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ORCIDBibTeX records: Daisuke Kihara
@article{DBLP:journals/corr/abs-2403-04200,
author = {Nabil Ibtehaz and
Ning Yan and
Masood Mortazavi and
Daisuke Kihara},
title = {ACC-ViT : Atrous Convolution's Comeback in Vision Transformers},
journal = {CoRR},
volume = {abs/2403.04200},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2403.04200},
doi = {10.48550/ARXIV.2403.04200},
eprinttype = {arXiv},
eprint = {2403.04200},
timestamp = {Wed, 03 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2403-04200.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SubramaniyaTK23,
author = {Sai Raghavendra Maddhuri Venkata Subramaniya and
Genki Terashi and
Daisuke Kihara},
title = {Enhancing cryo-EM maps with 3D deep generative networks for assisting
protein structure modeling},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad494},
doi = {10.1093/BIOINFORMATICS/BTAD494},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SubramaniyaTK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/miccai/IbtehazK23,
author = {Nabil Ibtehaz and
Daisuke Kihara},
editor = {Hayit Greenspan and
Anant Madabhushi and
Parvin Mousavi and
Septimiu Salcudean and
James Duncan and
Tanveer F. Syeda{-}Mahmood and
Russell H. Taylor},
title = {ACC-UNet: {A} Completely Convolutional UNet Model for the 2020s},
booktitle = {Medical Image Computing and Computer Assisted Intervention - {MICCAI}
2023 - 26th International Conference, Vancouver, BC, Canada, October
8-12, 2023, Proceedings, Part {III}},
series = {Lecture Notes in Computer Science},
volume = {14222},
pages = {692--702},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-3-031-43898-1\_66},
doi = {10.1007/978-3-031-43898-1\_66},
timestamp = {Sat, 14 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/miccai/IbtehazK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2308-13680,
author = {Nabil Ibtehaz and
Daisuke Kihara},
title = {ACC-UNet: {A} Completely Convolutional UNet model for the 2020s},
journal = {CoRR},
volume = {abs/2308.13680},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2308.13680},
doi = {10.48550/ARXIV.2308.13680},
eprinttype = {arXiv},
eprint = {2308.13680},
timestamp = {Fri, 01 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2308-13680.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cg/GagliardiRFBRHA22,
author = {Luca Gagliardi and
Andrea Raffo and
Ulderico Fugacci and
Silvia Biasotti and
Walter Rocchia and
Hao Huang and
Boulbaba Ben Amor and
Yi Fang and
Yuanyuan Zhang and
Xiao Wang and
Charles Christoffer and
Daisuke Kihara and
Apostolos Axenopoulos and
Stelios K. Mylonas and
Petros Daras},
title = {{SHREC} 2022: Protein-ligand binding site recognition},
journal = {Comput. Graph.},
volume = {107},
pages = {20--31},
year = {2022},
url = {https://doi.org/10.1016/j.cag.2022.07.005},
doi = {10.1016/J.CAG.2022.07.005},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cg/GagliardiRFBRHA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fbinf/KagayaFJK22,
author = {Yuki Kagaya and
Sean Flannery and
Aashish Jain and
Daisuke Kihara},
title = {ContactPFP: Protein Function Prediction Using Predicted Contact Information},
journal = {Frontiers Bioinform.},
volume = {2},
year = {2022},
url = {https://doi.org/10.3389/fbinf.2022.896295},
doi = {10.3389/FBINF.2022.896295},
timestamp = {Fri, 28 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fbinf/KagayaFJK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fbinf/WangKHZUK22,
author = {Xiao Wang and
Mizuho Kittaka and
Yilin He and
Yiwei Zhang and
Yasuyoshi Ueki and
Daisuke Kihara},
title = {OC{\_}Finder: Osteoclast Segmentation, Counting, and Classification
Using Watershed and Deep Learning},
journal = {Frontiers Bioinform.},
volume = {2},
year = {2022},
url = {https://doi.org/10.3389/fbinf.2022.819570},
doi = {10.3389/FBINF.2022.819570},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fbinf/WangKHZUK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/MonroeK22,
author = {Lyman Monroe and
Daisuke Kihara},
title = {Using steered molecular dynamic tension for assessing quality of computational
protein structure models},
journal = {J. Comput. Chem.},
volume = {43},
number = {17},
pages = {1140--1150},
year = {2022},
url = {https://doi.org/10.1002/jcc.26876},
doi = {10.1002/JCC.26876},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/MonroeK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cvpr/Wang0TKC22,
author = {Xiao Wang and
Haoqi Fan and
Yuandong Tian and
Daisuke Kihara and
Xinlei Chen},
title = {On the Importance of Asymmetry for Siamese Representation Learning},
booktitle = {{IEEE/CVF} Conference on Computer Vision and Pattern Recognition,
{CVPR} 2022, New Orleans, LA, USA, June 18-24, 2022},
pages = {16549--16558},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/CVPR52688.2022.01607},
doi = {10.1109/CVPR52688.2022.01607},
timestamp = {Wed, 05 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cvpr/Wang0TKC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2203-10035,
author = {Ilja Gubins and
Marten L. Chaillet and
Gijs van der Schot and
M. Cristina Trueba and
Remco C. Veltkamp and
Friedrich F{\"{o}}rster and
Xiao Wang and
Daisuke Kihara and
Emmanuel Moebel and
Nguyen P. Nguyen and
Tommi A. White and
Filiz Bunyak and
Giorgos Papoulias and
Stavros Gerolymatos and
Evangelia I. Zacharaki and
Konstantinos Moustakas and
Xiangrui Zeng and
Sinuo Liu and
Min Xu and
Yaoyu Wang and
Cheng Chen and
Xuefeng Cui and
Fa Zhang},
title = {{SHREC} 2021: Classification in cryo-electron tomograms},
