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Wyszukujesz frazę ""Molecular Sequence Annotation"" wg kryterium: Temat


Tytuł :
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases.
Corporate Authors :
RNAcentral Consortium
Źródło :
Nucleic acids research [Nucleic Acids Res] 2021 Jan 08; Vol. 49 (D1), pp. D212-D220.
Typ publikacji :
Journal Article; Research Support, N.I.H., Intramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Molecular Sequence Annotation*
Software*
Databases, Nucleic Acid/*organization & administration
RNA, Untranslated/*genetics
Animals ; Apicomplexa/classification ; Apicomplexa/genetics ; Base Sequence ; Betacoronavirus/classification ; Betacoronavirus/genetics ; Databases, Nucleic Acid/supply & distribution ; Fungi/classification ; Fungi/genetics ; Gene Ontology ; Humans ; Internet ; Nucleic Acid Conformation ; RNA, Untranslated/classification ; RNA, Untranslated/metabolism ; Sequence Analysis, RNA
Czasopismo naukowe
Tytuł :
Graph embeddings on gene ontology annotations for protein-protein interaction prediction.
Autorzy :
Zhong X; School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China. .
Rajapakse JC; School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, Singapore.
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Źródło :
BMC bioinformatics [BMC Bioinformatics] 2020 Dec 16; Vol. 21 (Suppl 16), pp. 560. Date of Electronic Publication: 2020 Dec 16.
Typ publikacji :
Journal Article
MeSH Terms :
Gene Ontology*
Molecular Sequence Annotation*
Protein Interaction Mapping/*methods
Animals ; Area Under Curve ; Computational Biology/methods ; Humans ; Mice ; ROC Curve ; Saccharomyces cerevisiae/genetics ; Task Performance and Analysis
Czasopismo naukowe
Tytuł :
Integrating comprehensive functional annotations to boost power and accuracy in gene-based association analysis.
Autorzy :
Quick C; Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA.; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
Wen X; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
Abecasis G; Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA.; Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA.
Boehnke M; Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA.
Kang HM; Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA.
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Źródło :
PLoS genetics [PLoS Genet] 2020 Dec 15; Vol. 16 (12), pp. e1009060. Date of Electronic Publication: 2020 Dec 15 (Print Publication: 2020).
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
Genome-Wide Association Study/*methods
Molecular Sequence Annotation/*methods
Algorithms ; Genome-Wide Association Study/standards ; Humans ; Molecular Sequence Annotation/standards ; Polymorphism, Genetic ; Quantitative Trait Loci ; Reproducibility of Results
Czasopismo naukowe
Tytuł :
A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins.
Autorzy :
Makrodimitris S; Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands.; Keygene N.V., Wageningen, the Netherlands.
Reinders M; Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands.; Leiden Computational Biology Center, Leiden University Medical Center, Leiden, the Netherlands.
van Ham R; Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands.; Keygene N.V., Wageningen, the Netherlands.
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Źródło :
PloS one [PLoS One] 2020 Nov 25; Vol. 15 (11), pp. e0242723. Date of Electronic Publication: 2020 Nov 25 (Print Publication: 2020).
Typ publikacji :
Journal Article
MeSH Terms :
Arabidopsis*/genetics
Arabidopsis*/metabolism
Arabidopsis Proteins*/genetics
Arabidopsis Proteins*/metabolism
Escherichia coli*/genetics
Escherichia coli*/metabolism
Escherichia coli Proteins*/genetics
Escherichia coli Proteins*/metabolism
Lycopersicon esculentum*/genetics
Lycopersicon esculentum*/metabolism
Molecular Sequence Annotation*
Saccharomyces cerevisiae*/genetics
Saccharomyces cerevisiae*/metabolism
Saccharomyces cerevisiae Proteins*/genetics
Saccharomyces cerevisiae Proteins*/metabolism
Protein Interaction Maps/*physiology
Czasopismo naukowe
Tytuł :
Ten simple rules for annotating sequencing experiments.
Autorzy :
Stevens I; Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.; Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.
Mukarram AK; Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
Hörtenhuber M; Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
Meehan TF; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
Rung J; Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.; Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
Daub CO; Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.; Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.
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Źródło :
PLoS computational biology [PLoS Comput Biol] 2020 Oct 05; Vol. 16 (10), pp. e1008260. Date of Electronic Publication: 2020 Oct 05 (Print Publication: 2020).
Typ publikacji :
Editorial; Research Support, Non-U.S. Gov't
MeSH Terms :
Genomics*/methods
Genomics*/standards
Molecular Sequence Annotation*/methods
Molecular Sequence Annotation*/standards
Sequence Analysis, DNA*/methods
Sequence Analysis, DNA*/standards
Computational Biology ; Gene Ontology ; Metadata
Raport
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 :
Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome.
Autorzy :
Triant DA; Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
Le Tourneau JJ; Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
Diesh CM; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA.
Unni DR; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94608, USA.
Shamimuzzaman M; Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
Walsh AT; Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
Gardiner J; Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
Goldkamp AK; Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, 74078, USA.
Li Y; Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
Nguyen HN; Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.; MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA.
