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With expanding data archives opportunity arises to augment replicate numbers when conditions of interest overlap. Despite correction procedures for estimating transcript abundance, a source of ambiguity is transcript level intra-condition count variation; as indicated by disjointed results between analysis tools. We present TVscript, a tool that removes reference-based transcripts associated with intra-condition count variation above specified thresholds and we explore the effects of such variation on differential expression analysis. Initially iterative differential expression analysis involving simulated counts, where levels of intra-condition variation and sets of over represented transcripts are explicitly specified, was performed. Then counts derived from inter- and intra-study data representing brain samples of dogs, wolves and foxes (wolves\n                    <jats:italic>vs<\/jats:italic>\n                    . dogs and aggressive\n                    <jats:italic>vs<\/jats:italic>\n                    . tame foxes) were used. For simulations, the sensitivity in detecting differentially expressed transcripts increased after removing hyper-variable transcripts, although at levels of intra-condition variation above 5% detection became unreliable. For real data, prior to applying TVscript, \u224820% of the transcripts identified as being differentially expressed were associated with high levels of intra-condition variation, an over representation relative to the reference set. As transcripts harbouring such variation were removed pre-analysis, a discordance from 26 to 40% in the lists of differentially expressed transcripts is observed when compared to those obtained using the non-filtered reference. The removal of transcripts possessing intra-condition variation values within (and above) the 97\n                    <jats:sup>th<\/jats:sup>\n                    and 95\n                    <jats:sup>th<\/jats:sup>\n                    percentiles, for wolves\n                    <jats:italic>vs<\/jats:italic>\n                    . dogs and aggressive\n                    <jats:italic>vs<\/jats:italic>\n                    . tame foxes, maximized the sensitivity in detecting differentially expressed transcripts as a result of alterations within gene-wise dispersion estimates. Through analysis of our real data the support for seven genes with potential for being involved with selection for tameness is provided. TVscript is available at:\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/sourceforge.net\/projects\/tvscript\/\" xlink:type=\"simple\">https:\/\/sourceforge.net\/projects\/tvscript\/<\/jats:ext-link>\n                    .\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0274591","type":"journal-article","created":{"date-parts":[[2022,9,22]],"date-time":"2022-09-22T13:51:03Z","timestamp":1663854663000},"page":"e0274591","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["On taming the effect of transcript level intra-condition count variation during differential expression analysis: A story of dogs, foxes and wolves"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6988-9993","authenticated-orcid":true,"given":"Diana","family":"Lobo","sequence":"first","affiliation":[]},{"given":"Raquel","family":"Linheiro","sequence":"additional","affiliation":[]},{"given":"Raquel","family":"Godinho","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6212-0962","authenticated-orcid":true,"given":"John Patrick","family":"Archer","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,9,22]]},"reference":[{"key":"pone.0274591.ref001","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: A revolutionary tool for transcriptomics","volume":"10","author":"Z Wang","year":"2009","journal-title":"Nat Rev Genet"},{"key":"pone.0274591.ref002","article-title":"A survey of best practices for RNA-seq data analysis","volume":"17","author":"A Conesa","year":"2016","journal-title":"Genome Biol"},{"key":"pone.0274591.ref003","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1101\/pdb.top084970","article-title":"RNA Sequencing and Analysis","volume":"2015","author":"KR Kukurba","year":"2015","journal-title":"Cold Spring Harb Protoc"},{"key":"pone.0274591.ref004","first-page":"621","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"A Mortazavi","year":"2008","journal-title":"Nat Methods 2008 57"},{"key":"pone.0274591.ref005","article-title":"Accurate quantification of transcriptome from RNA-Seq data by effective length normalization","volume":"39","author":"S