@article{madison_tahir_broeck_phan_horn_sozzani_2024, title={Cell-material interactions in 3D bioprinted plant cells}, url={https://doi.org/10.1101/2024.01.30.578043}, DOI={10.1101/2024.01.30.578043}, abstractNote={Abstract}, author={Madison, Imani and Tahir, Maimouna and Broeck, Lisa Van and Phan, Linh and Horn, Timothy and Sozzani, Rosangela}, year={2024}, month={Feb} }
 @article{van den broeck_bhosale_song_fonseca de lima_ashley_zhu_zhu_van de cotte_neyt_ortiz_et al._2023, title={Functional annotation of proteins for signaling network inference in non-model species}, volume={14}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-023-40365-z}, DOI={10.1038/s41467-023-40365-z}, abstractNote={Abstract}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Van den Broeck, Lisa and Bhosale, Dinesh Kiran and Song, Kuncheng and Fonseca de Lima, Cássio Flavio and Ashley, Michael and Zhu, Tingting and Zhu, Shanshuo and Van De Cotte, Brigitte and Neyt, Pia and Ortiz, Anna C. and et al.}, year={2023}, month={Aug} }
 @misc{amin_van den broeck_de smet_locke_sozzani_2023, title={Optimal Brain Dissection in Dense Autoencoders: Towards Determining Feature Importance in -Omics Data}, url={http://dx.doi.org/10.1109/bip60195.2023.10379275}, DOI={10.1109/BIP60195.2023.10379275}, abstractNote={Recently, there has been increased interest in ma-chine learning explainability. Understanding the complex relationship between input features of a model and their respective outputs is of increased relevance, especially in biological science. In this paper, we introduce Optimal Brain Dissection (OBD), an innovative methodology designed to examine the importance of first-layer connections in a biology-inspired autoencoder. We incorporated regulator-target interactions within the first autoencoder layer, representing biological regulatory networks, and identified their importance to the reconstruction error, a critical aspect in navigating the complexity of high-dimensional omics data. Through a combination of pruning techniques and counterfactual reasoning, OBD offers a method to quantify feature importance, factoring in both weight magnitude and time-to-laziness. To implement this method, we propose a Dense Autoencoder (DAE) architecture, aiming for increased efficiency and reduced computation. Tailored for omics data, the DAE employs skip concatenations and circumvents non-existent target-target interactions. Our approach aims to understand the relative importance of connections for autoencoder performance, a critical step towards better counter-factual reasoning for neural networks.}, journal={2023 IEEE 5th International Conference on BioInspired Processing (BIP)}, publisher={IEEE}, author={Amin, Fin and Van den Broeck, Lisa and De Smet, Ive and Locke, Anna M. and Sozzani, Rossangela}, year={2023}, month={Nov} }
 @article{madison_gillan_peace_gabrieli_broeck_jones_sozzani_2023, title={Phosphate starvation: response mechanisms and solutions}, volume={8}, ISSN={["1460-2431"]}, url={https://doi.org/10.1093/jxb/erad326}, DOI={10.1093/jxb/erad326}, abstractNote={Abstract}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Madison, Imani and Gillan, Lydia and Peace, Jasmine and Gabrieli, Flavio and Broeck, Lisa and Jones, Jacob L. and Sozzani, Rosangela}, editor={Ort, DonaldEditor}, year={2023}, month={Aug} }
 @inproceedings{mahatma_broeck_morffy_staller_strader_sozzani_2023, title={Prediction and functional characterization of transcriptional activation domains}, url={https://doi.org/10.1109/CISS56502.2023.10089768}, DOI={10.1109/CISS56502.2023.10089768}, abstractNote={Gene expression is induced by transcription factors (TFs) through their activation domains (ADs). However, ADs are unconserved, intrinsically disordered sequences without a secondary structure, making it challenging to recognize and predict these regions and limiting our ability to identify TFs. Here, we address this challenge by leveraging a neural network approach to systematically predict ADs. As input for our neural network, we used computed properties for amino acid (AA) side chain and secondary structure, rather than relying on the raw sequence. Moreover, to shed light on the features learned by our neural network and greatly increase interpretability, we computed the input properties most important for an accurate prediction. Our findings further highlight the importance of aromatic and negatively charged AA and reveal the importance of unknown AA properties. Taking advantage of these most important features, we used an unsupervised learning approach to classify the ADs into 10 subclasses, which can further be explored for AA specificity and AD functionality. Overall, our pipeline, relying on supervised and unsupervised machine learning, shed light on the non-linear properties of ADs.}, author={Mahatma, Saloni and Broeck, Lisa Van and Morffy, Nicholas and Staller, Max V and Strader, Lucia C and Sozzani, Rosangela}, year={2023}, month={Mar} }
