An, Y. et al. TransFactor-Prediction of pro-viral SARS-CoV-2 host factors using a protein language model. Bioinformatics 41:btaf491 (2025) Ouologuem, S. et al. Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data. Bioinformatics 41, i314-i322 (2025) Ali, M. et al. GraphCompass: Spatial metrics for differential analyses of cell organization across conditions. Bioinformatics 40, i548-i557 (2024) Astaburuaga-García, R.* et al. RUCova: Removal of unwanted covariance in mass cytometry data. Bioinformatics 40:btae669 (2024) Dorešić, D. ; Grein, S.* & Hasenauer, J. Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data. Bioinformatics 40, i558-i566 (2024) Hagenberg, J. et al. longmixr: A tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types. Bioinformatics 40:btae137 (2024) Heumos, S.* et al. Cluster-efficient pangenome graph construction with nf-core/pangenome. Bioinformatics 40:btae609 (2024) Stock, M. ; Popp, N. ; Fiorentino, J. & Scialdone, A. Topological benchmarking of algorithms to infer Gene Regulatory Networks from Single-Cell RNA-seq Data. Bioinformatics 40:btae267 (2024) Wang, J.* ; Horlacher, M. ; Cheng, L.* & Winther, O.* DeepLocRNA: An interpretable deep learning model for predicting RNA subcellular localisation with domain-specific transfer-learning. Bioinformatics 40:btae065 (2024) Alamoudi, E.* et al. FitMultiCell: simulating and parameterizing computational models of multi-scale and multi-cellular processes. Bioinformatics 39:btad674 (2023) Hecker, D.* ; Behjati Ardakani, F.* ; Karollus, A.* ; Gagneur, J. & Schulz, M.H.* The adapted activity-by-contact model for enhancer-gene assignment and its application to single-cell data. Bioinformatics 39:btad062 (2023) Heumos, L. et al. mlf-core: A framework for deterministic machine learning. Bioinformatics 39:8 (2023) Huth, M. et al. Accessibility of covariance information creates vulnerability in Federated Learning frameworks. Bioinformatics 39:9 (2023) Kardell, O. ; Breimann, S.* & Hauck, S.M. mpwR: An R package for comparing performance of mass spectrometry-based proteomic workflows. Bioinformatics 39:3 (2023) Schälte, Y. et al. pyPESTO: A modular and scalable tool for parameter estimation for dynamic models. Bioinformatics 39:btad711 (2023) Vilov, S. & Heinig, M. DeepSom: A CNN-based approach to somatic variant calling in WGS samples without a matched normal. Bioinformatics 39:9 (2023) Weidner, L. ; Hemmler, D. ; Rychlik, M.* & Schmitt-Kopplin, P. DBDIpy: A Python library for processing of untargeted datasets from real-time plasma ionization mass spectrometry. Bioinformatics 39:2 (2023) Yuzeir, A.* et al. IntestLine: A shiny-based application to map the rolled intestinal tissue onto a line. Bioinformatics 39:2 (2023) Chetnik, K.* et al. maplet: An extensible R toolbox for modular and reproducible metabolomics pipelines. Bioinformatics 38, 1168-1170 (2022) Habermann, D.* et al. HAMdetector: A Bayesian regression model that integrates information to detect HLA-associated mutations. Bioinformatics 38, 2428-2436 (2022) Ogris, C. ; Castresana-Aguirre, M.* & Sonnhammer, E.L.L.* PathwAX II: Network-based pathway analysis with interactive visualization of network crosstalk. Bioinformatics 38, 2659-2660 (2022) Salzer, L. ; Witting, M. & Schmitt-Kopplin, P. MobilityTransformR: An R package for effective mobility transformation of CE-MS data. Bioinformatics 38, 4044-4045 (2022) Fröhlich, F.* et al. AMICI: High-performance sensitivity analysis for large ordinary differential equation models. Bioinformatics 37, 3676-3677 (2021) Schmiester, L. ; Weindl, D. & Hasenauer, J. Efficient gradient-based parameter estimation for dynamic models using qualitative data. Bioinformatics 37, 4493-4500 (2021) Angerer, P. ; Fischer, D.S. ; Theis, F.J. ; Scialdone, A. & Marr, C. Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data. Bioinformatics 36, 4291-4295 (2020) Dorigatti, E. & Schubert, B. Joint epitope selection and spacer design for string-of-beads vaccines. Bioinformatics 36, 2, i643-i650 (2020) Haselimashhadi, H.