Title | Column 1 | Column 2 | Column 3 | Column 4 | Column 5 | Column 6 | Column 7 | Column 8 | Column 9 | Column 10 | Column 11 | Column 12 | Column 13 | Column 14 | Column 15 | Column 16 | Column 17 | Column 18 | Column 19 | Column 20 | Column 21 | Column 22 | Column 23 | Column 24 | Column 25 | Column 26 | Column 27 | Column 28 | Column 29 | Column 30 | Column 31 | Column 32 | Column 33 | Column 34 | Column 35 | Column 36 | Column 37 | Column 38 | Column 39 | Column 40 | Column 41 | Column 42 | Column 43 | Column 44 | Column 45 | Column 46 | Column 47 | Column 48 | Column 49 | Column 50 | Column 51 | Column 52 | Column 53 | Column 54 | Column 55 | Column 56 | Column 57 | Column 58 | Column 59 | Column 60 | Column 61 | Column 62 | Column 63 | Column 64 | Column 65 | Column 66 | Column 67 | Column 68 | Column 69 | Column 70 | Column 71 | Column 72 | Column 73 | Column 74 | Column 75 | Column 76 | Column 77 | Column 78 | Column 79 | Column 80 | Column 81 | Column 82 | Column 83 | Column 84 | Column 85 | Column 86 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Key | Item Type | Publication Year | Author | Title | Publication Title | ISBN | ISSN | DOI | Url | Abstract Note | Date | Date Added | Date Modified | Access Date | Pages | Num Pages | Issue | Volume | Number Of Volumes | Journal Abbreviation | Short Title | Series | Series Number | Series Text | Series Title | Publisher | Place | Language | Rights | Type | Archive | Archive Location | Library Catalog | Call Number | Extra | Notes | File Attachments | Link Attachments | Manual Tags | Automatic Tags | Editor | Series Editor | Translator | Contributor | Attorney Agent | Book Author | Cast Member | Commenter | Composer | Cosponsor | Counsel | Interviewer | Producer | Recipient | Reviewed Author | Scriptwriter | Words By | Guest | Number | Edition | Running Time | Scale | Medium | Artwork Size | Filing Date | Application Number | Assignee | Issuing Authority | Country | Meeting Name | Conference Name | Court | References | Reporter | Legal Status | Priority Numbers | Programming Language | Version | System | Code | Code Number | Section | Session | Committee | History | Legislative Body |
EZPXY27A | journalArticle | 2023 | Limberis, Jason D.; Metcalfe, John Z. | primerJinn: a tool for rationally designing multiplex PCR primer sets for amplicon sequencing and performing in silico PCR | BMC Bioinformatics | 1471-2105 | 10.1186/s12859-023-05609-1 | Multiplex PCR amplifies numerous targets in a single tube reaction and is essential in molecular biology and clinical diagnostics. One of its most important applications is in the targeted sequencing of pathogens. Despite this importance, few tools are available for designing multiplex primers. | 2023-12-12 | 2025-02-15 01:49:57 | 2025-02-15 01:49:57 | 2025-02-15 01:49:57 | 468 | 1 | 24 | BMC Bioinformatics | primerJinn | BioMed Central | /Users/karolina/Zotero/storage/JZ8AG223/Limberis and Metcalfe - 2023 - primerJinn a tool for rationally designing multiplex PCR primer sets for amplicon sequencing and pe.pdf; /Users/karolina/Zotero/storage/F93JNC9J/s12859-023-05609-1.html | Multiplex PCR; PCR; Primer design; Targeted sequencing | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
UX4842PK | journalArticle | 2009 | Mori, Yasuyoshi; Notomi, Tsugunori | Loop-mediated isothermal amplification (LAMP): a rapid, accurate, and cost-effective diagnostic method for infectious diseases | Journal of Infection and Chemotherapy: Official Journal of the Japan Society of Chemotherapy | 1341-321X | 10.1007/s10156-009-0669-9 | Loop-mediated isothermal amplification (LAMP) is an established nucleic acid amplification method offering rapid, accurate, and cost-effective diagnosis of infectious diseases. This technology has been developed into commercially available detection kits for a variety of pathogens including bacteria and viruses. The current focus on LAMP methodology is as a diagnostic system to be employed in resource-limited laboratories in developing countries, where many fatal tropical diseases are endemic. The combination of LAMP and novel microfluidic technologies such as Lab-on-a-chip may facilitate the realization of genetic point-of-care testing systems to be used by both developed and developing countries in the near future. This review will describe the