Biology subjects

Muller, S.

Publications and source records attributed to Muller, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Nodule organogenesis in Medicago truncatula requires local stage-specific auxin biosynthesis and transport

The importance of auxin in plant organ development including root nodule formation is well established. Using auxin reporter constructs the spatiotemporal auxin distribution pattern during nodule development has previously been illustrated. However, our understanding of how this pattern is built-up and maintained still remains elusive. To this end, we studied how the auxin gradient visualized by DR5 expression patterns at different stages of nodule development in Medicago truncatula (Medicago), is correlated with the spatiotemporal expression patterns of known auxin biosynthesis and auxin transport genes. In addition, we record the MtPIN10-GFP expression pattern and polar positioning on the cell plasma membranes during nodule primordium development to investigate the auxin flux. RNA interference and the application of auxin synthesis blockers were used to demonstrate the relevance of biosynthesis and transport at the initial stages of the nodulation process. Our results show that upon rhizobium inoculation, preceding the first mitotic activity, a specific set of MtYUCs and MtPINs as well as MtLAX2 are expressed in the pericycle contributing to the creation of an auxin maximum. Overall, we demonstrate that dynamic spatiotemporal expression of both, MtYUCs and MtPINs, result in specific auxin outputs in subsequent stages of nodule primordia and nodule meristem formation.

plant biology↗

bioRxiv2023

Acute effects of psilocybin on the dynamics of gaze fixations during visual aesthetic perception

RationaleSerotonergic psychedelics are remarkable for their capacity to induce variable yet reproducible modifications to human consciousness The most salient acute effects of these compounds include perceptual alterations, predominantly in the visual domain, yet to date these alterations have been mostly documented only by subjective reports. ObjectivesWe used eye-tracking to quantify the effects of low vs. high doses of psilocybin mushrooms on the eye movements that underlie the exploration of complex visual stimuli, focusing on the particular case of aesthetic perception. ResultsFollowing a double-blind placebo-controlled design under semi-naturalistic conditions, we demonstrated that high doses of psilocybin result in a more local visual exploration of paintings, and thus in a less entropic fixation probability distribution. Participants reported heightened emotional response and state of flow under the high dose condition. ConclusionsThese findings are consistent with an effect of psilocybin on gaze fixation mediated by altered perception of low-level visual information, such as textures, shapes and colors. Our work also highlights the possibility of investigating psychedelics by addressing their effect on behavior under complex naturalistic conditions, which contributes to maintaining subject engagement while also increasing the ecological validity of the findings.

animal behavior and cognition↗

bioRxiv2023

eNODAL: an experimentally guided nutriomics data clustering method to unravel complex drug-diet interactions

Unraveling the complex interplay between nutrients and drugs via their effects on omics features could revolutionize our fundamental understanding of nutritional physiology, personalized nutrition and ultimately human health-span. Experimental studies in nutrition are starting to use large-scale omics experiments to pick apart the effects of such interacting factors. However, the high dimensionality of the omics features, coupled with complex fully-factorial experimental designs together pose a challenge to the analysis. Current strategies for analyzing such types of data are based on between-feature correlations. However, these techniques risk overlooking important signals that arise from the experimental design and produce clusters that are hard to interpret. We present a novel approach for analyzing high-dimensional outcomes in nutriomics experiments, termed experiment-guided NutriOmics DatA cLustering (eNODAL). This three-step hybrid framework takes advantage of both ANOVA-type analyses and unsupervised learning methods to extract maximum information from experimental nutriomics studies. First, eNODAL categorizes the omics features into interpretable groups based on the significance of response to the different experimental variables using an ANOVA-like test. Such groups may include the main effects of a nutritional intervention, and drug exposure, or their interaction. Second, consensus clustering is performed within each interpretable group to further identify subclusters of features with similar response profiles to these experimental factors. Third, eNODAL annotates these subclusters based on their experimental responses and biological pathways enriched within the subcluster. We validate eNODAL using data from a mouse experiment to test for the interaction effects of macronutrient intake and drugs that target aging mechanisms in mice.

bioinformatics↗

bioRxiv2023

"Candidatus Siderophilus nitratireducens": a psychrophilic, nap-dependent nitrate-reducing iron oxidizer within the new order Siderophiliales

