Corresponding author

1.  Y Xiang, T Sapir, P Rouillard, M Ferrand, JM Jiménez-Gómez (2022) Interaction between photoperiod and variation in circadian rhythms in tomato. BMC Plant Biol. doi:10.1186/s12870-022-03565-1.

2.  L Zhang, JM Jiménez-Gómez (2020) Functional Analysis of FRIGIDA Using Naturally Occurring Variation in Arabidopsis thaliana. Plant Journal. doi:10.1111/tpj.14716.

3.  NA Müller, L Zhang, M Koornneef and JM Jiménez-Gómez (2018) Mutations in EID1 and LNK2 caused light-conditional clock deceleration during tomato domestication. PNAS. doi:10.1073/pnas.1801862115.

4.  S Soyk, NA Müller, SJ Park, I Schmalenbach, K Jiang, R Hayama, L Zhang, J Van Eck, JM Jiménez-Gómez* and ZB Lippman* (*Co-corresponding) (2017) Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato. Nature Genetics. doi:10.1038/ng.3733.

5.  NA Müller, CL Wijnen, A Srinivasan, M Ryngajllo, I Ofner, T Lin, A Ranjan, D West, JN Maloof, NR Sinha, S Huang, D Zamir and JM Jiménez-Gómez (2016) Domestication selected for deceleration of the circadian clock in cultivated tomato. Nature Genetics. doi:10.1038/ng.3447.

6.  NA Müller and JM Jiménez-Gómez (2016) Analysis of Circadian Leaf Movements. Environmental Responses in Plants: Methods and Protocols. doi:10.1007/978-1-4939-3356-3_7.

7.  I Schmalenbach, L Zhang, M Reymond and JM Jiménez-Gómez (2014) The relationship between flowering time and growth responses to drought in the Arabidopsis Landsberg erecta x Antwerp-1 population. Frontiers in Plant Science. doi:10.3389/fpls.2014.00609.

8.  I Schmalenbach, L Zhang, M Ryngajllo and JM Jiménez-Gómez (2014) Functional analysis of the Landsberg erecta allele of FRIGIDA. BMC Plant Biology. doi:10.1186/s12870-014-0218-2.

9.  JM Jiménez-Gómez (2014) Network types and their application in natural variation studies in plants. Current Opinion in Plant Biology. doi:10.1016/j.pbi.2014.02.010.

10.  JM Jiménez-Gómez (2011) Next generation quantitative genetics in plants. Frontiers in Plant Physiology. doi:10.3389/fpls.2011.00077.

First author

11.  D Koenig*, JM Jiménez-Gómez* (*Co-first), S Kimura, D Fulop, DH Chitwood, LR Headland, R Kumar, MF Covington, U Kumar Devisetty, AV Tat, T Tohge, A Bolger, K Schneeberger, S Ossowski, C Lanz, G Xiong, M Taylor-Teeples, SM Brady, M Pauly, D Weigel, B Usadel, AR Fernie, J Peng, NR Sinha and JN Maloof (2013) Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. PNAS. doi:10.1073/pnas.1309606110.

12.  JM Jiménez-Gómez, J Corwin, B Joseph, JN Maloof and DJ Kliebenstein (2011) Genomic analysis of QTLs and genes altering natural variation in stochastic noise. PLoS Genetics. doi:10.1371/journal.pgen.1002295.

13.  JM Jiménez-Gómez, A Wallace and JN Maloof (2010) Network Analysis Identifies ELF3 as a QTL for the Shade Avoidance Response in Arabidopsis. PLoS Genetics. doi:10.1371/journal.pgen.1001100.

14.  JM Jiménez-Gómez and JN Maloof (2009) Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biology. doi:10.1186/1471-2229-9-85.

15.  JM Jiménez-Gómez and JN Maloof (2009) Plant research accelerates along the bioinformatics superhighway: symposium on plant sensing, response and adaptation to the environment. EMBO reports. doi:10.1038/embor.2009.116.

16.  JM Jiménez-Gómez, C Alonso-Blanco, A Borja, G Anastasio, T Angosto, R Lozano and JM Martínez-Zapater (2007) Quantitative genetic analysis of flowering time in tomato. Genome. doi:10.1139/g07-009.