journal = {CoRR},
volume = {abs/2203.10035},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2203.10035},
doi = {10.48550/ARXIV.2203.10035},
eprinttype = {arXiv},
eprint = {2203.10035},
timestamp = {Wed, 06 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2203-10035.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2204-00613,
author = {Xiao Wang and
Haoqi Fan and
Yuandong Tian and
Daisuke Kihara and
Xinlei Chen},
title = {On the Importance of Asymmetry for Siamese Representation Learning},
journal = {CoRR},
volume = {abs/2204.00613},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2204.00613},
doi = {10.48550/ARXIV.2204.00613},
eprinttype = {arXiv},
eprint = {2204.00613},
timestamp = {Wed, 06 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2204-00613.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SubramaniyaTJKK21,
author = {Sai Raghavendra Maddhuri Venkata Subramaniya and
Genki Terashi and
Aashish Jain and
Yuki Kagaya and
Daisuke Kihara},
title = {Protein contact map refinement for improving structure prediction
using generative adversarial networks},
journal = {Bioinform.},
volume = {37},
number = {19},
pages = {3168--3174},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab220},
doi = {10.1093/BIOINFORMATICS/BTAB220},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SubramaniyaTJKK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cg/RaffoFBRLOZHZPL21,
author = {Andrea Raffo and
Ulderico Fugacci and
Silvia Biasotti and
Walter Rocchia and
Yonghuai Liu and
Ekpo Otu and
Reyer Zwiggelaar and
David Hunter and
Evangelia I. Zacharaki and
Eleftheria Psatha and
Dimitrios Laskos and
Gerasimos Arvanitis and
Konstantinos Moustakas and
Tunde Aderinwale and
Charles Christoffer and
Woong{-}Hee Shin and
Daisuke Kihara and
Andrea Giachetti and
Huu{-}Nghia Nguyen and
Tuan{-}Duy Nguyen and
Vinh{-}Thuyen Nguyen{-}Truong and
Danh Le{-}Thanh and
Hai{-}Dang Nguyen and
Minh{-}Triet Tran},
title = {{SHREC} 2021: Retrieval and classification of protein surfaces equipped
with physical and chemical properties},
journal = {Comput. Graph.},
volume = {99},
pages = {1--21},
year = {2021},
url = {https://doi.org/10.1016/j.cag.2021.06.010},
doi = {10.1016/J.CAG.2021.06.010},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cg/RaffoFBRLOZHZPL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/MoriTMKS21,
author = {Takaharu Mori and
Genki Terashi and
Daisuke Matsuoka and
Daisuke Kihara and
Yuji Sugita},
title = {Efficient Flexible Fitting Refinement with Automatic Error Fixing
for De Novo Structure Modeling from Cryo-EM Density Maps},
journal = {J. Chem. Inf. Model.},
volume = {61},
number = {7},
pages = {3516--3528},
year = {2021},
url = {https://doi.org/10.1021/acs.jcim.1c00230},
doi = {10.1021/ACS.JCIM.1C00230},
timestamp = {Thu, 16 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/MoriTMKS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ChristofferCBAK21,
author = {Charles Christoffer and
Siyang Chen and
Vijay Bharadwaj and
Tunde Aderinwale and
Vidhur Kumar and
Matin Hormati and
Daisuke Kihara},
title = {LZerD webserver for pairwise and multiple protein-protein docking},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Webserver-Issue},
pages = {359--365},
year = {2021},
url = {https://doi.org/10.1093/nar/gkab336},
doi = {10.1093/NAR/GKAB336},
timestamp = {Tue, 06 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/ChristofferCBAK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tip/WangKLQ21,
author = {Xiao Wang and
Daisuke Kihara and
Jiebo Luo and
Guo{-}Jun Qi},
title = {EnAET: {A} Self-Trained Framework for Semi-Supervised and Supervised
Learning With Ensemble Transformations},
journal = {{IEEE} Trans. Image Process.},
volume = {30},
pages = {1639--1647},
year = {2021},
url = {https://doi.org/10.1109/TIP.2020.3044220},
doi = {10.1109/TIP.2020.3044220},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tip/WangKLQ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/3dor/GubinsCSTVF0KMN21,
author = {Ilja Gubins and
Marten L. Chaillet and
Gijs van der Schot and
M. Cristina Trueba and
Remco C. Veltkamp and
Friedrich F{\"{o}}rster and
Xiao Wang and
Daisuke Kihara and
Emmanuel Moebel and
Nguyen P. Nguyen and
Tommi A. White and
Filiz Bunyak and
Giorgos Papoulias and
Stavros Gerolymatos and
Evangelia I. Zacharaki and
Konstantinos Moustakas and
Xiangrui Zeng and
Sinuo Liu and
Min Xu and
Yaoyu Wang and
Cheng Chen and
Xuefeng Cui and
Fa Zhang},
editor = {Silvia Biasotti and
Roberto M. Dyke and
Yu{-}Kun Lai and
Paul L. Rosin and
Remco C. Veltkamp},
title = {{SHREC} 2021: Classification in Cryo-electron Tomograms},
booktitle = {14th Eurographics Workshop on 3D Object Retrieval, 3DOR 2021 - Short
Papers, Virtual Event, 2-3 September 2021},
pages = {5--17},
publisher = {Eurographics Association},
year = {2021},
url = {https://doi.org/10.2312/3dor.20211307},
doi = {10.2312/3DOR.20211307},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/3dor/GubinsCSTVF0KMN21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/3dor/LangenfeldACST021,
author = {Florent Langenfeld and
Tunde Aderinwale and
Charles Christoffer and
Woong{-}Hee Shin and
Genki Terashi and
Xiao Wang and
Daisuke Kihara and
Halim Benhabiles and
Karim Hammoudi and
Adnane Cabani and
F{\'{e}}ryal Windal and
Mahmoud Melkemi and
Ekpo Otu and
Reyer Zwiggelaar and
David Hunter and
Yonghuai Liu and
L{\'{e}}a Sirugue and
Huu{-}Nghia H. Nguyen and
Tuan{-}Duy H. Nguyen and
Vinh{-}Thuyen Nguyen{-}Truong and
Danh Le and
Hai{-}Dang Nguyen and
