{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T07:32:01Z","timestamp":1771572721023,"version":"3.50.1"},"reference-count":108,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,9,27]],"date-time":"2021-09-27T00:00:00Z","timestamp":1632700800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,9,27]],"date-time":"2021-09-27T00:00:00Z","timestamp":1632700800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Transmissible cancers lie at the intersection of oncology and infectious disease, two traditionally divergent fields for which gene expression studies are particularly useful for identifying the molecular basis of phenotypic variation. In oncology, transcriptomics studies, which characterize the expression of thousands of genes, have identified processes leading to heterogeneity in cancer phenotypes and individual prognoses. More generally, transcriptomics studies of infectious diseases characterize interactions between host, pathogen, and environment to better predict population-level outcomes. Tasmanian devils have been impacted dramatically by a transmissible cancer (devil facial tumor disease; DFTD) that has led to widespread population declines. Despite initial predictions of extinction, populations have persisted at low levels, due in part to heterogeneity in host responses, particularly between sexes. However, the processes underlying this variation remain unknown.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We sequenced transcriptomes from healthy and DFTD-infected devils, as well as DFTD tumors, to characterize host responses to DFTD infection, identify differing host-tumor molecular interactions between sexes, and investigate the extent to which tumor gene expression varies among host populations. We found minimal variation in gene expression of devil lip tissues, either with respect to DFTD infection status or sex. However, 4088 genes were differentially expressed in tumors among our sampling localities. Pathways that were up- or downregulated in DFTD tumors relative to normal tissues exhibited the same patterns of expression with greater intensity in tumors from localities that experienced DFTD for longer. No mRNA sequence variants were associated with expression variation.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Expression variation among localities may reflect morphological differences in tumors that alter ratios of normal-to-tumor cells within biopsies. Phenotypic variation in tumors may arise from environmental variation or differences in host immune response that were undetectable in lip biopsies, potentially reflecting variation in host-tumor coevolutionary relationships among sites that differ in the time since DFTD arrival.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12864-021-07994-4","type":"journal-article","created":{"date-parts":[[2021,9,27]],"date-time":"2021-09-27T13:06:43Z","timestamp":1632748003000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection"],"prefix":"10.1186","volume":"22","author":[{"given":"Christopher P.","family":"Kozakiewicz","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexandra K.","family":"Fraik","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Austin H.","family":"Patton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manuel","family":"Ruiz-Aravena","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David G.","family":"Hamilton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rodrigo","family":"Hamede","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hamish","family":"McCallum","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul A.","family":"Hohenlohe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark J.","family":"Margres","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Menna E.","family":"Jones","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew","family":"Storfer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,9,27]]},"reference":[{"issue":"8","key":"7994_CR1","doi-asserted-by":"publisher","first-page":"686","DOI":"10.1038\/embor.2013.92","volume":"14","author":"FDSE Melo","year":"2013","unstructured":"Melo FDSE, Vermeulen L, Fessler E, Medema JP. Cancer heterogeneity\u2014a multifaceted view. EMBO Rep. 2013;14(8):686\u201395. https:\/\/doi.org\/10.1038\/embor.2013.92.","journal-title":"EMBO Rep"},{"issue":"7","key":"7994_CR2","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1038\/nrclinonc.2015.73","volume":"12","author":"D Zardavas","year":"2015","unstructured":"Zardavas D, Irrthum A, Swanton C, Piccart M. Clinical management of breast cancer heterogeneity. Nat Rev Clin Oncol. 2015;12(7):381\u201394. https:\/\/doi.org\/10.1038\/nrclinonc.2015.73.","journal-title":"Nat Rev Clin Oncol"},{"issue":"7","key":"7994_CR3","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1038\/nrc2173","volume":"7","author":"C Sotiriou","year":"2007","unstructured":"Sotiriou C, Piccart MJ. Taking gene-expression profiling to the clinic: when will molecular signatures become relevant to patient care? Nat Rev Cancer. 2007;7(7):545\u201353. https:\/\/doi.org\/10.1038\/nrc2173.","journal-title":"Nat Rev Cancer"},{"issue":"2","key":"7994_CR4","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1038\/nrg.2017.96","volume":"19","author":"M Cie\u015blik","year":"2018","unstructured":"Cie\u015blik M, Chinnaiyan AM. Cancer transcriptome profiling at the juncture of clinical translation. Nat Rev Genet. 2018;19(2):93\u2013109. https:\/\/doi.org\/10.1038\/nrg.2017.96.","journal-title":"Nat Rev Genet"},{"key":"7994_CR5","doi-asserted-by":"publisher","first-page":"34534","DOI":"10.18632\/oncotarget.15837","volume":"8","author":"M Li","year":"2017","unstructured":"Li M, Sun Q, Wang X. Transcriptional landscape of human cancers. Oncotarget. 