2023.4～2024.3

• Omachi Y,Saito N,Furusawa C , Rare-event sampling analysis uncovers the fitness landscape of the genetic code , PLoS Comput. Biol. , 2023
  


• Takano S,Takahashi H,Yama Y,Miyazaki R,Furusawa C,Tsuru S , Inference of transcriptome signatures of Escherichia coli in long-term stationary phase , Sci. Rep. , 2023
  


• Tsutsumi M,Saito N,Koyabu D,Furusawa C , A deep learning approach for morphological feature extraction based on variational auto-encoder: an application to mandible shape , NPJ Syst. Biol. Appl. , 2023
  


• Sone M,Navanopparatsakul K,Takahashi S,Furusawa C,Hirasawa T , Loss of function of Hog1 improves glycerol assimilation in Saccharomyces cerevisiae , World J. Microbiol. Biotechnol. , 2023
  


• Shibai A,Izutsu M,Kotani H,Furusawa C , Non-monotonic Relationship between Mutation Rate and Speed of adaptation under Antibiotic Exposure in Escherichia coli , Preprint , 2023
  


• Kanai Y,Tsuru S,Furusawa C , Insertion sequences: simple mobile elements with rich ecological and evolutionary structures , Elsevier , 2023
  


• Himeoka Y,Furusawa C , Perturbation-response analysis ofin silicometabolic dynamics in nonlinear regime: Hard-coded responsiveness in the cofactors and network sparsity , Preprint , 2023
  


• Sato TU,Furusawa C,Kaneko K , Prediction of cross-fitness for adaptive evolution to different environmental conditions: Consequence of phenotypic dimensional reduction , Phys. Rev. Res. , 2023
  


• Maeda T,Furusawa C , Laboratory evolution of antimicrobial resistance in bacteria to develop rational treatment strategies , Antibiotics (Basel) , 2024
  


• Uchida Y,Tsutsumi M,Ichii S,Irie N,Furusawa C , Deciphering the origin of developmental stability: The role of intracellular expression variability in evolutionary conservation , Evolution and Development , 2024
  


• Fujiwara T,Shingyoji C,Higuchi H , Versatile properties of dynein molecules underlying regulation in flagellar oscillation , Sci. Rep. , 2023
  


• Kondo Y,Sasaki K,Higuchi H , Fast backward steps and detachment of single kinesin molecules measured under a wide range of loads , Traffic , 2023
  


• Uwamichi M,Li H,Zhao Z,Yao Y,Higuchi H,Kawaguchi K,Sano M , Experimental identification of force, velocity, and nematic order relationships in active nematic cell monolayers , Preprint , 2024
  


• Rutjes F , Connecting chemical worlds , Chem. Int. , 2023
  


• Zhang Y,Goto Y,Suga H , Discovery, biochemical characterization, and bioengineering of cyanobactin prenyltransferases , Trends Biochem. Sci. , 2023
  


• Warashina S,Sato H,Zouda M,Takahashi M,Wada Y,Passioura T,Suga H,Watanabe Y,Matsumoto K,Mukai H , Two-chain mature hepatocyte growth factor-specific positron emission tomography imaging in tumors using 64Cu-labeled HiP-8, a nonstandard macrocyclic peptide probe , Mol. Pharm. , 2023
  


• Suzuki T,Yi C,Song J , Wolf Prize in Chemistry 2023: A celebration for chemical biology , ACS Chem. Biol. , 2023
  


• Sivakumar K,Venkadasamy VL,Amudhan G,Ann KJ,Goud GK,Nayani K,Gogoi J,Kuncha SK,Mainkar PS,Kruparani SP,Sankaranarayanan R , Design principles and functional basis of enantioselectivity of alanyl-tRNA synthetase and a chiral proofreader during protein biosynthesis , Nucleic Acids Res. , 2023
  


• Ma X,Bakhtina M,Shulgina I,Cantara WA,Kuzmishin Nagy AB,Goto Y,Suga H,Foster MP,Musier-Forsyth K , Structural basis of tRNAPro acceptor stem recognition by a bacterial trans-editing domain , Nucleic Acids Res. , 2023
  


• White SH , Fifty years of biophysics at the membrane frontier , Annu. Rev. Biophys. , 2023
  


• Ikenoue T,Oono M,So M,Yamakado H,Arata T,Takahashi R,Kawata Y,Suga H , A RaPID macrocyclic peptide that inhibits the formation of α-synuclein amyloid fibrils , Chembiochem , 2023
  


• Burkart M,Ishikawa F , Non-ribosomal peptide biosynthesis and engineering: Methods and protocols , Springer US , 2023
  


• Katoh T,Suga H , Translation initiation with exotic amino acids using EF-P-responsive artificial initiator tRNA , Nucleic Acids Research , 2023
  


• Goto Y,Suga H , Ribosomal synthesis of peptides bearing noncanonical backbone structures via chemical posttranslational modifications , Methods Mol. Biol. , 2023
  


• Saha A,Suga H,Brik A , Combining chemical protein synthesis and random nonstandard peptides integrated discovery for modulating biological processes , Acc. Chem. Res. , 2023
  


• Miura T,Malla TR,Owen CD,Tumber A,Brewitz L,McDonough MA,Salah E,Terasaka N,Katoh T,Lukacik P,Strain-Damerell C,Mikolajek H,Walsh MA,Kawamura A,Schofield CJ,Suga H , In vitro selection of macrocyclic peptide inhibitors containing cyclic γ2,4-amino acids targeting the SARS-CoV-2 main protease , Nat. Chem. , 2023
  


• Kawakami N,Sato H,Terasaka N,Matsumoto K,Suga H , MET-activating ubiquitin multimers , Angew. Chem. Weinheim Bergstr. Ger. , 2023
  


• Franck C,Patel K,Walport LJ,Christie M,Norman A,Passioura T,Suga H,Payne RJ,Mackay JP , Discovery and characterization of cyclic peptides selective for the C-terminal bromodomains of BET family proteins , Structure , 2023
  


• Katoh T,Suga H , A comprehensive analysis of translational misdecoding pattern and its implication on genetic code evolution , Nucleic Acids Res. , 2023
  


