A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators

Authors: Ke, Yuji ^{1, 2, 10}, Pujol, Vincent ^{3, 4, 10}, Staut, Jasper ^{1, 2, 10}, Pollaris, Lotte ^{3, 4}, Seurinck, Ruth ^{3, 4}, Eekhout, Thomas ^{1, 2, 5}, Grones, Carolin ^{1, 2, 8}, Saura-Sanchez, Maite ^{1, 2}, Van Bel, Michiel ^{1, 2}, Vuylsteke, Marnik ⁶, Ariani, Andrea ⁷, Liseron-Monfils, Christophe ^{7, 9}, Vandepoele, Klaas ^{1, 2, ∗}, Saeys, Yvan ^{3, 4, ∗∗}, De Rybel, Bert ^{1, 2, 11, ∗∗∗}

Source: In Cell Reports 25 February 2025 44(2)

Neoantigen-targeted dendritic cell vaccination in lung cancer patients induces long-lived T cells exhibiting the full differentiation spectrum

Authors: Ingels, Joline, De Cock, Laurenz, Stevens, Dieter, Mayer, Rupert L., Théry, Fabien, Sanchez, Guillem Sanchez, Vermijlen, David, Weening, Karin, De Smet, Saskia, Lootens, Nele, Brusseel, Marieke, Verstraete, Tasja, Buyle, Jolien, Van Houtte, Eva, Devreker, Pam, Heyns, Kelly, De Munter, Stijn, Van Lint, Sandra, Goetgeluk, Glenn, Bonte, Sarah, Billiet, Lore, Pille, Melissa, Jansen, Hanne, Pascal, Eva, Deseins, Lucas, Vantomme, Lies, Verdonckt, Maarten, Roelandt, Ria, Eekhout, Thomas, Vandamme, Niels, Leclercq, Georges, Taghon, Tom, Kerre, Tessa, Vanommeslaeghe, Floris, Dhondt, Annemieke, Ferdinande, Liesbeth, Van Dorpe, Jo, Desender, Liesbeth, De Ryck, Frederic, Vermassen, Frank, Surmont, Veerle, Impens, Francis, Menten, Björn, Vermaelen, Karim, Vandekerckhove, Bart

Source: In Cell Reports Medicine 21 May 2024 5(5)

Entrepreneurs' mobile phone appropriation and technical efficiency of informal firms in Dakar (Senegal)

Authors: Eekhout, Thomas, Berrou, Jean‐Philippe, Combarnous, François

Source: Journal of international development. 35(6):1429-1455

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190085382.0x000001&indx=1&recIds=ETOCvdc_100190085382.0x000001

Distinctive and complementary roles of E2F transcription factors during plant replication stress responses

Authors: Nisa, Maherun, Eekhout, Thomas, Bergis, Clara, Pedroza-Garcia, Jose-Antonio, He, Xiaoning, Mazubert, Christelle, Vercauteren, Ilse, Cools, Toon, Brik-Chaouche, Rim, Drouin-Wahbi, Jeannine, Chmaiss, Layla, Latrasse, David, Bergounioux, Catherine, Vandepoele, Klaas, Benhamed, Moussa, De Veylder, Lieven, Raynaud, Cécile

Source: In Molecular Plant 7 August 2023 16(8):1269-1282

Rocks in the auxin stream : Wound-induced auxin accumulation and ERF115 expression synergistically drive stem cell regeneration

Authors: Canher, Balkan, Heyman, Jefri, Savina, Maria, Devendran, Ajay, Eekhout, Thomas, Vercauteren, Ilse, Prinsen, Els, Matosevich, Rotem, Xu, Jian, Mironova, Victoria, De Veylder, Lieven

Source: Proceedings of the National Academy of Sciences of the United States of America, 2020 Jul . 117(28), 16667-16677.

Access URL: https://www.jstor.org/stable/26935261

A single-cell morpho-transcriptomic map of brassinosteroid action in the Arabidopsis root

Authors: Graeff, Moritz, Rana, Surbhi, Wendrich, Jos R., Dorier, Julien, Eekhout, Thomas, Aliaga Fandino, Ana Cecilia, Guex, Nicolas, Bassel, George W., De Rybel, Bert, Hardtke, Christian S.

Source: In Molecular Plant 6 December 2021 14(12):1985-1999

The stem cell niche transcription factor ETHYLENE RESPONSE FACTOR 115 participates in aluminum‐induced terminal differentiation in Arabidopsis roots.

