[HTML][HTML] Ancient pathogen genomics as an emerging tool for infectious disease research

MA Spyrou, KI Bos, A Herbig, J Krause - Nature Reviews Genetics, 2019 - nature.com
Over the past decade, a genomics revolution, made possible through the development of
high-throughput sequencing, has triggered considerable progress in the study of ancient …

The true story of the HD-Zip family

FD Ariel, PA Manavella, CA Dezar, RL Chan - Trends in plant science, 2007 - cell.com
The HD-Zip family of transcription factors is unique to the plant kingdom. These proteins
exhibit the singular combination of a homeodomain with a leucine zipper acting as a …

[HTML][HTML] AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination

TC Terwilliger, D Liebschner, TI Croll, CJ Williams… - Nature …, 2024 - nature.com
Artificial intelligence-based protein structure prediction methods such as AlphaFold have
revolutionized structural biology. The accuracies of these predictions vary, however, and …

IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era

BQ Minh, HA Schmidt, O Chernomor… - Molecular biology …, 2020 - academic.oup.com
Abstract IQ-TREE (http://www. iqtree. org, last accessed February 6, 2020) is a user-friendly
and widely used software package for phylogenetic inference using maximum likelihood …

Evolutionary history, potential intermediate animal host, and cross‐species analyses of SARS‐CoV‐2

X Li, J Zai, Q Zhao, Q Nie, Y Li, BT Foley… - Journal of medical …, 2020 - Wiley Online Library
To investigate the evolutionary history of the recent outbreak of severe acute respiratory
syndrome coronavirus 2 (SARS‐CoV‐2) in China, a total of 70 genomes of virus strains from …

Transmission dynamics and evolutionary history of 2019‐nCoV

X Li, W Wang, X Zhao, J Zai, Q Zhao… - Journal of medical …, 2020 - Wiley Online Library
To investigate the time origin, genetic diversity, and transmission dynamics of the recent
2019‐nCoV outbreak in China and beyond, a total of 32 genomes of virus strains sampled …

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

J Trifinopoulos, LT Nguyen… - Nucleic acids …, 2016 - academic.oup.com
This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for
IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE …

Potential of large “first generation” human‐to‐human transmission of 2019‐nCoV

X Li, J Zai, X Wang, Y Li - Journal of medical virology, 2020 - Wiley Online Library
To investigate the genetic diversity, time origin, and evolutionary history of the 2019‐nCoV
outbreak in China and Thailand, a total of 12 genome sequences of the virus with known …

[HTML][HTML] A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals

P Simion, H Philippe, D Baurain, M Jager, DJ Richter… - Current biology, 2017 - cell.com
Resolving the early diversification of animal lineages has proven difficult, even using
genome-scale datasets. Several phylogenomic studies have supported the classical …

Ultrafast approximation for phylogenetic bootstrap

BQ Minh, MAT Nguyen… - Molecular biology and …, 2013 - academic.oup.com
Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the
clade support of phylogenetic trees. However, with the rapidly growing amount of data, this …