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Burge Lab @daSpliceIsRight

We study gene expression & RNA processing (RBPs, splicing, transcription) using experimental and computational methods at @MITBiology!

Joined January 2018
  • Tweets 202
  • Following 56
  • Followers 2,176
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Burge Lab@daSpliceIsRight
10 Jul 2024
Excited to share our model for interpreting RNAseq data in terms of splicing factor regulation. "In the spirit of accuracy, all splicing factors are depicted as cats" - @LaptopBiologist biorxiv.org/content/10.1101/…

KATMAP: Inferring splicing factor activity and regulatory targets from knockdown data

It is well-established that splicing factors (SFs) regulate splicing in a position-dependent manner. However, despite extensive experimental work focused on this regulation, quantifying SF regulatory...

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Congrats to Dr. Kowal on her PhD work reaching print! @ejkk0
Emma Kowal@ejkk0
26 Feb 2025
My PhD project from @daSpliceIsRight Lab/@MITBiology is out now in @NAR_Open! Thanks for great feedback & pleasant review process. Absolutely thrilled to be sharing this work w the world 🥰🤪 now onto the next chapter... 🐈🐈‍⬛😸😻academic.oup.com/nar/article…
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Emma Kowal@ejkk0
26 Feb 2025
My PhD project from @daSpliceIsRight Lab/@MITBiology is out now in @NAR_Open! Thanks for great feedback & pleasant review process. Absolutely thrilled to be sharing this work w the world 🥰🤪 now onto the next chapter... 🐈🐈‍⬛😸😻academic.oup.com/nar/article…

Sequence-dependent and -independent effects of intron-mediated enhancement learned from thousands...

Abstract. Spliceosomal introns are a ubiquitous feature of eukaryotic genes, whose presence often boosts the expression of their host gene, a phenomenon kn

academic.oup.com
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(B)URGENT NEWS!!! Join us in congratulating Jen, a post-doc in our lab, who successfully completed a half-marathon. Brian, Jen's cat, dons her medal:
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We present newly-minted PhD, Dr. Kowal (@ejkk0)'s exciting work on how different intron sequences enhance gene expression! Read to discover what motifs create the strongest introns as well as other intriguing insights from her large-scale screen: biorxiv.org/content/10.1101/…

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Emma is also currently searching for a Boston-based scientist role where she can contribute her skills to a meaningful mission on a dynamic team. Reach out if you're looking for a molecular/computational biologist w/ deep expertise in RNA, splicing, gene expression, & NGS assays!
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Prashant Bhat@_prashantbhat
31 Oct 2024
Elegant study by @ejkk0 & @daSpliceIsRight identifying 5'UTR intron sequences that enhance mRNA expression. Cool to see the integ. reporter higher Dox leading to greater intron-med. enhancement. Suggests a feedback loop between transcription & splicing to boost gene expression!
Emma Kowal@ejkk0
30 Oct 2024
My PhD work is live on bioRxiv today! :) biorxiv.org/content/10.1101/…
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Krysta Coyle, PhD 👩🏽‍🔬@molecularkrysta
3 Oct 2024
Great talk on KATMAP from @LaptopBiologist in the Burge lab (@daSpliceIsRight) - looking forward to applying this tool! #RNACanadaARN biorxiv.org/content/10.1101/…
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MIT Biology@MITBiology
8 Oct 2024
Congratulations to Biograd Hannah Jacobs! She was recently selected as an MIT Prize for Open Data Winner for her project on detecting naturally variable human exons in publicly available RNA sequencing data to aid in understanding health and disease @daSpliceIsRight
MIT Libraries@mitlibraries
8 Oct 2024
Congratulations to the winners of the 2024 MIT Prize for Open Data! Celebrate the winners and hear about their projects Oct. 22 at Hayden Library. @scienceMIT @MITdusp @MIT_CEE @MITelectionlab @mitenergy @MITMechE @MITBiology @MIT_CSAIL @MITEECS @MIT_SRP ow.ly/nW2C50TG4SB
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Congratulations to Kira, PhD student in our lab, and Keegan, former technician for both winning poster awards at the recent GRC on Post-transcriptional Gene Regulation!
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CB lab head, Chris, is participating in a team Iron Man in 2 weeks with two other dads of daughters with epilepsy. He will be doing the swimming leg and they are raising funds for @CureEpilepsy to support more research. Support them here: gofund.me/b317230c
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Check out this feature on @MadeleineOudin- for her deeply inspiring efforts on epilepsy in her lab alternative splicing expertise from our lab, to understand SCN8A mechanisms, and help Margot - and other kiddos like her - get the treatment they need! now.tufts.edu/2024/03/25/tuf…

