#Genomics

Recommended reading for all researchers
Data Management for Researchers By Dr Kristin Briney
https://www.amazon.com.au/Data-Management-Researchers-Kristin-Briney/dp/1784270113
#Genomics #bioinformatics

"Given the abundant use of sequences in recent public health crises, it is important to examine how the geographical source of infectious disease outbreaks can be traced and investigated through phylodynamic analyses of genomes..."

New review article in The Lancet Microbe

Approaches and challenges to inferring the geographical source of infectious disease outbreaks using genomic data

https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(23)00296-3/fulltext

#InfectiousDiseases #outbreak #genomics

New article is out! Thanks to Knowable Magazine for the in-depth discussion!

#Kākāpō #genomics #conservation #biology #bird #birds

https://knowablemagazine.org/article/living-world/2023/saving-endangered-flightless-birds-of-new-zealand

Noticed my old #introduction was a bit outdated, so here's a new one.

I'm a computer scientist, bioinformatician and sometimes applied mathematician, using and developing machine learning methods for biology and health care. I mostly work on genomics data, but also on small organic molecules and electronic health records.

ME/CFS is affecting every area of my life, including how much I work and go out of my home.

#bioinformatics #machineLearning #genomics

1/2

I just stumbled over TFlink which is a type of aggregator of databases of transcription factor targets. I will be using this for pathway analysis to understand RNA expression and chromatin modifications #Genomics #Epigenetics #bioinformatics
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9480832/

#Bioinformatics
#Genomics
#Hivemind

Any votes for favorite method for de novo transcript assembly? I don't need genome-wide. There's just one locus that was the target of Cas9 in an experiment we're helping analyze. Bulk transfection for knockout with no clone selection. Supposedly the western showed no protein. But the RNA-Seq shows absolutely no difference in transcript levels. Trying to figure out if the target triggered isoform switching rather than out of frame for all transcripts.

Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts

https://www.nature.com/articles/s41467-023-43236-9

#phages #viruses #evolution #genomics

Postdoctoral Fellow in Phylogenomics/Bioinformatics

#academicjobs #postdocjobs #genomics #evolution #microbiology

https://jobrxiv.org/job/uc-santa-barbara-27778-postdoctoral-fellow-in-phylogenomics-bioinformatics/

Study finds novel #gene #evolution in the #decaploid #pitcher_plant #Nepenthes gracilis.

#genomics #subgenomes

https://phys.org/news/2023-11-gene-evolution-decaploid-pitcher-nepenthes.html

Poisonous #invasive #plant exhibits twice as many #genes as expected.

#genomics #hogweed #Heracleum #furanocoumarin #conservation

https://phys.org/news/2023-11-poisonous-invasive-genes.html#google_vignette

Verheyen Lab in the #SFU Department of Molecular Biology and Biochemistry in Greater Vancouver is looking for a Postdoc or Research Associate to work on #CIHR funded project: Functional genomic studies of Cdk8/CDK19 in development and disease. Check out the ad here: https://verheyenlab.weebly.com/uploads/4/7/1/1/47119107/2023_verheyen_postdoc_ad.pdf #MolecularBiology #Drosophila #CellBiology #genomics

In a new podcast, you can listen to The Lancet Microbe's Rebecca Barksby discuss this series with Professor Kate Baker

The Lancet Microbe in conversation with Kate Baker on harnessing genomics for antimicrobial resistance surveillance

https://thelancetmicrobe.buzzsprout.com/1794195/14023731-kate-baker-on-harnessing-genomics-for-antimicrobial-resistance-surveillance

#AMR #genomics #InfectiousDiseases #IDMastodon

Unearthing how a #carnivorous #fungus traps and digests #worms.

#genomics #RNAseq #metalloproteases #Arthrobotrys

https://phys.org/news/2023-11-unearthing-carnivorous-fungus-digests-worms.html

Decoding #anthocyanin impact: #Genetic insights into #plant defense and #growth trade-offs.

#reactive_oxygen #stress #genomics #transcriptomics #ANT1 #MYB #Solanum

https://phys.org/news/2023-11-decoding-anthocyanin-impact-genetic-insights.html

New bioinformatician position open in the lab, to work as part of the e-OMIX team:

- Establish bioinformatics pipelines for preprocessing omics data.
- Adhere to interoperability standards established by the FIHR consortium.
- Integrate different types of omics data.
- Conceive and automate data analyses pipelines.
- Develop/contribute to #Bioconductor packages.

More details
- https://jobrxiv.org/job/uclouvain-27778-bioinformatician/
- https://www.eomix.be/

#job #bioinformatics #proteomics #genomics #transcriptomics

Looking for a way to sidestep the costs of generating phylogenetic trees?
In this #insilicotalk, David Dylus introduces #Read2Tree, a tool developed within the group of @dessimoz which enables rapid inference of phylogenetic trees from raw sequencing reads.
If you're passionate about comparative genomics and eager to learn how to construct phylogenetic trees efficiently, this is a must-watch!
👉 https://www.sib.swiss/in-silico-talks/read2tree-inferring-phylogenetic-trees-from-raw-sequencing-data
#Phylogenetics #Genomics #Bioinformatics #ComputationalBiology

Rediscovery of rare marine #amoeba #Rhabdamoeba marina.

#genomics #phylogenetics

https://phys.org/news/2023-11-rediscovery-rare-marine-amoeba-rhabdamoeba.html

Scientists claim to have solved the #damselfly #color mystery.

#genomics #evolution #inter_sexual #mimicry

https://phys.org/news/2023-11-scientists-damselfly-mystery.html

@QueerMatters
When I was going the other way, from #science into #Javascript, it looked like there were jobs at companies that provided scientific things (like #genomics companies, or Takara-style companies) but the language to know was #Python

Not sure how to find software jobs in pure science, tho. Unless you're doing a PhD and you can make it about "I coded this experiment", I'm not sure the money is there for a coder to help a bunch of scientists

Deciphering #grape #development: A molecular #phenology scale for grapevine berry maturation.

