2018年度(2017.4~2018.3)
2017年度(2016.4~2017.3)
2016年度(2016.4~2017.3)
- *Hiroki Kojima, Tom Froese, Mizuki Oka, Hiroyuki Iizuka andTakashi Ikegami,
T. A Sensorimotor Signature of the Transition to Conscious Social Perception: Co-regulation of Active and Passive Touch.,
Frontiers in psychology 8, 1778 (2017). - Sinapayen, L., & Ikegami, T.,Online fitting of computational cost to environmental complexity: Predictive coding with the ε-network,Proceedings of the 14th European Conference on Artificial Life 2017 14, 380-387 (2017).
- Doi, I., Ikegami, T., Masumori, A., Kojima, H., Ogawa K., & Ishiguro,
H.,
A new design principle for an autonomous robot,
Proceedings of the 14th European Conference on Artificial Life 2017 14, 490-466 (2017). - Masumori, A., Sinapayen, L., & Ikegami, T.,
Learning by Stimulation Avoidance Scale to Large Neural Networks,
Proceedings of the 14th European Conference on Artificial Life 2017 14, 275-282 (2017). - Masumori, A., Maruyama, N., Mita, T., Bakkum, D., Frey, U., Takahashi,
H.,& Ikegami, T.,
Learning by Stimulation Avoidance in Cultured Neuronal Cells,
The 2nd International Symposium on Swarm Behavior and Bio-Inspired Robotics(SWARM 2017) , 275-282 (2017). - Maruyama, N., Hashimoto, Y., Mototake, Y., Saito, D., & Ikegami, T.,
Revisiting Classification of Large Scale Flocking,
The 2nd International Symposium on Swarm Behavior and Bio-Inspired Robotics(SWARM 2017) , 307-310 (2017). - Hashimoto, Y., Ikegami, T.,
Novelty production in tagging crowds,
The 2nd International Symposium on Swarm Behavior and Bio-Inspired Robotics(SWARM 2017), 311-312 (2017). - Yugi K., Kuroda S.,
Metabolism as a signal generator across trans-omic networks at distinct time scales,
Curr. Opin. Sys. Biol. 8, 59-66 (2018). - Ueno A, Omori Y, Sugita Y, Watanabe S, Chaya T, Kozuka T, Kon T, Yoshida S, Matsushita K, Kuwahara R, Kajimura N, Okada Y, *Furukawa T.,
Lrit1, a retinal transmembrane protein, regulates selective synapse formation in cone photoreceptor cells and visual acuity.,
Cell Reports 22, 3562-3573 (2018). - Ohashi, K., Fujii, M., Uda, S., Kubota, H., Komada, H., Sakaguchi, K., Ogawa, W., Kuroda, S.,
Increase in hepatic and decrease in peripheral insulin clearance characterize abnormal temporal patterns of serum insulin in diabetic subjects,
NPJ Syst. Biol. 4, 14 (2018). - Seohyun Lee, Hyuno Kim, Hideo Higuchi,
Focus Stabilization by Axial Position Feedback in Biomedical Imaging Microscopy,
IEEE Sensors Applications Symposium 2018, 309-314 (2018). - Motoshi Kaya, Yoshiaki Tani, Takumi Washio, Toshiaki Hisada and Hideo Higuchi,
Coordinated force generation of skeletal myosins in myofilaments through motor coupling,
Nature Communications 8, 16036 (2017). - Akira Adachi, Satoshi Senmatsu, Ryuta Asada, Takuya Abe, Charles S. Hoffman, Kunihiro Ohta, *Kouji Hirota,
Interplay between chromatin modulators and histone acetylation regulates the formation of accessible chromatin in the upstream regulatory region of fission yeast fbp1.,
Genes & Genetic Systems , in press (2018). - Atsushi Kamimura, *Kunihiko Kaneko,
Exponential growth for self-reproduction in a catalytic reaction network: relevance of a minority molecular species and crowdedness,
New Journal of Physics 20, 035001 (2018). - K. Tokuyama, Y. Toya, T. Horinouchi, C. Furusawa, F. Matsuda, *H. Shimizu,
Application of adaptive laboratory evolution to overcome a flux limitation in an Escherichia coli production strain.,
Biotechnology and Bioengineering, 1-10 (2018). - C. Furusawa, T. Horinouchi, T. Maeda,,
Toward prediction and control of antibiotic-resistance evolution,
Current Opinion in Biotechnology 54, 45-59 (2018). - *Takaki Yamamoto and Masaki Sano,
Theoretical model of chirality-induced helical self-propulsion,
Phys. Rev. E 97, 012607/1-11 (2018). - T. Hirasawa, M. Saito, K. Yoshikawa, C. Furusawa,,
Integrated Analysis of the Transcriptome and Metabolome of Corynebacterium glutamicum during Penicillin-Induced Glutamic Acid Production,
Biotechnology Journal 1700612, 1-11 (2018). - Daiki Nishiguchi, Junichiro Iwasawa, Hong-Ren Jiang and Masaki Sano,
Flagellar dynamics of chains of active Janus particles fueled by an AC electric field,
New Journal of Physics 20, 015002/1-14 (2018).
