PuSH - HMGU Publikationen https://push-zb.helmholtz-munich.de PuSH - Publikationen-Server des Helmholtz Zentrums München de-de <![CDATA[Moutakanni, T.* et al. Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy. PLoS Comput. Biol. 21:e1013828 (2026)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=76405&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=76405&la=de Tue, 13 Jan 2026 00:00:00 +0000 <![CDATA[Flöge, K. et al. OneProt: Towards multi-modal protein foundation models via latent space alignment of sequence, structure, binding sites and text encoders. PLoS Comput. Biol. 21:e1013679 (2025)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=75992&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=75992&la=de Fri, 14 Nov 2025 00:00:00 +0000 <![CDATA[Hedrich, N.L.* ; Schulz, E. ; Hall-McMaster, S.* & Schuck, N.W.* An inductive bias for slowly changing features in human reinforcement learning. PLoS Comput. Biol. 20, 30:e1012568 (2024)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=72534&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=72534&la=de Thu, 28 Nov 2024 00:00:00 +0000 <![CDATA[Klinger, B.* et al. Quantitative modeling of signaling in aggressive B cell lymphoma unveils conserved core network. PLoS Comput. Biol. 20:e1012488 (2024)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=71897&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=71897&la=de Mon, 04 Nov 2024 00:00:00 +0000 <![CDATA[Lang, P.F.* ; Penas, D.R.* ; Banga, J.R.* ; Weindl, D. & Novak, B.* Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells. PLoS Comput. Biol. 20:e1011151 (2024)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=69764&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=69764&la=de Tue, 16 Jan 2024 00:00:00 +0000 <![CDATA[Wang, Z.* ; Hasenauer, J. & Schälte, Y. Missing data in amortized simulation-based neural posterior estimation. PLoS Comput. Biol. 20:e1012184 (2024)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=70857&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=70857&la=de Fri, 28 Jun 2024 00:00:00 +0000 <![CDATA[Zoller, H.* ; Garcia Perez, C. ; Betel Geijo Fernández, J.* & zu Castell, W. Measuring and understanding information storage and transfer in a simulated human gut microbiome. PLoS Comput. Biol. 20:e1012359 (2024)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=71743&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=71743&la=de Tue, 29 Oct 2024 00:00:00 +0000 <![CDATA[Huang, S.* ; Alier, E. ; Kilbertus, N. & Pfister, N.* Supervised learning and model analysis with compositional data. PLoS Comput. Biol. 19:e1011240 (2023)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=68404&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=68404&la=de Wed, 18 Oct 2023 00:00:00 +0000 <![CDATA[Lakrisenko, P. et al. Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks. PLoS Comput. Biol. 19:e1010783 (2023)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=67115&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=67115&la=de Fri, 10 Mar 2023 00:00:00 +0000 <![CDATA[Roca-Martínez, J.* ; Dhondge, H.* ; Sattler, M. & Vranken, W.F.* Deciphering the RRM-RNA recognition code: A computational analysis. PLoS Comput. Biol. 19:e1010859 (2023)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=67253&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=67253&la=de Tue, 24 Jan 2023 00:00:00 +0000 <![CDATA[Simonetto, C. ; Mansmann, U.* & Kaiser, J.C. Shape-specific characterization of colorectal adenoma growth and transition to cancer with stochastic cell-based models. PLoS Comput. Biol. 19:e1010831 (2023)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=67252&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=67252&la=de Tue, 24 Jan 2023 00:00:00 +0000 <![CDATA[Ullmann, T.* ; Peschel, S. ; Finger, P.* ; Müller, C.L. & Boulesteix, A.L.* Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering. PLoS Comput. Biol. 19:e1010820 (2023)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=67183&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=67183&la=de Wed, 11 Jan 2023 00:00:00 +0000 <![CDATA[Fiorentino, J. & Scialdone, A. The role of cell geometry and cell-cell communication in gradient sensing. PLoS Comput. Biol. 18:e1009552 (2022)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=64644&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=64644&la=de Tue, 19 Jul 2022 00:00:00 +0000 <![CDATA[Schuh, L. et al. Altered expression response upon repeated gene repression in single yeast cells. PLoS Comput. Biol. 18:e1010640 (2022)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=66482&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=66482&la=de Fri, 25 Nov 2022 00:00:00 +0000 <![CDATA[Sommer, A. et al. A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota. PLoS Comput. Biol. 18:e1010044 (2022)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=65016&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=65016&la=de Thu, 09 Jun 2022 00:00:00 +0000 <![CDATA[Karollus, A.