Showing 1 - 20 results of 37 for search '"Sequence Analysis, RNA methods"', query time: 1.38s Refine Results
1
Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

Authors: Viacheslav Mylka, Irina Matetovici, Suresh Poovathingal, Jeroen Aerts, Niels Vandamme, Ruth Seurinck, Kevin Verstaen, Gert Hulselmans, Silvie Van den Hoecke, Isabelle Scheyltjens, Kiavash Movahedi, Hans Wils, Joke Reumers, Jeroen Van Houdt, Stein Aerts, Yvan Saeys

Contributors: Laboratory of Molecullar and Cellular Therapy, Department of Bio-engineering Sciences, Basic (bio-) Medical Sciences

Source: GENOME BIOLOGY

Subject Terms: Animals, Antibodies/chemistry, COVID-19/blood, Case-control studies, Cell Line, Tumor, Cell Nucleus/chemistry, Humans, Lipids/chemistry, Mice, Inbred BALB C, Mice, Inbred C57BL, Neutrophils/chemistry, Sequence Analysis, RNA/methods, Single-Cell Analysis/methods, Cellular and Molecular Neuroscience, Biology and Life Sciences, Medicine and Health Sciences, Hashing, scRNA-seq, MULTI-seq, CITE-seq, Sample multiplexing, Science & Technology, Life Sciences & Biomedicine, Biotechnology & Applied Microbiology, Genetics & Heredity

File Description: application/pdf; Electronic

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::76e7752632cd02f28fbaed875f367966
https://hdl.handle.net/20.500.14017/5aaad9b8-237f-48cd-870f-045bc4a6e128

2
Gut mucosa dissociation protocols influence cell type proportions and single-cell gene expression levels

Authors: Werna T. C. Uniken Venema, Aarón D. Ramírez-Sánchez, Emilia Bigaeva, Sebo Withoff, Iris Jonkers, Rebecca E. McIntyre, Mennatallah Ghouraba, Tim Raine, Rinse K. Weersma, Lude Franke, Eleonora A. M. Festen, Monique G. P. van der Wijst

Contributors: Molecular Neuroscience and Ageing Research (MOLAR), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Stem Cell Aging Leukemia and Lymphoma (SALL)

Source: essn: 2045-2322
nlmid: 101563288
Scientific Reports, 12:9897. Nature Publishing Group

Subject Terms: Collagenases, Flow Cytometry/methods, Gene Expression, Gene Expression Profiling/methods, Intestinal Mucosa, Peptide Hydrolases, Sequence Analysis, RNA/methods, Single-Cell Analysis/methods, Article, 692/308/2056, 631/337/2019, Flow Cytometry, Gene Expression Profiling, Sequence Analysis, RNA, Single-Cell Analysis, Multidisciplinary, Sequence Analysis, RNA/methods

File Description: application/pdf

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9feb7c5ffcd2a1c94d8ab8e4546a9977

3
Chord: an ensemble machine learning algorithm to identify doublets in single-cell RNA sequencing data

Authors: Ke-Xu Xiong, Han-Lin Zhou, Cong Lin, Jian-Hua Yin, Karsten Kristiansen, Huan-Ming Yang, Gui-Bo Li

Source: Xiong, K-X, Zhou, H-L, Lin, C, Yin, J-H, Kristiansen, K, Yang, H-M & Li, G-B 2022, ' Chord : an ensemble machine learning algorithm to identify doublets in single-cell RNA sequencing data ', Communications Biology, vol. 5, 510 . https://doi.org/10.1038/s42003-022-03476-9

Subject Terms: General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology, Medicine (miscellaneous), Algorithms, Machine Learning, Sequence Analysis, RNA/methods, Single-Cell Analysis/methods, Software

File Description: application/pdf

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a5ade7d4351e4ee058b902d4f8980c45
https://doi.org/10.1038/s42003-022-03476-9

