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Tytuł :
PALMER: improving pathway annotation based on the biomedical literature mining with a constrained latent block model.
Autorzy :
Nam JH; Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA.; School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea.
Couch D; Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA.
da Silveira WA; School of Biological Sciences, Queen's University Belfast, Belfast, UK.
Yu Z; Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA.
Chung D; Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA. .
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Źródło :
BMC bioinformatics [BMC Bioinformatics] 2020 Oct 02; Vol. 21 (1), pp. 432. Date of Electronic Publication: 2020 Oct 02.
Typ publikacji :
Journal Article
MeSH Terms :
Algorithms*
Data Mining*
Models, Theoretical*
Molecular Sequence Annotation*
Publications*
Computer Simulation ; Gene Ontology ; Gene Regulatory Networks ; Humans ; Multigene Family ; Systems Biology
Czasopismo naukowe
Tytuł :
Evaluating the informativeness of deep learning annotations for human complex diseases.
Autorzy :
Dey KK; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA. .
van de Geijn B; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
Kim SS; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
Hormozdiari F; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
Kelley DR; Calico Labs, South San Francisco, CA, USA.
Price AL; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA. .; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .
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Źródło :
Nature communications [Nat Commun] 2020 Sep 17; Vol. 11 (1), pp. 4703. Date of Electronic Publication: 2020 Sep 17.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
Deep Learning*
Molecular Sequence Annotation*
Disease/*genetics
Alleles ; Genetic Predisposition to Disease ; Genome, Human ; Genome-Wide Association Study ; Histones/genetics ; Humans ; Linkage Disequilibrium ; Models, Genetic ; Phenotype ; Polymorphism, Single Nucleotide
Czasopismo naukowe
Tytuł :
A comprehensive rat transcriptome built from large scale RNA-seq-based annotation.
Autorzy :
Ji X; Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.; School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
Li P; Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.; Massachusetts General Hospital, Harvard Medical School, 51 Blossom St, Boston, MA 02114, USA.
Fuscoe JC; National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA.
Chen G; Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.
Xiao W; Massachusetts General Hospital, Harvard Medical School, 51 Blossom St, Boston, MA 02114, USA.
Shi L; Center for Pharmacogenomics, School of Pharmacy, Fudan University, Shanghai, 200438, China.
Ning B; National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA.
Liu Z; National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA.
Hong H; National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA.
Wu J; Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.
Liu J; School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
Guo L; National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA.
Kreil DP; Department of Biotechnology, Boku University Vienna, 1190 Muthgasse 18, Austria.
Łabaj PP; Department of Biotechnology, Boku University Vienna, 1190 Muthgasse 18, Austria.; Małopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7A, 30-387 Kraków, Poland.
Zhong L; Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning 530021, China.
Bao W; SAS Institute Inc., Cary, NC, 27513, USA.
Huang Y; Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning 530021, China.
He J; Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning 530021, China.
Zhao Y; Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning 530021, China.
Tong W; National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA.
Shi T; Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2020 Sep 04; Vol. 48 (15), pp. 8320-8331.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Molecular Sequence Annotation*
Genome/*genetics
RNA-Seq/*methods
Transcriptome/*genetics
Alternative Splicing/genetics ; Animals ; High-Throughput Nucleotide Sequencing ; Humans ; Rats ; Whole Exome Sequencing
Czasopismo naukowe
Tytuł :
[Comprehensive re-annotation of protein-coding genes for prokaryotic genomes by Z-curve and similarity-based methods].
Autorzy :
Liu S; School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China.
Zeng Z; School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China.
Zeng FC; Department of Biochemistry and Molecular Biology, School of Basic Medicine, Southwest Medical University, Luzhou 646000,China.
Du MZ; Department of Biochemistry and Molecular Biology, School of Basic Medicine, Southwest Medical University, Luzhou 646000,China.
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Źródło :
Yi chuan = Hereditas [Yi Chuan] 2020 Jul 20; Vol. 42 (7), pp. 691-702.