2017年度(2016.4~2017.3)
- Eng Kuan Moo, Daniel R.Peterson, Timothy R. Leonard, Motoshi Kaya and Walter Herzog,
In vivo muscle force and muscle power during near-maximal frog jumps.,
PloS one (2017). - Lana Sinapayen, Atsushi Masumori, Takashi Ikegami,
Learning by Stimulation Avoidance: A Principle to Control Spiking Neural Networks Dynamics.,
PLoS One 12(2), e0170388 (2017). - Takumi Washio, Toshiaki Hisada, Seine A. Shintani and Hideo Higuchi,
Analysis of spontaneous oscillations for a three state power stroke model,
Physical Review E. 95, 022411 (2017). - Takaho Tsuchiya, Masashi Fujii, Naoki Matsuda, Katsuyuki Kunida, Shinsuke Uda, Hiroyuki Kubota, Katsumi Konishi, *Shinya Kuroda,
System identification of signaling dependent gene expression with different time-scale data,
PLOS Computational Biology 13(12), e1005913 (2017). - Napo K. M. Cheung, Ryohei Nakamura, Ayako Uno, Masahiko Kumagai, Hiroto
S. Fukushima, Shinichi Morishita & Hiroyuki Takeda*,
Unlinking the methylome pattern from uncleotide sequence, revealed by large-scale in vivo genome engineering and methylome editing in medaka fish,
PloS Genetics 13, e1007123 (2017). - Suguru Takagi, Benjamin T. Cocanougher, Sawako Niki, Dohjin Miyamoto, Hiroshi Kohsaka, Hokuto Kazama, Richard D. Fetter, James W. Truman, Marta Zlatic, Albert Cardona and *Akinao Nose,
Divergent connectivity of homologous command-like neurons mediates segment-specific touch responses in Drosophila,
Neuron 96(6), 1373-1387 (2017). - James R. Krycer, Katsuyuki Yugi, Akiyoshi Hirayama, Daniel J. Fazakerley, Lake-Ee Quek, Richard Scalzo, Satoshi Ohno, Mark P. Hodson, Satsuki Ikeda, Futaba Shoji, Kumi Suzuki, Westa Domanova, Benjamin L. Parker, Marin E. Nelson, Sean J. Humphrey, Nigel Turner, Kyle L. Hoehn, Gregory J. Cooney, Tomoyoshi Soga, *Shinya Kuroda and *David E. James,
Dynamic metabolomics reveals that insulin primes the adipocyte for glucose metabolism,
Cell Reports 21(12), 3536-3547 (2017). - Takayuki Katoh, Yoshihiko Iwane, *Hiroaki Suga,
Logical engineering of D-arm and T-stem of tRNA that enhances d-amino acid incorporation.,
Nucleic Acids Research 45, 12601–12610 (2017). - 古澤力, 前田智也, 堀之内貴明,
ラボ内での全自動進化実験システムの構築,
実験医学別冊「あなたのラボにAI×ロボットがやってくる(夏目徹 編) (2017). - Ryan Kniewel, Hajime Murakami, Yan Liu, Masaru Ito, Kunihiro Ohta, Nancy M. Hollingsworth and *Scott Keeney,
Histone H3 threonine 11 phosphorylation is catalyzed directly by the meiosis-specific kinase Mek1 and provides a molecular readout of Mek1 activity in vivo. ,
GENETICS 207, 1313-1333 (2017). - Chiba K, Chien K, Sobu Y, Hata S, Kato S, Nakaya T, Okada Y, Nairn AC, Kinjo M, Taru H, Wang R, Suzuki T.,
Phosphorylation of KLC1 modifies interaction with JIP1 and abolishes the enhanced fast velocity of APP transport by kinesin-1 ,
MOLECULAR BIOLOGY OF THE CELL 28, 3857-3869 (2017). - Kazuki Ichikawa, Shingo Tomioka, Yuta Suzuki, Ryohei Nakamura, Koichiro
Doi, Jun Yoshimura, Masahiko Kumagai, Yusuke Inoue, Yui Uchida, Naoki Irie,
Hiroyuki Takeda* & Shinich Morishita*,
Centromere evolution and CpG methylation during vertebrate speciation ,
Nature Communications 1833, 1-11 (2017). - Tsukasa Kusakizako,Yoshiki Tanaka, Christopher J. Hipolito, *Hiroaki Suga, Osamu Nureki,
Crystallographic analysis of MATE-type multidrug exporter with its inhibitors.,
Methods Mol Biol. 1700, 7-57 (2017). - *Nobuto Takeuchi, Paulien Hogeweg, Kunihiko Kaneko,
Conceptualizing the Origin of Life in terms of Evolution,
Philosophical Transactions of the Royal Society A 375, 20160346 (2017). - Atsushi Shibai, Yusuke Takahashi, Yuka Ishizawa, Daisuke Motooka, Shota Nakamura, Bei-Wen Ying, and *Saburo Tsuru,
Mutation accumulation under UV radiation in Escherichia coli,
Scientific Reports 7(14531), 1-12 (2017). - Jo Marie Bacusmo, Alexandra B. Kuzmishin, William A. Cantara, Yuki Goto,
*Hiroaki Suga & Karin Musier-Forsyth,
Quality control by trans-editing factor prevents global mistranslation of non-protein amino acid α-aminobutyrate,
RNA Biol., 1-10 (2017). - *石原秀至、澤井哲,
細胞内反応場のゆらぎと細胞運動,
パリティ 32, 22-25 (2017). - Ryo Yokota, Yuki Kaminaga, Tetsuya J. Kobayashi,
Quantification of Inter-Sample Differences in T-Cell Receptor Repertoires Using Sequence-Based Information.,
Frontier Immunology 8, 1500 (2017). - T. S. Hatakeyama, *C. Furusawa, ,
Metabolic dynamics restricted by conserved carriers: Jamming and feedback,
PLOS COMPUTATIONAL BIOLOGY 13-11, e1005847 (2017). - K. Tanabe, N. Sakata, H. Shimizu, *C. Furusawa,,
Prediction of Cross-resistance and Collateral Sensitivity by Gene Expression profiles and Genomic Mutations,
SCIENTIFIC REPORTS 7, 14009 (2017). - Sanki Tashiro Yuki Nishihara Kazuto Kugou Kunihiro Ohta *Junko Kanoh,
Subtelomeres constitute a safeguard for gene expression and chromosome homeostasis,
Nucleic Acids Research 45, 10333-10349 (2017). - 岡田康志,
超解像顕微鏡によるライブイメージング,
生体の科学 68(5), 378-379 (2017). - 小田有沙,平田祥人,太田邦史,合原一幸,
Hi-Cという染色体の立体パズルを解く,
実験医学 最強のステップUPシリーズ シングルセル解析プロトコール 別冊, 313-318 (2017). - Haiyang Hu, Masahiro Uesaka, Song Guo, Kotaro Shimai, Tsai-Ming Lu, Fang Li, Satoko Fujimoto, Masato Ishikawa, Shiping Liu, Yohei Sasagawa, Guojie Zhang, Shigeru Kuratani, Jr-Kai Yu, Takehiro G. Kusakabe, Philipp Khaitovich, Naoki Irie*; the EXPANDE Consortium,
Constrained vertebrate evolution by pleiotropic genes,
Nature Ecology & Evolution 1, 1722-1730 (2017). - Ryohei Nakamura, Ayako Uno, Masahiko Kumagai, Shinichi Morishita&Hiroyuki Takeda*,Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts ,Epigenetics & Chromatin 110, 44 (2017).