* ; Avsec, Ž.* & Gagneur, J. Predicting mean ribosome load for 5'UTR of any length using deep learning. PLoS Comput. Biol. 17, e1008982 (2021)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=64380&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=64380&la=de Thu, 24 Feb 2022 00:00:00 +0000 <![CDATA[Schmiester, L. et al. PEtab-Interoperable specification of parameter estimation problems in systems biology. PLoS Comput. Biol. 17:e1008646 (2021)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=61210&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=61210&la=de Tue, 13 Apr 2021 00:00:00 +0000 <![CDATA[Dorigatti, E. & Schubert, B. Graph-theoretical formulation of the generalized epitope-based vaccine design problem. PLoS Comput. Biol. 16:e1008237 (2020)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=60446&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=60446&la=de Fri, 06 Nov 2020 00:00:00 +0000 <![CDATA[Hager, P. ; Mewes, H.-W.* ; Rohlfs, M.* ; Klein, C.* & Jeske, T. SmartPhase: Accurate and fast phasing of heterozygous variant pairs for genetic diagnosis of rare diseases. PLoS Comput. Biol. 16:e1007613 (2020)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=58103&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=58103&la=de Fri, 28 Feb 2020 00:00:00 +0000 <![CDATA[Knauer-Arloth, J. et al. DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning. PLoS Comput. Biol. 16:e1007616 (2020)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=58031&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=58031&la=de Wed, 18 Mar 2020 00:00:00 +0000 <![CDATA[Raimundez-Alvarez, E. et al. Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines. PLoS Comput. Biol. 16:e1007147 (2020)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=58492&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=58492&la=de Tue, 24 Mar 2020 00:00:00 +0000 <![CDATA[Münch, K.* ; Münch, R.* ; Biedendieck, R.* ; Jahn, D.* & Müller, J. Evolutionary model for the unequal segregation of high copy plasmids. PLoS Comput. Biol. 15:e1006724 (2019)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=55725&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=55725&la=de Mon, 25 Mar 2019 00:00:00 +0000 <![CDATA[Blazquez-Navarro, A.* et al. Differential T cell response against BK virus regulatory and structural antigens: A viral dynamics modelling approach. PLoS Comput. Biol. 14:e1005998 (2018)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=53757&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=53757&la=de Fri, 06 Jul 2018 00:00:00 +0000 <![CDATA[Fröhlich, F. ; Kaltenbacher, B.* ; Theis, F.J. & Hasenauer, J. Scalable parameter estimation for genome-scale biochemical reaction networks. PLoS Comput. Biol. 13:e1005331 (2017)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=50368&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=50368&la=de Sat, 31 Dec 2016 00:00:00 +0000 <![CDATA[Lepik, K.* et al. C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis. PLoS Comput. Biol. 13:e1005766 (2017)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=52281&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=52281&la=de Wed, 08 Nov 2017 00:00:00 +0000 <![CDATA[Rueedi, R.* et al. Metabomatching: Using genetic association to identify metabolites in proton NMR spectroscopy. PLoS Comput. Biol. 13, e1005839:e1005839 (2017)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=52451&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=52451&la=de Mon, 04 Dec 2017 00:00:00 +0000 <![CDATA[Fröhlich, F. et al. Inference for stochastic chemical kinetics using moment equations and system size expansion. PLoS Comput. Biol. 12:e1005030 (2016)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=49150&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=49150&la=de Fri, 29 Jul 2016 00:00:00 +0000 <![CDATA[Jagiella, N. ; Müller, B.* ; Müller, M.* ; Vignon-Clementel, I.E.* & Drasdo, D.* Inferring growth control mechanisms in growing multi-cellular spheroids of NSCLC cells from spatial-temporal image data. PLoS Comput. Biol. 12:e1004412 (2016)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=47994&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=47994&la=de Mon, 29 Feb 2016 00:00:00 +0000 <![CDATA[Lechner, M.