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Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers.

Darolti I, Wright AE, Sandkam BA, Morris J, Bloch NI, Farré M, Fuller RC, Bourne GR, Larkin DM, Breden F, Mank JE.

Proc Natl Acad Sci U S A. 2019 Sep 17;116(38):19031-19036. doi: 10.1073/pnas.1905298116. Epub 2019 Sep 4.


On the power to detect rare recombination events.

Wright AE, Darolti I, Bloch NI, Oostra V, Sandkam BA, Buechel SD, Kolm N, Breden F, Vicoso B, Mank JE.

Proc Natl Acad Sci U S A. 2019 Jun 25;116(26):12607-12608. doi: 10.1073/pnas.1905555116. Epub 2019 Jun 18. No abstract available.


Inferred Allelic Variants of Immunoglobulin Receptor Genes: A System for Their Evaluation, Documentation, and Naming.

Ohlin M, Scheepers C, Corcoran M, Lees WD, Busse CE, Bagnara D, Thörnqvist L, Bürckert JP, Jackson KJL, Ralph D, Schramm CA, Marthandan N, Breden F, Scott J, Matsen Iv FA, Greiff V, Yaari G, Kleinstein SH, Christley S, Sherkow JS, Kossida S, Lefranc MP, van Zelm MC, Watson CT, Collins AM.

Front Immunol. 2019 Mar 18;10:435. doi: 10.3389/fimmu.2019.00435. eCollection 2019. Review.


Outcomes of distal biceps tendon reattachment using the ToggleLoc™ fixation device with ZipLoop™ technology with single mini-open technique.

Alech-Tournier F, Elkholti K, Locquet V, Ninou M, Gibert N, Pozzetto M, Breden F, Rostoucher P, Marc A, Erhard L, Vogels J.

Eur J Orthop Surg Traumatol. 2019 May;29(4):925-931. doi: 10.1007/s00590-019-02376-9. Epub 2019 Feb 7.


Reviewing guppy color vision: integrating the molecular and physiological variation in visual tuning of a classic system for sensory drive.

Sandkam B, Dalton B, Breden F, Carleton K; Handling editor: Becky Fuller.

Curr Zool. 2018 Aug;64(4):535-545. doi: 10.1093/cz/zoy047. Epub 2018 Jun 9.


iReceptor: A platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories.

Corrie BD, Marthandan N, Zimonja B, Jaglale J, Zhou Y, Barr E, Knoetze N, Breden FMW, Christley S, Scott JK, Cowell LG, Breden F.

Immunol Rev. 2018 Jul;284(1):24-41. doi: 10.1111/imr.12666. Review.


Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data.

Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen Iv FA, Wine Y, Laserson U, Klatzmann D, Douek DC, Lefranc MP, Collins AM, Bubela T, Kleinstein SH, Watson CT, Cowell LG, Scott JK, Kepler TB.

Front Immunol. 2017 Nov 1;8:1418. doi: 10.3389/fimmu.2017.01418. eCollection 2017.


Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data.

Rubelt F, Busse CE, Bukhari SAC, Bürckert JP, Mariotti-Ferrandiz E, Cowell LG, Watson CT, Marthandan N, Faison WJ, Hershberg U, Laserson U, Corrie BD, Davis MM, Peters B, Lefranc MP, Scott JK, Breden F; AIRR Community, Luning Prak ET, Kleinstein SH.

Nat Immunol. 2017 Nov 16;18(12):1274-1278. doi: 10.1038/ni.3873. No abstract available.


Genomic Environment Impacts Color Vision Evolution in a Family with Visually Based Sexual Selection.

Sandkam BA, Joy JB, Watson CT, Breden F.

Genome Biol Evol. 2017 Nov 1;9(11):3100-3107. doi: 10.1093/gbe/evx228.


Comment on "A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data".

Watson CT, Matsen FA 4th, Jackson KJL, Bashir A, Smith ML, Glanville J, Breden F, Kleinstein SH, Collins AM, Busse CE.

J Immunol. 2017 May 1;198(9):3371-3373. doi: 10.4049/jimmunol.1700306. No abstract available.


Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation.

Wright AE, Darolti I, Bloch NI, Oostra V, Sandkam B, Buechel SD, Kolm N, Breden F, Vicoso B, Mank JE.

Nat Commun. 2017 Jan 31;8:14251. doi: 10.1038/ncomms14251.


