Daisuke Kihara

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 52

Top Topics

Shape Retrieval

Protein Structure

Grand Challenge

Computational Biology

Top Venues

J. Chem. Inf. Model.

Publications

Nabil Ibtehaz, Ning Yan, Masood S. Mortazavi, Daisuke Kihara
ACC-ViT : Atrous Convolution's Comeback in Vision Transformers. CoRR (2024)
Haoran Li, Xingjian Li, Jiahua Shi, Huaming Chen, Bo Du, Daisuke Kihara, Johan Barthelemy, Jun Shen, Min Xu
Vox-UDA: Voxel-wise Unsupervised Domain Adaptation for Cryo-Electron Subtomogram Segmentation with Denoised Pseudo Labeling. CoRR (2024)
Nabil Ibtehaz, Ning Yan, Masood S. Mortazavi, Daisuke Kihara
Fusion of regional and sparse attention in Vision Transformers. CoRR (2024)
Nabil Ibtehaz, Daisuke Kihara
ACC-UNet: A Completely Convolutional UNet model for the 2020s. CoRR (2023)
Daisuke Kihara
Editorial: Expert opinions in protein bioinformatics: 2022. Frontiers Bioinform. 3 (2023)
Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, Daisuke Kihara
Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling. Bioinform. 39 (8) (2023)
Nabil Ibtehaz, Daisuke Kihara
ACC-UNet: A Completely Convolutional UNet Model for the 2020s. MICCAI (3) (2023)
Xiao Wang, Haoqi Fan, Yuandong Tian, Daisuke Kihara, Xinlei Chen
On the Importance of Asymmetry for Siamese Representation Learning. CVPR (2022)
Xiao Wang, Haoqi Fan, Yuandong Tian, Daisuke Kihara, Xinlei Chen
On the Importance of Asymmetry for Siamese Representation Learning. CoRR (2022)
Lyman Monroe, Daisuke Kihara
Using steered molecular dynamic tension for assessing quality of computational protein structure models. J. Comput. Chem. 43 (17) (2022)
Luca Gagliardi, Andrea Raffo, Ulderico Fugacci, Silvia Biasotti, Walter Rocchia, Hao Huang, Boulbaba Ben Amor, Yi Fang, Yuanyuan Zhang, Xiao Wang, Charles Christoffer, Daisuke Kihara, Apostolos Axenopoulos, Stelios K. Mylonas, Petros Daras
SHREC 2022: Protein-ligand binding site recognition. Comput. Graph. 107 (2022)
Ilja Gubins, Marten L. Chaillet, Gijs van der Schot, M. Cristina Trueba, Remco C. Veltkamp, Friedrich Förster, Xiao Wang, Daisuke Kihara, Emmanuel Moebel, Nguyen P. Nguyen, Tommi A. White, Filiz Bunyak, Giorgos Papoulias, Stavros Gerolymatos, Evangelia I. Zacharaki, Konstantinos Moustakas, Xiangrui Zeng, Sinuo Liu, Min Xu, Yaoyu Wang, Cheng Chen, Xuefeng Cui, Fa Zhang
SHREC 2021: Classification in cryo-electron tomograms. CoRR (2022)
Xiao Wang, Mizuho Kittaka, Yilin He, Yiwei Zhang, Yasuyoshi Ueki, Daisuke Kihara
OC_Finder: Osteoclast Segmentation, Counting, and Classification Using Watershed and Deep Learning. Frontiers Bioinform. 2 (2022)
Yuki Kagaya, Sean Flannery, Aashish Jain, Daisuke Kihara
ContactPFP: Protein Function Prediction Using Predicted Contact Information. Frontiers Bioinform. 2 (2022)
Florent Langenfeld, Tunde Aderinwale, Charles Christoffer, Woong-Hee Shin, Genki Terashi, Xiao Wang, Daisuke Kihara, Halim Benhabiles, Karim Hammoudi, Adnane Cabani, Féryal Windal, Mahmoud Melkemi, Ekpo Otu, Reyer Zwiggelaar, David Hunter, Yonghuai Liu, Léa Sirugue, Huu-Nghia H. Nguyen, Tuan-Duy H. Nguyen, Vinh-Thuyen Nguyen-Truong, Danh Le, Hai-Dang Nguyen, Minh-Triet Tran, Matthieu Montès