• Chen H,Katoh T,Suga H , Macrocyclic peptides closed by a thioether-bipyridyl unit that grants cell membrane permeability , ACS Bio Med Chem Au , 2023
  


• Lemma B,Zhang D,Vamisetti GB,Wentz BG,Suga H,Brik A,Lubkowski J,Fushman D , Mechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation , Nat. Commun. , 2023
  


• Zhang Y,Hamada K,Satake M,Sengoku T,Goto Y,Suga H , Switching prenyl donor specificities of cyanobactin prenyltransferases , J. Am. Chem. Soc. , 2023
  


• Dengler S,Howard RT,Morozov V,Tsiamantas C,Huang WE,Liu Z,Dobrzanski C,Pophristic V,Brameyer S,Douat C,Suga H,Huc I , Display selection of a hybrid foldamer-peptide macrocycle , Angew. Chem. Int. Ed Engl. , 2023
  


• Chang JS,Vinogradov AA,Zhang Y,Goto Y,Suga H , Deep learning-driven library design for the DE Novo discovery of bioactive thiopeptides , ACS Cent. Sci. , 2023
  


• Low JKK,Patel K,Jones N,Solomon P,Norman A,Maxwell JWC,Pachl P,Matthews JM,Payne RJ,Passioura T,Suga H,Walport LJ,Mackay JP , mRNA display reveals a class of high-affinity bromodomain-binding motifs that are not found in the human proteome , J. Biol. Chem. , 2023
  


• Ishii S,Chino H,Ode KL,Kurikawa Y,Ueda HR,Matsuura A,Mizushima N,Itakura E , CCPG1 recognizes endoplasmic reticulum luminal proteins for selective ER-phagy , Mol. Biol. Cell , 2023
  


• Kon K,Ode K,Mano T,Fujishima H,Tone D,Shimizu C,Shiono S,Yada S,Garﾃｧon J,Kaneko M,Shinohara Y,Takahashi RR,Yamada R,Shi S,Sumiyama K,Kiyonari H,Susaki E,Ueda HR , Cortical parvalbumin neurons are responsible for homeostatic sleep rebound through CaMKII activation , bioRxiv , 2023
  


• Shintani-Domoto Y,Ode KL,Nomura S,Abe H,Ueda HR,Sakatani T,Ohashi R , Elucidation of the mechanism of amyloid A and transthyretin formation using mass spectrometry-based absolute quantification , Virchows Arch. , 2023
  


• Wang Y,Cao S,Tone D,Fujishima H,Yamada RG,Ohno RI,Shi S,Matsuzawa K,Kaneko M,Ukai-Tadenuma M,Ukai H,Hanashima C,Kiyonari H,Sumiyama K,Ode KL,Ueda HR , Post-synaptic competition between calcineurin and PKA regulates mammalian sleep-wake cycles , Preprint , 2023
  


• Nonaka H,Sakamoto S,Shiraiwa K,Ishikawa M,Tamura T,Okuno K,Kondo T,Kiyonaka S,Susaki EA,Shimizu C,Ueda HR,Kakegawa W,Arai I,Yuzaki M,Hamachi I , Bioorthogonal chemical labeling of endogenous neurotransmitter receptors in living mouse brains , Proc. Natl. Acad. Sci. U. S. A. , 2024
  


• Watanabe RR,Kiper BT,Zarco-Zavala M,Hara M,Kobayashi R,Ueno H,Garcﾃｭa-Trejo JJ,Li CB,Noji H , Rotary properties of hybrid F1-ATPases consisting of subunits from different species , iScience , 2023
  


• Guo P,Noji H,Yengo CM,Zhao Z,Grainge I , Biological nanomotors with linear, rotation, or revolution motion mechanism , CRC Press , 2023
  


• Sano O , Partial differential equations , World Scientific Publishing , 2023
  


• Guo P,Wang A , Biomotors and their nanobiotechnology applications , CRC Press , 2023
  


• Ueno H,Sano M,Hara M,Noji H , Digital cascade assays for ADP- or ATP-producing enzymes using a femtoliter reactor array device , ACS Sens. , 2023
  


• Noji H , Rocking out biophysics in IUPAB2024 Kyoto! , Biophys. Physicobiol. , 2023
  


• Ichikawa Y,Hukushima K , Dataset size dependence of rate-distortion curve and threshold of posterior collapse in linear VAE , Preprint , 2023
  


• Yoshiyama K,Hukushima K , Higher-order tensor renormalization group study of the J_{1}-J_{2} Ising model on a square lattice , Phys. Rev. E. , 2023
  


• Yamaguchi M,Shiraishi N,Hukushima K , Proof of avoidability of the quantum first-order transition in transverse magnetization in quantum annealing of finite-dimensional spin glasses , J. Stat. Phys. , 2024
  


• Shiraishi K,Mizuno H,Ikeda A , Johari-Goldstein ﾎｲ relaxation in glassy dynamics originates from two-scale energy landscape , Proc. Natl. Acad. Sci. U. S. A. , 2023
  


• Hara Y,Mizuno H,Ikeda A , Microrheology near jamming , Preprint , 2023
  


• Viviana Palacio-Betancur, Julio C Armas-Pérez, Juan P Hernández-Ortiz, Juan J de Pablo, Norihiro Oyama, Hideyuki Mizuno, Atsushi Ikeda , Where physics meets chemistry meets biology for fundamental soft matter research , Soft Matter , 2023
  


• Hara Y,Mizuno H,Ikeda A , Heterogeneity and low-frequency vibrations in bidisperse sphere packings , Preprint , 2023
  


• Takaha Y,Mizuno H,Ikeda A , Arrhenius temperature dependence of the crystallization time of deeply supercooled liquids , Phys. Rev. Res. , 2024
  


• Kamijima T,Ito S,Dechant A,Sagawa T , Thermodynamic uncertainty relations for steady-state thermodynamics , Phys. Rev. E. , 2023
  


