{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T18:05:24Z","timestamp":1740161124681,"version":"3.37.3"},"reference-count":46,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2022,6,7]],"date-time":"2022-06-07T00:00:00Z","timestamp":1654560000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2022,6,7]],"date-time":"2022-06-07T00:00:00Z","timestamp":1654560000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/100001655","name":"Grayson-Jockey Club Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001655","id-type":"DOI","asserted-by":"publisher"}]},{"name":"usda nrsp-8"},{"DOI":"10.13039\/100016749","name":"UC Davis Center for Equine Health","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100016749","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100009615","name":"Uniwersytet Rolniczy im. Hugona Ko\u0142\u0142\u0105taja w Krakowie","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009615","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Appl Genetics"],"published-print":{"date-parts":[[2022,9]]},"DOI":"10.1007\/s13353-022-00705-z","type":"journal-article","created":{"date-parts":[[2022,6,7]],"date-time":"2022-06-07T12:13:19Z","timestamp":1654603999000},"page":"571-581","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Another lesson from unmapped reads: in-depth analysis of RNA-Seq reads from various horse tissues"],"prefix":"10.1007","volume":"63","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5979-144X","authenticated-orcid":false,"given":"Artur","family":"Gurgul","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tomasz","family":"Szmato\u0142a","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ewa","family":"Oc\u0142o\u0144","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Igor","family":"Jasielczuk","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ewelina","family":"Semik-Gurgul","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carrie J.","family":"Finno","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jessica L.","family":"Petersen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rebecca","family":"Bellone","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erin N.","family":"Hales","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tomasz","family":"Z\u0105bek","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zbigniew","family":"Arent","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ma\u0142gorzata","family":"Kotula-Balak","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Monika","family":"Bugno-Poniewierska","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,6,7]]},"reference":[{"issue":"5","key":"705_CR1","doi-asserted-by":"publisher","first-page":"e433","DOI":"10.1016\/j.crvasa.2013.11.001","volume":"56","author":"H Alici","year":"2014","unstructured":"Alici H, Ercan S, Davutoglu V (2014) Brucella infective endocarditis. Cor Vasa 56(5):e433\u2013e435. https:\/\/doi.org\/10.1016\/j.crvasa.2013.11.001","journal-title":"Cor Vasa"},{"key":"705_CR2","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B (Methodological) 57:289\u2013300. https:\/\/doi.org\/10.1111\/j.2517-6161.1995.tb02031","journal-title":"Journal of the Royal Statistical Society: Series B (Methodological)"},{"issue":"Suppl 12","key":"705_CR3","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1186\/s12859-017-1821-7","volume":"18","author":"CM Bosworth","year":"2017","unstructured":"Bosworth CM, Grandhi S, Gould MP, LaFramboise T (2017) Detection and quantification of mitochondrial DNA deletions from next-generation sequence data. BMC Bioinformatics 18(Suppl 12):407. https:\/\/doi.org\/10.1186\/s12859-017-1821-7","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"705_CR4","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","volume":"12","author":"B Buchfink","year":"2014","unstructured":"Buchfink B, Xie C, Huson DH (2014) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12(1):59\u201360. https:\/\/doi.org\/10.1038\/nmeth.3176","journal-title":"Nat Methods"},{"issue":"6","key":"705_CR5","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1111\/age.12717","volume":"49","author":"EN Burns","year":"2018","unstructured":"Burns EN, Bordbari MH, Mienaltowski MJ, Affolter VK, Barro MV, Gianino F, Gianino G, Giulotto E, Kalbfleisch TS, Katzman SA, Lassaline M, Leeb T, Mack M, M\u00fcller EJ, MacLeod JN, Ming-Whitfield B, Alanis CR, Raudsepp T, Scott E, Vig S, Zhou H, Petersen JL, Bellone RR, Finno CJ (2018) Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project. Anim Genet 49(6):564\u2013570. https:\/\/doi.org\/10.1111\/age.12717","journal-title":"Anim Genet"},{"issue":"8","key":"705_CR6","doi-asserted-by":"publisher","first-page":"15423","DOI":"10.3390\/ijms140815423","volume":"14","author":"G Bussotti","year":"2013","unstructured":"Bussotti G, Notredame C, Enright AJ (2013) Detecting and comparing non-coding RNAs in the high-throughput era. Int J Mol Sci 14(8):15423\u201315458. https:\/\/doi.org\/10.3390\/ijms140815423","journal-title":"Int J Mol Sci"},{"key":"705_CR7","doi-asserted-by":"crossref","unstructured":"Chen J, Dai Z, Cao C, Zhang Q, Liu H, Sun X (2012) Next-generation sequencing data processing: analysis of unmapped reads and extremely high mapped peaks. 5th Int Conf BioMed Eng Informa 893\u201397.\u00a0https:\/\/ieeexplore.ieee.org\/document\/6512933","DOI":"10.1109\/BMEI.2012.6512933"},{"key":"705_CR8","doi-asserted-by":"publisher","first-page":"712","DOI":"10.1186\/1471-2164-13-712","volume":"13","author":"O C\u00f4t\u00e9","year":"2012","unstructured":"C\u00f4t\u00e9 O, Lillie BN, Hayes MA, Clark ME, van den Bosch L, Katavolos P, Viel L, Bienzle D (2012) Multiple secretoglobin 1A1 genes are differentially expressed in horses. BMC Genomics 13:712. https:\/\/doi.org\/10.1186\/1471-2164-13-712","journal-title":"BMC Genomics"},{"issue":"24","key":"705_CR9","doi-asserted-by":"publisher","first-page":"3207","DOI":"10.1093\/bioinformatics\/btp579","volume":"25","author":"JF Degner","year":"2009","unstructured":"Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, Pritchard JK (2009) Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinform (oxford, England) 25(24):3207\u20133212. https:\/\/doi.org\/10.1093\/bioinformatics\/btp579","journal-title":"Bioinform (oxford, England)"},{"key":"705_CR10","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1186\/s12864-020-07183-9","volume":"21","author":"S Dhorne-Pollet","year":"2020","unstructured":"Dhorne-Pollet S, Barrey E, Pollet N (2020) A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants. BMC Genomics 21:785. https:\/\/doi.org\/10.1186\/s12864-020-07183-9","journal-title":"BMC Genomics"},{"issue":"2","key":"705_CR11","doi-asserted-by":"publisher","first-page":"E321","DOI":"10.1152\/ajpendo.1998.274.2.E321274(2):E321-27","volume":"274","author":"F Diraison","year":"1998","unstructured":"Diraison F, Beylot M (1998) Role of human liver lipogenesis and reesterification in triglycerides secretion and in FFA reesterification. Am J Phys-Endocrinol Metab 274(2):E321\u2013E327. https:\/\/doi.org\/10.1152\/ajpendo.1998.274.2.E321274(2):E321-27","journal-title":"Am J Phys-Endocrinol Metab"},{"issue":"3","key":"705_CR12","doi-asserted-by":"publisher","first-page":"895","DOI":"10.3390\/biology1030895","volume":"1","author":"M Dodt","year":"2012","unstructured":"Dodt M, Roehr JT, Ahmed R, Dieterich C (2012) FLEXBAR-Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms. Biol (Basel) 1(3):895\u2013905. https:\/\/doi.org\/10.3390\/biology1030895","journal-title":"Biol (Basel)"},{"issue":"5","key":"705_CR13","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1038\/hdy.2014.85","volume":"114","author":"A Gouin","year":"2015","unstructured":"Gouin A, Legeai F, Nouhaud P, Whibley A, Simon JC, Lemaitre C (2015) Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads. Heredity (edinb) 114(5):494\u2013501. https:\/\/doi.org\/10.1038\/hdy.2014.85","journal-title":"Heredity (edinb)"},{"issue":"7","key":"705_CR14","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1038\/nbt.1883","volume":"29","author":"MG Grabherr","year":"2011","unstructured":"Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644\u2013652. https:\/\/doi.org\/10.1038\/nbt.1883","journal-title":"Nat Biotechnol"},{"issue":"1","key":"705_CR15","doi-asserted-by":"publisher","first-page":"11093","DOI":"10.1038\/s41598-019-47405-z","volume":"9","author":"MS Hasan","year":"2019","unstructured":"Hasan MS, Wu X, Zhang L (2019) Uncovering missed indels by leveraging unmapped reads. Sci Rep 9(1):11093. https:\/\/doi.org\/10.1038\/s41598-019-47405-z","journal-title":"Sci Rep"},{"issue":"12","key":"705_CR16","doi-asserted-by":"publisher","first-page":"689","DOI":"10.1038\/s41574-019-0256-9.Erratum.In:NatRevEndocrinol","volume":"15","author":"L Hodson","year":"2020","unstructured":"Hodson L Gunn PJ (2019) The regulation of hepatic fatty acid synthesis and partitioning: the effect of nutritional state. Nat Rev Endocrinol 15(12):689\u2013700. https:\/\/doi.org\/10.1038\/s41574-019-0256-9.Erratum.In:NatRevEndocrinol","journal-title":"Nat Rev Endocrinol"},{"issue":"1","key":"705_CR17","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/nar\/gkn923","volume":"37","author":"W da Huang","year":"2009","unstructured":"da Huang W, Sherman BT, Lempicki RA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37(1):1\u201313. https:\/\/doi.org\/10.1093\/nar\/gkn923","journal-title":"Nucleic Acids Res"},{"issue":"6215","key":"705_CR18","doi-asserted-by":"publisher","first-page":"1320","DOI":"10.1126\/science.1253451","volume":"346","author":"ED Jarvis","year":"2014","unstructured":"Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabald\u00f3n T, Capella-Guti\u00e9rrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-N\u00fa\u00f1ez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, J\u00f8nsson KA, Johnson W, Koepfli KP, O\u2019Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alstr\u00f6m P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G (2014) Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346(6215):1320\u20131331. https:\/\/doi.org\/10.1126\/science.1253451","journal-title":"Science"},{"issue":"1","key":"705_CR19","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1186\/s12879-018-3134-5","volume":"18","author":"R Kaden","year":"2018","unstructured":"Kaden R, Ferrari S, Jinnerot T, Lindberg M, Wahab T, Lavander M (2018) Brucella abortus: determination of survival times and evaluation of methods for detection in several matrices. BMC Infect Dis 18(1):259. https:\/\/doi.org\/10.1186\/s12879-018-3134-5","journal-title":"BMC Infect Dis"},{"issue":"8","key":"705_CR20","doi-asserted-by":"publisher","first-page":"826","DOI":"10.15252\/msb.156172","volume":"11","author":"M Kazemian","year":"2015","unstructured":"Kazemian M, Ren M, Lin JX, Liao W, Spolski R, Leonard WJ (2015) Comprehensive assembly of novel transcripts from unmapped human RNA-Seq data and their association with cancer. Mol Syst Biol 11(8):826. https:\/\/doi.org\/10.15252\/msb.156172","journal-title":"Mol Syst Biol"},{"key":"705_CR21","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1007\/978-1-4939-3369-3_13","volume":"1399","author":"KP Keegan","year":"2016","unstructured":"Keegan KP, Glass EM, Meyer F (2016) MG-RAST, a metagenomics service for analysis of microbial community structure and function. Methods Mol Biol 1399:207\u2013233. https:\/\/doi.org\/10.1007\/978-1-4939-3369-3_13","journal-title":"Methods Mol Biol"},{"issue":"2","key":"705_CR22","doi-asserted-by":"publisher","first-page":"65","DOI":"10.3390\/tropicalmed3020065","volume":"3","author":"MZ Khan","year":"2018","unstructured":"Khan MZ, Zahoor M (2018) An overview of brucellosis in cattle and humans, and