Professor in #Genomics @Sorbonne_Univ_. Interested in omics, core facilities management, bioinformatics and time organization methods.
Paris, France
Joined August 2017
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With a special focus on Omics tools
#NewNProt: A Review providing a guide to packaging and #containerization of #computational methods bit.ly/4aT2w2W
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The #LRGASP study is out in @naturemethods! This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis for long reads such as @nanopore #RNAseq #Transcriptomics
We are excited to publish our second-ever Registered Report! The #LRGASP Consortium evaluated various methods for transcript identification and quantification using long-read sequencing technologies. @anaconesa @TheSheynkmanLab @TheBrooksLab @calizavi
nature.com/articles/s41592-0…
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A must-read for compared performance, sample compatibility, cost, and workflow of single-cell kits from 10 companies across four technology classes. #SingleCell #RNAseq
Comparative Analysis of Commercial Single-Cell RNA Sequencing Technologies biorxiv.org/content/10.1101/…
"Spatial data should not be specifically corrected for library size prior to analysis, and algorithms designed for #scRNAseq data should be adopted with caution." #SpatialTranscriptomics
“Library size confounds biology in spatial transcriptomics data” finally out in Genome biology!
TL;DR
- LS normalisation is bad for domain identification.
- Exercise caution in adapting scRNA-seq methods to ST
- New normalisation methods needed for ST
rdcu.be/dE93v
Stéphane Le Crom retweeted
Reliable, fully local RAG agents with Llama3
With the release of Llama3, there's high interest in agents that run reliably & locally (e.g., on your laptop).
Here, we show to how build reliable local agents using LangGraph and Llama3-8b from scratch.
As a example, we combine ideas from 3 advanced RAG papers (Adaptive RAG, Corrective RAG, and Self-RAG) into a single control flow in LangGraph.
We run this locally w/ open source embeddings c/o @nomic_ai, @trychroma vectorstore, @tavilyai for web search, and Llama3-8b via @ollama.
Code:
github.com/langchain-ai/lang…
Video:
youtu.be/-ROS6gfYIts
A very interesting article on the best practices to be applied when carrying out a methodological comparison of omics tools. #transcriptomics #NGS
Challenges and best practices in omics benchmarking go.nature.com/48UWPRf #Review by Thomas G. Brooks, Nicholas F. Lahens, Antonijo Mrčela & Gregory R. Grant @Penn @ITMATbioinf
Free to read: rdcu.be/dvPOj
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Stéphane Le Crom retweeted
Accessible #ResearchInfrastructures are key for fostering Europe’s innovation potential!
For the latest #HorizonEU INFRA call, we’ve received 163 research proposals with a requested budget of €1,038 billion💶
32 projects are expected to be funded🤝🏻
🔗 europa.eu/!XbQg4w
ALT A visual with a blue background and a microscope. It shows the received number of proposals and the corresponding budget requested for the three calls.
Stéphane Le Crom retweeted
🤖 So #ChatGPT wrote the first sentence of this @ElsevierConnect article. Any other parts of the article too? How come none of the coauthors, Editor-in-Chief, reviewers, typesetters noticed? How can this happen with regular peer-review? pubpeer.com/publications/CAA…
ALT https://pubpeer.com/publications/CAABBF887348FB2D1C0329E0A27BE6
Stéphane Le Crom retweeted
Finally out!
“Challenges and perspectives in computational deconvolution of genomics data”. Kudos Drs Garmire, Teschendorff & team!!
🙏🏼@GarmireGroup for including me. @naturemethods for publishing!
nature.com/articles/s41592-0…
Stéphane Le Crom retweeted
A paper in Nature group on the use of nanopores for single-molecule proteomics sequencing. This would still be a challenge for complex samples, but a step forward in the use of nanopores for #NextGenProteomics nature.com/articles/s41592-0…
Stéphane Le Crom retweeted
First TurBOT shipped and ready to go.
You'll be able to hear more about TurBOT at #ECCMID2024 and at London Calling 2024 (#nanoporeconf).
Learn more about TurBOT here: bit.ly/48N8oJI #WYMM
Stéphane Le Crom retweeted
The #ESFRI Landscape Analysis is now complete! Today the 87th Forum approved the #LandscapeAnalysis report, expected to be published by the and of May 2024
Read more about the LA process & the contributions of #ESFRIStakeholders👇
esfri.eu/landscape_analysis
#ResearchInfrastructures
Stéphane Le Crom retweeted
iconPCR: Super-Flexible qPCR Thermocycler Oft Dreamed, Now Delivered
#AGBT24 launch of N6 Tec iconPCR has me very excited
omicsomics.blogspot.com/2024…
Stéphane Le Crom retweeted
Researchers at the @CityUHongKong have used @nanopore direct #RNAsequencing to evaluate 10 computational tools developed for studying modifications on viral #RNAs. rna-seqblog.com/researchers-…
Stéphane Le Crom retweeted
#CTLS is pleased to announce that applications are now open for the 2024 CTLS Professional Development Course for #CoreFacility Staff.
ctls-org.eu/ctls-professiona…
#corefacilities #ProfessionalDevelopment #sharedresources #technologyplatforms
Stéphane Le Crom retweeted
I have updated the #NextGenSequencing specs for the @UltimaGenomics UG100 instrument, which a "deli-fridge" sized competitor to the $ILMN Illumina NovaSeqX "fridge-freezer" sequencer. Single-end median 300bp, 6Tbp 12h run, ~20,000 hg30x/year, $100/genome. bit.ly/ngsspecs
NanOlympicsMod – benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing rna-seqblog.com/nanolympicsm… via @@RNASeqBlog
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Stéphane Le Crom retweeted
Correcting myself about the Oxford @nanopore P2/P2 Solo: this is only for PromethION flowcells. So the smallest combo covering all flowcell sizes currently is: MinION Mk1b (USB-C version) and P2 Solo.
