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Transcriptomic regulation of seasonal coat color change in hares.

Ferreira MS, Alves PC, Callahan CM, Giska I, Farelo L, Jenny H, Mills LS, Hackländer K, Good JM, Melo-Ferreira J.

Ecol Evol. 2020 Jan 15;10(3):1180-1192. doi: 10.1002/ece3.5956. eCollection 2020 Feb.


ACTN2 variant associated with a cardiac phenotype suggestive of left-dominant arrhythmogenic cardiomyopathy.

Good JM, Fellmann F, Bhuiyan ZA, Rotman S, Pruvot E, Schläpfer J.

HeartRhythm Case Rep. 2019 Oct 7;6(1):15-19. doi: 10.1016/j.hrcr.2019.10.001. eCollection 2020 Jan. No abstract available.


An Annotated Draft Genome of the Mountain Hare (Lepus timidus).

Marques JP, Seixas FA, Farelo L, Callahan CM, Good JM, Montgomery WI, Reid N, Alves PC, Boursot P, Melo-Ferreira J.

Genome Biol Evol. 2020 Jan 1;12(1):3656-3662. doi: 10.1093/gbe/evz273.


A New Variant in the MYH11 Gene in a Familial Case of Thoracic Aortic Aneurysm.

Pucci L, Pointet A, Good JM, Davoine E, Cina V, Zanchi F, Deglise S, Duchosal LM, Kirsch M.

Ann Thorac Surg. 2020 Apr;109(4):e279-e281. doi: 10.1016/j.athoracsur.2019.07.030. Epub 2019 Aug 29.


The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards.

Harris RB, Irwin K, Jones MR, Laurent S, Barrett RDH, Nachman MW, Good JM, Linnen CR, Jensen JD, Pfeifer SP.

Heredity (Edinb). 2020 Jan;124(1):1-14. doi: 10.1038/s41437-019-0257-4. Epub 2019 Aug 9. Review.


Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change.

Bi K, Linderoth T, Singhal S, Vanderpool D, Patton JL, Nielsen R, Moritz C, Good JM.

PLoS Genet. 2019 May 3;15(5):e1008119. doi: 10.1371/journal.pgen.1008119. eCollection 2019 May.


A high-throughput method for unbiased quantitation and categorization of nuclear morphology†.

Skinner BM, Rathje CC, Bacon J, Johnson EEP, Larson EL, Kopania EEK, Good JM, Yousafzai G, Affara NA, Ellis PJI.

Biol Reprod. 2019 May 1;100(5):1250-1260. doi: 10.1093/biolre/ioz013.


Automated Nuclear Cartography Reveals Conserved Sperm Chromosome Territory Localization across 2 Million Years of Mouse Evolution.

Skinner BM, Bacon J, Rathje CC, Larson EL, Kopania EEK, Good JM, Affara NA, Ellis PJI.

Genes (Basel). 2019 Feb 1;10(2). pii: E109. doi: 10.3390/genes10020109.


The genomic basis of environmental adaptation in house mice.

Phifer-Rixey M, Bi K, Ferris KG, Sheehan MJ, Lin D, Mack KL, Keeble SM, Suzuki TA, Good JM, Nachman MW.

PLoS Genet. 2018 Sep 24;14(9):e1007672. doi: 10.1371/journal.pgen.1007672. eCollection 2018 Sep.


Spermatogenesis and the Evolution of Mammalian Sex Chromosomes.

Larson EL, Kopania EEK, Good JM.

Trends Genet. 2018 Sep;34(9):722-732. doi: 10.1016/j.tig.2018.06.003. Epub 2018 Aug 1. Review.


Cascading speciation among mutualists and antagonists in a tree-beetle-fungi interaction.

Bracewell RR, Vanderpool D, Good JM, Six DL.

Proc Biol Sci. 2018 Jun 27;285(1881). pii: 20180694. doi: 10.1098/rspb.2018.0694.


Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares.

Jones MR, Mills LS, Alves PC, Callahan CM, Alves JM, Lafferty DJR, Jiggins FM, Jensen JD, Melo-Ferreira J, Good JM.