5
Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

Authors: Ao Chen, Sha Liao, Mengnan Cheng, Kailong Ma, Liang Wu, Yiwei Lai, Xiaojie Qiu, Jin Yang, Jiangshan Xu, Shijie Hao, Xin Wang, Huifang Lu, Xi Chen, Xing Liu, Xin Huang, Zhao Li, Yan Hong, Yujia Jiang, Jian Peng, Shuai Liu, Mengzhe Shen, Chuanyu Liu, Quanshui Li, Yue Yuan, Xiaoyu Wei, Huiwen Zheng, Weimin Feng, Zhifeng Wang, Yang Liu, Zhaohui Wang, Yunzhi Yang, Haitao Xiang, Lei Han, Baoming Qin, Pengcheng Guo, Guangyao Lai, Pura Muñoz-Cánoves, Patrick H. Maxwell, Jean Paul Thiery, Qing-Feng Wu, Fuxiang Zhao, Bichao Chen, Mei Li, Xi Dai, Shuai Wang, Haoyan Kuang, Junhou Hui, Liqun Wang, Ji-Feng Fei, Ou Wang, Xiaofeng Wei, Haorong Lu, Bo Wang, Shiping Liu, Ying Gu, Ming Ni, Wenwei Zhang, Feng Mu, Ye Yin, Huanming Yang, Michael Lisby, Richard J. Cornall, Jan Mulder, Mathias Uhlén, Miguel A. Esteban, Yuxiang Li, Longqi Liu, Xun Xu, Jian Wang

Source: Chen, A, Liao, S, Cheng, M, Ma, K, Wu, L, Lai, Y, Qiu, X, Yang, J, Xu, J, Hao, S, Wang, X, Lu, H, Chen, X, Liu, X, Huang, X, Li, Z, Hong, Y, Jiang, Y, Peng, J, Liu, S, Shen, M, Liu, C, Li, Q, Yuan, Y, Wei, X, Zheng, H, Feng, W, Wang, Z, Liu, Y, Wang, Z, Yang, Y, Xiang, H, Han, L, Qin, B, Guo, P, Lai, G, Muñoz-Cánoves, P, Maxwell, P H, Thiery, J P, Wu, Q-F, Zhao, F, Chen, B, Li, M, Dai, X, Wang, S, Kuang, H, Hui, J, Wang, L, Fei, J-F, Wang, O, Wei, X, Lu, H, Wang, B, Liu, S, Gu, Y, Ni, M, Zhang, W, Mu, F, Yin, Y, Yang, H, Lisby, M, Cornall, R J, Mulder, J, Uhlén, M, Esteban, M A, Li, Y, Liu, L, Xu, X & Wang, J 2022, ' Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays ', Cell, vol. 185, no. 10, pp. 1777-1792.e21 . https://doi.org/10.1016/j.cell.2022.04.003

Subject Terms: Animals, DNA/genetics, Embryo, Mammalian, Female, Gene Expression Profiling/methods, Mammals/genetics, Mice, Organogenesis/genetics, Pregnancy, Sequence Analysis, RNA/methods, Single-Cell Analysis/methods, Transcriptome/genetics, Brain, Cell atlas, Cell differentiation, Cell lineages, Development, Developmental diseases, Mouse organogenesis, Progenitors, Single-cell, Spatial transcriptomics, General Biochemistry, Genetics and Molecular Biology

File Description: application/pdf

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fabc9798c1368f1bac28825cf4ea3d4b
https://curis.ku.dk/portal/da/publications/spatiotemporal-transcriptomic-atlas-of-mouse-organogenesis-using-dna-nanoballpatterned-arrays(dd123904-163c-4267-bf46-c612c3bc3492).html

6
Single-cell RNA sequencing technologies and applications:A brief overview

Authors: Dragomirka Jovic, Xue Liang, Hua Zeng, Lin Lin, Fengping Xu, Yonglun Luo