- Ryuta Asada Miki Umeda Akira Adachi Satoshi Senmatsu Takuya Abe Hiroshi Iwasaki Kunihiro Ohta Charles S. Hoffman *Kouji Hirota,
Recruitment and delivery of the fission yeast Rst2 transcription factor via a local genome structure counteracts repression by Tup1-family corepressors. ,
Nucleic Acids Res. 45, 9361-9371 (2017). - Takayuki Katoh, Yoshihiko Iwane & *Hiroaki Suga,
tRNA engineering for manipulating genetic code.,
RNA Biol. 2017 Jul 19, 1-8 (2017). - Yusuke Inoue, Tomonori Saga, Takumi Aikawa, Masahiko Kumagai, Atsuko Shimada,
Yasushi Kawaguchi, Kiyoshi Naruse, Shinichi Morishita, Akihiko Koga &
Hiroyuki Takeda*,
Complete fusion of a transposon and herpesvirus created the Teratorn mobile element in medaka fish ,
Nature Communications 15, 551 (2017). - *Shuji Ishihara, Philippe Marcq, and Kaoru Sugimura,
From cells to tissue: A continuum model of epithelial mechanics,
Physical Review E 96, 022418/1-14 (2017). - Byung-Sik Shin, Takayuki Katoh, Erik Gutierrez, Joo-Ran Kim, *Hiroaki Suga, Thomas E. Dever,
Amino acid substrates impose polyamine, eIF5A, or hypusine requirement for peptide synthesis,
Nucleic Acids Res. 45(14), 8392-8402 (2017). - Masahiko Ueda, Nobuto Takeuchi, *Kunihiko Kaneko,
Stronger selection can slow down evolution driven by recombination on a smooth fitness landscape,
PLoS ONE 12(8), e0183120 (2017). - *Nobuto Takeuchi, Paulien Hogeweg, Kunihiko Kaneko,
The origin of a primordial genome through spontaneous symmetry breaking,
Nature Communications 8, 250 (2017). - Kwesi Teye, Koji Hashimoto, Sanae Numata, Kunihiro Ohta, Marek Haftek &
*Takashi Hashimoto,
Altmetric: 1More detailArticle | OPENMultimerization is required for antigen binding activity of an engineered IgM/IgG chimeric antibody recognizing a skin-related antigen,
Scientific Reports 7, 8212 (2017). - T. Horinouchi, A. Sakai, H. Kotani, K Tanabe, *C. Furusawa,
Improvement of isopropanol tolerance of Escherichia coli using adaptive laboratory evolution and omics technologies,
JOURNAL OF BIOTECHNOLOGY 255, 47-56 (2017). - Yu Sakurai , Wataru Mizumura, Manami Murata, Tomoya Hada, Shoshiro Yamamoto, Kenichiro Ito, Kazuhiro Iwasaki, Takayuki Katoh, Yuki Goto, Asako Takagi, Michinori Kohara, *Hiroaki Suga, and Hideyoshi Harashima,
Efficient siRNA delivery by lipid nanoparticles modified with a nonstandard macrocyclic peptide for EpCAM-targeting,
Mol. Pharmaceutics 14 (10), 3290–3298 (2017). - Louise J. Walport, Richard Obexer, *HiroakiSuga,
Strategies for transitioning macrocyclic peptides to cell-permeable drug leads,
Curr Opin Biotechnol. 48, 242-250 (2017). - Eric M. Danhart, Marina Bakhtina, William A. Cantara, Alexandra B. Kuzmishin, Xiao Ma, Brianne L. Sanford, Oscar Vargas-Rodriguez, Marija Košutić, Yuki Goto, *Hiroaki Suga, Kotaro Nakanishi, Ronald Micura, Mark P. Foster and Karin Musier-Forsyth,
Conformational and chemical selection by a trans-acting editing domain,
Proc Natl Acad Sci U S A 114(33), E6774-E6783 (2017). - *Hirotaka Matsumoto, Hisanori Kiryu, Chikara Furusawa, Minoru S. H. Ko, Shigeru B. H. Ko, Norio Gouda, Tetsutaro Hayashi, Itoshi Nikaido,
SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation,
BIOINFORMATICS 33-15, 2314-2321 (2017). - *畠山哲央, 金子邦彦,
生体リズムの頑健性と可塑性,
生物物理 57, 186-190 (2017). - Tadasu Nozaki, Ryosuke Imai, Mai Tanbo, Ryosuke Nagashima, Sachiko Tamura, Tomomi Tani, Yasumasa Joti, Masaru Tomita, Kayo Hibino, Masato T. Kanemaki, Kerstin S. Wendt, Yasushi Okada, Takeharu Nagai, Kazuhiro Maeshima,
Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging,
MOLECULAR CELL 67, 282-293 (2017). - Tetsuya Hiraiwa, Erina Kuranaga and *Tatsuo Shibata,
Wave propagation of junctional remodeling in collective cell movement of epithelial tissue: Numerical simulation study,
frontiers in Cell and Developmental Biology 5, 66/1-15 (2017). - Yuma Fujimoto, Takahiro Sagawa, *Kunihiko Kaneko,
Hierarchical prisoner’s dilemma in hierarchical game for resource competition,
New Journal of Physics 19, 073008 (2017). - 小澤高嶺 太田邦史,
「昆虫の形態の多様性とエピゲノム」—子供のころの疑問を明らかに ,
生物の科学 遺伝 4, 314-318 (2017). - Tetsuya J. Kobayashi, Yuki Sughiyama ,
Information thermodynamic structure in population dynamics in fluctuating environment,
Physical Review E 96, 012402 (2017). - Masashi K. Kajita, Kazuyuki Aihara, Tetsuya J. Kobayashi,
Balancing specificity, sensitivity, and speed of ligand discrimination by zero-order ultraspecificity,
Physical Review E 96, 012405 (2017). - 岡田康志,
超解像顕微鏡で観える生物現象,
医学の歩み 262(5), 573-579 (2017). - Kazuki Harada, Tetsuya Kitaguchi, Taichi Kamiya, Kyaw Htet Aung, Kazuaki Nakamura, Kunihiro Ohta and *Takashi Tsuboi,
