Alex M. Valm

LGBTQ+ realities in the biological sciences

This study surveys LGBTQ+ biologists to assess workplace climate and belonging, finding lower morale and exclusionary experiences among transgender and gender non-conforming scientists.

A decrease in specific health-associated commensals is linked to progressive periodontal tissue destruction independent of dysbiotic community profiles

This study tracks microbiome and host changes during periodontitis in mice, finding health-associated bacteria correlate with tissue integrity and immune cell infiltration.

Metagenomic and transcriptomic signatures of periodontitis in companion dogs

This study identifies metagenomic and transcriptomic signatures of periodontitis in companion dogs, revealing microbial and host gene expression changes associated with disease progression.

Cross hybridization Inference for Phylogenetic Resolution (CIPHR)-FISH enables microbiome imaging with strain level taxonomic resolution

CIPHR-FISH improves microbiome imaging by enabling strain-level taxonomic resolution through machine learning and probe design, revealing spatial community structures in zebrafish.

BEEP Learning: Multi-View Image Decomposition for Massively Multiplexed Biological Fluorescence Microscopy

This paper introduces BEEP learning, a machine learning framework for multi-view fluorescence unmixing that improves discrimination of fluorophores in multiplexed imaging.

Inosine misincorporation into mRNA triggers the integrated stress response and activates an innate immune gene expression signature

This study shows that inosine misincorporation into mRNA activates the integrated stress response and an innate immune gene expression signature, linking ITPase deficiency to cellular stress.

A Framework of Multi-View Machine Learning for Biological Spectral Unmixing of Fluorophores with Overlapping Excitation and Emission Spectra

This paper introduces a multi-view machine learning framework to improve spectral unmixing of overlapping fluorophores in fluorescence microscopy images.

Unmixing Fluorescence Image Data with Sparse and Low-Rank Poisson Regression

This paper introduces a sparse and low-rank Poisson unmixing method to improve fluorescence image unmixing accuracy in low signal-to-noise regimes with overlapping fluorophores.

A feedback loop between heterochromatin and the nucleopore complex controls germ-cell to oocyte transition during Drosophila oogenesis