Nitrate leaching from agricultural soils is increasingly found in groundwater, a primary source of drinking water worldwide. This nitrate influx can potentially stimulate the biological oxidation of iron in anoxic groundwater reservoirs. Nitrate-reducing iron-oxidizing (NRFO) bacteria have been extensively studied in laboratory settings, yet their ecophysiology in natural environments remains largely unknown. To this end, we established a pilot-scale filter on nitrate-rich groundwater to elucidate the structure and metabolism of nitrate-reducing iron-oxidizing microbiomes under oligotrophic conditions mimicking natural groundwaters. The enriched community stoichiometrically removed iron and nitrate consistently with NRFO metabolism. Genome-resolved metagenomics revealed the underlying metabolic network between the dominant iron-dependent denitrifying autotrophs and the less abundant organoheterotrophs. The most abundant genome belonged to a new Candidate order, named Siderophiliales. This new species, "Candidatus Siderophilus nitratireducens", carries central genes to iron oxidation (cytochrome c cyc2), carbon fixation (rbc), and for the sole periplasmic nitrate reductase (nap). To our knowledge, this is the first report of nap-based lithoautotrophic growth, and we demonstrate that iron oxidation coupled to dissimilatory reduction of nitrate to nitrite is thermodynamically favourable under realistic Fe3+/Fe2+ and [Formula] concentration ratios. Ultimately, by bridging the gap between laboratory investigations and real-world conditions, this study provides insights into the intricate interplay between nitrate and iron in groundwater ecosystems, and expands our understanding of NRFOs taxonomic diversity and ecological role.

microbiology↗

bioRxiv2023

Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria

Each genome encodes some codons more frequently than their synonyms (codon usage bias), but codons are also arranged more frequently into specific pairs (codon pair bias). Recoding viral genomes and yeast or bacterial genes with non-optimal codon pairs has been shown to decrease gene expression. Gene expression is thus importantly regulated not only by the use of particular codons but by their proper juxtaposition. We therefore hypothesized that non-optimal codon pairing could likewise attenuate Mtb genes. We explored the role of codon pair bias by recoding Mtb genes (rpoB, mmpL3, ndh) and assessing their expression in the closely related and tractable model organism M. smegmatis. To our surprise, recoding caused the expression of multiple smaller protein isoforms from all three genes. We confirmed that these smaller proteins were not due to protein degradation, but instead issued from new transcription initiation sites positioned within the open reading frame. New transcripts gave rise to intragenic translation initiation sites, which in turn led to the expression of smaller proteins. We next identified the nucleotide changes associated with these new sites of transcription and translation. Our results demonstrated that apparently benign, synonymous changes can drastically alter gene expression in mycobacteria. More generally, our work expands our understanding of the codon-level parameters that control translation and transcription initiation. IMPORTANCEMycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, one of the deadliest infectious diseases worldwide. Previous studies have established that synonymous recoding to introduce rare codon pairings can attenuate viral pathogens. We hypothesized that non-optimal codon pairing could be an effective strategy for attenuating gene expression to create a live vaccine for Mtb. We instead discovered that these synonymous changes enabled the transcription of functional mRNA that initiated in the middle of the open reading frame and from which many smaller protein products were expressed. To our knowledge, this is the first report that synonymous recoding of a gene in any organism can create or induce intragenic transcription start sites.

molecular biology↗

bioRxiv2022

Meta-omics profiling of full-scale groundwater rapid sand filters explains stratification of iron, ammonium and manganese removals

Rapid sand filters (RSF) are an established and widely applied technology for groundwater treatment. Yet, the underlying interwoven biological and physical-chemical reactions controlling the sequential removal of iron, ammonia and manganese remain poorly understood. To resolve the contribution and interactions between the individual reactions, we studied two full-scale drinking water treatment plant configurations, namely (i) one dual-media (anthracite and quartz sand) filter and (ii) two single-media (quartz sand) filters in series. In situ and ex situ activity tests were combined with mineral coating characterization and metagenome-guided metaproteomics along the depth of each filter. Both plants exhibited comparable performances and process compartmentalization, with most of ammonium and manganese removal occurring only after complete iron depletion. Within each compartment, the homogeneity of the media coating and genome-based microbial composition highlighted the effect of backwashing on filter media mixing. In stark contrast, intra-compartment contaminant removal was highly stratified following decreasing substrate availability along the filter height. This apparent and long-standing conflict was resolved by quantifying the expressed proteome at different filter heights, revealing a consistent stratification of proteins catalysing ammonia oxidation and protein-based relative abundances of nitrifying genera. This implies that microorganisms adapt their protein pool to the available nutrient load at a faster rate than the backwash mixing frequency. Ultimately, these results show the unique and complementary potential of metaproteomics to understand metabolic adaptations and interactions in highly dynamic ecosystems.

