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Items: 1 to 50 of 112

1.

Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses.

Yourick MR, Sandkam BA, Gammerdinger WJ, Escobar-Camacho D, Nandamuri SP, Clark FE, Joyce B, Conte MA, Kocher TD, Carleton KL.

Mol Ecol Resour. 2019 Jul 20. doi: 10.1111/1755-0998.13062. [Epub ahead of print]

PMID:
31325910
2.

Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes.

Conte MA, Joshi R, Moore EC, Nandamuri SP, Gammerdinger WJ, Roberts RB, Carleton KL, Lien S, Kocher TD.

Gigascience. 2019 Apr 1;8(4). pii: giz030. doi: 10.1093/gigascience/giz030.

3.

Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes.

Clark FE, Conte MA, Kocher TD.

Genes (Basel). 2018 Dec 5;9(12). pii: E610. doi: 10.3390/genes9120610.

4.

Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.

Gammerdinger WJ, Kocher TD.

Genes (Basel). 2018 Oct 4;9(10). pii: E480. doi: 10.3390/genes9100480. Review.

5.

Understanding Student Perceptions and Practices for Pre-Lecture Content Reading in the Genetics Classroom.

Gammerdinger WJ, Kocher TD.

J Microbiol Biol Educ. 2018 Jul 31;19(2). pii: jmbe-19-79. doi: 10.1128/jmbe.v19i2.1371. eCollection 2018.

6.

Transcriptome display during tilapia sex determination and differentiation as revealed by RNA-Seq analysis.

Tao W, Chen J, Tan D, Yang J, Sun L, Wei J, Conte MA, Kocher TD, Wang D.

BMC Genomics. 2018 May 15;19(1):363. doi: 10.1186/s12864-018-4756-0.

7.

Novel Sex Chromosomes in 3 Cichlid Fishes from Lake Tanganyika.

Gammerdinger WJ, Conte MA, Sandkam BA, Ziegelbecker A, Koblmüller S, Kocher TD.

J Hered. 2018 Jun 27;109(5):489-500. doi: 10.1093/jhered/esy003.

PMID:
29444291
8.

A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions.

Conte MA, Gammerdinger WJ, Bartie KL, Penman DJ, Kocher TD.

BMC Genomics. 2017 May 2;18(1):341. doi: 10.1186/s12864-017-3723-5.

9.

An allelic series at pax7a is associated with colour polymorphism diversity in Lake Malawi cichlid fish.

Roberts RB, Moore EC, Kocher TD.

Mol Ecol. 2017 May;26(10):2625-2639. doi: 10.1111/mec.13975. Epub 2017 Jan 21.

10.

Comparative analysis of a sex chromosome from the blackchin tilapia, Sarotherodon melanotheron.

Gammerdinger WJ, Conte MA, Baroiller JF, D'Cotta H, Kocher TD.

BMC Genomics. 2016 Oct 18;17(1):808.

11.

Dynamic Sequence Evolution of a Sex-Associated B Chromosome in Lake Malawi Cichlid Fish.

Clark FE, Conte MA, Ferreira-Bravo IA, Poletto AB, Martins C, Kocher TD.

J Hered. 2017 Jan;108(1):53-62. Epub 2016 Sep 14.

PMID:
27630131
12.

Integrated analysis of miRNA and mRNA expression profiles in tilapia gonads at an early stage of sex differentiation.

Tao W, Sun L, Shi H, Cheng Y, Jiang D, Fu B, Conte MA, Gammerdinger WJ, Kocher TD, Wang D.

BMC Genomics. 2016 May 4;17:328. doi: 10.1186/s12864-016-2636-z.

13.

A Tandem Duplicate of Anti-Müllerian Hormone with a Missense SNP on the Y Chromosome Is Essential for Male Sex Determination in Nile Tilapia, Oreochromis niloticus.

Li M, Sun Y, Zhao J, Shi H, Zeng S, Ye K, Jiang D, Zhou L, Sun L, Tao W, Nagahama Y, Kocher TD, Wang D.

PLoS Genet. 2015 Nov 20;11(11):e1005678. doi: 10.1371/journal.pgen.1005678. eCollection 2015 Nov.

