Discover and read the best of Twitter Threads about #GENOMICS

Most recents (24)

A short story about #bioinformatics, #genomics, bacterial reference #standards and the challenges and complexity of doing reproducible science. (Names changed to protect the innocent! ☺)

🧬🧬👍👍

A thread...
1/ Dr. Amy discovers a cool new bacteria and does whole genome sequencing on it and publishes the results. "This is the first time this genome has been sequenced, and will pave the way for groundbreaking research in the future!"
2/ 9 months later, while the manuscript is still under review, Dr. Amy deposits the strain into the ATCC collection for safe keeping. ATCC gives her a strain ID and she uses that in the publication the following year.
Read 16 tweets
JPM Healthcare Daily Roundup #JPM2021

The first day of the conference hasn't disappointed, especially if you're a fan of talking cubes. What is this mysterious object and what sorcery is inside?

See disclosures at the end.
The Tempus One, meant to be carried in a doctor's coat or sat at the bedside, is a physical manifestation of @TempusLabs' genomic and phenotypic data-lake. Oncologists can ask One all sorts of questions regarding their patients, though I'm unsure if it'll (...)
(...) just reflex you to a computer after a sufficiently difficult question. I'm sure we'll learn more soon. Has this sort of form-factor been tried before?

I'm just hoping it has adjustable humor/honesty settings like TARS from Interstellar.

Moving right along.
Read 15 tweets
"Greater Brisbane will be entering a 3-day lockdown. That will be Metro North, Metro South, West Moreton," said Ms Palaszczuk

Good luck Brisbane. Don’t worry, everyone must be scared into taking this vaccine

@BoliqueAna 🙏 Image
Take a look at Henry Palaszczuk

Board Member- Gene Technology Alliance

Advancements where #genomics meets #blockchain 🧬 genomic research and #DNA database expansion. Including Artificial intelligence medium.com/@gtablockchain…
Read 8 tweets
'The Genome UK strategy outlines the ambition to create the most advanced genomic healthcare system in the world, underpinned by the latest scientific advances, to deliver better health outcomes at lower cost.' @CSOSue @EBIBristol
.@CSOSue highlights the case of Jessica who was aged 4 when a genetic cause for her seizures was found as part of the #100kGenomesProject @GenomicsEngland and analysis suggested a change to her diet could help make her condition more manageable @EBIBristol #Genomics
.@CSOSue giving examples of the excellent genomic testing services being offered in the NHS Genomic Medicine Service including the Rapid Exome Sequencing service @RDEhospitals @ExeterExomes run by @EllardSian and the familial hypercholesterolaemia service run by @SWGLH
Read 4 tweets
I'm thrilled to present my first first-author paper on the evolution of gigantism in the #capybara, the world's largest rodent! 😃 Thanks to co-authors @CrawfordAJ @eenork @frozenzoo @OfficialSMBE #MBE #cienciacriolla 🧶👇 1/21 bit.ly/3mmgqlp
Body size evolution is central in biology. We know that body size co-evolves with many organismal traits (e.g. longevity, home range 🏠, generation time ⏰, predation risk, organ allometries 💪, etc.) within and between spp.
2/21
Yet, we know little about how body size itself evolves 🧐. For instance, body size in mammals varies over 8 orders of magnitude! 🤯
3/21
Read 24 tweets
We wrote a review on the potential of genome sequencing technologies in autism
@lornahoulihan @lgallagh_louise

authors.elsevier.com/a/1bnrL3A54zZV…

@AutismTCD @MaynoothBiology @scienceirel @MaynoothUni @tcddublin
#AutismGenomics #BelieveInScience

Let me tell you more (1/5)
WHY study the genetics of autism?

Studying genetics helps us to understand the biology of autism and brings us towards improved diagnosis and medical decision-making (2/5)

#ThinkGenetics #AutismGenomics Image
HOW can we identify genetic variants in ASD?

