It's time to stop making t-SNE & UMAP plots. In a new preprint w/ Tara Chari we show that while they display some correlation with the underlying high-dimension data, they don't preserve local or global structure & are misleading. They're also arbitrary.🧵biorxiv.org/content/10.110…

It's finally out!✨Check out the latest 📰 from myself and @FOAylward in The ISME Journal where we recover & explore genomes of jumbo phages that occupy distinct niches throughout the ocean 🌊🧬🗺️🦠 This project has meant a lot to me✨hope you enjoy the read! nature.com/articles/s4139…

New review —> Discovery of Diverse CRISPR-Cas Systems and Expansion of the Genome Engineering Toolbox pubs.acs.org/doi/10.1021/ac…

Mirusviruses are plankton-infecting relatives of herpesviruses (nature.com/articles/s4158…). They were found after many years of genome-resolved metagenomic surveys of #TaraOceans using #anvio and #Evolution for guidance. Here is a blog covering this journey: anvio.org/blog/mirus-dis…

In silico methods for predicting functional synonymous variants genomebiology.biomedcentral.com/articles/10.11…

Here is a gif describing our use of "phylogeny-guided genome-resolved metagenomics" Cooking ingredients: (1) #TaraOceans ('omics) (2) A relevant marker gene (#phylogeny) (3) #anvio metabins (constrained binning) The #anvio metabins were key. More at anvio.org/blog/constrain…

What is happening in single-cell genomics?! A new paper by YUHAN HAO et al. on data "harmonization" nature.com/articles/s4158… claims to improve on previous work (LHS fig.). But that's just a trick. What it actually shows is that no method works (same fig. w/ full y-axis RHS). 1/🧵

16 resources for re-analyzing public expression data. 👇 🧵

Excited to hear @colinhillucc speak about the virome at Karolinska Institutet

Learn Bayesian statistics buff.ly/42j5pWf tidyverse code buff.ly/3a7iusA #rstats

Public data are a gold mine for bioinformatics. Ten Resources for easy access public genomic data: 👇 🧵

New community list to keep track of approaches and analytic methods for repeated measures #omics (single/multi-) studies in the style of Michael Love's awesome-multi-omics: github.com/smdabdoub/awes… #stats #RStats #bioinformatics #metagenomics #microbiome #metabolomics

Interested in 16S rRNA amplicon sequencing on Oxford Nanopore ? Check out our preprint (first-authored by the amazing Xuan.L), where we validate high-throughput UMI-based sequencing of 16S rRNA genes using Q20+ chemistry. TLDR: 3 is the magic number!🪄🧬 tinyurl.com/46pba94k (1/8)

Want to find the right resolution for #singlecell subpopulations in your #scRNAseq, #scATACseq, #scMultiome, #spatial, and other #omics data sets? I'm excited to share our new tool TMCI for #datavisualization! Pre-print: biorxiv.org/content/10.110… Code: github.com/schwartzlab-me…

Impressive work from @vagar112 Taka Inoue et al on shared and cell type specific activity of promoters and enhancers via lentiMPRA. Training and evaluating models of activity from biochemical and sequence features, and more. 1/3 x.com/vagar112/statu…

Our paper is out today! Bacterial genomics has exploded in recent years, but, with a few exceptions, researchers have ignored bacterial epigenomes. We analyzed hundreds of Bacteroides (and friends) isolates and found astonishing epigenomic diversity. rdcu.be/dgvAy

And finally, if like me you are excited about the prospects of "multi 'omics", i.e. paired metaG / metaT / other cool measurements on the same samples, keep an eye on data.microbiomedata.org (National Microbiome Data Collaborative ) 🤩

Out now in Nature Microbiology, from Bridget McGivern and the EMERGE team. We investigated a long held view in peatland systems- the enzyme latch theory- from a microbial perspective. DOE Office of Science U.S. National Science Foundation CSU College of Agricultural Sciences (1/n) nature.com/articles/s4156…

Vaping transforms your oral microbiome! 🦠 Our new npj Biofilms and Microbiomes study shows e-cig aerosols fuel dense, virulent, antibiotic-resistant biofilms. 👉 nature.com/articles/s4152… #Microbiome #Biofilms #Vaping #OralHealth #Research