Lysophosphatidylinositol-induced activation of the cation channel TRPV2 triggers glucagon-like peptide-1 secretion in enteroendocrine L cells. ,
J. Biol. Chem. 292, 10855-10864 (2017). - Yusuke Himeoka, *Kunihiko Kaneko,
Theory for transitions between log and stationary phases: universal laws for lag time,
Physical Review X 7, 021049 (2017). - Hidenori Nakaoka, *Yuichi Wakamoto,
Aging, mortality, and the fast growth trade-off of Schizosaccharomyces pombe,
PLoS Biology 15, e2001109 (2017). - M. Yoshida, S. G. Reyes, S. Tsuda, T. Horinouchi, C. Furusawa,*L. Cronin, ,
Time-programmable drug dosing allows the manipulation, suppression and reversal of antibiotic drug resistance in vitro,
NATURE COMMUNICATIONS 8, 15589 (2017). - A. Germond, V. Kumar, T. Ichimura, J. Moreau, C. Furusawa, H. Fujita,,
Raman spectroscopy as a tool for ecology and evolution,
JOURNAL OF THE ROYAL SOCIETY INTERFACE 14, 131 (2017). - Keita Kamino, Yohei Kondo, Akihiko Nakajima, Mai Honda-Kitahara, Kunihiko Kaneko, and *Satoshi Sawai,
Fold-change detection and scale-invariance of cell-cell signaling in social amoeba,
Proceedings of the National Academy of Sciences of the United States of America 114(21), E4149-E4157 (2017). - Xiao Song, Lu-yi Lu, Toby Passioura, *Hiroaki Suga,
Macrocyclic peptide inhibitors for the protein-protein interaction of Zaire Ebola virus protein 24 and karyopherin alpha 5,
Org Biomol Chem 15(24), 5155-5160 (2017). - S. Suzuki, T. Horinouchi, *C. Furusawa,,
Acceleration and suppression of resistance development by antibiotic combinations,
BMC GENOMICS 18, 328 (2017). - *Kyogo Kawaguchi, Ryoichiro Kageyama & *Masaki Sano,
Topological defects control collective dynamics in neural progenitor cell cultures,
Nature 545, 327–331 (2017). - Shintaro Yamada, Mika Okamura, Arisa Oda, Hiroshi Murakami, Kunihiro Ohta and *Takatomi Yamada,
Correlation of meiotic DSB formation and transcription initiation around fission yeast recombination hotspots,
GENETICS 206, 801-809 (2017). - Akane Kawamura, Martin Münzel, Tatsuya Kojima, Clarence Yapp, Bhaskar Bhushan,
Yuki Goto, Anthony Tumber, Takayuki Katoh, Oliver N. F. King, Toby Passioura,
Louise J. Walport, Stephanie B. Hatch, Sarah Madden, Susanne Müller, Paul
E. Brennan, Rasheduzzaman Chowdhury, Richard J. Hopkinson, *Hiroaki Suga
& Christopher J. Schofield,
Highly selective inhibition of histone demethylases by de novo macrocyclic peptides,
Nat Commun. 8, 14773 (2017). - *Takaki Yamamoto and Masaki Sano,
Chirality-induced helical self-propulsion of cholesteric liquid crystal droplets,
Soft Matter 13, 3328-3333 (2017). - Hao Yu, Patricia Dranchak, Zhiru Li, Ryan MacArthur, Matthew S. Munson,
Nurjahan Mehzabeen, Nathan J. Baird, Kevin P. Battalie, David Ross, Scott
Lovell, Clotilde K. S. Carlow, *Hiroaki Suga & James Inglese,
Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases,
Nat Commun 8, 14932 (2017). - Takashi Amoh, Keiji Murakami, Reiko Kariyama, Kenji Hori, Yasuhiko Irie, Darija Viducic, Katsuhiko Hirota, Jun Igarashi, *Hiroaki Suga, Hiromi Kumon, Yoichiro Miyake,
A pseudomonas aeruginosa quorum-sensing autoinducer analog enhances the activity of antibiotics against resistant strains,
J Med Invest 64(1.2), 101-109 (2017). - Robustness of spatial patterns in buffered reaction-diffusion systems and its reciprocity with phase plasticity,
Tetsuhiro S. Hatakeyama, *Kunihiko Kaneko,
Physical Review E, Rapid Communication 95, 030201(R) (2017). - Richard Obexer, Louise J. Walport, *Hiroaki Suga,
Exploring sequence space: harnessing chemical and biological diversity towards new peptide leads,
Curr Opin Chem Biol. 38, 52-61 (2017). - Yui Uchida*, Masahiro Uesaka, Takayoshi Yamamoto, Hiroyuki Takeda and Naoki Irie*,
Embryonic lethality is not sufficient to explain hourglass-like conservation of vertebrate embryos,
EvoDevo 9:7, 1-11 (2017). - Jonathan T.Young, Tetsuhiro S. Hatakeyama, *Kunihiko Kaneko,
Dynamics Robustness of Linear Signaling Cascades,
PLOS Computational Biology 13, e1005434 (2017). - *Nen Saito, Kunihiko Kaneko,
Embedding dual function into molecular motors through collective motion,
Scientific Reports 7, 44288 (2017). - Seino A.K. Jongkees, Sami Caner, Christina Tysoe, Gary D. Brayer, Stephen G. Withers, *Hiroaki Suga,
Rapid discovery of potent and selective glycosidase-inhibiting de novo peptides,
Cell Chem Biol 24(3), 381-390 (2017). - 大橋郁、藤井雅史、小川渉、*黒田真也,
血糖値恒常性システムの数理モデル解析,
実験医学 35(5), 830-833 (2017). - Masashi Fujii, Kaoru Ohashi, Yasuaki Karasawa, Minori Hikichi and *Shinya Kuroda,