#fruit #agriculture #genomics #transcriptomics

https://phys.org/news/2023-11-deciphering-grape-molecular-phenology-scale.html

Wired: Dr. Alison Todd’s Inventions May Save Your Life https://www.wired.com/story/women-in-science-alison-todd/ #Tech #wired #TechNews #IT #Technology via @morganeogerbc #Science/Biotech #Science/Health #WomeninScience #antibiotics #medicine #genetics #Genomics #diseases #Science #biotech #health #cancer

💡 That's a wrap on our #OMAUpdate2024 highlights! Dive into the new OMA browser to explore these features and more. Your feedback is always welcome! #Genomics #Bioinformatics https://omabrowser.org

🔍 Check out our revamped Local Synteny Viewer for comparing genomic neighborhoods across extant and ancestral genomes. A powerful tool for genomic research. #Synteny #Genomics #OMAUpdate2024

The Lancet Microbe's new 5-paper series is now online

Harnessing genomics for antimicrobial resistance surveillance

https://www.thelancet.com/series/amr-genomics

#AMR #genomics #InfectiousDiseases #IDMastodon #WAAW

Thrilled to share our latest preprint: "Evidence of Root Anatomy Driving Local Adaptation in Mexican Maize" 🌽 🍿

Amazing job done by Chloee McLaughlin https://chloeemclaughlin.wordpress.com/, and the team !

📊 Key Findings:

Traits favoring reduced axial conductance found in cooler, drier highland areas.

🌐 Implications:

Candidate genes identified linking root anatomy and environmental variation.

🔓 Link: https://doi.org/10.1101/2023.11.14.567017

#MaizeAdaptation #RootAnatomy #Genomics #GRANAR #MECHA

Hello science friends! Can anyone point me towards some resources that I could use learn how to do a de novo genome assembly from long reads (@nanopore)? Mammalian species, no reference genome exists. An equally exciting and daunting task.... Please share #neuroscience #genomics

Oslo Bioinformatics Workshop Week 2023, December 11th-15th.

Genome annotation, ML in #genomics, #DMP, #usegalaxy, #snakemake (@Lexnederbragt), #apptainer, #docker, transcription factors (@ievarau) #nextflow (@ewels) and much more.

https://www.mn.uio.no/sbi/english/events/oslo-bioinformatics-workshop-week-2023/index.html

🧬 New in #OMAUpdate2024: We've significantly expanded our coverage of bacteria and archaea, including Asgardarchaeota, for a deeper understanding of microbial genome evolution. #Genomics #Microbiology

🚀 Exciting news from the OMA team! Our 2024 update brings a host of improvements to our orthology knowledgebase. Stay tuned for a series of highlights! #OMAUpdate2024 #Genomics #Bioinformatics
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad1020/7420097

Adapting to climate change: #Mutation enables flour #beetles to speed up their #development.

#genomics #evolution #CYP18a1 #ecdysone

https://phys.org/news/2023-11-climate-mutation-enables-flour-beetles.html

This, err.... seems bad?

https://www.theguardian.com/technology/2023/nov/12/private-uk-health-data-donated-medical-research-shared-insurance-companies

#biobank #dataprivacy #genomics

Mummified baboons point to the direction of the fabled land of Punt #genomics #mtDNA #egypt #history
https://arstechnica.com/science/2023/11/mummified-baboons-point-to-the-direction-of-the-fabled-land-of-punt/

Registration is now open for our Workshop to Establish State-of-the-Art #Mollusc #Genomics:
https://meetings.embo.org/event/24-mollusc-genomics

This 3-day meeting will be held 28-31 May 2024 in Namur, Belgium. Talks will also be streamed.

Travel and childcare grants are available. More details are on the website.

In-person registration is limited to 50 people, and will favor participants who contribute a talk or poster. So register now! Deadline 15 Dec 2023.

#biodiversity #evolution #ecology

The Reactome Pathway Knowledgebase 2024: Solidifying Reactome's place as undisputed champ in pathway curation
#Genomics #Bioinformatics
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad1025/7369850

#Genetic analysis shows head #lice #evolution mirrors #human #migration and colonization in the Americas.

#genomics #anthropology

https://phys.org/news/2023-11-genetic-analysis-lice-evolution-mirrors.html

I'm generating clusters from a large, sparse matrix (clustering a diverse set of genomes using protein family occurrence).

I've played around with SOM and various hierarchical clustering methods with different distance metrics. An other suggestions for obvious things I should try?

#statistics #unsupervisedlearning #genomics #bioinformatics

Engineered yeast breaks new record: a genome with over 50% synthetic DNA https://www.nature.com/articles/d41586-023-03495-4 #Science #Biology #Genetics #DNA #Genomics @science @biology

“Researchers trying to rebuild the Scottish #wildcat (Felis silvestris) population are gaining insights from ancient #genomics.

At a wildlife park in the Scottish Highlands, a captive-breeding programme is considering an audacious breeding strategy to eliminate the house-cat #DNA that has infiltrated the wildcat genome.

To help them to unpick the problem, researchers analysed the genomes of dozens of ancient and modern #cats.”

https://www.nature.com/articles/d41586-023-03451-2

biggest comparative #genomics #bioinformatics news in a long time:

GeneMark finally dropped the requirement for that super-annoying license key file!!!

Made deployment via Docker or conda impossible, led to all kinds of errors on network-mounted file-systems, expired randomly and led to silent failures. so happy it's finally gone

https://github.com/Gaius-Augustus/BRAKER/releases/tag/v3.0.4

Our paper on the genomic basis and evolution of female colour polymorphism in damselflies is finally published in "Nature Ecology & Evolution"! Thankyou to all the co-authors from France, Japan and Sweden, including my PhD-student Sofie Nilén in #SvenssonLab

https://www.nature.com/articles/s41559-023-02243-1

#damselflies #Odonata #evolution #genomics #insects #inversion

PhD position in viral evolution and diversity @foaylward

Virginia Tech

Funded PhD positions in the Aylward Lab to study the #evolution and #genomics of giant #viruses. Both computational and wet-lab projects available.

