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Tytuł :
Mitochondrial respiratory chain function promotes extracellular matrix integrity in cartilage.
Autorzy :
Bubb K; Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Biochemistry, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany.
Holzer T; Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Biochemistry, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany.
Nolte JL; Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
Krüger M; Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
Wilson R; Central Science Laboratory, University of Tasmania, Hobart, Tasmania, Australia.
Schlötzer-Schrehardt U; Department of Ophthalmology, University Hospital Erlangen, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany.
Brinckmann J; Department of Dermatology, Institute of Virology and Cell Biology, University of Lübeck, Lübeck, Germany.
Altmüller J; Cologne Center for Genomics, University of Cologne, Cologne, Germany; Berlin Institute of Health at Charité, Core Facility Genomics, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Aszodi A; Department for Orthopaedics and Trauma Surgery, Musculoskeletal University Center Munich (MUM), University Hospital, Ludwig-Maximilians-University (LMU), Munich, Germany.
Fleischhauer L; Department for Orthopaedics and Trauma Surgery, Musculoskeletal University Center Munich (MUM), University Hospital, Ludwig-Maximilians-University (LMU), Munich, Germany; Center for Applied Tissue Engineering and Regenerative Medicine, Munich University of Applied Sciences, Munich, Germany.
Clausen-Schaumann H; Center for Applied Tissue Engineering and Regenerative Medicine, Munich University of Applied Sciences, Munich, Germany.
Probst K; Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Biochemistry, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany.
Brachvogel B; Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Biochemistry, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany. Electronic address: .
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Źródło :
The Journal of biological chemistry [J Biol Chem] 2021 Oct; Vol. 297 (4), pp. 101224. Date of Electronic Publication: 2021 Sep 22.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
RNA-Seq*
Single-Cell Analysis*
Cartilage/*metabolism
Extracellular Matrix/*metabolism
Femur/*metabolism
Animals ; Electron Transport ; Extracellular Matrix/genetics ; Mice ; Mice, Transgenic
Czasopismo naukowe
Tytuł :
Single-Cell RNA Sequencing Reveals Endothelial Cell Transcriptome Heterogeneity Under Homeostatic Laminar Flow.
Autorzy :
Liu Z; Integrative Program for Biological & Genome Sciences (Z.L., D.L.R., V.L.B.).; McAllister Heart Institute (Z.L., D.L.R., V.L.B.).
Ruter DL; Integrative Program for Biological & Genome Sciences (Z.L., D.L.R., V.L.B.).; Now with KBI Biopharma, Inc, RTP, NC (D.L.R.).; McAllister Heart Institute (Z.L., D.L.R., V.L.B.).; Lineberger Comprehensive Cancer Center (D.L.R., Y.J., V.L.B.).
Quigley K; Department of Chemistry (K.Q.).
Tanke NT; Curriculum in Cell Biology and Physiology (N.T.T., V.L.B.).
Jiang Y; Lineberger Comprehensive Cancer Center (D.L.R., Y.J., V.L.B.).; Department of Biostatistics (Y.J.).; Department of Genetics (Y.J.).
Bautch VL; Integrative Program for Biological & Genome Sciences (Z.L., D.L.R., V.L.B.).; McAllister Heart Institute (Z.L., D.L.R., V.L.B.).; Lineberger Comprehensive Cancer Center (D.L.R., Y.J., V.L.B.).; Curriculum in Cell Biology and Physiology (N.T.T., V.L.B.).; Department of Biology, University of North Carolina, Chapel Hill (V.L.B.).
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Źródło :
Arteriosclerosis, thrombosis, and vascular biology [Arterioscler Thromb Vasc Biol] 2021 Oct; Vol. 41 (10), pp. 2575-2584. Date of Electronic Publication: 2021 Aug 26.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
Gene Expression Profiling*
Mechanotransduction, Cellular*
RNA-Seq*
Single-Cell Analysis*
Transcriptome*
Human Umbilical Vein Endothelial Cells/*metabolism
Animals ; Cells, Cultured ; Humans ; Mice ; Microscopy, Fluorescence ; Regional Blood Flow ; Stress, Mechanical
Czasopismo naukowe
Tytuł :
Human nasal wash RNA-Seq reveals distinct cell-specific innate immune responses in influenza versus SARS-CoV-2.
Autorzy :
Gao KM; Department of Medicine and.
