Statistics of large-scale sequence searching. - Rainer Spang; Martin Vingron (Bioinform., 1998)

A new method for modeling protein evolution. - Tobias Müller 001; Rainer Spang; Martin Vingron (German Conference on Bioinformatics, 1999)

Sequence Database Search Using Jumping Alignments. - Rainer Spang; Marc Rehmsmeier; Jens Stoye (ISMB, 2000)

Sequence Database Search Using Jumping Alignments. - Constantin Bannert; Marc Rehmsmeier; Rainer Spang; Jens Stoye (German Conference on Bioinformatics, 2001)

Limits of homology detection by pairwise sequence comparison. - Rainer Spang; Martin Vingron (Bioinform., 2001)

Prediction and uncertainty in the analysis of gene expression profiles. - Rainer Spang; Carrie Blanchette; Harry Zuzan; Jeffrey R. Marks; Joseph Nevins; Mike West (Silico Biol., 2002)

A Novel Approach to Remote Homology Detection: Jumping Alignments. - Rainer Spang; Marc Rehmsmeier; Jens Stoye (J. Comput. Biol., 2002)

Finding disease specific alterations in the co-expression of genes. - Dennis Kostka; Rainer Spang (ISMB/ECCB (Supplement of Bioinformatics), 2004)

A Stochastic Downhill Search Algorithm for Estimating the Local False Discovery Rate. - Stefanie Scheid; Rainer Spang (IEEE ACM Trans. Comput. Biol. Bioinform., 2004)

Probabilistic Soft Interventions in Conditional Gaussian Networks. - Florian Markowetz; Steffen Grossmann; Rainer Spang (AISTATS, 2005)

Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data. - Claudio Lottaz; Rainer Spang (Bioinform., 2005)

Non-transcriptional pathway features reconstructed from secondary effects of RNA interference. - Florian Markowetz; Jacques Bloch; Rainer Spang (Bioinform., 2005)

twilight; a Bioconductor package for estimating the local false discovery rate. - Stefanie Scheid; Rainer Spang (Bioinform., 2005)

stam - a Bioconductor compliant R package for structured analysis of microarray data. - Claudio Lottaz; Rainer Spang (BMC Bioinform., 2005)

Permutation Filtering: A Novel Concept for Significance Analysis of Large-Scale Genomic Data. - Stefanie Scheid; Rainer Spang (RECOMB, 2006)

OrderedList - a bioconductor package for detecting similarity in ordered gene lists. - Claudio Lottaz; Xinan Yang; Stefanie Scheid; Rainer Spang (Bioinform., 2006)

Selecting normalization genes for small diagnostic microarrays. - Jochen Jaeger; Rainer Spang (BMC Bioinform., 2006)

Automated in-silico detection of cell populations in flow cytometry readouts and its application to leukemia disease monitoring. - Joern Toedling; Peter Rhein; Richard Ratei; Leonid Karawajew; Rainer Spang (BMC Bioinform., 2006)

Similarities of Ordered Gene Lists. - Xinan Yang; Stefan Bentink; Stefanie Scheid; Rainer Spang (J. Bioinform. Comput. Biol., 2006)

Nested effects models for high-dimensional phenotyping screens. - Florian Markowetz; Dennis Kostka; Olga G. Troyanskaya; Rainer Spang (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Annotation-based distance measures for patient subgroup discovery in clinical microarray studies. - Claudio Lottaz; Joern Toedling; Rainer Spang (Bioinform., 2007)

Inferring cellular networks - a review. - Florian Markowetz; Rainer Spang (BMC Bioinform., 2007)

Compensating for Unknown Confounders in Microarray Data Analysis Using Filtered Permutations. - Stefanie Scheid; Rainer Spang (J. Comput. Biol., 2007)

Analyzing gene perturbation screens with nested effects models in R and bioconductor. - Holger Fröhlich; Tim Beißbarth; Achim Tresch; Dennis Kostka; Juby Jacob; Rainer Spang; Florian Markowetz (Bioinform., 2008)

Detecting hierarchical structure in molecular characteristics of disease using transitive approximations of directed graphs. - Juby Jacob; Marcel Jentsch; Dennis Kostka; Stefan Bentink; Rainer Spang (Bioinform., 2008)

Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures. - Dennis Kostka; Rainer Spang (PLoS Comput. Biol., 2008)

ReseqChip: Automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly. - Marian Thieme; Claudio Lottaz; Harald Niederstätter; Walther Parson; Rainer Spang; Peter J. Oefner (BMC Bioinform., 2009)

Estimating classification probabilities in high-dimensional diagnostic studies. - Inka J. Appel; Wolfram Gronwald; Rainer Spang (Bioinform., 2011)

Genomic data integration using guided clustering. - Matthias Maneck; Alexandra Schrader; Dieter Kube; Rainer Spang (Bioinform., 2011)

Considering Unknown Unknowns - Reconstruction of Non-confoundable Causal Relations in Biological Networks. - Mohammad Javad Sadeh; Giusi Moffa; Rainer Spang (RECOMB, 2013)

Considering Unknown Unknowns: Reconstruction of Nonconfoundable Causal Relations in Biological Networks. - Mohammad Javad Sadeh; Giusi Moffa; Rainer Spang (J. Comput. Biol., 2013)

Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction. - Sebastian Dümcke; Johannes Bräuer; Benedict Anchang; Rainer Spang; Niko Beerenwinkel; Achim Tresch (Bioinform., 2014)

A statistical approach to virtual cellular experiments: improved causal discovery using accumulation IDA (aIDA). - Franziska Taruttis; Rainer Spang; Julia C. Engelmann (Bioinform., 2015)

