Kate Dubarry
@airendaie.bsky.social
EFI Innovation Fellow. Postdoc @UoE IRR. Single-cell, bioinformatics, human critical illness, livestock genomics, first gen. Into culture change & helping others. Entrepreneurship. Fluent in sarcasm.
August 10, 2025 at 4:21 PM
Did my first ever race this morning. 13.1km in 1:30:33 at the Edinburgh #kilomathon and absolutely loved it!
April 6, 2025 at 1:19 PM
Did my first ever race this morning. 13.1km in 1:30:33 at the Edinburgh #kilomathon and absolutely loved it!
In 5 months I've gone from "never running unless I'm chased by angry bears" (there's no bears in the UK 😂) to running my first race. So pleased with how far I've come. 2 weeks to go! Love training with @nikerunclubapp.bsky.social and @coachbennett.bsky.social #running
March 23, 2025 at 3:45 PM
In 5 months I've gone from "never running unless I'm chased by angry bears" (there's no bears in the UK 😂) to running my first race. So pleased with how far I've come. 2 weeks to go! Love training with @nikerunclubapp.bsky.social and @coachbennett.bsky.social #running
Let's go get that bag I guess. And by bag I mean UMAPS coming out my ears and muffled cries of "WHAT DOES IT MEEEEAAAN" emanating from under my desk.
Also jokes on me we use @parse.bsky.social but haven't been able to snag a coffee cup off them so I guess today I'm a @10xgenomics.bsky.social grll
Also jokes on me we use @parse.bsky.social but haven't been able to snag a coffee cup off them so I guess today I'm a @10xgenomics.bsky.social grll
March 21, 2025 at 8:14 AM
Let's go get that bag I guess. And by bag I mean UMAPS coming out my ears and muffled cries of "WHAT DOES IT MEEEEAAAN" emanating from under my desk.
Also jokes on me we use @parse.bsky.social but haven't been able to snag a coffee cup off them so I guess today I'm a @10xgenomics.bsky.social grll
Also jokes on me we use @parse.bsky.social but haven't been able to snag a coffee cup off them so I guess today I'm a @10xgenomics.bsky.social grll
Reposted by Kate Dubarry
Superb work by Wouter @Zouters & @OlgaPushkarev developing ChromatinHD, two scale-adaptive #machinelearning models & interpretation tools that use #scRNAseq + #scATACseq data to better understand how chromatin accessibility relates to gene expression doi.org/10.1038/s414...
Happy 2025 everyone 🎆 !
Happy 2025 everyone 🎆 !
ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning - Nature Communications
Functional chromatin changes occur at different scales. Here, the authors introduce ChromatinHD, a method that characterises differential and predictive chromatin accessibility changes in a scale-adap...
doi.org
January 6, 2025 at 2:05 PM
Superb work by Wouter @Zouters & @OlgaPushkarev developing ChromatinHD, two scale-adaptive #machinelearning models & interpretation tools that use #scRNAseq + #scATACseq data to better understand how chromatin accessibility relates to gene expression doi.org/10.1038/s414...
Happy 2025 everyone 🎆 !
Happy 2025 everyone 🎆 !
Reposted by Kate Dubarry
Introducing METAGENE-1🧬, an open-source 7B-parameter metagenomics foundation model pretrained on 1.5 trillion base pairs. Built for pandemic monitoring, pathogen detection, and biosurveillance, with SOTA results across many genomics tasks.
🧵1/
🧵1/
January 6, 2025 at 5:04 PM
Introducing METAGENE-1🧬, an open-source 7B-parameter metagenomics foundation model pretrained on 1.5 trillion base pairs. Built for pandemic monitoring, pathogen detection, and biosurveillance, with SOTA results across many genomics tasks.
🧵1/
🧵1/
Reposted by Kate Dubarry
Estimating cell compositions and cell-type-specific expressions from GWAS data using invariant causal prediction, deep learning and regularized matrix completion: Bridging GWAS and single-cell resolution in Biobank-scale studi #SingleCell 🧪🧬🖥️
https://www.researchsquare.com/article/rs-5451188/latest
https://www.researchsquare.com/article/rs-5451188/latest
December 31, 2024 at 11:32 AM
Estimating cell compositions and cell-type-specific expressions from GWAS data using invariant causal prediction, deep learning and regularized matrix completion: Bridging GWAS and single-cell resolution in Biobank-scale studi #SingleCell 🧪🧬🖥️
https://www.researchsquare.com/article/rs-5451188/latest
https://www.researchsquare.com/article/rs-5451188/latest
Reposted by Kate Dubarry
Single-cell RNA sequencing analysis reveals new insights for intersex gonad initiation and early sex differentiation of goats https://www.biorxiv.org/content/10.1101/2024.12.31.630861v1
December 31, 2024 at 4:31 PM
Single-cell RNA sequencing analysis reveals new insights for intersex gonad initiation and early sex differentiation of goats https://www.biorxiv.org/content/10.1101/2024.12.31.630861v1
Reposted by Kate Dubarry
Reposted by Kate Dubarry
Prof. Karen Liu's fantastic journey, full of hope, not dissimilar to mine.
thenode.biologists.com/i-dont-think... #Altcareers #Careers Congrats also to @dev-journal.bsky.social : first "post directly to Bluesky" button from a journal that I've yet seen in the wild!
thenode.biologists.com/i-dont-think... #Altcareers #Careers Congrats also to @dev-journal.bsky.social : first "post directly to Bluesky" button from a journal that I've yet seen in the wild!
