* names in bold are/were lab members
2024
FJ Martínez Rivas, D Wozny, Z Xue, E Gilbault, T Sapir, M Rouille, A Ricou, J Medina, LD Noël, E Lauber, A Voxeur, O Loudet, G Clément, JM Jiménez-Gómez "Parallel Evolution of Salinity Tolerance in Arabidopsis thaliana Accessions from Cape Verde Islands" BioRxiv [link]
Z Xue, M Ferrand, E Gilbault, O Zurfluh, G Clément, A Marmagne, S Huguet, JM Jiménez-Gómez, A Krapp, C Meyer, O Loudet "Natural variation in response to combined water and nitrogen deficiencies in Arabidopsis" The Plant Cell [link]
F Perez-Alfocea, M Borghi, JJ Guerrero, AR Jimenez, JM Jiménez-Gómez, AR Fernie and I Bartomeus "Pollinator-assisted plant phenotyping, selection, and breeding for crop resilience to abiotic stresses" Plant Journal [link]
2023
B Renau-Morata , J Cebolla-Cornejo, L Carrillo , D Gil-Villar, R Martí, JM Jiménez-Gómez, A Granell, AJ Monforte, J Medina, RV Molina, SG Nebauer "Identification of Solanum pimpinellifolium genome regions for increased resilience to nitrogen deficiency in cultivated tomato" Scientia Horticulturae [link]
MG Sterken, H Nijveen, M van Zanten, JM Jiménez-Gómez, N Geshnizjani, LAJ Willems, J Rienstra, HWM Hilhorst, W Ligterink, BL Snoek. "Plasticity of maternal environment dependent expression-QTLs of tomato seeds". Theor Appl Genet [link]
2022
I Shwartz, C Yahav, N Kovetz, M Levy, A Israeli, M Bar, KL Duval, EG Krall, N Teboul , JM Jiménez-Gómez, RB Deal , N Ori. "The VIL gene CRAWLING ELEPHANT controls maturation and differentiation in tomato via polycomb silencing". PLoS Genetics [link]
J dos Reis Moreira, A Quiñones, B Silvestre Lira, JM Robledo, SJ Curtin, MH Vicente, DM Ribeiro, M Ryngajllo, JM Jiménez-Gómez, LE Pereira Peres, M Rossi, A Zsögön. "SELF PRUNING 3C is a flowering repressor that modulates seed germination, root architecture, and drought responses".
J Exp Botany [link]
Y Xiang, T Sapir, P Rouillard, M Ferrand, JM Jiménez-Gómez. "Interaction between photoperiod and variation in circadian rhythms in tomato". BioRXiv [link]
2020
M Domínguez, E Dugas, M Benchouaia, B Leduque, JM Jiménez-Gómez, V Colot, L Quadrana. "The impact of transposable elements on tomato diversity". Nature Communications [link]
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. "ENO regulates tomato fruit size through the floral meristem development network". PNAS [link]
TJM Van Dooren, A Bortolini Silveira, E Gilbault, JM Jiménez-Gómez, A Martin, L Bach, S Tisné, L Quadrana, O Loudet and V Colot "Mild drought induces phenotypic and DNA methylation plasticity but no transgenerational effects in Arabidopsis". J Exp Botany [link]
L Zhang and JM Jiménez-Gómez. "Functional Analysis of FRIGIDA Using Naturally Occurring Variation in Arabidopsis thaliana". The Plant Journal [link]
2019
S Soyk, ZH Lemmon, FJ Sedlazeck, JM Jiménez-Gómez, M Alonge, SF Hutton, J Van Eck, MC Schatz and ZB Lippman. "Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato". Nature Plants [link]
R Huertas, R Catalá, JM Jiménez-Gómez, MM Castellano, P Crevillén, M Piñeiro, JA Jarillo and J Salinas. "Arabidopsis Sme1 regulates plant development and response to abiotic stress by determining spliceosome activity specificity". The Plant Cell [link]
E Fantini, M Sulli, L Zhang, G Aprea, JM Jiménez-Gómez, A Bendahmane, G Perrotta, G Giuliano and P Facella. "Pivotal roles of cryptochromes 1a and 2 in tomato development and physiology". Plant Physiology [link]
Y Hu, A Mesihovic, JM Jiménez-Gómez, S Röth, P Gebhardt, D Bublak, A Bovy, KD Scharf, E Schleiff, S Fragkostefanakis. "Natural variation in HsfA2 pre‐mRNA splicing is associated with changes in thermotolerance during tomato domestication". New Phytologist [link]
2018
E Olate, JM Jiménez-Gómez, L Holuigue, J Salinas. "NPR1 mediates a novel regulatory pathway in cold acclimation by interacting with HSFA1 factors". Nature Plants [link]
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. "Allele specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato". Plant Journal [link]
NA Müller, L Zhang, M Koornneef, JM Jiménez-Gómez."Mutations in EID1 and LNK2 caused light-conditional clock deceleration during tomato domestication". PNAS [link]
2017
S Soyk, NA Müller, SJ Park, I Schmalenbach, Ke Jiang, Ryosuke Hayama, Lei Zhang, Joyce Van Eck, JM Jiménez-Gómez, Zachary B Lippman."Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato". Nature Genetics [link]
GU Balcke, S Bennewitz, N Bergau, B Athmer, A Henning, P Majovsky, JM Jiménez-Gómez, W Hoehenwarter, A Tissier. “Multiomics of tomato glandular trichomes reveals distinct features of central carbon metabolism supporting high productivity of specialized metabolites”. The Plant Cell [link]
E Magnani, JM Jiménez-Gómez, L Soubigou-Taconnat, L Lepiniec, E Fiume. “Profiling the onset of somatic embryogenesis in Arabidopsis” BMC Genomics, [link]
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. “A ‘footprint’ of desiccation tolerance in the genome of Xerophyta viscosa”. Nature Plants [link]
C Bazakos, M Hanemian, C Trontin, JM Jiménez-Gómez, O Loudet. “New Strategies and Tools in Quantitative Genetics: How to Go from the Phenotype to the Genotype”. Annual Review of Plant Biology [link]
MF Alvarez, M Angarita, MC Delgado, C Garcia, JM Jiménez-Gómez, C Gebhardt, T Mosquera. “Identification of novel associations of candidate genes with resistance to late blight in Solanum tuberosum Group Phureja” Frontiers in Plant Science [link]
EAR Serin, LB Snoek, H Nijveen, LAJ Willems, JM Jiménez-Gómez, HWM Hilhorst, W Ligterink. “Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population” Frontiers in Plant Science [link].
