Harlan Barker

One major focus was having cross-species functionality, so the tool uses Ensembl IDs and can make predictions in 317 different species, including all model organisms. Looking forward (hoping) to seeing how the community uses this to advance transcriptional biology research!

This article presents a tool that integrates multiple data types to improve the accuracy of transcription factor binding site (TFBS) prediction.

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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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

Why it matters:
Our results strengthen the idea that subtle tuning of gene activity helped sculpt human-specific cognitive abilities, along with the neuropsychiatric risks that hitchhike on that evolutionary journey.

- In an autism dataset 15 of these TFs and 16 of their target genes are differentially expressed in autism vs. control, most commonly upregulated in developing neurons and downregulated in SV2C- and somatostatin-expressing interneurons, oligodendrocytes.

- The target genes cluster around pathways linked to neurodevelopment (including autism-related processes), craniofacial and connective-tissue biology, tracheal and prostate function, and vision.

What we found:
- Using our tool TFBSFootprinter, we screened the non-coding genome and uncovered 110 transcription factors (TFs) whose binding differs, potentially altering expression of 75 target genes.
- The TFs are enriched for vision, motor neurons, homeobox, and brain.

Background:
- Protein-coding changes between modern humans and Neanderthals are surprisingly scarce—just 96 sites. Regulatory changes are far richer.

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...

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

Logo of ELLIS Institute Finland (line drawn map of Europe)

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.

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...

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!

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 🧬🖥️🧪

Thanks for sharing. I think that it is underutilized for study outside of single cell analyses. In one of our recent studies we used it to correlate cells based on various phenotype measurements after FACS.

If it’s a pre-print somewhere I’d be interested to see your article, or share it after pub!

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 ...

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....

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?

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...

Previously Unknown Life Forms Discovered Within Human Microbiomes
astrobiology.com/2024/12/prev... #astrobiology #genomics #microbiology

Are you sure it’s your first, or maybe just the worst?? 🙈

deevybee.blogspot.com/2024/12/finl...
re @zbmed.bsky.social new contract

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...

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...

🖥️🧬🧪

Side note: Greg Bear wrote a great sci-fi series which incorporates Planet X and is the first fiction I’ve ever read which incorporates a more comprehensive view of the extrasolar bodies of the solar system.

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!

GitHub - thirtysix/population_genetics_AADR: Interactive visualization of population genetics data for ~10,000 modern and ancient individuals. Interactive visualization of population genetics data for ~10,000 modern and ancient individuals. - thirtysix/population_genetics_AADR

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Code for running the analysis and generating the interactive plot here:
github.com/thirtysix/po...

2/3
I grabbed a starting set of 16,765 ancient and modern humans found at AARD (reich.hms.harvard.edu/allen-ancien...), compiled by the David Reich lab, processed the data with ADMIXTOOLS2 and PLINK, and then created an interactive visualization using Python and Bokeh.

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*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

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.

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

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...

Cartoon summary of experimental setup, showing young adult male low-social rhesus monkeys voluntarily inhaling though a nebulizer to get a juice reward.

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/...

Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