I don't think I would’ve been better off being a biologist to begin with - the Node
No such thing as a standard career path – an interview with Karen Liu
thenode.biologists.com
December 30, 2024 at 3:44 PM
Prof. Karen Liu's fantastic journey, full of hope, not dissimilar to mine.
thenode.biologists.com/i-dont-think... #Altcareers #Careers Congrats also to @dev-journal.bsky.social : first "post directly to Bluesky" button from a journal that I've yet seen in the wild!
thenode.biologists.com/i-dont-think... #Altcareers #Careers Congrats also to @dev-journal.bsky.social : first "post directly to Bluesky" button from a journal that I've yet seen in the wild!
Reposted by Kate Dubarry
Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics Platforms 🧬🖥️🧪 biorxiv.org/cgi/content/...
Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics Platforms
Recent advancements in spatial transcriptomics technologies have significantly enhanced resolution and throughput, underscoring an urgent need for systematic benchmarking. To address this, we collecte...
biorxiv.org
December 26, 2024 at 8:27 AM
Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics Platforms 🧬🖥️🧪 biorxiv.org/cgi/content/...
Reposted by Kate Dubarry
#MedSky🧪 #IDSky #pharmasky #publichealh This phase I&II #Clinicaltrial provides preliminary evidence supporting the Tx of #COVID19 patients with moderate/severe symptoms using NK from #COVID19 convalescent donors is feasible & safe.
www.cell.com/iscience/ful...
www.cell.com/iscience/pdf...
www.cell.com/iscience/ful...
www.cell.com/iscience/pdf...
December 29, 2024 at 8:21 PM
#MedSky🧪 #IDSky #pharmasky #publichealh This phase I&II #Clinicaltrial provides preliminary evidence supporting the Tx of #COVID19 patients with moderate/severe symptoms using NK from #COVID19 convalescent donors is feasible & safe.
www.cell.com/iscience/ful...
www.cell.com/iscience/pdf...
www.cell.com/iscience/ful...
www.cell.com/iscience/pdf...
Reposted by Kate Dubarry
#MedSky🧪#Immunosky #Bcell immunity carries the inherent risk of deviating into #autoimmunity & malignancy, which are both strongly associated with genetic variants or alterations that increase immune signaling @nature.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Diverse mutational landscapes in human lymphocytes - Nature
Sequencing of individual human lymphocyte clones shows that they are highly prone to mutations, with higher burdens in memory cells than in naive cells arising from mutational processes associated wit...
www.nature.com
December 29, 2024 at 12:32 PM
#MedSky🧪#Immunosky #Bcell immunity carries the inherent risk of deviating into #autoimmunity & malignancy, which are both strongly associated with genetic variants or alterations that increase immune signaling @nature.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Kate Dubarry
#MedSky🧪 #IDSky #Episky The study suggest that #sepsis mortality could increase 18-to 46-fold within 5 yrs of the emergence of a single pan-resistant E. coli strain. Failure to prevent the emergence of pan-resistance would have direconsequences for #publichealth @nature.bsky.social
rdcu.be/d4QZP
rdcu.be/d4QZP
Predicting sepsis mortality into an era of pandrug-resistant E. coli through modeling
Communications Medicine - Koch et al. model scenarios of emergence of a single pan-resistant Escherichia coli strain in the United States. Findings suggest dire mortality outcomes and highlight the...
rdcu.be
December 27, 2024 at 12:14 PM
#MedSky🧪 #IDSky #Episky The study suggest that #sepsis mortality could increase 18-to 46-fold within 5 yrs of the emergence of a single pan-resistant E. coli strain. Failure to prevent the emergence of pan-resistance would have direconsequences for #publichealth @nature.bsky.social
rdcu.be/d4QZP
rdcu.be/d4QZP
Reposted by Kate Dubarry
Genome-wide association analyses in dairy heifers highlight genes overlapping with mouse and human fertility and human health traits https://www.biorxiv.org/content/10.1101/2024.12.19.629410v1
December 22, 2024 at 1:35 AM
Genome-wide association analyses in dairy heifers highlight genes overlapping with mouse and human fertility and human health traits https://www.biorxiv.org/content/10.1101/2024.12.19.629410v1
Reposted by Kate Dubarry
Spatial-DC: a robust deep learning-based method for deconvolution of spatial proteomics www.biorxiv.org/cont...
