FAIRsoft-A practical implementation of FAIR principles for research software.

MOTIVATION: Software plays a crucial and growing role in research. Unfortunately, the computational component in Life Sciences research is often challenging to reproduce and verify. It could be undocumented, opaque, contain unknown errors that affect the outcome, or be directly unavailable and impossible to use for others. These issues are detrimental to the overall quality of scientific research. One step to address this problem is the formulation of principles that research software in the domain should meet to ensure its quality and sustainability, resembling the FAIR (Findable, Accessible, Interoperable, and Reusable) Data Principles. RESULTS: We present here a comprehensive series of quantitative indicators based on a pragmatic interpretation of the FAIR Principles and their implementation on OpenEBench, ELIXIR's open platform providing both support for scientific benchmarking and an active observatory of quality-related features for Life Sciences research software. The results serve to understand the current practices around research software quality-related features and provide objective indications for improving them. AVAILABILITY: Software metadata, from 11 different sources, collected, integrated and analysed in the context of this manuscript are available at https://doi.org/10.5281/zenodo.7311067. Code used for software metadata retrieval and processing is available in the following repository https://gitlab.bsc.es/inb/elixir/software-observatory/FAIRsoft_ETL. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.

The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these data to address challenges in transcript isoform detection, quantification and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. Incorporating additional orthogonal data and replicate samples is advised when aiming to detect rare and novel transcripts or using reference-free approaches. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

Rare disease research workflow using multilayer networks elucidates the molecular determinants of severity in Congenital Myasthenic Syndromes.

Exploring the molecular basis of disease severity in rare disease scenarios is a challenging task provided the limitations on data availability. Causative genes have been described for Congenital Myasthenic Syndromes (CMS), a group of diverse minority neuromuscular junction (NMJ) disorders; yet a molecular explanation for the phenotypic severity differences remains unclear. Here, we present a workflow to explore the functional relationships between CMS causal genes and altered genes from each patient, based on multilayer network community detection analysis of complementary biomedical information provided by relevant data sources, namely protein-protein interactions, pathways and metabolomics. Our results show that CMS severity can be ascribed to the personalized impairment of extracellular matrix components and postsynaptic modulators of acetylcholine receptor (AChR) clustering. This work showcases how coupling multilayer network analysis with personalized -omics information provides molecular explanations to the varying severity of rare diseases; paving the way for sorting out similar cases in other rare diseases.

RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.

RegulonDB is a database that contains the most comprehensive corpus of knowledge of the regulation of transcription initiation of Escherichia coli K-12, including data from both classical molecular biology and high-throughput methodologies. Here, we describe biological advances since our last NAR paper of 2019. We explain the changes to satisfy FAIR requirements. We also present a full reconstruction of the RegulonDB computational infrastructure, which has significantly improved data storage, retrieval and accessibility and thus supports a more intuitive and user-friendly experience. The integration of graphical tools provides clear visual representations of genetic regulation data, facilitating data interpretation and knowledge integration. RegulonDB version 12.0 can be accessed at https://regulondb.ccg.unam.mx.

WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows.

The inherent diversity of approaches in proteomics research has led to a wide range of software solutions for data analysis. These software solutions encompass multiple tools, each employing different algorithms for various tasks such as peptide-spectrum matching, protein inference, quantification, statistical analysis, and visualization. To enable an unbiased comparison of commonly used bottom-up label-free proteomics workflows, we introduce WOMBAT-P, a versatile platform designed for automated benchmarking and comparison. WOMBAT-P simplifies the processing of public data by utilizing the sample and data relationship format for proteomics (SDRF-Proteomics) as input. This feature streamlines the analysis of annotated local or public ProteomeXchange data sets, promoting efficient comparisons among diverse outputs. Through an evaluation using experimental ground truth data and a realistic biological data set, we uncover significant disparities and a limited overlap in the quantified proteins. WOMBAT-P not only enables rapid execution and seamless comparison of workflows but also provides valuable insights into the capabilities of different software solutions. These benchmarking metrics are a valuable resource for researchers in selecting the most suitable workflow for their specific data sets. The modular architecture of WOMBAT-P promotes extensibility and customization. The software is available at https://github.com/wombat-p/WOMBAT-Pipelines.

Perilesional edema diameter associated with brain metastases as a predictive factor of response to radiotherapy in non-small cell lung cancer.

