@daSpliceIsRight

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

 Cambridge, MA
genes.mit.edu/burgelab/
Joined January 2018
  • Tweets202
  • Following56
  • Followers2.2K
64Media
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...

biorxiv.org
1
13
54
4,381
Congrats to Dr. Kowal on her PhD work reaching print! @ejkk0
Emma Kowal@ejkk026 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
1
1
4
728
Burge Lab retweeted
Emma Kowal@ejkk026 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
4
1
25
1,616
(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:
8
528
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/…
2
1
20
943
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!
3
305
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@ejkk030 Oct 2024
My PhD work is live on bioRxiv today! :) biorxiv.org/content/10.1101/…

Sequence determinants of intron-mediated enhancement learned from thousands of random introns

Spliceosomal introns are a ubiquitous feature of eukaryotic genes, whose presence often boosts the expression of their host gene, a phenomenon known as intron-mediated enhancement (IME). IME has been...

biorxiv.org
1
2
18
2,185
Great talk on KATMAP from @LaptopBiologist in the Burge lab (@daSpliceIsRight) - looking forward to applying this tool! #RNACanadaARN biorxiv.org/content/10.1101/…
3
7
834
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@mitlibraries8 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

MIT Prize for Open Data | Open Data @ MIT

To highlight the value of open data at MIT, and to encourage the next generation of researchers, the MIT School of Science and the MIT Libraries present the MIT Prize for Open Data. Congratulations...

libraries.mit.edu
2
6
1,533
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!
10
752
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
1
13
844
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
17
1,054
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...

biorxiv.org
1
9
45
4,219
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
1
5
19
2,764
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 - xitter.cf/daSpliceIsRight/status…
Burge Lab@daSpliceIsRight14 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 🧵👇

Quantifying negative selection in human 3’ UTRs uncovers constrained targets of RNA-binding proteins

Many non-coding variants associated with phenotypes occur in 3’ untranslated regions (3’ UTRs) and may affect interactions with RNA-binding proteins (RBPs) to regulate post-transcriptional gene...

biorxiv.org
712
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@nupharm113 Nov 2023
Preprint Alert: Molecular and Cellular Context Influences SCN8A Variant Function. doi.org/10.1101/2023.11.11.5… #SCN8A #ionchannels #epilepsy
1
2
16
3,804
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
1
3
739
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…
1
4
41
3,544
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
6
26
2,314
Thanks Xuebing! Excited to visit!
Xuebing Wu@wu_xuebing12 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.'
3
685
Load more