Source: Jovic, D, Liang, X, Zeng, H, Lin, L, Xu, F & Luo, Y 2022, ' Single-cell RNA sequencing technologies and applications : A brief overview ', Clinical and Translational Medicine, vol. 12, no. 3, e694 . https://doi.org/10.1002/ctm2.694

Subject Terms: Animals, Gene Expression Profiling/methods, Sequence Analysis, RNA/methods, Single-Cell Analysis/methods, Technology, Whole Exome Sequencing, ATLAS, BETA-CELL, GENE-EXPRESSION, GENOME-WIDE EXPRESSION, MESSENGER-RNA, PHENOTYPIC HETEROGENEITY, REVEALS, RNA sequencing, SEQ ANALYSIS, SPATIAL TRANSCRIPTOMICS, STROMAL CELLS, big data, precision medicine, regenerative medicine, single cell, Molecular Medicine, Medicine (miscellaneous)

File Description: application/pdf

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fe3c7f9c3a207a59ae231fb3e3ef571a
https://curis.ku.dk/portal/da/publications/singlecell-rna-sequencing-technologies-and-applications(a27923bb-68d1-4138-a6d3-50e61c9398dc).html

7
Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies

Authors: Buys de Barbanson, Nico Battich, Marvin E. Tanenbaum, Lenno Krenning, Alexander van Oudenaarden, Hans Clevers, Joep Beumer, Chloé S. Baron

Contributors: Hubrecht Institute for Developmental Biology and Stem Cell Research

Source: Science, 367(6482), 1151-1156. American Association for the Advancement of Science (AAAS)

Subject Terms: Animals, Humans, Indicators and Reagents/chemistry, K562 Cells, Mice, RNA Stability, RNA, Messenger/metabolism, Sequence Analysis, RNA/methods, Single-Cell Analysis/methods, Transcription, Genetic, Uridine/analogs & derivatives, RNA, Messenger/metabolism, Sequence Analysis, RNA/methods, Transcription, Genetic, Multidisciplinary, Transcription (biology), Cell, medicine.anatomical_structure, medicine, Messenger RNA, Cell cycle, Gene expression, Cell biology, Biology, Cellular differentiation, Stem cell

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4ce8c483eeafd24ebf33ea24464326ea

HTML Full Text     PDF Full Text
8
Tailoring the resolution of single-cell RNA sequencing for primary cytotoxic T cells

Authors: Kanev, Kristiyan, Roelli, Patrick, Wu, Ming, Wurmser, Christine, Delorenzi, Mauro, Pfaffl, Michael W., Zehn, Dietmar

Source: Nature Communications
Nature communications, vol. 12, no. 1, pp. 569
Nature Communications, Vol 12, Iss 1, Pp 1-11 (2021)

Subject Terms: Article, Gene expression analysis, RNA sequencing, Lymphocyte differentiation, Infection, Animals, Gene Expression Profiling/methods, High-Throughput Nucleotide Sequencing/methods, Humans, Mice, RNA/genetics, RNA, Messenger/genetics, Reproducibility of Results, Sequence Analysis, RNA/methods, Single-Cell Analysis/methods, T-Lymphocytes, Cytotoxic/cytology, T-Lymphocytes, Cytotoxic/metabolism, Science

File Description: application/pdf

Access URL: https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::0d2add2555507393937f9419b3038488
http://europepmc.org/articles/PMC7835213

9
A Chlamydia trachomatis 23S rRNA G1523A variant escaping detection in the Aptima Combo 2 assay (Hologic) was widespread across Denmark in July–September 2019

Authors: Tobias Müller Vang, Lene Nielsen, Ida Grønbaek, Jørgen Skov Jensen, Steen Hoffmann, Rikke Kristine Nielsen, Ronza Hadad, Magnus Unemo, Marianne Nielsine Skov, Henrik Westh, Birte Kolmos, Lasse Jessen Schwartz, Jens Kjølseth Møller, Marlene Olsen, Lenette Sandborg Weinreich

