Publications
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Corresponding authors of each publication are marked with asterisks (*).

2026

  1. Cell-Size Confinement Drives Size-Dependent Scaling of Intracellular Reaction-Diffusion Waves for Robust Patterning
    #S Takada, #S Kohyama, M Yanagisawa, N Doi, N Yoshinaga*, K Fujiwara*.
    (#: contributed equally to this work)
    Small Science 6(4), e202500643

    2. Review

  2. Mirror life at the crossroads: Report on the symposia in Japan for discussion toward mirror life synthesis
    K Fujiwara*, W Aoki, C Furusawa, A Hasegawa, G Hayashi, D Kiga, K Mikami, S Takada, Y Shimizu.
    Biophysics and Physicobiology 23(1), e230008

    3. 解説記事・総説

  3. 鏡像生命創成への技術と社会のロードマップ
    藤原 慶、見上公一
    実験医学 2026年4月号 pp.42-45

    4. 2025

      Review

    1. Beyond Simplifications: Overlooked Physics of Macromolecular Behaviors in Living Cells
      M Yanagisawa*, K Fujiwara*.
      Macromolecules 58(18), pp.9557-9566

      2. 解説記事・総説

    2. 細胞空間における界面が反応拡散波の形成と特性に与える効果
      藤原 慶、髙田咲良
      Colloid & Interface Communications 50(4), pp.42-45

    3. 見えてきた「隣人」としての鏡像生命
      大澤博隆、藤原 慶
      S-Fマガジン(早川文庫) 2026年2月号(2025年12月25日出版)、p.94-97

      4. 著書

    4. 鏡の国の生き物をつくる SFで踏み出す鏡像生命学の世界 (日刊工業新聞)
      監修・著：藤原慶、監修：大澤博隆、長谷川愛
      著：柞刈湯葉、八島游舷、麦原遼、茜灯里、瀬名秀明
      ISBN:9784526084034

      5. 2024

      1. STALL-seq: mRNA-display selection of bacterial and eukaryotic translational arrest sequences from large random-sequence libraries
        T Hamano, Y Nagumo, T Umehara, K Hirono, K Fujiwara, H Taguchi, Y Chadani, N Doi*
        J. Biol. Chem. 300(12), 107978

      2. Cell-free protein expression by a reconstituted transcription-translation system energized by sugar catabolism
        G Sato, S Miyazawa, N Doi, K Fujiwara*
        Molecules 29(13), 2956, DOI: 10.3390/molecules29132956

      3. Metabolic tug-of-war between glycolysis and translation revealed by a biochemical reconstitution
        G Sato, S Kinoshita, TG Yamada, S Arai, T Kitaguchi, A Funahashi, N Doi, K Fujiwara*
        ACS Synthetic Biology 13(5), 1572-1581, DOI: 10.1021/acssynbio.4c00209

        4. Review

      4. Artificial cell system as a tool for investigating pattern formation mechanisms of intracellular reaction-diffusion waves
        S Takada*, K Fujiwara.
        Biophysics and Physicobiology 21(4), e210022

        5. 2023

        1. Multimolecular Competition Effect as a Modulator of Protein Localization and Biochemical Networks in Cell-size Space
          S Nishikawa, G Sato, S Takada, S Kohyama, G Honda, M Yanagisawa, Y Hori, N Doi, N Yoshinaga, K Fujiwara*
          Advanced Science 11(6), 2308030. DOI:10.1002/advs.202308030

        2. Phase-Separated Giant Liposomes for Stable Elevation of α-Hemolysin Concentration in Lipid Membranes
          M Kobayashi,H Noguchi, G Sato, C Watanabe, K Fujiwara*, M Yanagisawa*
          Langmuir 39, 32, pp.11481-11489, DOI:10.1021/acs.langmuir.3c02019

          3. 総説

        3. 生命の折り合い：単純と複雑の調和
          藤原 慶、栁澤実穂
          現代化学, 2024年1月号, pp. 26-28 (2023)

        4. 酵素をひたすら混ぜる研究
          藤原 慶
          生物工学会誌, 101(12) pp. 639 (2023)

          5. 2022

          1. Cytoplasmic delivery of siRNA using human-derived membrane penetration-enhancing peptide
            M Nakamura, K Fujiwara, N Doi*.
            J Nanobiotech 20, 458, DOI;10.1186/s12951-022-01667-4