---
#proteomics #prot-preprint
---
#proteomics #prot-preprint
December 21, 2024 at 1:00 PM
Spatial-DC: a robust deep learning-based method for deconvolution of spatial proteomics www.biorxiv.org/cont...
---
#proteomics #prot-preprint
---
#proteomics #prot-preprint
Reposted by Kate Dubarry
Happy Advent! 🎄 Day 15. Today you should identify what might be problematic in the text.
#researchintegrity
#researchintegrityadventcalendar
papermills.tilda.ws/advent - all cases Days 1-15
papermills.tilda.ws/advent15 - case Day 15
#researchintegrity
#researchintegrityadventcalendar
papermills.tilda.ws/advent - all cases Days 1-15
papermills.tilda.ws/advent15 - case Day 15
December 15, 2024 at 12:57 AM
Happy Advent! 🎄 Day 15. Today you should identify what might be problematic in the text.
#researchintegrity
#researchintegrityadventcalendar
papermills.tilda.ws/advent - all cases Days 1-15
papermills.tilda.ws/advent15 - case Day 15
#researchintegrity
#researchintegrityadventcalendar
papermills.tilda.ws/advent - all cases Days 1-15
papermills.tilda.ws/advent15 - case Day 15
This crystallises all that I believe to be true about good science. I see Night Science around me often, but never had a word for it until now. Science is not only the Positivist tradition of hypothesis testing. Good scientists figure out how to shift between the two.
Night science is all about being OPEN to new ideas, while Day science is all about being CLOSED in a particular experimental design. It’s crazy hard, but the full scientific process requires us to be good at both.
December 13, 2024 at 10:02 PM
This crystallises all that I believe to be true about good science. I see Night Science around me often, but never had a word for it until now. Science is not only the Positivist tradition of hypothesis testing. Good scientists figure out how to shift between the two.
Reposted by Kate Dubarry
I think one low cost, high impact intervention to improve peer review is training trainees on what peer review should look like. I wrote this guide for my students: github.com/jtleek/reviews that includes an opinionated approach to what is/isn't important in review (pretty computationally flavored)
December 12, 2024 at 4:22 PM
I think one low cost, high impact intervention to improve peer review is training trainees on what peer review should look like. I wrote this guide for my students: github.com/jtleek/reviews that includes an opinionated approach to what is/isn't important in review (pretty computationally flavored)
Reposted by Kate Dubarry
The tech bro fascination with eugenics is so on brand. The idea that you could make accurate, actionable predictions from individual genotypes (with all their complex, non-linear interactions) from averaged, linearly modeled population-level genomic statistics is just another big data fantasy
December 12, 2024 at 4:13 PM
The tech bro fascination with eugenics is so on brand. The idea that you could make accurate, actionable predictions from individual genotypes (with all their complex, non-linear interactions) from averaged, linearly modeled population-level genomic statistics is just another big data fantasy
I am so privileged to work in such a great place
December 12, 2024 at 9:34 AM
I am so privileged to work in such a great place
Reposted by Kate Dubarry
We love sharing tools! Check out this "ecosystem of tools and resources, omnideconv, simplifying the application, benchmarking, and optimization of deconvolution methods" of second-gen methods for cell-type deconvolution of transcriptomic data.
Great collaboration with @itisalist.bsky.social ✨
We hope our study and set of tools and resources can be helpful to the scientific community 💫
📝 preprint: doi.org/10.1101/2024...
🛠️ omnideconv ecosystem: omnideconv.org
Please repost and help us spread the word!
6/6
We hope our study and set of tools and resources can be helpful to the scientific community 💫
📝 preprint: doi.org/10.1101/2024...
🛠️ omnideconv ecosystem: omnideconv.org
Please repost and help us spread the word!
6/6
Benchmarking second-generation methods for cell-type deconvolution of transcriptomic data
In silico cell-type deconvolution from bulk transcriptomics data is a powerful technique to gain insights into the cellular composition of complex tissues. While first-generation methods used precompu...
doi.org
December 11, 2024 at 7:30 PM
We love sharing tools! Check out this "ecosystem of tools and resources, omnideconv, simplifying the application, benchmarking, and optimization of deconvolution methods" of second-gen methods for cell-type deconvolution of transcriptomic data.
Love this unusual viewpoint on Prince's Street!
Edinburgh O'Clock - 3 minutes to every hour. - we run fast so you don't miss your train.
A new hourly image to brighten your day taken in #Scotland very often #Edinburgh and shared with love by Tom Duffin
@tomduffinphotos.bsky.social.
Please repost with your own caption.
A new hourly image to brighten your day taken in #Scotland very often #Edinburgh and shared with love by Tom Duffin
@tomduffinphotos.bsky.social.
Please repost with your own caption.
December 9, 2024 at 10:49 AM
Love this unusual viewpoint on Prince's Street!
Reposted by Kate Dubarry
New method compresses terabytes of genomic data into gigabytes medicalxpress.com/news/2024-12...
December 6, 2024 at 3:03 PM
New method compresses terabytes of genomic data into gigabytes medicalxpress.com/news/2024-12...