14.

An improved genome reference for the African cichlid, Metriaclima zebra.

Conte MA, Kocher TD.

BMC Genomics. 2015 Sep 22;16:724. doi: 10.1186/s12864-015-1930-5.

15.

Structure and decay of a proto-Y region in Tilapia, Oreochromis niloticus.

Gammerdinger WJ, Conte MA, Acquah EA, Roberts RB, Kocher TD.

BMC Genomics. 2014 Nov 17;15:975. doi: 10.1186/1471-2164-15-975.

16.

The genomic substrate for adaptive radiation in African cichlid fish.

Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier J, Johnson J, Alcazar R, Noh HJ, Russell P, Aken B, Alföldi J, Amemiya C, Azzouzi N, Baroiller JF, Barloy-Hubler F, Berlin A, Bloomquist R, Carleton KL, Conte MA, D'Cotta H, Eshel O, Gaffney L, Galibert F, Gante HF, Gnerre S, Greuter L, Guyon R, Haddad NS, Haerty W, Harris RM, Hofmann HA, Hourlier T, Hulata G, Jaffe DB, Lara M, Lee AP, MacCallum I, Mwaiko S, Nikaido M, Nishihara H, Ozouf-Costaz C, Penman DJ, Przybylski D, Rakotomanga M, Renn SCP, Ribeiro FJ, Ron M, Salzburger W, Sanchez-Pulido L, Santos ME, Searle S, Sharpe T, Swofford R, Tan FJ, Williams L, Young S, Yin S, Okada N, Kocher TD, Miska EA, Lander ES, Venkatesh B, Fernald RD, Meyer A, Ponting CP, Streelman JT, Lindblad-Toh K, Seehausen O, Di Palma F.

Nature. 2014 Sep 18;513(7518):375-381. doi: 10.1038/nature13726. Epub 2014 Sep 3.

17.

Origin and evolution of B chromosomes in the cichlid fish Astatotilapia latifasciata based on integrated genomic analyses.

Valente GT, Conte MA, Fantinatti BE, Cabral-de-Mello DC, Carvalho RF, Vicari MR, Kocher TD, Martins C.

Mol Biol Evol. 2014 Aug;31(8):2061-72. doi: 10.1093/molbev/msu148. Epub 2014 Apr 26.

PMID:
24770715
18.

Mapping of pigmentation QTL on an anchored genome assembly of the cichlid fish, Metriaclima zebra.

O'Quin CT, Drilea AC, Conte MA, Kocher TD.

BMC Genomics. 2013 Apr 27;14:287. doi: 10.1186/1471-2164-14-287.

19.

Lineage-specific expansion of vomeronasal type 2 receptor-like (OlfC) genes in cichlids may contribute to diversification of amino acid detection systems.

Nikaido M, Suzuki H, Toyoda A, Fujiyama A, Hagino-Yamagishi K, Kocher TD, Carleton K, Okada N.

Genome Biol Evol. 2013;5(4):711-22. doi: 10.1093/gbe/evt041.

20.

A deleterious effect associated with UNH159 is attenuated in twin embryos of an inbred line of blue tilapia Oreochromis aureus.

Shirak A, Palti Y, Bern O, Kocher TD, Gootwine E, Seroussi E, Hulata G, Ron M, Avtalion RR.

J Fish Biol. 2013 Jan;82(1):42-53. doi: 10.1111/j.1095-8649.2012.03474.x. Epub 2012 Nov 26.

PMID:
23331137
21.

Origins of shared genetic variation in African cichlids.

Loh YH, Bezault E, Muenzel FM, Roberts RB, Swofford R, Barluenga M, Kidd CE, Howe AE, Di Palma F, Lindblad-Toh K, Hey J, Seehausen O, Salzburger W, Kocher TD, Streelman JT.

Mol Biol Evol. 2013 Apr;30(4):906-17. doi: 10.1093/molbev/mss326. Epub 2012 Dec 28.

22.

Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish.

Mazzuchelli J, Kocher TD, Yang F, Martins C.

