Harlan Barker
@harlanbarker.bsky.social
Scientist, American in Finland. Doing bioinformatics, cancer, single-cell RNA-Seq transcriptomics, and ancient DNA research at Tampere University and University of Oulu.
🧪🧬 🖥️
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
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
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...
www.tandfonline.com
July 26, 2025 at 4:48 AM
🧪🧬 🖥️
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
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
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
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
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...
www.csbj.org
June 3, 2025 at 11:24 AM
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
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
Reposted by Harlan Barker
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
February 4, 2025 at 3:16 PM
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
Nice compilation of Finnish researchers.
Tässä vuoden ensimmäinen #FollowFriday Tiedespesiaali!
Tässä ketjussa 89 tiede-ja tutkimustoimijaa seurattavaksi🧵: (koko 1576:n lista lopussa)
1/10
@ivaskalab.bsky.social
@jarkkokoivunen.bsky.social
@mattilalab.bsky.social
@amnamusic.bsky.social
@akiratakedalab.bsky.social
@jain-shruti.bsky.social
Tässä ketjussa 89 tiede-ja tutkimustoimijaa seurattavaksi🧵: (koko 1576:n lista lopussa)
1/10
@ivaskalab.bsky.social
@jarkkokoivunen.bsky.social
@mattilalab.bsky.social
@amnamusic.bsky.social
@akiratakedalab.bsky.social
@jain-shruti.bsky.social
January 25, 2025 at 1:53 PM
Nice compilation of Finnish researchers.
Reposted by Harlan Barker
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...
Please let me know if you’d like to be added!
bsky.app/start/did:pl...
November 17, 2024 at 7:26 PM
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...
Please let me know if you’d like to be added!
bsky.app/start/did:pl...
Reposted by Harlan Barker
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!
Please comment if you would like to be added: go.bsky.app/5h7VaGm
Looking forward to the discussions!
December 15, 2024 at 9:22 AM
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!
Please comment if you would like to be added: go.bsky.app/5h7VaGm
Looking forward to the discussions!
Reposted by Harlan Barker
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) https://chatgpt.com/g/g-677277d002608191887af1a9c0a9e832-gene-info 🧵 1/4 🧬🖥️🧪
December 30, 2024 at 2:30 PM
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) https://chatgpt.com/g/g-677277d002608191887af1a9c0a9e832-gene-info 🧵 1/4 🧬🖥️🧪
Reposted by Harlan Barker
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....
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 ...
www.embopress.org
January 3, 2025 at 9:30 AM
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....
Reposted by Harlan Barker
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?
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?
November 28, 2024 at 2:36 PM
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?
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?
Reposted by Harlan Barker
Previously Unknown Life Forms Discovered Within Human Microbiomes
astrobiology.com/2024/12/prev... #astrobiology #genomics #microbiology
astrobiology.com/2024/12/prev... #astrobiology #genomics #microbiology
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...
astrobiology.com
December 29, 2024 at 7:32 PM
Previously Unknown Life Forms Discovered Within Human Microbiomes
astrobiology.com/2024/12/prev... #astrobiology #genomics #microbiology
astrobiology.com/2024/12/prev... #astrobiology #genomics #microbiology
Reposted by Harlan Barker
Reposted by Harlan Barker
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...
🖥️🧬🧪
Stephen R Quake, The Tabula Sapiens Consortium
bioRxiv 2024.12.03.626516; doi: doi.org/10.1101/2024...
🖥️🧬🧪
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...
doi.org
December 18, 2024 at 11:31 PM
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...
🖥️🧬🧪
Stephen R Quake, The Tabula Sapiens Consortium
bioRxiv 2024.12.03.626516; doi: doi.org/10.1101/2024...
🖥️🧬🧪
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!
It's hard to believe there could be a giant planet in the solar system that we haven't seen. But these are exciting times! We should know within the next two years either way. www.scientificamerican.com/article/if-p...
We May Be on the Brink of Finding the Real Planet Nine
If there’s a hidden world in the solar system, a new telescope should find it
www.scientificamerican.com
December 19, 2024 at 7:56 AM
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!
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
*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
December 17, 2024 at 9:11 AM
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
*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
Reposted by Harlan Barker
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
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
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.
www.thelancet.com
December 11, 2024 at 11:39 PM
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
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
Reposted by Harlan Barker
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...
December 16, 2024 at 9:25 AM
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...
Reposted by Harlan Barker
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/...
December 4, 2024 at 10:16 PM
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/...
Reposted by Harlan Barker
Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪
There are already many articles for which there is more attention on Bluesky than on other comparable micro-blogging sites, meaning the academic community and the general public have clearly adopted Bluesky as one of its core places to disseminate and discuss new research.
A Place of Joy.
A Place of Joy.
December 3, 2024 at 2:10 PM
Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪
Reposted by Harlan Barker
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 .
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
December 2, 2024 at 1:57 PM
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 .
Reposted by Harlan Barker
What a great community! It's still not too late to join the #PancreaticCancer Starter Pack.
go.bsky.app/2FHVVL6
go.bsky.app/2FHVVL6
December 1, 2024 at 9:33 PM
What a great community! It's still not too late to join the #PancreaticCancer Starter Pack.
go.bsky.app/2FHVVL6
go.bsky.app/2FHVVL6
Reposted by Harlan Barker
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...).
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.
www.jobs.cam.ac.uk
November 29, 2024 at 12:11 PM
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...).
A starter pack for researchers, groups, and folks in Tampere, Finland.
go.bsky.app/KB8tVST
go.bsky.app/KB8tVST
November 27, 2024 at 9:57 AM
A starter pack for researchers, groups, and folks in Tampere, Finland.
go.bsky.app/KB8tVST
go.bsky.app/KB8tVST
Reposted by Harlan Barker
November 19, 2024 at 10:05 AM
Reposted by Harlan Barker
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
go.bsky.app/Q9svkYf
November 20, 2024 at 9:40 PM
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
go.bsky.app/Q9svkYf
Reposted by Harlan Barker
Starting a list of oncology related peopl. Please tell me more to add. Or any similar listd go.bsky.app/GKXp9Fy @n8pennell.bsky.social
November 10, 2024 at 9:54 PM
Starting a list of oncology related peopl. Please tell me more to add. Or any similar listd go.bsky.app/GKXp9Fy @n8pennell.bsky.social