Phenomics: the next challenge

D Houle, DR Govindaraju, S Omholt - Nature reviews genetics, 2010 - nature.com
A key goal of biology is to understand phenotypic characteristics, such as health, disease
and evolutionary fitness. Phenotypic variation is produced through a complex web of …

Genotype–phenotype mapping and the end of the 'genes as blueprint'metaphor

M Pigliucci - … Transactions of the Royal Society B …, 2010 - royalsocietypublishing.org
In a now classic paper published in 1991, Alberch introduced the concept of genotype–
phenotype (G→ P) mapping to provide a framework for a more sophisticated discussion of …

System-wide molecular evidence for phenotypic buffering in Arabidopsis

J Fu, JJB Keurentjes, H Bouwmeester, T America… - Nature …, 2009 - nature.com
We profiled 162 lines of Arabidopsis for variation in transcript, protein and metabolite
abundance using mRNA microarrays, two-dimensional polyacrylamide gel electrophoresis …

Control of cell identity by the nuclear receptor HNF4 in organ pathophysiology

V Dubois, B Staels, P Lefebvre, MP Verzi, J Eeckhoute - Cells, 2020 - mdpi.com
Hepatocyte Nuclear Factor 4 (HNF4) is a transcription factor (TF) belonging to the nuclear
receptor family whose expression and activities are restricted to a limited number of organs …

Mechanisms and evolution of control logic in prokaryotic transcriptional regulation

SAFT van Hijum, MH Medema… - … and Molecular Biology …, 2009 - Am Soc Microbiol
SUMMARY A major part of organismal complexity and versatility of prokaryotes resides in
their ability to fine-tune gene expression to adequately respond to internal and external …

Phenotypic heterogeneity in human genetic diseases: ultrasensitivity-mediated threshold effects as a unifying molecular mechanism

YH Sun, YL Wu, BY Liao - Journal of Biomedical Science, 2023 - Springer
Phenotypic heterogeneity is very common in genetic systems and in human diseases and
has important consequences for disease diagnosis and treatment. In addition to the many …

Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver

V Dubois, C Gheeraert, W Vankrunkelsven… - Molecular systems …, 2020 - embopress.org
Liver injury triggers adaptive remodeling of the hepatic transcriptome for repair/regeneration.
We demonstrate that this involves particularly profound transcriptomic alterations where …

Macrophage polarization reflects T cell composition of tumor microenvironment in pediatric classical Hodgkin lymphoma and has impact on survival

MHM Barros, P Segges, G Vera-Lozada, R Hassan… - PloS one, 2015 - journals.plos.org
Macrophages have been implicated in the pathogenesis of classical Hodgkin lymphoma
(cHL) and have been suggested to have a negative impact on outcome. Most studies …

Changes in gene expression predictably shift and switch genetic interactions

X Li, J Lalić, P Baeza-Centurion, R Dhar… - Nature …, 2019 - nature.com
Non-additive interactions between mutations occur extensively and also change across
conditions, making genetic prediction a difficult challenge. To better understand the plasticity …

A framework for evolutionary systems biology

L Loewe - BMC systems biology, 2009 - Springer
Background Many difficult problems in evolutionary genomics are related to mutations that
have weak effects on fitness, as the consequences of mutations with large effects are often …