Daisuke Kihara

According to our database, Daisuke Kihara authored at least 58 papers between 2006 and 2020.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2020

Path-LZerD: Predicting Assembly Order of Multimeric Protein Complexes.

Genki Terashi, Charles Christoffer, Daisuke Kihara

Proceedings of the Protein-Protein Interaction Networks, Methods and Protocols., 2020

2DKD: a toolkit for content-based local image search.

Julian S. Deville, Daisuke Kihara, Atilla Sit

Source Code Biol. Medicine, 2020

MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry.

Genki Terashi, Yuki Kagaya, Daisuke Kihara

J. Chem. Inf. Model., 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, Mahmoud Melkemi, Andrea Giachetti, Stelios K. Mylonas, Apostolos Axenopoulos, Petros Daras, Ekpo Otu, Matthieu Montès

Comput. Graph., 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, Xuefeng Cui, Fa Zhang, Emmanuel Moebel, Xiao Wang, Daisuke Kihara, Xiangrui Zeng, Min Xu, Nguyen P. Nguyen, Tommi White, Filiz Bunyak

Comput. Graph., 2020

Protein docking model evaluation by 3D deep convolutional neural networks.

Xiao Wang, Genki Terashi, Charles Christoffer, Mengmeng Zhu, Daisuke Kihara

Bioinform., 2020

A Simple But Effective Bert Model for Dialog State Tracking on Resource-Limited Systems.

Tuan Manh Lai, Quan Hung Tran, Trung Bui, Daisuke Kihara

Proceedings of the 2020 IEEE International Conference on Acoustics, 2020

2019

Study of the Variability of the Native Protein Structure.

Xusi Han, Woong-Hee Shin, Charles Christoffer, Genki Terashi, Lyman Monroe, Daisuke Kihara

Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 3, 2019

Three-dimensional Krawtchouk descriptors for protein local surface shape comparison.

Atilla Sit, Woong-Hee Shin, Daisuke Kihara

Pattern Recognit., 2019

A global map of the protein shape universe.

Xusi Han, Atilla Sit, Charles Christoffer, Siyang Chen, Daisuke Kihara

PLoS Comput. Biol., 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

EnAET: Self-Trained Ensemble AutoEncoding Transformations for Semi-Supervised Learning.

Xiao Wang, Daisuke Kihara, Jiebo Luo, Guo-Jun Qi

CoRR, 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

Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences.

Aashish Jain, Daisuke Kihara

Bioinform., 2019

A Gated Self-attention Memory Network for Answer Selection.

Tuan Manh Lai, Quan Hung Tran, Trung Bui, Daisuke Kihara

Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing, 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

Proceedings of the High Performance Computing - 6th Latin American Conference, 2019

Protein Shape Retrieval Contest.

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

Proceedings of the 12th Eurographics Workshop on 3D Object Retrieval, 2019

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, 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

Proceedings of the 12th Eurographics Workshop on 3D Object Retrieval, 2019

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

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

2017

Modeling disordered protein interactions from biophysical principles.

Lenna X. Peterson, Amitava Roy, Charles Christoffer, Genki Terashi, Daisuke Kihara

PLoS Comput. Biol., 2017

A Study of the Boltzmann Sequence-Structure Channel.

Abram Magner, Daisuke Kihara, Wojciech Szpankowski

Proc. IEEE, 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

DextMP: deep dive into text for predicting moonlighting proteins.

Ishita K. Khan, Mansurul Bhuiyan, Daisuke Kihara

Bioinform., 2017

Protein Shape Retrieval.

Na Song, Daniela Craciun, Charles Christoffer, Xusi Han, Daisuke Kihara, Guillaume Levieux, Matthieu Montès, Hong Qin, Pranjal Sahu, Genki Terashi, Haiguang Liu

Proceedings of the 10th Eurographics Workshop on 3D Object Retrieval, 2017

2016

Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein-Ligand Binding Prediction in CSAR 2013 and 2014.

Xiaolei Zhu, Woong-Hee Shin, Hyungrae Kim, Daisuke Kihara

J. Chem. Inf. Model., 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

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

Genome-scale prediction of moonlighting proteins using diverse protein association information.

Ishita K. Khan, Daisuke Kihara

Bioinform., 2016

Ensemble-based evaluation for protein structure models.