BMC Genomics. 2012 Sep 9;13:463. doi: 10.1186/1471-2164-13-463.

23.

A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs.

Guyon R, Rakotomanga M, Azzouzi N, Coutanceau JP, Bonillo C, D'Cotta H, Pepey E, Soler L, Rodier-Goud M, D'Hont A, Conte MA, van Bers NE, Penman DJ, Hitte C, Crooijmans RP, Kocher TD, Ozouf-Costaz C, Baroiller JF, Galibert F.

BMC Genomics. 2012 Jun 6;13:222. doi: 10.1186/1471-2164-13-222.

24.

A small number of genes underlie male pigmentation traits in Lake Malawi cichlid fishes.

O'Quin CT, Drilea AC, Roberts RB, Kocher TD.

J Exp Zool B Mol Dev Evol. 2012 May;318(3):199-208. doi: 10.1002/jez.b.22006.

PMID:
22544717
25.

Circular DNA intermediate in the duplication of Nile tilapia vasa genes.

Fujimura K, Conte MA, Kocher TD.

PLoS One. 2011;6(12):e29477. doi: 10.1371/journal.pone.0029477. Epub 2011 Dec 22.

26.

Chromosome differentiation patterns during cichlid fish evolution.

Poletto AB, Ferreira IA, Cabral-de-Mello DC, Nakajima RT, Mazzuchelli J, Ribeiro HB, Venere PC, Nirchio M, Kocher TD, Martins C.

BMC Genet. 2012 Jan 19;13:2. doi: 10.1186/1471-2156-13-2. No abstract available.

27.

Tol2-mediated transgenesis in tilapia (Oreochromis niloticus).

Fujimura K, Kocher TD.

Aquaculture. 2011 Oct 1;319(3-4):342-346.

28.

Craniofacial divergence and ongoing adaptation via the hedgehog pathway.

Roberts RB, Hu Y, Albertson RC, Kocher TD.

Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13194-9. doi: 10.1073/pnas.1018456108. Epub 2011 Jul 25.

29.

Comparative cytogenetic mapping of Sox2 and Sox14 in cichlid fishes and inferences on the genomic organization of both genes in vertebrates.

Mazzuchelli J, Yang F, Kocher TD, Martins C.

Chromosome Res. 2011 Jul;19(5):657-67. doi: 10.1007/s10577-011-9225-4. Epub 2011 Jun 21.

30.

Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus).

Soler L, Conte MA, Katagiri T, Howe AE, Lee BY, Amemiya C, Stuart A, Dossat C, Poulain J, Johnson J, Di Palma F, Lindblad-Toh K, Baroiller JF, D'Cotta H, Ozouf-Costaz C, Kocher TD.

BMC Genomics. 2010 Nov 16;11:636. doi: 10.1186/1471-2164-11-636.

31.

Genetic and physical mapping of sex-linked AFLP markers in Nile tilapia (Oreochromis niloticus).

Lee BY, Coutanceau JP, Ozouf-Costaz C, D'Cotta H, Baroiller JF, Kocher TD.

Mar Biotechnol (NY). 2011 Jun;13(3):557-62. doi: 10.1007/s10126-010-9326-7. Epub 2010 Oct 7.

32.

Chromosome evolution in African cichlid fish: contributions from the physical mapping of repeated DNAs.

Ferreira IA, Poletto AB, Kocher TD, Mota-Velasco JC, Penman DJ, Martins C.

Cytogenet Genome Res. 2010;129(4):314-22. doi: 10.1159/000315895. Epub 2010 Jul 6.

33.

Chromosome differentiation patterns during cichlid fish evolution.

Poletto AB, Ferreira IA, Cabral-de-Mello DC, Nakajima RT, Mazzuchelli J, Ribeiro HB, Venere PC, Nirchio M, Kocher TD, Martins C.

BMC Genet. 2010 Jun 15;11:50. doi: 10.1186/1471-2156-11-50. Erratum in: BMC Genet. 2012 Jan 19;13:2.

34.

An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags.

Lee BY, Howe AE, Conte MA, D'Cotta H, Pepey E, Baroiller JF, di Palma F, Carleton KL, Kocher TD.

