Publications
Journal Article (118)
1.
Journal Article
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options. Nucleic Acids Research, gkad985 (2023)
2.
Journal Article
5 (2), lqad057 (2023)
Cooperativity boosts affinity and specificity of proteins with multiple RNA-binding domains. NAR: genomics and bioinformatics 3.
Journal Article
Fast and accurate protein structure search with Foldseek. Nature Biotechnology (2023)
4.
Journal Article
78 (5), pp. 1148 - 1168 (2023)
Protease allergens as initiators–regulators of allergic inflammation. Allergy: European Journal of Allergy and Clinical Immunology 5.
Journal Article
5 (1), lqad007 (2023)
RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton. NAR: genomics and bioinformatics 6.
Journal Article
19 (6), pp. 679 - 682 (2022)
ColabFold: making protein folding accessible to all. Nature Methods 7.
Journal Article
8 (15), eabj8633 (2022)
Cln5 represents a new type of cysteine-basedS-depalmitoylase linked to neurodegeneration. Science Advances 8.
Journal Article
18 (2), e9816 (2022)
Large-scale analysis of Drosophila core promoter function using synthetic promoters. Molecular Systems Biology 9.
Journal Article
37 (19), pp. 3364 - 3366 (2021)
SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts. Bioinformatics 10.
Journal Article
37 (18), pp. 3029 - 3031 (2021)
Fast and sensitive taxonomic assignment to metagenomic contigs. Bioinformatics 11.
Journal Article
37, pp. i308 - i316 (2021)
Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins. Bioinformatics 12.
Journal Article
37 (Suppl. 1), pp. i308 - i316 (2021)
Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins. Bioinformatics 13.
Journal Article
368 (12), fnab067 (2021)
Going to extremes: A metagenomic journey into the dark matter of life. FEMS Microbiology Letters 14.
Journal Article
22, 142 (2021)
Tejaas: reverse regression increases power for detecting trans-eQTLs. Genome Biology 15.
Journal Article
3 (2), lquab026 (2021)
Bayesian Markov models improve the prediction of binding motifs beyond first order. NAR: Genomics and Bioinformatics 16.
Journal Article
10, e65381 (2021)
Evidence for additive and synergistic action of mammalian enhancers during cell fate determination. eLife 17.
Journal Article
49 (D1), pp. D298 - D308 (2021)
DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Research 18.
Journal Article
72 (1), e108 (2020)
Protein sequence analysis using the MPI Bioinformatics Toolkit. Current Protocols in Bioinformatics 19.
Journal Article
79 (6), p. 1066 (2020)
A high-throughput screen for transcription activation domains reveals their sequence features and permits prediction by deep learning (Correction). Molecular Cell 20.
Journal Article
78 (5), pp. 890 - 902.e6 (2020)
A high-throughput screen for transcription activation domains reveals their sequence features and permits prediction by deep learning. Molecular Cell 21.
Journal Article
8, 48 (2020)
MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. Microbiome 22.
Journal Article
30 (1), pp. 4 - 14 (2020)
Mechanisms for active regulation of biomolecular condensates. Trends in Cell Biology 23.
Journal Article
47 (17), pp. 8961 - 8974 (2019)
Reconstructing complex lineage trees from scRNA-seq data using MERLoT. Nucleic Acids Research 24.
Journal Article
35 (18), pp. 3517 - 3519 (2019)
PROSSTT: Probabilistic simulation of single-cell RNA-seq data for complex differentiation processes. Bioinformatics 25.
Journal Article
20 (1), 473 (2019)
HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics 26.
Journal Article
35 (16), pp. 2856 - 2858 (2019)
MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics 27.
Journal Article
10 (1), 2909 (2019)
Lysine/RNA-interactions drive and regulate biomolecular condensation. Nature Communications 28.
Journal Article
16, pp. 603 - 606 (2019)
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold. Nature Methods 29.
Journal Article
8, e47040 (2019)
Transcriptome maps of general eukaryotic RNA degradation factors. eLife 30.
Journal Article
14 (12), e1007856 (2018)
Bayesian multiple logistic regression for case-control GWAS. PLoS Genetics 31.
Journal Article
14 (11), e1006526 (2018)
Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction. PLoS Computational Biology 32.
Journal Article
430 (15), pp. 2237 - 2243 (2018)
A completely reimplemented MPI Bioinformatics Toolkit with a new HHpred server at its core. Journal of Molecular Biology 33.
Journal Article
8, 9938 (2018)
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports 34.
Journal Article
46 (W1), pp. W215 - W220 (2018)
The BaMM web server for de-novo motif discovery and regulatory sequence analysis. Nucleic Acids Research 35.
Journal Article
9, 2542 (2018)
Clustering huge protein sequence sets in linear time. Nature Communications 36.
Journal Article
35 (11), pp. 1026 - 1028 (2017)
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology 37.
Journal Article
33 (19), pp. 3113 - 3114 (2017)
WIsH: Who is the host? Predicting prokaryotic hosts from metagenomic phage contigs. Bioinformatics 38.
Journal Article
6, e25637 (2017)
RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases. eLife 39.
Journal Article
66 (1), pp. 38 - 49 (2017)
Genome-wide analysis of RNA polymerase II termination at protein-coding genes. Molecular Cell 40.
Journal Article
355 (6322), pp. 248 - 249 (2017)
Big-data approaches to protein structure prediction. Science 41.
Journal Article
45 (D1), pp. D170 - D176 (2017)
Uniclust databases of clustered and deeply annotated protein sequences and alignments. Nucleic Acids Research 42.
Journal Article
44 (13), pp. 6055 - 6069 (2016)
Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences. Nucleic Acids Research 43.
Journal Article
44 (W1), pp. W410 - W415 (2016)
The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucleic Acids Research 44.
Journal Article
32 (9), pp. 1323 - 1330 (2016)
MMseqs software suite for fast and deep clustering and searching of large protein sequence sets. Bioinformatics 45.
Journal Article
61 (2), pp. 247 - 259 (2016)
Modulations of DNA contacts by linker histones and post-translational modifications determine the mobility and modifiability of nucleosomal H3 tails. Molecular Cell 46.
Journal Article
4, e09410 (2015)
A vocabulary of ancient peptides at the origin of folded proteins. eLife 47.
Journal Article
11 (10), e1004343 (2015)
Automatic prediction of protein 3D Structures by probabilistic multi-template homology modeling. PLoS Computational Biology 48.
Journal Article
83 (10), pp. 1849 - 1858 (2015)
Structure of Ctk3, a subunit of the RNA polymerase II CTD kinase complex, reveals a non-canonical CTD-interacting domain fold. Proteins: Structure, Function, and Bioinformatics 49.
Journal Article
31 (5), pp. 674 - 681 (2015)
Context similarity scoring improves protein sequence alignments in the midnight zone. Bioinformatics 50.
Journal Article
31 (11), pp. 1729 - 1737 (2015)
bbcontacts: Prediction of β-strand pairing from direct coupling patterns. Bioinformatics