Профиль

Alex Crits-Christoph

Computational microbiologist I like to post about: microbial genomics, microbial ecology, evolution, micro+plant biotechnology, climate, symbiosis, virology, ag, sci publishing and policy

5,1 тыс. подписчиков1,9 тыс. подписок2,2 тыс. постов
Публикации
⟳ Репост от Alex Crits-Christoph
Alison Feder

A few months ago, @elena-romero.bsky.social published a paper showing that HIV escape from broadly neutralizing antibody 10-1074 is driven by very recurrent mutation. In her latest, she asks - just how soft are the signatures of these sweeps? www.biorxiv.org/content/10.6...

Haplotype and diversity signatures of ultra-soft selective sweeps in HIV-1Many urgent medical and agricultural challenges are driven by resistance evolution via soft selective sweeps of multiple simultaneous mutations. Standard approaches to detect these mutations involve g...www.biorxiv.org
⟳ Репост от Alex Crits-Christoph
Nature Reviews Microbiology

New online! Eggerthella lenta: metabolism, pathogenesis and therapeutic implications

Eggerthella lenta: metabolism, pathogenesis and therapeutic implicationsNature Reviews Microbiology, Published online: 23 July 2026; doi:10.1038/s41579-026-01344-5Advancing microbiome research beyond well-studied bacterial species is key to understanding the full functional diversity and potential of the human gut microbiome. In this Review, Turnbaugh and colleagues explore the unique metabolism and pathogenic potential of Eggerthella lenta, supporting the feasibility and utility of studying diverse human-associated bacterial species.dlvr.it
⟳ Репост от Alex Crits-Christoph
Yang Liu

When we talk with AI researchers, one question comes up most frequently: do you have datasets focused on mutations at key protein positions? Until now, building libraries for that usually meant a lot of DNA synthesis. We developed HGT-DGR as a faster and cheaper way to make them.

bioRxivpreprint

Continuous target-specific mutagenesis and rapid gene evolution by diversity-generating retroelements in Escherichia coli https://www.biorxiv.org/content/10.64898/2026.07.21.739853v1

⟳ Репост от Alex Crits-Christoph
Nadine Ziemert

Looking for BGCs in large metagenomic datasets? Our new biorxiv preprint introduces metaSMASH, a scalable fork of antiSMASH designed specifically for metagenome-scale BGC detection and analysis : www.biorxiv.org/cgi/content/... Thanks @canerbagci.bsky.social and @kblin.bsky.social ❤️

metaSMASH: Scalable Biosynthetic Gene Cluster Detection for Large Metagenomic AssembliesantiSMASH is widely used for biosynthetic gene cluster (BGC) detection and annotation, but its standard workflow is poorly suited to large metagenomic assemblies, where massive contig counts create severe runtime bottlenecks and complicate downstream result exploration. We present metaSMASH, a re-engineered fork of antiSMASH for metagenome-scale BGC analysis. metaSMASH preserves the original antiSMASH detection and annotation logic while introducing streaming, memory-bounded execution, record-level parallelisation, optional output filtering, and an interactive dashboard for large result sets. Across 25 benchmark metagenome datasets, metaSMASH reproduced identical BGC detection results while dramatically reducing computational cost. Relative to the default antiSMASH configuration, metaSMASH was a geometric-mean 38x faster. It also outperformed an ad hoc chunked antiSMASH workflow: in the default configuration it achieved a geometric-mean 2.9x speed-up and 1.7x lower peak memory, and with extended-analysis modules enabled it was 2.7x faster and used 3.1x less memory while completing all datasets, whereas the ad hoc workflow ran out of memory on the two largest assemblies. By substantially reducing the computational burden of large-scale metagenome analysis without sacrificing result equivalence, metaSMASH makes routine mining of assembled metagenomes more practical and provides a scalable foundation for natural product discovery from complex microbial communities. ### Competing Interest Statement The authors have declared no competing interest. German Center for Infection Research, TTU Novel Antibiotics 09.716 Volkswagen Foundation, 0072511-00www.biorxiv.org
Alex Crits-Christoph

There are a lot of very wrong things in the OSTP report, but this one is just silly for multiple reasons? The average tenure of an employee at unicorn tech and biotech startups in SF is just 2-4 years. www.inc.com/business-ins... (Maybe just a bit higher post 2022 slump?)

Here's the Average Tenure for Tech Workers in Silicon Valley's Top 15 CompaniesA new report shows that software and internet companies had the highest employee turnover in 2017, compared with other major industries.www.inc.comCarl T. Bergstrom

15. I keep coming back to this line. It is willful misrepresentation of our federal funding agencies' mission beyond discovery: developing that R&D workforce (and a pipeline of ideas) that flow into the private sector so beloved to our author. We employ trainEES because trainING is what we do.

⟳ Репост от Alex Crits-Christoph
Steven Robbins

In addition to GC and strain bias, certain taxa showed systematically underestimated completeness via CheckM1 and 2, so historically much more likely to get erroneously thrown away in fragmented short read MAGs—a 3rd reason for the existence of Ghost Taxa. A sub-🧵. bsky.app/profile/stev...

Steven Robbins

It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.nature.com/articles/s41...

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