From dacc69ca4581c621efa63751f06065dbd388a40d Mon Sep 17 00:00:00 2001 From: Mick Date: Mon, 12 Aug 2019 15:43:23 -0700 Subject: [PATCH] capitalized journal titles in bib --- latex/wgd.bbl | 56 +++++++++++++++++++-------------------- latex/wgd.bib | 72 +++++++++++++++++++++++++------------------------- latex/wgd.blg | 2 +- latex/wgd.log | 4 +-- latex/wgd.pdf | Bin 1470305 -> 1470315 bytes 5 files changed, 67 insertions(+), 67 deletions(-) diff --git a/latex/wgd.bbl b/latex/wgd.bbl index 9c1fbdf..cdf4be7 100644 --- a/latex/wgd.bbl +++ b/latex/wgd.bbl @@ -12,14 +12,14 @@ Anders, S., P.~T. Pyl, and W.~Huber, 2015. \bibitem[{Arumuganathan and Earle(1991)}]{arumuganathan1991} Arumuganathan, K. and E.~Earle, 1991. \newblock Nuclear dna content of some important plant species. -\newblock Plant molecular biology reporter 9:208--218. +\newblock Plant Molecular Biology Reporter 9:208--218. \bibitem[{Barker et~al.(2009)Barker, Vogel, and Schranz}]{barker2009} Barker, M.~S., H.~Vogel, and M.~E. Schranz, 2009. \newblock Paleopolyploidy in the brassicales: analyses of the cleome transcriptome elucidate the history of genome duplications in arabidopsis and other brassicales. -\newblock Genome biology and evolution 1:391--399. +\newblock Genome Biology and Evolution 1:391--399. \bibitem[{Birchler and Veitia(2012)}]{birchler2012} Birchler, J.~A. and R.~A. Veitia, 2012. @@ -43,20 +43,20 @@ Bolger, A.~M., M.~Lohse, and B.~Usadel, 2014. Cannon, S.~B., A.~Mitra, A.~Baumgarten, N.~D. Young, and G.~May, 2004. \newblock The roles of segmental and tandem gene duplication in the evolution of large gene families in arabidopsis thaliana. -\newblock BMC plant biology 4:10. +\newblock BMC Plant Biology 4:10. \bibitem[{Coate and Doyle(2010)}]{coate2010} Coate, J.~E. and J.~J. Doyle, 2010. \newblock Quantifying whole transcriptome size, a prerequisite for understanding transcriptome evolution across species: an example from a plant allopolyploid. -\newblock Genome biology and evolution 2:534--546. +\newblock Genome Biology and Evolution 2:534--546. \bibitem[{Coate and Doyle(2011)}]{coate2011} ---{}---{}---, 2011. \newblock Divergent evolutionary fates of major photosynthetic gene networks following gene and whole genome duplications. -\newblock Plant signaling \& behavior 6:594--597. +\newblock Plant Signaling \& Behavior 6:594--597. \bibitem[{Coate et~al.(2016)Coate, Song, Bombarely, and Doyle}]{coate2016} Coate, J.~E., M.~J. Song, A.~Bombarely, and J.~J. Doyle, 2016. @@ -68,14 +68,14 @@ Coate, J.~E., M.~J. Song, A.~Bombarely, and J.~J. Doyle, 2016. Conant, G.~C., J.~A. Birchler, and J.~C. Pires, 2014. \newblock Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time. -\newblock Current opinion in plant biology 19:91--98. +\newblock Current Opinion in Plant Biology 19:91--98. \bibitem[{Defoort et~al.(2019)Defoort, Van~de Peer, and Carretero-Paulet}]{defoort2019} Defoort, J., Y.~Van~de Peer, and L.~Carretero-Paulet, 2019. \newblock The evolution of gene duplicates in angiosperms and the impact of protein-protein interactions and the mechanism of duplication. -\newblock Genome biology and evolution . +\newblock Genome Biology and Evolution . \bibitem[{Dong et~al.(2019)Dong, Lau, Song, Ierullo, Esteban, Wu, Sivieng, Nahal, Gaudinier, Pasha et~al.}]{dong2019} @@ -83,7 +83,7 @@ Dong, S., V.~Lau, R.~Song, M.~Ierullo, E.~Esteban, Y.~Wu, T.~Sivieng, H.~Nahal, A.~Gaudinier, A.~Pasha, et~al., 2019. \newblock Proteome-wide, structure-based prediction of protein-protein interactions/new molecular interactions viewer. -\newblock Plant physiology 179:1893--1907. +\newblock Plant Physiology 179:1893--1907. \bibitem[{Doyle and Coate(2019)}]{doyle2019} Doyle, J.