Winston Timp
@timp0
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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
Winston Timp (https://timplab.org/) is searching for new postdoctoral fellows to join his research lab at Johns Hopkins. This position would focus on projects involving sequencing technology develo...
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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.
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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.
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We generated single-cell long-read hippocampal data from 17 total mice subjected to one of three contextual experiences: Fear-conditioned (C+), Unconditioned (U+), or Naive (N). 20% of experience-variable isoforms arise from genes with no detectable difference at the gene level.
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Using @10xGenomics Genomics and @nanopore sequencing, we generated the first single-cell long-read dataset of the mouse hippocampus. For example, S100a16, a calcium-binding protein, has cell-type alternative isoforms undetectable with standard 10X 3’ short-read data:
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We are excited to announce our most recent preprint “Single-cell long-read sequencing of the experience-induced transcriptome” ( https://t.co/Qts0K63OmJ) led by @sheridan in collaboration with Richard Huganir. A few highlights:
biorxiv.org
Neural activity drives transcriptional events that are critical for learning. Activity-induced transcript isoform expression and alternative splicing are cell-type specific events typically obscured...
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🦖 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
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Direct detection of 8-oxo-dG using nanopore sequencing. #DNAmodifications #Nanopore #Sequencing @nanopore @NatureComms
https://t.co/dSA7vsKyxX
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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.”
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NEW review article from Henikoff and Ahmad about emerging epigenomic mapping technologies to study chromatin regulation. Very comprehensive - great for beginners and experts alike! https://t.co/KOOHsRLpFm
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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: https://t.co/TZ754nqt2V Sequence
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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!
Meet Kimberley Billingsley, PhD! 🎉 As a Gates Sr. AD Fellow, she will use high-resolution methylation data to develop predictive models for ADRD, identify epigenetic signatures for better risk stratification and early detection, and establish accurate biomarkers. #ADRD
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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/
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A milestone for our lab! Here's a full text link:
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing https://t.co/lh9zsE4Jdg
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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.
Adaptively integrated sequencing and assembly of near-complete genomes https://t.co/FZ58HX394d
#biorxiv_genomic
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Uncalled4: a toolkit for nanopore signal alignment, analysis and visualization of DNA and RNA modifications. https://t.co/lh0swHAKmr
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New online! Computational analysis of DNA methylation from long-read sequencing https://t.co/Nntw3xnklU
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📣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: https://t.co/bZAkdj3oSG
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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)
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Our preprint is out! We hacked the @nanopore sequencer to read amino acids and PTMs along protein strands. This opens up the possibility for barcode sequencing at the protein level for highly multiplexed assays, PTM monitoring, and protein identification! https://t.co/hVdNFa7ti4
biorxiv.org
The ability to sequence single protein molecules in their native, full-length form would enable a more comprehensive understanding of proteomic diversity. Current technologies, however, are limited...
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