Mark R@markrobinsonca@{genomic.social,bsky.social}

statistical bioinformatics; canadian/swiss; #methodsmatter #rstats; open science advocate; grumpy towards prestige worshippers, excessive admin and bros.

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

Interested in benchmarking computational methods in computational biology, generally?

Save the date, submit an abstract, join us next March in Ascona!

Conference website:
https://t.co/wBqBh5yFj4

Please retweet and/or tell your colleagues!

[PCI Genomics @PCIgenomics]

@miriplass 📝 A recommendation of this preprint from @GermainPl, Jiayi Wang, and @markrobinsonca
: https://t.co/PRGSfIuiyF

Thank you to the recommender and two reviewers for evaluating this manuscript! 🙌

[Lukas Weber @lmwebr]

We are excited to share our online book and preprint on “Orchestrating Spatial Transcriptomics Analysis with Bioconductor” (OSTA)!

[bioRxiv Bioinfo @biorxiv_bioinfo]

Analysis of anatomical multi-cellular structures from spatial omics data using sosta https://t.co/c72r08wXKQ #biorxiv_bioinfo

[Simone Tiberi @tiberi_simone]

DESpace2: a novel framework to compare spatial expression patterns between conditions (e.g., healthy vs. diseased), from spatial omics data.

Aim: identifying genes with distinct spatial structures (DSP) between groups of samples.

1/3

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

Guest Editors:
Mark Robinson, University of Zurich
Fritz Joachim Sedlazeck, Baylor College of Medicine
Hong-Bin Shen, Shanghai Jiao Tong University
Jean Yee Hwa Yang, The University of Sydney
Xin Maizie Zhou, Vanderbilt University

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

Heads-up that Genome Biology is starting a new benchmark collection ("Benchmarks v2.0"):
https://t.co/vwErrEPaQ1

[Malte Luecken @MDLuecken]

Looking forward to giving my talk on community-driven benchmarking via Open Problems tomorrow at the first Ascona benchmarking meeting. @markrobinsonca really knows how to put on a conference in this beautiful location! Half of my lab came along :).

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

Quick update. We have a pretty exciting lineup of topics/speakers in and around benchmarking that will be presented in Ascona at the end of the month:

https://t.co/CBJg0punVr

There are few registration slots left, so if you are interested to join us, get in touch.

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

Interested in benchmarking computational methods in computational biology, generally?

Save the date, submit an abstract, join us next March in Ascona!

Conference website:
https://t.co/wBqBh5yFj4

Please retweet and/or tell your colleagues!

[Siyuan Luo @Siyuan__Luo]

Excited to share our work on selecting validation metrics for single-cell and spatial omics! Learn to evaluate embeddings, graphs, clustering, and spatial domains with biological relevance. Discover poem, our R package with new spatially-aware metrics! https://t.co/6ki7DhmLEC

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

This is getting exciting. Over 20 abstracts submitted. The committee will be looking at them next week. Looking forward to these discussions.

There is still time to submit (due Monday 18th).

Google form link:
https://t.co/zGGZ9Xd60E

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

Interested in benchmarking computational methods in computational biology, generally?

Save the date, submit an abstract, join us next March in Ascona!

Conference website:
https://t.co/wBqBh5yFj4

Please retweet and/or tell your colleagues!

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

Abstract submission and pre-registration is now open:
https://t.co/zGGZ9Xd60E

(due November 18th 2024, 6pm, time zone of your choice)

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

Interested in benchmarking computational methods in computational biology, generally?

Save the date, submit an abstract, join us next March in Ascona!

Conference website:
https://t.co/wBqBh5yFj4

Please retweet and/or tell your colleagues!

[Anshul Kundaje @anshulkundaje]

https://t.co/QCtOIaybOj

Nice benchmark of single cell "foundation models" (scGPT, scFoundation) and GEARS (a GNN model) further hyped as "virtual cell models" against linear baselines on perturbation prediction.

Long-story short: they can't beat the linear baselines. 1/

[Anshul Kundaje @anshulkundaje]

Before folks jump to the next level with even bigger, more complex models, can u plz come together with others who have expertise on how to set up benchmarks & baselines to really test whether u r actually making progress? 3/

[Belinda Phipson @BelindaPhipson]

Yes!!!

@EurekaPrizes
@WEHI_research

[Stephen Turner 🦋 @stephenturner.us @strnr]

Weekly recap: What I'm reading this week in de-extinction and patent law, ATAC-seq benchmarking, large animal genomes, SV genotyping with long reads, cell type-specific enhancer prediction, AI in biosecurity, https://t.co/wI4QvdcFf2

[Clint Miller @clintomics]

New benchmarking study of 8 pipelines and 5 widely used methods for scATAC data analysis..includes embedding, graph and partition-based metrics and useful recommendations by data complexity and downstream tasks. Snakemake workflow: https://t.co/XxZnbBUZWp https://t.co/x9MH9Kbwpg

[Simone Tiberi @tiberi_simone]

*DifferentialRegulation* out in Biostatistics: https://t.co/dyWXV2QzwD

A Bayesian hierarchical method to identify differences in splicing dynamics (i.e. gene regulation) between conditions.

It works on bulk and single-cell RNA-seq.

Also on Bioconductor: https://t.co/dJeOSWoQMr

[UZH Science @UZH_Science]

We are #hiring!
Join our Department of Molecular Life Sciences @UZH_en as Assistant Professor #tenuretrack in "BioImaging and Data Analysis"!
https://t.co/aYAzlSDCPD
Apply until 30th June 2024 at https://t.co/ACtk2fnM93!

#BioVisionCenter #imageanalysis #computervision #AI #ML

[Maarten Vanhove @MPM_Vanhove]

Absolutely. To me, Gold OA is one of the most discouraging and wasteful aspects of practising science, propagating enormous inequality, gatekeeping, and Matthew effects.