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Tytuł :
Identifying of miR-98-5p/IGF1 axis contributes breast cancer progression using comprehensive bioinformatic analyses methods and experiments validation.
Autorzy :
Sun D; Clinical Pharmacology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121001, China.
Luo X; Clinical Laboratory, The Third Affiliated Hospital of Jinzhou Medical University, Jinzhou 121000, China.
Ma L; Intensive Care Unit, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121001, China.
Wang Y; Blood Transfusion Department, The Third Affiliated Hospital of Jinzhou Medical University, Jinzhou 121000, China.
Zhang F; Intensive Care Unit, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121001, China. Electronic address: .
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Źródło :
Life sciences [Life Sci] 2020 Nov 15; Vol. 261, pp. 118435. Date of Electronic Publication: 2020 Sep 17.
Typ publikacji :
Journal Article
MeSH Terms :
Gene Expression Regulation, Neoplastic*
Gene Regulatory Networks*
Breast Neoplasms/*genetics
Insulin-Like Growth Factor I/*genetics
MicroRNAs/*genetics
Animals ; Cell Line, Tumor ; Computational Biology ; Disease Progression ; Female ; Gene Ontology ; Humans ; Mice, Inbred BALB C ; Mice, Nude
Czasopismo naukowe
Tytuł :
Comprehensive analysis of differentially expressed microRNAs and mRNAs involved in diabetic corneal neuropathy.
Autorzy :
Zhang Y; Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan 430060, China; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao 266071, China.
Jiang H; Qingdao Eye Hospital of Shandong First Medical University, Qingdao 266071, China; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao 266071, China.
Dou S; Qingdao Eye Hospital of Shandong First Medical University, Qingdao 266071, China; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao 266071, China.
Zhang B; Qingdao Eye Hospital of Shandong First Medical University, Qingdao 266071, China; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao 266071, China.
Qi X; Qingdao Eye Hospital of Shandong First Medical University, Qingdao 266071, China; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao 266071, China.
Li J; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao 266071, China.
Zhou Q; Qingdao Eye Hospital of Shandong First Medical University, Qingdao 266071, China; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao 266071, China.
Li W; Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan 430060, China; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao 266071, China.
Chen C; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao 266071, China.
Wang Q; Qingdao Eye Hospital of Shandong First Medical University, Qingdao 266071, China; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao 266071, China. Electronic address: .
Xie L; Qingdao Eye Hospital of Shandong First Medical University, Qingdao 266071, China; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao 266071, China. Electronic address: .
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Źródło :
Life sciences [Life Sci] 2020 Nov 15; Vol. 261, pp. 118456. Date of Electronic Publication: 2020 Sep 19.
Typ publikacji :
Journal Article
MeSH Terms :
Gene Regulatory Networks*
Corneal Diseases/*genetics
Diabetic Neuropathies/*genetics
MicroRNAs/*genetics
RNA, Messenger/*genetics
Animals ; Cornea/innervation ; Cornea/pathology ; Corneal Diseases/pathology ; Diabetic Neuropathies/pathology ; Hyperglycemia/genetics ; Hyperglycemia/pathology ; Male ; Mice, Inbred C57BL
Czasopismo naukowe
Tytuł :
An integrative gene network-based approach to uncover the cellular and molecular infrastructures of schizophrenia.
Autorzy :
Bozorgmehr A; Iran Psychiatric Hospital, Iran University of Medical Sciences (IUMS), Tehran, Iran. Electronic address: .
Sadeghi B; Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran. Electronic address: .
Tabatabaei Zavari ES; Stem Cell Preparation Unit, Eye Research Center, Farabi Eye Hospital, Tehran University of Medical Sciences (TUMS), Tehran, Iran.
Bahrami E; Science and Research Branch, Islamic Azad University, Tehran, Iran.
Zamani F; Department of Psychology, Kharazmi University, Tehran, Iran.