• Hoshino M,Nagayama R,Yoshimura K,Yamagishi JF,Ito S , Geometric speed limit for acceleration by natural selection in evolutionary processes , Phys. Rev. Res. , 2023
  


• Kolchinsky A,Ohga N,Ito S , Thermodynamic bound on spectral perturbations , arXiv e-prints , 2023
  


• Ohga N,Ito S,Kolchinsky A , Thermodynamic bound on the asymmetry of cross-correlations , Phys. Rev. Lett. , 2023
  


• Nagayama R,Yoshimura K,Kolchinsky A,Ito S , Geometric thermodynamics of reaction-diffusion systems: Thermodynamic trade-off relations and optimal transport for pattern formation , Preprint , 2023
  


• Sekizawa D,Ito S,Oizumi M , Decomposing thermodynamic dissipation of linear Langevin systems via oscillatory modes and its application to neural dynamics , Preprint , 2023
  


• Ito S , Geometric thermodynamics for the Fokker–Planck equation: stochastic thermodynamic links between information geometry and optimal transport , Inf. Geom. , 2024
  


• Fujimoto Y,Ito S , Game-theoretical approach to minimum entropy productions in information thermodynamics , Phys. Rev. Res. , 2024
  


• Pham TM,Kaneko K , Double-replica theory for evolution of genotype-phenotype interrelationship , Phys. Rev. Res. , 2023
  


• Sakata A,Kaneko K , Evolutionary shaping of low-dimensional path facilitates robust and plastic switching between phenotypes , Phys. Rev. Res. , 2023
  


• Kaneko K , Constructing universal phenomenology for biological cellular systems: an idiosyncratic review on evolutionary dimensional reduction , J. Stat. Mech. , 2024
  


• Ikawa K,Hiro S,Kondo S,Ohsawa S,Sugimura K , Coronin-1 promotes directional cell rearrangement in Drosophila wing epithelium , Cell Structure and Function , 2023
  


• Gauquelin E,Kuromiya K,Namba T,Ikawa K,Fujita Y,Ishihara S,Sugimura K , Mechanical convergence in mixed populations of mammalian epithelial cells , Eur. Phys. J. E Soft Matter , 2024
  


• Zhu W,Dong H,Xu R,You J,Yan DZ,Xiong C,Wu J,Bi K , Botrytis cinerea BcCDI1 protein triggers both plant cell death and immune response , Front. Plant Sci. , 2023
  


• Sasaki Y,Gonzﾃ｡lez-Tobﾃｳn J,Hino Y,Jin C,Li T,Nguyen TAN,Oakley B,Stevens D , 12th Japan-US seminar in Plant Pathology meeting report , Mol. Plant. Microbe. Interact. , 2023
  


• Hiruma K,Aoki S,Takino J,Higa T,Utami YD,Shiina A,Okamoto M,Nakamura M,Kawamura N,Ohmori Y,Sugita R,Tanoi K,Sato T,Oikawa H,Minami A,Iwasaki W,Saijo Y , A fungal sesquiterpene biosynthesis gene cluster critical for mutualist-pathogen transition in Colletotrichum tofieldiae , Nat. Commun. , 2023
  


• Takagi M,Hirata R,Aihara Y,Hayashi Y,Mizutani-Aihara M,Ando E,Yoshimura-Kono M,Tomiyama M,Kinoshita T,Mine A,Toda Y , Image-based quantification of Arabidopsis thaliana stomatal aperture from leaf images , Plant Cell Physiol. , 2023
  


• Mehlferber EC,Debray R,Conover AE,Sherman JK,Kaulbach G,Reed R,McCue KF,Ferrel JE,Khanna R,Koskella B , Phyllosphere microbial associations improve plant reproductive success , Front. Plant Sci. , 2023
  


• Ito M,Tajima Y,Ogawa-Ohnishi M,Nishida H,Nosaki S,Noda M,Sotta N,Kawade K,Kamiya T,Fujiwara T,Matsubayashi Y,Suzaki T , IMA peptides regulate root nodulation and nitrogen homeostasis by providing iron according to internal nitrogen status , Nat. Commun. , 2024
  


• Ujimatsu R,Takino J,Nakamura M,Haba H,Minami A,Hiruma K , A fungal transcription factorBOT6facilitates the transition of a beneficial root fungus into an adapted anthracnose pathogen , Preprint , 2024
  


• Hirai H,Sen Y,Tamura M,Ohta K , TOR inactivation triggers heterochromatin formation in rDNA during glucose starvation , Cell Rep. , 2023
  


• Sugiyama M,Ozawa T,Ohta K,Okada K,Niimi T,Yamaguchi K,Shigenobu S,Okada Y , Transcriptomic and functional screening of weapon formation genes implies significance of cell adhesion molecules and female-biased genes in broad-horned flour beetle , PLoS Genet. , 2023
  


• Tai YT,Fukuda T,Morozumi Y,Hirai H,Oda AH,Kamada Y,Akikusa Y,Kanki T,Ohta K,Shiozaki K , Fission yeast TORC1 promotes cell proliferation through Sfp1, a transcription factor involved in ribosome biogenesis , Mol. Cell. Biol. , 2023
  


• Morozumi Y,Mahayot F,Nakase Y,Soong JX,Yamawaki S,Sofyantoro F,Imabata Y,Oda AH,Tamura M,Kofuji S,Akikusa Y,Shibatani A,Ohta K,Shiozaki K , Rapamycin-sensitive mechanisms confine the growth of fission yeast below the temperatures detrimental to cell physiology , iScience , 2024
  


• Tsuchiya N,Oizumi M,Yamada M , Qualia Structure B Grant Proposal S75 76 77 , PsyArXiv , 2023
  


• Tsuchiya N,Saigo H,Phillips S,Taguchi S,Ishihara Y,Moriguchi Y,Nakano T,Koizumi A,Yamada M,Oizumi M,Horii T,Saji N,Taniguchi T , Qualia Structure Proposal (japanese Version) , OSF , 2023
  


• Kiyooka D,Oomoto I,Kitazono J,Kobayashi M,Matsubara C,Kobayashi K,Murayama M,Oizumi M , Single-cell resolution functional networks during sleep are segregated into spatially intermixed modules , Preprint , 2023
  