microbiology↗

bioRxiv2022

Origin, exposure routes and xenobiotics impart nanoplastics with toxicity on freshwater bivalves

Various environmental aged plastic wastes were collected in the environment and crushed to the nanometric scale to get a mix of nanoplastics (NPs) of different natures - mostly polyolefins (PE, PP), polyesters (PET) and polyvinylics (PS and PVC) - and undefined shapes (noted NP-L, mean hydrodynamic diameter at 285 nm). We aimed to test the toxicity of NPs of environmentally relevance on freshwater bivalves and compare results to commonly used styrenic NP-PS (206 nm). Corbicula fluminea were exposed to four different conditions with NPs (0.008 to 10 g/L), for 21 days and kept under depuration conditions for 21 additional days: 1) waterborne exposure to NP-L, 2) diet borne exposure to NP-L, 3) synergic waterborne exposure to NP-L and AlCl3 salt (1 mg/L), 4) waterborne exposure to NP-PS. Enzyme activities, gene expressions and behavioural tests were assessed. Trophic and synergic exposures with Al triggered more gene modulations than direct exposure to NP-L (namely on 12s, atg12, gal, segpx, p53 and ache). NP-PS were also more harmful than NP-L, but only at high concentrations (10 g/L). The effects of each treatment lasted until 7 days of depuration and no more gene inductions were observed after 21 days in clean water. Very few effects were shown on phenol-oxidase (PO), and glutathione S-transferase (GST). However, the inhibition of acetylcholinesterase (AchE) was concomitant with an increase of the filtration activity of bivalves exposed to NP-L (trophic route) and NP-PS, suggesting neurotoxic effects. By disturbing the ventilatory activity, NPs could have direct effects on xenobiotic accumulation and excretion capacities. The results point out how the structure, aging, exposure routes and additional xenobiotics can interact with adverse outcomes of NPs in bivalves. These findings underline the importance to consider naturally aged environmental NPs in ecotoxicological studies rather than synthetic latexes, i.e. crosslinked nanospheres prepared from virgin polymers. This manuscript presents the first data of toxicity on freshwater organisms exposed to nanoplastics coming from natural sources. Whereas the majority of papers are dealing with non-environmentally representative plastics (mainly commercially-available polystyrene latexes) to evaluate nanoplastic effects on organisms, this study develops methods to prepare model nanoplastics from plastic wastes collected in rivers, and to assess their real adverse effects on aquatic organisms. Our results show significant differences between the inflammatory effects triggered by nanoplastics coming from natural sources and polystyrene nanobeads. This work suggests that the data published so far in the literature may underestimate the toxicity of nanoplastics spread into the environment on the aquatic organisms at the bottom of the food chain, which might consequently impart halieutic resources on the long term.

pharmacology and toxicology↗

bioRxiv2022

Mapping the landscape of genetic dependencies in chordoma

Identifying the spectrum of genes required for cancer cell survival can reveal essential cancer circuitry and therapeutic targets, but such a map remains incomplete for many cancer types. We applied genome-scale CRISPR-Cas9 loss-of-function screens to map the landscape of selectively essential genes in chordoma, a bone cancer with few validated targets. This approach confirmed a known chordoma dependency, TBXT (T; brachyury), and identified a range of additional dependencies, including PTPN11, ADAR, PRKRA, LUC7L2, SRRM2, SLC2A1, SLC7A5, FANCM, and THAP1. CDK6, SOX9, and EGFR, genes previously implicated in chordoma biology, were also recovered. We found genomic and transcriptomic features that predict specific dependencies, including interferon-stimulated gene expression, which correlates with ADAR dependence and is elevated in chordoma. Validating the therapeutic relevance of dependencies, small-molecule inhibitors of SHP2, encoded by PTPN11, had potent preclinical efficacy against chordoma. Our results generate an emerging map of chordoma dependencies to enable biological and therapeutic hypotheses.

cancer biology↗

bioRxiv2022

HSPA8 chaperone complex drives chaperone-mediated autophagy regulation in acute promyelocytic leukemia differentiation