 @article{gaudinier_broeck_moreno-risueño_rodriguez-medina_sozzani_brady_2023, title={Quantitative Modeling of the Short-Term Response to Nitrogen Availability that Coordinates Early Events in Lateral Root Initiation}, url={https://doi.org/10.1101/2023.12.05.570292}, DOI={10.1101/2023.12.05.570292}, abstractNote={Abstract}, author={Gaudinier, Allison and Broeck, Lisa Van and Moreno-Risueño, Miguel and Rodriguez-Medina, Joel and Sozzani, Rosangela and Brady, Siobhan M.}, year={2023}, month={Dec} }
 @article{beretta_franchini_din_lacchini_broeck_sozzani_orozco-arroyo_caporali_adam_jouannic_et al._2023, title={The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice}, volume={4}, ISSN={["1365-313X"]}, url={https://doi.org/10.1111/tpj.16229}, DOI={10.1111/tpj.16229}, abstractNote={SUMMARY}, journal={PLANT JOURNAL}, author={Beretta, Veronica M. and Franchini, Emanuela and Din, Israr Ud and Lacchini, Elia and Broeck, Lisa and Sozzani, Rosangela and Orozco-Arroyo, Gregorio and Caporali, Elisabetta and Adam, Helene and Jouannic, Stefan and et al.}, year={2023}, month={Apr} }
 @article{broeck_schwartz_krishnamoorthy_spurney_tahir_melvin_gobble_peters_muhammad_li_et al._2022, title={Establishing a reproducible approach for the controllable deposition and maintenance of plants cells with 3D bioprinting}, volume={3}, url={https://doi.org/10.1101/2022.03.25.485804}, DOI={10.1101/2022.03.25.485804}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Broeck, Lisa Van and Schwartz, Michael F and Krishnamoorthy, Srikumar and Spurney, Ryan J and Tahir, Maimouna Abderamane and Melvin, Charles and Gobble, Mariah and Peters, Rachel and Muhammad, Atiyya and Li, Baochun and et al.}, year={2022}, month={Mar} }
 @article{broeck_schwartz_krishnamoorthy_tahir_spurney_madison_melvin_gobble_nguyen_peters_et al._2022, title={Establishing a reproducible approach to study cellular functions of plant cells with 3D bioprinting}, url={https://doi.org/10.1126/sciadv.abp9906}, DOI={10.1126/sciadv.abp9906}, abstractNote={Capturing cell-to-cell signals in a three-dimensional (3D) environment is key to studying cellular functions. A major challenge in the current culturing methods is the lack of accurately capturing multicellular 3D environments. In this study, we established a framework for 3D bioprinting plant cells to study cell viability, cell division, and cell identity. We established long-term cell viability for bioprinted Arabidopsis and soybean cells. To analyze the generated large image datasets, we developed a high-throughput image analysis pipeline. Furthermore, we showed the cell cycle reentry of bioprinted cells for which the timing coincides with the induction of core cell cycle genes and regeneration-related genes, ultimately leading to microcallus formation. Last, the identity of bioprinted Arabidopsis root cells expressing endodermal markers was maintained for longer periods. The framework established here paves the way for a general use of 3D bioprinting for studying cellular reprogramming and cell cycle reentry toward tissue regeneration.}, journal={Science Advances}, author={Broeck, Lisa Van and Schwartz, Michael F. and Krishnamoorthy, Srikumar and Tahir, Maimouna Abderamane and Spurney, Ryan J. and Madison, Imani and Melvin, Charles and Gobble, Mariah and Nguyen, Thomas and Peters, Rachel and et al.}, year={2022}, month={Oct} }
 @article{broeck_bhosale_song_lima_ashley_zhu_zhu_cotte_neyt_ortiz_et al._2022, title={Functional annotation of proteins for signaling network inference in non-model species}, url={https://doi.org/10.21203/rs.3.rs-2201240/v1}, DOI={10.21203/rs.3.rs-2201240/v1}, abstractNote={Abstract}, author={Broeck, Lisa Van and Bhosale, Dinesh and Song, Kuncheng and Lima, Cássio Fonseca and Ashley, Michael and Zhu, Tingting and Zhu, Shanshuo and Cotte, Brigitte Van De and Neyt, Pia and Ortiz, Anna and et al.}, year={2022}, month={Nov} }