Typ publikacji :
Journal Article
MeSH Terms :
Genome, Archaeal*/genetics
Genome, Bacterial*/genetics
Molecular Sequence Annotation*
Genes, Bacterial ; Open Reading Frames ; Prokaryotic Cells
Czasopismo naukowe
Tytuł :
Partitioning gene-based variance of complex traits by gene score regression.
Autorzy :
Zhang W; Quantitative Life Science, McGill University, Montreal, Quebec, Canada.
Li SY; Department of Computer Science, McGill University, Montreal, Quebec, Canada.
Liu T; Department of Computer Science, McGill University, Montreal, Quebec, Canada.
Li Y; Quantitative Life Science, McGill University, Montreal, Quebec, Canada.; Department of Computer Science, McGill University, Montreal, Quebec, Canada.
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Źródło :
PloS one [PLoS One] 2020 Aug 20; Vol. 15 (8), pp. e0237657. Date of Electronic Publication: 2020 Aug 20 (Print Publication: 2020).
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Molecular Sequence Annotation*
Genome-Wide Association Study/*statistics & numerical data
Multifactorial Inheritance/*genetics
Transcriptome/*genetics
Gene Expression Regulation/genetics ; Genetic Predisposition to Disease ; Genome, Human/genetics ; Genotype ; Humans ; Linkage Disequilibrium ; Models, Genetic ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait Loci
Czasopismo naukowe
Tytuł :
Index and biological spectrum of human DNase I hypersensitive sites.
Autorzy :
Meuleman W; Altius Institute for Biomedical Sciences, Seattle, WA, USA. .
Muratov A; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Rynes E; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Halow J; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Lee K; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Bates D; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Diegel M; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Dunn D; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Neri F; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Teodosiadis A; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Reynolds A; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Haugen E; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Nelson J; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Johnson A; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Frerker M; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Buckley M; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Sandstrom R; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Vierstra J; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Kaul R; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Stamatoyannopoulos J; Altius Institute for Biomedical Sciences, Seattle, WA, USA. .; Department of Genome Sciences, University of Washington, Seattle, WA, USA. .; Division of Oncology, Department of Medicine, University of Washington, Seattle, WA, USA. .
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Źródło :
Nature [Nature] 2020 Aug; Vol. 584 (7820), pp. 244-251. Date of Electronic Publication: 2020 Jul 29.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Molecular Sequence Annotation*
Chromatin/*genetics
DNA/*metabolism
Deoxyribonuclease I/*metabolism
Chromatin/chemistry ; Chromatin/metabolism ; DNA/chemistry ; DNA/genetics ; Gene Expression Regulation ; Genes/genetics ; Genome, Human/genetics ; Humans ; Promoter Regions, Genetic/genetics ; Regulatory Sequences, Nucleic Acid/genetics
Czasopismo naukowe
Tytuł :
CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities.
Autorzy :
Kondratenko Y; Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia, 199004. .
Korobeynikov A; Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia, 199004.; Department of Statistical Modelling, St. Petersburg State University, St. Petersburg, Russia, 198515.
Lapidus A; Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia, 199004.
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Źródło :
BMC bioinformatics [BMC Bioinformatics] 2020 Jul 24; Vol. 21 (Suppl 12), pp. 303. Date of Electronic Publication: 2020 Jul 24.
Typ publikacji :
Journal Article
MeSH Terms :
High-Throughput Nucleotide Sequencing*
Molecular Sequence Annotation*
Software*
Databases, Genetic ; Humans ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics
Czasopismo naukowe
Tytuł :
Conserved unique peptide patterns (CUPP) online platform: peptide-based functional annotation of carbohydrate active enzymes.
Autorzy :
Barrett K; Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
Hunt CJ; Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
Lange L; LLa-BioEconomy, Research & Advisory, 2500 Valby, Denmark.
Meyer AS; Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2020 Jul 02; Vol. 48 (W1), pp. W110-W115.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Carbohydrate Metabolism*
Molecular Sequence Annotation*
Software*
Enzymes/*chemistry
Enzymes/*genetics
Algorithms ; Enzymes/classification ; Enzymes/metabolism ; Internet ; Peptides/chemistry ; Sequence Analysis, DNA ; Sequence Analysis, Protein
Czasopismo naukowe
Tytuł :
SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update).
