Winston Timp

Interested in a #postdoc position to develop new sequencing methods? Come work with us! Work includes but is not limited to epigenetics, RNA mods, and single-cell/spatial transcriptomics. docs.google.com/document/d/1ZM…

We assembled the acrocentric short arms of 23 samples from a 4-generation pedigree, revealing unique mutational and recombination patterns from these highly repetitive regions that are usually excluded in the genetic analysis. Preprint: biorxiv.org/content/10.648…

Finally, in CA1 engram (Fos+) neurons, we found upregulated isoforms (Egr1-201, Junb-201, Arpc2-201) and downregulated isoforms (Plp1-201). Notably, Arpc2-201—a learning-linked cytoskeletal isoform—suggests structural remodeling during engram activation.

For example Baiap2; which encodes an abundant scaffolding protein (Irsp53) in the postsynaptic density. We observed no differential expression, only differential splicing, resulting in loss of the C-terminal PDZ binding motif, needed for postsynaptic density localization.

We are excited to announce our most recent preprint “Single-cell long-read sequencing of the experience-induced transcriptome” (biorxiv.org/content/10.110…) led by @sheridan in collaboration with Richard Huganir. A few highlights:

🦖 Something HUGE just hatched. Plasmidsaurus now offers RNA sequencing for gene expression analysis with: • As fast as 3 day turnaround • $50/sample for academia, $80 for industry • Up to ~10M unique transcript 3’ end reads per sample • Interactive results that let you explore changes in genes and pathways Explore Plasmidsaurus RNA-Seq today.

Direct detection of 8-oxo-dG using nanopore sequencing. #DNAmodifications #Nanopore #Sequencing @nanopore @NatureComms nature.com/articles/s4146…

3050 Ti added. github.com/Kirk3gaard/202…

Knowledge is power. In the studio, Matt Loose shared insights on rapid CNS profiling — and how one participant told him: “Even if the answer isn’t what you want, it’s better than not knowing at all.”

NEW review article from Henikoff and Ahmad about emerging epigenomic mapping technologies to study chromatin regulation. Very comprehensive - great for beginners and experts alike! sciencedirect.com/science/articl…

Ski fast…and sequence faster. Plasmidsaurus now lives in Germany! 🇩🇪 Overnight sequencing for ALL of Europe Pickup ~4PM → Results 8AM 🦖 Dropboxes in 14 European countries...and the dino is looking for MORE! Request your free dropbox here: shorturl.at/cplXq Sequence plasmids, amplicons, bacteria, libraries, yeast, AAV, microbiomes, eukaryotes…sequence everything. No primers needed. Big love to Dr Jan Müller, PI at the Medical University Innsbruck, Austria, for starring in this video!

Excited & very lucky to be part of the Gates Sr. AD Fellowship ✨ Using CARD’s long-read epigenetic data 🧬 to build better predictive models of ADRD & making all models & methods openly available (open science FTW!🔓). Looking forward to collaborating with this awesome group!

A decade ago, we had thousands of bacterial genomes. Now, we have millions. How to scale computational methods? Our paper in @naturemethods answers this: use evolutionary history to guide compression and search. …From terabytes to tens of GBs… w/@Baym @ZaminIqbal et al. 🧵1/

A milestone for our lab! Here's a full text link: rdcu.be/egmYb

Introducing cornetto, an adaptive genome assembly paradigm using @nanopore adaptive sampling. - greatly reduces cost per genome assembly - reference agnostic, so works for non-humans - assembly just using saliva - & many more Relies on 2 excellent software #readfish & #hifiasm.

Uncalled4: a toolkit for nanopore signal alignment, analysis and visualization of DNA and RNA modifications. nature.com/articles/s4159…

New online! Computational analysis of DNA methylation from long-read sequencing bit.ly/4cjxUtl

📣Our 24-reaction CUT&RUN Kit is here! Everything you love about our 48 reaction CUT&RUN kit in an affordable and convenient kit size. Perfect for: ✔️First-time CUT&RUN users ✔️Running small experiments ✔️Testing new cells or targets Check it out: hubs.la/Q02_Zs7v0

It's my pleasure to present the next big preprint from SheqLab! An exciting application of our O-MAP platform that I hope will transform the study of nuclear architecture. If you've ever wanted to dissect the subnuclear "neighborhood" around an individual locus, read on! (1/30)