Publications

Journal Article (12)

1.
Journal Article
Contreras-Garrido, A.; Galanti, D.; Movilli, A.; Becker, C.; Bossdorf, O.; Drost, H.-G.; Weigel, D.: Transposon dynamics in the emerging oilseed crop Thlaspi arvense. PLOS Genetics 20 (1), e1011141 (2024)
2.
Journal Article
Grigorjew, A.; Gynter, A.; Dias, F.; Buchfink, B.; Drost, H.-G.; Tomescu, A.: Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD. Genome Biology: Biology for the Post-Genomic Era 24 (1), 168 (2023)
3.
Journal Article
Barrera-Redondo, J.; Lotharukpong, J.; Drost, H.-G.; Coelho, S.: Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra. Genome Biology 24 (1), 54 (2023)
4.
Journal Article
Srikant, T.; Yuan, W.; Berendzen, K.; Contreras Garrido, A.; Drost, H.-G.; Schwab, R.; Weigel, D.: Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation. Genome Biology 23 (1), 263 (2022)
5.
Journal Article
Edgar, R.; Taylor, J.; Lin, V.; Altman, T.; Barbera, P.; Meleshko, T.; Lohr, D.; Novakovsky, G.; Buchfink, B.; Al-Shayeb , B. et al.; Banfield, J.; de la Peña , M.; Korobeynikov, A.; Chikhi, R.; Babaian, A.: Petabase-scale sequence alignment catalyses viral discovery. Nature 602 (7895), pp. 142 - 147 (2022)
6.
Journal Article
Cerruti, E.; Gisbert, C.; Drost, H.-G.; Valentino, D.; Valentino, D.; Portis, E.; Barchi, L.; Prohens, J.; Lanteri, S.; Comino, C. et al.; Catoni, M.: Grafting vigour is associated with DNA de-methylation in eggplant. Horticulture Research 8 (1), 241 (2021)
7.
Journal Article
Moutsopoulos, I.; Maischak, L.; Lauzikaite, E.; Vasquez Urbina, S.; Williams, E.; Drost, H.-G.; Mohorianu, I.: noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise. Nucleic Acids Research 49 (14), e83 (2021)
8.
Journal Article
Buchfink, B.; Reuter, K.; Drost, H.-G.: Sensitive protein alignments at tree-of-life scale using DIAMOND. Nature methods 18 (4), pp. 366 - 368 (2021)
9.
Journal Article
Srikant, T.; Drost, H.-G.: How Stress Facilitates Phenotypic Innovation Through Epigenetic Diversity. Frontiers in Plant Science 11, 606800 (2021)
10.
Journal Article
Drost, H.-G.: LTRpred: de novo annotation of intact retrotransposons. The Journal of Open Source Software 5 (50), 2170 (2020)
11.
Journal Article
Exposito-Alonso, M.; Drost, H.-G.; Burbano, H.; Weigel, D.: The Earth BioGenome project: opportunities and challenges for plant genomics and conservation. The Plant Journal 102 (2), pp. 222 - 229 (2020)
12.
Journal Article
Drost, H.-G.; Sanchez, D.: Becoming a Selfish Clan: Recombination Associated to Reverse-Transcription in LTR Retrotransposons. Genome Biology and Evolution 11 (12), pp. 3382 - 3392 (2019)

Book Chapter (1)

13.
Book Chapter
Benoit, M.; Drost, H.-G.: A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants. In: Methods in Molecular Biology, Vol. 2250. Springer, US (2021)

Meeting Abstract (2)

14.
Meeting Abstract
Barrera-Redondo, J.; Lotharukpong, J.; Drost, H.-G.; Coelho, S.: Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra. In SMBE 2023, pp. 385 - 386. Society for Molecular Biology and Evolution Conference 2023 (SMBE 2023), Ferrara, Italy, July 23, 2023 - July 27, 2023. (2023)
15.
Meeting Abstract
Teasdale, L.; Shirsekar, G.; Collenberg, M.; Murray, K.; Contreras Garrido, A.; van Ess, L.; Juettner, j.; Lanz, C.; Fitz, J.; Drost, H.-G. et al.; Weigel, D.: Challenges of annotating complex genes in the Arabidopsis long read genome collection. In 33rd International Conference on Arabidopsis Research (ICAR 2023), WS02-06. 33rd International Conference on Arabidopsis Research (ICAR 2023), Chiba, Japan, June 05, 2023 - June 06, 2023. (2023)

Talk (3)

16.
Talk
Drost, H.-G.: Sensitive clustering of 20 billion protein sequences at tree-of-life scale using DIAMOND2 DeepClust. Max-Planck-Campus Tübingen: Distinguished Speaker Seminar Series (DSSS), Tübingen, Germany (2023)
17.
Talk
Buchfink, B.; Reuter, K.: Diamond. Future Opportunities for Software in Research 2022, Plön, Germany (2022)
18.
Talk
Buchfink, B.: Sensitive tree-of-life scale protein alignment using DIAMOND. Brazilian Webinars on Bioinformatics (2021)

Thesis - Master (1)

19.
Thesis - Master
Behr, C.: Harnessing Protein Language Models to improve classic Local Pairwise Alignments for more sensitive and scalable Deep Homology Detection. Master, Ebherhard-Karls-Universität, Tübingen, Germany (2022)

Preprint (1)

20.
Preprint
Buchfink, B.; Ashkenazy, H.; Reuter, K.; Kennedy, J.; Drost, H.-G.: Sensitive clustering of protein sequences at tree-of-life scale using DIAMOND DeepClust. (submitted)
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