Contributor

17.  FJ Yuste-Lisbona, JM Jiménez-Gómez, C Capel and R Lozano (2021) Effective Mapping by Sequencing to Isolate Causal Mutations in the Tomato Genome. Crop Breeding. doi:10.1007/978-1-0716-1201-9_7.

18.  M Domínguez, E Dugas, M Benchouaia, B Leduque, JM Jiménez-Gómez, V Colot, L Quadrana (2020) The impact of transposable elements on tomato diversity. Nature Communications. doi:10.1038/s41467-020-17874-2.

19.  FJ Yuste-Lisbona, A Fernández-Lozano, B Pineda, S Bretones, A Ortíz-Atienza, B García-Sogo, NA Müller, T Angosto, J Capel, V Moreno, JM Jiménez-Gómez and R Lozano (2020) ENO regulates tomato fruit size through the floral meristem development network. PNAS. doi:10.1073/pnas.1913688117.

20.  TJM Van Dooren, A Bortolini Silveira, E Gilbault, JM Jiménez-Gómez, A Martin, L Bach, S Tisné, L Quadrana, O Loudet and V Colot (2020) Mild drought induces phenotypic and DNA methylation plasticity but no transgenerational effects in Arabidopsis. J Exp Botany. doi:10.1093/jxb/eraa132.

21.  Y Hu, A Mesihovic, JM Jiménez-Gómez, S Röth, P Gebhardt, D Bublak, A Bovy, KD Scharf, E Schleiff, S Fragkostefanakis (2020) Natural variation in HsfA2 pre-mRNA splicing is associated with changes in thermotolerance during tomato domestication. New Phytologist. doi:10.1111/nph.16221.

22.  S Soyk, ZH Lemmon, FJ Sedlazeck, JM Jiménez-Gómez, M Alonge, SF Hutton, J Van Eck, MC Schatz and ZB Lippman (2019) Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato. Nature Plants. doi:10.1038/s41477-019-0422-z.

23.  R Huertas, R Catalá, JM Jiménez-Gómez, MM Castellano, P Crevillén, M Piñeiro, JA Jarillo and J Salinas (2019) Arabidopsis Sme1 regulates plant development and response to abiotic stress by determining spliceosome activity specificity. The Plant Cell. doi:10.1105/tpc.18.00689.

24.  E Fantini, M Sulli, L Zhang, G Aprea, JM Jiménez-Gómez, A Bendahmane, G Perrotta, G Giuliano and P Facella (2019) Pivotal roles of cryptochromes 1a and 2 in tomato development and physiology. Plant Physiology. doi:10.1104/pp.18.00793.

25.  E Albert, R Duboscq, M Latreille, S Santoni, M Beukers, JP Bouchet, F Bitton, J Gricourt, C Poncet, V Gautier, JM Jiménez-Gómez, G Rigaill and M Causse (2018) Allele specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato. Plant Journal. doi:10.1111/tpj.14057.

26.  E Olate, JM Jiménez-Gómez, L Holuigue and J Salinas (2018) NPR1 mediates a novel regulatory pathway in cold acclimation by interacting with HSFA1 factors. Nature Plants. doi:10.1038/s41477-018-0254-2.

27.  A Ashoub, N Müller, JM Jiménez-Gómez and W Brüggemann (2018) Prominent alterations of wild barley leaf transcriptome in response to individual and combined drought acclimation and heat shock conditions. Physiologia Plantarum. doi:10.1111/ppl.12667.

28.  GU Balcke, S Bennewitz, N Bergau, B Athmer, A Henning, P Majovsky, JM Jiménez-Gómez, W Hoehenwarter and A Tissier (2017) Multi-omics of tomato glandular trichomes reveals distinct features of central carbon metabolism supporting high productivity of specialized metabolites. The Plant Cell. doi:10.1105/tpc.17.00060.