SHREC 2021: Surface-based Protein Domains Retrieval. 3DOR (2021)
Takaharu Mori, Genki Terashi, Daisuke Matsuoka, Daisuke Kihara, Yuji Sugita
Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps. J. Chem. Inf. Model. 61 (7) (2021)
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, Konstantinos Moustakas, Tunde Aderinwale, Charles Christoffer, Woong-Hee Shin, Daisuke Kihara, Andrea Giachetti, Huu-Nghia Nguyen, Tuan-Duy Nguyen, Vinh-Thuyen Nguyen-Truong, Danh Le-Thanh, Hai-Dang Nguyen, Minh-Triet Tran
SHREC 2021: Retrieval and classification of protein surfaces equipped with physical and chemical properties. Comput. Graph. 99 (2021)
Ilja Gubins, Marten L. Chaillet, Gijs van der Schot, M. Cristina Trueba, Remco C. Veltkamp, Friedrich Förster, Xiao Wang, Daisuke Kihara, Emmanuel Moebel, Nguyen P. Nguyen, Tommi A. White, Filiz Bunyak, Giorgos Papoulias, Stavros Gerolymatos, Evangelia I. Zacharaki, Konstantinos Moustakas, Xiangrui Zeng, Sinuo Liu, Min Xu, Yaoyu Wang, Cheng Chen, Xuefeng Cui, Fa Zhang
SHREC 2021: Classification in Cryo-electron Tomograms. 3DOR (2021)
Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, Aashish Jain, Yuki Kagaya, Daisuke Kihara
Protein contact map refinement for improving structure prediction using generative adversarial networks. Bioinform. 37 (19) (2021)
Xiao Wang, Daisuke Kihara, Jiebo Luo, Guo-Jun Qi
EnAET: A Self-Trained Framework for Semi-Supervised and Supervised Learning With Ensemble Transformations. IEEE Trans. Image Process. 30 (2021)
Charles Christoffer, Siyang Chen, Vijay Bharadwaj, Tunde Aderinwale, Vidhur Kumar, Matin Hormati, Daisuke Kihara
LZerD webserver for pairwise and multiple protein-protein docking. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Tuan Manh Lai, Quan Hung Tran, Trung Bui, Daisuke Kihara
A Simple But Effective Bert Model for Dialog State Tracking on Resource-Limited Systems. ICASSP (2020)
Julian S. Deville, Daisuke Kihara, Atilla Sit
2DKD: a toolkit for content-based local image search. Source Code Biol. Medicine 15 (1) (2020)
Ilja Gubins, Marten L. Chaillet, Gijs van der Schot, Remco C. Veltkamp, Friedrich Förster, Yu Hao, Xiaohua Wan, Xuefeng Cui, Fa Zhang, Emmanuel Moebel, Xiao Wang, Daisuke Kihara, Xiangrui Zeng, Min Xu, Nguyen P. Nguyen, Tommi A. White, Filiz Bunyak
SHREC 2020: Classification in cryo-electron tomograms. Comput. Graph. 91 (2020)
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, Mahmoud Melkemi, Andrea Giachetti, Stelios K. Mylonas, Apostolos Axenopoulos, Petros Daras, Ekpo Otu, Matthieu Montès
SHREC 2020: Multi-domain protein shape retrieval challenge. Comput. Graph. 91 (2020)
Genki Terashi, Yuki Kagaya, Daisuke Kihara
MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry. J. Chem. Inf. Model. 60 (5) (2020)
Xiao Wang, Genki Terashi, Charles Christoffer, Mengmeng Zhu, Daisuke Kihara
Protein docking model evaluation by 3D deep convolutional neural networks. Bioinform. 36 (7) (2020)
