2024

1.  Kojima Y, Mii S, Hayashi S, Hirose H, Ishikawa M, Akiyama M, Enomoto A, Shimamura T,Single-cell Colocalization analysis using a generative model,Cell Syst.,Vol.15,Issue2, 180-192.e7,2024.  
2.  Hashimoto M, Kojima Y, Sakamoto T, Ozato Y, Nakano Y, Abe T, Hosoda K, Saito H, Higuchi S, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Hata T, Nagayama S, Kagawa K, Goto Y, Utou M, Gamachi A, Imamura K, Kuze Y, Zenkoh J, Suzuki A, Takahashi K, Niida A, Hirose H, Hayashi S, Koseki J, Fukuchi S, Murakami K, Yoshizumi T, Kadomatsu K, Tobo T, Oda Y, Uemura M, Eguchi H, Doki Y, Mori M, Oshima M, Shibata T, Suzuki Y, Shimamura T, Mimori K,Spatial and single-cell colocalisation analysis reveals MDK-mediated immunosuppressive environment with regulatory T cells in colorectal carcinogenesis,EBioMedicine. 2024 Apr 9:105102. doi: 10.1016/j.ebiom.2024.105102. Epub ahead of print. PMID: 38614865.
3. Majima K, Kojima Y, Minoura K, Abe K, Hirose H, Shimamura T, LineageVAE: Reconstructing Historical Cell States and Transcriptomes toward Unobserved Progenitors,Bioinf. https://doi.org/10.1093/bioinformatics/btae520,2024.
4. Mizukoshi C, Kojima Y, Nomura S, Hayashi S, Abe K, Shimamura T, DeepKINET: a deep generative model for estimating single-cell RNA splicing and degradation rates, Genome Biol., 25, Article No.229,2024. 

2023

1. Ishikawa M, Sugino S, Masuda Y, Tarumoto Y, Seto Y, Taniyama N, Wagai F, Yamauchi Y, Kojima Y, Kiryu H, Yusa K, Eiraku M, Mochizuki A, RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations,Commun. Biol., Vol.6, Ariticle Number1290, 2023
2. Nakahara R, Aki S, Sugaya M, Hirose H, Kato M, Maeda K, Sakamoto D M, Kojima Y, Nishida M, Ando R, Muramatsu M, Pan M, Tsuchida R, Matsumura Y, Yanai H, Takano H, Yao R, Sando S, Shibuya M, Sakai J, Kodama T, Kidoya H, Shimamura T, Osawa T,Hypoxia activates SREBP2through Golgidisassembly in bone marrow-derived monocytesfor enhanced tumor growth,EMBO J.,DOI:10.15252/embj.2023114032
3. Genuth M, Kojima Y(Co-First), Jülich D, Kiryu H, Holley S, Automated time-lapse data segmentation reveals in vivo cell state dynamics, Sci. Adv.,Vol.9,Issue22, DOI: 10.1126/sciadv.adf1814.,2023
4. Koseki J, Hayashi S, Kojima Y, Hirose H, Shimamura T,  Topological data analysis of protein structure and inter/intra-molecular interaction changes attributable to amino acid mutations,Comput. Struct. Biotechnol. J., Vol.21, 2950-2959, 2023.
5. Ozato Y, Kojima Y(Co-First), Kobayashi Y, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Kagawa K, Goto Y, Udo M, Gamachi A, Imamura K, Kuze Y, Zenkou J, Suzuki A, Niida A, Sakamoto T, Hirose H, Hayashi S, Koseki J, Oki E, Fukuchi S, Oshima M, Tobo T, Nagayama S, Doki Y, Eguchi H, Mori M, Shibata T, Suzuki Y, Shimamura T, Mimori K, Spatial and single-cell transcriptomics decipher the cellular environment containing HLA-G+ cancer cells and SPP1+ macrophages in colorectal cancer,Cell Reports, Vol. 42, Issue 1, 111929, 2023.
   

2022

1.  Nagaharu K, Kojima Y (Co-First), Hirose H, Minoura K, Hinohara K, Minami H, Kageyama Y, Sugimoto Y, Masuya M, Nii S, Seki M, Suzuki Y, Tawara I, Shimamura T, Katayama N, Nishikawa H, Ohishi K, A bifurcation concept for B-lymphoid/plasmacytoid dendritic cells with largely fluctuating transcriptome dynamics, Cell Reports, Vol.40, Issue 9, 111260, 2022.

2021

1. Isoyama S, Mori S, Sugiyama D, Kojima Y, Tada Y, Shitara K, Hinohara K, Dan S, Nishikawa H,Cancer immunotherapy with PI3K and PD-1 dual-blockade via optimal modulation of T cell activation signal,  J. ImmunoTher. Cancer, Vol.9, Issue 8, e002279, 2021.

2020

1. Kojima Y, Matsumoto H, Kiryu H, Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations, Bioinformatics, Vol.36, Issue 1, 221-231, 2020.

2019

1. Kiryu H, Ichikawa Y, Kojima Y, TMRS: an algorithm for computing the time to the most recent substitution event from a multiple alignment column, Algorithms Mol. Bio., Vol.14, Issue23, 2019.