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Tytuł:
SmithHunter: a workflow for the identification of candidate smithRNAs and their targets.
Autorzy:
Marturano G; Department of Life Sciences, University of Siena, 53100, Siena, Italy.
Carli D; Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy.
Cucini C; Department of Life Sciences, University of Siena, 53100, Siena, Italy.
Carapelli A; Department of Life Sciences, University of Siena, 53100, Siena, Italy.; National Biodiversity Future Center (NBFC), 90133, Palermo, Italy.
Plazzi F; Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy.
Frati F; Department of Life Sciences, University of Siena, 53100, Siena, Italy.; National Biodiversity Future Center (NBFC), 90133, Palermo, Italy.
Passamonti M; Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy. .
Nardi F; Department of Life Sciences, University of Siena, 53100, Siena, Italy.; National Biodiversity Future Center (NBFC), 90133, Palermo, Italy.
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2024 Sep 02; Vol. 25 (1), pp. 286. Date of Electronic Publication: 2024 Sep 02.
Typ publikacji:
Journal Article
MeSH Terms:
Workflow*
Bivalvia*/genetics
Sequence Analysis, RNA*/methods
Animals ; Software ; Genome, Mitochondrial/genetics ; RNA/genetics ; RNA, Mitochondrial/genetics
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Single-cell RNA sequencing integrated with bulk RNA sequencing analysis reveals the protective effects of lactate-mediated lactylation of microglia-related proteins on spinal cord injury.
Autorzy:
Zhang B; Department of Orthopedic Surgery, Shanghai Changzheng Hospital, Navy Medical University, Shanghai, China.
Li F; Department of Orthopedic Surgery, Shanghai Changzheng Hospital, Navy Medical University, Shanghai, China.
Shi Y; Department of Orthopedic Surgery, Shanghai Changzheng Hospital, Navy Medical University, Shanghai, China.
Ji C; Department of Orthopedic Surgery, Shanghai Changzheng Hospital, Navy Medical University, Shanghai, China.
Kong Q; Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Sun K; Department of Orthopedic Surgery, Shanghai Changzheng Hospital, Navy Medical University, Shanghai, China.; Department of Orthopedics, Naval Medical Center of PLA, Shanghai, China.
Sun X; Department of Orthopedic Surgery, Shanghai Changzheng Hospital, Navy Medical University, Shanghai, China.
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Źródło:
CNS neuroscience & therapeutics [CNS Neurosci Ther] 2024 Sep; Vol. 30 (9), pp. e70028.
Typ publikacji:
Journal Article
MeSH Terms:
Spinal Cord Injuries*/metabolism
Microglia*/drug effects
Microglia*/metabolism
Mice, Inbred C57BL*
Lactic Acid*/metabolism
Sequence Analysis, RNA*/methods
Single-Cell Analysis*
Animals ; Mice ; Male ; Neuroprotective Agents/pharmacology ; Glycolysis/drug effects ; Glycolysis/physiology
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Single-cell RNA sequencing data analysis utilizing multi-type graph neural networks.
Autorzy:
Xu L; College of Computer Science and Technology, Harbin Engineering University, Harbin, 150001, Heilongjiang, China.
Li Z; College of Computer Science and Technology, Harbin Engineering University, Harbin, 150001, Heilongjiang, China. Electronic address: .
Ren J; College of Computer Science and Technology, Harbin Engineering University, Harbin, 150001, Heilongjiang, China.
Liu S; College of Computer Science and Technology, Harbin Engineering University, Harbin, 150001, Heilongjiang, China.
Xu Y; College of Engineering, Tokyo Institute of Technology, Tokyo, 226-0026, Tokyo, Japan.
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Źródło:
Computers in biology and medicine [Comput Biol Med] 2024 Sep; Vol. 179, pp. 108921. Date of Electronic Publication: 2024 Jul 25.
Typ publikacji:
Journal Article
MeSH Terms:
Single-Cell Analysis*/methods
Neural Networks, Computer*
Sequence Analysis, RNA*/methods
Humans ; Algorithms
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Tytuł:
scGAAC: A graph attention autoencoder for clustering single-cell RNA-sequencing data.
