Theo Nelson (@MakeBrainHappy) header
Theo Nelson (@MakeBrainHappy) profile picture

Theo Nelson

@MakeBrainHappy

Bioinformatics ; Nanopore Direct-RNA Sequencing & Epitranscriptomics @mason_lab

youtube.com/@makethebrainhappy-scientificex
Joined January 2017
  • Tweets230
  • Following114
  • Followers71
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Photo by Theo Nelson (@MakeBrainHappy)Photo by Theo Nelson (@MakeBrainHappy)Photo by Theo Nelson (@MakeBrainHappy)Photo by Theo Nelson (@MakeBrainHappy)Photo by Theo Nelson (@MakeBrainHappy)Photo by Theo Nelson (@MakeBrainHappy)Photo by Theo Nelson (@MakeBrainHappy)Photo by Theo Nelson (@MakeBrainHappy)Photo by Theo Nelson (@MakeBrainHappy)
Replying to @mason_lab @coregenomics @CatharineAquino @nanopore @mitenjain
We have been excited to implement the latest @nanopore models released at the Boston Community Meeting in @mason_lab. These are true multi-modification callers for inosine, m5C, m6A, and pseudouridine. The accuracy metrics are attached below. @Stoibs11
Image from Theo Nelson (@MakeBrainHappy)
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dkNET (@dkNET_Info) profile picture
dkNET@dkNET_InfoOct 19
📢 Join us this Friday for the #dkNET #webinar "A Hormone Cell Atlas Maps the Human #Endocrine System at Cellular Resolution" 🎤 Lijiang Fei, PhD, University of Cambridge 📅 Friday, Oct 23, 2026 | 11 AM–12 PM PT 🔗 dknet.org/about/blog/2952 #Endocrinology #SingleCell
Image from dkNET (@dkNET_Info)
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Chris Mason (@mason_lab) profile picture
Chris Mason
@mason_labOct 17
"Modulator Resolves Transcript-, Allele-, and Condition-associated RNA Modification Differences from Direct RNA Sequencing." biorxiv.org/content/10.64898… our lab's cool new algorithm and epitranscritpome analysis tool set led by Theo @MakeBrainHappy in partnership with the Horner lab. Check it out!
Modulator Resolves Transcript-, Allele-, and Condition-associated RNA Modification Differences from...

Modulator Resolves Transcript-, Allele-, and Condition-associated RNA Modification Differences from...

Nanopore direct-RNA sequencing (DRS) reports RNA modifications on single molecules, but there is no comprehensive algorithm for processing, aligning, and differentiating base modifications across...

biorxiv.org
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Congratulations to Michael Goneos for delivering an excellent prize-winning talk: "Pilot discovery of allele-specific RNA modifications." Thank you D.C. for a great time at ISMB 2026! #ISMB #HITseq #Nanopore @mason_lab @ISMBinfo @iscb
Image from Theo Nelson (@MakeBrainHappy)
Image from Theo Nelson (@MakeBrainHappy)
Image from Theo Nelson (@MakeBrainHappy)
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Evan Appleton (@evappleton) profile picture
Evan Appleton@evappletonJun 22
Hot off the press at @naturemethods - our work to Derive elephant iPSCs! nature.com/articles/s41592-0…
Derivation of elephant induced pluripotent stem cells

Derivation of elephant induced pluripotent stem cells

Nature Methods - This study reports the first successful derivation of elephant induced pluripotent stem cells.

nature.com
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Cancer Cell (@Cancer_Cell) profile picture
Cancer Cell@Cancer_CellMay 1
Online Now: Activated T cell extracellular vesicle DNA transfer enhances antigen presentation and anti-tumor immunity dlvr.it/TSKVFp
Image from Cancer Cell (@Cancer_Cell)
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Chris Mason (@mason_lab) profile picture
Chris Mason
@mason_labMay 1
"Activated T cell extracellular vesicle DNA transfer enhances antigen presentation and anti-tumor immunity" sciencedirect.com/science/ar…
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Anne Loft (@AnneloftSdu) profile picture
Anne Loft@AnneloftSdu14 May 2025
Check out our new roadmap for single cell analyses of adipose tissue at @NatMetabolism 🧐 Thrilled to share our work put together by amazing colleagues from Adipose Bionetwork in @humancellatlas 🤩 Huge thanks to my fellow co-coordinators @susmandrup Evan D. Rosen and Margo Emont
Nature Metabolism (@NatMetabolism) profile pictureNature Metabolism
@NatMetabolism13 May 2025
Towards a consensus atlas of human and mouse adipose tissue at single-cell resolution go.nature.com/43rCoet
Towards a consensus atlas of human and mouse adipose tissue at single-cell resolution

Towards a consensus atlas of human and mouse adipose tissue at single-cell resolution

Nature Metabolism - In this Review, the authors present a roadmap towards achieving consensus on development, analysis and interpretation of single-cell transcriptomics data in adipose tissue,...