Minh{-}Triet Tran and
Matthieu Mont{\`{e}}s},
editor = {Silvia Biasotti and
Roberto M. Dyke and
Yu{-}Kun Lai and
Paul L. Rosin and
Remco C. Veltkamp},
title = {{SHREC} 2021: Surface-based Protein Domains Retrieval},
booktitle = {14th Eurographics Workshop on 3D Object Retrieval, 3DOR 2021 - Short
Papers, Virtual Event, 2-3 September 2021},
pages = {19--26},
publisher = {Eurographics Association},
year = {2021},
url = {https://doi.org/10.2312/3dor.20211308},
doi = {10.2312/3DOR.20211308},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/3dor/LangenfeldACST021.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangTCZK20,
author = {Xiao Wang and
Genki Terashi and
Charles Christoffer and
Mengmeng Zhu and
Daisuke Kihara},
title = {Protein docking model evaluation by 3D deep convolutional neural networks},
journal = {Bioinform.},
volume = {36},
number = {7},
pages = {2113--2118},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btz870},
doi = {10.1093/BIOINFORMATICS/BTZ870},
timestamp = {Fri, 25 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangTCZK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cg/LangenfeldPLRAT20,
author = {Florent Langenfeld and
Yuxu Peng and
Yu{-}Kun Lai and
Paul L. Rosin and
Tunde Aderinwale and
Genki Terashi and
Charles Christoffer and
Daisuke Kihara and
Halim Benhabiles and
Karim Hammoudi and
Adnane Cabani and
F{\'{e}}ryal Windal and
Mahmoud Melkemi and
Andrea Giachetti and
Stelios K. Mylonas and
Apostolos Axenopoulos and
Petros Daras and
Ekpo Otu and
Matthieu Mont{\`{e}}s},
title = {{SHREC} 2020: Multi-domain protein shape retrieval challenge},
journal = {Comput. Graph.},
volume = {91},
pages = {189--198},
year = {2020},
url = {https://doi.org/10.1016/j.cag.2020.07.013},
doi = {10.1016/J.CAG.2020.07.013},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cg/LangenfeldPLRAT20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cg/GubinsCSVFHWCZM20,
author = {Ilja Gubins and
Marten L. Chaillet and
Gijs van der Schot and
Remco C. Veltkamp and
Friedrich F{\"{o}}rster and
Yu Hao and
Xiaohua Wan and
Xuefeng Cui and
Fa Zhang and
Emmanuel Moebel and
Xiao Wang and
Daisuke Kihara and
Xiangrui Zeng and
Min Xu and
Nguyen P. Nguyen and
Tommi A. White and
Filiz Bunyak},
title = {{SHREC} 2020: Classification in cryo-electron tomograms},
journal = {Comput. Graph.},
volume = {91},
pages = {279--289},
year = {2020},
url = {https://doi.org/10.1016/j.cag.2020.07.010},
doi = {10.1016/J.CAG.2020.07.010},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cg/GubinsCSVFHWCZM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/TerashiKK20,
author = {Genki Terashi and
Yuki Kagaya and
Daisuke Kihara},
title = {MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density
Maps with Symmetry},
journal = {J. Chem. Inf. Model.},
volume = {60},
number = {5},
pages = {2634--2643},
year = {2020},
url = {https://doi.org/10.1021/acs.jcim.9b01110},
doi = {10.1021/ACS.JCIM.9B01110},
timestamp = {Wed, 01 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/TerashiKK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/scfbm/DevilleKS20,
author = {Julian S. Deville and
Daisuke Kihara and
Atilla Sit},
title = {2DKD: a toolkit for content-based local image search},
journal = {Source Code Biol. Medicine},
volume = {15},
number = {1},
year = {2020},
url = {https://doi.org/10.1186/s13029-020-0077-1},
doi = {10.1186/S13029-020-0077-1},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/scfbm/DevilleKS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icassp/LaiTBK20,
author = {Tuan Manh Lai and
Quan Hung Tran and
Trung Bui and
Daisuke Kihara},
title = {A Simple But Effective Bert Model for Dialog State Tracking on Resource-Limited
Systems},
booktitle = {2020 {IEEE} International Conference on Acoustics, Speech and Signal
Processing, {ICASSP} 2020, Barcelona, Spain, May 4-8, 2020},
pages = {8034--8038},
publisher = {{IEEE}},
year = {2020},
url = {https://doi.org/10.1109/ICASSP40776.2020.9053975},
doi = {10.1109/ICASSP40776.2020.9053975},
timestamp = {Thu, 23 Jul 2020 16:19:28 +0200},
biburl = {https://dblp.org/rec/conf/icassp/LaiTBK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:series/mimb/TerashiCK20,
author = {Genki Terashi and
Charles Christoffer and
Daisuke Kihara},
editor = {Stefan Canzar and
Francisca Rojas Ringeling},
title = {Path-LZerD: Predicting Assembly Order of Multimeric Protein Complexes},
booktitle = {Protein-Protein Interaction Networks, Methods and Protocols},
series = {Methods in Molecular Biology},
volume = {2074},
pages = {95--112},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-1-4939-9873-9\_8},
doi = {10.1007/978-1-4939-9873-9\_8},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/series/mimb/TerashiCK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JainK19,
author = {Aashish Jain and
Daisuke Kihara},
title = {Phylo-PFP: improved automated protein function prediction using phylogenetic
distance of distantly related sequences},
journal = {Bioinform.},
volume = {35},
number = {5},
pages = {753--759},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty704},
doi = {10.1093/BIOINFORMATICS/BTY704},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JainK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KhanJRBK19,
author = {Ishita K. Khan and
Aashish Jain and
Reda Rawi and
Halima Bensmail and
Daisuke Kihara},
title = {Prediction of protein group function by iterative classification on
functional relevance network},
journal = {Bioinform.},
volume = {35},
number = {8},