Autorzy:
Zhang L; School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China.
Xiang H; School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China.
Wang F; School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China.
Chen Z; School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China.
Shen M; School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China.
Ma J; School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China; Department of Veterinary Biosciences, Melbourne Veterinary School, the University of Melbourne, Parkville, Victoria 3010, Australia. Electronic address: .
Liu H; School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China.
Zheng H; School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China. Electronic address: .
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Źródło:
Methods (San Diego, Calif.) [Methods] 2024 Sep; Vol. 229, pp. 115-124. Date of Electronic Publication: 2024 Jun 29.
Typ publikacji:
Journal Article
MeSH Terms:
Single-Cell Analysis*/methods
Sequence Analysis, RNA*/methods
Humans ; Cluster Analysis ; RNA-Seq/methods ; Algorithms ; Software
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Single-cell RNA sequencing of cystic fibrosis liver disease explants reveals endothelial complement activation.
Autorzy:
Declercq M; Department of Development and Regeneration, Woman and Child Unit, KU Leuven, Leuven, Belgium.; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium.
Treps L; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium.; Nantes Université, INSERM UMR 1307, CNRS UMR 6075, Université d'Angers, CRCI2NA, Nantes, France.
Geldhof V; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium.
Conchinha NV; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium.; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
de Rooij LPMH; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium.; The CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
Subramanian A; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium.; Department of Biotechnology, Indian Institute of Technology, Hyderabad, Telangana, India.
Feyeux M; Nantes Université, CHU Nantes, CNRS, Inserm, BioCore, US16, SFR Bonamy, Nantes, France.
Cotinat M; Nantes Université, INSERM UMR 1307, CNRS UMR 6075, Université d'Angers, CRCI2NA, Nantes, France.
Boeckx B; Laboratory for Translational Genetics, Center for Cancer Biology, VIB, Leuven, Belgium.; Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
Vinckier S; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium.
Dupont L; Department of Pneumology, UZ Leuven, Leuven, Belgium.; Department of Chronic Diseases and Metabolism, Respiratory Diseases and Thoracic Surgery, KU Leuven, Leuven, Belgium.
Vermeulen F; Department of Development and Regeneration, Woman and Child Unit, KU Leuven, Leuven, Belgium.; Department of Pediatrics, Pediatric Pulmonology, University Hospital of Leuven, Leuven, Flanders, Belgium.
Boon M; Department of Development and Regeneration, Woman and Child Unit, KU Leuven, Leuven, Belgium.; Department of Pediatrics, Pediatric Pulmonology, University Hospital of Leuven, Leuven, Flanders, Belgium.
Proesmans M; Department of Development and Regeneration, Woman and Child Unit, KU Leuven, Leuven, Belgium.; Department of Pediatrics, Pediatric Pulmonology, University Hospital of Leuven, Leuven, Flanders, Belgium.
Libbrecht L; Department of Pathology, Cliniques Universitaires Saint-Luc, Brussels, Belgium.; Department of Pathology, AZ Groeninge, Kortrijk, Belgium.; Laboratory of Hepatology, KU Leuven, Leuven, Belgium.
Pirenne J; Transplantation Research Group, Department of Immunology, Microbiology and Transplantation, KU Leuven, Leuven, Belgium.; Department of Abdominal Transplant Surgery, University Hospitals Leuven, Leuven, Belgium.
Monbaliu D; Transplantation Research Group, Department of Immunology, Microbiology and Transplantation, KU Leuven, Leuven, Belgium.; Department of Abdominal Transplant Surgery, University Hospitals Leuven, Leuven, Belgium.
Jochmans I; Transplantation Research Group, Department of Immunology, Microbiology and Transplantation, KU Leuven, Leuven, Belgium.; Department of Abdominal Transplant Surgery, University Hospitals Leuven, Leuven, Belgium.
Dewerchin M; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium.
Eelen G; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium.
