jp flores (he/him)

#Introductions Hi! 🤠 I’m JP (he/him), and I’m a PhD candidate at UNC Chapel Hill studying the role of 3D chromatin structure in response to environmental stress 🧬 I host the From where does it STEM? podcast, write/edit for GeneBites, & more! website: jpflores.rbind.io instagram: @jpflores_31

🚨the latest from the lab! 😃👇🏻 www.science.org/doi/10.1126/...

🚨Preprint from our lab🚨 How and when did TADs emerge during evolution? 🐁🐟🪰 HINT: the diversification of CTCF regulation and functions enabled new mechanisms of 3D chromatin folding 🧬 With Liene Astica & @rdacemel.bsky.social Link: www.biorxiv.org/content/10.6... Bluetorial 1/15👇

The 4DN Center for 3D Structure and Physics of the Genome proudly presents: "Stepwise reorganization of chromosome conformation and nuclear organization during stem cell differentiation". www.biorxiv.org/content/10.6...

In February 2026, we captured this photo of Dr. JP Flores from the Scientist Network for Advancing Policy (SNAP) as he ran across the plenary stage at the 2026 annual meeting of the American Association for the Advancement of Science (AAAS) in Phoenix, Arizona.

Quantitative changes in 3D contact predict changes in enhancer-promoter regulation upon cohesin depletion @jengreitz.bsky.social www.nature.com/articles/s41...

IMO the paper of the year in the gene regulation field - such a clean and clear study, showing how promoter-enhancer contacts mediate transcriptional activation. www.cell.com/cell/abstrac...

Order Matters: Ambient RNA correction confounds doublet detection in single-cell RNA sequencing https://www.biorxiv.org/content/10.64898/2026.10.13.758369v1

How does gene expression change during regeneration? Are specific enhancers activated or is there extensive genome re-modelling? Working with the team of Guillermo Orsi, we show that insect (cricket) and crustacean (Parhyale) genomes become re-modelled on a genome-wide scale.

The time has come! Vienna and I are moving to Milan, Italy tonight to start a 3mo Fulbright 😊 Ci vediamo presto!

How can histone acetyl-transferase acetylate a specific histone tail residue ? Using cryo-EM, we captured the MSL complex in a stable post-catalytic state, visualising the acetyl group on H4K16, a central mark for gene regulation authors.elsevier.com/sd/article/S...

Excited to share PostChicago, our lab's new R/Bioconductor package for the analysis of Capture-(Hi)C data downstream of loop calling. We present two of its applications: Meta-profiling of interactions and detection of crosslinking artefacts: www.biorxiv.org/content/10.6...

Very interesting historical perspective on cohesin and its role in transcriptional regulation: link.springer.com/article/10.1...

Systematic mapping of enhancers, silencers, and topological elements using prime editing deletion screens www.biorxiv.org/content/10.6... Check out our preprint on next-generation tech for mapping distal regulatory effects! We’re excited to help set this up - please get in touch Thread 👇

The archaeon Sukunaarchaeum mirabile, associated with dinoflagellates, has a genome of only 238 kbp🧬🤯 #archaea #symbiosis #eukaryotes #protists #MicroSky @currentbiology.bsky.social www.cell.com/current-biol...

And… I am SO excited to share the first research preprint from my group! In this paper we determined several cryoEM structures to visualize the entire cell-to-cell bridging complex formed by TAM receptor and ligand, bringing into 3D a common graphical depiction. www.biorxiv.org/content/10.6...