~J. and J.~E. Coate, 2019. @@ -98,7 +98,7 @@ Edger, P.~P., J.~C. Hall, A.~Harkess, M.~Tang, J.~Coombs, S.~Mohammadin, M.~E. \newblock Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses. -\newblock American journal of botany 105:463--469. +\newblock American Journal of Botany 105:463--469. \bibitem[{Edger and Pires(2009)}]{edger2009} Edger, P.~P. and J.~C. Pires, 2009. @@ -110,19 +110,19 @@ Edger, P.~P. and J.~C. Pires, 2009. Freeling, M., 2009. \newblock Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. -\newblock Annual review of plant biology 60:433--453. +\newblock Annual Review of Plant Biology 60:433--453. \bibitem[{Grob and Grossniklaus(2017)}]{grob2017} Grob, S. and U.~Grossniklaus, 2017. \newblock Chromosome conformation capture-based studies reveal novel features of plant nuclear architecture. -\newblock Current opinion in plant biology 36:149--157. +\newblock Current Opinion in Plant Biology 36:149--157. \bibitem[{Grob et~al.(2014)Grob, Schmid, and Grossniklaus}]{grob2014} Grob, S., M.~W. Schmid, and U.~Grossniklaus, 2014. \newblock Hi-c analysis in arabidopsis identifies the knot, a structure with similarities to the flamenco locus of drosophila. -\newblock Molecular cell 55:678--693. +\newblock Molecular Cell 55:678--693. \bibitem[{Guo et~al.(1996)Guo, Davis, and Birchler}]{guo1996} Guo, M., D.~Davis, and J.~A. Birchler, 1996. @@ -134,7 +134,7 @@ Guo, M., D.~Davis, and J.~A. Birchler, 1996. Hakes, L., J.~W. Pinney, S.~C. Lovell, S.~G. Oliver, and D.~L. Robertson, 2007. \newblock All duplicates are not equal: the difference between small-scale and genome duplication. -\newblock Genome biology 8:R209. +\newblock Genome Biology 8:R209. \bibitem[{Hou et~al.(2018)Hou, Shi, Chen, Islam, Johnson, Kanno, Huettel, Yen, Hsu, Ji et~al.}]{hou2018} @@ -149,7 +149,7 @@ Katju, V. and U.~Bergthorsson, 2018. \newblock Old trade, new tricks: insights into the spontaneous mutation process from the partnering of classical mutation accumulation experiments with high-throughput genomic approaches. -\newblock Genome biology and evolution 11:136--165. +\newblock Genome Biology and Evolution 11:136--165. \bibitem[{Konrad et~al.(2018)Konrad, Flibotte, Taylor, Waterston, Moerman, Bergthorsson, and Katju}]{konrad2018} @@ -176,7 +176,7 @@ Liu, C., Y.-J. Cheng, J.-W. Wang, and D.~Weigel, 2017. Love, M.~I., W.~Huber, and S.~Anders, 2014. \newblock Moderated estimation of fold change and dispersion for rna-seq data with deseq2. -\newblock Genome biology 15:550. +\newblock Genome Biology 15:550. \bibitem[{Lynch and Conery(2000)}]{lynch2000} Lynch, M. and J.~S. Conery, 2000. @@ -191,7 +191,7 @@ Lynch, M. and J.~S. Conery, 2000. \bibitem[{Panchy et~al.(2016)Panchy, Lehti-Shiu, and Shiu}]{panchy2016} Panchy, N., M.~Lehti-Shiu, and S.-H. Shiu, 2016. \newblock Evolution of gene duplication in plants. -\newblock Plant physiology 171:2294--2316. +\newblock Plant Physiology 171:2294--2316. \bibitem[{Papp et~al.(2003)Papp, Pal, and Hurst}]{papp2003} Papp, B., C.~Pal, and L.~D. Hurst, 2003. @@ -203,7 +203,7 @@ Papp, B., C.~Pal, and L.~D. Hurst, 2003. Pertea, M., D.~Kim, G.~M. Pertea, J.~T. Leek, and S.~L. Salzberg, 2016. \newblock Transcript-level expression analysis of rna-seq experiments with hisat, stringtie and ballgown. -\newblock Nature protocols 11:1650. +\newblock Nature Protocols 11:1650. \bibitem[{Pirrello et~al.(2018)Pirrello, Deluche, Frangne, Gevaudant, Maza, Djari, Bourge, Renaudin, Brown, Bowler et~al.}]{pirrello2018} @@ -225,7 +225,7 @@ Qiao, X., H.~Yin, L.~Li, R.~Wang, J.~Wu, J.~Wu, and S.