Background: Different prognostic scales exist in patients with brain metastasis, particularly in lung cancer. The Graded Prognostic Assessment for lung cancer using molecular markers (Lung-molGPA index) for brain metastases is a powerful prognostic tool that effectively identifies patients at different risks. However, these scales do not include perilesional edema diameter (PED) associated with brain metastasis. Current evidence suggests that PED might compromise the delivery and efficacy of radiotherapy to treat BM. This study explored the association between radiotherapy efficacy, PED extent, and gross tumor diameter (GTD). Aim: The aim of this study was to evaluate the intracranial response (iORR), intracranial progression-free survival (iPFS), and overall survival (OS) according to the extent of PED and GT. Methods: Out of 114 patients with BM at baseline or throughout the disease, 65 were eligible for the response assessment. The GTD and PED sum were measured at BM diagnosis and after radiotherapy treatment. According to a receiver operating characteristic (ROC) curve analysis, cutoff values were set at 27 mm and 17 mm for PED and GT, respectively. Results: Minor PED was independently associated with a better iORR [78.8% vs. 50%, OR 3.71 (95% CI 1.26-10.99); p = 0.018] to brain radiotherapy. Median iPFS was significantly shorter in patients with major PED [6.9 vs. 11.8 months, HR 2.9 (95% CI 1.7-4.4); p < 0.001] independently of other prognostic variables like the Lung-molGPA and GTD. A major PED also negatively impacted the median OS [18.4 vs. 7.9 months, HR 2.1 (95% CI 1.4-3.3); p = 0.001]. Conclusion: Higher PED was associated with an increased risk of intracranial progression and a lesser probability of responding to brain radiotherapy in patients with metastatic lung cancer. We encourage prospective studies to confirm our findings.

DEBBIE: The Open Access Database of Experimental Scaffolds and Biomaterials Built Using an Automated Text Mining Pipeline.

Biomaterials research output has experienced an exponential increase over the last three decades. The majority of research is published in the form of scientific articles and is therefore available as unstructured text, making it a challenging input for computational processing. Computational tools are becoming essential to overcome this information overload. Among them, text mining systems present an attractive option for the automated extraction of information from text documents into structured datasets. This work presents the first automated system for biomaterial related information extraction from the National Library of Medicine's premier bibliographic database (MEDLINE) research abstracts into a searchable database. The system is a text mining pipeline that periodically retrieves abstracts from PubMed and identifies research and clinical studies of biomaterials. Thereafter, the pipeline identifies sixteen concept types of interest in the abstract using the Biomaterials Annotator, a tool for biomaterials Named Entity Recognition (NER). These concepts of interest, along with the abstract and relevant metadata are then deposited in DEBBIE, the Database of Experimental Biomaterials and their Biological Effect. DEBBIE is accessible through a web application that provides keyword searches and displays results in an intuitive and meaningful manner, aiming to facilitate an efficient mapping and organization of biomaterials information.

Progressive arousal: a new concept and definition for premature ejaculation.

Background: Premature ejaculation (PE) is a nosologic entity with issues in its conceptualization and definition. Aim: To understand if the altered sexual response in men with PE is in the orgasm phase, as currently assumed, or the arousal phase with difficulties in modulating, regulating, or decreasing sexual arousal. Methods: Men were recruited who looked for help for PE and met the diagnostic criteria according to clinical standards. The participants completed a sociodemographic survey and the Premature Ejaculation Diagnostic Tool. They also performed a masturbation exercise with a maximum of 5 stops, with the intention of prolonging the arousal phase. The time of the exercise was measured from the beginning of genital masturbation to ejaculation. Outcomes: We calculated the total time of the exercise, the median time at each start, and the number of dropouts. We performed a pairwise comparison analysis between starts and made a survival curve representing the percentage of men who remained in the exercise. Results: A total of 481 men with PE participated (mean ± SD; age, 29.25 ± 8.72 years). We found that the expected median survival time until ejaculation was 317.00 seconds (95% CI, 288.34-345.65). However, the average time during stimulation decreased as the exercise progressed, and statistically significant differences were observed in their pairwise comparison (P < .001). Also, the chances of ejaculation increased as the exercise progressed, with 62.16% of the participants ejaculating before the end of the exercise. The results indicated increasing sexual arousal, where stops in stimulation were progressively less effective at maintaining ejaculation times at starts. Clinical Implications: We showed that the arousal phase is altered in PE, not the orgasm phase, and this could finally have implications in the diagnosis and/or treatment of this condition. Strengths and Limitations: The analysis of the times at starts and stops in a masturbation exercise in men with PE, had been barely addressed before. In the future, it would be important to verify the effect of stops during sexual intercourse and to incorporate a control group of men without PE. Conclusions: We propose a new conceptualization and definition for PE: progressive arousal disorder is the inability to modulate, regulate, or decrease arousal during any sexual activity, even with brief stops during sexual stimulation, causing unwanted ejaculation.

