Kuntz SG, Eisen MB (2015). Oxygen changes drive non-uniform scaling in Drosophila melanogaster embryogenesis.
Journal  PubMed  PMC  Preprint  Data:Figshare  

Paris M, Villalta JE, Eisen MB, Lott SE (2015). Sex Bias and Maternal Contribution to Gene Expression Divergence in Drosophila Blastoderm Embryos.
Journal  PubMed  PMC  Data:GEO  

Combs PA, Eisen MB (2015). Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols.
Journal  PubMed  PMC  Web  Data:GEO  

MacManes MD, Eisen MB (2014). Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus.
Journal  PubMed  PMC  Preprint  Data:SRA  Data:DRYAD  

Li XY, Harrison MM, Villalta JE, Kaplan T, Eisen MB (2014). Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition.
Journal  PubMed  PMC  Preprint  Data:GEO  

Kuntz SG, Eisen MB (2014). Drosophila embryogenesis scales uniformly across temperature in developmentally diverse species.
Journal  PubMed  PMC  Preprint  Data:DRYAD  

Lott SE, Villalta JE, Zhou Q, Bachtrog D, Eisen MB (2014). Sex-specific embryonic gene expression in species with newly evolved sex chromosomes.
Journal  PubMed  PMC  Data:GEO  

Paris M, Kaplan T, Li XY, Villalta JE, Lott SE et al. (2013). Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression.
Journal  PubMed  PMC  Web  Data:GEO  

Combs PA, Eisen MB (2013). Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.
Journal  PubMed  PMC  Web  Data:GEO  

MacManes MD, Eisen MB (2013). Improving transcriptome assembly through error correction of high-throughput sequence reads.
Journal  PubMed  PMC  Data:DRYAD  Software:SCRIPTS  

Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B et al. (2007). Evolution of genes and genomes on the Drosophila phylogeny.
Journal  PubMed  Data:FLYBASE  Data:WORKING