The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation and comparative genomics across the vertebrate subphylum and key model organisms. The Ensembl annotation pipeline is capable of integrating experimental and reference data from multiple providers into a single integrated resource. Here, we present 94 newly annotated and re-annotated genomes, bringing the total number of genomes offered by Ensembl to 227. This represents the single largest expansion of the resource since its inception. We also detail our continued efforts to improve human annotation, developments in our epigenome analysis and display, a new tool for imputing causal genes from genome-wide association studies and visualisation of variation within a 3D protein model. Finally, we present information on our new website. Both software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license) and data updates made available four times a year.

The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.

Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed to efficiently deliver annotation at scale for all eukaryotic life, and it also provides deep comprehensive annotation for key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the annotation of new assemblies. Here, we report the release of the greatest annual number of newly annotated genomes in the history of Ensembl via our dedicated Ensembl Rapid Release platform (http://rapid.ensembl.org). We have also developed a new method to generate comparative analyses at scale for these assemblies and, for the first time, we have annotated non-vertebrate eukaryotes. Meanwhile, we continually improve, extend and update the annotation for our high-value reference vertebrate genomes and report the details here. We have a range of specific software tools for specific tasks, such as the Ensembl Variant Effect Predictor (VEP) and the newly developed interface for the Variant Recoder. All Ensembl data, software and tools are freely available for download and are accessible programmatically.

Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years. During that time, our resources, services and tools have continually evolved in line with both the publicly available genome data and the downstream research and applications that utilise the Ensembl platform. In recent years we have witnessed a dramatic shift in the genomic landscape. There has been a large increase in the number of high-quality reference genomes through global biodiversity initiatives. In parallel, there have been major advances towards pangenome representations of higher species, where many alternative genome assemblies representing different breeds, cultivars, strains and haplotypes are now available. In order to support these efforts and accelerate downstream research, it is our goal at Ensembl to create high-quality annotations, tools and services for species across the tree of life. Here, we report our resources for popular reference genomes, the dramatic growth of our annotations (including haplotypes from the first human pangenome graphs), updates to the Ensembl Variant Effect Predictor (VEP), interactive protein structure predictions from AlphaFold DB, and the beta release of our new website.

Young women living with HIV in the United States face many social and psychological challenges, including involvement in health care and secondary prevention efforts. The factors that put these young women at risk for HIV acquisition initially, such as poverty, gender roles, cultural norms, and limited perceived control over sexual relationships, continue to place them at risk for both adverse mental and physical health outcomes that impact their daily lives and secondary prevention efforts. This study utilized focus groups with young HIV-positive women in order to better understand their perceived problems and pressures and to inform a developmentally appropriate secondary prevention intervention for young HIV-positive women that could be implemented in clinical care settings. Focus groups with young HIV-positive women were convened in three U.S. cities: Baltimore, Chicago, and Tampa. A total of 17 young, HIV-positive women, age range 17-24 (mean age = 21), participated in the focus groups. This article describes the psychological and social challenges these young women face as well as their suggestions regarding secondary HIV prevention intervention components.

Black young men who have sex with men (BYMSM) are the group most disproportionately impacted by HIV in the United States and most in need of efficacious interventions to address community-level factors that increase their vulnerability to HIV. The House Ball Community (HBC) is a distinct social network within the larger BYMSM community that may be particularly vulnerable to social norms and stigma around HIV. This study tailored an evidence-based, community-level popular opinion leader (OL) intervention for use within the HBC. The intervention, called POSSE, was then piloted to evaluate feasibility, acceptability and preliminary efficacy. Recruiting opinion leaders from the community and training them to deliver risk reduction messages was found to be feasible and highly acceptable. Community-level surveys (n=406) were completed over 5 waves of data collection. Overall exposure to the intervention increased across waves. Statistically significant (p < .05) declines were observed for multiple sexual partners, condomless anal intercourse with any male partners and with male partners of unknown HIV status. HIV stigma declined as well, but the trend was not statistically significant.

This study qualitatively examined the social-ecological stressors that youth experience during the first year following an HIV diagnosis. Thirty HIV-positive youth (16 males, 14 females) between the ages of 16-24 participated in either focus groups or individual interviews. All sessions were transcribed and themes were identified through cross-case and comparative analyses. Participants reported experiencing stressors within multiple social-ecological systems, including interactions with their families, sexual partners, health care providers, work, and school. The results from this study highlight the need for youth-focused services that assist with multiple layers of stressors during the first year following an HIV diagnosis.

This article describes the influence of a group-based behavioral intervention for adolescents and young adults newly diagnosed with HIV (Project ACCEPT) on four dimensions of HIV-related stigma-personalized stigma, disclosure concerns, negative self-image, and concern with public attitudes about people with HIV-as measured by the Berger HIV Stigma Scale. Stigma was addressed in a holistic manner during the intervention by providing HIV/AIDS-related information, facilitating the acquisition of coping skills, and providing contact with other youth living with HIV in order to improve social support. Fifty youth (28 male, 22 female; mean age=19.24 years) newly diagnosed with HIV from four geographically diverse clinics participated in a one-group pretest-posttest design study whereby they received the intervention over a 12-week period, and completed assessments at baseline, post-intervention, and 3-month follow-up. Results from the combined sample (males and females) revealed overall reductions in stigma in three dimensions: personalized stigma, disclosure concerns, and negative self-image, although only the combined-sample effects for negative self-image were maintained at 3-month follow-up. Gender-specific analyses revealed that the intervention reduced stigma for males across all four dimensions of stigma, with all effects being maintained to some degree at the 3-month follow-up. Only personalized stigma demonstrated a decrease for females, although this effect was not maintained at the 3-month follow-up; while the other three types of stigma increased at post-intervention and 3-month follow-up. Findings are discussed in terms of gender specific outcomes and the need for a different type of intervention to reduce stigma for young women.