Shahbazi A; Cellular and Molecular Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran; Department of Neuroscience, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran. Electronic address: .
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Źródło :
Life sciences [Life Sci] 2020 Nov 01; Vol. 260, pp. 118345. Date of Electronic Publication: 2020 Aug 24.
Typ publikacji :
Journal Article
MeSH Terms :
Gene Expression Regulation*
Gene Regulatory Networks*
Genetic Predisposition to Disease*
Polymorphism, Single Nucleotide*
Biomarkers/*analysis
Schizophrenia/*genetics
Genome-Wide Association Study ; Humans
Czasopismo naukowe
Tytuł :
A novel lncRNA-miRNA-mRNA competitive endogenous RNA network for uveal melanoma prognosis constructed by weighted gene co-expression network analysis.
Autorzy :
Yu H; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China.
Cheng Y; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China.
Li W; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China.
Li Z; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China.
Wu P; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China.
Qiu S; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China.
Zeng B; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China.
Huang B; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China. Electronic address: .
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Źródło :
Life sciences [Life Sci] 2020 Nov 01; Vol. 260, pp. 118409. Date of Electronic Publication: 2020 Sep 11.
Typ publikacji :
Journal Article
MeSH Terms :
Gene Expression Regulation, Neoplastic*
Gene Regulatory Networks*
Biomarkers, Tumor/*genetics
Melanoma/*pathology
MicroRNAs/*genetics
RNA, Long Noncoding/*genetics
RNA, Messenger/*genetics
Uveal Neoplasms/*pathology
Apoptosis ; Cell Proliferation ; Humans ; Melanoma/genetics ; Prognosis ; Survival Rate ; Tumor Cells, Cultured ; Uveal Neoplasms/genetics
SCR Disease Name :
Uveal melanoma
Czasopismo naukowe
Tytuł :
LAMP: disease classification derived from layered assessment on modules and pathways in the human gene network.
Autorzy :
Mi Z; Beijing Advanced Innovation Center for Big Data and Brain Computing and LMIB, Beihang University, Beijing, China.; Peng Cheng Laboratory, Shenzhen, Guangdong Province, China.; School of Mathematical Sciences and Shenyuan Honors College, Beihang University, Beijing, China.
Guo B; Beijing Advanced Innovation Center for Big Data and Brain Computing and LMIB, Beihang University, Beijing, China. .; Peng Cheng Laboratory, Shenzhen, Guangdong Province, China. .; School of Mathematical Sciences and Shenyuan Honors College, Beihang University, Beijing, China. .
Yang X; Beijing Advanced Innovation Center for Big Data and Brain Computing and LMIB, Beihang University, Beijing, China.; Peng Cheng Laboratory, Shenzhen, Guangdong Province, China.; School of Mathematical Sciences and Shenyuan Honors College, Beihang University, Beijing, China.
Yin Z; Beijing Advanced Innovation Center for Big Data and Brain Computing and LMIB, Beihang University, Beijing, China.; Peng Cheng Laboratory, Shenzhen, Guangdong Province, China.; School of Mathematical Sciences and Shenyuan Honors College, Beihang University, Beijing, China.
Zheng Z; Beijing Advanced Innovation Center for Big Data and Brain Computing and LMIB, Beihang University, Beijing, China.; Peng Cheng Laboratory, Shenzhen, Guangdong Province, China.; School of Mathematical Sciences and Shenyuan Honors College, Beihang University, Beijing, China.
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Źródło :
BMC bioinformatics [BMC Bioinformatics] 2020 Oct 30; Vol. 21 (1), pp. 487. Date of Electronic Publication: 2020 Oct 30.
Typ publikacji :
Journal Article
MeSH Terms :
Algorithms*
Gene Regulatory Networks*
Disease/*classification
Disease/*genetics
Signal Transduction/*genetics
Cluster Analysis ; Genetic Therapy ; Humans
Czasopismo naukowe
Tytuł :
Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells.
Autorzy :
Tarbier M; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
Mackowiak SD; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
Frade J; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.
