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| http://dx.doi.org/10.1007/s11306-014-0755-6 | DOI Listing |
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CASTER: Direct species tree inference from whole-genome alignments.
Science
January 2025
Electrical and Computer Engineering Department, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA.
Genomes contain mosaics of discordant evolutionary histories, challenging the accurate inference of the tree of life. While genome-wide data are routinely used for discordance-aware phylogenomic analyses, due to modeling and scalability limitations, the current practice leaves out large chunks of genomes. As more high-quality genomes become available, we urgently need discordance-aware methods to infer the tree directly from a multiple genome alignment.
View Article and Find Full Text PDFModeling Biases from Low-Pass Genome Sequencing to Enable Accurate Population Genetic Inferences.
Mol Biol Evol
January 2025
Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA.
Low-pass genome sequencing is cost-effective and enables analysis of large cohorts. However, it introduces biases by reducing heterozygous genotypes and low-frequency alleles, impacting subsequent analyses such as model-based demographic history inference. Several approaches exist for inferring an unbiased allele frequency spectrum (AFS) from low-pass data, but they can introduce spurious noise into the AFS.
View Article and Find Full Text PDFDecoding the Therapeutic Target SVEP1: Harnessing Molecular Trait GWASs to Unravel Mechanisms of Human Disease.
Annu Rev Pharmacol Toxicol
January 2025
Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA; email:
Although human genetics has substantial potential to illuminate novel disease pathways and facilitate drug development, identifying causal variants and deciphering their mechanisms remain challenging. We believe these challenges can be addressed, in part, by creatively repurposing the results of molecular trait genome-wide association studies (GWASs). In this review, we introduce techniques related to molecular GWASs and unconventionally apply them to understanding , a human coronary artery disease risk locus.
View Article and Find Full Text PDFUsing a Composite Summary of Daily Sex Hormones to Gauge Time Until Menopause: A Focus on Pregnanediol Glucuronide (PDG).
J Clin Endocrinol Metab
January 2025
Preventive and Behavioral Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA.
Context: The timing of a woman's final menstrual period (FMP) in relation to her age is considered a valuable indicator of overall health, being associated with cardiovascular, bone health, reproductive, and general mortality outcomes.
Objective: This work aimed to evaluate the relationship between hormones and the "time to FMP" when daily hormone trajectories are characterized by their 1) entropy, and 2) deviation from premenopausal/stable cycle patterns (representing a textbook "gold standard"; GS).
Methods: As part of the Study of Women's Health Across the Nation, urinary luteinizing hormone (LH), follicle-stimulating hormone (FSH), estrogen conjugates (E1C), and pregnanediol glucuronide (PDG) were measured daily from a multiracial sample of 549 mid-life women for the duration of one menstrual cycle.
Catalyst-derived hierarchy in 2D imine-based covalent organic frameworks.
Nanoscale
January 2025
Dept. of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA.
Identifying facile strategies for hierarchically structuring crystalline porous materials is critical for realizing diffusion length scales suitable for broad applications. Here, we elucidate synthesis-structure-function relations governing how room temperature catalytic conditions can be exploited to tune covalent organic framework (COF) growth and thereby access unique hierarchical morphologies without the need to introduce secondary templates or structure directing molecules. Specifically, we demonstrate how scandium triflate, an efficient catalyst involved in the synthesis of imine-based COFs, can be exploited as an effective growth modifier capable of selectively titrating terminal amines on 2D COF layers to facilitate anisotropic crystal growth.
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