Kentaro Shimizu

发表

A weighted average difference method for detecting differentially expressed genes from microarray data

Koji Kadota, Yuji Nakai, Kentaro Shimizu, 2008, Algorithms for Molecular Biology.

Automatic generation of bioinformatics tools for predicting protein–ligand binding sites

Kentaro Shimizu, Yusuke Komiyama, Masaki Banno, 2015, Bioinform..

Prediction of Carbohydrate-Binding Proteins from Sequences Using Support Vector Machines

Kentaro Shimizu, Mizuki Morita, Seizi Someya, 2010, Adv. Bioinformatics.

New Evaluation Method and Result of Video Compression Ratio and Quality for Telesurgery in Neurosurgery

Hiroshi Iseki, Takashi Suzuki, Kentaro Shimizu, 2009 .

Computational Protocol for Screening GPI-anchored Proteins

Kentaro Shimizu, Kazuya Sumikoshi, Cao Wei, 2009, BICoB.

A server framework in the Act 8 operating system

Kentaro Shimizu, Shiki Okasaka, 1999 .

Office in the cloud: Web-based cloud platform for Telcos services

Kentaro Shimizu, Naoki Uchida, Masafumi Suzuki, 2013, 2013 17th International Conference on Intelligence in Next Generation Networks (ICIN).

Parallel algorithm for efficient calculation of second derivatives of conformational energy function in internal coordinates

Kentaro Shimizu, Shugo Nakamura, Mitsunori Ikeguchi, 1998, J. Comput. Chem..

A Portable Logic Simulation System

Kentaro Shimizu, 1984 .

Prediction of MoRFs Based on n-gram Convolutional Neural Network

Kentaro Shimizu, Fang Chun, Yoshitaka Moriwaki, 2019 .

Prediction of Protein-Protein Interaction Sites Using Only Sequence Information and Using Both Sequence and Structural Information

Kentaro Shimizu, Masanori Kakuta, Shugo Nakamura, 2008 .

Identifying MoRFs in Disordered Proteins Using Enlarged Conserved Features

Kentaro Shimizu, Daming Zhu, Chun Fang, 2018, ICBCB 2018.

High-Density Scanning Combined with Digital Image of Real Objects for Complete Reproduction of Cultural Artifacts

Kentaro Shimizu, Junta Doi, Wataru Sato, 2006, 2006 IEEE International Conference on Multisensor Fusion and Integration for Intelligent Systems.

Development of an ab initio protein structure prediction system ABLE.

Kentaro Shimizu, Tsuyoshi Inoue, Takashi Ishida, 2003, Genome informatics. International Conference on Genome Informatics.

Identification of GPI-(like)-Anchored Proteins by Using SVM

Kentaro Shimizu, Cao Wei, K. Shimizu, 2006, First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06).

3P-012 Folding simulation of the B-domain of staphylococcal protein A(The 46th Annual Meeting of the Biophysical Society of Japan)

Kentaro Shimizu, Tohru Terada, Kenichiro Nishi, 2008 .

Access route control by an extended key/lock scheme

Kentaro Shimizu, Masahiro Sowa, Soichi Shigeta, 2001, Comput. Syst. Sci. Eng..

Flexible User-Definable Memory Coherence Scheme in Distributed Shared Memory of GALAXY

Mamoru Maekawa, Kentaro Shimizu, Pradeep Kumar Sinha, 1991, EDMCC.

Commentary: A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines

Kentaro Shimizu, Koji Kadota, K. Kadota, 2020, Frontiers in Genetics.

Accurate Classification of Differential Expression Patterns in a Bayesian Framework With Robust Normalization for Multi-Group RNA-Seq Count Data

Koji Kadota, Kentaro Shimizu, Takayuki Osabe, 2019, Bioinformatics and biology insights.

High-Density Surface Reconstruction of Fine Arts and Documents for Complete Reproduction and Counterfeit Detection

Kentaro Shimizu, Junta Doi, Masakazu Sekijima, 2007, 2007 IEEE International Conference on Networking, Sensing and Control.

