Evolutionary constraint and innovation across hundreds of placental mammals
Zoonomia is the largest comparative genomics resource for mammals produced to date. By
aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect …
aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect …
Deep cis-regulatory homology of the butterfly wing pattern ground plan
A Mazo-Vargas, AM Langmüller, A Wilder… - Science, 2022 - science.org
Butterfly wing patterns derive from a deeply conserved developmental ground plan yet are
diverse and evolve rapidly. It is poorly understood how gene regulatory architectures can …
diverse and evolve rapidly. It is poorly understood how gene regulatory architectures can …
A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence
M Ivanković, JN Brand, L Pandolfini, T Brown… - Nature …, 2024 - nature.com
The planarian Schmidtea mediterranea is being studied as a model species for
regeneration, but the assembly of planarian genomes remains challenging. Here, we report …
regeneration, but the assembly of planarian genomes remains challenging. Here, we report …
A chromosome-level reference genome and pangenome for barn swallow population genomics
Insights into the evolution of non-model organisms are limited by the lack of reference
genomes of high accuracy, completeness, and contiguity. Here, we present a chromosome …
genomes of high accuracy, completeness, and contiguity. Here, we present a chromosome …
False-positive IRESes from Hoxa9 and other genes resulting from errors in mammalian 5′ UTR annotations
C Akirtava, GE May… - Proceedings of the …, 2022 - National Acad Sciences
Hyperconserved genomic sequences have great promise for understanding core biological
processes. It has been recently proposed that scores of hyperconserved 5′ untranslated …
processes. It has been recently proposed that scores of hyperconserved 5′ untranslated …
Improving the performance of supervised deep learning for regulatory genomics using phylogenetic augmentation
Motivation Supervised deep learning is used to model the complex relationship between
genomic sequence and regulatory function. Understanding how these models make …
genomic sequence and regulatory function. Understanding how these models make …
Addiction-associated genetic variants implicate brain cell type-and region-specific cis-regulatory elements in addiction neurobiology
Recent large genome-wide association studies have identified multiple confident risk loci
linked to addiction-associated behavioral traits. Most genetic variants linked to addiction …
linked to addiction-associated behavioral traits. Most genetic variants linked to addiction …
Relating enhancer genetic variation across mammals to complex phenotypes using machine learning
Protein-coding differences between species often fail to explain phenotypic diversity,
suggesting the involvement of genomic elements that regulate gene expression such as …
suggesting the involvement of genomic elements that regulate gene expression such as …
Vocal learning–associated convergent evolution in mammalian proteins and regulatory elements
Vocal production learning (“vocal learning”) is a convergently evolved trait in vertebrates. To
identify brain genomic elements associated with mammalian vocal learning, we integrated …
identify brain genomic elements associated with mammalian vocal learning, we integrated …
Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin
Background Evolutionary conservation is an invaluable tool for inferring functional
significance in the genome, including regions that are crucial across many species and …
significance in the genome, including regions that are crucial across many species and …