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Harlan Barker

@harlanbarker.bsky.social
761 followers 3.1K following 28 posts

Scientist, American in Finland. Doing bioinformatics, cancer, single-cell RNA-Seq transcriptomics, and ancient DNA research at Tampere University and University of Oulu.

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Harlan Barker @harlanbarker.bsky.social · 29/07/2026
𝗦𝗵𝗼𝗿𝘁 𝘃𝗲𝗿𝘀𝗶𝗼𝗻 I made a github repo and dashboard cataloging 1,900+ regulatory genomics tools/resources: thirtysix.github.io/awesome-regu... I had no idea there were so many!
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Harlan Barker @harlanbarker.bsky.social · 26/07/2025
🧪🧬 🖥️ Our latest article has been published: TFBSFootprinter - a multiomics computational tool for predicting transcription factor binding sites across vertebrate species. www.tandfonline.com/doi/full/10.... #Bioinformatics #GeneRegulation #Transcription #ComputationalBiology
tandfonline.com
TFBSFootprinter: a multiomics tool for prediction of transcription factor binding sites in vertebrate species
Transcription factor (TF) proteins play a critical role in the regulation of eukaryotic gene expression via sequence-specific binding to genomic locations known as transcription factor binding site...
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Harlan Barker @harlanbarker.bsky.social · 03/06/2025
Our article is now published in Computational & Structural Biotechnology Journal. 🧪🧬 🖥️ Evolution is in the details: Regulatory differences in modern human and Neanderthal. Barker HR, Parkkila S, Tolvanen MEE (2025). 🔗 Full open-access article: www.csbj.org/article/S200... #EvoBio
csbj.org
Evolution is in the details: Regulatory differences in modern human and Neanderthal
Transcription factor (TF) proteins play a critical role in the regulation of eukaryote gene expression via sequence-specific binding to genomic locations known as TF binding sites. We studied sites of...
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ELLIS Institute Finland @ellisinstitute.fi · 04/02/2025
ELLIS Institute Finland is hiring Principal Investigators in AI + machine learning. World-class resources for research incl. LUMI supercomputer, generous starting package & professorship affiliation with a university in the world’s happiest country! Apply by March 9: ellisinstitute.fi/PI-recruit
Logo of ELLIS Institute Finland (line drawn map of Europe)
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Harlan Barker @harlanbarker.bsky.social · 25/01/2025
Nice compilation of Finnish researchers.
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Darcy Burbage, DNP, RN, AOCN @darcyburbage.bsky.social · 17/11/2024
Inspired by the other great starter packs, the Oncology Nurses on BlueSky starter pack is up! Please let me know if you’d like to be added! bsky.app/start/did:pl...
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Chrats Melkonian @cmelkonian.bsky.social · 15/12/2024
A new #StarterPack with scientist specialized in microbial bioinformatics - #MicroBioInf. Please comment if you would like to be added: go.bsky.app/5h7VaGm Looking forward to the discussions!
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Stephen Turner @stephenturner.us · 30/12/2024
I made a "gene info" custom GPT. Paste in a list of human gene symbols. It'll run some python code against a custom knowledge base to provide information about those genes (from RefSeq) chatgpt.com/g/g-677277d002608191887… 🧵 1/4 🧬🖥️🧪
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Ester Hammond @hammond-lab.bsky.social · 03/01/2025
Great start to 2025. Tumor hypoxia promotes immune evasion by autophagy-mediated downregulation of MHC class I expression leading to reduced antigen presentation. Great work from @halaestephan.bsky.social www.embopress.org/doi/full/10....
embopress.org
Hypoxia promotes tumor immune evasion by suppressing MHC-I expression and antigen presentation | The EMBO Journal
imageimageHypoxia contributes to cancer resistance to both standard therapies and immunotherapy. This work demonstrates that tumor hypoxia promotes immune evasion by autophagy-mediated downregulation ...