The FAIR Cookbook - the essential resource for and by FAIR doers.

The notion that data should be Findable, Accessible, Interoperable and Reusable, according to the FAIR Principles, has become a global norm for good data stewardship and a prerequisite for reproducibility. Nowadays, FAIR guides data policy actions and professional practices in the public and private sectors. Despite such global endorsements, however, the FAIR Principles are aspirational, remaining elusive at best, and intimidating at worst. To address the lack of practical guidance, and help with capability gaps, we developed the FAIR Cookbook, an open, online resource of hands-on recipes for "FAIR doers" in the Life Sciences. Created by researchers and data managers professionals in academia, (bio)pharmaceutical companies and information service industries, the FAIR Cookbook covers the key steps in a FAIRification journey, the levels and indicators of FAIRness, the maturity model, the technologies, the tools and the standards available, as well as the skills required, and the challenges to achieve and improve data FAIRness. Part of the ELIXIR ecosystem, and recommended by funders, the FAIR Cookbook is open to contributions of new recipes.

Validación del instrumento Infant Malnutrition and Feeding Checklist for Congenital Heart Disease, una herramienta para identificar riesgo de desnutrición y dificultades de alimentación en lactantes con cardiopatías congénitas / Validation of the instrument “Infant Malnutrition and Feeding Checklist for Congenital Heart Disease”, a tool to identify risk of malnutrition and feeding difficulties in infants with congenital heart disease

Introducción: actualmente, se han diseñado diversas herramientas para detectar oportunamente el riesgo de desnutrición en niños hospitalizados. En aquellos con diagnóstico de cardiopatías congénitas (CC), solo existe una herramienta desarrollada en Canadá, llamada Infant Malnutrition and Feeding Checklist for Congenital Heart Disease (IMFC:CHD), la cual fue diseñada en idioma inglés. Objetivo: evaluar la validez y confiabilidad de la adaptación en español de la herramienta IMFC:CHD en lactantes con CC. Métodos: estudio transversal de validación realizado en dos etapas: la primera, de traducción y adaptación transcultural de la herramienta; y la segunda, de validación de la nueva herramienta traducida, donde se obtuvieron las evidencias de confiabilidad y validez. Resultados: en la primera etapa se obtuvo la herramienta traducida y adaptada al idioma español; para la segunda etapa se incluyeron 24 lactantes con diagnóstico de CC. Se evaluó la validez de criterio concurrente entre la herramienta de tamizaje y la evaluación antropométrica, obteniéndose un acuerdo sustancial (κ = 0,660, IC 95 %: 0,36-0,95). Para la validez de criterio predictiva, la cual fue comparada con los días de estancia hospitalaria, se obtuvo un acuerdo moderado (κ = 0,489, IC 95 %: 0,1-0,8). La confiabilidad de la herramienta se evaluó mediante consistencia externa, midiendo la concordancia interobservador, y se obtuvo un acuerdo sustancial (κ = 0,789, IC 95 %: 0,5-0,9); la reproducibilidad de la herramienta mostró un acuerdo casi perfecto (κ = 1, IC 95 %: 0,9-1,0). Conclusiones: la herramienta IMFC:CHD mostró una adecuada validez y confiabilidad, por lo que podría considerarse un recurso útil para la identificación de desnutrición grave. (AU)