Autorzy :
Oscanoa J; Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK.
Sivapalan L; Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK.
Gadaleta E; Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK.
Dayem Ullah AZ; Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK.
Lemoine NR; Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK.
Chelala C; Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2020 Jul 02; Vol. 48 (W1), pp. W185-W192.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Genetic Variation*
Genome, Human*
Molecular Sequence Annotation*
Software*
Humans ; Internet ; Neoplasms/genetics
Czasopismo naukowe
Tytuł :
AnnoLnc2: the one-stop portal to systematically annotate novel lncRNAs for human and mouse.
Autorzy :
Ke L; School of Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI) and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China.
Yang DC; School of Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI) and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China.
Wang Y; School of Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI) and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China.
Ding Y; Beijing Institute of Radiation Medicine, Beijing 100850, China.
Gao G; School of Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI) and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2020 Jul 02; Vol. 48 (W1), pp. W230-W238.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Molecular Sequence Annotation*
Software*
RNA, Long Noncoding/*chemistry
RNA, Long Noncoding/*metabolism
Animals ; Evolution, Molecular ; Gene Expression Regulation ; Humans ; Mice ; RNA, Long Noncoding/genetics
Czasopismo naukowe
Tytuł :
Perspectives on ENCODE.
Autorzy :
Snyder MP; Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA. .; Cardiovascular Institute, Stanford School of Medicine, Stanford, CA, USA. .
Gingeras TR; Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Moore JE; University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.
Weng Z; University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.; Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, Shanghai, China.; Bioinformatics Program, Boston University, Boston, MA, USA.
Gerstein MB; Yale University, New Haven, CT, USA.
Ren B; Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.; Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA.
Hardison RC; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Stamatoyannopoulos JA; Altius Institute for Biomedical Sciences, Seattle, WA, USA.; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Department of Medicine, University of Washington, Seattle, WA, USA.
Graveley BR; Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA.
Feingold EA; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Pazin MJ; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Pagan M; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Gilchrist DA; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Hitz BC; Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
Cherry JM; Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
Bernstein BE; Broad Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Mendenhall EM; Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA.; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
Zerbino DR; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
Frankish A; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
Flicek P; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
Myers RM; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
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Corporate Authors :
ENCODE Project Consortium
Źródło :
Nature [Nature] 2020 Jul; Vol. 583 (7818), pp. 693-698. Date of Electronic Publication: 2020 Jul 29.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
Databases, Genetic*/standards
Databases, Genetic*/trends
Genomics*/standards
Genomics*/trends
Molecular Sequence Annotation*/standards
Genome/*genetics
Animals ; Binding Sites ; Chromatin/genetics ; Chromatin/metabolism ; DNA Methylation ; Gene Expression Regulation/genetics ; Genome, Human/genetics ; Histones/metabolism ; Humans ; Mice ; Quality Control ; Regulatory Sequences, Nucleic Acid/genetics ; Transcription Factors/metabolism
Czasopismo naukowe
Tytuł :
G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation.
Autorzy :
Sargent L; Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, United States of America.
Liu Y; Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Leung W; Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America.
Mortimer NT; School of Biological Sciences, Illinois State University, Normal, Illinois, United States of America.
Lopatto D; Department of Psychology, Grinnell College, Grinnell, Iowa, United States of America.
Goecks J; Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, United States of America.
Elgin SCR; Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America.
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Źródło :
PLoS computational biology [PLoS Comput Biol] 2020 Jun 04; Vol. 16 (6), pp. e1007863. Date of Electronic Publication: 2020 Jun 04 (Print Publication: 2020).
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
Genome*
Molecular Sequence Annotation*
Software*
Computational Biology/*education
Computational Biology/*methods
Genomics/*education
Genomics/*methods
Algorithms ; Animals ; Base Sequence ; Computer Graphics ; Databases, Genetic ; Drosophila melanogaster ; Humans ; Sequence Analysis, RNA ; Students ; User-Computer Interface
Czasopismo naukowe
Tytuł :
VADR: validation and annotation of virus sequence submissions to GenBank.
