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Tytuł :
TIPP2: metagenomic taxonomic profiling using phylogenetic markers.
Autorzy :
Shah N; Department of Computer Science, University of Maryland College Park, College Park, MD, 02740, USA.
Molloy EK; Department of Computer Science, University of California Los Angeles, CA, 90095, USA.
Pop M; Department of Computer Science, University of Maryland College Park, College Park, MD, 02740, USA.
Warnow T; Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
DeepSurf: A surface-based deep learning approach for the prediction of ligand binding sites on proteins.
Autorzy :
Mylonas SK; Information Technologies Institute, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece.
Axenopoulos A; Information Technologies Institute, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece.
Daras P; Information Technologies Institute, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
Adversarial generation of gene expression data.
Autorzy :
Viñas R; Department of Computer Science and Technology, University of Cambridge, UK.; Department of Computer Science, University College London, UK.
Andrés-Terré H; Department of Computer Science and Technology, University of Cambridge, UK.
Liò P; Department of Computer Science and Technology, University of Cambridge, UK.
Bryson K; Department of Computer Science, University College London, UK.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
lgpr: An interpretable nonparametric method for inferring covariate effects from longitudinal Data.
Autorzy :
Timonen J; Department of Computer Science, Aalto University, Espoo, 00076, Finland.
Mannerström H; Department of Computer Science, Aalto University, Espoo, 00076, Finland.
Vehtari A; Department of Computer Science, Aalto University, Espoo, 00076, Finland.
Lähdesmäki H; Department of Computer Science, Aalto University, Espoo, 00076, Finland.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
Genome-scale de novo assembly using ALGA.
Autorzy :
Swat S; Poland, Poznan University of Technology, Institute of Computing Science, Piotrowo 2, 60-965 Poznan.
Laskowski A; Poland, Poznan University of Technology, Institute of Computing Science, Piotrowo 2, 60-965 Poznan.
Badura J; Poland, Poznan University of Technology, Institute of Computing Science, Piotrowo 2, 60-965 Poznan.
Frohmberg W; Poland, Poznan University of Technology, Institute of Computing Science, Piotrowo 2, 60-965 Poznan.
Wojciechowski P; Poland, Poznan University of Technology, Institute of Computing Science, Piotrowo 2, 60-965 Poznan.; Poland, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan.
Swiercz A; Poland, Poznan University of Technology, Institute of Computing Science, Piotrowo 2, 60-965 Poznan.; Poland, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan.
Kasprzak M; Poland, Poznan University of Technology, Institute of Computing Science, Piotrowo 2, 60-965 Poznan.
Blazewicz J; Poland, Poznan University of Technology, Institute of Computing Science, Piotrowo 2, 60-965 Poznan.; Poland, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
bbeaR: an R package and framework for epitope-specific antibody profiling.
Autorzy :
Suprun M; Department of Pediatrics, Allergy and Immunology.
Ellis RJ; Addiction Institute of Mount Sinai.
Sampson HA; Department of Pediatrics, Allergy and Immunology.
Suárez-Fariñas M; Department of Population Health Science and Policy.; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
IsoMiRmap-fast, deterministic, and exhaustive mining of isomiRs from short RNA-seq datasets.
Autorzy :
Loher P; Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.
Karathanasis N; Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.
Londin E; Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.
Bray P; Department of Medicine, University of Utah, Salt Lake City, Utah, 84112.
Pliatsika V; Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.
Telonis AG; Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.
Rigoutsos I; Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
SWOTein: a structure-based approach to predict stability Strengths and Weaknesses of prOTEINs.
Autorzy :
Hou Q; Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Shandong 250002, P. R. China.; National Institute of Health Data Science of China, Shandong University, Shandong 250002, P. R. China.; Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium.
Pucci F; Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium.; Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe, 1050 Brussels, Belgium.
Ancien F; Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium.; Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe, 1050 Brussels, Belgium.
Kwasigroch JM; Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium.
Bourgeas R; Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium.
Rooman M; Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium.; Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe, 1050 Brussels, Belgium.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
Cellinker: a platform of ligand-receptor interactions for intercellular communication analysis.
Autorzy :
Zhang Y; Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China.
Liu T; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
Wang J; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
Zou B; Department of Statistics, University of California Davis, Davis, California, USA.
Li L; Department of Pathology, Harbin Medical University, Harbin 150081, China.
Yao L; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
Chen K; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
Ning L; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
Wu B; Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China.
Zhao X; Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China.; Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
Wang D; Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China.; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.; Dermatology Hospital, Southern Medical University, Guangzhou 510091, China.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
Alignment-free Genomic Analysis via a Big Data Spark Platform.
Autorzy :
Petrillo UF; Dipartimento di Scienze Statistiche, Università di Roma - La Sapienza, Rome, 00185, Italy.
Palini F; Dipartimento di Scienze Statistiche, Università di Roma - La Sapienza, Rome, 00185, Italy.
Cattaneo G; Dipartimento di Informatica, Università di Salerno, Fisciano (SA), 84084, Italy.
Giancarlo R; Dipartimento di Matematica ed Informatica, Università di Palermo, Palermo, 90133, Italy.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
Bios2cor: an R package integrating dynamic and evolutionary correlations to identify functionally important residues in proteins.
Autorzy :
Taddese B; CNRS UMR 6015-INSERM 1083, MITOVASC Laboratory, FRANCE, 3 rue Roger Amsler 49100 ANGERS.