* et al. Soft windowing application to improve analysis of high-throughput phenotyping data. Bioinformatics 36, 1492-1500 (2020) Lotfollahi, M. ; Naghipourfar, M. ; Theis, F.J. & Wolf, F.A. Conditional out-of-distribution generation for unpaired data using transfer VAE. Bioinformatics 36, 2, i610-i617 (2020) Porubsky, D.* et al. breakpointR: An R/Bioconductor package to localize strand state changes in Strand-seq data. Bioinformatics 36, 1260-1261 (2020) Schälte, Y. & Hasenauer, J. Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation. Bioinformatics 36, 1, 551-559 (2020) Schmiester, L. ; Schälte, Y. ; Fröhlich, F. ; Hasenauer, J. & Weindl, D. Efficient parameterization of large-scale dynamic models based on relative measurements. Bioinformatics 36, 594-602 (2020) Solovey, M. & Scialdone, A. COMUNET: A tool to explore and visualize intercellular communication. Bioinformatics 36, 4296-4300 (2020) Do, K.T. ; Rasp, D.J.N.P. ; Kastenmüller, G. ; Suhre, K. & Krumsiek, J. MoDentify: Phenotype-driven module identification in metabolomics networks at different resolutions. Bioinformatics 35, 532-534 (2019) Gilly, A. et al. Very low-depth whole-genome sequencing in complex trait association studies. Bioinformatics 35, 2555-2561 (2019) Hamad, S. et al. HitPickV2: A web server to predict targets of chemical compounds. Bioinformatics 35, 1239-1240 (2019) Hass, H.* et al. Benchmark problems for dynamic modeling of intracellular processes. Bioinformatics 35, 3073-3082 (2019) Jeske, T. et al. DEUS: An R package for accurate small RNA profiling based on differential expression of unique sequences. Bioinformatics 35, 4834-4836 (2019) Villaverde, A.F.* ; Fröhlich, F. ; Weindl, D. ; Hasenauer, J. & Banga, J.R.* Benchmarking optimization methods for parameter estimation in large kinetic models. Bioinformatics 35, 830-838 (2019) Ballnus, B. ; Schaper, S.* ; Theis, F.J. & Hasenauer, J. Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering. Bioinformatics 34, 494-501 (2018) Klinger, E. ; Rickert, D. & Hasenauer, J. pyABC: Distributed, likelihood-free inference. Bioinformatics 34, 3591-3593 (2018) Loos, C. ; Krause, S. & Hasenauer, J. Hierarchical optimization for the efficient parametrization of ODE models. Bioinformatics 34, 4266-4273 (2018) Stapor, P. et al. PESTO: Parameter EStimation TOolbox. Bioinformatics 34, 705-707 (2018) Stapor, P. ; Fröhlich, F. & Hasenauer, J. Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis. Bioinformatics 34, 151-159 (2018) Chlis, N.-K. ; Wolf, F.A. & Theis, F.J. Model-based branching point detection in single-cell data by K-Branches clustering. Bioinformatics 33, 3211-3219 (2017) Dirmeier, S.* ; Fuchs, C. ; Müller, N.S. & Theis, F.J. netReg: Network-regularized linear models for biological association studies. Bioinformatics 34, 896-898 (2017) Fröhlich, F. ; Theis, F.J. ; Rädler, J.O.* & Hasenauer, J. Parameter estimation for dynamical systems with discrete events and logical operations. Bioinformatics 33, 1049-1056 (2017) Hastreiter, M. et al. KNIME4NGS: A comprehensive toolbox for next generation sequencing analysis. Bioinformatics 33, 1565-1567 (2017) Hilsenbeck, O.* et al. fastER: A user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy. Bioinformatics 33, 2020-2028 (2017) Jaravine, V.* ; Raffegerst, S.* ; Schendel, D.J.* & Frishman, D. Assessment of cancer and virus antigens for cross-reactivity in human tissues. Bioinformatics 33, 104-111 (2017) Kazeroonian, A. ; Theis, F.J. & Hasenauer, J. A scalable moment-closure approximation for large-scale biochemical reaction networks. Bioinformatics 33, i293-i300 (2017) Ligon, T.S.* et al. GenSSI 2.0: Multi-experiment structural identifiability analysis of SBML models. Bioinformatics 34, 1421-1423 (2017) Maier, C. ; Loos, C. & Hasenauer, J. Robust parameter estimation for dynamical systems from outlier-corrupted data. Bioinformatics 33, 1-8 (2017) Zheng, J.