Journal Papers & Preprints

(* = corresponding author)

Selected Publications

2023

• 2023 – Adrian Contreras-Garrido, Dario Galanti, Andrea Movilli, Claude Becker, Oliver Bossdorf, Hajk-Georg Drost*, Detlef Weigel*. Transposon dynamics in the emerging oilseed crop Thlaspi arvense. bioRxiv, 2023.05.24.542068 (2023)

• 2023 – Benjamin Buchfink, Haim Ashkenazy, Klaus Reuter,  John A. Kennedy, Hajk-Georg Drost*. Sensitive clustering of protein sequences at tree-of-life scale using DIAMOND DeepClust. bioRxiv, 2023.01.24.525373 (2023).

• 2023 – Andreas Grigorjew, Artur Gynter, Fernando Dias, Benjamin Buchfink, Hajk-Georg Drost*, and Alexandru I. Tomescu*. Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD. bioRxiv, 2023.01.11.523286 (2023).

• 2023 – Josué Barrera-Redondo*, Jaruwatana Sodai Lotharukpong, Hajk-Georg Drost* and Susana M Coelho*. Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra. Genome Biology, 24:54 (2023).

2022

• 2022 – Thanvi Srikant, Wei Yuan, Kenneth Wayne Berendzen, Adrian Contreras Garrido, Hajk-Georg Drost, Rebecca Schwab, Detlef Weigel. Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation. Genome Biology, 23:263 (2022).

• 2022 – Robert C. Edgar, Jeff Taylor, Victor Lin, Tomer Altman, Pierre Barbera, DmitryMeleshko, Dan Lohr, Gherman Novakovsky, Benjamin Buchfink, Basem Al-Shayeb, Jillian F. Banfield, Marcos de la Peña, Anton Korobeynikov, Rayan Chikhi, and Artem Babaian. Petabase-scale sequence alignment catalyses viral discovery. Nature, 602, 142 – 147 (2022).
  • Media Coverage: New dangers? Computers uncover 100,000 novel viruses in old genetic data

2021

• 2021 – B Buchfink, K Reuter, HG Drost*. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nature Methods, 18, 366–368 (2021).
  • Media Coverage: Speeding up sequence alignment across the tree of life and Die Banane in uns and Google for the Tree of Life
  • Recommended by Faculty Opinion (former F1000Prime): Sensitive protein alignments at tree-of-life scale using DIAMOND

• 2021 – I Moutsopoulos, L Maischak, E Lauzikaite, SA Vasquez Urbina, Eleanor C Williams, HG Drost, II Mohorianu. noisyR: Enhancing biological signal in sequencing datasets by characterising random technical noise. Nucleic Acids Research, 49 (14), e83 (2021).

• 2021 – T Srikant and HG Drost*. How Stress Facilitates Phenotypic Innovation Through Epigenetic Diversity. Frontiers in Plant Science, 11 (2021). Article style: Hypothesis and Theory

• 2021 – M Benoit, HG Drost*. A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants. In: Cho J. (eds) Plant Transposable Elements. Methods in Molecular Biology, vol 2250. Humana, New York, NY (2021). 

• 2021 – E Cerruti, C Gisbert, HG Drost, D Valentino, E Portis, L Barchi, J Prohens, S Lanteri, C Comino, M Catoni. Epigenetic bases of grafting-induced vigour in eggplant. Horticulture Research, 8(1), 241 (2021).

2020

• 2020 – HG Drost*. LTRpred: de novo annotation of intact retrotransposons. Journal of Open Source Software, 5(50), 2170 (2020).
  • Documentation: https://hajkd.github.io/LTRpred/articles/Introduction.html

• 2020 – M Exposito-Alonso, HG Drost, HA Burbano, D Weigel. The Earth BioGenome project: Opportunities and Challenges for Plant Genomics and Conservation. The Plant Journal, 102, 222-229 (2020).