          2. Controlling the periodicity of a reaction-diffusion wave in artificial cells by a two-way energy supplier
            S Takada, N Yoshinaga, N Doi, K Fujiwara*.
            ACS Nano, 16(10), 16853-16861, DOI:10.1021/acsnano.2c06756

          3. Mode selection mechanism in traveling and standing waves revealed by Min wave reconstituted in artificial cells
            S Takada, N Yoshinaga*, N Doi, K Fujiwara*.
            Science Advances, 8, eabm8460, DOI:10.1126/sciadv.abm8460

          4. Characterization of the membrane penetration-enhancing peptide S19 derived from human syncytin-1 for the intracellular delivery of TAT-fused proteins
            M Suzuki, K Iwaki, M Kikuchi, K Fujiwara, N Doi*.
            Biochem Biophys Res Comm, 586:63-67, DOI:10.1016/j.bbrc.2021.11.065

            5. 総説

          5. Min波の人工細胞内再構成とそこから見えた細胞サイズ空間効果
            光山 隼史、義永 那津人、藤原 慶
            生物物理, 62(1):19-23

            6. Review

          6. Cell-Size Space Regulates the Behavior of Confined Polymers: From Nano- and Micromaterials Science to Biology
            M Yanagisawa*, C Watanabe, N Yoshinaga, K Fujiwara*.
            Langmuir, 38(39), 11811?11827, DOI:10.1021/acs.langmuir.2c01397

            7. 2021

            1. Activation of a diluted E. coli cell-free transcription-translation system within liposomes by hypertonic concentration
              Y Matsui, T Akui, N Doi, K Fujiwara*.
              STAR protocols, 2(4):101003, doi:10.1016/j.xpro.2021.101003.

            2. Transcription-translation of Escherichia coli genome within artificial cells
              T Deyama, Y Matsui, Y Chadani, Y Sekine, N Doi, K Fujiwara*.
              Chemical Communications, 57, pp.10367-10370, DOI: 10.1039/d1cc04401j

            3. System concentration shift as a regulator of transcription-translation system within liposomes
              #T Akui, #K Fujiwara*, G Sato, M Takinoue, SM Nomura, N. Doi.
              (#: contributed equally to this work)
              iScience, 24(8), 102859, DOI:10.1016/j.isci.2021.102859

            4. Switching ON of transcription-translation system using GUV fusion by co-supplementation of calcium with long-chain polyethylene glycol
              Y Uwaguchi, K Fujiwara*, N Doi.
              ChemBioChem, 22, 2319-2324, DOI:10.1002/cbic.202100100

            5. A relationship between NTP and cell extract concentration for cell-free protein expression
              K Takahashi, G Sato, N Doi, K Fujiwara*
              Life, 11(3), 237, DOI:10.3390/life11030237

              6. 和文

            6. 大学の枠を越えたオンライン生体分子デザイン コン ペティションの 取り組み
              村田智、葛谷明紀、藤原 慶、平 順一、川又生吹、佐藤佑介、瀧ノ上正浩、野村 M. 慎一郎、角五 彰、堀 豊、安部桂太
              工学教育, 69 巻 4 号 pp. 4_31-4_39

              7. 翻訳

            7. Synthetic Biology 合成生物学 (ニュートンプレス)
              原著：Synthetic Biology: A Very Short Introduction (Jamie A. Davies)
              監訳: 藤原 慶、訳：徳永 美恵

              8. 著書

            8. これだけ！ 生化学 第2版 (秀和システム)
              著：生化学若い研究者の会 (執筆、編集を分担)、監修：稲垣賢二

              9. 2020

              1. Conformational equilibrium of MinE regulates allowable concentration ranges of a protein wave for cell division
                S Kohyama, K Fujiwara*, N Yoshinaga, N Doi
                Nanoscale, 12, 11960 - 11970, doi: 10.1039/D0NR00242A

              2. Self-Organization Assay for Min Proteins of Escherichia coli in Micro-droplets Covered with Lipids
                S Kohyama, K Fujiwara*, N Yoshinaga, N Doi
                bio-protocol, 10(6): e3561, doi: 10.21769/BioProtoc.3561

              3. Microfluidic screening system based on boron-doped diamond electrodes and dielectrophoretic sorting for directed evolution of NAD(P)-dependent oxidoreductases.
                H Goto, Y Kanai, A Yotusui, S Shimokihara, S Shitara, R Oyobiki, K Fujiwara, T Watanabe, Y Einaga, Y Matsumoto, N Miki, N Doi*
                Lab on a chip, 20(4):852-861, doi: 10.1039/C9LC01263J

