Ruqian Lyu YOU? Author Swipe

Last 10y

A spatial transcriptomic atlas of acute neonatal lung injury across development and disease severity Open

Saahithi Mallapragada, Ruqian Lyu, Arianna L. Williams-Katek, B Fischer, Annika Vannan , et al. · 2025

Mapping the spatial and temporal transcriptional relationships during lung development is fundamental to understanding regeneration and chronic lung disease; however, the classification of samples as control or disease is especially challe…

A spatial transcriptomic atlas of acute neonatal lung injury across development and disease severity Open

Saahithi Mallapragada, Ruqian Lyu, Arianna L. Williams-Katek, B Fischer, Annika Vannan , et al. · 2025

A molecular understanding of lung organogenesis requires delineation of the timing and regulation of the cellular transitions that ultimately form and support a surface capable of gas exchange. While the advent of single-cell transcriptomi…

SpatialRNA: a python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset Open

Ruqian Lyu, Annika Vannan, Jonathan A. Kropski, Nicholas E. Banovich, Davis J. McCarthy · 2025

Image-based spatial transcriptomics deliver gene expression measurements of RNA transcripts in tissue slices with single-molecule resolution and spatial context preserved. Modern Graph Neural Network (GNN) models are promising methods for …

Spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis Open

Annika Vannan, Ruqian Lyu, Arianna L. Williams-Katek, Nicholas M. Negretti, Evan D. Mee , et al. · 2025

Large-scale changes in the structure and cellular makeup of the distal lung are a hallmark of pulmonary fibrosis (PF), but the spatial contexts that contribute to disease pathogenesis have remained uncertain. Using image-based spatial tran…

Image-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis Open

Annika Vannan, Ruqian Lyu, A. Williams, Nicholas M. Negretti, Evan D. Mee , et al. · 2023

The human lung is structurally complex, with a diversity of specialized epithelial, stromal and immune cells playing specific functional roles in anatomically distinct locations, and large-scale changes in the structure and cellular makeup…

Fancm has dual roles in the limiting of meiotic crossovers and germ cell maintenance in mammals Open

Vanessa Tsui, Ruqian Lyu, Stevan Novakovic, Jessica M. Stringer, Jessica E. M. Dunleavy , et al. · 2023

Meiotic crossovers are required for accurate chromosome segregation and producing new allelic combinations. Meiotic crossover numbers are tightly regulated within a narrow range, despite an excess of initiating DNA double-strand breaks. He…

Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma Open

Agustin Sgro, Joseph Cursons, Charlene Waryah, Eleanor Woodward, Momeneh Foroutan , et al. · 2023

Additional file 13 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma Open

Agustin Sgro, Joseph Cursons, Charlene Waryah, Eleanor Woodward, Momeneh Foroutan , et al. · 2023

Additional file 13: Data S2. Related to Fig. 1. mRNA transcript abundance, probe methylation (beta) values, and copy number variation data for all TCGA liver samples (including matched adjacent normal liver tissue). Corresponds to pre-tran…

Additional file 14 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma Open

Agustin Sgro, Joseph Cursons, Charlene Waryah, Eleanor Woodward, Momeneh Foroutan , et al. · 2023

Additional file 14: Data S3. Related to Fig. 1. z-score normalized mRNA transcript abundance, probe methylation (beta) values, and copy number variation for all TCGA liver samples (including matched adjacent normal liver tissue). Correspon…

Additional file 15 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma Open

Agustin Sgro, Joseph Cursons, Charlene Waryah, Eleanor Woodward, Momeneh Foroutan , et al. · 2023

Additional file 15: Data S4. Related to Fig. 2, Fig. 3, Fig. 4, and Fig. 6. Comparison of the fold change in mRNA expression for the tumor suppressor genes targeted individually or multiplexed by CRISPRa system (SpdCas9-VPR and MS2-MCP-p65…

Additional file 16 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma Open

Agustin Sgro, Joseph Cursons, Charlene Waryah, Eleanor Woodward, Momeneh Foroutan , et al. · 2023

Additional file 16: Data S5. Related to Figs. 3, 4, and 7. Comprehensive bioinformatic analysis of predicted potential off-targets for the ten TSGs targeted by CRISPRa technology utilizing the most active gRNAs.

Additional file 17 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma Open

Agustin Sgro, Joseph Cursons, Charlene Waryah, Eleanor Woodward, Momeneh Foroutan , et al. · 2023

Additional file 17: Data S6. Related to Figure S6. Probe methylation (beta) values for HHIP in transiently transfected Hep3B cells with SpdCas9-VPR and MS2-MCP-p65-HSF1, or SpdCas9-TET1-CD and MS2-MCP-p65-HSF1 targeting HHIP promoter.