Xusi Han, Atilla Sit, Charles Christoffer, Siyang Chen, Daisuke Kihara
A global map of the protein shape universe. PLoS Comput. Biol. 15 (4) (2019)
Florent Langenfeld, Apostolos Axenopoulos, Halim Benhabiles, Petros Daras, Andrea Giachetti, Xusi Han, Karim Hammoudi, Daisuke Kihara, Tuan Manh Lai, Haiguang Liu, Mahmoud Melkemi, Stelios K. Mylonas, Genki Terashi, Yufan Wang, Féryal Windal, Matthieu Montès
Protein Shape Retrieval Contest. 3DOR@Eurographics (2019)
Aashish Jain, Daisuke Kihara
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences. Bioinform. 35 (5) (2019)
Ishita K. Khan, Aashish Jain, Reda Rawi, Halima Bensmail, Daisuke Kihara
Prediction of protein group function by iterative classification on functional relevance network. Bioinform. 35 (8) (2019)
Tuan Manh Lai, Quan Hung Tran, Trung Bui, Daisuke Kihara
A Simple but Effective BERT Model for Dialog State Tracking on Resource-Limited Systems. CoRR (2019)
Tuan Manh Lai, Quan Hung Tran, Trung Bui, Daisuke Kihara
A Gated Self-attention Memory Network for Answer Selection. EMNLP/IJCNLP (1) (2019)
Tuan Manh Lai, Quan Hung Tran, Trung Bui, Daisuke Kihara
A Gated Self-attention Memory Network for Answer Selection. CoRR (2019)
Woong-Hee Shin, Daisuke Kihara
Predicting binding poses and affinity ranking in D3R Grand Challenge using PL-PatchSurfer2.0. J. Comput. Aided Mol. Des. 33 (12) (2019)
Atilla Sit, Woong-Hee Shin, Daisuke Kihara
Three-dimensional Krawtchouk descriptors for protein local surface shape comparison. Pattern Recognit. 93 (2019)
Ilja Gubins, Gijs van der Schot, Remco C. Veltkamp, Friedrich Förster, Xuefeng Du, Xiangrui Zeng, Zhenxi Zhu, Lufan Chang, Min Xu, Emmanuel Moebel, Antonio Martínez-Sánchez, Charles Kervrann, Tuan Manh Lai, Xusi Han, Genki Terashi, Daisuke Kihara, Benjamin A. Himes, Xiaohua Wan, Jingrong Zhang, Shan Gao, Yu Hao, Zhilong Lv, Xiaohua Wan, Zhidong Yang, Zijun Ding, Xuefeng Cui, Fa Zhang
Classification in Cryo-Electron Tomograms. 3DOR@Eurographics (2019)
Manuel Zumbado Corrales, Luis Castillo-Valverde, José Salas-Bonilla, Julio Víquez-Murillo, Daisuke Kihara, Juan Esquivel-Rodríguez
Matching of EM Map Segments to Structurally-Relevant Bio-molecular Regions. CARLA (2019)
Xiao Wang, Daisuke Kihara, Jiebo Luo, Guo-Jun Qi
EnAET: Self-Trained Ensemble AutoEncoding Transformations for Semi-Supervised Learning. CoRR (2019)
Lenna X. Peterson, Yoichiro Togawa, Juan Esquivel-Rodríguez, Genki Terashi, Charles Christoffer, Amitava Roy, Woong-Hee Shin, Daisuke Kihara
Modeling the assembly order of multimeric heteroprotein complexes. PLoS Comput. Biol. 14 (1) (2018)
Satwica Yerneni, Ishita K. Khan, Qing Wei, Daisuke Kihara
IAS: Interaction Specific GO Term Associations for Predicting Protein-Protein Interaction Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (4) (2018)
Abram Magner, Daisuke Kihara, Wojciech Szpankowski
A Study of the Boltzmann Sequence-Structure Channel. Proc. IEEE 105 (2) (2017)
Lenna X. Peterson, Amitava Roy, Charles Christoffer, Genki Terashi, Daisuke Kihara