Authors: Larsen, Paul B., He, Shiyang, Meyer, Taylor J., Szurman‐Zubrzycka, Miriam, Alfs, Carolin, Kwasniewska, Jolanta, Pervis, Alexandra, Gajecka, Monika, Veerabahu, Aishwarya, Beaulieu, Taylor R., Bolaris, Stephen C., Eekhout, Thomas, De Veylder, Lieven, Abel, Steffen, Szarejko, Iwona, Murn, Jernej

Source: Plant, Cell & Environment; Nov2024, Vol. 47 Issue 11, p4432-4448, 17p

Subject Terms: DNA repair, TRANSCRIPTION factors, STEM cell niches, GAMMA rays, DNA damage, ROOT growth

The plant WEE1 kinase is involved in checkpoint control activation in nematode-induced galls

Authors: Cabral, Danila, Banora, Mohamed Youssef, Antonino, José Dijair, Rodiuc, Natalia, Vieira, Paulo, Coelho, Roberta R., Chevalier, Christian, Eekhout, Thomas, Engler, Gilbert, De Veylder, Lieven, Grossi-de-Sa, Maria Fatima, de Almeida Engler, Janice

Source: The New Phytologist, 2020 Jan 01. 225(1), 430-447.

Access URL: https://www.jstor.org/stable/26874260

Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing.

Authors: Rijk, Peter De^1,2, Watzeels, Tijs^2,3, Küçükali, Fahri^2,3, Dongen, Jasper Van^2,3, Faura, Júlia^2,4, Willems, Patrick^5,6,7,8, Deyn, Lara De^2,3, Duchateau, Lena^2,3, Grones, Carolin^5,6, Eekhout, Thomas^5,6,9, Pooter, Tim De^1,2, Joris, Geert^1,2, Rombauts, Stephane^5,6, Rybel, Bert De^5,6, Rademakers, Rosa^2,4, Breusegem, Frank Van^5,6, Strazisar, Mojca^1,2, Sleegers, Kristel^2,3, Coster, Wouter De^2,4, wouter.decoster@uantwerpen.be

Source: Bioinformatics; Sep2024, Vol. 40 Issue 9, p1-10, 10p

A Spatiotemporal DNA Endoploidy Map of the Arabidopsis Root Reveals Roles for the Endocycle in Root Development and Stress Adaptation

Authors: Bhosale, Rahul, Boudolf, Veronique, Cuevas, Fabiola, Lu, Ran, Eekhout, Thomas, Hu, Zhubing, Van Isterdael, Gert, Lambert, GeorginaM., Xu, Fan, Nowack, Moritz K., Smith, Richard S., Vercauteren, Ilse, De Rycke, Riet, Storme, Veronique, Beeckman, Tom, Larkin, John C., Kremer, Anna, Höfte, Herman, Galbraith, David W., Kumpf, Robert P., Maere, Steven, De Veylder, Lieven

Source: Plant Cell, 2018 Oct 01. 30(10), 2330-2351.

Access URL: https://www.jstor.org/stable/90026100

Tissue-Specific Control of the Endocycle by the Anaphase Promoting Complex/Cyclosome Inhibitors UVI4 and DEL1

Authors: Heyman, Jefri, Polyn, Stefanie, Eekhout, Thomas, De Veylder, Lieven

Source: Plant Physiology, 2017 Sep 01. 175(1), 303-313.

Access URL: https://www.jstor.org/stable/26375395

Modification of DNA Checkpoints to Confer Aluminum Tolerance

Authors: Eekhout, Thomas, Larsen, Paul, De Veylder, Lieven

Source: In Trends in Plant Science February 2017 22(2):102-105

Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.

Authors: Grones, Carolin^1,2 (AUTHOR), Eekhout, Thomas^1,2,3 (AUTHOR), Shi, Dongbo^4,5 (AUTHOR), Neumann, Manuel⁶ (AUTHOR), Berg, Lea S⁷ (AUTHOR), Ke, Yuji^1,2 (AUTHOR), Shahan, Rachel^8,9 (AUTHOR), Cox Jr, Kevin L¹⁰ (AUTHOR), Gomez-Cano, Fabio¹¹ (AUTHOR), Nelissen, Hilde^1,2 (AUTHOR), Lohmann, Jan U⁵ (AUTHOR), Giacomello, Stefania¹² (AUTHOR), Martin, Olivier C¹³ (AUTHOR), Cole, Benjamin¹⁴ (AUTHOR), Wang, Jia-Wei¹⁵ (AUTHOR), Kaufmann, Kerstin⁶ (AUTHOR), Raissig, Michael T⁷ (AUTHOR), Palfalvi, Gergo¹⁶ (AUTHOR), Greb, Thomas⁵ (AUTHOR), Libault, Marc^2,17 (AUTHOR) libaultm@missouri.edu

Source: Plant Cell. Apr2024, Vol. 36 Issue 4, p812-828. 17p.