~Zhang, 2018. \newblock Different modes of gene duplication show divergent evolutionary patterns and contribute differently to the expansion of gene families involved in important fruit traits in pear (pyrus bretschneideri). -\newblock Frontiers in plant science 9:161. +\newblock Frontiers in Plant Science 9:161. \bibitem[{Ravi and Chan(2010)}]{ravi2010} Ravi, M. and S.~W. Chan, 2010. @@ -250,13 +250,13 @@ Rodgers-Melnick, E., S.~P. Mane, P.~Dharmawardhana, G.~T. Slavov, O.~R. Crasta, S.~H. Strauss, A.~M. Brunner, and S.~P. DiFazio, 2012. \newblock Contrasting patterns of evolution following whole genome versus tandem duplication events in populus. -\newblock Genome research 22:95--105. +\newblock Genome Research 22:95--105. \bibitem[{Rogers et~al.(2017)Rogers, Shao, and Thornton}]{rogers2017} Rogers, R.~L., L.~Shao, and K.~R. Thornton, 2017. \newblock Tandem duplications lead to novel expression patterns through exon shuffling in drosophila yakuba. -\newblock PLoS genetics 13:e1006795. +\newblock PLoS Genetics 13:e1006795. \bibitem[{Schlapfer et~al.(2017)Schlapfer, Zhang, Wang, Kim, Banf, Chae, Dreher, Chavali, Nilo-Poyanco, Bernard et~al.}]{schlapfer2017} @@ -264,7 +264,7 @@ Schlapfer, P., P.~Zhang, C.~Wang, T.~Kim, M.~Banf, L.~Chae, K.~Dreher, A.~K. Chavali, R.~Nilo-Poyanco, T.~Bernard, et~al., 2017. \newblock Genome-wide prediction of metabolic enzymes, pathways and gene clusters in plants. -\newblock Plant physiology Pp. pp--01942. +\newblock Plant Physiology Pp. pp--01942. \bibitem[{Schnable et~al.(2011)Schnable, Springer, and Freeling}]{schnable2011} Schnable, J.~C., N.~M. Springer, and M.~Freeling, 2011. @@ -277,18 +277,18 @@ Schnable, J.~C., N.~M. Springer, and M.~Freeling, 2011. Schnable, J.~C., X.~Wang, J.~C. Pires, and M.~Freeling, 2012. \newblock Escape from preferential retention following repeated whole genome duplications in plants. -\newblock Frontiers in plant science 3:94. +\newblock Frontiers in Plant Science 3:94. \bibitem[{Spoelhof et~al.(2017)Spoelhof, Soltis, and Soltis}]{spoelhof2017} Spoelhof, J.~P., P.~S. Soltis, and D.~E. Soltis, 2017. \newblock Pure polyploidy: closing the gaps in autopolyploid research. -\newblock Journal of systematics and evolution 55:340--352. +\newblock Journal of Systematics and Evolution 55:340--352. \bibitem[{Springer et~al.(2010)Springer, Weissman, and Kirschner}]{springer2010} Springer, M., J.~S. Weissman, and M.~W. Kirschner, 2010. \newblock A general lack of compensation for gene dosage in yeast. -\newblock Molecular systems biology 6:368. +\newblock Molecular Systems Biology 6:368. \bibitem[{Stupar et~al.(2007)Stupar, Bhaskar, Yandell, Rensink, Hart, Ouyang, Veilleux, Busse, Erhardt, Buell et~al.}]{stupar2007} @@ -318,7 +318,7 @@ Tasdighian, S., M.~Van~Bel, Z.~Li, Y.~Van~de Peer, L.~Carretero-Paulet, and Visger, C.~J., G.~K.-S. Wong, Y.~Zhang, P.~S. Soltis, and D.~E. Soltis, 2019. \newblock Divergent gene expression levels between diploid and autotetraploid tolmiea relative to the total transcriptome, the cell, and biomass. -\newblock American journal of botany 106:280--291. +\newblock American Journal of Botany 106:280--291. \bibitem[{Wang et~al.(2015)Wang, Liu, Roqueiro, Grimm, Schwab, Becker, Lanz, and Weigel}]{wang2015} @@ -326,13 +326,13 @@ Wang, C., C.~Liu, D.~Roqueiro, D.~Grimm, R.~Schwab, C.~Becker, C.~Lanz, and D.~Weigel, 2015. \newblock Genome-wide analysis of local chromatin packing in arabidopsis thaliana. -\newblock Genome research 25:246--256. +\newblock Genome Research 25:246--256. \bibitem[{Wang et~al.(2013)Wang, Tan, and Paterson}]{wang2013} Wang, Y., X.~Tan, and A.~H. Paterson, 2013. \newblock Different patterns of gene structure divergence following gene duplication in arabidopsis. -\newblock BMC genomics 14:652. +\newblock BMC Genomics 14:652. \bibitem[{Wang et~al.