Website: eurekalabs.ai GitHub: github.com/EurekaLabsAI 𝕏: Eureka Labs

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/

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

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!

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

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?

Intracellular spatial transcriptomic analysis toolkit (InSTAnT) | Nature Communications nature.com/articles/s4146…

Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing. #AlternativeSplicing #LongRead #Sequencing bioRxiv 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/…

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!

STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging | bioRxiv ⁦Dr. Jasmine Plummer 👩🏻‍🔬🧬🇨🇦🇺🇸⁩ ⁦Holger Heyn⁩ ⁦@pascual_reguant⁩ ⁦@eliseinsing⁩ ⁦CNAG⁩ ⁦Adelaide Centre for Epigenetics⁩ ⁦St. Jude Research⁩ 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)

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…

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 Earlham Institute covering everything from animal, bacteria, plants, humans, short+long seq, spatial - and more!

🥶🥶 #PSGARS I #UCL

A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq Nanopore long-read data biorxiv.org/content/10.110… #biorxiv_bioinfo

Three-dimensional spatial transcriptomics at isotropic resolution enabled by generative deep learning biorxiv.org/content/10.110… #biorxiv_bioinfo

My supervisor, MarioniLab , will be giving a keynote at the scverse conference. His contributions to single-cell and spatial transcriptomics have shaped much of the field, and I’m looking forward to hearing his perspective on where computational biology is headed.