Small-Volume effect enables robust, sensitive, and efficient information transfer in the spine,
Biophysical Journal 112(4), 813-826 (2017). - *Yohei Murakami, Masanori Koyama, Shigeyuki Oba, Shinya Kuroda and Shin Ishii,
Model-based control of the temporal patterns of intracellular signaling in silico,
Biophysics and Physicobiology 14, 29-40 (2017). - 岡田康志,
ライブイメージングのための高速超解像蛍光顕微鏡法,
O plus E 39(2), 74-178 (2017). - Katsuyuki Yugi and Shinya Kuroda ,
Metabolism-Centric Trans-Omics,
Cell Systems 4(1), 19-20 (2017). - H. Shimizu, C. Furusawa, T. Hirasawa, K. Yoshikawa, Y. Toya, T. Shirai, F. Matsuda,,
Omics-Integrated Approach for Metabolic State Analysis of Microbial Processes: Innovationsand Future Directions,
Applied Bioengineering -, 213-236 (2017). - Toby Passioura, *Hiroaki Suga,
A RaPID way to discover nonstandard macrocyclic peptide modulators of drug targets,
Chem Commun (Camb) 53(12), 1931-1940 (2017). - Yuki Sughiyama, Tetsuya J. Kobayashi,
Steady-state thermodynamics for population growth in fluctuating environments,
Physical Review E 95, 012131 (2017). - oichi Kosodo, Taeko Suetsugu, Tetsuya J. Kobayashi, Fumio Matsuzaki,
Systematic time-dependent visualization and quantitation of the neurogenic rate in brain organoids,
Biochemical and Biophysical Research Communications 483, 94-100 (2017). - *Taro Toyota, Taisuke Banno, Juan M. Castro, and Masayuki Imai,
Locomotion and transformation of underwater micrometer-sized molecular aggregates under chemical stimuli,
J. Phys. Soc. Jpn. 86, 101006 (2017). - *能瀬聡直、高坂洋史、伏木彬,
光によるショウジョウバエ中枢回路の機能解剖,
生体の科学 68(5), 478-479 (2017). - 岡田康志,
共焦点顕微鏡の光学系を用いた超解像顕微鏡法,
顕微鏡 52(2), 62-66 (2017). - 岡田康志,
超解像顕微鏡研究の最前線,
顕微鏡 52(2), 61 (2017). - S. Suzuki, T. Horinouchi, *C. Furusawa, ,
Expression profiling of antibiotic resistant bacteria obtained by laboratory evolution,
Methods Mol Biol. 1520, 263-279 (2017). - C. Furusawa,
Analysis of Drug Resistance Using Experimental Evolution,
Yakugaku Zasshi 137, 373-376 (2017). - Takahiro Kohsokabe, Kunihiko Kaneko,
Boundary-Induced Pattern Formation from Temporal Oscillation: Spatial Map Analysis,
Europhysics Letters 116, 48005/1-6 (2017). - 樋口秀男,
生物物理学と他の領域をゆらぐ,理学部ニュース 48, 08 (2017).
- 中岡秀憲, 梅谷実樹, *若本祐一,
1細胞レベルの環境応答と選択の計測,
化学と生物, in press. - Ryohei Seki, Cai Li, Qi Fang, Shinichi Hayashi, Shiro Egawa, Jiang Hu,
Luohao Xu, Hailin Pan, Mao Kondo, Tomohiko Sato, Haruka Matsubara, Namiko
Kamiyama, Keiichi Kitajima, Daisuke Saito, Yang Liu, M. Thomas P. Gilbert,
Qi Zhou, Xing Xu, Toshihiko Shiroishi, Naoki Irie*, Koji Tamura* &
Guojie Zhang*,
Functional roles of aves class-specific cis-regulatory elements on macroevolution of bird-specific features,
Nature Communications 8, 14229 (2017). - Taro Ozaki, Kona Yamashita, Yuki Goto, Morito Shimomura, Shohei Hayashi, Shumpei Asamizu, Yoshinori Sugai, Haruo Ikeda, Hiroaki Suga, Hiroyasu Onaka,
Dissection of goadsporin biosynthesis by in vitro reconstitution leading to designer analoges expressed in vivo,
Nature Communications 8, 14207 (2017). - S. A. K. Jongkees, S. Umemoto, Hiroaki Suga,
Linker-free incorporation of carbohydrates into in vitro displayed macrocyclic peptides,
Chemical Science 8, 1474-1481 (2017).
- Takayuki Katoh, Kenya Tajima, Hiroaki Suga,
Consecutive Elongation of D-Amino Acids in Translation,
Cell Chemical Biology 24, 46-54 (2017). - *豊田太郎, 風山祐輝, 大崎寿久, 竹内昌治,
ジャイアントベシクルのダイナミクスと人工細胞型センサーへの展開,
分析化学 65, 715-727 (2017).
- Tomoyuki Mano, *Jean-Baptiste Delfau, Junichiro Iwasawa, and Masaki Sano,
Optimal run-and-tumble based transportation of a Janus particle with active steering,
Proceedings of the National Academy of Sciences 114(13), E2580-E2589 (2017). - *Daiki Nishiguchi, Ken H. Nagai, Hugues Chate, and Masaki Sano,
Long-range nematic order and anomalous fluctuations in suspensions of swimming filamentous bacteria,
Physical Review E 95, 020601(R) /1-6 (2017). - *J.-B. Delfau, John J. Molina and M. Sano,
Collective behavior of strongly confined suspensions of squirmers,
Europhysics Letters 114, 24001/1-5 (2016). - Hideki Terajima, *Hikari Yoshitane, Haruka Ozaki, Yutaka Suzuki,Shigeki Shimba, Shinya Kuroda, Wataru Iwasaki and *Yoshitaka Fukada,
ADARB1 catalyzes circadian A-to-I editing and regulates RNA rhythm,
Nature Genetics 49, 146-151 (2017). - Teruyuki Matsunaga, Hiroshi Kohsaka, and *Akinao Nose,
Gap junction-mediated signaling from motor neurons regulates motor generation in the central circuits of larval Drosophila,
The Jounal of Neuroscience 37(8), 2045-2060 (2017).