                4. 2019

                1. Regulation of spatiotemporal patterning in artificial cells by a defined protein expression system
                  #A Yoshida, #S Kohyama, #K Fujiwara*, S Nishikawa, N Doi
                  (#: contributed equally to this work)
                  Chemical Science, 10, pp. 11064-11072 (2019), doi: 10.1039/C9SC02441G

                2. Cell-sized confinement controls generation and stability of a protein wave for spatiotemporal regulation in cells
                  S Kohyama, N Yoshinaga*, M Yanagisawa, K Fujiwara*, N Doi
                  eLife, doi: 10.7554/eLife.44591

                  3. 展望記事

                3. 酵素を内包した人工細胞が拓く新しい醸造業や医薬品の開発
                  藤原 慶, MDB 技術予測レポート, 項目36, (2019)

                  4. 2018

                  1. A dual system using compartmentalized partnered replication for selection of arsenic-responsive transcriptional regulator
                    SL Aye, K Fujiwara, N Doi*
                    J. Biochem., 164(5), pp. 341-348, doi.org/10.1093/jb/mvy055

                  2. Engineering of DNA polymerase I from Thermus thermophilus using compartmentalized self-replication
                    SL Aye, K Fujiwara, A Ueki, N Doi*
                    Biochem. Biophys. Res. Comm., 499(2), pp. 170-176

                  3. Increasing elasticity through changes in the secondary structure of gelatin by gelation in a microsized lipid space
                    A Sakai, #Y Murayama, #K Fujiwara,T Fujisawa, S Sasaki, S Kidoaki, M Yanagisawa*
                    (#: contributed equally to this work)
                    ACS Central Science, 4(4), pp.477-483

                  4. Artificial cell fermentation as a platform for highly efficient cascade conversion
                    K Fujiwara*, T Adachi, N Doi
                    ACS Synthetic Biology, 7(2), pp 363-370 (2018), doi: 10.1021/acssynbio.7b00365

                    5. Review

                  5. Single micrometer-sized gels: Unique mechanics and characters for applications
                    M Yanagisawa*, C Watanabe, K Fujiwara
                    Gels, 4(2), 29, (2018); doi:10.3390/gels4020029

                    6. 総説

                  6. 細胞サイズ脂質膜小胞による”発酵”生産の可能性
                    藤原 慶, バイオサイエンスとインダストリ－, 76(4) pp. 302-303 (2018)

                    7. 2017

                    1. Liposomal internal viscosity affects the fate of membrane deformation induced by hypertonic treatment
                      #K Fujiwara*, #M Yanagisawa*
                      (#: contributed equally to this work)
                      Soft Matter, 13, pp. 9192-9198 (2017)

                    2. Universal glass-forming behavior of in vitro and living cytoplasm
                      #K Nishizawa, #K Fujiwara, M Ikenaga, N Nakajo, M Yanagisawa, and D Mizuno*
                      (#: contributed equally to this work)
                      Scientific Report, 7, Article number: 15143 (2017). doi:10.1038/s41598-017-14883-y

                    3. In vitro transcription-translation using bacterial genome as a template to reconstitute intracellular profile
                      #K Fujiwara*, #T Sawamura, T Niwa, T Deyama, SM Nomura, H Taguchi, N Doi
                      (#: contributed equally to this work)
                      Nucleic Acids Research, 45(19), pp. 11449-11458 (2017) DOI: 10.1093/nar/gkx776

                    4. DNA cytoskeleton for stabilizing artificial cells.
                      C Kurokawa, K Fujiwara, M Morita, I Kawamata, Y Kawagishi, A Sakai, Y Murayama, S M. Nomura, S Murata, M Takinoue*, M Yanagisawa*
                      Proc. Natl. Acad. Sci. USA, 114(28), pp. 7228-7233 (2017), doi: 10.1073/pnas.1702208114

                    5. Human-derived fusogenic peptides for the intracellular delivery of proteins.
                      K Sudo, K Niikura, K Iwaki, S Kohyama, K Fujiwara, N Doi*
                      J. Control. Release, 255(10), pp. 1-11 (2017), doi:10.1016/j.jconrel.2017.03.398