Source: Hadad, R, Jensen, J S, Westh, H, Grønbæk, I, Schwartz, L J, Nielsen, L, Vang, T M, Nielsen, R, Weinreich, L S, Skov, M N, Olsen, M, Møller, J K, Kolmos, B, Unemo, M & Hoffmann, S 2020, ' A Chlamydia trachomatis 23S rRNA G1523A variant escaping detection in the Aptima Combo 2 assay (Hologic) was widespread across Denmark in July–September 2019 ', A P M I S. Acta Pathologica, Microbiologica et Immunologica Scandinavica, vol. 128, no. 6, pp. 440-444 . https://doi.org/10.1111/apm.13043
Hadad, R, Skov Jensen, J, Westh, H, Grønbaek, I, Jessen Schwartz, L, Nielsen, L, Müller Vang, T, Nielsen, R, Sandborg Weinreich, L, Skov, M N, Olsen, M, Kjølseth Møller, J, Kolmos, B, Unemo, M & Hoffmann, S 2020, ' A Chlamydia trachomatis 23S rRNA G1523A variant escaping detection in the Aptima Combo 2 assay (Hologic) was widespread across Denmark in July-September 2019 ', APMIS-Journal of Pathology, Microbiology and Immunology, vol. 128, no. 6, pp. 440-444 . https://doi.org/10.1111/apm.13043
Hadad, R, Jensen, J S, Westh, H, Grønbaek, I, Schwartz, L J, Nielsen, L, Vang, T M, Nielsen, R, Weinreich, L S, Skov, M N, Olsen, M, Møller, J K, Kolmos, B, Unemo, M & Hoffmann, S 2020, ' A Chlamydia trachomatis 23S rRNA G1523A variant escaping detection in the Aptima Combo 2 assay (Hologic) was widespread across Denmark in July-September 2019 ', A P M I S. Acta Pathologica, Microbiologica et Immunologica Scandinavica, vol. 128, no. 6, pp. 440-444 . https://doi.org/10.1111/apm.13043

Subject Terms: 23S rRNA, Aptima Combo 2 assay, C1515T, Chlamydia trachomatis, Denmark, FI-nvCT, G1523A, new variant, Microbiology (medical), General Medicine, Immunology and Allergy, Pathology and Forensic Medicine, Chlamydia trachomatis infection, medicine.disease_cause, medicine, Nucleic Acid Amplification Tests, 23S ribosomal RNA, business.industry, business, New variant, Dual target, Highly sensitive, Virology, Single sample, Chlamydia Infections/diagnosis, Chlamydia trachomatis/genetics, Denmark/epidemiology, Female, Gonorrhea/diagnosis, Humans, Male, Neisseria gonorrhoeae/genetics, Nucleic Acid Amplification Techniques/methods, RNA, Bacterial/genetics, RNA, Ribosomal, 23S/genetics, Sensitivity and Specificity, Sequence Analysis, RNA/methods

File Description: application/pdf

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d059c0a521bae27620a1301f9a95e7c0
https://findresearcher.sdu.dk:8443/ws/files/170280566/apm.13043.pdf

10
NOseq: amplicon sequencing evaluation method for RNA m6A sites after chemical deamination

Authors: Yuri Motorin, Julian König, Jean-Yves Roignant, Claudia Höbartner, Aurellia Galliot, Florian Pichot, Thomas Kemmer, Mark Helm, Virginie Marchand, Maksim V. Sednev, Andreas Hildebrandt, Stephan Werner, Tina Lence

Contributors: Johannes Gutenberg - Universität Mainz (JGU), Ingénierie, Biologie et Santé en Lorraine (IBSLor), Université de Lorraine (UL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Würzburg, Institute of Molecular Biology (IMB), Center for Integrative Genomics - Institute of Bioinformatics, Génopode (CIG), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL)-Université de Lausanne (UNIL), Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Université de Lausanne = University of Lausanne (UNIL)-Université de Lausanne = University of Lausanne (UNIL)