historical, current, and future developments of such technologies. | 2009-04 | 2025-02-15 01:50:59 | 2025-02-15 01:50:59 | 62-69 | 2 | 15 | J Infect Chemother | Loop-mediated isothermal amplification (LAMP) | eng | PubMed | PMID: 19396514 PMCID: PMC7087713 | /Users/karolina/Zotero/storage/YBVRP2HI/Mori and Notomi - 2009 - Loop-mediated isothermal amplification (LAMP) a rapid, accurate, and cost-effective diagnostic meth.pdf; | Animals; Bacteria; Communicable Diseases; Eukaryota; Humans; Nucleic Acid Amplification Techniques; Point-of-Care Systems; Time Factors; Viruses | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CWW7JD8J | journalArticle | 2019 | Kaygusuz, Doğukan; Vural, Sümeyra; Aytekin, Ali Özhan; Lucas, Stuart James; Elitas, Meltem | DaimonDNA: A portable, low-cost loop-mediated isothermal amplification platform for naked-eye detection of genetically modified organisms in resource-limited settings | Biosensors and Bioelectronics | 0956-5663 | 10.1016/j.bios.2019.111409 | https://www.sciencedirect.com/science/article/pii/S0956566319304889 | The steady increase in commercialization of genetically modified organisms (GMOs) demands low-cost, rapid and portable GMO-detection methods that are technically and economically sustainable. Traditional nucleic acid detection platforms are still expensive, immobile and generate complex read-outs to be analyzed by experienced personal. Herein, we report the development of a portable, rapid and user-friendly GMO-detection biosensor, DaimonDNA. The system specifically amplifies the target DNA using loop-mediated isothermal amplification (LAMP) and provides real-time, naked-eye detection with Hydroxynaphthol blue reagent in less than 30 min. The construction of the platform relies on 3D printing and off-the-shelf electronic components that makes it extremely low-cost (<25 Euro), light weight (108 g), mobile (6 × 6 × 3 cm) and suitable for field deployment. We present the detection of the soybean lectin gene as a species control, and P35S as a transgene element found in many GMO varieties. We confirmed specificity of the DaimonDNA biosensor using” RoundUp Ready (RRS)” and MON89788 soybean genomic DNA with P35S and lectin primer sets. We characterized sensitivity of our system using 76.92, 769.2 and 7692 copies of RRS soybean genomic DNA in a non-GMO background. We benchmarked the DNA amplification and detection efficiency of our system against a thermocycling machine by quantifying the images obtained from gel electrophoresis and showed that our system is comparable to most other reported isothermal amplification techniques. This system can also be used for widespread point-of-care or field-based testing that is infrequently performed due to the lack of rapid, inexpensive, user-friendly and portable methods. | 2019-09-15 | 2025-02-15 01:52:09 | 2025-02-15 01:52:09 | 2025-02-15 01:52:09 | 111409 | 141 | Biosensors and Bioelectronics | DaimonDNA | ScienceDirect | /Users/karolina/Zotero/storage/DMRK8MR3/S0956566319304889.html | Biosensor; Genetically modified organisms (GMO); Loop-mediated isothermal amplification (LAMP); Low-cost; Naked-eye detection; Portable | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NA65UVGB | webpage | practical guide to amplicon and metagenomic analysis of microbiome data | Protein & Cell | Oxford Academic | https://academic.oup.com/proteincell/article/12/5/315/6724529 | 2025-02-15 01:52:49 | 2025-02-15 01:52:49 | 2025-02-15 01:52:49 | /Users/karolina/Zotero/storage/H7E25TMZ/6724529.html | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
4XTDZ5J4 | journalArticle | 2024 | Kalendar, Ruslan; Shevtsov, Alexandr; Otarbay, Zhenis; Ismailova, Aisulu | In silico PCR analysis: a comprehensive bioinformatics tool for enhancing nucleic acid amplification assays | Frontiers in Bioinformatics | 2673-7647 | 10.3389/fbinf.2024.1464197 | https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2024.1464197/full | 2024-10-07 | 2025-02-15 01:53:24 | 2025-02-15 01:53:24 | 2025-02-15 01:53:24 | 4 | Front. Bioinform. | In silico PCR analysis | English | Frontiers | Publisher: Frontiers | /Users/karolina/Zotero/storage/P4JNH2KC/Kalendar et al. - 2024 - In silico PCR analysis a comprehensive bioinformatics tool for enhancing nucleic acid amplification.pdf | bisulfite conversion; degenerate PCR; genotyping; In silico