Basic Information

Email Address

• Email Address

  shiomi.akifumi.5vkyoto-u.ac.jp

Professional Memberships

• From Apr. 2021, To Present

  The Japan Society of Mechanical Engneers
• From Apr. 2019, To Present

  The Biophysical Society of Japan
• From Apr. 2015, To Present

  The Japanese Conference on the Biochemistry of Lipids
• From Apr. 2014, To Present

  The Biochemical Society

Academic Degree

• 23 Mar. 2017

  京都大学修士（工学）
• 23 Mar. 2020

  京都大学博士（工学）

Academic Resume (Undergraduate School/Majors)

• 京都大学, 工学部工業化学科, 卒業

Research History

• From Apr. 2025, To Present

  Kyoto University, The Hakubi Center for Advanced Research, Program-Specific Associate Professor, Hakubi Researcher
• From Apr. 2022, To Mar. 2025

  RIKEN, Microfluidics RIKEN Hakubi Research Team, Special Postdoctoral Researcher
• From Apr. 2023, To Mar. 2024

  University of California, Los Angeles, Bioengineering, Visiting scholar
• From Apr. 2020, To Mar. 2022

  RIKEN, Microfluidics RIKEN Hakubi Research Team, postdoctoral Researcher
• From Apr. 2017, To Mar. 2020

  Kyoto University, Graduate School of Engineering, 日本学術振興会特別研究員DC1

ID,URL

• ORCID ID

  0000-0002-9277-2301

• J-Global ID

  202001000612096810

• Researcher number

  60880557

researchmap URL

• https://researchmap.jp/akifumi_shiomi

Research

Research Interests

• Single-cell RNA sequencing
• phospholipids
• plasma membrane
• Cell mechanics

Research Areas

• Life sciences, Bioorganic chemistry, リン脂質
• Life sciences, Cell biology, 細胞形態
• Life sciences, Biophysics, 細胞の機械特性

Papers

• Identification of a transient receptor potential channel that is regulated by phospholipid asymmetry

  Riku Nakanishi; Akira Murakami; Emi Sasaki; Masaki Tsuchiya; Miki Suzuki; Akifumi Shiomi; Kohjiro Nagao; Tomohiko Taguchi; Masato Umeda; Kunitoshi Uchida; Yuji Hara

  bioRxiv, 10 Aug. 2026

  
• Abstract Tu0066: The Role of Type VIII Collagen in Modulating Endothelial Cell Stiffness in Inflammation

  Qian Li; Lifang Ye; Karina Bender; Jonathan Phan; Akifumi Shiomi; Sriharsha Talapaneni; Yonghong Meng; Dino Di Carlo; Yin Tintut; Linda Demer; Jeffrey Hsu

  Arteriosclerosis, Thrombosis, and Vascular Biology, Apr. 2025

  
• Proteostatic defect drives biophysical remodeling that triggers cell competition

  Wonjae Song; Mai Yukitake; Kei Kozawa; Nanami Sato; Jiaying Wen; Zehao Dai; Susumu Ishikawa; Akifumi Shiomi; Hirofumi Shintaku; Seiichiro Ishihara; Hisashi Haga; Yasuyuki Fujita

  iScience, Aug. 2026, Peer-reviewed

  
• Δ9–fatty Acid Desaturase Regulates Cell Membrane Deformation

  Kohjiro Nagao; Takumi Oka; Akifumi Shiomi; Ayano Ochi; Yuji Hara; Hiroyuki Saito; Masato Umeda

  MEMBRANE, 06 Apr. 2026, Peer-reviewed

  
• High-throughput mechanical phenotyping and transcriptomics of single cells.