Roskams T; Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven and University Hospitals Leuven, Leuven, Belgium.
Verleden S; Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, Leuven, Belgium.; Department of ASTARC, University of Antwerp, Wilrijk, Belgium.
Lambrechts D; Laboratory for Translational Genetics, Center for Cancer Biology, VIB, Leuven, Belgium.; Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
Carmeliet P; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium.; Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
Witters P; Department of Development and Regeneration, Woman and Child Unit, KU Leuven, Leuven, Belgium.; Department of Paediatrics and Metabolic Center, University Hospitals Leuven, Leuven, Belgium.
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Źródło:
Liver international : official journal of the International Association for the Study of the Liver [Liver Int] 2024 Sep; Vol. 44 (9), pp. 2382-2395. Date of Electronic Publication: 2024 Jun 07.
Typ publikacji:
Journal Article
MeSH Terms:
Cystic Fibrosis*/genetics
Single-Cell Analysis*
Endothelial Cells*/metabolism
Sequence Analysis, RNA*
Complement Activation*
Humans ; Liver/pathology ; Liver/metabolism ; Male ; Female ; Adult ; Liver Cirrhosis/genetics ; Liver Cirrhosis/pathology ; Liver Diseases/genetics
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Association Between COVID-19 and Neurological Diseases: Evidence from Large-Scale Mendelian Randomization Analysis and Single-Cell RNA Sequencing Analysis.
Autorzy:
Huang L; Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China.
Wang Y; Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China.; International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing, China.
He Y; Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China.
Huang D; Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China.
Wen T; Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China.
Han Z; Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China. .
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Źródło:
Molecular neurobiology [Mol Neurobiol] 2024 Sep; Vol. 61 (9), pp. 6354-6365. Date of Electronic Publication: 2024 Feb 01.
Typ publikacji:
Journal Article
MeSH Terms:
COVID-19*/genetics
Mendelian Randomization Analysis*
Single-Cell Analysis*
Nervous System Diseases*/genetics
Nervous System Diseases*/virology
Sequence Analysis, RNA*/methods
Humans ; SARS-CoV-2/genetics ; Epilepsy/genetics ; Epilepsy/virology ; Bipolar Disorder/genetics ; Bipolar Disorder/virology
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Tytuł:
NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs.
Autorzy:
Saville L; Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E3N4, Canada.; Paul Albrechtsen Research Institute, CCMB, Winnipeg, MB, R3E3N4, Canada.; Southern Alberta Genome Sciences Centre, Lethbridge, AB, T1K3M4, Canada.; Canadian Centre for Behavioral Neuroscience, Lethbridge, AB, T1K3M4, Canada.
Wu L; Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E3N4, Canada.; Paul Albrechtsen Research Institute, CCMB, Winnipeg, MB, R3E3N4, Canada.
Habtewold J; Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E3N4, Canada.; Paul Albrechtsen Research Institute, CCMB, Winnipeg, MB, R3E3N4, Canada.
Cheng Y; Southern Alberta Genome Sciences Centre, Lethbridge, AB, T1K3M4, Canada.; Canadian Centre for Behavioral Neuroscience, Lethbridge, AB, T1K3M4, Canada.
Gollen B; Southern Alberta Genome Sciences Centre, Lethbridge, AB, T1K3M4, Canada.; Canadian Centre for Behavioral Neuroscience, Lethbridge, AB, T1K3M4, Canada.
Mitchell L; Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E3N4, Canada.; Paul Albrechtsen Research Institute, CCMB, Winnipeg, MB, R3E3N4, Canada.; Southern Alberta Genome Sciences Centre, Lethbridge, AB, T1K3M4, Canada.; Canadian Centre for Behavioral Neuroscience, Lethbridge, AB, T1K3M4, Canada.
Stuart-Edwards M; Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E3N4, Canada.; Paul Albrechtsen Research Institute, CCMB, Winnipeg, MB, R3E3N4, Canada.; Southern Alberta Genome Sciences Centre, Lethbridge, AB, T1K3M4, Canada.; Canadian Centre for Behavioral Neuroscience, Lethbridge, AB, T1K3M4, Canada.
