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Bioinformatics publications
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Stonin1 (STON1) is an endocytic protein but its role in cancer remains unclear. Here, we investigated the immune role of STON1 in kidney renal clear cell carcinoma (KIRC). We undertook bioinformatics analyses of the expression and clinical significance of STON1 in KIRC through a series of public databases, and the role of STON1 in the tumor microenvironment and the predictive value for immunotherapy and targeted treatment in KIRC were identified with R packages.
18p
vischultz
20-10-2023
3
1
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Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. We describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research.
9p
visteverogers
24-06-2023
8
2
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Biology has entered the era of big data with the advent of high-throughput omics technologies. Biological databases provide public access to petabytes of data and information facilitating knowledge discovery.
19p
vitzuyu2711
29-09-2021
12
2
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Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantially reduce the amount of culturing needed before a high quality genome can be recovered.
18p
vilichoo2711
23-06-2021
12
1
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LINC01116 is a recently identified oncogenic lncRNA in glioma. Diferential expression analysis using the public gene expression analysis tool GEPIA revealed the upregulation of LINC01116 in lung cancer. We studied the functions of LINC01116 in small cell lung cancer (SCLC).
6p
vimichigan2711
26-03-2021
12
2
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Independent data sources can be used to augment post-marketing drug safety signal detection. The vast amount of publicly available biomedical literature contains rich side effect information for drugs at all clinical stages.
10p
vikentucky2711
26-11-2020
8
1
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The scientific literature contains millions of microbial gene identifiers within the full text and tables, but these annotations rarely get incorporated into public sequence databases. We propose to utilize the Open Access (OA) subset of PubMed Central (PMC) as a gene annotation database and have developed an R package called pmcXML to automatically mine and extract locus tags from full text, tables and supplements.
8p
vikentucky2711
26-11-2020
15
0
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Mandatory deposit of raw microarray data files for public access, prior to study publication, provides significant opportunities to conduct new bioinformatics analyses within and across multiple datasets.
11p
vikentucky2711
26-11-2020
11
0
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Accurate somatic mutation-calling is essential for insightful mutation analyses in cancer studies. Several mutation-callers are publicly available and more are likely to appear. Nonetheless, mutation-calling is still challenging and there is unlikely to be one established caller that systematically outperforms all others.
8p
vikentucky2711
26-11-2020
5
1
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Bacterial pathogenicity represents a major public health concern worldwide. Secretion systems are a key component of bacterial pathogenicity, as they provide the means for bacterial proteins to penetrate host-cell membranes and insert themselves directly into the host cells’ cytosol.
9p
vikentucky2711
26-11-2020
7
0
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Emerging viral diseases, most of which are caused by the transmission of viruses from animals to humans, pose a threat to public health. Discovering pathogenic viruses through surveillance is the key to preparedness for this potential threat.
9p
vikentucky2711
26-11-2020
9
1
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Text mining is increasingly used in the biomedical domain because of its ability to automatically gather information from large amount of scientific articles. One important task in biomedical text mining is relation extraction, which aims to identify designated relations among biological entities reported in literature.
18p
vikentucky2711
26-11-2020
5
1
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Meta-analysis has become a popular approach for high-throughput genomic data analysis because it often can significantly increase power to detect biological signals or patterns in datasets. However, when using public-available databases for meta-analysis, duplication of samples is an often encountered problem, especially for gene expression data.
3p
vikentucky2711
26-11-2020
12
1
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The growing wealth of public available gene expression data has made the systemic studies of how genes interact in a cell become more feasible. Liquid association (LA) describes the extent to which coexpression of two genes may vary based on the expression level of a third gene (the controller gene).
8p
vikentucky2711
26-11-2020
9
1
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This article demonstrates the adaptation of BitTorrent to private collaboration networks in an authenticated, authorized and encrypted manner while retaining the same characteristics of standard BitTorrent.
6p
vikentucky2711
26-11-2020
8
1
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Current biomedical research needs to leverage and exploit the large amount of information reported in scientific publications. Automated text mining approaches, in particular those aimed at finding relationships between entities, are key for identification of actionable knowledge from free text repositories.
17p
vikentucky2711
26-11-2020
12
2
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Quantifying gene expression by RNA-Seq has several advantages over microarrays, including greater dynamic range and gene expression estimates on an absolute, rather than a relative scale. Nevertheless, microarrays remain in widespread use, demonstrated by the ever-growing numbers of samples deposited in public repositories.
11p
vikentucky2711
24-11-2020
3
1
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Genomic data production is at its highest level and continues to increase, making available novel primary data and existing public data to researchers for exploration. Here we explore the consequences of “batch” correction for biological discovery in two publicly available expression datasets.
10p
vioklahoma2711
19-11-2020
7
2
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The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, which makes now C. gigas becoming a model organism among lophotrochozoans, the under-described sister clade of ecdysozoans within protostomes.
12p
vioklahoma2711
19-11-2020
8
1
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The Cancer Genome Atlas (TCGA) is a pool of molecular data sets publicly accessible and freely available to cancer researchers anywhere around the world. However, wide spread use is limited since an advanced knowledge of statistics and statistical software is required.
7p
vioklahoma2711
19-11-2020
9
2
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