Acute myeloid leukemia (AML) is a cancer of the hematopoietic system characterized by the hyperproliferation of undifferentiated cells of the myeloid lineage. While most of AML therapy are focusing on tumor debulking, all-trans retinoic acid (ATRA) induces differentiation in acute promeylocytic leukemia (APL) a particular subtype. Macroautophagy has been extensively investigated in the context of various cancers and is often dysregulated in AML where it can have context-dependent pro- or anti-leukemogenic effects. On the contrary, the implications of chaperone-mediated autophagy (CMA) on the pathophysiology of diseases are still being explored and its role in AML has remained elusive. To answer our questions we took advantages of human AML primary samples and databases. Furthermore, we used ATRA-sensitive (NB4) and -resistant (NB4-R1) cells to further dissect a potential function for CMA in ATRA-mediated neutrophil differentiation. NB4-R1 cells are unique in that they do respond to retinoic acid transcriptionally, but do not mature in response to retinoid signaling alone unless maturation is triggered by adding cAMP. Here, we report that CMA related mRNA transcripts are higher expressed in immature hematopoietic cells as compared to neutrophils. In line, lysosomal degradation of mCherry-KFERQ CMA reporter decreases during ATRA-induced differentiation of APL cells. On the other hand, using NB4-R1 cells we found that macroautophagy flux primed the ATRA resistant NB4-R1 cells to differentiate upon ATRA treatment, but reduced association of LAMP-2A and HSPA8 is necessary for complete neutrophil maturation. Accordingly, depletion of HSPA8 attenuated CMA activity and facilitated APL differentiation. In contrast, maintaining high CMA activity by ectopic expression of LAMP-2A impeded APL differentiation. Overall, our findings demonstrate that both normal and APL neutrophil differentiation require CMA downregulation and this pathway is predominantly dependent on HSPA8 assisted by other co-chaperones.

cancer biology↗

bioRxiv2022

Characterization of non-human primate dura in health and neurodegeneration

Brain meninges and associated vasculature participate in brain clearance and are implicated in many neurological conditions such as Alzheimers disease, meningitis, multiple sclerosis, stroke, and traumatic brain injury. However, most of our knowledge concerning brain clearance via meninges is based on rodent data, and relevance to human disease remains unclear. One of the technical barriers in studies of meningeal physiology in health and disease is that existing imaging modalities are suboptimal for large and optically non-transparent meningeal tissue of humans and non-human primate (NHP) animal models. To address this barrier, we performed first characterization of NHP dura by high resolution confocal microscopy of clarified tissue. We investigated vascular structures and resident cells in normal monkeys and primate models of tauopathy and synucleinopathy. We demonstrated the presence of an extensive meningeal vascular network covering the entire tissue surface with resolution to the smallest capillaries. This is also the first work to map lymphatic vessels in the dura of non-human primate (NHP). Overall, the NHP lymphatic meningeal system resembles the anatomy found in rat dura, but it is more complex. Analysis of dura from NPH models of tauopathy and synucleinopathy revealed an association with disease-specific biomarkers (amyloid, tau, -synuclein) with both the blood and lymphatic vasculature. This work has broad relevance to many brain diseases where solute accumulation and abnormal macromolecular clearance is a part of the pathogenesis.

neuroscience↗

bioRxiv2022

Discovery of a druggable copper-signaling pathway that drives cell plasticity and inflammation

Inflammation is a complex physiological process triggered in response to harmful stimuli. It involves specialized cells of the immune system able to clear sources of cell injury and damaged tissues to promote repair. Excessive inflammation can occur as a result of infections and is a hallmark of several diseases. The molecular basis underlying inflammatory responses are not fully understood. Here, we show that the cell surface marker CD44, which characterizes activated immune cells, acts as a metal transporter that promotes copper uptake. We identified a chemically reactive pool of copper(II) in mitochondria of inflammatory macrophages that catalyzes NAD(H) redox cycling by activating hydrogen peroxide. Maintenance of NAD+ enables metabolic and epigenetic programming towards the inflammatory state. Targeting mitochondrial copper(II) with a rationally-designed dimer of metformin triggers distinct metabolic and epigenetic states that oppose macrophage activation. This drug reduces inflammation in mouse models of bacterial and viral (SARS-CoV-2) infections, improves well-being and increases survival. Identifying mechanisms that regulate the plasticity of immune cells provides the means to develop next-generation medicine. Our work illuminates the central role of copper as a regulator of cell plasticity and unveils a new therapeutic strategy based on metabolic reprogramming and the control of epigenetic cell states.

