EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences. - Jianjun Hu; Yifeng D. Yang; Daisuke Kihara (BMC Bioinform., 2006)

Tracing Lineage in Multi-version Scientific Databases. - Mingwu Zhang; Daisuke Kihara; Sunil Prabhakar 001 (BIBE, 2007)

Salient critical points for meshes. - Yu-Shen Liu; Min Liu 018; Daisuke Kihara; Karthik Ramani (Symposium on Solid and Physical Modeling, 2007)

Function Prediction of uncharacterized proteins. - Troy Hawkins; Daisuke Kihara (J. Bioinform. Comput. Biol., 2007)

Combining gene sequence similarity and textual information for gene function annotation in the literature. - Luo Si; Danni Yu; Daisuke Kihara; Yi Fang 003 (Inf. Retr., 2008)

ESG: extended similarity group method for automated protein function prediction. - Meghana Chitale; Troy Hawkins; Changsoon Park; Daisuke Kihara (Bioinform., 2009)

3D-SURFER: software for high-throughput protein surface comparison and analysis. - David La; Juan Esquivel-Rodríguez; Vishwesh Venkatraman; Bin Li; Lee Sael; Stephen Ueng; Steven Ahrendt; Daisuke Kihara (Bioinform., 2009)

Protein-protein docking using region-based 3D Zernike descriptors. - Vishwesh Venkatraman; Yifeng D. Yang; Lee Sael; Daisuke Kihara (BMC Bioinform., 2009)

Application of 3D Zernike descriptors to shape-based ligand similarity searching. - Vishwesh Venkatraman; Padmasini Chakravarthy; Daisuke Kihara (J. Cheminformatics, 2009)

Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP. - Troy Hawkins; Meghana Chitale; Daisuke Kihara (BMC Bioinform., 2010)

Improved protein surface comparison and application to low-resolution protein structure data. - Lee Sael; Daisuke Kihara (BMC Bioinform., 2010)

Characterization and Classification of Local Protein Surfaces Using Self-Organizing Map. - Lee Sael; Daisuke Kihara (Int. J. Knowl. Discov. Bioinform., 2010)

Quantification of Protein Group Coherence and Pathway Assignment Using Functional Association. - Meghana Chitale; Shriphani Palakodety; Daisuke Kihara (BMC Bioinform., 2011)

Protein domain recurrence and order can enhance prediction of protein functions. - Mario Abdel Messih; Meghana Chitale; Vladimir B. Bajic; Daisuke Kihara; Xin Gao 001 (Bioinform., 2012)

Evaluation of multiple protein docking structures using correctly predicted pairwise subunits. - Juan Esquivel-Rodríguez; Daisuke Kihara (BMC Bioinform., 2012)

Protein docking prediction using predicted protein-protein interface. - Bin Li; Daisuke Kihara (BMC Bioinform., 2012)

Constructing patch-based ligand-binding pocket database for predicting function of proteins. - Lee Sael; Daisuke Kihara (BMC Bioinform., 2012)

Effective inter-residue contact definitions for accurate protein fold recognition. - Chao Yuan; Hao Chen; Daisuke Kihara (BMC Bioinform., 2012)

Evaluation of Arterial Stiffness during the Flow-Mediated Dilation Test. - Harutoyo Hirano; Daisuke Kihara; Hiroki Hirano; Yuichi Kurita; Teiji Ukawa; Tsuneo Takayanagi; Haruka Morimoto; Ryuji Nakamura; Noboru Saeki; Yukihito Higashi; Masashi Kawamoto; Masao Yoshizumi; et al. (SMC, 2013)

In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment. - Meghana Chitale; Ishita K. Khan; Daisuke Kihara (BMC Bioinform., 2013)

The International Society of Computational Biology presents: the Great Lakes Bioinformatics Conference, May 16-18, 2014, Cincinnati, Ohio. - Jim Cavalcoli; Lonnie R. Welch; Bruce J. Aronow; Sorin Draghici; Daisuke Kihara (Bioinform., 2014)

Comparison of Image Patches Using Local Moment Invariants. - Atilla Sit; Daisuke Kihara (IEEE Trans. Image Process., 2014)

Phase transitions in a sequence-structure channel. - Abram Magner; Daisuke Kihara; Wojciech Szpankowski (ITA, 2015)

PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool. - Ishita K. Khan; Qing Wei; Meghana Chitale; Daisuke Kihara (Bioinform., 2015)

Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0. - Xiaolei Zhu 001; Yi Xiong 002; Daisuke Kihara (Bioinform., 2015)

Navigating 3D electron microscopy maps with EM-SURFER. - Juan Esquivel-Rodríguez; Yi Xiong 002; Xusi Han; Shuomeng Guang; Charles Christoffer; Daisuke Kihara (BMC Bioinform., 2015)

GenoBase: comprehensive resource database of Escherichia coli K-12. - Yuta Otsuka; Ai Muto; Rikiya Takeuchi; Chihiro Okada; Motokazu Ishikawa; Koichiro Nakamura; Natsuko Yamamoto; Hitomi Dose; Kenji Nakahigashi; Shigeki Tanishima; Sivasundaram Suharnan; Wataru Nomura; et al. (Nucleic Acids Res., 2015)

The Boltzmann sequence-structure channel. - Abram Magner; Daisuke Kihara; Wojciech Szpankowski (ISIT, 2016)

Ensemble-based evaluation for protein structure models. - Michal Jamróz 001; Andrzej Kolinski; Daisuke Kihara (Bioinform., 2016)

Genome-scale prediction of moonlighting proteins using diverse protein association information. - Ishita K. Khan; Daisuke Kihara (Bioinform., 2016)

Ranking protein-protein docking results using steered molecular dynamics and potential of mean force calculations. - Laura J. Kingsley; Juan Esquivel-Rodríguez; Ying Yang; Daisuke Kihara; Markus A. Lill (J. Comput. Chem., 2016)

PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation. - Woong-Hee Shin; Charles Christoffer; Ji-Bo Wang; Daisuke Kihara (J. Chem. Inf. Model., 2016)

Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein-Ligand Binding Prediction in CSAR 2013 and 2014. - Xiaolei Zhu 001; Woong-Hee Shin; Hyungrae Kim; Daisuke Kihara (J. Chem. Inf. Model., 2016)

Protein Shape Retrieval. - Na Song; Daniela Craciun; Charles Christoffer; Xusi Han; Daisuke Kihara; Guillaume Levieux; Matthieu Montès; Hong Qin 001; Pranjal Sahu; Genki Terashi; Haiguang Liu (3DOR@Eurographics, 2017)

DextMP: deep dive into text for predicting moonlighting proteins. - Ishita K. Khan; Mansurul Bhuiyan; Daisuke Kihara (Bioinform., 2017)

NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology. - Qing Wei; Ishita K. Khan; Ziyun Ding; Satwica Yerneni; Daisuke Kihara (BMC Bioinform., 2017)

A Study of the Boltzmann Sequence-Structure Channel. - Abram Magner; Daisuke Kihara; Wojciech Szpankowski (Proc. IEEE, 2017)

Modeling disordered protein interactions from biophysical principles. - Lenna X. Peterson; Amitava Roy; Charles Christoffer; Genki Terashi; Daisuke Kihara (PLoS Comput. Biol., 2017)

Modeling the assembly order of multimeric heteroprotein complexes. - Lenna X. Peterson; Yoichiro Togawa; Juan Esquivel-Rodríguez; Genki Terashi; Charles Christoffer; Amitava Roy; Woong-Hee Shin; Daisuke Kihara (PLoS Comput. Biol., 2018)

IAS: Interaction Specific GO Term Associations for Predicting Protein-Protein Interaction Networks. - Satwica Yerneni; Ishita K. Khan; Qing Wei; Daisuke Kihara (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Classification in Cryo-Electron Tomograms. - Ilja Gubins; Gijs van der Schot; Remco C. Veltkamp; Friedrich Förster; Xuefeng Du; Xiangrui Zeng; Zhenxi Zhu; Lufan Chang; Min Xu 009; Emmanuel Moebel; Antonio Martínez-Sánchez; Charles Kervrann; et al. (3DOR@Eurographics, 2019)

Protein Shape Retrieval Contest. - Florent Langenfeld; Apostolos Axenopoulos; Halim Benhabiles; Petros Daras; Andrea Giachetti 001; Xusi Han; Karim Hammoudi; Daisuke Kihara; Tuan Manh Lai; Haiguang Liu; Mahmoud Melkemi; Stelios K. Mylonas; et al. (3DOR@Eurographics, 2019)

Matching of EM Map Segments to Structurally-Relevant Bio-molecular Regions. - Manuel Zumbado Corrales; Luis Castillo-Valverde; José Salas-Bonilla; Julio Víquez-Murillo; Daisuke Kihara; Juan Esquivel-Rodríguez (CARLA, 2019)