Haight T; Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E3N4, Canada.; Paul Albrechtsen Research Institute, CCMB, Winnipeg, MB, R3E3N4, Canada.; Southern Alberta Genome Sciences Centre, Lethbridge, AB, T1K3M4, Canada.; Canadian Centre for Behavioral Neuroscience, Lethbridge, AB, T1K3M4, Canada.
Mohajerani M; Canadian Centre for Behavioral Neuroscience, Lethbridge, AB, T1K3M4, Canada.
Zovoilis A; Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E3N4, Canada. .; Paul Albrechtsen Research Institute, CCMB, Winnipeg, MB, R3E3N4, Canada. .; Southern Alberta Genome Sciences Centre, Lethbridge, AB, T1K3M4, Canada. .; Canadian Centre for Behavioral Neuroscience, Lethbridge, AB, T1K3M4, Canada. .
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Źródło:
Genome biology [Genome Biol] 2024 Aug 28; Vol. 25 (1), pp. 233. Date of Electronic Publication: 2024 Aug 28.
Typ publikacji:
Journal Article
MeSH Terms:
RNA, Untranslated*/genetics
Sequence Analysis, RNA*/methods
Nanopore Sequencing*/methods
Animals ; Mice ; Humans ; RNA, Messenger/genetics ; Brain/metabolism
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Single-cell RNA sequencing of nc886, a non-coding RNA transcribed by RNA polymerase III, with a primer spike-in strategy.
Autorzy:
Shin GJ; Department of Microbiology, The Catholic University of Korea, Seoul, Korea.; Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul, Korea.
Choi BH; Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea.
Eum HH; Department of Microbiology, The Catholic University of Korea, Seoul, Korea.
Jo A; Department of Microbiology, The Catholic University of Korea, Seoul, Korea.
Kim N; Department of Microbiology, The Catholic University of Korea, Seoul, Korea.
Kang H; Department of Microbiology, The Catholic University of Korea, Seoul, Korea.; Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul, Korea.
Hong D; Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul, Korea.; Department of Medical Informatics, The Catholic University of Korea, Seoul, Korea.
Jang JJ; Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea.
Lee HH; Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea.
Lee YS; Division of Rare Cancer, Research Institute, National Cancer Center, Goyang, Korea.
Lee YS; Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea.
Lee HO; Department of Microbiology, The Catholic University of Korea, Seoul, Korea.; Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul, Korea.
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Źródło:
PloS one [PLoS One] 2024 Aug 27; Vol. 19 (8), pp. e0301562. Date of Electronic Publication: 2024 Aug 27 (Print Publication: 2024).
Typ publikacji:
Journal Article
MeSH Terms:
Single-Cell Analysis*/methods
RNA Polymerase III*/genetics
RNA Polymerase III*/metabolism
RNA, Untranslated*/genetics
Sequence Analysis, RNA*/methods
Humans ; Transcription, Genetic ; DNA Primers/genetics ; Gene Expression Profiling/methods
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing.
Autorzy:
Tan L; Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.
Guo Z; Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.
Shao Y; Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.
Ye L; Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.
Wang M; Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.
Deng X; Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.; Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China.
Chen S; State Key Lab of Chemical Biology and Drug Discovery and Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hong Kong, China.
Li R; Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, 518057, China.; Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.; Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China.
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Źródło:
Nucleic acids research [Nucleic Acids Res] 2024 Aug 27; Vol. 52 (15), pp. 8746-8762.
Typ publikacji:
Journal Article
MeSH Terms:
Escherichia coli*/genetics
Escherichia coli*/metabolism
Staphylococcus aureus*/genetics
Staphylococcus aureus*/metabolism
Transcriptome*/genetics
RNA, Bacterial*/genetics
RNA, Bacterial*/metabolism
Sequence Analysis, RNA*/methods
Nanopore Sequencing*/methods
High-Throughput Nucleotide Sequencing/methods ; Operon/genetics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Adenosine/analogs & derivatives ; Adenosine/metabolism ; Adenosine/genetics ; Nanopores ; Gene Expression Regulation, Bacterial ; Gene Expression Profiling/methods
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Connectivity Network Feature Sharing in Single-Cell RNA Sequencing Data Identifies Rare Cells.
