cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000822
title: Drosophila bipectinata genome sequencing project

description: The <i>Drosophila bipectinata<i> genome is being sequenced by the Baylor College of Medicine as part of the modENCODE project to provide comparative sequencing data for the identification of functional DNA elements in the <i>D. melanogaster</i> genome.</i></i>
DOI: 10.26036/cnphis0000823
title: Drosophila elegans genome sequencing project

description: The <i>Drosophila elegans<i> genome is being sequenced by the Baylor College of Medicine as part of the modENCODE project to provide comparative sequencing data for the identification of functional DNA elements in the <i>D. melanogaster</i> genome.</i></i>
DOI: 10.26036/cnphis0000825
title: Drosophila kikkawai genome sequencing project

description: The <i>Drosophila kikkawai<i> genome is being sequenced by the Baylor College of Medicine as part of the modENCODE project to provide comparative sequencing data for the identification of functional DNA elements in the <i>D. melanogaster</i> genome.</i></i>
DOI: 10.26036/cnphis0000826
title: Drosophila rhopaloa genome sequencing project

description: The <i>Drosophla rhopaloa</i> genome is being sequenced by the Baylor College of Medicine as part of the modENCODE project to provide comparative sequencing data for the identification of functional DNA elements in the <i>D. melanogaster</i> genome.
DOI: 10.26036/cnphis0000827
title: Drosophila takahashii genome sequencing project

description: The <i>Drosophila takahashii<i> genome is being sequenced by the Baylor College of Medicine as part of the modENCODE project to provide comparative sequencing data for the identification of functional DNA elements in the <i>D. melanogaster</i> genome.</i></i>
DOI: 10.26036/cnphis0000828
title: Drosophila eugracilis genome sequencing

description: Scope: Monoisolate; Material: Genome; Capture: Whole; Method type: Sequencing The Drosophila eugracilis genome is being sequenced by the Baylor College of Medicine as part of the modENCODE project to provide comparative sequencing data for the identification of functional DNA elements in the D. melanogaster genome
DOI: 10.26036/cnphis0000829
title: Transcriptome Analysis of Silver Carp (Hypophthalmichthys molitrix) by Paired-End RNA Sequencing

description: In this study, we performed de novo transcriptome assembly and analysis of the 17.10 million short-read sequences produced by Illumina paired-end sequencing technology. Using an improved multiple k-mer contig assembling methods coupled with further scaffolding, 85759 sequences were obtained. There were 23044 sequences annotated with 3423 GO terms for 104196 term occurrences and the three corresponding organizing principles. A total of 38200 assembled sequences were involved in 218 predicted KEGG metabolic pathways. We also recovered 41 genes out of 44 genes involving in the biosynthesizing of glutathione and out of which 8 genes were identified having experienced positive selection between silver carp and zebrafish using likelihood ratio test.
DOI: 10.14455/nrct.fas.2018.76
title: เกลือสมุทรสุดวิเศษ : วิถีเกลือ วิถีชุมชน
DOI: 10.14455/nrct.img.2018.381
title: การประยุกต์ใช้เทคนิค Inter-Simple Sequence Repeat (ISSR) เพื่อหาเครื่องหมายโมเลกุลจำเพาะเจาะจงกับกล้วยไม้สกุลหวาย (Dendrobium Sw.) ในประเทศไทยที่มีสารกลุ่ม bibenzyl
DOI: 10.26036/cnphis0000082
title: Exome sequencing of (ITU) Indian Telugu in the UK HapMap population

description: Exome sequencing of (ITU) Indian Telugu in the UK HapMap population. DNA for sequencing was extracted from lymphoblastoid cell line.
DOI: 10.26036/cnphis0000088
title: Whole genome sequencing of (ITU) Indian Telugu in the UK HapMap population

description: Whole genome sequencing of (ITU) Indian Telugu in the UK HapMap population. DNA for sequencing was extracted from lymphoblastoid cell line.
DOI: 10.26036/cnphis0000089
title: Whole genome sequencing of (STU) Sri Lankan Tamil in the UK HapMap population

description: -
DOI: 10.26036/cnphis0000824
title: Drosophila ficusphila genome sequencing project

