Publications and Media

@article{WOS:001673578400001,

title = {A novel approach to assessing the tracking accuracy of crop phenology  for multi-orbit and multi-feature Sentinel-1 time series},

author = {Johannes Low and Christopher Conrad and Steven Hill and Michael Thiel and Tobias Ullmann and Insa Otte},

doi = {10.1016/j.srs.2026.100370},

issn = {2666-0172},

year  = {2026},

date = {2026-06-01},

urldate = {2026-06-01},

journal = {SCIENCE OF REMOTE SENSING},

volume = {13},

keywords = {Canola, DEMMIN, DiP-ZAZIkI, InSAR coherence, Phenology, Sugar beet, Wheat},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001681509300001,

title = {Fast barcode calling based on k-mer distances},

author = {Riko Corwin Uphoff and Steffen Schuler and Ivo Grosse and Matthias Muller-Hannemann},

doi = {10.1093/pnasnexus/pgag001},

year  = {2026},

date = {2026-02-01},

urldate = {2026-02-01},

journal = {PNAS NEXUS},

volume = {5},

number = {2},

keywords = {Algorithm engineering, DiP-Hyperspace, DNA barcode calling, Spatial transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001643722100001,

title = {Machine Learning-Driven Enzyme Mining: Opportunities, Challenges, and  Future Perspectives},

author = {Felix Moorhoff and Yanzi Zhang and Sizhe Qiu and Wenjuan Dong and David Medina-Ortiz and Jing Zhao and Mehdi D. Davari},

doi = {10.1021/acscatal.5c04814},

issn = {2155-5435},

year  = {2026},

date = {2026-01-01},

urldate = {2026-01-01},

journal = {ACS CATALYSIS},

volume = {16},

number = {1},

pages = {12-30},

keywords = {Biocatalysis, DiP-BioCasNavi, Enzyme discovery, Machine learning},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001631204600001,

title = {Whole-genome resequencing of the wild barley diversity collection: a  resource for identifying and exploiting genetic variation for cultivated  barley improvement},

author = {Rebecca Spanner and Ahmad H. Sallam and Yu Guo and Murukarthick Jayakodi and Axel Himmelbach and Anne Fiebig and Jamie Simmons and Gerit Bethke and Yoonjung Lee and Luis Willian Pacheco Arge and Yinjie Qiu and Ana Badea and Michael Baum and Francois Belzile and Roi Ben-David and Robert Brueggeman and Austin Case and Luigi Cattivelli and Michael Davis and Christoph Dockter and Jaroslav Dolezel and Antonin Dreiseitl and Ryan Gavin and Lior Glick and Stephan Greiner and Ruth Hamilton and Patrick M. Hayes and Scott Heisel and Cynthia Henson and Benjamin Kilian and Takao Komatsuda and Chengdao Li and Cheng Liu and Ramamurthy Mahalingam and Maren Maruschewski and Oadi Matny and Andreas Maurer and Klaus F. X. Mayer and Itay Mayrose and Matthew Moscou and Gary J. Muehlbauer and Youko Oono and Frank Ordon and Hakan Ozkan and Ales Pecinka and Dragan Perovic and Klaus Pillen and Mohammad Pourkheirandish and Joanne Russell and Jan Safar and Silvio Salvi and Miguel Sanchez-Garcia and Kazuhiro Sato and Thomas Schmutzer and Uwe Scholz and Jeness Scott and Gurcharn Singh Brar and Kevin P. Smith and Mark E. Sorrells and Manuel Spannagl and Nils Stein and Alessandro Tondelli and Roberto Tuberosa and James Tucker and Thomas Turkington and Jan Valkoun and Ramesh Pal Singh Verma and Marcus A. Vinje and Maria Korff and Jason G. Walling and Robbie Waugh and Roger P. Wise and Brande B. H. Wulff and Shengming Yang and Guoping Zhang and Peter L. Morrell and Martin Mascher and Brian J. Steffenson},

doi = {10.1093/g3journal/jkaf261},

issn = {2160-1836},

year  = {2026},

date = {2026-01-01},

urldate = {2026-01-01},

journal = {G3-GENES GENOMES GENETICS},

volume = {16},

number = {1},

abstract = {To exploit allelic variation in Hordeum vulgare subsp. spontaneum, the 

 Wild Barley Diversity Collection was subjected to paired-end Illumina 

 sequencing at similar to 9 x depth and evaluated for several agronomic 

 traits. We discovered 240.2 million single nucleotide polymorphisms 

 (SNPs) after alignment to the Morex V3 assembly and 24.4 million short 

 (1 to 50 bp) insertions and deletions. A genome-wide association study 

 of lemma color identified one marker-trait association (MTA) on 

 chromosome 1H close to HvBlp, the cloned gene controlling black lemma. 