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Peter W🤓 @wang.social · 28/11/2024
Happy Thanksgiving, everyone! While you are drinking wine and drowning in turkey, I would encourage folks to think about: What if Bluesky really is our shot at breaking the web2/socmedia stranglehold on collective sensemaking... What kinds of trillionaire and sovereign attacks are coming?
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Astrobiology @astrobiology.bsky.social · 29/12/2024
Previously Unknown Life Forms Discovered Within Human Microbiomes astrobiology.com/2024/12/prev... #astrobiology #genomics #microbiology
astrobiology.com
Previously Unknown Life Forms Discovered Within Human Microbiomes - Astrobiology
Editor’s note: A team of researchers at Stanford University discovered objects they named “obelisks” in the human mouth and gut. The obelisks are microscopic, circular bits of genetic material that co...
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Dorothy Bishop @deevybee.bsky.social · 23/12/2024
deevybee.blogspot.com/2024/12/finl... re @zbmed.bsky.social new contract
deevybee.blogspot.com
Finland vs. Germany: the case of MDPI
It's been an odd week for the academic publisher MDPI. On 16th December, Finland's Publication Forum (known as JUFO) announced that from J...
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Joan @resabut.bsky.social · 18/12/2024
Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues Stephen R Quake, The Tabula Sapiens Consortium bioRxiv 2024.12.03.626516; doi: doi.org/10.1101/2024... 🖥️🧬🧪
doi.org
Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues
The Tabula Sapiens is a reference human cell atlas containing single cell transcriptomic data from more than two dozen organs and tissues. Here we report Tabula Sapiens 2.0 which includes data from ni...
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Harlan Barker @harlanbarker.bsky.social · 19/12/2024
Great bit of writing on a fascinating topic! My grandma got me a subscription to @sciam.bsky.social as a kid and reading it was one of the reasons I became a scientist. I have to admit I haven’t subscribed in awhile (not sure I can get it here in Finland) but I’m going to look into it again!
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Harlan Barker @harlanbarker.bsky.social · 17/12/2024
1/3 *Of interest to fellow ancient DNA researchers* 🧪 Working on scRNA-Seq data I got excited when I attended an EMBL symposium on ancient DNA and realized some of the same visualization methods (e.g., UMAP) could be applied to ancient DNA. *Final results: umap-aadr.herokuapp.com/main_umap
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Eric Topol @erictopol.bsky.social · 11/12/2024
Why do some people, despite SARS-CoV-2 exposure, not develop an infection? An ultra-early interferon response blocks Covid www.thelancet.com/journals/ebi... adds to protection from pre-existing, cross-reactive T cells in some people
thelancet.com
An ultra-early, transient interferon-associated innate immune response associates with protection from SARS-CoV-2 infection despite exposure
Our interferon-associated signature of early SARS-CoV-2 infection characterises a subgroup of exposed, uninfected contacts in three independent cohorts who may have successfully aborted infection prior to induction of adaptive immunity. The earlier transient upregulation of signature genes in PCR-negative compared to PCR-positive CHIM volunteers suggests that ultra-early interferon-associated innate immune responses correlate with, and may contribute to, protection against SARS-CoV-2 infection.
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Joachim Goedhart @joachimgoedhart.bsky.social · 16/12/2024
There are now 24 step-by-step guides, explaining how to create these ⬇️ data visualizations with R/ggplot2 - I hope this is a useful resource. Find them all here: joachimgoedhart.github.io/DataViz-prot...
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Proceedings of the National Academy of Sciences @pnas.org · 04/12/2024
Male rhesus monkeys with autism-like traits that voluntarily inhaled arginine vasopressin showed improved facial recognition and responded better to social overtures from other monkeys, as compared with monkeys who inhaled a placebo. In PNAS: www.pnas.org/doi/10.1073/...
Cartoon summary of experimental setup, showing young adult male low-social rhesus monkeys voluntarily inhaling though a nebulizer to get a juice reward.