Process migration in the GALAXY distributed operating system

Xiaohua Jia, Mamoru Maekawa, Kentaro Shimizu, 1991, [1991] Proceedings. The Fifth International Parallel Processing Symposium.

Hierarchical object groups in distributed operating systems

Mamoru Maekawa, Kentaro Shimizu, Jun Hamano, 1988, [1988] Proceedings. The 8th International Conference on Distributed.

A Multimedia Workstation, Yougao

Yu Gu, Mamoru Maekawa, Kentaro Shimizu, 1991 .

Automatic Improvement of Scheduling Policies in Parsley Parallel Programming Environment

Kentaro Shimizu, Masakazu Sekijima, Shugo Nakamura, 2002, IASTED PDCS.

A normalization strategy for comparing tag count data

Koji Kadota, Kentaro Shimizu, Tomoaki Nishiyama, 2012, Algorithms for Molecular Biology.

2P071 Generality of the protein structure prediction method based on molecular dynamics simulation with secondary structure information(The 48th Annual Meeting of the Biophysical Society of Japan)

Kentaro Shimizu, Tohru Terada, Asahiko Nishimura, 2010 .

Improving the reliability of name resolution mechanism in distributed operating systems

Mamoru Maekawa, Kentaro Shimizu, Pradeep Kumar Sinha, 1992, [1992] Proceedings of the 12th International Conference on Distributed Computing Systems.

Linked Open Data Construction of Purpose Oriented Interactomics by Integration of Life Sciences LOD

Fumihiro Kato, Kentaro Shimizu, Yusuke Komiyama, 2014 .

Process Creation and Date Sharing in a Single Address Space Operating System

Kentaro Shimizu, Shusuke Okamoto, Masahiro Sowa, 1998 .

A Paraellel and Nonblocking Updating Mechanism for Replicated Directory Files in Distributed Systems

Xiaohua Jia, Mamoru Maekawa, Kentaro Shimizu, 1994, J. Parallel Distributed Comput..

Coarse‐grained molecular dynamics simulations of protein–ligand binding

Kentaro Shimizu, Tohru Terada, Tatsuki Negami, 2014, J. Comput. Chem..

Performance Evaluation of Global Page Placement Policies in Massively Parallel Systems

Kentaro Shimizu, Hyo Ashihara, Tadaaki Miyata, 1997 .

High-Precision Geometric Modeling of 3D Artifacts for Virtual Restoration

Kentaro Shimizu, Junta Doi, Wataru Sato, 2006, 2006 IEEE Symposium on Virtual Environments, Human-Computer Interfaces and Measurement Systems.

Design of an ASIC for digital audio signal level meters

Ming Zhang, Kentaro Shimizu, Shungang Wei, 1994, Proceedings Seventh Annual IEEE International ASIC Conference and Exhibit.

CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing

Kentaro Shimizu, Koki Tsuyuzaki, Itoshi Nikaido, 2018, Genome Biology.

Office on Demand: New cloud service platform for carrier

Kentaro Shimizu, Naoki Uchida, Shinyo Muto, 2012, 2012 16th International Conference on Intelligence in Next Generation Networks.

Time-of-Reduction-Recovery Predicton in Neural Networks of Variable Topology to Improve Enzyme Classification

Kentaro Shimizu, Junta Doi, Yasuo Kuhara, 1998, NC.

BUDDY-system: A web site for constructing a dataset of protein pairs between ligand-bound and unbound states

Kentaro Shimizu, Shugo Nakamura, Tohru Terada, 2011, BMC Research Notes.

Tape winding device for tire-building machines

Kentaro Shimizu, Osamu Fujiki, Mitsuru Hitotsuyanagi, 1991 .

Editor's Introduction: Parallel and Distributed Operating Systems

Kentaro Shimizu, 1992 .

Parallel algorithm for efficient calculation of second derivatives of conformational energy function in internal coordinates

Kentaro Shimizu, Shugo Nakamura, Mitsunori Ikeguchi, 1998 .

