Sökresultat - "expression analysis"

Development of a MVI associated HCC prognostic model through single cell transcriptomic analysis and 101 machine learning algorithms.

Zhang J; Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, China., Zhang Z; Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, China., Yang C; Department of Gynaecology and Obstetrics Department, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, China., Liu Q; Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, China. qingguangliu@xjtu.edu.cn., Song T; Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, China. 13572431619@163.com.

Evaluation Study; Journal Article; Validation Study , 2025

Single-cell transcriptomics of clinical grade adipose-derived regenerative cells reveals consistency between donors independent of gender and BMI.

Bjerre FA; Department of Clinical Research, University of Southern Denmark, Odense, Denmark.; Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark.; Andersen Group, University of Southern Denmark, Odense, Denmark., Nielsen JV; Department of Clinical Research, University of Southern Denmark, Odense, Denmark.; Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark., Burton M; Department of Clinical Research, University of Southern Denmark, Odense, Denmark.; Department of Clinical Genetics, Odense University Hospital, Odense, Denmark., Dhumale P; Department of Clinical Research, University of Southern Denmark, Odense, Denmark.; Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark., Jørgensen MG; Department of Clinical Research, University of Southern Denmark, Odense, Denmark.; Research Unit for Plastic Surgery, Odense University Hospital, Odense, Denmark., Hansen ST; Department of Clinical Research, University of Southern Denmark, Odense, Denmark.; Department of Urology, Odense University Hospital, Odense, Denmark., Lund L; Department of Clinical Research, University of Southern Denmark, Odense, Denmark.; Department of Urology, Odense University Hospital, Odense, Denmark., Thomassen M; Department of Clinical Research, University of Southern Denmark, Odense, Denmark.; Department of Clinical Genetics, Odense University Hospital, Odense, Denmark., Sørensen JA; Department of Clinical Research, University of Southern Denmark, Odense, Denmark.; Research Unit for Plastic Surgery, Odense University Hospital, Odense, Denmark., Andersen DC; Department of Clinical Research, University of Southern Denmark, Odense, Denmark.; Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark.; Andersen Group, University of Southern Denmark, Odense, Denmark., Jensen CH; Department of Clinical Research, University of Southern Denmark, Odense, Denmark. charken@health.sdu.dk.; Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark. charken@health.sdu.dk.; Andersen Group, University of Southern Denmark, Odense, Denmark. charken@health.sdu.dk.

Comparative Study; Journal Article , 2025

Utilizing sc-linker to integrate single-cell RNA sequencing and human genetics to identify cell types and driver genes associated with non-small cell lung cancer.

Zhou Y; Department of Radiation Oncology, Xiamen Cancer Center, Xiamen Key Laboratory of Radiation Oncology, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, China.; Department of Nuclear Medicine and Minnan PET Center, Xiamen Key Laboratory of Radiopharmaceuticals, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, China., Zhao L; Department of Radiation Oncology, Xiamen Cancer Center, Xiamen Key Laboratory of Radiation Oncology, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, China.; Department of Nuclear Medicine and Minnan PET Center, Xiamen Key Laboratory of Radiopharmaceuticals, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, China., Cai M; Department of Rheumatology and Clinical Immunology, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, China., Luo D; Department of Radiation Oncology, Xiamen Cancer Center, Xiamen Key Laboratory of Radiation Oncology, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, China.; Department of Nuclear Medicine and Minnan PET Center, Xiamen Key Laboratory of Radiopharmaceuticals, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, China., Pang Y; Department of Radiation Oncology, Xiamen Cancer Center, Xiamen Key Laboratory of Radiation Oncology, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, China.; Department of Nuclear Medicine and Minnan PET Center, Xiamen Key Laboratory of Radiopharmaceuticals, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, China., Chen J; Department of Radiation Oncology, Xiamen Cancer Center, Xiamen Key Laboratory of Radiation Oncology, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, China.; Department of Nuclear Medicine and Minnan PET Center, Xiamen Key Laboratory of Radiopharmaceuticals, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, China., Luo Q; Department of Radiation Oncology, Xiamen Cancer Center, Xiamen Key Laboratory of Radiation Oncology, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, China. qcluo@xmu.edu.cn., Lin Q; Department of Radiation Oncology, Xiamen Cancer Center, Xiamen Key Laboratory of Radiation Oncology, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, China. linqin05@163.com.

Dataset; Journal Article , 2025

Single-cell RNA sequencing reveals the dysfunctional characteristics of PBMCs in patients with type 2 diabetes mellitus.

Zhao J; Department of Endocrinology Two, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China.; Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China.; Diabetes Institute, Anhui Academy Chinese Medicine, Hefei, China., Fang Z; Department of Endocrinology Two, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China.; Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China.; Diabetes Institute, Anhui Academy Chinese Medicine, Hefei, China.