Lee","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"pone.0274591.ref006","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation","volume":"28","author":"C Trapnell","year":"2010","journal-title":"Nat Biotechnol"},{"key":"pone.0274591.ref007","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1093\/bioinformatics\/btp113","article-title":"Statistical inferences for isoform expression in RNA-Seq","volume":"25","author":"H Jiang","year":"2009","journal-title":"Bioinformatics"},{"key":"pone.0274591.ref008","doi-asserted-by":"crossref","first-page":"1344","DOI":"10.1126\/science.1158441","article-title":"The transcriptional landscape of the yeast genome defined by RNA sequencing","volume":"320","author":"U Nagalakshmi","year":"2008","journal-title":"Science (80-)"},{"key":"pone.0274591.ref009","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"MI Love","year":"2014","journal-title":"Genome Biol"},{"key":"pone.0274591.ref010","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"MD Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"pone.0274591.ref011","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1038\/nbt.1910","article-title":"Sequencing technology does not eliminate biological variability","volume":"29","author":"KD Hansen","year":"2011","journal-title":"Nat Biotechnol"},{"key":"pone.0274591.ref012","doi-asserted-by":"crossref","first-page":"1725","DOI":"10.1093\/bib\/bby045","article-title":"Physiological RNA dynamics in RNA-Seq analysis","volume":"20","author":"Z Xu","year":"2019","journal-title":"Brief Bioinform"},{"key":"pone.0274591.ref013","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1186\/1471-2164-12-293","article-title":"RNA-seq: Technical variability and sampling","volume":"12","author":"LM McIntyre","year":"2011","journal-title":"BMC Genomics"},{"key":"pone.0274591.ref014","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1093\/bioinformatics\/btt688","article-title":"RNA-seq differential expression studies: More sequence or more replication?","volume":"30","author":"Y Liu","year":"2014","journal-title":"Bioinformatics"},{"key":"pone.0274591.ref015","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1261\/rna.053959.115","article-title":"How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?","volume":"22","author":"NJ Schurch","year":"2016","journal-title":"RNA"},{"key":"pone.0274591.ref016","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1186\/1471-2164-13-484","article-title":"Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing","volume":"13","author":"JA Robles","year":"2012","journal-title":"BMC Genomics"},{"key":"pone.0274591.ref017","first-page":"1","article-title":"Massive mining of publicly available RNA-seq data from human and mouse","volume":"9","author":"A Lachmann","year":"2018","journal-title":"Nat Commun 2018 91"},{"key":"pone.0274591.ref018","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1007\/978-1-0716-1103-6_4","article-title":"Processing and Analysis of RNA-seq Data from Public Resources. Methods in Molecular Biology","author":"Y Zoabi","year":"2021","journal-title":"Methods Mol Biol"},{"key":"pone.0274591.ref019","first-page":"1","article-title":"Meta-analysis of RNA-seq expression data across species, tissues and studies","volume":"16","author":"PH Sudmant","year":"2015","journal-title":"Genome Biol 2015 161"},{"key":"pone.0274591.ref020","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1186\/1471-2105-15-91","article-title":"Differential meta-analysis of RNA-seq data from multiple studies","volume":"15","author":"A Rau","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"pone.0274591.ref021","doi-asserted-by":"crossref","first-page":"107515","DOI":"10.1016\/j.compbiolchem.2021.107515","article-title":"Gene expression analysis of combined RNA-seq experiments using a receiver operating characteristic calibrated procedure","volume":"93","author":"SL Jeng","year":"2021","journal-title":"Comput Biol 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complex non-genetic factors in gene expression levels greatly increases power in eQTL studies","volume":"6","author":"O Stegle","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"pone.0274591.ref026","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1038\/nbt.3000","article-title":"Detecting and correcting systematic variation in large-scale RNA sequencing data","volume":"32","author":"S Li","year":"2014","journal-title":"Nat Biotechnol"},{"key":"pone.0274591.ref027","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s12859-019-2599-6","article-title":"Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data","volume":"20","author":"T