Kévin Lebrigand, PhD
@kevinlebrigandHead bioinformatics platform @IPMC_sophia, Nice, France. Single Cell, Nanopore, Spatial transcriptomics
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Spatial isoform Transcriptomics (SiT) is now published in @NAR_Open Combining @10xGenomics #Visium and @nanopore long-read, we explore the spatial landscape of gene expression isoforms in mouse brain sections. @pbarbry @joalunatkthse @fr_genomics @CNRS doi.org/10.1093/nar/gk…
Please join us for our free Technology Live Virtual Symposium on Spatial Biology this October 29th! natureconferences.streamgo.live/spatial-biolog… Speakers include Rong Fan, Andrea Radtke, Long Cai, Sarah Teichmann and many more!
Most protein function predictors only make predictions for labels seen in training. We used LLM embeddings of text describing protein function to train ProtNote, which can generalize to new functional labels described in free text. Code is available for everybody to try!
Single cell folks @ #LRUA24 - if you're interested in single cell #longread sequencing consider registering interest to our next symposium! This annual meeting held @EarlhamInst covering everything from animal, bacteria, plants, humans, short+long seq, spatial - and more!
🗓️ Mark your calendars! The Norwich #SingleCell and #Spatial Symposium with @biouea returns in 2025. Register your interest now to join us 18-19 June, exploring the latest technologies, research, and applications in single-cell and spatial genomics. okt.to/S6uOYH
We are excited to introduce LoRNA-SH, a frontier RNA foundation model that leverages long-read transcriptomics and long-context inputs to learn and predict the transcriptome architecture with base-pair resolution: biorxiv.org/content/10.110…
🧑💻With CellWhisperer, your personal single-cell RNA-seq expert and assistant is waiting to talk to you! • Watch a short demo & try it out: cellwhisperer.bocklab.org • Analyze your own data: github.com/epigen/cellwhi… • Read the preprint on bioRxiv: biorxiv.org/content/10.110… (7/9)
STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging | bioRxiv @DrJasPlummer @hoheyn @pascual_reguant @eliseinsing @cnag_eu @ACEpigenetics @StJudeResearch biorxiv.org/content/10.110…
This article completely misses the point. A major issue in biology right now is that engaging in data generation does not demand a substantial time investment in bioinformatics research. cell.com/cell/fulltext/…
🚨 Mark your calendars! The "Trans Mucus Network" symposium is happening from Nov 28-30, 2024, in Lille! This event brings together multidisciplinary expertise. Find the program, registration, and abstract submission details here: transmucusnetwork2024.univ-lille.fr Please share!
Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing. #AlternativeSplicing #LongRead #Sequencing @biorxivpreprint biorxiv.org/content/10.110…
Intracellular spatial transcriptomic analysis toolkit (InSTAnT) | Nature Communications nature.com/articles/s4146…
nature.com/articles/natur… This work tried to decompose the factors that influence protein abundance. Has similar work been done for transcript abundance? i.e. how predictive is chromatin accessibility and the dna sequence itself in predicting transcript abundance?
Learning how to share my scientific talks from home (v5) In this abbreviated talk, I discuss considerations for #geneexpression count normalization in #singlecell imaging-based #spatiallytranscriptomics 📽️: youtu.be/phzYB9rmcEg?si… #bioinformatics #dataanalysis #AcademicTwitter
Reading the reviews of a rejected proposal makes my blood boil. R3 states that the project doesn't develop a new methodology but "only" novel bioinformatics methods. How long will this disregard for computational research continue? Try to do your sequencing data analysis by hand!
Now is the time to submit abstracts for #LRUA24! This is a great opportunity to share your long-read work with leading experts. Both talks and posters will be selected For submission, visit the conference website: lrua2024.se Abstract deadline is Aug 21st
Recently @NimwegenLab wrote "the single-cell genomics/epigenomics field is by far the most dysfunctional that I have ever encountered." x.com/NimwegenLab/st… Same for me. The normalization of this situation is super frustrating and very, very sad. 5/
I'm sorry but I honestly feel that this kind of shock-and-awe approach to science is doing terrible damage. I'm a theorist that has interests spanning multiple areas but the single-cell genomics/epigenomics field is by far the most dysfunctional that I have ever encountered. 1/n
Website: eurekalabs.ai GitHub: github.com/EurekaLabsAI 𝕏: @EurekaLabsAI
Today we report in @natBME the systematic application of six recent prime editing developments to enable efficient and functional correction of CFTR F508del, the predominant mutation that causes cystic fibrosis (CF), in primary airway cells from CF patients.…
New research from our group. CapTrap-seq, a library preparation protocol for high-fidelity full-length RNA sequencing rdcu.be/dL3z with @carninci @buszczynska and others. The paper in @NatureComms includes a link to a layman version of the paper in #Catalan (#Català)
Spatial transcriptomics and @nanopore long reads? Yes you can. See @kevinlebrigand et al 2023 NAR publication on spatial landscape with long reads! academic.oup.com/nar/article/51…
Are computational biologists the drivers of research? 7 years ago I co-wrote an editorial about how computational biologists are no longer just supportive, but are now running the show. Today I would write how every biologist should also be computational. genomebiology.biomedcentral.com/articles/10.11…
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