#SIB Early Career Award very very deserved to Maria Brbic https://people.epfl.ch/maria.brbic, who is an outstanding #SingleCell #machinelearning scientist with a great commitment to equality and inclusivity in science and to #OpenSource #BC2basel #EDI

Marius Lange #BC2basel: increasing complexity of #SingleCell data leads to problems of temporal, spatial and spatio-temporal mapping. The solution proposed is optimal transport applications, implemented in Moscot:
https://moscot.readthedocs.io/en/latest/
https://www.biorxiv.org/content/10.1101/2023.05.11.540374v2 #SpatialTranscriptomics #scRNAseq

🎉 Exciting News!
This week has been a whirlwind of milestones and achievements that I'm thrilled to share with all of you!💛(1/5)

#academicchatter #cancerresearch #thesis #genomics #singlecell #bioinformatics

Senior Bioinformatician Hematology

Erasmus Medical Center

Come and join our team as a senior bioinformatician at the Erasmus MC, the Netherlands. #bioinformatics #haemonc

See the full job description on jobRxiv: https://jobrxiv.org/job/erasmus-medical-center-27778-senior-bioinformatician-hematology/?feed_id=55149

#ScienceJobs #hiring #research #bioinformatics #singlecell
Rotterdam #Net...
https://jobrxiv.org/job/erasmus-medical-center-27778-senior-bioinformatician-hematology/?feed_id=55149

#scRNAseq #singlecell #pathwayAnalysis
Seems really easy to use, and return good results:

ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis - ScienceDirect

https://www.sciencedirect.com/science/article/pii/S1535947620600159?via%3Dihub

Really interesting approach for #singlecell analysis: "Isolating salient variations of interest in single-cell data with contrastiveVI" by Ethan Weinberger from @suinleelab Preprint is available here: https://www.biorxiv.org/content/10.1101/2021.12.21.473757v3.full

As you may (or may not) have noticed, STRING v12.0 has been released! So what's new? #bioinformatics #singlecell #textmining
https://youtube.com/shorts/sdcmZWTHumw?feature=share

Spatial transcriptomics of plant-fungal interactions🌱🍄

New Preprint with Karen Serrano, Margot Bezrutczyk, Henrik Scheller, and @bcoli

"Spatial Co-transcriptomics Reveals Discrete Stages of the Arbuscular Mycorrhizal Symbiosis"

https://www.biorxiv.org/content/10.1101/2023.08.02.551648v1

@LBNLBioSci #plantmicrobial #symbiosis #microbiome #singlecell #transcriptomes #plants #fungi

GAGE-seq for 3D genome and transcriptome co-profiling within the same single cell
https://www.biorxiv.org/content/10.1101/2023.07.20.549578v1
#singlecell #transcriptome #Genomics

Excellent #singlecell @bioconductor workshop today at the #ismbeccb2023

I have update my {cellula} #Rstats package for #singlecell RNA-seq analysis with a few new things:

- removed a lot of obligatory dependencies to make first install light

- application of {tricycle} for cell cycle calculation, and a circular plot for the assignments

- color management with color vision deficiency-friendly palettes and other presets

- a third trajectory inference method (a simplified version of PAGA + DPT), although it is still very much a WIP

https://github.com/gdagstn/cellula

The new issue of @genomeresearch is now live. Follow the link to new research on #singlecell glucocorticoid immune response, interchromosomal rearrangement detection in cattle, and more! 🐄https://tinyurl.com/GenomeRes-33-6

New tool for multimodal single cell data integration
MultiVI: deep generative model for the integration of multimodal data
#singlecell #bioinformatics #python

Videos of the #SIB course “Gene expression made useful easily: tools and database of Bgee” (Frederic Bastian & @marcrr):
Introduction of trainers https://www.youtube.com/watch?v=vjrTq0fGCTk
Overview of Bgee https://www.youtube.com/watch?v=x8Fypkwlmuw
Data integration in Bgee https://www.youtube.com/watch?v=hTx4fk77DZ4
Bgee data access https://www.youtube.com/watch?v=5cbXWL9quCA
Bgee tools https://www.youtube.com/watch?v=iUSjT9wDbmU
#biocuration #bioinformatics #RNAseq #SingleCell #GeneExpression #training

This really weird title for a C. elegans scRNA-seq atlas reminds me of @Odedrechavi who said that "metazoan" in a paper abstract means the work is about fly or nematode.
https://www.science.org/doi/10.1126/sciadv.adg0506
#SingleCell #nematode #Metazoa

A few days left to register with early bird rate to our #BC2 #ISBSIB workshop "Standardization of single-cell metadata: an Open Research Data initiative" with Jason Hilton of #cellxgene & David Osumi-Sutherland #EBI #SingleCell #FAIRdata #bioinformatics #biocuration #HumanCellAtlas #FlyCellAtlas https://www.bc2.ch/tutorials-workshops

Very helpful & thorough assessment of the effect of background counts (ambient RNA, etc) on single-cell RNA-seq analyses: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02978-x #singlecell #compbio #openaccess

Computational Scientist

Icahn School of Medicine at Mount Sinai

Come join our team as a #computationalScientist: #multiOmics modeling of #myeloma, including #singleCell, #spatialTranscriptomics and #flowCytometry

See the full job description on jobRxiv: https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-computational-scientist-5/?feed_id=47998

#ScienceJobs #hi...
https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-computational-scientist-5/?feed_id=47998

Postdoctoral Researcher

Icahn School of Medicine at Mount Sinai

Come join our team as a #bioinformatics postdoc: #multiOmics modeling of #myeloma, including #singleCell, #spatialTranscriptomics and #flowCytometry

See the full job description on jobRxiv: https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-postdoctoral-researcher-4/?feed_id=47893

#ScienceJobs #hi...
https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-postdoctoral-researcher-4/?feed_id=47893

MT @: A great opportunity for #SingleCell omics, #MassSpec, & #imaging #MassSpec researchers to publish their advances on pushing tech towards single-cell analyses, sensitivity & resolution JPR is not only about proteins -- metabolites, lipids, glycans, drugs, exposome, all welcome!Theo @thalexandrov and I will serve as editors for a Special Issue of @JProteomeRes Single-Cell Omics

Submissions before January 31, 2024 can be included in the special issue.

Information: https://axial.acs.org/biology-and-biological-chemistry/call-for-papers-single-cell-omics?utm_source=twttr&utm_medium=sm&utm_campaign=IC001_ST0002D_T000331_jprobs_Single-Cell_Omics_Call_for_Papers&src=IC001_ST0002D_T000331_jprobs_Single-Cell_Omics_Call_for_Paper