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This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan Albert,
Zero-shot evaluation reveals limitations of single-cell foundation models | Genome Biology | Full Text (genomebiology.biomedcentral.com)
Foundation models such as scGPT and Geneformer have not been rigorously evaluated in a setting where they are used without any further training (i.e., zero-shot). Understanding the performance of models in zero-shot settings is critical to applications that exclude the ability to fine-tune, such as discovery settings where labels are unknown. Our evaluation of the zero-shot performance of Geneformer and scGPT suggests that, in some cases, these models may face reliability challenges and could be outperformed by simpler methods.
submitted by: Istvan Albert
GitHub - louisaslett/kalis-bmc: Sources and materials for kalis R package paper (github.com)
kalis: A Modern Implementation of the Li & Stephens Model for Local Ancestry Inference in R
Blog post: https://kalis.louisaslett.com/articles/lct_example.html
submitted by: Istvan Albert
On the ancestry and evolution of the extinct dire wolf | bioRxiv (www.biorxiv.org)
Dire wolves (Aenocyon dirus) are extinct predators of Pleistocene North America. Although phenotypically similar to living wolves (Canis lupus), dire wolves have yet to be placed confidently in the canid family tree. We generated 3.4x and 12.8x paleogenomes from two well-preserved dire wolves dating to > 13,000 and > 72,000 years ago, and estimated consensus species trees for these and 10 canid species. Our results revealed that ~2/3 of dire wolf ancestry is derived from a lineage sister to the clade comprising the gray wolf, coyote, and dhole, and the remaining ~1/3 from a lineage near the base of Canini diversity. We identified 80 genes evolving under diversifying selection in dire wolves.
submitted by: Istvan Albert
Refining filtering criteria for accurate taxonomic classification of ancient metagenomic data | bioRxiv (www.biorxiv.org)
axonomic profiling is a key component of ancient metagenomic analysis, however it is also susceptible to false-positive identifications. In particular, classification tools from the Kraken family, such as Kraken2 and KrakenUniq, are highly sensitive to the choice of filtering options. To address this issue, various filtering approaches have been proposed. In this study, I conduct a comprehensive benchmarking of different filtering strategies using simulated microbial and environmental ancient metagenomic data. I evaluate these approaches based on the balance between sensitivity and specificity of ground truth reconstruction (F1-score), and propose an optimal thresholding strategy tailored to specific sequencing depths in ancient metagenomic datasets.
submitted by: Istvan Albert
A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines | Nature Methods (www.nature.com)
To evaluate the ability to study RNA transcript expression, we profiled seven human cell lines with five different RNA-sequencing protocols, including short-read cDNA, Nanopore long-read direct RNA, amplification-free direct cDNA and PCR-amplified cDNA sequencing, and PacBio IsoSeq, with multiple spike-in controls, and additional transcriptome-wide N6-methyladenosine profiling data. We describe differences in read length, coverage, throughput and transcript expression, reporting that long-read RNA sequencing more robustly identifies major isoforms.
submitted by: Istvan Albert
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