See the full job description on jobRxiv: https://jobrxiv.org/job/virginia-tech-27778-funded-phd-position/?feed_id=64662

#ScienceJobs #hiring #research
Blacksburg #UnitedStatesUS ...
https://jobrxiv.org/job/virginia-tech-27778-funded-phd-position/?feed_id=64662

New #algae species rewrites understanding of #reef systems.

#Corallinales #Porolithon #genomics #biodiversity

https://phys.org/news/2023-11-algae-species-rewrites-reef.html

Since November 1st, Charles Underwood has joined our institute as professor of Plant genome engineering. Read more about Charles and his research on our website! @Radboud_uni #biology #plantgenome #cellbiology #genetics #genomics #agriculturalsciences #biotechnology https://www.ru.nl/en/about-us/news/charles-underwood-appointed-professor-of-plant-genome-engineering

#Genomics #Genetics #Bioinformatics #HiveMind

The T2T has been really interesting for the human reference. Is there a similar push for mice? Given how reliant we are on a relatively small number of core mouse strains, I would think a mouse strain T2T would be incredibly valuable.

#Bioinformatics
#Genomics
#ComputationalBiology
#Servers
#HomeLab
We may have some small budget still set aside to replace an old, dead server in the lab. Thoughts on thread ripper builds? I've considered maybe an i9 Raptor Lake. But it'll primarily be a work horse server. The eCores won't help so much. Thread ripper will give many more (performance) cores at a higher cost. Thoughts? Experiences? Reliability?

Subject: 2023 Patricia A. Marshall Lecture: Charmaine Royal, Ph.D. on "Genomics and Equity in the 21st Century" You can livestream this lecture on genomics and equity in the 21st Century. Looks pretty interesting. Use the CR code in the image. #healthequity #genomics

How #Kelp Keeps a Record of Environmental Calamity https://undark.org/2023/10/31/bull-kelp-destruction/

Integrating kelp #genomics analyses and geological data to reveal ancient #earthquake impacts https://royalsocietypublishing.org/doi/10.1098/rsif.2023.0105

"On a coastal rock platform near #Rārangi, #NewZealand, the team stumbled on another pocket of odd kelp #genetics. The kelp, they found, shared the genes of a population from 300 kilometers away. Something had clearly happened here."

Friends - we are looking for reviewers for a #genomics focused package - sourmash.

We’d like atleast one person with a solid genomics background but the second can be more packaging, usability, docs, etc etc focused. Please spread the word in your communities!!

more here:
https://pyopensci.discourse.group/t/looking-for-genomics-package-reviewers/388

#openscience #python #opensource #science

Today's learning resource

Understanding the difference between #ComputationalBiology & #Bioinformatics
and what each is used for.

https://graduate.northeastern.edu/resources/computational-biology-vs-bioinformatics/

#STEM #science #education #computerScience #biology #lifelongLearning
--------------------------------
For Students/Researchers :

Have you tried the CRISPR-based map that ties every human gene to its job function?

https://news.mit.edu/2022/crispr-based-map-ties-every-human-gene-to-its-function-0609

https://gwps.wi.mit.edu/

#STEM #edtech #biology #genetics #genomics #fediscience #ScienceMastodon

#Fungal #evolution discovered: #Mycena can now invade living #hosts.

#DNA #genomics #mutualism #nitrogen

https://phys.org/news/2023-10-fungal-evolution-mycena-invade-hosts.html

#Mouse #Mummies Show Life Persists in #Mars-like Environment https://www.scientificamerican.com/article/mouse-mummies-show-life-persists-in-mars-like-environment1/

#Genomic insights into the mystery of #MouseMummies on the summits of #Atacama #volcanoes https://www.cell.com/current-biology/fulltext/S0960-9822(23)01161-2

"#Scientists had expected life at the summits to be limited to #microbes... Instead a new analysis suggests that #mice found living on the peaks aren’t outliers but representatives of a fairly persistent population."

#genomics #extremophiles #mammals #animals #astrobiology #AtacamaDesert

Our recent review article "The five pillars of computational reproducibility: bioinformatics and beyond" has just been published 😀
I'm very thankful to everyone who contributed suggestions and critiques of our work including my colleagues, twitter friends and peer-reviewers 🙏
https://academic.oup.com/bib/article/24/6/bbad375/7326135
#Genomics
#Bioinformatics

An historically Black medical college and pharmaceutical industry group began a program to increase the numbers of people of African descent in genomic databases.

https://sciencebusiness.technewslit.com/?p=45355

#News #Press #Science #Business #Africa #Black #Diaspora #Genomics #Research #Sequencing #Databases #PopulationGenetics #Diversity #GeneticCounseling #HBCU #HealthEquity

For the Tiniest #Archaea, A Genomic Switch of Friend or Foe https://jgi.doe.gov/scihi-for-the-tiniest-archaea-a-genomic-switch-of-friend-or-foe/

A predicted #CRISPR-mediated #symbiosis between uncultivated archaea: Sarah Esser et al. https://www.nature.com/articles/s41564-023-01439-2

"Meta-#omics datasets show that CRISPR-Cas systems determine mutualism or parasitism between some archaeal hosts and their hitchhikers."

#microbes #microorganisms #microbiology #genomics

Okay, simple finding. GitHub has pretty strict file size quotas: 100 MB. You can use Git LFS to go beyond that, but then you only have ~2GB of LFS storage across your whole `Pro` GitHub account. So my hope to use Github->Zenodo archiving for any file, is a bit premature for >100 MB files.

In other news, I came across this tool: https://github.com/datalad/datalad , which seems neat.

Does anyone have experience with it?

#DataLad #genomics

Now published in Peer Community Journal, #genomics section: "COVFlow: phylodynamics analyses of viruses from selected #SARSCoV2 genome sequences" https://doi.org/10.24072/pcjournal.333

This got lost amid this week’s outbreak of war in Israel.