  Akifumi Shiomi; Taikopaul Kaneko; Kaori Nishikawa; Arata Tsuchida; Takashi Isoshima; Mayuko Sato; Kiminori Toyooka; Kentaro Doi; Hidekazu Nishikii; Hirofumi Shintaku

  Nature communications, 17 May 2024, Peer-reviewed, Lead author

  Access this paper :

  
• Secretory GFP reconstitution labeling of neighboring cells interrogates cell–cell interactions in metastatic niches

  Misa Minegishi; Takahiro Kuchimaru; Kaori Nishikawa; Takayuki Isagawa; Satoshi Iwano; Kei Iida; Hiromasa Hara; Shizuka Miura; Marika Sato; Shigeaki Watanabe; Akifumi Shiomi; Yo Mabuchi; Hiroshi Hamana; Hiroyuki Kishi; Tatsuyuki Sato; Daigo Sawaki; Shigeru Sato; Yutaka Hanazono; Atsushi Suzuki; Takahide Kohro; Tetsuya Kadonosono; Tomomi Shimogori; Atsushi Miyawaki; Norihiko Takeda; Hirofumi Shintaku; Shinae Kizaka-Kondoh; Satoshi Nishimura

  Nature Communications, 05 Dec. 2023, Peer-reviewed

  
• The mechanosensitive ion channel PIEZO1 promotes satellite cell function in muscle regeneration

  Kotaro Hirano; Masaki Tsuchiya; Akifumi Shiomi; Seiji Takabayashi; Miki Suzuki; Yudai Ishikawa; Yuya Kawano; Yutaka Takabayashi; Kaori Nishikawa; Kohjiro Nagao; Eiji Umemoto; Yasuo Kitajima; Yusuke Ono; Keiko Nonomura; Hirofumi Shintaku; Yasuo Mori; Masato Umeda; Yuji Hara

  Life Science Alliance, Nov. 2022, Peer-reviewed

  
• Extreme deformability of insect cell membranes is governed by phospholipid scrambling

  Akifumi Shiomi; Kohjiro Nagao; Nobuhiro Yokota; Masaki Tsuchiya; Utako Kato; Naoto Juni; Yuji Hara; Masayuki X. Mori; Yasuo Mori; Kumiko Ui-Tei; Motohide Murate; Toshihide Kobayashi; Yuri Nishino; Atsuo Miyazawa; Akihisa Yamamoto; Ryo Suzuki; Stefan Kaufmann; Motomu Tanaka; Kazuya Tatsumi; Kazuyoshi Nakabe; Hirofumi Shintaku; Semen Yesylevsky; Mikhail Bogdanov; Masato Umeda

  Cell Reports, Jun. 2021, Peer-reviewed, Lead author

  Access this paper :

  
• Changes in the physicochemical properties of fish cell membranes during cellular senescence.

  Akifumi Shiomi; Kohjiro Nagao; Hisae Kasai; Yuji Hara; Masato Umeda

  Bioscience, biotechnology, and biochemistry, Mar. 2020, Peer-reviewed, Lead author

  
• Cell surface flip-flop of phosphatidylserine is critical for PIEZO1-mediated myotube formation.

  Masaki Tsuchiya; Yuji Hara; Masaki Okuda; Karin Itoh; Ryotaro Nishioka; Akifumi Shiomi; Kohjiro Nagao; Masayuki Mori; Yasuo Mori; Junichi Ikenouchi; Ryo Suzuki; Motomu Tanaka; Tomohiko Ohwada; Junken Aoki; Motoi Kanagawa; Tatsushi Toda; Yosuke Nagata; Ryoichi Matsuda; Yasunori Takayama; Makoto Tominaga; Masato Umeda

  Nature communications, 24 May 2018, Peer-reviewed

  Access this paper :

  

Misc.

• 毛利隆元急死をめぐる毒殺説の形成――赤川元保・和智誠春誅殺事件の再検討

  塩見晃史

  歴史研究, Apr. 2026, Peer-reviewed, Lead author, Corresponding author

  
• 須々万沼城の戦い再考

  塩見 晃史

  歴史研究, Feb. 2025, Peer-reviewed, Lead author, Corresponding author

  
• ELASTomics：細胞の力学特性と遺伝子発現の統合解析法

  塩見 晃史; 金子 泰洸; ポール; 西川 香里; 土田 新; 新宅 博文

  生物物理, Jan. 2025, Peer-reviewed, Lead author

  
• Regulation of cell deformability by phospholipid transport

  Akifumi Shiomi; Kohjiro Nagao; Masato Umeda

  生化学, Jan. 2022, Lead author

  
• リン脂質スクランブラーゼにより昆虫細胞は高い変形能を獲得する

  Akifumi Shiomi, Kohjiro Nagao, Masato Umeda

  実験医学, Nov. 2021, Lead author

  
• Phospholipid transporters in Drosophila melanogaster

  Kohjiro Nagao; Akifumi Shiomi; Masato Umeda

  生体の科学, May 2016

  