 @article{thomas_broeck_spurney_sozzani_frank_2022, title={Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation}, volume={34}, ISSN={["1532-298X"]}, url={https://doi.org/10.1093/plcell/koab246}, DOI={10.1093/plcell/koab246}, abstractNote={Abstract}, number={1}, journal={PLANT CELL}, publisher={Oxford University Press (OUP)}, author={Thomas, Hannah and Broeck, Lisa and Spurney, Ryan and Sozzani, Rosangela and Frank, Margaret}, year={2022}, month={Jan}, pages={535–556} }
 @article{broeck_spurney_fisher_schwartz_clark_nguyen_madison_gobble_long_sozzani_2021, title={A hybrid model connecting regulatory interactions with stem cell divisions in the root}, volume={2}, url={https://doi.org/10.1017/qpb.2021.1}, DOI={10.1017/qpb.2021.1}, abstractNote={Abstract}, journal={Quantitative Plant Biology}, publisher={Cambridge University Press (CUP)}, author={Broeck, Lisa Van and Spurney, Ryan J. and Fisher, Adam P. and Schwartz, Michael and Clark, Natalie M. and Nguyen, Thomas T. and Madison, Imani and Gobble, Mariah and Long, Terri and Sozzani, Rosangela}, year={2021} }
 @article{kim_van den broeck_karre_choi_christensen_wang_jo_cho_balint‐kurti_2021, title={Analysis of the transcriptomic, metabolomic, and gene regulatory responses to
            <i>Puccinia sorghi
            in maize}, volume={22}, ISSN={1464-6722 1364-3703}, url={http://dx.doi.org/10.1111/mpp.13040}, DOI={10.1111/mpp.13040}, abstractNote={Abstract}, number={4}, journal={Molecular Plant Pathology}, publisher={Wiley}, author={Kim, Saet‐Byul and Van den Broeck, Lisa and Karre, Shailesh and Choi, Hoseong and Christensen, Shawn A. and Wang, Guan‐Feng and Jo, Yeonhwa and Cho, Won Kyong and Balint‐Kurti, Peter}, year={2021}, month={Feb}, pages={465–479} }
 @misc{schwartz_peters_hunt_abdul-matin_broeck_sozzani_2021, title={Divide and Conquer: The Initiation and Proliferation of Meristems}, volume={40}, ISSN={["1549-7836"]}, url={http://dx.doi.org/10.1080/07352689.2021.1915228}, DOI={10.1080/07352689.2021.1915228}, abstractNote={Abstract In contrast to animals, which complete organogenesis early in their development, plants continuously produce organs, and structures throughout their entire lifecycle. Plants achieve the continuous growth of organs through the initiation and maintenance of meristems that populate the plant body. Plants contain two apical meristems, one at the shoot and one root, to produce the lateral organs of the shoot and the cell files of the root, respectively. Additional meristems within the plant produce branches while others produce the cell types within the vasculature system. Throughout development, plants must balance producing organs and maintaining their meristems, which requires tightly controlled regulations. This review focuses on the various plant meristems, how cells within these meristems maintain their identity, and particularly the molecular players that regulate stem cell maintenance. In addition, we summarize cell types which share molecular features with meristems, but do not follow the same rules regarding maintenance, including pericycle and rachis founder cells. Together, these populations of cells contribute to the entire organogenesis of plants.}, number={2}, journal={CRITICAL REVIEWS IN PLANT SCIENCES}, publisher={Informa UK Limited}, author={Schwartz, Michael F. and Peters, Rachel and Hunt, Aitch M. and Abdul-Matin, Abdul-Khaliq and Broeck, Lisa and Sozzani, Rosangela}, year={2021}, month={Mar}, pages={147–156} }
 @article{thomas_broeck_spurney_sozzani_frank_2021, title={Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation}, volume={2}, url={https://doi.org/10.1101/2021.02.26.433082}, DOI={10.1101/2021.02.26.433082}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Thomas, Hannah and Broeck, Lisa Van and Spurney, Ryan and Sozzani, Rosangela and Frank, Margaret}, year={2021}, month={Feb} }
 @article{franchini_beretta_din_lacchini_broeck_sozzani_orozco-arroyo_adam_jouannic_gregis_et al._2021, title={The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice}, volume={5}, url={https://doi.org/10.1101/2021.05.03.442460}, DOI={10.1101/2021.05.03.442460}, abstractNote={ABSTRACT}, publisher={Cold Spring Harbor Laboratory}, author={Franchini, Emanuela and Beretta, Veronica M. and Din, Israr Ud and Lacchini, Elia and Broeck, Lisa Van and Sozzani, Rosangela and Orozco-Arroyo, Gregorio and Adam, Hélène and Jouannic, Stefan and Gregis, Veronica and et al.}, year={2021}, month={May} }