Source: Nucleic Acids Research
Nucleic Acids Research, Oxford University Press, 2020, ⟨10.1093/nar/gkaa1173⟩
Nucleic acids research, vol. 49, no. 4, pp. e23

Subject Terms: AcademicSubjects/SCI00010, Narese/13, Methods Online, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], ComputingMilieux_MISCELLANEOUS, Adenosine/analogs & derivatives, Adenosine/analysis, Algorithms, Animals, Chromatography, Liquid, Deamination, Drosophila melanogaster/genetics, HEK293 Cells, HeLa Cells, High-Throughput Nucleotide Sequencing/methods, Humans, RNA/chemistry, RNA, Long Noncoding/chemistry, RNA, Messenger/chemistry, RNA, Ribosomal, 18S/chemistry, Sequence Alignment, Sequence Analysis, RNA/methods, Tandem Mass Spectrometry, Genetics, Amplicon, Transcriptome, Sequence alignment, Ribosomal RNA, Computational biology, Biology, RNA, Bisulfite sequencing, Sequence analysis

File Description: application/pdf

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7a5a3da39a645358b584c4beb2957407
http://europepmc.org/articles/PMC7913672

11
Genetic diversity and drug resistance of HIV-1 among infected pregnant women newly diagnosed in Luanda, Angola

Authors: Carlos Silva de Jesus, Cruz S. Sebastião, Domingos Jandondo, Zoraima Neto, Marinela Mirandela, Miguel Brito, Amilcar Tanuri, Joana Morais, José Carlos Couto-Fernandez

Contributors: NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM)

Source: Repositório Científico de Acesso Aberto de Portugal
Repositório Científico de Acesso Aberto de Portugal (RCAAP)
instacron:RCAAP
PLoS ONE, Vol 14, Iss 11, p e0225251 (2019)
PLoS ONE

Subject Terms: Adolescent, Adult, Angola, Anti-HIV Agents/pharmacology, Cross-Sectional Studies, Drug Resistance, Viral, Female, Genetic Variation, Genotyping Techniques, HIV Infections/diagnosis, HIV-1/classification, Humans, Phylogeny, Population Surveillance, Pregnancy, Pregnancy Complications, Infectious/virology, Sample Size, Sequence Analysis, RNA/methods, Young Adult, pol Gene Products, Human Immunodeficiency Virus/genetics, SDG 3 - Good Health and Well-being, Medicine, Science, Multidisciplinary, Antibiotic resistance, Drug resistance, Population, education.field_of_study, education, Genetic variation, Reverse transcriptase, Subtyping, Biology, Sequence analysis, Nucleoside Reverse Transcriptase Inhibitor, Virology, HIV infection, Antiretroviral therapy, Antimicrobial resistance, Epidemiology, Human genetics, Luanda, Project Pró-África CNPq n˚ 440145/2015-5, Research Article, Biology and Life Sciences, Microbiology, Medical Microbiology, Microbial Pathogens, Viral Pathogens, Immunodeficiency Viruses, HIV, HIV-1, Medicine and Health Sciences, Pathology and Laboratory Medicine, Pathogens, Organisms, Viruses, RNA viruses, Retroviruses, Lentivirus, Women's Health, Maternal Health, Obstetrics and Gynecology, Immunology, Vaccination and Immunization, Antiviral Therapy, Antiretroviral Therapy, Public and Occupational Health, Preventive Medicine, Microbial Control, Antimicrobial Resistance, Pharmacology, HIV epidemiology, People and Places, Geographical Locations, Africa, Genetics, Human Genetics

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1fa8500391911f6a800b1b8c7485d7e6

12
RNA sequencing and swarm intelligence-enhanced classification algorithm development for blood-based disease diagnostics using spliced blood platelet RNA