description: The <i>Drosophila ficusphila</i> genome is being sequenced by the Baylor College of Medicine as part of the modENCODE project to provide comparative sequencing data for the identification of functional DNA elements in the <i>D. melanogaster</i> genome.
DOI: 10.26036/cnphis0000830
title: LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders

description: Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. To date, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we used high-throughput 454 sequencing to generate genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders, based on which we explored the transposable element landscape of salamanders.
DOI: 10.26036/cnphis0000831
title: LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders

description: Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. To date, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we used high-throughput 454 sequencing to generate genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders, based on which we explored the transposable element landscape of salamanders.
DOI: 10.26036/cnphis0000832
title: LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders

description: Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. To date, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we used high-throughput 454 sequencing to generate genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders, based on which we explored the transposable element landscape of salamanders.
DOI: 10.26036/cnphis0000833
title: LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders

description: Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. To date, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we used high-throughput 454 sequencing to generate genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders, based on which we explored the transposable element landscape of salamanders.
DOI: 10.26036/cnphis0000834
title: LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders

description: Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. To date, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we used high-throughput 454 sequencing to generate genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders, based on which we explored the transposable element landscape of salamanders.
DOI: 10.26036/cnphis0000835
title: LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders

description: Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. To date, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we used high-throughput 454 sequencing to generate genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders, based on which we explored the transposable element landscape of salamanders.
DOI: 10.26036/cnphis0000836
title: Drosophila ficusphila Transcriptome or Gene expression

description: This RNAseq data is to support the Drosophila ficusphila genome project at Baylor College of Medicine Human genome Sequencing Center, to provide comparative sequencing data for the identification of functional DNA elements in the D.melanogaster genome. This transcriptome data will be used to annotate gene models in Drosophila ficusphila to aid the comparisons. This part of the larger modENCODE comparative genome project.
DOI: 10.14455/nrct.fas.2018.80
title: ผ้าสร้อยดอกหมากสารคาม
DOI: 10.14455/nrct.img.2018.384
title: หุ่นยนต์ทำความสะอาดชายหาด ฝีมือคนไทย(ภายใต้โครงการ “ปตท.สผ. รักษ์ทะเล รักษ์ชายหาด” )
DOI: 10.14457/cmu.the.2009.738
title: ผลของเชื้อราอาร์บัสคูลาร์มายคอร์ไรซา ต่อต้นกล้ากาแฟอราบิก้า [Coffea arabica L.] เพื่อใช้ผลิตกาแฟในระบบเกษตรอินทรีย์
DOI: 10.14457/cmu.the.2009.739
title: ผลของการตัดช่อดอกต่อการเปลี่ยนแปลงปริมาณคาร์โบไฮเดรตธาตุอาหารในใบ การออกดอกชุดที่สองและคุณภาพผลของลำไย
DOI: 10.26036/cnphis0000096
title: 1000 Plant (1KP) Transcriptomes : The pilot study.

description: 1KP is an international multidisciplinary consortium acquiring large-scale gene sequences for the Viridiplantae (green plants), incorporating at some phylogenetic/taxonomic level nearly all known species from angiosperms to algae.This pilot study is the first 85 species of the &gt;1000 species to be sequenced.
DOI: 10.26036/cnphis0000098
title: Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

description: The gastrointestinal tracts of mammalians are sterile in utero and colonized by microorganisms immediately after delivery. The subsequent development of the infant gut microbiota involves a complex succession of microbes, driven by factors such as gestational age, mode of delivery, antibiotic use, hygiene, geographical zone and type of feeding.
DOI: 10.26036/cnphis0000099
title: RNA-Seq analysis and transcriptome assembly for Blackberry (Rubus sp. Var. Lochness) fruit

