Discover and read the best of Twitter Threads about #genomics

Most recents (24)

This is a thread about how anyone can use publicly accessible sequence databases and free software to discover new things about #genomes, #biology, and life on earth.

#Bioinformatics #Genomics #Evolution #Science #MolecularBiology #DNA #Research #DataScience #LifeSciences Image
Genomes are absolutely loaded with complex information, most of which we still don’t understand.

Complete and near complete genome sequences are now available for many organisms.

However, decoding the information in these genomes remains a slow and difficult process. Image
A large proportion of most published genome sequences consist of DNA that is incompletely understood in terms of its evolutionary origins and functional significance. Image
Read 21 tweets
$NTLA and $REGN report initial data from ph1 study of #ATTR for NTLA-2001. All patients across the two doses showed 92-94% TTR reduction at day 28.
#crispr #genomics #genetherapy #biology #biotech
At both dose levels, $NTLA-2001 was generally well tolerated. 2 patients reported transient infusion reactions, which was the only observed treatment-related adverse event.
$NTLA-2001 is an in-vivo administered #genetherapy.
It is one of the first few in-vivo #GeneTherapy being tested. Congrats to the $NTLA and $REGN teams.
Read 4 tweets
🆕: ⚠️Not so mild 🦠#COVID19
in this immunosuppressed patient
- development of atypical, severe, acute 🧠 meningitis
ijidonline.com/article/S1201-… #bioinformatics #womeninstem #openscience #scicomm #snrtg #genomics #immunology Image
This patient could not have wound up in better hands:
National Institute of Infectious Diseases
“Lazzaro Spallanzani” IRCCS- Rome, 🇮🇹 Italy
👍 great job treating this patient,
sequencing and monitoring🧬the 🦠strain,
...and saving her life
#openscience #scicomm
I have found only a handful of reports in literature of
🦠Sars-Cov-2 induced🧠 meningitis. I thought there would be more. Caveat: it's exceedingly rare, but it does happen.
Read 4 tweets
7⃣+ months of Norovirus🦠positivity➕
in this ⚠️Primary Immunodeficiency patient
▪️ Rx-resistant
🧬-> intra-host evolution led to a unique norovirus strain
bit.ly/3RbH53d #bioinformatics #openscience #scicomm #itrtg #raredisease #genomics #immunology Image
Very much in line with what has been seen
in some persistent🦠Sars-Cov-2 infections in immunocompromised hosts.
▪️ viral-clearance failure
▪️ within-host viral evolution/mutations
*the report gives no indication on the fate of the patient.
⚠️Immunocompromised patients ⚠️as atypical
"outliers" with almost every🦠infectious pathogen (circa 2017).
❗️ PLEASE doctors - keep a good 👁️eye on those
with compromised immune-systems
jiac-j.com/article/S1341-… #openscience #scicomm #meded Image
Read 4 tweets
A LinkedIn post by Sarah Hartley-Kane on the UK becoming the 'Silicon Valley of Global Genomics' linkedin.com/posts/sarahhk_… Image
The cost of a whole genome is probably already in the $100 mark, but not widely available: the only companies that have shown realistic goals towards the $100 genome are: MGI Tech with their DNBSEQ-T7 and T10x4 large instruments, together with @UltimaGenomics with their U100 ... Image
which is expected to be commercially available in 2023 and produces $1/Gb reads (albeit short-reads with homopolymer noise), and $ONT.L Oxford @nanopore, which is currently closing into the $2/Gb mark of Q20+ single pass reads on the PromethION flowcells Image
Read 10 tweets
1/
It’s another Thursday, and that means it’s time for another #tweetorial! Today, we want to show you how you can view RefSeq #annotations on Ensembl 🥳

#bioinf #genomics #assembly #EnsemblTraining
2/
While Ensembl gene models are annotated directly on the reference genome, #RefSeq are annotated on mRNA sequences. In other words: genome browsers will have different annotation methods, so you might be interested in comparing these annotations side-by-side 📖🤔
3/
👂🏽You say you want to make direct comparisons of annotations between @NCBI’s RefSeq and Ensembl? Now is your time to try it out on Ensembl! 🏃🏽
Read 9 tweets
1/ You’ve sequenced your samples and identified variants. Great! 🙌

