Sven Rahmann
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View article: Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index
Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index Open
Motivation The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many countries have strict privacy and data protection guidelines for human sequence data, so microb…
View article: Smaller and More Flexible Cuckoo Filters
Smaller and More Flexible Cuckoo Filters Open
We provide the git repository (cuckoo-filter-git.tar.gz) which includes the code of a windowed Cuckoo filter implementation and the workflows to reproduce the results presented in the linked paper.In addition, we provide a docker file (Doc…
View article: Activation of NF‐κB Signaling by Optogenetic Clustering of IKKα and β
Activation of NF‐κB Signaling by Optogenetic Clustering of IKKα and β Open
Molecular optogenetics allows the control of molecular signaling pathways in response to light. This enables the analysis of the kinetics of signal activation and propagation in a spatially and temporally resolved manner. A key strategy fo…
View article: Integrated flexible DNA methylation-chromatin segmentation modeling enhances epigenomic state annotation
Integrated flexible DNA methylation-chromatin segmentation modeling enhances epigenomic state annotation Open
DNA methylation and histone modifications together shape the cell-type-specific epigenomic landscape. To enable a more comprehensive genome-wide annotation, we developed EpiSegMixMeth (ESMM), the first truly integrative segmentation model …
View article: Swiftly identifying strongly unique k-mers
Swiftly identifying strongly unique k-mers Open
Motivation Short DNA sequences of length k that appear in a single location (e.g., at a single genomic position, in a single species from a larger set of species, etc.) are called unique k-mers . They are useful for placing sequenced DNA f…
View article: Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index
Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index Open
Motivation The first step when working with DNA sequence data of human-derived microbiomes is usually to remove human contamination for two reasons. First, many countries have strict privacy and data protection guidelines for human sequenc…
View article: A comprehensive review and evaluation of species richness estimation
A comprehensive review and evaluation of species richness estimation Open
Motivation The statistical problem of estimating the total number of distinct species in a population (or distinct elements in a multiset), given only a small sample, occurs in various areas, ranging from the unseen species problem in ecol…
View article: Tumor Necrosis Factor‐Alpha Inhibits the Replication of Patient‐Derived Archetype BK Polyomavirus While Activating Rearranged Strains
Tumor Necrosis Factor‐Alpha Inhibits the Replication of Patient‐Derived Archetype BK Polyomavirus While Activating Rearranged Strains Open
To date, no drugs are approved for BK polyomavirus (BKPyV) reactivation, a major cause of nephropathy after kidney transplantation. Recently, tumor necrosis factor‐α (TNF‐α) blockade has been proposed as a promising therapy, however, the e…
View article: Blocked Bloom Filters with Choices
Blocked Bloom Filters with Choices Open
Probabilistic filters are approximate set membership data structures that represent a set of keys in small space, and answer set membership queries without false negative answers, but with a certain allowed false positive probability. Such…
View article: A Review and Evaluation of Species Richness Estimation
A Review and Evaluation of Species Richness Estimation Open
Motivation The statistical problem of estimating the total number of distinct species in a population (or distinct elements in a multiset), given only a small sample, occurs in various areas, ranging from the unseen species problem in ecol…
View article: Lossless Approximate Pattern Matching: Automated Design of Efficient Search Schemes
Lossless Approximate Pattern Matching: Automated Design of Efficient Search Schemes Open
This study introduces a pioneering approach to automate the creation of search schemes for lossless approximate pattern matching. Search schemes are combinatorial structures that define a series of searches over a partitioned pattern. Each…
View article: Activation of NF-κB signaling by optogenetic clustering of IKKα and β
Activation of NF-κB signaling by optogenetic clustering of IKKα and β Open
A large percentage of proteins form higher-order structures in order to fulfill their function. These structures are crucial for the precise spatial and temporal regulation of the cellular signaling network. Investigation of this network r…
View article: Mibianto: ultra-efficient online microbiome analysis through <i>k</i>-mer based metagenomics
Mibianto: ultra-efficient online microbiome analysis through <i>k</i>-mer based metagenomics Open
