Shuichi Onami

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 20

Top Venues

bioRxiv : the preprint server for biology

Scientific data

BMC bioinformatics

Science advances

RIKEN Center for Biosystems Dynamics Research

The Graduate University for Advanced Studies, SOKENDAI (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

RIKEN Center for Biosystems Dynamics Research Apr 01 2018

Japan

Team Leader

Education History

The Graduate University for Advanced Studies, SOKENDAI Apr 01 1994 - Mar 31 1998

Japan

PHD

Publications

Yuki Yamagata, Tsubasa Fukuyama, Shuichi Onami, Hiroshi Masuya
Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective. Scientific data 11 (1) (2024)
Yuki Yamagata, Tsubasa Fukuyama, Shuichi Onami, Hiroshi Masuya
Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective. Scientific data 11 (1) (2024)
Daniel Yutaka Sprague, Kevin Rusch, Raymond L Dunn, Jackson M Borchardt, Steven Ban, Greg Bubnis, Grace Chiu, Chentao Wen, Ryoga Suzuki, Shivesh Chaudhary, Hyun Jee Lee, Zikai Yu, Benjamin K Dichter, Ryan Ly, Shuichi Onami, Hang Lu, Koutarou D Kimura, Eviatar I Yemini, Saul Kato
Unifying community-wide whole-brain imaging datasets enables robust automated neuron identification and reveals determinants of neuron positioning in C. elegans . bioRxiv : the preprint server for biology (2024)
Daniel Yutaka Sprague, Kevin Rusch, Raymond L Dunn, Jackson M Borchardt, Greg Bubnis, Grace C Chiu, Chentao Wen, Ryoga Suzuki, Shivesh Chaudhary, Benjamin Dichter, Ryan Ly, Shuichi Onami, Hang Lu, Kotaro Kimura, Eviatar I Yemini, Saul Kato
Unifying community-wide whole-brain imaging datasets enables robust automated neuron identification and reveals determinants of neuron positioning in C. elegans . bioRxiv : the preprint server for biology (2024)
Nikki Bialy, Frank Alber, Brenda J Andrews, Michael Angelo, Brian J Beliveau, Lacramioara Bintu, Alistair Nicol Boettiger, Ulrike Boehm, Claire M Brown, Mahmoud Bukar Maina, James J Chambers, Beth A Cimini, Kevin W Eliceiri, Rachel Errington, Orestis Faklaris, Nathalie Gaudreault, Ronald N Germain, Wojtek J Goscinski, David Grünwald, Michael Halter, Dorit Hanein, John W Hickey, Judith Lacoste, Alex Laude, Emma Lundberg, Jian Ma, Leonel Malacrida, Josh Moore, Glyn Nelson, Elizabeth Kathleen Neumann, Roland Nitschke, Shuichi Onami, Jaime A Pimentel, Anne L Plant, Andrea J Radtke, Bikash Sabata, Denis Schapiro, Johannes Schöneberg, Jeffrey M Spraggins, Damir Sudar, Wouter-Michiel Vierdag, Niels Volkmann, Carolina Wählby, Siyuan Steven Wang, Ziv Rafael Yaniv, Caterina Strambio-De-Castilla
Harmonizing the Generation and Pre-publication Stewardship of FAIR Image data. ArXiv (2024)
Yuki Yamagata, Tsubasa Fukuyama, Shuichi Onami, Hiroshi Masuya
Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective. Scientific data 11 (1) (2024)
Towako Hiraki-Kajiyama, Nobuhiko Miyasaka, Reiko Ando, Noriko Wakisaka, Hiroya Itoga, Shuichi Onami, Yoshihiro Yoshihara
An atlas and database of neuropeptide gene expression in the adult zebrafish forebrain. The Journal of comparative neurology 532 (6) (2024)
Daniel Yutaka Sprague, Kevin Rusch, Raymond L Dunn, Jackson M Borchardt, Steven Ban, Greg Bubnis, Grace C Chiu, Chentao Wen, Ryoga Suzuki, Shivesh Chaudhary, Hyun Jee Lee, Zikai Yu, Benjamin K Dichter, Ryan Ly, Shuichi Onami, Hang Lu, Koutarou D Kimura, Eviatar I Yemini, Saul Kato
Unifying community-wide whole-brain imaging datasets enables robust automated neuron identification and reveals determinants of neuron positioning in C. elegans . bioRxiv : the preprint server for biology (2024)