• Sasaki M,Takeda K,Abe K,Oizumi M , Unsupervised alignment in neuroscience: Introducing a toolbox for Gromov-Wasserstein optimal transport , Preprint , 2023
  


• Sekizawa D,Ito S,Oizumi M , Decomposing thermodynamic dissipation of linear Langevin systems via oscillatory modes and its application to neural dynamics , Preprint , 2023
  


• Kobayashi M,Noguchi H,Sato G,Watanabe C,Fujiwara K,Yanagisawa M , Phase-separated giant liposomes for stable elevation of ﾎｱ-hemolysin concentration in lipid membranes , Langmuir , 2023
  


• Shono M,Honda G,Yanagisawa M,Yoshikawa K,Shioi A , Spontaneous formation of uniform cell-sized microgels through water/water phase separation , Small , 2023
  


• Kanakubo Y,Watanabe C,Yamamoto J,Yanagisawa N,Sakuta H,Nikoubashman A,Yanagisawa M , Cell-sized confinements alter molecular diffusion in concentrated polymer solutions due to length-dependent wetting of polymers , ACS Mater. Au , 2023
  


• Tokita M,Uwataki M,Yamashita Y,Hara T,Yanagisawa M , Frictional properties of phase-separated agarose hydrogels in water permeation , Soft Matter , 2023
  


• Shono M,Aburatani K,Yanagisawa M,Yoshikawa K,Shioi A , Periodic alignment of binary droplets via a microphase separation of a tripolymer solution under tubular confinement , ACS Macro Lett. , 2024
  


• Nishikawa S,Sato G,Takada S,Kohyama S,Honda G,Yanagisawa M,Hori Y,Doi N,Yoshinaga N,Fujiwara K , Multimolecular competition effect as a modulator of protein localization and biochemical networks in cell-size space , Adv. Sci. (Weinh.) , 2024
  


• Okura T,Tahara M,Otsuki N,Sato M,Takeuchi K,Takeda M , Generation of a photocontrollable recombinant bovine parainfluenza virus type 3 , Microbiol. Immunol. , 2023
  


• Koganezawa Y,Wakamoto Y,Sato M,Umetani M , Detecting photoactivatable Cre-mediated gene deletion efficiency in Escherichia coli , Bio Protoc. , 2023
  


• Otabe T,Nihongaki Y,Sato M , A split CRISPR-Cpf1 platform for inducible gene activation , Methods Mol. Biol. , 2023
  


• Kato H,Okawa R,Ogasawara T,Hoshino Y,Hidaka N,Koga M,Kinoshita Y,Kobayashi H,Taniguchi Y,Fukumoto S,Nangaku M,Makita N,Hoshi K,Nakano K,Ito N , Effect of conventional treatment on dental complications and ectopic ossifications among 30 adults with XLH , J. Clin. Endocrinol. Metab. , 2023
  


• Sugawara Y,Kato H,Nagasaki M,Yoshida Y,Fujisawa M,Minegishi N,Yamamoto M,Nangaku M , CFH-CFHR1 hybrid genes in two cases of atypical hemolytic uremic syndrome , J. Hum. Genet. , 2023
  


• Yamaguchi S,Atarashi T,Okada A,Nasu S,Yamauchi T,Arase Y,Aizawa T,Nangaku M,Kadowaki T , Impact of the COVID-19 pandemic on health check-ups: A nationwide questionnaire survey in 639 healthcare facilities in Japan Society of Ningen Dock , JMA J. , 2023
  


• Li Q,Nishi H,Inoue R,Ueda S,Nangaku M , Chronic kidney disease prevalence and awareness in middle age and young old: Regional comparative study in Japan , Nephrology (Carlton) , 2023
  


• Kawabata C,Hirakawa Y,Inagi R,Nangaku M , Acetate attenuates kidney fibrosis in an oxidative stress-dependent manner , Physiol. Rep. , 2023
  


• Green JB,Mottl AK,Bakris G,Heerspink HJ,Mann JF,McGill JB,A , Design of the COmbinatioN effect of FInerenone anD EmpaglifloziN in participants with chronic kidney disease and type 2 diabetes using a UACR Endpoint study (CONFIDENCE) , Nephrology Dialysis Transplantation , 2023
  


• Nangaku M,Takama H,Ichikawa T,Mukai K,Kojima M,Suzuki Y,A , Randomized, double-blind, placebo-controlled phase 3 study of bardoxolone methyl in patients with diabetic kidney disease: design and baseline characteristics of the AYAME study , Nephrology Dialysis Transplantation , 2023
  


• Matsuura R,Komaru Y,Hamasaki Y,Nangaku M,Doi K , Benefit of higher blood pressure target in severe acute kidney injury treated by continuous renal replacement therapy , Shock , 2023
  


• Cherney DZI,de Zeeuw D,Heerspink HJL,Cardona J,Desch M,Wenz A,Schulze F,Nangaku M , Safety, tolerability, pharmacodynamics and pharmacokinetics of the soluble guanylyl cyclase activator BI 685509 in patients with diabetic kidney disease: A randomized trial , Diabetes Obes. Metab. , 2023
  


• Saigusa H,Mimura I,Kurata Y,Tanaka T,Nangaku M , Hypoxia-inducible lncRNA MIR210HG promotes HIF1ﾎｱ expression by inhibiting miR-93-5p in renal tubular cells , FEBS J. , 2023
  


• Nangaku M , Global perspective of kidney diseases: Challenges and changes , Nephrology (Carlton) , 2023
  


• Yamazaki T,Mimura I,Kurata Y,Tanaka T,Nangaku M , Dznep, a histone modification inhibitor, inhibits HIF1ﾎｱ binding to TIMP2 gene and suppresses TIMP2 expression under hypoxia , Physiol. Rep. , 2023
  


• Yoshida T,Matsuura R,Komaru Y,Miyamoto Y,Yoshimoto K,Hamasaki Y,Noiri E,Nangaku M,Doi K , Different roles of functional and structural renal markers measured at discontinuation of renal replacement therapy for acute kidney injury , Blood Purif. , 2023
  