Modeling disordered protein interactions from biophysical principles. PLoS Comput. Biol. 13 (4) (2017)
Qing Wei, Ishita K. Khan, Ziyun Ding, Satwica Yerneni, Daisuke Kihara
NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology. BMC Bioinform. 18 (1) (2017)
Ishita K. Khan, Mansurul Bhuiyan, Daisuke Kihara
DextMP: deep dive into text for predicting moonlighting proteins. Bioinform. 33 (14) (2017)
Na Song, Daniela Craciun, Charles Christoffer, Xusi Han, Daisuke Kihara, Guillaume Levieux, Matthieu Montès, Hong Qin, Pranjal Sahu, Genki Terashi, Haiguang Liu
Protein Shape Retrieval. 3DOR@Eurographics (2017)
Laura J. Kingsley, Juan Esquivel-Rodríguez, Ying Yang, Daisuke Kihara, Markus A. Lill
Ranking protein-protein docking results using steered molecular dynamics and potential of mean force calculations. J. Comput. Chem. 37 (20) (2016)
Abram Magner, Daisuke Kihara, Wojciech Szpankowski
The Boltzmann sequence-structure channel. ISIT (2016)
Ishita K. Khan, Daisuke Kihara
Genome-scale prediction of moonlighting proteins using diverse protein association information. Bioinform. 32 (15) (2016)
Woong-Hee Shin, Charles Christoffer, Ji-Bo Wang, Daisuke Kihara
PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation. J. Chem. Inf. Model. 56 (9) (2016)
Xiaolei Zhu, Woong-Hee Shin, Hyungrae Kim, Daisuke Kihara
Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein-Ligand Binding Prediction in CSAR 2013 and 2014. J. Chem. Inf. Model. 56 (6) (2016)
Michal Jamróz, Andrzej Kolinski, Daisuke Kihara
Ensemble-based evaluation for protein structure models. Bioinform. 32 (12) (2016)
Yuta Otsuka, Ai Muto, Rikiya Takeuchi, Chihiro Okada, Motokazu Ishikawa, Koichiro Nakamura, Natsuko Yamamoto, Hitomi Dose, Kenji Nakahigashi, Shigeki Tanishima, Sivasundaram Suharnan, Wataru Nomura, Toru Nakayashiki, Walid G. Aref, Barry R. Bochner, Tyrrell Conway, Michael Gribskov, Daisuke Kihara, Kenneth E. Rudd, Yukako Tohsato, Barry L. Wanner, Hirotada Mori
K-12. Nucleic Acids Res. 43 (Database-Issue) (2015)
Juan Esquivel-Rodríguez, Yi Xiong, Xusi Han, Shuomeng Guang, Charles Christoffer, Daisuke Kihara
Navigating 3D electron microscopy maps with EM-SURFER. BMC Bioinform. 16 (2015)
Ishita K. Khan, Qing Wei, Meghana Chitale, Daisuke Kihara
PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool. Bioinform. 31 (2) (2015)
Abram Magner, Daisuke Kihara, Wojciech Szpankowski
Phase transitions in a sequence-structure channel. ITA (2015)
Xiaolei Zhu, Yi Xiong, Daisuke Kihara
Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0. Bioinform. 31 (5) (2015)
Jim Cavalcoli, Lonnie R. Welch, Bruce J. Aronow, Sorin Draghici, Daisuke Kihara
The International Society of Computational Biology presents: the Great Lakes Bioinformatics Conference, May 16-18, 2014, Cincinnati, Ohio. Bioinform. 30 (1) (2014)
Atilla Sit, Daisuke Kihara
Comparison of Image Patches Using Local Moment Invariants. IEEE Trans. Image Process. 23 (5) (2014)
Meghana Chitale, Ishita K. Khan, Daisuke Kihara
In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment. BMC Bioinform. 14 (S-3) (2013)