pages = {1388--1394},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty787},
doi = {10.1093/BIOINFORMATICS/BTY787},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KhanJRBK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ShinK19,
author = {Woong{-}Hee Shin and
Daisuke Kihara},
title = {Predicting binding poses and affinity ranking in {D3R} Grand Challenge
using PL-PatchSurfer2.0},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {12},
pages = {1083--1094},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00222-y},
doi = {10.1007/S10822-019-00222-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ShinK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/HanSCCK19,
author = {Xusi Han and
Atilla Sit and
Charles Christoffer and
Siyang Chen and
Daisuke Kihara},
title = {A global map of the protein shape universe},
journal = {PLoS Comput. Biol.},
volume = {15},
number = {4},
year = {2019},
url = {https://doi.org/10.1371/journal.pcbi.1006969},
doi = {10.1371/JOURNAL.PCBI.1006969},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/HanSCCK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pr/SitSK19,
author = {Atilla Sit and
Woong{-}Hee Shin and
Daisuke Kihara},
title = {Three-dimensional Krawtchouk descriptors for protein local surface
shape comparison},
journal = {Pattern Recognit.},
volume = {93},
pages = {534--545},
year = {2019},
url = {https://doi.org/10.1016/j.patcog.2019.05.019},
doi = {10.1016/J.PATCOG.2019.05.019},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/pr/SitSK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/3dor/LangenfeldABDGH19,
author = {Florent Langenfeld and
Apostolos Axenopoulos and
Halim Benhabiles and
Petros Daras and
Andrea Giachetti and
Xusi Han and
Karim Hammoudi and
Daisuke Kihara and
Tuan Manh Lai and
Haiguang Liu and
Mahmoud Melkemi and
Stelios K. Mylonas and
Genki Terashi and
Yufan Wang and
F{\'{e}}ryal Windal and
Matthieu Mont{\`{e}}s},
editor = {Silvia Biasotti and
Guillaume Lavou{\'{e}} and
Remco C. Veltkamp},
title = {Protein Shape Retrieval Contest},
booktitle = {12th Eurographics Workshop on 3D Object Retrieval, 3DOR@Eurographics
2019, Genoa, Italy, May 5-6, 2019},
pages = {25--31},
publisher = {Eurographics Association},
year = {2019},
url = {https://doi.org/10.2312/3dor.20191058},
doi = {10.2312/3DOR.20191058},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/3dor/LangenfeldABDGH19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/3dor/GubinsSVFDZZCXM19,
author = {Ilja Gubins and
Gijs van der Schot and
Remco C. Veltkamp and
Friedrich F{\"{o}}rster and
Xuefeng Du and
Xiangrui Zeng and
Zhenxi Zhu and
Lufan Chang and
Min Xu and
Emmanuel Moebel and
Antonio Mart{\'{\i}}nez{-}S{\'{a}}nchez and
Charles Kervrann and
Tuan Manh Lai and
Xusi Han and
Genki Terashi and
Daisuke Kihara and
Benjamin A. Himes and
Xiaohua Wan and
Jingrong Zhang and
Shan Gao and
Yu Hao and
Zhilong Lv and
Xiaohua Wan and
Zhidong Yang and
Zijun Ding and
Xuefeng Cui and
Fa Zhang},
editor = {Silvia Biasotti and
Guillaume Lavou{\'{e}} and
Remco C. Veltkamp},
title = {Classification in Cryo-Electron Tomograms},
booktitle = {12th Eurographics Workshop on 3D Object Retrieval, 3DOR@Eurographics
2019, Genoa, Italy, May 5-6, 2019},
pages = {49--54},
publisher = {Eurographics Association},
year = {2019},
url = {https://doi.org/10.2312/3dor.20191061},
doi = {10.2312/3DOR.20191061},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/3dor/GubinsSVFDZZCXM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/carla/CorralesCSVKE19,
author = {Manuel Zumbado Corrales and
Luis Castillo{-}Valverde and
Jos{\'{e}} Salas{-}Bonilla and
Julio V{\'{\i}}quez{-}Murillo and
Daisuke Kihara and
Juan Esquivel{-}Rodr{\'{\i}}guez},
editor = {Juan Luis Crespo{-}Mari{\~{n}}o and
Esteban Meneses{-}Rojas},
title = {Matching of {EM} Map Segments to Structurally-Relevant Bio-molecular
Regions},
booktitle = {High Performance Computing - 6th Latin American Conference, {CARLA}
2019, Turrialba, Costa Rica, September 25-27, 2019, Revised Selected
Papers},
series = {Communications in Computer and Information Science},
volume = {1087},
pages = {464--478},
publisher = {Springer},
year = {2019},
url = {https://doi.org/10.1007/978-3-030-41005-6\_32},
doi = {10.1007/978-3-030-41005-6\_32},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/carla/CorralesCSVKE19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/emnlp/LaiTBK19,
author = {Tuan Manh Lai and
Quan Hung Tran and
Trung Bui and
Daisuke Kihara},
editor = {Kentaro Inui and
Jing Jiang and
Vincent Ng and
Xiaojun Wan},
title = {A Gated Self-attention Memory Network for Answer Selection},
booktitle = {Proceedings of the 2019 Conference on Empirical Methods in Natural
Language Processing and the 9th International Joint Conference on
Natural Language Processing, {EMNLP-IJCNLP} 2019, Hong Kong, China,
November 3-7, 2019},
pages = {5952--5958},
publisher = {Association for Computational Linguistics},
year = {2019},
url = {https://doi.org/10.18653/v1/D19-1610},
doi = {10.18653/V1/D19-1610},
timestamp = {Thu, 07 Apr 2022 09:14:07 +0200},
biburl = {https://dblp.org/rec/conf/emnlp/LaiTBK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/bioinf/HanSCTMK19,
author = {Xusi Han and
Woong{-}Hee Shin and
Charles Christoffer and
Genki Terashi and
Lyman Monroe and
Daisuke Kihara},
editor = {Shoba Ranganathan and
Michael Gribskov and
Kenta Nakai and
Christian Sch{\"{o}}nbach},
title = {Study of the Variability of the Native Protein Structure},
booktitle = {Encyclopedia of Bioinformatics and Computational Biology - Volume