• Sankoda A,Nagae Y,Waki K,Sze WT,Oba K,Mieno M,Nangaku M,Yamauchi T,Ohe K , Glycemic control, renal progression, and use of telemedicine phone consultations among Japanese patients with type 2 diabetes mellitus during the COVID-19 pandemic: Retrospective cohort study , JMIR Diabetes , 2023
  


• Kikuchi K,Nangaku M,Ryuzaki M,Yamakawa T,Ota Y,Hanafusa N,Sakai K,Kanno Y,Ando R,Shinoda T,Wakino S,Nakamoto H,Takemoto Y,Akizawa T,COVID-19 Task Force Committee of the Japanese Association of Dialysis Physicians, the Japanese Society for Dialysis Therapy, and the Japanese Society of Nephrology , Efficacy of molnupiravir and sotrovimab in Japanese dialysis patients with COVID-19 in clinical practice during the Omicron (BA.1 and BA.2) pandemic , Ther. Apher. Dial. , 2023
  


• Hidaka N,Murata H,Tachikawa K,Osaki K,Sekiyama T,Kinoshita Y,Kato H,Hoshino Y,Kimura S,Sunouchi T,Watanabe S,Nangaku M,Makita N,Michigami T,Ito N , The effect of asfotase Alfa on plasma and urine pyrophosphate levels and pseudofractures in a patient with adult-onset hypophosphatasia , JBMR Plus , 2023
  


• Yoshimoto K,Matsuura R,Komaru Y,Yoshida T,Miyamoto Y,Hamasaki Y,Inokuchi R,Nangaku M,Doi K , Solute clearance evaluation and filter clotting prediction in continuous renal replacement therapy , J. Clin. Med. , 2023
  


• Hagino K,Ichihashi N , In vitro transcription/translation-coupled DNA replication through partial regeneration of 20 aminoacyl-tRNA synthetases , ACS Synth. Biol. , 2023
  


• Yukawa K,Mizuuchi R,Ichihashi N , How prebiotic complexity increases through Darwinian evolution , Elsevier , 2023
  


• Seo K,Ichihashi N , Investigation of compatibility between DNA replication, transcription, and translation for in vitro central dogma , ACS Synth. Biol. , 2023
  


• Ohta K,Shimizu T,Oshima T,Ichihashi N , Genetic analysis of Bacillus subtilis stable L-forms obtained via long-term cultivation , J. Gen. Appl. Microbiol. , 2023
  


• Mizuuchi R,Ichihashi N , Minimal RNA self-reproduction discovered from a random pool of oligomers , Chemical Science , 2023
  


• Seo K,Hagino K,Ichihashi N , Progresses in cell-free in vitro evolution , Adv. Biochem. Eng. Biotechnol. , 2023
  


• Ueda K,Mizuuchi R,Ichihashi N , Emergence of linkage between cooperative RNA replicators encoding replication and metabolic enzymes through experimental evolution , PLoS Genet. , 2023
  


• Nozaki T,Shinkai S,Ide S,Higashi K,Tamura S,Shimazoe MA,Nakagawa M,Suzuki Y,Okada Y,Sasai M,Onami S,Kurokawa K,Iida S,Maeshima K , Condensed but liquid-like domain organization of active chromatin regions in living human cells , Sci. Adv. , 2023
  


• Shibuya R,Kajimoto S,Yaginuma H,Ariyoshi T,Okada Y,Nakabayashi T , In situ quantification of biomolecular concentration of cytoplasmic membraneless organelles in a living cell , Preprint , 2023
  


• Tanaka H,Okada Y,Nakayamada S,Miyazaki Y,Namba S,Sonehara K,Shirai Y,Yamamoto K,Sonomoto K,Tanaka Y , OP0001 DECONVOLUTING IMMUNOLOGICAL AND CLINICAL HETEROGENEITY ACROSS AUTOIMMUNE RHEUMATIC DISEASES BY COHORT-WIDE IMMUNO-PHENOTYPING , BMJ Publishing Group Ltd , 2023
  


• Fukuda T,Furukawa K,Maruyama T,Yamashita SI,Noshiro D,Song C,Ogasawara Y,Okuyama K,Alam JM,Hayatsu M,Saigusa T,Inoue K,Ikeda K,Takai A,Chen L,Lahiri V,Okada Y,Shibata S,Murata K,Klionsky DJ,Noda NN,Kanki T , The mitochondrial intermembrane space protein mitofissin drives mitochondrial fission required for mitophagy , Mol. Cell , 2023
  


• Takao D,Kyunai YM,Okada Y,Satoh A , A primer on deep learning-based cellular image classification of changes in the spatial distribution of the Golgi apparatus after experimental manipulation , Methods Mol. Biol. , 2023
  


• Katoh TA,Omori T,Ishikawa T,Okada Y,Hamada H , Biophysical analysis of mechanical signals in immotile cilia of mouse embryonic nodes using advanced microscopic techniques , Bio Protoc. , 2023
  


• Okamoto K,Fujita H,Okada Y,Shinkai S,Onami S,Abe K,Fujimoto K,Sasaki K,Shioi G,Watanabe TM , Single-molecule tracking of Nanog and Oct4 in living mouse embryonic stem cells uncovers a feedback mechanism of pluripotency maintenance , EMBO J. , 2023
  


• Totsuka NM,Kuwana S,Sawai S,Oka K,Sasakura Y,Hotta K , Distribution changes of non-self-test cells and self-tunic cells surrounding the outer body during Ciona metamorphosis , Dev. Dyn. , 2023
  


• Uwamichi M,Miura Y,Kamiya A,Imoto D,Sawai S , Random walk and cell morphology dynamics in Naegleria gruberi , Front. Cell Dev. Biol. , 2023
  


• Sando S , Development of hyperpolarized NMR molecular probes for biological applications , Bull. Chem. Soc. Jpn. , 2023
  


