Publications
Journal Article (11)
1.
Journal Article
24 (1), 168 (2023)
Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD. Genome Biology: Biology for the Post-Genomic Era 2.
Journal Article
24 (1), 54 (2023)
Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra. Genome Biology 3.
Journal Article
23 (1), 263 (2022)
Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation. Genome Biology 4.
Journal Article
602 (7895), pp. 142 - 147 (2022)
Petabase-scale sequence alignment catalyses viral discovery. Nature 5.
Journal Article
8 (1), 241 (2021)
Grafting vigour is associated with DNA de-methylation in eggplant. Horticulture Research 6.
Journal Article
49 (14), e83 (2021)
noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise. Nucleic Acids Research 7.
Journal Article
18 (4), pp. 366 - 368 (2021)
Sensitive protein alignments at tree-of-life scale using DIAMOND. Nature methods 8.
Journal Article
11, 606800 (2021)
How Stress Facilitates Phenotypic Innovation Through Epigenetic Diversity. Frontiers in Plant Science 9.
Journal Article
5 (50), 2170 (2020)
LTRpred: de novo annotation of intact retrotransposons. The Journal of Open Source Software 10.
Journal Article
102 (2), pp. 222 - 229 (2020)
The Earth BioGenome project: opportunities and challenges for plant genomics and conservation. The Plant Journal 11.
Journal Article
11 (12), pp. 3382 - 3392 (2019)
Becoming a Selfish Clan: Recombination Associated to Reverse-Transcription in LTR Retrotransposons. Genome Biology and Evolution Book Chapter (1)
12.
Book Chapter
2250. Springer, US (2021)
A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants. In: Methods in Molecular Biology, Vol. Meeting Abstract (1)
13.
Meeting Abstract
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)
14.
Talk
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)
15.
Talk
Diamond. Future Opportunities for Software in Research 2022, Plön, Germany (2022)
16.
Talk
Sensitive tree-of-life scale protein alignment using DIAMOND. Brazilian Webinars on Bioinformatics (2021)
Thesis - Master (1)
17.
Thesis - Master
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 (2)
18.
Preprint
Transposon dynamics in the emerging oilseed crop Thlaspi arvense. (submitted)
19.
Preprint
Sensitive clustering of protein sequences at tree-of-life scale using DIAMOND DeepClust. (submitted)