Autorzy :
Schäffer AA; Cancer Data Science Laboratory National, Cancer Insitute, National Institutes of Health, Bethesda, 20892, MD, USA.; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA.
Hatcher EL; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA.
Yankie L; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA.
Shonkwiler L; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA.; Massachusetts Institute of Technology, Cambridge, MA, USA.
Brister JR; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA.
Karsch-Mizrachi I; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA.
Nawrocki EP; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA. .
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Źródło :
BMC bioinformatics [BMC Bioinformatics] 2020 May 24; Vol. 21 (1), pp. 211. Date of Electronic Publication: 2020 May 24.
Typ publikacji :
Journal Article
MeSH Terms :
Betacoronavirus*/genetics
Coronavirus Infections*/genetics
Databases, Nucleic Acid*
Molecular Sequence Annotation*/standards
Pandemics*
Pneumonia, Viral*/genetics
Software*
DNA Viruses ; Genomics ; Humans ; Viruses
SCR Disease Name :
COVID-19
Czasopismo naukowe
Tytuł :
CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments.
Autorzy :
Ekiz HA; Division of Microbiology and Immunology, Department of Pathology, University of Utah, 15 N. Medical Dr. East, JMRB, Salt Lake City, UT, 84112, USA. .; Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Dr, Salt Lake City, UT, 84112, USA. .
Conley CJ; Bioinformatics Shared Resource, Hunstman Cancer Institute, University of Utah, 2000 Circle of Hope Dr, Salt Lake City, UT, 84112, USA.
Stephens WZ; Division of Microbiology and Immunology, Department of Pathology, University of Utah, 15 N. Medical Dr. East, JMRB, Salt Lake City, UT, 84112, USA.; Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Dr, Salt Lake City, UT, 84112, USA.
O'Connell RM; Division of Microbiology and Immunology, Department of Pathology, University of Utah, 15 N. Medical Dr. East, JMRB, Salt Lake City, UT, 84112, USA. .; Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Dr, Salt Lake City, UT, 84112, USA. .
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Źródło :
BMC bioinformatics [BMC Bioinformatics] 2020 May 15; Vol. 21 (1), pp. 191. Date of Electronic Publication: 2020 May 15.
Typ publikacji :
Journal Article
MeSH Terms :
Internet*
Molecular Sequence Annotation*
Sequence Analysis, RNA*
Single-Cell Analysis*
Software*
Algorithms ; Animals ; Base Sequence ; Cell Aggregation ; Cluster Analysis ; Databases, Genetic ; Humans ; Mice
Czasopismo naukowe
Tytuł :
Comprehensive proteomics and functional annotation of mouse brown adipose tissue.
Autorzy :
Li J; Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, China.
Li J; Key Laboratory of Endocrinology of Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
Zhao WG; Key Laboratory of Endocrinology of Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
Sun HD; Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, China.
Guo ZG; Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, China.
Liu XY; Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, China.
Tang XY; Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, China.
She ZF; State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Diabetes Research Center of Chinese Academy of Medical Sciences, Beijing, China.
Yuan T; Key Laboratory of Endocrinology of Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
Liu SN; State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Diabetes Research Center of Chinese Academy of Medical Sciences, Beijing, China.
Liu Q; State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Diabetes Research Center of Chinese Academy of Medical Sciences, Beijing, China.
Fu Y; Key Laboratory of Endocrinology of Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
Sun W; Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, China.
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Źródło :
PloS one [PLoS One] 2020 May 06; Vol. 15 (5), pp. e0232084. Date of Electronic Publication: 2020 May 06 (Print Publication: 2020).