A Gated Self-attention Memory Network for Answer Selection. - Tuan Manh Lai; Quan Hung Tran; Trung Bui; Daisuke Kihara (EMNLP/IJCNLP (1), 2019)

Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences. - Aashish Jain; Daisuke Kihara (Bioinform., 2019)

Prediction of protein group function by iterative classification on functional relevance network. - Ishita K. Khan; Aashish Jain; Reda Rawi; Halima Bensmail; Daisuke Kihara (Bioinform., 2019)

EnAET: Self-Trained Ensemble AutoEncoding Transformations for Semi-Supervised Learning. - Xiao Wang 004; Daisuke Kihara; Jiebo Luo 001; Guo-Jun Qi (CoRR, 2019)

Predicting binding poses and affinity ranking in D3R Grand Challenge using PL-PatchSurfer2.0. - Woong-Hee Shin; Daisuke Kihara (J. Comput. Aided Mol. Des., 2019)

A global map of the protein shape universe. - Xusi Han; Atilla Sit; Charles Christoffer; Siyang Chen; Daisuke Kihara (PLoS Comput. Biol., 2019)

Three-dimensional Krawtchouk descriptors for protein local surface shape comparison. - Atilla Sit; Woong-Hee Shin; Daisuke Kihara (Pattern Recognit., 2019)

Study of the Variability of the Native Protein Structure. - Xusi Han; Woong-Hee Shin; Charles Christoffer; Genki Terashi; Lyman Monroe; Daisuke Kihara (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

A Simple But Effective Bert Model for Dialog State Tracking on Resource-Limited Systems. - Tuan Manh Lai; Quan Hung Tran; Trung Bui; Daisuke Kihara (ICASSP, 2020)

Protein docking model evaluation by 3D deep convolutional neural networks. - Xiao Wang 013; Genki Terashi; Charles Christoffer; Mengmeng Zhu; Daisuke Kihara (Bioinform., 2020)

SHREC 2020: Classification in cryo-electron tomograms. - Ilja Gubins; Marten L. Chaillet; Gijs van der Schot; Remco C. Veltkamp; Friedrich Förster; Yu Hao; Xiaohua Wan 001; Xuefeng Cui; Fa Zhang 001; Emmanuel Moebel; Xiao Wang 004; Daisuke Kihara; et al. (Comput. Graph., 2020)

SHREC 2020: Multi-domain protein shape retrieval challenge. - Florent Langenfeld; Yuxu Peng; Yu-Kun Lai; Paul L. Rosin; Tunde Aderinwale; Genki Terashi; Charles Christoffer; Daisuke Kihara; Halim Benhabiles; Karim Hammoudi; Adnane Cabani; Féryal Windal; et al. (Comput. Graph., 2020)

MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry. - Genki Terashi; Yuki Kagaya; Daisuke Kihara (J. Chem. Inf. Model., 2020)

2DKD: a toolkit for content-based local image search. - Julian S. Deville; Daisuke Kihara; Atilla Sit (Source Code Biol. Medicine, 2020)

Path-LZerD: Predicting Assembly Order of Multimeric Protein Complexes. - Genki Terashi; Charles Christoffer; Daisuke Kihara (Protein-Protein Interaction Networks, 2020)

SHREC 2021: Classification in Cryo-electron Tomograms. - Ilja Gubins; Marten L. Chaillet; Gijs van der Schot; M. Cristina Trueba; Remco C. Veltkamp; Friedrich Förster; Xiao Wang 004; Daisuke Kihara; Emmanuel Moebel; Nguyen P. Nguyen; Tommi A. White; Filiz Bunyak; et al. (3DOR, 2021)

SHREC 2021: Surface-based Protein Domains Retrieval. - Florent Langenfeld; Tunde Aderinwale; Charles Christoffer; Woong-Hee Shin; Genki Terashi; Xiao Wang 004; Daisuke Kihara; Halim Benhabiles; Karim Hammoudi; Adnane Cabani; Féryal Windal; Mahmoud Melkemi; et al. (3DOR, 2021)

Protein contact map refinement for improving structure prediction using generative adversarial networks. - Sai Raghavendra Maddhuri Venkata Subramaniya; Genki Terashi; Aashish Jain; Yuki Kagaya; Daisuke Kihara (Bioinform., 2021)

