CompBio Postdoc interested in HumanGenetics, NeuroEpigenomics & Addiction @unige_en
Geneva, Switzerland
Joined December 2014
- Tweets349
- Following415
- Followers262
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Dr. Anna Ramisch retweeted
🔥🧬Finally out!🧬🔥 Check out our latest study in Nature Genetics uncovering a surprising phenomenon of convergent co-regulated promoters cocoProms doi.org/10.1038/s41588-024-0…
🧑🤝🧑I'm happy to be part of such an amazing team!
🧵
Dr. Anna Ramisch retweeted
Very excited to share that our manuscript on cis-eQTL analysis of adipose tissue gene expression in 2,344 samples is now out in Nature Genetics
rdcu.be/d5ov4
See thread from lead author @SarahBrotman below
I’m excited to share that this manuscript is now published in Nature Genetics! 🧪🧬 🖥️
nature.com/articles/s41588-0…
The AdipoExpress data can be accessed here: zenodo.org/records/13845120
An interactive browser of the colocalization results can be accessed here: adipose.colocus.app
Dr. Anna Ramisch retweeted
Delineating the effective use of self-supervised learning in single-cell genomics @NatMachIntell @fabian_theis nature.com/articles/s42256-0…
Dr. Anna Ramisch retweeted
I'm very excited to share that I’ve started as a group leader @karolinskainst. I am looking for curious, enthusiastic and collaborative postdocs and assistants (pre-PhD) to join us to decipher regulation of hypoxia cell states that govern systems oxygen homeostasis 1/3
Dr. Anna Ramisch retweeted
New benchmarking study of 8 pipelines and 5 widely used methods for scATAC data analysis..includes embedding, graph and partition-based metrics and useful recommendations by data complexity and downstream tasks. Snakemake workflow: github.com/RoseYuan/sc_chrom… genomebiology.biomedcentral.…
Dr. Anna Ramisch retweeted
Really happy for @aline_real25 to be getting this out. Major implication for me is I've always assumed gwas hits will be explained by expression as it has to mediate then. But here @aline_real25 shows these expression effects can take many forms, not all picked up by common tech
I am excited to share our new preprint with @anavinuela, @AnnaRamisch, @arnsbr, and @dermitzakis! We used direct RNA long-read seq on 60 LCLs from the 1000 Genomes Project to study genetic regulation of transcript abundance & RNA modifications (m6A).
researchsquare.com/article/r….
So happy that our preprint is finally out! If you're interested in the advantages of long-read direct RNA sequencing in population studies, this is for you.
I am excited to share our new preprint with @anavinuela, @AnnaRamisch, @arnsbr, and @dermitzakis! We used direct RNA long-read seq on 60 LCLs from the 1000 Genomes Project to study genetic regulation of transcript abundance & RNA modifications (m6A).
researchsquare.com/article/r….
Dr. Anna Ramisch retweeted
I am excited to share our new preprint with @anavinuela, @AnnaRamisch, @arnsbr, and @dermitzakis! We used direct RNA long-read seq on 60 LCLs from the 1000 Genomes Project to study genetic regulation of transcript abundance & RNA modifications (m6A).
researchsquare.com/article/r….
Dr. Anna Ramisch retweeted
We are looking for a bioinformatician @cdf1530 @CirbCdf in Paris to analyse genomic/epigenetic datasets🧬 in the context of a synergy @ERC_Research long term program. See below and apply😎 RT🙏
Dr. Anna Ramisch retweeted
‼️New Epigenetics Review ‼️
Read here at @GenesDev where we discuss brief history of various epigenetic modulator classes 🧬, their links to multiple disease types 😷, and their potential for (combined or novel) therapeutic targeting 💊!
m.genesdev.cshlp.org/content…
Dr. Anna Ramisch retweeted
Check out our lab's recent #preprint by Hanna Schwaemmle and our collaborators @unige_en. We asked how do cells assemble functional SWI/SNF chromatin remodeling complexes? The key is to make just the right amount of each subunit!
biorxiv.org/content/10.1101/…
Dr. Anna Ramisch retweeted
Des scientifiques de l’#UNIGE ont identifié les séquences génétiques régulant l’activité des gènes responsables de la croissance osseuse.
@guillaumeandrey @F_Darbellay
#science #médecine #recherche #génétique
ow.ly/cfek50SizmR
Dr. Anna Ramisch retweeted
Figeno, my visualization tool for genomics🎨🧬, is now published in Bioinformatics! doi.org/10.1093/bioinformati…
It can generate publication-quality figures for sequencing data along genomic coordinates: bigwig, HiC, @nanopore data with base modifications, and WGS with CNAs and SVs.
Dr. Anna Ramisch retweeted
How do enhancers work over distances that sometimes exceed megabases? Excited to share our work led by @gracecbower where we uncover a unique sequence signature globally associated with long-range enhancer-promoter interactions in developing limb buds: biorxiv.org/content/10.1101/… 1/
Dr. Anna Ramisch retweeted
Characterizing >100,000 sequences in primary neurons and organoids and deep learning to decode regulatory activity. Amazing work from @Chengyu_Deng_, @seawhalen, Katie Pollard, @LabNowakowski and others as part of #PsychENCODE in @ScienceMagazine.
science.org/doi/10.1126/scie…
Dr. Anna Ramisch retweeted
Ana @anavinuela is motivating us to look at eQTLs beyond gene counts to transcript counts from long read sequencing data
Ana et al used @oxfordnanopore to generate 🧬 data
#BoG24
Dr. Anna Ramisch retweeted
Excited to share with the single-cell community the most recent work of @tmontsay and @AEsteveCodina from @cnag_eu, something we think will be a game-changer in #scRNAseq quality control: biorxiv.org/content/10.1101/… @biorxivpreprint
Get ready for the tweetorial!
1/10
Dr. Anna Ramisch retweeted
Inspired by @lpachter and team's exploration of scRNA-seq pipelines, we face similar challenges in scATAC-seq, only magnified! After 5 years of tackling these inconsistencies with my advisor @JunhyongKim , Here is a summary (and some solutions😃) 1/n #Genomics #Bioinformatics
The choice of whether to use Seurat or Scanpy for single-cell RNA-seq analysis typically comes down to a preference of R vs. Python. But do they produce the same results? In biorxiv.org/content/10.1101/… w/ @Josephmrich et al. we take a close look. The results are 👀 1/🧵
Dr. Anna Ramisch retweeted
Excited to share Nicheformer! Led by @Alejandro__TL & @AnnaCSchaar, Nicheformer is a foundation model for single-cell & spatial omics. Its innovation is going beyond disassociated analysis to capture & predict local tissue context at single-cell level. biorxiv.org/content/10.1101/…
Dr. Anna Ramisch retweeted
The difference in @10xGenomics' Cell Ranger's default between version 6 and 7 is discussed in this thread, but it's such a big deal that it's worth its own thread.
tl;dr: in v7 Cell Ranger changed how it produces the gene count matrix leading to a huge difference in results. 1/
The choice of whether to use Seurat or Scanpy for single-cell RNA-seq analysis typically comes down to a preference of R vs. Python. But do they produce the same results? In biorxiv.org/content/10.1101/… w/ @Josephmrich et al. we take a close look. The results are 👀 1/🧵