TY - JOUR AU - Brown, S. J. AU - Shippy, T. D. AU - Miller, S. AU - Bolognesi, R. AU - Beeman, R. W. AU - Lorenzen, M. D. PY - 2009 DA - 2009// TI - The red flour beetle, Tribolium castaneum (Coleoptera): a model for studies of development and pest biology JO - Cold Spring Harb Protoc VL - 2009 UR - https://doi.org/10.1101/pdb.emo126 DO - 10.1101/pdb.emo126 ID - Brown2009 ER - TY - JOUR AU - Klingler, M. PY - 2004 DA - 2004// JO - Tribolium Curr Biol VL - 14 UR - https://doi.org/10.1016/j.cub.2004.08.004 DO - 10.1016/j.cub.2004.08.004 ID - Klingler2004 ER - TY - JOUR AU - Schröder, R. AU - Beermann, A. AU - Wittkopp, N. AU - Lutz, R. PY - 2008 DA - 2008// TI - From development to biodiversity--Tribolium castaneum, an insect model organism for short germband development JO - Dev Genes Evol VL - 218 UR - https://doi.org/10.1007/s00427-008-0214-3 DO - 10.1007/s00427-008-0214-3 ID - Schröder2008 ER - TY - JOUR AU - Panfilio, K. A. PY - 2008 DA - 2008// TI - Extraembryonic development in insects and the acrobatics of blastokinesis JO - Dev Biol VL - 313 UR - https://doi.org/10.1016/j.ydbio.2007.11.004 DO - 10.1016/j.ydbio.2007.11.004 ID - Panfilio2008 ER - TY - JOUR AU - Posnien, N. AU - Schinko, J. B. AU - Kittelmann, S. AU - Bucher, G. PY - 2010 DA - 2010// TI - Genetics, development and composition of the insect head - a beetle’s view JO - Arthropod Struct Dev. VL - 39 UR - https://doi.org/10.1016/j.asd.2010.08.002 DO - 10.1016/j.asd.2010.08.002 ID - Posnien2010 ER - TY - JOUR AU - Tautz, D. PY - 2004 DA - 2004// JO - Segmentation Dev Cell VL - 7 UR - https://doi.org/10.1016/j.devcel.2004.08.008 DO - 10.1016/j.devcel.2004.08.008 ID - Tautz2004 ER - TY - JOUR AU - Davis, G. K. AU - Patel, N. H. PY - 2002 DA - 2002// TI - SHORT, LONG, AND BEYOND: Molecular and embryological approaches to insect segmentation JO - Annu Rev Entomol VL - 47 UR - https://doi.org/10.1146/annurev.ento.47.091201.145251 DO - 10.1146/annurev.ento.47.091201.145251 ID - Davis2002 ER - TY - BOOK AU - Snodgrass, R. PY - 1954 DA - 1954// TI - Insect metamorphosis: Smithsonian miscellaneous collections, V122, no. 9 PB - Literary Licensing CY - Washington ID - Snodgrass1954 ER - TY - JOUR AU - Bäumer, D. AU - Strohlein, N. M. AU - Schoppmeier, M. PY - 2012 DA - 2012// TI - Opposing effects of notch-signaling in maintaining the proliferative state of follicle cells in the telotrophic ovary of the beetle Tribolium JO - Front Zool VL - 9 UR - https://doi.org/10.1186/1742-9994-9-15 DO - 10.1186/1742-9994-9-15 ID - Bäumer2012 ER - TY - JOUR AU - Tomoyasu, Y. AU - Wheeler, S. R. AU - Denell, R. E. PY - 2005 DA - 2005// TI - Ultrabithorax is required for membranous wing identity in the beetle Tribolium castaneum JO - Nature. VL - 433 UR - https://doi.org/10.1038/nature03272 DO - 10.1038/nature03272 ID - Tomoyasu2005 ER - TY - JOUR AU - Hu, Y. AU - Schmitt-Engel, C. AU - Schwirz, J. AU - Stroehlein, N. AU - Richter, T. AU - Majumdar, U. PY - 2018 DA - 2018// TI - A morphological novelty evolved by co-option of a reduced gene regulatory network and gene recruitment in a beetle JO - Proc R Soc B VL - 