A Ashoub, N Müller, JM Jiménez‐Gómez, W Brüggemann. “Prominent alterations of wild barley leaf transcriptome in response to individual and combined drought acclimation and heat shock conditions”Physiologia Plantarum [link].
2016
NA Müller, CL Wijnen, A Srinivasan, M Ryngajllo, I Ofner, T Lin, A Ranjan, D West, JN Maloof, NR Sinha, S Huang, D Zamir, JM Jiménez-Gómez “Domestication selected for deceleration of the circadian clock in cultivated tomato”. Nature Genetics [link]
NA Müller, JM Jiménez-Gómez. “Analysis of Circadian Leaf Movements”. Environmental Responses in Plants: Methods and Protocols [link]
M Bar, A Israeli, M Levy, HB Gera, JM Jiménez-Gómez, S Kouril, P Tarkowski, and N Ori. “CLAUSA Is a MYB Transcription Factor That Promotes Leaf Differentiation by Attenuating Cytokinin Signaling”. The Plant Cell [link]
A Srinivasan, JM Jiménez-Gómez, F Fornara, W Soppe, V Brambilla. “Alternative splicing enhances transcriptome complexity in desiccating seeds”. J. Integr. Plant Biol. [link]
C Perea-Resa, C Carrasco-López, R Catalá, V Turečková, O Novak, W Zhang, LE Sieburth, JM Jiménez-Gómez and J Salinas. “The LSM1-7 complex controls plant adaptation to adverse environmental conditions by promoting selective mRNA decapping”. The Plant Cell [link]
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, C Gebhardt. "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 [link]
2014
I Schmalenbach, L Zhang, M Reymond, JM Jiménez-Gómez. “The relationship between flowering time and growth responses to drought in the Arabidopsis Landsberg erecta x Antwerp-1 population”. Frontiers in Plant Science [link]
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, AR Fernie. "The genome of the stress-tolerant wild tomato species Solanum pennellii". Nature Genetics [link]
J Gloggnitzer, S Akimcheva, A Srinivasan, B Kusenda, N Riehs, H Stampfl, J Bautor, B Dekrout, C Jonak, JM Jiménez-Gómez, JE Parker, K Riha. "Nonsense-Mediated mRNA Decay Modulates Immune Receptor Levels to Regulate Plant Antibacterial Defense". Cell Host & Microbe [link]
I Schmalenbach, L Zhang, M Ryngajllo, JM Jiménez-Gómez. “Functional analysis of the Landsberg erecta allele of FRIGIDA”. BMC Plant Biology [link]
JM Jiménez-Gómez. “Network types and their application in natural variation studies in plants”. Current Opinion in Plant Biology [link]
2013
DH Chitwood, R Kumar, LR Headland, A Ranjan, MF Covington, Y Ichihashi, D Fulop, JM Jiménez-Gómez, J Peng, JN Maloof and NR Sinha. "A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines". The Plant Cell [link]
D Koenig*, JM Jiménez-Gómez*, 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. “Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato”. PNAS [link]
2012
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, BJ Staskawicz. “Fine genetic mapping of RXopJ4, a bacterial spot disease resistance locus from Solanum pennellii LA716”. Theor Appl Genet [link]
DH Chitwood, LR Headland, DL Filiault, R Kumar, JM Jiménez-Gómez, AV Schrager, DS Park, J Peng, NR Sinha and JN Maloof. “Native environment modulates leaf size and response to simulated foliar shade across wild tomato species”. PLoS ONE [link]
2011
JM Jiménez-Gómez, J Corwin, B Joseph, JN Maloof and DJ Kliebenstein. "Genomic Analysis of QTLs and Genes Altering Natural Variation in Stochastic Noise". PLoS Genetics [link]
R Kerwin, JM Jiménez-Gómez, SL Harmer, JN Maloof and DJ Kliebenstein. "Network Quantitative Trait Loci Mapping of Circadian Clock Outputs Identifies Metabolic Pathway-to-Clock Linkages in Arabidopsis". The Plant Cell [link]
JM Jiménez-Gómez. "Next generation quantitative genetics in plants". Frontiers in Plant Physiology[link]
2010
JM Jiménez-Gómez, A Wallace and JN Maloof. "Network Analysis Identifies ELF3 as a QTL for the Shade Avoidance Response in Arabidopsis". PLoS Genetics [link]
2009
JM Jimenez-Gomez and JM Maloof." Sequence diversity in three tomato species: SNPs, markers, and molecular evolution". BMC Plant Biology [link]
JM Jiménez-Gómez and JN Maloof. "Plant research accelerates along the (bio)informatics superhighway. Symposium on Plant Sensing, Response and Adaptation to the Environment". EMBO Reports [link]
2007
JM Jiménez-Gómez C Alonso-Blanco, A Borja, G Anastasio, T Angosto, R Lozano and JM Martínez-Zapater. "Quantitative genetic analysis of flowering time in tomato". Génome [link]