DUOS
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DUOS
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相关论文
13Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth
Gydush Gregory•Nguyen Erica•Bae Jin H.•Blewett Timothy•Rhoades Justin等 20 人
Nature Biomedical Engineering
2022
•2022/3/17
•00 p.1-10
Assaying for large numbers of low-frequency mutations requires sequencing at extremely high depth and accuracy. Increasing sequencing depth aids the detection of low-frequency mutations yet limits the number of loci that can be simultaneously probed. Here we report a method for the accurate tracking...
BiomarkersBiotechnologyCancerMedical researchMolecular biology
10.1038/S41551-022-00855-9
ISSN:2157-846X
A molecular single-cell lung atlas of lethal COVID-19
Johannes C. Melms•Jana Biermann•Huachao Huang•Yiping Wang•Ajay Nair等 43 人
Nature
2021
•2021/4/29
•00 p.1-6
Respiratory failure is the leading cause of death in patients with severe SARS-CoV-2 infection1,2, but the host response at the lung tissue level is poorly understood. Here we performed single-nucleus RNA sequencing of about 116,000 nuclei from the lungs of nineteen individuals who died of COVID-19 ...
Cellular signalling networksInfectionSARS-CoV-2
10.1038/S41586-021-03569-1
ISSN:0028-0836
Deciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics
Avishay Spitzer•Kevin C. Johnson•Masashi Nomura•Luciano Garofano•Djamel Nehar-belaid等 46 人
Nature Genetics
2025
•2025/5/9
•Vol.57 No.5 p.1168-1178
The evolution of isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GBM) after standard-of-care therapy remains poorly understood. Here we analyzed matched primary and recurrent GBMs from 59 patients using single-nucleus RNA sequencing and bulk DNA sequencing, assessing the longitudinal evolution...
CNS cancerData processing
10.1038/S41588-025-02168-4
ISSN:1061-4036
A concerted neuron–astrocyte program declines in ageing and schizophrenia
Emi Ling•James Nemesh•Melissa Goldman•Nolan Kamitaki•Nora Reed等 23 人
Nature
2024
•2024/3/6
•00 p.1-8
Human brains vary across people and over time; such variation is not yet understood in cellular terms. Here we describe a relationship between people’s cortical neurons and cortical astrocytes. We used single-nucleus RNA sequencing to analyse the prefrontal cortex of 191 human donors aged 22–97 year...
GenomicsMolecular neuroscienceNeural ageingSchizophreniaTranscriptomics
10.1038/S41586-024-07109-5
ISSN:0028-0836
Longitudinal changes in DNA methylation in IDH-mutant glioma fuel disease progression through altered cell state differentiation
Masashi Nomura•Ramya Raviram•Joshua S. Schiffman•Lillian Bussema•Vivian Lu等 22 人
Nature Genetics
2026
•2026/6/22
•00 p.1-10
The progression of isocitrate dehydrogenase-mutant glioma (IDH-G) from slow-growing tumor to fatal disease is associated with transcriptional and DNA methylation changes that remain poorly understood. Here, we profiled a longitudinal cohort of 36 IDH-G samples from 19 patients by joint-capture multi...
CNS cancerEpigenetics
10.1038/S41588-026-02642-7
ISSN:1061-4036
Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion
Chris J. Frangieh•Johannes C. Melms•Pratiksha I. Thakore•Kathryn R. Geiger-Schuller•Patricia Ho等 22 人
Nature Genetics
2021
•2021/3/1
•Vol.53 No.3 p.332-341
Resistance to immune checkpoint inhibitors (ICIs) is a key challenge in cancer therapy. To elucidate underlying mechanisms, we developed Perturb-CITE-sequencing (Perturb-CITE-seq), enabling pooled clustered regularly interspaced short palindromic repeat (CRISPR)–Cas9 perturbations with single-cell t...
Functional genomicsHigh-throughput screeningMelanomaSystems analysisTumour immunology
10.1038/S41588-021-00779-1
ISSN:1061-4036
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
Toni M. Delorey•Carly G. K. Ziegler•Graham Heimberg•Rachelly Normand•Yiming Yang等 109 人
Nature
2021
•2021/4/29
•00 p.1-8
COVID-19, which is caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple organ failure1–4, but little is known about its pathophysiology. Here we generated single-cell atlases of 24 lung, 16 kidney, 16 liver and 19 heart autopsy tissue samples and spatial atlases of 14...