“For the first time, ancient DNA has been recovered from the bodies of ancient Israelites living in the First Temple period." by David Reich & co collaborating with Israeli counterparts.

https://www.haaretz.com/archaeology/2023-10-09/ty-article/in-first-archaeologists-extract-dna-of-ancient-israelites/0000018b-138a-d2fc-a59f-d39b21fd0000

#AncientDNA #Archaeology #Genomics #History #israel

I'm looking for a tool like `backlocate` from https://github.com/lindenb/jvarkit
(CC @yokofakun ) and the tool `proteinToGenome` from https://bioconductor.org/packages/release/bioc/html/ensembldb.html , in order to liftover polypeptide coordinates (i.e. domain annotations) back into genome coordinates. It's not a totally trivial liftover, as my genes have introns. But, my GFF doesn't have the `start_codon` and `stop_codon` that `backlocate` requires, and `proteinToGenome` only works with gene annotations hosted on Ensembl. Thoughts? #genomics

How dormant #plant #traits could be reawakened to unlock #fertiliser_free #farming.

#evolution #mycorhizae #soil #microbiome #genomics #FoodSecurity

https://theconversation.com/how-dormant-plant-traits-could-be-reawakened-to-unlock-fertiliser-free-farming-211235

Image of the map in all its glory. One of the curiosities is that one linkage group contains ~28% of the markers, consistent with previous karyotyping. I have frequently supposed that this large chromosome might be associated with the supergene - but this is not the case.
#supergenes #genomics #snails

Fine mapping of the Cepaea 🐌 shell colour and mid-banded loci using a high-density linkage 🧬 map, new paper out today in Heredity 🎺🥂 Nothing is ever straightforward in snail genomics! Culmination of much work by PhD student Maggie Johansen. Open access: https://doi.org/10.1038/s41437-023-00648-z.
#BBSRC #Genomics #snails #heredity #newpaper #openaccess #supergenes

Anyone work at a company they like that's hiring #PhD #research interns for summer 2024? Interested in roles related to #ComputerScience #DataVisualization #ExplainableAI #Genomics #Bioinformatics #SoftwareEngineering #ML #interpretability #EDA #DataAnalytics

I'm a third year PhD student in Computer Science at an R1 university (completed MS coursework), and a dual citizen USA/EU :) Thanks for boosting! #GetFediHired

“At SIB, we know that expertise in life science data is critical to solving the world's most pressing challenges.”

You can also read more on the history of our organization and the work of our members in the #SIBProfile 2023: https://issuu.com/sibswissinstituteofbioinformatics/docs/sib_profile_2023

#bioinformatics #computationalbiology #datascience #biodiversity #opendata #datascience #genomics #proteomics #programming #python #artificialintelligence #machinelearning #biocuration #biology #ecology #bigdata #cancer #scicomm

Genomic histories shaped by whaling and 16,000 years of isolation https://ecoevocommunity.nature.com/posts/genomic-histories-shaped-by-whaling-and-16-000-years-of-isolation #genomics #whales

The genomic footprint of whaling and isolation in fin whale populations https://www.nature.com/articles/s41467-023-40052-z

"The population of the Eastern North #Pacific fin #whale population was reduced 99% during the 20th-century #whaling period, whereas the Gulf of #California population remained small and isolated for 16,000 years. This contrasting histories have affected the #genomes of both populations."

What could go wrong?
#genomics #bioinformatics
https://www.biorxiv.org/content/10.1101/2023.09.08.556814v1

Final paper from Marine Duhamel's PhD and second installment of our project on the causes and consequences of #recombination suppression in #sex determining #Chromosomes

The dynamics of #transposable #elements accumulation in non-recombining regions

Fully formatted, #peer reviewed and #openaccess at
https://www.nature.com/articles/s41467-023-41413-4

#seXYevol #EvolutionaryBiology #bioinformatics #FungiFriday #Genomics

I've gone live!

Crush Crush

#Biology #Bioinformatics #OneHealth #Gaming #Streaming #LifeScience #Tech #Transcriptomics #SingleCell #Genomics #Sequencing #Animals #neuhier

https://fex.techbio.eu

📢 Exciting News! 🚀 Don't miss out on this opportunity!

There are still a few seats left for our October courses. Ready to boost your data analysis skills? Join us now: https://physalia-courses.org/courses-workshops/ 💪📊

#DataAnalysis #Rstats #Genomics #Bioinformatics #Python #DataScience

I used to blog a *lot*. When I was a scientist trying to get into #SciComms, I would force myself to write at least 3 posts a week for my #genomics blog.

In 2014 I wrote a post: ‘Understanding MAPQ scores in SAM files: does 37 = 42?’

http://www.acgt.me/blog/2014/12/16/understanding-mapq-scores-in-sam-files-does-37-42

Community-initiated genomics
Ancient DNA is used to connect enslaved African Americans to modern descendants
#slavery #genomics #ethicalresearch #catoctinfurnaces
https://www.science.org/doi/full/10.1126/science.adj2380

If you're looking for resources to teach #machineLearning and some of its applications to #genomics or #chemoinformatics: I post most of my teaching materials on my website https://cazencott.info/index.php/pages/Teaching and they are available under a CC-BY license if you want to reuse them.

I consider it part of my job as a public servant to make what I create publicly available, but not everyone shares this take...

Scientists pinpoint moment humanity almost went extinct 😨
https://www.ctvnews.ca/sci-tech/scientists-say-they-have-pinpointed-the-moment-humanity-almost-went-extinct-1.6548340

* humanity almost wiped out 900,000 yrs ago
* global population dwindled to 1,280 reproducing individuals
* population stayed this small for about 117,000 yrs

Did our ancestors nearly die out?
https://www.science.org/doi/10.1126/science.adj9484

Genomic inference of severe human bottleneck during the Early to Middle Pleistocene transition
https://www.science.org/doi/abs/10.1126/science.abq7487

https://en.wikipedia.org/wiki/Population_bottleneck

#humanity #extinction #genomics #PopulationBottleneck

There is an opening for an assistant professor in Computational Medical Genomics at ETH Zurich.
#career #genomics

Please find details here:

https://ethz.ch/en/the-eth-zurich/working-teaching-and-research/faculty/faculty-affairs/ausgeschriebene-professuren/ingenieurwissenschaften/assistenzprofessur--tenure-track--fuer-computational-medical-gen.html

Graffiti of an axolotl with a double-helix tail (in Parque Viveros de Coyoacán).

