Keith Robison @OmicsOmicsBlog
Computational biologist in drug discovery since '96. omicsomics.blogspot.com Boston, MA Joined February 2010-
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Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice. #HiC #Multiomic #SingleCell #3Dgenome #scRNAseq #scATACseq #OlfactoryReceptor @naturemethods nature.com/articles/s4159…
Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References #AnnualReview #GenomicsHumanGenetics #GenomeSequencing #Pangenome #ReferenceGenomes @EimearEKenny @khmiga @JMonlong @rajivmccoy @BenedictPaten @mike_schatz annualreviews.org/content/journa…
Wait...what?? I just came across this whilst looking for something else: French railways in 1949 started running trains between Paris and Strasbourg that had pneumatic tyres? I presume it didn't go well...
I think there is a huge benefit to standardizing a chunked on-disk binary typed arrays (e.g. Zarr) to store VCF data. Then, build bioinformatics and population genomics software on top of this format. bio2zarr is alpha but I'm very excited: github.com/sgkit-dev/bio2…
2: We still don’t have a complete understanding of population stratification, with many sub-threshold effects potentially overfitting to stratification [Aw et al. 2024]. The extent to which this impacts significant variants also remains unknown [Berg et al. 2019 eLife].
1: "in pointing at everything, genetics would point at nothing" [Goldstein 2009]: As GWAS implicates thousands of loci/genes (ex: 21% of the genome for height; [Yengo 2022]) the value becomes less clear unless these genes can be tied to coherent disease mechanisms/pathways.
It pains me to see facile critiques of GWAS on here from our clinical/biostats friends while the many actually good reasons to be critical of GWAS get little attention. So here's a thread on what GWAS does, what critics get wrong, and where GWAS is genuinely still lacking. 🧵:
Great GWAS paper diving deep into the contributions of germline variants to kidney cancer in 29k cases and >800k controls. I particularly love the discovery of a VHL 3' UTR variant, seen in ~10% of African and ~0.01% of European ancestries, that increase the risk of clear cell…
The seriously hobbled Orange Line train that took 45+ minutes from NEMC to Wellington continued on Crazy that the MBTA didn’t pull it out of service @transitmatters @MBTA
Updating to R 4.4.0 isn't a bad idea right now hiddenlayer.com/research/r-bit…
People don’t realize how monumentally massive the rare disease opportunity actually is. $200M average market value X 10,000 rare diseases = $2 trillion You know what else equals $2T? The market caps of the top 10 BioPharma companies. $2T up for grabs? Who’s going to take it?
I wonder how many bugs are introduced into science annually just because the default software installs on clusters are often quite outdated. I'm lobbying our IT to update bcftools from 1.6 to 1.20 — 1.6 is from 2017!
Strange Ask: Anyone have access to fresh cacao flowers they could overnight to my lab? Work will be toward saving our chocolate and enhancing crop resilience. DM's open if anyone has leads. Please RT. TYIA! 🍫🌱🌺🧬
Scientists have discovered dimethyl sulfide—a molecule thought to have only living sources—on a cold, lifeless comet. scim.ag/6Ke
Aha. So DMS, a potential biosignature (oh hey there exoplanet K2-18b) has been found on a comet, and unless that comet is covered in algae (it’s not) then you can make DMS without needing biology. Biosignatures are tricky things. Nice story from @elisecutts!
Aha. So DMS, a potential biosignature (oh hey there exoplanet K2-18b) has been found on a comet, and unless that comet is covered in algae (it’s not) then you can make DMS without needing biology. Biosignatures are tricky things. Nice story from @elisecutts!
Cell Simulation as Cell Segmentation | bioRxiv biorxiv.org/content/10.110…
"Egyptian Genome Project aims to sequence genomic variants of 100,000 apparently healthy Egyptian adults, with around 8,000 individuals suspected to have a genetic disease, as well as 200 ancient Egyptian mummies." 🔥 Elmonem et al. Nat Gen nature.com/articles/s4158…
@GenomicsCow @OmicsOmicsBlog This was pretty unexpected because it's a massive gift to the large diagnostics players. They still have to update their QSRs but that's a way lower lift than having to submit every NYS test. It's also a gift to AMCs who now have a ton of power as test development incubators.
@coregenomics @PacBio @OmicsOmicsBlog @AlbertVilella @mehtamanal @CatharineAquino Over on Nava Whiteford’s ASeq Discord server it was announced that all of the San Diego location people were given 60 days notice. I think that’s about 150 people. I’m sure there were others let go in the Bay Area as well.