285 UR - https://doi.org/10.1098/rspb.2018.1373 DO - 10.1098/rspb.2018.1373 ID - Hu2018 ER - TY - JOUR AU - Noh, M. Y. AU - Muthukrishnan, S. AU - Kramer, K. J. AU - Arakane, Y. PY - 2016 DA - 2016// TI - Cuticle formation and pigmentation in beetles JO - Curr Opin Insect Sci VL - 17 UR - https://doi.org/10.1016/j.cois.2016.05.004 DO - 10.1016/j.cois.2016.05.004 ID - Noh2016 ER - TY - JOUR AU - King, B. AU - Denholm, B. PY - 2014 DA - 2014// TI - Malpighian tubule development in the red flour beetle (Tribolium castaneum) JO - Arthropod Struct Dev VL - 43 UR - https://doi.org/10.1016/j.asd.2014.08.002 DO - 10.1016/j.asd.2014.08.002 ID - King2014 ER - TY - JOUR AU - Li, J. AU - Lehmann, S. AU - Weißbecker, B. AU - Ojeda Naharros, I. AU - Schütz, S. AU - Joop, G. PY - 2013 DA - 2013// TI - Odoriferous defensive stink gland Transcriptome to identify novel genes necessary for Quinone synthesis in the red flour beetle, Tribolium castaneum JO - PLoS Genet VL - 9 UR - https://doi.org/10.1371/journal.pgen.1003596 DO - 10.1371/journal.pgen.1003596 ID - Li2013 ER - TY - JOUR AU - Hunt, T. AU - Bergsten, J. AU - Levkanicova, Z. AU - Papadopoulou, A. AU - John, O. S. AU - Wild, R. PY - 2007 DA - 2007// TI - A comprehensive phylogeny of beetles reveals the evolutionary origins of a Superradiation JO - Science. VL - 318 UR - https://doi.org/10.1126/science.1146954 DO - 10.1126/science.1146954 ID - Hunt2007 ER - TY - JOUR AU - Merzendorfer, H. AU - Kim, H. S. AU - Chaudhari, S. S. AU - Kumari, M. AU - Specht, C. A. AU - Butcher, S. PY - 2012 DA - 2012// TI - Genomic and proteomic studies on the effects of the insect growth regulator diflubenzuron in the model beetle species Tribolium castaneum JO - Insect Biochem Mol Biol VL - 42 UR - https://doi.org/10.1016/j.ibmb.2011.12.008 DO - 10.1016/j.ibmb.2011.12.008 ID - Merzendorfer2012 ER - TY - STD TI - Ulrich J, Dao VA, Majumdar U, Schmitt-Engel C, Schwirz J, Schultheis D, et al. Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target. BMC Genomics. 2015;16. https://doi.org/10.1186/s12864-015-1880-y. ID - ref17 ER - TY - JOUR AU - Berghammer, A. J. AU - Klingler, M. AU - Wimmer, E. A. PY - 1999 DA - 1999// TI - A universal marker for transgenic insects JO - Nature. VL - 402 UR - https://doi.org/10.1038/46463 DO - 10.1038/46463 ID - Berghammer1999 ER - TY - JOUR AU - Koniszewski, N. D. B. AU - Kollmann, M. AU - Bigham, M. AU - Farnworth, M. AU - He, B. AU - Büscher, M. PY - 2016 DA - 2016// TI - The insect central complex as model for heterochronic brain development-background, concepts, and tools JO - Dev Genes Evol VL - 226 UR - https://doi.org/10.1007/s00427-016-0542-7 DO - 10.1007/s00427-016-0542-7 ID - Koniszewski2016 ER - TY - JOUR AU - Lorenzen, M. D. AU - Berghammer, A. J. AU - Brown, S. J. AU - Denell, R. E. AU - Klingler, M. AU - Beeman, R. W. PY - 2003 DA - 2003// TI - piggyBac-mediated germline transformation in the beetle Tribolium castaneum JO - Insect Mol Biol VL - 12 UR - https://doi.org/10.1046/j.1365-2583.2003.00427.x DO - 10.1046/j.1365-2583.2003.00427.x ID - Lorenzen2003 ER - TY - JOUR AU - Sarrazin, A. F. AU - Peel, A. D. AU - Averof, M. PY - 2012 DA - 2012// TI - A Segmentation Clock with Two-Segment Periodicity in Insects JO - Science VL - 336 UR - https://doi.org/10.1126/science.1218256 DO - 10.1126/science.1218256 ID - Sarrazin2012 ER - TY - JOUR AU - Schinko, J. B. AU - Weber, M. AU - Viktorinova, I. AU - Kiupakis, A. AU - Averof, M. AU - Klingler, M. PY - 2010 DA - 2010// TI - Functionality of the GAL4/UAS system in Tribolium requires the use of endogenous core promoters JO - BMC Dev Biol VL - 10 UR - https://doi.org/10.1186/1471-213X-10-53 DO - 10.1186/1471-213X-10-53 ID - Schinko2010 ER - TY - JOUR AU - Schinko, J. B. AU - Hillebrand, K. AU - Bucher, G. PY - 2012 DA - 2012// TI - Heat shock-mediated misexpression of genes in the beetle Tribolium castaneum JO - Dev Genes Evol VL - 222 UR - https://doi.org/10.1007/s00427-012-0412-x DO - 10.1007/s00427-012-0412-x ID - Schinko2012 ER - TY - JOUR AU - Trauner, J. AU - Schinko, J. AU - Lorenzen, M. AU - Shippy, T. AU - Wimmer, E. AU - Beeman, R. W. PY - 2009 DA - 2009// TI - Large-scale insertional mutagenesis of a coleopteran stored grain pest, the red flour beetle Tribolium castaneum, identifies embryonic lethal mutations and enhancer traps JO - BMC Biol VL - 7 UR - https://doi.org/10.1186/1741-7007-7-73 DO - 10.1186/1741-7007-7-73 ID - Trauner2009 ER - TY - JOUR AU - Beermann, A. AU - Jay, D. G. AU - Beeman, R. W. AU - Hulskamp, M. AU - Tautz, D. AU - Jürgens, G. PY - 2001 DA - 2001// TI - The short antennae gene of Tribolium is required for limb development and encodes the orthologue of the Drosophila distal-less protein JO - Development. VL - 128 ID - Beermann2001 ER - TY - JOUR AU - Brown, S. J. AU - Mahaffey, J. P. AU - Lorenzen, M. D. AU - Denell, R. E. AU - Mahaffey, J. W. PY - 1999 DA - 1999// TI - Using RNAi to investigate orthologous homeotic gene function during development of distantly related insects JO - Evol Dev VL - 1 UR - https://doi.org/10.1046/j.1525-142x.1999.99013.x DO - 10.1046/j.1525-142x.1999.99013.x ID - Brown1999 ER - TY - JOUR AU - Peel, A. D. AU - Schanda, J. AU - Grossmann, D. AU - Ruge, F. AU - Oberhofer, G. AU - Gilles, A. F. PY - 2013 DA - 2013// TI - Tc-knirps plays different roles in the specification of antennal and mandibular parasegment boundaries and is regulated by a pair-rule gene in the beetle Tribolium castaneum JO - BMC Dev Biol VL - 13 UR - https://doi.org/10.1186/1471-213X-13-25 DO - 10.1186/1471-213X-13-25 ID - Peel2013 ER - TY - JOUR AU - Curtis, C. D. AU - Brisson, J. A. AU - DeCamillis, M. A. AU - Shippy, T. D. AU - Brown, S. J. AU - Denell, R. E. PY - 2001 DA - 2001// TI - Molecular characterization of cephalothorax, the Tribolium ortholog of sex combs reduced JO - Genesis. VL - 30 UR - https://doi.org/10.1002/gene.1027 DO - 10.1002/gene.1027 ID - Curtis2001 ER - TY - JOUR AU - Bucher, G. AU - Scholten, J. AU - Klingler, M. PY - 2002 DA - 2002// TI - Parental RNAi in Tribolium (Coleoptera) JO - Curr Biol VL - 12 UR - https://doi.org/10.1016/S0960-9822(02)00666-8 DO - 10.1016/S0960-9822(02)00666-8 ID - Bucher2002 ER - TY - JOUR AU - Tomoyasu, Y. AU - Denell, R. E. PY - 2004 DA - 2004// TI - Larval RNAi in Tribolium (Coleoptera) for analyzing adult development JO - Dev Genes Evol VL - 214 UR - https://doi.org/10.1007/s00427-004-0434-0 DO - 10.1007/s00427-004-0434-0 ID - Tomoyasu2004 ER - TY - JOUR AU - Tomoyasu, Y. AU - Miller, S. C. AU - Tomita, S. AU - Schoppmeier, M. AU - Grossmann, D. AU - Bucher, G. PY - 2008 DA - 2008// TI - Exploring systemic RNA interference in insects: a genome-wide survey for RNAi genes in Tribolium JO - Genome Biol VL - 9 UR - https://doi.org/10.1186/gb-2008-9-1-r10 DO - 10.1186/gb-2008-9-1-r10 ID - Tomoyasu2008 ER - TY - JOUR AU - Schmitt-Engel, C. AU - Schultheis, D. AU - Schwirz, J. AU - Ströhlein, N. AU - Troelenberg, N. AU - Majumdar, U. PY - 2015 DA - 2015// TI - The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology JO - Nat Commun VL - 6 UR - https://doi.org/10.1038/ncomms8822 DO - 10.1038/ncomms8822 ID - Schmitt-Engel2015 ER - TY - JOUR AU - Dönitz, J. AU - Schmitt-Engel, C. AU - Grossmann, D. AU - Gerischer, L. AU - Tech, M. AU - Schoppmeier, M. PY - 2015 DA - 2015// TI - iBeetle-base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1054 DO - 10.1093/nar/gku1054 ID - Dönitz2015 ER - TY - JOUR AU - Dönitz, J. AU - Gerischer, L. AU - Hahnke, S. AU - Pfeiffer, S. AU - Bucher, G. PY - 2018 DA - 2018// TI - Expanded and updated data and a query pipeline for iBeetle-base JO - Nucleic Acids Res VL - 46 UR - https://doi.org/10.1093/nar/gkx984 DO - 10.1093/nar/gkx984 ID - Dönitz2018 ER - TY - JOUR AU - Gilles, A. F. AU - Schinko, J. B. AU - Averof, M. PY - 2015 DA - 2015// TI - Efficient CRISPR-mediated gene targeting and transgene replacement in the beetle Tribolium castaneum JO - Dev Camb Engl VL - 142 ID - Gilles2015 ER - TY - STD TI - Gilles AF, Schinko JB, Schacht MI, Enjolras C, Averof M. Clonal analysis by tunable CRISPR-mediated excision. bioRxiv. 2018:394221. https://doi.org/10.1101/394221. ID - ref36 ER - TY - JOUR AU - Kim, H. S. AU - Murphy, T. AU - Xia, J. AU - Caragea, D. AU - Park, Y. AU - Beeman, R. W. PY - 2010 DA - 2010// TI - BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkp807 DO - 10.1093/nar/gkp807 ID - Kim2010 ER - TY - JOUR AU - Richards, S. AU - Gibbs, R. A. AU - Weinstock, G. M. AU - Brown, S. J. AU - Denell, R. AU - Beeman, R. W. PY - 2008 DA - 2008// TI - The genome of the model beetle and pest Tribolium castaneum JO - Nature. VL - 452 UR - https://doi.org/10.1038/nature06784 DO - 10.1038/nature06784 ID - Richards2008 ER - TY - JOUR AU - Lorenzen, M. D. PY - 2005 DA - 2005// TI - Genetic linkage maps of the red flour beetle, Tribolium castaneum, based on bacterial artificial chromosomes and expressed sequence tags JO - Genetics. VL - 170 UR - https://doi.org/10.1534/genetics.104.032227 DO - 10.1534/genetics.104.032227 ID - Lorenzen2005 ER - TY - JOUR AU - Boetzer, M. AU - Pirovano, W. PY - 2012 DA - 2012// TI - Toward almost closed genomes with GapFiller JO - Genome Biol VL - 13 UR - https://doi.org/10.1186/gb-2012-13-6-r56 DO - 10.1186/gb-2012-13-6-r56 ID - Boetzer2012 ER - TY - STD TI - Shelton JM, Coleman MC, Herndon N, Lu N, Lam ET, Anantharaman T, et al. Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool. BMC Genomics. 2015;16. https://doi.org/10.1186/s12864-015-1911-8. ID - ref41 ER - TY - JOUR AU - Stanke, M. AU - Diekhans, M. AU - Baertsch, R. AU - Haussler, D. PY - 2008 DA - 2008// TI - Using native and syntenically mapped cDNA alignments to improve de novo gene finding JO - Bioinformatics. VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn013 DO - 10.1093/bioinformatics/btn013 ID - Stanke2008 ER - TY - JOUR AU - Kent, W. J. PY - 2002 DA - 2002// TI - BLAT---the BLAST-like alignment tool JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.229202 DO - 10.1101/gr.229202 ID - Kent2002 ER - TY - JOUR AU - Simão, F. A. AU - Waterhouse, R. M. AU - Ioannidis, P. AU - Kriventseva, E. V. AU - Zdobnov, E. M. PY - 2015 DA - 2015// TI - BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs JO - Bioinformatics. VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv351 DO - 10.1093/bioinformatics/btv351 ID - Simão2015 ER - TY - JOUR AU - Gramates, L. S. AU - Marygold, S. J. AU - Santos, G. AU - Urbano, J. -. M. AU - Antonazzo, G. AU - Matthews, B. B. PY - 2017 DA - 2017// TI - FlyBase at 25: looking to the future JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1016 DO - 10.1093/nar/gkw1016 ID - Gramates2017 ER - TY - JOUR AU - Elsik, C. G. AU - Worley, K. C. AU - Bennett, A. K. AU - Beye, M. AU - Camara, F. AU - Childers, C. P. PY - 2014 DA - 2014// TI - Finding the missing honey bee genes: lessons learned from a genome upgrade JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-86 DO - 10.1186/1471-2164-15-86 ID - Elsik2014 ER - TY - JOUR AU - Schwager, E. E. AU - Sharma, P. P. AU - Clarke, T. AU - Leite, D. J. AU - Wierschin, T. AU - Pechmann, M. PY - 2017 DA - 2017// TI - The house spider genome reveals an ancient whole-genome duplication during arachnid evolution JO - BMC Biol VL - 15 UR - https://doi.org/10.1186/s12915-017-0399-x DO - 10.1186/s12915-017-0399-x ID - Schwager2017 ER - TY - JOUR AU - O’Leary, N. A. AU - Wright, M. W. AU - Brister, J. R. AU - Ciufo, S. AU - Haddad, D. AU - McVeigh, R. PY - 2016 DA - 2016// TI - Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1189 DO - 10.1093/nar/gkv1189 ID - O’Leary2016 ER - TY - JOUR AU - Raible, F. AU - Tessmar-Raible, K. AU - Osoegawa, K. AU - Wincker, P. AU - Jubin, C. AU - Balavoine, G. PY - 2005 DA - 2005// TI - Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii JO - Science. VL - 310 UR - https://doi.org/10.1126/science.1119089 DO - 10.1126/science.1119089 ID - Raible2005 ER - TY - JOUR AU - Otu, H. H. AU - Sayood, K. PY - 2003 DA - 2003// TI - A new sequence distance measure for phylogenetic tree construction JO - Bioinformatics. VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg295 DO - 10.1093/bioinformatics/btg295 ID - Otu2003 ER - TY - JOUR AU - Ulitsky, I. AU - Burstein, D. AU - Tuller, T. AU - Chor, B. PY - 2006 DA - 2006// TI - The average common substring approach to phylogenomic reconstruction JO - J Comput Biol J Comput Mol Cell Biol VL - 13 UR - https://doi.org/10.1089/cmb.2006.13.336 