nature.com
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Simon Duerr (@simonduerr) profile picture
Simon Duerr@simonduerr28 Oct 2024
This is great! @NIAIDNews have launched a collection of public domain illustrations (currently 550 individual icons) bioart.niaid.nih.gov/
Image from Simon Duerr (@simonduerr)
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Our work from the @Axiom_Space Ax-2 missions has been published! Thank you to Dr. Bader Shirah for leading this monumental effort, our partners across academia & the team at @IIAS_NLC for making this happen. Truly a good year for space-based neuroscience research. 🧠🚀👩🏽‍⚕️🏥🌠
Image from Dr. Shawna Pandya (@shawnapandya)
Image from Dr. Shawna Pandya (@shawnapandya)
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BioDecoded (@BioDecoded) profile picture
BioDecoded@BioDecoded26 Feb 2022
Contamination detection in genomic data: more is not enough | Genome Biology genomebiology.biomedcentral.… #BioInformatics
Image from BioDecoded (@BioDecoded)
Image from BioDecoded (@BioDecoded)
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Do you remember when you joined Twitter? I do! #MyTwitterAnniversary
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Theo Nelson retweeted
dana_peer (@dana_peer) profile picture
dana_peer@dana_peer13 Jan 2022
(1) Finally out, after one of the most painful and long reviews (with nitpicky reviews, see my last comment) is a method that I am extremely proud of and excited about. One of the best in my career: nature.com/articles/s41592-0…
CellRank for directed single-cell fate mapping

CellRank for directed single-cell fate mapping

Nature Methods - CellRank infers directed cell state transitions and cell fates incorporating RNA velocity information into a graph based Markov process.

nature.com
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🎮 Multiplayer IGV, anyone? Here's a sneak peek of a prototype I built to enable scientists to collaborate on a shared IGV.js view. It uses WebSockets and Cloudflare Durable Objects to sync state.
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🩹Bioprinting bandages 🩺Cancer research 👕Space stain remover 🔬Student experiments And more will launch aboard the next @Space_Station commercial resupply launch! Explore the research: go.nasa.gov/339gHDD

Science Launching on SpaceX's 24th Cargo Resupply Mission to Station

The 24th SpaceX cargo resupply services mission, targeted to launch in late December from Kennedy Space Center, carries scientific research and technology demos to the International Space Station.

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Li Song (@mourisl) profile picture
Li Song@mourisl12 Nov 2021
Our newest work Chromap for fast chromatin profiling analysis is published on Nature Communications today! Chromap significantly reduces the pain of waiting in the era of deep sequencing and single-cell analysis. @haowen_zhang @XShirleyLiu @lh3lh3 nature.com/articles/s41467-0…
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Learn about partial fraction decomposition in a new article contributed to #makethebrainhappy makethebrainhappy.com/2021/0… #mathematics #partialfractions #decomposition #math #mathedu #matheducation
Theo Nelson retweeted
Li Song (@mourisl) profile picture
Li Song@mourisl19 Jun 2021
Are the ChIP-seq/(sc)ATAC-seq/Hi-C communities jealous of RNA-seq community for fast data processing with Kallisto/Salmon? With joint forces from @haowen_zhang @XShirleyLiu @lh3lh3, we are thrilled to present Chromap for fast chromatin profiling analysis. biorxiv.org/content/10.1101/…
Fast alignment and preprocessing of chromatin profiles with Chromap

Fast alignment and preprocessing of chromatin profiles with Chromap

We present Chromap, an ultrafast method for aligning and preprocessing high throughput chromatin profiles. Chromap is comparable to BWA-MEM and Bowtie2 in alignment accuracy and is over 10 times...

biorxiv.org
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sina (@sinabooeshaghi) profile picture
sina
@sinabooeshaghi24 May 2021
`ffq` (Fetch FastQ) is a new command line tool that makes it easier to find #sequencing data from the SRA / GEO / ENA. Importantly `ffq` does not download files, just file metadata / download links in #json format github.com/pachterlab/ffq developed by @lioscro and myself.
Image from sina (@sinabooeshaghi)
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New Video available on MakeTheBrainHappy - Scientific Exploration: #BioInformatics #computationalbiology #compbio #sequencing #rnasequencing - How do you calculate effective counts? youtube.com/watch?v=NkyAsXs5…
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A little feature of the latest #bioinformatics #computationalbiology #compbio video on MakeTheBrainHappy - Scientific Exploration, answering how you can calculate effective length in order to correct for length-based differences in RNA count matrices!
RNA-Seq Blog (@RNASeqBlog) profile pictureRNA-Seq Blog@RNASeqBlog29 Apr 2021
Here we describe what the mean fragment length represents and how to calculate the effective length for an #RNAsequencing experiment. - @MakeBrainHappy rna-seqblog.com/the-concepts…
The Concepts of Mean Fragment Length and Effective Length in RNA Sequencing

The Concepts of Mean Fragment Length and Effective Length in RNA Sequencing

Before we can perform normalization on the counts we need to calculate an effective length which is dependent on the mean fragment length...

rna-seqblog.com
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