Catuara-Solarz S; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.
Biryukova I; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
Gelali E; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.
Menéndez DB; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.
Zapata L; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.; Center for Evolution and Cancer, The Institute of Cancer Research, London, UK.
Ossowski S; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.; Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain.; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
Bienko M; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.
Gallant CJ; Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
Friedländer MR; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden. .
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Źródło :
Nature communications [Nat Commun] 2020 Oct 28; Vol. 11 (1), pp. 5445. Date of Electronic Publication: 2020 Oct 28.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Gene Regulatory Networks*
Protein Interaction Maps*
Cell Nucleus/*genetics
Animals ; Cell Line ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Knockout Techniques ; Genetic Variation ; Mice ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Mouse Embryonic Stem Cells/cytology ; Mouse Embryonic Stem Cells/metabolism ; RNA-Seq ; Ribonuclease III/deficiency ; Ribonuclease III/genetics ; Ribonuclease III/metabolism ; Single-Cell Analysis ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcriptome
Czasopismo naukowe
Tytuł :
PyGNA: a unified framework for geneset network analysis.
Autorzy :
Fanfani V; School of Biological Science, The University of Edinburgh, Edinburgh, EH9 3BF, UK.
Cassano F; School of Biological Science, The University of Edinburgh, Edinburgh, EH9 3BF, UK.
Stracquadanio G; School of Biological Science, The University of Edinburgh, Edinburgh, EH9 3BF, UK. .
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Źródło :
BMC bioinformatics [BMC Bioinformatics] 2020 Oct 22; Vol. 21 (1), pp. 476. Date of Electronic Publication: 2020 Oct 22.
Typ publikacji :
Journal Article
MeSH Terms :
Gene Regulatory Networks*
Programming Languages*
Software*
Algorithms ; Computer Simulation ; Sequence Analysis, RNA ; Stochastic Processes
Czasopismo naukowe
Tytuł :
Differential gene regulatory pattern in the human brain from schizophrenia using transcriptomic-causal network.
Autorzy :
Yazdani A; Department of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Genetic Medicine Building, CB#7361, Chapel Hill, NC, 27599-7264, USA. .
Mendez-Giraldez R; Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA.
Yazdani A; Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Kosorok MR; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
Roussos P; Department of Psychiatry, Pamela Sklar Division of Psychiatric Genomics and Friedman Brain Institute, Icahn School of Medicine At Mount Sinai, Hess CSM Building Floor 9 Room 107, 1470 Madison Ave, New York, NY, 10029, USA. .; Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, 10468, USA. .
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Źródło :
BMC bioinformatics [BMC Bioinformatics] 2020 Oct 21; Vol. 21 (1), pp. 469. Date of Electronic Publication: 2020 Oct 21.
Typ publikacji :
Journal Article
MeSH Terms :
Computational Biology*
Gene Regulatory Networks*
Transcriptome*
Brain/*metabolism
Schizophrenia/*genetics
Humans
Czasopismo naukowe
Tytuł :
Network perturbation analysis in human bronchial epithelial cells following SARS-CoV2 infection.
Autorzy :
Nunnari G; Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy. Electronic address: .
Sanfilippo C; IRCCS Centro Neurolesi Bonino Pulejo, Strada Statale 113, C.da Casazza, 98124, Messina, Italy. Electronic address: .
Castrogiovanni P; Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Italy. Electronic address: .
Imbesi R; Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Italy. Electronic address: .i.
Li Volti G; Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 97, 95125, Catania, Italy. Electronic address: .
Barbagallo I; Department of Drug Sciences, University of Catania, Viale Andrea Doria, 6, 95125, Catania, Italy. Electronic address: .
Musumeci G; Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Italy. Electronic address: .
Di Rosa M; Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Italy. Electronic address: .
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Źródło :
Experimental cell research [Exp Cell Res] 2020 Oct 15; Vol. 395 (2), pp. 112204. Date of Electronic Publication: 2020 Jul 28.
