Yannis Nevers, Tamsin E. M. Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, Laura Portell-Silva, Laia Codo, Salvatore Cosentino, Marina Marcet-Houben, Anna Vlasova, Laetitia Poidevin, Arnaud Kress, Mark Hickman, Emma Persson, Ivana Piližota, Cristina Guijarro-Clarke, the OpenEBench team, the Quest for Orthologs Consortium, Wataru Iwasaki, Odile Lecompte, Erik Sonnhammer, David S. Roos, Toni Gabaldón, David Thybert, Paul D. Thomas, Yanhui Hu, David M Emms, Elspeth Bruford, Salvador Capella-Gutierrez, Maria J Martin, Christophe Dessimoz, and Adrian Altenhoff. The Quest for Orthologs orthology benchmark service in 2022. Nucleic Acids Research, 50, W623–W632. (2022)

Joel H. Nitta, Brent D. Mishler, Wataru Iwasaki, and Atsushi Ebihara. Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation. American Journal of Botany, 109, 727-745. (2022)

Tsukasa Fukunaga and Wataru Iwasaki. Inverse Potts model improves accuracy of phylogenetic profiling. Bioinformatics, 38, 1794-1800. (2022)

Naoki Konno, Yusuke Kijima, Keito Watano, Soh Ishiguro, Keiichiro Ono, Mamoru Tanaka, Hideto Mori, Nanami Masuyama, Dexter Pratt, Trey Ideker, Wataru Iwasaki, and Nozomu Yachie. Deep distributed computing to reconstruct extremely large lineage trees. Nature Biotechnology, 40, 566-575. (2022)

Tsukasa Fukunaga and Wataru Iwasaki. Mirage: Estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families. Bioinformatics Advances, published online. (2021)

Nanako Kanno, Shingo Kato, Moriya Ohkuma, Motomu Matsui, Wataru Iwasaki, and Shinsuke Shigeto. Machine learning-assisted single-cell Raman fingerprinting for in situ and nondestructive classification of prokaryotes. iScience, 24, 102975. (2021)

Yuka W Iwasaki, Sira Sriswasdi, Yasuha Kinugasa, Jun Adachi, Yasunori Horikoshi, Aoi Shibuya, Wataru Iwasaki, Satoshi Tashiro, Takeshi Tomonaga, and Haruhiko Siomi. Piwi–piRNA complexes induce stepwise changes in nuclear architecture at target loci. EMBO Journal, 40, e108345. (2021)

Benjamin Linard, Ingo Ebersberger, Shawn E. McGlynn, Natasha Glover, Tomohiro Mochizuki, Mateus Patricio, Odile Lecompte, Yannis Nevers, QFO Consortium, Paul D. Thomas, Toni Gabaldón, Erik Sonnhammer, Christophe Dessimoz, and Ikuo Uchiyama. Ten Years of Collaborative Progress in the Quest for Orthologs. Molecular Biology and Evolution, 38, 3033-3045. (2021)

Tomoyuki Mikami and Wataru Iwasaki. The flipping t‐ratio test: phylogenetically informed assessment of the Pareto theory for phenotypic evolution. Methods in Ecology and Evolution, 12, 696-706. (2021)

Shotaro Hirase, Ayumi Tezuka, Atsushi J. Nagano, Mana Sato, Sho Hosoya, Kiyoshi Kikuchi, and Wataru Iwasaki. Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population. Evolution, 75, 176-194. (2021)