An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic.
Sudhir Kumar , Qiqing Tao , Steven Weaver , Maxwell Sanderford
Molecular Biology and Evolution
1
2021
Somatic evolutionary timings of driver mutations.
Karen Gomez , Sayaka Miura , Louise A Huuki , Brianna S Spell
BMC Cancer 18 ( 1) 85 -85
13
2018
Using disease-associated coding sequence variation to investigate functional compensation by human paralogous proteins
Sayaka Miura , Stephanie Tate , Sudhir Kumar ,
Evolutionary Bioinformatics 11 ( 11) 245 -251
2015
Delineation of Tumor Migration Paths by Using a Bayesian Biogeographic Approach
Antonia Chroni , Tracy Vu , Sayaka Miura , Sudhir Kumar
Cancers 11 ( 12) 1880
3
2019
Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data
Sayaka Miura , Tracy Vu , Jiamin Deng , Tiffany Buturla
Scientific Reports 10 ( 1) 3498
7
2020
A new method for inferring timetrees from temporally sampled molecular sequences.
Sayaka Miura , Koichiro Tamura , Qiqing Tao , Louise A Huuki
PLOS Computational Biology 16 ( 1)
5
2020
PathFinder: Bayesian inference of clone migration histories in cancer.
Sudhir Kumar , Antonia Chroni , Koichiro Tamura , Maxwell Sanderford
Bioinformatics 36
2020
Evolutionary changes of the target sites of two microRNAs encoded in the Hox gene cluster of Drosophila and other insect species.
Sayaka Miura , Masafumi Nozawa , Masatoshi Nei
Genome Biology and Evolution 3 ( 3) 129 -139
17
2011
Origins and Evolution of MicroRNA Genes in Drosophila Species
Masafumi Nozawa , Sayaka Miura , Masatoshi Nei
Genome Biology and Evolution 2 ( 2) 180 -189
96
2010
Origins and evolution of microRNA genes in plant species.
Masafumi Nozawa , Sayaka Miura , Masatoshi Nei
Genome Biology and Evolution 4 ( 3) 230 -239
244
2012
A new method for inferring timetrees from temporally sampled molecular sequences
Sayaka Miura , Koichiro Tamura , Sergei L Kosakovsky Pond , Louise A Huuki
bioRxiv 620187
1
2019
Predicting clone genotypes from tumor bulk sequencing of multiple samples.
Sayaka Miura , Karen Gomez , Oscar Murillo , Louise A Huuki
Bioinformatics 34 ( 23) 4017 -4026
16
2018
Computational enhancement of single-cell sequences for inferring tumor evolution.
Sayaka Miura , Louise A Huuki , Tiffany Buturla , Tracy Vu
Bioinformatics 34 ( 17)
15
2018
Migrations of cancer cells through the lens of phylogenetic biogeography
Antonia Chroni , Sayaka Miura , Olumide Oladeinde , Vivian Aly
Scientific Reports 11 ( 1) 17184
5
2021
Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy
Antonella Amendola , Marta Canuti , Silvia Bianchi , Sudhir Kumar
Environmental Research 215 113979
2
2022
TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity
Marcos A Caraballo-Ortiz , Sayaka Miura , Maxwell Sanderford , Tenzin Dolker
Bioinformatics 38 ( 10) 2719 -2726
6
2022
The durability of immunity against reinfection by SARS-CoV-2: a comparative evolutionary study
Jeffrey P Townsend , Hayley B Hassler , Zheng Wang , Sayaka Miura
The Lancet Microbe 2 ( 12) e666 -e675
184
2021
Molecular evidence for SARS-CoV-2 in samples collected from patients with Morbilliform eruptions since late summer 2019 in Lombardy, Northern Italy
Antonella Amendola , Marta Canuti , Silvia Bianchi , Sudhir Kumar
15
2021
A phylogenetic approach to study the evolution of somatic mutational processes in cancer
Sayaka Miura , Tracy Vu , Jiyeong Choi , Jeffrey P Townsend
Communications Biology 5 ( 1) 617 -617
5
2022
Clone phylogenetics reveals metastatic tumor migrations, maps, and models
Antonia Chroni , Sayaka Miura , Lauren Hamilton , Tracy Vu
Cancers 14 ( 17) 4326 -4326
4
2022