The axolotl possesses a genome approximately ten times larger than that of humans and is notable for its extensive regenerative capabilities, which include the ability to regrow limbs and vital organs. These features make it a subject of interest in the fields of regenerative medicine and developmental biology.

#axolotl #genomics #science #cdmx #StreetArt

crosshap from my former PhD student Jacob Marsh is now out in Bioinformatics!

It's an R-based tool that visualises phenotype-haplotype-associations in a region of interest. We used it to explore population diversity around specific candidate genes; follow-up papers are under peer review.

Paper: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad518/7247532
Repo: https://jacobimarsh.github.io/crosshap/

#bioinformatics #genomics

Tambets, K., Yunusbayev, B., Hudjashov, G. et al. Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations. Genome Biol 19, 139 (2018). https://doi.org/10.1186/s13059-018-1522-1 #OpenAccess #OA #Article #Science #Demography #History #Language #Languages #Population #Genetics #PopulationGenetics #Genomics #Biology #Geography #Europe #Asia #Academia #Academic #Academics @science @biology

AIMS-2-Trials is launching #EAGER (European #Autism #GEnomics Registry) to recruit 1,500. This is lead by King’s College.

They 'discussed autistic community concerns and risks associated with genetic research and data sharing via the Autism Sharing Initiative.’ which ‘is lead by Dean Hartley, Senior Director of Discovery and Translational Science at Autism Speaks.’ Seriously?

https://www.aims-2-trials.eu/2023/08/02/new-project-european-autism-genomics-registry/

(AIMS-2-Trials grant agreement: https://gizmonaut.net/autism-documents/)

@actuallyautistic

It was a pleasure to work with Jason Ladner and Jason Sahl on this insightful look at how pathogen genomics can be leveraged post #COVID19 to understand and track other pathogen and emerging #epidemics

#pandemic #genomics #pathogen #virus #bacteria #sequencing #GlobalHealth

From: @PLOSBiology
https://fediscience.org/@PLOSBiology/110819074844875384

Scientists in the Natural Sciences - Applied Sciences

• Published (not necessarily in field)

Please Message For Additions, Deletions or Edits

Agricultural Science (#AgriculturalScience)
Birge, Traci @TraciInFinland
Bommarco, Riccardo @bommarco
Cardinael, Rémi @remicardinael
Ehlers, Melf-Hinrich @Melf
ETH Zürich @crop_science_eth
Hepworth, Craig @floridafruitgeek
Malek, Žiga @zigamalek
Morris, Ed R @Edrmorris
Nordquist, Rebecca @renordquist
Plieninger, Tobias @plieninger
Rodriguez, Carolina @CRodriguez
Schwerdtner, Ulrike @UliSchwerdtner

Aerospace Engineering (#AeroSpaceEngineering)
Dubos, Gregory @astroptere
LaPrade, Sherie @astrosherie
Ellison, Doug @doug_ellison
Hutt, Jason T @jathhutt

Biophysics (#Biophysics)
Bagley, Bryce Allen @babagley
Delpierre, Julien @JulienDelpierre
Dmitrieff, Serge @dmitrieff
Étienne, Jocelyn @jocelyn_etienne
Giorgino, Toni @giorginolab
Haase, Albrecht @neurophysics
Kennard, Andrew @askennard
Michieletto, Davide @dmichiel
Lew, Matthew D @lewlab
Meesters, Christian @rupdecat
Neher, Richard @richardneher
Plested, Andrew @andrewplested
Popescu, Gabriela K @PopStarLab
Rowland, David James @drdrowland
Sadoine, Mayuri @MayuriSadoine
Schwarz, Ulrich Sebastian @UlrichSchwarz
Wallace, Mark I @markianwallace

Biomedical Science (#BiomedicalScience)
Aldrich, Chris @chrisaldrich
Konrad, David @dbkonrad

Biotremology (#Biotremology)
López, Juan José Díez @Tremoneta

Climate Science (#ClimateScience)
Brettschneider, Brian @Climatologist49
Campbell, Micheline @michcampbell
Cobb, Kim @coralsncaves
Gironella, Fritzi G @fagg
Gleick, Peter @petergleick
Gowan, Evan J @DrEvanGowan
Hawkins, Ed @ed_hawkins
Hayhoe, Katharine @kathhayhoe
Karmalkar, Ambarish @akarma
Labe, Zach M @ZLabe
LeGrande, Allegra Nicole @atthenius
Marelle, Louis @louismarelle
Mottram, Ruth @Ruth_Mottram
Pollice, Robert @robpollice
Rahmstorf, Stefan @rahmstorf

Climatology (#Climatology)
Dupont, Claire @Cladupont
Lucht, Wolfgang @W_Lucht
Wagner, Gernot @gwagner

Engineering (#Engineering)
Aldrich, Chris @chrisaldrich
Bean, Keri @PlanetaryKeri
Ellison, Doug @doug_ellison
Famelis, Michalis @mfamelis
Gill, Kevin M @kevinmgill
Haas, Charles @ProfCharlesHaas
Hulse, Daniel @Daniel_Hulse
Walker-Franklin, Imari @calimari

Environmental Science (#EnvironmentalScience)
Brander, Susanne M @smbrander
Feldwick, Mark @MarkIngs
Glückler, Ramesh @rglueckler
Gusmão, Felipe @fgusmao
Jehn, Florian Ulrich @florianjehn
Jones, Oliver AH @Dr_Oli_Jones
Killam, Daniel @dantheclamman
Mann, Michael E @MichaelEMann
McKinney, Zeke J @ZekeMD
Osborn, Mark @MicrobialLife
O'Shea, Bethany @DrBethRocks
Pyle, Greg @gregpyle
Sigmund, Gabriel @GabrielS
Sims, Kerry @DrKerryS
Sultana, Farhana @farhanasultana
Tate, Brandon K @brandontate
Walker-Franklin, Imari @calimari
Weintraub, Michael N @mnweintraub
Zourek, Leonard @leonardzourek

