peer reviewed journal articles
† Advised graduate student
‡ Undergraduate student
§ Lowell High School student
* Equal contributions
‡ Undergraduate student
§ Lowell High School student
* Equal contributions
- ‡Luna SK and Chain FJJ (2021) Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development. Genes.
- †Dacey DP and Chain FJJ (2021) Concatenation of paired-end reads improves taxonomic classification of amplicons for profiling microbial communities. BMC Bioinformatics
- Pagsuyoin SA, Luo J and Chain FJJ (2021) Effects of sewer biofilm on the degradation of drugs in sewage: A microcosm study. Journal of Hazardous Materials
- Chain FJJ and Assis R (2021) BLAST from the past: impacts of evolving approaches on studies of evolution by gene duplication. Genome Biology and Evolution
- §Huang KM and Chain FJJ (2021) Copy number variations and young duplicate genes have high methylation levels in sticklebacks. Evolution
- †Dacey DP and Chain FJJ (2020) The challenges of microbial control of mosquito-borne diseases due to the gut microbiome. Frontiers in Genetics
- †Suresh S, Crease TJ, Cristescu ME and Chain FJJ (2020) Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure. BMC Genomics
- ‡Beeber D and Chain FJJ (2020) crispRdesignR: A Versatile Guide RNA Design Package in R for CRISPR/Cas9 Applications. Journal of Genomics. See TOOLS for more information
- Martin GK, Beisner BE, Chain FJJ, Cristescu ME, del Giorgio PA and Derry AM. (2020) Freshwater zooplankton metapopulations and metacommunities respond differently to environmental and spatial variation. Ecology
- Schmitz JF, Chain FJJ and Bornberg-Bauer E (2020) Evolution of novel genes in three-spined stickleback populations. Heredity
- Millette KL, Fugère V, Debyser C, Greiner A, Chain FJJ and Gonzalez A (2019) No consistent effects of humans on animal genetic diversity worldwide. Ecology Letters
- †Huang Y, Feulner PGD, Eizaguirre C, Lenz TL, Bornberg-Bauer E, Milinski M, Reusch TBH and Chain FJJ (2019) Genome-wide genotype-expression relationships reveal both copy number and single nucleotide differentiation contribute to differential gene expression between stickleback ecotypes. Genome Biology and Evolution
- Chain FJJ, Finlayson S, Crease T and Cristescu ME (2019) Variation in transcriptional responses to copper exposure across Daphnia pulex lineages. Aquatic Toxicology
- Chain FJJ, Flynn JM, Bull JK and Cristescu ME (2019) Accelerated rates of large-scale mutations in the presence of copper and nickel. Genome Research
- Bull JK, Flynn JM, Chain FJJ and Cristescu ME (2019) Fitness and genomic consequences of chronic exposure to low levels of copper and nickel in Daphnia pulex mutation accumulation lines. G3: Genes, Genomes, Genetics
- Zhang GK, Chain FJJ, Abbott CL and Cristescu ME (2018) Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities. Evolutionary Applications
- ‡Eckert IMK, Littlefair JE, Zhang GK, Chain FJJ, Crease TJ and Cristescu ME (2018) Bioinformatics for Biomonitoring: Species Detection and Diversity Estimates Across Next-Generation Sequencing Platforms. Advances in Ecological Research
- Scott R, Zhan A, Brown EA, Chain FJJ, Cristescu ME, Gras R and MacIsaac HJ (2018) Optimization and performance testing of a sequence processing pipeline applied to detection of nonindigenous species. Evolutionary Applications
- Flynn JM, Chain FJJ, Schoen DJ and Cristescu ME (2017) Spontaneous Mutation Accumulation in Daphnia pulex in Selection-Free vs. Competitive Environments. Molecular Biology and Evolution
- Chain FJJ, Brown EA, MacIsaac HJ and Cristescu ME (2016) Metabarcoding reveals strong spatial structure and temporal turnover of zooplankton communities in marine and freshwater ports. Diversity and Distributions
- †Huang Y, Chain FJJ, Panchal M, Eizaguirre C, Kalbe M, Lenz TL, Samonte IE, Stoll M, Bornberg-Bauer E, Reusch TBH, Milinski M and Feulner PGD (2016) Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks. Molecular Ecology
