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Daniel P. Koenig, Ph.D. - Publications

Affiliations: 
2010 Genetics University of California, Davis, Davis, CA 
Area:
Genetics, Botany Biology
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32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Brown KE, Koenig D. On the hidden temporal dynamics of plant adaptation. Current Opinion in Plant Biology. 70: 102298. PMID 36126489 DOI: 10.1016/j.pbi.2022.102298  0.301
2019 Koenig D, Hagmann J, Li R, Bemm F, Slotte T, Nueffer B, Wright SI, Weigel D. Long-term balancing selection drives evolution of immunity genes in . Elife. 8. PMID 30806624 DOI: 10.7554/Elife.43606  0.55
2019 Koenig D, Hagmann J, Li R, Bemm F, Slotte T, Neuffer B, Wright SI, Weigel D. Author response: Long-term balancing selection drives evolution of immunity genes in Capsella Elife. DOI: 10.7554/Elife.43606.048  0.479
2018 Seymour DK, Chae E, Arioz BI, Koenig D, Weigel D. Transmission ratio distortion is frequent in Arabidopsis thaliana controlled crosses. Heredity. PMID 29955170 DOI: 10.1038/S41437-018-0107-9  0.474
2016 Seymour DK, Chae E, Grimm DG, Martín Pizarro C, Habring-Müller A, Vasseur F, Rakitsch B, Borgwardt KM, Koenig D, Weigel D. Genetic architecture of nonadditive inheritance in Arabidopsis thaliana hybrids. Proceedings of the National Academy of Sciences of the United States of America. PMID 27803326 DOI: 10.1073/Pnas.1615268113  0.726
2016 Martinez CC, Koenig D, Chitwood DH, Sinha NR. A Sister of PIN1 gene in tomato (Solanum lycopersicum) defines leaf and flower organ initiation patterns by maintaining epidermal auxin flux. Developmental Biology. PMID 27554165 DOI: 10.1016/J.Ydbio.2016.08.011  0.522
2015 Rawat V, Abdelsamad A, Pietzenuk B, Seymour DK, Koenig D, Weigel D, Pecinka A, Schneeberger K. Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data. Plos One. 10: e0137391. PMID 26382944 DOI: 10.1371/Journal.Pone.0137391  0.562
2015 Steige KA, Reimegård J, Koenig D, Scofield DG, Slotte T. Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella. Molecular Biology and Evolution. 32: 2501-14. PMID 26318184 DOI: 10.1093/Molbev/Msv169  0.393
2015 Koenig D, Weigel D. Beyond the thale: comparative genomics and genetics of Arabidopsis relatives. Nature Reviews. Genetics. 16: 285-98. PMID 25854181 DOI: 10.1038/Nrg3883  0.579
2014 Seymour DK, Koenig D, Hagmann J, Becker C, Weigel D. Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization. Plos Genetics. 10: e1004785. PMID 25393550 DOI: 10.1371/Journal.Pgen.1004785  0.721
2014 Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R, ... ... Koenig D, et al. The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Genetics. 46: 1034-8. PMID 25064008 DOI: 10.1038/Ng.3046  0.756
2014 Agren JÃ…, Wang W, Koenig D, Neuffer B, Weigel D, Wright SI. Mating system shifts and transposable element evolution in the plant genus Capsella. Bmc Genomics. 15: 602. PMID 25030755 DOI: 10.1186/1471-2164-15-602  0.564
2014 Garcês HM, Koenig D, Townsley BT, Kim M, Sinha NR. Truncation of LEAFY COTYLEDON1 protein is required for asexual reproduction in Kalanchoë daigremontiana. Plant Physiology. 165: 196-206. PMID 24664206 DOI: 10.1104/Pp.114.237222  0.748
2013 Koenig D, Jiménez-Gómez JM, Kimura S, Fulop D, Chitwood DH, Headland LR, Kumar R, Covington MF, Devisetty UK, Tat AV, Tohge T, Bolger A, Schneeberger K, Ossowski S, Lanz C, et al. Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proceedings of the National Academy of Sciences of the United States of America. 110: E2655-62. PMID 23803858 DOI: 10.1073/Pnas.1309606110  0.759
2013 Slotte T, Hazzouri KM, Ã…gren JA, Koenig D, Maumus F, Guo YL, Steige K, Platts AE, Escobar JS, Newman LK, Wang W, Mandáková T, Vello E, Smith LM, Henz SR, et al. The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nature Genetics. 45: 831-5. PMID 23749190 DOI: 10.1038/Ng.2669  0.768