29.  MC Costa, MA Artur, J Maia, E Jonkheer, M Derks, H Nijveen, B Williams, S Mundree, JM Jiménez-Gómez, T Hesselink, E Schijlen, W Ligterink, M Oliver, J Farrant and H Hilhorst (2017) A footprint of desiccation tolerance in the genome of Xerophyta viscosa. Nature Plants. doi:10.1038/nplants.2017.38.

30.  E Magnani, JM Jiménez-Gómez, L Soubigou-Taconnat, L Lepiniec and E Fiume (2017) Profiling the onset of somatic embryogenesis in Arabidopsis. BMC Genomics. doi:10.1186/s12864-017-4391-1.

31.  EAR Serin, LB Snoek, H Nijveen, LAJ Willems, JM Jiménez-Gómez, HWM Hilhorst and W Ligterink (2017) Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population. Frontiers in Plant Science. doi:10.3389/fgene.2017.00201.

32.  MF Alvarez, M Angarita, MC Delgado, C Garcia, JM Jiménez-Gómez, C Gebhardt and T Mosquera (2017) Identification of novel associations of candidate genes with resistance to late blight in Solanum tuberosum Group Phureja. Frontiers in Plant Science. doi:10.3389/fpls.2017.01040.

33.  C Bazakos, M Hanemian, C Trontin, JM Jiménez-Gómez and O Loudet (2017) New Strategies and Tools in Quantitative Genetics: How to Go from the Phenotype to the Genotype. Annual Review of Plant Biology. doi:10.1146/annurev-arplant-042916-040820.

34.  M Bar, A Israeli, M Levy, HB Gera, JM Jiménez-Gómez, S Kouril, P Tarkowski and N Ori (2016) CLAUSA Is a MYB Transcription Factor That Promotes Leaf Differentiation by Attenuating Cytokinin Signaling. The Plant Cell. doi:10.1105/tpc.16.00211.

35.  T Mosquera, MF Alvarez, JM Jiménez-Gómez, MS Muktar, MJ Paulo, S Steinemann, J Li, A Draffehn, A Hofmann, J Lübeck, J Strahwald, E Tacke, HR Hofferbert, B Walkemeier and C Gebhardt (2016) Targeted and Untargeted Approaches Unravel Novel Candidate Genes and Diagnostic SNPs for Quantitative Resistance of the Potato (Solanum tuberosum L.)  to Phytophthora infestans Causing the Late Blight Disease. PLoS One. doi:10.1371/journal.pone.0156254.

36.  A Srinivasan, JM Jiménez-Gómez, F Fornara, W Soppe and V Brambilla (2016) Alternative splicing enhances transcriptome complexity in desiccating seeds. J Integr Plant Biol. doi:10.1111/jipb.12482.

37.  C Perea-Resa, C Carrasco-López, R Catalá, V Turecková, O Novak, W Zhang, LE Sieburth, JM Jiménez-Gómez and J Salinas (2016) The LSM1-7 complex controls plant adaptation to adverse environmental conditions by promoting selective mRNA decapping. The Plant Cell. doi:10.1105/tpc.15.00867.

38.  SM Bush, L Carriedo, D Fulop, Y Ichihashi, MF Covington, R Kumar, A Ranjan, DH Chitwood, L Headland, DL Filiault, JM Jiménez-Gómez, NR Sinha and JN Maloof (2015) Auxin signaling is a common factor underlying natural variation in tomato shade avoidance. bioRxiv. doi:10.1101/031088.

39.  A Bolger, F Scossa, ME Bolger, C Lanz, F Maumus, T Tohge, H Quesneville, S Alseekh, I Sørensen, G Lichenstein, EA Fich, M Conte, H Keller, K Schneeberger, R Schwacke, I Ofner, J Vrebalov, Y Xu, S Osorio, SA Aflitos, E Schijlen, JM Jiménez-Gómez, M Ryngajllo, S Kimura, R Kumar, D Koenig, LR Headland, JN Maloof, N Sinha, RCHJ van Ham, RK Lankhorst, L Mao, A Vogel, B Arsova, R Panstruga, Z Fei, JKC Rose, D Zamir, F Carrari, JJ Giovannoni, D Weigel, B Usadel and AR Fernie (2014) The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Genetics. doi:10.1038/ng.3046.

