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List of works by Takashi Gojobori

A comparison of the molecular clock of hepatitis C virus in the United States and Japan predicts that hepatocellular carcinoma incidence in the United States will increase over the next two decades ⬇️

scientific article

A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing

scientific article

A genome-wide survey of the genes for planar polarity signaling or convergent extension-related genes in Ciona intestinalis and phylogenetic comparisons of evolutionary conserved signaling components

scientific article published in October 2003

A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes

scientific article published on 10 March 2004

A new database (GCD) on genome composition for eukaryote and prokaryote genome sequences and their initial analyses

scientific article

A non-sulfated chondroitin stabilizes membrane tubulation in cnidarian organelles

scientific article

A polymerase chain reaction-based method for cloning novel members of a gene family using a combination of degenerate and inhibitory primers

scientific article published in May 2002

A prioritization analysis of disease association by data-mining of functional annotation of human genes

scientific article

A reduction in selective immune pressure during the course of chronic hepatitis C correlates with diminished biochemical evidence of hepatic inflammation

scientific article published on 15 December 2006

A web-based interactive developmental table for the ascidian Ciona intestinalis, including 3D real-image embryo reconstructions: I. From fertilized egg to hatching larva

scientific article

Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda

scientific article

Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae).

scientific article

Alternative splicing in human transcriptome: functional and structural influence on proteins.

scientific article

An evolutionary origin and selection process of goldfish

scientific article

Basin-scale seasonal changes in marine free-living bacterioplankton community in the Ofunato Bay

article

Biased biological functions of horizontally transferred genes in prokaryotic genomes

scientific article

Binary classification of protein molecules into intrinsically disordered and ordered segments ⬇️

scientific article published on June 22, 2011

Brachyury-downstream gene sets in a chordate, Ciona intestinalis: integrating notochord specification, morphogenesis and chordate evolution

scientific article published in January 2008

Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity

scientific article

CIBEX: center for information biology gene expression database

scientific article published on October 2003

CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies

scientific article

Cancer-related mutations in BRCA1-BRCT cause long-range structural changes in protein-protein binding sites: a molecular dynamics study

scientific article published in January 2007

Cilium evolution: identification of a novel protein, nematocilin, in the mechanosensory cilium of Hydra nematocytes

scientific article published on 17 July 2008

Clone identification in Japanese flowering cherry (<i>Prunus</i> subgenus <i>Cerasus</i>) cultivars using nuclear SSR markers ⬇️

scientific article published on November 1, 2012

Cloning and functional analysis of ascidian Mitf in vivo: insights into the origin of vertebrate pigment cells

scientific article published in December 2003

Coevolution of axon guidance molecule Slit and its receptor Robo

scientific article

Comparative analysis of gene expression for convergent evolution of camera eye between octopus and human

scientific article

Comparative analysis of the base biases at the gene terminal portions in seven eukaryote genomes

scientific article

Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens

scientific article

Comparative genome analyses of nervous system-specific genes

scientific article published on 20 December 2005

Comparative genome analysis of three eukaryotic parasites with differing abilities to transform leukocytes reveals key mediators of Theileria-induced leukocyte transformation

scientific article

Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine-Dalgarno sequence in prokaryotes

scientific article

Comparative genomics of bidirectional gene pairs and its implications for the evolution of a transcriptional regulation system

scientific article

Comparative miRNAs analysis of Two contrasting broccoli inbred lines with divergent head-forming capacity under temperature stress

scientific article published in December 2015

Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence

scientific article (publication date: 24 June 2003)

Comparative study of flux redistribution of metabolic pathway in glutamate production by two coryneform bacteria

scientific article published in March 2005

Comparison of gene expression profile of epiretinal membranes obtained from eyes with proliferative vitreoretinopathy to that of secondary epiretinal membranes

scientific article

Computational analysis and functional expression of ancestral copepod luciferase

scientific article published on 23 July 2013

Corrigendum: The genome of Chenopodium quinoa

scientific article published in Nature

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

scientific article published on 8 January 2007

DDBJ dealing with mass data produced by the second generation sequencer

scientific article

DDBJ in preparation for overview of research activities behind data submissions.

