TY - JOUR AU - Roux, J. AU - Rosikiewicz, M. AU - Robinson-Rechavi, M. PY - 2015 DA - 2015// TI - What to compare and how: Comparative transcriptomics for Evo-Devo JO - J Exp Zool B Mol Dev Evol VL - 324 UR - https://doi.org/10.1002/jez.b.22618 DO - 10.1002/jez.b.22618 ID - Roux2015 ER - TY - JOUR AU - Pantalacci, S. AU - Semon, M. PY - 2015 DA - 2015// TI - Transcriptomics of developing embryos and organs: A raising tool for evo-devo JO - J Exp Zool B Mol Dev Evol VL - 324 UR - https://doi.org/10.1002/jez.b.22595 DO - 10.1002/jez.b.22595 ID - Pantalacci2015 ER - TY - JOUR AU - Papatsenko, D. AU - Levine, M. AU - Goltsev, Y. PY - 2011 DA - 2011// TI - Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles JO - PLoS Biol VL - 9 UR - https://doi.org/10.1371/journal.pbio.1000584 DO - 10.1371/journal.pbio.1000584 ID - Papatsenko2011 ER - TY - JOUR AU - Treutlein, B. AU - Brownfield, D. G. AU - Wu, A. R. AU - Neff, N. F. AU - Mantalas, G. L. AU - Espinoza, F. H. PY - 2014 DA - 2014// TI - Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq JO - Nature VL - 509 UR - https://doi.org/10.1038/nature13173 DO - 10.1038/nature13173 ID - Treutlein2014 ER - TY - JOUR AU - Scialdone, A. AU - Tanaka, Y. AU - Jawaid, W. AU - Moignard, V. AU - Wilson, N. K. AU - Macaulay, I. C. PY - 2016 DA - 2016// TI - Resolving early mesoderm diversification through single-cell expression profiling JO - Nature VL - 535 UR - https://doi.org/10.1038/nature18633 DO - 10.1038/nature18633 ID - Scialdone2016 ER - TY - JOUR AU - Anavy, L. AU - Levin, M. AU - Khair, S. AU - Nakanishi, N. AU - Fernandez-Valverde, S. L. AU - Degnan, B. M. PY - 2014 DA - 2014// TI - BLIND ordering of large-scale transcriptomic developmental timecourses JO - Development VL - 141 UR - https://doi.org/10.1242/dev.105288 DO - 10.1242/dev.105288 ID - Anavy2014 ER - TY - JOUR AU - Gerrard, D. T. AU - Berry, A. A. AU - Jennings, R. E. AU - Piper Hanley, K. AU - Bobola, N. AU - Hanley, N. A. PY - 2016 DA - 2016// TI - An integrative transcriptomic atlas of organogenesis in human embryos JO - Elife VL - 5 UR - https://doi.org/10.7554/eLife.15657 DO - 10.7554/eLife.15657 ID - Gerrard2016 ER - TY - JOUR AU - Francesconi, M. AU - Lehner, B. PY - 2015 DA - 2015// TI - Reconstructing and analysing cellular states, space and time from gene expression profiles of many cells and single cells JO - Mol Biosyst VL - 11 UR - https://doi.org/10.1039/C5MB00339C DO - 10.1039/C5MB00339C ID - Francesconi2015 ER - TY - JOUR AU - Pankey, M. S. AU - Minin, V. N. AU - Imholte, G. C. AU - Suchard, M. A. AU - Oakley, T. H. PY - 2014 DA - 2014// TI - Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid JO - Proc Natl Acad Sci U S A VL - 111 UR - https://doi.org/10.1073/pnas.1416574111 DO - 10.1073/pnas.1416574111 ID - Pankey2014 ER - TY - JOUR AU - Tian, X. AU - Strassmann, J. E. AU - Queller, D. C. PY - 2013 DA - 2013// TI - Dictyostelium development shows a novel pattern of evolutionary conservation JO - Mol Biol Evol VL - 30 UR - https://doi.org/10.1093/molbev/mst007 DO - 10.1093/molbev/mst007 ID - Tian2013 ER - TY - JOUR AU - Levin, M. AU - Anavy, L. AU - Cole, A. G. AU - Winter, E. AU - Mostov, N. AU - Khair, S. PY - 2016 DA - 2016// TI - The mid-developmental transition and the evolution of animal body plans JO - Nature VL - 531 UR - https://doi.org/10.1038/nature16994 DO - 10.1038/nature16994 ID - Levin2016 ER - TY - JOUR AU - Kalinka, A. T. AU - Varga, K. M. AU - Gerrard, D. T. AU - Preibisch, S. AU - Corcoran, D. L. AU - Jarrells, J. PY - 2010 DA - 2010// TI - Gene expression divergence recapitulates the developmental hourglass model JO - Nature VL - 468 UR - https://doi.org/10.1038/nature09634 DO - 10.1038/nature09634 ID - Kalinka2010 ER - TY - JOUR AU - Levin, M. AU - Hashimshony, T. AU - Wagner, F. AU - Yanai, I. PY - 2012 DA - 2012// TI - Developmental milestones punctuate gene expression in the Caenorhabditis embryo JO - Dev Cell VL - 22 UR - https://doi.org/10.1016/j.devcel.2012.04.004 DO - 10.1016/j.devcel.2012.04.004 ID - Levin2012 ER - TY - JOUR AU - Wang, Z. AU - Young, R. L. AU - Xue, H. AU - Wagner, G. P. PY - 2011 DA - 2011// TI - Transcriptomic analysis of avian digits reveals conserved and derived digit identities in birds JO - Nature VL - 477 UR - https://doi.org/10.1038/nature10391 DO - 10.1038/nature10391 ID - Wang2011 ER - TY - JOUR AU - Tschopp, P. AU - Sherratt, E. AU - Sanger, T. J. AU - Groner, A. C. AU - Aspiras, A. C. AU - Hu, J. K. PY - 2014 DA - 2014// TI - A relative shift in cloacal location repositions external genitalia in amniote evolution JO - Nature VL - 516 UR - https://doi.org/10.1038/nature13819 DO - 10.1038/nature13819 ID - Tschopp2014 ER - TY - JOUR AU - Kin, K. AU - Nnamani, M. C. AU - Lynch, V. J. AU - Michaelides, E. AU - Wagner, G. P. PY - 2015 DA - 2015// TI - Cell-type phylogenetics and the origin of endometrial stromal cells JO - Cell Rep VL - 10 UR - https://doi.org/10.1016/j.celrep.2015.01.062 DO - 10.1016/j.celrep.2015.01.062 ID - Kin2015 ER - TY - JOUR AU - Angelini, D. R. AU - Kaufman, T. C. PY - 2005 DA - 2005// TI - Insect appendages and comparative ontogenetics JO - Dev Biol VL - 286 UR - https://doi.org/10.1016/j.ydbio.2005.07.006 DO - 10.1016/j.ydbio.2005.07.006 ID - Angelini2005 ER - TY - JOUR AU - Ruvinsky, I. AU - Gibson-Brown, J. J. PY - 2000 DA - 2000// TI - Genetic and developmental bases of serial homology in vertebrate limb evolution JO - Development VL - 127 ID - Ruvinsky2000 ER - TY - JOUR AU - Duboc, V. AU - Logan, M. P. PY - 2011 DA - 2011// TI - Regulation of limb bud initiation and limb-type morphology JO - Dev Dyn VL - 240 UR - https://doi.org/10.1002/dvdy.22582 DO - 10.1002/dvdy.22582 ID - Duboc2011 ER - TY - JOUR AU - Weatherbee, S. D. AU - Carroll, S. B. PY - 1999 DA - 1999// TI - Selector genes and limb identity in arthropods and vertebrates JO - Cell VL - 97 UR - https://doi.org/10.1016/S0092-8674(00)80737-0 DO - 10.1016/S0092-8674(00)80737-0 ID - Weatherbee1999 ER - TY - JOUR AU - Valen, L. PY - 1994 DA - 1994// TI - Serial homology: the crests and cusps of mammalian teeth JO - Acta Palaeontol Pol VL - 38 ID - Valen1994 ER - TY - JOUR AU - Weiss, K. AU - Stock, D. AU - Zhao, Z. AU - Buchanan, A. AU - Ruddle, F. AU - Shashikant, C. PY - 1998 DA - 1998// TI - Perspectives on genetic aspects of dental patterning JO - Eur J Oral Sci VL - 106 UR - https://doi.org/10.1111/j.1600-0722.1998.tb02154.x DO - 10.1111/j.1600-0722.1998.tb02154.x ID - Weiss1998 ER - TY - JOUR AU - Mann, R. S. AU - Carroll, S. B. PY - 2002 DA - 2002// TI - Molecular mechanisms of selector gene function and evolution JO - Curr Opin Genet Dev VL - 12 UR - https://doi.org/10.1016/S0959-437X(02)00344-1 DO - 10.1016/S0959-437X(02)00344-1 ID - Mann2002 ER - TY - JOUR AU - Cobourne, M. T. AU - Sharpe, P. T. PY - 2003 DA - 2003// TI - Tooth and jaw: molecular mechanisms of patterning in the first branchial arch JO - Arch Oral Biol VL - 48 UR - https://doi.org/10.1016/S0003-9969(02)00208-X DO - 10.1016/S0003-9969(02)00208-X ID - Cobourne2003 ER - TY - JOUR AU - Bininda-Emonds, O. R. AU - Jeffery, J. E. AU - Sanchez-Villagra, M. R. AU - Hanken, J. AU - Colbert, M. AU - Pieau, C. PY - 2007 DA - 2007// TI - Forelimb-hindlimb developmental timing changes across tetrapod phylogeny JO - BMC Evol Biol VL - 7 UR - https://doi.org/10.1186/1471-2148-7-182 DO - 10.1186/1471-2148-7-182 ID - Bininda-Emonds2007 ER - TY - JOUR AU - Richardson, M. K. AU - Gobes, S. M. AU - Leeuwen, A. C. AU - Polman, J. A. AU - Pieau, C. AU - Sanchez-Villagra, M. R. PY - 2009 DA - 2009// TI - Heterochrony in limb evolution: developmental mechanisms and natural selection JO - J Exp Zool B Mol Dev Evol VL - 312 UR - https://doi.org/10.1002/jez.b.21250 DO - 10.1002/jez.b.21250 ID - Richardson2009 ER - TY - JOUR AU - Taher, L. AU - Collette, N. M. AU - Murugesh, D. AU - Maxwell, E. AU - Ovcharenko, I. AU - Loots, G. G. PY - 2011 DA - 2011// TI - Global gene expression analysis of murine limb development JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0028358 DO - 10.1371/journal.pone.0028358 ID - Taher2011 ER - TY - JOUR AU - Laugel-Haushalter, V. AU - Paschaki, M. AU - Thibault-Carpentier, C. AU - Dembele, D. AU - Dolle, P. AU - Bloch-Zupan, A. PY - 2013 DA - 2013// TI - Molars and incisors: show your microarray IDs JO - BMC Res Notes VL - 6 UR - https://doi.org/10.1186/1756-0500-6-113 DO - 10.1186/1756-0500-6-113 ID - Laugel-Haushalter2013 ER - TY - JOUR AU - Jernvall, J. AU - Thesleff, I. PY - 2012 DA - 2012// TI - Tooth shape formation and tooth renewal: evolving with the same signals JO - Development VL - 139 UR - https://doi.org/10.1242/dev.085084 DO - 10.1242/dev.085084 ID - Jernvall2012 ER - TY - JOUR AU - Tucker, A. AU - Sharpe, P. PY - 2004 DA - 2004// TI - The cutting-edge of mammalian development; how the embryo makes teeth JO - Nat Rev Genet VL - 5 UR - https://doi.org/10.1038/nrg1380 DO - 10.1038/nrg1380 ID - Tucker2004 ER - TY - JOUR AU - Weiss, K. M. AU - Stock, D. W. AU - Zhao, Z. PY - 1998 DA - 1998// TI - Dynamic interactions and the evolutionary genetics of dental patterning JO - Crit Rev Oral Biol Med VL - 9 UR - https://doi.org/10.1177/10454411980090040101 DO - 10.1177/10454411980090040101 ID - Weiss1998 ER - TY - JOUR AU - Ferguson, C. A. AU - Tucker, A. S. AU - Sharpe, P. T. PY - 2000 DA - 2000// TI - Temporospatial cell interactions regulating mandibular and maxillary arch patterning JO - Development VL - 127 ID - Ferguson2000 ER - TY - JOUR AU - Zhao, Z. AU - Stock, D. AU - Buchanan, A. AU - Weiss, K. PY - 2000 DA - 2000// TI - Expression of Dlx genes during the development of the murine dentition JO - Dev Genes Evol VL - 210 UR - https://doi.org/10.1007/s004270050314 DO - 10.1007/s004270050314 ID - Zhao2000 ER - TY - JOUR AU - Salazar-Ciudad, I. PY - 2008 DA - 2008// TI - Tooth morphogenesis in vivo, in vitro, and in silico JO - Curr Top Dev Biol VL - 81 UR - https://doi.org/10.1016/S0070-2153(07)81012-X DO - 10.1016/S0070-2153(07)81012-X ID - Salazar-Ciudad2008 ER - TY - JOUR AU - Salazar-Ciudad, I. PY - 2012 DA - 2012// TI - Tooth patterning and evolution JO - Curr Opin Genet Dev VL - 22 UR - https://doi.org/10.1016/j.gde.2012.10.006 DO - 10.1016/j.gde.2012.10.006 ID - Salazar-Ciudad2012 ER - TY - JOUR AU - Jernvall, J. AU - Thesleff, I. PY - 2000 DA - 2000// TI - Reiterative signaling and patterning during mammalian tooth morphogenesis JO - Mech Dev VL - 92 UR - https://doi.org/10.1016/S0925-4773(99)00322-6 DO - 10.1016/S0925-4773(99)00322-6 ID - Jernvall2000 ER - TY - JOUR AU - Thesleff, I. AU - Keranen, S. AU - Jernvall, J. PY - 2001 DA - 2001// TI - Enamel knots as signaling centers linking tooth morphogenesis and odontoblast differentiation JO - Adv Dent Res VL - 15 UR - https://doi.org/10.1177/08959374010150010401 DO - 10.1177/08959374010150010401 ID - Thesleff2001 ER - TY - JOUR AU - Landin, M. A. AU - Nygard, S. AU - Shabestari, M. G. AU - Babaie, E. AU - Reseland, J. E. AU - Osmundsen, H. PY - 2015 DA - 2015// TI - Mapping the global mRNA transcriptome during development of the murine first molar JO - Front Genet VL - 6 UR - https://doi.org/10.3389/fgene.2015.00047 DO - 10.3389/fgene.2015.00047 ID - Landin2015 ER - TY - JOUR AU - O’Connell, D. J. AU - Ho, J. W. AU - Mammoto, T. AU - Turbe-Doan, A. AU - O’Connell, J. T. AU - Haseley, P. S. PY - 2012 DA - 2012// TI - A Wnt-bmp feedback circuit controls intertissue signaling dynamics in tooth organogenesis JO - Sci Signal VL - 5 ID - O’Connell2012 ER - TY - JOUR AU - Peterkova, R. AU - Hovorakova, M. AU - Peterka, M. AU - Lesot, H. PY - 2014 DA - 2014// TI - Three-dimensional analysis of the early development of the dentition JO - Aust Dent J VL - 59 UR - https://doi.org/10.1111/adj.12130 DO - 10.1111/adj.12130 ID - Peterkova2014 ER - TY - JOUR AU - Cam, Y. AU - Fausser, J. L. AU - Vonesch, J. L. AU - Peterkova, R. AU - Peterka, M. AU - Halaskova, M. PY - 2002 DA - 2002// TI - Asymmetrical morphogenesis and medio-lateral positioning of molars during mouse development JO - Eur J Oral Sci VL - 110 UR - https://doi.org/10.1034/j.1600-0722.2002.00140.x DO - 10.1034/j.1600-0722.2002.00140.x ID - Cam2002 ER - TY - JOUR AU - Biben, C. AU - Wang, C. C. AU - Harvey, R. P. PY - 2002 DA - 2002// TI - NK-2 class homeobox genes and pharyngeal/oral patterning: Nkx2-3 is required for salivary gland and tooth morphogenesis JO - Int J Dev Biol VL - 46 ID - Biben2002 ER - TY - JOUR AU - Mitsiadis, T. A. AU - Drouin, J. PY - 2008 DA - 2008// TI - Deletion of the Pitx1 genomic locus affects mandibular tooth morphogenesis and expression of the Barx1 and Tbx1 genes JO - Dev Biol VL - 313 UR - https://doi.org/10.1016/j.ydbio.2007.10.055 DO - 10.1016/j.ydbio.2007.10.055 ID - Mitsiadis2008 ER - TY - JOUR AU - Ferguson, C. A. AU - Tucker, A. S. AU - Christensen, L. AU - Lau, A. L. AU - Matzuk, M. M. AU - Sharpe, P. T. PY - 1998 DA - 1998// TI - Activin is an essential early mesenchymal signal in tooth development that is required for patterning of the murine dentition JO - Genes Dev VL - 12 UR - https://doi.org/10.1101/gad.12.16.2636 DO - 10.1101/gad.12.16.2636 ID - Ferguson1998 ER - TY - JOUR AU - Jia, S. AU - Zhou, J. AU - Gao, Y. AU - Baek, J. A. AU - Martin, J. F. AU - Lan, Y. PY - 2013 DA - 2013// TI - Roles of Bmp4 during tooth morphogenesis and sequential tooth formation JO - Development VL - 140 UR - https://doi.org/10.1242/dev.081927 DO - 10.1242/dev.081927 ID - Jia2013 ER - TY - JOUR AU - Aberg, T. AU - Wang, X. P. AU - Kim, J. H. AU - Yamashiro, T. AU - Bei, M. AU - Rice, R. PY - 2004 DA - 2004// TI - Runx2 mediates FGF signaling from epithelium to mesenchyme during tooth morphogenesis JO - Dev Biol VL - 270 UR - https://doi.org/10.1016/j.ydbio.2004.02.012 DO - 10.1016/j.ydbio.2004.02.012 ID - Aberg2004 ER - TY - JOUR AU - Wang, X. P. AU - Suomalainen, M. AU - Jorgez, C. J. AU - Matzuk, M. M. AU - Wankell, M. AU - Werner, S. PY - 2004 DA - 2004// TI - Modulation of activin/bone morphogenetic protein signaling by follistatin is required for the morphogenesis of mouse molar teeth JO - Dev Dyn VL - 231 UR - https://doi.org/10.1002/dvdy.20118 DO - 10.1002/dvdy.20118 ID - Wang2004 ER - TY - JOUR AU - Qiu, M. AU - Bulfone, A. AU - Ghattas, I. AU - Meneses, J. J. AU - Christensen, L. AU - Sharpe, P. T. PY - 1997 DA - 1997// TI - Role of the Dlx homeobox genes in proximodistal patterning of the branchial arches: mutations of Dlx-1, Dlx-2, and Dlx-1 and -2 alter morphogenesis of proximal skeletal and soft tissue structures derived from the first and second arches JO - Dev Biol VL - 185 UR - https://doi.org/10.1006/dbio.1997.8556 DO - 10.1006/dbio.1997.8556 ID - Qiu1997 ER - TY - JOUR AU - Thomas, B. L. AU - Tucker, A. S. AU - Qui, M. AU - Ferguson, C. A. AU - Hardcastle, Z. AU - Rubenstein, J. L. PY - 1997 DA - 1997// TI - Role of Dlx-1 and Dlx-2 genes in patterning of the murine dentition JO - Development VL - 124 ID - Thomas1997 ER - TY - JOUR AU - Jeong, J. AU - Li, X. AU - McEvilly, R. J. AU - Rosenfeld, M. G. AU - Lufkin, T. AU - Rubenstein, J. L. PY - 2008 DA - 2008// TI - Dlx genes pattern mammalian jaw primordium by regulating both lower jaw-specific and upper jaw-specific genetic programs JO - Development VL - 135 UR - https://doi.org/10.1242/dev.019778 DO - 10.1242/dev.019778 ID - Jeong2008 ER - TY - JOUR AU - Schmitt, R. AU - Lesot, H. AU - Vonesch, J. L. AU - Ruch, J. V. PY - 1999 DA - 1999// TI - Mouse odontogenesis in vitro: the cap-stage mesenchyme controls individual molar crown morphogenesis JO - Int J Dev Biol VL - 43 ID - Schmitt1999 ER - TY - STD TI - Tooth and Craniofacial Development Group of the Developmental Biology Programme IoB, University of Helsinki: Bite-it database. Tooth and Craniofacial Development Group of the Developmental Biology Programme, Institute of Biotechnology, University of Helsinki. http://bite-it.helsinki.fi. UR - http://bite-it.helsinki.fi ID - ref52 ER - TY - JOUR AU - Kaur, H. AU - Mao, S. AU - Li, Q. AU - Sameni, M. AU - Krawetz, S. A. AU - Sloane, B. F. PY - 2012 DA - 2012// TI - RNA-Seq of human breast ductal carcinoma in situ models reveals aldehyde dehydrogenase isoform 5A1 as a novel potential target JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0050249 DO - 10.1371/journal.pone.0050249 ID - Kaur2012 ER - TY - JOUR AU - Lisi, S. AU - Peterkova, R. AU - Peterka, M. AU - Vonesch, J. L. AU - Ruch, J. V. AU - Lesot, H. PY - 2003 DA - 2003// TI - Tooth morphogenesis and pattern of odontoblast differentiation JO - Connect Tissue Res VL - 44 UR - https://doi.org/10.1080/03008200390152278 DO - 10.1080/03008200390152278 ID - Lisi2003 ER - TY - JOUR AU - Harjunmaa, E. AU - Kallonen, A. AU - Voutilainen, M. AU - Hamalainen, K. AU - Mikkola, M. L. AU - Jernvall, J. PY - 2012 DA - 2012// TI - On the difficulty of increasing dental complexity JO - Nature VL - 483 UR - https://doi.org/10.1038/nature10876 DO - 10.1038/nature10876 ID - Harjunmaa2012 ER - TY - JOUR AU - Rutishauser, R. AU - Moline, P. PY - 2005 DA - 2005// TI - Evo-devo and the search for homology (“sameness”) in biological systems JO - Theory Biosci VL - 124 UR - https://doi.org/10.1007/BF02814485 DO - 10.1007/BF02814485 ID - Rutishauser2005 ER - TY - JOUR AU - Minelli, A. PY - 2003 DA - 2003// TI - The origin and evolution of appendages JO - Int J Dev Biol VL - 47 ID - Minelli2003 ER - TY - JOUR AU - Hu, B. AU - Nadiri, A. AU - Kuchler-Bopp, S. AU - Perrin-Schmitt, F. AU - Peters, H. AU - Lesot, H. PY - 2006 DA - 2006// TI - Tissue engineering of tooth crown, root, and periodontium JO - Tissue Eng VL - 12 UR - https://doi.org/10.1089/ten.2006.12.2069 DO - 10.1089/ten.2006.12.2069 ID - Hu2006 ER - TY - JOUR AU - Ouimette, J. F. AU - Jolin, M. L. AU - L’Honore, A. AU - Gifuni, A. AU - Drouin, J. PY - 2010 DA - 2010// TI - Divergent transcriptional activities determine limb identity JO - Nat Commun VL - 1 UR - https://doi.org/10.1038/ncomms1036 DO - 10.1038/ncomms1036 ID - Ouimette2010 ER - TY - JOUR AU - Moullec, N. PY - 1978 DA - 1978// TI - Contribution to the morphological study of mouse odontogenesis. Causality of tooth differentiation (author’s transl) JO - Arch Anat Histol Embryol VL - 61 ID - Moullec1978 ER - TY - JOUR AU - Salazar-Ciudad, I. AU - Jernvall, J. PY - 2010 DA - 2010// TI - A computational model of teeth and the developmental origins of morphological variation JO - Nature VL - 464 UR - https://doi.org/10.1038/nature08838 DO - 10.1038/nature08838 ID - Salazar-Ciudad2010 ER - TY - JOUR AU - Irie, N. AU - Kuratani, S. PY - 2011 DA - 2011// TI - Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis JO - Nat Commun VL - 2 UR - https://doi.org/10.1038/ncomms1248 DO - 10.1038/ncomms1248 ID - Irie2011 ER - TY - JOUR AU - Piasecka, B. AU - Lichocki, P. AU - Moretti, S. AU - Bergmann, S. AU - Robinson-Rechavi, M. PY - 2013 DA - 2013// TI - The hourglass and the early conservation models--co-existing patterns of developmental constraints in vertebrates JO - PLoS Genet VL - 9 UR - https://doi.org/10.1371/journal.pgen.1003476 DO - 10.1371/journal.pgen.1003476 ID - Piasecka2013 ER - TY - JOUR AU - Quint, M. AU - Drost, H. G. AU - Gabel, A. AU - Ullrich, K. K. AU - Bonn, M. AU - Grosse, I. PY - 2012 DA - 2012// TI - A transcriptomic hourglass in plant embryogenesis JO - Nature VL - 490 UR - https://doi.org/10.1038/nature11394 DO - 10.1038/nature11394 ID - Quint2012 ER - TY - JOUR AU - Wang, Z. AU - Pascual-Anaya, J. AU - Zadissa, A. AU - Li, W. AU - Niimura, Y. AU - Huang, Z. PY - 2013 DA - 2013// TI - The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2615 DO - 10.1038/ng.2615 ID - Wang2013 ER - TY - JOUR AU - Lesot, H. AU - Hovorakova, M. AU - Peterka, M. AU - Peterkova, R. PY - 2014 DA - 2014// TI - Three-dimensional analysis of molar development in the mouse from the cap to bell stage JO - Aust Dent J VL - 59 UR - https://doi.org/10.1111/adj.12132 DO - 10.1111/adj.12132 ID - Lesot2014 ER - TY - JOUR AU - Rothova, M. AU - Peterkova, R. AU - Tucker, A. S. PY - 2012 DA - 2012// TI - Fate map of the dental mesenchyme: dynamic development of the dental papilla and follicle JO - Dev Biol VL - 366 UR - https://doi.org/10.1016/j.ydbio.2012.03.018 DO - 10.1016/j.ydbio.2012.03.018 ID - Rothova2012 ER - TY - JOUR AU - Giese, A. AU - Bjerkvig, R. AU - Berens, M. E. AU - Westphal, M. PY - 2003 DA - 2003// TI - Cost of migration: invasion of malignant gliomas and implications for treatment JO - J Clin Oncol VL - 21 UR - https://doi.org/10.1200/JCO.2003.05.063 DO - 10.1200/JCO.2003.05.063 ID - Giese2003 ER - TY - JOUR AU - Duncan, T. AU - Su, T. T. PY - 2004 DA - 2004// TI - Embryogenesis: coordinating cell division with gastrulation JO - Curr Biol VL - 14 UR - https://doi.org/10.1016/j.cub.2004.03.050 DO - 10.1016/j.cub.2004.03.050 ID - Duncan2004 ER - TY - JOUR AU - Francesconi, M. AU - Lehner, B. PY - 2014 DA - 2014// TI - The effects of genetic variation on gene expression dynamics during development JO - Nature VL - 505 UR - https://doi.org/10.1038/nature12772 DO - 10.1038/nature12772 ID - Francesconi2014 ER - TY - JOUR AU - Tsang, J. C. AU - Yu, Y. AU - Burke, S. AU - Buettner, F. AU - Wang, C. AU - Kolodziejczyk, A. A. PY - 2015 DA - 2015// TI - Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells JO - Genome Biol VL - 16 UR - https://doi.org/10.1186/s13059-015-0739-5 DO - 10.1186/s13059-015-0739-5 ID - Tsang2015 ER - TY - JOUR AU - Kowalczyk, M. S. AU - Tirosh, I. AU - Heckl, D. AU - Rao, T. N. AU - Dixit, A. AU - Haas, B. J. PY - 2015 DA - 2015// TI - Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells JO - Genome Res VL - 25 UR - https://doi.org/10.1101/gr.192237.115 DO - 10.1101/gr.192237.115 ID - Kowalczyk2015 ER - TY - JOUR AU - Buettner, F. AU - Natarajan, K. N. AU - Casale, F. P. AU - Proserpio, V. AU - Scialdone, A. AU - Theis, F. J. PY - 2015 DA - 2015// TI - Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells JO - Nat Biotechnol VL - 33 UR - https://doi.org/10.1038/nbt.3102 DO - 10.1038/nbt.3102 ID - Buettner2015 ER - TY - JOUR AU - O’Duibhir, E. AU - Lijnzaad, P. AU - Benschop, J. J. AU - Lenstra, T. L. AU - Leenen, D. AU - Groot Koerkamp, M. J. PY - 2014 DA - 2014// TI - Cell cycle population effects in perturbation studies JO - Mol Syst Biol VL - 10 UR - https://doi.org/10.15252/msb.20145172 DO - 10.15252/msb.20145172 ID - O’Duibhir2014 ER - TY - JOUR AU - Israel, J. W. AU - Martik, M. L. AU - Byrne, M. AU - Raff, E. C. AU - Raff, R. A. AU - McClay, D. R. PY - 2016 DA - 2016// TI - Comparative developmental transcriptomics reveals rewiring of a highly