Houxiang Zhu
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View article: Arsenic regulates ALKBH1 abundance and substrate specificity to promote translation and tumorigenicity
Arsenic regulates ALKBH1 abundance and substrate specificity to promote translation and tumorigenicity Open
The mechanisms that underlie arsenic tumorigenicity remain incompletely understood. Here, we show that arsenic regulates the abundance and the demethylase activity of ALKBH1, which, in turn, promotes arsenic-induced skin tumorigenesis. At …
View article: Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages
Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages Open
View article: 8066 Compensatory Signatures of Islet Cells That Protect Obese Humans From Diabetes
8066 Compensatory Signatures of Islet Cells That Protect Obese Humans From Diabetes Open
Disclosure: H. Kim: None. Y. Li: None. H. Zhu: None. K. El Jellas: None. N. Shukla: None. Z. Ren: None. K. Fukuda: None. M. Chen: None. R. Kulkarni: Advisory Board Member; Self; Novo Nordisk, Inversago, Biomea, REDD. The increasing prevale…
View article: LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA
LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA Open
View article: Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages
Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages Open
Breast cancer is a heterogeneous disease, and treatment is guided by biomarker profiles representing distinct molecular subtypes. Breast cancer arises from the breast ductal epithelium, and experimental data suggests breast cancer subtypes…
View article: Author Correction: Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma
Author Correction: Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma Open
View article: Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma
Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma Open
Identifying tumor-cell-specific markers and elucidating their epigenetic regulation and spatial heterogeneity provides mechanistic insights into cancer etiology. Here, we perform snRNA-seq and snATAC-seq in 34 and 28 human clear cell renal…
View article: Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer
Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer Open
View article: Chromatin accessibility shapes tumor architecture and microenvironment in clear cell renal cell carcinoma
Chromatin accessibility shapes tumor architecture and microenvironment in clear cell renal cell carcinoma Open
The molecular landscape of clear cell renal cell carcinoma (ccRCC) has been annotated by a number of large-scale sequencing studies, complemented by recent proteomics efforts. However, these bulk analyses are limited by the diverse cell po…
View article: Pollock: fishing for cell states
Pollock: fishing for cell states Open
Motivation The use of single-cell methods is expanding at an ever-increasing rate. While there are established algorithms that address cell classification, they are limited in terms of cross platform compatibility, reliance on the availabi…
View article: Proteogenomic characterization of pancreatic ductal adenocarcinoma
Proteogenomic characterization of pancreatic ductal adenocarcinoma Open
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 1…
View article: A proteogenomic portrait of lung squamous cell carcinoma
A proteogenomic portrait of lung squamous cell carcinoma Open
View article: Proteogenomic and metabolomic characterization of human glioblastoma
Proteogenomic and metabolomic characterization of human glioblastoma Open
View article: Spatial drivers and pre-cancer populations collaborate with the microenvironment in untreated and chemo-resistant pancreatic cancer
Spatial drivers and pre-cancer populations collaborate with the microenvironment in untreated and chemo-resistant pancreatic cancer Open
SUMMARY Pancreatic Ductal Adenocarcinoma (PDAC) is a lethal disease with limited treatment options and poor survival. We studied 73 samples from 21 patients (7 treatment-naïve and 14 treated with neoadjuvant regimens), analyzing distinct s…
View article: CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity
CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity Open
The CRISPR-Cpf1 system has been successfully applied in genome editing. However, target efficiency of the CRISPR-Cpf1 system varies among different gRNA sequences. We reanalyzed the published CRISPR-Cpf1 gRNAs data and found many sequence …
View article: CRISPR-RT: a web application for designing CRISPR-C2c2 crRNA with improved target specificity
CRISPR-RT: a web application for designing CRISPR-C2c2 crRNA with improved target specificity Open
Summary CRISPR-Cas systems have been successfully applied in genome editing. Recently, the CRISPR-C2c2 system has been reported as a tool for RNA editing. Here we describe CRISPR-RT (CRISPR RNA-Targeting), the first web application to help…
View article: CRISPR-RT: A web service for designing CRISPR-C2c2 crRNA with improved target specificity
CRISPR-RT: A web service for designing CRISPR-C2c2 crRNA with improved target specificity Open
CRISPR-Cas systems have been successfully applied in genome editing. Recently, the CRISPR-C2c2 system has been reported as a tool for RNA editing. Here we describe CRISPR-RT (CRISPR R NA- T argeting), the first web service to help biologis…
View article: CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization
CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization Open
The CRISPR system holds much promise for successful genome engineering, but therapeutic, industrial and research applications will place high demand on improving the specificity and efficiency of this tool. CT-Finder ( http://bioinfolab.mi…