Subject Terms: *TRANSCRIPTOMES, *PLANT molecular biology, *DATA warehousing, *PLANT genes, *BEST practices, *DEVELOPMENTAL biology

The Arabidopsis SIAMESE-RELATED Cyclin-Dependent Kinase Inhibitors SMR5 and SMR7 Regulate the DNA Damage Checkpoint in Response to Reactive Oxygen Species

Authors: Yi, Dalong, Kamei, Claire Lessa Alvim, Cools, Toon, Vanderauwera, Sandy, Takahashi, Naoki, Okushima, Yoko, Eekhout, Thomas, Yoshiyama, Kaoru Okamoto, Larkin, John, Van den Daele, Hilde, Conklin, Phillip, Britt, Anne, Umeda, Masaaki, De Veylder, Lieven

Source: The Plant Cell, 2014 Jan 01. 26(1), 296-309.

Access URL: https://www.jstor.org/stable/43190665

Cell type–specific attenuation of brassinosteroid signaling precedes stomatal asymmetric cell division.

Authors: Eun-­Ji Kim, Cheng Zhang, Boyu Guo, Eekhout, Thomas, Houbaert, Anaxi, Wendrich, Jos R., Vandamme, Niels, Tiwari, Manish, Simon-­-­Vezo, Claire, Vanhoutte, Isabelle, Saeys, Yvan, Kun Wang, Yuxian Zhu, De Rybel, Bert, Russinova, Eugenia

Source: Proceedings of the National Academy of Sciences of the United States of America; 9/5/2023, Vol. 120 Issue 36, p1-12, 32p

Subject Terms: CELL division, STOMATA, SCAFFOLD proteins, ARABIDOPSIS thaliana, CELL communication

PAT1-type GRAS-domain proteins control regeneration by activating DOF3.4 to drive cell proliferation in Arabidopsis roots.

Authors: Bisht, Anchal^1,2 (AUTHOR), Eekhout, Thomas^1,2 (AUTHOR) lieven.deveylder@psb.vib-ugent.be, Canher, Balkan^1,2 (AUTHOR), Lu, Ran^1,2 (AUTHOR), Vercauteren, Ilse^1,2 (AUTHOR), Jaeger, Geert De^1,2 (AUTHOR), Heyman, Jefri^1,2 (AUTHOR), Veylder, Lieven De^1,2 (AUTHOR) lieven.deveylder@psb.vib-ugent.be

Source: Plant Cell. May2023, Vol. 35 Issue 5, p1513-1531. 19p.

Subject Terms: *CELL proliferation, *GENE expression, *CELL division, *TRANSCRIPTION factors, *ARABIDOPSIS, *PROTEINS, *ZINC-finger proteins

Plant lineage-specific PIKMIN1 drives APC/^CCCS52A2 E3-ligase activity-dependent cell division.

Authors: Willems, Alex, Yuanke Liang, Heyman, Jefri, Depuydt, Thomas, Eekhout, Thomas, Canher, Balkan, Van den Daele, Hilde, Vercauteren, Ilse, Vandepoele, Klaas, De Veylder, Lieven

Source: Plant Physiology; Mar2023, Vol. 191 Issue 3, p1574-1595, 22p

Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single‐cell transcriptomics.

Authors: Tenorio Berrío, Rubén^1,2 (AUTHOR), Verhelst, Eline^1,2 (AUTHOR), Eekhout, Thomas^1,2,3 (AUTHOR), Grones, Carolin^1,2 (AUTHOR), De Veylder, Lieven^1,2 (AUTHOR), De Rybel, Bert^1,2 (AUTHOR), Dubois, Marieke^1,2 (AUTHOR) marieke.dubois@psb.vib-ugent.be

Source: New Phytologist. Mar2025, p1. 19p. 5 Illustrations, 2 Charts.

Non-cell autonomous and spatiotemporal signalling from a tissue organizer orchestrates root vascular development.

Authors: Yang, BaoJun, Minne, Max, Brunoni, Federica, Plačková, Lenka, Petřík, Ivan, Sun, Yanbiao, Nolf, Jonah, Smet, Wouter, Verstaen, Kevin, Wendrich, Jos R., Eekhout, Thomas, Hoyerová, Klára, Van Isterdael, Gert, Haustraete, Jurgen, Bishopp, Anthony, Farcot, Etienne, Novák, Ondřej, Saeys, Yvan, De Rybel, Bert

Source: Nature Plants; Nov2021, Vol. 7 Issue 11, p1485-1494, 10p

Lack of RNase H2 activity rescues HU-sensitivity of WEE1 deficient plants

Authors: Eekhout, Thomas, Kalhorzadeh, Pooneh, De Veylder, Lieven

Source: Plant signaling & behavior. 10(4)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100050607217.0x000001&indx=1&recIds=ETOCvdc_100050607217.0x000001