Authors: Nik Sol, Thomas Wurdinger, Myron G. Best, Sjors G J G In 't Veld

Contributors: Neurosurgery, VU University medical center, Neurology, CCA - Imaging and biomarkers, CCA - Cancer biology and immunology

Source: Nature protocols, 14(4), 1206-1234. Nature Publishing Group
Best, M G, in ’t Veld, S G J G, Sol, N & Wurdinger, T 2019, ' RNA sequencing and swarm intelligence–enhanced classification algorithm development for blood-based disease diagnostics using spliced blood platelet RNA ', Nature Protocols, vol. 14, no. 4, pp. 1206-1234 . https://doi.org/10.1038/s41596-019-0139-5
Nature Protocols, 14(4), 1206-1234. Nature Publishing Group

Subject Terms: Biomarkers/blood, Blood Platelets/chemistry, Computational Biology/methods, DNA, Complementary/analysis, High-Throughput Nucleotide Sequencing/methods, Humans, RNA Splicing, RNA, Messenger/analysis, Sequence Analysis, RNA/methods, Support Vector Machine/statistics & numerical data, ComputingMethodologies_PATTERNRECOGNITION, General Biochemistry, Genetics and Molecular Biology, FASTQ format, RNA extraction, Swarm intelligence, Gene, Computer science, Statistical classification, RNA, Algorithm, Selection (genetic algorithm), Database normalization, DNA, Complementary/analysis, Messenger/analysis, Sequence Analysis, RNA/methods

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a1ceba9b2d503e83af1539396b591443
https://pure.amc.nl/en/publications/rna-sequencing-and-swarm-intelligenceenhanced-classification-algorithm-development-for-bloodbased-disease-diagnostics-using-spliced-blood-platelet-rna(bd266aca-a41d-463a-881e-0646f08b8547).html

13
Transcriptional profiling of human microglia reveals grey-white matter heterogeneity and multiple sclerosis-associated changes

Authors: Jörg Hamann, Suzanne S. M. Miedema, Mark R. Mizee, Inge Huitinga, Marlijn van der Poel, Joachim L. Schultze, Thomas Ulas, Adelia, Sander W. Tas, Karianne G. Schuurman, Boy Helder, Cheng-Chih Hsiao

Contributors: Netherlands Institute for Neuroscience (NIN), AII - Inflammatory diseases, Graduate School, Experimental Immunology, Clinical Immunology and Rheumatology

Source: Nature Communications, 10:1139. Nature Publishing Group
Nature Communications
Nature communications, 10(1). Nature Publishing Group
Nature Communications, Vol 10, Iss 1, Pp 1-13 (2019)

Subject Terms: Aged, 80 and over, Case-Control Studies, Female, Gene Expression Profiling/methods, Gene Expression Regulation, Glycolysis/genetics, Gray Matter/metabolism, Humans, Iron/metabolism, Magnetic Resonance Imaging, Male, Membrane Proteins/genetics, Metabolic Networks and Pathways/genetics, Microglia/metabolism, Middle Aged, Multiple Sclerosis/genetics, Receptors, G-Protein-Coupled/genetics, Purinergic P2Y12/genetics, Sequence Analysis, RNA/methods, White Matter/metabolism, Article, Aged, 80 and over, Receptors, G-Protein-Coupled/genetics, Receptors, Purinergic P2Y12/genetics, Sequence Analysis, RNA/methods, Science, sense organs, skin and connective tissue diseases, lcsh:Science, lcsh:Q, General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, GPR56, Grey matter, medicine.anatomical_structure, medicine, White matter, Multiple sclerosis, medicine.disease, Biology, Gene expression, Transcriptome, Cell biology, Microglia, Regulation of gene expression

File Description: application/pdf

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ca80112a31c0c1a26e0ca851188f89cd

14
s ·nr:a visual analytics framework for contextual analyses of private and public RNA-seq data