Science. 2018 Jun 22;360(6395):1355-1358. doi: 10.1126/science.aar5273.


The Evolution of Polymorphic Hybrid Incompatibilities in House Mice.

Larson EL, Vanderpool D, Sarver BAJ, Callahan C, Keeble S, Provencio LL, Kessler MD, Stewart V, Nordquist E, Dean MD, Good JM.

Genetics. 2018 Jul;209(3):845-859. doi: 10.1534/genetics.118.300840. Epub 2018 Apr 24.


Function and underlying mechanisms of seasonal colour moulting in mammals and birds: what keeps them changing in a warming world?

Zimova M, Hackländer K, Good JM, Melo-Ferreira J, Alves PC, Mills LS.

Biol Rev Camb Philos Soc. 2018 Aug;93(3):1478-1498. doi: 10.1111/brv.12405. Epub 2018 Mar 5. Review.


Winter color polymorphisms identify global hot spots for evolutionary rescue from climate change.

Mills LS, Bragina EV, Kumar AV, Zimova M, Lafferty DJR, Feltner J, Davis BM, Hackländer K, Alves PC, Good JM, Melo-Ferreira J, Dietz A, Abramov AV, Lopatina N, Fay K.

Science. 2018 Mar 2;359(6379):1033-1036. doi: 10.1126/science.aan8097. Epub 2018 Feb 15.


Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares.

Marques JP, Ferreira MS, Farelo L, Callahan CM, Hackländer K, Jenny H, Montgomery WI, Reid N, Good JM, Alves PC, Melo-Ferreira J.

Sci Data. 2017 Dec 5;4:170178. doi: 10.1038/sdata.2017.178.


Maturation of Cerebellar Purkinje Cell Population Activity during Postnatal Refinement of Climbing Fiber Network.

Good JM, Mahoney M, Miyazaki T, Tanaka KF, Sakimura K, Watanabe M, Kitamura K, Kano M.

Cell Rep. 2017 Nov 21;21(8):2066-2073. doi: 10.1016/j.celrep.2017.10.101.


Rapid neo-sex chromosome evolution and incipient speciation in a major forest pest.

Bracewell RR, Bentz BJ, Sullivan BT, Good JM.

Nat Commun. 2017 Nov 17;8(1):1593. doi: 10.1038/s41467-017-01761-4.


Whole exome sequencing of wild-derived inbred strains of mice improves power to link phenotype and genotype.

Chang PL, Kopania E, Keeble S, Sarver BAJ, Larson E, Orth A, Belkhir K, Boursot P, Bonhomme F, Good JM, Dean MD.

Mamm Genome. 2017 Oct;28(9-10):416-425. doi: 10.1007/s00335-017-9704-9. Epub 2017 Aug 17.


The transcriptional landscape of seasonal coat colour moult in the snowshoe hare.

Ferreira MS, Alves PC, Callahan CM, Marques JP, Mills LS, Good JM, Melo-Ferreira J.

Mol Ecol. 2017 Aug;26(16):4173-4185. doi: 10.1111/mec.14177. Epub 2017 Jun 7.


Phylogenomic Insights into Mouse Evolution Using a Pseudoreference Approach.

Sarver BA, Keeble S, Cosart T, Tucker PK, Dean MD, Good JM.

Genome Biol Evol. 2017 Mar 1;9(3):726-739. doi: 10.1093/gbe/evx034.


Comparative Phylogenomic Assessment of Mitochondrial Introgression among Several Species of Chipmunks (Tamias).

Sarver BA, Demboski JR, Good JM, Forshee N, Hunter SS, Sullivan J.

Genome Biol Evol. 2017 Jan 1;9(1):7-19. doi: 10.1093/gbe/evw254.


Range expansion underlies historical introgressive hybridization in the Iberian hare.

Marques JP, Farelo L, Vilela J, Vanderpool D, Alves PC, Good JM, Boursot P, Melo-Ferreira J.

Sci Rep. 2017 Jan 25;7:40788. doi: 10.1038/srep40788.