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Molecular Sequence Annotation*/methods
Proteomics*/methods
Adipose Tissue, Brown/*metabolism
Proteome/*metabolism
Adipose Tissue, Brown/chemistry ; Animals ; Chromatography, High Pressure Liquid ; Chromatography, Liquid ; Databases, Protein ; Female ; Mice ; Mice, Inbred C57BL ; Proteome/analysis ; Tandem Mass Spectrometry
Czasopismo naukowe
Tytuł :
Transcript expression-aware annotation improves rare variant interpretation.
Autorzy :
Cummings BB; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA.
Karczewski KJ; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
Kosmicki JA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.; Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA.
Seaby EG; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.; Genomic Informatics Group, University Hospital Southampton, Southampton, UK.
Watts NA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
Singer-Berk M; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Mudge JM; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
Karjalainen J; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Satterstrom FK; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
O'Donnell-Luria AH; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
Poterba T; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Seed C; Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Solomonson M; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
Alföldi J; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
Daly MJ; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
MacArthur DG; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .; Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA. .; Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Syndney, Australia. .; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia. .
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Corporate Authors :
Genome Aggregation Database Production Team
Genome Aggregation Database Consortium
Źródło :
Nature [Nature] 2020 May; Vol. 581 (7809), pp. 452-458. Date of Electronic Publication: 2020 May 27.
Typ publikacji :
Journal Article
MeSH Terms :
Molecular Sequence Annotation*/standards
Transcription, Genetic*
Disease/*genetics
Haploinsufficiency/*genetics
Loss of Function Mutation/*genetics
Transcriptome/*genetics
Autism Spectrum Disorder/genetics ; Datasets as Topic ; Developmental Disabilities/genetics ; Exons/genetics ; Female ; Genotype ; Humans ; Intellectual Disability/genetics ; Male ; Poisson Distribution ; RNA, Messenger/analysis ; RNA, Messenger/genetics ; Rare Diseases/diagnosis ; Rare Diseases/genetics ; Reproducibility of Results ; Whole Exome Sequencing
Czasopismo naukowe
Tytuł :
Sequencing and Functional Annotation of the Whole Genome of Shiraia bambusicola .
Autorzy :
Ren X; College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, China.; Institute of biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, 550006, China.; Guizhou Key Laboratory of Agricultural Biotechnology, Guiyang, Guizhou, 550006, China, and.
Liu Y; Institute of biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, 550006, China.; Guizhou Key Laboratory of Agricultural Biotechnology, Guiyang, Guizhou, 550006, China, and.
Tan Y; Institute of biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, 550006, China.; Guizhou Key Laboratory of Agricultural Biotechnology, Guiyang, Guizhou, 550006, China, and.
Huang Y; Institute of biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, 550006, China.; Guizhou Key Laboratory of Agricultural Biotechnology, Guiyang, Guizhou, 550006, China, and.
Liu Z; Guizhou Key Laboratory of Agricultural Biotechnology, Guiyang, Guizhou, 550006, China, and .; Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, 550006, China.
Jiang X; College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, China, .
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Źródło :
G3 (Bethesda, Md.) [G3 (Bethesda)] 2020 Jan 07; Vol. 10 (1), pp. 23-35. Date of Electronic Publication: 2020 Jan 07.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Genome, Fungal*
Molecular Sequence Annotation*
Ascomycota/*genetics
Ascomycota/classification ; Base Composition ; Fungal Proteins/genetics ; Fungal Proteins/metabolism ; Open Reading Frames ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Whole Genome Sequencing
Czasopismo naukowe
Tytuł :
Multi-species annotation of transcriptome and chromatin structure in domesticated animals.
Autorzy :
Foissac S; GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France. .
Djebali S; GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.
Munyard K; Curtin University, School of Pharmacy & Biomedical Sciences, CHIRI Biosciences, Perth, 24105, Australia.
Vialaneix N; MIAT, Université de Toulouse, INRA, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.
Rau A; GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350, France.
Muret K; PEGASE, Agrocampus-Ouest, INRA, Saint-Gilles Cedex, F-35590, France.
Esquerré D; GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.; INRA, US1426, GeT-PlaGe, Genotoul, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.
Zytnicki M; MIAT, Université de Toulouse, INRA, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.