conserved gene regulatory network during a major life history switch in the sea urchin genus Heliocidaris JO - PLoS Biol VL - 14 UR - https://doi.org/10.1371/journal.pbio.1002391 DO - 10.1371/journal.pbio.1002391 ID - Israel2016 ER - TY - JOUR AU - Fushan, A. A. AU - Turanov, A. A. AU - Lee, S. G. AU - Kim, E. B. AU - Lobanov, A. V. AU - Yim, S. H. PY - 2015 DA - 2015// TI - Gene expression defines natural changes in mammalian lifespan JO - Aging Cell VL - 14 UR - https://doi.org/10.1111/acel.12283 DO - 10.1111/acel.12283 ID - Fushan2015 ER - TY - JOUR AU - Brawand, D. AU - Soumillon, M. AU - Necsulea, A. AU - Julien, P. AU - Csardi, G. AU - Harrigan, P. PY - 2011 DA - 2011// TI - The evolution of gene expression levels in mammalian organs JO - Nature VL - 478 UR - https://doi.org/10.1038/nature10532 DO - 10.1038/nature10532 ID - Brawand2011 ER - TY - BOOK AU - Gould, S. PY - 1977 DA - 1977// TI - Ontogeny and Phylogeny PB - Belknap Press of Harvard University Press CY - Cambridge ID - Gould1977 ER - TY - JOUR AU - Liu, X. AU - Somel, M. AU - Tang, L. AU - Yan, Z. AU - Jiang, X. AU - Guo, S. PY - 2012 DA - 2012// TI - Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.127324.111 DO - 10.1101/gr.127324.111 ID - Liu2012 ER - TY - JOUR AU - Somel, M. AU - Franz, H. AU - Yan, Z. AU - Lorenc, A. AU - Guo, S. AU - Giger, T. PY - 2009 DA - 2009// TI - Transcriptional neoteny in the human brain JO - Proc Natl Acad Sci U S A VL - 106 UR - https://doi.org/10.1073/pnas.0900544106 DO - 10.1073/pnas.0900544106 ID - Somel2009 ER - TY - JOUR AU - Somel, M. AU - Rohlfs, R. AU - Liu, X. PY - 2014 DA - 2014// TI - Transcriptomic insights into human brain evolution: acceleration, neutrality, heterochrony JO - Curr Opin Genet Dev VL - 29 UR - https://doi.org/10.1016/j.gde.2014.09.001 DO - 10.1016/j.gde.2014.09.001 ID - Somel2014 ER - TY - JOUR AU - Yanai, I. AU - Peshkin, L. AU - Jorgensen, P. AU - Kirschner, M. W. PY - 2011 DA - 2011// TI - Mapping gene expression in two Xenopus species: evolutionary constraints and developmental flexibility JO - Dev Cell VL - 20 UR - https://doi.org/10.1016/j.devcel.2011.03.015 DO - 10.1016/j.devcel.2011.03.015 ID - Yanai2011 ER - TY - JOUR AU - Yuan, Y. AU - Chen, Y. P. AU - Ni, S. AU - Xu, A. G. AU - Tang, L. AU - Vingron, M. PY - 2011 DA - 2011// TI - Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series JO - BMC Bioinf VL - 12 UR - https://doi.org/10.1186/1471-2105-12-347 DO - 10.1186/1471-2105-12-347 ID - Yuan2011 ER - TY - JOUR AU - Raff, R. A. W. G. PY - 1989 DA - 1989// TI - Heterochrony: developmental mechanisms and evolutionary results JO - J Evol Biol VL - 2 UR - https://doi.org/10.1046/j.1420-9101.1989.2060409.x DO - 10.1046/j.1420-9101.1989.2060409.x ID - Raff1989 ER - TY - JOUR AU - Peterka, M. AU - Lesot, H. AU - Peterkova, R. PY - 2002 DA - 2002// TI - Body weight in mouse embryos specifies staging of tooth development JO - Connect Tissue Res VL - 43 UR - https://doi.org/10.1080/03008200290000673 DO - 10.1080/03008200290000673 ID - Peterka2002 ER - TY - JOUR AU - Jernvall, J. AU - Aberg, T. AU - Kettunen, P. AU - Keranen, S. AU - Thesleff, I. PY - 1998 DA - 1998// TI - The life history of an embryonic signaling center: BMP-4 induces p21 and is associated with apoptosis in the mouse tooth enamel knot JO - Development VL - 125 ID - Jernvall1998 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, S. L. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with Bowtie 2 JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - JOUR AU - Kim, D. AU - Pertea, G. AU - Trapnell, C. AU - Pimentel, H. AU - Kelley, R. AU - Salzberg, S. L. PY - 2013 DA - 2013// TI - TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions JO - Genome Biol VL - 14 UR - https://doi.org/10.1186/gb-2013-14-4-r36 DO - 10.1186/gb-2013-14-4-r36 ID - Kim2013 ER - TY - JOUR AU - Anders, S. AU - Pyl, P. T. AU - Huber, W. PY - 2015 DA - 2015// TI - HTSeq--a Python framework to work with high-throughput sequencing data JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btu638 DO - 10.1093/bioinformatics/btu638 ID - Anders2015 ER - TY - STD TI - R Core Team. R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2016. https://www.R-project.org/. UR - https://www.R-project.org/ ID - ref90 ER - TY - BOOK AU - Wickham, H. PY - 2009 DA - 2009// TI - ggplot2: Elegant Graphics for Data Analysis PB - Springer-Verlag CY - New York UR - https://doi.org/10.1007/978-0-387-98141-3 DO - 10.1007/978-0-387-98141-3 ID - Wickham2009 ER - TY - JOUR AU - Love, M. I. AU - Huber, W. AU - Anders, S. PY - 2014 DA - 2014// TI - Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0550-8 DO - 10.1186/s13059-014-0550-8 ID - Love2014 ER - TY - JOUR AU - Dray, S. AU - Dufour, A. -. B. PY - 2007 DA - 2007// TI - The ade4 package: implementing the duality diagram for ecologists JO - J Stat Softw VL - 22 UR - https://doi.org/10.18637/jss.v022.i04 DO - 10.18637/jss.v022.i04 ID - Dray2007 ER - TY - JOUR AU - Eden, E. AU - Navon, R. AU - Steinfeld, I. AU - Lipson, D. AU - Yakhini, Z. PY - 2009 DA - 2009// TI - GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists JO - BMC Bioinf VL - 10 UR - https://doi.org/10.1186/1471-2105-10-48 DO - 10.1186/1471-2105-10-48 ID - Eden2009 ER - TY - JOUR AU - Falcon, S. AU - Gentleman, R. PY - 2007 DA - 2007// TI - Using GOstats to test gene lists for GO term association JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btl567 DO - 10.1093/bioinformatics/btl567 ID - Falcon2007 ER - TY - JOUR AU - Hashimshony, T. AU - Feder, M. AU - Levin, M. AU - Hall, B. K. AU - Yanai, I. PY - 2015 DA - 2015// TI - Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer JO - Nature VL - 519 UR - https://doi.org/10.1038/nature13996 DO - 10.1038/nature13996 ID - Hashimshony2015 ER - TY - JOUR AU - Gaujoux, R. AU - Seoighe, C. PY - 2013 DA - 2013// TI - Cell Mix: a comprehensive toolbox for gene expression deconvolution JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt351 DO - 10.1093/bioinformatics/btt351 ID - Gaujoux2013 ER - TY - JOUR AU - Zhong, Y. AU - Wan, Y. W. AU - Pang, K. AU - Chow, L. M. AU - Liu, Z. PY - 2013 DA - 2013// TI - Digital sorting of complex tissues for cell type-specific gene expression profiles JO - BMC Bioinf VL - 14 UR - https://doi.org/10.1186/1471-2105-14-89 DO - 10.1186/1471-2105-14-89 ID - Zhong2013 ER - TY - JOUR AU - Gruneberg, H. PY - 1965 DA - 1965// TI - Genes and genotypes affecting the teeth of the mouse JO - J Embryol Exp Morphol VL - 14 ID - Gruneberg1965 ER - TY - JOUR AU - Lochovska, K. AU - Peterkova, R. AU - Pavlikova, Z. AU - Hovorakova, M. PY - 2015 DA - 2015// TI - Sprouty gene dosage influences temporal-spatial dynamics of primary enamel knot formation JO - BMC Dev Biol VL - 15 UR - https://doi.org/10.1186/s12861-015-0070-0 DO - 10.1186/s12861-015-0070-0 ID - Lochovska2015 ER - TY - JOUR AU - Prochazka, J. AU - Pantalacci, S. AU - Churava, S. AU - Rothova, M. AU - Lambert, A. AU - Lesot, H. PY - 2010 DA - 2010// TI - Patterning by heritage in mouse molar row development JO - Proc Natl Acad Sci U S A VL - 107 UR - https://doi.org/10.1073/pnas.1002784107 DO - 10.1073/pnas.1002784107 ID - Prochazka2010 ER - TY - JOUR AU - Cameron, T. L. AU - Belluoccio, D. AU - Farlie, P. G. AU - Brachvogel, B. AU - Bateman, J. F. PY - 2009 DA - 2009// TI - Global comparative transcriptome analysis of cartilage formation in vivo JO - BMC Dev Biol VL - 9 UR - https://doi.org/10.1186/1471-213X-9-20 DO - 10.1186/1471-213X-9-20 ID - Cameron2009 ER -