Authors: Jan-Wilhelm Kornfeld, Paul Klemm, Peter Frommolt

Source: Klemm, P, Frommolt, P & Kornfeld, J W 2019, ' s ·nr : a visual analytics framework for contextual analyses of private and public RNA-seq data ', BMC Genomics, vol. 20, 85 . https://doi.org/10.1186/s12864-018-5396-0
BMC Genomics
BMC Genomics, Vol 20, Iss 1, Pp 1-12 (2019)

Subject Terms: Animals, Computer Graphics, Gene Expression Profiling/methods, High-Throughput Nucleotide Sequencing/methods, Mice, Sequence Analysis, RNA/methods, Software, User-Computer Interface, Next-generation sequencing, RNA-seq, Analysis workflow, Visual analytics, Visualization, GUI, GO analysis, Gene filtering, Differentially expressed genes, lcsh:Biotechnology, lcsh:TP248.13-248.65, lcsh:Genetics, lcsh:QH426-470, Genetics, Biotechnology, RNA-Seq, Experimental data, Data science, Login, Context (language use), Differential expression, SIMPLE (military communications protocol), Biology

File Description: application/pdf

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::54aeabfcfd38b5241463dd06aad0267f
https://findresearcher.sdu.dk:8443/ws/files/146020480/s12864_018_5396_0.pdf

15
Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers

Authors: Phillip D. Zamore, Pei Hsuan Wu, Zhiping Weng, Timothy J. Beane, Yu Fu

Source: BMC Genomics
BMC Genomics, Vol 19, Iss 1, Pp 1-14 (2018)
BMC genomics, Vol. 19, No 1 (2018) P. 531

Subject Terms: Genetics, Biotechnology, RNA-Seq, Computational biology, DNA microarray, Deep sequencing, Genomic library, RNA, Small RNA, Proteomics, Biology, Polymerase chain reaction, law.invention, law, natural sciences, genetic processes, Methodology Article, RNA-seq, Small RNA-seq, Unique molecular identifier, UMI, PCR duplicates, PCR cycle, Starting material, Sequencing depth, Transcriptome, Ribognome, lcsh:Biotechnology, lcsh:TP248.13-248.65, lcsh:Genetics, lcsh:QH426-470, Animals, Gene Library, Male, Mice, Polymerase Chain Reaction, RNA / chemistry, RNA / isolation & purification, RNA / metabolism, Reproducibility of Results, Sequence Analysis, RNA / methods, Testis / metabolism, Nucleotide, chemistry.chemical_classification, chemistry, Regulation of gene expression, Function (biology), Identifier

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2fb55ebe33b2ecd0a8c4eacbab0adecc
https://doi.org/10.1186/s12864-018-4933-1

16
Colorimetric assessment of BCR-ABL1 transcripts in clinical samples via gold nanoprobes

Authors: Patrícia Ribeiro, Raquel Vinhas, Cláudia Correia, Alexandra R. Fernandes, Aida Botelho de Sousa, Pedro V. Baptista, Alexandra Lourenço

Source: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Agência para a Sociedade do Conhecimento (UMIC)-FCT-Sociedade da Informação
instacron:RCAAP

Subject Terms: Biochemistry, Analytical Chemistry, Colloidal gold, Chemistry, Nanoprobe, Molecular probe, Polymerase chain reaction, law.invention, law, DNA, chemistry.chemical_compound, Computational biology, Molecular biology, Bioanalysis, Oligonucleotide, Fusion transcript, HSAC HEM, Colorimetry/methods, Fusion Proteins, bcr-abl/genetics, Gold/chemistry, Leukemia, Myeloid/genetics, Metal Nanoparticles/chemistry, Molecular Probe Techniques, Molecular Probes/chemistry, RNA, Neoplasm/genetics, Reproducibility of Results, Sensitivity and Specificity, Sequence Analysis, RNA/methods, Transcription Factors/genetics, Tumor Cells, Cultured

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::04c42fdb23481fb80cab940bb29d49fe
https://doi.org/10.1007/s00216-016-9622-9