Derrien T; UMR6290 IGDR, CNRS, Université Rennes 1, Rennes, France.
Bardou P; GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.
Blanc F; GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350, France.
Cabau C; GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.
Crisci E; GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350, France.; Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA.
Dhorne-Pollet S; GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350, France.
Drouet F; UMR1282 ISP, INRA, Nouzilly, F-37380, France.
Faraut T; GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.
Gonzalez I; MIAT, Université de Toulouse, INRA, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.
Goubil A; GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350, France.
Lacroix-Lamandé S; UMR1282 ISP, INRA, Nouzilly, F-37380, France.
Laurent F; UMR1282 ISP, INRA, Nouzilly, F-37380, France.
Marthey S; GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350, France.
Marti-Marimon M; GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.
Momal-Leisenring R; GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350, France.
Mompart F; GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.
Quéré P; UMR1282 ISP, INRA, Nouzilly, F-37380, France.
Robelin D; GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.
Cristobal MS; GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.
Tosser-Klopp G; GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.
Vincent-Naulleau S; IRCM, CEA, Université Paris Saclay, Jouy-en-Josas, F-78350, France.
Fabre S; GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.
Pinard-Van der Laan MH; GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350, France.
Klopp C; MIAT, Université de Toulouse, INRA, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.
Tixier-Boichard M; GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350, France.
Acloque H; GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326, France.; GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350, France.
Lagarrigue S; PEGASE, Agrocampus-Ouest, INRA, Saint-Gilles Cedex, F-35590, France.
Giuffra E; GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350, France. .
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Źródło :
BMC biology [BMC Biol] 2019 Dec 30; Vol. 17 (1), pp. 108. Date of Electronic Publication: 2019 Dec 30.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Molecular Sequence Annotation*
Transcriptome*
Animals, Domestic/*genetics
Chromatin/*genetics
Animals ; Cattle ; Chickens ; Goats ; Phylogeny ; Sus scrofa
Czasopismo naukowe
Tytuł :
De Novo RNA-seq and Functional Annotation of Haemaphysalis longicornis.
Autorzy :
Niu D; Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, No.76 Yanta West Road, Xi'an, 710061, China.
Zhao Y; Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, No.76 Yanta West Road, Xi'an, 710061, China. .
Yang Y; Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, No.76 Yanta West Road, Xi'an, 710061, China.
Yang R; Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, No.76 Yanta West Road, Xi'an, 710061, China.
Gong X; Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, No.76 Yanta West Road, Xi'an, 710061, China.
Hu L; Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, No.76 Yanta West Road, Xi'an, 710061, China.
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Źródło :
Acta parasitologica [Acta Parasitol] 2019 Dec; Vol. 64 (4), pp. 807-820. Date of Electronic Publication: 2019 Aug 15.
Typ publikacji :
Journal Article
MeSH Terms :
Molecular Sequence Annotation*
RNA-Seq*
Ixodidae/*genetics
Animals ; Dogs/parasitology ; Female ; Open Reading Frames ; RNA/genetics
Czasopismo naukowe
Tytuł :
The mitochondrial genome of Morchella importuna (272.2 kb) is the largest among fungi and contains numerous introns, mitochondrial non-conserved open reading frames and repetitive sequences.
Autorzy :
Liu W; Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China.
Cai Y; Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan 430070, China.
Zhang Q; Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China.
Chen L; Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China.
Shu F; Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China.
Ma X; Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan 430070, China.
Bian Y; Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China. Electronic address: .
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Źródło :
International journal of biological macromolecules [Int J Biol Macromol] 2020 Jan 15; Vol. 143, pp. 373-381. Date of Electronic Publication: 2019 Dec 09.
Typ publikacji :
Journal Article
MeSH Terms :
Molecular Sequence Annotation*
Ascomycota/*genetics
Genome, Mitochondrial/*genetics
Ascomycota/classification ; Introns/genetics ; Mitochondria/genetics ; Open Reading Frames/genetics ; Phylogeny ; Repetitive Sequences, Nucleic Acid/genetics
Czasopismo naukowe

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