(2011)Wang, Wang, Tang, Tan, Ficklin, Feltus, and Paterson}]{wang2011} @@ -340,7 +340,7 @@ Wang, Y., X.~Wang, H.~Tang, X.~Tan, S.~P. Ficklin, F.~A. Feltus, and A.~H. Paterson, 2011. \newblock Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. -\newblock PloS one 6:e28150. +\newblock PloS One 6:e28150. \bibitem[{Xie et~al.(2019)Xie, Zhang, Zhang, Wang, Hu, and Wu}]{xie2019} Xie, T., F.-G. Zhang, H.-Y. Zhang, X.-T. Wang, J.-H. Hu, and X.-M. Wu, 2019. diff --git a/latex/wgd.bib b/latex/wgd.bib index cd0992b..d4b7016 100644 --- a/latex/wgd.bib +++ b/latex/wgd.bib @@ -1,7 +1,7 @@ @article{freeling2009, title={Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition}, author={Freeling, Michael}, - journal={Annual review of plant biology}, + journal={Annual Review of Plant Biology}, volume={60}, pages={433--453}, year={2009}, @@ -38,7 +38,7 @@ @article{blanc2004 @article{lamesch2011, title={The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools}, author={Lamesch, Philippe and Berardini, Tanya Z and Li, Donghui and Swarbreck, David and Wilks, Christopher and Sasidharan, Rajkumar and Muller, Robert and Dreher, Kate and Alexander, Debbie L and Garcia-Hernandez, Margarita and others}, - journal={Nucleic acids research}, + journal={Nucleic Acids Research}, volume={40}, number={D1}, pages={D1202--D1210}, @@ -58,7 +58,7 @@ @article{yu2010 @article{liang2018, title={Functional divergence between subgenomes and gene pairs after whole genome duplications}, author={Liang, Zhikai and Schnable, James C}, - journal={Molecular plant}, + journal={Molecular Plant}, volume={11}, number={3}, pages={388--397}, @@ -68,7 +68,7 @@ @article{liang2018 @article{wang2013, title={Different patterns of gene structure divergence following gene duplication in Arabidopsis}, author={Wang, Yupeng and Tan, Xu and Paterson, Andrew H}, - journal={BMC genomics}, + journal={BMC Genomics}, volume={14}, number={1}, pages={652}, @@ -78,7 +78,7 @@ @article{wang2013 @article{schlapfer2017, title={Genome-wide prediction of metabolic enzymes, pathways and gene clusters in plants}, author={Schlapfer, Pascal and Zhang, Peifen and Wang, Chuan and Kim, Taehyong and Banf, Michael and Chae, Lee and Dreher, Kate and Chavali, Arvind K and Nilo-Poyanco, Ricardo and Bernard, Thomas and others}, - journal={Plant physiology}, + journal={Plant Physiology}, pages={pp--01942}, year={2017}, publisher={Am Soc Plant Biol} @@ -96,7 +96,7 @@ @article{lynch2000 @article{jin2016, title={PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants}, author={Jin, Jinpu and Tian, Feng and Yang, De-Chang and Meng, Yu-Qi and Kong, Lei and Luo, Jingchu and Gao, Ge}, - journal={Nucleic acids research}, + journal={Nucleic Acids Research}, pages={gkw982}, year={2016}, publisher={Oxford University Press} @@ -115,7 +115,7 @@ @article{berman2002 @article{dong2019, title={Proteome-wide, structure-based prediction of protein-protein interactions/new molecular interactions viewer}, author={Dong, Shaowei and Lau, Vincent and Song, Richard and Ierullo, Matthew and Esteban, Eddi and Wu, Yingzhou and Sivieng, Teeratham and Nahal, Hardeep and Gaudinier, Allison and Pasha, Asher and others}, - journal={Plant physiology}, + journal={Plant Physiology}, volume={179}, number={4}, pages={1893--1907}, @@ -167,7 +167,7 @@ @article{hou2018 @article{veitia2015, title={Gene dosage imbalances: action, reaction, and models}, author={Veitia, Reiner A and Potier, Marie Claude}, -journal={Trends in biochemical sciences}, +journal={Trends in Biochemical Sciences}, volume={40}, number={6}, pages={309--317}, @@ -195,7 +195,7 @@ @incollection{lynch2003a @article{lynch2003b, title={The origins of genome complexity}, author={Lynch, Michael and Conery, John S}, - journal={science}, + journal={Science}, volume={302}, number={5649}, pages={1401--1404}, @@ -215,7 +215,7 @@ @article{doyle2019 @article{spoelhof2017, title={Pure polyploidy: closing the gaps in autopolyploid research}, author={Spoelhof, Jonathan P and Soltis, Pamela S and Soltis, Douglas E}, - journal={Journal of systematics and evolution}, + journal={Journal of Systematics and Evolution}, volume={55}, number={4}, pages={340--352}, @@ -235,7 +235,7 @@ @article{ravi2010 @article{arumuganathan1991, title={Nuclear DNA content of some important plant species}, author={Arumuganathan, Ka and Earle, ED}, - journal={Plant molecular biology reporter}, + journal={Plant Molecular Biology Reporter}, volume={9}, number={3}, pages={208--218}, @@ -255,7 +255,7 @@ @article{bolger2014 @article{pertea2016, title={Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown}, author={Pertea, Mihaela and Kim, Daehwan and Pertea, Geo M and Leek, Jeffrey T and Salzberg, Steven L}, - journal={Nature protocols}, + journal={Nature Protocols}, volume={11}, number={9}, pages={1650}, @@ -275,7 +275,7 @@ @article{anders2015 @article{love2014, title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2}, author={Love, Michael I and Huber, Wolfgang and Anders, Simon}, - journal={Genome biology}, + journal={Genome Biology}, volume={15}, number={12}, pages={550}, @@ -285,7 +285,7 @@ @article{love2014 @article{cannon2004, title={The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana}, author={Cannon, Steven B and Mitra, Arvind and Baumgarten, Andrew and Young, Nevin D and May, Georgiana}, - journal={BMC plant biology}, + journal={BMC Plant Biology}, volume={4}, number={1}, pages={10}, @@ -295,7 +295,7 @@ @article{cannon2004 @article{coate2010, title={Quantifying whole transcriptome size, a prerequisite for understanding transcriptome evolution across species: an example from a plant allopolyploid}, author={Coate, Jeremy E and Doyle, Jeff J}, - journal={Genome biology and evolution}, + journal={Genome Biology and Evolution}, volume={2}, pages={534--546}, year={2010}, @@ -314,7 +314,7 @@ @article{robinson2018 @article{visger2019, title={Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass}, author={Visger, Clayton J and Wong, Gane K-S and Zhang, Yong and Soltis, Pamela S and Soltis, Douglas E}, - journal={American journal of botany}, + journal={American Journal of Botany}, volume={106}, number={2}, pages={280--291}, @@ -325,7 +325,7 @@ @article{visger2019 @article{katju2018, title={Old trade, new tricks: insights into the spontaneous mutation process from the partnering of classical mutation accumulation experiments with high-throughput genomic approaches}, author={Katju, Vaishali and Bergthorsson, Ulfar}, - journal={Genome biology and evolution}, + journal={Genome Biology and Evolution}, volume={11}, number={1}, pages={136--165}, @@ -355,7 +355,7 @@ @article{papp2003 @article{edger2018, title={Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses}, author={Edger, Patrick P and Hall, Jocelyn C and Harkess, Alex and Tang, Michelle and Coombs, Jill and Mohammadin, Setareh and Schranz, M Eric and Xiong, Zhiyong and Leebens-Mack, James and Meyers, Blake C and others}, - journal={American journal of botany}, + journal={American Journal of Botany}, volume={105}, number={3}, pages={463--469}, @@ -365,7 +365,7 @@ @article{edger2018 @article{panchy2016, title={Evolution of gene duplication in plants}, author={Panchy, Nicholas and Lehti-Shiu, Melissa and Shiu, Shin-Han}, - journal={Plant