Genotype–environment associations to reveal the molecular basis of environmental adaptation

JR Lasky, EB Josephs, GP Morris - The Plant Cell, 2023 - academic.oup.com
A fundamental goal in plant biology is to identify and understand the variation underlying
plants' adaptation to their environment. Climate change has given new urgency to this goal …

Functional variation in the non-coding genome: molecular implications for food security

G Gullotta, A Korte, S Marquardt - Journal of Experimental …, 2023 - academic.oup.com
The growing world population, in combination with the anticipated effects of climate change,
is pressuring food security. Plants display an impressive arsenal of cellular mechanisms …

Proteogenomic links to human metabolic diseases

M Koprulu, J Carrasco-Zanini, E Wheeler… - Nature …, 2023 - nature.com
Studying the plasma proteome as the intermediate layer between the genome and the
phenome has the potential to identify new disease processes. Here, we conducted a cis …

Genome‐wide association study and network analysis of in vitro transformation in Populus trichocarpa support key roles of diverse phytohormone pathways and …

MF Nagle, J Yuan, D Kaur, C Ma… - New …, 2024 - Wiley Online Library
Wide variation in amenability to transformation and regeneration (TR) among many plant
species and genotypes presents a challenge to the use of genetic engineering in research …

Epigenetics as a mediator of genetic risk in osteoarthritis: role during development, homeostasis, aging, and disease progression

D Richard, TD Capellini… - American Journal of …, 2023 - journals.physiology.org
The identification of genomic loci that are associated with osteoarthritis (OA) has provided a
starting point for understanding how genetic variation activates catabolic processes in the …

cisDynet: An integrated platform for modeling gene‐regulatory dynamics and networks

T Zhu, X Zhou, Y You, L Wang, Z He, D Chen - Imeta, 2023 - Wiley Online Library
Chromatin accessibility sequencing has been widely used for uncovering genetic regulatory
mechanisms and inferring gene regulatory networks. However, effectively integrating large …

Disease-associated non-coding variants alter NKX2-5 DNA-binding affinity

EG Peña-Martínez, A Rivera-Madera… - … et Biophysica Acta (BBA …, 2023 - Elsevier
Genome-wide association studies (GWAS) have mapped over 90% of disease-or trait-
associated variants within the non-coding genome, like cis-regulatory elements (CREs). Non …

Efferocytosis in atherosclerosis

SS Adkar, NJ Leeper - Nature Reviews Cardiology, 2024 - nature.com
Cardiovascular disease is the leading cause of death worldwide, and it commonly results
from atherosclerotic plaque progression. One of the increasingly recognized drivers of …

Decoding polygenic diseases: advances in noncoding variant prioritization and validation

IM Chin, ZA Gardell, MR Corces - Trends in Cell Biology, 2024 - cell.com
Genome-wide association studies (GWASs) provide a key foundation for elucidating the
genetic underpinnings of common polygenic diseases. However, these studies have …

iPS cell generation-associated point mutations include many C> T substitutions via different cytosine modification mechanisms

R Araki, T Suga, Y Hoki, K Imadome… - Nature …, 2024 - nature.com
Genomic aberrations are a critical impediment for the safe medical use of iPSCs and their
origin and developmental mechanisms remain unknown. Here we find through WGS …