Roberts C; Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
Zhao Z; Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
Alexander LJ; USDA-ARS-PA-Livestock & Range Research Lab, Miles City, MT, 59301, USA.
Decker JE; Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.; MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA.
Schnabel RD; Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.; MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA.
Schroeder SG; USDA-ARS Animal Genomics and Improvement Lab, Beltsville, MD, 20705, USA.
Sonstegard TS; Acceligen, Eagan, MN, 55121, USA.
Taylor JF; Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
Rivera RM; Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
Hagen DE; Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, 74078, USA.
Elsik CG; Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.; MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA.; Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
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Źródło :
Animal genetics [Anim Genet] 2020 Oct; Vol. 51 (5), pp. 675-682. Date of Electronic Publication: 2020 Jun 14.
Typ publikacji :
Journal Article
MeSH Terms :
Databases, Genetic*
Genome*
Molecular Sequence Annotation*
Online Systems*
Animals ; Cattle/genetics
Czasopismo naukowe
Tytuł :
Haplotype-resolved genome analyses of a heterozygous diploid potato.
Autorzy :
Zhou Q; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.; Peng Cheng Laboratory, Shenzhen, China.
Tang D; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Huang W; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
Yang Z; College of Horticulture, Northwest Agriculture and Forest University, Yangling, China.
Zhang Y; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Hamilton JP; Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
Visser RGF; Plant Breeding, Wageningen University and Research, Wageningen, the Netherlands.
Bachem CWB; Plant Breeding, Wageningen University and Research, Wageningen, the Netherlands.
Robin Buell C; Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
Zhang Z; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.; College of Horticulture, Qingdao Agricultural University, Qingdao, China.
Zhang C; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Huang S; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China. .; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China. .
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Źródło :
Nature genetics [Nat Genet] 2020 Oct; Vol. 52 (10), pp. 1018-1023. Date of Electronic Publication: 2020 Sep 28.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Molecular Sequence Annotation*
Genome, Plant/*genetics
Haplotypes/*genetics
Solanum tuberosum/*genetics
Alleles ; Diploidy ; Heterozygote ; Tetraploidy
Czasopismo naukowe
Tytuł :
Synchrotron-based FTIR microspectroscopy of protein aggregation and lipids peroxidation changes in human cataractous lens epithelial cells.
Autorzy :
Kreuzer M; CELLS-ALBA, Carrer de la Llum 2-26, Cerdanyola del Valles, 08290, Barcelona, Spain.
Dučić T; CELLS-ALBA, Carrer de la Llum 2-26, Cerdanyola del Valles, 08290, Barcelona, Spain. .
Hawlina M; Eye Hospital, University Medical Centre, Grablovičeva 46, 1000, Ljubljana, Slovenia.
Andjelic S; Eye Hospital, University Medical Centre, Grablovičeva 46, 1000, Ljubljana, Slovenia. .
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Źródło :
Scientific reports [Sci Rep] 2020 Sep 23; Vol. 10 (1), pp. 15489. Date of Electronic Publication: 2020 Sep 23.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Lipid Peroxidation*
Molecular Sequence Annotation*
Cataract/*metabolism
Epithelium, Corneal/*metabolism
Lens, Crystalline/*metabolism
Adult ; Aged ; Aged, 80 and over ; Cataract/pathology ; Epithelium, Corneal/pathology ; Female ; Humans ; Lens, Crystalline/pathology ; Male ; Middle Aged ; Spectroscopy, Fourier Transform Infrared ; Synchrotrons
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 :
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 :
[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 :
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 :
Occupancy maps of 208 chromatin-associated proteins in one human cell type.
Autorzy :
Partridge EC; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
Chhetri SB; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.; Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA.; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MA, USA.
Prokop JW; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.; Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA.
Ramaker RC; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
Jansen CS; Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA.
Goh ST; Division of Biology, California Institute of Technology, Pasadena, CA, USA.
Mackiewicz M; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
Newberry KM; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
Brandsmeier LA; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
Meadows SK; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
Messer CL; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
Hardigan AA; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
Coppola CJ; Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA.
Dean EC; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.; Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.
Jiang S; Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA.
Savic D; Pharmaceutical Sciences Department, St Jude Children's Research Hospital, Memphis, TN, USA.
Mortazavi A; Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA.
Wold BJ; Division of Biology, California Institute of Technology, Pasadena, CA, USA.
Myers RM; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA. .
Mendenhall EM; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA. .; Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA. .
Pokaż więcej
Źródło :
Nature [Nature] 2020 Jul; Vol. 583 (7818), pp. 720-728. Date of Electronic Publication: 2020 Jul 29.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
Chromatin Immunoprecipitation Sequencing*
Molecular Sequence Annotation*
Chromatin/*genetics
Chromatin/*metabolism
DNA-Binding Proteins/*metabolism
Regulatory Sequences, Nucleic Acid/*genetics
Datasets as Topic ; Enhancer Elements, Genetic/genetics ; Hep G2 Cells ; Humans ; Nucleotide Motifs/genetics ; Promoter Regions, Genetic/genetics ; Protein Binding ; Transcription Factors/metabolism
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

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