Li, Y.* ; Hu, Q.* ; Han, S.* ; Wang-Sattler, R. ; Du, W.*
Multi-manifolds fusing hyperbolic graph network balanced by pareto optimization for identifying spatial domains of spatial transcriptomics.
Brief. Bioinform. 26:bbaf162 (2025)
Grexa, I.* ; Iván, Z.Z.* ; Migh, E.* ; Kovács, F.* ; Bolck, H.A.* ; Zheng, X.* ; Mund, A.* ; Moshkov, N.* ; Miczán, V.* ; Koos, K.* ; Horvath, P.
SuperCUT, an unsupervised multimodal image registration with deep learning for biomedical microscopy.
Brief. Bioinform. 25:bbae029 (2024)
Heylen, D.* ; Pusparum, M.* ; Kuliesius, J.* ; Wilson, J.* ; Park, Y.-C. ; Jamiołkowski, J.* ; D'Onofrio, V.* ; Valkenborg, D.* ; Aerts, J.* ; Ertaylan, G.* ; Hooyberghs, J.*
Synthetic plasma pool cohort correction for affinity-based proteomics datasets allows multiple study comparison.
Brief. Bioinform. 26:bbae657 (2024)
Zahedi, R.P.* ; Ghamsari, R.* ; Argha, A.* ; Macphillamy, C.* ; Beheshti, A.* ; Alizadehsani, R.* ; Lovell, N.H.* ; Lotfollahi, M. ; Alinejad-Rokny, H.*
Deep learning in spatially resolved transcriptfomics: A comprehensive technical view.
Brief. Bioinform. 25:bbae082 (2024)
Henao, J. ; Lauber, M.* ; Azevedo, M. ; Grekova, A. ; Theis, F.J. ; List, M.* ; Ogris, C. ; Schubert, B.
Multi-omics regulatory network inference in the presence of missing data.
Brief. Bioinform. 24:13 (2023)
Horlacher, M. ; Cantini, G. ; Hesse, J. ; Schinke, P. ; Goedert, N. ; Londhe, S. ; Moyon, L. ; Marsico, A.
A systematic benchmark of machine learning methods for protein-RNA interaction prediction.
Brief. Bioinform. 24:bbad307 (2023)
Wang, J.* ; Horlacher, M. ; Cheng, L.* ; Winther, O.*
RNA trafficking and subcellular localization-a review of mechanisms, experimental and predictive methodologies.
Brief. Bioinform. 24:14 (2023)
Han, S. ; Huang, J. ; Foppiano, F. ; Prehn, C. ; Adamski, J.* ; Suhre, K.* ; Li, Y.* ; Matullo, G.* ; Schliess, F.* ; Gieger, C. ; Peters, A. ; Wang-Sattler, R.
TIGER: Technical variation elimination for metabolomics data using ensemble learning architecture.
Brief. Bioinform. 23:bbab535 (2022)
Jeong, Y.* ; Barros De Andrade E Sousa, L. ; Thalmeier, D. ; Toth, R.* ; Ganslmeier, M.* ; Breuer, K.* ; Plass, C.* ; Lutsik, P.*
Systematic evaluation of cell-type deconvolution pipelines for sequencing-based bulk DNA methylomes.
Brief. Bioinform. 23:bbac248 (2022)
Villaverde, A.F.* ; Pathirana, D.* ; Fröhlich, F. ; Hasenauer, J.* ; Banga, J.R.*
A protocol for dynamic model calibration.
Brief. Bioinform. 23:bbab387 (2022)
Deutelmoser, H.* ; Scherer, D.* ; Brenner, H.* ; Waldenberger, M. ; Suhre, K.* ; Kastenmüller, G. ; Lorenzo Bermejo, J.*
Robust Huber-LASSO for improved prediction of protein, metabolite and gene expression levels relying on individual genotype data.
Brief. Bioinform. 22:bbaa230 (2021)
Peschel, S. ; Müller, C.L. ; von Mutius, E. ; Boulesteix, A.L.* ; Depner, M.
NetCoMi: Network construction and comparison for microbiome data in R.
Brief. Bioinform. 22, DOI: 10.1093/bib/bbaa290 (2021)
Guala, D.* ; Ogris, C. ; Müller, N.S. ; Sonnhammer, E.L.L.*
Genome-wide functional association networks: Background, data & state-of-the-art resources.
Brief. Bioinform. 21, 1224-1237 (2020)
Hoksza, D.* ; Gawron, P.* ; Ostaszewski, M.* ; Hasenauer, J. ; Schneider, R.*
Closing the gap between formats for storing layout information in systems biology.
Brief. Bioinform. 21, 1249-1260 (2020)
Hoksza, D.* ; Gawron, P.* ; Ostaszewski, M.* ; Hasenauer, J. ; Schneider, R.*
Closing the gap between formats for storing layout information in systems biology.
Brief. Bioinform. 22, 608 (2020)
Omony, J. ; Nussbaumer, T. ; Gutzat, R.*
DNA methylation analysis in plants: review of computational tools and future perspectives.
Brief. Bioinform. 21, 906-918 (2020)
Pitea, A. ; Kondofersky, I.* ; Sass, S. ; Theis, F.J. ; Müller, N.S. ; Unger, K.
Copy number aberrations from Affymetrix SNP 6.0 genotyping data-how accurate are commonly used prediction approaches?
Brief. Bioinform. 21, 272-281 (2020)
Ostaszewski, M.* ; Gebel, S.* ; Kuperstein, I.* ; Mazein, A.* ; Zinovyev, A.* ; Dogrusoz, U.* ; Hasenauer, J. ; Fleming, R.M.T.* ; Le Novère, N.* ; Gawron, P.* ; Ligon, T.* ; Niarakis, A.* ; Nickerson, D.A.* ; Weindl, D. ; Balling, R.* ; Barillot, E.* ; Auffray, C.* ; Schneider, R.*
Community-driven roadmap for integrated disease maps.
Brief. Bioinform. 20, 659-670 (2019)
Villmann, T.* ; Schleif, F.M.* ; Kostrzewa, M.* ; Walch, A.K. ; Hammer, B.*
Classification of mass-spectrometric data in clinical proteomics using learning vector quantization methods.
Brief. Bioinform. 9, 129-143 (2008)
Yuille, M.* ; van Ommen, G.J.* ; Bréchot, C.* ; Cambon-Thomsen, A.* ; Dagher, G.* ; Landegren, U.* ; Litton, J.E.* ; Pasterk, M.* ; Peltonen, L.* ; Taussig, M.* ; Wichmann, H.-E. ; Zatloukal, K.*
Biobanking for Europe.
Brief. Bioinform. 9, 14-24 (2008)
Mueller, J.C.
Linkage disequilibrium for different scales and applications.
Brief. Bioinform. 5, 1-10 (2004)
Werner, T.
The state of the art of mammalian promoter recognition.
Brief. Bioinform. 4, 22-30 (2003)
Hrabě de Angelis, M. ; Strivens, M.*
Large-scale production of mouse phenotypes : the search for animal models for inherited diseases in humans.
Brief. Bioinform. 2, 170-180 (2001)
Werner, T.
Identification and functional modelling of DNA sequence elements of transcription.
Brief. Bioinform. 1, 372-380 (2000)