Christmas et al. Evolutionary constraint and innovation across hundreds of placental mammals

Sullivan et al. Leveraging base pair mammalian constraint to understand genetic variation and human disease

Andrews et al. Mammalian evolution of human cis-regulatory elements and transcription factor binding sites

  • All data and code are deposited at Zenodo (doi:10.5281/ZENODO.7149205).


Foley at al. A genomic timescale for placental mammal evolution


Kaplow et al. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

  • Publicly available ATAC-seq data was obtained from Gene Expression Omnibus accessions GSE161374, GSE146897, GSE137311, and GSE159815; China National GeneBank accession CNP0000198; and ArrayExpress accession E-MTAB-2633.
  • Unpublished ATAC-seq data generated by the Pfenning Lab can be found at GSE187366.
  • Tree used for the phenotype association pipeline can be obtained by contacting the Zoonomia Consortium and will be released prior to publication.
  • Publicly available genomes and annotations were downloaded from NCBI Publicly available genomes and annotations were downloaded from NCBI.
  • Publicly available human Hi-C data was accessed at
  • Mouse cortex Dip-C data was downloaded from Gene Expression Omnibus accession GSE146397.
  • Motif discovery results and machine learning models can be found at
  • Machine learning model predictions can be obtained from the UCSC Genome Browser (
  • New code for this work can be found at


Keough et al. Three-dimensional genome re-wiring in loci with human accelerated regions


Kirilenko et al. Integrating gene annotation with orthology inference at scale


Moon et. al. Comparative genomics of balto, a famous historic dog, captures lost diversity of 1920s sled dogs

  • Raw sequencing reads for Balto and Alaskan sled dogs have been deposited to the NCBI Sequence Read Archive under BioProject accession PRJNA786530.

Osmanski et al. Insights into mammalian TE diversity via the curation of 248 mammalian genome assemblies

  • All assemblies are available in Genbank, TE consensus sequences are available via the Dfam database. 
  • All other data is available in the supplementary materials; code used in the analysis is available at

Wilder et al. The contribution of historical processes to contemporary extinction risk in placental mammals

  • The data presented in this paper are detailed in supplementary materials.
  • Summary data and analysis scripts are available at
  • NCBI accession numbers for sequence data used in analyses are given in table S1.


Xue et al. The functional and evolutionary impacts of human-specific deletions in conserved elements

  • Oligo libraries used in this study are available upon request. CRISPR-modified SK-N-SH for the LOXL2-associated hCONDEL-edited cell lines are available upon request.
  • All additional unique/stable reagents generated in this study are available without restriction, or with a Materials Transfer Agreement.