3},
pages = {606--619},
publisher = {Elsevier},
year = {2019},
url = {https://doi.org/10.1016/b978-0-12-809633-8.20148-9},
doi = {10.1016/B978-0-12-809633-8.20148-9},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/reference/bioinf/HanSCTMK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1909-09696,
author = {Tuan Manh Lai and
Quan Hung Tran and
Trung Bui and
Daisuke Kihara},
title = {A Gated Self-attention Memory Network for Answer Selection},
journal = {CoRR},
volume = {abs/1909.09696},
year = {2019},
url = {http://arxiv.org/abs/1909.09696},
eprinttype = {arXiv},
eprint = {1909.09696},
timestamp = {Wed, 11 Dec 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1909-09696.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1910-12995,
author = {Tuan Manh Lai and
Quan Hung Tran and
Trung Bui and
Daisuke Kihara},
title = {A Simple but Effective {BERT} Model for Dialog State Tracking on Resource-Limited
Systems},
journal = {CoRR},
volume = {abs/1910.12995},
year = {2019},
url = {http://arxiv.org/abs/1910.12995},
eprinttype = {arXiv},
eprint = {1910.12995},
timestamp = {Thu, 31 Oct 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1910-12995.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1911-09265,
author = {Xiao Wang and
Daisuke Kihara and
Jiebo Luo and
Guo{-}Jun Qi},
title = {EnAET: Self-Trained Ensemble AutoEncoding Transformations for Semi-Supervised
Learning},
journal = {CoRR},
volume = {abs/1911.09265},
year = {2019},
url = {http://arxiv.org/abs/1911.09265},
eprinttype = {arXiv},
eprint = {1911.09265},
timestamp = {Fri, 13 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1911-09265.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/PetersonTETCRSK18,
author = {Lenna X. Peterson and
Yoichiro Togawa and
Juan Esquivel{-}Rodr{\'{\i}}guez and
Genki Terashi and
Charles Christoffer and
Amitava Roy and
Woong{-}Hee Shin and
Daisuke Kihara},
title = {Modeling the assembly order of multimeric heteroprotein complexes},
journal = {PLoS Comput. Biol.},
volume = {14},
number = {1},
year = {2018},
url = {https://doi.org/10.1371/journal.pcbi.1005937},
doi = {10.1371/JOURNAL.PCBI.1005937},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/PetersonTETCRSK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/YerneniKWK18,
author = {Satwica Yerneni and
Ishita K. Khan and
Qing Wei and
Daisuke Kihara},
title = {{IAS:} Interaction Specific {GO} Term Associations for Predicting
Protein-Protein Interaction Networks},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {15},
number = {4},
pages = {1247--1258},
year = {2018},
url = {https://doi.org/10.1109/TCBB.2015.2476809},
doi = {10.1109/TCBB.2015.2476809},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/YerneniKWK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KhanBK17,
author = {Ishita K. Khan and
Mansurul Bhuiyan and
Daisuke Kihara},
title = {DextMP: deep dive into text for predicting moonlighting proteins},
journal = {Bioinform.},
volume = {33},
number = {14},
pages = {i83--i91},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx231},
doi = {10.1093/BIOINFORMATICS/BTX231},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KhanBK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WeiKDYK17,
author = {Qing Wei and
Ishita K. Khan and
Ziyun Ding and
Satwica Yerneni and
Daisuke Kihara},
title = {NaviGO: interactive tool for visualization and functional similarity
and coherence analysis with gene ontology},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {177:1--177:13},
year = {2017},
url = {https://doi.org/10.1186/s12859-017-1600-5},
doi = {10.1186/S12859-017-1600-5},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WeiKDYK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pieee/MagnerKS17,
author = {Abram Magner and
Daisuke Kihara and
Wojciech Szpankowski},
title = {A Study of the Boltzmann Sequence-Structure Channel},
journal = {Proc. {IEEE}},
volume = {105},
number = {2},
pages = {286--305},
year = {2017},
url = {https://doi.org/10.1109/JPROC.2016.2608797},
doi = {10.1109/JPROC.2016.2608797},
timestamp = {Fri, 02 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/pieee/MagnerKS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/PetersonRCTK17,
author = {Lenna X. Peterson and
Amitava Roy and
Charles Christoffer and
Genki Terashi and
Daisuke Kihara},
title = {Modeling disordered protein interactions from biophysical principles},
journal = {PLoS Comput. Biol.},
volume = {13},
number = {4},
year = {2017},
url = {https://doi.org/10.1371/journal.pcbi.1005485},
doi = {10.1371/JOURNAL.PCBI.1005485},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/PetersonRCTK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/3dor/SongCCHKLMQSTL17,
author = {Na Song and
Daniela Craciun and
Charles Christoffer and
Xusi Han and
Daisuke Kihara and
Guillaume Levieux and
Matthieu Mont{\`{e}}s and
Hong Qin and
Pranjal Sahu and
Genki Terashi and
Haiguang Liu},
editor = {Ioannis Pratikakis and
Florent Dupont and
Maks Ovsjanikov},
title = {Protein Shape Retrieval},
booktitle = {10th Eurographics Workshop on 3D Object Retrieval, 3DOR@Eurographics
2017, Lyon, France, April 23-24, 2017},
publisher = {Eurographics Association},
year = {2017},
url = {https://doi.org/10.2312/3dor.20171055},
doi = {10.2312/3DOR.20171055},
timestamp = {Tue, 27 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/3dor/SongCCHKLMQSTL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JamrozKK16,
author = {Michal Jamr{\'{o}}z and
Andrzej Kolinski and
Daisuke Kihara},