Autorzy:
Wang S; Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum (East China), Qingdao 266580, China.
Li H; Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum (East China), Qingdao 266580, China.
Liu Y; College of Science, China University of Petroleum (East China), Qingdao 266580, China.
Pang S; Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum (East China), Qingdao 266580, China.
Qiao S; The College of Software, Tiangong University, Tianjin 300387, China.
Su J; School of AI and Advanced Computing, XJTLU Entrepreneur College (Taicang), Xi'an Jiaotong-Liverpool University, Suzhou 215123, Jiangsu, China.
Wang S; School of Information and Control Engineering, Qingdao University of Technology, Qingdao 266525, China.
Zhang Y; College of Mathematics and Systems Science, Shandong University of Science and Technology, Qingdao 266590, China.
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Źródło:
Journal of chemical information and modeling [J Chem Inf Model] 2024 Aug 26; Vol. 64 (16), pp. 6596-6609. Date of Electronic Publication: 2024 Aug 03.
Typ publikacji:
Journal Article
MeSH Terms:
Single-Cell Analysis*/methods
Sequence Analysis, RNA*/methods
Humans
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing.
Autorzy:
Volteras D; Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK.
Shahrezaei V; Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK. Electronic address: .
Thomas P; Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK. Electronic address: .
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Źródło:
Cell systems [Cell Syst] 2024 Aug 21; Vol. 15 (8), pp. 694-708.e12. Date of Electronic Publication: 2024 Aug 08.
Typ publikacji:
Journal Article
MeSH Terms:
Single-Cell Analysis*/methods
Sequence Analysis, RNA*/methods
Transcription, Genetic*/genetics
Gene Expression Regulation*/genetics
Cell Cycle*/genetics
Humans ; Bayes Theorem ; Transcriptome/genetics ; Stochastic Processes
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Single-cell RNA sequencing reveals the effects of high-fat diet on oocyte and early embryo development in female mice.
Autorzy:
Zhu Q; Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.; Graduate School, Nanjing Medical University, Nanjing, China.
Li F; Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, China.
Wang H; Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, China.
Wang X; Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.
Xiang Y; Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.
Ding H; Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.
Wu H; Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.; Graduate School, Dalian Medical University, Dalian, China.
Xu C; Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.
Weng L; Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.; Graduate School, Nanjing University Of Chinese Medicine, Nanjing, China.
Cai J; Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.; Graduate School, Nanjing University Of Chinese Medicine, Nanjing, China.
Xu T; Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.; Graduate School, Nanjing University Of Chinese Medicine, Nanjing, China.
Liang N; Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.; Graduate School, Dalian Medical University, Dalian, China.
Hong X; Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.; Graduate School, Nanjing Medical University, Nanjing, China.
Xue M; Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.; Graduate School, Dalian Medical University, Dalian, China.
Ge H; Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China. .; Graduate School, Nanjing Medical University, Nanjing, China. .; Graduate School, Nanjing University Of Chinese Medicine, Nanjing, China. .; Graduate School, Dalian Medical University, Dalian, China. .
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Źródło:
Reproductive biology and endocrinology : RB&E [Reprod Biol Endocrinol] 2024 Aug 20; Vol. 22 (1), pp. 105. Date of Electronic Publication: 2024 Aug 20.
Typ publikacji:
Journal Article
MeSH Terms:
Diet, High-Fat*/adverse effects
Oocytes*/metabolism
Embryonic Development*/genetics
Embryonic Development*/drug effects
Single-Cell Analysis*
Obesity*/genetics
Obesity*/metabolism
Sequence Analysis, RNA*
Animals ; Female ; Mice ; Mice, Inbred C57BL ; Pregnancy ; Blastocyst/metabolism
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Genome-wide and cell-type-selective profiling of in vivo small noncoding RNA:target RNA interactions by chimeric RNA sequencing.