 Four MTAs were identified for seedling stem rust resistance, including 2 

 novel loci on chromosomes 1H and 6H and one co-locating to the complex 

 RMRL1-RMRL2 locus on 5H. The whole-genome sequence data described herein 

 will facilitate the identification and utilization of new alleles for 

 barley improvement.},

keywords = {Genomic data, Sequencing, Variant analysis},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001616552400001,

title = {Best Practices for Machine Learning-Assisted Protein Engineering},

author = {Fabio Herrera-Rocha and David Medina-Ortiz and Fabian Mauz and Juergen Pleiss and Mehdi D. Davari},

doi = {10.1021/acs.jcim.5c01983},

issn = {1549-9596},

year  = {2025},

date = {2025-12-01},

urldate = {2025-12-01},

journal = {JOURNAL OF CHEMICAL INFORMATION AND MODELING},

volume = {65},

number = {23},

pages = {12655-12667},

keywords = {DiP-LeFos, Machine learning, Optimization, Protein engineering},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001622101600001,

title = {Lipid MRI in plant science: principles and potential areas of  application},

author = {Ljudmilla Borisjuk and Thomas Neuberger and Hardy Rolletschek},

doi = {10.1093/jxb/eraf479},

issn = {0022-0957},

year  = {2025},

date = {2025-11-01},

urldate = {2025-11-01},

journal = {JOURNAL OF EXPERIMENTAL BOTANY},

keywords = {Artificial intelligence, DiP-Magdi, Lipid imaging, Magnetic resonance imaging, NMR spectroscopy, Phenotyping},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001593332300001,

title = {Tillering plasticity of drought-stressed barley genotypes under  different re-watering regimes},

author = {Sahel Soleimani and Philip Wichmann and Klaus Pillen and Kerstin Neumann and Andreas Maurer},

doi = {10.1186/s12870-025-07504-8},

issn = {1471-2229},

year  = {2025},

date = {2025-10-01},

urldate = {2025-10-01},

journal = {BMC PLANT BIOLOGY},

volume = {25},

number = {1},

abstract = {Background One future challenge of agriculture will be maintaining food 

 security in times of climate change. Future plant breeding, therefore, 

 has to account for the genotypes\' survival during drought and a good 

 recovery ability after rainfall events. We aimed at investigating the 

 re-tillering behavior of selected barley genotypes (cultivars and wild 

 barley introgression lines) in different drought and re-watering 

 scenarios, which were applied in a high-throughput phenotyping facility. 

 Re-tillering describes the activation of additional tillers after 

 post-stress irrigation. Results Twenty-three selected genotypes of the 

 barley NAM population HEB-25, along with three control genotypes, were 

 evaluated in four replicates under five distinct treatment conditions. 

 In this experiment, re-tillering was particularly pronounced in an 

 alternating watering and stress treatment, where the resumption of 

 irrigation post-stress enabled full recovery of the plants. However, it 

 was noted that while re-watering after a stress period promotes tiller 

 activation and the development of fertile ears, it also tends to 

 increase the number of sterile ears. The degree of sterile ear formation 

 varied significantly among different genotypes, highlighting the 

 critical role of genetic factors in modulating plant responses to 

 re-tillering and post-stress irrigation. It is important to note that 

 excessive re-tillering has been shown to exhibit a negative correlation 

 with fertile ear weight. Conclusions The impact of focusing on tiller 

 number and re-tillering behavior in future barley breeding may be 

 significant, particularly in the context of climate change. By selecting 

 for genotypes with appropriate tillering plasticity, breeders can 

 develop barley varieties that are more resilient to stress conditions 

 such as drought.},

keywords = {Drought tolerance, Genotype, Plant Breeding, Quantitative trait},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001574260900001,

title = {UPLC-ESI-TOF-MS Profiling of Metabolome Alterations in Barley  (Hordeum vulgare L.) Leaves Induced by Bipolaris  sorokiniana},

