TY - JOUR AU - Hake, S. AU - Ross-Ibarra, J. PY - 2015 DA - 2015// TI - Genetic, evolutionary and plant breeding insights from the domestication of maize JO - eLife VL - 4 UR - https://doi.org/10.7554/eLife.05861 DO - 10.7554/eLife.05861 ID - Hake2015 ER - TY - STD TI - FAO. FAOSTAT: crops. http://www.fao.org/faostat/en/#data/QC. 2018. UR - http://www.fao.org/faostat/en/#data/QC ID - ref2 ER - TY - STD TI - Eurostat. Green maize by area, production and humidity. https://ec.europa.eu/eurostat/web/products-datasets/-/tag00101. 2018. UR - https://ec.europa.eu/eurostat/web/products-datasets/-/tag00101 ID - ref3 ER - TY - CHAP AU - Sood, S. AU - Flint-Garcia, S. AU - Willcox, M. C. AU - Holland, J. B. ED - Tuberosa, R. ED - Graner, A. ED - Frison, E. PY - 2014 DA - 2014// TI - Mining natural variation for maize improvement: selection on phenotypes and genes BT - Genomics of Plant Genetic Resources: Volume 1. Managing, Sequencing and Mining Genetic Resources PB - Springer CY - Dordrecht, The Netherlands ID - Sood2014 ER - TY - JOUR AU - Tenaillon, M. I. AU - Charcosset, A. PY - 2011 DA - 2011// TI - A European perspective on maize history JO - C R Biol VL - 334 UR - https://doi.org/10.1016/j.crvi.2010.12.015 DO - 10.1016/j.crvi.2010.12.015 ID - Tenaillon2011 ER - TY - STD TI - Haberer G, Bauer E, Kamal N, Gundlach H, Fischer I, Seidel MA, Spannagl M, Marcon C, Ruban A, Urbany C, Nemri A, Hochholdinger F, Ouzunova M, Houben A, Schön C-C, Mayer KFX. European maize genomes unveil pan-genomic dynamics of repeats and genes. bioRxiv. 2019;766444. ID - ref6 ER - TY - JOUR AU - Rodríguez, V. M. AU - Romay, M. C. AU - Ordás, A. AU - Revilla, P. PY - 2010 DA - 2010// TI - Evaluation of European maize (Zea mays L.) germplasm under cold conditions JO - Genet Resour Crop Evol VL - 57 UR - https://doi.org/10.1007/s10722-009-9529-9 DO - 10.1007/s10722-009-9529-9 ID - Rodríguez2010 ER - TY - JOUR AU - Strigens, A. AU - Schipprack, W. AU - Reif, J. C. AU - Melchinger, A. E. PY - 2013 DA - 2013// TI - Unlocking the genetic diversity of maize landraces with doubled haploids opens new avenues for breeding JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0057234 DO - 10.1371/journal.pone.0057234 ID - Strigens2013 ER - TY - JOUR AU - Greaves, J. A. PY - 1996 DA - 1996// TI - Improving suboptimal temperature tolerance in maize - the search for variation JO - J Exp Bot VL - 47 UR - https://doi.org/10.1093/jxb/47.3.307 DO - 10.1093/jxb/47.3.307 ID - Greaves1996 ER - TY - JOUR AU - Haldimann, P. PY - 1998 DA - 1998// TI - Low growth temperature-induced changes to pigment composition and photosynthesis in Zea mays genotypes differing in chilling sensitivity JO - Plant Cell Environ VL - 21 UR - https://doi.org/10.1046/j.1365-3040.1998.00260.x DO - 10.1046/j.1365-3040.1998.00260.x ID - Haldimann1998 ER - TY - JOUR AU - Foyer, C. H. AU - Vanacker, H. AU - Gomez, L. D. AU - Harbinson, J. PY - 2002 DA - 2002// TI - Regulation of photosynthesis and antioxidant metabolism in maize leaves at optimal and chilling temperatures JO - Plant Physiol Biochem VL - 40 UR - https://doi.org/10.1016/S0981-9428(02)01425-0 DO - 10.1016/S0981-9428(02)01425-0 ID - Foyer2002 ER - TY - JOUR AU - Rymen, B. AU - Fiorani, F. AU - Kartal, F. AU - Vandepoele, K. AU - Inze, D. AU - Beemster, G. T. S. PY - 2007 DA - 2007// TI - Cold nights impair leaf growth and cell cycle progression in maize through transcriptional changes of cell cycle genes JO - Plant Physiol VL - 143 UR - https://doi.org/10.1104/pp.106.093948 DO - 10.1104/pp.106.093948 ID - Rymen2007 ER - TY - JOUR AU - Sobkowiak, A. AU - Jończyk, M. AU - Jarochowska, E. AU - Biecek, P. AU - Trzcinska-Danielewicz, J. AU - Leipner, J. AU - Fronk, J. AU - Sowiński, P. PY - 2014 DA - 2014// TI - Genome-wide transcriptomic analysis of response to low temperature reveals candidate genes determining divergent cold-sensitivity of maize inbred lines JO - Plant Mol Biol VL - 85 UR - https://doi.org/10.1007/s11103-014-0187-8 DO - 10.1007/s11103-014-0187-8 ID - Sobkowiak2014 ER - TY - JOUR AU - Farooq, M. AU - Aziz, T. AU - Wahid, A. AU - Lee, D. -. J. AU - Siddique, K. H. M. PY - 2009 DA - 2009// TI - Chilling tolerance in maize: agronomic and physiological approaches JO - Crop Pasture Sci VL - 60 UR - https://doi.org/10.1071/CP08427 DO - 10.1071/CP08427 ID - Farooq2009 ER - TY - JOUR AU - Mao, J. AU - Yu, Y. AU - Yang, J. AU - Li, G. AU - Li, C. AU - Qi, X. AU - Wen, T. AU - Hu, J. PY - 2017 DA - 2017// TI - Comparative transcriptome analysis of sweet corn seedlings under low-temperature stress JO - Crop J VL - 5 UR - https://doi.org/10.1016/j.cj.2017.03.005 DO - 10.1016/j.cj.2017.03.005 ID - Mao2017 ER - TY - JOUR AU - Battal, P. AU - Erez, M. E. AU - Turker, M. AU - Berber, I. PY - 2008 DA - 2008// TI - Molecular and physiological changes in maize (Zea mays) induced by exogenous NAA, ABA and MeJa during cold stress JO - Ann Bot Fenn VL - 45 UR - https://doi.org/10.5735/085.045.0302 DO - 10.5735/085.045.0302 ID - Battal2008 ER - TY - JOUR AU - Khan, M. I. R. AU - Fatma, M. AU - Per, T. S. AU - Anjum, N. A. AU - Khan, N. A. PY - 2015 DA - 2015// TI - Salicylic acid-induced abiotic stress tolerance and underlying mechanisms in plants JO - Front Plant Sci VL - 6 ID - Khan2015 ER - TY - JOUR AU - Aroca, R. AU - Tognoni, F. AU - Irigoyen, J. J. AU - Sánchez-Díaz, M. AU - Pardossi, A. PY - 2001 DA - 2001// TI - Different root low temperature response of two maize genotypes differing in chilling sensitivity JO - Plant Physiol Biochem VL - 39 UR - https://doi.org/10.1016/S0981-9428(01)01335-3 DO - 10.1016/S0981-9428(01)01335-3 ID - Aroca2001 ER - TY - JOUR AU - Melkonian, J. AU - Yu, L. X. AU - Setter, T. L. PY - 2004 DA - 2004// TI - Chilling responses of maize (Zea mays L.) seedlings: root hydraulic conductance, abscisic acid, and stomatal conductance JO - J Exp Bot VL - 55 UR - https://doi.org/10.1093/jxb/erh215 DO - 10.1093/jxb/erh215 ID - Melkonian2004 ER - TY - JOUR AU - Nagel, K. A. AU - Kastenholz, B. AU - Jahnke, S. AU - Dusschoten, D. AU - Aach, T. AU - Mühlich, M. AU - Truhn, D. AU - Scharr, H. AU - Terjung, S. AU - Walter, A. AU - Schurr, U. PY - 2009 DA - 2009// TI - Temperature responses of roots: impact on growth, root system architecture and implications for phenotyping JO - Funct Plant Biol VL - 36 UR - https://doi.org/10.1071/FP09184 DO - 10.1071/FP09184 ID - Nagel2009 ER - TY - STD TI - Breitkopf A. Monatliche Durchschnittstemperatur in Deutschland von Juni 2018 bis Juni 2019. https://de.statista.com/statistik/daten/studie/5564/umfrage/monatliche-durchschnittstemperatur-in-deutschland/Statista. 