PDF Full Text
19
switchde:inference of switch-like differential expression along single-cell trajectories

Authors: Campbell, Kieran R., Yau, Christopher

Source: Campbell, K R & Yau, C 2017, ' switchde : inference of switch-like differential expression along single-cell trajectories ', Bioinformatics (Oxford, England), vol. 33, no. 8, pp. 1241-1242 . https://doi.org/10.1093/bioinformatics/btw798
Bioinformatics

Subject Terms: Gene Expression Profiling/methods, Models, Genetic, Models, Statistical, Sequence Analysis, RNA/methods, Single-Cell Analysis, Software, Applications Notes, Gene Expression

Access URL: https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::29b69cd17fa4d9499d36642094f399b0
https://www.research.manchester.ac.uk/portal/en/publications/switchde(754f1160-1211-468c-bc73-f36a886574ae).html

20
RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics

Authors: Nik Sol, François Rustenburg, Bauke Ylstra, Bakhos A. Tannous, Josephine C. Dorsman, Heleen Verschueren, Bart A. Westerman, Pieter Wesseling, Egbert F. Smit, Jihane Tannous, Najim Ameziane, Jan Koster, Irsan E. Kooi, Henk M.W. Verheul, Edward Post, Myron G. Best, Thomas Wurdinger, David P. Noske, Pepijn Schellen, Jaap C. Reijneveld, R. Jonas A. Nilsson

Contributors: Neurosurgery, Neurology, Human genetics, Pathology, Pulmonary medicine, Medical oncology, CCA - Disease profiling, Oncogenomics, Amsterdam Gastroenterology Endocrinology Metabolism, Cancer Center Amsterdam

Source: Cancer Cell, 28(5), 666. Cell Press
Cancer Cell, 28(5), 666-676. Cell Press
Cancer Cell
Best, M G, Sol, N, Kooi, E I, Tannous, J, Westerman, A, Rustenburg, F, Schellen, P, Verschueren, H, Post, E, Koster, J, Ylstra, B, Ameziane, N, Dorsman, J, Smit, E F, Verheul, H M, Noske, D P, Reijneveld, J C, Nilsson, R J A, Tannous, B A, Wesseling, P & Wurdinger, T 2015, ' RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics ', Cancer Cell, vol. 28, no. 5, pp. 666-676 . https://doi.org/10.1016/j.ccell.2015.09.018
Cancer Cell, 28, 666-76
Cancer cell, 28(5), 666-676. Cell Press

Subject Terms: Oncology, Cell Biology, Cancer Research, Adult, Aged, 80 and over, Biomarkers, Tumor/blood, Blood Platelets/metabolism, Class I Phosphatidylinositol 3-Kinases, ErbB Receptors/genetics, Female, Gene Expression Profiling/methods, Gene Ontology, Humans, Male, Middle Aged, Mutation, Neoplasms/blood, Pathology, Molecular/methods, Phosphatidylinositol 3-Kinases/genetics, Proto-Oncogene Proteins c-met/genetics, Proto-Oncogene Proteins p21(ras)/genetics, Receptor, ErbB-2/genetics, Reproducibility of Results, Sensitivity and Specificity, Sequence Analysis, RNA/methods, Signal Transduction/genetics, Support Vector Machine, Young Adult, Cancer and Oncology, Cancer och onkologi, Cellbiologi, Article, Primary tumor, medicine.disease, medicine, RNA, Cancer research, Cancer, KRAS, medicine.disease_cause, Biology, Gene expression profiling, Messenger RNA, MRNA Sequencing, Platelet, Aged, 80 and over, Biomarkers, Tumor/blood, Pathology, Molecular/methods, Receptor, ErbB-2/genetics, Sequence Analysis, RNA/methods

File Description: image/pdf; application/pdf

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::16e6f8b66ce2ad8929b91af1171d0d1e
https://dspace.library.uu.nl/handle/1874/350405

Search Tools: Get RSS Feed — Email this Search