Introduction: currently, various tools have been designed to timely detect the risk of malnutrition in hospitalized children. In those with a diagnosis of congenital heart disease (CHD), there is only one tool developed in Canada: Infant Malnutrition and Feeding Checklist for Congenital Heart Disease (IMFC:CHD), which was designed in English. Objective: to evaluate the validity and reliability of the Spanish adaptation of the IMFC:CHD tool in infants with CHD. Methods: cross-sectional validation study carried out in two stages. The first, of translation and cross-cultural adaptation of the tool, and the second, of validation of the new translated tool, where evidence of reliability and validity were obtained. Results: in the first stage, the tool was translated and adapted to the Spanish language; for the second stage, 24 infants diagnosed with CHD were included. The concurrent criterion validity between the screening tool and the anthropometric evaluation was evaluated, obtaining a substantial agreement (κ = 0.660, 95 % CI: 0.36-0.95) and for the predictive criterion validity, which was compared with the days of hospital stay, moderate agreement was obtained (κ = 0.489, 95 % CI: 0.1-0.8). The reliability of the tool was evaluated through external consistency, measuring theinter-observer agreement, obtaining a substantial agreement (κ = 0.789, 95 % CI: 0.5-0.9), and the reproducibility of the tool showed an almost perfect agreement (κ = 1, CI 95 %: 0.9-1.0). Conclusions: the IMFC:CHD tool showed adequate validity and reliability, and could be considered as a useful resource for the identification of severe malnutrition. (AU)

[Validation of the instrument "Infant Malnutrition and Feeding Checklist for Congenital Heart Disease", a tool to identify risk of malnutrition and feeding difficulties in infants with congenital heart disease]. / Validación del instrumento Infant Malnutrition and Feeding Checklist for Congenital Heart Disease, una herramienta para identificar riesgo de desnutrición y dificultades de alimentación en lactantes con cardiopatías congénitas.

Introduction: Introduction: currently, various tools have been designed to timely detect the risk of malnutrition in hospitalized children. In those with a diagnosis of congenital heart disease (CHD), there is only one tool developed in Canada: Infant Malnutrition and Feeding Checklist for Congenital Heart Disease (IMFC:CHD), which was designed in English. Objective: to evaluate the validity and reliability of the Spanish adaptation of the IMFC:CHD tool in infants with CHD. Methods: cross-sectional validation study carried out in two stages. The first, of translation and cross-cultural adaptation of the tool, and the second, of validation of the new translated tool, where evidence of reliability and validity were obtained. Results: in the first stage, the tool was translated and adapted to the Spanish language; for the second stage, 24 infants diagnosed with CHD were included. The concurrent criterion validity between the screening tool and the anthropometric evaluation was evaluated, obtaining a substantial agreement (κ = 0.660, 95 % CI: 0.36-0.95) and for the predictive criterion validity, which was compared with the days of hospital stay, moderate agreement was obtained (κ = 0.489, 95 % CI: 0.1-0.8). The reliability of the tool was evaluated through external consistency, measuring the inter-observer agreement, obtaining a substantial agreement (κ = 0.789, 95 % CI: 0.5-0.9), and the reproducibility of the tool showed an almost perfect agreement (κ = 1, CI 95 %: 0.9-1.0). Conclusions: the IMFC:CHD tool showed adequate validity and reliability, and could be considered as a useful resource for the identification of severe malnutrition.

Introducción: Introducción: actualmente, se han diseñado diversas herramientas para detectar oportunamente el riesgo de desnutrición en niños hospitalizados. En aquellos con diagnóstico de cardiopatías congénitas (CC), solo existe una herramienta desarrollada en Canadá, llamada Infant Malnutrition and Feeding Checklist for Congenital Heart Disease (IMFC:CHD), la cual fue diseñada en idioma inglés. Objetivo: evaluar la validez y confiabilidad de la adaptación en español de la herramienta IMFC:CHD en lactantes con CC. Métodos: estudio transversal de validación realizado en dos etapas: la primera, de traducción y adaptación transcultural de la herramienta; y la segunda, de validación de la nueva herramienta traducida, donde se obtuvieron las evidencias de confiabilidad y validez. Resultados: en la primera etapa se obtuvo la herramienta traducida y adaptada al idioma español; para la segunda etapa se incluyeron 24 lactantes con diagnóstico de CC. Se evaluó la validez de criterio concurrente entre la herramienta de tamizaje y la evaluación antropométrica, obteniéndose un acuerdo sustancial (κ = 0,660, IC 95 %: 0,36-0,95). Para la validez de criterio predictiva, la cual fue comparada con los días de estancia hospitalaria, se obtuvo un acuerdo moderado (κ = 0,489, IC 95 %: 0,1-0,8). La confiabilidad de la herramienta se evaluó mediante consistencia externa, midiendo la concordancia interobservador, y se obtuvo un acuerdo sustancial (κ = 0,789, IC 95 %: 0,5-0,9); la reproducibilidad de la herramienta mostró un acuerdo casi perfecto (κ = 1, IC 95 %: 0,9-1,0). Conclusiones: la herramienta IMFC:CHD mostró una adecuada validez y confiabilidad, por lo que podría considerarse un recurso útil para la identificación de desnutrición grave.

