@misc{noauthor_httpwwwsequenceontologyorg_nodate,
	title = {http://www.sequenceontology.org/},
	shorttitle = {http},
	url = {http://www.sequenceontology.org/},
	language = {en-US},
	urldate = {2024-08-01},
	file = {Snapshot:/home/yume/Zotero/storage/L3YQIYUL/www.sequenceontology.org.html:text/html},
}

@article{frankish_gencode_2019,
	title = {{GENCODE} reference annotation for the human and mouse genomes},
	volume = {47},
	issn = {1362-4962},
	doi = {10.1093/nar/gky955},
	abstract = {The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend the GENCODE gene annotation. Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.},
	language = {eng},
	number = {D1},
	journal = {Nucleic Acids Research},
	author = {Frankish, Adam and Diekhans, Mark and Ferreira, Anne-Maud and Johnson, Rory and Jungreis, Irwin and Loveland, Jane and Mudge, Jonathan M. and Sisu, Cristina and Wright, James and Armstrong, Joel and Barnes, If and Berry, Andrew and Bignell, Alexandra and Carbonell Sala, Silvia and Chrast, Jacqueline and Cunningham, Fiona and Di Domenico, Tomás and Donaldson, Sarah and Fiddes, Ian T. and García Girón, Carlos and Gonzalez, Jose Manuel and Grego, Tiago and Hardy, Matthew and Hourlier, Thibaut and Hunt, Toby and Izuogu, Osagie G. and Lagarde, Julien and Martin, Fergal J. and Martínez, Laura and Mohanan, Shamika and Muir, Paul and Navarro, Fabio C. P. and Parker, Anne and Pei, Baikang and Pozo, Fernando and Ruffier, Magali and Schmitt, Bianca M. and Stapleton, Eloise and Suner, Marie-Marthe and Sycheva, Irina and Uszczynska-Ratajczak, Barbara and Xu, Jinuri and Yates, Andrew and Zerbino, Daniel and Zhang, Yan and Aken, Bronwen and Choudhary, Jyoti S. and Gerstein, Mark and Guigó, Roderic and Hubbard, Tim J. P. and Kellis, Manolis and Paten, Benedict and Reymond, Alexandre and Tress, Michael L. and Flicek, Paul},
	month = jan,
	year = {2019},
	pmid = {30357393},
	pmcid = {PMC6323946},
	keywords = {Animals, Computational Biology, Databases, Genetic, Genome, Human, Genomics, Humans, Internet, Mice, Molecular Sequence Annotation, Pseudogenes, Software},
	pages = {D766--D773},
	file = {Full Text:/home/yume/Zotero/storage/6JNTGDLZ/Frankish et al. - 2019 - GENCODE reference annotation for the human and mou.pdf:application/pdf},
}

@misc{noauthor_bam_nodate,
	title = {{BAM} {File} {Format}},
	url = {https://support.illumina.com/help/BS_App_RNASeq_Alignment_OLH_1000000006112/Content/Source/Informatics/BAM-Format.htm},
	urldate = {2024-08-01},
	file = {BAM File Format:/home/yume/Zotero/storage/4DTFGIN2/BAM-Format.html:text/html},
}