* et al. LD Hub: A centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis. Bioinformatics 33, 272-279 (2017) Angerer, P. et al. Destiny: Diffusion maps for large-scale single-cell data in R. Bioinformatics 32, 1241-1243 (2016) Geissen, E.M.* et al. MEMO - multi-experiment mixture model analysis of censored data. Bioinformatics 32, 2464-2472 (2016) Hross, S. & Hasenauer, J. Analysis of CFSE time-series data using division-, age- and label-structured population models. Bioinformatics 32, 2321-2329 (2016) Arnold, M. ; Raffler, J. ; Pfeufer, A. ; Suhre, K. & Kastenmüller, G. SNiPA: An interactive, genetic variant-centered annotation browser. Bioinformatics 31, 1334-1336 (2015) Haase, K.* ; Raffegerst, S.H. ; Schendel, D.J. & Frishman, D. Expitope: A web server for epitope expression. Bioinformatics 31, 1854-1856 (2015) Haghverdi, L. ; Buettner, F. & Theis, F.J. Diffusion maps for high-dimensional single-cell analysis of differentiation data. Bioinformatics 31, 2989-2998 (2015) Kim, D.K.* et al. EVpedia: A community web portal for extracellular vesicles research. Bioinformatics 31, 933-939 (2015) Matos, M.R.* ; Knapp, B. & Kaderali, L.* lpNet: A linear programming approach to reconstruct signal transduction networks. Bioinformatics 31, 3231-3233 (2015) Ocone, A. ; Haghverdi, L. ; Müller, N.S. & Theis, F.J. Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data. Bioinformatics 31, i89-i96 (2015) Petri, T.* ; Altmann, S.* ; Geistlinger, L.* ; Zimmer, R.* & Küffner, R. Addressing false discoveries in network inference. Bioinformatics 31, 2836-2843 (2015) Raue, A.* et al. Data2Dynamics: A modeling environment tailored to parameter estimation in dynamical systems. Bioinformatics 31, 3558-3560 (2015) Sass, S. ; Buettner, F. ; Müller, N.S. & Theis, F.J. RAMONA: A web application for gene set analysis on multilevel omics data. Bioinformatics 31, 128-130 (2015) Andor, N. ; Harness, J.V.* ; Müller, S.* ; Mewes, H.-W. & Petritsch, C.* EXPANDS: Expanding ploidy and allele frequency on nested subpopulations. Bioinformatics 30, 50-60 (2014) Buettner, F. ; Moignard, V.* ; Göttgens, B.* & Theis, F.J. Probabilistic PCA of censored data: Accounting for uncertainties in the visualisation of high-throughput single-cell qPCR data. Bioinformatics 30, 1867-1875 (2014) Liu, X. & Campillos, M. Unveiling new biological relationships using shared hits of chemical screening assay pairs. Bioinformatics 30, i579-i586 (2014) März, M.* et al. Challenges in RNA virus bioinformatics. Bioinformatics 30, 1793-1799 (2014) Nussbaumer, T. et al. RNASeqExpressionBrowser - a web interface to browse and visualize high-throughput expression data. Bioinformatics 30, 2519-2520 (2014) Vogt, I. ; Prinz, J. ; Worf, K.* & Campillos, M. Systematic analysis of gene properties influencing organ system phenotypes in mammalian perturbations. Bioinformatics 30, 3093-3100 (2014) Liu, X. ; Vogt, I. ; Haque, T. & Campillos, M. HitPick: A web server for hit identification and target prediction of chemical screenings. Bioinformatics 29, 1910-1912 (2013) Rivas, M.A.* et al. Assessing association between protein truncating variants and quantitative traits. Bioinformatics 29, 2419-2426 (2013) Buettner, F. & Theis, F.J. A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst. Bioinformatics 28, i626-i632 (2012) Ellwanger, D.C. ; Büttner, F.A. ; Mewes, H.-W. & Stuempflen, V. The sufficient minimal set of miRNA seed types. Bioinformatics 27, 1346-1350 (2011) Smialowski, P. ; Frishman, D. & Kramer, S.* Pitfalls of supervised feature selection. Bioinformatics 26, 440-443 (2010) Dietmann, S. ; Georgii, E.* ; Antonov, A.* ; Tsuda, K.* & Mewes, H.-W. The DICS repository: Module-assisted analysis of disease-related gene lists. Bioinformatics 25, 830-831 (2009) Georgii, E.* ; Dietmann, S. ; Uno, T.* ; Pagel, P. & Tsuda, K.