author = {Lisa Kurzweil and Timo D. Stark and Karina Hille and Felix Hoheneder and Jana Mrtva and Johann Hausladen and Miriam Lenk and Mohammed Saddik Motawia and Nicole Strittmatter and A. Corina Vlot and Klaus Pillen and Mette Sorensen and Birger L. Moller and Ralph Hueckelhoven and Corinna Dawid},

doi = {10.1021/acs.jafc.5c05419},

issn = {0021-8561},

year  = {2025},

date = {2025-10-01},

urldate = {2025-10-01},

journal = {JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY},

volume = {73},

number = {39},

pages = {24662-24687},

abstract = {Spot blotch of barley (Hordeum vulgare L.), caused by Bipolaris 

 sorokiniana, is responsible for major losses in crop yield. 

 Breeding-resistant barley varieties have proven to be an effective 

 countermeasure for protecting agricultural production. Plants react to 

 pathogen attacks by up-regulating secondary metabolites. Marker 

 compounds for a B. sorokiniana infection are examined by untargeted 

 UPLC-TOF-MS metabolomics and lipidomics techniques. Through the analysis 

 of nine quantitatively resistant and susceptible barley genotypes, 

 derived from the nested association mapping population HEB-25, followed 

 by structure identification experiments and spore germination assays, 57 

 metabolites are identified. In addition to previously known metabolites, 

 the unknown compounds 5-carboxydidehydroblumenol C-9-O-ss-d-glucoside 

 (46) and grasshopper ketone 3-sulfate (47) were elucidated. 

 5-Carboxyblumenol C-9-O-ss-d-glucoside (45) was described for the first 

 time in barley leaves. Pheophytin derivatives, oxylipins, 

 linolenate-conjugated lipids, and flavone glycosides were described for 

 the first time in connection with infections by phytopathogenic fungi or 

 resistance in barley.},

keywords = {Lipids, Metabolomics, MS imaging, Plant stress},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001565394900001,

title = {Integrating the landscape scale supports SAR-based detection and  assessment of the phenological development at the field level},

author = {Johannes Low and Steven Hill and Insa Otte and Christoph Friedrich and Michael Thiel and Tobias Ullmann and Christopher Conrad},

doi = {10.3389/frsen.2025.1610005},

year  = {2025},

date = {2025-08-01},

urldate = {2025-08-01},

journal = {FRONTIERS IN REMOTE SENSING},

volume = {6},

keywords = {DEMMIN, DiP-ZAZIkI, InSAR coherence, Phenology, Sentinel-1},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001513545300001,

title = {New loci and candidate genes in spring two-rowed barley detected through  meta-analysis of a field trial European network},

author = {Francesc Montardit-Tarda and Ana M. Casas and William T. B. Thomas and Florian Schnaithmann and Rajiv Sharma and Salar Shaaf and Chiara Campoli and Joanne Russell and Luke Ramsay and Micha M. Bayer and Stefano Delbono and Marko Jaaskelainen and Maitry Paul and Frederick L. Stoddard and Andrea Visioni and Andrew J. Flavell and Klaus Pillen and Benjamin Kilian and Andreas Graner and Laura Rossini and Robbie Waugh and Luigi Cattivelli and Alan H. Schulman and Alessandro Tondelli and Ernesto Igartua},

doi = {10.1007/s00122-025-04934-8},

issn = {0040-5752},

year  = {2025},

date = {2025-07-01},

urldate = {2025-07-01},

journal = {THEORETICAL AND APPLIED GENETICS},

volume = {138},

number = {7},

abstract = {Key messageA dense genome-wide meta-analysis provides new QTLs, reveals 