- Brown EA, Chain FJJ, Zhan A, MacIsaac HJ and Cristescu ME (2016) Early detection of aquatic invaders using metabarcoding. Diversity and Distributions
- Clare EL, Chain FJJ, Littlefair JE and Cristescu ME (2016) The effects of parameter choice on defining molecular operational taxonomic units and resulting ecological analyses of metabarcoding data. Genome
- Adamowicz SJ, Chain FJJ, Clare EL, Deiner K, Dinca V, Elias-Gutierrez M, Hausmann A, Hogg ID, Kekkonen M, Lijtmaer DA, Naaum A, Steinke D, Valdez-Moreno M, Van der Bank M, Wilson J-J and Xu J (2016) From Barcodes to Biomes: Special Issues from the 6th International Barcode of Life Conference. Genome
- Baltazar-Soares M, Bracamonte S, Bayer T, Chain FJJ, Hanel R, Harrod C and Eizaguirre C (2016) Evaluating the adaptive potential of the European eel: insights into the genetic status of an endangered species. PeerJ
- Chain FJJ (2015) Sex-biased expression of young genes in Silurana (Xenopus) tropicalis. Cytogenetic and Genome Research, special issue on Xenopus Genomics
- *Feulner PGD, *Chain FJJ, *Panchal M, †Huang Y, Eizaguirre C, Kalbe M, Lenz TL, Samonte IE, Stoll M, Bornberg-Bauer E, Reusch TBH and Milinski M (2015) Genomics of divergence along a continuum of parapatric population differentiation. PLoS Genetics
- ‡Flynn JM, Brown EA, Chain FJJ, MacIsaac HJ and Cristescu ME (2015) Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods. Ecology and Evolution
- Brown EA, Chain FJJ, Crease TJ, MacIsaac HJ and Cristescu ME (2015) Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities? Ecology and Evolution
- *Chain FJJ, *Feulner PGD, *Panchal M, Eizaguirre C, Kalbe M, Lenz TL, Samonte IE, Stoll M, Bornberg-Bauer E., Milinski M and Reusch TBH (2014) Extensive copy-number variation of young genes across stickleback populations. PLoS Genetics
- Chain FJJ and Feulner PGD (2014) Ecological and evolutionary implications of genomic structural variations. Frontiers in Genetics
- Zhan A, Song H, Brown EA, Chain FJJ, Therriault TW, Abbott CL, Heath DD, Cristescu ME and MacIsaac HJ (2014) Reproducibility of pyrosequencing data for biodiversity assessment in complex communities. Methods in Ecology and Evolution
- Guo B, Chain FJJ, Bornberg-Bauer E, Leder EH and Merilä J (2013) Genomic divergence between nine- and three-spined sticklebacks. BMC Genomics
- Stiebens V, Merino SE, Roder C, Chain FJJ, Lee PLM and Eizaguirre C (2013) Living on the edge: how philopatry maintains adaptive potential. Proc. R. Soc. B.
- 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) A large pseudoautosomal region on the sex chromosomes of the frog Silurana tropicalis. Genome Biology and Evolution
- Shen JJ, Dushoff J, Bewick AJ, Chain FJJ and Evans BJ (2013) Genomic dynamics of transposable elements in the Western Clawed Frog (Silurana tropicalis). Genome Biology and Evolution
- Stiebens VA, Merino SE, Chain FJJ and Eizaguirre C (2013) Evolution of MHC class I genes in the endangered loggerhead sea turtle (Caretta caretta) revealed by 454 amplicon sequencing. BMC Evolutionary Biology
- *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 (2012) Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks. Molecular Ecology
- Bewick AJ, Chain FJJ, Heled J and Evans BJ (2012) The Pipid root. Systematic Biology
- Chain FJJ, Dushoff J and Evans BJ (2011) The odds of duplicate gene persistence after polyploidization. BMC Genomics
- Chain FJJ, Ilieva D and Evans BJ (2008) Single-species microarrays and comparative transcriptomics. PLoS One
- Chain FJJ, Ilieva D and Evans BJ (2008) Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization. BMC Evolutionary Biology
- Chain FJJ and Evans BJ (2006) Multiple mechanisms promote the retained expression of gene duplicates in the tetraploid frog Xenopus laevis. PLoS Genetics