Challenges and prospects in the analysis of large-scale gene expression data. - Jan Ihmels; Sven Bergmann (Briefings Bioinform., 2004)

Defining transcription modules using large-scale gene expression data. - Jan Ihmels; Sven Bergmann; Naama Barkai (Bioinform., 2004)

Set-up of a Unit-Selection Synthesis with a Prominent Voice. - Stefan Breuer; Sven Bergmann; Ralf Dragon; Sebastian Möller 001 (LREC, 2006)

EuroDia: a beta-cell gene expression resource. - Robin Liechti; Gábor Csárdi; Sven Bergmann; Frédéric Schütz; Thierry Sengstag; Sylvia F. Boj; Joan-Marc Servitja; Jorge Ferrer; Leentje Van Lommel; Frans Schuit; Sonia Klinger; Bernard Thorens; et al. (Database J. Biol. Databases Curation, 2010)

Modular analysis of gene expression data with R. - Gábor Csárdi; Zoltán Kutalik; Sven Bergmann (Bioinform., 2010)

ExpressionView - an interactive viewer for modules identified in gene expression data. - Andreas Lüscher; Gábor Csárdi; Aitana Morton de Lachapelle; Zoltán Kutalik; Bastian Peter; Sven Bergmann (Bioinform., 2010)

FastEpistasis: a high performance computing solution for quantitative trait epistasis. - Thierry Schüpbach; Ioannis Xenarios; Sven Bergmann; Karen Kapur (Bioinform., 2010)

Connecting Points by Smooth Connection Functions Defines Shapes in the Smoothest Possible Way. - Alex Alon; Sven Bergmann (SHAPES, 2011)

A New Scaling Measure Quantifies the Conservation of Proportions of Gene Expression Profiles in Developing Organic Shapes. - Aitana Morton de Lachapelle; Sven Bergmann (SHAPES, 2011)

Using Transcription Modules to Identify Expression Clusters Perturbed in Williams-Beuren Syndrome. - Charlotte N. Henrichsen; Gábor Csárdi; Marie-Thérèse Zabot; Carmela Fusco; Sven Bergmann; Giuseppe Merla; Alexandre Reymond (PLoS Comput. Biol., 2011)

Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human. - Barbara Piasecka; Marc Robinson-Rechavi; Sven Bergmann (Bioinform., 2012)

Iterative Estimation of Rigid-Body Transformations - Application to Robust Object Tracking and Iterative Closest Point. - Micha Hersch; Aude Billard; Sven Bergmann (J. Math. Imaging Vis., 2012)

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. - Heinz Stockinger; Adrian M. Altenhoff; Konstantin Arnold; Amos Bairoch; Frederic B. Bastian; Sven Bergmann; Lydie Bougueleret; Philipp Bucher; Mauro Delorenzi; Lydie Lane; Philippe Le Mercier; Frédérique Lisacek; et al. (Nucleic Acids Res., 2014)

Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics. - David Lamparter 002; Daniel Marbach; Rico Rueedi; Zoltán Kutalik; Sven Bergmann (PLoS Comput. Biol., 2016)

Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility. - David Lamparter 002; Daniel Marbach; Rico Rueedi; Sven Bergmann; Zoltán Kutalik (PLoS Comput. Biol., 2017)

Metabomatching: Using genetic association to identify metabolites in proton NMR spectroscopy. - Rico Rueedi; Roger Mallol; Johannes Raffler; David Lamparter 002; Nele Friedrich; Peter Vollenweider; Gérard Waeber; Gabi Kastenmüller; Zoltán Kutalik; Sven Bergmann (PLoS Comput. Biol., 2017)

Interoperable and scalable data analysis with microservices: applications in metabolomics. - Payam Emami Khoonsari; Pablo A. Moreno; Sven Bergmann; Joachim Burman; Marco Capuccini; Matteo Carone; Marta Cascante; Pedro de Atauri; Carles Foguet; Alejandra N. González-Beltrán; Thomas Hankemeier; Kenneth Haug; et al. (Bioinform., 2019)

MONET: a toolbox integrating top-performing methods for network modularization. - Mattia Tomasoni; Sergio Gómez; Jake Crawford; Weijia Zhang 001; Sarvenaz Choobdar; Daniel Marbach; Sven Bergmann (Bioinform., 2020)

Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic labeling experiment. - Micha Hersch; Adriano Biasini; Ana C. Marques; Sven Bergmann (BMC Bioinform., 2022)

Cross-GWAS coherence test at the gene and pathway level. - Daniel Krefl; Sven Bergmann (PLoS Comput. Biol., 2022)

PascalX: a Python library for GWAS gene and pathway enrichment tests. - Daniel Krefl; Alessandro Brandulas Cammarata; Sven Bergmann (Bioinform., 2023)