2017;8:34534\u201351. https:\/\/doi.org\/10.18632\/oncotarget.15837.","journal-title":"Oncotarget"},{"key":"7994_CR6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-016-0028-x","volume":"7","author":"J Espinal-Enr\u00edquez","year":"2017","unstructured":"Espinal-Enr\u00edquez J, Fresno C, Anda-J\u00e1uregui G, Hern\u00e1ndez-Lemus E. RNA-Seq based genome-wide analysis reveals loss of inter-chromosomal regulation in breast cancer. Sci Rep. 2017;7:1\u201319.","journal-title":"Sci Rep"},{"key":"7994_CR7","doi-asserted-by":"publisher","unstructured":"Calon A, Lonardo E, Berenguer-Llergo A, Espinet E, Hernando-Momblona X, Iglesias M, et al. Stromal gene expression defines poor-prognosis subtypes in colorectal cancer. Nat Genet. 2015;47(4):320\u20139. https:\/\/doi.org\/10.1038\/ng.3225.","DOI":"10.1038\/ng.3225"},{"key":"7994_CR8","doi-asserted-by":"publisher","unstructured":"Smith BA, Sokolov A, Uzunangelov V, Baertsch R, Newton Y, Graim K, et al. A basal stem cell signature identifies aggressive prostate cancer phenotypes. Proc Natl Acad Sci U S A. 2015;112(47):E6544\u201352. https:\/\/doi.org\/10.1073\/pnas.1518007112.","DOI":"10.1073\/pnas.1518007112"},{"key":"7994_CR9","doi-asserted-by":"publisher","unstructured":"Marisa L, de Reyni\u00e8s A, Duval A, Selves J, Gaub MP, Vescovo L, et al. Gene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic value. PLoS Med. 2013;10(5):e1001453. https:\/\/doi.org\/10.1371\/journal.pmed.1001453.","DOI":"10.1371\/journal.pmed.1001453"},{"key":"7994_CR10","doi-asserted-by":"publisher","unstructured":"Zhao J, Guo C, Xiong F, Yu J, Ge J, Wang H, et al. Single cell RNA-seq reveals the landscape of tumor and infiltrating immune cells in nasopharyngeal carcinoma. Cancer Lett. 2020;477:131\u201343. https:\/\/doi.org\/10.1016\/j.canlet.2020.02.010.","DOI":"10.1016\/j.canlet.2020.02.010"},{"key":"7994_CR11","doi-asserted-by":"publisher","unstructured":"Hotaling S, Shah AA, McGowan KL, Tronstad LM, Giersch JJ, Finn DS, et al. Mountain stoneflies may tolerate warming streams: Evidence from organismal physiology and gene expression. Glob Chang Biol. 2020. https:\/\/doi.org\/10.1111\/gcb.15294.","DOI":"10.1111\/gcb.15294"},{"issue":"3","key":"7994_CR12","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1016\/j.aquatox.2008.08.010","volume":"90","author":"MF Oleksiak","year":"2008","unstructured":"Oleksiak MF. Changes in gene expression due to chronic exposure to environmental pollutants. Aquat Toxicol. 2008;90(3):161\u201371. https:\/\/doi.org\/10.1016\/j.aquatox.2008.08.010.","journal-title":"Aquat Toxicol"},{"key":"7994_CR13","doi-asserted-by":"publisher","first-page":"7866 LP","DOI":"10.1073\/pnas.1018580108","volume":"108","author":"C Bonneaud","year":"2011","unstructured":"Bonneaud C, Balenger SL, Russell AF, Zhang J, Hill GE, Edwards SV. Rapid evolution of disease resistance is accompanied by functional changes in gene expression in a wild bird. Proc Natl Acad Sci. 2011;108:7866 LP\u20137871. https:\/\/doi.org\/10.1073\/pnas.1018580108.","journal-title":"Proc Natl Acad Sci"},{"issue":"2","key":"7994_CR14","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1111\/mec.15327","volume":"29","author":"A Ellison","year":"2020","unstructured":"Ellison A, Zamudio K, Lips K, Muletz-Wolz C. Temperature-mediated shifts in salamander transcriptomic responses to the amphibian-killing fungus. Mol Ecol. 2020;29(2):325\u201343. https:\/\/doi.org\/10.1111\/mec.15327.","journal-title":"Mol Ecol"},{"issue":"1","key":"7994_CR15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.tig.2015.10.001","volume":"32","author":"EA Ostrander","year":"2016","unstructured":"Ostrander EA, Davis BW, Ostrander GK. Transmissible tumors: breaking the cancer paradigm. Trends Genet. 2016;32(1):1\u201315. https:\/\/doi.org\/10.1016\/j.tig.2015.10.001.","journal-title":"Trends Genet"},{"key":"7994_CR16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.ppat.1005904","volume":"12","author":"MJ Metzger","year":"2016","unstructured":"Metzger MJ, Goff SP. A sixth modality of infectious disease: contagious cancer from devils to clams and beyond. PLoS Pathog. 2016;12:1\u20137.","journal-title":"PLoS Pathog"},{"issue":"3","key":"7994_CR17","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1007\/s10393-007-0126-0","volume":"4","author":"SB Pyecroft","year":"2007","unstructured":"Pyecroft SB, Pearse AM, Loh R, Swift K, Belov K, Fox N, et al. Towards a case definition for devil facial tumour disease: what is it? Ecohealth. 2007;4(3):346\u201351. https:\/\/doi.org\/10.1007\/s10393-007-0126-0.","journal-title":"Ecohealth."},{"issue":"3","key":"7994_CR18","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1007\/s10393-007-0118-0","volume":"4","author":"H McCallum","year":"2007","unstructured":"McCallum H, Tompkins DM, Jones M, Lachish S, Marvanek S, Lazenby B, et al. Distribution and impacts of Tasmanian devil facial tumor disease. Ecohealth. 2007;4(3):318\u201325. https:\/\/doi.org\/10.1007\/s10393-007-0118-0.","journal-title":"Ecohealth."},{"issue":"2","key":"7994_CR19","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1016\/j.biocon.2006.04.010","volume":"131","author":"CE Hawkins","year":"2006","unstructured":"Hawkins CE, Baars C, Hesterman H, Hocking GJ, Jones ME, Lazenby B, et al. Emerging disease and population decline of an island endemic, the Tasmanian devil Sarcophilus harrisii. Biol Conserv. 2006;131(2):307\u201324. https:\/\/doi.org\/10.1016\/j.biocon.2006.04.010.","journal-title":"Biol Conserv"},{"issue":"3","key":"7994_CR20","doi-asserted-by":"publisher","first-page":"1368","DOI":"10.1111\/1365-2664.13088","volume":"55","author":"BT Lazenby","year":"2018","unstructured":"Lazenby BT, Tobler MW, Brown WE, Hawkins CE, Hocking GJ, Hume F, et al. Density trends and demographic signals uncover the long-term impact of transmissible cancer in Tasmanian devils. J Appl Ecol. 2018;55(3):1368\u201379. https:\/\/doi.org\/10.1111\/1365-2664.13088.","journal-title":"J Appl Ecol"},{"issue":"8","key":"7994_CR21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1007098","volume":"14","author":"A Storfer","year":"2018","unstructured":"Storfer A, Hohenlohe PA, Margres MJ, Patton A, Fraik AK, Lawrance M, et al. The devil is in the details: genomics of transmissible cancers in Tasmanian devils. PLoS Pathog. 