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for - follow up - paper - Could physiology rescue genomics?

to - Could physiology rescue genomics? - https://hyp.is/bslQ-BVVEe-hgF-rrNmjrA/academic.oup.com/biolinnean/article/139/4/357/6604006

https://zoonomiaproject.org/

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Workflow 1. Cross-linking 2. Chromatin fragmentation 3. Immunoprecipitation of chromatin 4. DNA recovery and purification 5. Sequencing of DNA

ChIP-seq is concerned with testing for protein DNA interactions.

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It would be really interesting to compare the patterns you observe here with the X-like genome inversion patterns that we and others have reported (e.g., see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC16139/). These patterns basically show that the distance a gene is from the origin of replication is conserved but the side of the origin it is on is not.

Those inversion patterns have been seen in some but not all comparisons of closely related bacterial and archaeal genomes. So it seems there are some taxa where the distance a gene is from the origin is not conserved over evolutionary time. It would be interesting to know if these taxa show the X-like patternb you report for gene expression.

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dodgy labs might mark variant as pathogenic and link to assessment criteria but apply them wrongly. These might be detected if other labs post conflicting assessments. But for ultrarare variants, no other lab might have submitted that variant

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ReconfigBehSci. (2022, January 10). RT @GeraldGmboowa: Genomic epidemiology of SARS-CoV-2 in Africa focused on different 🌍regions @AfricaCDC https://bit.ly/3tcDuJl. Using A… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1480595472834338827

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Singh, Urvashi B., Mercy Rophina, Dr Rama Chaudhry, Vigneshwar Senthivel, Kiran Bala, Rahul C. Bhoyar, Bani Jolly, et al. “Variants of Concern Responsible for SARS-CoV-2 Vaccine Breakthrough Infections from India.” OSF Preprints, June 3, 2021. https://doi.org/10.31219/osf.io/fgd4x.

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Faria, N. R., Mellan, T. A., Whittaker, C., Claro, I. M., Candido, D. da S., Mishra, S., Crispim, M. A. E., Sales, F. C. S., Hawryluk, I., McCrone, J. T., Hulswit, R. J. G., Franco, L. A. M., Ramundo, M. S., Jesus, J. G. de, Andrade, P. S., Coletti, T. M., Ferreira, G. M., Silva, C. A. M., Manuli, E. R., … Sabino, E. C. (2021). Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. https://doi.org/10.1126/science.abh2644

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Merrick, J. (2021, April 20). Covid-19 variants: South African strain is causing the most concern for UK scientists. iNews. https://inews.co.uk/news/politics/covid-19-variants-south-african-strain-is-causing-the-most-concern-for-uk-scientists-965679?utm_term=Autofeed&ito=social_itw_theipaper&utm_medium=Social&utm_source=Twitter#Echobox=1618951521

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GDC purpose/summary: https://youtu.be/LY5SkHJplxc?t=118

API endpoint filters are given as % encoded JSON: https://youtu.be/VT-chUoq-oo?t=221

Fields reference for endpoint:files: https://api.gdc.cancer.gov/files/_mapping

Fields reference for endpoint:genes: https://api.gdc.cancer.gov/genes/_mapping

New migrations to the UK are being tracked by citizen science projects to see if this is related to climate change http://srs.britishspiders.org.uk/portal/p/Wasp+Spider

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See also StackExchange https://biology.stackexchange.com/questions/86312/as-large-scale-sequencing-projects-progress-do-we-need-a-new-name-for-chromosome

Check out the peer review report for this article: http://www.plantcell.org/content/plantcell/suppl/2019/07/13/tpc.18.00606.DC2/tpc18.00606.PRR-Griffiths.pdf

We do not have to worry about both bases in both strands. Any one strand is fine. Because A always pairs with T and C always pairs with G.

"variable" typically means gene or locus in the context of biological data.

Perhaps the most important measure to keep precision medicine initiate alive. Surge in risk and treatment response prediction in genomic assays is of little value without practical means of affordable molecular profiling of a patient's tumor or more importantly, pre-diagnosis genomic screen.

National Geographic and others have dubbed it "Fishzilla" http://natgeotv.com/asia/fishzilla/about

Database URL is here: http://gsa.big.ac.cn/

Note: metadata is INSDC format, but this database isn't part of the INSDC, so you'll still need to submit your data to one of those databases to meet internationally recognised mandates

According to BMC Biology, 2016 was "the year of the Wisent"dx.doi.org/10.1186/s12915-016-0329-3

The ENCODE portal is the official canonical source for ENCODE data and data from other related projects.

BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

More information also in this blog interview with the first author: http://blogs.biomedcentral.com/gigablog/2016/06/08/introducing-gigwa-genotype-investigator-genome-wide-analyses/

This has now migrated to: http://gigagalaxy.net/

This paper was studied in a case study that lead to some corrections. See the paper here: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127612

These policies have been built on the Fort Lauderdale principles, see the original policies from 2003 https://www.genome.gov/10506537/

This was sequenced at the same time and is available from http://dx.doi.org/10.5524/100003

This was sequenced at the same time and is available as dataset http://dx.doi.org/10.5524/100002

The unusual data released strategy involving crowdsourcing on twitter, is discussed in more detail in this blog http://blogs.biomedcentral.com/gigablog/2011/08/03/notes-from-an-e-coli-tweenome-lessons-learned-from-our-first-data-doi/

The dockerised workflows are discussed in more detail in this blog posting here: http://blogs.biomedcentral.com/gigablog/2015/07/30/fermenting-reproducible-research-revolution/

See also this population genomics study in Nature Genetics that uses this data: http://www.nature.com/ng/journal/v45/n1/full/ng.2494.html See also this blog posting on data citation of this data (and related problems): http://blogs.biomedcentral.com/gigablog/2012/12/21/promoting-datacitation-in-nature/

The panda and polar bear datasets should have been included in the data section rather than hidden in the URLs section. Production removed the DOIs and used (now dead) URLs instead, but for the working links and insight see the following blog: http://blogs.biomedcentral.com/gigablog/2012/12/21/promoting-datacitation-in-nature/

More on the backstory and other papers using and citing this data before the Cell publication in ths blog posting: http://blogs.biomedcentral.com/gigablog/2014/05/14/the-latest-weapon-in-publishing-data-the-polar-bear/

This is going to be a good talk. Get your coffee, open your eyes, and open your mind! A pattern that could actually scale up - worth a try! Disagree? reply here.

Poorly studied in some part to its very high degree of heterozygosity. You can get some more insight here, where it was nominated as a "top ten genome" http://www.homolog.us/blogs/blog/2015/05/08/top-ten-genomes-ix-pacific-oyster/

See Nature doi:10.1038/nature11236 for more on how LFR works: http://www.nature.com/nature/journal/v487/n7406/full/nature11236.html