Presentations

• Mechano sequencing of single cells

  Hirofumi Shintaku; Akifumi Shiomi; Misa Minegishi; Keiji Nozaki; Junichi Murai; Taikopaul Kaneko

  Pacifichem 2025, 18 Dec. 2026, Invited

  
• Beyond mechanical phenotyping;novel methods for integrated analysis of mechanical phenotyping and transcriptome

  Akifumi Shiomi; Taikopaul Kaneko; Kaori Nishikawa; Di Carlo Dino; Hirofumi Shintaku

  The 48th Annual Meeting of the Molecular Biology Society of Japan, 04 Dec. 2025, Invited

  
• Deciphering the molecular mechanisms regulating cell mechanics

  Akifumi Shiomi

  Hakubi seminar, 18 Nov. 2025, Invited

  
• Microfluidics-Based Integration of Mechanical Phenotyping and Transcriptomics

  Akifumi SHIOMI; Taikopaul KANEKO; Kaori NISHIKAWA; Dino Di Carlo; Hirofumi SHINTAKU

  The 16th Symposium on Micro-Nano Science and Technology, 11 Nov. 2025

  
• Identification of the mechanical causality of extruding directionality of loser cells under cell competition by mechanical inference integrated with cell surface tension

  Jin Kitamura; Junichi Murai; Akifumi Shiomi; Misa Minegishi; Mahmoud N. Abdelmoez; Taikopaul Kaneko; Hirofumi Shintaku

  GloBIAS Bioimage Analysis Conference, 26 Oct. 2025

  
• 異分野融合の架け橋〜西国の覇者の上洛からセルメカニクスまで

  塩見晃史

  京都を学ぶ 〜知がつなぐ時代と分野の架け橋〜, 24 Oct. 2025, Invited

  
• High-throughput profiling of the cell mechanics with unbiased transcriptional screening in cancer cells

  Akifumi Shiomi; Taikopaul Kaneko; Kaori Nishikawa; Dino Di Carlo; Hirofumi Shintaku

  The 84th Annual Meeting of the Japaneses Cancer Association, 25 Sep. 2025, Invited

  
• Nano-Electrokinetics Links Hidden Transcriptomic Dynamics to Stochastic Single-Cell Behavior

  Hirofumi Shintaku; Akifumi Shiomi; Taikopaul Kaneko; Misa Minegishi; Kotaro Torii; Arata Tsuchida

  The 63rd Annual Meeting of the Biophysical Society of Japan, 26 Sep. 2025, Invited

  
• ELASTomics: combined analysis of mechanical phenotype and transcriptome during aging

  Akifumi Shiomi; Taikopaul Kaneko; Kaori Nishikawa; Hirofumi Shintaku

  The ageing genome: from mechanisms to disease EMBL Symposium, 12 Jun. 2025

  
• Spatio-tensional transcriptomics to dissect mechanical cell-cell interaction

  Junichi Murai; Mahmoud N. Abdelmoez; Akifumi Shiomi; Misa Minegishi; Taikopaul Kaneko; Hirofumi Shintaku

  Physics and Chemistry of Microfluidics Gordon Research Conference, 04 Jun. 2025

  
• MECHANOmics: Combined analysis of mechanical phenotype of cell deformability and transcriptome at single-cell resolution

  Akifumi Shiomi; Taikopaul Kaneko; Kaori Nishikawa; Dino Di Carlo; Hirofumi Shintaku

  2025 Physics and Chemistry of Microfluidics Gordon Research Conference, 04 Jun. 2025

  
• Development of Microfluidic Sequence Automation for Spatio-tensional Transcriptomics

  Junichi Murai; Mahmoud N. Abdelmoez; Akifumi Shiomi; Misa Minegishi; Taikopaul Kaneko; Hirofumi Shintaku

  Physics and Chemistry of Microfluidics Gordon Research Seminar, 31 May 2025

  
• The mechanical phenotyping integrated with transcriptomics for single cells

  Akifumi SHIOMI; Taikopaul KANEKO; Kaori NISHIKAWA; Arata TSUCHIDA; Dino Di Carlo; Hirofumi SHINTAKU

