02/2023 - Bounding the average causal effect in Mendelian randomisation studies with multiple proposed instruments: An application to prenatal alcohol exposure and attention deficit hyperactivity disorder
Background As large-scale observational data become more available, caution regarding causal assumptions remains critically important. This may be especially true for Mendelian randomisation (MR), an increasingly popular approach. Point estimation in MR usually requires strong, often implausible homogeneity assumptions beyond the core instrumental conditions. Bounding, which does not require homogeneity assumptions, is infrequently applied in […]
01/2023 - A heuristic algorithm solving the mutual-exclusivity sorting problem
Motivation Binary (or boolean) matrices provide a common effective data representation adopted in several domains of computational biology, especially for investigating cancer and other human diseases. For instance, they are used to summarise genetic aberrations—copy number alterations or mutations—observed in cancer patient cohorts, effectively highlighting combinatorial relations among them. One of these is the tendency […]
01/2023 - An interactive web application for processing, correcting, and visualizing genome-wide pooled CRISPR-Cas9 screens
A limitation of pooled CRISPR-Cas9 screens is the high false-positive rate in detecting essential genes arising from copy-number-amplified genomics regions. To solve this issue, we previously developed CRISPRcleanR: a computational method implemented as R/python package and in a dockerized version. CRISPRcleanR detects and corrects biased responses to CRISPR-Cas9 targeting in an unsupervised fashion, accurately reducing […]
01/2023 - The molecular structure of IFT-A and IFT-B in anterograde intraflagellar transport trains
Anterograde intraflagellar transport (IFT) trains are essential for cilia assembly and maintenance. These trains are formed of 22 IFT-A and IFT-B proteins that link structural and signaling cargos to microtubule motors for import into cilia. It remains unknown how the IFT-A/-B proteins are arranged into complexes and how these complexes polymerize into functional trains. Here […]
01/2023 - Partial Identification of the Average Causal Effect in Multiple Study Populations: The Challenge of Combining Mendelian Randomization Studies
Background: Researchers often use random-effects or fixed-effects meta-analysis to combine findings from multiple study populations. However, the causal interpretation of these models is not always clear, and they do not easily translate to settings where bounds, rather than point estimates, are computed. Methods: If bounds on an average causal effect of interest in a well-defined […]
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