Congratulations to Alli Gombolay (PhD), Courtney Astore (MS), Sonali Gupta (MS), and Aaron Pfennig (MS) who were recognized as the 2020 Outstanding Students in Bioinformatics at Georgia Tech. Each student received a monetary award funded by the J. Leland Jackson Endowed Fellowships Fund in Bioinformatics. Students were selected for demonstrated excellence in their academic studies and their bioinformatics research. We would like to thank our faculty selection committee, Jung Choi, Matt Torres, and Soojin Yi, for evaluating the many nominations received this year.
Alli Gombolay (PhD) is a rising 6th year Bioinformatics doctoral student, advised by Professor Francesca Storici. As a Ph.D. student in Professor Storici’s lab, one of Alli’s main projects has been developing Ribose-Map, the first bioinformatics toolkit for the comprehensive analysis of high-throughput ribonucleotide sequencing data to gain insight into the biological mechanisms that regulate the presence of ribonucleotides in DNA and their effects on genome stability, DNA metabolism, and ultimately human disease. Alli’s work on developing Ribose-Map led to a first-author (and corresponding-author) publication in Nucleic Acids Research. In addition, she also applied Ribose-Map to uncover biological signatures of ribonucleotide incorporation in the DNA of different species, strains, and genotypes of yeast and published this work as co-first author in Nature Communications. Furthermore, Alli has recently developed a protocol for Ribose-Map that will help researchers of all skill-levels apply Ribose-Map to their own sequencing data and interpret the results. She submitted this protocol to Nature Protocols as first-author (and co-corresponding author), and it is currently under review. In addition to four completed publications, Alli has given 13 professional presentations. Finally, she is the inventor of Ribose-Map invention disclosure for new software for analysis of ribose-seq data. According to Professor Storici, “Alli’s work has opened up a series of research lines in the lab, and has markedly contributed to the funding awards our lab received in the last several years, as well as to preparation of new grant applications. Alli has already made impressive achievements and there is no doubt she will continue to make significant contributions to the advancement of science and technology.”
Courtney Astore (MS) is a joint PhD and MS Bioinformatics student who is finishing her MS Bioinformatics degree this fall. Courtney works in Professor Jeffrey Skolnick’s group where she has contributed to the development of a novel algorithm that predicts disease comorbidities, LeMeDISCO, for which a paper is in preparation. LeMeDISCO is advantageous over previously developed methods as it uses a high-coverage disease library with more complete mode of action protein profiles (from her group’s previously developed algorithm, MEDICASCY) that are attributed with each disease. Further, the comorbidity predictions are purely based on shared molecular mechanisms that overlap disease pairs, which is different than previous techniques that merely use text mining and/or other clinical association-based methods. This method is translational as they can determine protein targets with high comorbidity enrichment to determine repurposed drugs to treat an individual disease profile. Courtney’s group has already began applying it to specific disease cases in determining repurposed drugs. For example, they used LeMeDISCO to determine potentially severe adverse events associated with COVID-19 by inputting a set of SARS-CoV-2 interacting human proteins and another set of GWAS identified risk genes, for which a paper is also in-preparation. Professor Skolnick notes, “During the time Courtney has been a member of my research group, I have been uniformly impressed by her curiosity, drive, and passion for science. She asks excellent questions and seeks to excel in all that she does.”
Sonali Gupta (MS) works at the Jordan Lab, where she analyzed whole-genome sequences of 7,000+ foodborne bacterial pathogens. She applied machine learning algorithms to predict the PulseNet pulsed-field gel electrophoresis banding pattern identifiers given the whole genome sequence of unknown foodborne pathogens. Sonali and her team developed a two-level model to predict serotypes and PFGE classes sequentially with an overall accuracy of 72%. Sonali presented her work as a poster at the Biological Sciences Ph.D. Recruitment 2020. She will also be writing and submitting a manuscript for this research during Fall 2020 semester. In summer 2020, Sonali completed an internship with bluebird bio, where she benchmarked Seurat data integration methods for various single-cell RNA sequencing datasets. This work will help guide many of the team's analyses in the future. Professor Jordan says, “Sonali is one of the very best MS students that have come through my lab over the last 14 years. She worked on a high-risk project to classify microbial pathogens that cause foodborne illness, in collaboration with CDC’s PulseNet epidemiological network. Sonali completely turned the project around, fundamentally changed our approach to the problem, and developed her own method, essentially completing the work in two semesters.”
Aaron Pfennig (MS) joined Professor Mark Borodovsky and his team at the beginning of his master’s program in August 2019. Aaron’s work encompassed development of a new algorithm and a pipeline for analysis of viral genomes with genetic code changing along the DNA sequence as well as description of discoveries of the viruses (phages) possessing such unusual properties. Structural and functional annotation of the newly characterized phages residing in the space of human microbiome revealed details of possible evolutionary developed strategies for overcoming bacteria anti-defense mechanisms. Remarkably, the phages with recoded TAG stop codon appear to be able to infect bacteria with the standard genetic code. The results of this multifaceted project will help advance our knowledge on human associated viruses. Currently, they are wrapping up the preparation of a manuscript for publication. Mark Borodovsky notes, “In my thirty-year time conducting Bioinformatics research at Georgia Tech I have rarely, if ever, seen so capable student. In addition to his learning abilities, Aaron is well organized and his productivity is spectacular.” Aaron completed his MS Bioinformatics degree in August, and has just begun his PhD study in the Quantitative Biosciences interdisciplinary graduate program at Georgia Tech.