Using High-Throughput Sequencing to Characterize the Development of the Antibody Repertoire During Infections: A Case Study of HIV-1.

Breden F, Watson CT.

Adv Exp Med Biol. 2017;1053:245-263. doi: 10.1007/978-3-319-72077-7_12. Review.


VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.

Toby IT, Levin MK, Salinas EA, Christley S, Bhattacharya S, Breden F, Buntzman A, Corrie B, Fonner J, Gupta NT, Hershberg U, Marthandan N, Rosenfeld A, Rounds W, Rubelt F, Scarborough W, Scott JK, Uduman M, Vander Heiden JA, Scheuermann RH, Monson N, Kleinstein SH, Cowell LG.

BMC Bioinformatics. 2016 Oct 6;17(Suppl 13):333.


Erratum: IGHV1-69 polymorphism modulates anti-influenza antibody repertoires, correlates with IGHV utilization shifts and varies by ethnicity.

Avnir Y, Watson CT, Glanville J, Peterson EC, Tallarico AS, Bennett AS, Qin K, Fu Y, Huang CY, Beigel JH, Breden F, Zhu Q, Marasco WA.

Sci Rep. 2016 Apr 29;6:23876. doi: 10.1038/srep23876. No abstract available.


IGHV1-69 polymorphism modulates anti-influenza antibody repertoires, correlates with IGHV utilization shifts and varies by ethnicity.

Avnir Y, Watson CT, Glanville J, Peterson EC, Tallarico AS, Bennett AS, Qin K, Fu Y, Huang CY, Beigel JH, Breden F, Zhu Q, Marasco WA.

Sci Rep. 2016 Feb 16;6:20842. doi: 10.1038/srep20842. Erratum in: Sci Rep. 2016 Apr 29;6:23876.


Poecilia picta, a Close Relative to the Guppy, Exhibits Red Male Coloration Polymorphism: A System for Phylogenetic Comparisons.

Lindholm AK, Sandkam B, Pohl K, Breden F.

PLoS One. 2015 Nov 3;10(11):e0142089. doi: 10.1371/journal.pone.0142089. eCollection 2015.


Color vision varies more among populations than among species of live-bearing fish from South America.

Sandkam BA, Young CM, Breden FM, Bourne GR, Breden F.

BMC Evol Biol. 2015 Oct 16;15:225. doi: 10.1186/s12862-015-0501-3.


Developmental plasticity in vision and behavior may help guppies overcome increased turbidity.

Ehlman SM, Sandkam BA, Breden F, Sih A.

J Comp Physiol A Neuroethol Sens Neural Behav Physiol. 2015 Dec;201(12):1125-35. doi: 10.1007/s00359-015-1041-4. Epub 2015 Oct 1.


Cancer susceptibility and reproductive trade-offs: a model of the evolution of cancer defences.

Boddy AM, Kokko H, Breden F, Wilkinson GS, Aktipis CA.

Philos Trans R Soc Lond B Biol Sci. 2015 Jul 19;370(1673). pii: 20140220. doi: 10.1098/rstb.2014.0220.


The locus of sexual selection: moving sexual selection studies into the post-genomics era.

Wilkinson GS, Breden F, Mank JE, Ritchie MG, Higginson AD, Radwan J, Jaquiery J, Salzburger W, Arriero E, Barribeau SM, Phillips PC, Renn SC, Rowe L.

J Evol Biol. 2015 Apr;28(4):739-55. doi: 10.1111/jeb.12621. Epub 2015 Apr 17. Review.


Beauty in the eyes of the beholders: colour vision is tuned to mate preference in the Trinidadian guppy (Poecilia reticulata).

Sandkam B, Young CM, Breden F.

Mol Ecol. 2015 Feb;24(3):596-609. doi: 10.1111/mec.13058.


Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity.

Watson CT, Steinberg KM, Graves TA, Warren RL, Malig M, Schein J, Wilson RK, Holt RA, Eichler EE, Breden F.

Genes Immun. 2015 Jan-Feb;16(1):24-34. doi: 10.1038/gene.2014.56. Epub 2014 Oct 23.


Antibody engineering and therapeutics, The Annual Meeting of the Antibody Society: December 8-12, 2013, Huntington Beach, CA.