                      6. 著書

                    6. ペプチド医薬品のスクリーニング・安定化・製剤化技術
                      技術情報協会, 「1-4. mRNAディスプレイ法によるペプチドのスクリーニング」
                      須藤慧, 藤原 慶, 土居信英

                    7. 人工細胞の創製とその応用
                      CMC出版, 植田充美編,「3-4. 無細胞システムによる生命システムの理解」, 藤原 慶

                      8. 2016

                      1. In vitro selection of bispecific diabody fragments using covalent bicistronic DNA display.
                        M Nakayama, S Komiya, K Fujiwara, K Horisawa, N Doi*
                        Biochem. Biophys. Res. Comm., 478(16), pp. 606-611 (2016)

                      2. Biochemical preparation of cell extract for cell-free protein synthesis without physical disruption.
                        K Fujiwara*, N Doi
                        PLOS ONE, 11(4): e0154614. (2016) doi:10.1371/journal.pone.0154614

                      3. Identification of novel in vivo obligate GroEL/ES substrates based on data from a cell-free proteomics approach.
                        T Niwa, K Fujiwara, H Taguchi*
                        FEBS Lett., 590 (2), pp. 251-257 (2016)

                        4. 翻訳

                      4. 自然世界の高分子 (吉岡書店, 原題：Giant Molecules)
                        原著：Alexander Y. Grosberg and Alexei R. Khokhlov、監訳: 田中 基彦、鴇田 正之
                        訳: 田中 基彦、鴇田 正之、柳沢 実穂、坂上 貴洋、藤原 慶

                        5. 著書

                      5. DNA分子デザインのすべて～BIOMOD虎の巻
                        CBT学会eBOOK、分子ロボティクス研究会編(1章3,4,5,11の執筆担当：藤原 慶)

                        6. 2015

                        1. PURE mRNA display for in vitro selection of single-chain antibodies.
                          Y Nagumo, K Fujiwara, K Horisawa, H Yanagawa, N Doi*
                          J. Biochem., 159(5), pp. 519-526 (2015)

                        2. Droplet-Shooting and Size-Filtration (DSSF) Method for Synthesis of Cell-Sized Liposomes with Controlled Lipid Compositions.
                          M Morita, H Onoe, M Yanagisawa, H Ito, M Ichikawa, K Fujiwara, H Saito, M Takinoue*
                          ChemBioChem, 16 (14), pp. 2029-2035 (2015), DOI: 10.1002/cbic.201500354

                        3. Generation of monodisperse cell-sized microdroplets using a centrifuge-based axisymmetric co-flowing microfluidic device.
                          H Yamashita, M Morita, H Sugiura, K Fujiwara, H Onoe, M Takinoue*
                          J. Biosci. Bioeng., 119 (4), pp. 492-495 (2015), DOI: 10.1016/j.jbiosc.2014.09.018

                        4. Peptide sequences converting polyglutamine into a prion in yeast.
                          W Odani, K Urata, M Okuda, S Okuma, H Koyama, CG Pack, K Fujiwara, T Nojima, M Kinjo, S Kawai-Noma, H Taguchi*
                          FEBS Lett., 282 (3), pp. 477-490 (2015)

                          5. 総説

                        5. 高分子混雑効果を細胞モデル系から読み解く
                          柳澤 実穂, 藤原 慶
                          生物物理, 55(5) pp. 246-249 (2015)

                        2014

                        1. Multiple patterns of polymer gels in microspheres due to the interplay among phase separation, wetting, and gelation.
                          M Yanagisawa*, S Nigorikawa, T Sakaue, K Fujiwara, M Tokita.
                          Proc. Natl. Acad. Sci. USA, 111 (45), 15894-15899 (2014)

                        2. Conversion of a Chaperonin GroEL-Independent Protein into an Obligate Substrate.
                          T Ishimoto, K Fujiwara, T Niwa, H Taguchi*.
                          J. Biol. Chem., 289: 32073-32080 (2014)

                        3. Introducing Micrometer-Sized Artificial Objects into Live Cells: A Method for Cell-Giant Unilamellar Vesicle Electrofusion.
                          AC Saito, T Ogura, K Fujiwara, S Murata, SM Nomura*.
                          PLoS ONE, (9), e106853 (2014)

                        4. Generation of Giant Unilamellar Liposomes Containing Biomacromolecules at Physiological Intracellular Concentrations using Hypertonic Conditions.
                          K Fujiwara*, M Yanagisawa*.
                          ACS Synthetic Biology, 3 (12), pp 870-874 (2014): 10.1021/sb4001917