 @article{krishnamoorthy_schwartz_broeck_hunt_horn_sozzani_2021, title={Tissue Regeneration with Hydrogel Encapsulation: A Review of Developments in Plants and Animals}, url={https://doi.org/10.34133/2021/9890319}, DOI={10.34133/2021/9890319}, abstractNote={
            Hydrogel encapsulation has been widely utilized in the study of fundamental cellular mechanisms and has been shown to provide a better representation of the complex
            in vivo
            microenvironment in natural biological conditions of mammalian cells. In this review, we provide a background into the adoption of hydrogel encapsulation methods in the study of mammalian cells, highlight some key findings that may aid with the adoption of similar methods for the study of plant cells, including the potential challenges and considerations, and discuss key findings of studies that have utilized these methods in plant sciences.
          }, journal={BioDesign Research}, author={Krishnamoorthy, Srikumar and Schwartz, Michael F. and Broeck, Lisa Van and Hunt, Aitch and Horn, Timothy J. and Sozzani, Rosangela}, year={2021}, month={Jan} }
 @article{doydora_gatiboni_grieger_hesterberg_jones_mclamore_peters_sozzani_van den broeck_duckworth_2020, title={Accessing Legacy Phosphorus in Soils}, volume={4}, ISSN={2571-8789}, url={http://dx.doi.org/10.3390/soilsystems4040074}, DOI={10.3390/soilsystems4040074}, abstractNote={Repeated applications of phosphorus (P) fertilizers result in the buildup of P in soil (commonly known as legacy P), a large fraction of which is not immediately available for plant use. Long-term applications and accumulations of soil P is an inefficient use of dwindling P supplies and can result in nutrient runoff, often leading to eutrophication of water bodies. Although soil legacy P is problematic in some regards, it conversely may serve as a source of P for crop use and could potentially decrease dependence on external P fertilizer inputs. This paper reviews the (1) current knowledge on the occurrence and bioaccessibility of different chemical forms of P in soil, (2) legacy P transformations with mineral and organic fertilizer applications in relation to their potential bioaccessibility, and (3) approaches and associated challenges for accessing native soil P that could be used to harness soil legacy P for crop production. We highlight how the occurrence and potential bioaccessibility of different forms of soil inorganic and organic P vary depending on soil properties, such as soil pH and organic matter content. We also found that accumulation of inorganic legacy P forms changes more than organic P species with fertilizer applications and cessations. We also discuss progress and challenges with current approaches for accessing native soil P that could be used for accessing legacy P, including natural and genetically modified plant-based strategies, the use of P-solubilizing microorganisms, and immobilized organic P-hydrolyzing enzymes. It is foreseeable that accessing legacy P will require multidisciplinary approaches to address these limitations.}, number={4}, journal={Soil Systems}, publisher={MDPI AG}, author={Doydora, Sarah and Gatiboni, Luciano and Grieger, Khara and Hesterberg, Dean and Jones, Jacob L. and McLamore, Eric S. and Peters, Rachel and Sozzani, Rosangela and Van den Broeck, Lisa and Duckworth, Owen W.}, year={2020}, month={Dec}, pages={74} }
 @article{van den broeck_gordon_inzé_williams_sozzani_2020, title={Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling}, volume={11}, ISSN={1664-8021}, url={http://dx.doi.org/10.3389/fgene.2020.00457}, DOI={10.3389/fgene.2020.00457}, abstractNote={Plant responses to environmental and intrinsic signals are tightly controlled by multiple transcription factors (TFs). These TFs and their regulatory connections form gene regulatory networks (GRNs), which provide a blueprint of the transcriptional regulations underlying plant development and environmental responses. This review provides examples of experimental methodologies commonly used to identify regulatory interactions and generate GRNs. Additionally, this review describes network inference techniques that leverage gene expression data to predict regulatory interactions. These computational and experimental methodologies yield complex networks that can identify new regulatory interactions, driving novel hypotheses. Biological properties that contribute to the complexity of GRNs are also described in this review. These include network topology, network size, transient binding of TFs to DNA, and competition between multiple upstream regulators. Finally, this review highlights the potential of machine learning approaches to leverage gene expression data to predict phenotypic outputs.}, journal={Frontiers in Genetics}, publisher={Frontiers Media SA}, author={Van den Broeck, Lisa and Gordon, Max and Inzé, Dirk and Williams, Cranos and Sozzani, Rosangela}, year={2020}, month={May} }