Oxford Nanopore @nanopore
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18K Followers 1K Following Goodbye Twitter 👋 You can now find me on bsky. I'll also try and post research updates more frequently on my lab homepage, linked below ⬇️Shawn Baker @SanDiegOmics
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1 Followers 363 FollowingFilip Wiberg @FilipWiber22619
0 Followers 5 FollowingLiz Worthey @lizworthey
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2K Followers 1K Following Co-founder/CEO of @sanogenetics. Researcher in genomics and rare disorders. Host of https://t.co/yXvLIgEGfs 🎙️CCCAOL @lkhyo13
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44K Followers 2K Following Bren Professor of Computational Biology @caltech. Blog at https://t.co/FFQzhEsmhi. Tweets represent my views, not my employer's. #methodsmatterOxford Nanopore @nanopore
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5K Followers 2K Following AgBio genomics expert. Exploring new horizons & disruptive innovations in DNA, RNA & Protein sequencing, single cell & spatial omics. 🌱 🥬 🍉 🍏 🫑 🌶 🌽🫐🍌🍓Heng Li @lh3lh3
10K Followers 207 Following Associate professor of biomedical informatics at @HarvardDBMI and @dfcidatascience𝕐 (@[email protected].. @nomad421
8K Followers 939 Following Associate Professor of CS @ University of Maryland. Proud Rust advocate! I ♥ science & compiled, statically-typed programming languages! Views are my own.Jonathan Jacobs 🧬�.. @bioinformer
9K Followers 3K Following Authenticity and data provenance in #genomics + #bioinformatics. Also #scicom, @officialATCC #gaming #DnD #EDM #punk @ Home ♟👾🎮 🎸he/himEwan Birney @ewanbirney
50K Followers 2K Following Deputy Director General of EMBL, Director of EMBL-EBI. I have an insatiable love of biology. @[email protected]. I also work with ONT, Dovetail + GeL.Sebastian S. Cocioba�.. @ATinyGreenCell
24K Followers 8K Following Amateur 🌿 Biologist • Aspiring 🌺 Designer Researcher at Binomica Labs • Degreeless Heathen • Petunia Breeder • Open Lab Notebook: https://t.co/umYTLluuuwTorsten Seemann @torstenseemann
16K Followers 2K Following Microbial genomics, bioinformatics software, training. A/Prof ORCID: 0000-0001-6046-610X Retro 8-bit computers; VIC=20, C=64, C=128.Nils Homer @nilshomer
6K Followers 747 Following I write software for Biologists. Founder @fulcrumgenomics, Bioinformatician, Computer Scientist, Coder, Father of 2xGirls. Opinions are my own.Gary Schroth @Genomics_Guy
4K Followers 3K Following Inspired by Smart People, Genomics, Innovation, RNA, Science, Politics, Travel, Sports, Truth, Music, EVs, and Dogs. All opinions are my own.Michael Schatz @mike_schatz
16K Followers 1K Following Bloomberg Distinguished Professor of Computer Science and Biology at Johns Hopkins Universityantisense. @razoralign
13K Followers 64 Following We do not know about death, because we never know about life. https://t.co/5L9IhaBKH5Vega Shah @dr_alphalyrae
12K Followers 3K Following life sciences software 🧬 product strategy 👩🏻💻 writer & futurist 🚀 previously scientist at @JGI, @UW & @UCBerkeley 👩🏻🔬 views are all mine ✨Adam Phillippy @aphillippy
18K Followers 1K Following Goodbye Twitter 👋 You can now find me on bsky. I'll also try and post research updates more frequently on my lab homepage, linked below ⬇️Shawn Baker @SanDiegOmics
2K Followers 201 Following Genomics expert with 20+ years experience in R&D, marketing, and business consulting. Also at https://t.co/ZYxXrDzuaK and https://t.co/Psjayl6JYgSteven Salzberg 💙�.. @StevenSalzberg1
19K Followers 235 Following Bloomberg Distinguished Professor of BME, CS, and Biostats at Johns Hopkins University, tennis player, blogger at Forbes: https://t.co/7SZhlbYPtn…Sasha Gusev @SashaGusevPosts
9K Followers 3K Following Statistical geneticist. Associate Prof at @DanaFarber | @harvardmed | @DFCIPopSciDirk Haussecker @RNAiAnalyst
18K Followers 509 Following There are no alternative truths. Please do not allow evil to spread and destroy our freedom of life. Not investment adviceDr. Elinne Becket - @.. @bielleogy
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1K Followers 3K Following Dad. Kiwi in Canada. Posts + opinions are my own. Global Market Development - Population Genomics at Illumina #genomics #dna #nextgenerationsequencingStephen Quake @StephenQuake