• Sakamoto DM,Tamura I,Yi B,Hasegawa S,Saito Y,Yamada N,Takakusagi Y,Kubota SI,Kobayashi M,Harada H,Hanaoka K,Taki M,Nangaku M,Tainaka K,Sando S , Whole-body and whole-organ 3D imaging of hypoxia using an activatable covalent fluorescent probe compatible with tissue clearing , ACS Nano , 2024
  


• Sugimoto H,Hironaka KI,Nakamura T,Yamada T,Miura H,Otowa-Suematsu N,Fujii M,Hirota Y,Sakaguchi K,Ogawa W,Kuroda S , Improved detection of decreased glucose handling capacities via novel continuous glucose monitoring-derived indices: AC_mean and AC_Var , Preprint , 2023
  


• Maehara H,Kokaji T,Hatano A,Suzuki Y,Matsumoto M,Nakayama KI,Egami R,Tsuchiya T,Ozaki H,Morita K,Shirai M,Li D,Terakawa A,Uematsu S,Hironaka KI,Ohno S,Kubota H,Araki H,Miura F,Ito T,Kuroda S , DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle , Sci. Rep. , 2023
  


• Sugimoto H,Hironaka KI,Yamada T,Sakaguchi K,Ogawa W,Kuroda S , DI/cle, a measure consisting of insulin sensitivity, secretion, and clearance, captures diabetic states , J. Clin. Endocrinol. Metab. , 2023
  


• Nie M,Nagata S,Oda H,Takeuchi S , Millimeter-thick 3D tissues constructed by densely cellularized core-shell microfluidic bioprinting , Biofabrication , 2023
  


• Nie M,Shima A,Takeuchi S , Centimeter-Scale Cultured Whole-Cut Chicken Meat Fabricated Using a Microfabricated Hollow Fiber Bioreactor , IEEE , 2023
  


• Hashimoto I,Osaki T,Sugiura H,Mimura H,Takamori S,Miki N,Takeuchi S , Reproducible reformation of a bilayer lipid membrane using microair bubbles , Droplet , 2023
  


• Hashimoto I,Osaki T,Sugiura H,Mimura H,Takamori S,Miki N,Takeuchi S , Back cover, volume 2, number 3, July 2023 , Droplet , 2023
  


• Morita K,Morimoto Y,Takeuchi S , Biohybrid tensegrity actuator driven by selective contractions of multiple skeletal muscle tissues , Biofabrication , 2023
  


• Nie M,Truckenmﾃｼller R,Takeuchi S , Microfabrication technology in tissue engineering , Elsevier , 2023
  


• Louis F,Furuhashi M,Yoshinuma H,Takeuchi S,Matsusaki M , Mimicking Wagyu beef fat in cultured meat: Progress in edible bovine adipose tissue production with controllable fatty acid composition , Mater. Today Bio , 2023
  


• Inagaki S,Morimoto Y,Suzuki IK,Emoto K,Takeuchi S , Co-culture system of human skin equivalents with mouse neural spheroids , J. Biosci. Bioeng. , 2023
  


• Nie M,Shima A,Takeuchi S , Centimeter-scale perfusable cultured meat with densely packed, highly aligned muscle fibers via hollow fiber bioreactor , Preprint , 2023
  


• Yoshito M,Hironobu O,Kaneyasu N,Midori KN,Hiroaki O,Shoji T,Masanori M , Technological Development to Construct Brain窶冱 Neural Circuits , IEICE Proceedings Series , 2023
  


• Takamori S,Mimura H,Osaki T,Takeuchi S , A microfluidic device for selective pairing and electrofusion of cell-sized liposomes , Sens. Actuators B Chem. , 2023
  


• Ogishi K,Osaki T,Mimura H,Hashimoto I,Morimoto Y,Miki N,Takeuchi S , Real-time quantitative characterization of ion channel activities for automated control of a lipid bilayer system , Biosens. Bioelectron. , 2023
  


• Sakai K,Miura S,Teshima TF,Goto T,Takeuchi S,Yamaguchi M , Small-artery-mimicking multi-layered 3D co-culture in a self-folding porous graphene-based film , Nanoscale Horiz , 2023
  


• Mimura H,Osaki T,Takamori S,Nakao K,Takeuchi S , Lipid bilayer reformation using the wiping blade for improved ion channel analysis , Anal. Chem. , 2023
  


• Gao Y,Kainuma S,Yang M,Ishihara S,Inoue D , Galvanic corrosion behavior of hot-dip Al and 55Al窶纏n coatings applied to steel bolted joints in atmospheric environments , Constr. Build. Mater. , 2023
  


• Yamashita S,Ishihara S,Graner F , Apical constriction requires patterned apical surface remodeling to synchronize cellular deformation , Preprint , 2023
  


• Nishide R,Ishihara S , Oscillatory and chaotic pattern dynamics driven by surface curvature , Preprint , 2024
  


• Nishide R,Ishihara S , Weakly nonlinear analysis of Turing pattern dynamics on curved surfaces , Preprint , 2024
  


• Gauquelin E,Kuromiya K,Namba T,Ikawa K,Fujita Y,Ishihara S,Sugimura K , Mechanical convergence in mixed populations of mammalian epithelial cells , Eur. Phys. J. E Soft Matter , 2024
  


• Salter C,Ikegami T , Sensing performance: from Balinese character to Japanese androids , Theatre Perform. Des. , 2023
  


• Doi I,Deng W,Ikegami T , Spontaneous and information-induced bursting activities in honeybee hives , Sci. Rep. , 2023
  


• Kojima H,Ikegami T , Implementation of lenia as a reaction-diffusion system , MIT Press , 2023
  


• Adachi R,Kojima H,Ikegami T , Life-like Behavior of an Oil Droplet in an Aqueous Surfactant Solution: Comparative Analysis with Tetrahymena Movement and Numerical Investigation , MIT Press , 2023
  


• Yoshida T,Masumori A,Maruyama N,Smith J,Ikegami T , Development of concept representation of behavior through mimicking and imitation in a humanoid robot alter3 , MIT Press , 2023
  


• Maruyama N,Crosscombe M,Dobata S,Ikegami T , Emergence of Differentiation of Deterministic/Stochastic Behavior in Ants窶・Collectives , MIT Press , 2023
  