GeneticsSARS-CoV-2Viral infection
10.1038/S41586-021-03570-8
ISSN:0028-0836
A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors
Michal Slyper•Caroline B. M. Porter•Orr Ashenberg•Julia Waldman•Eugene Drokhlyansky等 50 人
Nature Medicine
2020
•2020/5/11
•Vol.26 No.5 p.792-802
Single-cell genomics is essential to chart tumor ecosystems. Although single-cell RNA-Seq (scRNA-Seq) profiles RNA from cells dissociated from fresh tumors, single-nucleus RNA-Seq (snRNA-Seq) is needed to profile frozen or hard-to-dissociate tumors. Each requires customization to different tissue an...
Biological techniquesCancerComputational biology and bioinformaticsGene expression analysisGenomic analysis
10.1038/S41591-020-0844-1
ISSN:1078-8956
The genetic architecture of DNA replication timing in human pluripotent stem cells
Ding Qiliang•Edwards Matthew M.•Wang Ning•Zhu Xiang•Bracci Alexa N.等 18 人
Nature Communications
2021
•2021/11/19
•Vol.12 No.1 p.1-18
DNA replication follows a strict spatiotemporal program that intersects with chromatin structure but has a poorly understood genetic basis. To systematically identify genetic regulators of replication timing, we exploited inter-individual variation in human pluripotent stem cells from 349 individual...
DNA replicationEpigeneticsGenomePopulation genetics
10.1038/S41467-021-27115-9
ISSN:2041-1723
Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment
Hwang William L.•Jagadeesh Karthik A.•Guo Jimmy A.•Hoffman Hannah I.•Yadollahpour Payman等 65 人
Nature Genetics
2022
•2022/7/28
•Vol.54 No.8 p.1178-1191
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and treatment-refractory cancer. Molecular stratification in pancreatic cancer remains rudimentary and does not yet inform clinical management or therapeutic development. Here, we construct a high-resolution molecular landscape of the cellul...
Gene expressionPancreatic cancerTranscriptomics
10.1038/S41588-022-01134-8
ISSN:1061-4036
Genomic and transcriptomic correlates of immunotherapy response within the tumor microenvironment of leptomeningeal metastases
Prakadan Sanjay M.•Alvarez-Breckenridge Christopher A.•Markson Samuel C.•Kim Albert E.•Klein Robert H.等 29 人
Nature Communications
2021
•2021/10/12
•Vol.12 No.1 p.1-10
Leptomeningeal disease (LMD) is a devastating complication of solid tumor malignancies, with dire prognosis and no effective systemic treatment options. Over the past decade, the incidence of LMD has steadily increased due to therapeutics that have extended the survival of cancer patients, highlight...
Cancer immunotherapyCNS cancerGenomicsMetastasis
10.1038/S41467-021-25860-5
ISSN:2041-1723
An immune-cell signature of bacterial sepsis
Miguel Reyes•Michael R. Filbin•Roby P. Bhattacharyya•Kianna Billman•Thomas Eisenhaure等 11 人
Nature Medicine
2020
•2020/2/17
•Vol.26 No.3 p.333-340
Dysregulation of the immune response to bacterial infection can lead to sepsis, a condition with high mortality. Multiple whole-blood gene-expression studies have defined sepsis-associated molecular signatures, but have not resolved changes in transcriptional states of specific cell types. Here, we ...
Bacterial infectionDiagnostic markersMonocytes and macrophagesRNA sequencingSepsis
10.1038/S41591-020-0752-4
ISSN:1078-8956
B cells promote atrial fibrillation via autoantibodies
Masahiro Yamazoe•Kenneth K. Y. Ting•I-Hsiu Lee•Aneesh Bapat•Andrew Lewis等 25 人
Nature Cardiovascular Research
2025
•2025/10/8
•Vol.4 No.10 p.1381-1396
Atrial fibrillation, the most frequent cardiac arrhythmia, causes heart failure and stroke. Here we describe that combining the typical risk factors of atrial fibrillation (hypertension, obesity and mitral valve regurgitation (HOMER)) activates adaptive immunity in wild-type mice, ultimately causing...
Cardiovascular diseasesInflammation
10.1038/S44161-025-00724-Z
ISSN:2731-0590