Filters








27 Hits in 9.5 sec

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

Marina Lizio, Jayson Harshbarger, Imad Abugessaisa, Shuei Noguchi, Atsushi Kondo, Jessica Severin, Chris Mungall, David Arenillas, Anthony Mathelier, Yulia A. Medvedeva, Andreas Lennartsson, Finn Drabløs (+13 others)
2016 Nucleic Acids Research  
We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives.  ...  We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization  ...  ACKNOWLEDGEMENTS The authors would like to thank all of the members in the FANTOM consortium for fruitful collaboration.  ... 
doi:10.1093/nar/gkw995 pmid:27794045 pmcid:PMC5210666 fatcat:5z6fqqnewbbi7a5mwaipsgmi44

The Use and Abuse of -Omes [chapter]

Sonja J. Prohaska, Peter F. Stadler
2011 Msphere  
In spite of the great success stories ofomics projects over the last decade much remains to be understood, not only at the technological but also at the conceptual level.  ...  The diverse fields of -omics research share a common logical structure combining a cataloging effort for a particular class of molecules or interactions, the underlying -ome, and a quantitative aspect  ...  In distinction from genomes, transcriptomes vary between cell types, developmental state, and in dependence of environmental stimuli.  ... 
doi:10.1007/978-1-61779-027-0_8 pmid:21370084 fatcat:2qh2chwz5vbq5k4jgn6vyaugjm

Integrative mapping of the dog epigenome: reference annotation for comparative inter-tissue and cross-species studies [article]

Keun Hong Son, Mark Borris Docdoc Aldonza, A-Reum Nam, Kang-Hoon Lee, Jeong-Woon Lee, Kyung-Ju Shin, Keunsoo Kang, Je-Yoel Cho
2022 bioRxiv   pre-print
Through the integrative next generation sequencing of transcriptomes paired with histone marks and DNA methylome profiling of 11 adult tissue types, implemented in a cross-species approach, we generated  ...  Ultimately, we delineated conserved epigenomic changes at the tissue- and species-specific resolutions.  ...  Acknowledgement We thank the members of Je-Yoel Cho lab for insightful discussions and technical aid during sample collection, Jong-Koo Kang for facilitating the donation program at College of Veterinary  ... 
doi:10.1101/2022.07.22.501075 fatcat:v2qxqne24ng6nic25u2o7gq46i

Approaches to Identify and Characterise the Post-Transcriptional Roles of lncRNAs in Cancer

Jean-Michel Carter, Daniel Aron Ang, Nicholas Sim, Andrea Budiman, Yinghui Li
2021 Non-Coding RNA  
The sheer diversity of mechanisms requires diverse resources and methods that have been developed and refined over the past decade.  ...  We provide an overview of computational resources as well as proven low-to-high throughput techniques to enable identification and characterisation of lncRNAs in their complex interactive contexts.  ...  Conflicts of Interest: The authors declare no conflicts of interest.  ... 
doi:10.3390/ncrna7010019 pmid:33803328 pmcid:PMC8005986 fatcat:lzlrqxk6cfgkff3kqawy6zdwvy

Detecting and Comparing Non-Coding RNAs in the High-Throughput Era

Giovanni Bussotti, Cedric Notredame, Anton Enright
2013 International Journal of Molecular Sciences  
of new methods to align RNAs and the analysis of high-throughput data.  ...  In recent years there has been a growing interest in the field of non-coding RNA.  ...  Acknowledgments The authors wish to acknowledge Roderic Guigó for the helpful comments and suggestions.  ... 
doi:10.3390/ijms140815423 pmid:23887659 pmcid:PMC3759867 fatcat:nl7u3xv3irdp3kyrisfwd5aize

The mouse genome

J. L. Guenet
2005 Genome Research  
In the same way, and as another consequence of the sequencing, the discovery of many single nucleotide polymorphisms and the development of new tools and resources, like the Collaborative Cross, will contribute  ...  in the mouse genome.  ...  It is also dedicated to the scientists at Harwell and Bar Harbor who gave generously of their time to teach me the basics of Mouse Genetics.  ... 
doi:10.1101/gr.3728305 pmid:16339371 fatcat:4ccwkesopzezzlzbwyigcr55rq

CellO: Comprehensive and hierarchical cell type classification of human cells with the Cell Ontology

Matthew N. Bernstein, Zhongjie Ma, Michael Gleicher, Colin N. Dewey
2020 iScience  
Cell type annotation is a fundamental task in the analysis of single-cell RNA-sequencing data.  ...  CellO's comprehensive training set enables it to run out of the box on diverse cell types and achieves competitive or even superior performance when compared to existing state-of-the-art methods.  ...  Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. Nucleic Acids Res. 45, D737-D743. Ma, F., and Pellegrini, M. (2020).  ... 
doi:10.1016/j.isci.2020.101913 pmid:33364592 pmcid:PMC7753962 fatcat:i4sqfiad2naslno73ohm4sathy