PCR; PCR primer and probe analysis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2R6UC85I | journalArticle | 2008 | Tomita, Norihiro; Mori, Yasuyoshi; Kanda, Hidetoshi; Notomi, Tsugunori | Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products | Nature Protocols | 1750-2799 | 10.1038/nprot.2008.57 | As the human genome is decoded and its involvement in diseases is being revealed through postgenome research, increased adoption of genetic testing is expected. Critical to such testing methods is the ease of implementation and comprehensible presentation of amplification results. Loop-mediated isothermal amplification (LAMP) is a simple, rapid, specific and cost-effective nucleic acid amplification method when compared to PCR, nucleic acid sequence-based amplification, self-sustained sequence replication and strand displacement amplification. This protocol details an improved simple visual detection system for the results of the LAMP reaction. In LAMP, a large amount of DNA is synthesized, yielding a large pyrophosphate ion by-product. Pyrophosphate ion combines with divalent metallic ion to form an insoluble salt. Adding manganous ion and calcein, a fluorescent metal indicator, to the reaction solution allows a visualization of substantial alteration of the fluorescence during the one-step amplification reaction, which takes 30–60 min. As the signal recognition is highly sensitive, this system enables visual discrimination of results without costly specialized equipment. This detection method should be helpful in basic research on medicine and pharmacy, environmental hygiene, point-of-care testing and more. | 2008-05 | 2025-02-15 01:54:10 | 2025-02-15 01:54:10 | 2025-02-15 01:54:10 | 877-882 | 5 | 3 | Nat Protoc | en | 2008 Springer Nature Limited | Publisher: Nature Publishing Group | Analytical Chemistry; Biological Techniques; Computational Biology/Bioinformatics; general; Life Sciences; Microarrays; Organic Chemistry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
6JJ3VIVL | journalArticle | 2021 | Lopez-Rincon, Alejandro; Tonda, Alberto; Mendoza-Maldonado, Lucero; Mulders, Daphne G. J. C.; Molenkamp, Richard; Perez-Romero, Carmina A.; Claassen, Eric; Garssen, Johan; Kraneveld, Aletta D. | Classification and specific primer design for accurate detection of SARS-CoV-2 using deep learning | Scientific Reports | 2045-2322 | 10.1038/s41598-020-80363-5 | In this paper, deep learning is coupled with explainable artificial intelligence techniques for the discovery of representative genomic sequences in SARS-CoV-2. A convolutional neural network classifier is first trained on 553 sequences from the National Genomics Data Center repository, separating the genome of different virus strains from the Coronavirus family with 98.73% accuracy. The network’s behavior is then analyzed, to discover sequences used by the model to identify SARS-CoV-2, ultimately uncovering sequences exclusive to it. The discovered sequences are validated on samples from the National Center for Biotechnology Information and Global Initiative on Sharing All Influenza Data repositories, and are proven to be able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. Next, one of the sequences is selected to generate a primer set, and tested against other state-of-the-art primer sets, obtaining competitive results. Finally, the primer is synthesized and tested on patient samples (n = 6 previously tested positive), delivering a sensitivity similar to routine diagnostic methods, and 100% specificity. The proposed methodology has a substantial added value over existing methods, as it is able to both automatically identify promising primer sets for a virus from a limited amount of data, and deliver effective results in a minimal amount of time. Considering the possibility of future pandemics, these characteristics are invaluable to promptly create specific detection methods for diagnostics. | 2021-01-13 | 2025-02-15 01:56:00 | 2025-02-15 01:56:00 | 2025-02-15 01:56:00 | 947 | 1 | 11 | Sci Rep | en | 2021 The Author(s) | Publisher: Nature Publishing Group | /Users/karolina/Zotero/storage/CSNVKDMY/Lopez-Rincon et al. - 2021 - Classification and specific primer design for accurate detection of SARS-CoV-2 using deep learning.pdf | Classification and taxonomy; Computer science; Viral infection |