its serological and molecular diagnosis in control strategies. Trop Med Infectious Dis 3(2):65. https:\/\/doi.org\/10.3390\/tropicalmed3020065","journal-title":"Trop Med Infectious Dis"},{"issue":"4","key":"705_CR23","doi-asserted-by":"publisher","first-page":"R36","DOI":"10.1186\/gb-2013-14-4-r36","volume":"14","author":"D Kim","year":"2013","unstructured":"Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14(4):R36","journal-title":"Genome Biol"},{"issue":"1","key":"705_CR24","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/s12864-018-5378-2","volume":"20","author":"VN Laine","year":"2019","unstructured":"Laine VN, Gossmann TI, van Oers K, Visser ME, Groenen MAM (2019) Exploring the unmapped DNA and RNA reads in a songbird genome. BMC Genomics 20(1):19. https:\/\/doi.org\/10.1186\/s12864-018-5378-2","journal-title":"BMC Genomics"},{"issue":"11","key":"705_CR25","doi-asserted-by":"publisher","first-page":"1359","DOI":"10.3390\/genes11111359","volume":"11","author":"HY Lee","year":"2020","unstructured":"Lee HY, Kim JY, Kim KH, Jeong S, Cho Y, Kim N (2020) Gene expression profile in similar tissues using transcriptome sequencing data of whole-body horse skeletal muscle. Genes 11(11):1359. https:\/\/doi.org\/10.3390\/genes11111359","journal-title":"Genes"},{"issue":"12","key":"705_CR26","doi-asserted-by":"publisher","first-page":"892","DOI":"10.1016\/j.tig.2019.09.006","volume":"35","author":"H Lee","year":"2019","unstructured":"Lee H, Zhang Z, Krause HM (2019) Long noncoding RNAs and repetitive elements: junk or intimate evolutionary partners? Trends Genet 35(12):892\u2013902. https:\/\/doi.org\/10.1016\/j.tig.2019.09.006","journal-title":"Trends Genet"},{"issue":"4","key":"705_CR27","doi-asserted-by":"publisher","first-page":"e40","DOI":"10.5808\/GI.2019.17.4.e40","volume":"17","author":"Y Lee","year":"2019","unstructured":"Lee Y, Park K, Koh I (2019) Analysis of unmapped regions associated with long deletions in Korean whole genome sequences based on short read data. Genomics Inform 17(4):e40\u2013e40. https:\/\/doi.org\/10.5808\/GI.2019.17.4.e40","journal-title":"Genomics Inform"},{"key":"705_CR28","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1016\/j.gde.2017.10.002","volume":"48","author":"Z Li","year":"2018","unstructured":"Li Z, Qin F, Li H (2018) Chimeric RNAs and their implications in cancer. Curr Opin Genet Dev 48:36\u201343. https:\/\/doi.org\/10.1016\/j.gde.2017.10.002","journal-title":"Curr Opin Genet Dev"},{"key":"705_CR29","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. https:\/\/doi.org\/10.1186\/s13059-014-0550-8","journal-title":"Genome Biol"},{"issue":"W1","key":"705_CR30","doi-asserted-by":"publisher","first-page":"W566","DOI":"10.1093\/nar\/gkv468","volume":"43","author":"T Metsalu","year":"2015","unstructured":"Metsalu T, Vilo J (2015) ClustVis: a web tool for visualizing clustering of multivariate data using principal component analysis and heatmap. Nucleic Acids Res 43(W1):W566-570. https:\/\/doi.org\/10.1093\/nar\/gkv468","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"705_CR31","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1186\/s12915-019-0690-0","volume":"17","author":"SJ Park","year":"2019","unstructured":"Park SJ, Onizuka S, Seki M, Suzuki Y, Iwata T, Nakai K (2019) A systematic sequencing-based approach for microbial contaminant detection and functional inference. BMC Biol 17(1):72. https:\/\/doi.org\/10.1186\/s12915-019-0690-0","journal-title":"BMC Biol"},{"issue":"1","key":"705_CR32","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1007\/s12686-017-0951-6","volume":"11","author":"J Pei","year":"2019","unstructured":"Pei J, Chu M, Bao P, Sha Z, Ding X, Yan P, Guo X (2019) The complete mitochondrial genome of Sanhe Horse (Equus caballus). Conserv Genet Resour 11(1):11\u201314. https:\/\/doi.org\/10.1007\/s12686-017-0951-6","journal-title":"Conserv Genet