Graph Inference from a Walk for TRees of Bounded Degree 3 is NP-Complete. - Osamu Maruyama; Satoru Miyano (MFCS, 1995)

Extracting Best Consensus Motifs from Positive and Negative Examples. - Erika Tateishi; Osamu Maruyama; Satoru Miyano (STACS, 1996)

Inferring a Tree from Walks. - Osamu Maruyama; Satoru Miyano (Theor. Comput. Sci., 1996)

Toward Genomic Hypothesis Creator: View Designer for Discovery. - Osamu Maruyama; Tomoyuki Uchida; Takayoshi Shoudai; Satoru Miyano (Discovery Science, 1998)

Identification of Gene Regulatory Networks by Strategic Gene Disruptions and Gene Overexpressions. - Tatsuya Akutsu; Satoru Kuhara; Osamu Maruyama; Satoru Miyano (SODA, 1998)

Designing Views in HypothesisCreator: System for Assisting in Discovery. - Osamu Maruyama; Tomoyuki Uchida; Kim Lan Sim; Satoru Miyano (Discovery Science, 1999)

VML: A View Modeling Language for Computational Knowledge Discovery. - Hideo Bannai; Yoshinori Tamada; Osamu Maruyama; Satoru Miyano (Discovery Science, 2001)

Learning Conformation Rules. - Osamu Maruyama; Takayoshi Shoudai; Emiko Furuichi; Satoru Kuhara; Satoru Miyano (Discovery Science, 2001)

Views: Fundamental Building Blocks in the Process of Knowledge Discovery. - Hideo Bannai; Yoshinori Tamada; Osamu Maruyama; Kenta Nakai; Satoru Miyano (FLAIRS, 2001)

HypothesisCreator: Concepts for Accelerating the Computational Knowledge Discovery Process. - Hideo Bannai; Yoshinori Tamada; Osamu Maruyama; Satoru Miyano (Electron. Trans. Artif. Intell., 2001)

Toward Drawing an Atlas of Hypothesis Classes: Approximating a Hypothesis via Another Hypothesis Model. - Osamu Maruyama; Takayoshi Shoudai; Satoru Miyano (Discovery Science, 2002)

Foundations of Designing Computational Knowledge Discovery Processes. - Yoshinori Tamada; Hideo Bannai; Osamu Maruyama; Satoru Miyano (Progress in Discovery Science, 2002)

Extensive feature detection of N-terminal protein sorting signals. - Hideo Bannai; Yoshinori Tamada; Osamu Maruyama; Kenta Nakai; Satoru Miyano (Bioinform., 2002)

Fast algorithm for extracting multiple unordered short motifs using bit operations. - Osamu Maruyama; Hideo Bannai; Yoshinori Tamada; Satoru Kuhara; Satoru Miyano (Inf. Sci., 2002)

Finding optimal degenerate patterns in DNA sequences. - Daisuke Shinozaki; Tatsuya Akutsu; Osamu Maruyama (ECCB, 2003)

Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model. - Tatsuya Akutsu; Satoru Kuhara; Osamu Maruyama; Satoru Miyano (Theor. Comput. Sci., 2003)

Extensive Search for Discriminative Features of Alternative Splicing. - Hiroki Sakai; Osamu Maruyama (Pacific Symposium on Biocomputing, 2004)

Searching for Regulatory Elements of Alternative Splicing Events Using Phylogenetic Footprinting. - Daichi Shigemizu; Osamu Maruyama (WABI, 2004)

Reconstructing phylogenetic trees of prokaryote genomes by randomly sampling oligopeptides. - Osamu Maruyama; Akiko Matsuda; Satoru Kuhara (Int. J. Bioinform. Res. Appl., 2005)

Evaluating Protein Sequence Signatures Inferred from Protein-Protein Interaction Data by Gene Ontology Annotations. - Osamu Maruyama; Hideki Hirakawa; Takao Iwayanagi; Yoshiko Ishida; Shizu Takeda; Jun Otomo; Satoru Kuhara (BIBM, 2008)

NWE: Node-weighted expansion for protein complex prediction using random walk distances. - Osamu Maruyama; Ayaka Chihara (BIBM, 2010)

Heterodimeric protein complex identification. - Osamu Maruyama (BCB, 2011)

Noninvasive miniaturized mass-flow meter using a curved cannula for implantable axial flow blood pump. - Ryo Kosaka; Masahiro Nishida; Osamu Maruyama; Takashi Yamane 001 (EMBC, 2011)

Improvement of hemocompatibility for hydrodynamic levitation centrifugal pump by optimizing step bearings. - Ryo Kosaka; Toru Yada; Masahiro Nishida; Osamu Maruyama; Takashi Yamane 001 (EMBC, 2011)

Infrequent, Unexpected, and Contrast Pattern Discovery from Bacterial Genomes by Genome-wide Comparative Analysis. - Daisuke Ikeda; Osamu Maruyama; Satoru Kuhara (BIOINFORMATICS, 2013)

Noninvasive blood-flow meter using a curved cannula with zero compensation for an axial flow blood pump. - Ryo Kosaka; Kyohei Fukuda; Masahiro Nishida; Osamu Maruyama; Takashi Yamane 001 (EMBC, 2013)

Fluid dynamic design for low hemolysis in a hydrodynamically levitated centrifugal blood pump. - Tomotaka Murashige; Ryo Kosaka; Masahiro Nishida; Osamu Maruyama; Takashi Yamane 001; Katsuyuki Kuwana; Yasuo Kawaguchi (EMBC, 2013)