2016年度(2016.4~2017.3)
- Takashi Ikegami, Naoto Horibe, M Hanczyc,
Potential Memory Effects in Self-Moving Oil Droplets,
INTERNATIONAL JOURNAL OF UNCONVENTIONAL COMPUTING 11, 345-355 (2016). - Do Won Hwang, Namryeong Bahng, Kenichiro Ito, Seunggyun Ha, Mee Young Kim, Eunji Lee, *Hiroaki Suga, Dong Soo Lee,
In vivo targeting of c-Met using a non-standard macrocyclic peptide in gastric carcinoma,
Cancer Lett 385, 144-149 (2016). - *Chikara Furusawa, Tomoyuki Yamaguchi,
Robust and accurate discrimination of self/non-self antigen presentations by regulatory T cell suppression,
PLoS One 11(9), e0163134 (2016). - Shingo Suzuki, Takaaki Horinouchi, *Chikara Furusawa,
Phenotypic changes associated with the fitness cost in antibiotic resistant Escherichia coli strains,
Molecular Biosystems 12(2), 414-20 (2016). - *古澤力, 鈴木真吾, 堀之内貴明,
大腸菌進化実験を用いた遺伝子発現量からの抗生物質耐性メカニズムの解析,
バイオサイエンスとインダストリー 74(2), 138-140 (2016). - Nen Saito and Kunihiko Kaneko,
Collective motion switches motor direction along filament,
Scientific reports, in press. - Kenji Shinoda and Kunihiko Kaneko,
Chaotic Griffiths Phase with Anomalous Lyapunov Spectra in Coupled Map Networks,
Physical Review Letters 117, 254101/1-6 (2016). - Jumpei F Yamagishi, Nen Saito, Kunihiko Kaneko,
Symbiotic Cell Differentiation and Cooperative Growth in Multicellular Aggregates,
PLOS Computational Biology 12(10), e1005042/1-17 (2016). - Tomoki Kurikawa, Kunihiko Kaneko,
Dynamic Organization of Hierarchical Memories,
PLoS ONE 11, e0162640/1-19 (2016). - Nen Saito, Yuki Sughiyama, and Kunihiko Kaneko,
Motif analysis for small-number effects in chemical reaction dynamics,
The Journal of Chemical Physics 145, 094111/1-7 (2016). - Yohei Saito, Yuki Sughiyama, Kunihiko Kaneko, and Tetsuya J. Kobayashi,
Discreteness-induced transitions in multibody reaction systems,
Physical Review E 94, 022140/1-8 (2016). - Atsushi Kamimura, Kunihiko Kaneko,
Negative scaling relationship between molecular diversity and resource abundances,
Physical Review E 93, 062419/1-13 (2016). - Benjamin Pfeuty and Kunihiko Kaneko,
Requirements for efficient cell-type proportioning: regulatory timescales, stochasticity and lateral inhibition,
Physical Biology 13, 026007/1-9 (2016). - Nobuto Takeuchi, Kunihiko Kaneko, Paulien Hogeweg,
Evolutionarily stable disequilibrium: endless dynamics of evolution in a stationary population,
Proceedings of the Royal Society B 283, 20153109 (2016). - Yusuke Himeoka and Kunihiko Kaneko,
Enzyme oscillation can enhance the thermodynamic efficiency of cellular metabolism:consequence of anti-phase coupling between reaction flux and affinity,
Physical Biology 13, 026002/1-12 (2016). - 高井啓, 岡田康志,
3色の高輝度発光タンパク質プローブの開発と応用,
Journal of Japanese Biochemical Society 88(5), 669-673 (2016). - 岡田康志,
超解像蛍光顕微鏡法の現状と生体イメージングへの応用,
レーザー研究 44(10), 643-647 (2016). - 岡田康志,
超解像蛍光顕微鏡,
Clinical Neuroscience 34(6), 638-642 (2016). - Morito Sakuma, Sayaka Kita, and Hideo Higuchi,
Quantitative evaluation of malignant gliomas damage induced by photoactivation of IR700 dye,
Science and Technology of Advanced Materials 22, 473-482 (2016). - Gaigai Yu, Hiroyuki Onodera, Yuki Aono, Fuun Kawano, Yoshibumi Ueda, Akihiro Furuya, Hideyuki Suzuki, and *Moritoshi Sato,
Optical manipulation of the alpha subunits of heterotrimeric G proteins using photoswitchable dimerization systems,
Scientific Reports 6, 35777 (2016). - Fuun Kawano, Risako Okazaki, Masayuki Yazawa, and *Moritoshi Sato,
A photoactivatable Cre–loxP recombination system for optogenetic genome engineering,
Nature Chemical Biology 12, 1059-1064 (2016). - Keiji Fushimi, Takahiro Nakajima, Yuki Aono, Tatsuro Yamamoto, Ni-Ni-Win, Masahiko Ikeuchi, Moritoshi Sato and *Rei Narikawa,
Photoconversion and fluorescence properties of a red/green-type cyanobacteriochrome AM1_C0023g2 that binds not only phycocyanobilin but also biliverdin,
Frontiers in Microbiology 7, 588 (2016). - *佐藤守俊,
CRISPR-Cas9システムの光操作技術,
実験医学増刊号「All about ゲノム編集」 34, 47-52 (2016). - Takasho Nozoe, Edo Kussell, and *Yuichi Wakamoto,
Inferring fitness landscapes and selection on phenotypic states from single-cell genealogical data,
PLoS Genetics ad(3), e1006653 (2017). - Mikihiro Hashimoto, Takashi Nozoe, Hidenori Nakaoka, Reiko Okura, Sayo Akiyoshi, Kunihiko Kaneko, Edo Kussell, and *Yuichi Wakamoto,
Noise-driven growth rate gain in clonal cellular populations,
PNAS 113, 3251-3256 (2016). - Maroš Pleška, Long Qian, Reiko Okura, Tobias Bergmiller, Yuichi Wakamoto, Edo Kussell, and *Călin C. Guet,
Bacterial autoimmunity due to a restriction-modification system,
Current Biology 26, 404-409 (2016). - Ayako Uno, Ryohei Nakamura, Tatsuya Tsukahara, Wei Qu, Sumio Sugano,
Yutaka Suzuki, Shinichi Morishita, and Hiroyuki Takeda,