Derr AG; Department of Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA.
Guo Z; Department of Medicine and.
Nündel K; Department of Medicine and.
Marshak-Rothstein A; Department of Medicine and.
Finberg RW; Department of Medicine and.
Wang JP; Department of Medicine and.
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Źródło :
JCI insight [JCI Insight] 2021 Nov 22; Vol. 6 (22). Date of Electronic Publication: 2021 Nov 22.
Typ publikacji :
Journal Article; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
COVID-19*/genetics
COVID-19*/immunology
Immunity, Innate*
Influenza A virus*/genetics
Influenza A virus*/immunology
Influenza, Human*/genetics
Influenza, Human*/immunology
Macrophages*/immunology
Macrophages*/virology
RNA-Seq*
SARS-CoV-2*/genetics
SARS-CoV-2*/immunology
Adult ; Female ; Humans ; Male ; Nasal Lavage
Czasopismo naukowe
Tytuł :
DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data.
Autorzy :
Chen J; Department of Computer Science, Hong Kong Baptist University, Waterloo Road, Kowloon Tong, Hong Kong.
Cheong C; Department of Computer Science, Hong Kong Baptist University, Waterloo Road, Kowloon Tong, Hong Kong.
Lan L; Department of Computer Science, Hong Kong Baptist University, Waterloo Road, Kowloon Tong, Hong Kong.
Zhou X; Department of Biomedical Engineering, Vanderbilt University, Vanderbilt Place Nashville, 37235, TN, USA.
Liu J; Department of Computer Science, Hong Kong Baptist University, Waterloo Road, Kowloon Tong, Hong Kong.
Lyu A; School of Chinese Medicine, Hong Kong Baptist University, Waterloo Road, Kowloon Tong, Hong Kong.
Cheung WK; Department of Computer Science, Hong Kong Baptist University, Waterloo Road, Kowloon Tong, Hong Kong.
Zhang L; Department of Computer Science, Hong Kong Baptist University, Waterloo Road, Kowloon Tong, Hong Kong.
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Źródło :
Briefings in bioinformatics [Brief Bioinform] 2021 Nov 05; Vol. 22 (6).
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
RNA-Seq*
Software*
COVID-19/*genetics
SARS-CoV-2/*genetics
Algorithms ; COVID-19/epidemiology ; COVID-19/virology ; Cluster Analysis ; Gene Regulatory Networks/genetics ; Humans ; Neural Networks, Computer ; SARS-CoV-2/pathogenicity ; Single-Cell Analysis
Czasopismo naukowe
Tytuł :
circFL-seq reveals full-length circular RNAs with rolling circular reverse transcription and nanopore sequencing.
Autorzy :
Liu Z; Institute of Systems Biomedicine, Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China , NHC Key Laboratory of Medical Immunology (Peking University), Beijing, China.
Tao C; Department of Human Anatomy, Histology & Embryology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
Li S; Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
Du M; Department of Microbiology & Infectious Disease Center, School of Basic Medical Science Peking University Health Science Center, Beijing, China.
Bai Y; Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
Hu X; Institute of Systems Biomedicine, Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China , NHC Key Laboratory of Medical Immunology (Peking University), Beijing, China.
Li Y; Chinese Institute for Brain Research, Beijing, China.
Chen J; Chinese Institute for Brain Research, Beijing, China.
Yang E; Institute of Systems Biomedicine, Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China , NHC Key Laboratory of Medical Immunology (Peking University), Beijing, China.; Department of Microbiology & Infectious Disease Center, School of Basic Medical Science Peking University Health Science Center, Beijing, China.; Chinese Institute for Brain Research, Beijing, China.
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Źródło :
ELife [Elife] 2021 Oct 14; Vol. 10. Date of Electronic Publication: 2021 Oct 14.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Nanopore Sequencing*
Reverse Transcription*
RNA, Circular/*chemistry
RNA-Seq/*methods
Cell Line ; Humans ; Protein Isoforms/metabolism ; RNA-Seq/instrumentation
Czasopismo naukowe
Tytuł :
A single-cell guide to retinal development: Cell fate decisions of multipotent retinal progenitors in scRNA-seq.
Autorzy :
Shiau F; John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA.
Ruzycki PA; John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA.
Clark BS; John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA. Electronic address: .
