Three decades of work on
plant stem cells.

2026

• WUSCHEL modulates jasmonate signaling to control the balance between growth and defense in the shoot apical meristem. Fan P, Boumpas P, Wenzl C, Ma Y, Poschet G, Zhao J, Greb T, Lohmann JU
  bioRxiv
• The role of DOF transcription factors in generating specificity during plant development. Hidalgo I, Lohmann JU
  J. Exp. Botany

2025

• The cell wall controls stem cell fate in the Arabidopsis shoot apical meristem. Zerin T, Ruiz-Duarte P, Schürholz AK, Schlamp T, Ma Y, Bevilacqua C, El Arbi N, Wenzl C, Miotk A, Prevedel R, Greb T, Lohmann JU, Wolf S
  bioRxiv
• A single-cell multi-omics atlas of rice. Wang X, Huang H, Kang J, Jiang S, Wang K, Li D, Xie S, Liu C, Li C, Yang L, Lohmann JU, Liang Z, Gu X
  Nature
• MicroRNA control of stem cell reconstitution and growth in root regeneration. Baulies JL, Rodríguez RE, Liebsch D, Zhao X, Zeng J, Bald L, Schommer C, Lohmann JU, Palatnik JF
  Nature Plants
• The hidden architects: nitric oxide and redox dynamics in plant stem cell homeostasis. Zeng J, Zhao X, Lohmann JU
  BioEssays

2024

• Cell-to-cell mobility of the stem cell inducing WUSCHEL transcription factor is controlled by a balance of transport and retention. Fuchs M, Stiehl T, Marciniak-Czochra A, Lohmann JU
  bioRxiv
• TOR kinase controls Arabidopsis shoot development by translational repression of cytokinin catabolic enzymes. Janocha D, Pfeiffer A, Dong Y, Novák O, Strnad M, Ryabova LA, Lohmann JU
  bioRxiv
• ARGONAUTE10 controls cell fate specification and formative cell divisions in the Arabidopsis root. El Arbi N, Schürholz AK, Handl MU, Schiffner A, Hidalgo Prados I, Schnurbusch L, Wenzl C, Zhao X, Zeng J, Lohmann JU, Wolf S
  EMBO J.
• Best practices for the execution, analysis and data storage of plant single cell/nucleus transcriptomics. Grones C, Eekhout T, Shi D, Neumann M, Berg LS, Ke Y, Shahan R, Cox KL, Nelissen H, Lohmann JU, Giacomello S, Martin OC, Cole B, Wang JW, Kaufmann K, Raissig MT, Palfalvi G, Greb T, Libault M, De Rybel B
  Plant Cell

2023

• Nitric oxide controls shoot meristem activity via regulation of DNA methylation. Zeng J, Zhao X, Liang Z, Hidalgo I, Gebert M, Fan P, Wenzl C, Gornik SG, Lohmann JU
  Nature Communications
• SNF1-RELATED KINASE 1 and TARGET OF RAPAMYCIN control light-responsive splicing events and developmental characteristics in etiolated Arabidopsis seedlings. Saile J, Wießner-Kroh T, Erbstein K, Obermüller DM, Pfeiffer A, Janocha D, Lohmann J, Wachter A
  Plant Cell
• 3D imaging reveals apical stem cell responses to ambient temperature. Wenzl C, Lohmann JU
  Cells & Development
• TOR acts as metabolic gatekeeper for auxin-dependent lateral root initiation in Arabidopsis thaliana. Stitz M, Kuster D, Reinert M, Schepetilnikov M, Berthet B, Reyes‐Hernández J, Janocha D, Artins A, Boix M, Henriques R, Pfeiffer A, Lohmann J, Gaquerel E, Maizel A
  EMBO J.
• OBERON3 and SUPPRESSOR OF MAX2 1-LIKE proteins form a regulatory module specifying phloem identity. Wallner ES, Tonn N, Shi D, Luzzietti L, Wanke F, Hunziker P, Xu Y, Jung I, Lopéz-Salmerón V, Gebert M, Wenzl C, Lohmann JU, Harter K, Greb T
  Nature Communications

2022

• Chromatin accessibility illuminates single-cell regulatory dynamics of rice root tips. Feng D, Liang Z, Wang Y, Yao J, Yuan Z, Hu G, Qu R, Xie S, Li D, Yang L, Zhao X, Ma Y, Lohmann JU, Gu X
  BMC Biology
• Multi-angle in vivo imaging of the Arabidopsis thaliana shoot apical meristem (SAM). Fuchs M, Lohmann JU
  Methods Mol. Biol.