Resour"},{"issue":"S26","key":"705_CR33","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1111\/j.2042-3306.1998.tb05133.x","volume":"30","author":"CC Pollitt","year":"1998","unstructured":"Pollitt CC, Daradka M (1998) Equine laminitis basement membrane pathology: loss of type IV collagen, type VII collagen and laminin immunostaining. Equine Vet J 30(S26):139\u2013144. https:\/\/doi.org\/10.1111\/j.2042-3306.1998.tb05133.x","journal-title":"Equine Vet J"},{"issue":"6","key":"705_CR34","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26(6):841\u2013842. https:\/\/doi.org\/10.1093\/bioinformatics\/btq033","journal-title":"Bioinformatics"},{"issue":"6","key":"705_CR35","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1016\/j.stem.2009.04.002","volume":"4","author":"EL Rawlins","year":"2009","unstructured":"Rawlins EL, Okubo T, Xue Y, Brass DM, Auten RL, Hasegawa H, Wang F, Hogan BL (2009) The role of Scgb1a1+ Clara cells in the long-term maintenance and repair of lung airway, but not alveolar, epithelium. Cell Stem Cell 4(6):525\u2013534. https:\/\/doi.org\/10.1016\/j.stem.2009.04.002","journal-title":"Cell Stem Cell"},{"issue":"6","key":"705_CR36","doi-asserted-by":"publisher","first-page":"796","DOI":"10.1089\/cmb.2012.0022","volume":"19","author":"S Schbath","year":"2012","unstructured":"Schbath S, Martin V, Zytnicki M, Fayolle J, Loux V, Gibrat J-F (2012) Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. J Comput Biol 19(6):796\u2013813. https:\/\/doi.org\/10.1089\/cmb.2012.0022","journal-title":"J Comput Biol"},{"issue":"3","key":"705_CR37","doi-asserted-by":"publisher","first-page":"R28","DOI":"10.1186\/gb-2013-14-3-r28","volume":"14","author":"HB Shaffer","year":"2013","unstructured":"Shaffer HB, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning APJ, Li Y, Literman R, McGaugh SE, Mork L, O\u2019Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK (2013) The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol 14(3):R28\u2013R28. https:\/\/doi.org\/10.1186\/gb-2013-14-3-r28","journal-title":"Genome Biol"},{"issue":"4","key":"705_CR38","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.1016\/j.celrep.2017.10.001","volume":"21","author":"AR Sonawane","year":"2017","unstructured":"Sonawane AR, Platig J, Fagny M, Chen CY, Paulson JN, Lopes-Ramos CM, DeMeo DL, Quackenbush J, Glass K, Kuijjer ML (2017) Understanding Tissue-Specific Gene Regulation. Cell Rep 21(4):1077\u20131088. https:\/\/doi.org\/10.1016\/j.celrep.2017.10.001","journal-title":"Cell Rep"},{"issue":"1","key":"705_CR39","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1186\/1756-0500-5-85","volume":"5","author":"A Tiessen","year":"2012","unstructured":"Tiessen A, P\u00e9rez-Rodr\u00edguez P, Delaye-Arredondo LJ (2012) Mathematical modeling and comparison of protein size distribution in different plant, animal, fungal and microbial species reveals a negative correlation between protein size and protein number, thus providing insight into the evolution of proteomes. BMC Res Notes 5(1):85. https:\/\/doi.org\/10.1186\/1756-0500-5-85","journal-title":"BMC Res Notes"},{"issue":"1","key":"705_CR40","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1016\/j.ygeno.2016.11.009","volume":"109","author":"T Usman","year":"2017","unstructured":"Usman T, Hadlich F, Demasius W, Weikard R, K\u00fchn C (2017) Unmapped reads from cattle RNAseq data: a source for missing and misassembled sequences in the reference assemblies and for detection of pathogens in the host. Genomics 109(1):36\u201342. https:\/\/doi.org\/10.1016\/j.ygeno.2016.11.009","journal-title":"Genomics"},{"key":"705_CR41","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1186\/1471-2105-8-417","volume":"8","author":"AX Wang","year":"2007","unstructured":"Wang AX, Ruzzo WL, Tompa M (2007) How accurately is ncRNA aligned within whole-genome multiple alignments? BMC Bioinform 8:417. https:\/\/doi.org\/10.1186\/1471-2105-8-417","journal-title":"BMC