Sequencing of the whole genome and the whole exome is made possible by Next-Generation Sequencing technologies. These techniques allow us to look at many types of genetic variation across the genome. (3/5)

#NGS #Genomics Image
Read 5 tweets
Rapid whole genome (🧬) sequencing (rWGS) is one of the most exciting (and benevolent) collisions of #AI and #genomics I can think of.

rWGS can diagnose a critically ill child in minutes where previously it took years.

illumina.com/company/news-c…
A few years ago, Illumina ($ILMN) and Rady Children's Hospital (@RadyGenomics) collaborated to offer sequencing services for diagnosing critically-ill infants and toddlers.

Roughly 70% of rare diseases are genetic and they can take five years to diagnose.
As sequencing costs dropped and #AI got faster, this collaboration became Project Baby Bear: a pilot study for rWGS's diagnostic yield, clinical utility, and health economics in practice.

Several innovative companies joined Rady's in creating a rapid diagnostic pipeline.
Read 14 tweets
Today I shared 4 materials to introduce a PhD student about molecular pathway analysis. I mentor this student remotely back in India since late 2017. Here are the list of 4 papers. What does #Bioinformatics #Genomics #ScienceTwitter think of this list?

1. bioinformatics.mdanderson.org/MicroarrayCour…
Read 5 tweets
Our updated analysis on #SARSCoV2 clades in India, now peer-reviewed and published in OFID by @OxUniPress. In collaboration with @vinodscaria @IGIBSocial. Congratulations to the entire team.
doi.org/10.1093/ofid/o…
#Genomics #IndiaFightsCOVID19
I’ve never done one of these before, but I’m gonna make a thread of tweets explaining the key findings, and more importantly what our paper doesn’t show. 1/n
First and foremost, there is no conclusive evidence at present that any clade of SARS-CoV-2 is associated with increased mortality or severity of the disease. 2/n
Read 11 tweets
Daily Bookmarks to GAVNet 09/05/2020 greeneracresvaluenetwork.wordpress.com/2020/09/05/dai…
Tracking the COVID-19 pandemic in Australia using genomics | Nature Communications

nature.com/articles/s4146…

#tracking #COVID19 #pandemic #Genomics
Why efficiency is dangerous and slowing down makes life better | Psyche Ideas

psyche.co/ideas/why-effi…

#optimization #efficiency
Read 8 tweets
📢🎉The work of #Bat1K is featured on the cover in the latest issue of @nature: “Six reference-quality #genomes reveal evolution of #bat adaptations” 🦇🧬 #bats Our thread 👇 on the paper:nature.com/articles/s4158… 📸: Olivier Farcy(1/n) Image
📢Have you ever wondered how 🦇 manage to do what they do? #bats have extraordinary adaptations, including powered #flight, laryngeal #echolocation, #vocal #learning and an exceptional #longevity with unique #immunity and resistance to #cancer! 📸: @DanielWhitby5 (2/n) Image
A #Bat1K team led by @Sonja_Vernes @EmmaTeeling1 @hillermich @TheGeneMyers has just published the raw genetic material that codes for these unique 🦇 adaptations and #superpowers in @nature! #bats #genomics #cool! (3/n) Image
Read 32 tweets
I'm excited to share my first postdoc manuscript (and first-ever preprint!) from Dianne Newman’s lab @caltech. This was a wonderful collaboration with Linda Thomashow and David Weller @USDA_ARS. tinyurl.com/ydynmqhq.