Quantifying microbiome species and composition from metagenomic assays is often challenging due to its time-consuming nature and computational complexity. In Bioinformatics, k-mer-based approaches were long established to expedite the anal…
View article: Three-Year Mortality of Older Hospitalized Patients with Osteosarcopenia: Data from the OsteoSys Study
Three-Year Mortality of Older Hospitalized Patients with Osteosarcopenia: Data from the OsteoSys Study Open
Osteosarcopenia, the concurrent presence of sarcopenia and osteopenia/osteoporosis, poses a significant health risk to older adults, yet its impact on clinical outcomes is not fully understood. The aim of this prospective, longitudinal mul…
View article: EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery
EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery Open
Motivation Automated chromatin segmentation based on ChIP-seq (chromatin immunoprecipitation followed by sequencing) data reveals insights into the epigenetic regulation of chromatin accessibility. Existing segmentation methods are constra…
View article: Pancreatic cancer acquires resistance to MAPK pathway inhibition by clonal expansion and adaptive DNA hypermethylation
Pancreatic cancer acquires resistance to MAPK pathway inhibition by clonal expansion and adaptive DNA hypermethylation Open
Background Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with poor prognosis. It is marked by extraordinary resistance to conventional therapies including chemotherapy and radiation, as well as to essentially all targeted…
View article: Additional file 1 of Pancreatic cancer acquires resistance to MAPK pathway inhibition by clonal expansion and adaptive DNA hypermethylation
Additional file 1 of Pancreatic cancer acquires resistance to MAPK pathway inhibition by clonal expansion and adaptive DNA hypermethylation Open
Additional file 1. Supplementary Tables 3–5, 7
View article: Design of Worst-Case-Optimal Spaced Seeds
Design of Worst-Case-Optimal Spaced Seeds Open
Read mapping (and alignment) is a fundamental problem in biological sequence analysis. For speed and computational efficiency, many popular read mappers tolerate only a few differences between the read and the corresponding part of the ref…
View article: EpiSegMix: A Flexible Distribution Hidden Markov Model with Duration Modeling for Chromatin State Discovery
EpiSegMix: A Flexible Distribution Hidden Markov Model with Duration Modeling for Chromatin State Discovery Open
Motivation Automated chromatin segmentation based on ChIP-seq data reveals insights into the epigenetic regulation of chromatin accessibility. Existing segmentation methods are constrained by simplifying modeling assumptions, which may hav…
View article: 2.3 Cancer Diagnostics and Therapy from Molecular Data
2.3 Cancer Diagnostics and Therapy from Molecular Data Open
The past decade has seen unprecedented progress in the survival chances of cancer patients as a consequence of new treatments targeting tumor-specific cellular processes, which have been uncovered by molecular genetic analyses. From a data…
View article: 2.6 Protein Complex Similarity
2.6 Protein Complex Similarity Open
Proteins have manifold functions in living cells, including structural integrity, transport, defense against pathogens, or message transmission, to name but a few. Recent advances in Machine Learning appear to have solved the protein foldi…
View article: Non-responsiveness to cardioprotection by ischaemic preconditioning in Ossabaw minipigs with genetic predisposition to, but without the phenotype of the metabolic syndrome
Non-responsiveness to cardioprotection by ischaemic preconditioning in Ossabaw minipigs with genetic predisposition to, but without the phenotype of the metabolic syndrome Open
The translation of successful preclinical and clinical proof-of-concept studies on cardioprotection to the benefit of patients with reperfused acute myocardial infarction has been difficult so far. This difficulty has been attributed to co…
View article: Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing
Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing Open
Occurrence of extra-chromosomal circular DNA is a phenomenon frequently observed in tumor cells, and the presence of such DNA has been recognized as a marker of adverse outcome across cancer types. We here describe a computational workflow…
View article: Epigenetic plasticity via adaptive DNA hypermethylation and clonal expansion underlie resistance to oncogenic pathway inhibition in pancreatic cancer
Epigenetic plasticity via adaptive DNA hypermethylation and clonal expansion underlie resistance to oncogenic pathway inhibition in pancreatic cancer Open
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with poor prognosis. Drug resistance is the major cause for therapeutic failure in PDAC patients with progressive disease. The mechanisms underlying resistance formation are c…