Causal Modeling of Cancer-Stromal Communication Identifies PAPPA as a Novel Stroma-Secreted Factor Activating NFκB Signaling in Hepatocellular Carcinoma. - Julia C. Engelmann; Thomas Amann; Birgitta Ott-Rötzer; Margit Nützel; Yvonne Reinders; Jörg Reinders; Wolfgang E. Thasler; Theresa Kristl; Andreas Teufel; Christian G. Huber; Peter J. Oefner; Rainer Spang; et al. (PLoS Comput. Biol., 2015)

Analyzing synergistic and non-synergistic interactions in signalling pathways using Boolean Nested Effect Models. - Martin Pirkl; Elisabeth Hand; Dieter Kube; Rainer Spang (Bioinform., 2016)

Reference point insensitive molecular data analysis. - Michael Altenbuchinger; Thorsten Rehberg; Helena U. Zacharias; Frank Stämmler; K. Dettmer; D. Weber; Andreas Hiergeist; A. Gessner; E. Holler; Peter J. Oefner; Rainer Spang (Bioinform., 2017)

Molecular signatures that can be transferred across different omics platforms. - Michael Altenbuchinger; Philipp Schwarzfischer; Thorsten Rehberg; Jörg Reinders; Christian W. Kohler; Wolfram Gronwald; Julia Richter; Monika Szczepanowski; Neus Masqué-Soler; Wolfram Klapper; Peter J. Oefner; Rainer Spang (Bioinform., 2017)

Loss-Function Learning for Digital Tissue Deconvolution. - Franziska Görtler; Stefan Solbrig; Tilo Wettig; Peter J. Oefner; Rainer Spang; Michael Altenbuchinger (RECOMB, 2018)

Modelling cancer progression using Mutual Hazard Networks. - Rudolf Schill; Stefan Solbrig; Tilo Wettig; Rainer Spang (Bioinform., 2020)

Low-rank tensor methods for Markov chains with applications to tumor progression models. - Peter Georg; Lars Grasedyck; Maren Klever; Rudolf Schill; Rainer Spang; Tilo Wettig (CoRR, 2020)

Loss-Function Learning for Digital Tissue Deconvolution. - Franziska Görtler; Marian Schön; Jakob Simeth; Stefan Solbrig; Tilo Wettig; Peter J. Oefner; Rainer Spang; Michael Altenbuchinger (J. Comput. Biol., 2020)

DTD: An R Package for Digital Tissue Deconvolution. - Marian Schön; Jakob Simeth; Paul Heinrich; Franziska Görtler; Stefan Solbrig; Tilo Wettig; Peter J. Oefner; Michael Altenbuchinger; Rainer Spang (J. Comput. Biol., 2020)

BITES: balanced individual treatment effect for survival data. - Stefan Schrod; Andreas Schäfer 005; Stefan Solbrig; Robert Lohmayer; Wolfram Gronwald; Peter J. Oefner; Tim Beißbarth; Rainer Spang; Helena U. Zacharias; Michael Altenbuchinger (Bioinform., 2022)

Anomaly detection in mixed high-dimensional molecular data. - Lena Buck; Tobias Schmidt; Maren Feist; Philipp Schwarzfischer; Dieter Kube; Peter J. Oefner; Helena U. Zacharias; Michael Altenbuchinger; Katja Dettmer; Wolfram Gronwald; Rainer Spang (Bioinform., 2023)

Overcoming Observation Bias for Cancer Progression Modeling. - Rudolf Schill; Maren Klever; Andreas Lösch; Y. Linda Hu; Stefan Vocht; Kevin Rupp; Lars Grasedyck; Rainer Spang; Niko Beerenwinkel (RECOMB, 2024)

Modeling metastatic progression from cross-sectional cancer genomics data. - Kevin Rupp; Andreas Lösch; Y. Linda Hu; Chenxi Nie; Rudolf Schill; Maren Klever; Simon Pfahler; Lars Grasedyck; Tilo Wettig; Niko Beerenwinkel; Rainer Spang (Bioinform., 2024)

dabih - encrypted data storage and sharing platform. - Michael Huttner; Jakob Simeth; Renato Liguori; Fulvia Ferrazzi; Rainer Spang (CoRR, 2024)

Correcting for Observation Bias in Cancer Progression Modeling. - Rudolf Schill; Maren Klever; Andreas Lösch; Y. Linda Hu; Stefan Vocht; Kevin Rupp; Lars Grasedyck; Rainer Spang; Niko Beerenwinkel (J. Comput. Biol., 2024)

Taming numerical imprecision by adapting the KL divergence to negative probabilities. - Simon Pfahler; Peter Georg; Rudolf Schill; Maren Klever; Lars Grasedyck; Rainer Spang; Tilo Wettig (Stat. Comput., 2024)

Differentiated uniformization: a new method for inferring Markov chains on combinatorial state spaces including stochastic epidemic models. - Kevin Rupp; Rudolf Schill; Jonas Süskind; Peter Georg; Maren Klever; Andreas Lösch; Lars Grasedyck; Tilo Wettig; Rainer Spang (Comput. Stat., 2024)

Reconstructing Disease Histories in Huge Discrete State Spaces. - Rudolf Schill; Maren Klever; Kevin Rupp; Y. Linda Hu; Andreas Lösch; Peter Georg; Simon Pfahler; Stefan Vocht; Stefan Hansch; Tilo Wettig; Lars Grasedyck; Rainer Spang (Künstliche Intell., 2025)

AI in Precision Medicine. - Rainer Spang; Bernd Ludwig (Künstliche Intell., 2025)