Literature

Ribo-Seq:

McGlincy NJ, Ingolia NT.Transcriptome-wide measurement of translation by ribosome profiling. Methods. 2017 Aug 15;126:112-129.
doi: 10.1016/j.ymeth.2017.05.028. 

Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 2009 Apr 10;324(5924):218-23.
doi: 10.1126/science.1168978. 

Aspden JL, Eyre-Walker YC, Phillips RJ, Amin U, Mumtaz MA, Brocard M, Couso JP. Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq. Elife. 2014 Aug 21;3:e03528.
doi: 10.7554/eLife.03528. 

Legendre R, Baudin-Baillieu A, Hatin I, Namy O. RiboTools: a Galaxy toolbox for qualitative ribosome profiling analysis. Bioinformatics. 2015 Aug 1;31(15):2586-8.
doi: 10.1093/bioinformatics/btv174. 

Popa A, Lebrigand K, Paquet A, Nottet N, Robbe-Sermesant K, Waldmann R, Barbry P. RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing. F1000Res. 2016 Jun 9;5:1309.
doi: 10.12688/f1000research.8964.1. 

Li W, Wang W, Uren PJ, Penalva LOF, Smith AD. Riborex: fast and flexible identification of differential translation from Ribo-seq data. Bioinformatics. 2017 Jun 1;33(11):1735-1737.
doi: 10.1093/bioinformatics/btx047. 

Xiao Z, Zou Q, Liu Y, Yang X. Genome-wide assessment of differential translations with ribosome profiling data. Nat Commun. 2016 Apr 4;7:11194.
doi: 10.1038/ncomms11194. 

Carja O, Xing T, Wallace EWJ, Plotkin JB, Shah P. riboviz: analysis and visualization of ribosome profiling datasets. BMC Bioinformatics. 2017 Oct 25;18(1):461.
doi: 10.1186/s12859-017-1873-8. 

Ingolia NT. Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet. 2014 Mar;15(3):205-13.
doi: 10.1038/nrg3645. 

Ingolia NT. Ribosome Footprint Profiling of Translation throughout the Genome. Cell. 2016 Mar 24;165(1):22-33.
doi: 10.1016/j.cell.2016.02.066. 

 

 

RAD-seq:

Cariou M1, Duret L, Charlat S. Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization. Ecol Evol. 2013 Apr;3(4):846-52.
doi: 10.1002/ece3.512.

Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH. Stacks: building and genotyping Loci de novo from short-read sequences. G3 (Bethesda). 2011 Aug;1(3):171-82.
doi: 10.1534/g3.111.000240.

Emerson KJ, Merz CR, Catchen JM, Hohenlohe PA, Cresko WA, Bradshaw WE, Holzapfel CM. Resolving postglacial phylogeography using high-throughput sequencing. Proc Natl Acad Sci U S A. 2010 Sep 14;107(37):16196-200.
doi: 10.1073/pnas.1006538107.

Miller MR1, Dunham JP, Amores A, Cresko WA, Johnson EA. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res. 2007 Feb;17(2):240-8.
doi: 10.1101/gr.5681207.

Davey JW1, Blaxter ML. RADSeq: next-generation population genetics. Brief Funct Genomics. 2010 Dec;9(5-6):416-23.
doi: 10.1093/bfgp/elq031. 

Malinsky M, Trucchi E, Lawson DJ, Falush D. RADpainter and fineRADstructure: population inference from RADseq data. Mol Biol Evol. 2018 Feb 20.
doi: 10.1093/molbev/msy023.

Chong Z1, Ruan J, Wu CI. Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads. Bioinformatics. 2012 Nov 1;28(21):2732-7.
doi: 10.1093/bioinformatics/bts482.

 

 

Whole-Exome Sequencing:

Belkadi A, Bolze A, Itan Y, Cobat A, Vincent QB, Antipenko A, Shang L, Boisson B, Casanova JL, Abel L. Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants. Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):5473-8.
doi: 10.1073/pnas.1418631112. 

Hintzsche J, Kim J, Yadav V, Amato C, Robinson SE, Seelenfreund E, Shellman Y, Wisell J, Applegate A, McCarter M, Box N, Tentler J, De S, Robinson WA, Tan AC. IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples. J Am Med Inform Assoc. 2016 Jul;23(4):721-30.
doi: 10.1093/jamia/ocw022. 

Gao X, Xu J, Starmer J. Fastq2vcf: a concise and transparent pipeline for whole-exome sequencing data analyses. BMC Res Notes. 2015 Mar 8;8:72.
doi: 10.1186/s13104-015-1027-x. 

Rennert H, Eng K, Zhang T, Tan A, Xiang J, Romanel A, Kim R, Tam W, Liu YC, Bhinder B, Cyrta J, Beltran H, Robinson B, Mosquera JM, Fernandes H, Demichelis F, Sboner A, Kluk M, Rubin MA, Elemento O. Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care. NPJ Genom Med. 2016;1. pii: 16019.
doi: 10.1038/npjgenmed.2016.19. 

Li J, Doyle MA, Saeed I, Wong SQ, Mar V, Goode DL, Caramia F, Doig K, Ryland GL, Thompson ER, Hunter SM, Halgamuge SK, Ellul J, Dobrovic A, Campbell IG, Papenfuss AT, McArthur GA, Tothill RW. Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human and mouse genomes: a virtual appliance approach for instant deployment. PLoS One. 2014 Apr 21;9(4):e95217.
doi: 10.1371/journal.pone.0095217. 

Luo R, Wong YL, Law WC, Lee LK, Cheung J, Liu CM, Lam TW. BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU. PeerJ. 2014 Jun 3;2:e421.
doi: 10.7717/peerj.421. 

 

 

 

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