2018;14(8):e1007098. https:\/\/doi.org\/10.1371\/journal.ppat.1007098.","journal-title":"PLoS Pathog"},{"key":"7994_CR22","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1126\/science.1180616","volume":"327","author":"EP Murchison","year":"2010","unstructured":"Murchison EP, Tovar C, Hsu A, Bender HS, Kheradpour P, Rebbeck CA, et al. The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. Science (80- ). 2010;327:84\u20137.","journal-title":"Science (80- )"},{"issue":"8","key":"7994_CR23","doi-asserted-by":"publisher","DOI":"10.4161\/onci.25235","volume":"2","author":"HV Siddle","year":"2013","unstructured":"Siddle HV, Kaufman J. How the devil facial tumor disease escapes host immune responses. Oncoimmunology. 2013;2(8):e25235. https:\/\/doi.org\/10.4161\/onci.25235.","journal-title":"Oncoimmunology."},{"key":"7994_CR24","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1016\/j.ccell.2018.03.013","volume":"33","author":"MR Stammnitz","year":"2018","unstructured":"Stammnitz MR, Coorens THH, Gori KC, Hayes D, Fu B, Wang J, et al. The origins and vulnerabilities of two transmissible cancers in Tasmanian devils. Cancer Cell. 2018;33:607\u2013619.e15. https:\/\/doi.org\/10.1016\/j.ccell.2018.03.013.","journal-title":"Cancer Cell"},{"issue":"9","key":"7994_CR25","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pone.0024475","volume":"6","author":"GK Brown","year":"2011","unstructured":"Brown GK, Kreiss A, Lyons AB, Woods GM. Natural killer cell mediated cytotoxic responses in the tasmanian devil. PLoS One. 2011;6(9):1\u201310. https:\/\/doi.org\/10.1371\/journal.pone.0024475.","journal-title":"PLoS One"},{"key":"7994_CR26","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1126\/science.aau8936","volume":"365","author":"A Patchett","year":"2019","unstructured":"Patchett A, Woods G. Targeting transmissible cancers in animals. Science (80- ). 2019;365:438\u201340.","journal-title":"Science (80- )"},{"issue":"13","key":"7994_CR27","doi-asserted-by":"publisher","first-page":"5103","DOI":"10.1073\/pnas.1219920110","volume":"110","author":"HV Siddle","year":"2013","unstructured":"Siddle HV, Kreiss A, Tovar C, Yuen CK, Cheng Y, Belov K, et al. Reversible epigenetic down-regulation of MHC molecules by devil facial tumour disease illustrates immune escape by a contagious cancer. Proc Natl Acad Sci U S A. 2013;110(13):5103\u20138. https:\/\/doi.org\/10.1073\/pnas.1219920110.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"7994_CR28","doi-asserted-by":"publisher","first-page":"1087","DOI":"10.1093\/beheco\/arz054","volume":"30","author":"DG Hamilton","year":"2019","unstructured":"Hamilton DG, Jones ME, Cameron EZ, McCallum H, Storfer A, Hohenlohe PA, et al. Rate of intersexual interactions affects injury likelihood in Tasmanian devil contact networks. Behav Ecol. 2019;30(4):1087\u201395. https:\/\/doi.org\/10.1093\/beheco\/arz054.","journal-title":"Behav Ecol"},{"issue":"1","key":"7994_CR29","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1111\/j.1365-2656.2012.02025.x","volume":"82","author":"RK Hamede","year":"2013","unstructured":"Hamede RK, Mccallum H, Jones M. Biting injuries and transmission of Tasmanian devil facial tumour disease. J Anim Ecol. 2013;82(1):182\u201390. https:\/\/doi.org\/10.1111\/j.1365-2656.2012.02025.x.","journal-title":"J Anim Ecol"},{"issue":"5","key":"7994_CR30","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1111\/j.1365-2656.2007.01272.x","volume":"76","author":"S Lachish","year":"2007","unstructured":"Lachish S, Jones M, McCallum H. The impact of disease on the survival and population growth rate of the Tasmanian devil. J Anim Ecol. 2007;76(5):926\u201336. https:\/\/doi.org\/10.1111\/j.1365-2656.2007.01272.x.","journal-title":"J Anim Ecol"},{"issue":"12","key":"7994_CR31","doi-asserted-by":"publisher","first-page":"3379","DOI":"10.1890\/08-1763.1","volume":"90","author":"H McCallum","year":"2009","unstructured":"McCallum H, Jones M, Hawkins C, Hamede R, Lachish S, Sinn DL, et al. Transmission dynamics of Tasmanian devil facial tumor disease may lead to disease-induced extinction. Ecology. 2009;90(12):3379\u201392. https:\/\/doi.org\/10.1890\/08-1763.1.","journal-title":"Ecology."},{"issue":"6","key":"7994_CR32","doi-asserted-by":"publisher","first-page":"770","DOI":"10.1111\/ele.12776","volume":"20","author":"K Wells","year":"2017","unstructured":"Wells K, Hamede RK, Kerlin DH, Storfer A, Hohenlohe PA, Jones ME, et al. Infection of the fittest: devil facial tumour disease has greatest effect on individuals with highest reproductive output. Ecol Lett. 2017;20(6):770\u20138. https:\/\/doi.org\/10.1111\/ele.12776.","journal-title":"Ecol Lett"},{"issue":"3","key":"7994_CR33","doi-asserted-by":"publisher","DOI":"10.1002\/ecy.2613","volume":"100","author":"K Wells","year":"2019","unstructured":"Wells K, Hamede RK, Jones ME, Hohenlohe PA, Storfer A, McCallum HI. Individual and temporal variation in pathogen load predicts long-term impacts of an emerging infectious disease. Ecology. 2019;100(3):e02613. https:\/\/doi.org\/10.1002\/ecy.2613.","journal-title":"Ecology."