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Źródło :
Developmental biology [Dev Biol] 2021 Oct; Vol. 478, pp. 41-58. Date of Electronic Publication: 2021 Jun 17.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Review
MeSH Terms :
RNA-Seq*
Single-Cell Analysis*
Multipotent Stem Cells/*cytology
Retina/*growth & development
Retinal Neurons/*cytology
Animals ; Cell Lineage ; Gene Expression Regulation, Developmental ; Humans ; Multipotent Stem Cells/metabolism ; Neural Stem Cells/cytology ; Neural Stem Cells/metabolism ; Neurogenesis ; Retina/cytology ; Retina/embryology ; Retinal Diseases/genetics ; Retinal Diseases/metabolism ; Retinal Diseases/pathology ; Retinal Neurons/metabolism ; Transcriptome
Czasopismo naukowe
Tytuł :
Relationship between the Phenylpropanoid Pathway and Dwarfism of Paspalum seashore Based on RNA-Seq and iTRAQ.
Autorzy :
Zhang Y; College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing 210095, China.
Liu J; College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing 210095, China.
Yu J; College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing 210095, China.
Zhang H; College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing 210095, China.
Yang Z; College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing 210095, China.
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Źródło :
International journal of molecular sciences [Int J Mol Sci] 2021 Sep 03; Vol. 22 (17). Date of Electronic Publication: 2021 Sep 03.
Typ publikacji :
Journal Article
MeSH Terms :
Gene Expression Regulation, Plant*
Mutation*
Paspalum*/genetics
Paspalum*/metabolism
Proteomics*
RNA-Seq*
Whole Exome Sequencing
Czasopismo naukowe
Tytuł :
Comparative Transcriptome Analysis of Human Adipose-Derived Stem Cells Undergoing Osteogenesis in 2D and 3D Culture Conditions.
Autorzy :
Kim BC; Department of Dentistry, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea.
Kwack KH; Department of Dentistry, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea.
Chun J; Department of Dentistry, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea.
Lee JH; Department of Oral Microbiology, School of Dentistry, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea.; Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea.
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Źródło :
International journal of molecular sciences [Int J Mol Sci] 2021 Jul 26; Vol. 22 (15). Date of Electronic Publication: 2021 Jul 26.
Typ publikacji :
Comparative Study; Journal Article
MeSH Terms :
Cell Culture Techniques*
Osteogenesis*
RNA-Seq*
Adipose Tissue/*metabolism
Stem Cells/*metabolism
Adipose Tissue/cytology ; Humans ; Stem Cells/cytology
Czasopismo naukowe
Tytuł :
Are dropout imputation methods for scRNA-seq effective for scHi-C data?
Autorzy :
Han C; Ohio State University.
Xie Q; Ohio State University.
Lin S; Translational Data Analytics Institute at the Ohio State University.
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Źródło :
Briefings in bioinformatics [Brief Bioinform] 2021 Jul 20; Vol. 22 (4).
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
Algorithms*
Computer Simulation*
RNA, Small Cytoplasmic*/genetics
RNA, Small Cytoplasmic*/metabolism
RNA-Seq*
Single-Cell Analysis*
Software*
Humans
Czasopismo naukowe
Tytuł :
Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq.
Autorzy :
Vivek AT; National Institute of Plant Genome Research in New Delhi, India.
Kumar S; National Institute of Plant Genome Research in New Delhi.
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Źródło :
Briefings in bioinformatics [Brief Bioinform] 2021 Jul 20; Vol. 22 (4).
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't; Review
MeSH Terms :
Databases, Nucleic Acid*
Gene Expression Regulation, Plant*
Plants*/genetics
Plants*/metabolism
RNA, Plant*/biosynthesis
RNA, Plant*/genetics
RNA, Untranslated*/biosynthesis
RNA, Untranslated*/genetics
RNA-Seq*
Software*
Czasopismo naukowe
Tytuł :
scAPAtrap: identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data.
Autorzy :
Wu X; Department of Automation in Xiamen University.
Liu T; Department of Automation in Xiamen University.
Ye C; College of the Environment and Ecology in Xiamen University.
Ye W; Department of Automation in Xiamen University.
Ji G; Department of Automation in Xiamen University.
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Źródło :
Briefings in bioinformatics [Brief Bioinform] 2021 Jul 20; Vol. 22 (4).