40.  J Gloggnitzer, S Akimcheva, A Srinivasan, B Kusenda, N Riehs, H Stampfl, J Bautor, B Dekrout, C Jonak, JM Jiménez-Gómez, JE Parker and K Riha (2014) Nonsense-Mediated mRNA Decay Modulates Immune Receptor Levels to Regulate Plant Antibacterial Defense. Cell Host and Microbe. doi:10.1016/j.chom.2014.08.010.

41.  DH Chitwood, R Kumar, LR Headland, A Ranjan, MF Covington, Y Ichihashi, D Fulop, JM Jiménez-Gómez, J Peng, JN Maloof and NR Sinha (2013) A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines. The Plant Cell. doi:10.1105/tpc.113.112391.

42.  M Sharlach, D Dahlbeck, L Liu, J Chiu, JM Jiménez-Gómez, S Kimura, D Koenig, JN Maloof, N Sinha, GV Minsavage, JB Jones, RE Stall and BJ Staskawicz (2012) Fine genetic mapping of RXopJ4, a bacterial spot disease resistance locus from Solanum pennellii LA716. Theor Appl Genet. doi:10.1007/s00122-012-2004-6.

43.  DH Chitwood, LR Headland, DL Filiault, R Kumar, JM Jiménez-Gómez, AV Schrager, DS Park, J Peng, NR Sinha and  JN Maloof (2012) Native environment modulates leaf size and response to simulated foliar shade across wild tomato species. PLoS One. doi:10.1371/journal.pone.0029570.

44.  RE Kerwin, JM Jiménez-Gómez, SL Harmer, JN Maloof and DJ Kliebenstein (2011) Network QTL mapping of circadian clock outputs identifies metabolic pathway to clock linkages in Arabidopsis. The Plant Cell. doi:10.1105/tpc.110.082065.

Current mentor of 1 Postdoc, 2 PhD students and 1 Technician

Past mentor of 6 Postdocs; 4 PhDs; 4 Technicians; 6 Master Students; 5 Undergraduates; 3 Visiting Scientists

Dec 2021 to now: Cientifico Titular. Head of the "Adaptive Genetics and Genomics" group. Centro de Biotecnología y Genómica de Plantas (CBGP), UPM-INIA, Spain

Jan 2019 to Dec 2021: Directeur de Recherche classe 2. Head of the "Adaptive Genetics and Genomics" group. Institut Jean-Pierre Bourgin, INRA-Versailles, France

Mar 2013 to Dec 2018: Charge de Recherche classe 1. Head of the "Adaptive Genetics and Genomics" group. Institut Jean-Pierre Bourgin, INRA-Versailles, France

Oct 2010 to Dec 2015: Group Leader. Head of the "Adaptive Genetics and Genomics" group. Max Planck Institute for Plant Breeding Research, Cologne, Germany.

Feb 2006 to Sep 2010: Postdoctoral fellow. Work on plant natural variation, genetics and genomics. University of California Davis, under the supervision of Julin N Maloof, PhD.

Feb 2005 to Oct 2005: Postdoctoral fellow. Work on Characterization of the TYLCV virus resistance gene in tomato. University of Almeria, Spain, under the supervision of Dr. Rafael Lozano Ruiz.

Sep 2000 to Feb 2005: PhD. Thesis title: “Quantitative genetic analysis of flowering time in tomato”. Centre for National Biotechnology (CNB-CSIC), Madrid, Spain, under the supervision of Dr. Jose Miguel Martínez-Zapater.

Sep 1996 to Feb 1999: B. Sc. in Biology. Specialty Biotechnology. Universidad Complutense de Madrid, Madrid, Spain.

EDITORIAL TASKS

Monitoring Editor at Plant Physiology

FUNDING

Coordinator in 5 grants, WP holder in 4 grants

COMMUNICATIONS

4 times Keynote speaker in international conferences; 10 times Invited speaker in international conferences/workshops/retreats; 19 times Invited speaker at research institutions; 8 times Oral presentation selected among abstracts; 2 times Poster presenter

OTHERS

Participated in 9 Thesis committees

Taught in 6 Master Courses