  The 15th Symposium on Micro-Nano Science and Technology, 27 Nov. 2024

  
• Integration of mechanical phenotyping and transcriptomics by ELASTomics and MECHANOmics

  Akifumi Shiomi; Taikopaul Kaneko; Kaori Nishikawa; Dino Di Carlo; Hirofumi Shintaku

  The 52nd Naito Conference, 03 Oct. 2024

  
• Combined analysis of static and dynamic cell-mechanics with unbiased transcriptomics for thousands of single cells

  Akifumi Shiomi; Taikopaul Kaneko; Kaori Nishikawa; Dino Di Carlo; Hirofumi Shintaku

  IUPAB2024, 25 Jun. 2024

  
• Combined analysis of static and dynamic cell mechanics with unbiased transcriptomics for thousands of single cells

  Akifumi Shiomi; Taikopaul Kaneko; Kaori Nishikawa; Dino Di Carlo; Hirofumi Shintaku

  International Symposium on Mechanical control of biological self-organization, 18 Jun. 2024

  
• Combined Analysis of Cell Mechanics and Transcriptome

  Akifumi Shiomi

  IEEE-NEMS 2024, 03 May 2024, Invited

  
• Combined analysis of mechanical properties and transcriptome in thousands of single cells

  Akifumi Shiomi; Taikopaul Kaneko; Kaori Nishikawa; Hirofumi Shintaku

  The 61th Annual Meeting of the Biophysical Society of Japan, 14 Nov. 2023, Invited

  
• ELASTOMICS: HIGH-THROUGHPUT MECHANICAL PHENOTYPING AND TRANSCRIPTOMICS OF SINGLE CELLS

  Akifumi Shiomi; Taikopaul Kaneko; Kaori Nishikawa; Hirofumi Shintaku

  microTAS 2023, 16 Oct. 2023

  
• ELASTomics: Combined analysis of mechanical phenotype of cellular surface and transcriptome at single-cell resolution

  Akifumi SHIOMI; Taikopaul KANEKO; Kaori NISHIKAWA; Hirofumi SHINTAKU

  2023 Physics and Chemistry of Microfluidics Gordon Research Conference, 07 Jun. 2023

  
• ELASTomics: Combined analysis of mechanical phenotype of cellular surface and transcriptome at single-cell resolution

  Akifumi SHIOMI; Taikopaul KANEKO; Kaori NISHIKAWA; Hirofumi SHINTAKU

  2023 Physics and Chemistry of Microfluidics Gordon Research Seminar, 04 Jun. 2023

  
• Combined analysis of mechanical phenotype of cellular membrane and transcriptome in cellular senescence

  Akifumi SHIOMI; Taikopaul KANEKO; Kaori NISHIKAWA; Hirofumi SHINTAKU

  Micro-Nano Science & Technology Division in JSME, 16 Nov. 2022

  
• Combined analysis of mechanical phenotype of cellular membrane and transcriptome using nanoelectroporation

  Akifumi SHIOMI; Taikopaul KANEKO; Kaori NISHIKAWA; Hirofumi SHINTAKU

  The 95rd Annual Meeting of the Japanese Biochemical Society, 09 Nov. 2022

  
• 微小電気穿孔法を用いた細胞の膜張力と遺伝子発現の統合解析

  Akifumi SHIOMI; Taikopaul KANEKO; Kaori NISHIKAWA; Hirofumi SHINTAKU

  Single cell Genomics Japan 2022, 30 Aug. 2022

  
• Profiling of membrane-mechanical phenotype and gene expression in thousands of single cells

  Akifumi Shiomi; Taikopaul Kaneko; Kaori Nishikawa; Hirofumi Shintaku

  Pacifichem 2021, 21 Dec. 2021

  
• A combined analysis of membrane-mechanical phenotyping and transcriptomics using nanoelectroporation