cell biology↗

bioRxiv2022

Natural language signatures of psilocybin microdosing

Serotonergic psychedelics are being studied as novel treatments for mental health disorders and as facilitators of improved well-being, mental function and creativity. Recent studies have found mixed results concerning the effects of low doses of psychedelics ("microdosing") on these domains. However, microdosing is generally investigated using instruments designed to assess larger doses of psychedelics, which might lack sensitivity and specificity for this purpose. Following a double-blind and placebo-controlled experimental design, we explored natural language as a resource to identify speech produced under the acute effects of psilocybin microdoses, focusing on variables known to be affected by higher doses: verbosity, semantic variability and sentiment scores. Except for semantic variability, these metrics presented significant differences between a typical active microdose of 0.5 g of psilocybin mushrooms and an inactive placebo condition. Moreover, machine learning classifiers trained using these metrics were capable of distinguishing between conditions with high accuracy (AUC{approx}0.8). Our results constitute first proof that low doses of serotonergic psychedelics can be identified from unconstrained natural speech, with potential for widely applicable, affordable, and ecologically valid monitoring of microdosing schedules.

pharmacology and toxicology↗

bioRxiv2021

Microevidence for microdosing with psilocybin mushrooms: a double-blind placebo-controlled study of subjective effects, behavior, creativity, perception, cognition, and brain activity

The use of low sub-hallucinogenic doses of psychedelics ("microdosing") has gained popularity in recent years. Although anecdotal reports claim multiple benefits associated with this practice, the lack of placebo-controlled studies limits our knowledge of microdosing and its effects. Moreover, research conducted in laboratory settings might fail to capture the motivation of individuals engaged in microdosing protocols. We recruited 34 individuals planning to microdose with psilocybin mushrooms (Psilocybe cubensis), one of the materials most frequently used for this purpose. Following a double-blind placebo-controlled design, we investigated the effects of 0.5 g dried mushrooms on subjective experience, behavior, creativity, perception, cognition, and brain activity. The reported acute effects were significantly more intense for the active dose compared to the placebo, which could be explained by unblinding. For the other measurements, we observed either null effects or a trend towards cognitive impairment and, in the case of EEG, towards reduced theta band spectral power. Our findings support the possibility that expectation effects underlie at least some of the anecdotal benefits attributed to microdosing with psilocybin mushrooms.

neuroscience↗

bioRxiv2021

CLUH controls astrin-1 expression to couple mitochondrial metabolism to cell cycle progression

Proliferating cells undergo metabolic changes in synchrony with cell cycle progression and cell division. Mitochondria provide fuel, metabolites, and ATP during different phases of the cell cycle, however it is not completely understood how mitochondrial function and the cell cycle are coordinated. CLUH is a post-transcriptional regulator of mRNAs encoding mitochondrial proteins involved in oxidative phosphorylation and several metabolic pathways. Here, we show a role of CLUH in regulating the expression of astrin, which is involved in metaphase to anaphase progression, centrosome integrity, and mTORC1 inhibition. We find that CLUH binds both the SPAG5 mRNA and its product astrin, and controls the synthesis and the stability of the full-length astrin-1 isoform. We show that CLUH interacts with astrin-1 specifically during interphase. Astrin-depleted cells show mTORC1 hyperactivation and enhanced anabolism. On the other hand, cells lacking CLUH show decreased astrin levels and increased mTORC1 signaling, but cannot sustain anaplerotic and anabolic pathways. In absence of CLUH, cells fail to grow during G1, and progress faster through the cell cycle, indicating dysregulated matching of growth, metabolism and cell cycling. Our data reveal a role of CLUH in coupling growth signaling pathways and mitochondrial metabolism with cell cycle progression.