Clinical Trial; Journal Article , 2025

cDNA Synthesis and Quantitative PCR (qPCR) for Gene Expression Analysis

Arunachalam, Karuppusamy^Aff3, Sreeja, Puthanpura Sasidharan^Aff4, Arunachalam, Karuppusamy^Aff1, Sreeja, Puthanpura Sasidharan^Aff2

Exploring the Perturbation of Biological Processes Caused by Gene Upregulation Using Knock-In Transfection, Transcriptomics, and Bioinformatics Analysis

Garcia, Isabella R.^Aff4, Larcombe, Lee D.^Aff4

Moll, Jürgen^Aff2, Carotta, Sebastian^Aff3, Walker, John M.^Aff1

Predicting lung aging using scRNA-Seq data.

Song Q; Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America., Singh A; Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America., McDonough JE; Faculty of Health Sciences, McMaster University, Ontario, Canada., Adams TS; Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America., Vos R; Department of Pediatrics (Division of Pulmonology) and Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America., De Man R; Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America., Myers G; Department of Pediatrics (Division of Pulmonology) and Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America., Ceulemans LJ; Department of Respiratory Medicine, KU Leuven, Leuven, Belgium., Vanaudenaerde BM; Department of Respiratory Medicine, KU Leuven, Leuven, Belgium., Wuyts WA; Department of Respiratory Medicine, KU Leuven, Leuven, Belgium., Yan X; Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America., Schupp J; Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America., Hagood JS; Department of Pediatrics (Division of Pulmonology) and Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America., Kaminski N; Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America., Bar-Joseph Z; Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.; Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

Journal Article , 2024

Meta-analysis of single-cell RNA sequencing co-expression in human neural organoids reveals their high variability in recapitulating primary tissue.

Werner JM; The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America., Gillis J; The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.; Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.

Journal Article; Meta-Analysis , 2024

Identification of psoriasis-associated immune marker G3BP2 through single-cell RNA sequencing and meta analysis.

Gao S; Department of Dermatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China., Fan H; Department of Dermatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China., Wang T; Department of Dermatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China., Chen J; Department of Dermatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China.

Journal Article; Meta-Analysis; Research Support, Non-U.S. Gov't , 2024

Transcriptomics of Human Brain Tissue in Parkinson's Disease: a Comparison of Bulk and Single-cell RNA Sequencing.

Fiorini MR; The Montreal Neurological Institute-Hospital, Montreal, QC, Canada.; Department of Human Genetics, McGill University, Montreal, QC, Canada., Dilliott AA; The Montreal Neurological Institute-Hospital, Montreal, QC, Canada.; Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada., Thomas RA; The Montreal Neurological Institute-Hospital, Montreal, QC, Canada. rhalena.thomas@mcgill.ca.; Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada. rhalena.thomas@mcgill.ca., Farhan SMK; The Montreal Neurological Institute-Hospital, Montreal, QC, Canada. sali.farhan@mcgill.ca.; Department of Human Genetics, McGill University, Montreal, QC, Canada. sali.farhan@mcgill.ca.; Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada. sali.farhan@mcgill.ca.

Journal Article; Review; Comparative Study , 2024

A single-cell RNA-seq dataset describing macrophages in NSCLC tumor and peritumor tissues.

Li A; Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China., Wang H; Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China., Zhang L; Thoracic Surgery Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China., Zhao Q; Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China., Yang Y; Thoracic Surgery Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China. fccyangy1@zzu.edu.cn., Zhang Y; Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China. yizhang@zzu.edu.cn.; School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China. yizhang@zzu.edu.cn., Yang L; Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China. fccyangl1@zzu.edu.cn.; School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China. fccyangl1@zzu.edu.cn.

Dataset; Journal Article , 2024

RNA-Seq and Gene Set Enrichment Analysis (GSEA) in Peripheral Blood Mononuclear Cells (PBMCs)

Wen, Fayuan^{Aff4, Aff5}, Kumari, Namita^{Aff5, Aff6}, Taylor Vi, James G.^{Aff5, Aff6, Aff7, Aff8}

Raghavachari, Nalini^Aff2, Garcia-Reyero, Natalia^Aff3, Walker, John M.^Aff1

Integrating large-scale single-cell RNA sequencing in central nervous system disease using self-supervised contrastive learning.

Fang Y; Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China., Chen J; School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, Guangdong, China., Wang H; Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.; Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Neurospine center, China International Neuroscience Institute, Beijing, China., Wang S; Department of Neurosurgery, 900th Hospital, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China., Chang M; Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China., Chen Q; School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, Guangdong, China., Shi Q; Chinese University of Hong Kong (Shenzhen) School of Medicine, People's Republic of China, Shenzhen, Guangdong, China., Xian L; Department of Neurosurgery, 900th Hospital, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China., Feng M; Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. fengming@pumch.cn., Hu B; School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, Guangdong, China. hubaotian@hit.edu.cn., Wang R; Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. wangrz@126.com.; Chinese University of Hong Kong (Shenzhen) School of Medicine, People's Republic of China, Shenzhen, Guangdong, China. wangrz@126.com.