physiology}, + journal={Plant Physiology}, volume={171}, number={4}, pages={2294--2316}, @@ -375,7 +375,7 @@ @article{panchy2016 @article{conant2014, title={Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time}, author={Conant, Gavin C and Birchler, James A and Pires, J Chris}, - journal={Current opinion in plant biology}, + journal={Current Opinion in Plant Biology}, volume={19}, pages={91--98}, year={2014}, @@ -394,7 +394,7 @@ @article{edger2009 @article{lu2016, title={Experimental evolution reveals interplay between Sch9 and polyploid stability in yeast}, author={Lu, Yi-Jin and Swamy, Krishna BS and Leu, Jun-Yi}, - journal={PLoS genetics}, + journal={PLoS Genetics}, volume={12}, number={11}, pages={e1006409}, @@ -404,7 +404,7 @@ @article{lu2016 @article{hebert2014, title={The intrinsic and extrinsic effects of N-linked glycans on glycoproteostasis}, author={Hebert, Daniel N and Lamriben, Lydia and Powers, Evan T and Kelly, Jeffery W}, - journal={Nature chemical biology}, + journal={Nature Chemical Biology}, volume={10}, number={11}, pages={902}, @@ -434,7 +434,7 @@ @article{zhang2015 @article{defoort2019, title={The evolution of gene duplicates in angiosperms and the impact of protein-protein interactions and the mechanism of duplication}, author={Defoort, Jonas and Van de Peer, Yves and Carretero-Paulet, Lorenzo}, - journal={Genome biology and evolution}, + journal={Genome Biology and Evolution}, year={2019} } @article{xie2019, @@ -449,13 +449,13 @@ @article{xie2019 @article{defoort2019, title={The evolution of gene duplicates in angiosperms and the impact of protein-protein interactions and the mechanism of duplication}, author={Defoort, Jonas and Van de Peer, Yves and Carretero-Paulet, Lorenzo}, - journal={Genome biology and evolution}, + journal={Genome Biology and Evolution}, year={2019} } @article{barker2009, title={Paleopolyploidy in the Brassicales: analyses of the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and other Brassicales}, author={Barker, Michael S and Vogel, Heiko and Schranz, M Eric}, - journal={Genome biology and evolution}, + journal={Genome Biology and Evolution}, volume={1}, pages={391--399}, year={2009}, @@ -464,7 +464,7 @@ @article{barker2009 @article{coate2011, title={Divergent evolutionary fates of major photosynthetic gene networks following gene and whole genome duplications}, author={Coate, Jeremy E and Doyle, Jeff J}, - journal={Plant signaling \& behavior}, + journal={Plant Signaling \& Behavior}, volume={6}, number={4}, pages={594--597}, @@ -504,7 +504,7 @@ @article{riddle2006 @article{rogers2017, title={Tandem duplications lead to novel expression patterns through exon shuffling in Drosophila yakuba}, author={Rogers, Rebekah L and Shao, Ling and Thornton, Kevin R}, - journal={PLoS genetics}, + journal={PLoS Genetics}, volume={13}, number={5}, pages={e1006795}, @@ -514,7 +514,7 @@ @article{rogers2017 @article{rodgers2012, title={Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus}, author={Rodgers-Melnick, Eli and Mane, Shrinivasrao P and Dharmawardhana, Palitha and Slavov, Gancho T and Crasta, Oswald R and Strauss, Steven H and Brunner, Amy M and DiFazio, Stephen P}, - journal={Genome research}, + journal={Genome Research}, volume={22}, number={1}, pages={95--105}, @@ -524,7 +524,7 @@ @article{rodgers2012 @article{springer2010, title={A general lack of compensation for gene dosage in yeast}, author={Springer, Michael and Weissman, Jonathan S and Kirschner, Marc W}, - journal={Molecular systems biology}, + journal={Molecular Systems Biology}, volume={6}, number={1}, pages={368}, @@ -560,7 +560,7 @@ @article{zhou2011 @article{wang2015, title={Genome-wide