 breeding history trends and identifies new candidate genes for yield, 

 plant height, grain weight, and heading time of spring 

 barley.AbstractThis study contributes new knowledge on quantitative 

 trait loci (QTLs) and candidate genes for adaptive traits and yield in 

 two-rowed spring barley. A meta-analysis of a network of field trials, 

 varying in latitude and sowing date, with 151 cultivars across several 

 European countries, increased QTL detection power compared to 

 single-trial analyses. The traits analysed were heading date (HD), plant 

 height (PH), thousand-grain weight (TGW), and grain yield (GY). Breaking 

 down the analysis by the main genotype-by-environment trends revealed 

 QTLs and candidate genes specific to conditions like sowing date and 

 latitude. A historical look on the evolution of QTL frequencies revealed 

 that early selection focused on PH and TGW, likely due to their high 

 heritability. GY selection occurred later, facilitated by reduced 

 variance in other traits. The study observed that favourable alleles for 

 plant height were often fixed before those for grain yield and TGW. Some 

 regions showed linkage in repulsion, suggesting targets for future 

 breeding. Several candidate genes were identified, including known genes 

 and new candidates based on orthology with rice. Remarkably, the 

 deficiens allele of gene Vrs1 appears associated with higher GY. These 

 findings provide valuable insights for barley breeders aiming to improve 

 yield and other agronomic traits.},

keywords = {Agricultural Genetics, Drought tolerance, Genotype, Plant Breeding, Quantitative trait},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001430386400001,

title = {Profiling and Bioactivity of Polyphenols from the Omani Medicinal Plant  Terminalia dhofarica (syn. Anogeissus dhofarica)},

author = {Jonas Kappen and Luay Rashan and Katrin Franke and Ludger A. Wessjohann},

doi = {10.3390/molecules30040952},

year  = {2025},

date = {2025-02-01},

urldate = {2025-02-01},

journal = {MOLECULES},

volume = {30},

number = {4},

keywords = {Antibiotic, DiP-Hyperspace, NMR spectroscopy, Phytochemical profiling, Structure elucidation, UHPLC-HRMS},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001411678300001,

title = {A barley pan-transcriptome reveals layers of genotype-dependent  transcriptional complexity},

author = {Wenbin Guo and Miriam Schreiber and Vanda B. Marosi and Paolo Bagnaresi and Morten Egevang Jorgensen and Katarzyna B. Braune and Ken Chalmers and Brett Chapman and Viet Dang and Christoph Dockter and Anne Fiebig and Geoffrey B. Fincher and Agostino Fricano and John Fuller and Allison Haaning and Georg Haberer and Axel Himmelbach and Murukarthick Jayakodi and Yong Jia and Nadia Kamal and Peter Langridge and Chengdao Li and Qiongxian Lu and Thomas Lux and Martin Mascher and Klaus F. X. Mayer and Nicola Mccallum and Linda Milne and Gary J. Muehlbauer and Martin T. S. Nielsen and Sudharsan Padmarasu and Pai Rosager Pedas and Klaus Pillen and Curtis Pozniak and Magnus W. Rasmussen and Kazuhiro Sato and Thomas Schmutzer and Uwe Scholz and Danuta Schueler and Hana Simkova and Birgitte Skadhauge and Nils Stein and Nina W. Thomsen and Cynthia Voss and Penghao Wang and Ronja Wonneberger and Xiao-Qi Zhang and Guoping Zhang and Luigi Cattivelli and Manuel Spannagl and Micha Bayer and Craig Simpson and Runxuan Zhang and Robbie Waugh},

doi = {10.1038/s41588-024-02069-y},

issn = {1061-4036},

year  = {2025},

date = {2025-02-01},

urldate = {2025-02-01},

journal = {NATURE GENETICS},

volume = {57},

number = {2},

abstract = {A pan-transcriptome describes the transcriptional and 

 post-transcriptional consequences of genome diversity from multiple 

 individuals within a species. We developed a barley pan-transcriptome 

 using 20 inbred genotypes representing domesticated barley diversity by 

 generating and analyzing short- and long-read RNA-sequencing datasets 

 from multiple tissues. To overcome single reference bias in transcript 

 quantification, we constructed genotype-specific reference transcript 

 datasets (RTDs) and integrated these into a linear pan-genome framework 

 to create a pan-RTD, allowing transcript categorization as core, shell 

 or cloud. Focusing on the core (expressed in all genotypes), we observed 

 significant transcript abundance variation among tissues and between 

 genotypes driven partly by RNA processing, gene copy number, structural 

 rearrangements and conservation of promotor motifs. Network analyses 

 revealed conserved co-expression module::tissue correlations and 

 frequent functional diversification. To complement the 

 pan-transcriptome, we constructed a comprehensive cultivar (cv.) Morex 

 gene-expression atlas and illustrate how these combined datasets can be 

 used to guide biological inquiry.},

keywords = {Gene expression, Pan-genome, Pan-transcriptome, Plant genetics, RNA sequencing},

pubstate = {published},

tppubtype = {article}

}