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K. Shimizu · SciRah

Researcher profile · Semantic Scholar

K. Shimizu

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K. Shimizu — researcher profile on SciRah

h-index: 27
Works: 263
Citations: 3,039

Most-cited papers

TCC: an R package for comparing tag count data with robust normalization strategies
Jian-Qiang Sun, T. Nishiyama, K. Shimizu, K. Kadota
2013BMC Bioinformatics554 citations Open access
Semantic Scholar
TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data
Wei-Shun Su, Jian-Qiang Sun, K. Shimizu, K. Kadota
2019BMC Research Notes112 citations Open access
Semantic Scholar
Trisaccharide containing α2,3-linked sialic acid is a receptor for mumps virus
M. Kubota, K. Takeuchi, S. Watanabe, S. Ohno +12 more
2016Proceedings of the National Academy of Sciences of the United States of America97 citations Open access
Semantic Scholar
A normalization strategy for comparing tag count data
K. Kadota, T. Nishiyama, K. Shimizu
2012Algorithms for Molecular Biology90 citations Open access
Semantic Scholar
Evaluation of methods for differential expression analysis on multi-group RNA-seq count data
Min Tang, Jian-Qiang Sun, K. Shimizu, K. Kadota
2015BMC Bioinformatics74 citations Open access
Semantic Scholar
Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results
Shitao Zhao, Jian-Qiang Sun, K. Shimizu, K. Kadota
2018Biological Procedures Online40 citations Open access
Semantic Scholar
NRBP1-Containing CRL2/CRL4A Regulates Amyloid β Production by Targeting BRI2 and BRI3 for Degradation.
T. Yasukawa, Aya Tsutsui, C. Tomomori-Sato, S. Sato +8 more
2020Cell Reports39 citations Open access
Semantic Scholar
Mechanism of self/nonself-discrimination in Brassica self-incompatibility
K. Murase, Yoshitaka Moriwaki, Tomoyuki Mori, Xiao Liu +14 more
2020Nature Communications36 citations Open access
Semantic Scholar
Prediction of Antifungal Peptides by Deep Learning with Character Embedding
Chun Fang, Yoshitaka Moriwaki, Caihong Li, K. Shimizu
2019IPSJ Transactions on Bioinformatics33 citations Open access
Semantic Scholar
Comparative analysis of membrane protein structure databases.
K. Shimizu, W. Cao, Gul Saad, M. Shoji +1 more
2018Biochimica et Biophysica Acta - Biomembranes30 citations Open access
Semantic Scholar
Coarse‐grained molecular dynamics simulations of protein–ligand binding
Tatsuki Negami, K. Shimizu, T. Terada
2014Journal of Computational Chemistry30 citations
Semantic Scholar
Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family
T. Kashima, Kouki Okumura, A. Ishiwata, Machika Kaieda +9 more
2021Journal of Biological Chemistry29 citations Open access
Semantic Scholar
Mechanism for folate‐independent aldolase reaction catalyzed by serine hydroxymethyltransferase
Y. Chiba, T. Terada, Masafumi Kameya, K. Shimizu +3 more
2012The FEBS Journal29 citations Open access
Semantic Scholar
Heme binding mechanism of structurally similar iron-regulated surface determinant near transporter domains of Staphylococcus aureus exhibiting different affinities for heme.
Yoshitaka Moriwaki, T. Terada, José M. M. Caaveiro, Yousuke Takaoka +3 more
2013Biochemistry26 citations
Semantic Scholar
Quercetin 3,5,7,3′,4′-pentamethyl ether from Kaempferia parviflora directly and effectively activates human SIRT1
Mimin Zhang, Peng Lu, T. Terada, Miaomiao Sui +15 more
2021Communications Biology25 citations Open access
Semantic Scholar
Development of a deep learning-based method to identify “good” regions of a cryo-electron microscopy grid
Yuichi Yokoyama, T. Terada, K. Shimizu, Kouki Nishikawa +5 more
2020Biophysical Reviews24 citations Open access
Semantic Scholar
Selective binding of antimicrobial porphyrins to the heme‐receptor IsdH‐NEAT3 of Staphylococcus aureus