description: There is an increasing interest in berries, especially blackberries in the diet, because of recent reports of their health benefits due to their high content of flavonoids. A broad range of genomic tools are available for other Rosaceae species but these tools are still lacking in the Rubus genus, thus limiting gene discovery and the breeding of improved varieties. De novo RNA-seq of blackberry grown under field conditions was performed using Illumina Hiseq 2000. Almost 9 billion nucleotide bases were sequenced in total. Following assembly, 42,062 unigenes were detected. For functional annotation, 33,040 (NR), 32,762 (NT), 21,932 (Swiss-Prot), 20,134 (KEGG), 13,676 (COG), 24,168 (GO) unigenes were annotated using different databases; in total 34,552 annotated unigenes were identified. For protein prediction analysis, the number of coding DNA sequences (CDS) that mapped to the protein database was 32,540. Non redundant (NR), annotation showed that 25,418 genes (77.5%) has the highest similarity with Fragaria vesca subespecies vesca. A reanalysis was undertaken by aligning the reads with this reference genome for a deeper analysis of the transcriptome. In this reanalysis, 67,845 SNP were found, 462 alternative splicing events were analyzed, and the distribution of the reads on the reference chromosomes was established. We demonstrated that de novo assembly, using Trinity and later annotation with Blast using different databases, were complementary to alignment to the reference sequence using SOAPaligner/SOAP2. The Fragaria reference genome belongs to a species of the same family as blackberry (Rosaceae) but to a different genus. Since blackberries are tetraploids, the possibility of artefactual gene chimeras resulting from mis-assembly was tested with one of the genes sequenced by RNAseq, Chalcone Synthase (CHS). cDNAs encoding this protein gene were cloned and sequenced. Primers designed on the assembled sequences accurately distinguished different contigs, at least for the chalcone synthase genes. We prepared and analysed transcriptome data from ripe blackberries, for which prior genomic information was limited. This sequence information will improve the knowledge of this important and healthy fruit, providing an invaluable new tool for biological research.
DOI: 10.26036/cnphis0000837
title: Drosophila rhopaloa Transcriptome or Gene expression

description: This RNAseq data is to support the Drosophila rhopaloa genome project at Baylor College of Medicine Human genome Sequencing Center, to provide comparative sequencing data for the identification of functional DNA elements in the D.melanogaster genome. This transcriptome data will be used to annotate gene models in Drosophila rhopaloa to aid the comparisons. This part of the larger modENCODE comparative genome project.
DOI: 10.26036/cnphis0000838
title: Drosophila biarmipes Transcriptome or Gene expression

description: This RNAseq data is to support the Drosophila biarmipes genome project at Baylor College of Medicine Human genome Sequencing Center, to provide comparative sequencing data for the identification of functional DNA elements in the D.melanogaster genome. This transcriptome data will be used to annotate gene models in Drosophila biarmipes to aid the comparisons. This part of the larger modENCODE comparative genome project.
DOI: 10.26036/cnphis0000839
title: Drosophila bipectinata Transcriptome or Gene expression

description: This RNAseq data is to support the Drosophila bipectinata genome project at Baylor College of Medicine Human genome Sequencing Center, to provide comparative sequencing data for the identification of functional DNA elements in the D.melanogaster genome. This transcriptome data will be used to annotate gene models in Drosophila bipectinata to aid the comparisons. This part of the larger modENCODE comparative genome project.
DOI: 10.26036/cnphis0000840
title: Drosophila elegans Transcriptome or Gene expression

description: This RNAseq data is to support the Drosophila elegans genome project at Baylor College of Medicine Human genome Sequencing Center, to provide comparative sequencing data for the identification of functional DNA elements in the D.melanogaster genome. This transcriptome data will be used to annotate gene models in Drosophila elegans to aid the comparisons. This part of the larger modENCODE comparative genome project.
DOI: 10.26036/cnphis0000841
title: Drosophila eugracilis Transcriptome or Gene expression

description: This RNAseq data is to support the Drosophila eugracilis genome project at Baylor College of Medicine Human genome Sequencing Center, to provide comparative sequencing data for the identification of functional DNA elements in the D.melanogaster genome. This transcriptome data will be used to annotate gene models in Drosophila eugracilis to aid the comparisons. This part of the larger modENCODE comparative genome project.
DOI: 10.26036/cnphis0000842
title: Drosophila takahashii Transcriptome or Gene expression

description: This RNAseq data is to support the Drosophila takahashii genome project at Baylor College of Medicine Human genome Sequencing Center, to provide comparative sequencing data for the identification of functional DNA elements in the D.melanogaster genome. This transcriptome data will be used to annotate gene models in Drosophila takahashii to aid the comparisons. This part of the larger modENCODE comparative genome project.
DOI: 10.26036/cnphis0000843
title: Heliconius melpomene aglaope Variation