2019. UR - https://de.statista.com/statistik/daten/studie/5564/umfrage/monatliche-durchschnittstemperatur-in-deutschland/Statista ID - ref21 ER - TY - STD TI - Landwirtschaftskammer Nordrhein-Westfalen. Saatzeit für Mais. https://www.landwirtschaftskammer.de/landwirtschaft/ackerbau/mais/saatzeit-pdf.pdf. 2015. UR - https://www.landwirtschaftskammer.de/landwirtschaft/ackerbau/mais/saatzeit-pdf.pdf ID - ref22 ER - TY - JOUR AU - Mock, J. J. AU - McNeill, M. J. PY - 1979 DA - 1979// TI - Cold tolerance of maize inbred lines adapted to various latitudes in North America JO - Crop Sci VL - 19 UR - https://doi.org/10.2135/cropsci1979.0011183X001900020017x DO - 10.2135/cropsci1979.0011183X001900020017x ID - Mock1979 ER - TY - JOUR AU - Hund, A. AU - Fracheboud, Y. AU - Soldati, A. AU - Frascaroli, E. AU - Salvi, S. AU - Stamp, P. PY - 2004 DA - 2004// TI - QTL controlling root and shoot traits of maize seedlings under cold stress JO - Theor Appl Genet VL - 109 UR - https://doi.org/10.1007/s00122-004-1665-1 DO - 10.1007/s00122-004-1665-1 ID - Hund2004 ER - TY - JOUR AU - Arshad, M. A. AU - Azooz, R. H. PY - 1996 DA - 1996// TI - Tillage effects on soil thermal properties in a semiarid cold region JO - Soil Sci Soc Am J VL - 60 UR - https://doi.org/10.2136/sssaj1996.03615995006000020032x DO - 10.2136/sssaj1996.03615995006000020032x ID - Arshad1996 ER - TY - JOUR AU - Chaikam, V. AU - Molenaar, W. AU - Melchinger, A. E. AU - Boddupalli, P. M. PY - 2019 DA - 2019// TI - Doubled haploid technology for line development in maize: technical advances and prospects JO - Theor Appl Genet VL - 132 UR - https://doi.org/10.1007/s00122-019-03433-x DO - 10.1007/s00122-019-03433-x ID - Chaikam2019 ER - TY - JOUR AU - Hölker, A. C. AU - Mayer, M. AU - Presterl, T. AU - Bolduan, T. AU - Bauer, E. AU - Ordas, B. AU - Brauner, P. C. AU - Ouzunova, M. AU - Melchinger, A. E. AU - Schön, C. C. PY - 2019 DA - 2019// TI - European maize landraces made accessible for plant breeding and genome-based studies JO - Theor Appl Genet VL - 132 UR - https://doi.org/10.1007/s00122-019-03428-8 DO - 10.1007/s00122-019-03428-8 ID - Hölker2019 ER - TY - JOUR AU - Revilla, P. AU - Boyat, A. AU - Álvarez, A. AU - Gouesnard, B. AU - Ordás, B. AU - Rodríguez, V. M. AU - Ordás, A. AU - Malvar, R. A. PY - 2006 DA - 2006// TI - 2006. Contribution of autochthonous maize populations for adaptation to European conditions JO - Euphytica VL - 152 UR - https://doi.org/10.1007/s10681-006-9214-4 DO - 10.1007/s10681-006-9214-4 ID - Revilla2006 ER - TY - JOUR AU - Peter, R. AU - Eschholz, T. W. AU - Stamp, P. AU - Liedgens, M. PY - 2009 DA - 2009// TI - Swiss Flint maize landraces - a rich pool of variability for early vigour in cool environments JO - Field Crops Res VL - 110 UR - https://doi.org/10.1016/j.fcr.2008.07.015 DO - 10.1016/j.fcr.2008.07.015 ID - Peter2009 ER - TY - JOUR AU - Schneider, D. N. AU - Freitag, N. M. AU - Liedgens, M. AU - Feil, B. AU - Stamp, P. PY - 2011 DA - 2011// TI - Early growth of field-grown swiss flint maize landraces JO - Maydica VL - 