Author

Miki Kojima

RIKEN Center for Integrative Medical Sciences

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 4 Immunology· 1 Neuroscience· 1

Signature Assays, Organisms & Methods

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Organism:human· 5 Approach:statistical model· 5 Research Focus:cell type annotation· 4 Research Focus:differential expression· 4 Assay:scRNA-seq· 4 Assay:bulk RNA-seq· 2 Research Focus:gene regulatory network inference· 2 Research Focus:benchmarking· 1

Frequent Co-Authors

Piero CarninciiD· 5 shared Yoshinari AndoiD· 5 shared Chung-Chau HoniD· 4 shared Jay W. ShiniD· 4 shared Jonathan MoodyiD· 4 shared Tsukasa Kouno· 4 shared Jen-Chien ChangiD· 3 shared Akari SuzukiiD· 2 shared

Activity by Year

2020-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 43 mutual co-author links

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5 shared papersGenomics

Piero CarninciORCID

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Author profile →

6 papers

Recent·Most cited

ASCL1 primes medullary thymic epithelial cell programs required for central tolerance

Nobuko Akiyama, Kenta Horie, Kano Namiki, Jen-Chien Chang, Maki Miyauchi, Takahisa Miyao, Nanako Uchida, Naho Hagiwara, Masaki Yoshida, Mizuki Morota, Tsukasa Kouno, Miki Kojima, Jonathan Moody, Yoshinari Ando, Hirotake Ichise, , Taishin Akiyama

The paper identifies ASCL1 as a key regulator of mTEC function and central tolerance by analyzing single-cell RNA sequencing data from thymoma patients and mouse models.

bioRxiv · Aug 6, 2025 · PreprintImmunology

Systematic evaluation of single-cell multimodal data integration for comprehensive human reference atlas.

Mario Acera Mateos, Xian Adiconis, Jessica-Kanglin Li, Doménica Marchese, Ginevra Caratù, Chung-Chau Hon, Prabha Tiwari, Miki Kojima, Beate Vieth, Michael A. Murphy, Sean Simmons, Thomas Lefévre, Irene Claes, Christopher Lund O'Connor, Rajasree Menon, , Elisabetta Mereu

This paper benchmarks multimodal single-cell data integration methods to improve kidney reference atlas quality by identifying adaptive states and rare cell types.

bioRxiv · Mar 6, 2025 · PreprintGenomics

Single-cell analysis of human diversity in circulating immune cells

Kian Hong Kock, Le Min Tan, Kyung Yeon Han, Yoshinari Ando, Damita Jevapatarakul, Ankita Chatterjee, Quy Xiao Xuan Lin, Eliora Violain Buyamin, Radhika Sonthalia, Deepa Rajagopalan, Yoshihiko Tomofuji, Shvetha Sankaran, Mi-So Park, Mai Abe, Juthamard Chantaraamporn, , Shyam Prabhakar

The paper presents AIDA, a diverse single-cell RNA-seq atlas of immune cells, revealing sub-continental diversity impacts on immune cell properties and identifying functional genetic variants.

bioRxiv · Jun 30, 2024 · PreprintGenomics

Integrative Transcriptomics Reveals Layer 1 Astrocytes Altered in Schizophrenia

Julio Leon, Satoshi Yoshinaga, Mizuki Hino, Atsuko Nagaoka, Yoshinari Ando, Jonathan Moody, Miki Kojima, Ayako Kitazawa, Kanehiro Hayashi, Kazunori Nakajima, Carlo Condello, Piero Carninci, Yasuto Kunii, Chung-Chau Hon, Jay W. Shin, Ken‐ichiro Kubo

The paper identifies altered layer 1 astrocytes in schizophrenia using spatial and single-nucleus transcriptomics of the anterior cingulate cortex.

bioRxiv · Jun 27, 2024 · PreprintNeuroscience

A single-cell atlas of transcribed cis-regulatory elements in the human genome

Jonathan Moody, Tsukasa Kouno, Miki Kojima, Ikuko Koya, Julio Leon, Akari Suzuki, Akira Hasegawa, Taishin Akiyama, Nobuko Akiyama, Masayuki Amagai, Jen-Chien Chang, Ayano Fukushima‐Nomura, Mika Handa, Kazunori Hino, Mizuki Hino, , Chung-Chau Hon

The paper constructs a single-cell atlas of transcribed cis-regulatory elements in the human genome, revealing gene regulation patterns and trait-gene relationships across cell populations.

bioRxiv · Nov 13, 2023 · PreprintGenomics

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

Jordan A. Ramilowski, Chi Wai Yip, Saumya Agrawal, Jen-Chien Chang, Yari Ciani, Ivan V. Kulakovskiy, Mickaël Mendez, Jasmine Li Ching Ooi, John F. Ouyang, Nick Parkinson, Andreas Petri, Leonie Roos, Jessica Severin, Kayoko Yasuzawa, Imad Abugessaisa, , Chinatsu Yamamoto

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.

Genome Research · Jul 1, 2020Peer-reviewedGenomics