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Bluesky @bsky.app · 03/12/2024
Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪
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Leopold Parts @leopoldparts.bsky.social · 02/12/2024
Does my mutation have the same impact as yours? Population genetics 🤠 🥸 🤓 🤡 meets single cell CRISPRi ⚡ ! www.biorxiv.org/content/10.1... Led by Claudia Feng, Oliver Stegle, Britta Velten, @sangerinstitute.bsky.social .
lnkd.in
LinkedIn
This link will take you to a page that’s not on LinkedIn
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Victor Javier @vjsanchez.bsky.social · 01/12/2024
What a great community! It's still not too late to join the #PancreaticCancer Starter Pack. go.bsky.app/2FHVVL6
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Steve Russell @steverus.bsky.social · 29/11/2024
The School of Biological Sciences in Cambridge is recruiting an Associate Professor or G11 Professor in Evolutionary Genomics www.jobs.cam.ac.uk/job/49389/. The post builds on our successful cross-department research theme in Functional and Evolutionary Genomics (www.bio.cam.ac.uk/research/fun...).
jobs.cam.ac.uk
Associate Professor / Professor of Evolutionary Genomics - Job Opportunities - University of Cambridge
Associate Professor / Professor of Evolutionary Genomics in the Department of Genetics at the University of Cambridge.
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Harlan Barker @harlanbarker.bsky.social · 27/11/2024
A starter pack for researchers, groups, and folks in Tampere, Finland. go.bsky.app/KB8tVST
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Ákos T Kovács @evolvedbiofilm.bsky.social · 19/11/2024
Biofilm Starter Pack on the Blue place go.bsky.app/HF1jeCQ
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Dr Katherine Duncan @kateduncan.bsky.social · 20/11/2024
If you are new to 🦋 and are interested in microbial natural products - here’s some starter packs to help connect us go.bsky.app/72NeGsT and go.bsky.app/4xnRN52 - there’s also one set up by @danudwary.secondarymetabolism.com here go.bsky.app/Q9svkYf
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Rafael Santana-Davila @valdesan.bsky.social · 10/11/2024
Starting a list of oncology related peopl. Please tell me more to add. Or any similar listd go.bsky.app/GKXp9Fy @n8pennell.bsky.social
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Souvik Bhattacharyya @souvik-uthealth.bsky.social · 12/11/2024
Hello Blueskis. Here is a starter pack of General Microbiology. It's a small list currently. Please feel free to self-nominate and I will add you. go.bsky.app/QgSQHJ9
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Harlan Barker @harlanbarker.bsky.social · 26/11/2024
📢 @unioulu.bsky.social in @cellpress.bsky.social Our lab's latest research on high-grade serous ovarian cancer (HGSOC). We used single-cell transcriptomics, cell painting, and drug testing to profile normal (HOSE1C and HOSE2C) and malignant ovarian cells. www.cell.com/molecular-th... 🧪 #oncsky
sciencedirect.com
Molecular and functional profiling of primary normal ovarian cells defines insights into cancer development and drug responses
Patients with ovarian cancer, especially the high-grade serous ovarian cancer (HGSOC) subtype, face poor prognosis due to late diagnosis and treatment…
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Jon Lim, FRCP PhD @drjonlim.bsky.social · 25/11/2024
🧑‍🔬🏛️👩‍⚕️ Lots of our #CancerImmunology community now here 🦋, including @jimallisonphd.bsky.social 🏅! #AcademicSky #ImmunoSky #OncSky #StarterPack 1 is already full 🙌, so starting a another one. Let's continue growing! - Pack 1️⃣: go.bsky.app/PRdmHCP - Pack 2️⃣: go.bsky.app/93eqJbs
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Adam M Novak @adamnovak.graphs.vg · 07/11/2024
I arrived like an hour ago and already I have a #pangenomics / #bioinformatics starter pack for you: go.bsky.app/UsodJmy
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scverse @scverse.bsky.social · 16/11/2024
Explore the scverse Starter Pack! Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place. go.bsky.app/UvFMa8d
