Hannah Long (@hannahlong) Bsky

Morally relevant features warranting ethical oversight in human stem cell-based embryo models Nature Cell Biology - This Perspective presents a set of attributes by which to evaluate human stem cell-based embryo models that not only include morally relevant embryo features but also take...

Following several years (!) of discussion and rumination, our team of excellent colleagues - Martin Pera, @nicolasrivron.bsky.social, @amartinezarias.bsky.social, Karen Sermon and Nienke de Graeff - have published a new ethical perspective on SCBEM #embryomodels rdcu.be/fcklG [1/5]

1 week ago 29 11 1 0

A functional overlap between actively transcribed genes and chromatin insulator elements - The EMBO Journal The mammalian genome is organised into large topologically associating domains (TADs) and smaller sub-TADs or enhancer-promoter loops, which may contribute to the regulation of gene expression. These ...

#WIMMReads
🧪 From Jim Hughes, Douglas Higgs and Mira Kassouf: actively transcribed genes can define chromatin boundaries, linking gene activity directly to 3D genome organisation.

Read more 👇

#GenomeBiology #Chromatin #WIMM @rdm.ox.ac.uk @medsci.ox.ac.uk #AkademicSky

1 month ago 3 3 0 0

Redirecting

Really pleased to share the *final* version of @katiegelder.bsky.social's super work, profiling the functional roles of #IDRs in CBP. Published today 🎉

🔗https://doi.org/10.1016/j.celrep.2026.117109

#IDRs #condensates #transcription #CBP #generegulation #enhancers (1/7)

1 month ago 24 10 2 0

We are looking for two exceptional Research Assistants!

1) Experimental, to drive forward quantitative studies of transcription factor function in development

2) computational, to develop and apply cutting-edge deep learning models of gene regulation.

Links below

2 months ago 2 2 1 0

Array-CNCC: precise aggregation and arrayed plating facilitate quantitative phenotyping of human cranial neural crest cells and craniofacial disease modelling Facial development is highly sensitive to genetic and environmental perturbation, with craniofacial malformation associated with over one-third of congenital birth defects. The face arises during an early and largely inaccessible window of embryonic development, with a large contribution from transient and multipotent cranial neural crest cells (CNCCs). Assessment of the molecular and cellular mechanisms driving normal and disordered human facial development therefore relies greatly on the use of in vitro cellular models. Here, we adapted a neurosphere-based CNCC differentiation protocol to facilitate robust quantification of early specification and migration events. Introduction of single-cell aggregation with arrayed plating enabled standardisation of neurosphere size, growth and patterning. Inclusion of fibronectin coating enhanced the efficiency of neurosphere attachment and synchronicity of CNCC migration timing. To demonstrate application of the Array-CNCC method, we developed a strategy for mosaic co-culture, which can facilitate differentiation of wildtype untreated cells directly alongside cells exposed to distinct drug treatments or genetic alterations. Finally, we present a screening approach which we use to test the impact of distinct extracellular matrix components on neurosphere morphology, CNCC migration and gene expression. Together, the Array-CNCC method is highly amenable to quantitative phenotyping and screening approaches, enabling enhanced craniofacial disease modelling with both cellular and molecular readouts. ### Competing Interest Statement The authors have declared no competing interest. Medical Research Council, MC\_UU\_00035/12, MC\_ST\_00035 Wellcome Trust, https://ror.org/029chgv08, 227712/Z/23/Z

📣 Preprint alert!

I am happy to share that our neural crest manuscript is now available on BioRxiv! www.biorxiv.org/content/10.6...

3 months ago 5 5 0 0

SS18::SSX activates Polycomb target genes without BAF ❌
Instead, transcription relies on EP300 via the SS18 QPGY domain
www.biorxiv.org/content/10.6...
➡️ Coactivator targeting emerges as a new therapeutic strategy in synovial sarcoma 🎯
Team work from @banitolab.bsky.social and @uoe-igc.bsky.social

2 months ago 22 16 3 0

Array-CNCC: precise aggregation and arrayed plating facilitate quantitative phenotyping of human cranial neural crest cells and craniofacial disease modelling www.biorxiv.org/content/10.64898/2026.01...

3 months ago 1 2 0 0

This was a fantastic collaborative effort - many congratulations to first authors Ewa and Kasia!

@ewaoz.bsky.social
@km-milto.bsky.social

And a big thank you to everyone who provided support, input and inspiration along the way.

2 months ago 5 0 0 1

📣 I'm excited to share our latest preprint!

We adapt and characterise a neurosphere-based CNCC differentiation protocol, and demonstrate utility for quantitative phenotyping and craniofacial disease modelling! 🧫

Read about Array-CNCC here:
www.biorxiv.org/content/10.6...

@uoe-igc.bsky.social

2 months ago 49 14 2 1

🎉 Many congratulations to Kasia Milto who successfully defended her thesis last week! It was so wonderful to have Kasia as the first PhD student in the lab, and to co-supervise with Jenny Nichols. So proud!

@km-milto.bsky.social
@uoe-igc.bsky.social

2 months ago 17 0 1 1

Super line-up of chromatin, epigenetics and gene regulation speakers coming your way from @aicc-ireland.bsky.social over the next 5 months!

3 months ago 4 1 0 0

ASPEN: Robust detection of allelic dynamics in single cell RNA-seq Author summary One powerful way to study regulation is to examine hybrids between two inbred species, where each gene has two distinct parental copies, or alleles. Measuring how much each allele is ex...