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Databases, Nucleic Acid*
Genome*
RNA 3' Polyadenylation Signals*
RNA-Seq*
Single-Cell Analysis*
Software*
Molecular Sequence Annotation
Czasopismo naukowe
Tytuł :
Transcriptome analysis of gene expression changes upon enzymatic dissociation in skeletal myoblasts.
Autorzy :
Miyawaki-Kuwakado A; Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
Wu Q; Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
Harada A; Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
Tomimatsu K; Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
Fujii T; Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
Maehara K; Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
Ohkawa Y; Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
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Źródło :
Genes to cells : devoted to molecular & cellular mechanisms [Genes Cells] 2021 Jul; Vol. 26 (7), pp. 530-540. Date of Electronic Publication: 2021 Jun 08.
Typ publikacji :
Journal Article
MeSH Terms :
Transcriptome*
Myoblasts/*metabolism
RNA-Seq/*methods
Animals ; Cell Line ; Mice ; Myoblasts/drug effects ; NIH 3T3 Cells ; RNA-Seq/standards ; Trypsin/pharmacology
Czasopismo naukowe
Tytuł :
Confronting false discoveries in single-cell differential expression.
Autorzy :
Squair JW; Center for Neuroprosthetics and Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.; NeuroRestore, Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.; International Collaboration on Repair Discoveries (ICORD), University of British Columbia, Vancouver, BC, Canada.
Gautier M; Center for Neuroprosthetics and Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.; NeuroRestore, Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
Kathe C; Center for Neuroprosthetics and Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.; NeuroRestore, Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
Anderson MA; Center for Neuroprosthetics and Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.; NeuroRestore, Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
James ND; Center for Neuroprosthetics and Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.; NeuroRestore, Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
Hutson TH; Center for Neuroprosthetics and Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.; NeuroRestore, Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
Hudelle R; Center for Neuroprosthetics and Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.; NeuroRestore, Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
Qaiser T; International Collaboration on Repair Discoveries (ICORD), University of British Columbia, Vancouver, BC, Canada.
Matson KJE; Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
Barraud Q; Center for Neuroprosthetics and Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.; NeuroRestore, Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
Levine AJ; Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
La Manno G; Center for Neuroprosthetics and Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
Skinnider MA; Center for Neuroprosthetics and Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. .; NeuroRestore, Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland. .; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada. .
Courtine G; Center for Neuroprosthetics and Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. .; NeuroRestore, Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland. .
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Źródło :
Nature communications [Nat Commun] 2021 Sep 28; Vol. 12 (1), pp. 5692. Date of Electronic Publication: 2021 Sep 28.
Typ publikacji :
Journal Article; Research Support, N.I.H., Intramural; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Data Accuracy*
Models, Statistical*
RNA-Seq/*methods
Single-Cell Analysis/*methods
Animals ; Biological Variation, Individual ; Biological Variation, Population ; Datasets as Topic ; Gene Expression Regulation ; Humans ; Mice ; RNA-Seq/statistics & numerical data ; Rabbits ; Rats ; Single-Cell Analysis/statistics & numerical data ; Swine
Czasopismo naukowe
Tytuł :
Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning.
Autorzy :
Körtel N; Institute of Molecular Biology (IMB), Mainz 55128, Germany.
Rücklé C; Institute of Molecular Biology (IMB), Mainz 55128, Germany.
Zhou Y; Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt 60438, Germany.
Busch A; Institute of Molecular Biology (IMB), Mainz 55128, Germany.
Hoch-Kraft P; Institute of Molecular Biology (IMB), Mainz 55128, Germany.
Sutandy FXR; Institute of Molecular Biology (IMB), Mainz 55128, Germany.; Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt 60590, Germany.
Haase J; Institute of Molecular Medicine, Sect. Molecular Cell Biology, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Halle 06120, Germany.
Pradhan M; Institute of Molecular Biology (IMB), Mainz 55128, Germany.
Musheev M; Institute of Molecular Biology (IMB), Mainz 55128, Germany.
Ostareck D; Department of Intensive Care Medicine, University Hospital RWTH Aachen, Aachen 52074, Germany.
Ostareck-Lederer A; Department of Intensive Care Medicine, University Hospital RWTH Aachen, Aachen 52074, Germany.
Dieterich C; Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg 69120, Germany.; German Centre for Cardiovascular Research (DZHK) - Partner Site Heidelberg/Mannheim, Heidelberg 69120, Germany.
Hüttelmaier S; Institute of Molecular Medicine, Sect. Molecular Cell Biology, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Halle 06120, Germany.