Now, here's how you can use @ensembl to find out the effect of your variants on #protein structures and interactions. A thread...🧵

#genomics #bioinformatics #tweetorial #Ensembltraining 🧬 A screenshot from Ensembl's Alphafold protein viewer with va
2/ The Variant Effect Predictor (VEP) is what you’re going to need for this task. You can find it in the blue header from the @ensembl homepage: ensembl.org/info/docs/tool…

#VEP Screenshot of Ensembl's homepage with annotated arrow pointi
3/ Click the ‘Launch VEP’ button to open the VEP web tool and enter your input data using instructions in the documentation:
👉ensembl.org/info/docs/tool… Screenshot of Ensembl's VEP web interface documentation and
Read 10 tweets
Major update for small cell #lung cancer! #LCSM

With @juliensage + @FoundationATCG, our paper now on @bioRxiv:

►Genomic analysis of *3,600* pts with SCLC; largest SCLC study to date!

►Multiple interesting findings discussed in this 🧵
biorxiv.org/content/10.110…
🧵2
This study is unique in many ways:

> The #SCLC cohort studied came mostly from community sites --> representing a more typical “real-world” cohort of SCLC.
> The genomic data are tied to clinical data + outcomes.

#LCSM
🧵3
To the best of our knowledge, our study analyzes the largest number of SCLC tumors from African ancestry to date:
> n=256 AFR cases
> 7.1% of the entire cohort
#Diversity in clinical studies is critical!!
See tweet 🧵9 for more details.
Read 15 tweets
Our many-years-in-the-making EpiC Dog epigenome paper is finally out as preprint @biorxivpreprint
Close collaboration with our lab's lead bioinformatician @new__hong & MBD-seq aficionado @MethylAReum, spearheaded by our versatile PI @je_yoel @SNUnow #Epigenome #Genomics #Dog A🧵
While still in early stage format, EpiC Dog is a culmination of our efforts to annotate functional elements of dog genome enabled by chromatin states discovery and profiling super-enhancer and DNA methylome landscapes across multiple tissue types. See also BarkBase and DoGA /2
Modern dogs are champions of modern genetics. They empower us with their evolution and diversification of phenotypic traits from morphology to behavior. One reason dog genomics has become >popular compared to genomic studies of other domesticated mammals, but who's comparing? /3
Read 14 tweets
Looking at a little Strategy: 🧵

I hope putting out my game plan will help other get ideas on how to do a strategy for investing to maximize returns.
1/ I am finally getting comfortable with my strategy. I have a set amount now that I am contributing to each of my portfolios for #biotech, #tech and #crypto. My plan is to use the any rallies to fade some of the companies I want get rid of that disappointed me.
2/ Then I want to use that cash to accumulate more of the companies I like. The max tax loss I can take for a year about $3,000. That would reduce my taxes and get me back about 25% or $750 in tax savings. It will work out like getting some cash back on those losers.
Read 14 tweets
Yesterday, I completed my months-long quest to accurately identify all sci-fields emerging in WW other than the well-established Neuro ⬇️
For, it's been long since we noticed emerging scientific tangents that span diverse fields like: #ML, #Materials_Science, #Pharmacology, #Genomics, #Open_Hardware, etc
Awesome -- But, how does one possibly map all these frontiers without employing actual people to read and annotate dozens of hundreds of abstracts at a time?
Read 16 tweets
Brand 🆕 insight into the mechanism of
anti-interferon (IFN)–γ autoantibodies
- implications for 🧬Inborn Errors of Immunity⚠️
and 🦠SarsCov2
#bioinformatics #openscience #scicomm #immunology #genomics #raredisease
These auto-ABs are linked 🦠to:
1⃣ Primary Immunodeficiencies / "IEIs": susceptibility to certain infections
2⃣ Susceptibility to severe and fatal COVID-19
The anti-interferon (IFN)–γ autoantibody
➡️🦠#COVID19 connection
bit.ly/3yGDbaY #bioinformatics #openscience #scicomm
Read 4 tweets
🦠9⃣-MONTH Sars-Cov-2 infection in an
immunocompromised patient
⚠️ with more than 20 🧬viral mutations
academic.oup.com/cid/advance-ar… #bioinformatics #openscience #scicomm #snrtg #immunology #genomics Image
Getting 💉vaccinated💉: 1⃣ protects the immunocompromised from SarsCov2, and 2⃣: protects ALL OF US from the emergence of new🦠variants🧬
Our lives our interconnected. Shielding the most vulnerable is in our collective best-interest.
Read 6 tweets
1/ Do you need reference sequence files from #Ensembl? All of the different files available can be confusing. Here’s a thread to help you decide which files you need…🧵

