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2020 – today
- 2024
[i9]Nabil Ibtehaz, Ning Yan, Masood S. Mortazavi, Daisuke Kihara:
ACC-ViT : Atrous Convolution's Comeback in Vision Transformers. CoRR abs/2403.04200 (2024)- [i8]Nabil Ibtehaz, Ning Yan, Masood S. Mortazavi, Daisuke Kihara:
Fusion of regional and sparse attention in Vision Transformers. CoRR abs/2406.08859 (2024) - [i7]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 abs/2406.18610 (2024) - 2023
- [j55]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) - [j54]Daisuke Kihara:
Editorial: Expert opinions in protein bioinformatics: 2022. Frontiers Bioinform. 3 (2023) - [c15]Nabil Ibtehaz, Daisuke Kihara:
ACC-UNet: A Completely Convolutional UNet Model for the 2020s. MICCAI (3) 2023: 692-702 - [i6]Nabil Ibtehaz, Daisuke Kihara:
ACC-UNet: A Completely Convolutional UNet model for the 2020s. CoRR abs/2308.13680 (2023) - 2022
- [j53]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: 20-31 (2022) - [j52]Yuki Kagaya, Sean Flannery, Aashish Jain, Daisuke Kihara:
ContactPFP: Protein Function Prediction Using Predicted Contact Information. Frontiers Bioinform. 2 (2022) - [j51]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) - [j50]Lyman Monroe, Daisuke Kihara:
Using steered molecular dynamic tension for assessing quality of computational protein structure models. J. Comput. Chem. 43(17): 1140-1150 (2022) - [c14]Xiao Wang, Haoqi Fan, Yuandong Tian, Daisuke Kihara, Xinlei Chen:
On the Importance of Asymmetry for Siamese Representation Learning. CVPR 2022: 16549-16558 - [i5]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 abs/2203.10035 (2022) - [i4]Xiao Wang, Haoqi Fan, Yuandong Tian, Daisuke Kihara, Xinlei Chen:
On the Importance of Asymmetry for Siamese Representation Learning. CoRR abs/2204.00613 (2022) - 2021
- [j49]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): 3168-3174 (2021) - [j48]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: 1-21 (2021) - [j47]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): 3516-3528 (2021) - [j46]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): 359-365 (2021) - [j45]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: 1639-1647 (2021) - [c13]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: 5-17 - [c12]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: 19-26 - 2020
- [j44]Xiao Wang, Genki Terashi, Charles Christoffer, Mengmeng Zhu, Daisuke Kihara:
Protein docking model evaluation by 3D deep convolutional neural networks. Bioinform. 36(7): 2113-2118 (2020) - [j43]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: 189-198 (2020) - [j42]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: 279-289 (2020) - [j41]Genki Terashi, Yuki Kagaya, Daisuke Kihara:
MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry. J. Chem. Inf. Model. 60(5): 2634-2643 (2020) - [j40]Julian S. Deville, Daisuke Kihara, Atilla Sit:
2DKD: a toolkit for content-based local image search. Source Code Biol. Medicine 15(1) (2020) - [c11]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: 8034-8038 - [p1]Genki Terashi, Charles Christoffer, Daisuke Kihara:
Path-LZerD: Predicting Assembly Order of Multimeric Protein Complexes. Protein-Protein Interaction Networks 2020: 95-112
2010 – 2019
- 2019
- [j39]Aashish Jain, Daisuke Kihara:
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences. Bioinform. 35(5): 753-759 (2019) - [j38]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): 1388-1394 (2019) - [j37]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): 1083-1094 (2019) - [j36]Xusi Han, Atilla Sit, Charles Christoffer, Siyang Chen, Daisuke Kihara:
A global map of the protein shape universe. PLoS Comput. Biol. 15(4) (2019) - [j35]Atilla Sit, Woong-Hee Shin, Daisuke Kihara:
Three-dimensional Krawtchouk descriptors for protein local surface shape comparison. Pattern Recognit. 93: 534-545 (2019) - [c10]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: 25-31 - [c9]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: 49-54 - [c8]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: 464-478 - [c7]Tuan Manh Lai, Quan Hung Tran, Trung Bui, Daisuke Kihara:
A Gated Self-attention Memory Network for Answer Selection. EMNLP/IJCNLP (1) 2019: 5952-5958 - [r1]Xusi Han, Woong-Hee Shin, Charles Christoffer, Genki Terashi, Lyman Monroe, Daisuke Kihara:
Study of the Variability of the Native Protein Structure. Encyclopedia of Bioinformatics and Computational Biology (3) 2019: 606-619 - [i3]Tuan Manh Lai, Quan Hung Tran, Trung Bui, Daisuke Kihara:
A Gated Self-attention Memory Network for Answer Selection. CoRR abs/1909.09696 (2019) - [i2]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 abs/1910.12995 (2019) - [i1]Xiao Wang, Daisuke Kihara, Jiebo Luo, Guo-Jun Qi:
EnAET: Self-Trained Ensemble AutoEncoding Transformations for Semi-Supervised Learning. CoRR abs/1911.09265 (2019) - 2018
- [j34]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) - [j33]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): 1247-1258 (2018) - 2017
