Metabarcoding reveals strong spatial structure and temporal turnover of zooplankton communities in marine and freshwater ports

Chain FJJ, Brown EA, MacIsaac HJ and Cristescu ME. (2016) Diversity and Distributions

The effects of parameter choice on defining molecular operational taxonomic units and resulting ecological analyses of metabarcoding data

Clare E, Chain FJJ, Littlefair JE and Cristescu ME. (2016) Genome

Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks

Huang Y, Chain FJJ, Panchal M, Eizaguirre C, Kalbe M, Lenz TL, Samonte IE, Stoll M, Bornberg-Bauer E., Reusch TBH and Milinski M. (2016) Molecular Ecology. 25 (4)

Evaluating the adaptive potential of the European eel: is the immunogenetic status recovering?

Baltazar-Soares M, Bracamonte SE, Bayer T, Chain FJJ, Hanel R, Harrod C and Eizaguirre C. (2016) PeerJ

Sex-biased expression of young genes in Silurana (Xenopus) tropicalis

Chain FJJ. (2015). Xenopus Genomics special issue in Cytogenetic and Genome Research. 145 (3-4)

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

Flynn JM, Brown EA, Chain FJJ, MacIsaac HJ and Cristescu ME.  (2015). Ecology and Evolution. 5 (11)

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?

Brown EA, Chain FJJ, Crease TJ, MacIsaac HJ and Cristescu ME. (2015). Ecology and Evolution. 5 (11)

Genomics of divergence along a continuum of parapatric population differentiation

Feulner PGD*, Chain FJJ*, Panchal M*, Huang Y, Eizaguirre C, Samonte IE, Kalbe M, Lenz TL, Stoll M, Bornberg-Bauer E, Reusch TBH and Milinski M. (2015)  PLoS Genetics. 11(2): e1004966

Extensive copy-number variation of young genes across stickleback populations

Chain FJJ*, Feulner PGD*, Panchal M*, Eizaguirre C, Samonte IE, Kalbe M, Lenz TL,  Stoll M, Bornberg-Bauer E, Milinski M and Reusch TBH. (2014)  PLoS Genetics. 10(12): e1004830

Ecological and evolutionary implications of genomic structural variations

Chain FJJ and Feulner PGD. (2014). Frontiers in Genetics. 5 (326)

Reproducibility of pyrosequencing data for biodiversity assessment in complex communities

Zhan A, Song H, Brown E, Chain FJJ, Therriault TW, Abbott CL, Heath DD, Cristescu ME and MacIsaac HJ. (2014) Methods in Ecology and Evolution 5 (9)

Genomic divergence between nine- and three-spined sticklebacks

Guo B, Chain FJJ, Bornberg-Bauer E, Leder EH and Merilä J. (2013). BMC Genomics. 14 (756)

Living on the edge: how philopatry maintains adaptive potential

Stiebens VA, Merino SE, Roder C, Chain FJJ, Lee PLM, Eizaguirre C. (2013) Proceedings of The Royal Society B. 280 (1763)

A large pseudoautosomal region on the sex chromosomes of the frog Silurana tropicalis

Bewick AJ, Chain FJJ, Zimmerman LB, Sesay A, Gilchrist MJ, Owens N, Seifertova E, Krylov V, Macha J, Tlapakova T, Kubickova S, Cernohorska H, Zarsky V, Evans BJ (2013) Genome Biology and Evolution. 5 (6)

Genomic dynamics of transposable elements in the Western Clawed Frog (Silurana tropicalis)

Shen JJ, Dushoff J, Bewick AJ, Chain FJJ and Evans BJ (2013) Genome Biology and Evolution. 5 (5)

Evolution of MHC class I genes in the endangered loggerhead sea turtle (Caretta caretta) revealed by 454 amplicon sequencing

Stiebens VA, Merino SE, Chain FJJ and Eizaguirre C (2013) BMC Evolutionary Biology. 13:95

Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks

Feulner PGD*, Chain FJJ*, Panchal M*, Eizaguirre C, Kalbe M, Lenz TL, Mundry M, Samonte IE, Stoll M, Milinski M, Reusch TBH, Bornberg-Bauer E. (2013)  Molecular Ecology. 22:635-649

The Pipid root

Bewick AJ, Chain FJJ, Heled J, Evans BJ. (2012) Systematic Biology. 61 (6)

The odds of duplicate gene persistence after polyploidization 

Chain FJJ, Dushoff J, Evans BJ. (2011)  BMC Genomics. 12:599

Single-species microarrays and comparative transcriptomics

Chain FJJ, Ilieva D, Evans BJ. (2008)  PLoS ONE. 3(9): e3279

Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization

Chain FJJ, Ilieva D, Evans BJ. (2008)  BMC Evolutionary Biology. 8:43.

Multiple mechanisms promote the retained expression of gene duplicates in the tetraploid frog Xenopus laevis

Chain FJJ and Evans BJ. (2006)  PLoS Genetics. 2(4):e56.