Additional file 12 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma Open

Agustin Sgro, Joseph Cursons, Charlene Waryah, Eleanor Woodward, Momeneh Foroutan , et al. · 2023

Additional file 12: Data S1. Related to Fig. 1. Assigned 'integrated cluster' (iClust) groups for TCGA liver cancer samples where available (from the original TCGA-LIHC manuscript), together with inferred iClusters for unspecified samples,…

Meiotic crossover detection from single-cell DNA sequencing of sperm cells and bulk DNA sequencing of BC1F1 pups Open

Ruqian Lyu · 2022

This repository contains: The preprocessing workflows (in Snakemake files) for analysing the single-cell DNA sequencing of sperm cells and bulk DNA sequencing from Fancm mice for crossover detection The HTML analysis reports The R scripts …

sgcocaller and comapr: personalised haplotype assembly and comparative crossover map analysis using single-gamete sequencing data Open

Ruqian Lyu, Vanessa Tsui, Wayne Crismani, Ruijie Liu, Heejung Shim , et al. · 2022

Profiling gametes of an individual enables the construction of personalised haplotypes and meiotic crossover landscapes, now achievable at larger scale than ever through the availability of high-throughput single-cell sequencing technologi…

<i>Fancm</i> regulates meiotic double-strand break repair pathway choice in mammals Open

Vanessa Tsui, Ruqian Lyu, Stevan Novakovic, Jessica M. Stringer, Jessica E. M. Dunleavy , et al. · 2022

Meiotic crossovers are required for accurate chromosome segregation and to produce new allelic combinations. Meiotic crossover numbers are tightly regulated within a narrow range, despite an excess of initiating DNA double-strand breaks. H…

Proliferation drives quorum sensing of microbial products in human macrophage populations Open

Nadia Rajab, Linden J. Gearing, Ruqian Lyu, Yair D. J. Prawer, Paul W. Angel , et al. · 2022

Macrophages coordinate the initial host inflammatory response to tissue infection, as well as mediating the reparative phase, by producing growth factors that promote tissue repair. One model of this functional dichotomy is that peripheral…

Case Report: Hypoglycemia Due to a Novel Activating Glucokinase Variant in an Adult – a Molecular Approach Open

Anojian Koneshamoorthy, Dilan Seniveratne-Epa, Genevieve Calder, Matthew Sawyer, Thomas W. H. Kay , et al. · 2022

We present a case of an obese 22-year-old man with activating GCK variant who had neonatal hypoglycemia, re-emerging with hypoglycemia later in life. We investigated him for asymptomatic hypoglycemia with a family history of hypoglycemia. …

sgcocaller and comapr: personalised haplotype assembly and comparative crossover map analysis using single-gamete sequencing data Open

Ruqian Lyu, Vanessa Tsui, Wayne Crismani, Ruijie Liu, Heejung Shim , et al. · 2022

Profiling gametes of an individual enables the construction of personalised haplotypes and meiotic crossover landscapes, now achievable at larger scale than ever through the availability of high-throughput single-cell sequencing technologi…

Key signaling networks are dysregulated in patients with the adipose tissue disorder, lipedema Open

Musarat Ishaq, Nadeeka Bandara, Steven Morgan, Cameron J. Nowell, Ahmad M. Mehdi , et al. · 2021

Personalized genome structure via single gamete sequencing Open

Ruqian Lyu, Vanessa Tsui, Davis J. McCarthy, Wayne Crismani · 2021

Genetic maps have been fundamental to building our understanding of disease genetics and evolutionary processes. The gametes of an individual contain all of the information required to perform a de novo chromosome-scale assembly of an indi…

Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes Open

Davis J. McCarthy, Raghd Rostom, Yuanhua Huang, Daniel J. Kunz, Petr Danecek , et al. · 2020

Bulk and single-cell DNA sequencing has enabled reconstructing clonal substructures of somatic tissues from frequency and cooccurrence patterns of somatic variants. However, approaches to characterize phenotypic variations between clones a…

Referee report. For: Fluent genomics with plyranges and tximeta [version 1; peer review: 1 approved, 1 approved with reservations] Open

Ruqian Lyu, PuXue Qiao · 2020

Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signatures Open

Dharmesh D. Bhuva, Momeneh Foroutan, Yi Xie, Ruqian Lyu, Joseph Cursons , et al. · 2019

Advances in RNA sequencing (RNA-seq) technologies that measure the transcriptome of biological samples have revolutionised our ability to understand transcriptional regulatory programs that underpin diseases such as cancer. We recently pub…

Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signatures Open

Dharmesh D. Bhuva, Momeneh Foroutan, Yi Xie, Ruqian Lyu, Joseph Cursons , et al. · 2019

Advances in RNA sequencing (RNA-seq) technologies that measure the transcriptome of biological samples have revolutionised our ability to understand transcriptional regulatory programs that underpin diseases such as cancer. We recently pub…

Using singscore to predict mutations in acute myeloid leukemia from transcriptomic signatures Open

Dharmesh D. Bhuva, Momeneh Foroutan, Yi Xie, Ruqian Lyu, Joseph Cursons , et al. · 2019

Advances in RNA sequencing (RNA-seq) technologies that measure the transcriptome of biological samples have revolutionised our ability to understand transcriptional regulatory programs that underpin diseases such as cancer. We recently pub…

Single sample scoring of molecular phenotypes Open

Momeneh Foroutan, Dharmesh D. Bhuva, Ruqian Lyu, Kristy Horan, Joseph Cursons , et al. · 2018

Additional file 2: of Single sample scoring of molecular phenotypes Open

Momeneh Foroutan, Dharmesh D. Bhuva, Ruqian Lyu, Kristy Horan, Joseph Cursons , et al. · 2018

This includes IDs for 500 of the overlapping samples between the TCGA breast cancer RNA-seq and microarray data. (TXT 8 kb)

Defining a landscape of molecular phenotypes using a simple single sample scoring method Open

Momeneh Foroutan, Dharmesh D. Bhuva, Kristy Horan, Ruqian Lyu, Joseph Cursons , et al. · 2017

Background Gene set scoring provides a useful approach for quantifying concordance between sample transcriptomes and selected molecular signatures. Most methods use information from all samples to score an individual sample, leading to uns…

Fetching topic information...