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Author Details

Wataru Iwasaki
the University of Tokyo
2006
96
26
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36630500Machine learning enables prediction of metabolic system evolution in bacteria.Sci Adv2023
37963895Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years.Nat Commun2023
37673872A fungal sesquiterpene biosynthesis gene cluster critical for mutualist-pathogen transition in Colletotrichum tofieldiae.Nat Commun2023
37309722AlphaCutter: Efficient removal of non-globular regions from predicted protein structures.Proteomics2023
37438353Chromosome genome assembly and annotation of the spiny red gurnard (Chelidonichthys spinosus).Sci Data2023
36857197MitoFish, MitoAnnotator, and MiFish Pipeline: Updates in 10 Years.Mol Biol Evol2023
34747029Long reads and Hi-C sequencing illuminate the two-compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis.New Phytol2022
37938339Unexpected absence of ribosomal protein genes from metagenome-assembled genomes.ISME Commun2022
35771653Mirage 2.0: fast and memory-efficient reconstruction of gene-content evolution considering heterogeneous evolutionary patterns among gene families.Bioinformatics2022
35435239Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation.Am J Bot2022
35634928Convergent copy number increase of genes associated with freshwater colonization in fishes.Philos Trans R Soc Lond B Biol Sci2022
35630964High-Density and Monodisperse Electrochemical Gold Nanoparticle Synthesis Utilizing the Properties of Boron-Doped Diamond Electrodes.Nanomaterials (Basel)2022
35552456The Quest for Orthologs orthology benchmark service in 2022.Nucleic Acids Res2022
36092417An open and continuously updated fern tree of life.Front Plant Sci2022
35922439Metal deposition and shape reproduction at biological temperatures on cell-level samples.Sci Rep2022
36386892Nondestructive microbial discrimination using single-cell Raman spectra and random forest machine learning algorithm.STAR Protoc2022
36083456Lifestyle Evolution Analysis by Binary-State Speciation and Extinction (BiSSE) Model.Methods Mol Biol2022
35060594Inverse Potts model improves accuracy of phylogenetic profiling.Bioinformatics2022
34992246Deep distributed computing to reconstruct extremely large lineage trees.Nat Biotechnol2022
33165944Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population.Evolution2021
36700099Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families.Bioinform Adv2021
33877468Correction to: Assessment of Polygala paniculata (Polygalaceae) characteristics for evolutionary studies of legume-rhizobia symbiosis.J Plant Res2021
34887400Massive image-based single-cell profiling reveals high levels of circulating platelet aggregates in patients with COVID-19.Nat Commun2021
34485857Machine learning-assisted single-cell Raman fingerprinting for <i>in situ</i> and nondestructive classification of prokaryotes.iScience2021
33956892Correction: Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8.PLoS One2021
34337769Piwi-piRNA complexes induce stepwise changes in nuclear architecture at target loci.EMBO J2021
31364707Graph Splitting: A Graph-Based Approach for Superfamily-Scale Phylogenetic Tree Reconstruction.Syst Biol2020
31828682Assessment of Polygala paniculata (Polygalaceae) characteristics for evolutionary studies of legume-rhizobia symbiosis.J Plant Res2020
33117966Environmental Atlas of Prokaryotes Enables Powerful and Intuitive Habitat-Based Analysis of Community Structures.iScience2020
33024051Metatranscriptomics by <i>In Situ</i> RNA Stabilization Directly and Comprehensively Revealed Episymbiotic Microbial Communities of Deep-Sea Squat Lobsters.mSystems2020
32357172Logicome Profiler: Exhaustive detection of statistically significant logic relationships from comparative omics data.PLoS One2020
32374845The Quest for Orthologs benchmark service and consensus calls in 2020.Nucleic Acids Res2020
30635580Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community.Nat Commun2019
30032301SonicParanoid: fast, accurate and easy orthology inference.Bioinformatics2019
31548428A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators.Proc Natl Acad Sci U S A2019
31428688Functional D-box sequences reset the circadian clock and drive mRNA rhythms.Commun Biol2019
31341962Genome and transcriptome evolve separately in recently hybridized Trichosporon fungi.Commun Biol2019
30870453Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8.PLoS One2019
31127303A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios.Mol Biol Evol2019
31026590Recognition and delineation of yeast genera based on genomic data: Lessons from Trichosporonales.Fungal Genet Biol2019
29027707A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved 'natural' hybrid genomes.Yeast2018
29476140Proteorhodopsin variability and distribution in the North Pacific Subtropical Gyre.ISME J2018
29668970MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding.Mol Biol Evol2018
29494765Correlation between Electronic Shell Structure and Inertness of Cu <sub>n</sub><sup>+</sup> toward O<sub>2</sub> Adsorption at n = 15, 21, 41, and 49.J Phys Chem A2018
29410487Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia.ISME J2018
29540790Demonstration of the potential of environmental DNA as a tool for the detection of avian species.Sci Rep2018
29460198Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus⿿ÿ⿿yedoensis 'Somei-yoshino' across the Japanese archipelago.J Plant Res2018
28028038Function and evolution of a Lotus japonicus AP2/ERF family transcription factor that is required for development of infection threads.DNA Res2017
28103804Inactivity periods and postural change speed can explain atypical postural change patterns of Caenorhabditis elegans mutants.BMC Bioinformatics2017
28321065Small Bowel Obstruction Caused by the Ingestion of a Wooden Toothpick: The CT findings and a Literature Review.Intern Med2017
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ETH Zurich, Universitatstr. 6
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Stockholm University
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Erick Antezana
Norwegian University of Science and Technology
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Hiroshima University
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Release 1.2