The @zeitlingerlab.bsky.social is pleased to announce @sergio-gma91.bsky.social’s preprint “High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo” (www.biorxiv.org/content/10.6...). TLDR; TFIID behaves differently depending on promoter type. More below:

How can Bioconductor methods become more reusable across different workflow ecosystems? Our latest blog explores how Bioconductor, Galaxy & nf-core contributors used a single-cell workflow to test the BiocJobs approach & advance research software interoperability. Read the full post: bit.ly/4y4ZuUB

💜Applications are OPEN for the 2027 #DisabledInSTEM Mentorship Program! Join our 7th year of connecting disabled people in STEM with mentors & community. Mentors can be disabled or nondisabled allies! 📅 Apply by Dec. 11 Mentees: forms.gle/121MAZgCWBHW...
 Mentors: forms.gle/LU1NFBxCz43M...

Delighted to see our latest paper out in @natgenet.nature.com ! The brilliant @jhamley98.bsky.social developed MCCv, allowing chromatin architecture to be visualised at base-pair resolution for each allele—a powerful way to identify functional genetic variants. www.nature.com/articles/s41... 🧵

We are excited to share research, but I want to take some time to share a little about myself. I LOVE science, but I also spend a lot of time advocating for more inclusive science. This work is promoted by my own obstacles in pursuing science which I talk about here: www.cell.com/cell/fulltex...

1\ We know a bit about how 3D chromatin interactions are formed, but what do we know about how they are disrupted? We asked this question in our latest preprint: doi.org/10.64898/202..., focusing on the massive loss of promoter interactions during neuronal differentiation.

🧬 New paper in Bioinformatics Advances: "Loopcity: An R package for the detection of chromatin loop communities from Hi-C data"  Read it here: https://doi.org/10.1093/bioadv/vbag269 Authors include: @jpflores.rbind.io

Fun project by Sarah, me and @dphansti.bsky.social ! Thanks to @bioinfoadv.bsky.social for the thread 😊

RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) www.biorxiv.org/content/10.6...

Two tools for plotting genomics data: figeno: Tool for making genomics figures in #python. github.com/CompEpigen/... Plotting Multi-omic Data with plotgardener in #rstats phanstiellab.github.io/plotgardene...

Open peer review can mean different things, from publishing review reports to sharing reviewer identities or connecting review with preprints. We explore different approaches to making peer review more transparent: buff.ly/6Vrxhfl #PeerReviewWeek #PRW2026

❗Postdoc positions available! We have multiple fully funded openings in the lab - please reach out if you’re interested. I’ll be at CSHL Epigenetics and Chromatin this week, so come find me if you’d like to learn more about the lab or potential projects

🧪🧬New preprint We present cryo-EM structures of reconstituted CTCF–nucleosome complexes, showing CTCF dimerization drives nucleosome oligomerization into defined higher-order assemblies. Disrupting CTCF–CTCF interfaces in mESCs reduces looping and impairs differentiation. tinyurl.com/CTCF-nucleos...

Excited to share our new preprint on in situ chromatin structure of the inactive X chromosome in differentiated female mouse embryonic stem cells. www.biorxiv.org/content/10.6... 🧵1/8

The talented @isa-ozdemir.bsky.social wrote a review of CHD remodelers, discussing all 9 family members and their roles in ES cells and early development. dx.doi.org/10.1002/bies... 1/2

(1/n) Excited to share close collab w @bloodgenes.bsky.social led by Varshini & Chun-jie et al How to induce expression of key genes while silencing much of the genome during Erythropoiesis? A: Matchmaker CREs load cohesin near key genes to promote looping & exp: www.biorxiv.org/content/10.6...

First preprint from the lab 🚨 We asked when and how global chromatin organization emerges during early development 🐟

Great to see this lovely functional genomics work from @gweykopf.bsky.social @jmarshlab.bsky.social @kennethbaillie.bsky.social @gorrellmsydney.bsky.social @simonbiddie.bsky.social published. What at first sight seemed to be non-coding turns out to be coding. www.nature.com/articles/s41...

🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇

The Neal lab is hiring a postdoctoral fellow to lead exciting structural and biophysical studies of membrane protein quality control! Competitive HHMI-scale salary + cutting-edge science + a genuinely wonderful and supportive lab culture. Please share widely with anyone who might be interested!