Autorzy:
Li X; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Mills WT 4th; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Jin DS; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Meffert MK; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address: .
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Źródło:
Cell reports methods [Cell Rep Methods] 2024 Aug 19; Vol. 4 (8), pp. 100836. Date of Electronic Publication: 2024 Aug 09.
Typ publikacji:
Journal Article
MeSH Terms:
RNA, Small Untranslated*/genetics
RNA, Small Untranslated*/metabolism
Sequence Analysis, RNA*/methods
Animals ; Mice ; Humans ; RNA-Induced Silencing Complex/metabolism ; RNA-Induced Silencing Complex/genetics ; Genome/genetics
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Tytuł:
scParser: sparse representation learning for scalable single-cell RNA sequencing data analysis.
Autorzy:
Zhao K; Department of Statistics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
So HC; School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China. .; KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Kunming Institute of Zoology and The Chinese University of Hong Kong, Hong Kong SAR, China. .; Department of Psychiatry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China. .; Margaret K.L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China. .; Brain and Mind Institute, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China. .; Hong Kong Branch of the Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, China. .
Lin Z; Department of Statistics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China. .
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Źródło:
Genome biology [Genome Biol] 2024 Aug 16; Vol. 25 (1), pp. 223. Date of Electronic Publication: 2024 Aug 16.
Typ publikacji:
Journal Article
MeSH Terms:
Single-Cell Analysis*/methods
Sequence Analysis, RNA*/methods
Humans ; RNA-Seq/methods ; Software
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets.
Autorzy:
Sprang M; Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, Mainz, 55128, Germany.
Möllmann J; Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, Mainz, 55128, Germany.
Andrade-Navarro MA; Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, Mainz, 55128, Germany. .
Fontaine JF; Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, Mainz, 55128, Germany.; Central Institute for Decision Support Systems in Crop Protection (ZEPP), Rüdesheimer Str. 60-68, Bad Kreuznach, 55545, Germany.
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Źródło:
Genome biology [Genome Biol] 2024 Aug 16; Vol. 25 (1), pp. 222. Date of Electronic Publication: 2024 Aug 16.
Typ publikacji:
Journal Article
MeSH Terms:
Sequence Analysis, RNA*
Humans ; Reproducibility of Results
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Ribosome Profiling and RNA Sequencing Reveal Translation and Transcription Regulation under Acute Heat Stress in Rainbow Trout ( Oncorhynchus mykiss , Walbaum , 1792 ) Liver.
Autorzy:
Zhao G; Department of College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
Liu Z; Department of College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
Quan J; Department of College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
Lu J; Department of College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
Li L; Department of College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
Pan Y; Department of College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
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Źródło:
International journal of molecular sciences [Int J Mol Sci] 2024 Aug 14; Vol. 25 (16). Date of Electronic Publication: 2024 Aug 14.
Typ publikacji:
Journal Article
MeSH Terms:
Oncorhynchus mykiss*/genetics
Heat-Shock Response*/genetics
Ribosomes*/metabolism
Ribosomes*/genetics
Protein Biosynthesis*/genetics
Liver*/metabolism
Sequence Analysis, RNA*
Animals ; Gene Expression Regulation ; Transcription, Genetic ; Gene Expression Profiling ; Fish Proteins/genetics ; Fish Proteins/metabolism ; Open Reading Frames/genetics ; Transcriptome ; Ribosome Profiling
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer.
Autorzy:
Byrne A; Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA.
Le D; Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA.
Sereti K; Department of Discovery Oncology, Genentech, South San Francisco, CA, USA.
Menon H; Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA.
Vaidya S; Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA.
Patel N; Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA.
Lund J; Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA.
Xavier-Magalhães A; Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA.
Shi M; Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA.
Liang Y; Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA.
Sterne-Weiler T; Department of Discovery Oncology, Genentech, South San Francisco, CA, USA.; Department of Oncology Bioinformatics, Genentech, South San Francisco, CA, USA.
Modrusan Z; Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA. .