Typ publikacji :
Journal Article
MeSH Terms :
Gene Regulatory Networks*
Transcriptome*
Bronchi/*metabolism
Coronavirus Infections/*genetics
Pneumonia, Viral/*genetics
Respiratory Mucosa/*metabolism
Bronchi/pathology ; Carcinoembryonic Antigen/genetics ; Carcinoembryonic Antigen/metabolism ; Coronavirus Infections/metabolism ; Drug Discovery/methods ; Dyneins/genetics ; Dyneins/metabolism ; GPI-Linked Proteins/genetics ; GPI-Linked Proteins/metabolism ; Granulocyte Colony-Stimulating Factor/genetics ; Granulocyte Colony-Stimulating Factor/metabolism ; Humans ; Immunity, Innate ; Machine Learning ; Pandemics ; Pneumonia, Viral/metabolism ; Up-Regulation
SCR Disease Name :
COVID-19
Czasopismo naukowe
Tytuł :
Genome-Wide Analysis of the FOXA1 Transcriptional Network Identifies Novel Protein-Coding and Long Noncoding RNA Targets in Colorectal Cancer Cells.
Autorzy :
Lazar SB; Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA.
Pongor L; Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, CCR, NCI, NIH, Bethesda, Maryland, USA.
Li XL; Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA.
Grammatikakis I; Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA.
Muys BR; Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA.
Dangelmaier EA; Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA.
Redon CE; Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, CCR, NCI, NIH, Bethesda, Maryland, USA.
Jang SM; Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, CCR, NCI, NIH, Bethesda, Maryland, USA.
Walker RL; Molecular Genetics Section, Genetics Branch, CCR, NCI, NIH, Bethesda, Maryland, USA.
Tang W; Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, Maryland, USA.
Ambs S; Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, Maryland, USA.
Harris CC; Molecular Genetics and Carcinogenesis Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, Maryland, USA.
Meltzer PS; Molecular Genetics Section, Genetics Branch, CCR, NCI, NIH, Bethesda, Maryland, USA.
Aladjem MI; Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, CCR, NCI, NIH, Bethesda, Maryland, USA.
Lal A; Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA .
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Źródło :
Molecular and cellular biology [Mol Cell Biol] 2020 Oct 13; Vol. 40 (21). Date of Electronic Publication: 2020 Oct 13 (Print Publication: 2020).
Typ publikacji :
Journal Article; Research Support, N.I.H., Intramural
MeSH Terms :
Gene Regulatory Networks*
Colorectal Neoplasms/*genetics
Hepatocyte Nuclear Factor 3-alpha/*genetics
RNA, Long Noncoding/*genetics
Adenocarcinoma/genetics ; Adenocarcinoma/pathology ; Anoikis/genetics ; Carcinoembryonic Antigen/genetics ; Carcinoembryonic Antigen/metabolism ; Cell Differentiation/genetics ; Cell Line, Tumor ; Chromatin Immunoprecipitation ; Colorectal Neoplasms/pathology ; Enhancer Elements, Genetic ; GPI-Linked Proteins/genetics ; GPI-Linked Proteins/metabolism ; Gene Expression Regulation, Neoplastic ; Genome-Wide Association Study ; Hepatocyte Nuclear Factor 3-alpha/metabolism ; High-Throughput Nucleotide Sequencing ; Humans ; Proteins/genetics ; Pseudogenes
Czasopismo naukowe
Tytuł :
Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors.
Autorzy :
Tu X; The State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Shandong, China.; State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
Mejía-Guerra MK; Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA. .
Valdes Franco JA; Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA.
Tzeng D; State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
Chu PY; State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
Shen W; State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
Wei Y; Department of Statistics, The Chinese University of Hong Kong, Hong Kong, China.
Dai X; The State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Shandong, China.
Li P; The State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Shandong, China. .
Buckler ES; Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA.; School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA.; Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, USA.
Zhong S; State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China. .