Bioinform"},{"key":"705_CR42","doi-asserted-by":"publisher","first-page":"1114","DOI":"10.1186\/s12864-015-2313-7","volume":"16","author":"LK Whitacre","year":"2015","unstructured":"Whitacre LK, Tizioto PC, Kim J, Sonstegard TS, Schroeder SG, Alexander LJ, Medrano JF, Schnabel RD, Taylor JF, Decker JE (2015) What\u2019s in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual. BMC Genomics 16:1114. https:\/\/doi.org\/10.1186\/s12864-015-2313-7","journal-title":"BMC Genomics"},{"issue":"6","key":"705_CR43","doi-asserted-by":"publisher","first-page":"676","DOI":"10.3109\/14653240903313974","volume":"11","author":"AP Wong","year":"2009","unstructured":"Wong AP, Keating A, Waddell TK (2009) Airway regeneration: the role of the Clara cell secretory protein and the cells that express it. Cytotherapy 11(6):676\u2013687. https:\/\/doi.org\/10.3109\/14653240903313974","journal-title":"Cytotherapy"},{"key":"705_CR44","doi-asserted-by":"publisher","first-page":"584310","DOI":"10.3389\/fimmu.2020.584310","volume":"11","author":"M Xu","year":"2020","unstructured":"Xu M, Yang W, Wang X, Nayak DK (2020) Lung secretoglobin Scgb1a1 influences alveolar macrophage-mediated inflammation and immunity. Front Immunol 11:584310. https:\/\/doi.org\/10.3389\/fimmu.2020.584310","journal-title":"Front Immunol"},{"issue":"10","key":"705_CR45","doi-asserted-by":"publisher","first-page":"2023","DOI":"10.1016\/j.humpath.2014.07.007","volume":"45","author":"EJ Young","year":"2014","unstructured":"Young EJ, Roushan MRH, Shafae S, Genta RM, Taylor SL (2014) Liver histology of acute brucellosis caused by Brucella melitensis. Hum Pathol 45(10):2023\u20132028. https:\/\/doi.org\/10.1016\/j.humpath.2014.07.007","journal-title":"Hum Pathol"},{"key":"705_CR46","doi-asserted-by":"publisher","unstructured":"Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, \u00d6deen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-N\u00fa\u00f1ez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farr\u00e9 M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, H\u00e5stad O, Sawyer RH, KimH, Kim K-W, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O\u2019Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alstr\u00f6m P, Fjelds\u00e5 J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DV, Houde P, Zhang Y, Yang H, Wang J, Avian Genome Consortium, Jarvis ED, Gilbert MTP, Wang J (2014) Comparative genomics reveals insights into avian genome evolution and adaptation. Science (New York, N.Y.) 346(6215):1311-20.\u00a0https:\/\/doi.org\/10.1126\/science.1251385","DOI":"10.1126\/science.1251385"}],"container-title":["Journal of Applied Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s13353-022-00705-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s13353-022-00705-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s13353-022-00705-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,8,11]],"date-time":"2022-08-11T03:30:23Z","timestamp":1660188623000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s13353-022-00705-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,7]]},"references-count":46,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2022,9]]}},"alternative-id":["705"],"URL":"https:\/\/doi.org\/10.1007\/s13353-022-00705-z","relation":{},"ISSN":["1234-1983","2190-3883"],"issn-type":[{"type":"print","value":"1234-1983"},{"type":"electronic","value":"2190-3883"}],"subject":[],"published":{"date-parts":[[2022,6,7]]},"assertion":[{"value":"13 January 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 April 2022","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 May 2022","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 June 2022","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All protocols were approved by the UCD Institutional Animal Care and Use Committee (Protocol #19037).","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}