2013 Grimm D, Hagmann J, Koenig D, Weigel D, Borgwardt K. Accurate indel prediction using paired-end short reads. Bmc Genomics. 14: 132. PMID 23442375 DOI: 10.1186/1471-2164-14-132  0.705
2013 Manavella PA, Koenig D, Rubio-Somoza I, Burbano HA, Becker C, Weigel D. Tissue-specific silencing of Arabidopsis SU(VAR)3-9 HOMOLOG8 by miR171a. Plant Physiology. 161: 805-12. PMID 23204429 DOI: 10.1104/Pp.112.207068  0.709
2013 Sharlach M, Dahlbeck D, Liu L, Chiu J, Jiménez-Gómez JM, Kimura S, Koenig D, Maloof JN, Sinha N, Minsavage GV, Jones JB, Stall RE, Staskawicz BJ. Fine genetic mapping of RXopJ4, a bacterial spot disease resistance locus from Solanum pennellii LA716. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 126: 601-9. PMID 23117718 DOI: 10.1007/S00122-012-2004-6  0.737
2012 Alakonya A, Kumar R, Koenig D, Kimura S, Townsley B, Runo S, Garces HM, Kang J, Yanez A, David-Schwartz R, Machuka J, Sinha N. Interspecific RNA interference of SHOOT MERISTEMLESS-like disrupts Cuscuta pentagona plant parasitism. The Plant Cell. 24: 3153-66. PMID 22822208 DOI: 10.1105/Tpc.112.099994  0.732
2012 Chitwood DH, Headland LR, Ranjan A, Martinez CC, Braybrook SA, Koenig DP, Kuhlemeier C, Smith RS, Sinha NR. Leaf asymmetry as a developmental constraint imposed by auxin-dependent phyllotactic patterning. The Plant Cell. 24: 2318-27. PMID 22722959 DOI: 10.1105/Tpc.112.098798  0.542
2012 Manavella PA, Koenig D, Weigel D. Plant secondary siRNA production determined by microRNA-duplex structure. Proceedings of the National Academy of Sciences of the United States of America. 109: 2461-6. PMID 22308502 DOI: 10.1073/Pnas.1200169109  0.692
2012 Zoulias N, Koenig D, Hamidi A, McCormick S, Kim M. A role for PHANTASTICA in medio-lateral regulation of adaxial domain development in tomato and tobacco leaves. Annals of Botany. 109: 407-18. PMID 22184618 DOI: 10.1093/Aob/Mcr295  0.558
2011 Becker C, Hagmann J, Müller J, Koenig D, Stegle O, Borgwardt K, Weigel D. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature. 480: 245-9. PMID 22057020 DOI: 10.1038/Nature10555  0.726
2011 Cao J, Schneeberger K, Ossowski S, Günther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C, Wang X, Ott F, Müller J, Alonso-Blanco C, Borgwardt K, et al. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nature Genetics. 43: 956-63. PMID 21874002 DOI: 10.1038/Ng.911  0.7
2011 Rowan BA, Weigel D, Koenig D. Developmental genetics and new sequencing technologies: the rise of nonmodel organisms. Developmental Cell. 21: 65-76. PMID 21763609 DOI: 10.1016/J.Devcel.2011.05.021  0.515
2011 Grimm DG, Hagmann J, Koenig D, Weigel D, Borgwardt K. Support vector machines for finding deletions and short insertions using paired-end short reads F1000research. 2. DOI: 10.7490/F1000Research.2126.1  0.422
2010 Koenig D, Sinha N. Evolution of leaf shape: A pattern emerges. Current Topics in Developmental Biology. 91: 169-83. PMID 20705182 DOI: 10.1016/S0070-2153(10)91006-5  0.577
2010 Ji J, Strable J, Shimizu R, Koenig D, Sinha N, Scanlon MJ. WOX4 promotes procambial development. Plant Physiology. 152: 1346-56. PMID 20044450 DOI: 10.1104/Pp.109.149641  0.601
2010 Uchida N, Kimura S, Koenig D, Sinha N. Coordination of leaf development via regulation of KNOX1 genes. Journal of Plant Research. 123: 7-14. PMID 19506991 DOI: 10.1007/S10265-009-0248-2  0.75
2009 David-Schwartz R, Koenig D, Sinha NR. LYRATE is a key regulator of leaflet initiation and lamina outgrowth in tomato. The Plant Cell. 21: 3093-104. PMID 19820188 DOI: 10.1105/Tpc.109.069948  0.584
2009 Koenig D, Bayer E, Kang J, Kuhlemeier C, Sinha N. Auxin patterns Solanum lycopersicum leaf morphogenesis. Development (Cambridge, England). 136: 2997-3006. PMID 19666826 DOI: 10.1242/Dev.033811  0.57
2008 Kimura S, Koenig D, Kang J, Yoong FY, Sinha N. Natural variation in leaf morphology results from mutation of a novel KNOX gene. Current Biology : Cb. 18: 672-7. PMID 18424140 DOI: 10.1016/J.Cub.2008.04.008  0.721
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