title = {Ensemble-based evaluation for protein structure models},
journal = {Bioinform.},
volume = {32},
number = {12},
pages = {314--321},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw262},
doi = {10.1093/BIOINFORMATICS/BTW262},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JamrozKK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KhanK16,
author = {Ishita K. Khan and
Daisuke Kihara},
title = {Genome-scale prediction of moonlighting proteins using diverse protein
association information},
journal = {Bioinform.},
volume = {32},
number = {15},
pages = {2281--2288},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw166},
doi = {10.1093/BIOINFORMATICS/BTW166},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KhanK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/KingsleyEYKL16,
author = {Laura J. Kingsley and
Juan Esquivel{-}Rodr{\'{\i}}guez and
Ying Yang and
Daisuke Kihara and
Markus A. Lill},
title = {Ranking protein-protein docking results using steered molecular dynamics
and potential of mean force calculations},
journal = {J. Comput. Chem.},
volume = {37},
number = {20},
pages = {1861--1865},
year = {2016},
url = {https://doi.org/10.1002/jcc.24412},
doi = {10.1002/JCC.24412},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/KingsleyEYKL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/ZhuSKK16,
author = {Xiaolei Zhu and
Woong{-}Hee Shin and
Hyungrae Kim and
Daisuke Kihara},
title = {Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein-Ligand
Binding Prediction in {CSAR} 2013 and 2014},
journal = {J. Chem. Inf. Model.},
volume = {56},
number = {6},
pages = {1088--1099},
year = {2016},
url = {https://doi.org/10.1021/acs.jcim.5b00625},
doi = {10.1021/ACS.JCIM.5B00625},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/ZhuSKK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/ShinCWK16,
author = {Woong{-}Hee Shin and
Charles Christoffer and
Ji{-}Bo Wang and
Daisuke Kihara},
title = {PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening
Method That Is Tolerant to Target and Ligand Structure Variation},
journal = {J. Chem. Inf. Model.},
volume = {56},
number = {9},
pages = {1676--1691},
year = {2016},
url = {https://doi.org/10.1021/acs.jcim.6b00163},
doi = {10.1021/ACS.JCIM.6B00163},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/ShinCWK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isit/MagnerKS16,
author = {Abram Magner and
Daisuke Kihara and
Wojciech Szpankowski},
title = {The Boltzmann sequence-structure channel},
booktitle = {{IEEE} International Symposium on Information Theory, {ISIT} 2016,
Barcelona, Spain, July 10-15, 2016},
pages = {255--259},
publisher = {{IEEE}},
year = {2016},
url = {https://doi.org/10.1109/ISIT.2016.7541300},
doi = {10.1109/ISIT.2016.7541300},
timestamp = {Wed, 16 Oct 2019 14:14:48 +0200},
biburl = {https://dblp.org/rec/conf/isit/MagnerKS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KhanWCK15,
author = {Ishita K. Khan and
Qing Wei and
Meghana Chitale and
Daisuke Kihara},
title = {{PFP/ESG:} automated protein function prediction servers enhanced
with Gene Ontology visualization tool},
journal = {Bioinform.},
volume = {31},
number = {2},
pages = {271--272},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btu646},
doi = {10.1093/BIOINFORMATICS/BTU646},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KhanWCK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhuXK15,
author = {Xiaolei Zhu and
Yi Xiong and
Daisuke Kihara},
title = {Large-scale binding ligand prediction by improved patch-based method
Patch-Surfer2.0},
journal = {Bioinform.},
volume = {31},
number = {5},
pages = {707--713},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btu724},
doi = {10.1093/BIOINFORMATICS/BTU724},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhuXK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Esquivel-Rodriguez15,
author = {Juan Esquivel{-}Rodr{\'{\i}}guez and
Yi Xiong and
Xusi Han and
Shuomeng Guang and
Charles Christoffer and
Daisuke Kihara},
title = {Navigating 3D electron microscopy maps with {EM-SURFER}},
journal = {{BMC} Bioinform.},
volume = {16},
pages = {181:1--181:9},
year = {2015},
url = {https://doi.org/10.1186/s12859-015-0580-6},
doi = {10.1186/S12859-015-0580-6},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Esquivel-Rodriguez15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/OtsukaMTOINYDNTSNNABCGKRTWM15,
author = {Yuta Otsuka and
Ai Muto and
Rikiya Takeuchi and
Chihiro Okada and
Motokazu Ishikawa and
Koichiro Nakamura and
Natsuko Yamamoto and
Hitomi Dose and
Kenji Nakahigashi and
Shigeki Tanishima and
Sivasundaram Suharnan and
Wataru Nomura and
Toru Nakayashiki and
Walid G. Aref and
Barry R. Bochner and
Tyrrell Conway and
Michael Gribskov and
Daisuke Kihara and
Kenneth E. Rudd and
Yukako Tohsato and
Barry L. Wanner and
Hirotada Mori},
title = {GenoBase: comprehensive resource database of \emph{Escherichia coli}
{K-12}},
journal = {Nucleic Acids Res.},
volume = {43},
number = {Database-Issue},
pages = {606--617},
year = {2015},
url = {https://doi.org/10.1093/nar/gku1164},
doi = {10.1093/NAR/GKU1164},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/OtsukaMTOINYDNTSNNABCGKRTWM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ita/MagnerKS15,
author = {Abram Magner and
Daisuke Kihara and
Wojciech Szpankowski},
title = {Phase transitions in a sequence-structure channel},
booktitle = {2015 Information Theory and Applications Workshop, {ITA} 2015, San
Diego, CA, USA, February 1-6, 2015},
pages = {235--239},
publisher = {{IEEE}},
year = {2015},