Stephenson W; Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA. .
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Źródło:
Nature communications [Nat Commun] 2024 Aug 12; Vol. 15 (1), pp. 6916. Date of Electronic Publication: 2024 Aug 12.
Typ publikacji:
Journal Article
MeSH Terms:
Single-Cell Analysis*/methods
Ovarian Neoplasms*/genetics
Sequence Analysis, RNA*/methods
Polymorphism, Single Nucleotide*
Humans ; Female ; Cell Line, Tumor ; High-Throughput Nucleotide Sequencing/methods ; Transcriptome/genetics ; RNA Isoforms/genetics ; Allelic Imbalance/genetics ; Gene Expression Profiling/methods ; Gene Expression Regulation, Neoplastic
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Tytuł:
RankCompV3: a differential expression analysis algorithm based on relative expression orderings and applications in single-cell RNA transcriptomics.
Autorzy:
Yan J; Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, 350122, China.
Zeng Q; Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, 350122, China.
Wang X; Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, 350122, China. .; The Second Affiliated Hospital, Fujian Medical University, Quanzhou, 362000, China. .
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2024 Aug 07; Vol. 25 (1), pp. 259. Date of Electronic Publication: 2024 Aug 07.
Typ publikacji:
Journal Article
MeSH Terms:
Single-Cell Analysis*/methods
Algorithms*
Gene Expression Profiling*/methods
Sequence Analysis, RNA*/methods
Transcriptome/genetics ; Humans ; Software
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Unravelling tRNA fragments in DENV pathogenesis: Insights from RNA sequencing.
Autorzy:
Madhry D; Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
Kumari K; Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
Meena V; Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
Roy R; Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
Verma B; Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India. .
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Źródło:
Scientific reports [Sci Rep] 2024 Aug 07; Vol. 14 (1), pp. 18357. Date of Electronic Publication: 2024 Aug 07.
Typ publikacji:
Journal Article
MeSH Terms:
RNA, Transfer*/genetics
RNA, Transfer*/metabolism
Dengue Virus*/genetics
Dengue Virus*/pathogenicity
Sequence Analysis, RNA*
Dengue*/virology
Dengue*/genetics
RNA, Small Untranslated*/genetics
Humans ; Gene Expression Profiling/methods
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Single-cell RNA sequencing reveals that an imbalance in monocyte subsets rather than changes in gene expression patterns is a feature of postmenopausal osteoporosis.
Autorzy:
Tao L; Department of Orthopedics, First Hospital of China Medical University, Shenyang, Liaoning, 110000, China.
Jiang W; Department of Orthopedics, First Hospital of China Medical University, Shenyang, Liaoning, 110000, China.
Li H; Department of Internal Medicine, Shanghai Pudong New Area People's Hospital, Shanghai, 200000, China.
Wang X; Department of Orthopedics, First Hospital of China Medical University, Shenyang, Liaoning, 110000, China.
Tian Z; Department of Orthopedics, First Hospital of China Medical University, Shenyang, Liaoning, 110000, China.
Yang K; Department of Orthopedics, First Hospital of China Medical University, Shenyang, Liaoning, 110000, China.
Zhu Y; Department of Orthopedics, First Hospital of China Medical University, Shenyang, Liaoning, 110000, China.
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Źródło:
Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research [J Bone Miner Res] 2024 Aug 05; Vol. 39 (7), pp. 980-993.
Typ publikacji:
Journal Article
MeSH Terms:
Monocytes*/metabolism
Monocytes*/pathology
Osteoporosis, Postmenopausal*/genetics
Osteoporosis, Postmenopausal*/metabolism
Osteoporosis, Postmenopausal*/blood
Single-Cell Analysis*
Sequence Analysis, RNA*
Humans ; Female ; Middle Aged ; Aged ; Gene Expression Regulation ; Transcriptome ; Lipopolysaccharide Receptors/metabolism
Czasopismo naukowe
Full Text Finder  Link otwiera się w nowym oknieSzczegóły
Wyświetlanie 1-20 z 19067

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