Tufts Researcher Takes on Epilepsy After Daughter’s Diagnosis

now.tufts.edu
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Want to understand how splicing decisions are actually made in the cell based on pre-mRNA sequence? PhD student Kayla McCue has been hard at work modelling just that, & we're very excited to announce that now you can read about it in her new preprint! biorxiv.org/content/10.1101/…

An Interpretable Model of pre-mRNA Splicing for Animal and Plant Genes

Pre-mRNA splicing is a fundamental step in gene expression, conserved across eukaryotes, in which the spliceosome recognizes motifs at the 3’ and 5’ splice sites (SS), excises introns and ligates...

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Check out our recent work on evolutionary constraint and #GeneticVariants in human 3' UTRs, now published with @SpringerNature in @NatureComms and available here! rdcu.be/duX2T

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See also: our thread breaking down some of the highlights of the methods and results of this work when it was released as a preprint - x.com/daSpliceIsRight/status…

Burge Lab@daSpliceIsRight
14 Dec 2022
New Burge Lab preprint! How do we interpret the impact of genetic variants in non-coding regions of the human genome? Led by Postdoc Scott Findlay, this work describes our efforts to validate classification of regulatory variants in 3ʹ UTRs: biorxiv.org/content/10.1101/… Short 🧵👇
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Madeleine Oudin@MadeleineOudin
13 Nov 2023
Alternative splicing matters for genetic diagnoses. Honored to be a part of this exciting work on the impact of splicing in SCN8A. Sodium channels undergo mutually exclusive alternative splicing, with higher 5N during development, shifting to exon 5A during early childhood.
Al George@nupharm1
13 Nov 2023
Preprint Alert: Molecular and Cellular Context Influences SCN8A Variant Function. doi.org/10.1101/2023.11.11.5… #SCN8A #ionchannels #epilepsy
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It's the season of decorative gourds 🎃💜 Bid on one of these stunning purple glass pumpkins, hand-made by grad student Connor Kenny, and you will also be supporting crucial, life-saving epilepsy research through the @SCN8AAlliance! givebutter.com/c/jGvNXz

Purple Glass Pumpkins for SCN8A

Hand-blown glass purple pumpkins from MIT

givebutter.com
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DHX15 is one of the helicases in the spliceosome. We found that it mediates splicing quality control by repressing the splicing of weak introns - but it can't do it alone! Teamwork makes the dream work, in the lab & in this paper, out now in Cell Reports! sciencedirect.com/science/ar…

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Neural Networks are often used as black box predictive tools, but do they have to be? biorxiv.org/content/10.1101/… Here we strive to create an interpretable model of RNA splicing based closely on the known binding & activity of RBPs, & improve RBP binding prediction along the way.

Improved modeling of RNA-binding protein motifs in an interpretable neural model of RNA splicing

Sequence-specific RNA-binding proteins (RBPs) play central roles in splicing decisions, but their exact binding locations and activities are difficult to predict. Here, we describe a modular splicing...

biorxiv.org
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Thanks Xuebing! Excited to visit!
Xuebing Wu@wu_xuebing
12 Oct 2023
Excited to welcome my PhD co-advisor Chris @daSpliceIsRight to visit us @ColumbiaSysBio on Oct 18. He will talk about 'Interpretable Models of RNA Splicing and Splicing Factor Activity.'
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