TY - JOUR AU - Zerbino, D. R. AU - Achuthan, P. AU - Akanni, W. AU - Amode, M. R. AU - Barrell, D. AU - Bhai, J. PY - 2018 DA - 2018// TI - Ensembl 2018 JO - Nucleic Acids Res VL - 46 UR - https://doi.org/10.1093/nar/gkx1098 DO - 10.1093/nar/gkx1098 ID - Zerbino2018 ER - TY - JOUR PY - 2017 DA - 2017// TI - UniProt: the universal protein knowledgebase JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1099 DO - 10.1093/nar/gkw1099 ID - ref2 ER - TY - BOOK AU - O’Leary, N. A. AU - Wright, M. W. AU - Brister, J. R. AU - Ciufo, S. AU - Haddad, D. AU - McVeigh, R. PY - 2016 DA - 2016// TI - Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation ID - O’Leary2016 ER - TY - BOOK AU - Thibaud-Nissen, F. AU - Souvorov, A. AU - Murphy, T. AU - DiCuccio, M. AU - Kitts, P. PY - 2013 DA - 2013// TI - Eukaryotic genome annotation pipeline. The NCBI H ID - Thibaud-Nissen2013 ER - TY - STD TI - Keller O, Odronitz F, Stanke M, Kollmar M, Waack S. Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species. BMC Bioinformatics. 2008;9. ID - ref5 ER - TY - STD TI - Venturini L, Caim S, Kaithakottil GG, Mapleson DL, Swarbreck D. Leveraging multiple transcriptome assembly methods for improved gene structure annotation. GigaScience. 2018;7:1–15. https://doi.org/10.1093/gigascience/giy093. ID - ref6 ER - TY - JOUR AU - Fushan, A. A. AU - Turanov, A. A. AU - Lee, S. G. AU - Kim, E. B. AU - Lobanov, A. V. AU - Yim, S. H. PY - 2015 DA - 2015// TI - Gene expression defines natural changes in mammalian lifespan JO - Aging Cell VL - 14 UR - https://doi.org/10.1111/acel.12283 DO - 10.1111/acel.12283 ID - Fushan2015 ER - TY - STD TI - Uhlén M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, et al. Towards a knowledge-based human protein atlas. Nat Biotechnol. 2010;28. ID - ref8 ER - TY - BOOK AU - Uhlén, M. AU - Fagerberg, L. AU - Hallström, B. M. AU - Lindskog, C. AU - Oksvold, P. AU - Mardinoglu, A. PY - 2015 DA - 2015// TI - Tissue-based map of the human proteome. Science (80- ) ID - Uhlén2015 ER - TY - STD TI - Bioinformatics Group at the Babraham Institute. FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Accessed 5 Nov 2018. UR - http://www.bioinformatics.babraham.ac.uk/projects/fastqc ID - ref10 ER - TY - BOOK AU - Fang, G. AU - Bhardwaj, N. AU - Robilotto, R. AU - Gerstein, M. B. PY - 2010 DA - 2010// TI - Getting started in gene Orthology and functional analysis ID - Fang2010 ER - TY - JOUR AU - Jun, G. AU - Wing, M. K. AU - Abecasis, G. R. AU - Kang, H. M. PY - 2015 DA - 2015// TI - An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data JO - Genome Res VL - 25 UR - https://doi.org/10.1101/gr.176552.114 DO - 10.1101/gr.176552.114 ID - Jun2015 ER - TY - JOUR AU - Huber, W. AU - Carey, V. J. AU - Gentleman, R. AU - Anders, S. AU - Carlson, M. AU - Carvalho, B. S. PY - 2015 DA - 2015// TI - Orchestrating high-throughput genomic analysis with Bioconductor JO - Nat Methods VL - 12 UR - https://doi.org/10.1038/nmeth.3252 DO - 10.1038/nmeth.3252 ID - Huber2015 ER - TY - JOUR AU - Liao, Y. AU - Smyth, G. K. AU - Shi, W. PY - 2014 DA - 2014// TI - featureCounts: an efficient general purpose program for assigning sequence reads to genomic features JO - Bioinformatics. VL - 30 UR - https://doi.org/10.1093/bioinformatics/btt656 DO - 10.1093/bioinformatics/btt656 ID - Liao2014 ER - TY - JOUR AU - Ewels, P. AU - Magnusson, M. AU - Lundin, S. AU - Käller, M. PY - 2016 DA - 2016// TI - MultiQC: summarize analysis results for multiple tools and samples in a single report JO - Bioinformatics. VL - 32 UR - https://doi.org/10.1093/bioinformatics/btw354 DO - 10.1093/bioinformatics/btw354 ID - Ewels2016 ER - TY - STD TI - Söllner JF, Leparc G, Hildebrandt T, Klein H, Thomas L, Stupka E, et al. An RNA-Seq atlas of gene expression in mouse