RNA sequencing: new technologies and applications in cancer research

M Hong, S Tao, L Zhang, LT Diao, X Huang… - Journal of hematology & …, 2020 - Springer
Over the past few decades, RNA sequencing has significantly progressed, becoming a
paramount approach for transcriptome profiling. The revolution from bulk RNA sequencing …

Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease

M Piwecka, N Rajewsky, A Rybak-Wolf - Nature Reviews Neurology, 2023 - nature.com
In the past decade, single-cell technologies have proliferated and improved from their
technically challenging beginnings to become common laboratory methods capable of …

Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species

N Li, Q He, J Wang, B Wang, J Zhao, S Huang… - Nature Genetics, 2023 - nature.com
Effective utilization of wild relatives is key to overcoming challenges in genetic improvement
of cultivated tomato, which has a narrow genetic basis; however, current efforts to decipher …

The m6A reader IGF2BP2 regulates glutamine metabolism and represents a therapeutic target in acute myeloid leukemia

H Weng, F Huang, Z Yu, Z Chen, E Prince, Y Kang… - Cancer Cell, 2022 - cell.com
Summary N 6-Methyladenosine (m 6 A) modification and its modulators play critical roles
and show promise as therapeutic targets in human cancers, including acute myeloid …

A transcriptional regulator that boosts grain yields and shortens the growth duration of rice

S Wei, X Li, Z Lu, H Zhang, X Ye, Y Zhou, J Li, Y Yan… - Science, 2022 - science.org
Complex biological processes such as plant growth and development are often under the
control of transcription factors that regulate the expression of large sets of genes and …

Contribution of ferroptosis and GPX4's dual functions to osteoarthritis progression

Y Miao, Y Chen, F Xue, K Liu, B Zhu, J Gao, J Yin… - …, 2022 - thelancet.com
Background Osteoarthritis (OA) is the most common joint disease and is the leading cause
of chronic disability among older people. Chondrocyte death and extracellular matrix (ECM) …

WormBase in 2022—data, processes, and tools for analyzing Caenorhabditis elegans

P Davis, M Zarowiecki, V Arnaboldi, A Becerra… - Genetics, 2022 - academic.oup.com
Abstract WormBase (www. wormbase. org) is the central repository for the genetics and
genomics of the nematode Caenorhabditis elegans. We provide the research community …

Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

P Qin, H Lu, H Du, H Wang, W Chen, Z Chen, Q He… - Cell, 2021 - cell.com
Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to
crop evolution, domestication, and improvement. Here, we assembled 31 high-quality …

[HTML][HTML] A route to de novo domestication of wild allotetraploid rice

H Yu, T Lin, X Meng, H Du, J Zhang, G Liu, M Chen… - Cell, 2021 - cell.com
Cultivated rice varieties are all diploid, and polyploidization of rice has long been desired
because of its advantages in genome buffering, vigorousness, and environmental …

TPM, FPKM, or normalized counts? A comparative study of quantification measures for the analysis of RNA-seq data from the NCI patient-derived models repository

Y Zhao, MC Li, MM Konaté, L Chen, B Das… - Journal of translational …, 2021 - Springer
Background In order to correctly decode phenotypic information from RNA-sequencing
(RNA-seq) data, careful selection of the RNA-seq quantification measure is critical for inter …