• Masumori A,Maruyama N,Ikegami T , Exploring Multi-Level Inter-Scale Information Flow in Large-Scale Boids Model , MIT Press , 2023
  


• Masumori A,Ikegami T , Embodied Time Perception: Effects of Time Delay on Hand Motion and Time Estimation in Virtual Environments , MIT Press , 2023
  


• Takata R,Tang Y,Tian Y,Maruyama N,Kojima H,Ikegami T , Evolving Collective AI: Simulation of Ants Communicating via Chemicals , MIT Press , 2023
  


• Froese T,Weber N,Shpurov I,Ikegami T , From autopoiesis to self-optimization: Toward an enactive model of biological regulation , Biosystems. , 2023
  


• Masumori A,Ikegami T , Spiking neural networks produce informational closure by stimulus avoidance , Biosystems. , 2023
  


• Stano P,Nehaniv C,Ikegami T,Damiano L,Witkowski O , Autopoiesis: Foundations of life, cognition, and emergence of self/other , Biosystems. , 2023
  


• Nicholas MW,Takashi I,Anna C , Hanging in there: Prenatal origins of antigravity homeostasis in humans , Preprint , 2023
  


• Yoshida T,Masumori A,Ikegami T , From text to motion: Grounding GPT-4 in a humanoid robot "Alter3" , Preprint , 2023
  


• Tottori T,Kobayashi TJ , Decentralized stochastic control with finite-dimensional memories: A memory limitation approach , Entropy (Basel) , 2023
  


• Zhang M,Hiki Y,Funahashi A,Kobayashi TJ , Mol-PECO: a deep learning model to predict human olfactory perception from molecular structures , Preprint , 2023
  


• Horiguchi SA,Kobayashi TJ , Cellular gradient flow structure linking single-cell-level rules and population-level dynamics , Phys. Rev. Res. , 2023
  


• Nakashima S,Kobayashi TJ , Population dynamics models for various forms of adaptation , The Biophysical Society of Japan , 2023
  


• Horie K,Namiki K,Kinoshita K,Miyauchi M,Ishikawa T,Hayama M,Maruyama Y,Hagiwara N,Miyao T,Murata S,Kobayashi TJ,Akiyama N,Akiyama T , Acute irradiation causes a long-term disturbance in the heterogeneity and gene expression profile of medullary thymic epithelial cells , Front. Immunol. , 2023
  


• Ishikawa T,Horie K,Takakura Y,Ohki H,Maruyama Y,Hayama M,Miyauchi M,Miyao T,Hagiwara N,Kobayashi TJ,Akiyama N,Akiyama T , T-cell receptor repertoire analysis of CD4-positive T cells from blood and an affected organ in an autoimmune mouse model , Genes Cells , 2023
  


• Zhang Y,Obuchi H,Toyota T , A practical guide to preparation and applications of giant unilamellar vesicles formed via centrifugation of water-in-oil emulsion droplets , Membranes (Basel) , 2023
  


• Kuzuya A,Nomura SI,Toyota T,Nakakuki T,Murata S , From molecular robotics to molecular cybernetics: The first step toward chemical artificial intelligence , IEEE Trans. Mol. Biol. Multiscale Commun. , 2023
  


• Nomoto T,Kimura H,Chiari L,Toyota T,Fujinami M , Flow-driven self-propulsion of oil droplet on a surfactant solution surface, as observed by time-resolved interfacial tension and surface flow speed measurements , Langmuir , 2024
  


• Uemura S , Comprehensive quantitative analysis of single-molecule proteins using ribosome fusion nanopore technology , Impact , 2023
  


• Narita H,Shima T,Iizuka R,Uemura S , N-terminal region of Drosophila melanogaster Argonaute2 forms amyloid-like aggregates , BMC Biol. , 2023
  


• Irie M,Kabata H,Sasahara K,Kurihara M,Shirasaki Y,Kamatani T,Baba R,Matsusaka M,Koga S,Masaki K,Miyata J,Araki Y,Kikawada T,Kabe Y,Suematsu M,Yamagishi M,Uemura S,Moro K,Fukunaga K , Annexin A1 is a cell-intrinsic metalloregulator of zinc in human ILC2s , Cell Rep. , 2023
  


• Ebata H,Shima T,Iizuka R,Uemura S , Accumulation of TERT in mitochondria exerts two opposing effects on apoptosis , FEBS Open Bio , 2023
  


• Tanaka Y,Yamagishi M,Motomura Y,Kamatani T,Oguchi Y,Suzuki N,Kiniwa T,Kabata H,Irie M,Tsunoda T,Miya F,Goda K,Ohara O,Funatsu T,Fukunaga K,Moro K,Uemura S,Shirasaki Y , Time-dependent cell-state selection identifies transiently expressed genes regulating ILC2 activation , Commun. Biol. , 2023
  


• Kamei KI,Kobayashi-Kirschvink KJ,Nozoe T,Nakaoka H,Umetani M,Wakamoto Y , Revealing global stoichiometry conservation architecture in cells from Raman spectral patterns , Preprint , 2023
  


• Sato Y,Yoshimura K,Matsuda K,Haraguchi T,Marumo A,Yamagishi M,Sato S,Ito K,Yajima J , Membrane-bound myosin IC drives the chiral rotation of the gliding actin filament around its longitudinal axis , Sci. Rep. , 2023
  


• Yanagi K,Komatsu T,Fujikawa Y,Kojima H,Okabe T,Nagano T,Ueno T,Hanaoka K,Urano Y , Development of pathway-oriented screening to identify compounds to control 2-methylglyoxal metabolism in tumor cells , Commun. Chem. , 2023
  


• Fujioka H,Kawatani M,Spratt SJ,Komazawa A,Misawa Y,Shou J,Mizuguchi T,Kosakamoto H,Kojima R,Urano Y,Obata F,Ozeki Y,Kamiya M , Activatable Raman probes utilizing enzyme-induced aggregate formation for selective ex vivo imaging , J. Am. Chem. Soc. , 2023
  


