61 Matching Annotations
  1. Last 7 days
    1. if you could correct this Gene would we have the future reassured and we can then avoid all of these diseases I very much doubt it and I think it's very dangerous 00:23:49 because

      for - adjacency - progress trap - Crispr - gene therapy - Denis Noble - human genome project

      adjacency - between - human genome project - gene therapy - Crispr - progress trap - adjacency relationship - The idea that we can find specific causal relationships between genes and disease and use gene therapy to cure disease, - an envisioned goal of the human genome project - can be very dangerous because - usually one gene collaborates with many other genes to bring about an effect - If we don't know all the relationships, we can bring about a progress trap

    1. if you look for those in the genome you will not find them 00:05:26 anywhere in the genome

      for - comparison - genome coding to computer program

    2. the message I've put here we wish them all 00:03:44 well because that's the ending of my new book coming out next month

      for - metaphor - refuting genome as - book of life

    3. a bit of size comparison

      for - size comparison - genome to cell

    4. biology Beyond The 00:00:19 genome

      for - book - Biology Beyond the Genome - author - scientist - biologist - Denis Noble - book - Understanding Living Systems

  2. Aug 2023
    1. About ten years ago, a massive breakthrough happened in genomic research technology. A method appeared which is called NGS, next generation sequencing, and this method significantly cuts time and costs of any genomic research. For example, have you ever heard about the Human Genome Project? It was quite a popular topic for science fiction some time ago. 00:03:10 This project launched in 1990 with the goal to decrypt all genomic information in a human organism. At that time, with the technology of the time, it took ten years and three billion dollars to reach the goals of this project. With NGS, all of that can be done in just one day at the cost of 15,000 dollars.
      • for: progress trap, cumulative cultural evolution, gene-culture co-evolution, speed of cultural evolution, human genome project
      • paraphrase
        • the human genome project took 10 years and cost 3 billion dollars
        • with NGS technology, 10 years later, the same job takes 1 day and costs $15,000 dollars
  3. Nov 2022
    1. Primers to target the DXS gene24 (one copy per genome) and the ampicillin resistance gene on the plasmid were created using the Primer3Plus design tool
  4. Oct 2022
    1. To perform bacterial genome assembly, we suggest using the third-party de novo assembly tool Flye3. This analysis package represents a complete pipeline, taking raw nanopore reads as input, and producing polished contigs as output. We also recommend one round of polishing with Medaka4. These tools can be found on GitHub
  5. Aug 2022
    1. ReconfigBehSci. (2021, December 12). RT @ryan_landay: > A new diverse genome has appeared within the B.1.1.529 lineage that has all of the shared mutations of B.1.1.529, some o… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1470066521615605766

  6. Jun 2022
    1. whole-genome sequencing (WGS) provides the highest possible subtyping resolution improving the surveillance, outbreak investigation, source attribution, and microbial population studies

      Purpose of WGS in population epidemiology

      1. Surveillance
      2. Outbreak Investigation
      3. Source attribution
      4. Microbial population
  7. Mar 2022
    1. BA.2 sub-lineage has even higher propensity to spread among people and has the ability to infect people who have been fully vaccinated and/or previously infected by escaping from neutralising antibodies induced by vaccination or infection.

      Omicron BA2 infects more in vaccinated

  8. Feb 2022
  9. Dec 2021
    1. Genome sequencing is complex, and only 38 laboratories across the country (https://bit.ly/3ED4vrP) have the ability to sequence a virus which is as infectious as this

      Viral Genome sequencing facility in India

      • 38 labs
  10. Oct 2021
  11. Sep 2021
    1. To identify early embryonic base substitutions, we analysed whole-genome sequences of blood samples from 279 individuals with breast cancer (mean sequencing coverage 32-fold; Supplementary Table 1) seeking mutations with VAFs ranging from 10% to 35%

      This is what the research is studying.

    1. Kraemer, M. U. G., Hill, V., Ruis, C., Dellicour, S., Bajaj, S., McCrone, J. T., Baele, G., Parag, K. V., Battle, A. L., Gutierrez, B., Jackson, B., Colquhoun, R., O’Toole, Á., Klein, B., Vespignani, A., COVID-19 Genomics UK (COG-UK) Consortium‡, Volz, E., Faria, N. R., Aanensen, D. M., … Pybus, O. G. (2021). Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science, 373(6557), 889–895. https://doi.org/10.1126/science.abj0113

  12. Aug 2021
    1. O’Toole, Á., Scher, E., Underwood, A., Jackson, B., Hill, V., McCrone, J. T., Colquhoun, R., Ruis, C., Abu-Dahab, K., Taylor, B., Yeats, C., du Plessis, L., Maloney, D., Medd, N., Attwood, S. W., Aanensen, D. M., Holmes, E. C., Pybus, O. G., & Rambaut, A. (2021). Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evolution, veab064. https://doi.org/10.1093/ve/veab064