Michal Jamróz, Andrzej Kolinski, Daisuke Kihara

Bioinform., 2016

The Boltzmann sequence-structure channel.

Abram Magner, Daisuke Kihara, Wojciech Szpankowski

Proceedings of the IEEE International Symposium on Information Theory, 2016

2015

GenoBase: comprehensive resource database of <i>Escherichia coli</i> 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, Toru Nakayashiki, Walid G. Aref, Barry R. Bochner, Tyrrell Conway, Michael Gribskov, Daisuke Kihara, Kenneth E. Rudd, Yukako Tohsato, Barry L. Wanner, Hirotada Mori

Nucleic Acids Res., 2015

Navigating 3D electron microscopy maps with EM-SURFER.

Juan Esquivel-Rodríguez, Yi Xiong, Xusi Han, Shuomeng Guang, Charles Christoffer, Daisuke Kihara

BMC Bioinform., 2015

Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0.

Xiaolei Zhu, Yi Xiong, Daisuke Kihara

Bioinform., 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

Phase transitions in a sequence-structure channel.

Abram Magner, Daisuke Kihara, Wojciech Szpankowski

Proceedings of the 2015 Information Theory and Applications Workshop, 2015

2014

Comparison of Image Patches Using Local Moment Invariants.

Atilla Sit, Daisuke Kihara

IEEE Trans. Image Process., 2014

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

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

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, Toshio Tsuji

Proceedings of the IEEE International Conference on Systems, 2013

2012

Effective inter-residue contact definitions for accurate protein fold recognition.

Chao Yuan, Hao Chen, Daisuke Kihara

BMC Bioinform., 2012

Constructing patch-based ligand-binding pocket database for predicting function of proteins.

Lee Sael, Daisuke Kihara

BMC Bioinform., 2012

Protein docking prediction using predicted protein-protein interface.

Bin Li, Daisuke Kihara

BMC Bioinform., 2012

Evaluation of multiple protein docking structures using correctly predicted pairwise subunits.

Juan Esquivel-Rodríguez, Daisuke Kihara

BMC Bioinform., 2012

Protein domain recurrence and order can enhance prediction of protein functions.

Mario Abdel Messih, Meghana Chitale, Vladimir B. Bajic, Daisuke Kihara, Xin Gao

Bioinform., 2012

2011

Quantification of Protein Group Coherence and Pathway Assignment Using Functional Association.

Meghana Chitale, Shriphani Palakodety, Daisuke Kihara

BMC Bioinform., 2011

2010

Characterization and Classification of Local Protein Surfaces Using Self-Organizing Map.

Lee Sael, Daisuke Kihara

Int. J. Knowl. Discov. Bioinform., 2010

Improved protein surface comparison and application to low-resolution protein structure data.

Lee Sael, Daisuke Kihara

BMC Bioinform., 2010

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

2009

Application of 3D Zernike descriptors to shape-based ligand similarity searching.

Vishwesh Venkatraman, Padmasini Chakravarthy, Daisuke Kihara

J. Cheminformatics, 2009

Protein-protein docking using region-based 3D Zernike descriptors.

Vishwesh Venkatraman, Yifeng D. Yang, Lee Sael, Daisuke Kihara

BMC 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

ESG: extended similarity group method for automated protein function prediction.

Meghana Chitale, Troy Hawkins, Changsoon Park, Daisuke Kihara

Bioinform., 2009

2008

Combining gene sequence similarity and textual information for gene function annotation in the literature.

Luo Si, Danni Yu, Daisuke Kihara, Yi Fang

Inf. Retr., 2008

2007

Function Prediction of uncharacterized proteins.

Troy Hawkins, Daisuke Kihara

J. Bioinform. Comput. Biol., 2007

Salient critical points for meshes.

Yu-Shen Liu, Min Liu, Daisuke Kihara, Karthik Ramani

Proceedings of the 2007 ACM Symposium on Solid and Physical Modeling, 2007

Tracing Lineage in Multi-version Scientific Databases.

Mingwu Zhang, Daisuke Kihara, Sunil Prabhakar

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

2006

EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences.

Jianjun Hu, Yifeng D. Yang, Daisuke Kihara

BMC Bioinform., 2006