* Enumeration of condition-dependent dense modules in protein interaction networks. Bioinformatics 25, 933-940 (2009) Wägele, B. et al. CRONOS: The cross-reference navigation server. Bioinformatics 25, 141-143 (2009) Kastenmüller, G. ; Gasteiger, J.* & Mewes, H.-W. An environmental perspective on large-scale genome clustering based on metabolic capabilities. Bioinformatics 24, i56-i62 (2008) Schachtner, R.* et al. Knowledge-based gene expression classification via matrix factorization. Bioinformatics 24, 1688-1697 (2008) Tetko, I.V. ; Rodchenkov, I. ; Walter, M.C. ; Rattei, T.* & Mewes, H.-W. Beyond the 'best' match: Machine learning annotation of protein sequences by integration of different sources of information. Bioinformatics 24, 621-628 (2008) Krumsiek, J. ; Arnold, R. & Rattei, T.* Gepard: A rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 23, 1026-1028 (2007) Pagel, P. ; Oesterheld, M. ; Stuempflen, V. & Frishman, D. The DIMA web resource-exploring the protein domain network. Bioinformatics 22, 997-998 (2006) Wang, Y. ; Hindemitt, T. & Mayer, K.F.X. Significant sequence similarities in promoters and precursors of Arabidopsis thaliana non-conserved microRNAs. Bioinformatics 22, 2585-2589 (2006) Arnold, R. et al. SIMAP - The similarity matrix of proteins. Bioinformatics 21, 42-46 (2005) Artamonova, I.I. ; Frishman, G. ; Gelfand, M.S.* & Frishman, D. Mining sequence annotation databanks for association patterns. Bioinformatics 21, 3, 49-57 (2005) Friedel, C.C.* et al. Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage. Bioinformatics 21, 1383-1388 (2005) Hindemitt, T. & Mayer, K.F.X. CREDO: A web-based tool for computational detection of conserved sequence motifs in noncoding sequences. Bioinformatics 21, 4304-4306 (2005) Pagel, P. et al. The MIPS mammalian protein-protein interaction database. Bioinformatics 21, 832-834 (2005) Tetko, I.V. et al. MIPS bacterial genomes functional annotation benchmark dataset. Bioinformatics 21, 2520-2521 (2005) Wahl, M.B. ; Heinzmann, U. & Imai, K. LongSAGE analysis significantly improves genome annotation: identifications of novel genes and alternative transcripts in the mouse. Bioinformatics 21, 1393-1400 (2005) Wahl, M.B. ; Heinzmann, U. & Imai, K. LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genome. Bioinformatics 21, 1389-1392 (2005) Antonov, A.V. ; Tetko, I.V. ; Mader, M.T. ; Budczies, J. & Mewes, H.-W. Optimization models for cancer classification: Extracting gene interaction information from microarray expression data. Bioinformatics 20, 644-652 (2004) Antonov, A.V. ; Tetko, I.V. ; Prokopenko, V.V.* ; Kosykh, D. & Mewes, H.-W. Web portal for classification of expression data using maximal margin linear programming. Bioinformatics 20, 3284-3285 (2004) Crass, T.* et al. The Helmholtz network for bioinformatics: An integrative web portal bioinformatics resources. Bioinformatics 20, 268-270 (2004) Müller, J.C. & Andreoli, C. Plotting haplotype-specific linkage disequilibrium patterns by extended haplotype homozygosity. Bioinformatics 19, 786-787 (2003) Wong, P.* ; Kolesov, G. ; Frishman, D. & Houry, W.A.* Phylogenetic Web Profiler. Bioinformatics 19, 782-783 (2003) Burckhardt, F. MOUSE (Mitochondrial and Other Useful SEquences) a compilation of population genetic markers. Bioinformatics 18, 890-891 (2002) Kolesov, G. ; Mewes, H.-W. & Frishman, D. SNAPper : gene order predicts gene function. Bioinformatics 18, 1017-1019 (2002) Morgenstern, B. et al. Exon discovery by genomic sequence alignment. Bioinformatics 18, 777-787 (2002) Frishman, D. et al. Functional and structural genomics using PEDANT. Bioinformatics 17, 44-57 (2001) Wjst, M. & Immervoll, T. An internet linkage and mutation database for the complex phenotype asthma. Bioinformatics 14, 827-828 (1998) Herrmann, G. ; Schön, A. ; Brack-Werner, R. & Werner, T. CONRAD: A method for identification of variable and conserved regions within proteins by scale-space filtering. Bioinformatics 12, 197-203 (1996)