Environmental Toxicology (#EnvironmentalToxicology)
Feldwick, Mark @MarkIngs
Hammer, Sjúrður @sjurdur
Pyle, Greg @gregpyle
Reichman, Suzie M @SuzieReichman
Whitehead, Andrew @andrewwhitehead

Epidemiology (#Epidemiology)
Alwan, Nisreen A @nisreen
Bassani, Diego G @dgbassani
Baxter, Nancy @enenbee
Bazaco, Michael @MCBazacoPhD
Bergstrom, Carl T @ct_bergstrom
Bolker, Ben @bbolker
Chiong, Winston @winstonchiong
D'Angelo, Nico @nicod
Feldman, Ryan @EMPoisonPharmD
Funk, Sebastian @sbfnk
Gonsalves, Gregg @gregggonsalves
Handel, Andreas @andreashandel
Hernan, Miguel @MiguelHernan
Hill, Edward M @EdMHill
Hyde, Zoë @DrZoeHyde
Jamal, Alainna J @alainnajj
Kinney, Gregory L @mycotropic
Kline, David @DavidKline
Kucharski, Adam @adamjkucharski
Ley, Sylvia @sylvialey
Meesters, Christian @rupdecat
Mekaru, Sumiko @Sumiko_Mekaru
Moss, Rob @rob_models
Murray, Eleanor J @epiellie
Newman, Kira L @KiraNewmanMDPhD
Pearce, Neil @nepearce
Peiper, Nicholas C @doctorpipes
Polis, Chelsea B @cbpolis
Salemi, Jason L @JasonSalemi
Schrom, John @johnschrom
Sesay, Cecirahim @cecirahim
Smith, Tara C @aetiology
Tennant, Peter WG @pwgtennant
Tobin, Martin D @martin_tobin
Wallace, Katrine @EpidemiologistKat
Walsh, Michael @EpiDoctor

Evolutionary Science (#EvolutionaryScience)
Albert, Victor A @PlantEvoGenomics
Anderson, Chris @c_n_anderson
Barber, Matthew F @bioBarber
Bergstrom, Carl T @ct_bergstrom
Bolker, Ben @bbolker
Clarke, John T @jclarkepaleo
Constantinides, Bede @bede
Davison, Angus @snailman
Débarre, Florence @flodebarre
Eisen, Jonathan @phylogenomics
Enquist, Brian J @bjenquist
Gregory, T Ryan @TRyanGregory
Hartberg, Yasha @yasha
Kennard, Andrew @askennard
Kristensen, Nadiah Pardede @nadiah
Kovács, Ákos T @EvolvedBiofilm
Leighton, Gavin M @GMcLeanLeighton
Lenski, Richard @RELenski
Meuthen, Denis @DenisMeuthen
Neher, Richard @richardneher
Nelson, Chase W @chasewnelson
Osmond, Matthew @mmosmond
Ralph, Peter L @petrelharp
Schürch, Roger @schuemaa
Stajich, Jason @hyphaltip
Strepsipzerg, Max Aubry @StrepsipZerg
Szala, Anna @anna
Vlieger, Leon @inqbiol
White, Rhys Thomas @Rhys

Food Science (#FoodScience)
Hammann, Simon @simonhammann
Kramer, Timo @Timo_Micro

Genetic Epidemiology (#GeneticEpidemiology)
Hodcroft, Emma @firefoxx66
Meesters, Christian @rupdecat
Tobin, Martin D @martin_tobin

Genomics (#Genomics)
Albert, Victor A @PlantEvoGenomics
Coassin, Stefan @stncsn
Constantinides, Bede @bede
Davison, Angus @snailman
Eisen, Jonathan @phylogenomics
Gregory, T Ryan @TRyanGregory
Gunter, Chris @girlscientist
Lenski, Richard @RELenski
MacLean, Dan @danmaclean
Mäklin, Tommi @themaklin
Maurizio, Paul L @paul
Meesters, Christian @rupdecat
Neher, Richard @richardneher
Nelson, Chase W @chasewnelson
Salter, Susannah J @zannah_du
Stajich, Jason @hyphaltip
Tobin, Martin D @martin_tobin
White, Rhys Thomas @Rhys
Zakour, Nouri Ben @genomiss

Information Technology (#InformationTechnology)
Wright, Bryan @catselbow

Medicine (#Medicine)
Alwan, Nisreen A @nisreen
Argyropoulos, Christos @ChristosArgyrop
Baxter, Nancy @enenbee
Bhattacharyya, Roby @roby
Briscoe, Joshua @jcbriscoe
Corman, Victor Max @vmcorman
Delaney, Brendan C @bcdelaney1
Feldman, Ryan @EMPoisonPharmD
Flores, Anthony R @pedIDDoc
Funk, Sebastian @sbfnk
Gebhard, Christian @basepair
Halama, Niels @halama_immuno
Jamal, Alainna J @alainnajj
McKinney, Zeke J @ZekeMD
Mohr, Emma @Mohr_lab
Newman, Kira L
@KiraNewmanMDPhD
Stone, Judy @drjudystone
Topolsky, Ivan @dryak
Trebach, Joshua D @jtrebach

Neuroscience (#NeuroScience)
Bellec, Pierre @pierre_bellec
Cardona, Albert @albertcardona
Case, Sami @samilcase
Chiong, Winston @winstonchiong
Desrochers, Theresa M @DesrochersLab
Elsilä, Lauri @laurielsila
Gellersen, Helena M @helenagellersen
Haun, Andrew M @amhaun
John, Yohan J @DrYohanJohn
Kachlicka, Magdalena @mkachlicka
Kanev, Jacob @jkanev
Karmarkar, Uma R @uma_karma
Leterrier, Christophe @christlet
Miller, Earl K @ekmiller
Moleman, Peter @MolemanPeter
Negwer, Moritz @moritz_negwer
Olsen, Rosanna @RosannaOlsen
O’Mara, Shane @shaneomara
Popescu, Gabriela K @PopStarLab
Schultz, Simon R @neuralengine
Timberlake, Ben @ByBenTimberlake
Wu, Wayne @attninaction
van Bree, Sander @sandervanbree

