Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages
Loss of limbs evolved many times in squamate reptiles. Here we investigated the genomic
basis of convergent limb loss in reptiles. We sequenced the genomes of a closely related …
basis of convergent limb loss in reptiles. We sequenced the genomes of a closely related …
Novel phylogenetic methods are needed for understanding gene function in the era of mega-scale genome sequencing
Ongoing large-scale genome sequencing projects are forecasting a data deluge that will
almost certainly overwhelm current analytical capabilities of evolutionary genomics. In …
almost certainly overwhelm current analytical capabilities of evolutionary genomics. In …
Vision-related convergent gene losses reveal SERPINE3's unknown role in the eye
H Indrischek, J Hammer, A Machate, N Hecker… - Elife, 2022 - elifesciences.org
Despite decades of research, knowledge about the genes that are important for
development and function of the mammalian eye and are involved in human eye disorders …
development and function of the mammalian eye and are involved in human eye disorders …
Evolutionary rewiring of regulatory networks contributes to phenotypic differences between human and mouse orthologous genes
Mouse models have been engineered to reveal the biological mechanisms of human
diseases based on an assumption. The assumption is that orthologous genes underlie …
diseases based on an assumption. The assumption is that orthologous genes underlie …
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 …
A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution
Genomes contain conserved non-coding sequences that perform important biological
functions, such as gene regulation. We present a phylogenetic method, PhyloAcc-C, that …
functions, such as gene regulation. We present a phylogenetic method, PhyloAcc-C, that …
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 …
Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits
C Stefen, F Wagner, M Asztalos, P Giere, P Grobe… - Mammalian …, 2022 - Springer
A new and uniquely structured matrix of mammalian phenotypes, MaTrics (Ma mmalian Tr
aits for Comparative Genom ics) in a digital form is presented. By focussing on mammalian …
aits for Comparative Genom ics) in a digital form is presented. By focussing on mammalian …
TFforge utilizes large-scale binding site divergence to identify transcriptional regulators involved in phenotypic differences
BE Langer, M Hiller - Nucleic acids research, 2019 - academic.oup.com
Abstract Changes in gene regulation are important for phenotypic and in particular
morphological evolution. However, it remains challenging to identify the transcription factors …
morphological evolution. However, it remains challenging to identify the transcription factors …
Recapitulating Evolutionary Divergence in a Single Cis-Regulatory Element Is Sufficient to Cause Expression Changes of the Lens Gene Tdrd7
JG Roscito, K Subramanian, R Naumann… - Molecular biology …, 2021 - academic.oup.com
Mutations in cis-regulatory elements play important roles for phenotypic changes during
evolution. Eye degeneration in the blind mole rat (BMR; Nannospalax galili) and other …
evolution. Eye degeneration in the blind mole rat (BMR; Nannospalax galili) and other …