@kudlalab

Group at @mrc_hgu @EdinUni_IGC @EdinburghUni, using synthetic biology and machine learning to understand genotype-phenotype relationships in RNA and proteins.

 Edinburgh, Scotland
Joined December 2020
  • Tweets63
  • Following125
  • Followers311
8Media
Codon optimization: #Pfizer #BioNTech vs #Moderna github.com/NAalytics/Assembl…
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Kudla lab retweeted
Joe Marsh@jmarshlab8 Jun 2024
Excited to see this work led by @kudlalab is now out, showing that PAX6 DNA binding measured in a yeast 1-hybrid deep mutational scan outperforms existing computational approaches for variant classification embopress.org/doi/full/10.10…

Deep mutational scanning quantifies DNA binding and predicts clinical outcomes of PAX6 variants

Molecular Systems Biology - Nonsense and missense mutations in the transcription factor PAX6 cause a wide range of eye development defects, including aniridia, microphthalmia and coloboma. To...

link.springer.com
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Kudla lab retweeted
Joe Marsh@jmarshlab19 Sep 2023
Excited to share our Perspective on the new AlphaMissense variant effect predictor tool from @GoogleDeepMind @ScienceMagazine science.org/doi/full/10.1126…

Predicting pathogenic protein variants

Machine-learning algorithm uses structure prediction to spot disease-causing mutations

science.org
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We have an open postdoctoral position on deep mutational scanning of transcription factor genes @kudlalab @mrc_hgu @varianteffects. Apply by 4th October! jobs.ac.uk/job/DCK493/resear…
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Hey @BBCSport, it's HOObert HOORcatch, not HUEbert HERcatch. In Polish, the letter "U" is always pronounced "OO". Simple.
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Kudla lab retweeted
MRC_HGU@mrc_hgu7 Feb 2023
Our partners @IIMCB_Poland are recruiting junior group leaders - excellent support available to start your independent career in this internationally recognised and vibrant scientific environment
IIMCB, Warsaw, Poland@IIMCB_Poland2 Feb 2023
📣 @IIMCB_Poland is recruiting‼ ✔ Who? Junior Group Leaders✌ 👉 All the details: bit.ly/3Y0fXYI #IIMCB #TeamingForExcellence #HorizonEurope #research #development #Science
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These are good points @lichuan_Bio @Xukang_AA.
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Thanks for these kind words @AbbeAtSea. Looking forward to meeting you and many other codon usage enthusiasts at our EMBO Workshop in Edinburgh next week!
The Lab LaBella@Lab_LaBella31 Mar 2022
Only 1 more week until the #EMBO_CU22 conference co-organized by Grzegorz Kudla @kudlalab at @EdinUni_IGC. Professor Kudla has made significant findings in the codon world by combining synthetic biology, next-gen sequencing, and computational modelling #3rdBaseThurs @rokaslab
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Nothing in genomics or transcriptomics makes sense except in the light of G/C content
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our paper is now out @Nature ! nature.com/articles/s41586-0… a 🧵on the excitement and value of Basic Science, DNA replication and repair, teamwork and collaboration, and the fundamental incompatibility of LEGO and DUPLO 1/n
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This is the best lab trick I've seen in ages.
Anca Farcas@AncaMFarcas2 Feb 2022
When your husband is a nerd who did his PhD in Scotland and uses IrnBru to stain his western blot membranes…it works amazingly if you ever run out of Ponceau!
Before

ALT Before

Nicely soaking

ALT Nicely soaking

Nicely stained

ALT Nicely stained

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Join us in Edinburgh for the 1st EMBO workshop on codon usage function, mechanism and evolution. Three weeks left to register!
MRC_HGU@mrc_hgu3 Feb 2022
Excited to be hosting an outstanding and diverse array of researchers with insight on the codon usage bias phenomenon. 1st EMBO workshop on codon usage function, mechanism and evolution at the Royal College of Physicians of Edinburgh, April 8-11, 2022 meetings.embo.org/event/21-c…

Codon usage: Function, mechanism and evolution

The degeneracy of genetic code allows 18 of the 20 standard amino acids to be encoded by two to six synonymous codons. Codon usage bias, the preference for certain synonymous codons is a feature of a…

meetings.embo.org
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Antibiotic resistance in the pathogenic bacterium Klebsiella pneumoniae mediated by a single synonymous mutation in outer membrane porin gene @TheFrankelLab @RouskinLab. biorxiv.org/content/10.1101/…
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Kudla lab retweeted
Bloom Lab
@jbloom_lab6 Dec 2021
We’ve created calculator that aggregates deep mutational scanning data to estimate how mutations to #SARSCoV2 RBD affect recognition by human polyclonal antibodies. The calculator emphasizes extensive antigenic change in #Omicron variant. jbloomlab.github.io/RBD_esca… (1/n)

An antibody-escape calculator for mutations to the SARS-CoV-2 receptor-binding domain

A key goal of SARS-CoV-2 surveillance is to rapidly identify viral variants with mutations that reduce neutralization by polyclonal antibodies elicited by vaccination or infection. Unfortunately,...

jbloomlab.github.io
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Add your name! Registration now open for the EMBO Workshop on RNA: Structure meets function, 27 June – 1 July 2022 in Åkersberga, Sweden meetings.embo.org/event/20-r… #EMBOrna

RNA: Structure meets function

High-throughput sequencing results in recent decades have revealed that transcription of the eukaryotic genome goes beyond coding regions and uncovered an overwhelming amount of novel functional RNAs…

meetings.embo.org
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New preprint!📜📢 "Structural features within the NORAD long noncoding RNA underlie efficient repression of Pumilio activity". A great collaboration between Sveta from my lab, @omerz213 @ericmiskalab @ericmiska and @kudlalab . What did we find? A 🧵 biorxiv.org/content/10.1101/… 1/11

Structural features within the NORAD long noncoding RNA underlie efficient repression of Pumilio...

It is increasingly appreciated that long non-coding RNAs (lncRNAs) carry out important functions in mammalian cells, but how these are encoded in their sequences and manifested in their structures...

biorxiv.org
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The #AI revolution in protein structure prediction continues, as researchers have unveiled a combination of programs that can determine which proteins are likely to interact with one another and what the resulting complexes look like. fcld.ly/ew2zce2

AI cracks the code of protein complexes—providing a road map for new drug targets

Software maps thousands of the partnered proteins that govern cell biology

science.org
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Kudla lab retweeted
MRC_HGU@mrc_hgu5 Nov 2021
Application is now for our 4 year #PhD programme including Human Genetics, Genomics and Disease and projects for International Quantitative Scientists. Closing date 7 January 2022, details here: ed.ac.uk/mrc-human-genetics-…
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Accessibility of translation initiation sites is the strongest predictor of heterologous protein expression in E. coli journals.plos.org/ploscompbi…

Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable...

Author summary Recombinant proteins are widely used as therapeutics, such as vaccines, monoclonal antibodies, hormones and enzymes. However, the success rate of recombinant protein production is...

journals.plos.org
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Kudla lab retweeted
MRC_HGU@mrc_hgu28 Sep 2021
We are recruiting for an early career group leader! Bring your cross-disciplinary expertise, innovative mathematical/computational approach to extract biomedical meaning from large datasets to help us understand the genetics of disease.Apply by October 21 elxw.fa.em3.oraclecloud.com/…
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🚨🚨RNA STRUCTURE SYMPOSIUM TODAY!🚨🚨 Schedule:
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