},{"issue":"1891","key":"7994_CR34","doi-asserted-by":"publisher","first-page":"20182239","DOI":"10.1098\/rspb.2018.2239","volume":"285","author":"M Ruiz-Aravena","year":"2018","unstructured":"Ruiz-Aravena M, Jones ME, Carver S, Estay S, Espejo C, Storfer A, et al. Sex bias in ability to cope with cancer: Tasmanian devils and facial tumour disease. Proc R Soc B Biol Sci. 2018;285(1891):20182239. https:\/\/doi.org\/10.1098\/rspb.2018.2239.","journal-title":"Proc R Soc B Biol Sci"},{"issue":"29","key":"7994_CR35","doi-asserted-by":"publisher","first-page":"10023","DOI":"10.1073\/pnas.0711236105","volume":"105","author":"ME Jones","year":"2008","unstructured":"Jones ME, Cockburn A, Hamede R, Hawkins C, Hesterman H, Lachish S, et al. Life-history change in disease-ravaged Tasmanian devil populations. Proc Natl Acad Sci U S A. 2008;105(29):10023\u20137. https:\/\/doi.org\/10.1073\/pnas.0711236105.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"7994_CR36","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1111\/j.1365-2656.2008.01494.x","volume":"78","author":"S Lachish","year":"2009","unstructured":"Lachish S, McCallum H, Jones M. Demography, disease and the devil: life-history changes in a disease-affected population of Tasmanian devils (Sarcophilus harrisii). J Anim Ecol. 2009;78(2):427\u201336. https:\/\/doi.org\/10.1111\/j.1365-2656.2008.01494.x.","journal-title":"J Anim Ecol"},{"issue":"1","key":"7994_CR37","doi-asserted-by":"publisher","first-page":"12684","DOI":"10.1038\/ncomms12684","volume":"7","author":"B Epstein","year":"2016","unstructured":"Epstein B, Jones M, Hamede R, Hendricks S, McCallum H, Murchison EP, et al. Rapid evolutionary response to a transmissible cancer in Tasmanian devils. Nat Commun. 2016;7(1):12684. https:\/\/doi.org\/10.1038\/ncomms12684.","journal-title":"Nat Commun"},{"key":"7994_CR38","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pone.0201838","volume":"13","author":"JN Hubert","year":"2018","unstructured":"Hubert JN, Zerjal T, Hospital F. Cancer- and behavior-related genes are targeted by selection in the Tasmanian devil (Sarcophilus harrisii). PLoS One. 2018;13:1\u201315.","journal-title":"PLoS One"},{"issue":"21","key":"7994_CR39","doi-asserted-by":"publisher","first-page":"4189","DOI":"10.1111\/mec.14853","volume":"27","author":"MJ Margres","year":"2018","unstructured":"Margres MJ, Jones ME, Epstein B, Kerlin DH, Comte S, Fox S, et al. Large-effect loci affect survival in Tasmanian devils (Sarcophilus harrisii) infected with a transmissible cancer. Mol Ecol. 2018;27(21):4189\u201399. https:\/\/doi.org\/10.1111\/mec.14853.","journal-title":"Mol Ecol"},{"issue":"11","key":"7994_CR40","doi-asserted-by":"publisher","first-page":"3012","DOI":"10.1093\/gbe\/evy229","volume":"10","author":"MJ Margres","year":"2018","unstructured":"Margres MJ, Ruiz-Aravena M, Hamede R, Jones ME, Lawrance MF, Hendricks SA, et al. The genomic basis of tumor regression in Tasmanian devils (Sarcophilus harrisii). Genome Biol Evol. 2018;10(11):3012\u201325. https:\/\/doi.org\/10.1093\/gbe\/evy229.","journal-title":"Genome Biol Evol"},{"key":"7994_CR41","doi-asserted-by":"publisher","unstructured":"Margres MJ, Ruiz-Aravena M, Hamede R, Chawla K, Patton AH, Lawrance MF, et al. Spontaneous tumor regression in Tasmanian devils associated with RASL11A activation. Genetics. 2020;:genetics.303428.2020. https:\/\/doi.org\/10.1534\/genetics.120.303428.","DOI":"10.1534\/genetics.120.303428"},{"key":"7994_CR42","doi-asserted-by":"crossref","unstructured":"Flies AS, Blackburn NB, Lyons AB, Hayball JD, Woods GM. Comparative analysis of immune checkpoint molecules and their potential role in the transmissible tasmanian devil facial tumor disease. Front Immunol. 2017;8 MAY:1\u201327.","DOI":"10.3389\/fimmu.2017.00513"},{"key":"7994_CR43","doi-asserted-by":"crossref","unstructured":"Flies AS, Bruce Lyons A, Corcoran LM, Papenfuss AT, Murphy JM, Knowles GW, et al. PD-L1 is not constitutively expressed on tasmanian devil facial tumor cells but is strongly upregulated in response to IFN-\u03b3 and can be expressed in the tumor microenvironment. Front Immunol. 2016;7 DEC:1\u201313.","DOI":"10.3389\/fimmu.2016.00581"},{"key":"7994_CR44","doi-asserted-by":"publisher","unstructured":"Kosack L, Wingelhofer B, Popa A, Orlova A, Agerer B, Vilagos B, et al. The ERBB-STAT3 axis drives Tasmanian devil facial tumor disease. Cancer Cell. 2019;35:125\u2013139.e9. https:\/\/doi.org\/10.1016\/j.ccell.2018.11.018.","DOI":"10.1016\/j.ccell.2018.11.018"},{"issue":"17","key":"7994_CR45","doi-asserted-by":"publisher","first-page":"3217","DOI":"10.1111\/mec.15558","volume":"29","author":"CP Kozakiewicz","year":"2020","unstructured":"Kozakiewicz CP, Ricci L, Patton AH, Stahlke AR, Hendricks SA, Margres MJ, et al. Comparative landscape genetics reveals differential effects of environment on host and pathogen genetic structure in Tasmanian devils (Sarcophilus harrisii) and their transmissible tumour. Mol Ecol. 2020;29(17):3217\u201333. https:\/\/doi.org\/10.1111\/mec.15558.","journal-title":"Mol Ecol"},{"issue":"3","key":"7994_CR46","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1038\/s41596-019-0128-8","volume":"14","author":"H Mi","year":"2019","unstructured":"Mi H, Muruganujan A, Huang X, Ebert D, Mills C, Guo X, et al. Protocol update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0). Nat Protoc. 2019;14(3):703\u201321. https:\/\/doi.org\/10.1038\/s41596-019-0128-8.","journal-title":"Nat Protoc"},{"issue":"2","key":"7994_CR47","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/fly.19695","volume":"6","author":"P Cingolani","year":"2012","unstructured":"Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly (Austin). 2012;6(2):80\u201392. https:\/\/doi.org\/10.4161\/fly.19695.","journal-title":"Fly (Austin)"},{"issue":"9","key":"7994_CR48","doi-asserted-by":"publisher","first-page":"e0216838","DOI":"10.1371\/journal.pone.0216838","volume":"14","author":"MO Adetunji","year":"2019","unstructured":"Adetunji MO, Lamont SJ, Abasht B, Schmidt CJ. Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data. PLoS One. 2019;14(9):e0216838\u20138. https:\/\/doi.org\/10.1371\/journal.pone.0216838.","journal-title":"PLoS One"},{"key":"7994_CR49","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.5362","volume":"6","author":"A Coudray","year":"2018","unstructured":"Coudray A, Battenhouse AM, Bucher P, Iyer VR. Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data. PeerJ. 2018;6:e5362. https:\/\/doi.org\/10.7717\/peerj.5362.","journal-title":"PeerJ."},{"issue":"7457","key":"7994_CR50","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1038\/nature12213","volume":"499","author":"MS Lawrence","year":"2013","unstructured":"Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013;499(7457):214\u20138. https:\/\/doi.org\/10.1038\/nature12213.","journal-title":"Nature."},{"issue":"5","key":"7994_CR51","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","volume":"144","author":"D Hanahan","year":"2011","unstructured":"Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144(5):646\u201374. https:\/\/doi.org\/10.1016\/j.cell.2011.02.013.","journal-title":"Cell."},{"issue":"1","key":"7994_CR52","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1016\/S0092-8674(00)81683-9","volume":"100","author":"D Hanahan","year":"2000","unstructured":"Hanahan D, Weinberg RA. The hallmarks of Cancer. Cell. 2000;100(1):57\u201370. https:\/\/doi.org\/10.1016\/S0092-8674(00)81683-9.","journal-title":"Cell."},{"key":"7994_CR53","doi-asserted-by":"publisher","unstructured":"Discher DE, Mooney DJ, Zandstra PW. Growth factors, matrices, and forces combine and control stem cells. Science (80- ). 2009;324:1673\u20131677. https:\/\/doi.org\/10.1126\/science.1171643.","DOI":"10.1126\/science.1171643"},{"issue":"2","key":"7994_CR54","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1002\/path.3031","volume":"226","author":"PG Gritsenko","year":"2012","unstructured":"Gritsenko PG, Ilina O, Friedl P. Interstitial guidance of cancer invasion. J Pathol. 2012;226(2):185\u201399. https:\/\/doi.org\/10.1002\/path.3031.","journal-title":"J Pathol"},{"issue":"10","key":"7994_CR55","doi-asserted-by":"publisher","first-page":"3028","DOI":"10.3390\/ijms19103028","volume":"19","author":"C Walker","year":"2018","unstructured":"Walker C, Mojares E, Del R\u00edo Hern\u00e1ndez A. Role of extracellular matrix in development and cancer progression. Int J Mol Sci. 2018;19(10):3028. https:\/\/doi.org\/10.3390\/ijms19103028.","journal-title":"Int J Mol Sci"},{"issue":"2","key":"7994_CR56","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1016\/j.radi.2006.12.001","volume":"14","author":"I Foster","year":"2008","unstructured":"Foster I. Cancer: a cell cycle defect. Radiography. 2008;14(2):144\u20139. https:\/\/doi.org\/10.1016\/j.radi.2006.12.001.","journal-title":"Radiography."},{"issue":"9","key":"7994_CR57","doi-asserted-by":"publisher","first-page":"3158","DOI":"10.1200\/JCO.1998.16.9.3158","volume":"16","author":"DG Kirsch","year":"1998","unstructured":"Kirsch DG, Kastan MB. Tumor-suppressor p53: implications for tumor development and prognosis. J Clin Oncol. 1998;16(9):3158\u201368. https:\/\/doi.org\/10.1200\/JCO.1998.16.9.3158.","journal-title":"J Clin Oncol"},{"issue":"6","key":"7994_CR58","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1002\/humu.20495","volume":"28","author":"A Petitjean","year":"2007","unstructured":"Petitjean A, Mathe E, Kato S, Ishioka C, Tavtigian SV, Hainaut P, et al. Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: lessons from recent developments in the IARC TP53 database. Hum Mutat. 2007;28(6):622\u20139. https:\/\/doi.org\/10.1002\/humu.20495.","journal-title":"Hum Mutat"},{"issue":"12","key":"7994_CR59","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1038\/nrc3399","volume":"12","author":"NJ Curtin","year":"2012","unstructured":"Curtin NJ. DNA repair dysregulation from cancer driver to therapeutic target. Nat Rev Cancer. 2012;12(12):801\u201317. https:\/\/doi.org\/10.1038\/nrc3399.","journal-title":"Nat Rev Cancer"},{"key":"7994_CR60","doi-asserted-by":"publisher","unstructured":"Chae YK, Anker JF, Carneiro BA, Chandra S, Kaplan J, Kalyan A, et al. Genomic landscape of DNA repair genes in cancer. Oncotarget. 2016;7:23312\u201321. https:\/\/doi.org\/10.18632\/oncotarget.8196.","DOI":"10.18632\/oncotarget.8196"},{"key":"7994_CR61","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1016\/j.pharmthera.2016.02.003","volume":"160","author":"NS Gavande","year":"2016","unstructured":"Gavande NS, VanderVere-Carozza PS, Hinshaw HD, Jalal SI, Sears CR, Pawelczak KS, et al. DNA repair targeted therapy: the past or future of cancer treatment? Pharmacol Ther. 2016;160:65\u201383. https:\/\/doi.org\/10.1016\/j.pharmthera.2016.02.003.","journal-title":"Pharmacol Ther"},{"key":"7994_CR62","doi-asserted-by":"publisher","unstructured":"Varga T, Aplan PD. Chromosomal aberrations induced by double strand DNA breaks. DNA Repair (Amst). 2005;4:1038\u201346. doi:https:\/\/doi.org\/10.1016\/j.dnarep.2005.05.004.","DOI":"10.1016\/j.dnarep.2005.05.004"},{"issue":"1","key":"7994_CR63","doi-asserted-by":"publisher","first-page":"8761","DOI":"10.1038\/s41598-017-08908-9","volume":"7","author":"RL Taylor","year":"2017","unstructured":"Taylor RL, Zhang Y, Sch\u00f6ning JP, Deakin JE. Identification of candidate genes for devil facial tumour disease tumourigenesis. Sci Rep. 2017;7(1):8761. https:\/\/doi.org\/10.1038\/s41598-017-08908-9.","journal-title":"Sci Rep"},{"issue":"1","key":"7994_CR64","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1186\/s12929-017-0374-4","volume":"24","author":"P Czerwi\u0144ska","year":"2017","unstructured":"Czerwi\u0144ska P, Mazurek S, Wiznerowicz M. The complexity of TRIM28 contribution to cancer. J Biomed Sci. 2017;24(1):63. https:\/\/doi.org\/10.1186\/s12929-017-0374-4.","journal-title":"J Biomed Sci"},{"issue":"27","key":"7994_CR65","doi-asserted-by":"publisher","first-page":"44141","DOI":"10.18632\/oncotarget.17390","volume":"8","author":"I Jov\u010devska","year":"2017","unstructured":"Jov\u010devska I, Zupanec N, Urlep \u017d, Vrani\u010d A, Matos B, Stokin CL, et al. Differentially expressed proteins in glioblastoma multiforme identified with a nanobody-based anti-proteome approach and confirmed by OncoFinder as possible tumor-class predictive biomarker candidates. Oncotarget. 