Harutoyo Hirano, Daisuke Kihara, Hiroki Hirano, Yuichi Kurita, Teiji Ukawa, Tsuneo Takayanagi, Haruka Morimoto, Ryuji Nakamura, Noboru Saeki, Yukihito Higashi, Masashi Kawamoto, Masao Yoshizumi, Toshio Tsuji
Evaluation of Arterial Stiffness during the Flow-Mediated Dilation Test. SMC (2013)
Bin Li, Daisuke Kihara
Protein docking prediction using predicted protein-protein interface. BMC Bioinform. 13 (2012)
Chao Yuan, Hao Chen, Daisuke Kihara
Effective inter-residue contact definitions for accurate protein fold recognition. BMC Bioinform. 13 (2012)
Mario Abdel Messih, Meghana Chitale, Vladimir B. Bajic, Daisuke Kihara, Xin Gao
Protein domain recurrence and order can enhance prediction of protein functions. Bioinform. 28 (18) (2012)
Lee Sael, Daisuke Kihara
Constructing patch-based ligand-binding pocket database for predicting function of proteins. BMC Bioinform. 13 (S-2) (2012)
Juan Esquivel-Rodríguez, Daisuke Kihara
Evaluation of multiple protein docking structures using correctly predicted pairwise subunits. BMC Bioinform. 13 (S-2) (2012)
Meghana Chitale, Shriphani Palakodety, Daisuke Kihara
Quantification of Protein Group Coherence and Pathway Assignment Using Functional Association. BMC Bioinform. 12 (2011)
Lee Sael, Daisuke Kihara
Characterization and Classification of Local Protein Surfaces Using Self-Organizing Map. Int. J. Knowl. Discov. Bioinform. 1 (1) (2010)
Lee Sael, Daisuke Kihara
Improved protein surface comparison and application to low-resolution protein structure data. BMC Bioinform. 11 (S-11) (2010)
Troy Hawkins, Meghana Chitale, Daisuke Kihara
Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP. BMC Bioinform. 11 (2010)
Meghana Chitale, Troy Hawkins, Changsoon Park, Daisuke Kihara
ESG: extended similarity group method for automated protein function prediction. Bioinform. 25 (14) (2009)
Vishwesh Venkatraman, Padmasini Chakravarthy, Daisuke Kihara
Application of 3D Zernike descriptors to shape-based ligand similarity searching. J. Cheminformatics 1 (2009)
David La, Juan Esquivel-Rodríguez, Vishwesh Venkatraman, Bin Li, Lee Sael, Stephen Ueng, Steven Ahrendt, Daisuke Kihara
3D-SURFER: software for high-throughput protein surface comparison and analysis. Bioinform. 25 (21) (2009)
Vishwesh Venkatraman, Yifeng D. Yang, Lee Sael, Daisuke Kihara
Protein-protein docking using region-based 3D Zernike descriptors. BMC Bioinform. 10 (2009)
Luo Si, Danni Yu, Daisuke Kihara, Yi Fang
Combining gene sequence similarity and textual information for gene function annotation in the literature. Inf. Retr. 11 (5) (2008)
Mingwu Zhang, Daisuke Kihara, Sunil Prabhakar
Tracing Lineage in Multi-version Scientific Databases. BIBE (2007)
Troy Hawkins, Daisuke Kihara
Function Prediction of uncharacterized proteins. J. Bioinform. Comput. Biol. 5 (1) (2007)
Yu-Shen Liu, Min Liu, Daisuke Kihara, Karthik Ramani
Salient critical points for meshes. Symposium on Solid and Physical Modeling (2007)
Jianjun Hu, Yifeng D. Yang, Daisuke Kihara
EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences. BMC Bioinform. 7 (2006)