and rat normal tissues. Sci Data. 2017;4. https://doi.org/10.1038/sdata.2017.185. ID - ref16 ER - TY - JOUR AU - Durnick, S. AU - Spellman, P. T. AU - Birney, E. AU - Huber, W. PY - 2009 DA - 2009// TI - Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt JO - Nat Protoc VL - 4 UR - https://doi.org/10.1038/nprot.2009.97 DO - 10.1038/nprot.2009.97 ID - Durnick2009 ER - TY - JOUR AU - Durinck, S. AU - Moreau, Y. AU - Kasprzyk, A. AU - Davis, S. AU - De, M. B. AU - Brazma, A. PY - 2005 DA - 2005// TI - BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis JO - Bioinformatics. VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti525 DO - 10.1093/bioinformatics/bti525 ID - Durinck2005 ER - TY - JOUR AU - Liu, J. AU - Li, G. AU - Chang, Z. AU - Yu, T. AU - Liu, B. AU - McMullen, R. PY - 2016 DA - 2016// TI - BinPacker: packing-based De novo transcriptome assembly from RNA-seq data JO - PLoS Comput Biol VL - 12 ID - Liu2016 ER - TY - JOUR AU - Bankevich, A. AU - Nurk, S. AU - Antipov, D. AU - Gurevich, A. A. AU - Dvorkin, M. AU - Kulikov, A. S. PY - 2012 DA - 2012// TI - SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing JO - J Comput Biol VL - 19 UR - https://doi.org/10.1089/cmb.2012.0021 DO - 10.1089/cmb.2012.0021 ID - Bankevich2012 ER - TY - JOUR AU - Smith-Unna, R. AU - Boursnell, C. AU - Patro, R. AU - Hibberd, J. M. AU - Kelly, S. PY - 2016 DA - 2016// TI - TransRate: reference-free quality assessment of de novo transcriptome assemblies JO - Genome Res VL - 26 UR - https://doi.org/10.1101/gr.196469.115 DO - 10.1101/gr.196469.115 ID - Smith-Unna2016 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - JOUR AU - Haas, B. J. AU - Papanicolaou, A. AU - Yassour, M. AU - Grabherr, M. AU - Philip, D. AU - Bowden, J. PY - 2013 DA - 2013// TI - De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with trinity JO - Nat Protoc VL - 8 UR - https://doi.org/10.1038/nprot.2013.084 DO - 10.1038/nprot.2013.084 ID - Haas2013 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with high accuracy and high throughput JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - JOUR AU - Tommaso, P. AU - Chatzou, M. AU - Floden, E. W. AU - Barja, P. P. AU - Palumbo, E. AU - Notredame, C. PY - 2017 DA - 2017// TI - Nextflow enables reproducible computational workflows JO - Nat Biotechnol VL - 35 UR - https://doi.org/10.1038/nbt.3820 DO - 10.1038/nbt.3820 ID - Tommaso2017 ER - TY - STD TI - Docker. https://www.docker.com/. Accessed 5 Nov 2018. UR - https://www.docker.com/ ID - ref26 ER - TY - STD TI - Pertea M, Shumate A, Pertea G, Varabyou A, Chang Y, Madugundu AK, et al. Thousands of large-scale RNA sequencing experiments yield a comprehensive new human gene list and reveal extensive transcriptional noise. bioRxiv. 2018. ID - ref27 ER - TY - JOUR AU - Wethmar, K. AU - Barbosa-Silva, A. AU - Andrade-Navarro, M. A. AU - Leutz, A. PY - 2014 DA - 2014// TI - uORFdb — a comprehensive literature database on eukaryotic uORF biology JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt952 DO - 10.1093/nar/gkt952 ID - Wethmar2014 ER - TY - STD TI - The Human Protein Atlas. The Tissue Atlas. https://www.proteinatlas.org/humanproteome/tissue. Accessed 17 Mar 2019. UR - https://www.proteinatlas.org/humanproteome/tissue ID - ref29 ER - TY - STD TI - Larsson J. eulerr: Area-proportional Euler and Venn diagrams with ellipses. 2018. https://cran.r-project.org/package=eulerr. UR - https://cran.r-project.org/package=eulerr ID - ref30 ER - TY - JOUR AU - Lex, A. AU - Gehlenborg, N. AU - Strobelt, H. AU - Vuillemot, R. AU - Pfister, H. PY - 2014 DA - 2014// TI - UpSet: visualization of intersecting sets JO - IEEE Trans Vis Comput Graph VL - 20 UR - https://doi.org/10.1109/TVCG.2014.2346248 DO - 10.1109/TVCG.2014.2346248 ID - Lex2014 ER -