N. Vu, Yoshitaka Moriwaki, Jose M. M. Caaveiro, T. Terada +4 more
2013Protein Science24 citations Open access
Semantic Scholar
Understanding the molecular mechanism underlying the high catalytic activity of p-hydroxybenzoate hydroxylase mutants for producing gallic acid.
Yoshitaka Moriwaki, M. Yato, T. Terada, S. Saito +9 more
2019Biochemistry23 citations
Semantic Scholar
Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C-6 Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C-6 Methyltransferase.
Hayama Tsutsumi, Yoshitaka Moriwaki, T. Terada, K. Shimizu +3 more
2021Angewandte Chemie22 citations
Semantic Scholar
CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing
Kenta Sato, Koki Tsuyuzaki, K. Shimizu, I. Nikaido
2018Genome Biology22 citations Open access
Semantic Scholar
A new method for evaluating the specificity of indirect readout in protein–DNA recognition
S. Yamasaki, T. Terada, H. Kono, K. Shimizu +1 more
2012Nucleic Acids Research20 citations Open access
Semantic Scholar
EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation
Keisuke Yanagisawa, Yoshitaka Moriwaki, T. Terada, K. Shimizu
2021Journal of Chemical Information and Modeling18 citations Open access
Semantic Scholar
Differential expression analysis using a model-based gene clustering algorithm for RNA-seq data
Takayuki Osabe, K. Shimizu, K. Kadota
2020BMC Bioinformatics17 citations Open access
Semantic Scholar
A Recently Formed Triploid Cardamine insueta Inherits Leaf Vivipary and Submergence Tolerance Traits of Parents
Jian-Qiang Sun, R. Shimizu-Inatsugi, Hugo Hofhuis, K. Shimizu +3 more
2020bioRxiv16 citations Open access
Semantic Scholar
Identifying short disorder-to-order binding regions in disordered proteins with a deep convolutional neural network method
Chun Fang, Yoshitaka Moriwaki, Aikui Tian, Caihong Li +1 more
2019J. Bioinform. Comput. Biol.16 citations Open access
Semantic Scholar
Accurate Classification of Differential Expression Patterns in a Bayesian Framework With Robust Normalization for Multi-Group RNA-Seq Count Data
Takayuki Osabe, K. Shimizu, K. Kadota
2019Bioinformatics and Biology Insights15 citations Open access
Semantic Scholar
Development of a sugar-binding residue prediction system from protein sequences using support vector machine
Masaki Banno, Yusuke Komiyama, W. Cao, Y. Oku +5 more
2017Comput. Biol. Chem.15 citations Open access
Semantic Scholar
A new entropy model for RNA: part III. Is the folding free energy landscape of RNA funnel shaped?
Wayne K. Dawson, T. Takai, N. Ito, K. Shimizu +1 more
2014Journal of Nucleic Acids Investigation14 citations Open access
Semantic Scholar
Prediction and analysis of antifreeze proteins
Ryosuke Miyata, Yoshitaka Moriwaki, T. Terada, K. Shimizu
2021Heliyon13 citations Open access
Semantic Scholar
Coarse-grained molecular dynamics simulation of protein conformational change coupled to ligand binding
Tatsuki Negami, K. Shimizu, T. Terada
2020Chemical Physics Letters13 citations
Semantic Scholar
Development of a protein–ligand-binding site prediction method based on interaction energy and sequence conservation
H. Tsujikawa, Kenta Sato, Cao Wei, Gul Saad +4 more
2016Journal of Structural and Functional Genomics13 citations Open access
Semantic Scholar
Automatic generation of bioinformatics tools for predicting protein–ligand binding sites
Yusuke Komiyama, Masaki Banno, K. Ueki, Gul Saad +1 more
2015Bioinform.13 citations Open access
Semantic Scholar
Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides
K. Hasegawa, Yoshitaka Moriwaki, T. Terada, Cao Wei +1 more
2022J. Bioinform. Comput. Biol.12 citations Open access
Semantic Scholar
Rapid Heme Transfer Reactions between NEAr Transporter Domains of Staphylococcus aureus: A Theoretical Study Using QM/MM and MD Simulations