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Źródło :
Nature communications [Nat Commun] 2020 Oct 09; Vol. 11 (1), pp. 5089. Date of Electronic Publication: 2020 Oct 09.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Gene Regulatory Networks*
Plant Leaves/*genetics
Transcription Factors/*genetics
Zea mays/*genetics
Chromatin Immunoprecipitation Sequencing ; Computational Biology/methods ; Machine Learning ; Plant Proteins/genetics ; Poaceae/genetics ; Transcription Factors/metabolism
Czasopismo naukowe
Tytuł :
Two-step mixed model approach to analyzing differential alternative RNA splicing.
Autorzy :
Luo L; Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico.; University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico.
Kang H; Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico.; University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico.
Li X; Department of Mathematics and Statistics, University of New Mexico, Albuquerque, New Mexico.
Ness SA; Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico.; University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico.
Stidley CA; Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico.
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Źródło :
PloS one [PLoS One] 2020 Oct 09; Vol. 15 (10), pp. e0232646. Date of Electronic Publication: 2020 Oct 09 (Print Publication: 2020).
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
Alternative Splicing*
Gene Regulatory Networks*
Carcinoma, Adenoid Cystic/*genetics
Gene Expression Profiling/*methods
Leukemia, Myeloid, Acute/*genetics
Algorithms ; Child ; Gene Expression Regulation, Neoplastic ; Humans ; Linear Models ; Models, Genetic ; RNA, Messenger/genetics ; Sequence Analysis, RNA/methods ; Whole Exome Sequencing
Czasopismo naukowe
Tytuł :
A fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida.
Autorzy :
Calero P; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.
Volke DC; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.
Lowe PT; School of Chemistry, University of St. Andrews, KY16 9ST St, Andrews, UK.
Gotfredsen CH; Department of Chemistry, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.
O'Hagan D; School of Chemistry, University of St. Andrews, KY16 9ST St, Andrews, UK.
Nikel PI; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark. .
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Źródło :
Nature communications [Nat Commun] 2020 Oct 07; Vol. 11 (1), pp. 5045. Date of Electronic Publication: 2020 Oct 07.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Gene Regulatory Networks*
Halogenation/*genetics
Metabolic Engineering/*methods
Pseudomonas putida/*metabolism
Synthetic Biology/*methods
Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Biosynthetic Pathways/genetics ; DNA-Directed RNA Polymerases/genetics ; Fluorides/metabolism ; Fluorine/metabolism ; Membrane Transport Proteins/genetics ; Membrane Transport Proteins/metabolism ; Mutation ; Pseudomonas putida/genetics ; RNA, Bacterial/genetics ; Riboswitch/genetics ; Viral Proteins/genetics
Czasopismo naukowe
Tytuł :
Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage.
Autorzy :
Espah Borujeni A; Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
Zhang J; Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
Doosthosseini H; Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
Nielsen AAK; Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
Voigt CA; Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .
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Źródło :
Nature communications [Nat Commun] 2020 Oct 05; Vol. 11 (1), pp. 5001. Date of Electronic Publication: 2020 Oct 05.
Typ publikacji :
Journal Article; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Gene Regulatory Networks*
DNA-Directed RNA Polymerases/*metabolism
Ribosomes/*metabolism
Escherichia coli/genetics ; Escherichia coli/growth & development ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Models, Theoretical ; Protein Biosynthesis ; RNA-Seq ; Synthetic Biology ; Transcription, Genetic
Czasopismo naukowe
Tytuł :
Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation.
Autorzy :
Xin J; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.; CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China.; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China.; Bio-X Program, Stanford University, Stanford, CA, 94305, USA.; University of Chinese Academy of Sciences, 100101, Beijing, China.
Zhang H; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China.
He Y; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China.; University of Chinese Academy of Sciences, 100101, Beijing, China.
Duren Z; Departments of Statistics, Stanford University, Stanford, CA, 94305, USA.; Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, 29646, USA.
Bai C; High Altitude Medical Research Center, School of Medicine, Tibetan University, 850000, Lhasa, China.
