
Davis, Scott B.;
Wisser, Randall J.

Publication type:

Article

BALCONY: an R package for MSA and functional compartments of protein variability analysis.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2294-z

By:

Płuciennik, Alicja;
Stolarczyk, Michał;
Bzówka, Maria;
Raczyńska, Agata;
Magdziarz, Tomasz;
Góra, Artur

Publication type:

Article

Multiple model species selection for transcriptomics analysis of non-model organisms.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 9, p. 137, doi. 10.1186/s12859-018-2278-z

By:

Pai, Tun-Wen;
Li, Kuan-Hung;
Yang, Cing-Han;
Hu, Chin-Hwa;
Lin, Han-Jia;
Wang, Wen-Der;
Chen, Yet-Ran

Publication type:

Article

Predicting diabetic retinopathy and identifying interpretable biomedical features using machine learning algorithms.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 9, p. 195, doi. 10.1186/s12859-018-2277-0

By:

Tsao, Hsin-Yi;
Chan, Pei-Ying;
Su, Emily Chia-Yu

Publication type:

Article

Efficient computation of motif discovery on Intel Many Integrated Core (MIC) Architecture.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 9, p. 185, doi. 10.1186/s12859-018-2276-1

By:

Peng, Shaoliang;
Cheng, Minxia;
Huang, Kaiwen;
Cui, YingBo;
Zhang, Zhiqiang;
Guo, Runxin;
Zhang, Xiaoyu;
Yang, Shunyun;
Liao, Xiangke;
Lu, Yutong;
Zou, Quan;
Shi, Benyun

Publication type:

Article

Biomedical event extraction based on GRU integrating attention mechanism.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 9, p. 177, doi. 10.1186/s12859-018-2275-2

By:

Li, Lishuang;
Wan, Jia;
Zheng, Jieqiong;
Wang, Jian

Publication type:

Article

BMCMDA: a novel model for predicting human microbe-disease associations via binary matrix completion.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 9, p. 169, doi. 10.1186/s12859-018-2274-3

By:

Shi, Jian-Yu;
Huang, Hua;
Zhang, Yan-Ning;
Cao, Jiang-Bo;
Yiu, Siu-Ming

Publication type:

Article

A graph-based approach for proteoform identification and quantification using top-down homogeneous multiplexed tandem mass spectra.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 9, p. 161, doi. 10.1186/s12859-018-2273-4

By:

Zhu, Kaiyuan;
Liu, Xiaowen

Publication type:

Article

Big data analysis for evaluating bioinvasion risk.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 9, p. 151, doi. 10.1186/s12859-018-2272-5

By:

Wang, Shengling;
Wang, Chenyu;
Wang, Shenling;
Ma, Liran

Publication type:

Article

ConnectedAlign: a PPI network alignment method for identifying conserved protein complexes across multiple species.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 9, p. 129, doi. 10.1186/s12859-018-2271-6

By:

Gao, Jianliang;
Song, Bo;
Hu, Xiaohua;
Yan, Fengxia;
Wang, Jianxin

Publication type:

Article

Drug response prediction model using a hierarchical structural component modeling method.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 9, p. 117, doi. 10.1186/s12859-018-2270-7

By:

Kim, Sungtae;
Choi, Sungkyoung;
Yoon, Jung-Hwan;
Kim, Youngsoo;
Lee, Seungyeoun;
Park, Taesung

Publication type:

Article

On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 9, p. 105, doi. 10.1186/s12859-018-2269-0

By:

Kundu, Soumya;
Bansal, Mukul S.

Publication type:

Article

GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 9, p. 95, doi. 10.1186/s12859-018-2268-1

By:

Wang, Dan;
Wang, Lusheng

Publication type:

Article

DeepSort: deep convolutional networks for sorting haploid maize seeds.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 9, p. 85, doi. 10.1186/s12859-018-2267-2

By:

Veeramani, Balaji;
Raymond, John W.;
Chanda, Pritam

Publication type:

Article

miREM: an expectation-maximization approach for prioritizing miRNAs associated with gene-set.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2292-1

By:

Abdul Hadi, Luqman Hakim;
Quy Xiao Xuan Lin;
Tri Tran Minh;
Loh, Marie;
Ng, Hong Kiat;
Salim, Agus;
Soong, Richie;
Benoukraf, Touati

Publication type:

Article

REHUNT: a reliable and open source package for restriction enzyme hunting.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2168-4

By:

Cheng, Yu-Huei;
Liaw, Jiun-Jian;
Kuo, Che-Nan

Publication type:

Article

Multi-class segmentation of neuronal structures in electron microscopy images.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2305-0

By:

Cetina, Kendrick;
Buenaposada, José M.;
Baumela, Luis

Publication type:

Article

BART: bioinformatics array research tool.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2308-x

By:

Amaral, Maria Luisa;
Erikson, Galina A.;
Shokhirev, Maxim N.

Publication type:

Article

PIPEBAR and OverlapPER: tools for a fast and accurate DNA barcoding analysis and paired-end assembly.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2307-y

By:

Nunes, Gisele Lopes;
de Lima, Talvâne Glauber Lopes;
Oliveira, Renato Renison Moreira;
Alves, Ronnie;
Oliveira, Guilherme

Publication type:

Article

PRS-on-Spark (PRSoS): a novel, efficient and flexible approach for generating polygenic risk scores.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2289-9

By:

Chen, Lawrence M.;
Yao, Nelson;
Garg, Elika;
Zhu, Yuecai;
Nguyen, Thao T. T.;
Pokhvisneva, Irina;
Hari Dass, Shantala A.;
Unternaehrer, Eva;
Gaudreau, Hélène;
Silveira, Patricia P.;
O’Donnell, Kieran J.;
Meaney, Michael J.;
Forest, Marie;
Greenwood, Celia M. T.;
McEwen, Lisa M.;
MacIsaac, Julia L.;
Kobor, Michael S.

Publication type:

Article

Fusion of encoder-decoder deep networks improves delineation of multiple nuclear phenotypes.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2285-0

By:

Khoshdeli, Mina;
Winkelmaier, Garrett;
Parvin, Bahram

Publication type:

Article

CircPrimer: a software for annotating circRNAs and determining the specificity of circRNA primers.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2304-1

By:

Zhong, Shanliang;
Wang, Jinyan;
Zhang, Qian;
Xu, Hanzi;
Feng, Jifeng

Publication type:

Article