url = {https://doi.org/10.1109/ITA.2015.7308994},
doi = {10.1109/ITA.2015.7308994},
timestamp = {Wed, 16 Oct 2019 14:14:51 +0200},
biburl = {https://dblp.org/rec/conf/ita/MagnerKS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CavalcoliWADK14,
author = {Jim Cavalcoli and
Lonnie R. Welch and
Bruce J. Aronow and
Sorin Draghici and
Daisuke Kihara},
title = {The International Society of Computational Biology presents: the Great
Lakes Bioinformatics Conference, May 16-18, 2014, Cincinnati, Ohio},
journal = {Bioinform.},
volume = {30},
number = {1},
pages = {148--149},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btt673},
doi = {10.1093/BIOINFORMATICS/BTT673},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CavalcoliWADK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tip/SitK14,
author = {Atilla Sit and
Daisuke Kihara},
title = {Comparison of Image Patches Using Local Moment Invariants},
journal = {{IEEE} Trans. Image Process.},
volume = {23},
number = {5},
pages = {2369--2379},
year = {2014},
url = {https://doi.org/10.1109/TIP.2014.2315923},
doi = {10.1109/TIP.2014.2315923},
timestamp = {Sun, 10 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tip/SitK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChitaleKK13,
author = {Meghana Chitale and
Ishita K. Khan and
Daisuke Kihara},
title = {In-depth performance evaluation of {PFP} and {ESG} sequence-based
function prediction methods in {CAFA} 2011 experiment},
journal = {{BMC} Bioinform.},
volume = {14},
number = {{S-3}},
pages = {S2},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-S3-S2},
doi = {10.1186/1471-2105-14-S3-S2},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChitaleKK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/smc/HiranoKHKUTMNSHKYT13,
author = {Harutoyo Hirano and
Daisuke Kihara and
Hiroki Hirano and
Yuichi Kurita and
Teiji Ukawa and
Tsuneo Takayanagi and
Haruka Morimoto and
Ryuji Nakamura and
Noboru Saeki and
Yukihito Higashi and
Masashi Kawamoto and
Masao Yoshizumi and
Toshio Tsuji},
title = {Evaluation of Arterial Stiffness during the Flow-Mediated Dilation
Test},
booktitle = {{IEEE} International Conference on Systems, Man, and Cybernetics,
Manchester, {SMC} 2013, United Kingdom, October 13-16, 2013},
pages = {3756--3759},
publisher = {{IEEE}},
year = {2013},
url = {https://doi.org/10.1109/SMC.2013.640},
doi = {10.1109/SMC.2013.640},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/smc/HiranoKHKUTMNSHKYT13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MessihCBKG12,
author = {Mario Abdel Messih and
Meghana Chitale and
Vladimir B. Bajic and
Daisuke Kihara and
Xin Gao},
title = {Protein domain recurrence and order can enhance prediction of protein
functions},
journal = {Bioinform.},
volume = {28},
number = {18},
pages = {444--450},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts398},
doi = {10.1093/BIOINFORMATICS/BTS398},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MessihCBKG12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiK12,
author = {Bin Li and
Daisuke Kihara},
title = {Protein docking prediction using predicted protein-protein interface},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {7},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-7},
doi = {10.1186/1471-2105-13-7},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YuanCK12,
author = {Chao Yuan and
Hao Chen and
Daisuke Kihara},
title = {Effective inter-residue contact definitions for accurate protein fold
recognition},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {292},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-292},
doi = {10.1186/1471-2105-13-292},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/YuanCK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Esquivel-RodriguezK12,
author = {Juan Esquivel{-}Rodr{\'{\i}}guez and
Daisuke Kihara},
title = {Evaluation of multiple protein docking structures using correctly
predicted pairwise subunits},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-2}},
pages = {S6},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-S2-S6},
doi = {10.1186/1471-2105-13-S2-S6},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Esquivel-RodriguezK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SaelK12,
author = {Lee Sael and
Daisuke Kihara},
title = {Constructing patch-based ligand-binding pocket database for predicting
function of proteins},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-2}},
pages = {S7},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-S2-S7},
doi = {10.1186/1471-2105-13-S2-S7},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SaelK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChitalePK11,
author = {Meghana Chitale and
Shriphani Palakodety and
Daisuke Kihara},
title = {Quantification of Protein Group Coherence and Pathway Assignment Using
Functional Association},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {373},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-373},
doi = {10.1186/1471-2105-12-373},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChitalePK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HawkinsCK10,
author = {Troy Hawkins and
Meghana Chitale and
Daisuke Kihara},
title = {Functional enrichment analyses and construction of functional similarity
networks with high confidence function prediction by {PFP}},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {265},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-265},
