Tim Warwick

Bioinformatics | Chromatin | RNA | Epigenetics
Researcher
@BrandesLab, @goetheuni, @CPI_ExStra @trr267

[Tim Warwick @tim_warwick]

Read the preprint @ https://t.co/3BEH8XmUvZ and let us know how to improve RADIAnT, send feature requests, get help with problem-solving and more @ https://t.co/Dnnn0XnLdB

[Tim Warwick @tim_warwick]

This project is the hard work of Simonida Zehr, with massive input from @TheMarcelSchulz in the frame of @trr267 (funded by @dfg_public), with major contributions from many people from @BrandesLab (@goetheuni) and @AstraZeneca / @Cambridge_Uni (Alessandro Bonetti + Emma Walsh)

[Tim Warwick @tim_warwick]

and finally, we generated RADICL-seq libraries from control endothelial cells and #EndMT-stimulated cells, and show that RADIAnT can be used to identify dynamic #chromatin-associated #lncRNAs

[Tim Warwick @tim_warwick]

In a benchmarking experiment using #Malat1 RAP-DNA data as a positive dataset, we found that RADIAnT outperformed previously proposed methods in the accurate recall of Malat1-DNA interactions

[Tim Warwick @tim_warwick]

Using published data from mESCs, we show that RADIAnT detects consistent RNA-DNA interactions across different ligation methods and experiments. RADIAnT uses a genomic binning approach which can be scaled to the quality and depth of the data to maximise statistical power

[Tim Warwick @tim_warwick]

RADIAnT makes up the final step of reads-to-interactions pipeline, built with #Snakemake, which is customisable by the user with regard to species, method and more, enabling parallelised and reproducible analysis of RNA-DNA ligation data

[Tim Warwick @tim_warwick]

Do you want to detect #RNA-#DNA interactions from RADICL-seq, Red-C or GRID-seq, but lack a reliable method? Then try RADIAnT, our new statistical framework for calling robust, consistent interactions from RNA-DNA ligation methods https://t.co/3BEH8XmUvZ

[Tim Warwick @tim_warwick]

Therefore, we developed a statistical approach that accounts for these factors - RADIAnT. RADIAnT builds a dataset-specific background model from the input data, against which RNA-DNA interactions can be called in a manner that accounts for gene locus proximity and RNA expression

[Tim Warwick @tim_warwick]

Whilst working with these data types, we noted that they were hugely influenced by nascent transcription and RNA expression levels, leading to potential overrepresentation of close-range interactions and underrepresentation of long-range interactions

[Kurian Lab @KurianLab]

@EVanNostrandLab dive into the new mysteries of snoRNAs in this exciting article.

Includes:
-chimeric eCLiP to map snoRNA-target RNA interactions
- SNORD89 guided 2'-O methylation of U2 leading to splicing regulation
- SNORD3-rRNA processing

https://t.co/b5H9gYBOMC
👏👏👏👏👏

[Institute for Cardiovascular Physiology @BrandesLab]

Did you know that there is a second glutamine metabolism pathway that generates α-ketoglutarate?

Check out our new pre-print from @FlaviaRezendeF describing the pathway, now on bioRxiv: https://t.co/DkVYktl8yO

(1/4)

[Tim Warwick @tim_warwick]

It was a pleasure to be involved in the project, supported by @CPI_ExStra @trr267 @goetheuni @dfg_public and @dzhk_germany, conducted at @BrandesLab here in Frankfurt! (4/4)

[Tim Warwick @tim_warwick]

How do ubiquitous chromatin remodeling complexes alter accessibility of cell-type specific enhancers? We analysed genome-wide #RNA-#DNA interactions and found enrichments in RNA binding at SWI/SNF-bound enhancers (1/4)

[James A. Oo @JamesAOo7]

Happy to share our pre-print on #lncRNA recruitment of SWI/SNF to cell type-specific #enhancers.

We performed several sequencing experiments to reveal the mechanism for how the highly conserved and ubiquitously expressed SWI/SNF finds its DNA targets genome-wide.

[Tim Warwick @tim_warwick]

Using Hi-C data, we could show that these enhancers are functionally required for the expression of linked genes in endothelial cells (3/4)

[Marcel Schulz - @[email protected] @TheMarcelSchulz]

Final poster day #ISMBECCB2023 ! 308 : @tim_warwick presents a method to predict RNA:DNA:DNA interactions using novel RNA:DNA interaction codes. TriplexAligner is able to predict triplex targets for RNAs using local alignments. @trr267 @dzhk_germany @BrandesLab @iRnaCosi 1/3

[Tim Warwick @tim_warwick]

and in case you can’t make the talk I’ll also have a poster later on (no. 308) where we can talk in more detail (if the paper is still on the board)!

[Tim Warwick @tim_warwick]

For anybody at #ISMBECCB2023 interested in mechanisms of regulatory #RNA, I’ll be giving a talk on our recently published method on prediction of RNA-DNA interactions at 12:20 TODAY in the iRNA session! @BrandesLab @TheMarcelSchulz @trr267 @CPI_ExStra

[Tim Warwick @tim_warwick]

Read the manuscript here: https://t.co/5ZvD58nyaP

[Marcel Schulz - @[email protected] @TheMarcelSchulz]

Come and see our science in 4 talks over the next three days at #ISMBECCB2023 in #Lyon @dzhk_germany @CPI_ExStra @InstCardReg_FFM