Wang","year":"2019","journal-title":"BMC Bioinformatics"},{"key":"pone.0274591.ref028","article-title":"Reproducibility of Methods to Detect Differentially Expressed Genes from Single-Cell RNA Sequencing","volume":"10","author":"T Mou","year":"2020","journal-title":"Front Genet"},{"key":"pone.0274591.ref029","doi-asserted-by":"crossref","first-page":"2734","DOI":"10.1038\/s41598-020-59516-z","article-title":"Variability in estimated gene expression among commonly used RNA-seq pipelines","volume":"10","author":"S Arora","year":"2020","journal-title":"Sci Rep"},{"key":"pone.0274591.ref030","doi-asserted-by":"crossref","first-page":"3470","DOI":"10.1016\/j.csbj.2021.05.040","article-title":"Robustness of differential gene expression analysis of RNA-seq","volume":"19","author":"A Stupnikov","year":"2021","journal-title":"Comput Struct Biotechnol J"},{"key":"pone.0274591.ref031","doi-asserted-by":"crossref","first-page":"e019015","DOI":"10.1371\/journal.pone.0190152","article-title":"RNA-Seq differential expression analysis: An extended review and a software tool","volume":"12","author":"J Costa-Silva","year":"2017","journal-title":"PLoS One"},{"issue":"3","key":"pone.0274591.ref032","doi-asserted-by":"crossref","first-page":"91172","DOI":"10.1371\/journal.pone.0091172","article-title":"An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts","volume":"9","author":"MP Hoeppner","year":"2014","journal-title":"PLoS One"},{"key":"pone.0274591.ref033","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1007\/s00335-013-9480-0","article-title":"Analysis of the canine brain transcriptome with an emphasis on the hypothalamus and cerebral cortex","volume":"24","author":"M Roy","year":"2013","journal-title":"Mamm Genome"},{"key":"pone.0274591.ref034","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1111\/acel.12283","article-title":"Gene expression defines natural changes in mammalian lifespan","volume":"14","author":"AA Fushan","year":"2015","journal-title":"Aging Cell"},{"key":"pone.0274591.ref035","doi-asserted-by":"crossref","first-page":"e1002962","DOI":"10.1371\/journal.pgen.1002962","article-title":"A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals","volume":"8","author":"FW Albert","year":"2012","journal-title":"PLoS Genet"},{"key":"pone.0274591.ref036","doi-asserted-by":"crossref","first-page":"10398","DOI":"10.1073\/pnas.1800889115","article-title":"Genomic responses to selection for tame\/aggressive behaviors in the silver fox (Vulpes vulpes)","volume":"115","author":"X Wang","year":"2018","journal-title":"Proc Natl Acad Sci"},{"key":"pone.0274591.ref037","doi-asserted-by":"crossref","first-page":"3115","DOI":"10.1093\/gbe\/evu245","article-title":"Domestication of the dog from the Wolf was promoted by enhanced excitatory synaptic plasticity: A hypothesis","volume":"6","author":"Y Li","year":"2014","journal-title":"Genome Biol Evol"},{"key":"pone.0274591.ref038","doi-asserted-by":"crossref","first-page":"1867","DOI":"10.1093\/molbev\/mst088","article-title":"Artificial selection on brain-expressed genes during the domestication of dog","volume":"30","author":"Y Li","year":"2013","journal-title":"Mol Biol Evol"},{"key":"pone.0274591.ref039","article-title":"The History of Farm Foxes Undermines the Animal Domestication Syndrome","author":"KA Lord","year":"2019","journal-title":"Trends Ecol Evol"},{"key":"pone.0274591.ref040","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1007\/s10519-010-9418-1","article-title":"Mapping loci for fox domestication: Deconstruction\/Reconstruction of a behavioral phenotype","volume":"41","author":"A Kukekova","year":"2011","journal-title":"Behav Genet"},{"key":"pone.0274591.ref041","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1534\/g3.117.300508","article-title":"Anterior Pituitary Transcriptome Suggests Differences in ACTH Release in Tame and Aggressive Foxes","volume":"8","author":"J Hekman","year":"2018","journal-title":"G3; Genes|Genomes|Genetics"},{"key":"pone.0274591.ref042","first-page":"1","article-title":"Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals","volume":"21","author":"Y Hou","year":"2020","journal-title":"BMC Genomics"},{"key":"pone.0274591.ref043","first-page":"D682","article-title":"Ensembl 2020","volume":"48","author":"AD Yates","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"pone.0274591.ref044","article-title":"Fast gapped-read alignment with Bowtie 2","author":"B Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"pone.0274591.ref045","first-page":"1","article-title":"TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions","volume":"14","author":"D Kim","year":"2013","journal-title":"Genome Biol"},{"key":"pone.0274591.ref046","first-page":"907","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"D Kim","year":"2019","journal-title":"Nat Biotechnol 2019 378"},{"key":"pone.0274591.ref047","unstructured":"Bushnell, Brian. BBMap: A Fast, Accurate, Splice-Aware Aligner. Conference: 9th Annual Genomics of Energy Environment Meeting. 