Contents list

2018 Soft Matter  
Each of the 55 IRCS carries up to seven SEG/Pas chromosomal segments with an average size of 13.4 Mb, totalizing 1.26% of the genome. The complete series covers 38% of the SEG/Pas genome.  ...  This study demonstrates that genetic control of bone shape can be efficiently dissected in the mouse using appropriate tools.  ...  high-resolution DNA tiling arrays (ChIP-chip).  ... 
doi:10.1039/c8sm90107d fatcat:tko5byj5izccvgfzmdsssx4mgm

Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish [article]

Damir Baranasic, Matthias Hoertenhuber, Piotr Balwierz, Tobias Zehnder, Abdul Kadir Mukarram, Chirag Nepal, Csilla Varnai, Yavor Hadzhiev, Ada Jimenez-Gonzalez, Nan Li, Joseph W. Wragg, Fabio D'Orazio (+40 others)
2021 bioRxiv   pre-print
developmental genomics to mammals.  ...  utility in experimental design.  ...  Acknowledgements Acknowledgements: We thank Max Haussler at UCSC, and Daniel Zerbino at EBI for facilitating access of DANIO-CODE track hubs in the UCSC and Ensembl genome browsers respectively.  ... 
doi:10.1101/2021.08.09.454869 fatcat:q3s6ty662zcvtcderzcstiazqe

Abstracts from the Human Genome Meeting 2018

2018 Human Genomics  
Acknowledgements Part of this research has been conducted using the UK Biobank Resource (application reference no. 19664).  ...  A14 Molecular Biological Elucidation of in vitro Spermatogenesis by Transcriptome Analysis Takeru Abe 1,3 , Hajime Nishimura 3 , Kazuaki Kojima 1 , Hiroyuki Sanjo 2 , Takuya Sato 1 , Harukazu Suzuki  ...  Results The sixth edition of the FANTOM project (FANTOM6) aims to systematically elucidate the function of lncRNAs in human by subjecting them to high-throughput perturbations in multiple cell types followed  ... 
doi:10.1186/s40246-018-0138-6 fatcat:nl6xhsuchzgbxik4pjwjvbbkie

HGM 2010 Programme / Abstract

2010 The HUGO Journal  
The identification of an EYS mutation in a dog affected with retinal progressive atrophy would provide a useful model for establishing future therapies for retinitis pigmentosa.  ...  Conclusion: Heterozygous patients in the two families studied may carry an intronic EYS mutation causing exon skipping.  ...  MIR@NT@N is a userfriendly web resource freely available at http://maia.genouest.org/demo/ Massive parallel high-throughput sequencing is now widely used to analyze the transcriptome or interactome at  ... 
doi:10.1007/s11568-010-9143-0 fatcat:oykxd6u7snfi5o7m6tst7wi6yq

Heart Enhancers: Development and Disease Control at a Distance

Xuefei Yuan, Ian C. Scott, Michael D. Wilson
2021 Frontiers in Genetics  
Recent synergistic advances in functional genomic technologies, combined with the developmental biology toolbox, have resulted in unprecedented genome-wide annotation of heart enhancers and their target  ...  Starting with early studies of vertebrate heart enhancers and ending with state-of-the-art genome-wide enhancer discovery and testing, we will review how studying heart enhancers in metazoan species has  ...  ACKNOWLEDGMENTS We apologize to the authors whose work could not be covered or thoroughly discussed in this review due to space limitations.  ... 
doi:10.3389/fgene.2021.642975 pmid:33777110 pmcid:PMC7987942 fatcat:oonhtriionbslgn5kezjnvpf44

Tissue-specific profiling reveals distinctive regulatory architectures for ubiquitous, germline and somatic genes [article]

Jacques Serizay, Yan Dong, Jurgen Janes, Michael A Chesney, Chiara Cerrato, Julie Ahringer
2020 bioRxiv   pre-print
Our results demonstrate fundamental differences in regulatory architectures of germline-active and somatic tissue-specific genes and provide a key resource for future studies.  ...  Despite increasingly detailed knowledge of gene expression patterns, the regulatory architectures that drive them are not well understood.  ...  Acknowledgments We thank all the members of the Ahringer lab and particularly F. Carelli and A. Frapporti for fruitful discussions and comments on the manuscript. We thank A. Appert and K.  ... 
doi:10.1101/2020.02.20.958579 fatcat:3rvq6zrkajdptm7fsqr6a63rle

Gramene (rice and other grasses database) [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
In large mammals, the males generally have more offspring than the females.  ...  PAX8 seems to be required for the differentiation of endoderm primordia into thyroxin-producing follicular cells. Goiterlike diseases are known in the majority of mammals.  ...  Its homologs are present in prokaryotes as well as in the mitochondria of yeast, insects, and mammals.  ... 
doi:10.1007/978-1-4020-6754-9_7111 fatcat:dsqojxeco5gwhgpgdcm22jb33y

Gout [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
In large mammals, the males generally have more offspring than the females.  ...  PAX8 seems to be required for the differentiation of endoderm primordia into thyroxin-producing follicular cells. Goiterlike diseases are known in the majority of mammals.  ...  Its homologs are present in prokaryotes as well as in the mitochondria of yeast, insects, and mammals.  ... 
doi:10.1007/978-1-4020-6754-9_7078 fatcat:igkfa5bydfeehhe7ekrw5dudny
« Previous Showing results 1 — 15 out of 27 results