Josh Moore, Daniela Basurto-Lozada, Sébastien Besson, John A Bogovic, Jordao Bragantini, Jackson M Brown, Jean-Marie Burel, Xavier Casas Moreno, Gustavo de Medeiros, Erin E Diel, David Gault, Satrajit S Ghosh, Ilan Gold, Yaroslav O Halchenko, Matthew Hartley, David Horsfall, Mark S Keller, Mark Kittisopikul, Gabor Kovacs, Aybüke Küpcü Yoldaş, Koji Kyoda, Albane le Tournoulx de la Villegeorges, Tong Li, Prisca Liberali, Dominik Lindner, Melissa Linkert, Joel Lüthi, Jeremy Maitlin-Shepard, Trevor Manz, Luca Marconato, Matthew McCormick, Merlin Lange, Khaled Mohamed, William Moore, Nils Norlin, Wei Ouyang, Buğra Özdemir, Giovanni Palla, Constantin Pape, Lucas Pelkmans, Tobias Pietzsch, Stephan Preibisch, Martin Prete, Norman Rzepka, Sameeul Samee, Nicholas J Schaub, Hythem Sidky, Ahmet Can Solak, David R Stirling, Jonathan Striebel, Christian Tischer, Daniel M Toloudis, Isaac Virshup, Petr Walczysko, Alan M Watson, Erin Weisbart, Frances Wong, Kevin A Yamauchi, Omer Ali Bayraktar, Beth A Cimini, Nils Gehlenborg, Muzlifah A Haniffa, Nathan A Hotaling, Shuichi Onami, Loïc Alain Royer, Stephan Saalfeld, Oliver Stegle, Fabian Joachim Theis, Jason R Swedlow
OME-Zarr: a cloud-optimized bioimaging file format with international community support. Histochemistry and cell biology (2023)
Tadasu Nozaki, Soya Shinkai, Satoru Ide, Koichi Higashi, Sachiko Tamura, Masa A Shimazoe, Masaki Nakagawa, Yutaka Suzuki, Yasushi Okada, Masaki Sasai, Shuichi Onami, Ken Kurokawa, Shiori Iida, Kazuhiro Maeshima
Condensed but liquid-like domain organization of active chromatin regions in living human cells. Science advances 9 (14) (2023)
Kazuko Okamoto, Hideaki Fujita, Yasushi Okada, Soya Shinkai, Shuichi Onami, Kuniya Abe, Kenta Fujimoto, Kensuke Sasaki, Go Shioi, Tomonobu M Watanabe
Single-molecule tracking of Nanog and Oct4 in living mouse embryonic stem cells uncovers a feedback mechanism of pluripotency maintenance. The EMBO journal (2023)
Yukihiko Kubota, Natsumi Ota, Hisashi Takatsuka, Takuma Unno, Shuichi Onami, Asako Sugimoto, Masahiro Ito
The PAF1 complex cell autonomously promotes oogenesis in Caenorhabditis elegans. Genes to cells : devoted to molecular & cellular mechanisms 27 (6) (2022)
Soya Shinkai, Hiroya Itoga, Koji Kyoda, Shuichi Onami
PHi-C2: interpreting Hi-C data as the dynamic 3D genome state. Bioinformatics (Oxford, England) 38 (21) (2022)
Jason R Swedlow, Pasi Kankaanpää, Siddhant Tripathi, Wojtek J Goscinski, Graham John Galloway, Leonel Malacrida, Ryan P Sullivan, Steffen Härtel Gründler, Claire M Brown, Christopher D Wood, Antje Keppler, Federica Paina, Ben Loos, Sara Zullino, Dario Livio Longo, Silvio Aime, Shuichi Onami
A global view of standards for open image data formats and repositories. Nature methods 18 (12) (2022)
Shiori Iida, Soya Shinkai, Yuji Itoh, Sachiko Tamura, Masato T Kanemaki, Shuichi Onami, Kazuhiro Maeshima
Single-nucleosome imaging reveals steady-state motion of interphase chromatin in living human cells. Science advances 8 (22) (2022)
Siddhant Tripathi, Wah Chiu, Lucy M Collinson, Michele C Darrow, Jan Ellenberg, David Grünwald, Jean-Karim Hériché, Andrii Iudin, Gabriel G Martins, Terry Meehan, Kedar Narayan, Ardan Patwardhan, Matthew Robert Geoffrey Russell, Helen R Saibil, Caterina Strambio-De-Castilla, Jason R Swedlow, Christian Tischer, Virginie Uhlmann, Paul Verkade, Mary Barlow, Omer Ali Bayraktar, Ewan Birney, Cesare Catavitello, Christopher J Cawthorne, Stephan Wagner-Conrad, Elizabeth Duke, Perrine Paul-Gilloteaux, Emmanuel M Gustin, Maria Harkiolaki, Pasi Kankaanpää, Thomas Lemberger, Jo McEntyre, Josh Moore, Andrew W Nicholls, Shuichi Onami, Helen Parkinson, Maddy Parsons, Marina Romanchikova, Nicholas Sofroniew, Jim Swoger, Nadine Utz, Lennard M Voortman, Frances Wong, Peijun Zhang, Gerard J Kleywegt, Alvis Brazma
REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. Nature methods 18 (12) (2022)
Momoko Imakubo, Jun Takayama, Hatsumi Okada, Shuichi Onami
Statistical image processing quantifies the changes in cytoplasmic texture associated with aging in Caenorhabditis elegans oocytes. BMC bioinformatics 22 (1) (2021)
Soya Shinkai, Masaki Nakagawa, Takeshi Sugawara, Yuichi Togashi, Hiroshi Ochiai, Ryuichiro Nakato, Yuichi Taniguchi, Shuichi Onami
PHi-C: deciphering Hi-C data into polymer dynamics. NAR genomics and bioinformatics 2 (2) (2020)
Koji Kyoda, Kenneth H L Ho, Yukako Tohsato, Hiroya Itoga, Shuichi Onami
BD5: An open HDF5-based data format to represent quantitative biological dynamics data. PloS one 15 (8) (2020)
Yusuke Azuma, Shuichi Onami
Biologically constrained optimization based cell membrane segmentation in C. elegans embryos. BMC bioinformatics 18 (1) (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Shuichi Onami