The Daily Bulletin

Please join us for the Computational Genomics Data Science and AI Panel on Tuesday, April 2, from 6:00 to 7:00 p.m. in Science and Mathematics Complex 151. This panel discussion is part of the Data Science and Analytics Seminar Spring 2024 Series.

PANELISTS

Daniel McSkimming, Lead Bioinformatician, Veterans Affairs National Oncology Program

• Artificial intelligence in medicine and biotech.
• Machine learning approaches are growing in data analytics.
• Analyzing imagery can improve cancer screening and detection.
• Proteins can be modeled as language?

Daniel McSkimming is a Buffalo native who grew up in West Seneca before attending the University at Buffalo for his bachelor's and master's degrees in mathematics. Before attending the University of Georgia for his Ph.D. in bioinformatics, Dr. McSkimming worked in a variety of data-oriented positions, including as a data manager for research labs, an actuarial analyst at Blue Cross Blue Shield, and an intelligence specialist in the United States Navy. He is currently the lead bioinformatician and supervisory data scientist for the VA's national Precision Oncology Program, where he uses gene sequencing technologies to identify medically relevant genomic variation in veterans with cancer. He has authored over two dozen papers, created and deployed machine-learning solutions to complex problems, and enjoys exploring the ability of deep learning networks to act creatively.

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Mark A. Gallo, Professor of Biology, Niagara University
Annotation and analysis of novel Staph bacteriophage genomes

• Isolation of phage—easy, right?
• DNA sequence analysis—why so many holes?
• Genome annotation—guilt by association.
• Challenges and triumphs with undergraduate researchers.

Mark Gallo is the Jack Hughes Endowed Program Director of Pre-professional Health at Niagara University. He began his education at the University of Pittsburgh, where he received his B.S. in biochemistry and biophysics and then his M.S. in biochemistry from the University of Pittsburgh Medical School. He then went to Cornell University, where he received his Ph.D. in microbiology for his research on the evolution of metabolic pathways in bacteria. Afterward, Dr. Gallo pursued postdoctoral research at the University of Wisconsin-Madison School of Pharmacy, where he helped elucidate the genetic pathway for the synthesis of daunorubicin/doxorubicin in Streptomyces. He has been at Niagara University for the past 28 years, where he continues to host an active research program with undergraduate students. His interests include the properties of Staphylococci associated with wild animals, notably their antibiotic resistance profiles. Recently Dr. Gallo has been productive with respect to the ability to isolate bacteriophage that can kill Staph, which can also be isolated from mammals with the end goal being the identification of strains useful for phage therapy.

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Phillip Shults, Research Entomologist, U.S. Department of Agriculture (USDA) Agricultural Research Service (ARS)
Delimiting species with genomics and machine learning

• Some insects can transmit disease-causing pathogens, and it is imperative that we be able to accurately identify these species.
• We used SNP data, obtained from genome sequencing, to investigate cryptic species in a group of insects.
• We used a random forest algorithm to optimized a set of molecular markers for species identification.
• The research branches of the government are always looking for computational biologists or bioinformaticians.

Phillip Shults earned his Ph.D. in entomology from Texas A&M University and has been studying bugs for the past 14 years. Currently, he is a research scientist with the USDA-ARS and has a lab focusing on the genomics of insects that transmit pathogens to livestock. Dr. Shults enjoys investing in his mentored students from various academic backgrounds, so they may achieve academic success and career goals.

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David Molik, Computational Biologist, U.S. Department of Agriculture (USDA) Agricultural Research Service (ARS)
David Molik is a computational biologist specializing in arthropod genomics and is currently working with the USDA-ARS. His experience includes a previous role within the same department at the Pacific Basin Agricultural Research Center, Tropical Crop and Commodity Protection Research Unit (USDA ARS PBARC TCCPRU), where he focused on developing heterochromatin computational software. This software is crucial for creating more precise and practical genomic tools for research in combating agricultural insect pests. Before his tenure at the USDA-ARS, he dedicated his efforts to his thesis at the University of Notre Dame. Before that, he was a scientific informatics developer at Cold Spring Harbor Laboratory.

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John Krolewsky, Adjunct Instructor, Biology and Data Science and Analytics, Buffalo State University
John Krolewsky is a physician-scientist interested in cancer biology and genomics. He was an undergrad at MIT (1977) and an M.D.-Ph.D. trainee at NYU (1984). He has worked at Columbia University, UC Irvine, and the University of Rochester. He “retired” in 2022 from Roswell Park Comprehensive Cancer Center in Buffalo, where he was previously the chair of Cancer Genomics and Genetics. Currently, he is an adjunct instructor in biology and data science and analytics at Buffalo State. He is continuing his research on prostate cancer genomics and helping to develop training programs in computational genomics and AI (using GPTs). He is based in Cambridge, Massachusetts, but also has a house in Buffalo, on Elmwood Avenue.

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Olga Novikova, Ph.D., Assistant Professor, Biology Department, Buffalo State University
Olga Novikova's main research interest is a dynamic of non-LTR and LTR retrotransposons in eukaryotic genomes and their evolutionary impact. Retrotransposable elements play an important role in evolution of eukaryotic organisms. They are ancient, ubiquitous, prevalent, and dynamic components of all eukaryote genomes. The dynamics of the retrotransposon life cycle results in the multiplication of these transposable elements, up to the point where they can occupy major fractions of the genomes, in a wide variety of eukaryotes. By their response to stress, invasiveness, promoter activity, and sheer numbers, as mobile promoters or transcriptional enhancers, retrotransposons can wreak many changes on the genome.