  Akifumi SHIOMI; Taikopaul KANEKO; Kaori NISHIKAWA; Hirofumi SHINTAKU

  The 59th Annual Meeting of the Biophysical Society of Japan, 25 Nov. 2021

  
• Membrane mechanical phenotyping combined with transcriptome analysis

  Akifumi SHIOMI; Taikopaul KANEKO; Kaori NISHIKAWA; Hirofumi SHINTAKU

  Mechanical Engineering Congress 2021 Japan, 07 Sep. 2021

  
• Phospholipid scramblase-mediated cell deformability

  塩見 晃史; 長尾 耕治郎; 従二 直人; 村手 源英; 小林 俊秀; 鈴木 量; 田中 求; 程 久美子; 新宅 博文; 梅田 眞郷

  The 93rd Annual Meeting of the Japanese Biochemical Society, 15 Sep. 2020, Invited

  
• リン脂質スクランブラーゼXKRによる昆虫細胞膜の高粘弾性変形能

  塩見 晃史; 長尾 耕治郎; 山本 暁久; 鈴木 量; 田中 求; 梅田 眞郷

  The 57th Annual Meeting of the Biophysical Society of Japan, 24 Sep. 2019

  
• 昆虫細胞の形質膜における特異な膜構築機構と変形能の解明

  塩見 晃史; 長尾 耕治郎; 山本暁久; 鈴木量; 田中 求; 梅田眞郷

  The 92nd Annual Meeting of the Japanese Biochemical Society, 18 Sep. 2019

  
• Extreme deformability of insect cell membranes is acquired by constitutive scrambling of phospholipids.

  Masato Umeda; Akifumi Shiomi; Kohjiro Nagao

  2019 Lipids, Molecular & Cellular Biology of Gordon Research Conferences

  
• The unique membrane formation and cellular deformability in Drosophila

  Shiomi Akifumi; Nagao Kohjiro; Toya Kaede; Suzuki Ryo; Tanaka Motomu; Ui-Tei kumiko; Umada Masato

  第91回日本生化学会大会

  
• リン脂質スクランブラーゼXKRによる細胞変形能の制御機構とその生理機能

  塩見晃史; 長尾耕治郎; 従二直人; 鈴木量; 田中求; 原雄二; 梅田眞郷

  第60回日本脂質生化学会

  
• The unique membrane formation and cellular deformability in Drosophila

  Akifumi Shiomi; Kohjiro Nagao; Naoto Juni; Ryo Suzuki; Motomu Tanaka; Kumiko Ui-Tei; Masato Umeda

  Consortium of Biological Sciences 2017 (ConBio2017)

  
• Remarkable deformability of insect cell is supported by constitutively active phospholipid scramblase.

  Kohjiro Nagao; Akifumi Shiomi; Masato Umeda

  Lipids, Molecular & Cellular Biology of Gordon Research Conferences 2017

  
• 昆虫細胞の特異な膜構築と変形能

  塩見晃史; 長尾耕治郎; 巽和也; 中部主敬; 鈴木量; 田中求; 梅田眞郷

  第59回日本脂質生化学会

  

Books and Other Publications

• Mechanical phenotyping with unbiased transcriptomics using nanopore-electroporation

  Akifumi Shiomi; Jin Kitamura; Junichi Murai; Taikopaul Kaneko; Misa Minegishi; Hirofumi Shintaku, Joint work, The CELL

  Mar. 2026

  
• 白眉センターだより Vol.23

  Joint editor

  Feb. 2026

  
• 次世代バイオテクノロジーへの招待

  塩見, 尚史; 塩見, 晃史

  大学教育出版, Nov. 2021

  Find Kyoto University's collection of books :

  
• 生命科学が解き明かす食と健康

  塩見, 尚史; 塩見, 晃史, Joint work

  大学教育出版, Apr. 2020

  Find Kyoto University's collection of books :

  
• 生命科学が解き明かす体の秘密

  塩見, 尚史; 塩見, 晃史, Joint work

  大学教育出版, Jun. 2017

  Find Kyoto University's collection of books :

  