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Rob Patro @robp.bsky.social · 12/11/2024
I made a starter pack for algorithmic genomics. It's certainly incomplete, but already has a ton of awesome peeps. Let me know if you know people I should add (with a focus on algorithms and data structures in genomics) go.bsky.app/TRWCnZs
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Bryan White, MS Bio, MPH 🧬 @crvscience.com · 14/11/2024
#EpiSky #MedSky 🧪🧬🖥️🛟🦠 Please help add to my “Public Health Data Trackers” starter pack. Infection rates, haplotype clusters, viral/bacterial genomics, positivity, ER rates, case reports, commentary on reports - we need it all. List is inclusive. Suggestions ⬇️ or DM. go.bsky.app/N4Hnryq
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Voilà: Francis Gagnon @chezvoila.com · 01/09/2024
Here you go. 🫡 Please share widely to help develop the dataviz community of Bluesky. 📊 go.bsky.app/R3nSyyy
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Johanna Joyce @johannajoyce.bsky.social · 23/11/2024
Both #Cancer #Research starter packs are now completely full! ~300 researchers, oncologists, students, postdocs, patient advocates, and organizations supporting cancer research 🧪🔬⚕️ I hope you'll find these useful to build our community here Pack 1: go.bsky.app/FEoaJMc Pack 2: go.bsky.app/6EcjWNA
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Rachel Pope @prehistorian.bsky.social · 24/11/2024
Prehistorians starter pack: go.bsky.app/R1ejt58
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Dr Rebecca Wragg Sykes @lemoustier.bsky.social · 11/11/2024
📣 🏺 A Palaeolithic #Archaeology & Human Origins people starter pack! Nearly 80 people here, if you work in these fields and want to be added, let me know (I'm keeping the list to trained/ qualified professional/academic/researchers etc at the moment) go.bsky.app/6hXVX57
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🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 10/11/2024
Genomics, evolution, and more starter pack! Help build community with this starter pack. This list is currently incomplete. Want to be included? Reply and I will remedy that! go.bsky.app/JjvzkWU
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David Fischer @davidsebfischer.bsky.social · 20/11/2024
To expedite the development of a network focussed on single-cell and spatial genomics on this platform, I started to collect accounts of scientists & groups that are broadly active in these fields. This is work in progress, DM if you want to be added or have suggestions! go.bsky.app/HZTJxbZ
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Raphael Gottardo @rgottardo.bsky.social · 24/11/2024
Ok, I tried to create my own list of people working on developing statistical or machine learning models applied to omics data. I am sure I missed a lot of cool people. If you'd like to be added, let me know. #Stats #ML #Omics go.bsky.app/73rcuJn
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Stephen Turner @stephenturner.us · 16/11/2024
Bluesky for Science Starter packs for genomics, bioinformatics, #Rstats, Nextflow. Moderation lists. Feeds. Let's rebuild the old scitwitter community and keep this place nice blog.stephenturner.us/p/bluesky-fo... 🧬🖥️🧪
blog.stephenturner.us
Bluesky for Science
Bluesky starter packs for genomics, bioinformatics, R, and Nextflow
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Su-In Lee @suinlee.bsky.social · 23/11/2024
Here is a #compbio starter kit! go.bsky.app/QVPoZXp To all the #Bioinformatics #Genomics #MachineLearning folks: please RP and let’s build this together!
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Willie Neiswanger @willieneis.bsky.social · 10/11/2024
I'm making a list of AI for Science researchers on bluesky — let me know if I missed you / if you'd like to join! go.bsky.app/AcP9Lix
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Harlan Barker @harlanbarker.bsky.social · 25/11/2024
Starter pack of academic journals on bluesky. Very helpful.
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