description: Heliconius butterflies are studied because their striking wing patterns show mimicry between different species in different locations. This sequence will be compared to our Heliconius melpomene reference sequence to identify the genetic changes underlying the differences and similarities in these wing patterns.
DOI: 10.26036/cnphis0000844
title: Heliconius cydno alithea Variation

description: Heliconius butterflies are studied because their striking wing patterns show mimicry between different species in different locations. This sequence will be compared to our Heliconius melpomene reference sequence to identify the genetic changes underlying the differences and similarities in these wing patterns.
DOI: 10.14457/cmu.the.2009.740
title: สมรรถนะของการเลี้ยงลูกและผลผลิตของแม่กระบือรีดนมพันธุ์เมซานา
DOI: 10.14457/cmu.the.2009.741
title: วาทกรรมของมิเชล ฟูโกต์ ต่อสถานภาพและบทบาทสตรีไทย ตามที่เสนอในนวนิยายของ คุณหญิงวิมล ศิริไพบูลย์
DOI: 10.14457/cmu.the.2009.742
title: ผลของระดับปุ๋ยไนโตรเจน ฟอสฟอรัส และโพแทสเซียม ต่อการเจริญเติบโต ผลผลิตและคุณภาพผลผลิตของพริกหนุ่มในดินชุดสันทราย
DOI: 10.14457/cmu.the.2009.743
title: สภาวะปริทันต์ของหญิงไทยวัยหมดประจำเดือน ที่มีความหนาแน่นของกระดูกต่ำ
DOI: 10.14457/cmu.the.2009.744
title: ผลของการโคชต่อการปฏิบัติของบิดามารดาในการดูแลเด็กป่วยโรคปอดอักเสบ
DOI: 10.14457/cmu.the.2009.746
title: เทคนิคการลดสัญญาณรบกวนในภาพคอมพิวเตดโทโมกราฟี ที่ได้จากการลดปริมาณรังสี
DOI: 10.14457/cmu.the.2009.747
title: ผลของการฉายรังสีแกมมาต่อการเจริญเติบโตของหญ้านวลน้อยและหญ้ามาเลเซีย
DOI: 10.14457/cmu.the.2009.748
title: แผนการผลิตพืชบนพื้นที่สูงที่เหมาะสมเชิงเศรษฐกิจและสิ่งแวดล้อมในระดับฟาร์ม ลุ่มน้ำแม่ศึก อำเภอแม่แจ่ม จังหวัดเชียงใหม่
DOI: 10.14457/cmu.the.2009.749
title: สัมพันธภาพในความแตกต่าง
DOI: 10.26036/cnphis0000095
title: Richness of human gut microbiome correlates with metabolic markers

description: We are facing a global metabolic health crisis provoked by an obesity epidemic. Here we report the human gut microbial composition in a population sample of 123 non-obese and 169 obese Danish individuals. We find two groups of individuals that differ by the number of gut microbial genes and thus gut bacterial richness. They harbour known and previously unknown bacterial species at different proportions; individuals with a low bacterial richness (23% of the population) are characterized by more marked overall adiposity, insulin resistance and dyslipidaemia and a more pronounced inflammatory phenotype when compared with high bacterial richness individuals. The obese individuals among the former also gain more weight over time. Only a few bacterial species are sufficient to distinguish between individuals with high and low bacterial richness, and even between lean and obese. Our classifications based on variation in the gut microbiome identify subsets of individuals in the general white adult population who may be at increased risk of progressing to adiposity-associated co-morbidities.
DOI: 10.26036/cnphis0000100
title: Gut and Oral Microbiome Dysbiosis in Rheumatoid Arthritis

description: Bacterial infection has long been implicated with rheumatoid arthritis (RA), but a systematic analysis of the probiotic and pathogenic microbiome in RA has been lacking. It is not clear whether and how the gut or oral microbial community is compositionally and functionally altered in RA, and whether and how the microbiota at different body sites overlap. Here we perform whole-genome shotgun sequencing for fecal, dental and salivary samples from a large cohort of RA patients, analyze metagenomic linkage groups to construct an RA classifier.
DOI: 10.26036/cnphis0000101
title: The 3000 Rice Genomes Project