• Nagano N,Ichihashi Y,Komatsu T,Matsuzaki H,Hata K,Watanabe T,Misawa Y,Suzuki M,Sakamoto S,Kagami Y,Kashiro A,Takeuchi K,Kanemitsu Y,Ochiai H,Watanabe R,Honda K,Urano Y , Development of fluorogenic substrates for colorectal tumor-related neuropeptidases for activity-based diagnosis , Chem. Sci. , 2023
  


• Shou J,Komazawa A,Wachi Y,Kawatani M,Fujioka H,Spratt SJ,Mizuguchi T,Oguchi K,Akaboshi H,Obata F,Tachibana R,Yasunaga S,Mita Y,Misawa Y,Kojima R,Urano Y,Kamiya M,Ozeki Y , Super-resolution vibrational imaging based on photoswitchable Raman probe , Sci. Adv. , 2023
  


• Iriki T,Iio H,Yasuda S,Masuta S,Kato M,Kosako H,Hirayama S,Endo A,Ohtake F,Kamiya M,Urano Y,Saeki Y,Hamazaki J,Murata S , Senescent cells form nuclear foci that contain the 26S proteasome , Cell Rep. , 2023
  


• Kunitake K,Mizuno T,Hattori K,Oneyama C,Kamiya M,Ota S,Urano Y,Kojima R , Barcoding of small extracellular vesicles with CRISPR-gRNA enables comprehensive, subpopulation-specific analysis of their biogenesis/release regulators , Preprint , 2023
  


• Echizen H,Hanaoka K,Shimamoto K,Hibi R,Toma-Fukai S,Ohno H,Sasaki E,Komatsu T,Ueno T,Tsuchiya Y,Watanabe Y,Otsuka T,Saito H,Nagatoishi S,Tsumoto K,Kojima H,Okabe T,Shimizu T,Urano Y , Discovery of a cystathionine ﾎｳ-lyase (CSE) selective inhibitor targeting active-site pyridoxal 5'-phosphate (PLP) via Schiff base formation , Sci. Rep. , 2023
  


• Tsuchimochi S,Wada-Hiraike O,Urano Y,Kukita A,Yamaguchi K,Honjo H,Taguchi A,Tanikawa M,Sone K,Mori-Uchino M,Tsuruga T,Oda K,Osuga Y , Characterization of a fluorescence imaging probe that exploits metabolic dependency of ovarian clear cell carcinoma , Sci. Rep. , 2023
  


• Takahashi R,Ishizawa T,Inagaki Y,Tanaka M,Ogasawara A,Kuriki Y,Fujita K,Kamiya M,Ushiku T,Urano Y,Hasegawa K , Real-time fluorescence imaging to identify cholangiocarcinoma in the extrahepatic biliary tree using an enzyme-activatable probe , Liver Cancer , 2023
  


• Kuriki Y,Sogawa M,Komatsu T,Kawatani M,Fujioka H,Fujita K,Ueno T,Hanaoka K,Kojima R,Hino R,Ueo H,Ueo H,Kamiya M,Urano Y , Modular design platform for activatable fluorescence probes targeting carboxypeptidases based on ProTide chemistry , J. Am. Chem. Soc. , 2024
  


• Watanabe G,Ishizawa T,Kuriki Y,Kamiya M,Ichida A,Kawaguchi Y,Akamatsu N,Kaneko J,Arita J,Kokudo N,Urano Y,Hasegawa K , Evaluation of pancreatic chymotrypsin activity for on-site prediction of clinically relevant postoperative pancreatic fistula , Pancreatology , 2024
  


• Hanaoka K,Ikeno T,Iwaki S,Deguchi S,Takayama K,Mizuguchi H,Tao F,Kojima N,Ohno H,Sasaki E,Komatsu T,Ueno T,Maeda K,Kusuhara H,Urano Y , A general fluorescence off/on strategy for fluorogenic probes: Steric repulsion-induced twisted intramolecular charge transfer (sr-TICT) , Sci. Adv. , 2024
  


• Ukegawa T,Komatsu T,Minoda M,Matsumoto T,Iwasaka T,Mizuno T,Tachibana R,Sakamoto S,Hanaoka K,Kusuhara H,Honda K,Watanabe R,Urano Y , Thioester-based coupled fluorogenic assays in microdevice for the detection of single-molecule enzyme activities of esterases with specified substrate recognition , Adv. Sci. (Weinh.) , 2024
  


• Shimizu T,Tanaka S,Kitagawa Y,Sakaguchi Y,Kamiya M,Takayanagi S,Takami H,Urano Y,Saito N , Advancement of fluorescent aminopeptidase probes for rapid cancer detection-current uses and neurosurgical applications , Front. Surg. , 2024
  


• Tsuyuzaki K,Yamamoto K,Toyoshima Y,Sato H,Kanamori M,Teramoto T,Ishihara T,Iino Y,Nikaido I , WormTensor: a clustering method for time-series whole-brain activity data from C. elegans , BMC Bioinformatics , 2023
  


• Tomioka M,Umemura Y,Ueoka Y,Chin R,Katae K,Uchiyama C,Ike Y,Iino Y , Antagonistic regulation of salt and sugar chemotaxis plasticity by a single chemosensory neuron in Caenorhabditis elegans , PLoS Genet. , 2023
  


• Kuze K,Tazawa UT,Suwazono K,Toyoshima Y,Iino Y , WormTracer: A precise method for worm posture analysis using temporal continuity , Preprint , 2023
  


• Matsumoto A,Toyoshima Y,Zhang C,Isozaki A,Goda K,Iino Y , Neuronal sensorimotor integration guiding salt concentration navigation in Caenorhabditis elegans , Proc. Natl. Acad. Sci. U. S. A. , 2024
  


• Toyoshima Y,Sato H,Nagata D,Kanamori M,Jang MS,Kuze K,Oe S,Teramoto T,Iwasaki Y,Yoshida R,Ishihara T,Iino Y , Ensemble dynamics and information flow deduction from whole-brain imaging data , PLoS Comput. Biol. , 2024
  

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【外部評価】
Report on UBI, 2016-2019
外部評価委員会報告