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Fabian L. M. Bernal

Publications and source records attributed to Fabian L. M. Bernal.

4 recordsLinked to original sources
arXiv2022

OncoEnrichR: cancer-dedicated gene set interpretation

Genome-scale screening experiments in cancer produce long lists of candidate genes that require extensive interpretation for biological insight and prioritization for follow-up studies. Interrogation of gene lists frequently represents a significant and time-consuming undertaking, in which experimental biologists typically combine results from a variety of bioinformatics resources in an attempt to portray and understand cancer relevance. As a means to simplify and strengthen the support for this endeavor, we have developed oncoEnrichR, a flexible bioinformatics tool that allows cancer researchers to comprehensively interrogate a given gene list along multiple facets of cancer relevance. oncoEnrichR differs from general gene set analysis frameworks through the integration of an extensive set of prior knowledge specifically relevant for cancer, including ranked gene-tumor type associations, literature-supported proto-oncogene and tumor suppressor gene annotations, target druggability data, regulatory interactions, synthetic lethality predictions, as well as prognostic associations, gene aberrations, and co-expression patterns across tumor types. The software produces a structured and user-friendly analysis report as its main output, where versions of all underlying data resources are explicitly logged, the latter being a critical component for reproducible science. We demonstrate the usefulness of oncoEnrichR through interrogation of two candidate lists from proteomic and CRISPR screens. oncoEnrichR is freely available as a web-based workflow hosted by the Galaxy platform (https://oncotools.elixir.no), and can also be accessed as a stand-alone R package (https://github.com/sigven/oncoEnrichR).

q-bio.GN↗
arXiv2020

Canted antiferromagnetism in high purity $\mathrm{NaFeF_3}$ prepared by a novel wet-chemical synthesis method

We report a novel synthesis method for, and structural and magnetic characterization of the fluoroperovskite $\mathrm{NaFeF_3}$. We have developed a wet-chemical method that allows preparation of large volumes of air-sensitive fluoroperovskites with high purity. $\mathrm{NaFeF_3}$ has a Néel temperature ($T_N$) of 90 K and a Weiss constant ($θ$) of -124 K, corresponding to dominant antiferromagnetic interactions. Below $T_N$, a slight difference is observed between zero-field and field cooled samples, indicating spin-canting and weak ferromagnetism. AC magnetometry confirms that weak ferromagnetism is inherent to $\mathrm{NaFeF_3}$ and not due to impurities. From powder neutron diffraction data, we describe the magnetic structure precisely as a weakly canted G-type (magnetic space group $Pn'ma'$). A ferromagnetic component is allowed in $Pn'ma'$, however, this component may be absent in zero magnetic fields and is too small to be confirmed on the basis of powder neutron diffraction data.

cond-mat.mtrl-sci↗
arXiv2014

Observation of the Sb2S3-type post-post-GdFeO3-perovskite: A model structure for high density ABX3 and A2X3 phases

Ten years have passed since the description of the perovskite to post-perovskite transition in MgSiO3 and its' impact on the mineralogy and rheology of the D" region at the base of the Earth's mantle. Much work has explored the mechanisms operating during this transformation and their influence on seismic response. In parallel, calculations in ABX3 systems have identified potential structures for a denser post-post-perovskite phase occurring at higher pressures. However, experiments have yet to elucidate any higher pressure form, beyond the CaIrO3-type. Here we describe the structures and transformations that lead to the crystallisation of a post-post-perovskite of Sb2S3-type in a GdFeO3-type fluoroperovskite at high pressure conditions. The use of single-crystal techniques gives unique access to the relative crystallographic orientations of all polymorphs. We use this information to extend this description to include other calculated and observed forms that are competitive in ABX3 and A2X3 stoichiometries (e.g. Sb2S3, a-Gd2S3, Be3N2) and provide substantial information on inter-relationships between these structures, which is critical to the interpretation of transition mechanisms, predicting transition sequences, to the expression of directional properties in those transformed structures when assessing their suitability to modelling e.g. their rheological response in deep-Earth and exoplanet interiors.

cond-mat.mtrl-sci↗