56 ID - Schneider2011 ER - TY - JOUR AU - Baldauf, J. A. AU - Marcon, C. AU - Lithio, A. AU - Vedder, L. AU - Altrogge, L. AU - Piepho, H. P. AU - Schoof, H. AU - Nettleton, D. AU - Hochholdinger, F. PY - 2018 DA - 2018// TI - Single-parent expression is a general mechanism driving extensive complementation of non-syntenic genes in maize hybrids JO - Curr Biol VL - 28 UR - https://doi.org/10.1016/j.cub.2017.12.027 DO - 10.1016/j.cub.2017.12.027 ID - Baldauf2018 ER - TY - JOUR AU - Jiao, Y. AU - Peluso, P. AU - Shi, J. AU - Liang, T. AU - Stitzer, M. C. AU - Wang, B. AU - Campbell, M. S. AU - Stein, J. C. AU - Wei, X. AU - Chin, C. S. AU - Guill, K. AU - Regulski, M. AU - Kumari, S. AU - Olson, A. AU - Gent, J. AU - Schneider, K. L. AU - Wolfgruber, T. K. AU - May, M. R. AU - Springer, N. M. AU - Antoniou, E. AU - McCombie, W. R. AU - Presting, G. G. AU - McMullen, M. AU - Ross-Ibarra, J. AU - Dawe, R. K. AU - Hastie, A. AU - Rank, D. R. AU - Ware, D. PY - 2017 DA - 2017// TI - Improved maize reference genome with single-molecule technologies JO - Nature VL - 546 UR - https://doi.org/10.1038/nature22971 DO - 10.1038/nature22971 ID - Jiao2017 ER - TY - JOUR AU - Frey, F. P. AU - Urbany, C. AU - Hüttel, B. AU - Reinhardt, R. AU - Stich, B. PY - 2015 DA - 2015// TI - Genome-wide expression profiling and phenotypic evaluation of European maize inbreds at seedling stage in response to heat stress JO - BMC Genomics VL - 16 UR - https://doi.org/10.1186/s12864-015-1282-1 DO - 10.1186/s12864-015-1282-1 ID - Frey2015 ER - TY - JOUR AU - Kollipara, K. P. AU - Saab, I. N. AU - Wych, R. D. AU - Lauer, M. J. AU - Singletary, G. W. PY - 2002 DA - 2002// TI - Expression profiling of reciprocal maize hybrids divergent for cold germination and desiccation tolerance JO - Plant Physiol VL - 129 UR - https://doi.org/10.1104/pp.000729 DO - 10.1104/pp.000729 ID - Kollipara2002 ER - TY - JOUR AU - Opitz, N. AU - Marcon, C. AU - Paschold, A. AU - Malik, W. A. AU - Lithio, A. AU - Brandt, R. AU - Piepho, H. P. AU - Nettleton, D. AU - Hochholdinger, F. PY - 2016 DA - 2016// TI - Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit JO - J Exp Bot VL - 67 UR - https://doi.org/10.1093/jxb/erv453 DO - 10.1093/jxb/erv453 ID - Opitz2016 ER - TY - JOUR AU - Opitz, N. AU - Paschold, A. AU - Marcon, C. AU - Malik, W. A. AU - Lanz, C. AU - Piepho, H. P. AU - Hochholdinger, F. PY - 2014 DA - 2014// TI - Transcriptomic complexity in young maize primary roots in response to low water potentials JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-741 DO - 10.1186/1471-2164-15-741 ID - Opitz2014 ER - TY - JOUR AU - Campbell, M. T. AU - Proctor, C. A. AU - Dou, Y. AU - Schmitz, A. J. AU - Phansak, P. AU - Kruger, G. R. AU - Zhang, C. AU - Walia, H. PY - 2015 DA - 2015// TI - Genetic and molecular characterization of submergence response identifies subtol6 as a major submergence tolerance locus in maize JO - PLoS One VL - 10 ID - Campbell2015 ER - TY - JOUR AU - Wang, B. AU - Tseng, E. AU - Regulski, M. AU - Clark, T. A. AU - Hon, T. AU - Jiao, Y. AU - Lu, Z. AU - Olson, A. AU - Stein, J. C. AU - Ware, D. PY - 2016 DA - 2016// TI - Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing JO - Nat Commun VL - 