Journal Article; Research Support, Non-U.S. Gov't , 2024

A gene regulatory network-aware graph learning method for cell identity annotation in single-cell RNA-seq data.

Zhao M; College of Computer Science and Control Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.; University of Chinese Academy of Sciences, Beijing 100190, China., Li J; College of Intelligence and Computing, Tianjin University, Tianjin 300350, China., Liu X; Computer Science and Engineering, University of South Carolina, Columbia, South Carolina 29208, USA., Ma K; College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China., Tang J; College of Computer Science and Control Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; guofei@csu.edu.cn jj.tang@siat.ac.cn., Guo F; School of Computer Science and Engineering, Central South University, Changsha 410083, China guofei@csu.edu.cn jj.tang@siat.ac.cn.

Journal Article , 2024

COMSE: analysis of single-cell RNA-seq data using community detection-based feature selection.

Luo Q; Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing, 100084, China.; MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China., Chen Y; School of Artificial Intelligence, Beijing Normal University, Beijing, 100875, China., Lan X; Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing, 100084, China. xlan@tsinghua.edu.cn.; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China. xlan@tsinghua.edu.cn.; MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China. xlan@tsinghua.edu.cn.

Journal Article , 2024

Robust analysis of allele-specific copy number alterations from scRNA-seq data with XClone.

Huang R; School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China., Huang X; School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China.; Center for Translational Stem Cell Biology, Hong Kong Science and Technology Park, Hong Kong SAR, China., Tong Y; Department of Pathology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China.; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China., Yan HYN; Department of Pathology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China.; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China., Leung SY; Department of Pathology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China.; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China.; The Jockey Club Centre for Clinical Innovation and Discovery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.; Centre for PanorOmic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China., Stegle O; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.; Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany., Huang Y; School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China. yuanhua@hku.hk.; Center for Translational Stem Cell Biology, Hong Kong Science and Technology Park, Hong Kong SAR, China. yuanhua@hku.hk.; Department of Statistics and Actuarial Science, The University of Hong Kong, Hong Kong SAR, China. yuanhua@hku.hk.

Journal Article , 2024

Highlighting immune features of the tumor ecosystem and prognostic value of Tfh and Th17 cell infiltration in head and neck squamous cell carcinoma by single-cell RNA-seq.

Tian Y; Department of Medical Oncology, Peking University First Hospital, Beijing, China., Liu C; Department of Radiation Oncology, Peking University First Hospital, Beijing, China., Yang W; Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China., Li X; Department of Medical Oncology, Peking University First Hospital, Beijing, China., Zhang M; Department of Radiation Oncology, Peking University People's Hospital, Beijing, China., Xiong Y; Department of Pathology, Peking University First Hospital, Beijing, China., Ren X; Department of Radiation Oncology, Peking University First Hospital, Beijing, China., Ma Z; Department of Neurology, Xi' an Aerospace General Hospital, Xian, China., Jin X; Department of Medical Oncology, Peking University First Hospital, Beijing, China., Wu Y; Department of Medical Oncology, Peking University First Hospital, Beijing, China., Dong X; Department of Medical Oncology, Peking University First Hospital, Beijing, China., Hu N; Department of Medical Oncology, Peking University First Hospital, Beijing, China., Xie Z; Department of Medical Oncology, Peking University First Hospital, Beijing, China., Qin Y; Department of Otolaryngology Head and Neck Surgery, Peking University First Hospital, Beijing, China. youngcaptain@sina.com., Wu S; Department of Medical Oncology, Peking University First Hospital, Beijing, China. skywu4923@sina.com.

Journal Article , 2024

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN.

Rosen Y; Department of Computer Science, Stanford University, Stanford, CA, USA., Brbić M; School of Computer and Communication Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland., Roohani Y; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA., Swanson K; Department of Computer Science, Stanford University, Stanford, CA, USA., Li Z; Department of Computer Science and Technology, Tsinghua University, Beijing, China., Leskovec J; Department of Computer Science, Stanford University, Stanford, CA, USA. jure@cs.stanford.edu.

Journal Article , 2024

Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis.

Hou W; Department of Biostatistics, Columbia University Mailman School of Public Health, New York City, NY, USA. wh2526@cumc.columbia.edu., Ji Z; Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA. zhicheng.ji@duke.edu.

Journal Article , 2024

Single-Cell RNA-Seq Debiased Clustering via Batch Effect Disentanglement.

Li Y, Lin Y, Hu P, Peng D, Luo H, Peng X

Journal Article; Research Support, Non-U.S. Gov't , 2024