Latest from our lab: dx.plos.org/10.1371/jour... Congratulations to Veronika for leading this work to model cis-regulatory dynamics in F1s using single-cell allelic data

4 months ago 13 3 1 0

Applications for our international #PhD program open until 11th Jan. Come work with us @uoe-igc.bsky.social and @hannahlong.bsky.social to understand DNMT3B in ICF syndrome or with our wonderful colleagues.
Details here:
institute-genetics-cancer.ed.ac.uk/igc-graduate...
#epigenetics Please repost 🙏

4 months ago 11 9 0 0

Excited to share our work at @natcomms.nature.com

We used single cell proteomics to define the functional heterogeneity of human neutrophils in glioblastoma, finding pro and anti-tumorigenic effector states invisible to scRNAseq.

SCP will revolutionise immunology, this is just the start

4 months ago 43 9 2 1

SET1/MLL complexes control transcription independently of H3K4me3 Histone H3 lysine 4 trimethylation (H3K4me3) at gene promoters is thought to play a central role in gene transcription. H3K4 methylation is deposited by the SET1 (A/B) and MLL (1-4) multi-protein comp...

An early Christmas present for those interested in chromatin and transcription! Fantastic work from @au-ho-yu.bsky.social and @aleksszczurek.bsky.social . Thanks to Inge and Michiel for their help. Please repost!

www.biorxiv.org/content/10.6...

4 months ago 133 65 10 6

JASPAR: An open-access database of transcription factor binding profiles JASPAR is the largest open-access database of curated and non-redundant transcription factor (TF) binding profiles from six different taxonomic groups.

JASPAR 2026 is out 🎉

The new release massively expands the TF motif collections and adds a dedicated DeepLearning collection of motifs learned from deep learning models.

Database: jaspar.elixir.no
Paper (NAR): doi.org/10.1093/nar/...

🧵1/2

4 months ago 63 28 1 0

Intro to Bedder – The Quinlan Lab

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.

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4 months ago 298 152 5 11

Don’t miss out on this opportunity- come and join us at the Oxford Organoid Hub working under the MRC-BHF REACT programme! If you love in vitro 3D models, the ❤️ and regenerative therapies, this is for you - apply by 18 Dec @oxforddpag.bsky.social @idrm.ox.ac.uk @rdm.ox.ac.uk

4 months ago 10 8 0 0

MRC four-year International PhD programme: Human Genetics, Genomics and Disease | IGC Graduate Research & Training | Institute of Genetics and Cancer Applications now open.

Exciting opportunity to work on a collaborative PhD project with Duncan and myself modeling ICF1 syndrome in human stem cell models 🧫

@sproullab.bsky.social
@uoe-igc.bsky.social

Applications are open for the MRC PhD programme in Human Genetics, Genomics and Disease at the University of Edinburgh!

4 months ago 4 0 0 0

Project 2: Use human ES cells to determine exactly how DNMT3B mutations cause ICF1 syndrome. Collaboration with @hannahlong.bsky.social:
institute-genetics-cancer.ed.ac.uk/igc-graduate...
Deadline 11th January 2026
This scheme is flexible if you are interested in other projects.
🧵 3/4

4 months ago 7 5 2 0

🚨 Multiple #PhD opportunities for lab or computational applicants. Do you want to understand the molecular basis of #epigenetic dysfunction in human disease?
Come work with our group at the fantastic, collaborative @uoe-igc.bsky.social in a beautiful, liveable city.
🧵 1/4
Please repost 🙏

4 months ago 20 17 1 2

BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants BRAIN-MAGNET, a convolutional neural network trained on 148,198 functionally tested non-coding regulatory elements, predicts enhancer activity directly from DNA sequence and identifies nucleotides ess...

Very pleased to share our latest paper published in Cell:
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants: Cell www.cell.com/cell/fulltex...
@cellpress.bsky.social, @cp-cell.bsky.social, @ruizhideng.bsky.social #enhancer
here is a thread about our findings:

5 months ago 12 9 2 2

Neanderthal DNA reveals how human faces form Subtle genomic variations between humans and Neanderthals provide clues to how DNA shapes our facial features.

Researchers have identified gene-regulatory variants that might have contributed to Neanderthals’ beefy jaws — offering a window on how the human face developed

go.nature.com/3Ke6StJ

5 months ago 34 7 0 3

Congratulations!

5 months ago 2 0 1 0

🚨Reposts appreciated‼️If I had read this PhD offer five years ago, I wouldn’t have hesitated for a second to apply 😉
Passionate about gene regulation, chromatin, and developmental biology? Just contact @radaiglesiaslab.bsky.social at @ibbtec.bsky.social 🧬✨

#PhD #3DGenome

5 months ago 36 37 0 3

Join us for our free inaugural lecture & drinks reception. @jorisveltman.bsky.social will talk about the genetic causes of rare disorders such as reproductive disorders & Charlie Lees will tell the 20‑year story of change in IBD.
More info & register👉 bit.ly/3J766hJ
@cmvm-edinburghuni.bsky.social

5 months ago 3 1 0 1

Neanderthal DNA enhances our understanding of face development

This Research Highlight showcases the work from Hannah Long @hannahlong.bsky.social, Kirsty Uttley @kirstyuttley.bsky.social, Hannah Jüllig @hannahjuellig.bsky.social and colleagues: journals.biologists.com/dev/article/...

5 months ago 21 7 2 2

Our latest paper has just been published in Cell!

doi.org/10.1016/j.ce...

We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.

5 months ago 209 79 6 11

Enjoy the start of this new adventure! And hopefully I’ll see you soon in Europe ☺️

5 months ago 0 0 0 0

Many congratulations Wendy, and to the whole team! Excited to see what you discover 🧬

5 months ago 0 0 0 0

Posts by Hannah Long