#microbialecology #plantmicrobe #genomics
Metabolite-mediated interactions shape microbial communities and can inhibit pathogen invasion. We focused on the ecology of phenazines, a family of bacterially produced redox-active antibiotics that can protect major crops from disease-causing microbes.
Phenazines are chemically diverse but are all derived from the same precursors, which are synthesized by conserved genes. We leveraged this knowledge to find which bacteria can make phenazines and to measure their abundance in the environment.
Read 12 tweets
Daily Bookmarks to GAVNet 6/02/2020-2

greeneracresvaluenetwork.wordpress.com/2020/06/02/dai…

What COVID-19 Means For The Future Of Capitalism, Democracy And Sustainability

medium.com/volans/what-co…

#coronavirus #future #capitalism #democracy #Sustainability
U.S. COVID-19 Contact Tracing Programs Designed for Failure, Despite Bloomberg Money; Why Can't the U.S. Copy the Lessons of Hong Kong's Success? | naked capitalism

nakedcapitalism.com/2020/05/u-s-co…

#tracing #failure #contact #Bloomberg
Stretch and flow: Research sheds light on unusual properties of well-known materials

phys.org/news/2020-05-u…

#research #flow #materials #Stretch
Read 12 tweets
Fortunately, there are no new strains of #SARSCoV2. Just changes in the letters of its RNA, a slow evolution, that enables precise genomic detective work, tracking of spread from one place to another. A great explainer: nytimes.com/interactive/20… @13pt @carlzimmer @NYTScience Image
It was that detective work by @nextstrain and the global #genomics collaborators to construct this macro picture, cool world map graphic wsj.com/graphics/coron…
This is one of my favorite infographics and it appeared in print form today @NYTScience Image
Read 3 tweets
A break from #SARSCoV2 to another challenge—very early diagnosis of #cancer. Just released @ScienceMagazine is a study of 10,000 women using a blood test (#genomics, proteins) and PET imaging w/ very high specificity of diagnosis (and low sensitivity)
science.sciencemag.org/content/early/…
As far as I know, this is the 1st prospective study to show very early diagnosis of #cancer in healthy people w/o symptoms and curative potential. For that it is groundbreaking. The authors acknowledge many limitations and the further work to be done
While a blood test + PET for very early #cancer detection in a large cohort healthy women was a highlight of the day, a hard look at the numbers are warranted. Especially false positives. @jocelynkaiser @ScienceMagazine reviews the caveats here sciencemag.org/news/2020/04/b…
Read 3 tweets
🚨🧬🦠Great News! Just received approval to provide @QIAGENBiox CLC #Genomics ProSuite for free to any and all #publichealth or clinical microbiology labs who are sequencing or doing #bioinformatics of #SARSCOV2, the #coronavirus that causes #COVID19. Read this thread for details
Everything that follows is UNOFFICIAL. However, it will be captured on a specific landing page on QIAGEN Digital Insights that will go live with on Friday. In the meantime, I wanted to get the message out ASAP.
Tons of labs globally are already using CLC for microbial genomics work, including SARSCOV2 bioinformatics analysis. To support these labs, and those that may not have CLC already, we will be providing a collection of resources to help them with their work. This will include...
Read 16 tweets
I read the @biorxivpreprint every day. I've recently been asked by various people what/why/how I read so here is a short thread that may be helpful to others: 1/
@biorxivpreprint I read abstracts of articles on the @biorxivpreprint every morning and every evening, and typically a few times during the day as well. I am sometimes delving into the main paper, usually starting with the supplement. 2/
@biorxivpreprint I search for articles on @Google using keywords (and filtering for "past 24 hours"), my lab has @SlackHQ channels where people post articles, I check @rxivist, and I read and search twitter by keywords for topics I'm interested in every day. I follow @biorxivpreprint. 3/
Read 25 tweets
A single day & the pivotal role of single-cell sequencing:
1. Olfactory cells
@NatureNeuro nature.com/articles/s4159…
2. Organoids @naturemethods
3. Intra-tumor heterogeneity @NatureCancer nature.com/articles/s4301…
4. Sepsis
@NatureMedicine
5. Gut #microbiome @NatImmunol
Read 3 tweets
Cataloguing #Cancer: The day after #WorldCancerDay2020, @nature @naturepub publishes 22 papers w/ majorl new insights from whole genome sequencing. The cover & my v brief summary of the papers; also @NatureGenet @NatureComms @NatureBiotech @nresearchnews
nature.com/collections/af…
@nature @Naturepub @NatureGenet @NatureComms @NatureBiotech @nresearchnews "The future of cancer #genomics lies in the clinic"
An even better summary of these papers and the requisite next steps in the @nature editorial nature.com/articles/d4158…
Read 6 tweets
We are excited to share our pub in #EvolutionaryApplications bit.ly/2GH3tzr comparing relatedness estimates for pairing recommendations in critically #endangered #birds from #Aotearoa #NZ 🇳🇿. See this #SciComm 🧵 for more! #Conservation #Genomics #ConGen #ConSERTeam 1/13
Around the 🌏, #conservation breeding programmes strategically pair the least related individuals to enhance recovery. This is like #Tinder for threatened species, only more information goes into pairing than swiping ⬅️ or ➡️. See my #3MT for more! 2/13

