AI Article Synopsis
- eMPRess is a software program designed for phylogenetic tree reconciliation using the duplication-transfer-loss model, helping users make more reliable inferences by addressing event costs and representative solutions.
- The software is freely accessible for download at http://www.cs.hmc.edu/empress.
- Additional supplementary data can be found on the Bioinformatics online platform.
Article Abstract
Summary: We describe eMPRess, a software program for phylogenetic tree reconciliation under the duplication-transfer-loss model that systematically addresses the problems of choosing event costs and selecting representative solutions, enabling users to make more robust inferences.
Availability And Implementation: eMPRess is freely available at http://www.cs.hmc.edu/empress.
Supplementary Information: Supplementary data are available at Bioinformatics online.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1093/bioinformatics/btaa978 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods.
ISME J
January 2024
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States.
Article Synopsis
- - The study explores the gut microbiome of dogs and cats, using extensive data from 2639 stool samples to improve understanding of how these microbes impact animal and human health.
- - It identifies 184 unique species-level genome bins in companion animals and 198 that are shared among dogs, cats, and humans, indicating potential host-specific adaptations of these microbes.
- - By analyzing the functional differences between these microbial lineages, the research highlights their significance for companion animal health and supports the "One Health" approach, which emphasizes the interconnectedness of human and animal health.
Chronic binge drinking-induced susceptibility to colonic inflammation is microbiome-dependent.
Gut Microbes
August 2024
Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Alterations in intestinal permeability and the gut microbiome caused by alcohol abuse are associated with alcoholic liver disease and with worsening of inflammatory bowel diseases (IBD) symptoms. To resolve the direct effects of chronic ethanol consumption on the colon and its microbiome in the absence of acute or chronic alcohol-induced liver disease, we developed a mouse model of chronic binge drinking that uncovers how alcohol may enhance susceptibility to colitis via the microbiota. Employing daily ethanol gavage, we recapitulate key features of binge ethanol consumption.
View Article and Find Full Text PDFStrain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes.
Nat Med
August 2024
Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Article Synopsis
- The study explores the complex relationship between gut microbes and type 2 diabetes (T2D), revealing that previous research has been inconsistent partly due to diverse study designs.
- Researchers analyzed over 8,000 microbial genomes from multiple cohorts across various countries, identifying specific bacteria linked to T2D, such as Clostridium bolteae and Butyrivibrio crossotus, which also impact glucose metabolism.
- The findings highlight the importance of within-species differences in microbial strains and their genetic variations, providing new insights into the biological mechanisms contributing to metabolic risks associated with T2D.
Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions.
Syst Biol
September 2024
Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 46 rue d'Ulm, 75 005 Paris, France.
Interspecific interactions, including host-symbiont associations, can profoundly affect the evolution of the interacting species. Given the phylogenies of host and symbiont clades and knowledge of which host species interact with which symbiont, two questions are often asked: "Do closely related hosts interact with closely related symbionts?" and "Do host and symbiont phylogenies mirror one another?." These questions are intertwined and can even collapse under specific situations, such that they are often confused one with the other.
View Article and Find Full Text PDFEmpRess: an eHealth implementation readiness checklist for dementia developed through an interview study of stakeholder needs.
Aging Ment Health
May 2024
Alzheimer Center Limburg, Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands.
Objective: This study aimed to create a tool to assess eHealth interventions for dementia by adapting an existing implementation readiness (ImpRess) checklist that assessed manualised interventions.
Methods: In Part 1, online semi-structured interviews with individual stakeholders ( = 9) with expertise in eHealth and dementia were conducted (response rate 83%). The Nonadoption, Abandonment, and challenges to the Scale-Up, Spread, and Sustainability of Health and care technologies (NASSS) framework was applied, both to guide the construction of the interview guide, as well as to use its subdomains as codes in the deductive qualitative thematic analysis.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!