2014."},{"key":"pone.0274591.ref048","first-page":"525","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"NL Bray","year":"2016","journal-title":"Nat Biotechnol 2016 345"},{"key":"pone.0274591.ref049","unstructured":"Linheiro R, Archer J. CSReadGen website. https:\/\/sourceforge.net\/projects\/csreadgen\/"},{"key":"pone.0274591.ref050","doi-asserted-by":"crossref","first-page":"e1009631","DOI":"10.1371\/journal.pcbi.1009631","article-title":"CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure","volume":"17","author":"R Linheiro","year":"2021","journal-title":"PLOS Comput Biol"},{"key":"pone.0274591.ref051","author":"D Lobo","year":"2022","journal-title":"On taming the effect of transcript level intra-condition count variation during differential expression analysis: a story of dogs, foxes and wolves: Example R Script for using DESeq2"},{"key":"pone.0274591.ref052","first-page":"1","article-title":"A benchmark of batch-effect correction methods for single-cell RNA sequencing data","volume":"21","author":"HTN Tran","year":"2020","journal-title":"Genome Biol"},{"key":"pone.0274591.ref053","unstructured":"R Development Core Team. R: A language and environment for statistical computing. Vienna, Austria. 2017. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http:\/\/www.R-project.org."},{"key":"pone.0274591.ref054","doi-asserted-by":"crossref","first-page":"3439","DOI":"10.1093\/bioinformatics\/bti525","article-title":"BioMart and Bioconductor: A powerful link between biological databases and microarray data analysis","volume":"21","author":"S Durinck","year":"2005","journal-title":"Bioinformatics"},{"key":"pone.0274591.ref055","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1073\/pnas.2010083118","article-title":"Dog domestication and the dual dispersal of people and dogs into the Americas","volume":"118","author":"AR Perri","year":"2021","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pone.0274591.ref056","doi-asserted-by":"crossref","first-page":"e0139857","DOI":"10.1371\/journal.pone.0139857","article-title":"Systematic Characteristic Exploration of the Chimeras Generated in Multiple Displacement Amplification through Next Generation Sequencing Data Reanalysis","volume":"6","author":"J Tu","year":"2015","journal-title":"PLoS One"},{"key":"pone.0274591.ref057","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1007\/s40484-019-0181-x","article-title":"Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era","volume":"7","author":"R Rizzi","year":"2019","journal-title":"Quant Biol"},{"key":"pone.0274591.ref058","author":"D Lobo","year":"2022","journal-title":"On taming the effect of transcript level intra-condition count variation during differential expression analysis: a story of dogs, foxes and wolves: Bowtie2 counts and kallisto abundances"},{"key":"pone.0274591.ref059","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1093\/sysbio\/46.4.622","article-title":"Molecular Systematics of the Canidae","volume":"46","author":"RK Wayne","year":"1997","journal-title":"Syst Biol"},{"key":"pone.0274591.ref060","first-page":"120","article-title":"Quantification of the effects of chimerism on read mapping, differential expression and annotation following short-read de novo assembly","volume":"11","author":"R Linheiro","year":"2022","journal-title":"F1000Research 2022 11120"},{"key":"pone.0274591.ref061","article-title":"Effect of de novo transcriptome assembly on transcript quantification","volume":"9","author":"PH Hsieh","year":"2019","journal-title":"Sci Rep"},{"key":"pone.0274591.ref062","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1146\/annurev-genom-090413-025358","article-title":"Alignment of Next-Generation Sequencing Reads","volume":"16","author":"K Reinert","year":"2015","journal-title":"Annu Rev Genomics Hum Genet"},{"key":"pone.0274591.ref063","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1093\/bib\/bbx008","article-title":"Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions","volume":"19","author":"C Evans","year":"2018","journal-title":"Brief Bioinform"},{"key":"pone.0274591.ref064","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0070388","article-title":"PCR-Induced