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Deep Learning–Based Identification of Tissue of Origin for Carcinomas of Unknown Primary Using MicroRNA Expression: Algorithm Development and Validation

Deep Learning–Based Identification of Tissue of Origin for Carcinomas of Unknown Primary Using MicroRNA Expression: Algorithm Development and Validation

Cup AI Dx [20] used m RNA gene expression data from The Cancer Genome Atlas (TCGA) data set to train a network based on the popular inception model [22] to identify the TOO, achieving an accuracy of 96.7% on a validation set of 354 TCGA metastatic samples. The TOD-CUP method [21] addressed the variation in m RNA platforms and used a gene expression rank–based majority vote algorithm to achieve an overall accuracy of 94%.

Ananya Raghu, Anisha Raghu, Jillian F Wise

JMIR Bioinform Biotech 2024;5:e56538

Authors’ Response to Peer Reviews of “Establishment of a Novel Fetal Ovine Heart Cell Line by Spontaneous Cell Fusion: Experimental Study”

Authors’ Response to Peer Reviews of “Establishment of a Novel Fetal Ovine Heart Cell Line by Spontaneous Cell Fusion: Experimental Study”

Response: In collaboration with national or international research centers, we will look forward to studying: The whole genome sequence and the mutation events after cell fusion that led to immortalization, Comparative study of the mitochondria genome of FOH-SA and Vero cell lines, and The molecular events of spontaneous cell fusion.

Khalid Suleiman, Mutaib Aljulidan, Gamaleldin Hussein, Habib Alkhalaf

JMIRx Bio 2024;2:e62911

Investigating the Effects of Hyperbaric Oxygen Treatment in Necrotizing Soft Tissue Infection With Transcriptomics and Machine Learning (the HBOmic Study): Protocol for a Prospective Cohort Study With Data Validation

Investigating the Effects of Hyperbaric Oxygen Treatment in Necrotizing Soft Tissue Infection With Transcriptomics and Machine Learning (the HBOmic Study): Protocol for a Prospective Cohort Study With Data Validation

It is not surprising that the human genome holds variants related to infection, given that infectious diseases have been the largest cause of death during our evolution [26]. The multifaceted, heterogeneous nature of disease may explain the lack of success with identification of biomarkers.

Julie Vinkel, Leonor Rib, Alfonso Buil, Morten Hedetoft, Ole Hyldegaard

JMIR Res Protoc 2022;11(11):e39252

Identification of a Novel c.3080delC JAG1 Gene Mutation Associated With Alagille Syndrome: Whole Exome Sequencing

Identification of a Novel c.3080delC JAG1 Gene Mutation Associated With Alagille Syndrome: Whole Exome Sequencing

Next-generation sequencing analysis, including either genome or exome sequences, have been recommended for the molecular diagnosis of neonatal or infantile intrahepatic cholestasis [22]. Whole exome sequencing (WES) allows sequencing of all expressed genes in the genome, which is substantial, considering the protein-coding regions cover approximately 85% of human disease-causing mutations [27]. In this study, using WES, we identified a novel JAG1 mutation associated with early onset of Alagille syndrome.

Deepak Panwar, Vandana Lal, Atul Thatai

JMIR Bioinform Biotech 2022;3(1):e33946

The Easy-to-Use SARS-CoV-2 Assembler for Genome Sequencing: Development Study

The Easy-to-Use SARS-CoV-2 Assembler for Genome Sequencing: Development Study

In the current COVID-19 epidemic, more than 6 million full genome sequences of SARS-Co V-2 have been deposited in publicly accessible databases in the arc of 1 year (ie, GISAID) [6,7]. SARS-Co V-2 genome surveillance on a global scale is permitting real-time analysis of the outbreak, with a direct impact on the public health response.

Martina Rueca, Emanuela Giombini, Francesco Messina, Barbara Bartolini, Antonino Di Caro, Maria Rosaria Capobianchi, Cesare EM Gruber

JMIR Bioinform Biotech 2022;3(1):e31536

Exploring the Use of Genomic and Routinely Collected Data: Narrative Literature Review and Interview Study

Exploring the Use of Genomic and Routinely Collected Data: Narrative Literature Review and Interview Study

Since 2001, when the Human Genome Project mapped and sequenced virtually every gene in the human genome, genetic sequencing technology has advanced rapidly in both the public and private domains. Next-generation sequencing costs have plummeted by almost 100%, and research opportunities have grown exponentially as a result [1].

Helen Ruth Daniels, Kerina Helen Jones, Sharon Heys, David Vincent Ford

J Med Internet Res 2021;23(9):e15739