Pharmacology (#Pharmacology)
Bartos, Piia @piiabartos
Case, Sami @samilcase
Elsilä, Lauri @laurielsila
Feldman, Ryan @EMPoisonPharmD
Konrad, David @dbkonrad
Moleman, Peter @MolemanPeter
Rutz, Adriano @adafede

Physiology (#Physiology)
Olson, Christopher R @ChristophROlson
Schumacher, Michael A @schumacher

Psychiatry (#Psychiatry)
Anderson, Chase TM @ChaseTMAnderson
Bortolotti, Lisa @lisabortolotti
Briscoe, Joshua @jcbriscoe
Eckert, Anna-Lena @eckertal
Grothe, Christine @christinegrothe
Lee, Kangjoo @kangjoolee
Turban, Jack L @jackturban
Urgelés, Diego @urgeles

Taxonomy (#Taxonomy)
Brabant, Craig @mutillidae
Brignoli, Gino @gino
Musetti, Luciana @DrLu_Musetti
Plazi Species @plazi_species

Toxicology (#Toxicology)
Feldman, Ryan @EMPoisonPharmD
Trebach, Joshua D @jtrebach

Veterinary Medicine (#VeterinaryMedicine)
Firth, Clair @Buxton_Vienna
Mekaru, Sumiko @Sumiko_Mekaru
Nordquist, Rebecca @renordquist
van Vlie, Arnoud @dutchscientist
Voss, Sarah J @Sarah_J_Voss
Wakeham, David @wakehamAMR

Wildlife Epidemiology (#WildlifeEpidemiology)
Shriner, Susan A @SusanAShriner

For more extensive lists consisting of academics on Mastodon Click Here. Also, for an excellent set of curated science, philosophy, and mathematics lists covering podcasts, Mastodon, and Bluesky Click Here

(Click to access Formal & Social Sciences)

(See Index For More Hashtags)

#SciFedi #Scientists #FediScientists

#SIB course:
"#Biodiversity #bioinformatics: from large-scale #phylogenomics to gene families and functions"
30.08-1.09 Lausanne #UNIL.
- key evolutionary concepts
- methodological approaches
- hands-on in comparative genomic analyses, protein-coding gene evolution and function across animal genomes, from model and non model species; using e.g. #OrthoDB, #BUSCO, #OMA @bgeedb
Trainers: @rmwaterhouse, N Glover, C Dessimoz, & me https://www.sib.swiss/training/course/20230830_COMGE #MolecularEvolution #Genomics #training

Redoing my #Introduction post as I've just moved over from Fediscience to this instance. 👋

Hi, I'm Callum. I am currently manager of a large insectary facility in the UK. I'm interested in #Mosquitoes #VectorControl #Genomics #Speciation and #Evolution.

Announcing #SIB Comparative genomics course, taught by Christophe Dessimoz, Natasha Glover, @rmwaterhouse and myself, 30 August - 01 September in Lausanne #UNIL
• Introduction to molecular evolution & phylogenetics
• Orthology-focused arthropod comparative genomics
• Duplication of genes and genomes, expression
with #SIB resources #OMA, #Orthodb #BUSCO and @bgeedb #ortholog #orthologs #paralog #duplication #MolecularEvolution #Genomics #bioinformatics #training @P_Palagi https://www.sib.swiss/training/course/20230830_COMGE

Hey there!
I'm a French researcher in developmental biology, focusing on mammalian sex determination and gonadal development at the genetic level. I have a PhD in bioinformatics but I do wet and dry lab.
I am a free (as in freedom) and open source software advocate, formerly actively involved in FOSS groups.
I love dataviz, photography, classic rock music, and playing video games.
I moved from another Mastodon instance.
#introductions #stem #DevBio #genetics #genomics #transcriptomics #SexDet

New #introduction since I'm parking over here at veganism dot social[1].

🎓 I'm a #PhD candidate in #HistSci and #STS (science & technology studies) at UW-Madison (that's the one in #Wisconsin, not Washington)

📚 I study how #data get used, shared, recombined, and abused in the sciences – current projects touch on #pollution regulation and social #genomics. I guess #opendata and #openscience are relevant tags here

✍️ I blog about some of the #books I'm #reading, each post ends with a #vegan recipe [2] :vegan:. Mostly these have been scholarly #history books, but I also read a lot of #SciFi / #SFF

📝 My day job/funding (proudly #union) is as an editorial assistant at Social Studies of Science[3]

[1] at least for the time being, as a #fedipact precautionary measure

[2] https://blog.bennettmcintosh.com/posts

[3] https://journals.sagepub.com/home/sss

Edit: 👋 #histodons

Biotech Start-Up to Discover Cystic Fibrosis Therapy

A new #biotechnology company is advancing #research to find a comprehensive #treatment for cystic fibrosis, and staked to a €2 million #seed #investment from its founder.

https://sciencebusiness.technewslit.com/?p=44920

#News #Science #Business #CysticFibrosis #Lungs #Genomics #Mutations #StartUp #Entrepreneurs #France #Inserm #Finance #VentureCapital

Ancient Britons built Stonehenge – then vanished. Is science closing in on their killers? - https://www.theguardian.com/commentisfree/2023/jun/19/ancient-britons-stonehenge-killers-plague-britain-migration fascinating stuff #genomics #linguistics

163 / Improving data archiving practices in ancient #genomics https://doi.org/10.1101/2023.05.15.540553

“ … a reliance on inconsistently structured supplementary materials, non-permanent websites, and direct requests to authors, is not a rigorous long-term solution for a data-intensive research field.”