2021

• Distinct and overlapping functions of Miscanthus sinensis MYB transcription factors SCM1 and MYB103 in lignin biosynthesis. Golfier P, Ermakova O, Unda F, Murphy EK, Xie J, He F, Zhang W, Lohmann JU, Mansfield SD, Rausch T, Wolf S
  Int. J. Mol. Sci.
• Independent parental contributions initiate zygote polarization in Arabidopsis thaliana. Wang K, Chen H, Ortega-Perez M, Miao Y, Ma Y, Henschen A, Lohmann JU, Laubinger S, Bayer M
  Current Biology
• Transcriptional landscape of rice roots at the single-cell resolution. Liu Q, Liang Z, Feng D, Jiang S, Wang Y, Du Z, Li R, Hu G, Zhang P, Ma Y, Lohmann JU*, Gu X
  Molecular Plant
• Casting the net — connecting auxin signaling to the plant genome. Ma Y, Wolf S, Lohmann JU
  CSH Perspect. Biol.

2020

• WUSCHEL triggers innate antiviral immunity in plant stem cells. Wu H, Qu X, Dong Z, Luo L, Shao C, Forner J, Lohmann JU, Su M, Xu M, Liu X, Zhu L, Zeng J, Liu S, Tian Z, Zhao Z
  Science
• Accurate and versatile 3D segmentation of plant tissues at cellular resolution. Wolny A, Cerrone L, Vijayan A, Tofanelli R, Barro AV, Louveaux M, Wenzl C, Strauss S, Wilson-Sánchez D, Lymbouridou R, Steigleder SS, Pape C, Bailoni A, Duran-Nebreda S, Bassel GW, Lohmann JU, Tsiantis M, Hamprecht FA, Schneitz K, Maizel A, Kreshuk A
  eLife
• Mathematical modeling of plant cell fate transitions controlled by hormonal signals. Klawe FZ, Stiehl T, Bastian P, Gaillochet C, Lohmann JU, Marciniak-Czochra A
  PLOS Comp. Biol.
• Temporal integration of auxin information for the regulation of patterning. Galvan-Ampudia CS, Guillaume C, Legrand J, Azais R, Brunoud G, Moussu S, Wenzl C, Lohmann JU, Godin C, Vernoux T
  eLife
• Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL. Sloan J, Hakenjos JP, Gebert M, Gumiero A, Stier G, Wild K, Sinning I, Lohmann JU
  Nature Communications
• Aiming for the top: non-cell autonomous control of shoot stem cells in Arabidopsis. Fuchs M, Lohmann JU
  J. Plant Res.

2019

• WUSCHEL acts as an auxin response rheostat to maintain apical stem cells in Arabidopsis. Ma Y, Miotk A, Sutikovic Z, Ermakova O, Wenzl C, Medzihradsky A, Gaillochet C, Forner J, Utan G, Brackmann K, Galvan-Ampudia CS, Vernoux T, Greb T, Lohmann JU
  Nature Communications
• An apical hypoxic niche sets the pace over shoot meristem activity. Weits DA, Kunkowska AB, Kamps CW, Portz KM, Packbier NK, Nemec Venza Z, Gaillochet C, Lohmann JU, Pedersen O, van Dongen JT, Licausi F
  Nature
• Plant-thickening mechanisms revealed. Wolf S, Lohmann JU
  Nature
• Inducible, cell type-specific expression in Arabidopsis thaliana through LhGR-mediated trans-activation. López-Salmerón V, Schürholz AK, Li Z, Schlamp T, Wenzl C, Lohmann JU, Greb T, Wolf S
  J. Vis. Exp.