2017;8(27):44141\u201358. https:\/\/doi.org\/10.18632\/oncotarget.17390.","journal-title":"Oncotarget."},{"issue":"5","key":"7994_CR66","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1007\/s10147-016-0979-8","volume":"21","author":"Y Wang","year":"2016","unstructured":"Wang Y, Jiang J, Li Q, Ma H, Xu Z, Gao Y. KAP1 is overexpressed in hepatocellular carcinoma and its clinical significance. Int J Clin Oncol. 2016;21(5):927\u201333. https:\/\/doi.org\/10.1007\/s10147-016-0979-8.","journal-title":"Int J Clin Oncol"},{"issue":"2","key":"7994_CR67","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1006\/dbio.2000.9887","volume":"227","author":"A Brennan","year":"2000","unstructured":"Brennan A, Dean CH, Zhang AL, Cass DT, Mirsky R, Jessen KR. Endothelins control the timing of Schwann cell generation in vitro and in vivo. Dev Biol. 2000;227(2):545\u201357. https:\/\/doi.org\/10.1006\/dbio.2000.9887.","journal-title":"Dev Biol"},{"issue":"7","key":"7994_CR68","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1038\/nn.2323","volume":"12","author":"A Woodhoo","year":"2009","unstructured":"Woodhoo A, Alonso MBD, Droggiti A, Turmaine M, D\u2019Antonio M, Parkinson DB, et al. Notch controls embryonic Schwann cell differentiation, postnatal myelination and adult plasticity. Nat Neurosci. 2009;12(7):839\u201347. https:\/\/doi.org\/10.1038\/nn.2323.","journal-title":"Nat Neurosci"},{"issue":"10","key":"7994_CR69","doi-asserted-by":"publisher","first-page":"20160553","DOI":"10.1098\/rsbl.2016.0553","volume":"12","author":"R Pye","year":"2016","unstructured":"Pye R, Hamede R, Siddle HV, Caldwell A, Knowles GW, Swift K, et al. Demonstration of immune responses against devil facial tumour disease in wild Tasmanian devils. Biol Lett. 2016;12(10):20160553. https:\/\/doi.org\/10.1098\/rsbl.2016.0553.","journal-title":"Biol Lett"},{"issue":"1","key":"7994_CR70","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.1038\/s41467-017-01027-z","volume":"8","author":"D Aran","year":"2017","unstructured":"Aran D, Camarda R, Odegaard J, Paik H, Oskotsky B, Krings G, et al. Comprehensive analysis of normal adjacent to tumor transcriptomes. Nat Commun. 2017;8(1):1077. https:\/\/doi.org\/10.1038\/s41467-017-01027-z.","journal-title":"Nat Commun"},{"issue":"1","key":"7994_CR71","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1007\/s00262-013-1480-0","volume":"63","author":"DW Gutkin","year":"2014","unstructured":"Gutkin DW, Shurin MR. Clinical evaluation of systemic and local immune responses in cancer: time for integration. Cancer Immunol Immunother. 2014;63(1):45\u201357. https:\/\/doi.org\/10.1007\/s00262-013-1480-0.","journal-title":"Cancer Immunol Immunother"},{"key":"7994_CR72","doi-asserted-by":"publisher","unstructured":"Fraik AK, Margres MJ, Epstein B, Barbosa S, Jones M, Hendricks S, et al. Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations. Evolution (N Y). 2020. https:\/\/doi.org\/10.1111\/evo.14023.","DOI":"10.1111\/evo.14023"},{"issue":"10","key":"7994_CR73","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3390\/genes10100801","volume":"10","author":"AK Fraik","year":"2019","unstructured":"Fraik AK, Quackenbush C, Margres MJ, Comte S, Hamilton DG, Kozakiewicz CP, et al. Transcriptomics of Tasmanian devil (Sarcophilus harrisii) ear tissue reveals homogeneous gene expression patterns across a heterogeneous landscape. Genes (Basel). 2019;10(10):1\u201315. https:\/\/doi.org\/10.3390\/genes10100801.","journal-title":"Genes (Basel)"},{"issue":"7","key":"7994_CR74","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0179741","volume":"12","author":"Z Zhang","year":"2017","unstructured":"Zhang Z, Chang Y, Zhang J, Lu Y, Zheng L, Hu Y, et al. HMGB3 promotes growth and migration in colorectal cancer by regulating WNT\/\u03b2-catenin pathway. PLoS One. 2017;12(7):e0179741. https:\/\/doi.org\/10.1371\/journal.pone.0179741.","journal-title":"PLoS One"},{"issue":"37","key":"7994_CR75","doi-asserted-by":"publisher","first-page":"13783","DOI":"10.1073\/pnas.0604006103","volume":"103","author":"MJ Nemeth","year":"2006","unstructured":"Nemeth MJ, Kirby MR, Bodine DM. Hmgb3 regulates the balance between hematopoietic stem cell self-renewal and differentiation. Proc Natl Acad Sci. 2006;103(37):13783\u20138. https:\/\/doi.org\/10.1073\/pnas.0604006103.","journal-title":"Proc Natl Acad Sci"},{"issue":"6","key":"7994_CR76","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1038\/s41419-020-2685-8","volume":"11","author":"D Sun","year":"2020","unstructured":"Sun D, Cao H, Yang L, Lin L, Hou B, Zheng W, et al. MiR-200b in heme oxygenase-1-modified bone marrow mesenchymal stem cell-derived exosomes alleviates inflammatory injury of intestinal epithelial cells by targeting high mobility group box 3. Cell Death Dis. 2020;11(6):480. https:\/\/doi.org\/10.1038\/s41419-020-2685-8.","journal-title":"Cell Death Dis"},{"issue":"7269","key":"7994_CR77","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1038\/nature08512","volume":"462","author":"H Yanai","year":"2009","unstructured":"Yanai H, Ban T, Wang Z, Choi MK, Kawamura T, Negishi H, et al. HMGB proteins function as universal sentinels for nucleic-acid-mediated innate immune responses. Nature. 2009;462(7269):99\u2013103. https:\/\/doi.org\/10.1038\/nature08512.","journal-title":"Nature."},{"issue":"1","key":"7994_CR78","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.coi.2010.11.006","volume":"23","author":"SE Ewald","year":"2011","unstructured":"Ewald SE, Barton GM. Nucleic acid sensing toll-like receptors in autoimmunity. Curr Opin Immunol. 