  13. Jul 2021
    1. Kraemer, M. U. G., Hill, V., Ruis, C., Dellicour, S., Bajaj, S., McCrone, J. T., Baele, G., Parag, K. V., Battle, A. L., Gutierrez, B., Jackson, B., Colquhoun, R., O’Toole, Á., Klein, B., Vespignani, A., Consortium‡, T. C.-19 G. U. (CoG-U., Volz, E., Faria, N. R., Aanensen, D., … Pybus, O. G. (2021). Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science. https://doi.org/10.1126/science.abj0113

  14. May 2021
  15. Apr 2021
  16. Mar 2021
    1. de Oliveira T, Lutucuta S, Nkengasong J, Morais J, Paixao JP, Neto Z, Afonso P, Miranda J, David K, Ingles L, Amilton P A P R R C, Freitas H R, Mufinda F, Tessema K S , Tegally H, San E J, Wilkinson E, Giandhari J, Pillay S, Giovanetti M, Naidoo Y, Katzourakis A, Ghafari M, Singh L, Tshiabuila D, Martin D, Lessells R. (2021) A Novel Variant of Interest of SARS-CoV-2 with Multiple Spike Mutations Detected through Travel Surveillance in Africa. medRxiv. https://www.krisp.org.za/publications.php?pubid=330. Accessed 26 March 2021.

  17. Feb 2021
    1. Miro Weinberger. (2020, December 3). Our 1st Covid-19 wastewater tests since Thanksgiving just came in—Virus levels are up significantly citywide. I hope that all of #BTV will look at this graph and see what I see: A call to action, to stop gathering with other households, and to get tested ASAP if you have https://t.co/8nxTwOOcFA [Tweet]. @MiroBTV. https://twitter.com/MiroBTV/status/1334613511692017664

  18. Jan 2021
    1. we developed a vastly improved INTEGRATE system that uses streamlined expression vectors to direct highly accurate insertions at ~100% efficiency effectively in a single orientation, independent of the cargo size, without requiring selection markers

      Efficiency sounds too exciting to not try!

  19. Aug 2020
    1. Ferretti, A. P., Kula, T., Wang, Y., Nguyen, D. M., Weinheimer, A., Dunlap, G. S., Xu, Q., Nabilsi, N., Perullo, C. R., Cristofaro, A. W., Whitton, H. J., Virbasius, A., Olivier, K. J., Baiamonte, L. B., Alistar, A. T., Whitman, E. D., Bertino, S. A., Chattopadhyay, S., & MacBeath, G. (2020). COVID-19 Patients Form Memory CD8+ T Cells that Recognize a Small Set of Shared Immunodominant Epitopes in SARS-CoV-2. MedRxiv, 2020.07.24.20161653. https://doi.org/10.1101/2020.07.24.20161653

    1. Guo, L., Boocock, J., Tome, J. M., Chandrasekaran, S., Hilt, E. E., Zhang, Y., Sathe, L., Li, X., Luo, C., Kosuri, S., Shendure, J. A., Arboleda, V. A., Flint, J., Eskin, E., Garner, O. B., Yang, S., Bloom, J. S., Kruglyak, L., & Yin, Y. (2020). Rapid cost-effective viral genome sequencing by V-seq. BioRxiv, 2020.08.15.252510. https://doi.org/10.1101/2020.08.15.252510

    1. Qu, J., Cai, Z., Liu, Y., Duan, X., Han, S., Zhu, Y., Jiang, Z., Zhang, Y., Zhuo, C., Liu, Y., Liu, Y., Liu, L., & Yang, L. (2020). Persistent bacterial coinfection of a COVID-19 patient caused by a genetically adapted Pseudomonas aeruginosa chronic colonizer. BioRxiv, 2020.08.05.238998. https://doi.org/10.1101/2020.08.05.238998

    1. Lednicky, J. A., Lauzardo, M., Fan, Z. H., Jutla, A. S., Tilly, T. B., Gangwar, M., Usmani, M., Shankar, S. N., Mohamed, K., Eiguren-Fernandez, A., Stephenson, C. J., Alam, M. M., Elbadry, M. A., Loeb, J. C., Subramaniam, K., Waltzek, T. B., Cherabuddi, K., Morris, J. G., & Wu, C.-Y. (2020). Viable SARS-CoV-2 in the air of a hospital room with COVID-19 patients. MedRxiv, 2020.08.03.20167395. https://doi.org/10.1101/2020.08.03.20167395

  20. Jul 2020
  21. Jun 2020
  22. May 2020
  23. Apr 2020
  24. Nov 2017
  25. Oct 2017
    1. Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation
  26. Sep 2017
    1. Major flaws in "Identification of individuals by trait prediction using whole-genome sequencing data"

      re Venter study in PNAS, claiming to be able to identify people based on whole genome data

    1. Plot a course through the genome Inspired by Google Maps, a suite of tools is allowing researchers to chart the complex conformations of chromosomes.

      mentioned tools are focused on (capture) Hi-C data

  27. Jul 2017
    1. Napoleon oak genome sequencing project web site: example of public engagement in tree genomics

  28. Jun 2017
  29. Sep 2016
    1. You must quit IGV and restart for this preference to take effect. The genome should appear in the drop-down list.

      restart may be insufficient; had to modify prefs.properties in ~/igv (removing old cached genome values) before i could see my genomes

  30. Apr 2016