Comparative analysis of genome and epigenome in the closely related medaka species identifies conserved sequence preferences for DNA hypomethylated domains,
Zoological Science 33, 368-365 (2016). - Takane Ozawa, Tomoko Mizuhara, Masataka Arata, Masakazu Shimada, Teruyuki Niimi, Kensuke Okada, *Yasukazu Okada, and *Kunihiro Ohta,
Histone deacetylases control module-specific phenotypic plasticity in beetle weapons,
PNAS 113, 15042–15047 (2016). - Koji Hashimoto, Kohei Kurosawa, Akiho Murayama, *Hidetaka Seo, and Kunihiro Ohta,
B Cell-Based Seamless Engineering of Antibody Fc Domains,
PLoS One 11, e0167232 (2016). - Naomichi Takemata and *Kunihiro Ohta,
Role of non-coding RNA transcription around gene regulatory elements in transcription factor recruitment,
RNA Biology 14, 1-5 (2016). - *Yoshito Hirata, *Arisa Oda, Kunihiro Ohta, and Kazuyuki Aihara,
Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots,
Scientific Reports 6, 34982 (2016). - Atsuko Miki, Josephine Galipon, Satoshi Sawai, Toshifumi Inada, and *Kunihiro Ohta,
RNA decay systems enhance reciprocal switching of sense and antisense transcripts in response to glucose starvation,
Genes to Cells 21, 1276-1289 (2016). - Naoyoshi Kumakura, Hiroka Otsuki, Masaru Ito, Mika Nomoto, Yasuomi Tada, Kunihiro Ohta, and *Yuichiro Watanabe,
Arabidopsis AtRRP44 has ribonuclease activity that is required for cell viability,
Plant Biotechnology 33, 77–85 (2016). - Risa Mitsumori, Tomoe Ohashi, Kazuto Kugou, Ayako Ichino ,Kei Taniguchi, Kunihiro Ohta, Hiroyuki Uchida, and *Masaya Oki,
Analysis of novel Sir3 binding regions in Saccharomyces cerevisiae,
The Journal of Biochemistry 160, 11-17 (2016). - Naomichi Takemata, Arisa Oda, Takatomi Yamada, Josephine Galipon, Tomoichiro Miyoshi, Yutaka Suzuki, Sumio Sugano, Charles S. Hoffman, Kouji Hirota,and *Kunihiro Ohta,
Local potentiation of stress-responsive genes by upstream noncoding transcription,
Nucleic Acids Research 44 , 5174-5189 (2016). - Sanki Tashiro, Tetsuya Handa, Atsushi Matsuda, Takuto Ban, Toru Takigawa, Kazumi Miyasato, Kojiro Ishii, Kazuto Kugou, Kunihiro Ohta, Yasushi Hiraoka, Hisao Masukata and *Junko Kanoh,
Shugoshin forms a specialized chromatin domain at subtelomeres that regulates transcription and replication timing,
Nature Communications 7, 10393 (2016). - Akihiko Nakajima, Motohiko Ishida, Taihei Fujimori, Yuichi Wakamoto, and Satoshi Sawai,
The Microfluidic lighthouse: an omnidirectional gradient generator,
Lab on a Chip 16, 4382-4394 (2016). - Satoshi Kuwana, Hiroshi Senoo, Satoshi Sawai, and Masashi Fukuzawa,
A novel, lineage-primed prestalk cell subtype involved in the morphogenesis of D. discoideum,
Developmental Biology 416, 286-299 (2016). - Fumihito Fukujin, Akihiko Nakajima, Nao Shimada, and Satoshi Sawai,
Self-organization of chemoattractant waves in Dictyostelium depends on F-actin and cell–substrate adhesion,
Journal of The Royal Society Interface 13 (2016). - Akihiko Nakajima, Satoshi Sawai,
Dissecting Spatial and Temporal Sensing in Dictyostelium Chemotaxis Using a Wave Gradient Generator,
Methods in Molecular Biology 1407, 107-122 (2016). - Naohiro Terasaka, Kazuki Futai, Takayuki Katoh, Hiroaki Suga,
A human microRNA precursor binding to folic acid discovered by small RNA transcriptomic SELEX,
RNA 22(12), 1918-1928 (2016). - Yukiko Matsunaga, Nasir K. Bashiruddin, Yu Kitago, Junichi Takagi, Hiroaki Suga ,
Allosteric inhibition of a semaphorin 4D receptor plexin B1 by a high affinity macrocyclic peptide,
Cell Chemical Biology 23, 1341-1350 (2016). - Yuki Goto, Hiroaki Suga,
A post-translational cyclodehydratase, PatD, tolerates sequence variation in the C-terminal region of the substrate peptides,
Chemistry Letters 45, 1247-1249 (2016). - Kazuki Futai, Naohiro Terasaka, Takayuki Katoh, Hiroaki Suga ,
tRid, an enabling method to isolate previously inaccessible small RNA fractions,
Methods 106, 105-111 (2016). - Takayuki Katoh, Ingo Wohlgemuth, Masanobu Nagano, Marina V. Rodnina, and Hiroaki Suga,
Essential structural elements in tRNA(Pro) for EF-P-mediated alleviation of translation stalling,
Nature Communications 7, 11657 (2016). - Yoshihiko Iwane, Azusa Hitomi, Hiroshi Murakami, Takayuki Katoh, Yuki Goto, and Hiroaki Suga,
Expanding the amino acid repertoire of ribosomal polypeptide synthesis via the artificial division of codon boxes,
Nature Chemistry 8(4), 317-325 (2016). - *Taisuke Banno, Yuki Tanaka, Kouichi Asakura, *Taro Toyota,
Self-propelled oil droplets and their morphological change to giant vesicles induced by a surfactant solution at low pH,
Langmuir 32, 9591-9597 (2016). - Taisuke Banno, Arisa Asami, Naoko Ueno, Hiroyuki Kitahata, Yuki Koyano, Kouichi Asakura, *Taro Toyota,
Deformable self-propelled micro-object comprising underwater oil droplets,
Scientific Reports 6, 31292 (2016). - *Yuno Natsume, Taro Toyota,