Chen L; CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China.; University of Chinese Academy of Sciences, 100101, Beijing, China.
Luo X; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China.; University of Chinese Academy of Sciences, 100101, Beijing, China.
Yan DS; School of Mathematical Science, Inner Mongolia University, 010021, Huhhot, China.
Zhang C; CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China.; University of Chinese Academy of Sciences, 100101, Beijing, China.
Zhu X; Departments of Statistics, Stanford University, Stanford, CA, 94305, USA.
Yuan Q; CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China.; University of Chinese Academy of Sciences, 100101, Beijing, China.
Feng Z; CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China.; University of Chinese Academy of Sciences, 100101, Beijing, China.
Cui C; High Altitude Medical Research Center, School of Medicine, Tibetan University, 850000, Lhasa, China.
Qi X; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China.
Ouzhuluobu; High Altitude Medical Research Center, School of Medicine, Tibetan University, 850000, Lhasa, China.
Wong WH; Bio-X Program, Stanford University, Stanford, CA, 94305, USA. .; Departments of Statistics, Stanford University, Stanford, CA, 94305, USA. .; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA. .
Wang Y; CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China. .; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China. .; University of Chinese Academy of Sciences, 100101, Beijing, China. .; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 330106, Hangzhou, China. .
Su B; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China. .; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China. .
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Źródło :
Nature communications [Nat Commun] 2020 Oct 01; Vol. 11 (1), pp. 4928. Date of Electronic Publication: 2020 Oct 01.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Gene Regulatory Networks*
Models, Genetic*
Acclimatization/*genetics
Chromatin/*metabolism
Ethnic Groups/*genetics
Altitude ; Altitude Sickness/ethnology ; Altitude Sickness/genetics ; Altitude Sickness/metabolism ; Basic Helix-Loop-Helix Transcription Factors/genetics ; Cell Hypoxia/genetics ; Cells, Cultured ; Chromatin/genetics ; Chromatin Immunoprecipitation Sequencing ; Disease Resistance/genetics ; Female ; Gene Expression Regulation ; Human Umbilical Vein Endothelial Cells ; Humans ; Hypoxia/genetics ; Hypoxia/metabolism ; Oxygen/metabolism ; Polymorphism, Single Nucleotide ; Pregnancy ; Primary Cell Culture ; RNA-Seq ; Regulatory Elements, Transcriptional/genetics ; Selection, Genetic ; Tibet/ethnology ; Transcription Factors/metabolism ; Whole Genome Sequencing
Czasopismo naukowe
Tytuł :
Identification of Hub genes associated with infection of three lung cell lines by SARS-CoV-2 with integrated bioinformatics analysis.
Autorzy :
Xie TA; Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China.
Han MY; Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China.
Su XR; Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China.
Li HH; Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China.
Chen JC; Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China.
Guo XG; Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China.; Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.; Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.; Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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Źródło :
Journal of cellular and molecular medicine [J Cell Mol Med] 2020 Oct; Vol. 24 (20), pp. 12225-12230. Date of Electronic Publication: 2020 Sep 14.
Typ publikacji :
Journal Article
MeSH Terms :
Gene Regulatory Networks*
Protein Interaction Maps*
Betacoronavirus/*isolation & purification
Biomarkers/*analysis
Computational Biology/*methods
Coronavirus Infections/*diagnosis
Lung/*metabolism
Pneumonia, Viral/*diagnosis
Cells, Cultured ; Coronavirus Infections/genetics ; Coronavirus Infections/metabolism ; Coronavirus Infections/virology ; Humans ; Lung/virology ; Pandemics ; Pneumonia, Viral/genetics ; Pneumonia, Viral/metabolism ; Pneumonia, Viral/virology
SCR Disease Name :
COVID-19
Czasopismo naukowe
Tytuł :
Potential genes and pathways along with immune cells infiltration in the progression of atherosclerosis identified via microarray gene expression dataset re-analysis.