 @article{clark_van den broeck_guichard_stager_tanner_blilou_grossmann_iyer-pascuzzi_maizel_sparks_et al._2020, title={Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big}, volume={71}, ISSN={1543-5008 1545-2123}, url={http://dx.doi.org/10.1146/annurev-arplant-050718-100038}, DOI={10.1146/annurev-arplant-050718-100038}, abstractNote={ The acquisition of quantitative information on plant development across a range of temporal and spatial scales is essential to understand the mechanisms of plant growth. Recent years have shown the emergence of imaging methodologies that enable the capture and analysis of plant growth, from the dynamics of molecules within cells to the measurement of morphometricand physiological traits in field-grown plants. In some instances, these imaging methods can be parallelized across multiple samples to increase throughput. When high throughput is combined with high temporal and spatial resolution, the resulting image-derived data sets could be combined with molecular large-scale data sets to enable unprecedented systems-level computational modeling. Such image-driven functional genomics studies may be expected to appear at an accelerating rate in the near future given the early success of the foundational efforts reviewed here. We present new imaging modalities and review how they have enabled a better understanding of plant growth from the microscopic to the macroscopic scale. }, number={1}, journal={Annual Review of Plant Biology}, publisher={Annual Reviews}, author={Clark, Natalie M. and Van den Broeck, Lisa and Guichard, Marjorie and Stager, Adam and Tanner, Herbert G. and Blilou, Ikram and Grossmann, Guido and Iyer-Pascuzzi, Anjali S. and Maizel, Alexis and Sparks, Erin E. and et al.}, year={2020}, month={Apr}, pages={789–816} }
 @article{clark_fisher_berckmans_van den broeck_nelson_nguyen_bustillo-avendaño_zebell_moreno-risueno_simon_et al._2020, title={Protein complex stoichiometry and expression dynamics of transcription factors modulate stem cell division}, volume={117}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.2002166117}, DOI={10.1073/pnas.2002166117}, abstractNote={
            Stem cells divide and differentiate to form all of the specialized cell types in a multicellular organism. In the
            Arabidopsis
            root, stem cells are maintained in an undifferentiated state by a less mitotically active population of cells called the quiescent center (QC). Determining how the QC regulates the surrounding stem cell initials, or what makes the QC fundamentally different from the actively dividing initials, is important for understanding how stem cell divisions are maintained. Here we gained insight into the differences between the QC and the cortex endodermis initials (CEI) by studying the mobile transcription factor SHORTROOT (SHR) and its binding partner SCARECROW (SCR). We constructed an ordinary differential equation model of SHR and SCR in the QC and CEI which incorporated the stoichiometry of the SHR-SCR complex as well as upstream transcriptional regulation of SHR and SCR. Our model prediction, coupled with experimental validation, showed that high levels of the SHR-SCR complex are associated with more CEI division but less QC division. Furthermore, our model prediction allowed us to propose the putative upstream SHR regulators SEUSS and WUSCHEL-RELATED HOMEOBOX 5 and to experimentally validate their roles in QC and CEI division. In addition, our model established the timing of QC and CEI division and suggests that SHR repression of QC division depends on formation of the SHR homodimer. Thus, our results support that SHR-SCR protein complex stoichiometry and regulation of SHR transcription modulate the division timing of two different specialized cell types in the root stem cell niche.