description: Background Rice, Oryza sativa L., is the staple food for half the world’s population. By 2030, rice production must increase by at least 50% to keep pace with population growth. Accelerated genetic gains in rice improvement are needed to mitigate the effects of climate change and loss of arable land and to ensure global food supply. Results Here, we briefly report an international effort on resequencing a core collection of 3000 rice accessions from 89 countries, and its deposition into GigaDB.org (http://dx.doi.org/10.5524/200001) and SRA as a global public good. The 3,000 sequenced rice genomes had an average sequencing depth of 14X, average genome coverages and mapping rates of 94.0% and 92.5%, respectively. About 18.9 million SNPs in rice were discovered when aligned to the reference genome of the temperate japonica variety, Nipponbare. Phylogenetic analyses based on SNP data confirmed differentiation of the O. sativa gene pool into 5 varietal groups – indica, aus/boro, basmati/sadri, tropical japonica and temperate japonica. Conclusions This data provides a foundation for large-scale discovery of novel alleles for important rice phenotypes using various bioinformatics and/or genetic approaches. It also serves to understand at a higher level of detail the genomic diversity within O. sativa. With the release of the sequencing data, the project calls for the global rice community to take advantage of this data as a foundation for establishing a global, public rice genetic/genomic database and information platform for advancing rice breeding technology for future rice improvement. Purified seeds of the sequenced accessions are (or will be available) from the IRGC or CNCGB as genetic stocks. Information on obtaining seeds from the IRGC can be found at this link (http://irri.org/our-work/seeds) and from the CNCGB can be found at this site (http://icgr.caas.net.cn/cgris_english.html).
DOI: 10.26036/cnphis0000102
title: A Catalogue of the Mouse Gut Metagenome

description: The importance of the gut microbiota for regulation of whole body metabolism, energy homeostasis, development of the immune system and even complex behavioural traits is well documented. The acquisition of comprehensive gene catalogues of the human gut metagenome using “next generation sequencing” has immensely advanced our insight into the complex metagenome-host genome interaction and the connection between common human diseases and the gut microbiota. Causal links are difficult to establish in humans, and therefore, mice still serve as important models for functional studies. We used HiSeq2000-based whole metagenome sequencing to establish a catalogue of 2.6 million non-redundant microbial genes from faecal samples of 184 mice representing different strains, fed different diets, obtained from different providers, and kept in different housing laboratories to secure high diversity and representation. Similar to the human gut microbiome, more than 99% of the genes in the catalogue were bacterial, suggesting that the mouse microbiota overall comprises between 800 and 900 bacterial species. A core mouse gut microbiome was defined at the genus level comprising 60 genera, 25 of which were shared with the core genera in the human gut microbiome. Although the mouse gut microbiome was functionally similar to its human counterpart, sharing 79.9% of its KEGG orthologous groups, only 4.0% of the mouse gut microbial genes were shared with those identified in human gut microbiome, emphasising the need for a specific mouse catalogue. We observed marked differences regarding provider, housing laboratory, strains, gender and feed, emphasizing the need for carefully controlled experimental conditions and caution comparing data from different laboratories. As we have accounted for these factors in creating the catalogue, it provides a useful reference for future studies, including studies using short reads for comprehensive analyses of the mouse gut microbiome.
DOI: 10.26036/cnphis0000103
title: Gut microbiome development along the colorectal adenoma-carcinoma sequence

description: Colorectal cancer, a commonly diagnosed cancer in the elderly, often develops slowly from benign polyps called adenoma. The gut microbiota, with its critical roles in nutrient metabolism and immune modulation, is believed to be directly involved in colorectal carcinogenesis. The identity and functional capacity of the adenoma- or carcinoma-related gut microbe(s), however, have not been surveyed in a comprehensive manner. Here we perform metagenomewide association study (MGWAS) on stools from healthy controls, advanced adenoma and carcinoma patients, revealing gene markers from over 100 bacterial strains enriched in each group.
DOI: 10.26036/cnphis0000104
title: 1000 Plant (1KP) Transcriptomes

description: 1KP is an international multidisciplinary consortium acquiring large-scale gene sequences for the Viridiplantae (green plants), incorporating at some phylogenetic/taxonomic level nearly all known species from angiosperms to algae.