                          5. Review

                        5. Reconstitution of intracellular environments in vitro and in artificial cells.
                          K Fujiwara*, M Yanagisawa, SM Nomura.
                          BIOPHYSICS, 10 (0), pp. 43-48 (2014)

                          6. 和文

                        6. DNAナノテクノロジーのためのアウトリーチツールの開発と評価.
                          吉澤 慧, 藤原 慶, 野村 M.慎一郎, 村田 智*
                          形の科学会誌, 2014, 29(2)： 表紙を飾りました

                          7. 紀要

                        7. The rapid synthesis of cell-sized liposomes by centrifuge-based microfluidic device.
                          M Morita, H Onoe, M Yanagisawa, K Fujiwara, H Saito, M Takinoue.
                          18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014, pp. 336-338 (2014)

                          8. 著書

                        8. これだけ！ 生化学 (秀和システム)
                          著：生化学若い研究者の会 (執筆、編集を分担)、監修：稲垣賢二

                        2013

                        1. A bacterial salt sensor created by multiplying phenotypes of GroE-depleted Escherichia coli.
                          K Fujiwara*, KB Aoi, SM Nomura*.
                          Analytical methods, 5 (21), 5918-5922 (2013)

                        2. Cooperative working of bacterial chromosome replication proteins generated by a reconstituted protein expression system.
                          K Fujiwara*, T Katayama, SM Nomura.
                          Nucleic Acids Research, 41 (14): 7176-7183 (2013) doi:10.1093/nar/gkt489

                        3. Condensation of an additive-free cell extract to mimic the conditions of live cells.
                          K Fujiwara*, SM Nomura*.
                          PLoS ONE 8(1): e54155 (2013) doi:10.1371/journal.pone.0054155

                        4. Physicochemical analysis from real-time imaging of liposome tubulation reveals the characteristic of individual F-BAR domain proteins.
                          Y Takiguchi, T Itoh, K Tsujita, S Yamada, M Yanagisawa, K Fujiwara, M Ichikawa, A Yamamoto, K Takiguchi*.
                          Langmuir, Jan 8;29(1):328-36 (2013)

                          5. 紀要

                        5. Molecular robotics approach for constructing artificial cell model
                          SM Nomura*, Y Sato, K Fujiwara.
                          12th European Conference on Artificial Life, ECAL, 488-491 (2013)

                        6. Construction of remote-control supramolecular micro-crawler
                          D Komatsu, K Fujiwara, SM Nomura*.
                          12th European Conference on Artificial Life, ECAL, 208-209 (2013)

                          7. 総説

                        7. 細胞内濃厚環境に近づいた無細胞発現系
                          藤原 慶, 野村 M. 慎一郎, 生物物理, 53(5), pp.262-263 (2013)

                        8. 細胞抽出液の濃縮技術～細胞再構築に向けた挑戦～
                          野村 M. 慎一郎, 藤原 慶, 月刊バイオインダストリ, Vol. 30、No.8, p.59-65 (2013)

                        2012

                        1. Cell-Sized Confinement in Microspheres Accelerate the Reaction of Gene Expression.
                          A Kato, M Yanagisawa, YT Sato, K Fujiwara, K Yoshikawa*.
                          Scientific Report, 2, Article number: 283 (2012)

                        2. Mechanism of overexpression of methionine synthase in chaperonin-depleted Escherichia coli.
                          K Fujiwara*, H Taguchi.
                          Microbiology, 158, 917-924 (2012)

                        2003-2011

                        1. A systematic survey of in vivo obligate chaperonin-dependent substrates.
                          K Fujiwara, Y Ishihama, K Nakahigashi, T Soga, H Taguchi*.
                          The EMBO Journal, Vol. 29, No.9, 1552-1564 (2010)

                        2. Filamentous morphology in GroE-depleted Escherichia coli induced by impaired folding of FtsE.
                          K Fujiwara, H Taguchi*.
                          J. Bacteriol., Vol. 189, No. 16, 5860-5966 (2007)

                        3. Involvement of the arginine repressor in lysine biosynthesis of Thermus thermophilus.
                          K Fujiwara, T Tsubouchi, T Kuzuyama, Nishiyama M*.
                          Microbiology, vol. 152, 3585-3594 (2006)

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