Garnier A; CNRS UMR 6015-INSERM 1083, MITOVASC Laboratory, FRANCE, 3 rue Roger Amsler 49100 ANGERS.
Deniaud M; CNRS UMR 6015-INSERM 1083, MITOVASC Laboratory, FRANCE, 3 rue Roger Amsler 49100 ANGERS.
Henrion D; CNRS UMR 6015-INSERM 1083, MITOVASC Laboratory, FRANCE, 3 rue Roger Amsler 49100 ANGERS.
Chabbert M; CNRS UMR 6015-INSERM 1083, MITOVASC Laboratory, FRANCE, 3 rue Roger Amsler 49100 ANGERS.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data.
Autorzy :
Posada-Céspedes S; Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland.; SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland.
Seifert D; Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland.; SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland.
Topolsky I; Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland.; SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland.
Jablonski KP; Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland.; SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland.
Metzner KJ; Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, 8091, Switzerland.; 4 Institute of Medical Virology, University of Zurich, Zurich, 8091, Switzerland.
Beerenwinkel N; Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland.; SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
PrInCE: an R/bioconductor package for protein-protein interaction network inference from co-fractionation mass spectrometry data.
Autorzy :
Skinnider MA; Michael Smith Laboratories, University of British Columbia, Vancouver, Columbia, Canada British.
Cai C; Michael Smith Laboratories, University of British Columbia, Vancouver, Columbia, Canada British.
Stacey RG; Michael Smith Laboratories, University of British Columbia, Vancouver, Columbia, Canada British.
Foster LJ; Michael Smith Laboratories, University of British Columbia, Vancouver, Columbia, Canada British.; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
DNAModAnnot: a R toolbox for DNA modification filtering and annotation.
Autorzy :
Hardy A; Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France.
Matelot M; Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France.
Touzeau A; Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France.
Klopp C; Plateforme bioinformatique Genotoul, UR875 Mathématique et Informatique Appliquée de Toulouse, INRA, 31326, Castanet-Tolosan, France.
Lopez-Roques C; INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France.
Duharcourt S; Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France.
Defrance M; Université Libre de Bruxelles, Interuniversity Institute of Bioinformatics in Brussels (IB2), Brussels, 1050, Belgium.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments.
Autorzy :
Chen Z; Department of Molecular Biophysics and Biochemistry.; Department of Computer Science, Yale University, New Haven, CT 06520, USA.
Zhang J; Department of Computer Science, University of California, Irvine, CA 92617, USA.
Liu J
Zhang Z; School of Electronic Engineering and Computer Science, Queen Mary University of London, London, E1 4NS, United Kingdom.
Zhu J; School of Electronic Engineering and Computer Science, Queen Mary University of London, London, E1 4NS, United Kingdom.
Lee D; Department of Genetics and Genomic Sciences.; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Xu M; Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
Gerstein M; Department of Molecular Biophysics and Biochemistry.; Department of Computer Science, Yale University, New Haven, CT 06520, USA.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
VPF-Class: Taxonomic assignment and host prediction of uncultivated viruses based on viral protein families.
Autorzy :
Pons JC; Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain.
Paez-Espino D; Department of Energy Joint Genome Institute, Berkeley, 94720, USA.
Riera G; Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain.
Ivanova N; Department of Energy Joint Genome Institute, Berkeley, 94720, USA.
Kyrpides NC; Department of Energy Joint Genome Institute, Berkeley, 94720, USA.
Llabrés M; Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology.
Autorzy :
Luo L; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Yan S; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Lai PT; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Veltri D; Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 209892, USA.
Oler A; Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 209892, USA.
Xirasagar S; Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 209892, USA.
Ghosh R; Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 209892, USA.
Similuk M; Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 209892, USA.
Robinson PN; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
Lu Z; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD 20894, USA.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
Compression of quantification uncertainty for scRNA-seq counts.
Autorzy :
Van Buren S; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA.
Sarkar H; Department of Computer Science, University of Maryland College Park, MD 20742, USA.; Center for Bioinformatics and Computational Biology, University of Maryland College Park, MD 20742, USA.
Srivastava A; New York Genome Center, New York, NY 10013, USA.; Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA.
Rashid NU; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA.; Lineberger Comprehensive Cancer Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Patro R; Department of Computer Science, University of Maryland College Park, MD 20742, USA.; Center for Bioinformatics and Computational Biology, University of Maryland College Park, MD 20742, USA.
Love MI; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA.; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 20. Date of Electronic Publication: 2021 Jan 20.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
CaMelia: imputation in single-cell methylomes based on local similarities between cells.
Autorzy :
Tang J; Department of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China.
Zou J; Department of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China.
Fan M; Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China.
Tian Q; Department of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China.
Zhang J; Department of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China.
Fan S; Department of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China.; Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 611731, China.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 18. Date of Electronic Publication: 2021 Jan 18.
Typ publikacji :
Journal Article
Czasopismo naukowe
Tytuł :
SubtypeDrug: a software package for prioritization of candidate cancer subtype-specific drugs.
Autorzy :
Han X; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Kong Q; College of Basic Medicine, Harbin Medical University, Harbin, China.
Liu C; College of Basic Medicine, Harbin Medical University, Harbin, China.
Cheng L; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Han J; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jan 18. Date of Electronic Publication: 2021 Jan 18.
Typ publikacji :
Journal Article
Czasopismo naukowe

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