7 ID - Wang2016 ER - TY - JOUR AU - Arora, K. AU - Panda, K. K. AU - Mittal, S. AU - Mallikarjuna, M. G. PY - 2017 DA - 2017// TI - RNAseq revealed the important gene pathways controlling adaptive mechanisms under waterlogged stress in maize JO - Sci Rep VL - 7 UR - https://doi.org/10.1038/s41598-016-0028-x DO - 10.1038/s41598-016-0028-x ID - Arora2017 ER - TY - JOUR AU - Fenza, M. AU - Hogg, B. AU - Grant, J. AU - Barth, S. PY - 2017 DA - 2017// TI - Transcriptomic response of maize primary roots to low temperatures at seedling emergence JO - PeerJ VL - 5 UR - https://doi.org/10.7717/peerj.2839 DO - 10.7717/peerj.2839 ID - Fenza2017 ER - TY - JOUR AU - Makarevitch, I. AU - Waters, A. J. AU - West, P. T. AU - Stitzer, M. AU - Hirsch, C. N. AU - Ross-Ibarra, J. AU - Springer, N. M. PY - 2015 DA - 2015// TI - Transposable elements contribute to activation of maize genes in response to abiotic stress JO - PLoS Genet VL - 11 UR - https://doi.org/10.1371/journal.pgen.1005566 DO - 10.1371/journal.pgen.1005566 ID - Makarevitch2015 ER - TY - JOUR AU - Tai, H. AU - Lu, X. AU - Opitz, N. AU - Marcon, C. AU - Paschold, A. AU - Lithio, A. AU - Nettleton, D. AU - Hochholdinger, F. PY - 2016 DA - 2016// TI - Transcriptomic and anatomical complexity of primary, seminal, and crown roots highlight root type-specific functional diversity in maize (Zea mays L.) JO - J Exp Bot VL - 67 UR - https://doi.org/10.1093/jxb/erv513 DO - 10.1093/jxb/erv513 ID - Tai2016 ER - TY - JOUR AU - Desikan, R. PY - 2001 DA - 2001// TI - A.-H.-Mackerness S, Hancock JT, Neill SJ. Regulation of the Arabidopsis transcriptome by oxidative stress JO - Plant Physiol VL - 127 UR - https://doi.org/10.1104/pp.127.1.159 DO - 10.1104/pp.127.1.159 ID - Desikan2001 ER - TY - JOUR AU - Shinozaki, K. AU - Yamaguchi-Shinozaki, K. AU - Seki, M. PY - 2003 DA - 2003// TI - Regulatory network of gene expression in the drought and cold stress responses JO - Current Opin Plant Biol VL - 6 UR - https://doi.org/10.1016/S1369-5266(03)00092-X DO - 10.1016/S1369-5266(03)00092-X ID - Shinozaki2003 ER - TY - JOUR AU - Li, N. AU - Yue, C. AU - Cao, H. AU - Qian, W. AU - Hao, X. AU - Wang, Y. AU - Wang, L. AU - Ding, C. AU - Wang, X. AU - Yang, Y. PY - 2018 DA - 2018// TI - Transcriptome sequencing dissection of the mechanisms underlying differential cold sensitivity in young and mature leaves of the tea plant (Camellia sinensis) JO - J Plant Physiol VL - 224–225 ID - Li2018 ER - TY - JOUR AU - Aslam, M. M. AU - Rehman, S. AU - Khatoon, A. AU - Jamil, M. AU - Yamaguchi, H. AU - Hitachi, K. AU - Tsuchida, K. AU - Li, X. AU - Sunohara, Y. AU - Matsumoto, H. AU - Komatsu, S. PY - 2019 DA - 2019// TI - Molecular responses of maize shoot to a plant derived smoke solution JO - Int J Mol Sci VL - 20 UR - https://doi.org/10.3390/ijms20061319 DO - 10.3390/ijms20061319 ID - Aslam2019 ER - TY - JOUR AU - Kimotho, R. N. AU - Baillo, E. H. AU - Zhang, Z. PY - 2019 DA - 2019// TI - Transcription factors involved in abiotic stress responses in Maize (Zea mays L.) and their roles in enhanced productivity in the post genomics era JO - PeerJ VL - 7 UR - https://doi.org/10.7717/peerj.7211 DO - 10.7717/peerj.7211 ID - Kimotho2019 ER - TY - JOUR AU - Zhang, B. AU - Liu, J. AU - Yang, Z. E. AU - Chen, E. Y. AU - Zhang, C. J. AU - Zhang, X. Y. AU - Li, F. G. PY - 2018 DA - 2018// TI - Genome-wide analysis of GRAS transcription factor gene family in Gossypium hirsutum L JO - BMC Genomics VL - 19 UR - https://doi.org/10.1186/s12864-017-4368-0 DO - 10.1186/s12864-017-4368-0 ID - Zhang2018 ER - TY - JOUR AU - Baute, J. AU - Herman, D. AU - Coppens, F. AU - Block, J. AU - Slabbinck, B. AU - Dell’Acqua, M. AU - Pè, M. E. AU - Maere, S. AU - Nelissen, H. AU - Inzé, D. PY - 2015 DA - 2015// TI - Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population JO - Genome Biol VL - 16 UR - https://doi.org/10.1186/s13059-015-0735-9 DO - 10.1186/s13059-015-0735-9 ID - Baute2015 ER - TY - JOUR AU - Lanubile, A. AU - Ferrarini, A. AU - Maschietto, V. AU - Delledonne, M. AU - Marocco, A. AU - Bellin, D. PY - 2014 DA - 2014// TI - Functional genomic analysis of constitutive and inducible defense responses to Fusarium verticillioides infection in maize genotypes with contrasting ear rot resistance JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-710 DO - 10.1186/1471-2164-15-710 ID - Lanubile2014 ER - TY - JOUR AU - Coll-Garcia, D. AU - Mazuch, J. AU - Altmann, T. AU - Müssig, C. PY - 2004 DA - 2004// TI - EXORDIUM regulates brassinosteroid-responsive genes JO - FEBS Lett VL - 563 UR - https://doi.org/10.1016/S0014-5793(04)00255-8 DO - 10.1016/S0014-5793(04)00255-8 ID - Coll-Garcia2004 ER - TY - JOUR AU - Taïbi, K. AU - Campo, A. D. AU - Vilagrosa, A. AU - Bellés, J. M. AU - López-Gresa, M. P. AU - López-Nicolás, J. M. AU - Mulet, J. M. PY - 2018 DA - 2018// TI - Distinctive physiological and molecular responses to cold stress among cold-tolerant and cold-sensitive Pinus halepensis seed sources JO - BMC Plant Biol VL - 18 UR - https://doi.org/10.1186/s12870-018-1464-5 DO - 10.1186/s12870-018-1464-5 ID - Taïbi2018 ER - TY - JOUR AU - Mayer, M. AU - Unterseer, S. AU - Bauer, E. AU - Leon, N. AU - Ordas, B. AU - Schön, C. -. C. PY - 2017 DA - 2017// TI - Is there an optimum level of diversity in utilization of genetic resources? JO - Theor Appl Genet VL - 130 UR - https://doi.org/10.1007/s00122-017-2959-4 DO - 10.1007/s00122-017-2959-4 ID - Mayer2017 ER - TY - JOUR AU - Röber, F. K. AU - Gordillo, G. A. AU - Geiger, H. H. PY - 2005 DA - 2005// TI - In vivo haploid induction in maize - performance of new inducers and significance of doubled haploid lines in hybrid breeding JO - Maydica VL - 50 ID - Röber2005 ER - TY - JOUR AU - Hoecker, N. AU - Keller, B. AU - Piepho, H. P. AU - Hochholdinger, F. PY - 2006 DA - 2006// TI - Manifestation of heterosis during early maize (Zea mays L.) root development JO - Theor Appl Genet VL - 112 UR - https://doi.org/10.1007/s00122-005-0139-4 DO - 10.1007/s00122-005-0139-4 ID - Hoecker2006 ER - TY - JOUR AU - Galkovskyi, T. AU - Mileyko, Y. AU - Bucksch, A. AU - Moore, B. AU - Symonova, O. AU - Price, C. A. AU - Topp, C. N. AU - Iyer-pascuzzi, A. S. AU - Zurek, P. R. AU - Fang, S. AU - Harer, J. AU - Benfey, P. N. AU - Weitz, J. S. PY - 2012 DA - 2012// TI - GiA roots: software for the high throughput analysis of plant root system architecture JO - BMC Plant Biol VL - 12 UR - https://doi.org/10.1186/1471-2229-12-116 