Appearance of crystalline pattern for colloidal particles encapsulated in giant vesicles,
Transactions of the Materials Research Society of Japan 41, 147-149 (2016). - Masahito Hayashi, Masayoshi Nishiyama, Yuki Kazayama, Taro Toyota, Yoshie Harada, *Kingo Takiguchi,
Reversible morphological control of tubulin-encapsulating giant liposomes by hydrostatic pressure,
Langmuir 32, 3794-3802 (2016). - Yuki Kazayama, Tetsuhiko Teshima, Toshihisa Osaki, *Shoji Takeuchi, *Taro Toyota,
Integrated microfluidic system for size-based selection and trapping of giant vesicles,
Analytical Chemistry 88, 1111-1116 (2016). - Kazuma Gotoh, Tomonori Nomoto, Taro Toyota, *Masanori Fujinami,
Effects of halide ions on the acceptor phase in spontaneous chemical oscillations in donor/membrane/acceptor systems,
Journal of Colloid and Interface Science 462, 351-358 (2016). - Yuno Natsume, *Taro Toyota,
Asymmetrical polyhedral configuration of giant vesicles induced by orderly array of encapsulated colloidal particles,
PLOS ONE 11, e0146683 (2016). - *豊田太郎, 本多智,
合成両親媒性分子で創る細胞様システム,
生物物理 56, 165-167 (2016). - Tetsuya Hiraiwa, and Guillaume Salbreux,
Role of Turnover in Active Stress Generation in a Filament Network,
Physical Review Letters 116, 188101 (2016). - *Takao Ohta, Mitsusuke Tarama and Masaki Sano,
Simple model of cell crawling,
Physica D 318-319, 3-11 (2016). - *John J. Molina, Kotaro Otomura, Hayato Shiba, Hideki Kobayashi, Masaki Sano, and Ryoichi Yamamoto,
Rheological evaluation of colloidal dispersions using the smoothed profile method: formulation and applications,
Journal of Fluid Mechanics 792, 590-619 (2016). - *Masaki Sano and Keiichi Tamai,
A Universal Transition to Turbulence in Channel Flow,
Nature Physics 12, 249-253 (2016). - *佐野雅己,
現象のモデル化と数理モデルの普遍性,
数理科学 631, 1-4 (2016). - Takanori Sano, Kentaro Kawata, Satoshi Ohono, Katsuyuki Yugi, Hiroaki Kakuda,Hiroyuki Kubota, Shinsuke Uda, Masashi Fujii, Katsuyuki Kunida, Daisuke Hoshino,Atsushi Hatano, Yuki Ito, Miharu Sato, Yutaka Suzuki, Shinya Kuroda,
Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin,
Science Signaling 9, ra112 (2016). - Takamasa Kudo, *Shinsuke Uda, Takaho Tsuchiya, Takumi Wada, Yasuaki Karasawa, Masashi Fujii, Takeshi H. Saito, *Shinya Kuroda,
Laguerre filter analysis with partial least square regression reveals a priming effect of ERK and CREB on c-FOS induction,
PLoS ONE 11, e0160548 (2016). - Sarah Filippi, Chris P. Barnes, Paul D.W. Kirk, Takamasa Kudo, Katsuyuki Kunida, Siobhan S. McMahon, Takaho Tsuchiya, Takumi Wada, Shinya Kuroda, and *Michael P.H. Stumpf ,
Robustness of MEK-ERK dynamics and origins of Cell-to-Cell variability in MAPK signaling,
Cell Reports 15, 2524-2535 (2016). - Eri Hasegawa, James W. Truman, and *Akinao Nose,
Identification of excitatory premotor interneurons which regulate local muscle contraction during Drosophila larval locomotion,
Scientific Reports 6, 30806 (2016). - Aleksandr Drozd, Olaf Witkowski, Satoshi Matsuoka, Takashi Ikegami,
Critical Mass in the Emergence of Collective Intelligence: a Parallelized Simulation of Swarms in Noisy Environments,
Artificial Life and Robotics 21, 317-323 (2016). - Tim Taylor, Mark Bedau, Alastair Channon, David Ackley, Wolfgang Banzhaf, Guillaume Beslon, Emily Dolson, Tom Froese, Simon Hickinbotham, Takashi Ikegami, Barry McMullin, Norman Packard, Steen Rasmussen, Nathaniel Virgo, Eran Agmon, Edward Clark, Simon McGregor,Charles Ofria, Glen Ropella, Lee Spector, Kenneth O. Stanley, Adam Stanton, Christopher Timperley, Anya Vostinar, and Michael Wiser,
Open-Ended Evolution: Perspectives from the OEE Workshop in York,
Artificial Life 22, 408-423 (2016). - Olaf Witkowski, Takashi Ikegami,
Emergence of Swarming Behavior: Foraging Agents Evolve Collective Motion Based on Signaling,
PLoS ONE 11(4), e0152756 (2016). - Julien Hubert and Takashi Ikegami,
How long did it last? Memorizing interval timings in a simple robotic task,
Proceedings of the Artificial Life Conference 2016, 406-407 (2016). - Martin Biehl, Takashi Ikegami, Daniel Polani,
Towards information based spatiotemporal patterns as a foundation for agent representation in dynamical systems,
Proceedings of the Artificial Life Conference 2016, 722-729 (2016). - *Yukinobu Arata, Michio Hiroshima, Chan-Gi Pack, Ravikrishna Ramanujam, Fumio Motegi, Kenichi Nakazato, Hitoshi Sawa, Tetsuya J. Kobayashi, Tatsuo Shibata, and Yasushi Sako,
Cortical Polarity of the RING Protein PAR-2 Is Maintained by Exchange Rate Kinetics at the Cortical-Cytoplasmic Boundary,
Cell Reports 16, 2156-2168 (2016). - *Tetsuya J. Kobayashi, Ryo Yokota, Kazuyuki Aihara,
Feedback Regulation and its Efficiency in Biochemical Networks,
Journal of Statistical Physics 162, 1425-1449 (2016). - *秋山泰身, 小林徹也,
システム生物学と免疫系の自己-非自己識別,
医学の歩み 259, 839-842 (2016).