DO - 10.1089/cmb.2006.13.336 ID - Ulitsky2006 ER - TY - JOUR AU - Ha, M. AU - Kim, V. N. PY - 2014 DA - 2014// TI - Regulation of microRNA biogenesis JO - Nat Rev Mol Cell Biol VL - 15 UR - https://doi.org/10.1038/nrm3838 DO - 10.1038/nrm3838 ID - Ha2014 ER - TY - JOUR AU - Bartel, D. P. PY - 2009 DA - 2009// TI - MicroRNAs: target recognition and regulatory functions JO - Cell. VL - 136 UR - https://doi.org/10.1016/j.cell.2009.01.002 DO - 10.1016/j.cell.2009.01.002 ID - Bartel2009 ER - TY - JOUR AU - Marco, A. n. t. o. n. i. o. AU - Hui, J. e. r. o. m. e. H. L. AU - Ronshaugen, M. a. t. t. h. e. w. AU - Griffiths-Jones, S. a. m. PY - 2010 DA - 2010// TI - Functional Shifts in Insect microRNA Evolution JO - Genome Biology and Evolution VL - 2 UR - https://doi.org/10.1093/gbe/evq053 DO - 10.1093/gbe/evq053 ID - Marco2010 ER - TY - JOUR AU - Ninova, M. AU - Ronshaugen, M. AU - Griffiths-Jones, S. PY - 2016 DA - 2016// TI - MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum JO - Genome Res VL - 26 UR - https://doi.org/10.1101/gr.193367.115 DO - 10.1101/gr.193367.115 ID - Ninova2016 ER - TY - JOUR AU - Enright, A. J. AU - John, B. AU - Gaul, U. AU - Tuschl, T. AU - Sander, C. AU - Marks, D. S. PY - 2003 DA - 2003// TI - MicroRNA targets in Drosophila JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2003-5-1-r1 DO - 10.1186/gb-2003-5-1-r1 ID - Enright2003 ER - TY - JOUR AU - Sun, K. AU - Jee, D. AU - Navas, L. F. AU - Duan, H. AU - Lai, E. C. PY - 2015 DA - 2015// TI - Multiple in vivo biological processes are mediated by functionally redundant activities of Drosophila mir-279 and mir-996 JO - PLoS Genet VL - 11 UR - https://doi.org/10.1371/journal.pgen.1005245 DO - 10.1371/journal.pgen.1005245 ID - Sun2015 ER - TY - JOUR AU - Arakane, Y. AU - Muthukrishnan, S. AU - Beeman, R. W. AU - Kanost, M. R. AU - Kramer, K. J. PY - 2005 DA - 2005// TI - Laccase 2 is the phenoloxidase gene required for beetle cuticle tanning JO - Proc Natl Acad Sci U A VL - 102 UR - https://doi.org/10.1073/pnas.0504982102 DO - 10.1073/pnas.0504982102 ID - Arakane2005 ER - TY - JOUR AU - Lai, Y. i. -. T. i. n. g. AU - Deem, K. e. v. i. n. D. AU - Borràs-Castells, F. e. r. r. a. n. AU - Sambrani, N. a. g. r. a. j. AU - Rudolf, H. e. i. k. e. AU - Suryamohan, K. u. s. h. a. l. AU - El-Sherif, E. z. z. a. t. AU - Halfon, M. a. r. c. S. AU - McKay, D. a. n. i. e. l. J. AU - Tomoyasu, Y. o. s. h. i. n. o. r. i. PY - 2018 DA - 2018// TI - Enhancer identification and activity evaluation in the red flour beetle,Tribolium castaneum JO - Development VL - 145 UR - https://doi.org/10.1242/dev.160663 DO - 10.1242/dev.160663 ID - Lai2018 ER - TY - JOUR AU - Hinrichs, A. S. PY - 2006 DA - 2006// TI - The UCSC genome browser database: update 2006 JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj144 DO - 10.1093/nar/gkj144 ID - Hinrichs2006 ER - TY - JOUR AU - Wu, T. D. AU - Nacu, S. PY - 2010 DA - 2010// TI - Fast and SNP-tolerant detection of complex variants and splicing in short reads JO - Bioinformatics. VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq057 DO - 