          }, number={26}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Clark, Natalie M. and Fisher, Adam P. and Berckmans, Barbara and Van den Broeck, Lisa and Nelson, Emily C. and Nguyen, Thomas T. and Bustillo-Avendaño, Estefano and Zebell, Sophia G. and Moreno-Risueno, Miguel A. and Simon, Rüdiger and et al.}, year={2020}, month={Jun}, pages={15332–15342} }
 @article{spurney_broeck_clark_fisher_balaguer_sozzani_2020, title={tuxnet: a simple interface to process RNA sequencing data and infer gene regulatory networks}, volume={101}, ISSN={["1365-313X"]}, url={https://doi.org/10.1111/tpj.14558}, DOI={10.1111/tpj.14558}, abstractNote={Summary}, number={3}, journal={PLANT JOURNAL}, author={Spurney, Ryan J. and Broeck, Lisa and Clark, Natalie M. and Fisher, Adam P. and Balaguer, Maria A. de Luis and Sozzani, Rosangela}, year={2020}, month={Feb}, pages={716–730} }
 @article{n_broeck l_s_cotte b_m_k_d_i_2018, title={Early mannitol-triggered changes in the Arabidopsis leaf (phospho)proteome reveal growth regulators.}, volume={8}, url={http://europepmc.org/abstract/med/30010984}, DOI={10.1093/jxb/ery261}, abstractNote={Drought is one of the most detrimental environmental stresses to which plants are exposed. Especially mild drought is relevant to agriculture and significantly affects plant growth and development. In plant research, mannitol is often used to mimic drought stress and study the underlying responses. In growing leaf tissue of plants exposed to mannitol-induced stress, a highly-interconnected gene regulatory network is induced. However, early signaling and associated protein phosphorylation events that likely precede part of these transcriptional changes are largely unknown. Here, we performed a full proteome and phosphoproteome analysis on growing leaf tissue of Arabidopsis plants exposed to mild mannitol-induced stress and captured the fast (within the first half hour) events associated with this stress. Based on this in-depth data analysis, 167 and 172 differentially regulated proteins and phosphorylated sites were found back, respectively. Additionally, we identified H(+)-ATPASE 2 (AHA2) and CYSTEINE-RICH REPEAT SECRETORY PROTEIN 38 (CRRSP38) as novel regulators of shoot growth under osmotic stress. Highlight We captured early changes in the Arabidopsis leaf proteome and phosphoproteome upon mild mannitol stress and identified AHA2 and CRRSP38 as novel regulators of shoot growth under osmotic stress}, journal={Journal of experimental botany}, author={N, Nikonorova and Broeck L, Van and S, Zhu and Cotte B and M, Dubois and K, Gevaert and D, Inzé and I, De Smet}, year={2018}, month={Aug} }
 @article{dubois_broeck l van_inzé_2018, title={The Pivotal Role of Ethylene in Plant Growth.}, volume={4}, url={http://europepmc.org/abstract/med/29428350}, DOI={10.1016/j.tplants.2018.01.003}, abstractNote={Being continuously exposed to variable environmental conditions, plants produce phytohormones to react quickly and specifically to these changes. The phytohormone ethylene is produced in response to multiple stresses. While the role of ethylene in defense responses to pathogens is widely recognized, recent studies in arabidopsis and crop species highlight an emerging key role for ethylene in the regulation of organ growth and yield under abiotic stress. Molecular connections between ethylene and growth-regulatory pathways have been uncovered, and altering the expression of ethylene response factors (ERFs) provides a new strategy for targeted ethylene-response engineering. Crops with optimized ethylene responses show improved growth in the field, opening new windows for future crop improvement. This review focuses on how ethylene regulates shoot growth, with an emphasis on leaves.}, journal={Trends in plant science}, author={Dubois, M and Broeck L Van and Inzé, D}, year={2018}, month={Apr} }
 @misc{e-mtab-6205 - the expression profiles of 31 transcription factors in wild-type col-0 plants upon mild osmotic stress, including 10 time points and different leaf tissues_2017, url={https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6205}, year={2017} }
 @misc{e-mtab-6209 - the expression profiles of 30 transcription factors in 17 inducible gain-of-function lines after activation of overexpression, including 5 time points_2017, url={https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6209}, year={2017} }