2018

• WEADE: a workflow for enrichment analysis and data exploration. Trost N, Rempel E, Ermakova O, Tamirisa S, Parcalabescu L, Boutros M, Lohmann JU, Lohmann I
  PLOS One
• Epigenetic reprogramming by histone acetyltransferase HAG1/AtGCN5 is required for pluripotency acquisition in Arabidopsis. Kim JY, Yang W, Forner J, Lohmann JU, Noh B, Noh YS
  EMBO J.
• A comprehensive tool set for inducible, cell type-specific gene expression in Arabidopsis. Schuerholz AK, Lopez-Salmeron V, Li Z, Forner F, Wenzl C, Gaillochet C, Augustin S, Vilches Barro A, Fuchs M, Gebert M, Vermeer JEM, Lohmann JU, Greb T, Wolf S
  Plant Physiology
• Decoding the regulatory logic of the Drosophila male stem cell system. Papagiannouli F, Tamirisa S, Rempel E, Ermakova O, Trost N, Zhou J, Mundorf J, Brunel S, Ruhland N, Boutros M, Lohmann JU, Lohmann I
  Cell Reports
• A molecular framework for functional versatility of HECATE transcription factors. Gaillochet C, Jamge S, van der Wal F, Angenent G, Immink R, Lohmann JU
  Plant Journal
• Spatial specificity of auxin responses coordinates wood formation. Brackmann K, Qi J, Gebert M, Jouannet V, Schlamp T, Grünwald K, Wallner ES, Novikova DD, Levitsky VG, Agustí J, Sanchez P, Lohmann JU, Greb T
  Nature Communications
• From signals to stem cells and back again. Janocha D, Lohmann JU
  Curr. Opin. Plant Biol.
• Identification of causal dependences in gene regulatory networks using algorithmic information theory. Lohmann JU, Janzig D
  Springer Lect. Notes

2017

• Control of plant cell fate transitions by transcriptional and hormonal signals. Gaillochet C, Stiehl T, Wenzl C, Ripoll JJ, Bailey-Steinitz LJ, Pfeiffer A, Miotk A, Hakenjos J, Forner J, Yanofsky MF, Marciniack-Czochra A, Lohmann JU
  eLife
• Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells. Luís Balaguer MA, Fisher AP, Clark NM, Fernandez-Espinosa MG, Möller BK, Weijers D, Lohmann JU, Williams C, Lorenzo O, Sozzani R
  PNAS
• RETINOBLASTOMA RELATED1 mediates germline entry in Arabidopsis. Zhao X, Bramsiepe J, Van Durme M, Komaki S, Prusicki MA, Maruyama D, Forner J, Medzihradszky A, Wijnker E, Harashima H, Lu Y, Schmidt A, Guthörl D, Logroño RS, Guan Y, Pochon G, Grossniklaus U, Laux T, Higashiyama T, Lohmann JU, Nowack MK, Schnittger A
  Science
• Beyond flexibility: controlling stem cells in an ever-changing environment. Peiffer A, Wenzl C, Lohmann JU
  Curr. Opin. Plant Biol.

2016

• Integration of light and metabolic signals for stem cell activation at the shoot apical meristem. Pfeiffer A, Janocha D, Dong Y, Medzihradszky A, Schöne S, Daum G, Suzaki T, Forner J, Langenecker T, Rempel E, Schmid M, Wirtz M, Hell R, Lohmann JU
  eLife
• Plant stem cells. Greb T, Lohmann JU
  Current Biology

2015

• Job sharing in the endomembrane system: vacuolar acidification requires the combined activity of V-ATPase and V-PPase. Kriegel A, Andrés Z, Medzihradszky A, Krüger F, Scholl S, Delang S, Patir-Nebioglu MG, Gute G, Yang H, Murphy AS, Peer WA, Pfeiffer A, Krebs W, Lohmann JU, Schumacher K
  Plant Cell
• Arabidopsis HECATE genes function in phytohormone control during gynoecium and fruit development. Schuster C, Gaillochet C, Lohmann JU
  Development
• Transcriptional co-activation of cytokinin-responsive genes by DELLA proteins. Marín-de la Rosa N, Pfeiffer A, Hill K, Locascio A, Bhalerao R, Miskolczi P, Grønlund AL, Wanchoo-Kohli A, Thomas SG, Bennett MJ, Lohmann JU, Blázquez MA, Alabadí D
  PLOS Genetics
• Germline-transmitted genome editing in Arabidopsis thaliana using TAL-effector-nucleases. Forner J, Pfeiffer A, Langenecker A, Manavella P, Lohmann JU
  PLOS One
• Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Yang H, von der Fecht-Bartenbach J, Friml J, Lohmann JU, Neuhäuser B, Ludewig U
  Funct. Plant Biol.
• The never-ending story: from pluripotency to plant developmental plasticity. Gaillochet C, Lohmann JU
  Development
• O cell, where art thou? The mechanisms of shoot meristem patterning. Gaillochet C, Daum D, Lohmann JU
  Curr. Opin. Plant Biol.

