ggseqlogo: a versatile R package for drawing sequence logos

ggplot2: Elegant Graphics for Data Analysis

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The Genetics of Transcription Factor DNA Binding Variation

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An atlas of substrate specificities for the human serine/threonine kinome

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Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening

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Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning

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The intrinsic substrate specificity of the human tyrosine kinome

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Bridge RNAs direct programmable recombination of target and donor DNA

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The RNA Atlas expands the catalog of human non-coding RNAs

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CRISPR-Cas9 cytidine and adenosine base editing of splice-sites mediates highly-efficient disruption of proteins in primary and immortalized cells

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Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition

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Determining the ERK-regulated phosphoproteome driving KRAS-mutant cancer

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Viroid-like colonists of human microbiomes

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Viroid-like colonists of human microbiomes

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In Vitro Kinase-to-Phosphosite Database (iKiP-DB) Predicts Kinase Activity in Phosphoproteomic Datasets

Mari, T., Mösbauer, K., Wyler, E., Landthaler, M., Drosten, C., & Selbach, M. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00198 · Cited by 70

Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands

Solleder, M., Guillaume, P., Racle, J., Michaux, J., Pak, H.-S., Müller, M., Coukos, G., Bassani-Sternberg, M., & Gfeller, D. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir119.001641 · Cited by 68

Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus

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Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon

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Predicting antibody binders and generating synthetic antibodies using deep learning

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Meta learning addresses noisy and under-labeled data in machine learning-guided antibody engineering

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Design principles of cell-state-specific enhancers in hematopoiesis

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eIF4A2 targets developmental potency and histone H3.3 transcripts for translational control of stem cell pluripotency

Li, D., Yang, J., Huang, X., Zhou, H., & Wang, J. (2022) · Science Advances · doi:10.1126/sciadv.abm0478 · Cited by 28

Bacterial Argonaute nucleases reveal different modes of DNA targeting in vitro and in vivo

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Uncovering the temporal dynamics and regulatory networks of thermal stress response in a hyperthermophile using transcriptomics and proteomics

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Structure of mechanically activated ion channel OSCA2.3 reveals mobile elements in the transmembrane domain

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LptM promotes oxidative maturation of the lipopolysaccharide translocon by substrate binding mimicry

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Acetylation-dependent regulation of core spliceosome modulates hepatocellular carcinoma cassette exons and sensitivity to PARP inhibitors

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Cryo-EM structure of endogenous Plasmodium falciparum Pfs230 and Pfs48/45 fertilization complex

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Sequential verification of transcription by Integrator and Restrictor

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Deep Conservation of Histone Variants in Thermococcales Archaea

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NetMHCphosPan - Pan-specific prediction of MHC class I antigen presentation of phosphorylated ligands

Refsgaard, C. T., Barra, C., Peng, X., Ternette, N., & Nielsen, M. (2021) · ImmunoInformatics · doi:10.1016/j.immuno.2021.100005 · Cited by 12

Template-based modeling of insect odorant receptors outperforms AlphaFold3 for ligand binding predictions

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Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families

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The fitness cost of spurious phosphorylation

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Molecular characterization of the permanent outer-inner membrane contact site of the mitochondrial genome segregation complex in trypanosomes

Stettler, P., Schimanski, B., Aeschlimann, S., & Schneider, A. (2024) · PLOS Pathogens · doi:10.1371/journal.ppat.1012635 · Cited by 10

Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

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Unravelling the Functional Diversity of Type III Polyketide Synthases in Fungi

Sokolova, N., Denisov, S. S., Hackl, T., & Haslinger, K. (2025) · Angewandte Chemie International Edition · doi:10.1002/anie.202514786 · Cited by 9

Deciphering the landscape of phosphorylated HLA-II ligands

Solleder, M., Racle, J., Guillaume, P., Coukos, G., Bassani-Sternberg, M., & Gfeller, D. (2022) · iScience · doi:10.1016/j.isci.2022.104215 · Cited by 9

Cholesterol efflux protein, ABCA1, supports anticancer functions of myeloid immune cells

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Investigating the ability of deep learning-based structure prediction to extrapolate and/or enrich the set of antibody CDR canonical forms

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Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome ortholog mutants of Saccharomyces cerevisiae

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Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

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Evolution and phylogenetic distribution of endo -α-mannosidase

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SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes

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Molecular characterization of the archaic HLA-B∗73:01 allele reveals presentation of a unique peptidome and skewed engagement by KIR2DL2

Ross, P., Hilton, H. G., Lodwick, J., Slezak, T., Guethlein, L. A., McMurtrey, C. P., Han, A. S., Nielsen, M., Yong, D., Dulberger, C. L., et al. (2025) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2025.110542 · Cited by 1

Crystal structure and nanobodies against domain 3 of the malaria parasite fusogen Plasmodium falciparum HAP2

(2026) · doi:10.1042/bcj20250297

Molecular characterization of the permanent outer-inner membrane contact site of the mitochondrial genome segregation complex in trypanosomes

(2024) · doi:10.1101/2024.10.03.616434