Bren Professor of Computational Biology @Caltech.edu. Blog at http://liorpachter.wordpress.com. Posts represent my views, not my employer's. #methodsmatter
Efficient sampling of reads (with replacement). www.biorxiv.org/content/10.6...
fastQpick: scalable bootstrap and subsampling of FASTQ readsfastQpick is a command-line tool and Python library for sampling FASTQ reads with replacement. Sampling with replacement turns a single FASTQ file into an arbitrary number of bootstrap replicates, whi...www.biorxiv.org
FWIW when writing www.biorxiv.org/content/10.6... we selected eLife papers specifically because of their CC BY license and we cited every preprint we used: "The papers below were analyzed by OpenEval. They are distributed by eLife under the CC-BY license." www.biorxiv.org/content/bior...
Science should be machine-readableWe develop a machine-automated approach for extracting results from papers, which we assess via a comprehensive review of the entire eLife corpus. Our method facilitates a direct comparison of machine...www.biorxiv.org
TL;DR: We've identified more than 100 cases of apparent manipulation in Thermo Fisher Scientific's antibody verification data. @sholtodavid.bsky.social @johanduchene.bsky.social reeserichardson.blog/2026/05/28/h...
How much of Thermo Fisher’s antibody data has been manipulated?We’ve documented more than 100 instances of apparent data manipulation in Thermo’s catalogreeserichardson.blog
Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis. Preprint (w/ Gian Marco Visani and Aayush Verma): www.biorxiv.org/content/10.6... Blog: dewitt-lab.github.io/posts/2026-0...
Additivity is all you need?Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis.dewitt-lab.github.ioIn fact when we worked on applying splits networks to political data (see preprints.apsanet.org/engage/apsa/...) we also experimented with building splits networks from single-cell data and it was quite effective.
The Split SenateThe theory of split systems provides a mathematical formalism for understanding and visualizing collections of partitions of sets into two parts. In particular, split networks, which generalize phylog...preprints.apsanet.org