Integrated multi-omics profiling yields a clinically relevant molecular classification for esophageal squamous cell carcinoma DOI Creative Commons
Zhihua Liu, Yahui Zhao,

Pengzhou Kong

et al.

Cancer Cell, Journal Year: 2022, Volume and Issue: 41(1), P. 181 - 195.e9

Published: Dec. 29, 2022

Language: Английский

A genome-wide association study of shared risk across psychiatric disorders implicates gene regulation during fetal neurodevelopment DOI
Andrew J. Schork, Hyejung Won, Vivek Appadurai

et al.

Nature Neuroscience, Journal Year: 2019, Volume and Issue: 22(3), P. 353 - 361

Published: Jan. 28, 2019

Language: Английский

Citations

201
UCSC Genome Browser enters 20th year DOI Creative Commons
Christopher M. Lee,

Galt P Barber,

Jonathan D. Casper

et al.

Nucleic Acids Research, Journal Year: 2019, Volume and Issue: unknown

Published: Oct. 25, 2019

The University of California Santa Cruz Genome Browser website (https://genome.ucsc.edu) enters its 20th year providing high-quality genomics data visualization and genome annotations to the research community. In past year, we have added a new option our web BLAT tool that allows search against all genomes, single-cell expression viewer (https://cells.ucsc.edu), 'lollipop' plot display mode for high-density variation data, RESTful API extraction custom-track backup feature. New datasets include Tabula Muris GeneHancer regulatory annotations, Cancer Atlas Pan-Cancer variants, Reference Consortium Patch sequences, ENCODE transcription factor binding site peaks clusters, Database Genomic Variants Gold Standard Variants, Genomenon Mastermind variants three multi-species alignment tracks.

Language: Английский

Citations

195
Mendelian randomization for studying the effects of perturbing drug targets DOI Creative Commons
Dipender Gill, Marios K. Georgakis, Venexia Walker

et al.

Wellcome Open Research, Journal Year: 2021, Volume and Issue: 6, P. 16 - 16

Published: Jan. 28, 2021

Drugs whose targets have genetic evidence to support efficacy and safety are more likely be approved after clinical development. In this paper, we provide an overview of how natural sequence variation in the genes that encode drug can used Mendelian randomization analyses offer insight into mechanism-based adverse effects. Large databases summary level association data increasingly available leveraged identify validate variants serve as proxies for target perturbation. As with all empirical research, has limitations including confounding, its consideration lifelong effects, issues related heterogeneity across different tissues populations. When appropriately applied, provides a useful framework using population improve success rates development pipeline.

Language: Английский

Citations

177
Dissecting spatial heterogeneity and the immune-evasion mechanism of CTCs by single-cell RNA-seq in hepatocellular carcinoma DOI Creative Commons
Yun‐Fan Sun, Liang Wu, Shiping Liu

et al.

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: July 2, 2021

Little is known about the transcriptomic plasticity and adaptive mechanisms of circulating tumor cells (CTCs) during hematogeneous dissemination. Here we interrogate transcriptome 113 single CTCs from 4 different vascular sites, including hepatic vein (HV), peripheral artery (PA), (PV) portal (PoV) using single-cell full-length RNA sequencing in hepatocellular carcinoma (HCC) patients. We reveal that transcriptional dynamics were associated with stress response, cell cycle immune-evasion signaling transportation. Besides, identify chemokine CCL5 as an important mediator for CTC immune evasion. Mechanistically, overexpression transcriptionally regulated by p38-MAX signaling, which recruites regulatory T (Tregs) to facilitate escape metastatic seeding CTCs. Collectively, our results a previously unappreciated spatial heterogeneity immune-escape mechanism CTC, may aid designing new anti-metastasis therapeutic strategies HCC.

Language: Английский

Citations

162
The Role of Natural Products as Sources of Therapeutic Agents for Innovative Drug Discovery DOI
Kevin Dzobo

Elsevier eBooks, Journal Year: 2021, Volume and Issue: unknown, P. 408 - 422

Published: April 2, 2021

Language: Английский

Citations

160
Genomic architecture of autism from comprehensive whole-genome sequence annotation DOI Creative Commons
Brett Trost, Bhooma Thiruvahindrapuram,

Ada J. S. Chan

et al.

Cell, Journal Year: 2022, Volume and Issue: 185(23), P. 4409 - 4427.e18

Published: Nov. 1, 2022

Language: Английский

Citations

155
Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex DOI Creative Commons
Ana Uzquiano, Amanda J. Kedaigle, Martina Pigoni

et al.

Cell, Journal Year: 2022, Volume and Issue: 185(20), P. 3770 - 3788.e27

Published: Sept. 1, 2022

Language: Английский

Citations

149
Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs DOI Creative Commons
Christ Leemans,

Marloes C.H. van der Zwalm,

Laura Brueckner

et al.

Cell, Journal Year: 2019, Volume and Issue: 177(4), P. 852 - 864.e14

Published: April 11, 2019

Language: Английский

Citations

148
Recognition and inhibition of SARS-CoV-2 by humoral innate immunity pattern recognition molecules DOI Open Access
Matteo Stravalaci, Isabel Pagani, Elvezia Maria Paraboschi

et al.

Nature Immunology, Journal Year: 2022, Volume and Issue: 23(2), P. 275 - 286

Published: Jan. 31, 2022

Language: Английский

Citations

137
Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity DOI
Steven Gazal, Omer Weissbrod, Farhad Hormozdiari

et al.

Nature Genetics, Journal Year: 2022, Volume and Issue: 54(6), P. 827 - 836

Published: June 1, 2022

Language: Английский

Citations

125