scientific article

DDBJ launches a new archive database with analytical tools for next-generation sequence data

scientific article

DDBJ progress report

scientific article

DDBJ working on evaluation and classification of bacterial genes in INSDC

scientific article

DESM: portal for microbial knowledge exploration systems

scientific article

Databases of the marine metagenomics

scientific article published on 28 October 2015

Degeneration after sexual differentiation in hydra and its relevance to the evolution of aging

scientific article

Detecting linkage between a trait and a marker in a random mating population without pedigree record

scientific article

Detection of apoptosis during planarian regeneration by the expression of apoptosis-related genes and TUNEL assay

scientific article

Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors

scientific article

Different Endosymbiotic Interactions in Two Hydra Species Reflect the Evolutionary History of Endosymbiosis

scientific article published on 19 June 2016

Differential evolutionary rates of duplicated genes in protein interaction network

scientific article published on 17 August 2006

Dissecting planarian central nervous system regeneration by the expression of neural-specific genes

scientific article published in April 2002

Distribution and effects of nonsense polymorphisms in human genes

scientific article

Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes

scientific article

Dopamine receptor genes and evolutionary differentiation in the domestication of fighting cocks and long-crowing chickens

scientific article

Dynamic evolution of endogenous retrovirus-derived genes expressed in bovine conceptuses during the period of placentation

scientific article published on January 2013

Dynamic evolution of translation initiation mechanisms in prokaryotes

scientific article

Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts

scientific article

Editor’s Report for Genome Biology and Evolution, 2013.

scientific article published on 7 December 2013

Endogenous non-retroviral RNA virus elements in mammalian genomes

scientific article

Estimation of ancestral gene set of bilaterian animals and its implication to dynamic change of gene content in bilaterian evolution

scientific article

Eukaryotic nuclear structure explains the evolutionary rate difference of ribosome export factors

scientific article

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees

scientific article

Evolution of Pacific Ocean and the Sea of Japan populations of the gobiid species, Pterogobius elapoides and Pterogobius zonoleucus, based on molecular and morphological analyses

scientific article

Evolution of bioluminescence in marine planktonic copepods

scientific article

Evolution of complex structures: minicollagens shape the cnidarian nematocyst

scientific article published on 03 August 2008

Evolution of metabolic networks by gain and loss of enzymatic reaction in eukaryotes

scientific article published on 15 December 2005

Evolution of vitamin B6 (pyridoxine) metabolism by gain and loss of genes

scientific article published on 13 October 2004

Evolutionarily conserved transcription factor Apontic controls the G1/S progression by inducing cyclin E during eye development

scientific article

Evolutionary Transitions of MicroRNA-Target Pairs

scientific article

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

scientific article published on 18 June 2013

Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus

scientific article (publication date: 24 June 2011)

Evolutionary history of dog rabies in Brazil ⬇️

scientific article published on October 6, 2010

Evolutionary origin of sex-related genes in the mouse brain

scientific article published on 17 July 2007

Evolutionary patterns of recently emerged animal duplogs

scientific article

Evolutionary process of amino acid biosynthesis in Corynebacterium at the whole genome level

scientific article

Exploration and grading of possible genes from 183 bacterial strains by a common protocol to identification of new genes: Gene Trek in Prokaryote Space (GTPS).

scientific article

Eye-like ocelloids are built from different endosymbiotically acquired components

scientific article

FARNA: knowledgebase of inferred functions of non-coding RNA transcripts

scientific article published on 24 October 2016

FGFR-related gene nou-darake restricts brain tissues to the head region of planarians

scientific article published in October 2002

Finding Nemo's Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula

article

Finding Nemo’s Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula

article

Function and evolutionary origin of unicellular camera-type eye structure

scientific article published in 2015

G-compass: a web-based comparative genome browser between human and other vertebrate genomes

scientific article published on 21 October 2009

GBE Editor's Report.

scientific article published on 19 November 2010

GBE Editor’s Report.

scientific article published on 31 October 2012

Gene cluster analysis method identifies horizontally transferred genes with high reliability and indicates that they provide the main mechanism of operon gain in 8 species of gamma-Proteobacteria

scientific article published on 21 December 2006

Gene dosage imbalance of human chromosome 21 in mouse embryonic stem cells differentiating to neurons

scientific article published on 27 April 2011

Gene expression profile of fibrovascular membranes from patients with proliferative diabetic retinopathy

scientific article

Genetic polymorphism of the swine major histocompatibility complex (SLA) class�I genes, SLA-1, -2 and -3 ⬇️

scientific article published on November 7, 2003

Genetic stability of human T lymphotropic virus type I despite antiviral pressures by CTLs

scientific article published on May 2007

Genome and transcriptome analysis of the food-yeast Candida utilis

scientific article (publication date: 2012)

Global Ramifications of Dust and Sandstorm Microbiota

scientific article published in 2018

H-DBAS: alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational

scientific article

H-DBAS: human-transcriptome database for alternative splicing: update 2010

scientific article

H-InvDB in 2009: extended database and data mining resources for human genes and transcripts

scientific article

H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery

scientific article

Haemophilus influenzae

scientific article published in March 2003

Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network

scholarly article

Human genome network platform: a resource for TFRN analysis

scientific article published in January 2014

Identification of neurotransmitter receptor genes under significantly relaxed selective constraint by orthologous gene comparisons between humans and rodents

scientific article published in November 2002

In silico chromosome staining: reconstruction of Giemsa bands from the whole human genome sequence

scientific article

In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters.