analysis of local chromatin packing in Arabidopsis thaliana}, author={Wang, Congmao and Liu, Chang and Roqueiro, Damian and Grimm, Dominik and Schwab, Rebecca and Becker, Claude and Lanz, Christa and Weigel, Detlef}, - journal={Genome research}, + journal={Genome Research}, volume={25}, number={2}, pages={246--256}, @@ -570,7 +570,7 @@ @article{wang2015 @article{schnable2012, title={Escape from preferential retention following repeated whole genome duplications in plants}, author={Schnable, James C and Wang, Xiaowu and Pires, J Chris and Freeling, Michael}, - journal={Frontiers in plant science}, + journal={Frontiers in Plant Science}, volume={3}, pages={94}, year={2012}, @@ -579,7 +579,7 @@ @article{schnable2012 @article{hakes2007, title={All duplicates are not equal: the difference between small-scale and genome duplication}, author={Hakes, Luke and Pinney, John W and Lovell, Simon C and Oliver, Stephen G and Robertson, David L}, - journal={Genome biology}, + journal={Genome Biology}, volume={8}, number={10}, pages={R209}, @@ -589,7 +589,7 @@ @article{hakes2007 @article{qiao2018, title={Different modes of gene duplication show divergent evolutionary patterns and contribute differently to the expansion of gene families involved in important fruit traits in pear (Pyrus bretschneideri)}, author={Qiao, Xin and Yin, Hao and Li, Leiting and Wang, Runze and Wu, Juyou and Wu, Jun and Zhang, Shaoling}, - journal={Frontiers in plant science}, + journal={Frontiers in Plant Science}, volume={9}, pages={161}, year={2018}, @@ -598,7 +598,7 @@ @article{qiao2018 @article{wang2011, title={Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms}, author={Wang, Yupeng and Wang, Xiyin and Tang, Haibao and Tan, Xu and Ficklin, Stephen P and Feltus, F Alex and Paterson, Andrew H}, - journal={PloS one}, + journal={PloS One}, volume={6}, number={12}, pages={e28150}, @@ -608,7 +608,7 @@ @article{wang2011 @article{grob2014, title={Hi-C analysis in Arabidopsis identifies the KNOT, a structure with similarities to the flamenco locus of Drosophila}, author={Grob, Stefan and Schmid, Marc W and Grossniklaus, Ueli}, - journal={Molecular cell}, + journal={Molecular Cell}, volume={55}, number={5}, pages={678--693}, @@ -618,7 +618,7 @@ @article{grob2014 @article{grob2017, title={Chromosome conformation capture-based studies reveal novel features of plant nuclear architecture}, author={Grob, Stefan and Grossniklaus, Ueli}, - journal={Current opinion in plant biology}, + journal={Current Opinion in Plant Biology}, volume={36}, pages={149--157}, year={2017}, diff --git a/latex/wgd.blg b/latex/wgd.blg index e16cb92..6b01432 100644 --- a/latex/wgd.blg +++ b/latex/wgd.blg @@ -9,7 +9,7 @@ Repeated entry---line 449 of file wgd.bib I'm skipping whatever remains of this entry You've used 56 entries, 2892 wiz_defined-function locations, - 927 strings with 16562 characters, + 926 strings with 16534 characters, and the built_in function-call counts, 39997 in all, are: = -- 3147 > -- 2529 diff --git a/latex/wgd.log b/latex/wgd.log index 5389ea8..bb2d900 100644 --- a/latex/wgd.log +++ b/latex/wgd.log @@ -1,4 +1,4 @@ -This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex 2016.5.22) 12 AUG 2019 13:59 +This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex 2016.5.22) 12 AUG 2019 15:42 entering extended mode restricted \write18 enabled. file:line:error style messages enabled. @@ -522,7 +522,7 @@ l/texlive/2016/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb> -Output written on wgd.pdf (21 pages, 1470305 bytes). +Output written on wgd.pdf (21 pages, 1470315 bytes). 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