cell biology↗

bioRxiv2021

Global Plant Extinction Risk Assessment Informs Novel Biodiversity Hotspots

Curbing biodiversity loss and its impact on ecosystem services, resilience and Natures Contributions to People is one of the main challenges of our generation (IPBES, 2019b, 2019a; Secretariat of the United Nations Convention on Biological Diversity, 2020). A global baseline assessment of the threat status of all of biodiversity is crucial to monitor the progress of conservation policies worldwide (Mace & al., 2000; Secretariat of the United Nations Convention on Biological Diversity, 2021) and target priority areas for conservation (Walker & al., 2021). However, the magnitude of the task seems insurmountable, as even listing the organisms already known to science is a challenge (Nic Lughadha & al., 2016; Borsch & al., 2020; Govaerts & al., 2021). A new approach is needed to overcome this stumbling block and scale-up the assessment of extinction risk. Here we show that analyses of natural history mega-datasets using artificial intelligence allows us to predict a baseline conservation status for all vascular plants and identify target areas for conservation corresponding to hotspots optimally capturing different aspects of biodiversity. We illustrate the strong potential of AI-based methods to reliably predict extinction risk on a global scale. Our approach not only retrieved recognized biodiversity hotspots but identified new areas that may guide future global conservation action (Myers & al., 2000; Brooks & al., 2006). To further work in this area and guide the targets of the post-2020 biodiversity framework (Diaz & al., 2020a; Secretariat of the United Nations Convention on Biological Diversity, 2020; Mair & al., 2021), it will be necessary to accelerate the acquisition of fundamental data and allow inclusion of social and economic factors (Possingham & Wilson, 2005).

plant biology↗

bioRxiv2021

Stabilising microbial communities by looped mass transfer

Creating structurally and functionally stable microbiomes would be greatly beneficial to biotechnology and human health but so far has proven challenging. Here, we propose a looped mass transfer design that keeps microbiomes constant over long periods of time. The effluent of five parallel reactors that began with the same inoculum, was mixed in a reactor that represented a regional pool. Part of this pool was transferred back to the five reactors. Community dynamics were monitored and visualized by quantitative microbial flow cytometry and selected taxonomic sequencing of whole communities and sorted subcommunities. The rescue effect, known from metacommunity theory, was the main stabilizing mechanism that led to the survival of subcommunities with zero netgrowth, especially at high mass transfer rates. The looped mass transfer approach promises to overcome notorious stochastic structural fluctuations in bioreactors and has the potential to design and stabilize communities that can perform desired functions.

microbiology↗

bioRxiv2021

The extracellular matrix gene, Svep1, orchestrates airway patterning and the transition from lung branching morphogenesis to alveolar maturation in the mouse

Disruptions in airway branching or alveolar differentiation during lung development can lead to severe respiratory deficiencies and neonatal death. The molecular mechanisms governing branching patterning and early alveolar formation remain elusive. Loss of Svep1 function in mice results in various developmental defects, including lung hypoplasia and perinatal lethality. Our examination of the lungs of Svep1 knockout (Svep1-/-) mouse embryos, both in vivo and in vitro, revealed that Svep1 mutants exhibit an increase in the number of disorganized distal airway tips and progressively greater disruption of lung lobe morphology over time and saccular development. Svep1 interacts with FGF signaling to regulate smooth muscle differentiation and, together with Fgf9, guides airway branching patterning. Transcriptomic data from the lungs of Svep1-/- embryos revealed dysregulated gene expression affecting saccular maturation. Our findings demonstrate that Svep1 is a key extracellular matrix player shaping airway morphology and influencing alveolar fate. These insights offer potential avenues for therapeutic interventions in congenital lung disorders.

developmental biology↗

bioRxiv2021

SurvBenchmark: comprehensive benchmarking study of survival analysis methods using both omics data and clinical data

Survival analysis is a branch of statistics that deals with both, the tracking of time and of the survival status simultaneously as the dependent response. Current comparisons of survival model performance mostly center on clinical data with classic statistical survival models, with prediction accuracy often serving as the sole metric of model performance. Moreover, survival analysis approaches for censored omics data have not been thoroughly investigated. The common approach is to binarise the survival time and perform a classification analysis. Here, we develop a benchmarking framework, SurvBenchmark, that evaluates a diverse collection of survival models for both clinical and omics datasets. SurvBenchmark not only focuses on classical approaches such as the Cox model, but it also evaluates state-of-art machine learning survival models. All approaches were assessed using multiple performance metrics, these include model predictability, stability, flexibility and computational issues. Our systematic comparison framework with over 320 comparisons (20 methods over 16 datasets) shows that the performances of survival models vary in practice over real-world datasets and over the choice of the evaluation metric. In particular, we highlight that using multiple performance metrics is critical in providing a balanced assessment of various models. The results in our study will provide practical guidelines for translational scientists and clinicians, as well as define possible areas of investigation in both survival technique and benchmarking strategies. Contactjean.yang@sydney.edu.au

bioinformatics↗