* ; Schwarz, M. ; Opitz, M.* & Frey, E.* Hierarchical post-transcriptional regulation of colicin E2 expression in Escherichia coli. PLoS Comput. Biol. 12:e1005243 (2016)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=50141&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=50141&la=de Tue, 20 Dec 2016 00:00:00 +0000 <![CDATA[Prinz, J. ; Vogt, I. ; Adornetto, G. & Campillos, M.J. A novel drug-mouse phenotypic similarity method detects molecular determinants of drug effects. PLoS Comput. Biol. 12, DOI: 10.1371/journal.pcbi.1005111 (2016)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=49699&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=49699&la=de Thu, 13 Oct 2016 00:00:00 +0000 <![CDATA[Hoffmann, T.* ; Krackhardt, A.M. & Antes, I.* Quantitative analysis of the association angle between T-cell receptor Vα/Vβ domains reveals important features for epitope recognition. PLoS Comput. Biol. 11:e1004244 (2015)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=46372&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=46372&la=de Sun, 19 Jul 2015 00:00:00 +0000 <![CDATA[Hasenauer, J. ; Hasenauer, C.* ; Hucho, T.* & Theis, F.J. ODE constrained mixture modelling: A method for unraveling subpopulation structures and dynamics. PLoS Comput. Biol. 10:e1003686 (2014)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=31729&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=31729&la=de Mon, 07 Jul 2014 00:00:00 +0000 <![CDATA[Tiedemann, H.B. et al. Fast synchronization of ultradian oscillators controlled by Delta-Notch signaling with Cis-inhibition. PLoS Comput. Biol. 10:e1003843 (2014)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=32429&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=32429&la=de Sat, 04 Oct 2014 00:00:00 +0000 <![CDATA[Poos, K.* et al. How microRNA and transcription factor co-regulatory networks affect osteosarcoma cell proliferation. PLoS Comput. Biol. 9:e1003210 (2013)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=27493&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=27493&la=de Thu, 26 Sep 2013 00:00:00 +0000 <![CDATA[Tyanova, S.* ; Cox, J.* ; Olsen, J.* ; Mann, M.* & Frishman, D. Phosphorylation variation during the cell cycle scales with structural propensities of proteins. PLoS Comput. Biol. 9:e1002842 (2013)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=23160&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=23160&la=de Thu, 07 Mar 2013 00:00:00 +0000 <![CDATA[Tiedemann, H.B. et al. From dynamic expression patterns to boundary formation in the presomitic mesoderm. PLoS Comput. Biol. 8:e1002586 (2012)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=8183&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=8183&la=de Wed, 25 Jul 2012 00:00:00 +0000 <![CDATA[Kowarsch, A. ; Fuchs, A.* ; Frishman, D. & Pagel, P. Correlated mutations: A hallmark of phenotypic amino acid substitutions. PLoS Comput. Biol. 6:e1000923 (2010)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=5753&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=5753&la=de Fri, 08 Oct 2010 00:00:00 +0000 <![CDATA[Marr, C. ; Theis, F.J. ; Liebovitch, L.S.* & Hütt, M.-T.* Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli. PLoS Comput. Biol. 6, 31:e1000836 (2010)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=5933&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=5933&la=de Wed, 20 Oct 2010 00:00:00 +0000 <![CDATA[Klamt, S.* ; Haus, U.-U.* & Theis, F.J. Hypergraphs and cellular networks. PLoS Comput. Biol. 5:e1000385 (2009)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=1606&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=1606&la=de Thu, 31 Dec 2009 00:00:00 +0000 <![CDATA[Wittmann, D.M. et al. Spatial analysis of expression patterns predicts genetic interactions at the mid-hindbrain boundary. PLoS Comput. Biol. 5:e1000569 (2009)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=1438&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=1438&la=de Thu, 31 Dec 2009 00:00:00 +0000 <![CDATA[Tetko, I.V. et al. Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana. PLoS Comput. Biol. 2, 136-145:e21 (2006)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=468&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=468&la=de Fri, 13 Oct 2006 00:00:00 +0000 <![CDATA[Wong, P. & Frishman, D. Fold designability, distribution and disease. PLoS Comput. Biol. 2, 392-402:e40 (2006)]]> https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=5750&la=de https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=5750&la=de Thu, 14 Dec 2006 00:00:00 +0000