Autorzy :
Xu J; State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Beijing, China.; Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
Yang Y; State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Beijing, China.; Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
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Źródło :
Vascular [Vascular] 2020 Oct; Vol. 28 (5), pp. 643-654. Date of Electronic Publication: 2020 May 07.
Typ publikacji :
Journal Article
MeSH Terms :
Gene Regulatory Networks*
Oligonucleotide Array Sequence Analysis*
Transcriptome*
Carotid Arteries/*immunology
Carotid Artery Diseases/*genetics
Carotid Artery Diseases/*immunology
Carotid Arteries/pathology ; Carotid Artery Diseases/pathology ; Databases, Genetic ; Disease Progression ; Gene Expression Regulation ; Humans ; Plaque, Atherosclerotic
Czasopismo naukowe
Tytuł :
Inference and multiscale model of epithelial-to-mesenchymal transition via single-cell transcriptomic data.
Autorzy :
Sha Y; Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA.; The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA.
Wang S; Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA.
Zhou P; Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA.
Nie Q; Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA.; The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA.; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2020 Sep 25; Vol. 48 (17), pp. 9505-9520.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Gene Expression Profiling*
Gene Regulatory Networks*
Models, Biological*
Embryonic Stem Cells/*pathology
Epithelial-Mesenchymal Transition/*physiology
Animals ; Cell Differentiation ; Embryonic Stem Cells/cytology ; Embryonic Stem Cells/physiology ; Epithelial-Mesenchymal Transition/genetics ; Gene Expression Regulation, Neoplastic ; Head and Neck Neoplasms/genetics ; Head and Neck Neoplasms/pathology ; Humans ; Mice ; Single-Cell Analysis ; Skin Neoplasms/genetics ; Skin Neoplasms/pathology ; Squamous Cell Carcinoma of Head and Neck/genetics ; Squamous Cell Carcinoma of Head and Neck/pathology
Czasopismo naukowe
Tytuł :
Role of SARS-CoV-2 in Altering the RNA-Binding Protein and miRNA-Directed Post-Transcriptional Regulatory Networks in Humans.
Autorzy :
Srivastava R; Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, USA.
Daulatabad SV; Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, USA.
Srivastava M; Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, USA.
Janga SC; Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, USA.; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN 46202, USA.; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN 46202, USA.
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Źródło :
International journal of molecular sciences [Int J Mol Sci] 2020 Sep 25; Vol. 21 (19). Date of Electronic Publication: 2020 Sep 25.
Typ publikacji :
Journal Article
MeSH Terms :
Gene Regulatory Networks*
RNA Processing, Post-Transcriptional*
Betacoronavirus/*genetics
Betacoronavirus/*metabolism
Coronavirus Infections/*virology
MicroRNAs/*genetics
Pneumonia, Viral/*virology
RNA-Binding Proteins/*metabolism
Gene Expression Regulation ; Genome, Viral ; Humans ; MicroRNAs/metabolism ; Pandemics ; Protein Interaction Maps ; RNA-Binding Proteins/genetics
SCR Disease Name :
COVID-19
Czasopismo naukowe
Tytuł :
Robust partitioning of microRNA targets from downstream regulatory changes.
Autorzy :
Patel RK; Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.; Graduate Field of Genetics, Genomics, and Development, Cornell University, Ithaca, New York 14853, USA.
West JD; Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.; Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, USA.
Jiang Y; Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.; Graduate Field of Genetics, Genomics, and Development, Cornell University, Ithaca, New York 14853, USA.
Fogarty EA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.
Grimson A; Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2020 Sep 25; Vol. 48 (17), pp. 9724-9746.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Gene Regulatory Networks*
Computational Biology/*methods
MicroRNAs/*genetics
Transcription Factors/*genetics
3' Untranslated Regions ; 5' Untranslated Regions ; Gene Expression Profiling ; HEK293 Cells ; Humans ; Open Reading Frames ; Sequence Analysis, RNA ; Transcription, Genetic
Czasopismo naukowe

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