Yoshitaka Moriwaki, T. Terada, K. Tsumoto, K. Shimizu
2015PLoS ONE12 citations Open access
Semantic Scholar
Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Nonheme Iron Oxygenase Carbazole 1,9a-Dioxygenase
K. Inoue, Y. Usami, Y. Ashikawa, Haruko Noguchi +11 more
2014Applied and Environmental Microbiology11 citations Open access
Semantic Scholar
MoRFPred_en: Sequence-based prediction of MoRFs using an ensemble learning strategy
Chun Fang, Yoshitaka Moriwaki, Caihong Li, K. Shimizu
2019J. Bioinform. Comput. Biol.10 citations
Semantic Scholar
Prediction of protein mononucleotide binding sites using AlphaFold2 and machine learning
S. Yamaguchi, H. Nakashima, Yoshitaka Moriwaki, T. Terada +1 more
2022Comput. Biol. Chem.8 citations Open access
Semantic Scholar
Structural analysis of β‐L‐arabinobiose‐binding protein in the metabolic pathway of hydroxyproline‐rich glycoproteins in Bifidobacterium longum
M. Miyake, T. Terada, M. Shimokawa, N. Sugimoto +5 more
2020The FEBS Journal8 citations
Semantic Scholar
Virtual screening identification of novel chemical inhibitors for aberrant interactions between pathogenic mutant SOD1 and tubulin
Kazunori Hirayama, Yuuki Fujiwara, T. Terada, K. Shimizu +2 more
2019Neurochemistry International7 citations
Semantic Scholar
Electron Transport in a Dioxygenase-Ferredoxin Complex: Long Range Charge Coupling between the Rieske and Non-Heme Iron Center
Wayne K. Dawson, R. Jono, T. Terada, K. Shimizu
2016PLoS ONE7 citations Open access
Semantic Scholar
A new entropy model for RNA: part II. Persistence-related entropic contributions to RNA secondary structure free energy calculations
Wayne K. Dawson, Kenji Yamamoto, K. Shimizu, G. Kawai
2013Journal of Nucleic Acids Investigation7 citations Open access
Semantic Scholar
QM/MM Study of the Catalytic Mechanism and Substrate Specificity of the Aromatic Substrate C-Methyltransferase Fur6.
Fan Zhao, Yoshitaka Moriwaki, Tomohiro Noguchi, K. Shimizu +2 more
2024Biochemistry6 citations
Semantic Scholar
Development of a prediction system for tail-anchored proteins
Shunsuke Shigemitsu, W. Cao, T. Terada, K. Shimizu
2016BMC Bioinformatics6 citations Open access
Semantic Scholar
Commentary: A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines
K. Kadota, K. Shimizu
2020Frontiers in Genetics5 citations Open access
Semantic Scholar
Dissecting the Stereocontrolled Conversion of Short-Lived Sulfenic Acid by Lachrymatory Factor Synthase
T. Arakawa, Yuta Sato, Masayuki Yamada, J. Takabe +10 more
20205 citations
Semantic Scholar
High-Throughput Sequencing of the Expressed Torafugu (Takifugu rubripes) Antibody Sequences Distinguishes IgM and IgT Repertoires and Reveals Evidence of Convergent Evolution
Xi Fu, Jian-Qiang Sun, E. Tan, K. Shimizu +3 more
2018Frontiers in Immunology5 citations Open access
Semantic Scholar
Identifying MoRFs in Disordered Proteins Using Enlarged Conserved Features
Chun Fang, Yoshitaka Moriwaki, Da-Ming Zhu, K. Shimizu
2018ICBCB 20185 citations
Semantic Scholar
Prediction of N-myristoylation modification of proteins by SVM
W. Cao, K. Sumikoshi, Shugo Nakamura, T. Terada +1 more
2011Bioinformation5 citations Open access
Semantic Scholar
A unique peptide-based pharmacophore identifies an inhibitory compound against the A-subunit of Shiga toxin
M. Watanabe-Takahashi, M. Senda, Ryunosuke Yoshino, M. Hibino +5 more
2022Scientific Reports4 citations Open access
Semantic Scholar
Functional characterisation of two ferric-ion coordination modes of TtFbpA, the periplasmic subunit of an ABC-type iron transporter from Thermus thermophilus HB8.
Peng Lu, Yoshitaka Moriwaki, Mimin Zhang, Yukie Katayama +11 more
2019Metallomics4 citations
Semantic Scholar

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