Bioinformatics and Molecular Evolution

We collaborate with experimental biologists to model the structure, function and evolution of proteins and RNAs. We are consulting now in work to be published on RNA-seq analysis in neural and microbial systems, metagenomic binning using tRNA signatures, analysis of tRNA evolution in eukaryotic genomes, and adaptation in bacterial protein synthesis.

The tRNA Interaction Network

We study the tRNA interaction network, a biological information processing system at the heart of protein synthesis in all living cells. Before ultimate execution at the ribosome, a network of tRNAs, other noncoding RNAs, and proteins interact in the cytoplasm to reliably associate amino acids to specific sets of anticodons. This network comprises much, perhaps most, of the material basis of the genetic code.

The Evolution of Human Languages

In our NSF INSPIRE Awarded “Molecules to Minds” projects, in collaborations with Bodo Winter, Rick Dale, and Suzanne Sindi, we are investigating the evolution of senses over words and modeling how population size, structure and diversity influence both the grammatical structure of human languages and how functions are distributed over those structures.

Evolutionary Molecular Systems Biology

The Ardell Laboratory at UC Merced is a computational biology lab. We use computers to investigate hypotheses about genomes and organisms as molecular information-processing systems. We are purely a “dry” lab of scientist-programmers, who analyze and integrate systems biological and genomic data using computational and statistical models. Our aim is to discover new principles governing information flow in living cells. Our goal is to better understand the nature and origin of life, particularly growth, stress-resistance, aging, and disease.

Ardell lab research concerns:

• The evolution of genetic and biological codes and signals, more generally — the evolution of structure-function mappings in biological macromolecules, such as genomes, RNAs and proteins.
• The evolution of tRNA identity and of the tRNA-protein interaction network underlying tRNA biosynthesis and function, including the decoding of genetic messages through translational protein synthesis.
• Molecular evolutionary systems biology and the application of tRNA Class-Informative Features (CIFs) as slowly evolving, vertically inherited, statistically and biolgically robust markers to resolve deep phylogenetic relationships in the Tree of Life.
• Macromolecular interactions as drug discovery targets in eukaryotic pathogens.
• Theoretical biology concerning the origins of genetic (sequence-based) and “biological” (network-based) encodings.

The Ardell Lab belongs to the Quantitative and Systems Biology Graduate Group and the Molecular Cell Biology Unit in the School of Natural Sciences, the Center for Computational Biology, and the Sierra Nevada Research Institute at UC Merced. Prof. Ardell is also an affiliate of the Cognitive and Information Sciences Graduate Group.

The Ardell Lab is also a partner in the National Science Foundation-funded Undergraduate Research Mentorship (URM) program in Computational Biology that is run by UC Merced’s Center for Computational Biology. The URM program is a fantastic way for UC Merced undergraduates to get involved in bioinformatics and computational biology research!