Almagro JC, Gilliland GL, Breden F, Scott JK, Sok D, Pauthner M, Reichert JM, Helguera G, Andrabi R, Mabry R, Bléry M, Voss JE, Laurén J, Abuqayyas L, Barghorn S, Ben-Jacob E, Crowe JE Jr, Huston JS, Johnston SA, Krauland E, Lund-Johansen F, Marasco WA, Parren PW, Xu KY.

MAbs. 2014 May-Jun;6(3):577-618. doi: 10.4161/mabs.28421. Epub 2014 Mar 3.


Population structure of guppies in north-eastern Venezuela, the area of putative incipient speciation.

Herdegen M, Alexander HJ, Babik W, Mavárez J, Breden F, Radwan J.

BMC Evol Biol. 2014 Feb 17;14(1):28. doi: 10.1186/1471-2148-14-28.


Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation.

Watson CT, Steinberg KM, Huddleston J, Warren RL, Malig M, Schein J, Willsey AJ, Joy JB, Scott JK, Graves TA, Wilson RK, Holt RA, Eichler EE, Breden F.

Am J Hum Genet. 2013 Apr 4;92(4):530-46. doi: 10.1016/j.ajhg.2013.03.004. Epub 2013 Mar 28.


Hybridization leads to sensory repertoire expansion in a gynogenetic fish, the Amazon molly (poecilia formosa): a test of the hybrid-sensory expansion hypothesis.

Sandkam BA, Joy JB, Watson CT, Gonzalez-Bendiksen P, Gabor CR, Breden F.

Evolution. 2013 Jan;67(1):120-30. doi: 10.1111/j.1558-5646.2012.01779.x. Epub 2012 Sep 7.


Estimating the proportion of variation in susceptibility to multiple sclerosis captured by common SNPs.

Watson CT, Disanto G, Breden F, Giovannoni G, Ramagopalan SV.

Sci Rep. 2012;2:770. doi: 10.1038/srep00770. Epub 2012 Oct 25.


Age-associated hyper-methylated regions in the human brain overlap with bivalent chromatin domains.

Watson CT, Disanto G, Sandve GK, Breden F, Giovannoni G, Ramagopalan SV.

PLoS One. 2012;7(9):e43840. doi: 10.1371/journal.pone.0043840. Epub 2012 Sep 24.


The immunoglobulin heavy chain locus: genetic variation, missing data, and implications for human disease.

Watson CT, Breden F.

Genes Immun. 2012 Jul;13(5):363-73. doi: 10.1038/gene.2012.12. Epub 2012 May 3. Review.


Regulatory function of conserved sequences upstream of the long-wave sensitive opsin genes in teleost fishes.

Tam KJ, Watson CT, Massah S, Kolybaba AM, Breden F, Prefontaine GG, Beischlag TV.

Vision Res. 2011 Nov;51(21-22):2295-303. doi: 10.1016/j.visres.2011.09.010. Epub 2011 Sep 25.


Comparison of antibody repertoires produced by HIV-1 infection, other chronic and acute infections, and systemic autoimmune disease.

Breden F, Lepik C, Longo NS, Montero M, Lipsky PE, Scott JK.

PLoS One. 2011 Mar 30;6(3):e16857. doi: 10.1371/journal.pone.0016857.


Revisiting the T-cell receptor alpha/delta locus and possible associations with multiple sclerosis.

Watson CT, Para AE, Lincoln MR, Ramagopalan SV, Orton SM, Morrison KM, Handunnetthi L, Handel AE, Chao MJ, Morahan J, Sadovnick AD, Breden F, Ebers GC.

Genes Immun. 2011 Mar;12(2):59-66. doi: 10.1038/gene.2010.65. Epub 2011 Jan 27. Review.


A major QTL controls susceptibility to spinal curvature in the curveback guppy.

Gorman KF, Christians JK, Parent J, Ahmadi R, Weigel D, Dreyer C, Breden F.

BMC Genet. 2011 Jan 26;12:16. doi: 10.1186/1471-2156-12-16.


Gene duplication and divergence of long wavelength-sensitive opsin genes in the guppy, Poecilia reticulata.

Watson CT, Gray SM, Hoffmann M, Lubieniecki KP, Joy JB, Sandkam BA, Weigel D, Loew E, Dreyer C, Davidson WS, Breden F.

J Mol Evol. 2011 Feb;72(2):240-52. doi: 10.1007/s00239-010-9426-z. Epub 2010 Dec 18.