Highly concurrent directory management in the Galaxy distributed system

Xiaohua Jia, Mamoru Maekawa, Kentaro Shimizu, 1990, Proceedings.,10th International Conference on Distributed Computing Systems.

Adaptive bidding load balancing algorithms in heterogeneous distributed systems

Kentaro Shimizu, Yongbing Zhang, Hisao Kameda, 1994, Proceedings of International Workshop on Modeling, Analysis and Simulation of Computer and Telecommunication Systems.

CPC (Cyclic Pipeline Computer) - An Architecture Suited for Josephson and Pipelined-Memory Machines

Kentaro Shimizu, Shuichi Ichikawa, Eiichi Goto, 1989, IEEE Trans. Computers.

Design and Implementation of a Parallel Programming Environment Based on Distributed Shared Arrays

Kentaro Shimizu, Wataru Kaneko, Shugo Nakamura, 2003, ISHPC.

The Galaxv Distributed Operating System

Mamoru Maekawa, Kentaro Shimizu, Xiaohua Jia, 1991 .

CHRACTERISTICS OF MEASURED BERTHING VELOCITY AND THE APPLICATION FOR FENDER DESIGN OF BERTHING SHIP

Kentaro Shimizu, Shigeru Ueda, Tatsuhiko Okada, 2013 .

Insight of the Signal Motif of GPI-(like)-anchored Proteins by using SVM

Kentaro Shimizu, Kazuya Sumikoshi, Cao Wei, 2006, BIOCOMP.

Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity

Koji Kadota, Yuji Nakai, Kentaro Shimizu, 2008, Algorithms for Molecular Biology.

1P-013 Development of protein local structure prediction method based on combination of multiple support vector machines(Protein:Structure, The 47th Annual Meeting of the Biophysical Society of Japan)

Kentaro Shimizu, Masanori Kakuta, Shugo Nakamura, 2009 .

Flow Control and Routing Algorithms in WAPSN

Kentaro Shimizu, Hisao Kameda, R. C. Betini, 1995, Comput. Commun..

Development of a prediction system for tail-anchored proteins

Kentaro Shimizu, Cao Wei, Tohru Terada, 2016, BMC Bioinformatics.

Preemptive Resource Management: Defending against Resource Monopolizing DoS

Kentaro Shimizu, Wataru Kaneko, Kenji Kono, 2003, Applied Informatics.

Programming environment based on distributed shared arrays for high-performance scientific computing

Kentaro Shimizu, Wataru Kaneko, Shugo Nakamura, 2004, 2004 International Symposium on Applications and the Internet Workshops. 2004 Workshops..

ROKU: a novel method for identification of tissue-specific genes

Koji Kadota, Yuji Nakai, Kentaro Shimizu, 2006, BMC Bioinformatics.

MoRFPred_en: Sequence-based prediction of MoRFs using an ensemble learning strategy

Kentaro Shimizu, Yoshitaka Moriwaki, Caihong Li, 2019, J. Bioinform. Comput. Biol..

Flexible address space sharing mechanisms in the GALAXY distributed operating system

Mamoru Maekawa, Kentaro Shimizu, P. K. Sinha, 1991, [1991 Proceedings] Tenth Annual International Phoenix Conference on Computers and Communications.

Prediction of protein structure classes and secondary structures by means of hidden Markov models

Kentaro Shimizu, Junta Doi, Shugo Nakamura, 1999, Systems and Computers in Japan.

Development of a sugar-binding residue prediction system from protein sequences using support vector machine

Kentaro Shimizu, Yusuke Komiyama, Masaki Banno, 2017, Comput. Biol. Chem..

TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data

Koji Kadota, Kentaro Shimizu, Jianqiang Sun, 2019, BMC Research Notes.

Evaluation of methods for differential expression analysis on multi-group RNA-seq count data

Min Tang, Koji Kadota, Kentaro Shimizu, 2015, BMC Bioinformatics.

