Results 51 to 60 of about 31,734 (247)

MrBayes 3: Bayesian phylogenetic inference under mixed models [PDF]

Bioinformatics, 2003
Abstract Summary: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g.
Fredrik Ronquist, John P. Huelsenbeck
openaire   +2 more sources

Single‐cell DNA methylation profiling: Technologies, computation, and applications in precision oncology

Molecular Oncology, EarlyView.
Single‐cell DNA methylation (scDNAme) profiling maps epimutational clonal evolution, revealing mechanisms of malignancy and therapeutic resistance across diverse cancer types. By providing a high‐resolution landscape of intratumoral heterogeneity, these technologies empower precise patient stratification, guide the development of enhanced ...
Ik Soo Kim
wiley   +1 more source

Intrapatient tumour heterogeneity and clonal evolution in an autopsy study of metastatic salivary gland cancer

Molecular Oncology, EarlyView.
Tumour heterogeneity and clonal evolution of metastatic salivary gland cancer were evaluated in two patients with adenoid carcinoma and one patient with myoepithelial carcinoma. Radiology‐guided autopsy enabled multi‐region sampling (total samples n = 149), followed by whole‐genome sequencing and phylogenetic reconstruction (17 tumour samples, 4–7 per ...
Gerben Lassche, Niels J. van Ruitenbeek, Charlotte Adang, Luke O'Gorman, Pui Yuen Lee, Willemijn M. Klein, Adriana C. H. van Engen‐van Grunsven, Jack A. Schalken, Sander Bervoets, Gerald W. Verhaegh, Carla M. L. van Herpen   +10 more
wiley   +1 more source

Practical guidelines for Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC) [version 2; peer review: 3 approved, 1 approved with reservations]

Open Research Europe
Phylogenetic estimation is, and has always been, a complex endeavor. Estimating a phylogenetic tree involves evaluating many possible solutions and possible evolutionary histories that could explain a set of observed data, typically by using a model of ...
Orlando Schwery, Joëlle Barido-Sottani, Chi Zhang, Rachel C. M. Warnock, April Marie Wright   +4 more
doaj   +1 more source

Phylogenetic inference under varying proportions of indel-induced alignment gaps

BMC Evolutionary Biology, 2009
Background The effect of alignment gaps on phylogenetic accuracy has been the subject of numerous studies. In this study, we investigated the relationship between the total number of gapped sites and phylogenetic accuracy, when the gaps were introduced ...
Gadagkar Sudhindra R, Dwivedi Bhakti
doaj   +1 more source

Molecular dynamics simulations of positively selected codons in FcγRI reveal novel biochemical binding properties

FEBS Open Bio, EarlyView.
Evolutionary analysis across 32 placental mammals identified positive selection at residues H148 and W149 in the immune receptor FcγR1. Ancestral reconstruction combined with molecular dynamics simulations reveals how these mutations may influence receptor structure and dynamics, providing insight into the evolution of antibody recognition and immune ...
David A. Young, Omar Arias‐Gaguancela, Fiona Gibson, Morgan Grainger, Jodie Score, Amit Nathubhai, Mauricio Cafiero, Lee Richard Machado   +7 more
wiley   +1 more source

The complete mitochondrial genome of Quasipaa exilispinosa (Anura: Dicroglossidae)

Mitochondrial DNA. Part B. Resources, 2020
The complete mitochondrial genome (mitogenome) of Quasipaa exilispinosa (Anura: Dicroglossidae) we sequenced can provide critical information for mitogenome evolution.
Yan-Qing Wu, Qiao-Er Chen, Jun Wu
doaj   +1 more source

Conformational Snapshots of CydDC in a Native Lipid Bilayer Coupling Heme Transport to Antibiotic Resistance

Advanced Science, EarlyView.
Phylogenetic and biochemical analyses of the heme transporter CydDC reveal its functional conservation throughout bacterial evolution and demonstrate its unique asymmetric allosteric mechanism. Furthermore, impairment of CydDC function directly affects bacterial antibiotic resistance and likely compromises antibiotic efficacy through drug efflux.
Lili Yang, Changbin Zhang, Mengyuan Lyu, Yongbo Luo, Jierou Zhang, Yujiao Chen, Lintao Luo, Wen Qiao, Xiangyangpeng Li, Yu Zhou, Zhongling Wei, Yuling Xiao, Qian Niu, Juan Zhou, Guanglin He, Binwu Ying, Zhaoming Su, Hao Chen, Xiaodi Tang, Haohao Dong   +19 more
wiley   +1 more source

Fast algorithms for computing phylogenetic divergence time

BMC Bioinformatics, 2017
Background The inference of species divergence time is a key step in most phylogenetic studies. Methods have been available for the last ten years to perform the inference, but the performance of the methods does not yet scale well to studies with ...
Ralph W. Crosby, Tiffani L. Williams
doaj   +1 more source

T2T Genome Assembly and Multi‐Omics Data Reveal Terrestrial Adaptation and Mucus Biosynthesis in Tropical Leatherleaf Slug (Laevicaulis alte)

Advanced Science, EarlyView.
A gap‐free genome assembly and multi‐omics comparison of the terrestrial slug Laevichaulis alte with an aquatic relative reveal that expansion of the VEGF family orchestrates mucus production, lipid metabolism, and immune defense—highlighting key molecular innovations for conquering life on land.
Gang Wang, Shaofang He, Zhongkai Wang, Aobo Pang, Xiaoli Sun, Rongchen Liu, Fang Wang, Sisi Chen, Zhijuan Bian, Dongcheng Wei, Liuhan Wu, Siyao Zhao, Qiuting Ji, Yiqi Sun, Niying Sun, Yushinta Fujaya, Boping Tang, Kianann Tan, Daizhen Zhang, Lianfu Chen   +19 more
wiley   +1 more source