2011;23(1):3\u20139. https:\/\/doi.org\/10.1016\/j.coi.2010.11.006.","journal-title":"Curr Opin Immunol"},{"issue":"6894","key":"7994_CR79","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1038\/nature00858","volume":"418","author":"P Scaffidi","year":"2002","unstructured":"Scaffidi P, Misteli T, Bianchi ME. Release of chromatin protein HMGB1 by necrotic cells triggers inflammation. Nature. 2002;418(6894):191\u20135. https:\/\/doi.org\/10.1038\/nature00858.","journal-title":"Nature."},{"issue":"1","key":"7994_CR80","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1158\/2159-8290.CD-15-0341","volume":"6","author":"M Neupane","year":"2016","unstructured":"Neupane M, Clark AP, Landini S, Birkbak NJ, Eklund AC, Lim E, et al. MECP2 is a frequently amplified oncogene with a novel epigenetic mechanism that mimics the role of activated RAS in malignancy. Cancer Discov. 2016;6(1):45\u201358. https:\/\/doi.org\/10.1158\/2159-8290.CD-15-0341.","journal-title":"Cancer Discov"},{"key":"7994_CR81","unstructured":"Zajchowski DA, Bartholdi MF, Gong Y, Webster L, Liu H-L, Munishkin A, et al. Identification of Gene Expression Profiles That Predict the Aggressive Behavior of Breast Cancer Cells. Cancer Res. 2001;61:5168 LP \u2013 5178. http:\/\/cancerres.aacrjournals.org\/content\/61\/13\/5168.abstract."},{"issue":"1","key":"7994_CR82","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/ncomms10798","volume":"7","author":"D Zhang","year":"2016","unstructured":"Zhang D, Park D, Zhong Y, Lu Y, Rycaj K, Gong S, et al. Stem cell and neurogenic gene-expression profiles link prostate basal cells to aggressive prostate cancer. Nat Commun. 2016;7(1):1\u201315. https:\/\/doi.org\/10.1038\/ncomms10798.","journal-title":"Nat Commun"},{"issue":"1","key":"7994_CR83","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1186\/s13059-015-0732-z","volume":"16","author":"PA Ruzycki","year":"2015","unstructured":"Ruzycki PA, Tran NM, Kefalov VJ, Kolesnikov AV, Chen S. Graded gene expression changes determine phenotype severity in mouse models of CRX-associated retinopathies. Genome Biol. 2015;16(1):171. https:\/\/doi.org\/10.1186\/s13059-015-0732-z.","journal-title":"Genome Biol"},{"issue":"3","key":"7994_CR84","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1016\/j.trsl.2015.02.004","volume":"166","author":"GYF Ho","year":"2015","unstructured":"Ho GYF, Jung HJ, Schoen RE, Wang T, Lin J, Williams Z, et al. Differential expression of circulating microRNAs according to severity of colorectal neoplasia. Transl Res. 2015;166(3):225\u201332. https:\/\/doi.org\/10.1016\/j.trsl.2015.02.004.","journal-title":"Transl Res"},{"issue":"1","key":"7994_CR85","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1111\/j.1523-1739.2011.01747.x","volume":"26","author":"RK Hamede","year":"2012","unstructured":"Hamede RK, Lachish S, Belov K, Woods G, Kreiss A, Pearse AM, et al. Reduced effect of Tasmanian devil facial tumor disease at the disease front. Conserv Biol. 2012;26(1):124\u201334. https:\/\/doi.org\/10.1111\/j.1523-1739.2011.01747.x.","journal-title":"Conserv Biol"},{"issue":"1814","key":"7994_CR86","doi-asserted-by":"publisher","first-page":"20151468","DOI":"10.1098\/rspb.2015.1468","volume":"282","author":"RK Hamede","year":"2015","unstructured":"Hamede RK, Pearse AM, Swift K, Barmuta LA, Murchison EP, Jones ME. Transmissible cancer in Tasmanian devils: localized lineage replacement and host population response. Proc R Soc B Biol Sci. 2015;282(1814):20151468. https:\/\/doi.org\/10.1098\/rspb.2015.1468.","journal-title":"Proc R Soc B Biol Sci"},{"key":"7994_CR87","doi-asserted-by":"crossref","unstructured":"Patton AH, Lawrance M, Margres MJ, Kozakiewicz CP, Hamede R, Ruiz-Aravena M, et al. A transmissible cancer shifts from emergence to endemism in Tasmanian devils. Science (80- ). 2020;370:eabb9772.","DOI":"10.1126\/science.abb9772"},{"key":"7994_CR88","doi-asserted-by":"publisher","unstructured":"Kwon YM, Gori K, Park N, Potts N, Swift K, Wang J, et al. Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils 2020. https:\/\/doi.org\/10.1371\/journal.pbio.3000926, 18, 11, e3000926.","DOI":"10.1371\/journal.pbio.3000926"},{"issue":"4","key":"7994_CR89","doi-asserted-by":"publisher","first-page":"972","DOI":"10.1111\/1365-2656.13166","volume":"89","author":"DJ Becker","year":"2020","unstructured":"Becker DJ, Albery GF, Kessler MK, Lunn TJ, Falvo CA, Czirj\u00e1k G\u00c1, et al. Macroimmunology: the drivers and consequences of spatial patterns in wildlife immune defence. J Anim Ecol. 2020;89(4):972\u201395. https:\/\/doi.org\/10.1111\/1365-2656.13166.","journal-title":"J Anim Ecol"},{"issue":"1","key":"7994_CR90","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-016-0956-2","volume":"17","author":"CR Williams","year":"2016","unstructured":"Williams CR, Baccarella A, Parrish JZ, Kim CC. Trimming of sequence reads alters RNA-Seq gene expression estimates. BMC Bioinformatics. 2016;17(1):1\u201313. https:\/\/doi.org\/10.1186\/s12859-016-0956-2.","journal-title":"BMC Bioinformatics"},{"key":"7994_CR91","doi-asserted-by":"publisher","unstructured":"Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. RNA-seq experiments with HISAT, StringTie and Ballgown , Nat Protoc 2016;11:1650\u20131667. doi:https:\/\/doi.org\/10.1038\/nprot.2016-095, 9.","DOI":"10.1038\/nprot.2016-095"},{"issue":"8","key":"7994_CR92","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","volume":"37","author":"D Kim","year":"2019","unstructured":"Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37(8):907\u201315. https:\/\/doi.org\/10.1038\/s41587-019-0201-4.","journal-title":"Nat Biotechnol"},{"issue":"1","key":"7994_CR93","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-019-1910-1","volume":"20","author":"S Kovaka","year":"2019","unstructured":"Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol. 2019;20(1):1\u201313. https:\/\/doi.org\/10.1186\/s13059-019-1910-1.","journal-title":"Genome Biol"},{"key":"7994_CR94","doi-asserted-by":"publisher","first-page":"D682","DOI":"10.1093\/nar\/gkz966","volume":"48","author":"AD Yates","year":"2019","unstructured":"Yates AD, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J, et al. Ensembl 2020. Nucleic Acids Res. 2019;48:D682\u20138. https:\/\/doi.org\/10.1093\/nar\/gkz966.","journal-title":"Nucleic Acids Res"},{"key":"7994_CR95","doi-asserted-by":"crossref","unstructured":"Pertea M, Pertea G. GFF Utilities: GffRead and GffCompare. F1000Research. 