The Composite Regulatory Basis of the Large X-Effect in Mouse Speciation.

Larson EL, Keeble S, Vanderpool D, Dean MD, Good JM.

Mol Biol Evol. 2017 Feb 1;34(2):282-295. doi: 10.1093/molbev/msw243.


Genomic imprinting, disrupted placental expression, and speciation.

Brekke TD, Henry LA, Good JM.

Evolution. 2016 Dec;70(12):2690-2703. doi: 10.1111/evo.13085. Epub 2016 Oct 28.


Contrasting Levels of Molecular Evolution on the Mouse X Chromosome.

Larson EL, Vanderpool D, Keeble S, Zhou M, Sarver BA, Smith AD, Dean MD, Good JM.

Genetics. 2016 Aug;203(4):1841-57. doi: 10.1534/genetics.116.186825. Epub 2016 Jun 17.


Genomics of hybridization and its evolutionary consequences.

Abbott RJ, Barton NH, Good JM.

Mol Ecol. 2016 Jun;25(11):2325-32. doi: 10.1111/mec.13685. No abstract available.


Harnessing the power of RADseq for ecological and evolutionary genomics.

Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA.

Nat Rev Genet. 2016 Feb;17(2):81-92. doi: 10.1038/nrg.2015.28. Epub 2016 Jan 5. Review.


Targeted capture in evolutionary and ecological genomics.

Jones MR, Good JM.

Mol Ecol. 2016 Jan;25(1):185-202. doi: 10.1111/mec.13304. Epub 2015 Jul 30. Review.


Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks.

Good JM, Vanderpool D, Keeble S, Bi K.

Evolution. 2015 Aug;69(8):1961-72. doi: 10.1111/evo.12712. Epub 2015 Jul 21.


Genetic and phenotypic influences on copulatory plug survival in mice.

Mangels R, Young B, Keeble S, Ardekani R, Meslin C, Ferreira Z, Clark NL, Good JM, Dean MD.

Heredity (Edinb). 2015 Dec;115(6):496-502. doi: 10.1038/hdy.2015.50. Epub 2015 Jun 24.


Developmental stress increases reproductive success in male zebra finches.

Crino OL, Prather CT, Driscoll SC, Good JM, Breuner CW.

Proc Biol Sci. 2014 Nov 22;281(1795). pii: 20141266. doi: 10.1098/rspb.2014.1266.


Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.

Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alföldi J, Martinez Barrio A, Pielberg G, Rafati N, Sayyab S, Turner-Maier J, Younis S, Afonso S, Aken B, Alves JM, Barrell D, Bolet G, Boucher S, Burbano HA, Campos R, Chang JL, Duranthon V, Fontanesi L, Garreau H, Heiman D, Johnson J, Mage RG, Peng Z, Queney G, Rogel-Gaillard C, Ruffier M, Searle S, Villafuerte R, Xiong A, Young S, Forsberg-Nilsson K, Good JM, Lander ES, Ferrand N, Lindblad-Toh K, Andersson L.

Science. 2014 Aug 29;345(6200):1074-1079. doi: 10.1126/science.1253714.


The genomic architecture of population divergence between subspecies of the European rabbit.

Carneiro M, Albert FW, Afonso S, Pereira RJ, Burbano H, Campos R, Melo-Ferreira J, Blanco-Aguiar JA, Villafuerte R, Nachman MW, Good JM, Ferrand N.

PLoS Genet. 2014 Aug 28;10(8):e1003519. doi: 10.1371/journal.pgen.1003519. eCollection 2014 Aug.


Parent-of-origin growth effects and the evolution of hybrid inviability in dwarf hamsters.

Brekke TD, Good JM.

Evolution. 2014 Nov;68(11):3134-48. doi: 10.1111/evo.12500. Epub 2014 Sep 10.


Divergence with gene flow within the recent chipmunk radiation (Tamias).

Sullivan J, Demboski JR, Bell KC, Hird S, Sarver B, Reid N, Good JM.

Heredity (Edinb). 2014 Sep;113(3):185-94. doi: 10.1038/hdy.2014.27. Epub 2014 Apr 30. Review.