Transitions Are the Major Source of Error in Cleaned Ultra-Deep Pyrosequencing Data","volume":"8","author":"J Brodin","year":"2013","journal-title":"PLoS One"},{"key":"pone.0274591.ref065","article-title":"Analysis of error profiles in deep next-generation sequencing data","volume":"20","author":"X Ma","year":"2019","journal-title":"Genome Biol"},{"key":"pone.0274591.ref066","article-title":"A powerful and flexible approach to the analysis of RNA sequence count data","author":"YH Zhou","year":"2011","journal-title":"Bioinformatics"},{"key":"pone.0274591.ref067","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1093\/biostatistics\/kxs033","article-title":"A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data","volume":"14","author":"H Wu","year":"2013","journal-title":"Biostatistics"},{"key":"pone.0274591.ref068","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1186\/1471-2105-11-422","article-title":"BaySeq: Empirical Bayesian methods for identifying differential expression in sequence count data","volume":"11","author":"TJ Hardcastle","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"pone.0274591.ref069","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1093\/biostatistics\/kxs031","article-title":"Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors","volume":"14","author":"MA Van De Wiel","year":"2013","journal-title":"Biostatistics"},{"key":"pone.0274591.ref070","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1111\/gbb.12017","article-title":"Domestication-related variation in social preferences in chickens is affected by genotype on a growth QTL","volume":"12","author":"A Wir\u00e9n","year":"2013","journal-title":"Genes, Brain Behav"},{"key":"pone.0274591.ref071","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1534\/genetics.109.102186","article-title":"Genetic architecture of tameness in a rat model of animal domestication","volume":"182","author":"FW Albert","year":"2009","journal-title":"Genetics"},{"key":"pone.0274591.ref072","doi-asserted-by":"crossref","first-page":"1074","DOI":"10.1126\/science.1253714","article-title":"Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication","volume":"345","author":"M Carneiro","year":"2014","journal-title":"Science (80-)"},{"key":"pone.0274591.ref073","doi-asserted-by":"crossref","first-page":"e100585","DOI":"10.1371\/journal.pgen.1005851","article-title":"Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs","volume":"12","author":"AH Freedman","year":"2016","journal-title":"PLoS 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Genomics"},{"key":"pone.0274591.ref077","doi-asserted-by":"crossref","first-page":"1277","DOI":"10.1534\/genetics.114.168948","article-title":"Genetic influences on brain gene expression in rats selected for tameness and aggression","volume":"198","author":"HO Heyne","year":"2014","journal-title":"Genetics"},{"key":"pone.0274591.ref078","doi-asserted-by":"crossref","first-page":"jcs212","DOI":"10.1242\/jcs.212803","article-title":"Integrin activity in neuronal connectivity","volume":"131","author":"J Lilja","year":"2018","journal-title":"J Cell Sci"},{"key":"pone.0274591.ref079","first-page":"389","article-title":"Cell adhesion molecules: selectins and integrins","volume":"19","author":"R Gonz\u00e1lez-Amaro","year":"1999","journal-title":"Crit Rev Immunol"},{"key":"pone.0274591.ref080","doi-asserted-by":"crossref","first-page":"1448","DOI":"10.1002\/ajmg.b.31126","article-title":"Risk gene variants for nicotine dependence in the CHRNA5-CHRNA3-CHRNB4 cluster are associated with cognitive performance","volume":"153","author":"G Winterer","year":"2010","journal-title":"Am J Med Genet Part B Neuropsychiatr Genet"},{"key":"pone.0274591.ref081","doi-asserted-by":"crossref","first-page":"2508","DOI":"10.1038\/npp.2009.80","article-title":"Cognitive flexibility is associated with KIBRA variant and modulated by recent tobacco use","volume":"34","author":"H Zhang","year":"2009","journal-title":"Neuropsychopharmacology"},{"key":"pone.0274591.ref082","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1016\/j.tcb.2016.11.002","article-title":"Tribbles in the 21st Century: The Evolving Roles of Tribbles Pseudokinases in Biology and Disease","volume":"27","author":"PA Eyers","year":"2017","journal-title":"Trends Cell Biol"},{"issue":"12","key":"pone.0274591.ref083","doi-asserted-by":"crossref","first-page":"e512","DOI":"10.1371\/journal.pone.0051284","article-title":"Inner Ear Morphology Is Perturbed in Two Novel Mouse Models of Recessive 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