Nature Search

The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies

Leming Shi
Wendell Jones
Weida Tong
ResearchOpen Access03 Jul 2007
Nature Precedings

P: 1
The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies

Leming Shi
Wendell Jones
Weida Tong
ResearchOpen Access02 Jul 2007
Nature Precedings

P: 1
Point defects in metal halide perovskites

Point defects can have a critical influence on carrier dynamics and ion migration in metal halide perovskites. This Review surveys recent understandings of point defects and discusses new insights into defect tolerance in these materials.

Nuo Xu
Xinrui Qi
Zhigang Zou
Reviews18 Aug 2025
Nature Reviews Physics

Volume: 7, P: 554-564
Author Correction: Engineering antiviral immune-like systems for autonomous virus detection and inhibition in mice

Yidan Wang
Ying Xu
Haifeng Ye
Amendments and CorrectionsOpen Access05 Jul 2023
Nature Communications

Volume: 14, P: 1
Synergistic immunotherapy of glioblastoma by dual targeting of IL-6 and CD40

Glioblastomas are generally resistant to treatment with immune checkpoint inhibitors. Here the authors show that IL6 blockade, in combination with a CD40 agonist, overcomes macrophage-mediated immunosuppression and sensitizes glioblastoma to immune checkpoint blockade in preclinical models.

Fan Yang
Zhenqiang He
Yi Fan
ResearchOpen Access08 Jun 2021
Nature Communications

Volume: 12, P: 1-15
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

The Sequencing Quality Control (SEQC) consortium shows that junction discovery and differential gene expression profiling with RNA-seq can be robust but transcript-level and absolute measurements remain challenging.

Zhenqiang Su
Paweł P Łabaj
Leming Shi
Research24 Aug 2014
Nature Biotechnology

Volume: 32, P: 903-914
Engineering antiviral immune-like systems for autonomous virus detection and inhibition in mice

The development of broad-spectrum antivirals is an important part of pandemic preparedness and response. Here the authors present ALICE, synthetic biology designer immune-like cells that act as a sense-and-destroy antiviral system can detect viruses from seven different genera, mimicking the human innate immune system.

Yidan Wang
Ying Xu
Haifeng Ye
ResearchOpen Access09 Dec 2022
Nature Communications

Volume: 13, P: 1-18
Machine learning-based integration develops an immune-derived lncRNA signature for improving outcomes in colorectal cancer

Identification of long non-coding RNA (lncRNA) signatures could be used to improve cancer clinical outcome. Here the authors developed a machine learning-based integrative procedure to construct a consensus immune-related lncRNA signature to predict prognosis, recurrence and treatment benefits in colorectal cancer.

Zaoqu Liu
Long Liu
Xinwei Han
ResearchOpen Access10 Feb 2022
Nature Communications

Volume: 13, P: 1-14
Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures

Differential gene expression experiments yield quantitative insight into biological activity and may be important in disease classification and treatment. Here, the authors analyse external spike-in RNA controls to provide a standard method to assess and compare experiment performance.

Sarah A. Munro
Steven P. Lund
Marc Salit
Research25 Sept 2014
Nature Communications

Volume: 5, P: 1-10
PDGF-mediated mesenchymal transformation renders endothelial resistance to anti-VEGF treatment in glioblastoma

Resistance to anti-angiogenic therapies often occurs in patients. Here, the authors demonstrate the role of PDGF signaling in GBM resistance to anti-VEGF treatment via a mechanism that involves endothelial-mesenchymal transformation and transcriptional regulation of VEGFR-2.

Tianrun Liu
Wenjuan Ma
Yi Fan
ResearchOpen Access27 Aug 2018
Nature Communications

Volume: 9, P: 1-13
The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

A comparison of RNA-seq and microarray data from samples treated with diverse drugs highlights a dependency of cross-platform concordance on treatment effect.

Charles Wang
Binsheng Gong
Weida Tong
Research24 Aug 2014
Nature Biotechnology

Volume: 32, P: 926-932
Vascular niche IL-6 induces alternative macrophage activation in glioblastoma through HIF-2α

Macrophages in the tumour microenvironment (TME) acquire tumour-promoting functions upon M2 polarization. Here the authors show, in a mouse model of glioblastoma, that endothelial cells in the TME induce macrophage M2 polarization via IL-6 and that depletion of endothelial IL-6 improves survival.

Qirui Wang
Zhenqiang He
Yi Fan
ResearchOpen Access08 Feb 2018
Nature Communications

Volume: 9, P: 1-15
Targeting CircAURKA prevents colorectal cancer progression via enhancing CTNNB1 protein degradation

Zhenqiang Sun
Pengyuan Dang
Junhong Hu
Research28 Sept 2024
Oncogene

Volume: 43, P: 3388-3401
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

Leming Shi
Leming Shi
William Slikker Jr
Research08 Sept 2006
Nature Biotechnology

Volume: 24, P: 1151-1161
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

The Microarray Quality Control consortium pitted 36 teams against each other to evaluate methods for creating genomic classifiers, computational tools for interpreting gene expression profiles. The performance of the classifiers on blinded validation data—and metadata on the analytic methods—reveal the challenges facing the field.

Leming Shi
Gregory Campbell
Russell D Wolfinger
Research30 Jul 2010
Nature Biotechnology

Volume: 28, P: 827-838
Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq

Joshua Xu
Zhenqiang Su
Leming Shi
ResearchOpen Access26 Aug 2014
Scientific Data

Volume: 1, P: 1-8
Genome-wide association study of aggressive behaviour in chicken

Zhenhui Li
Ming Zheng
Xiquan Zhang
ResearchOpen Access03 Aug 2016
Scientific Reports

Volume: 6, P: 1-11
Multicenter epidemiological analysis of related factors in 10,808 hospitalized children with lower limb and pelvic fractures in China

Xin Qiu
Tianfeng Zhu
Jian Fang
ResearchOpen Access13 Nov 2024
Scientific Reports

Volume: 14, P: 1-11
Optimising PHBV biopolymer production in haloarchaea via CRISPRi-mediated redirection of carbon flux

Lin et al. investigate the use of CRISPRi technology in haloarchaea to regulate the metabolic pathways related to PHBV synthesis to increase PHBV production in H. mediterranei. The authors report that repression of citrate synthase genes redirects metabolic flux and increases production of this degradable bioplastic, which could be used as an alternative to chemical synthetic plastic.

Lin Lin
Junyu Chen
Jing Han
ResearchOpen Access25 Aug 2021
Communications Biology

Volume: 4, P: 1-13
Farnesoid X receptor activation protects the kidney from ischemia-reperfusion damage

Zhibo Gai
Lei Chu
Gerd A. Kullak-Ublick
ResearchOpen Access29 Aug 2017
Scientific Reports

Volume: 7, P: 1-16
Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq

Binsheng Gong
Charles Wang
Joshua Xu
ResearchOpen Access26 Aug 2014
Scientific Data

Volume: 1, P: 1-10
Characteristics of children with IgA nephropathy

Nan Zhou
Hui Wang
Jian Ding
Research09 Jun 2022
Pediatric Research

Volume: 93, P: 715-719

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