Genome structures embossed by oligonucleotide-stickiness. - Koichi Nishigaki; Ayumu Saito (Bioinform., 2002)

AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction. - Ayumu Saito; Masao Nagasaki; Masaaki Oyama; Hiroko Kozuka-Hata; Kentaro Semba; Sumio Sugano; Tadashi Yamamoto; Satoru Miyano (BMC Bioinform., 2007)

Cell System Ontology: Representation for Modeling, Visualizing, and Simulating Biological Pathways. - Euna Jeong; Masao Nagasaki; Ayumu Saito; Satoru Miyano (Silico Biol., 2007)

ExonMiner: Web service for analysis of GeneChip Exon array data. - Kazuyuki Numata; Ryo Yoshida; Masao Nagasaki; Ayumu Saito; Seiya Imoto; Satoru Miyano (BMC Bioinform., 2008)

Systematic reconstruction of TRANSPATH data into Cell System Markup Language. - Masao Nagasaki; Ayumu Saito; Chen Li 007; Euna Jeong; Satoru Miyano (BMC Syst. Biol., 2008)

Foundations of Systems Biology - Using Cell Illustrator® and Pathway Databases. - Masao Nagasaki; Ayumu Saito; Atsushi Doi; Hiroshi Matsuno; Satoru Miyano (Springer, 2009)

Host-parasite relations of bacteria and phages can be unveiled by Oligostickiness, a measure of relaxed sequence similarity. - Shamim Ahmed; Ayumu Saito; Miho Suzuki; Naoto Nemoto; Koichi Nishigaki (Bioinform., 2009)

DA 1.0: parameter estimation of biological pathways using data assimilation approach. - Chuan Hock Koh; Masao Nagasaki; Ayumu Saito; Limsoon Wong; Satoru Miyano (Bioinform., 2010)

Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram. - Chen Li 007; Masao Nagasaki; Ayumu Saito; Satoru Miyano (BMC Syst. Biol., 2010)

Cell Illustrator 4.0: A Computational Platform for Systems Biology. - Masao Nagasaki; Ayumu Saito; Euna Jeong; Chen Li 007; Kaname Kojima; Emi Ikeda; Satoru Miyano (Silico Biol., 2010)

CSO validator: improving manual curation workflow for biological pathways. - Euna Jeong; Masao Nagasaki; Emi Ikeda; Yayoi Sekiya; Ayumu Saito; Satoru Miyano (Bioinform., 2011)

MIRACH: efficient model checker for quantitative biological pathway models. - Chuan Hock Koh; Masao Nagasaki; Ayumu Saito; Chen Li 007; Limsoon Wong; Satoru Miyano (Bioinform., 2011)

Systems biology model repository for macrophage pathway simulation. - Masao Nagasaki; Ayumu Saito; André Fujita; Georg Tremmel; Kazuko Ueno; Emi Ikeda; Euna Jeong; Satoru Miyano (Bioinform., 2011)

IRView: a database and viewer for protein interacting regions. - Shigeo Fujimori; Naoya Hirai; Kazuyo Masuoka; Tomohiro Oshikubo; Tatsuhiro Yamashita; Takanori Washio; Ayumu Saito; Masao Nagasaki; Satoru Miyano; Etsuko Miyamoto-Sato (Bioinform., 2012)

XiP: a computational environment to create, extend and share workflows. - Masao Nagasaki; André Fujita; Yayoi Sekiya; Ayumu Saito; Emi Ikeda; Chen Li 007; Satoru Miyano (Bioinform., 2013)

Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling. - Ayumu Saito; Masao Nagasaki; Hiroshi Matsuno; Satoru Miyano (Modeling in Systems Biology, The Petri Net Approach, 2016)

Towards a Practical Library for Monadic Equational Reasoning in Coq. - Ayumu Saito; Reynald Affeldt (MPC, 2022)

Experimenting with an Intrinsically-Typed Probabilistic Programming Language in Coq. - Ayumu Saito; Reynald Affeldt (APLAS, 2023)

Semantics of Probabilistic Programs using s-Finite Kernels in Coq. - Reynald Affeldt; Cyril Cohen; Ayumu Saito (CPP, 2023)

Point-JEPA: A Joint Embedding Predictive Architecture for Self-Supervised Learning on Point Cloud. - Ayumu Saito; Jiju Poovvancheri (CoRR, 2024)

Point-JEPA: A Joint Embedding Predictive Architecture for Self-Supervised Learning on Point Cloud. - Ayumu Saito; Prachi Kudeshia; Jiju Poovvancheri (WACV, 2025)