#genomics #bioinformatics #tweetorial #Ensembltraining🧬
2/ Whole-genome reference files for each species in Ensembl can be found on the FTP site 🧑‍🤝‍🧑🐭🐄🐶🐟

👉 ftp.ensembl.org

If you’re studying non-vertebrate species, you’ll need to use the Ensembl Genomes FTP site 🌾🦠🦟

👉 ftp.ensemblgenomes.org
3/ Let’s explore the different directories and files available
Read 16 tweets
. 🧬Exciting stuff! 🧬
Hope of a genetic-"fix" for youngsters with a rare blood disorder
newscientist.com/article/232451… #bioinformatics #snrtg #scicomm #openscience #technology #biotech #genomics #raredisease
The clinical trial results which prompted extending CRISPR treatment to kids for
🧬 Sickle-cell and Beta-Thalassemia🩸
bit.ly/3n4MwUO #openscience #scicomm
🧵(thread 3/3)
...more 🧬✂️DNA-editing hope:
1⃣ Inborn Errors of Immunity : frontiersin.org/articles/10.33… #bioinformatics #biotech #WomenInSTEM #openscience #scicomm
2⃣ 'CF', ... 🫁 ➕: frontiersin.org/articles/10.33… #immunology #genomics #raredisease
Read 5 tweets
One of the most devastating and heart-wrenching of the
~7,000 known rare diseases
A novel mutation🧬identified in
*⃣ "Epidermolysis Bullosa"*⃣
bmcmedgenomics.biomedcentral.com/articles/10.11… #bioinformatics #openscience #100daysofcode #snrtg #genomics #raredisease
Young patients with Epidermolysis Bullosa are known as
"Butterfly Children"
A novel gene therapy has shown dramatic and promising results for some of them:
science.org/content/articl… #openscience #biotech #scicomm
Epidemolysis Bullosa: frequently referred to as
'The worst disease you've never heard of'
chron.com/life/health/ar… #openscience #raredisease #scicomm
Read 4 tweets
⚠️Potentially dangerous
new 🦠#COVID19 variants🧬
▪️The pandemic won't end until we prevent this phenomenon
❗️Get💉 vaxxed to shield & protect the immunocompromised
ijidonline.com/article/S1201-… #bioinformatics #WomenInSTEM #openscience #snrtg #immunology #genomics #raredisease
. "NOBODY is safe from the virus until
we are ALL safe from the virus"
~Dr. Tedros Ghebreyesus (WHO Director General)
Viruses🦠do strange things when unchallenged for long periods of times in hosts.
Unfortunately mutating🧬is one of those things.
Read 8 tweets
New 🧬genetic loci linked to #COVID19 🦠susceptibility
♂️ ♀️ with gender specificity
- Results from a huge 🇪🇸 Spanish GWAS study
academic.oup.com/hmg/advance-ar… #bioinformatics #openscience #scicomm #immunology #virology #snrtg #genomics Image
🦠🧬'...variants in 3p21.31 and 21q22.11 loci only among males ♂️; and variants in 9q21.32 near TLE1 only among females ♀️'
Evidence continues to accumulate that:
at least *⃣ for some *⃣ , susceptibility to severe and fatal 🦠COVID may lie in the genes🧬.
Read 4 tweets
🧬"Recessive complete deficiencies of typeI IFN immunity may underlie ∼10% of hospitalizations for COVID-19 🦠pneumonia 🫁 in children"
👥It DID in these 12 youngsters
#bioinformatics #openscience #scicomm #WomenInSTEM #immunology #genomics #raredisease Image
Great work as always by Prof Jean-Laurent @casanova_lab & Co in elucidating genetic susceptibility to SarsCov2. Direct link to the paper: rupress.org/jem/article/21…
The current paper continues this line of research:
"Inborn errors of type I IFN immunity in patients
with life-threatening COVID-19"
science.org/doi/10.1126/sc… #openscience #scicomm
Read 4 tweets
“It was quite a surprise for us to find that this gene is a
critical part of our immune system"
_News: utsouthwestern.edu/newsroom/artic… #bioinformatics single cell #openscience #scicomm #snrtg
_Journal: science.org/doi/10.1126/sc… #immunology #genomics #raredisease Image
"RNA 🧬exosome is crucial for B cell development,
