Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences

K Kryukov, MT Ueda, S Nakagawa, T Imanishi - Bioinformatics, 2019 - academic.oup.com
DNA sequence databases use compression such as gzip to reduce the required storage
space and network transmission time. We describe Nucleotide Archival Format (NAF)—a new …

Sequence Compression Benchmark (SCB) database—A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences

K Kryukov, MT Ueda, S Nakagawa, T Imanishi - GigaScience, 2020 - academic.oup.com
Background Nearly all molecular sequence databases currently use gzip for data compression.
Ongoing rapid accumulation of stored data calls for a more efficient compression tool. …

[PDF][PDF] Genomic diversity of SARS-CoV-2 can be accelerated by mutations in the nsp14 gene

K Takada, MT Ueda, S Shichinohe, Y Kida, C Ono… - Iscience, 2023 - cell.com
Coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2),
encode a proofreading exonuclease, nonstructural protein 14 (nsp14), that helps ensure …

[HTML][HTML] Altered oligomeric states in pathogenic ALS2 variants associated with juvenile motor neuron diseases cause loss of ALS2-mediated endosomal function

K Sato, A Otomo, MT Ueda, Y Hiratsuka… - Journal of Biological …, 2018 - ASBMB
Familial amyotrophic lateral sclerosis type 2 (ALS2) is a juvenile autosomal recessive motor
neuron disease caused by the mutations in the ALS2 gene. The ALS2 gene product, ALS2/…

[HTML][HTML] Alopecia areata susceptibility variant in MHC region impacts expressions of genes contributing to hair keratinization and is involved in hair loss

…, N Motosugi, T Hatanaka, M Kimura, MT Ueda… - …, 2020 - thelancet.com
Background Alopecia areata (AA) is considered a highly heritable, T-cell-mediated autoimmune
disease of the hair follicle. However, no convincing susceptibility gene has yet been …

[HTML][HTML] Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains

MT Ueda, K Kryukov, S Mitsuhashi, H Mitsuhashi… - Mobile DNA, 2020 - Springer
Background Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections
of mammalian germline cells. A large proportion of ERVs lose their open reading frames (…

Functional mutations in spike glycoprotein of Zaire ebolavirus associated with an increase in infection efficiency

MT Ueda, Y Kurosaki, T Izumi, Y Nakano… - Genes to …, 2017 - Wiley Online Library
Functional mutations in spike glycoprotein of Zaire ebolavirus associated with an increase in
infection efficiency - Ueda - 2017 - Genes to Cells - Wiley Online … Mahoko Takahashi Ueda

Systematic survey of non-retroviral virus-like elements in eukaryotic genomes

K Kryukov, MT Ueda, T Imanishi, S Nakagawa - Virus research, 2019 - Elsevier
Endogenous viral elements (EVEs) are viral sequences that are endogenized in the host cell.
Recently, several eukaryotic genomes have been shown to contain EVEs. To improve the …

TRIM28 expression on dendritic cells prevents excessive T cell priming by silencing endogenous retrovirus

…, S Yamanaka, S Nakagawa, MT Ueda… - The Journal of …, 2021 - journals.aai.org
Acquired immune reaction is initiated by dendritic cells (DCs), which present Ags to a few
naive Ag-specific T cells. Deregulation of gene expression in DCs may alter the outcome of the …

[HTML][HTML] A role for gorilla APOBEC3G in shaping lentivirus evolution including transmission to humans

Y Nakano, K Yamamoto, MT Ueda, A Soper… - PLoS …, 2020 - journals.plos.org
The APOBEC3 deaminases are potent inhibitors of virus replication and barriers to cross-species
transmission. For simian immunodeficiency virus (SIV) to transmit to a new primate host…