Awards

• 21 Nov. 2025

  研究開発奨励賞(一般財団法人エヌエフ基金)
• 24 Apr. 2025

  日本機械学会奨励賞
• 17 Dec. 2024

  JST-CREST 多細胞 若手の会 2024 YORC発表賞
• 28 Jun. 2024

  IUPAB2024 Student and Early Career Researcher Poster Award
• 17 Feb. 2023

  Sysmex賞（シスメックス株式会社）
• 01 Nov. 2021

  若手招待講演賞（日本生物物理学会）
• 18 Sep. 2019

  日本生化学会若手優秀発表賞
• 25 Sep. 2019

  日本生物物理学会学生発表賞
• 01 Feb. 2022

  優秀講演論文表彰（日本機械学会）

External funds: Kakenhi

• 細胞の力学特性から解き明かす細胞競合

  Grant-in-Aid for Early-Career Scientists

  Basic Section 44010:Cell biology-related

  Kyoto University

  塩見 晃史

  From 01 Apr. 2025, To 31 Mar. 2028, Granted

  力学特性;多細胞;エレクトロポレーション;細胞競合

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-25K18469/
• 多細胞が織りなす協調的な力学秩序解析法の開発

  Grant-in-Aid for Transformative Research Areas (A)

  Transformative Research Areas, Section (III)

  Kyoto University

  塩見 晃史

  From 01 Apr. 2025, To 31 Mar. 2027, Granted

  力学特性;1細胞RNA-seq;エレクトロポレーション;空間情報

  https://kaken.nii.ac.jp/grant/KAKENHI-PUBLICLY-25H01806/
• 細胞の遺伝子発現と力学的境界条件が織りなすオルガノイドの生体秩序

  Grant-in-Aid for Transformative Research Areas (A)

  Transformative Research Areas, Section (III)

  Institute of Physical and Chemical Research

  塩見 晃史

  From 01 Apr. 2023, To 31 Mar. 2025, Project Closed

  1細胞RNA-seq;力学特性;細胞表面張力;変形能;エレクトロポレーション;マイクロ流路;細胞競合;機械特性;1細胞RNAシーケンシング;遺伝子発現;細胞集団ダイナミクス;オルガノイド;トラックエッチド膜;細胞老化

  https://kaken.nii.ac.jp/grant/KAKENHI-PUBLICLY-23H04724/
• Combined analysis of mechanical properties and transcriptome in thousands of single cells

  Grant-in-Aid for Early-Career Scientists

  Basic Section 44010:Cell biology-related

  Institute of Physical and Chemical Research

  Akifumi Shiomi

  From 01 Apr. 2022, To 31 Mar. 2025, Project Closed

  1細胞RNA-seq;機械特性;細胞表面張力;変形能;遺伝子発現;エレクトロポレーション;トラックエッチド膜;細胞老化;リン脂質;オミックス解析;膜張力;老化

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22K15113/
• Elucidation of molecular mechanisms underlying lipid-mediated myofiber regeneration

  Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))

  Medium-sized Section 59:Sports sciences, physical education, health sciences, and related fields

  University of Shizuoka

  Yuji Hara

  From 07 Oct. 2021, To 31 Mar. 2025, Project Closed

  脂質動態;脂質配向性;骨格筋再生;筋衛星細胞;骨格筋幹細胞;筋再生;機械受容イオンチャネル;細胞分裂;細胞融合;リン脂質;筋管形成;超解像イメージング;膜脂質動態

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-21KK0174/
• Measurement of single-cell dynamics with nanoelectroporation

  Grant-in-Aid for Challenging Research (Pioneering)

  Medium-sized Section 28:Nano/micro science and related fields

  Kyoto University;Institute of Physical and Chemical Research

  Hirofumi Shintaku

  From 09 Jul. 2021, To 31 Mar. 2024, Project Closed

  1細胞;RNA-sequencing;マイクロ流体工学;オミクス;電気泳動;造血幹細胞

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-21K18194/

Education

Teaching subject(s)

• From 01 Apr. 2026, To 31 Mar. 2027

  ILAS Seminar

  Z001, Spring, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2026, To 31 Mar. 2027

  Global Frontier in Life Science A

  1018, Spring, Graduate School of Biostudies, 2

Academic, Social Contribution

Committee Memberships

• From Apr. 2024, To Mar. 2025

  Field Expert Committee Members, The Biophysical Society of Japan

Academic Contribution

• 

  京都を学ぶ～知がつなぐ時代と分野の架け橋～

  Planning, management, etc.

  塩見晃史, From 24 Oct. 2025, To 24 Oct. 2025