Bioinformatics Seminar Spring 2023 Schedule
January 19th, 2023: Student Introductions
January 26th, 2023: Nick Miller (NorthShore University Health System): "Flype and Bioinformatics at Northshore."
Nick Miller graduated from Loyola with two bachelor's degrees in Biology and Bioinformatics in 2015 and graduated with his Masters in Computer Science in 2016. Nick has worked at NorthShore University Healthcare System on the FLYPE Bioinformatics platform since 2017. In 2021 he was promoted to Associate Director of Bioinformatics and continues to direct the FLYPE program. When not working Nick spends his time trying to keep up with his 2 dogs and 9 month old daughter.
February 2nd, 2023: Mary Makarious (NIH and University College London): "From Data to Insights: The Role of Bioinformatics in Parkinson's Research."
Mary Makarious graduated from Loyola in 2018 with degrees in Bioinformatics, Biology, and Behavioral/Cognitive Neuroscience. Since then, she has been working at the Laboratory of Neurogenetics at the National Institutes of Health (NIH). She is currently a Ph.D. candidate at University College London and the NIH and serves as the co-lead for the Data and Code Dissemination group at the Global Parkinson’s Genetics Program. Her research uses machine learning, data science, and bioinformatic techniques on large datasets to study the risk and progression of Parkinson’s disease and other neurodegenerative diseases. She is particularly passionate about serving underrepresented populations in science, training and mentorship, and open science initiatives.
February 9th, 2023: Dr. Ran Blekhman (University of Chicago): "Functional Genomics of Host-Microbiome Interactions."
Ran Blekhman studies the human microbiome—the collection of all microbes that live in and on the human body—and how these microbes interact with our own genome and genes. His laboratory uses high-throughput genomics technologies and employs computational, statistical, machine learning, and population genetic analytical approaches, with the goal of understanding how we interact with our microbial communities, how host-microbe interactions affect human disease, and how the symbiosis between us and our microbiome evolved. His research has been published in Nature Ecology and Evolution, Nature Microbiology, PLOS Biology, Science, Cell, and eLife, among other journals. He was named a Sloan Research Fellow in the field of computational and evolutionary molecular biology, and a Scialog: Microbiome, Neurobiology, and Disease Fellow. Dr. Blekhman studied biology and computer science at Tel Aviv University and holds a PhD in human genetics from the University of Chicago. He was a postdoctoral research associate at Cornell University, and was faculty at the University of Minnesota Twin Cities, where he was awarded a McKnight Land-Grant Professorship and recognized with a Northrop Professorship. In 2022, Dr. Blekhman moved to the University of Chicago, where he is an Associate Professor in the Section of Genetic Medicine.
February 16th, 2023: Jessica Mattick (PacBio): "Single-cell isoform sequencing with concatenated arrays: bioinformatics challenges & solutions."
Jessica Mattick worked as a lab manager in the Campbell lab in Loyola's department of microbiology and immunology for 4 years. She simultaneously completed her Masters in Computer Science from Loyola in 2021. During the fall of 2020 she was tasked with launching a COVID-19 saliva surveillance program called Safeguard Surveillance to provide same day testing to school children in the Chicago area. She currently works as a Bioinformatics Engineer at PacBio.
February 23rd, 2023: Dr. Amie Settlecowski (Field Museum): "Museum bird specimens provide conservation insights for Bachman's Sparrow and DNA for whole genome sequencing."
Amie is interested in understanding how ecological and evolutionary processes influence the maintenance or erosion of genetic variation and how that relates to species persistence. To date she has inferred phylogenetic relationships and population structure of various birds using molecular lab techniques and a combination of historical DNA from museum specimens and modern DNA from extant populations. Amie studied Ecology and Evolutionary Biology at Tulane University and received her PhD in Renewable Natural Resources with a concentration in Wildlife Biology from Louisiana State University. Now she is a postdoc at the Field Museum, working in the bird collection. She is currently working on characterizing the population genomic trajectories of Ethiopian montane forest perching birds and identifying how best to collect whole genome sequence data from century-old bird study skins.
March 2nd, 2023: Dr. Chris Marshall (Marquette University): "Adaptations in Biofilms: From clinics to climate change."
Dr. Chris Marshall is an Assistant Professor at Marquette University in the Department of Biological Sciences. Dr. Marshall earned his bachelor's degree from Virginia Tech majoring in Environmental Science. He then earned both his Master's and Ph.D. from the Medical University of South Carolina (MUSC) in the Department of Microbiology and Immunology. During his time at MUSC, Dr. Marshall studied several aspects of applied and environmental microbiology with Dr. Hal May. Following his Ph.D., Dr. Marshall won the prestigious Argonne Director's Fellowship at the Department of Energy's Argonne National Laboratory and University of Chicago to work on microbiomes with Dr. Jack Gilbert. Dr. Marshall then took a Research Assistant Professor position at the University of Pittsburgh studying the evolution of antibiotic resistance in high priority pathogens with Dr. Vaughn Cooper. Dr. Marshall joined Marquette University as a tenure track faculty in the Fall of 2019. He has over 40 publications, 2 published patent applications, and is an editor for the journal mSystems.
March 16th, 2023: Dr. Sabrina Absalon (Indiana University): "Decoding New Players in Plasmodium Nuclear Biology using Expansion Microscopy."
Sabrina earns her Ph.D. studying intraflagellar transport in the protozoan Trypanosoma brucei in Dr. Philippe Bastin's lab at Pasteur Institute, Paris. In 2019, after completing a postdoc in Dr. Jeff Dvorin's lab at Boston Children's Hospital, she joined Indiana University School of medicine as an assistant professor. Her lab focuses on deciphering the molecular mechanisms underlying nuclear multiplication during the intraerythrocytic and hepatic development cycle of Plasmodium falciparum, a malaria-causing parasite.
March 23rd, 2023: Dr. Justin Podowski (Argonne National Lab): "Linking Nitrifier Diversity and Nitrification Activity in the Laurentian Great Lakes."
Justin Podowski is an Assistant Data Scientist at Argonne National Laboratory and uses reconstruction of complex microbial communities to inform nuclear non-proliferation and detection of bioweapons. He received his PhD from the University of Chicago where he studied the microbial communities in the Laurentian Great Lakes, and his BS from the University of Illinois at Urbana Champaign.
March 30th, 2023: Dr. Catherine Putonti (Loyola University Chicago): You're More Phage than Human!"
Catherine did her graduate studies at the University of Houston, earning an MS and PhD in Computer Science, followed by an MS in Biology with a concentration in Evolutionary Biology & Ecology. She joined the faculty at Loyola University Chicago in 2007. Presently, she is a Professor in the Department of Biology as well as the Department of Microbiology & Immunology at the Stritch School of Medicine.
April 13th, 2023: Dr. Stepfanie Aguillon (Stanford University): "Integrating genomics and behavioral ecology to understand speciation."
Stepfanie is currently an independent Stanford Science Fellow working in collaboration with the lab of Dr. Molly Schumer. She received her BS and MS from the University of Arizona, where she worked on aggression and dispersal in western bluebirds. She obtained her PhD from Cornell University in 2021 where she developed the northern flicker system.
April 20th, 2023: MS Student Internship Presentations
Anthony Truckenbrod: "Operational Data Analysis at a Microbiological Testing Lab."
Zihan Zheng: "PyloriAR: Analyzing antibiotic resistance in Helicobacter pylori patients."
April 27th, 2023: Dr. Chris Oakley (Purdue University): "Cold comfort and change: unraveling the genetic basis of adaptation and maladaptation."