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Saul Pierotti

Computational biologist - Researcher at Leids Universitair Medisch Centrum (LUMC)

LUMC staff page Zeller lab profile Curriculum Vitae Nextflow practical course Medaka fish icons by Amos Pierotti EMBL‑EBI staff page
Last updated on July 9th, 2024

Software:

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zellerlab/siamcat
R package for statistical and machine learning analysis of microbiome data
(originally developped by Wirbel et al., currently developping an updated version with further capabilities)
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zellerlab/flexprofiler
Pipeline for large-scale microbiome taxonomic and functional profiling with multiple tools
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birneylab/flexlmm
Flexible linear mixed model framework for Genome Wide Association Studies
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birneylab/stitchimpute
Pipeline that uses STITCH for imputing genotypes from low-coverage NGS data in a population
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birneylab/varexplore
Pipeline for genetic variant prioritization after association studies

Work:

* Equal contribution
Medaka fish as a model for complex trait genetics
Saul Pierotti
PhD thesis, Apollo - University of Cambridge Repository, December 2nd, 2025, https://doi.org/10.17863/CAM.123664
Discovery and characterization of gene-by-environment and epistatic genetic effects in a vertebrate model
Bettina Welz*, Saul Pierotti*, Tomas Fitzgerald, Thomas Thumberger, Risa Suzuki, Philip Watson, Jana Fuss, Tiago Cordeiro da Trindade, Fanny Defranoux, Marcio Ferreira, Kiyoshi Naruse, Felix Loosli, Jakob Gierten, Joachim Wittbrodt, Ewan Birney
Cell genomics, Volume 6, Issue 5, 13 May, 2026, 101164, https://doi.org/10.1016/j.xgen.2026.101164
A panel of medaka isogenic lines suggests individual, seasonal, and sexual genetic variation of bdnf gene expression in the brain
Eleonora Rovegno, Christina Vasilopoulou, Saul Pierotti, Tomas Fitzgerald, Joachim Wittbrodt, Ewan Birney, Daniela Vallone4, Felix Loosli, Cristiano Bertolucci, Nicholas S. Foulkes, Tyrone Lucon-Xiccato.
Frontiers in Behavioral Neurosciences, Volume 20, April 22nd, 2026, https://doi.org/10.3389/fnbeh.2026.1681619
A Scalable, High-Throughput Optomotor Response Pipeline for Quantitative Analysis of Vision Using Infinity-Pools
Risa Suzuki, Damjan Kalšan, Norin Bhatti, Saul Pierotti, Gero Hofmann, Ewan Birney, Thomas Thumberger, Joachim Wittbrodt.
Preprint on Biorχiv, January 14th, 2026, https://doi.org/10.64898/2026.01.13.699264
Measurement and classification of bold–shy behaviours in medaka fish
Saul Pierotti*, Ian Brettell*, Tomas Fitzgerald, Cathrin Herder, Narendar Aadepu, Christian Pylatiuk, Joachim Wittbrodt, Ewan Birney, Felix Loosli
Bioinformatics, Volume 41, Issue 6, June 2025, btaf342, https://doi.org/10.1093/bioinformatics/btaf342
FlexLMM: a Nextflow linear mixed model framework for GWAS
Saul Pierotti, Tomas Fitzgerald, Ewan Birney.
Bioinformatics, Volume 41, Issue 1, January 2025, btaf021, https://doi.org/10.1093/bioinformatics/btaf021
Extensive Gene x Environment interactions in the outbred vertebrate genetics of a standard physiological phenotype
Saul Pierotti, Bettina Welz, Jakob Gierten, Beate Wittbrodt, Philip Watson, Sebastian Stricker, Marcio Ferreira, Fanny Defranoux, Risa Suzuki, Jana Fuß, Tomas Fitzgerald, Thomas Thumberger, Felix Loosli, Joachim Wittbrodt, Ewan Birney.
The Biology of Genomes, Cold Spring Harbor Laboratory, 2024.
Genotype imputation in F2 crosses of inbred lines
Saul Pierotti, Bettina Welz, Tomas Fitzgerald, Joachim Wittbrodt, Ewan Birney.
Bioinformatics Advances, Volume 4, Issue 1, 2024, vbae107, DOI: 10.1093/bioadv/vbae107

Research interests:

Gut microbiome in health and disease
Genetic and environmental interactions
Mixed effect models for genetics and microbiome data analysis
lmm_equation
Reproducibility in data science
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