SHREC 2021: Retrieval and classification of protein surfaces equipped with physical and chemical properties. - Andrea Raffo; Ulderico Fugacci; Silvia Biasotti; Walter Rocchia; Yonghuai Liu; Ekpo Otu; Reyer Zwiggelaar; David Hunter; Evangelia I. Zacharaki; Eleftheria Psatha; Dimitrios Laskos; Gerasimos Arvanitis; et al. (Comput. Graph., 2021)

Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps. - Takaharu Mori; Genki Terashi; Daisuke Matsuoka; Daisuke Kihara; Yuji Sugita (J. Chem. Inf. Model., 2021)

LZerD webserver for pairwise and multiple protein-protein docking. - Charles Christoffer; Siyang Chen; Vijay Bharadwaj; Tunde Aderinwale; Vidhur Kumar; Matin Hormati; Daisuke Kihara (Nucleic Acids Res., 2021)

EnAET: A Self-Trained Framework for Semi-Supervised and Supervised Learning With Ensemble Transformations. - Xiao Wang 013; Daisuke Kihara; Jiebo Luo 001; Guo-Jun Qi (IEEE Trans. Image Process., 2021)

On the Importance of Asymmetry for Siamese Representation Learning. - Xiao Wang; Haoqi Fan 001; Yuandong Tian; Daisuke Kihara; Xinlei Chen (CVPR, 2022)

SHREC 2022: Protein-ligand binding site recognition. - Luca Gagliardi; Andrea Raffo; Ulderico Fugacci; Silvia Biasotti; Walter Rocchia; Hao Huang 003; Boulbaba Ben Amor; Yi Fang 006; Yuanyuan Zhang; Xiao Wang; Charles Christoffer; Daisuke Kihara; et al. (Comput. Graph., 2022)

ContactPFP: Protein Function Prediction Using Predicted Contact Information. - Yuki Kagaya; Sean Flannery; Aashish Jain; Daisuke Kihara (Frontiers Bioinform., 2022)

OC_Finder: Osteoclast Segmentation, Counting, and Classification Using Watershed and Deep Learning. - Xiao Wang; Mizuho Kittaka; Yilin He; Yiwei Zhang; Yasuyoshi Ueki; Daisuke Kihara (Frontiers Bioinform., 2022)

Using steered molecular dynamic tension for assessing quality of computational protein structure models. - Lyman Monroe; Daisuke Kihara (J. Comput. Chem., 2022)

ACC-UNet: A Completely Convolutional UNet Model for the 2020s. - Nabil Ibtehaz; Daisuke Kihara (MICCAI (3), 2023)

Editorial: Expert opinions in protein bioinformatics: 2022. - Daisuke Kihara (Frontiers Bioinform., 2023)

Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling. - Sai Raghavendra Maddhuri Venkata Subramaniya; Genki Terashi; Daisuke Kihara (Bioinform., 2023)

SHREC2024: Non-rigid Complementary Shapes Retrieval in Protein-protein Interactions. - Taher Yacoub; Nika Zarubina; Camille Depenveiller; Hoang-Phuc Nguyen; Vinh-Toan Vong; Minh-Triet Tran; Yuki Kagaya; Tsukasa Nakamura; Daisuke Kihara; Florent Langenfeld; Matthieu Montès (3DOR (Short Papers), 2024)

Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences. - Sushmita Basu; Jing Yu; Daisuke Kihara; Lukasz A. Kurgan (Briefings Bioinform., 2024)

ACC-ViT : Atrous Convolution's Comeback in Vision Transformers. - Nabil Ibtehaz; Ning Yan; Masood S. Mortazavi; Daisuke Kihara (CoRR, 2024)

Fusion of regional and sparse attention in Vision Transformers. - Nabil Ibtehaz; Ning Yan; Masood S. Mortazavi; Daisuke Kihara (CoRR, 2024)

Vox-UDA: Voxel-wise Unsupervised Domain Adaptation for Cryo-Electron Subtomogram Segmentation with Denoised Pseudo-Labeling. - Haoran Li; Xingjian Li 002; Jiahua Shi; Huaming Chen; Bo Du 004; Daisuke Kihara; Johan Barthélemy; Jun Shen 001; Min Xu 009 (AAAI, 2025)

Aligning Proteins and Language: A Foundation Model for Protein Retrieval. - Qifeng Wu; Zhengzhe Liu; Han Zhu; Yizhou Zhao; Daisuke Kihara; Min Xu 009 (CoRR, 2025)