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Efficient graph-color compression with neighborhood-informed Bloom filters
(2017)bioRxivTechnological advancements in high throughput DNA sequencing have led to an exponential growth of sequencing data being produced and stored as a byproduct of biomedical research. Despite its public availability, a majority of this data remains inaccessible to the research com- munity through a lack efficient data representation and indexing solutions. One of the available techniques to represent read data on a more abstract level is its ...Working Paper -
Decentralized Privacy-Preserving Proximity Tracing
(2020)arXivThis document describes and analyzes a system for secure and privacy-preserving proximity tracing at large scale. This system, referred to as DP3T, provides a technological foundation to help slow the spread of SARS-CoV-2 by simplifying and accelerating the process of notifying people who might have been exposed to the virus so that they can take appropriate measures to break its transmission chain. The system aims to minimise privacy and ...Working Paper -
Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data
(2020)medRxivPathogen genomes provide insights into their evolution and epidemic spread. We sequenced 1,439 SARS-CoV-2 genomes from Switzerland, representing 3-7% of all confirmed cases per week. Using these data, we demonstrate that no one lineage became dominant, pointing against evolution towards general lower virulence. On an epidemiological level, we report no evidence of cryptic transmission before the first confirmed case. We find many early ...Working Paper -
Detection and surveillance of SARS-CoV-2 genomic variants in wastewater
(2021)medRxivThe emergence of SARS-CoV-2 mutants with altered transmissibility, virulence, or immunogenicity emphasizes the need for early detection and epidemiological surveillance of genomic variants. Wastewater samples provide an opportunity to assess circulating viral lineages in the community. We performed genomic sequencing of 122 wastewater samples from three locations in Switzerland to analyze the B.1.1.7, B.1.351, and P.1 variants of SARS-CoV-2 ...Working Paper -
Metannot: A succinct data structure for compression of colors in dynamic de Bruijn graphs
(2017)bioRxivMuch of the DNA and RNA sequencing data available is in the form of high-throughput sequencing (HTS) reads and is currently unindexed by established sequence search databases. Recent succinct data structures for indexing both reference sequences and HTS data, along with associated metadata, have been based on either hashing or graph models, but many of these structures are static in nature, and thus, not well-suited as backends for dynamic ...Working Paper -
Lineage recording reveals dynamics of cerebral organoid regionalization
(2020)bioRxivDiverse regions develop within cerebral organoids generated from human induced pluripotent stem cells (iPSCs), however it has been a challenge to understand the lineage dynamics associated with brain regionalization. Here we establish an inducible lineage recording system that couples reporter barcodes, inducible CRISPR/Cas9 scarring, and single-cell transcriptomics to analyze lineage relationships during cerebral organoid development. ...Working Paper -
In-situ and laboratory geotechnical investigations (CPTu, sediment coring) performed in Lake Lucerne (Switzerland) in 2018–2020
(2022)In the framework of an SNSF-funded SINERGIA project “Lake Tsunamis: Causes, Controls and Hazard” we performed dense geotechnical investigations along the slope-perpendicular profiles at 11 sites in Lake Lucerne, central Switzerland, where the slopes have failed in the past or might be susceptible to future failures. In total, 152 in-situ free-fall cone penetration tests with pore pressure measurement (CPTu) and laboratory analysis of 49 ...Report -
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Towards an Inclusive Future in AI
(2019)In response to the accelerating potential of artificial intelligence (AI) to transform our lives, various governments, multilateral bodies, and other organizations have produced high-level principles and guidelines for the ethical use of AI in recent years. Despite the staggering number of such documents (over 90 by October 2019), there appears to be a relatively high degree of convergence on the level of principles. «Inclusiveness» is ...Report -
psupertime: supervised pseudotime inference for single cell RNA-seq data with sequential labels
(2019)bioRxivSingle cell RNA-seq has been successfully combined with pseudotime inference methods to investigate biological processes which have sequential labels, such as time series studies of development and differentiation. Pseudotime methods developed to date ignore the labels, and where there is substantial variation in the data not associated with the labels (such as cell cycle variation or batch effects), they can fail to find relevant genes. ...Working Paper