 @article{broeck_dubois_vermeersch_storme_matsui_inzé_2017, title={From network to phenotype: the dynamic wiring of an Arabidopsis transcriptional network induced by osmotic stress}, volume={13}, url={https://doi.org/10.15252/msb.20177840}, DOI={10.15252/msb.20177840}, abstractNote={Plants have established different mechanisms to cope with environmental fluctuations and accordingly fine‐tune their growth and development through the regulation of complex molecular networks. It is largely unknown how the network architectures change and what the key regulators in stress responses and plant growth are. Here, we investigated a complex, highly interconnected network of 20 Arabidopsis transcription factors (TFs) at the basis of leaf growth inhibition upon mild osmotic stress. We tracked the dynamic behavior of the stress‐responsive TFs over time, showing the rapid induction following stress treatment, specifically in growing leaves. The connections between the TFs were uncovered using inducible overexpression lines and were validated with transient expression assays. This study resulted in the identification of a core network, composed of ERF6, ERF8, ERF9, ERF59, and ERF98, which is responsible for most transcriptional connections. The analyses highlight the biological function of this core network in environmental adaptation and its redundancy. Finally, a phenotypic analysis of loss‐of‐function and gain‐of‐function lines of the transcription factors established multiple connections between the stress‐responsive network and leaf growth.}, number={12}, journal={Molecular Systems Biology}, publisher={EMBO}, author={Broeck, Lisa Van and Dubois, Marieke and Vermeersch, Mattias and Storme, Veronique and Matsui, Minami and Inzé, Dirk}, year={2017}, month={Dec}, pages={961} }
 @article{time of day determines arabidopsis transcriptome and growth dynamics under mild drought._2017, volume={2}, url={http://europepmc.org/abstract/med/27479938}, DOI={10.1111/pce.12809}, abstractNote={Abstract}, journal={Plant, cell & environment}, year={2017}, month={Feb} }
 @article{ralfl34 regulates formative cell divisions in arabidopsis pericycle during lateral root initiation._2016, volume={8}, url={http://europepmc.org/abstract/med/27521602}, DOI={10.1093/jxb/erw281}, abstractNote={Highlight We describe the role of RALFL34 during early events in lateral root development, and demonstrate its specific importance in orchestrating formative cell divisions in the pericycle.}, journal={Journal of experimental botany}, year={2016}, month={Aug} }
 @article{the ethylene response factors erf6 and erf11 antagonistically regulate mannitol-induced growth inhibition in arabidopsis._2015, volume={9}, url={http://europepmc.org/abstract/med/25995327}, DOI={10.1104/pp.15.00335}, abstractNote={A negative feedback loop involving two Ethylene Response Factors fine-tunes growth inhibition and stress tolerance activation under mannitol-induced stress. Leaf growth is a tightly regulated and complex process, which responds in a dynamic manner to changing environmental conditions, but the mechanisms that reduce growth under adverse conditions are rather poorly understood. We previously identified a growth inhibitory pathway regulating leaf growth upon exposure to a low concentration of mannitol and characterized the ETHYLENE RESPONSE FACTOR (ERF)/APETALA2 transcription factor ERF6 as a central activator of both leaf growth inhibition and induction of stress tolerance genes. Here, we describe the role of the transcriptional repressor ERF11 in relation to the ERF6-mediated stress response in Arabidopsis (Arabidopsis thaliana). Using inducible overexpression lines, we show that ERF6 induces the expression of ERF11. ERF11 in turn molecularly counteracts the action of ERF6 and represses at least some of the ERF6-induced genes by directly competing for the target gene promoters. As a phenotypical consequence of the ERF6-ERF11 antagonism, the extreme dwarfism caused by ERF6 overexpression is suppressed by overexpression of ERF11. Together, our data demonstrate that dynamic mechanisms exist to fine-tune the stress response and that ERF11 counteracts ERF6 to maintain a balance between plant growth and stress defense.}, journal={Plant physiology}, year={2015}, month={Sep} }