Research

Welcome to my research page! I will update this page periodically with what kind of research I’m doing, as well as where I’m doing it. (As of now, this page is under construction.)

My research interests primarily lie in neuroscience, memory, neurodegenerative diseases, and genomics.

Aminode

Aminode is a web tool that I co-created with Junyan Guo that is capable of identifying regions of evolutionary importance in any protein. With precomputed and preloaded analyses for almost the entire human protein coding genome, all you need to do is to enter a gene name into Aminode to get a high quality evolutionary analysis. Try it out here: www.aminode.org. I lead this investigation at the Sardiello Lab in conjunction with my co-authors and good friends, Junyan Guo, Dr. Alberto di Ronza, and of course, Dr. Marco Sardiello.

Aminode works on a basis of evolutionary constraint. To put it simply, consider a gene that you, as a human, have in common with a fish. Evolutionary speaking, you and the fish are extremely distant relatives. You can therefore expect to see many differences in amino acids when comparing the two genes. However, if there is the same amino acid, at the same spot and in the same gene between the fish and you despite the evolutionary gap- that spot must be very important. Aminode is all about identifying these areas of conservation in proteins.

CLN8

Aminode generated analysis for the gene CLN8. The red line indicates conservation, and the yellow bars on top of the graph denotes evolutionary constrained regions (ECRs).

Above is an Aminode generated analysis, and it contains a lot of information inside. On the side, you can see all the species that were analyzed to produce this graph. The red line indicates conservation by substitution, so the lower the line, the more conserved that area is, and the more important it must be to the function of the protein. The yellow bar on top of the graph denotes evolutionary constrained regions (ECRs), which are areas that Aminode thinks are especially important due to the relative conservation of that area compared to the areas around it. At a glance, you can see the conservation of each column of amino acids by the color. Colors are assigned to each column using a gradient from green to blue, with green as the least conserved, and blue as the most conserved.

So what can you use Aminode for? Genetic disease is generally caused by mutations in the genome. Inside me (and you too), there are thousands and thousands of genetic mutations in our genome. But why don’t I have a genetic disease? After all, genetic diseases can be caused by mutations in DNA bases, right? This discrepancy is because a large amount of these mutations are silent, which mean it does not lead to an amino acid change in the protein that the gene encodes for. Furthermore, some of these mutations that do lead to an amino acid change are benign and not pathogenic since the amino acid substitution is not in an important enough part of the protein to completely produce a defect. Sometimes, however, one of these mutations are in the wrong spot- a spot that is integral to the protein function- and it causes a devastating genetic disease.

You can imagine that it is an incredibly hard task for clinical geneticists or medical doctors to correctly diagnose patients that are suspected to have a genetic disorder or disease. You would have to sift through a huge amount of silent and benign mutations to find the correct pathogenic mutation! With Aminode, we hope to make that process much easier. If the mutation is in an ECR, chances are good that it will be deleterious. Aminode can be of great use to clinical geneticists and other medical doctors in the field.

Picture1

Aminode generated graph for PPT1, with all patient mutations mapped onto the graph.

Don’t believe me? We took real patients, and the mutations that cause their disease, and mapped their mutation onto our analyses. Above is a sample graph, with patient mutations mapped onto the gene PPT1. The green dots are where there are pathogenic, deleterious mutations. Most of those dots fall into Aminode predicted ECRs! After analyzing the entire genome with all publicly known patient mutations, nearly 60% of mutations fall into the Aminode ECRs.

There are many more uses for Aminode, but I can’t fit it all here. Instead, you can read all about it in the full paper that has now been published at Scientific Reports!

Sardiello Lab

My work as an assistant at the Sardiello Lab revolves around attempting to cure the type 8 variant of Neuronal Ceroid Lipofuscinosis. I assist Dr. Alberto di Ronza with his work under the supervision of Dr. Marco Sardiello. Much of this work is still confidential, but we are making great headway. I hope to share with you all good news soon.

If you want to learn more about our research in general, see our website here!

National Aeronautics and Space Administration (NASA)

My work at NASA involved the investigation and evaluation the use of commercial EEG devices for astronautic usage. Data gathering is underway, and I will update this page soon. This work was conducted under the supervision of Chelsea Iwig, M.S., a NASA Human Factors engineer.