The landscape of expression and alternative splicing variation across human traits.

Understanding the consequences of individual transcriptome variation is fundamental to deciphering human biology and disease. We implement a statistical framework to quantify the contributions of 21 individual traits as drivers of gene expression and alternative splicing variation across 46 human tissues and 781 individuals from the Genotype-Tissue Expression project. We demonstrate that ancestry, sex, age, and BMI make additive and tissue-specific contributions to expression variability, whereas interactions are rare. Variation in splicing is dominated by ancestry and is under genetic control in most tissues, with ribosomal proteins showing a strong enrichment of tissue-shared splicing events. Our analyses reveal a systemic contribution of types 1 and 2 diabetes to tissue transcriptome variation with the strongest signal in the nerve, where histopathology image analysis identifies novel genes related to diabetic neuropathy. Our multi-tissue and multi-trait approach provides an extensive characterization of the main drivers of human transcriptome variation in health and disease.

mHealth system (ATOPE+) to support exercise prescription in breast cancer survivors: a reliability and validity, cross-sectional observational study (ATOPE study).

Physical exercise is known to be beneficial for breast cancer survivors (BCS). However, avoiding nonfunctional overreaching is crucial in this population, as they are in physiological dysregulation. These factors could decrease their exercise capacity or facilitate nonfunctional overreaching, which can increase their risk of additional morbidities and even all-cause mortality. The focus of this study is to evaluate the reliability and validity of the ATOPE+ mHealth system to estimate autonomic balance and specific wellness parameters associated with BCS' perceived load, thereby informing nonlinear prescriptions in individualized physical exercise programs for BCS.Twenty-two BCS were included in the reliability and validity analysis. Measures were taken for four days, including morning autonomic balance by heart rate variability, self-reported perception of recovery from exercise, sleep satisfaction, emotional distress and fatigue after exertion. Measures were taken utilizing the ATOPE+ mHealth system application. The results of these measures were compared with criterion instruments to assess validity.The reliability results indicated that the intraclass correlation coefficient (ICC) showed an excellent correlation for recovery (0.93; 95% CI 0.85-0.96) and distress (0.94, 95% CI 0.89-0.97) as well as good correlation for the natural logarithm of the mean square root differences of the standard deviation (LnRMSSD) (0.87; 95% CI 0.74-0.94). Sleep satisfaction also showed an excellent correlation with a weighted kappa of 0.83. The validity results showed no significant differences, except for fatigue. ATOPE+ is reliable and valid for remotely assessing autonomic balance, perception of recovery, sleep satisfaction and emotional distress in BCS; however, it is not for fatigue. This highlights that ATOPE+ could be an easy and efficient system used to assess readiness in BCS, and could help to improve their health by supporting the prescription of optimal and safe physical exercise. Trial registration NCT03787966 ClinicalTrials.gov, December 2019 [ATOPE project]. https://clinicaltrials.gov/ct2/show/NCT03787966 .

Detection of early seeding of Richter transformation in chronic lymphocytic leukemia.

Richter transformation (RT) is a paradigmatic evolution of chronic lymphocytic leukemia (CLL) into a very aggressive large B cell lymphoma conferring a dismal prognosis. The mechanisms driving RT remain largely unknown. We characterized the whole genome, epigenome and transcriptome, combined with single-cell DNA/RNA-sequencing analyses and functional experiments, of 19 cases of CLL developing RT. Studying 54 longitudinal samples covering up to 19 years of disease course, we uncovered minute subclones carrying genomic, immunogenetic and transcriptomic features of RT cells already at CLL diagnosis, which were dormant for up to 19 years before transformation. We also identified new driver alterations, discovered a new mutational signature (SBS-RT), recognized an oxidative phosphorylation (OXPHOS)high-B cell receptor (BCR)low-signaling transcriptional axis in RT and showed that OXPHOS inhibition reduces the proliferation of RT cells. These findings demonstrate the early seeding of subclones driving advanced stages of cancer evolution and uncover potential therapeutic targets for RT.

