Insertions and deletions: Computational methods, evolutionary dynamics, and biological applications
Insertions and deletions constitute the second most important source of natural genomic
variation. Insertions and deletions make up to 25% of genomic variants in humans and are …
variation. Insertions and deletions make up to 25% of genomic variants in humans and are …
Phyloformer: Fast, accurate and versatile phylogenetic reconstruction with deep neural networks
Phylogenetic inference aims at reconstructing the tree describing the evolution of a set of
sequences descending from a common ancestor. The high computational cost of state-of-the …
sequences descending from a common ancestor. The high computational cost of state-of-the …
[HTML][HTML] ConvexML: Scalable and accurate inference of single-cell chronograms from CRISPR/Cas9 lineage tracing data
CRISPR/Cas9 gene editing technology has enabled lineage tracing for thousands of cells in
vivo. However, most of the analysis of CRISPR/Cas9 lineage tracing data has so far been …
vivo. However, most of the analysis of CRISPR/Cas9 lineage tracing data has so far been …
The chloroplast genome sequence and phylogenetic analysis of Rubia alata Wall and Rubia ovatifolia Z. Ying Zhang. (Rubiaceae)
JZ Shi, XY Chen, YY **g, Y Yan, G Zhang… - Molecular Biology …, 2024 - Springer
Abstract Background Rubia alata Wall (R. alata) and Rubia ovatifolia Z. Ying Zhang (R.
ovatifolia) are unique medicinal plants native to China. Sequencing their chloroplast …
ovatifolia) are unique medicinal plants native to China. Sequencing their chloroplast …
[PDF][PDF] Novel Protein Evolution Models for Ancestral Sequence Reconstruction
A Ravoor - 2024 - digicoll.lib.berkeley.edu
Understanding the evolution of proteins over time is crucial to a variety of applications in
biology such as phylogenetic tree reconstruction, ancestral sequence reconstruction …
biology such as phylogenetic tree reconstruction, ancestral sequence reconstruction …
Ultrafast classical phylogenetic method beats large protein language models on variant effect prediction
S Prillo, WY Wu, YS Song - The Thirty-eighth Annual Conference on Neural … - openreview.net
Amino acid substitution rate matrices are fundamental to statistical phylogenetics and
evolutionary biology. Estimating them typically requires reconstructed trees for massive …
evolutionary biology. Estimating them typically requires reconstructed trees for massive …