➡️and defects can lead to severe human disease."
Mutations in the SKIV2L gene are associated with a severe inherited disorder, trichohepatoenteric syndrome (THES), with multisystem involvement but unknown disease mechanism."
Genotypes, phenotypes,
and faces of "Trichohepatoenteric Syndrome"
- some of the earliest known cases
cell.com/action/showPdf… #openscience #bioinformatics #scicomm Image
Read 5 tweets
Fatal ⚠️Inborn Error of Immunity🧬
"We present the first reported case of progressive multifocal leukoencephalopathy due to a mutation in the RAC2 gene"
jmedicalcasereports.biomedcentral.com/articles/10.11… #bioinformatics #openscience #snrtg #genomics #raredisease #immunology Image
"PML has been reported as a fatal complication in 26 patients with Primary Immunodefiiency due to various gene mutations. Our patient is the first case reported with PML due to mutations in the RAC2 gene."
Progressive Multifocal Leukoencephalopathy (PML):
▪️ rare, oft-times fatal disease resulting in destruction of the brain's white matter
🦠strongly associated with exposure to 'John Cunningham Polyomavirus'"
sciencedirect.com/topics/medicin… #openscience #scicomm Image
Read 4 tweets
Want to apply #deeplearning in your #regulatory #genomics analyses but overwhelmed by suite of interpretation tools? Check out ExplaiNN: interpretable and transparent neural networks for genomics with @NovakovskyG @ofornes @sara_mostafavi @WyWyWa 🧵👇
biorxiv.org/cgi/content/sh…
ExplaiNN is an adaptation of NAMs from @agarwl_ & team for genomic sequences - predictions are a linear combination of independent CNNs- each consisting of 1 conv. layer with a single filter and two FC layers. This seemingly simple approach performs similar to multi-layer CNNs1/6
It provides importance of discovered motifs by mere visualisation of weights of the output layer. No need for filter nullification or clustering of importance scores from attribution methods! ExplaiNN on ATAC-seq of mouse immune system recapitulates results of AITAC model 2/6
Read 10 tweets
1/As promised & after reading $NTLA latest Q1 2022 financial report here is my analysis regarding @intelliatx latest corporate status. I have focused only on the main issues that I found to be the most interesting & relevant. #CRISPR #GeneEditing #BioTech #FinTwit #Genomics👇
2/NTLA-2001 is the most advanced In-Vivo #CRISPR/#Cas9 #GeneEditing program in $NTLA portfolio & is aimed to treat Transthyretin Amyloidosis - (ATTR). NTLA-2001 could potentially halt & reverse the disease in a “one time” treatment by knocking out the TTR gene with a single dose
3/In February $NTLA has presented an updated clinical data from its Phase 1 study of NTLA-2001 which included 15 patients with ATTR amyloidosis. IMO NTLA-2001 readout looks promising & here is a summary that I wrote shortly after @intelliatx’s presentation of NTLA-2001👇
Read 14 tweets
1/ I have been spending a lot of time with the market selling off trying to share and teach about investing and how to build a portfolio to diversify across assets and risks.
2/ I think its good to take time when the market is down to focus on improving our game for the next time around. Since I am a biotech focused investor, I would like to share with you the trends within the biotech space I think could propel the next decade of innovation.
3/ If you know me already, these won't be very new to you. My first big concept is using tech in biotech with developing #AI, #ML and #Automation to drive down the costs and improve the success of clinical development.
Read 18 tweets

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