Structural and micro-anatomical changes in vertebrae associated with idiopathic-type spinal curvature in the curveback guppy model.

Gorman KF, Handrigan GR, Jin G, Wallis R, Breden F.

Scoliosis. 2010 Jun 7;5:10. doi: 10.1186/1748-7161-5-10.


IGHV4-39 deletion polymorphism does not associate with risk or outcome of multiple sclerosis.

Watson CT, Ramagopalan SV, Morrison KM, Ebers GC, Breden F.

J Neuroimmunol. 2010 Aug 25;225(1-2):164-6. doi: 10.1016/j.jneuroim.2010.04.012. Epub 2010 May 15.


Genomic organization of duplicated short wave-sensitive and long wave-sensitive opsin genes in the green swordtail, Xiphophorus helleri.

Watson CT, Lubieniecki KP, Loew E, Davidson WS, Breden F.

BMC Evol Biol. 2010 Mar 30;10:87. doi: 10.1186/1471-2148-10-87.


Multilevel and kin selection in a connected world.

Wade MJ, Wilson DS, Goodnight C, Taylor D, Bar-Yam Y, de Aguiar MA, Stacey B, Werfel J, Hoelzer GA, Brodie ED 3rd, Fields P, Breden F, Linksvayer TA, Fletcher JA, Richerson PJ, Bever JD, Van Dyken JD, Zee P.

Nature. 2010 Feb 18;463(7283):E8-9; discussion E9-10. doi: 10.1038/nature08809.


Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies.

Willing EM, Bentzen P, van Oosterhout C, Hoffmann M, Cable J, Breden F, Weigel D, Dreyer C.

Mol Ecol. 2010 Mar;19(5):968-84. doi: 10.1111/j.1365-294X.2010.04528.x. Epub 2010 Feb 8.


Disproportionate body lengths correlate with idiopathic-type curvature in the curveback guppy.

Gorman KF, Breden F.

Spine (Phila Pa 1976). 2010 Mar 1;35(5):511-6. doi: 10.1097/BRS.0b013e3181b52baf.


Idiopathic-type scoliosis is not exclusive to bipedalism.

Gorman KF, Breden F.

Med Hypotheses. 2009 Mar;72(3):348-52. doi: 10.1016/j.mehy.2008.09.052. Epub 2008 Dec 12.


Preface: behavior genetics for behavioral ecologists.

Boake CR, Breden F, Moore AJ.

Am Nat. 2002 Dec;160 Suppl 6:i. doi: 10.1086/345391. No abstract available.


Sex chromosomes and sexual selection in poeciliid fishes.

Lindholm A, Breden F.

Am Nat. 2002 Dec;160 Suppl 6:S214-24. doi: 10.1086/342898.


Genetic tools for studying adaptation and the evolution of behavior.

Boake CR, Arnold SJ, Breden F, Meffert LM, Ritchie MG, Taylor BJ, Wolf JB, Moore AJ.

Am Nat. 2002 Dec;160 Suppl 6:S143-59. doi: 10.1086/342902.


The molecular basis of color vision in colorful fish: four long wave-sensitive (LWS) opsins in guppies (Poecilia reticulata) are defined by amino acid substitutions at key functional sites.

Ward MN, Churcher AM, Dick KJ, Laver CR, Owens GL, Polack MD, Ward PR, Breden F, Taylor JS.

BMC Evol Biol. 2008 Jul 18;8:210. doi: 10.1186/1471-2148-8-210.


Conservation of synteny between guppy and Xiphophorus genomes.

Brummell M, Kazianis S, Davidson WS, Breden F.

Zebrafish. 2006;3(3):347-57. doi: 10.1089/zeb.2006.3.347.


The mutant guppy syndrome curveback as a model for human heritable spinal curvature.

Gorman KF, Tredwell SJ, Breden F.

Spine (Phila Pa 1976). 2007 Apr 1;32(7):735-41.


Teleosts as models for human vertebral stability and deformity.

Gorman KF, Breden F.

Comp Biochem Physiol C Toxicol Pharmacol. 2007 Feb;145(1):28-38. Epub 2006 Oct 19. Review.


Parallel evolution and vicariance in the guppy (Poecilia reticulata) over multiple spatial and temporal scales.

Alexander HJ, Taylor JS, Wu SS, Breden F.

Evolution. 2006 Nov;60(11):2352-69.


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