scientific article published on 22 May 2018

Increasing genetic diversity of hepatitis C virus in haemophiliacs with human immunodeficiency virus coinfection

scientific article published in September 2007

Induction of a noggin-like gene by ectopic DV interaction during planarian regeneration

scientific article published in October 2002

Infectious endogenous retroviruses in cats and emergence of recombinant viruses

scientific article

Influences of diurnal sampling bias on fixed-point monitoring of plankton biodiversity determined using a massively parallel sequencing-based technique

scientific article published on 14 October 2015

Innexin gap junctions in nerve cells coordinate spontaneous contractile behavior in Hydra polyps

scientific article published on 07 January 2014

Integrated database (2): Data oriented approach to genome network informatics

scientific article

Integrative annotation of 21,037 human genes validated by full-length cDNA clones

scientific article

Introduction to the Special Series

scientific article published on 6 October 2011

Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB).

scientific article

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs

scientific article

Length variation of CAG/CAA triplet repeats in 50 genes among 16 inbred mouse strains

scientific article

Long-range neural and gap junction protein-mediated cues control polarity during planarian regeneration

scientific article

Long-range neural and gap junction protein-mediated cues control polarity during planarian regeneration

Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs

scientific article published on 05 October 2008

Low genetic diversities of rabies virus populations within different hosts in Brazil

scientific article

Mapping human genetic diversity in Asia

scientific article

Mapping of chimpanzee full-length cDNAs onto the human genome unveils large potential divergence of the transcriptome

scientific article published on 20 April 2007

Marine Metagenome as A Resource for Novel Enzymes

scientific article

Marine metagenomics as a source for bioprospecting

scientific article (publication date: December 2015)

Maser: one-stop platform for NGS big data from analysis to visualization

scientific article published in January 2018

Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis

scientific article

Metagenome-based diversity analyses suggest a strong locality signal for bacterial communities associated with oyster aquaculture farms in Ofunato Bay

article

Metagenomic studies of the Red Sea.

scientific article published on 22 October 2015

Methods for incorporating the hypermutability of CpG dinucleotides in detecting natural selection operating at the amino acid sequence level

scientific article published on 06 July 2009

Microarray analysis of embryonic retinoic acid target genes in the ascidian Ciona intestinalis

scientific article

Midline governs axon pathfinding by coordinating expression of two major guidance systems

scientific article published on May 2009

Molecular characterization of the Pb recombination hotspot in the mouse major histocompatibility complex class II region

scientific article published on August 2002

Molecular evolutionary analyses implicate injection treatment for schistosomiasis in the initial hepatitis C epidemics in Japan

scientific article published on January 2005

Molecular hierarchy in neurons differentiated from mouse ES cells containing a single human chromosome 21.

scientific article

Multiple plastids collected by the dinoflagellate Dinophysis mitra through kleptoplastidy

scientific article published on 18 November 2011

Nematogalectin, a nematocyst protein with GlyXY and galectin domains, demonstrates nematocyte-specific alternative splicing in Hydra

scientific article

No Evidence for Temperature-Dependence of the COVID-19 Epidemic

scientific article published on 31 March 2020

Novel algorithm for automated genotyping of microsatellites

scientific article

Obituary: Masatoshi Nei (1931–2023) ⬇️

scholarly article published in 2023

Optimized ancestral state reconstruction using Sankoff parsimony

scientific article

Origin and evolutionary process of the CNS elucidated by comparative genomics analysis of planarian ESTs

scientific article published on 24 June 2003

Origins of Japanese flowering cherry (Prunus subgenus Cerasus) cultivars revealed using nuclear SSR markers

scientific article (publication date: 30 January 2014)

PATHcre8: A Tool That Facilitates the Searching for Heterologous Biosynthetic Routes

scientific article published on 16 November 2020

Patterns of nucleotide substitution in pseudogenes and functional genes

article

Phylogenetic analysis of the complete genome of 18 Norwalk-like viruses

scientific article published in August 2002

Pigment cell lineage-specific expression activity of the ascidian tyrosinase-related gene

scientific article

Prediction of protein-destabilizing polymorphisms by manual curation with protein structure

scientific article

Radical amino acid change versus positive selection in the evolution of viral envelope proteins

scientific article published on 24 August 2006

Rapid evolution of major histocompatibility complex class I genes in primates generates new disease alleles in humans via hitchhiking diversity

