The last manuscript from the lab is out! scMaSigPro to identify genes responsible for cell type fate decisions in #single-cell trajectory analyses. In collaboration with BioBam and under the Marie Skłodowska-Curie Actions INTERCEPT-MDS ITN project. tinyurl.com/2aksah72

Awesome work from Priyansh Srivastava, the Conesa Lab and BioBam teams!! Interested in #SingleCell trajectories? Check this out! 👀

SQANTI3 release alert🚨 Are you a SQANTI3 user? Go ahead and update your installation to v5.2.2, our newest release includes bug fixes, updates and improvements in classification of monoexons, genic introns, NIC and genic categories. Don't miss the update! github.com/ConesaLab/SQAN…

Very excited to share that our EOSC Portal OSCARS proposal was selected for funding! In the next 2 years, we'll collaborate with European Reference Genome Atlas to develop open-source pipelines for #SQANTI3 and #longreads supported genome annotation oscars-project.eu/oscars-first-o… ELIXIR Europe BCBHubCSIC

Our study on methods to detect subgenomic RNAs (sgRNA) is now out. This is work from Thomas Baudeau (from Camille Marchet @[email protected] and Mikаël Sаlson Mikaël Salson's groups), who visited my group last summer. doi.org/10.1093/nar/gk… 1/5

Me + Opentrons + KAUST on how you can automate PacBio Kinnex kits :-)

We've updated the PacBio Kinnex single-cell RNA SMRT Link v13.1 troubleshooting guide to cover what are the metrics you should expect and how to analyze not officially tested kits such as GEM-X. #bioinformatics pacb.com/wp-content/upl…

Use of 26 PacBio Iso-Seq cell line data to build a RNA foundation model LoRNA to predict transcriptome architecture, including isoform abundance, exonic structures, and variant pathogenicity. #bioinformatics biorxiv.org/content/10.110…

Sebra: PacBio Iso-Seq in pre-implantation embryo find novel isoforms rich in antisense and intergenic. Conserved in primates, suggesting driving recent evolution. pubmed.ncbi.nlm.nih.gov/37903791/

Super exciting to see what the future holds for nanopore beyond DNA and RNA sequencing nature.com/articles/s4158…

making a lot of pairwise alignments (PAF) and needed a way to confirm validity of both coordinates and alignment github.com/ekg/pafcheck

At #ECCB2024? Do not miss the highlight talk presentation of Conesa Lab member Alejandro Paniagua about our ELIXIR Europe tool #SQANTI3, at 10:15 h at Teatro Room. HiTSeq 2024 PacBio Oxford Nanopore LongTREC I2SysBio BCBHubCSIC . Thanks to CSIC INFRAS2024 for travel support!

Today I will be speaking at the Instituto de Neurociencias UMH-CSIC, hosted by Prof Angela Nieto BCBHubCSIC Casa de la Ciència CSIC València I2SysBio

BREAKING NEWS The 2024 #NobelPrize in Physiology or Medicine has been awarded to Victor Ambros and Gary Ruvkun for the discovery of microRNA and its role in post-transcriptional gene regulation.

This year’s medicine laureates Victor Ambros and Gary Ruvkun studied a relatively unassuming 1 mm long roundworm, C. elegans. Despite its small size, C. elegans possesses many specialised cell types such as nerve and muscle cells also found in larger, more complex animals,

I'll be taking part in a panel discussion at the BIA Techbio event on October 16. Excited for the discussion!

#Genomics is revolutionising how we understand #GeneticMaterial, offering incredible insights into how genes 🧬 function and interact. This session will explore how combining data from multiple #Biological layers—genomics, proteomics, #Metabolomics, and more—is unlocking new

Do not miss this awesome special issue! Lots of great contributions in LRS #genomics and #trancriptomics

Release of DeepVariant 1.8. Large speed improvement (~67% faster) via small model for easy sites. New Pangenome-aware option. Reduces error by ~30% for vg-mapped WGS ~10% for BWA WGS ~5% BWA exome. New config for custom model users, see release notes 1/3 github.com/google/deepvar…

Strobealign v0.16.0 has been released. It comes with both runtime and accuracy improvements. Full changelog here github.com/ksahlin/strobe…