Michael B. Eisen

This paper describes an unsupervised method to detect, track, and organize insect songs from continuous field recordings, identifying 10.9 million singers and 45 song types across 13 months of data.

This paper develops an automated pipeline for 3D localization of bird vocalizations using small passive acoustic arrays in complex soundscapes, achieving reliable spatial estimates for a majority of detections.

The paper identifies the Zld interactome in Drosophila embryos, revealing co-factors essential for ZGA, including dCBP, Fsh, and Smr, and shows RNAPII associates with Zld-bound enhancers.

The paper investigates transcriptional bursting strategies in endogenous and ectopic even-skipped expression in fruit flies, finding consistent bursting patterns despite different regulatory contexts.

The paper develops a method to generate variant libraries in vivo using base editing to study gene regulatory programs in multicellular organisms.

The paper analyzes evolutionary conservation in IDRs across Drosophila and finds widespread constraint but limited function-specific clustering compared to yeast.

The paper improves orthologous protein inference and alignment by leveraging genomic redundancy and introduces a new phylogenetic HMM method, applied to Drosophila genomes.

The paper tests whether intrinsic protein disorder drives subnuclear clustering of transcription factors in Drosophila embryos and finds that IDRs alone are insufficient for this clustering.

This study uses single-nucleus RNA-sequencing to analyze gene expression differences in Drosophila embryos, revealing spatially distinct clusters and differential expression in specific regions.

The paper investigates early dosage compensation in Drosophila melanogaster and finds that it occurs through a post-transcriptional mechanism rather than transcriptional regulation.

The paper assesses RNAi knockdown efficiency of dKDM5/lid in Drosophila embryos using qRT-PCR and finds significant variability between individual embryos.

The paper uses live imaging to study the transcriptional dynamics of the Drosophila even-skipped gene, revealing how transcriptional bursting shapes its stripe expression pattern.

The paper presents 23 whole-genome sequences from the Drosophila montium species group, providing a resource for evolutionary studies.

This study shows that transcription factors like Zelda and Bicoid form dynamic, transient hubs in Drosophila embryos that interact with active transcription sites.

This study shows chronic ethanol ingestion harms Drosophila health, with effects dependent on the presence of the gut microbiome.

The paper investigates Zelda's role in zygotic enhancer activity in Drosophila embryos, finding that most enhancers show limited effects from Zelda site mutations, while one loses activity entirely, and that chromatin environment influences Zelda's effect.

The paper shows that mutating sequences around Bicoid binding sites in a Drosophila enhancer has a greater impact on its activity than mutating the Bicoid sites themselves.

The paper investigates Zelda's role in early Drosophila embryogenesis, showing it enhances chromatin accessibility and coordinates enhancer activity with maternal factors.

The paper investigates convergent evolution of gene expression in two high-toothed stickleback populations, finding that trans regulatory changes are more shared than cis changes.

This paper introduces an alignment-free method for genome-wide association studies using k-mer counts, demonstrating its ability to detect associations with structural variations and sequences absent from reference genomes.

The paper investigates whether chromatin accessibility in early Drosophila embryos is driven by transcriptional activity or independent mechanisms, finding that accessibility is largely uniform and not directly linked to activity.

The paper maps chromatin contacts in Drosophila embryos to show that insulator boundaries align with polytene interbands and TADs.

The study investigates whether Or22 allelic variation explains differences in D. melanogaster's ability to discriminate yeast-produced volatiles, finding that Or22 is not the primary driver of sensitivity to YVN.

The paper uses live imaging in Drosophila embryos to show that Bicoid binds DNA with a rapid off-rate and forms localized hubs that enable concentration-sensitive regulation.

The paper identifies insulator elements in Drosophila embryos as boundaries between topologically associated domains (TADs) and links them to low density polytene interbands.

The paper sequences and annotates the genome of Parhyale hawaiensis, identifying key genes for development, immunity, and lignocellulose digestion, providing a resource for comparative studies.