Identifying short disorder-to-order binding regions in disordered proteins with a deep convolutional neural network method

Kentaro Shimizu, Caihong Li, Chun Fang, 2019, J. Bioinform. Comput. Biol..

Tyrosine Kinase Ligand-Receptor Pair Prediction by Using Support Vector Machine

Kentaro Shimizu, Yusuke Komiyama, Kokoro Ueki, 2015, Adv. Bioinformatics.

INVESTIGATION ON SERVICE YEARS OF LARGE RUBBER MARINE FENDERS

Kentaro Shimizu, Toshiro Kamada, Hitoshi Akiyama, 2017 .

An effective system for managing biological data

Wei Cao, Zhenglu Yang, Qian Li, 2016, 2016 International Conference on Behavioral, Economic and Socio-cultural Computing (BESC).

A Portable Logic Simulation System for Development of FLATS Machine

Kentaro Shimizu, 1984, RIMS Symposia on Software Science and Engineering.

Effects of Link Communication Time on Optimal Load Balancing in Tree Hierarchy Network Configurations

Kentaro Shimizu, Hisao Kameda, Jie Li, 1993 .

Distributed Shared Arrays: Portable Shared-Memory Programming Interface for Multiple Computer Systems

Kentaro Shimizu, Wataru Kaneko, Shugo Nakamura, 2004, Cluster Computing.

Multicanonical ab inito QM/MM molecular dynamics simulation of a peptide in an aqueous environment

Kentaro Shimizu, Tohru Terada, Yuusuke Watanabe, 2009, J. Comput. Chem..

Evaluating methods for ranking differentially expressed genes applied to microArray quality control data

Koji Kadota, Kentaro Shimizu, K. Kadota, 2011, BMC Bioinformatics.

2P448 Improvement to a Protein-Protein Docking Algorithm by Introducing Layers in Molecular Expression Space(48. Bioinformatics, genomics and proteomics (II),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Kentaro Shimizu, Kazuya Sumikoshi, Shugo Nakamura, 2006 .

Reuse of Reconstructed Model of Human Skull for Anthropological and Anthropoid Morphological Model Estimation

Kentaro Shimizu, Junta Doi, Masahiko Hoshi, 2006, 2006 IEEE International Conference on Information Reuse & Integration.

FLATS Architecture and its Evaluation

Mitsuhisa Sato, Masayuki Suzuki, Kentaro Shimizu, 1997 .

Methods for analyzing next-generation sequencing data IX.Genome annotation, visualization, and registration to DDBJ

Koji Kadota, Kentaro Shimizu, Yasukazu Nakamura, 2017 .

The Galaxy distributed operating system

Xiaohua Jia, Mamoru Maekawa, Kentaro Shimizu, 1991, Computer.

Network-transparent object naming and locating in the GALAXY distributed operating system

Mamoru Maekawa, Kentaro Shimizu, P. K. Sinha, 1991 .

1P060 Development of a protein tertiary structure prediction server(1. Protein structure and dynamics (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Kentaro Shimizu, Masanori Kakuta, Shugo Nakamura, 2006 .

Design of a Lisp machine - FLATS

Masanori Idesawa, M. Suzuki, Kentaro Shimizu, 1982, LFP '82.

3P297 Development of structure prediction server and model quality assessment platform for proteins(Bioinformatics: Structural genomics,The 48th Annual Meeting of the Biophysical Society of Japan)

Kentaro Shimizu, Masanori Kakuta, Shugo Nakamura, 2010 .

New method for parallel computation of Hessian matrix of conformational energy function in internal coordinates

Kentaro Shimizu, Shugo Nakamura, Mitsunori Ikeguchi, 2002, J. Comput. Chem..

TCC: an R package for comparing tag count data with robust normalization strategies

Koji Kadota, Kentaro Shimizu, Jianqiang Sun, 2013, BMC Bioinformatics.