2014

• A mechanistic framework of non-cell autonomous stem cell induction in Arabidopsis. Daum G, Medzihradszky A, Suzaki T, Lohmann JU
  PNAS
• Regulation of plant stem cell quiescence by a novel brassinosteroid signaling module. Vilarrasa-Blasi J, González-García M, Frigola D, Fàbregas N, Alexiou K, López-Bigas N, Rivas S, Jauneau A, Lohmann JU, Benfey PN, Ibañes M, Caño-Delgado A
  Developmental Cell
• A regulatory framework for shoot stem cell control integrating metabolic, transcriptional, and phytohormone signals. Schuster C, Gaillochet C, Medzihradszky A, Busch W, Daum G, Krebs M, Kehle A, Lohmann JU
  Developmental Cell
• Detection of mRNA expression patterns by non-radioactive in situ hybridization on histological sections of floral tissue. Medzihradszky A, Schneitz K, Lohmann JU
  Methods Mol. Biol.
• Live imaging of Arabidopsis development. von Wangenheim D, Daum G, Lohmann JU, Stelzer EK, Maizel A
  Methods Mol. Biol.

2013

• GreenGate — a novel, versatile, and efficient cloning system for plant transgenesis. Lampropoulos A, Sutikovic Z, Wenzl C, Maegele I, Lohmann JU*, Forner J
  PLOS One
• Developmental plasticity and adaptation in plants. Lohmann JU, Maizel A
  Mech. Development

2012

• Stem cells: a view from the roots. Somorjai IM, Lohmann JU, Holstein TW, Zhao Z
  Biotechnology J.

2011

• The bZIP transcription factor PERIANTHIA: a multifunctional hub for meristem control. Maier AT, Stehling-Sun S, Offenburger SL, Lohmann JU
  Front. Plant Sci.
• June bloom in Maratea. Parcy F, Lohmann JU
  Development

2010

• Hormonal control of the shoot stem cell niche. Zhao Z, Andersen SU, Ljung K, Dolezal K, Miotk A, Schultheiss SJ, Lohmann JU
  Nature
• Transcriptional regulation of a plant stem cell niche. Busch W, Miotk A, Ariel FD, Zhao Z, Forner J, Daum G, Suzaki T, Schuster C, Schultheiß SJ, Leibfried A, Haubeiß S, Ha N, Chan RL, Lohmann JU
  Developmental Cell
• Role of A-type Arabidopsis response regulators in meristem maintenance and regeneration. Buechel S, Leibfried A, To JPC, Zhao Z, Andersen SU, Kieber JJ, Lohmann JU
  Eur. J. Cell Biol.

2009

• KIRMES: Kernel-based identification of regulatory modules in euchromatic sequences. Schultheiss SJ, Busch W, Lohmann JU, Kohlbacher O, Rätsch G
  Bioinformatics
• Dual roles of the bZIP transcription factor PERIANTHIA in the control of floral architecture and homeotic gene expression. Maier AT, Stehling-Sun S, Wollmann H, Demar M, Hong RL, Haubeiß S, Weigel D, Lohmann JU
  Development
• DETORQUEO, QUIRKY, and ZERZAUST represent novel components involved in organ development mediated by the receptor-like kinase STRUBBELIG in Arabidopsis thaliana. Fulton L, Batoux M, Vaddepalli P, Yadav RK, Busch W, Andersen SU, Lohmann JU, Schneitz K
  PLOS Genetics
• Cell signaling and gene regulation. Lohmann JU, Nemhauser JL
  Curr. Opin. Plant Biol.