2019

• 2019 – HG Drost and DH Sanchez. Becoming a selfish clan: recombination associated to reverse-transcription in LTR retrotransposons. Genome Biology and Evolution, 11(12):3382–3392 (2019). Article style: Opinion and Perspective

• 2019 – M Benoit, HG Drost, M Catoni, Q Gouil, S Lopez-Gomollon, DC Baulcombe, J Paszkowski. Environmental and epigenetic regulation of Rider retrotransposons in tomato. PloS Genetics, 15(9): e1008370 (2019).
  • Reproducible Scripts: https://github.com/HajkD/RIDER
  • Media Coverage: Harnessing tomato jumping genes could help speed-breed drought-resistant crops; Drought stress triggers Rider retrotransposons; What do tomato plants have to do with the climate crisis?; Cambridge breakthrough in breeding drought-resistant crops; Tomato Jumping Genes Could Help Speed-breed Drought Resistant Crops

• 2019 – J Cho, M Benoit, M Catoni, HG Drost, A Brestovitsky, M Oosterbeek, and J Paszkowski. Sensitive detection of pre-integration intermediates of LTR retrotransposons in crop plants. Nature Plants, 5, 26-33 (2019).
  • Reproducible Scripts: https://github.com/HajkD/ALE

pre-2019

• 2018 – HG Drost*. Philentropy: Information Theory and Distance Quantification with R. Journal of Open Source Software, 3(26), 765 (2018).
  • Documentation: https://drostlab.github.io/philentropy/

• 2018 – A Gogleva, HG Drost, S Schornack. SecretSanta: flexible pipelines for functional secretome prediction. Bioinformatics, 34(13), 2295-2296 (2018).
  • Documentation: https://gogleva.github.io/SecretSanta/vignettes/SecretSanta-vignette.html
  • Media Coverage: SecretSanta: A new tool for deciphering the secret language of cell-to-cell communication

• 2018–HG Drost*, A Gabel, J Liu, M Quint, I Grosse. myTAI: evolutionary transcriptomics with R. Bioinformatics 34 (9), 1589-1590 (2018).
  • Documentation: https://drostlab.github.io/myTAI/

• 2017 – DH Sanchez#, H Gaubert#, HG Drost, NR Zabet, J Paszkowski. High-frequency recombination between members of an LTR retrotransposon family during transposition bursts. Nature Communications 8 (1): 1283 (2017). (# co-first)

• 2017–HG Drost* and J Paszkowski. Biomartr: genomic data retrieval with R.Bioinformatics 33(8): 1216-1217 (2017).
  • Documentation: https://ropensci.github.io/biomartr/

• 2017– H Gaubert#, DH Sanchez#, HG Drost, J Paszkowski. Developmental restriction of retrotransposition activated in Arabidopsis by environmental stress. Genetics 207 (2): 813-821 (2017). (# co-first)
  • Reproducible Scripts: https://github.com/HajkD/Gaubert_et_al_2017

• 2017 – HG Drost, P Janitza, I Grosse, M Quint. Cross-kingdom comparison of the developmental hourglass. Curr. Opinion in Genetics & Development 45, 69-75 (2017). Article style: Opinion and Perspective

• 2016–HG Drost*, J Bellstaedt, DS O‘Maoileidigh, AT Silva, A Gabel, C Weinholdt, PT Ryan, BJ Dekkers, L Bentsink, HW Hilhorst, W Ligterink, F Wellmer, I Grosse, M Quint*. Post-embryonic hourglass patterns mark ontogenetic transitions in plant development. Molecular Biology and Evolution 33 (5), 1158- 1163 (2016). (journal cover).
  • Reproducible Scripts: https://github.com/HajkD/post-embryo
  • Media Coverage: „Ich versuche, meine Umwelt zu verstehen“

• 2015 –HG Drost, A Gabel, I Grosse, M Quint. Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis. Molecular Biology and Evolution 32 (5), 1221-1231 (2015).
  • Reproducible Scripts: https://github.com/HajkD/Active-maintenance-of-phylotranscriptomic-hourglasses

• 2015 – PT Ryan#, DS O‘Maoileidigh#, HG Drost, et al. Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation. BMC Genomics 16, 488 (2015). (# co-first)

• 2013 – BJW Dekkers, S Pearce, RP van Bolderen-Veldkamp, A Marshall, P Widera, J Gilbert, HG Drost et al. Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination. Plant Physiology 163 (1), 205-215 (2013).

• 2012 – M Quint, HG Drost, A Gabel, KK Ullrich, M Boenn, I Grosse. A transcriptomic hourglass in plant embryogenesis. Nature 490 (7418), 89-101 (2012). (journal cover).
  • Additional analyses: https://github.com/HajkD/published_phylomaps
  • Media Coverage: Gewagt und gewonnen: Bachelor-Arbeit wird Nature-Story or english version

• 2012 – HG Drost*. Development of a phylogenetic transcriptome atlas of Arabidopsis thaliana embryo development. Lecture Notes in Informatics – Seminars, Vol. S-11, 175-178 (2012).