doi = {10.1186/1471-2105-11-265},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HawkinsCK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SaelK10,
author = {Lee Sael and
Daisuke Kihara},
title = {Improved protein surface comparison and application to low-resolution
protein structure data},
journal = {{BMC} Bioinform.},
volume = {11},
number = {{S-11}},
pages = {S2},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-S11-S2},
doi = {10.1186/1471-2105-11-S11-S2},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SaelK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijkdb/SaelK10,
author = {Lee Sael and
Daisuke Kihara},
title = {Characterization and Classification of Local Protein Surfaces Using
Self-Organizing Map},
journal = {Int. J. Knowl. Discov. Bioinform.},
volume = {1},
number = {1},
pages = {32--47},
year = {2010},
url = {https://doi.org/10.4018/jkdb.2010100203},
doi = {10.4018/JKDB.2010100203},
timestamp = {Thu, 18 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijkdb/SaelK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChitaleHPK09,
author = {Meghana Chitale and
Troy Hawkins and
Changsoon Park and
Daisuke Kihara},
title = {{ESG:} extended similarity group method for automated protein function
prediction},
journal = {Bioinform.},
volume = {25},
number = {14},
pages = {1739--1745},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp309},
doi = {10.1093/BIOINFORMATICS/BTP309},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChitaleHPK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LaEVLSUAK09,
author = {David La and
Juan Esquivel{-}Rodr{\'{\i}}guez and
Vishwesh Venkatraman and
Bin Li and
Lee Sael and
Stephen Ueng and
Steven Ahrendt and
Daisuke Kihara},
title = {3D-SURFER: software for high-throughput protein surface comparison
and analysis},
journal = {Bioinform.},
volume = {25},
number = {21},
pages = {2843--2844},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp542},
doi = {10.1093/BIOINFORMATICS/BTP542},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LaEVLSUAK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/VenkatramanYSK09,
author = {Vishwesh Venkatraman and
Yifeng D. Yang and
Lee Sael and
Daisuke Kihara},
title = {Protein-protein docking using region-based 3D Zernike descriptors},
journal = {{BMC} Bioinform.},
volume = {10},
pages = {407},
year = {2009},
url = {https://doi.org/10.1186/1471-2105-10-407},
doi = {10.1186/1471-2105-10-407},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/VenkatramanYSK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/VenkatramanCK09,
author = {Vishwesh Venkatraman and
Padmasini Chakravarthy and
Daisuke Kihara},
title = {Application of 3D Zernike descriptors to shape-based ligand similarity
searching},
journal = {J. Cheminformatics},
volume = {1},
pages = {19},
year = {2009},
url = {https://doi.org/10.1186/1758-2946-1-19},
doi = {10.1186/1758-2946-1-19},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/VenkatramanCK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ir/SiYKF08,
author = {Luo Si and
Danni Yu and
Daisuke Kihara and
Yi Fang},
title = {Combining gene sequence similarity and textual information for gene
function annotation in the literature},
journal = {Inf. Retr.},
volume = {11},
number = {5},
pages = {389--404},
year = {2008},
url = {https://doi.org/10.1007/s10791-008-9053-0},
doi = {10.1007/S10791-008-9053-0},
timestamp = {Tue, 17 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ir/SiYKF08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/HawkinsK07,
author = {Troy Hawkins and
Daisuke Kihara},
title = {Function Prediction of uncharacterized proteins},
journal = {J. Bioinform. Comput. Biol.},
volume = {5},
number = {1},
pages = {1--30},
year = {2007},
url = {https://doi.org/10.1142/S0219720007002503},
doi = {10.1142/S0219720007002503},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/HawkinsK07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibe/ZhangKP07,
author = {Mingwu Zhang and
Daisuke Kihara and
Sunil Prabhakar},
title = {Tracing Lineage in Multi-version Scientific Databases},
booktitle = {Proceedings of the 7th {IEEE} International Conference on Bioinformatics
and Bioengineering, {BIBE} 2007, October 14-17, 2007, Harvard Medical
School, Boston, MA, {USA}},
pages = {440--447},
publisher = {{IEEE} Computer Society},
year = {2007},
url = {https://doi.org/10.1109/BIBE.2007.4375599},
doi = {10.1109/BIBE.2007.4375599},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibe/ZhangKP07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sma/LiuLKR07,
author = {Yu{-}Shen Liu and
Min Liu and
Daisuke Kihara and
Karthik Ramani},
editor = {Bruno L{\'{e}}vy and
Dinesh Manocha},
title = {Salient critical points for meshes},
booktitle = {Proceedings of the 2007 {ACM} Symposium on Solid and Physical Modeling,
Beijing, China, June 4-6, 2007},
pages = {277--282},
publisher = {{ACM}},
year = {2007},
url = {https://doi.org/10.1145/1236246.1236285},
doi = {10.1145/1236246.1236285},
timestamp = {Thu, 15 Jul 2021 08:59:42 +0200},
biburl = {https://dblp.org/rec/conf/sma/LiuLKR07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HuYK06,
author = {Jianjun Hu and
Yifeng D. Yang and
Daisuke Kihara},
title = {{EMD:} an ensemble algorithm for discovering regulatory motifs in
{DNA} sequences},
journal = {{BMC} Bioinform.},
volume = {7},
pages = {342},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-342},
doi = {10.1186/1471-2105-7-342},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HuYK06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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