2020;9:1\u201317.","DOI":"10.12688\/f1000research.23297.1"},{"key":"7994_CR96","doi-asserted-by":"crossref","unstructured":"Soneson C, Love MI, Robinson MD. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research. 2015;4.","DOI":"10.12688\/f1000research.7563.1"},{"issue":"1","key":"7994_CR97","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2010","unstructured":"Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139\u201340. https:\/\/doi.org\/10.1093\/bioinformatics\/btp616.","journal-title":"Bioinformatics."},{"key":"7994_CR98","doi-asserted-by":"crossref","unstructured":"Lun ATL, Chen Y, Smyth GK. It\u2019s DE-licious: a recipe for differential expression analyses of RNA-seq experiments using quasi-likelihood methods in edgeR. In: Statistical Genomics. Springer; 2016. p. 391\u2013416.","DOI":"10.1007\/978-1-4939-3578-9_19"},{"issue":"7","key":"7994_CR99","doi-asserted-by":"publisher","first-page":"e47","DOI":"10.1093\/nar\/gkv007","volume":"43","author":"ME Ritchie","year":"2015","unstructured":"Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47\u20137. https:\/\/doi.org\/10.1093\/nar\/gkv007.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"7994_CR100","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995;57(1):289\u2013300. https:\/\/doi.org\/10.1111\/j.2517-6161.1995.tb02031.x.","journal-title":"J R Stat Soc Ser B"},{"issue":"92","key":"7994_CR101","doi-asserted-by":"publisher","first-page":"20130950","DOI":"10.1098\/rsif.2013.0950","volume":"11","author":"G Hong","year":"2014","unstructured":"Hong G, Zhang W, Li H, Shen X, Guo Z. Separate enrichment analysis of pathways for up- and downregulated genes. J R Soc Interface. 2014;11(92):20130950. https:\/\/doi.org\/10.1098\/rsif.2013.0950.","journal-title":"J R Soc Interface"},{"issue":"7","key":"7994_CR102","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0021800","volume":"6","author":"F Supek","year":"2011","unstructured":"Supek F, Bo\u0161njak M, \u0160kunca N, \u0160muc T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One. 2011;6(7):e21800. https:\/\/doi.org\/10.1371\/journal.pone.0021800.","journal-title":"PLoS One"},{"issue":"3","key":"7994_CR103","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1038\/ng1180","volume":"34","author":"VK Mootha","year":"2003","unstructured":"Mootha VK, Lindgren CM, Eriksson K-F, Subramanian A, Sihag S, Lehar J, et al. PGC-1\u03b1-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003;34(3):267\u201373. https:\/\/doi.org\/10.1038\/ng1180.","journal-title":"Nat Genet"},{"issue":"43","key":"7994_CR104","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545\u201350. https:\/\/doi.org\/10.1073\/pnas.0506580102.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"D1","key":"7994_CR105","doi-asserted-by":"publisher","first-page":"D649","DOI":"10.1093\/nar\/gkx1132","volume":"46","author":"A Fabregat","year":"2018","unstructured":"Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, et al. The Reactome pathway knowledgebase. Nucleic Acids Res. 2018;46(D1):D649\u201355. https:\/\/doi.org\/10.1093\/nar\/gkx1132.","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"7994_CR106","doi-asserted-by":"publisher","first-page":"e13984","DOI":"10.1371\/journal.pone.0013984","volume":"5","author":"D Merico","year":"2010","unstructured":"Merico D, Isserlin R, Stueker O, Emili A, Bader GD. Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One. 2010;5(11):e13984. https:\/\/doi.org\/10.1371\/journal.pone.0013984.","journal-title":"PLoS One"},{"key":"7994_CR107","doi-asserted-by":"publisher","unstructured":"Kucera M, Isserlin R, Arkhangorodsky A, Bader GD. AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations. F1000Research. 2016;5:1717. doi:https:\/\/doi.org\/10.12688\/f1000research.9090.1.","DOI":"10.12688\/f1000research.9090.1"},{"issue":"11","key":"7994_CR108","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303.metabolite","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models. Genome Res. 2003;13(11):2498\u2013504. https:\/\/doi.org\/10.1101\/gr.1239303.metabolite.","journal-title":"Genome Res"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-021-07994-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12864-021-07994-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-021-07994-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,27]],"date-time":"2021-09-27T13:07:01Z","timestamp":1632748021000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-021-07994-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,9,27]]},"references-count":108,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["7994"],"URL":"https:\/\/doi.org\/10.1186\/s12864-021-07994-4","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,9,27]]},"assertion":[{"value":"10 February 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 September 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 September 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All methods were carried out in accordance with relevant guidelines and regulations. All research involving use of animals and field activity was performed in compliance with the ARRIVE guidelines, under University of Tasmania ethics approval A13326 and Washington State University IACUC approval ASAF 6796,","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"698"}}