resources

List of research resources developed by the Fukushima Lab

GitHub Repositories

kfuku52/genegalleon Charting evolutionary histories across genes and species
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kfuku52/csubst Analyzing combinations of codon substitution histories
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kfuku52/amalgkit RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
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kfuku52/RADTE Divergence time estimation in the complex history of gene family evolution
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kfuku52/cdskit Processing protein-coding DNA sequences in frame
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kfuku52/nwkit Newick tree processing
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kfuku52/averagers Estimating average temperatures from historical daily extremes
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mkrg01/genome_assembly_pipeline An integrated pipeline for eukaryotic genome assembly and gene annotation
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mkrg01/permucn A tool to test associations between binary trait transitions and gene-family copy-number evolution from CAFE outputs
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Genomes

The viewers below use NCBI's official API to display representative scaffolds for each assembly.

Cephalotus follicularis (NCBI / CoGe / Publication)

Nepenthes gracilis (NCBI / CoGe / Publication)

Collaboration Network

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2007 2026
1+
Visible categories

Authors
Author Category Coauthored First Latest
Kenji Fukushima Principal investigator 42 2007 2026
Mitsuyasu Hasebe External collaborators 9 2008 2022
Rainer Hedrich External collaborators 8 2020 2025
Victor A. Albert External collaborators 8 2017 2026
Yoshikazu Hoshi External collaborators 8 2007 2020
Matthias Freund Current and former lab members 7 2020 2025
Dirk Becker External collaborators 5 2020 2025
André Marques External collaborators 4 2023 2026
David D. Pollock External collaborators 4 2017 2023
Jonathan Kirshner External collaborators 4 2025 2026
Tanya Renner External collaborators 4 2018 2025
Atsushi J. Nagano External collaborators 3 2022 2025
Gergő Pálfalvi External collaborators 3 2017 2021
Héctor Montero Current and former lab members 3 2023 2025
Ines Kreuzer External collaborators 3 2020 2025
Katsuya Nagano External collaborators 3 2007 2011
Michaela Richter External collaborators 3 2023 2025
Shuji Shigenobu External collaborators 3 2017 2022
Takanori Wakatake Current and former lab members 3 2022 2026
Tomoko F. Shibata External collaborators 3 2017 2022
Charlotte Lindqvist External collaborators 2 2023 2025
Chunfang Zheng External collaborators 2 2017 2025
David Sankoff External collaborators 2 2017 2025
Enrique Ibarra-Laclette External collaborators 2 2018 2025
Franziska Saul Current and former lab members 2 2020 2023
Gerd Vogg External collaborators 2 2023 2025
Gerhard Bringmann External collaborators 2 2023 2025
Jörg Schultz External collaborators 2 2020 2021
Kadeem J. Gilbert External collaborators 2 2022 2023
Ken Shirasu External collaborators 2 2023 2025
Kenichi Tsuda External collaborators 2 2021 2025
Kenji Suetsugu External collaborators 2 2023 2025
Kimberly M. Farr External collaborators 2 2017 2018
Laura Ávila Robledillo External collaborators 2 2025 2026
Luis Herrera-Estrella External collaborators 2 2018 2025
Masuko Kobori External collaborators 2 2008 2009
Mathias Scharmann External collaborators 2 2023 2025
Sachiko Masuda External collaborators 2 2023 2025
Saeko Masumoto External collaborators 2 2008 2009
Seisuke Kimura External collaborators 2 2014 2023

