Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

F Denoeud, S Henriet, S Mungpakdee, JM Aury… - Science, 2010 - science.org
Genomes of animals as different as sponges and humans show conservation of global
architecture. Here we show that multiple genomic features including transposon diversity …

Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes

SP Schrimpf, M Weiss, L Reiter, CH Ahrens… - PLoS …, 2009 - journals.plos.org
The nematode Caenorhabditis elegans is a popular model system in genetics, not least
because a majority of human disease genes are conserved in C. elegans. To generate a …

Models for the retention of duplicate genes and their biological underpinnings

R Assis, G Conant, B Holland, DA Liberles… - …, 2024 - pmc.ncbi.nlm.nih.gov
Gene content in genomes changes through several different processes, with gene
duplication being an important contributor to such changes. Gene duplication occurs over a …

On the need for mechanistic models in computational genomics and metagenomics

DA Liberles, AI Teufel, L Liu… - Genome biology and …, 2013 - academic.oup.com
Computational genomics is now generating very large volumes of data that have the
potential to be used to address important questions in both basic biology and biomedicine …

Toward a general model for the evolutionary dynamics of gene duplicates

A Konrad, AI Teufel, JA Grahnen… - Genome biology and …, 2011 - academic.oup.com
Gene duplication is an important process in the functional divergence of genes and
genomes. Several processes have been described that lead to duplicate gene retention …

Models for gene duplication when dosage balance works as a transition state to subsequent neo-or sub-functionalization

AI Teufel, L Liu, DA Liberles - BMC evolutionary biology, 2016 - Springer
Background Dosage balance has been described as an important process for the retention
of duplicate genes after whole genome duplication events. However, dosage balance is only …

Evolution under fluctuating environments explains observed robustness in metabolic networks

OS Soyer, T Pfeiffer - PLoS Computational Biology, 2010 - journals.plos.org
A high level of robustness against gene deletion is observed in many organisms. However, it
is still not clear which biochemical features underline this robustness and how these are …

Duplication of OsHAP family genes and their association with heading date in rice

Q Li, W Yan, H Chen, C Tan, Z Han… - Journal of …, 2016 - academic.oup.com
Abstract Heterotrimeric Heme Activator Protein (HAP) family genes are involved in the
regulation of flowering in plants. It is not clear how many HAP genes regulate heading date …

Sequence of a complete chicken BG haplotype shows dynamic expansion and contraction of two gene lineages with particular expression patterns

J Salomonsen, JA Chattaway, ACY Chan… - PLoS …, 2014 - journals.plos.org
Many genes important in immunity are found as multigene families. The butyrophilin genes
are members of the B7 family, playing diverse roles in co-regulation and perhaps in antigen …

The former annotated human pseudogene dihydrofolate reductase-like 1 (DHFRL1) is expressed and functional

G McEntee, S Minguzzi, K O'Brien… - Proceedings of the …, 2011 - National Acad Sciences
Human dihydrofolate reductase (DHFR) was previously thought to be the only enzyme
capable of the reduction of dihydrofolate to tetrahydrofolate; an essential reaction necessary …