Unlocking the vault: next-generation museum population genomics.

Bi K, Linderoth T, Vanderpool D, Good JM, Nielsen R, Moritz C.

Mol Ecol. 2013 Dec;22(24):6018-32. doi: 10.1111/mec.12516. Epub 2013 Oct 7.


Comparative population genomics of the ejaculate in humans and the great apes.

Good JM, Wiebe V, Albert FW, Burbano HA, Kircher M, Green RE, Halbwax M, André C, Atencia R, Fischer A, Pääbo S.

Mol Biol Evol. 2013 Apr;30(4):964-76. doi: 10.1093/molbev/mst005. Epub 2013 Jan 16.


Meiotic sex chromosome inactivation is disrupted in sterile hybrid male house mice.

Campbell P, Good JM, Nachman MW.

Genetics. 2013 Mar;193(3):819-28. doi: 10.1534/genetics.112.148635. Epub 2013 Jan 10.


The conflict within and the escalating war between the sex chromosomes.

Good JM.

PLoS Genet. 2012 Sep;8(9):e1002955. doi: 10.1371/journal.pgen.1002955. Epub 2012 Sep 13. No abstract available.


Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales.

Bi K, Vanderpool D, Singhal S, Linderoth T, Moritz C, Good JM.

BMC Genomics. 2012 Aug 17;13:403. doi: 10.1186/1471-2164-13-403.


The bonobo genome compared with the chimpanzee and human genomes.

Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoç E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, André C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MH, Andrés AM, Kelso J, Pääbo S.

Nature. 2012 Jun 28;486(7404):527-31. doi: 10.1038/nature11128.


The contribution of the Y chromosome to hybrid male sterility in house mice.

Campbell P, Good JM, Dean MD, Tucker PK, Nachman MW.

Genetics. 2012 Aug;191(4):1271-81. doi: 10.1534/genetics.112.141804. Epub 2012 May 17.


A novel mutation in SCN4A causes severe myotonia and school-age-onset paralytic episodes.

Yoshinaga H, Sakoda S, Good JM, Takahashi MP, Kubota T, Arikawa-Hirasawa E, Nakata T, Ohno K, Kitamura T, Kobayashi K, Ohtsuka Y.

J Neurol Sci. 2012 Apr 15;315(1-2):15-9. doi: 10.1016/j.jns.2011.12.015. Epub 2012 Jan 16.


Reduced representation methods for subgenomic enrichment and next-generation sequencing.

Good JM.

Methods Mol Biol. 2011;772:85-103. doi: 10.1007/978-1-61779-228-1_5. Review.


On characterizing adaptive events unique to modern humans.

Crisci JL, Wong A, Good JM, Jensen JD.

Genome Biol Evol. 2011;3:791-8. doi: 10.1093/gbe/evr075. Epub 2011 Jul 29.


Bonobos fall within the genomic variation of chimpanzees.

Fischer A, Prüfer K, Good JM, Halbwax M, Wiebe V, André C, Atencia R, Mugisha L, Ptak SE, Pääbo S.

PLoS One. 2011;6(6):e21605. doi: 10.1371/journal.pone.0021605. Epub 2011 Jun 29.


Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection.

Albert FW, Hodges E, Jensen JD, Besnier F, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Good JM, Green RE, Burbano HA, Plyusnina IZ, Trut L, Andersson L, Schöneberg T, Carlborg O, Hannon GJ, Pääbo S.

Heredity (Edinb). 2011 Sep;107(3):205-14. doi: 10.1038/hdy.2011.4. Epub 2011 Feb 9.


Extraordinary sequence divergence at Tsga8, an X-linked gene involved in mouse spermiogenesis.

Good JM, Vanderpool D, Smith KL, Nachman MW.

Mol Biol Evol. 2011 May;28(5):1675-86. doi: 10.1093/molbev/msq348. Epub 2010 Dec 24.


Genetic history of an archaic hominin group from Denisova Cave in Siberia.

Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, Pääbo S.

Nature. 2010 Dec 23;468(7327):1053-60. doi: 10.1038/nature09710.

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