DO - 10.1186/1471-2229-12-116 ID - Galkovskyi2012 ER - TY - STD TI - Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, Lightfoot S, Menzel W, Granzow M, Ragg T. The RIN: An RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol 2006;7, 1–14. ID - ref57 ER - TY - JOUR AU - Bolger, A. M. AU - Lohse, M. AU - Usadel, B. PY - 2014 DA - 2014// TI - Trimmomatic: a flexible trimmer for Illumina sequence data JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu170 DO - 10.1093/bioinformatics/btu170 ID - Bolger2014 ER - TY - JOUR AU - Kim, D. AU - Langmead, B. AU - Salzberg, S. L. PY - 2015 DA - 2015// TI - HISAT: a fast spliced aligner with low memory requirements JO - Nat Methods VL - 12 UR - https://doi.org/10.1038/nmeth.3317 DO - 10.1038/nmeth.3317 ID - Kim2015 ER - TY - JOUR AU - Li, H. AU - Handsaker, B. AU - Wysoker, A. AU - Fennell, T. AU - Ruan, J. AU - Homer, N. AU - Marth, G. AU - Abecasis, G. AU - Durbin, R. PY - 2009 DA - 2009// TI - The sequence alignment/map format and SAMtools JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 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 - 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 - Benjamini, Y. AU - Hochberg, Y. PY - 1995 DA - 1995// TI - Controlling the false discovery rate: a practical and powerful approach to multiple testing JO - J R Stat Soc Series B Stat Methodol VL - 57 ID - Benjamini1995 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. AU - Davis, A. P. AU - Dolinski, K. AU - Dwight, S. S. AU - Eppig, J. T. AU - Harris, M. A. PY - 2000 DA - 2000// TI - Gene ontology: tool for the unification of biology JO - Nat Genet VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Ashburner2000 ER - TY - JOUR PY - 2019 DA - 2019// TI - The gene ontology resource: 20 years and still GOing strong JO - Nucleic Acids Res VL - 47 UR - https://doi.org/10.1093/nar/gky1055 DO - 10.1093/nar/gky1055 ID - ref65 ER - TY - JOUR AU - Wimalanathan, K. AU - Friedberg, I. AU - Andorf, C. M. AU - Lawrence-Dill, C. J. PY - 2018 DA - 2018// TI - Maize GO annotation - methods, evaluation, and review (maize-GAMER) JO - Plant Direct VL - 2 UR - https://doi.org/10.1002/pld3.52 DO - 10.1002/pld3.52 ID - Wimalanathan2018 ER - TY - STD TI - Carlson M, Falcon S, Pages H, Li N. GO. db: A set of annotation maps describing the entire Gene Ontology. R package version, 3.7.0. 2018. ID - ref67 ER - TY - STD TI - Alexa AA, Rahnenfuhrer J, Alexa MA. Package ‘topGO’ - Enrichment analysis for gene ontology. R package version 2.37.0. 2019. ID - ref68 ER - TY - JOUR AU - Supek, F. AU - Bošnjak, M. AU - Škunca, N. AU - Tomislav, Š. PY - 2011 DA - 2011// TI - REVIGO summarizes and visualizes long lists of gene ontology terms JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0021800 DO - 10.1371/journal.pone.0021800 ID - Supek2011 ER - TY - JOUR AU - Shannon, P. AU - Markiel, A. AU - Ozier, O. AU - Baliga, N. S. AU - Wang, J. T. AU - Ramage, D. AU - Amin, N. AU - Schwikowski, B. AU - Ideker, T. PY - 2003 DA - 2003// TI - Cytoscape: a software environment for integrated models of biomolecular interaction networks JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1239303 DO - 10.1101/gr.1239303 ID - Shannon2003 ER -