4K Followers 334 Following Head of Science @chanzuckerberg | Professor of #bioengineering and Applied Physics @stanford | Prolific #inventor focused on nexus of #biology, #physics + #techMatthew Miller - 🧬.. @biodiversityge1
605 Followers 615 Following Developing new tools for conservation & biodiversity genomics in the Middle East, Africa, and Central Asia; exploring the world before it’s too late.Mike Yarski @Pore_xy
771 Followers 563 Following Father, (he/him), food and wine loving cyclist, Technical Services Manager @Nanopore. views are my own and retweets are not endorsementsWarren Bach @bach_warren
770 Followers 879 Following Nanopore - Strategic Relationship Manager, ANZ. Love talking science & creating bonsai. *all opinions and tweets are my ownOzSingleCell Omics @ozsinglecells
3K Followers 616 Following Oz Single Cell brings the Australian single cell community together #OzSingleCellKuan-Hao Chao @KuanHaoChao
243 Followers 215 Following CS PhD candidate in @StevenSalzberg1 & @ElaPertea lab at @JohnsHopkins @JHUCompSci 🧬💻 #NTUEEJian Zhou @zhou_jian
1K Followers 600 Following Computational biology, machine learning, genomics. Assistant Professor at UT SouthwesternRoya Bashier @bashier_roya
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30 Followers 50 Following #InfectiousDisease and #Multiomics Marketing Programs Manager at #Illumina. All views are my own. #StopAsianHateS2 Genomics @S2Genomics
162 Followers 148 Following Dedicated to advancing single-cell research by automating tissue preparation. #S2GenomicsCanopy Biosciences @CanopyBio
252 Followers 245 Following Providing access to cutting-edge spatial biology and multi-omic tools. We're redefining what's possible in Spatial BiologySTOmics @ST_Omics
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6K Followers 2K Following #AssociateProf #CompBio #Omics #WomenInScience #PrecisionMedicine #RareDisease #ME/CFS #hEDS #UndiagnosedDisease #SciFiNerd #Mama #Scottish #TexanOmicsveu @OmicsVeu
8 Followers 47 Following Experience an accelerated pace of multiplex Spatial Biology with cutting edge technologies and automation.Jeff Vierstra @jeffvierstra
923 Followers 272 Following Senior Investigator @ Altius Institute. Chromatin structure & function. Mountain shenanigans and skiing turns all year. 🇺🇸 🇨🇱Páidí Creed @paidicreed
821 Followers 1K Following Using software to understand biology at @biomodalhqMohamed AbdulHameed @curephile
501 Followers 985 Following Interests: #cheminformatics, comptox, drug design, #toxicogenomicsGoose Data (wa/wa) @GooseData
4K Followers 201 Following Biotech visionary. Looking for best drugs with goose data. Retweets mean honking endorsement.Michael Quail @Mq1Michael
54 Followers 202 FollowingPhillip Compeau @PhillipCompeau
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3K Followers 608 Following There is no conservation of misery! Writing (soon) @ https://t.co/ovfBxaCM9l Go to my Highlights to see my Threads!Factorial Biotechnolo.. @factorialBio
94 Followers 66 Following Life science tools company developing innovative, single-cell, multi-omic workflows.Tony Robinson @Tony_Robinson
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87K Followers 757 Following OSINT Analyst - Secret WEF Biolab Interior DecoratorNavy General Board @thegeneralboard
10K Followers 95 Following Examining naval history and maybe some current events.Channa Prakash @AgBioWorld
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1K Followers 904 Following med student on leave to study biomedical data science and do neuro research 🔬 👩💻curious about epigenetics, neuroscience & ai applications in medicineEnveda Biosciences @envedabio
2K Followers 46 Following Engineering new drugs from nature with knowledge graphs, metabolomics, and MLPhillip A Richmond @Phil_A_Richmond
635 Followers 854 Following Bioinformatics PhD. Follow the science wherever it leads you.Ingo Hartung @HartungIngo
14K Followers 780 Following MedChem @Merckgroup; drug discovery nerd in oncology, immunology & targeted protein degradation, soccer, politics or tapas can get into the way; my own viewsSally Church @MaverickNY
18K Followers 2K Following Scientist, cancer geek, journalist, Londoner, always curious, adventurer, explorer, immigrant, lover of curry, fine wine & footballNicky Whiffin @nickywhiffin