Paper Network

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2007 2026
1+

Papers
Paper Year Links Connection score
Contrasting centromere structures in carnivorous sundews uncover a dynamic evolutionary trajectory shaped by polyploidy and chromosomal remodeling 2025 13 51
Genomes of the Venus flytrap and close relatives unveil the roots of plant carnivory 2020 21 44
Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis 2023 15 44
Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory 2017 22 36
Impaired trap closure in the counting-deficient Venus flytrap mutant DYSCALCULIA is caused by cell wall biomechanics 2025 12 33
The digestive systems of carnivorous plants 2022 13 24
Carnivorous plant genomes 2018 15 23
Genome evolution and convergent innovation in the carnivorous plant Sarracenia purpurea 2025 9 19
Calcium dynamics during trap closure visualized in transgenic Venus flytrap 2020 14 16
Genome sequence of 12 Vigna species as a knowledge base of stress tolerance and resistance 2022 12 16
Tandem repeat rDNA sequences derived from parents were stably maintained in hexaploids of Drosera spathulata complex (Droseraceae) 2008 13 15
Complexity and innovation in carnivorous plant genomes 2026 7 15
How to grow a tree: Plant voltage-dependent cation channels in the spotlight of evolution 2021 7 12
A discordance of seasonally covarying cues uncovers misregulated phenotypes in the heterophyllous pitcher plant Cephalotus follicularis 2021 8 10
Contrasting patterns of the 5S and 45S rDNA evolutions in the Byblis liniflora complex (Byblidaceae) 2011 7 9
Drosera rotundifolia and Drosera tokaiensis suppress the activation of HMC-1 human mast cells 2009 7 9
Bitter gourd suppresses lipopolysaccharide-induced inflammatory responses 2008 7 9
Somatic chromosome differentiation in three species of the Byblis liniflora complex (Byblidaceae) 2008 7 9
A comparative study of karyotypes in two species of Byblis (Byblidaceae) 2007 7 9
Oriented cell division shapes carnivorous pitcher leaves of Sarracenia purpurea 2015 8 8
Adaxial–abaxial polarity: The developmental basis of leaf shape diversity 2014 8 8
Convergent losses of arbuscular mycorrhizal symbiosis in carnivorous plants 2025 7 8
On the origin of carnivory: Molecular physiology and evolution of plants on an animal diet 2021 7 7
Construction costs and tradeoffs in carnivorous pitcher plant leaves: towards a pitcher leaf economic spectrum 2025 3 4
Markov katana: A novel method for Bayesian resampling of parameter space applied to phylogenetic trees 2018 3 4
Detecting macroevolutionary genotype–phenotype associations using error-corrected rates of protein convergence 2023 3 3
Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution 2020 3 3
Transcriptomic heterochrony and completely cleistogamous flower development in the mycoheterotrophic orchid Gastrodia 2023 2 3
Transcriptomic prey-capture responses in convergently evolved carnivorous pitcher plants 2026 2 2
Convergent acquisition of disulfide-forming enzymes in malodorous flowers 2025 2 2
Molecular basis behind the isoprene emission diversity in Fagaceae 2025 2 2
Non-prey biotic interactions in carnivorous plants 2023 2 2
Genomic signature and evolutionary history of completely cleistogamous lineages in the non-photosynthetic orchid Gastrodia 2025 1 2
Emergence of isochorismate-based salicylic acid biosynthesis within Brassicales 2025 1 1
Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species 2021 1 1
Molecular phylogeny determined using chloroplast DNA inferred a new phylogenetic relationship of Rorippa aquatica (Eaton) EJ Palmer \& Steyermark (Brassicaceae)—lake cress 2014 1 1
Australian pitcher plant (Cephalotus follicularis) 2026 0 0
Decoding plant cell heterogeneity and dynamics across responses, development, to evolution with single-cell technologies 2026 0 0
Genomic cradle for thousands 2026 0 0
Convergent emergence of glucomannan β-galactosyltransferase activity in asterids and rosids 2024 0 0
Carnivorous plants: Unlocking the secrets of peristome geometry in pitcher plants 2023 0 0
Assembly and annotation of a draft genome of the medicinal plant Polygonum cuspidatum 2019 0 0

Study Organism Genus Counts

Papers scanned 42
Detected genera 21
Max papers per genus 7

The chart counts how many papers mention each genus in titles or abstracts. Each genus links to Wikipedia, NCBI Taxonomy, and GBIF.

Genus counts by number of papers

Detected genera
Genus Papers First Latest Wikipedia NCBI Taxonomy GBIF
Cephalotus 7 2017 2026 Wikipedia NCBI GBIF
Drosera 5 2008 2026 Wikipedia NCBI GBIF
Dionaea 5 2020 2026 Wikipedia NCBI GBIF
Nepenthes 5 2023 2026 Wikipedia NCBI GBIF
Arabidopsis 4 2020 2025 Wikipedia NCBI GBIF
Byblis 3 2007 2011 Wikipedia NCBI GBIF
Utricularia 3 2018 2026 Wikipedia NCBI GBIF
Gastrodia 2 2023 2025 Wikipedia NCBI GBIF
Sarracenia 2 2015 2025 Wikipedia NCBI GBIF
Vigna 1 2022 2022 Wikipedia NCBI GBIF
Polygonum 1 2019 2019 Wikipedia NCBI GBIF
Rorippa 1 2014 2014 Wikipedia NCBI GBIF
Quercus 1 2025 2025 Wikipedia NCBI GBIF
Aldrovanda 1 2020 2020 Wikipedia NCBI GBIF
Asarum 1 2025 2025 Wikipedia NCBI GBIF
Brocchinia 1 2025 2025 Wikipedia NCBI GBIF
Capparis 1 2025 2025 Wikipedia NCBI GBIF
Carica 1 2025 2025 Wikipedia NCBI GBIF
Momordica 1 2008 2008 Wikipedia NCBI GBIF
Roridula 1 2025 2025 Wikipedia NCBI GBIF
Solanum 1 2024 2024 Wikipedia NCBI GBIF

Internal Resources

kflab: This repository serves as the main platform for coordinating activities in the Kenji Fukushima Lab. It includes more than code: lab supply logistics, experimental-design discussions, and research-progress updates. New members should create a GitHub account and request an invitation from Kenji Fukushima.