BMC Genomics. 2010 Apr 30;11:278. doi: 10.1186/1471-2164-11-278.

35.

Identification of repetitive elements in the genome of Oreochromis niloticus: tilapia repeat masker.

Shirak A, Grabherr M, Di Palma F, Lindblad-Toh K, Hulata G, Ron M, Kocher TD, Seroussi E.

Mar Biotechnol (NY). 2010 Apr;12(2):121-5. doi: 10.1007/s10126-009-9236-8. Epub 2009 Nov 21.

36.

Multiple interacting loci control sex determination in lake Malawi cichlid fish.

Ser JR, Roberts RB, Kocher TD.

Evolution. 2010 Feb 1;64(2):486-501. doi: 10.1111/j.1558-5646.2009.00871.x. Epub 2009 Oct 23.

37.

Sexual conflict resolved by invasion of a novel sex determiner in Lake Malawi cichlid fishes.

Roberts RB, Ser JR, Kocher TD.

Science. 2009 Nov 13;326(5955):998-1001. doi: 10.1126/science.1174705. Epub 2009 Oct 1.

38.

Sex-linked markers and microsatellite locus duplication in the cichlid species Oreochromis tanganicae.

Cnaani A, Kocher TD.

Biol Lett. 2008 Dec 23;4(6):700-3. doi: 10.1098/rsbl.2008.0286.

39.

Copy number variation of lipocalin family genes for male-specific proteins in tilapia and its association with gender.

Shirak A, Golik M, Lee BY, Howe AE, Kocher TD, Hulata G, Ron M, Seroussi E.

Heredity (Edinb). 2008 Nov;101(5):405-15. doi: 10.1038/hdy.2008.68. Epub 2008 Jul 23.

40.

Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids.

Loh YH, Katz LS, Mims MC, Kocher TD, Yi SV, Streelman JT.

Genome Biol. 2008;9(7):R113. doi: 10.1186/gb-2008-9-7-r113. Epub 2008 Jul 10.

41.

Genetics of sex determination in tilapiine species.

Cnaani A, Lee BY, Zilberman N, Ozouf-Costaz C, Hulata G, Ron M, D'Hont A, Baroiller JF, D'Cotta H, Penman DJ, Tomasino E, Coutanceau JP, Pepey E, Shirak A, Kocher TD.

Sex Dev. 2008;2(1):43-54. doi: 10.1159/000117718. Epub 2008 Apr 15.

PMID:
18418034
42.

Special feature--roundtable discussion. Fish models for studying adaptive evolution and speciation.

Kocher TD, Jeffery WR, Parichy DM, Peichel CL, Streelman JT, Thorgaard GH.

Zebrafish. 2005;2(3):147-56. doi: 10.1089/zeb.2005.2.147.

PMID:
18248189
43.
45.

Evolutionary biology: evidence for sympatric speciation?

Schliewen UK, Kocher TD, McKaye KR, Seehausen O, Tautz D.

Nature. 2006 Dec 7;444(7120):E12-3; discussion E13.

PMID:
17151605
46.

Amh and Dmrta2 genes map to tilapia (Oreochromis spp.) linkage group 23 within quantitative trait locus regions for sex determination.

Shirak A, Seroussi E, Cnaani A, Howe AE, Domokhovsky R, Zilberman N, Kocher TD, Hulata G, Ron M.

Genetics. 2006 Nov;174(3):1573-81. Epub 2006 Sep 1.

47.

Genetic and developmental basis of cichlid trophic diversity.

Albertson RC, Kocher TD.

Heredity (Edinb). 2006 Sep;97(3):211-21. Epub 2006 Jul 12. Review.

48.

Axes of differentiation in the bower-building cichlids of Lake Malawi.

Kidd MR, Kidd CE, Kocher TD.

Mol Ecol. 2006 Feb;15(2):459-78.

PMID:
16448413
49.

Integration and evolution of the cichlid mandible: the molecular basis of alternate feeding strategies.

Albertson RC, Streelman JT, Kocher TD, Yelick PC.

Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16287-92. Epub 2005 Oct 26.

50.

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