Niehrs C; Institute of Molecular Biology (IMB), Mainz 55128, Germany.; Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany.
Rausch O; STORM Therapeutics Ltd, Cambridge CB22 3AT, UK.
Dominissini D; Cancer Research Center and Wohl Institute for Translational Medicine, Chaim Sheba Medical Center, Tel HaShomer, and Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel.
König J; Institute of Molecular Biology (IMB), Mainz 55128, Germany.
Zarnack K; Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt 60438, Germany.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2021 Sep 20; Vol. 49 (16), pp. e92.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Machine Learning*
RNA Processing, Post-Transcriptional*
Adenosine/*analogs & derivatives
RNA-Seq/*methods
Adenosine/chemistry ; Adenosine/metabolism ; Animals ; HEK293 Cells ; Humans ; Methyltransferases/genetics ; Methyltransferases/metabolism ; Mice ; Mouse Embryonic Stem Cells/metabolism ; Nucleotide Motifs ; RNA, Messenger/chemistry ; RNA, Messenger/metabolism ; RNA-Seq/standards ; Sensitivity and Specificity
Czasopismo naukowe
Tytuł :
RNA-seq profiling reveals PBMC RNA as a potential biomarker for hepatocellular carcinoma.
Autorzy :
Han Z; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Futian District, Shenzhen, 518033, Guangdong Province, China.; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China.
Feng W; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Futian District, Shenzhen, 518033, Guangdong Province, China.; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China.
Hu R; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Futian District, Shenzhen, 518033, Guangdong Province, China.; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China.
Ge Q; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
Ma W; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Futian District, Shenzhen, 518033, Guangdong Province, China.; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China.
Zhang W; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Futian District, Shenzhen, 518033, Guangdong Province, China.; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China.
Xu S; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Futian District, Shenzhen, 518033, Guangdong Province, China.; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China.
Zhan B; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Futian District, Shenzhen, 518033, Guangdong Province, China.; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China.
Zhang L; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Futian District, Shenzhen, 518033, Guangdong Province, China.; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China.
Sun X; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Futian District, Shenzhen, 518033, Guangdong Province, China. .; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China. .
Zhou X; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Futian District, Shenzhen, 518033, Guangdong Province, China. .; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China. .
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Źródło :
Scientific reports [Sci Rep] 2021 Sep 07; Vol. 11 (1), pp. 17797. Date of Electronic Publication: 2021 Sep 07.
Typ publikacji :
Comparative Study; Journal Article; Research Support, Non-U.S. Gov't; Validation Study
MeSH Terms :
RNA-Seq*
Biomarkers, Tumor/*blood
Carcinoma, Hepatocellular/*blood
Leukocytes, Mononuclear/*chemistry
Liver Neoplasms/*blood
RNA, Neoplasm/*blood
Carcinoma, Hepatocellular/genetics ; DNA Primers ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene Ontology ; Gene Regulatory Networks ; Humans ; Liver Neoplasms/genetics ; Male ; Real-Time Polymerase Chain Reaction
Czasopismo naukowe
Tytuł :
RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq data.
Autorzy :
Schmidt F; Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis St, 138672, Singapore.
Ranjan B; Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis St, 138672, Singapore.
Lin QXX; Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis St, 138672, Singapore.
Krishnan V; DUKE-NUS Medical School, 8 College Rd, 169857, Singapore.
Joanito I; Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis St, 138672, Singapore.
Honardoost MA; Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis St, 138672, Singapore.; Department of Medicine, School of Medicine, National University of Singapore, 1 Kent Ridge Road, level 10, NUHS Tower Block, 119228, Singapore.
Nawaz Z; Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis St, 138672, Singapore.
Venkatesh PN; Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis St, 138672, Singapore.
Tan J; Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis St, 138672, Singapore.
Rayan NA; Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis St, 138672, Singapore.