- [j32]Ishita K. Khan, Mansurul Bhuiyan, Daisuke Kihara:
DextMP: deep dive into text for predicting moonlighting proteins. Bioinform. 33(14): i83-i91 (2017) - [j31]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): 177:1-177:13 (2017) - [j30]Abram Magner, Daisuke Kihara, Wojciech Szpankowski:
A Study of the Boltzmann Sequence-Structure Channel. Proc. IEEE 105(2): 286-305 (2017) - [j29]Lenna X. Peterson, Amitava Roy, Charles Christoffer, Genki Terashi, Daisuke Kihara:
Modeling disordered protein interactions from biophysical principles. PLoS Comput. Biol. 13(4) (2017) - [c6]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 - 2016
- [j28]Michal Jamróz, Andrzej Kolinski, Daisuke Kihara:
Ensemble-based evaluation for protein structure models. Bioinform. 32(12): 314-321 (2016) - [j27]Ishita K. Khan, Daisuke Kihara:
Genome-scale prediction of moonlighting proteins using diverse protein association information. Bioinform. 32(15): 2281-2288 (2016) - [j26]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): 1861-1865 (2016) - [j25]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): 1088-1099 (2016) - [j24]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): 1676-1691 (2016) - [c5]Abram Magner, Daisuke Kihara, Wojciech Szpankowski:
The Boltzmann sequence-structure channel. ISIT 2016: 255-259 - 2015
- [j23]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): 271-272 (2015) - [j22]Xiaolei Zhu, Yi Xiong, Daisuke Kihara:
Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0. Bioinform. 31(5): 707-713 (2015) - [j21]Juan Esquivel-Rodríguez, Yi Xiong, Xusi Han, Shuomeng Guang, Charles Christoffer, Daisuke Kihara:
Navigating 3D electron microscopy maps with EM-SURFER. BMC Bioinform. 16: 181:1-181:9 (2015) - [j20]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:
GenoBase: comprehensive resource database of Escherichia coli K-12. Nucleic Acids Res. 43(Database-Issue): 606-617 (2015) - [c4]Abram Magner, Daisuke Kihara, Wojciech Szpankowski:
Phase transitions in a sequence-structure channel. ITA 2015: 235-239 - 2014
- [j19]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): 148-149 (2014) - [j18]Atilla Sit, Daisuke Kihara:
Comparison of Image Patches Using Local Moment Invariants. IEEE Trans. Image Process. 23(5): 2369-2379 (2014) - 2013
- [j17]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): S2 (2013) - [c3]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: 3756-3759 - 2012
- [j16]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): 444-450 (2012) - [j15]Bin Li, Daisuke Kihara:
Protein docking prediction using predicted protein-protein interface. BMC Bioinform. 13: 7 (2012) - [j14]Chao Yuan, Hao Chen, Daisuke Kihara:
Effective inter-residue contact definitions for accurate protein fold recognition. BMC Bioinform. 13: 292 (2012) - [j13]Juan Esquivel-Rodríguez, Daisuke Kihara:
Evaluation of multiple protein docking structures using correctly predicted pairwise subunits. BMC Bioinform. 13(S-2): S6 (2012) - [j12]Lee Sael, Daisuke Kihara:
Constructing patch-based ligand-binding pocket database for predicting function of proteins. BMC Bioinform. 13(S-2): S7 (2012) - 2011
- [j11]Meghana Chitale, Shriphani Palakodety, Daisuke Kihara:
Quantification of Protein Group Coherence and Pathway Assignment Using Functional Association. BMC Bioinform. 12: 373 (2011) - 2010
- [j10]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: 265 (2010) - [j9]Lee Sael, Daisuke Kihara:
Improved protein surface comparison and application to low-resolution protein structure data. BMC Bioinform. 11(S-11): S2 (2010) - [j8]Lee Sael, Daisuke Kihara:
Characterization and Classification of Local Protein Surfaces Using Self-Organizing Map. Int. J. Knowl. Discov. Bioinform. 1(1): 32-47 (2010)
2000 – 2009
- 2009
- [j7]Meghana Chitale, Troy Hawkins, Changsoon Park, Daisuke Kihara:
ESG: extended similarity group method for automated protein function prediction. Bioinform. 25(14): 1739-1745 (2009) - [j6]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): 2843-2844 (2009) - [j5]Vishwesh Venkatraman, Yifeng D. Yang, Lee Sael, Daisuke Kihara:
Protein-protein docking using region-based 3D Zernike descriptors. BMC Bioinform. 10: 407 (2009) - [j4]Vishwesh Venkatraman, Padmasini Chakravarthy, Daisuke Kihara:
Application of 3D Zernike descriptors to shape-based ligand similarity searching. J. Cheminformatics 1: 19 (2009) - 2008
- [j3]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): 389-404 (2008) - 2007
- [j2]Troy Hawkins, Daisuke Kihara:
Function Prediction of uncharacterized proteins. J. Bioinform. Comput. Biol. 5(1): 1-30 (2007) - [c2]Mingwu Zhang, Daisuke Kihara, Sunil Prabhakar:
Tracing Lineage in Multi-version Scientific Databases. BIBE 2007: 440-447 - [c1]Yu-Shen Liu, Min Liu, Daisuke Kihara, Karthik Ramani:
Salient critical points for meshes. Symposium on Solid and Physical Modeling 2007: 277-282 - 2006
- [j1]Jianjun Hu, Yifeng D. Yang, Daisuke Kihara:
EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences. BMC Bioinform. 7: 342 (2006)
Coauthor Index
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