BMC Bioinformatics
Papers 9340
1 page of 934 pages (9,340 results)
Published on Dec 1, 2019in BMC Bioinformatics2.51
Christine Ng1
Estimated H-index: 1
(OICR: Ontario Institute for Cancer Research),
Jeffrey Green2
Estimated H-index: 2
(OICR: Ontario Institute for Cancer Research)
+ 36 AuthorsMarco A. Albuquerque2
Estimated H-index: 2
(OICR: Ontario Institute for Cancer Research)
We introduce BPG, a framework for generating publication-quality, highly-customizable plots in the R statistical environment. This open-source package includes multiple methods of displaying high-dimensional datasets and facilitates generation of complex multi-panel figures, making it suitable for complex datasets. A web-based interactive tool allows online figure customization, from which R code can be downloaded for integration with computational pipelines. BPG provides a new approach for link...
Published on Dec 1, 2019in BMC Bioinformatics2.51
Jinghang Gu (Soochow University (Suzhou)), Fuqing Sun1
Estimated H-index: 1
(Capital Medical University)
+ 1 AuthorsGuodong Zhou29
Estimated H-index: 29
(Soochow University (Suzhou))
Automatically understanding chemical-disease relations (CDRs) is crucial in various areas of biomedical research and health care. Supervised machine learning provides a feasible solution to automatically extract relations between biomedical entities from scientific literature, its success, however, heavily depends on large-scale biomedical corpora manually annotated with intensive labor and tremendous investment. We present an attention-based distant supervision paradigm for the BioCreative-V CD...
Published on Dec 1, 2019in BMC Bioinformatics2.51
Zheng Gao (IU: Indiana University Bloomington), Gang Fu (Microsoft)+ 8 AuthorsYing Ding38
Estimated H-index: 38
(IU: Indiana University Bloomington)
Representation learning provides new and powerful graph analytical approaches and tools for the highly valued data science challenge of mining knowledge graphs. Since previous graph analytical methods have mostly focused on homogeneous graphs, an important current challenge is extending this methodology for richly heterogeneous graphs and knowledge domains. The biomedical sciences are such a domain, reflecting the complexity of biology, with entities such as genes, proteins, drugs, diseases, and...
Published on Jan 9, 2019in BMC Bioinformatics2.51
Morteza H. Chalabi (University of Southern Denmark), Vasileios Tsiamis (University of Southern Denmark)+ 2 AuthorsVeit Schwämmle23
Estimated H-index: 23
(University of Southern Denmark)
Translational and post-translational control mechanisms in the cell result in widely observable differences between measured gene transcription and protein abundances. Herein, protein complexes are among the most tightly controlled entities by selective degradation of their individual proteins. They furthermore act as control hubs that regulate highly important processes in the cell and exhibit a high functional diversity due to their ability to change their composition and their structure. Bett...
Published on Dec 1, 2019in BMC Bioinformatics2.51
Bie Verbist7
Estimated H-index: 7
(Janssen Pharmaceutica),
Eva Adriaensen + 6 AuthorsHans De Wolf4
Estimated H-index: 4
(Janssen Pharmaceutica)
Background The QuantiGene® Plex 2.0 platform (ThermoFisher Scientific) combines bDNA with the Luminex/xMAP magnetic bead capturing technology to assess differential gene expression in a compound exposure setting. This technology allows multiplexing in a single well of a 96 or 384 multi-well plate and can thus be used in high throughput drug discovery mode. Data interpretation follows a three-step normalization/transformation flow in which raw median fluorescent gene signals are transformed to fo...
Published in BMC Bioinformatics2.51
Akanksha Srivastava2
Estimated H-index: 2
(UWA: University of Western Australia),
Yuliya V. Karpievitch13
Estimated H-index: 13
(UWA: University of Western Australia)
+ -3 AuthorsRyan Lister36
Estimated H-index: 36
(UWA: University of Western Australia)
The development of whole genome bisulfite sequencing has made it possible to identify methylation differences at single base resolution throughout an entire genome. However, a persistent challenge in DNA methylome analysis is the accurate identification of differentially methylated regions (DMRs) between samples. Sensitive and specific identification of DMRs among different conditions requires accurate and efficient algorithms, and while various tools have been developed to tackle this problem, ...
Published in BMC Bioinformatics2.51
Ruochen Yang (SC: University of Southern California), Xi Chen (UIUC: University of Illinois at Urbana–Champaign), Idoia Ochoa6
Estimated H-index: 6
(UIUC: University of Illinois at Urbana–Champaign)
Mass Spectrometry (MS) is a widely used technique in biology research, and has become key in proteomics and metabolomics analyses. As a result, the amount of MS data has significantly increased in recent years. For example, the MS repository MassIVE contains more than 123TB of data. Somehow surprisingly, these data are stored uncompressed, hence incurring a significant storage cost. Efficient representation of these data is therefore paramount to lessen the burden of storage and facilitate its d...
Published on Jan 18, 2019in BMC Bioinformatics2.51
Jingrong Zhang2
Estimated H-index: 2
(CAS: Chinese Academy of Sciences),
Zihao Wang2
Estimated H-index: 2
(CAS: Chinese Academy of Sciences)
+ 4 AuthorsFa Zhang11
Estimated H-index: 11
(CAS: Chinese Academy of Sciences)
Background Cryo-electron microscopy (cryo-EM) has become a widely used tool for determining the structures of proteins and macromolecular complexes. To acquire the input for single-particle cryo-EM reconstruction, researchers must select hundreds of thousands of particles from micrographs. As the signal-to-noise ratio (SNR) of micrographs is extremely low, the performance of automated particle-selection methods is still unable to meet research requirements. To free researchers from this laboriou...
Published on Jan 11, 2019in BMC Bioinformatics2.51
Hezha Hassan (Bielefeld University), Siba Shanak2
Estimated H-index: 2
(Arab American University of Jenin)
Gene Ontology (GO) is a useful resource of controlled vocabulary that provides information about annotated genes. Based on such resource, finding the biological function is useful for biologists to come up with different hypotheses and help further investigations of an experiment. The biological function for desired genes and gene associations is picked up from a randomly chosen list or through the analysis of differential gene expression. Many tools have been developed to utilize GO knowledge a...
Published on Mar 6, 2019in BMC Bioinformatics2.51
Fuyi Li7
Estimated H-index: 7
Yang Zhang50
Estimated H-index: 50
+ 5 AuthorsSong Jiangning27
Estimated H-index: 27
Background As an important type of post-translational modification (PTM), protein glycosylation plays a crucial role in protein stability and protein function. The abundance and ubiquity of protein glycosylation across three domains of life involving Eukarya, Bacteria and Archaea demonstrate its roles in regulating a variety of signalling and metabolic pathways. Mutations on and in the proximity of glycosylation sites are highly associated with human diseases. Accordingly, accurate prediction of...