Ong ST; DUKE-NUS Medical School, 8 College Rd, 169857, Singapore.; Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
Prabhakar S; Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis St, 138672, Singapore.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2021 Sep 07; Vol. 49 (15), pp. 8505-8519.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Algorithms*
Cluster Analysis*
RNA, Small Cytoplasmic/*genetics
RNA-Seq/*methods
Single-Cell Analysis/*methods
Animals ; Arthritis, Rheumatoid/genetics ; Bone Marrow Cells/metabolism ; COVID-19/blood ; COVID-19/pathology ; Cohort Studies ; Datasets as Topic ; Humans ; Leukocytes, Mononuclear/metabolism ; Leukocytes, Mononuclear/pathology ; Mice ; Organ Specificity ; Quality Control ; RNA-Seq/standards ; Single-Cell Analysis/standards ; Transcriptome
Czasopismo naukowe
Tytuł :
MITGARD: an automated pipeline for mitochondrial genome assembly in eukaryotic species using RNA-seq data.
Autorzy :
Nachtigall PG; Laboratório Especial de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.
Grazziotin FG; Laboratório de Coleções Zoológicas, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.
Junqueira-de-Azevedo ILM; Laboratório Especial de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.
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Źródło :
Briefings in bioinformatics [Brief Bioinform] 2021 Sep 02; Vol. 22 (5).
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Genome, Mitochondrial*
RNA-Seq*
Software*
Bothrops/*genetics
Animals ; Bothrops/classification ; Eukaryotic Cells
Czasopismo naukowe
Tytuł :
Adaptive Total-Variation Regularized Low-Rank Representation for Analyzing Single-Cell RNA-seq Data.
Autorzy :
Liu JX; School of Computer Science, Qufu Normal University, Rizhao, China.
Wang CY; School of Computer Science, Qufu Normal University, Rizhao, China.
Gao YL; Qufu Normal University Library, Qufu Normal University, Rizhao, China.
Zhang Y; College of Mathematics and Systems Science, Shandong University of Science and Technology, Qingdao, China.
Wang J; School of Computer Science, Qufu Normal University, Rizhao, China. .
Li SJ; School of Computer Science, Qufu Normal University, Rizhao, China.
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Źródło :
Interdisciplinary sciences, computational life sciences [Interdiscip Sci] 2021 Sep; Vol. 13 (3), pp. 476-489. Date of Electronic Publication: 2021 Jun 02.
Typ publikacji :
Journal Article
MeSH Terms :
RNA-Seq*
Algorithms ; Cluster Analysis ; Gene Expression Profiling ; Single-Cell Analysis
Czasopismo naukowe
Tytuł :
Cross-species integration of single-cell RNA-seq resolved alveolar-epithelial transitional states in idiopathic pulmonary fibrosis.
Autorzy :
Huang KY; Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke-NUS Medical School, Singapore, Republic of Singapore.
Petretto E; Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke-NUS Medical School, Singapore, Republic of Singapore.
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Źródło :
American journal of physiology. Lung cellular and molecular physiology [Am J Physiol Lung Cell Mol Physiol] 2021 Sep 01; Vol. 321 (3), pp. L491-L506. Date of Electronic Publication: 2021 Jun 16.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Gene Expression Regulation*
Idiopathic Pulmonary Fibrosis*/genetics
Idiopathic Pulmonary Fibrosis*/metabolism
Idiopathic Pulmonary Fibrosis*/pathology
RNA-Seq*
Single-Cell Analysis*
Alveolar Epithelial Cells/*metabolism
Respiratory Mucosa/*metabolism
Alveolar Epithelial Cells/pathology ; Animals ; Disease Models, Animal ; Humans ; Mice ; Mice, Knockout ; Respiratory Mucosa/pathology ; Species Specificity
Czasopismo naukowe
Tytuł :
Identification and validation of 12 immune-related genes as a prognostic signature for colon adenocarcinoma.
Autorzy :
Tang D; The First Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China.
Huang W; The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
Yang Z; The First Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China.
Wu X; School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
Sang X; School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
Wang K; School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
Cao G; School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
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Źródło :
Journal of biochemical and molecular toxicology [J Biochem Mol Toxicol] 2021 Sep; Vol. 35 (9), pp. e22852. Date of Electronic Publication: 2021 Aug 15.
Typ publikacji :
Journal Article; Validation Study
MeSH Terms :
Adenocarcinoma*/genetics
Adenocarcinoma*/metabolism
Adenocarcinoma*/mortality
Colonic Neoplasms*/genetics
Colonic Neoplasms*/metabolism
Colonic Neoplasms*/mortality
Databases, Nucleic Acid*
Gene Expression Regulation, Neoplastic*
RNA-Seq*
Disease-Free Survival ; Female ; Humans ; Male ; Survival Rate
Czasopismo naukowe

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