RiboTxAlign maps and quantifies ribosome footprints using sample-specific transcript references, achieving high accuracy in genomic placement and transcript-level abundance estimation.

bioRxiv · Oct 21, 2026 · PreprintBioinformatics

Niche-targeted therapy via YAP/TAZ activation enhances hematopoietic regeneration

Shun Uemura, Masayuki Yamashita, Takako Yokomizo‐Nakano, Ayako Aihara, Takumi Iwawaki, Shuhei Koide, Yaeko Nakajima‐Takagi, Motohiko Oshima, Yoshiki Omatsu, Yuki Matsumoto, Yoshiaki Kubota, Bahityar Rahmutulla, Atsushi Kaneda, Miki Nishio, Akira Suzuki, , Atsushi Iwama

This study shows that activating YAP/TAZ improves bone marrow niche recovery and hematopoietic regeneration after myeloablative stress.

Blood · Jun 22, 2026Peer-reviewedCell Biology

Breast cancer identity is defined by specialized enhancer sets via lysine deacetylation

Hiroaki Tachiwana, Kohei Kumegawa, Ryota Matsudo, Ai Katsuma, Atsushi Okabe, Nao Yoshida, Xufeng Shu, Masaki Kato, Tamiko Minamisawa, Akihiro Ito, Hiroshi Kimurâ, Piero Carninci, Atsushi Kaneda, Yasukazu Daigaku, Reo Maruyama, Noriko Saitoh

The paper identifies hypoacetylation-defined enhancers in luminal breast cancer cells and links them to subtype-specific gene regulation and patient classification.

bioRxiv · Jul 31, 2025 · PreprintCancer Biology

An integrative transcriptional logic model of hepatic insulin resistance

Takumi Kitamoto, Taiyi Kuo, Atsushi Okabe, Atsushi Kaneda, Domenico Accili

This paper investigates the transcriptional regulation of lipid and glucose metabolic genes in hepatic insulin resistance, finding distinct regulatory patterns and a model for their coexistence in type 2 diabetes.

Proceedings of the National Academy of Sciences · Nov 3, 2021Peer-reviewedMolecular Biology