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1.
Chetnik, K.* et al.: maplet: An extensible R toolbox for modular and reproducible metabolomics pipelines. Bioinformatics 38, 1168-1170 (2022)
2.
Habermann, D.* et al.: HAMdetector: A Bayesian regression model that integrates information to detect HLA-associated mutations. Bioinformatics 38, 2428-2436 (2022)
3.
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)
4.
Fröhlich, F.* et al.: AMICI: High-performance sensitivity analysis for large ordinary differential equation models. Bioinformatics 37, 3676-3677 (2021)
5.
Schmiester, L. ; Weindl, D. & Hasenauer, J.: Efficient gradient-based parameter estimation for dynamic models using qualitative data. Bioinformatics 37, 4493-4500 (2021)
6.
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)
7.
Dorigatti, E. & Schubert, B.: Joint epitope selection and spacer design for string-of-beads vaccines. Bioinformatics 36, 2, i643-i650 (2020)
8.
Haselimashhadi, H.* et al.: Soft windowing application to improve analysis of high-throughput phenotyping data. Bioinformatics 36, 1492-1500 (2020)
9.
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)
10.
Porubsky, D.* et al.: breakpointR: An R/Bioconductor package to localize strand state changes in Strand-seq data. Bioinformatics 36, 1260-1261 (2020)
11.
Schälte, Y. & Hasenauer, J.: Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation. Bioinformatics 36, 1, 551-559 (2020)
12.
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)
13.
Solovey, M. & Scialdone, A.: COMUNET: A tool to explore and visualize intercellular communication. Bioinformatics 36, 4296-4300 (2020)
14.
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)
15.
Gilly, A. et al.: Very low-depth whole-genome sequencing in complex trait association studies. Bioinformatics 35, 2555-2561 (2019)
16.
Hamad, S. et al.: HitPickV2: A web server to predict targets of chemical compounds. Bioinformatics 35, 1239-1240 (2019)
17.
Hass, H.* et al.: Benchmark problems for dynamic modeling of intracellular processes. Bioinformatics 35, 3073-3082 (2019)
18.
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)
19.
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)
20.
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)