The Quest for Orthologs orthology benchmark service in 2022.

The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource to compare existing and new methods of orthology inference (the bedrock for many comparative genomics and phylogenetic analysis) over a standard dataset and through common procedures. The Quest for Orthologs Consortium is dedicated to maintaining the resource up to date, through regular updates of the Reference Proteomes and increasingly accessible data through the OpenEBench platform. For this update, we have added a new benchmark based on curated orthology assertion from the Vertebrate Gene Nomenclature Committee, and provided an example meta-analysis of the public predictions present on the platform.

Effect of Phentermine on Hepatic Steatosis in Bariatric Surgery: A Pilot Study.

OBJECTIVE: Hepatic steatosis is associated with increased surgical complications in bariatric surgery patients. We aimed to evaluate the effect of phentermine in reducing hepatic steatosis, adipose tissue, and surgical complications in patients undergoing bariatric surgery. METHODS: This was a two-arm, double-blind, randomized, controlled pilot trial of 64 adult subjects with BMI >35 kg/m2 selected for bariatric surgery randomized into phentermine group (15 mg once daily) or placebo group for 8 weeks. Both groups adhered to a hypocaloric diet (500 calories/day) and an individualized exercise program. The primary endpoint was reducing the frequency of hepatic steatosis measured by ultrasound and reducing adipose tissue through fat mass in total kilograms or percentage. Key secondary points were the prevalence of surgical complications. Baseline and final biochemical parameters and blood pressure too were assessments. RESULTS: In the phentermine group, the frequency of hepatic steatosis decreased by 19%, and the percentage of patients with a normal ultrasound increased from 9% to 28% (p = 0.05). Likewise, the decrease in fat mass in kilograms was more significant in the phentermine group (56.1 kg vs. 51.8 kg, p = 0.02). A significant reduction in the HOMA-IR index was observed regardless of weight loss. No differences in surgical complications were observed between groups. Phentermine was well-tolerated; no differences were observed in the frequency of adverse events between the groups. CONCLUSIONS: Phentermine decreased the proportion of individuals with hepatic steatosis by 19% and promoted a more significant fat mass loss in kilograms among candidates for bariatric surgery.

PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies.

PhylomeDB is a unique knowledge base providing public access to minable and browsable catalogues of pre-computed genome-wide collections of annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous genes, as well as to their corresponding phylogeny-based orthology and paralogy relationships. In addition, PhylomeDB trees and alignments can be downloaded for further processing to detect and date gene duplication events, infer past events of inter-species hybridization and horizontal gene transfer, as well as to uncover footprints of selection, introgression, gene conversion, or other relevant evolutionary processes in the genes and organisms of interest. Here, we describe the latest evolution of PhylomeDB (version 5). This new version includes a newly implemented web interface and several new functionalities such as optimized searching procedures, the possibility to create user-defined phylome collections, and a fully redesigned data structure. This release also represents a significant core data expansion, with the database providing access to 534 phylomes, comprising over 8 million trees, and homology relationships for genes in over 6000 species. This makes PhylomeDB the largest and most comprehensive public repository of gene phylogenies. PhylomeDB is available at http://www.phylomedb.org.

COVID-19 Flow-Maps an open geographic information system on COVID-19 and human mobility for Spain.

COVID-19 is an infectious disease caused by the SARS-CoV-2 virus, which has spread all over the world leading to a global pandemic. The fast progression of COVID-19 has been mainly related to the high contagion rate of the virus and the worldwide mobility of humans. In the absence of pharmacological therapies, governments from different countries have introduced several non-pharmaceutical interventions to reduce human mobility and social contact. Several studies based on Anonymized Mobile Phone Data have been published analysing the relationship between human mobility and the spread of coronavirus. However, to our knowledge, none of these data-sets integrates cross-referenced geo-localised data on human mobility and COVID-19 cases into one all-inclusive open resource. Herein we present COVID-19 Flow-Maps, a cross-referenced Geographic Information System that integrates regularly updated time-series accounting for population mobility and daily reports of COVID-19 cases in Spain at different scales of time spatial resolution. This integrated and up-to-date data-set can be used to analyse the human dynamics to guide and support the design of more effective non-pharmaceutical interventions.