10.1093/bioinformatics/btq057 ID - Wu2010 ER - TY - JOUR AU - Dippel, S. AU - Oberhofer, G. AU - Kahnt, J. AU - Gerischer, L. AU - Opitz, L. AU - Schachtner, J. PY - 2014 DA - 2014// TI - Tissue-specific transcriptomics, chromosomal localization, and phylogeny of chemosensory and odorant binding proteins from the red flour beetle Tribolium castaneum reveal subgroup specificities for olfaction or more general functions JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-1141 DO - 10.1186/1471-2164-15-1141 ID - Dippel2014 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. PY - 2000 DA - 2000// TI - Gene ontology: tool for the unification of biology JO - Gene Ontol Consortium Nat Genet VL - 25 ID - Ashburner2000 ER - TY - JOUR AU - Roberts, A. AU - Pachter, L. PY - 2013 DA - 2013// TI - Streaming fragment assignment for real-time analysis of sequencing experiments JO - Nat Methods VL - 10 UR - https://doi.org/10.1038/nmeth.2251 DO - 10.1038/nmeth.2251 ID - Roberts2013 ER - TY - JOUR AU - Kriventseva, E. V. AU - Tegenfeldt, F. AU - Petty, T. J. AU - Waterhouse, R. M. AU - Simão, F. A. AU - Pozdnyakov, I. A. PY - 2015 DA - 2015// TI - OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1220 DO - 10.1093/nar/gku1220 ID - Kriventseva2015 ER - TY - JOUR AU - Stamatakis, A. PY - 2006 DA - 2006// TI - RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models JO - Bioinformatics. VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl446 DO - 10.1093/bioinformatics/btl446 ID - Stamatakis2006 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: a multiple sequence alignment method with reduced time and space complexity JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-113 DO - 10.1186/1471-2105-5-113 ID - Edgar2004 ER - TY - JOUR AU - Capella-Gutierrez, S. AU - Silla-Martinez, J. M. AU - Gabaldon, T. PY - 2009 DA - 2009// TI - trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp348 DO - 10.1093/bioinformatics/btp348 ID - Capella-Gutierrez2009 ER - TY - JOUR AU - Zhang, H. AU - Gao, S. AU - Lercher, M. J. AU - Hu, S. AU - Chen, W. -. H. PY - 2012 DA - 2012// TI - EvolView, an online tool for visualizing, annotating and managing phylogenetic trees JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gks576 DO - 10.1093/nar/gks576 ID - Zhang2012 ER - TY - JOUR AU - Kozomara, A. AU - Griffiths-Jones, S. PY - 2014 DA - 2014// TI - miRBase: annotating high confidence microRNAs using deep sequencing data JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1181 DO - 10.1093/nar/gkt1181 ID - Kozomara2014 ER - TY - JOUR AU - St Pierre, S. E. AU - Ponting, L. AU - Stefancsik, R. AU - McQuilton, P. PY - 2014 DA - 2014// TI - FlyBase 102--advanced approaches to interrogating FlyBase JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1092 DO - 10.1093/nar/gkt1092 ID - St Pierre2014 ER - TY - JOUR AU - Agarwal, V. AU - Bell, G. W. AU - Nam, J. -. W. AU - Bartel, D. P. PY - 2015 DA - 2015// TI - Predicting effective microRNA target sites in mammalian mRNAs JO - eLife. VL - 4 UR - https://doi.org/10.7554/eLife.05005 DO - 10.7554/eLife.05005 ID - Agarwal2015 ER -