From: https://sci.kiwi/@josephguhlin/110499943900692808

#OpenData #RDM #aDNA

It's a while since I've written an #Introduction #Introductions #Connections #TwitterMigration post, where I use my large follower count to more richly connect the :fediverse:

So, please meet:

@alyssa - Alyssa is a #Linux hacker who works with #graphics drivers (THANK YOU!) and who is doing amazing things with #GPU stuff on Macs.

@adam42smith is Sebastian Karcher works in #qualitative #data at #Syracuse, and works closely with the @zotero project (also THANK YOU!)

@rachelcoldicutt researches #innovation and alternative #infrastructures, and helps build intentional #communities

@ed is Stefano Maffulli, the current Executive Director of the #OpenSource Initiative - @osi

@DianaOfPortland is Diana Larasen, and she works in #Leadership #Agility

@photocyte is Dr Tim Fallon, who is a #biologist, #biochemist and #genomics and #bioinformatics #postdoc at #UCSD

@bridgetbarrett is an incoming Assistant #Professor at CU Boulder in #Advertising - working in #MediaStudies and #SocialIdentity and #SocialMedia

Please share your own #ConnectionList - and help us create a strong and connected #Fediverse :fediverse: ❤️

Pharma Company Gains Precise Gene Edits in $2B Biotech Deal

A global drug maker is acquiring access to a #biotechnology company's precise #genome editing techniques to develop new #therapies for rare and cardiometabolic disorders.

https://sciencebusiness.technewslit.com/?p=44824

#News #Science #Business #Genomics #GeneEditing #Crispr #Enzymes #Chemistry #BasePairs #BaseEditing #Collaboration #Licensing #RareDiseases

Is your research described by one of these: #popgen, evol. #genomics/#epigenetics, #life-histories, #biotic interactions, eco-evolutionary dynamics, long-term #field studies, #anthropology?

Come and make us stronger! Full #professorship at Uni #Mainz. Lots of recent turnover has happened here with fantastic young faculty, we have a lot of exciting plans for the future!

https://karriere.uni-mainz.de/university-professor-of-evolutionary-biology/

Deadline 28 June!

@ecoevojobs

One genome is not enough to represent all of human diversity. Today, we're revolutionizing the human genome reference with a draft of a more robust, diverse, and complete genome reference - just released by the UC Santa Cruz co-led Human Pangenome Consortium.

This will be a game-changing resource for genomics and health research.

The future of genomics and personalized medicine is happening right here at @UCSCgenomics.

https://www.youtube.com/watch?v=EIMuBw_xZB0

#science #genomics #news #sciencenews

Crispr Therapy Shown to Remove E. Coli in Gut

New #research with lab #animals shows gene-edited viruses can target and remove harmful E. coli #bacteria from the #gut, including strains usually resistant to #antibiotics.

https://sciencebusiness.technewslit.com/?p=44760

#News #Science #Business #Biotechnology #Genomics #GeneEditing #Crispr #Ecoli #Preclinical #Microbiome #AntibioticResistance #GutMicrobes

UK develops genetic early warning system for future pandemics - https://www.theguardian.com/world/2023/apr/02/uk-develops-genetic-early-warning-system-for-future-pandemics "Project aims to roll out cheap, easy-to-use technology across the globe to spot emergence of any new health threats" #genomics

OUT TODAY in Tumour Virus Research:

Nearly everyone gets #HPV. Most infections are cleared by the immune system, but a small fraction go on to cause ~5% of all cancers. #Genomics is revealing why.

Lisa Mirabello & I review the latest. 1/8
🔗https://www.sciencedirect.com/science/article/pii/S2666679023000058

Yes, 1000 times yes!
"researchers should not use race as a proxy for describing human genetic variation. Race is a social concept, but it is often used in genomics and genetics research as a surrogate for describing human genetic differences, which is misleading, inaccurate, and harmful."
https://www.nationalacademies.org/news/2023/03/researchers-need-to-rethink-and-justify-how-and-why-race-ethnicity-and-ancestry-labels-are-used-in-genetics-and-genomics-research-says-new-report
#Racism #STEM #genetics #genomics #HumanGenetics

🧐There are still a few seats available for some of our courses in April!

www.physalia-courses.org

#Rstats #Binformatics #rspatial #Pangenomics #GeometricMorphometrics #Metagenomics #MultivariateAnalysis #Metabarcoding #Genomics

#introduction #how /4
So, this is how we think it works: we tell each other what we're up to and what we like/dislike, timelines will soon be full of interesting/relevant stuff 🤞

Regular or recurrent hashtags:
#semIDEEV - institutional weekly seminars #Ecology #Evolution
#CheesyFungi - research on the living stuff making your #cheese more interesting
#seXYevol - the #EvolutionaryBiology of sex chromosomes
#ShouldTryThis - new methods on #bioinformatics #popgen #Genomics
#FungiFriday

The genome is publicly available in NCBI GenBank. We have also deposited the sequence read data in the Sequence Read Archive (SRA) under BioProject PRJNA888783. You may access the #sequencedata for further #research at https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA888783

#genomics #dataanalysis #openaccess

The C. psittaci BF_amazon_parrot13 strain's complete #genome was sequenced, revealing a circular chromosome (1,160,701 bp, GenBank: CP110211) & a chlamydial #plasmid (7,553 bp, GenBank: CP110212) 🧬 #genomics #microbiology #_BRIG

Start-Up Creating Software to Simplify Biomedical Analytics

A new #enterprise began public operations to provide researchers with better #analytical tools for making sense of mountains of complex #genomics and related #biomedical #data.

https://sciencebusiness.technewslit.com/?p=44401

#News #Science #Business #Bioinformatics #Analytics #Software #Proteomics, #GeneExpression #Algorithms, #StartUp #Licensing

Next Monday, February 6th at 4pm Eastern, University of Michigan's Science, Technology, and Public Policy Program is hosting indigenous geneticist and bioethicist Krystal Tsosie, to talk about Indigenous DNA and data: Community approaches to equity in genomics and health.

It will be in person and live-streamed! You can register here: https://stpp.fordschool.umich.edu/event/2023/indigenous-dna-and-data-community-approaches-equity-genomics-and-health #indigenous #DNA #genomics #healthequity