Effect of impeller flow path on pump performance and impeller stability of the monopivot circulatory pump. - Masahiro Nishida; Kento Nakayama; Ryo Kosaka; Osamu Maruyama; Yasuo Kawaguchi; Katsuyuki Kuwana; Takashi Yamane 001 (EMBC, 2013)

Simultaneous determination of hemolysis and hematocrit in extracorporeal circulation by plasma surface reflectance spectroscopy. - Daisuke Sakota; Yuki Kani; Ryo Kosaka; Masahiro Nishida; Osamu Maruyama (EMBC, 2013)

Risk analysis and detection of thrombosis by measurement of electrical resistivity of blood. - Achyut Sapkota; Yuta Asakura; Osamu Maruyama; Ryo Kosaka; Takashi Yamane 001; Masahiro Takei (EMBC, 2013)

Heterodimeric protein complex identification by naïve Bayes classifiers. - Osamu Maruyama (BMC Bioinform., 2013)

PPSampler2: Predicting protein complexes more accurately and efficiently by sampling. - Chasanah Kusumastuti Widita; Osamu Maruyama (BMC Syst. Biol., 2013)

The Purity Measure for genomic Regions leads to Horizontally Transferred genes. - Yuta Taniguchi; Yasuhiro Yamada; Osamu Maruyama; Satoru Kuhara; Daisuke Ikeda (J. Bioinform. Comput. Biol., 2013)

A scale-free structure prior for Bayesian inference of Gaussian graphical models. - Osamu Maruyama; Shota Shikita (BIBM, 2014)

Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels. - Peiying Ruan; Morihiro Hayashida; Osamu Maruyama; Tatsuya Akutsu (BMC Bioinform., 2014)

Discovery of small protein complexes from PPI networks with size-specific supervised weighting. - Chern Han Yong; Osamu Maruyama; Limsoon Wong (BMC Syst. Biol., 2014)

ReSAPP: Predicting overlapping protein complexes by merging multiple-sampled partitions of proteins. - So Kobiki; Osamu Maruyama (J. Bioinform. Comput. Biol., 2014)

Regularizing predicted complexes by mutually exclusive protein-protein interactions. - Osamu Maruyama; Limsoon Wong (ASONAM, 2015)

Bearing gap adjustment for improvement of levitation performance in a hydrodynamically levitated centrifugal blood pump. - Ryo Kosaka; Fumihiko Yoshida; Masahiro Nishida; Osamu Maruyama; Yasuo Kawaguchi; Takashi Yamane 001 (EMBC, 2015)

Evaluation of erythrocyte flow at a bearing gap in a hydrodynamically levitated centrifugal blood pump. - Tomotaka Murashige; Ryo Kosaka; Daisuke Sakota; Masahiro Nishida; Yasuo Kawaguchi; Takashi Yamane 001; Osamu Maruyama (EMBC, 2015)

Development of a photon-cell interactive monte carlo simulation for non-invasive measurement of blood glucose level by Raman spectroscopy. - Daisuke Sakota; Ryo Kosaka; Masahiro Nishida; Osamu Maruyama (EMBC, 2015)

Hyperspectral imaging of vascular anastomosis associated with blood flow and hemoglobin concentration. - Daisuke Sakota; Eiki Nagaoka; Osamu Maruyama (EMBC, 2015)

Reaction mechanism of blood coagulation factors in shear flow field. - Koki Kawakami; Daisuke Sakota; Ryo Kosaka; Masahiro Nishida; Yasuo Kawaguchi; Osamu Maruyama (EMBC, 2016)

RocSampler: regularizing overlapping protein complexes in protein-protein interaction networks. - Osamu Maruyama; Yuki Kuwahara (BMC Bioinform., 2017)

DegSampler: Collapsed Gibbs Sampler for Detecting E3 Binding Sites. - Osamu Maruyama; Fumiko Matsuzaki (BIBE, 2018)

Development of an Intelligent Ventricular Assist Device with a Function of Sensorless Thrombus Detection. - Takuro Maruyama; Tomotaka Murashige; Daisuke Sakota; Osamu Maruyama; Wataru Hijikata (EMBC, 2018)

DegSampler3: Pairwise Dependency Model in Degradation Motif Site Prediction of Substrate Protein Sequences. - Osamu Maruyama; Fumiko Matsuzaki (BIBE, 2019)

A convolutional neural network-based regression model to infer the epigenetic crosstalk responsible for CG methylation patterns. - Wan Kin Au Yeung; Osamu Maruyama; Hiroyuki Sasaki (BMC Bioinform., 2021)

CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers. - Osamu Maruyama; Yinuo Li; Hiroki Narita; Hidehiro Toh; Wan Kin Au Yeung; Hiroyuki Sasaki (BMC Bioinform., 2022)

CBOEP: Generating negative enhancer-promoter interactions to train classifiers. - Tsukasa Koga; Osamu Maruyama (BCB, 2023)

Preservation of emotional context in tweet embeddings on social networking sites. - Osamu Maruyama; Asato Yoshinaga; Ken-Ichi Sawai (Artif. Life Robotics, 2024)

Class-balanced negative training sets for improving classifier model predictions of enhancer-promoter interactions. - Osamu Maruyama; Tsukasa Koga (BMC Bioinform., 2025)