scientific article

Rate of evolution in brain-expressed genes in humans and other primates

scientific article published in February 2007

Search for the evolutionary origin of a brain: planarian brain characterized by microarray

scientific article published on 2 April 2003

Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis

article

Seasonal changes in the communities of photosynthetic picoeukaryotes in Ofunato Bay as revealed by shotgun metagenomic sequencing

article

Selection pressure on human STR loci and its relevance in repeat expansion disease

scientific article published on 11 June 2016

Single-cell technologies in environmental omics

scientific article published on 13 October 2015

Speciation of two gobioid species, Pterogobius elapoides and Pterogobius zonoleucus revealed by multi-locus nuclear and mitochondrial DNA analyses

scientific article

Specific expression of Gsta4 in mouse cochlear melanocytes: a novel role for hearing and melanocyte differentiation

scientific article

Strong positive selection and recombination drive the antigenic variation of the PilE protein of the human pathogen Neisseria meningitidis

scientific article

Substitution rate and structural divergence of 5'UTR evolution: comparative analysis between human and cynomolgus monkey cDNAs

scientific article

Systems medicine and integrated care to combat chronic noncommunicable diseases

scientific article

TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB.

scientific article

TOWARDS COORDINATED INTERNATIONAL SUPPORT OF CORE DATA RESOURCES FOR THE LIFE SCIENCES

scientific article (publication date: 23 February 2017)

TP Atlas: integration and dissemination of advances in Targeted Proteins Research Program (TPRP)—structural biology project phase II in Japan ⬇️

scientific article published on May 29, 2012

Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay

article

The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments ⬇️

scientific article

The First Symbiont-Free Genome Sequence of Marine Red Alga, Susabi-nori (Pyropia yezoensis) ⬇️

scientific article published on March 11, 2013

The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions.

scientific article

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

scientific article

The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms

scientific article

The Promoter Signatures in Rice LEA Genes Can Be Used to Build a Co-expressing LEA Gene Network

article

The Rice Annotation Project Database (RAP-DB): 2008 update

scientific article

The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information

scientific article

The Temporal Sequence of the Mammalian Neocortical Neurogenetic Program Drives Mediolateral Pattern in the Chick Pallium ⬇️

scientific article published on March 15, 2012

The dynamic genome of Hydra

scientific article

The evolutionary emergence of cell type-specific genes inferred from the gene expression analysis of Hydra

scholarly article

The evolutionary origin of long-crowing chicken: its evolutionary relationship with fighting cocks disclosed by the mtDNA sequence analysis

scientific article

The evolutionary position of nematodes

scientific article published on 8 April 2002

The evolutionary relationship between gene duplication and alternative splicing

scientific article published on 12 September 2008

The evolutionary study of small RNA-directed gene silencing pathways by investigating RNase III enzymes

scientific article published on 31 January 2009

The expression of neural-specific genes reveals the structural and molecular complexity of the planarian central nervous system

scientific article

The genome sequence and structure of rice chromosome 1.

scientific article published in November 2002

The genome stability in Corynebacterium species due to lack of the recombinational repair system ⬇️

scientific article published on October 23, 2003

The mitochondrial genome of the pufferfish, Fugu rubripes, and ordinal teleostean relationships

scientific article published in August 2002

The origin and evolution of porcine reproductive and respiratory syndrome viruses

scientific article

The transcript repeat element: the human Alu sequence as a component of gene networks influencing cancer

scientific article published on August 2010

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

scientific article

Tissue- and stage-dependent dosage compensation on the neo-X chromosome in Drosophila pseudoobscura

scientific article published on 3 December 2013

Towards BioDBcore: a community-defined information specification for biological databases

scientific article

Towards BioDBcore: a community-defined information specification for biological databases

scientific article (publication date: 2011)

Transcriptional interferences in cis natural antisense transcripts of humans and mice

scientific article

Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions

scientific article

Two-step evolution of endosymbiosis between hydra and algae

scientific article

V-GAP: Viral genome assembly pipeline

scientific article

VaProS: a database-integration approach for protein/genome information retrieval

scientific article published on 23 December 2016

VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts

scientific article published on 25 October 2008

Welcome to Genome Biology and Evolution

scientific article published on 5 May 2009

Where is the origin of the Japanese gamecocks?

scientific article published in October 2003

Whole genome association study of rheumatoid arthritis using 27 039 microsatellites

scientific article

Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates

scientific article

Zuckerkandl Prize

scientific article published in February 2002

big data: The future of biocuration

scientific article

cimp1, a novel astacin family metalloproteinase gene from East African cichlids, is differentially expressed between species during growth

scientific article published on 27 April 2005

magp4 gene may contribute to the diversification of cichlid morphs and their speciation

scientific article published on 6 March 2006

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