Results 61 to 70 of about 436,281 (168)

Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single‐cell RNA sequencing analyses

Quantitative Biology
The transcriptome, the complete set of RNA molecules within a cell, plays a critical role in regulating physiological processes. The advent of RNA sequencing (RNA‐seq) facilitated by Next Generation Sequencing (NGS) technologies, has revolutionized ...
Jorge A. Tzec‐Interián, Daianna González‐Padilla, Elsa B. Góngora‐Castillo   +2 more
doaj   +1 more source

Procrustes is a machine-learning approach that removes cross-platform batch effects from clinical RNA sequencing data

Communications Biology
With the increased use of gene expression profiling for personalized oncology, optimized RNA sequencing (RNA-seq) protocols and algorithms are necessary to provide comparable expression measurements between exome capture (EC)-based and poly-A RNA-seq ...
Nikita Kotlov, Kirill Shaposhnikov, Cagdas Tazearslan, Madison Chasse, Artur Baisangurov, Svetlana Podsvirova, Dawn Fernandez, Mary Abdou, Leznath Kaneunyenye, Kelley Morgan, Ilya Cheremushkin, Pavel Zemskiy, Maxim Chelushkin, Maria Sorokina, Ekaterina Belova, Svetlana Khorkova, Yaroslav Lozinsky, Katerina Nuzhdina, Elena Vasileva, Dmitry Kravchenko, Kushal Suryamohan, Krystle Nomie, John Curran, Nathan Fowler, Alexander Bagaev   +24 more
doaj   +1 more source

sNucConv: A bulk RNA-seq deconvolution method trained on single-nucleus RNA-seq data to estimate cell-type composition of human adipose tissues

iScience
Summary: Deconvolution algorithms mostly rely on single-cell RNA-sequencing (scRNA-seq) data applied onto bulk RNA-sequencing (bulk RNA-seq) to estimate tissues’ cell-type composition, with performance accuracy validated on deposited databases.
Gil Sorek, Yulia Haim, Vered Chalifa-Caspi, Or Lazarescu, Maya Ziv-Agam, Tobias Hagemann, Pamela Arielle Nono Nankam, Matthias Blüher, Idit F. Liberty, Oleg Dukhno, Ivan Kukeev, Esti Yeger-Lotem, Assaf Rudich, Liron Levin   +13 more
doaj   +1 more source

Comparison of gene fusion detection algorithms reveals frequently overlooked driver fusions in hematologic malignancies

npj Precision Oncology
Accurate detection of driver gene fusions is essential for the diagnosis, treatment, and prognostic prediction of hematologic malignancies. Despite increasing reliance on RNA sequencing (RNA-seq) for fusion detection, its algorithms have not been ...
Zen Tamura, Yuki Saito, Yasunori Kogure, Yuji Oshikawa-Kumade, Suguru Fukuhara, Sumito Shingaki, Hirokazu Kariyazono, Yoshiya Kikukawa, Yuta Ito, Kota Mizuno, Yuichi Shiraishi, Kotoe Katayama, Seiya Imoto, Koji Izutsu, Koichi Murakami, Junji Koya, Keisuke Kataoka   +16 more
doaj   +1 more source

Introduction to RNA-seq

, 2015
RNA-seq is a useful sequencing-based technology for identifying a snapshot of the transcriptional output from the cell. It has been used to estimate gene expression levels and estimate the impact of different treatments on gene expression. A new generation of methods, based upon RNA-seq is gaining exciting insights into RNA:RNA interactions, RNA ...
openaire   +1 more source

Integrated RNA-seq and small RNA-seq profiling reveals tissue-associated transcriptional programs and candidate miRNA-mRNA relationships across tea floral tissues. [PDF]

Front Plant Sci
Xing F, Sun F, Xie Q, Li T, Yang J, Heng S, Xu L, Zhang W, Mao G.   +8 more
europepmc   +1 more source

Identification of Novel Transcriptional Alleles in Primary Prostate Cancer Cells and Cancer Stem Cells by Bulk RNA-Seq and Single-Cell RNA-Seq Analyses. [PDF]

Biomolecules
Hu WY, Lu R, Maienschein-Cline M, Xu D, Afradiasbagharani P, Birch LA, Nonn L, Kajdacsy-Balla A, Shioda T, Prins GS.   +9 more
europepmc   +1 more source

ARACRA: Automated RNA-seq Analysis for Chemical Risk Assessment. [PDF]

Comput Struct Biotechnol J
Sharma S, Kumar S, Biosca-Brull J, Deepika D, Kumar V.   +4 more
europepmc   +1 more source

Reporting and representation of population descriptors in public RNA-seq databases. [PDF]

Cell Genom
Gallego Romero I, Rodenberg G, Arner AM, Li L, Beasley IJ, Rossow R, Ryan N, Wang S, Lea AJ.   +8 more
europepmc   +1 more source

The circulating metatranscriptome in acute myeloid leukemia patients: an RNA-seq reanalysis. [PDF]

Front Microbiomes
Nguyen ADD, Kern R, Dombrovski T, LaFramboise T.   +3 more
europepmc   +1 more source