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We developed a new method (phastSim) to simulate sequence evolution along huge phylogenies, in particular pandemic-scale ones like in SARS-CoV-2 doi.org/10.1101/2021.0… with Goldman Group Russ Corbett Conor Walker Lukas Weilguny Yatish Turakhia

For those of you who love to explain complex mutation clusters parsimoniously (who doesn't?), the final version of Conor Walker's paper is now out at journals.plos.org/plosgenetics/a… - also feat. Aylwyn Scally and Nicola De Maio. And me. Cool figures too: this 👇 is part of S.Fig 10

Postdoc position in Goldman Group Group at EMBL-EBI, to join new multinatl collab project creating proof-of-principle high-throughput nanopore device for determining amino acid sequence and identity of proteins Full details at embl.org/jobs/position/… <1/2>

Last call; closing date on Monday. Please apply! If you don't apply, at least promise me you'll RT or pass to a friend. x.com/EBIgoldman/sta…

The impressively huge scale of SARS-CoV-2 sequencing has really stretched our ability to do phylogenetics, and is leading to some fantastic advances in methods. Here's one that Nicola De Maio from the Goldman Group group at EMBL-EBI contributed to. x.com/emblebi/status…

We are re-advertising this position! Please check-out 👇 the original thread 👇, pass to anyone you think might be interested, share with colleagues, RT ... x.com/EBIgoldman/sta…

We are still looking to hire a postdoc bioinformatician on this fascinating project. Please read/RT/pass on to anyone who might be interested: x.com/emblebi/status…

Congrats to the 2021 EvolCompGen Talk & Poster awardees for #ismbeccb2021 Best talk - Elise Parey (Camille Berthelot @camilleberthelot.bsky.social lab) Best poster - Vignesh Sridhar (Vignesh Sridhar, JRaviLab) Honorable mentions Talks - Uno Punto c Conor Walker @matteodelabre Posters - Elliot Majlessi

Glad to see this out. Here, we track ~700 clones across >300 individuals over ~13 years to unravel key aspects of clonal haematopoiesis (when there are genetically-defined subpopulations of haematopoietic stem cells in your bone marrow).

Simulating pandemic-scale genome sequencing datasets, e.g to benchmark your new analysis methods? Try phastSim, now updated to include indels (biorxiv.org/content/10.110…) [1/2]

Really chuffed to share our latest work from Sanjana Lab out in @nature today (nature.com/articles/s4158…). We tested >12,000 genes to find positive regulators of T cell proliferation to be used for next-gen #immunotherapies. A thread...

Groundbreaking work from Nicola De Maio Goldman Group and colleagues "we rewrite the classical Felsenstein pruning algorithm so that we can infer phylogenetic trees on at least 10 times larger datasets with higher accuracy than existing maximum likelihood methods. "

We've known for a long time that a large fraction of noncoding GWAS hits are not currently explained by eQTLs. Why?? I'm excited to share our new preprint on this! Take home: GWAS and eQTL assays maximize power for different types of variants. (1/n) biorxiv.org/content/10.110…

This is a brilliant preprint. It describes an experimental method for separately sequencing the paternal and maternal genomes. This goes beyond the standard "experimental phasing" - the method can also tell which chr is maternal and which is paternal. biorxiv.org/content/10.110…

We've made a draft human pangenome! 47 haplotype-resolved assemblies, two reference genomes, and five pangenome graphs!

A few months ago we posted a pre-print regarding a new approach to likelihood-based phylogenetics at short divergence scales (e.g. genomic epidemiology). I have now further optimized the code and updated the preprint doi.org/10.1101/2022.0…

If you were looking for evidence that isoforms are cool, all-pervasive in the 🧠, and everybody should study them at the single cell level, our work on mouse development and brain-region variability from the Hagen Tilgner / @[email protected] lab is now live Nature Neuroscience! 1/ nature.com/articles/s4159…

Super excited to share my lab's latest work on quantifying the private information leakage from single cell count matrices. Led by very first postdoc in the g2lab, brilliant Conor Walker, we showed that individuals can be reidentified 1/n cell.com/cell/fulltext/…