It’s important to get the relatedness value right for pairing, because mating between close relatives can result in negative fitness consequences, like ⬇️ hatching success 🐣(see bit.ly/3b4IILO). 3/13
Read 13 tweets
If you are interested in analyzing #SingleCell #RNAseq data in #Bioconductor using #rstats, please check out our paper Orchestrating single-cell analysis (OSCA) with @Bioconductor that was published in @naturemethods this week! #genomics #scRNAseq #dataviz #methodsmatter
@Bioconductor @naturemethods OSCA is a rich, reproducible, accessible (from beginners to experts!) resource with many #scRNAseq workflows & datasets. The resource is an online #bookdown book that compiles every night to track development by the open-source and open-development @Bioconductor #rstats community
@Bioconductor @naturemethods Now, OSCA is not the only set of packages / workflows for the analysis of #scRNAseq data. #Scanpy (scanpy.readthedocs.io/en/stable/) and #Seurat (satijalab.org/seurat/) and are two incredibly popular packages in #python and #rstats, respectively.
Read 9 tweets
Our work is now officially out in @MolBioEvol: #Malaria viewed through the lens of an eradicated European strain tinyurl.com/qkqmaxe. (1/7) #published #genomics
On our hunt for past malaria we were fortunate to obtain a collection of blood-stained medical #microscope #slides prepared for diagnostics purposes in 1944 in Spain, one of the last footholds of #malaria in Europe. (2/7)
From these slides, and with a bit of lab wizardry from the team @uni_copenhagen @IBE_Barcelona, we were able to obtain a full #Pvivax genome - we also obtained a #Pfalciparum partial genome tinyurl.com/y2wsljcj. (3/7)
Read 7 tweets
A bit outside my wheelhouse, but a very interesting conclusion on evolution of the genetic code biorxiv.org/content/10.110…. Observations from marine metagenomic data show that the standard genetic code conserves nitrogen and carbon. @DaveZeevi @LiatShenhav #Evolution #Genomics
For example, a substitution from Ala to Arg, in addition to changing biochemical properties, also “costs” a lot of carbon and nitrogen - disadvantageous when nutrients are limiting. The “conservativeness” of the code is the average atomic cost of a single bp change.
Reshuffling the genetic code gives less robustness for resource conservation, and the existing genetic code balances resource conservation with other properties like hydrophobicity or size. So it seems this is could be an important property of the genetic code!
Read 3 tweets
Interesting if true - for every pathogenic variant caught on a typical hereditary cancer panel, 95 variants of unknown significance appear, suggesting an acute need to resolve them ad hoc. This patent describes an interesting #deeplearning approach:

patentimages.storage.googleapis.com/7f/4f/78/64f99… Image
Having a proprietary VUS database is definitely an advantage, but I'm less clear if that will be the case in the medium/long term. We discover and reclassify variants constantly, and make no mistake that #genomics is still at the top of the first inning.
If so, then competitive databases need to keep up or be flexible enough to be amenable to the latest research. Right now, it seems like a reasonable strategy is to tackle phenotype/genotype relationships with a deep-learning frameworks inclusive of diverse clinical features.
Read 3 tweets

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