2008

• A quantitative and dynamic model for plant stem cell regulation. Geier F, Lohmann JU*, Gerstung M, Maier AT, Timmer J, Fleck C
  PLOS One
• DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana. Skirycz A, Radziejwoski A, Busch W, Hannah MA, Czeszejko J, Kwasniewski M, Zanor MI, Lohmann JU, De Veylder L, Witt I, Mueller-Roeber B
  Plant Journal
• Dual roles of the nuclear cap binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. Laubinger S, Sachsenberg T, Zeller G, Busch W, Lohmann JU, Rätsch G, Weigel D
  PNAS
• Reduced V-ATPase activity in the trans-Golgi network causes oxylipin-dependent hypocotyl growth inhibition. Brüx A, Liu TY, Krebs M, Stierhof YD, Lohmann JU, Miersch O, Wasternack C, Schumacher K
  Plant Cell
• Requirement of B2-type cyclin dependent kinases for meristem integrity in Arabidopsis thaliana. Andersen SU, Buechel S, Zhao Z, Ljung K, Novák O, Busch W, Schuster C, Lohmann JU
  Plant Cell
• Plant stem cells: divide et impera. Lohmann JU
  Springer (book ch.)

2007

• Distinct expression patterns of natural antisense transcripts in Arabidopsis. Henz SR, Cumbie J, Kasschau KD, Lohmann JU, Carrington JC, Weigel D, Schmid M
  Plant Physiology
• Profiling a plant: expression analysis in Arabidopsis. Busch W, Lohmann JU
  Curr. Opin. Plant Biol.

2006

• Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. Levesque MP, Vernoux T, Busch W, Cui H, Wang JY, Blilou I, Hassan H, Nakajima K, Matsumoto N, Lohmann JU, Scheres B, Benfey PN
  PLOS Biology
• Transgenic Hydra allow in vivo tracking of individual stem cells during morphogenesis in a basal metazoan. Wittlieb J, Khalturin K, Lohmann JU, Anton-Erxleben F, Bosch TCG
  PNAS

2005

• WUSCHEL controls meristem function by direct regulation of cytokinin-inducible response regulators. Leibfried A, To JPC, Stehling S, Busch W, Kehle A, Demar M, Kieber JJ, Lohmann JU
  Nature
• Integration of spatial and temporal information during floral induction in Arabidopsis. Wigge PA, Kim MC, Jaeger KE, Busch W, Schmid M, Lohmann JU, Weigel D
  Science
• A gene expression map of Arabidopsis thaliana development. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Schölkopf B, Weigel D, Lohmann JU
  Nature Genetics

2004

• From tough nuts to touch-me-nots. Lohmann JU, Weigel D
  Cell

2003

• Dissection of floral induction pathways using global expression analysis. Schmid M, Uhlenhaut NH, Godard F, Demar M, Bressan R, Weigel D, Lohmann JU
  Development

2002

• In vivo electroporation for genetic manipulations of whole Hydra polyps. Bosch TCG, Augustin R, Gellner K, Khalturin K, Lohmann JU
  Differentiation
• Building beauty — the genetic control of floral patterning. Lohmann JU, Weigel D
  Developmental Cell

2001

• A molecular link between stem cell regulation and floral patterning in Arabidopsis. Lohmann JU, Hong R, Hobe M, Busch MA, Parcy F, Simon R, Weigel D
  Cell

2000

• The novel peptide HEADY specifies apical fate in a simple radially symmetric metazoan. Lohmann JU, Bosch TCG
  Genes & Development
• Non-radioactive differential display of messenger RNA. Bosch TCG, Lohmann JU
  Humana Press

1999

• Silencing of developmental genes in Hydra. Lohmann JU, Endl I, Bosch TCG
  Dev. Biol.
• A head-activator binding protein is present in Hydra in a soluble and a membrane-anchored form. Hampe W, Urny J, Franke I, Hoffmeister-Ullerich SAH, Herrmann D, Petersen CM, Lohmann J, Schaller HC
  Development
• Head-specific gene expression in Hydra: complexity of DNA-protein interactions at the promoter of ks1 is inversely correlated to the head activation potential. Endl I, Lohmann JU, Bosch TCG
  PNAS

1997

• Systematic isolation of peptide signal molecules regulating development in Hydra: LWamide and PW families. Takahashi T, Muneoka Y, Lohmann J, de Haro M, Bosch TCG, David C, Bode H, Koizumi O, Shimizu H, Hatta M, Fujisawa T, Sugiyama T
  PNAS

1995

• REN, a rapid, efficient and non-radioactive method for differential display and isolation of mRNA. Lohmann J, Schickle HP, Bosch TCG
  BioTechniques

For older method papers (1995–1999) and additional book chapters not listed above, see the lab CV.