A Self-organizing State Space Approach to Inferring Time-Varying Causalities between Regulatory Proteins

Kentaro Shimizu, Osamu Hirose, K. Shimizu, 2010, ITBAM.

Parametric analysis of optimal load balancing in distributed computer systems

Kentaro Shimizu, Yongbing Zhang, Hisao Kameda, 1992 .

EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation

Kentaro Shimizu, Tohru Terada, Yoshitaka Moriwaki, 2021, J. Chem. Inf. Model..

DNA microarray cluster analysis reveals tissue similarity and potential neuron‐specific genes expressed in cranial sensory ganglia

Kentaro Shimizu, Shugo Nakamura, Keiko Abe, 2003, Journal of neuroscience research.

Evaluation of Two Outlier-Detection-Based Methods for Detecting Tissue-Selective Genes from Microarray Data

Koji Kadota, Kentaro Shimizu, Tomokazu Konishi, 2007, Gene regulation and systems biology.

A comparison of generalized Born methods in folding simulations

Kentaro Shimizu, Tohru Terada, T. Terada, 2008 .

Potential for assessing quality of protein structure based on contact number prediction

Kentaro Shimizu, Takashi Ishida, Shugo Nakamura, 2006, Proteins.

Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation

Kentaro Shimizu, Tohru Terada, Yutaka Ito, 2008, Proteins.

A generalized conformational energy function of DNA derived from molecular dynamics simulations

Kentaro Shimizu, Tohru Terada, Satoshi Yamasaki, 2009, Nucleic acids research.

Mechanism of the difference in the binding affinity of E. coli tRNAGln to glutaminyl-tRNA synthetase caused by noninterface nucleotides in variable loop.

Kentaro Shimizu, Shugo Nakamura, Tohru Terada, 2007, Biophysical journal.

Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates

Kentaro Shimizu, Mizuki Morita, Masanori Kakuta, 2012 .

A new method for evaluating the specificity of indirect readout in protein–DNA recognition

Kentaro Shimizu, Tohru Terada, Satoshi Yamasaki, 2012, Nucleic acids research.

Molecular Dynamics Simulations in Aqueous Solution: Application to Free Energy Calculation of Oligopeptides

Kentaro Shimizu, Koichi Tazaki and, 1998 .

Prediction of protein structure classes and secondary structures by means of hidden Markov models

Kentaro Shimizu, Shugo Nakamura, Mitsunori Ikeguchi, 1999, Systems and Computers in Japan.

A new entropy model for RNA: part II. Persistence-related entropic contributions to RNA secondary structure free energy calculations

Kentaro Shimizu, Gota Kawai, Kenji Yamamoto, 2013 .

Up-Regulation of Genes Related to the Ubiquitin-Proteasome System in the Brown Adipose Tissue of 24-h-Fasted Rats

Koji Kadota, Yuji Nakai, Kentaro Shimizu, 2008, Bioscience, biotechnology, and biochemistry.

Folding free‐energy landscape of a 10‐residue mini‐protein, chignolin

Kentaro Shimizu, Shugo Nakamura, Tohru Terada, 2006, FEBS letters.

HPLC Retention time prediction for metabolome analysi

Koji Kadota, Kentaro Shimizu, Masanori Kakuta, 2010, Bioinformation.

Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations

Kentaro Shimizu, Tohru Terada, Ryuichiro Ishitani, 2008 .

Accurate prediction of native tertiary structure of protein using molecular dynamics simulation with the aid of the knowledge of secondary structures

Kentaro Shimizu, Tohru Terada, Tadaomi Furuta, 2009 .

Development of a protein–ligand-binding site prediction method based on interaction energy and sequence conservation

Kentaro Shimizu, Gul Saad, Kazuya Sumikoshi, 2016, Journal of Structural and Functional Genomics.

A fast protein-protein docking algorithm using series expansion in terms of spherical basis functions.

Kentaro Shimizu, Kazuya Sumikoshi, Shugo Nakamura, 2005, Genome informatics. International Conference on Genome Informatics.