4K Followers 759 Following Associate Prof & Henry Dale Fellow @bdi_oxford @HumanGeneticsOx | Computational Rare Disease Genomics | Non-coding | @StAnnesCollege | @nickywhiffin.bsky.socialErik Garrison @erikgarrison
4K Followers 1K Following (pan)genomes from many points of view. Assistant Professor UTHSC MemphisJonathan Ware @ReassessHistory
13K Followers 372 Following Enquiries: DM. Military Historian. 'Valuable' according to IWM. Jocks, Dragons and Sospans: Through Normandy with 53rd Welsh Division (2022). #WW2 #SWW #History@ENERGY @SecGranholm @JigarShahDC This is awesome! So why isn’t it happening everywhere? Two major roadblocks: permitting and $. Acquiring necessary permits can be time-consuming. And even though reconductoring saves $ in the long run, advanced conductors are more expensive than regular wires. 7/12
@ENERGY @SecGranholm @JigarShahDC Reconductoring can be: - cheaper, than building new transmission lines; - faster, by using existing rights of way; and - could quadruple projected transmission capacity added by 2035 While saving $85 billion. 6/12
@ENERGY @SecGranholm @JigarShahDC Maybe the most exciting solution is advanced reconductoring, which is a fancy way of saying replacing old wires with new lines made of modern materials that can carry more than twice as much electricity. Same towers. Same rights-of-way. Twice the power. 5/12
@CatharineAquino @SanDiegOmics @real_poobah @OmicsOmicsBlog @coregenomics @PacBio @AlbertVilella @mehtamanal so can Xitter. Genomics Cow, Grand Poohbah, genomix kid to name a few who pop up here frequently.
@AntoBeck @SanDiegOmics @real_poobah @OmicsOmicsBlog @coregenomics @PacBio @AlbertVilella @mehtamanal It’s anonymous and can be nasty ( maybe that’s why it’s interesting).
@AntoBeck @SanDiegOmics @real_poobah @OmicsOmicsBlog @coregenomics @PacBio @AlbertVilella @mehtamanal True. Just came back from a conference where we had a discussion about who the cow could be. He is famous!
Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity. #5mC #5hmC #DNAmethylation #MethylationFidelity #MaintenanceMethylation @NatureSMB nature.com/articles/s4159…
Yes, my mother was a nun; she was also a nurse who saw what hospitals were like before roe v wade. She also, unlike MAGA, actually read the Bible; and knew that criminalizing abortion has nothing to do w/the teachings of Jesus. If trump supporters would read the Jesus parts…
@JohnFugelsang @BuffaloSmitty71 @RobynJLeader Talking about abortions, and you wanna talk about Trump? Your Nun mother would be so upset with you 🤦♂️
@FelixSchlang The FAA temporarily opens up the firmament for the rocket, that's why rockets need launch licenses.
i understand the historical reasons for the term, but "organelle" is such a useless and misleading grab bag term even if you restrict it to membrane bound organelles, it includes structures with utterly different origins and basic biology
@primalpoly I sorta think there’s an unspoken assumption in this response
Lots of smart people who I respect on here are posting about pronatalism recently but I just don’t get it. Doesn’t increasing immigration solve any declining birth rate problems over the next ~century and have massive humanitarian externalities?
@SanDiegOmics @AntoBeck @real_poobah @OmicsOmicsBlog @coregenomics @PacBio @AlbertVilella @mehtamanal I go there but I don’t like the negativity 😅
@CatharineAquino @SanDiegOmics @real_poobah @OmicsOmicsBlog @coregenomics @PacBio @AlbertVilella @mehtamanal I find it more "real"
Powell used an ice axe and battering ram to break windows to gain entry into the Capitol on January 6. She pushed against barricades, encouraged others to attack police officers, and gave directions to rioters with a bullhorn. After it was over she posted on social media "IT WAS…
Prison-Bound J6 Rioter Tells CNN's Donie O'Sullivan 'I Know Trump Will Pardon Me' If He Wins In Stunning Exchange mediaite.com/a/tknhp
Black Canyon of the Gunnison. It's so much steeper and narrower than the Grand Canyon, and you can see and hear the river from the rim! Black Canyon KNOWS it's a canyon, Grand seems to think it might be a maze or a landscape painting with no perspective and a lot of pastel.
I challenge you to walk through a midsized European city one spring afternoon, then argue something about falling behind America.