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Open AccessBaseline ctDNA gene alterations as a biomarker of survival after panitumumab and chemotherapy in metastatic colorectal cancer
Certain genetic alterations and right-sided primary tumor location are associated with resistance to anti-epidermal growth factor (EGFR) treatment in metastatic colorectal cancer (mCRC). The phase 3 PARADIGM t...
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Article
Open AccessTransposable elements potentiate radiotherapy-induced cellular immune reactions via RIG-I-mediated virus-sensing pathways
Radiotherapy (RT) plus immunotherapy is a promising modality; however, the therapeutic effects are insufficient, and the molecular mechanism requires clarification to further develop combination therapies. Her...
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Article
Further notice of omics profiles of fecal and oral microbiota change in irritable bowel syndrome patients with diarrhea and symptom exacerbation
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Open AccessOmics profiles of fecal and oral microbiota change in irritable bowel syndrome patients with diarrhea and symptom exacerbation
Irritable bowel syndrome (IBS) is a disorder of gut–brain interaction, including dysregulation of the hypothalamic–pituitary–adrenal axis with salivary cortisol changes. However, the role of gastrointestinal m...
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Article
NOTCH gene alterations in metastatic colorectal cancer in the Nationwide Cancer Genome Screening Project in Japan (SCRUM-Japan GI-SCREEN)
Activated Notch receptor signaling has been implicated in tumor growth and progression in colorectal cancer (CRC). However, the pathogenic relevance of NOTCH gene alterations remains unclear. The aim of this stud...
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Open AccessComprehensive screening for drugs that modify radiation-induced immune responses
Combination therapy based on radiotherapy and immune checkpoint inhibitors (ICIs) was recently reported as effective for various cancers. The radiation-induced immune response (RIIR) is an essential feature in...
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Article
Open AccessMachine learning approaches to predict gestational age in normal and complicated pregnancies via urinary metabolomics analysis
The elucidation of dynamic metabolomic changes during gestation is particularly important for the development of methods to evaluate pregnancy status or achieve earlier detection of pregnancy-related complicat...
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Article
Clinical utility of circulating tumor DNA sequencing in advanced gastrointestinal cancer: SCRUM-Japan GI-SCREEN and GOZILA studies
Comprehensive genomic profiling enables genomic biomarker detection in advanced solid tumors. Here, to evaluate the utility of circulating tumor DNA (ctDNA) genoty**, we compare trial enrollment using ctDNA ...
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Alternative splicing of APOBEC3D generates functional diversity and its role as a DNA mutator
The apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) protein family members have cytidine deaminase activity and can induce cytosine to uracil transition in nucleic acid. The main funct...
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Open AccessComparative sequence analysis of patient-matched primary colorectal cancer, metastatic, and recurrent metastatic tumors after adjuvant FOLFOX chemotherapy
In the era of genome-guided personalized cancer treatment, we must understand chemotherapy-induced genomic changes in tumors. This study evaluated whether adjuvant FOLFOX chemotherapy modifies the mutational p...
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Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis ‘Somei-yoshino’ across the Japanese archipelago
Recent studies have shown that environmental DNA is found almost everywhere. Flower petal surfaces are an attractive tissue to use for investigation of the dispersal of environmental DNA in nature as they are ...
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Article
mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide
The polypeptide SPAR is encoded by a long non-coding RNA, localizes to the late endosome and lysosome, and regulates muscle regeneration by inhibiting mTORC1.
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Open AccessThe Babesia bovis gene and promoter model: an update from full-length EST analysis
Babesia bovis is an apicomplexan parasite that causes babesiosis in infected cattle. Genomes of pathogens contain promising information that can facilitate the development of methods for controlling infections. A...
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Open AccessBioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHac...
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Open AccessProfiling ascidian promoters as the primordial type of vertebrate promoter
CpG islands are observed in mammals and other vertebrates, generally escape DNA methylation, and tend to occur in the promoters of widely expressed genes. Another class of promoter has lower G+C and CpG conten...
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Open AccessThe 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications
The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively ...
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Article
Open AccessEffects of Alu elements on global nucleosome positioning in the human genome
Understanding the genome sequence-specific positioning of nucleosomes is essential to understand various cellular processes, such as transcriptional regulation and replication. As a typical example, the 10-bp ...
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Article
Open AccessWeak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs
Interspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms. A number of studies have compared protein sequences or promoter sequences be...
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Article
Genome-wide demethylation during neural differentiation of P19 embryonal carcinoma cells
Epigenetic regulation including DNA methylation plays an important role in several differentiation processes. We profiled global DNA methylation in the neural differentiation of P19 embryonic carcinoma cells u...
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Article
Complete sequencing and characterization of 21,243 full-length human cDNAs
As a base for human transcriptome and functional genomics, we created the “full-length long Japan” (FLJ) collection of sequenced human cDNAs. We determined the entire sequence of 21,243 selected clones and fou...
