Larry Mays Seminars in Bioinformatics

Zoom link for December 1, 2023: click here (Meeting ID: 916 4758 5746, Passcode: 0471277)

UNC Charlotte’s Department of Bioinformatics and Genomics (BiG) hosts a weekly seminar series named after Dr. Lawrence Mays (Emeritus Faculty). The Larry Mays Seminars in Bioinformatics covers research within Bioinformatics, Genomics, and Computational Biology. Seminars are free and open to the public. Seminars take place on Fridays at 2:30- 3:30 PM. All seminars are hosted from the Bioinformatics building, room 105. Please contact Dr. Denis Jacob Machado or Dr. Laurel Yohe for questions or suggestions.

The seminars are also a one-credit graduate course (BINF-6600 and BINF-8600 combined). The instructor for the Fall 2023 semester is Dr. Jacob Machado and Dr. Yohe in Spring 2024. Students enrolled in BINF-6600 or BINF-8600 can see course details on CANVAS.

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Schedule for the Spring semester of 2024:

• 1/19 (in person): Dr. Aaron Bivins, Lousiana State University
• 1/26 (remote): Dr. Liliana Dávalos, Stony Brook University
• 2/2 (in person): Dr. Morgan Carter, UNC Charlotte (CIPHER)
• 2/9 (in person): Dr. Yaniv Brandvain, University of Minnesota
• 2/16 (in person): Dr. Wynn Meyer, Lehigh University
• 2/23 (in person): Dr. Philipp Brand, Rockefeller University
• 3/1/24 (in person): Dr. Juan Vivero-Escoto, UNC Charlotte (CIPHER)
• 3/8/24: No seminar, Spring Break
• 3/15/24 (in person): Dr. Alejandro Damian-Serrano, University of Oregon
• 3/22/24 TBD
• 3/29/24: No seminar, Refresh Week
• 4/5/24: Dr. Bob Goldstein, UNC Chapel Hill
• 4/12/24: Dr. Meredith Yeager, National Cancer Institute
• 4/19/24: Dr. Elise Lauterbur, University of Arizona
• 4/26/24: No seminar, Spring Break

Zoom link for in-person attendance is available upon request. Please e-mail Dr. Laurel Yohe (lyohe1@uncc.edu) for the link.

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PREVIOUS EVENTS (FALL 2023)

I. September 8, 2023: UNC Charlotte’s HPC student group will introduce a new training module for our research clusters.

The Charlotte HPC Group gave the 9/8 seminar. This new student organization is focused on advancing high-performance computational skills for users of all levels across campus. They do this through various means, including in-person workshops, peer support, and online Canvas training. This day, they briefly showed the new module and told us about some of the other activities they have on the horizon. This seminar was informative for people who are new to the cluster or don’t even have an account and for more experienced users who want to expand their knowledge and find additional resources. The module is already available to the 49er community. Please use this form to request additional information.

II. September 15, 2023: Dr. Ward Wheeler talks about multi-armed bandits, Thompson sampling, and machine learning in phylogenetic graph search, among other topics.

Dr. Ward Wheeler visited in person on 9/15 coming from the Division of Invertebrate Zoology American Museum of Natural History, New York, NY, USA. In his talk, he talked about something cool called the multi-armed bandit problem in the context of phylogenetic graph searching. He uses a technique called Thompson sampling on a bunch of ‘search-bandits’ to help focus on search strategies that work best. This smart random sampling method turns out to be super effective in creating really good phylogenetic graphs, and it’s quicker than other random search methods. It’s like an unsupervised machine learning strategy that we can use on all sorts of phylogenetic data, even if we don’t know much about them beforehand.

III. September 22, 2023: Dr. Lucas Czeck talks about population genetic statistics for the next generation of pool sequencing.

In recent decades, so-called Evolve-and-Resequence (E&R) experiments have become a popular approach to survey rapid evolution of populations over multiple generations. These experiments allow us to measure shifts in the allele frequencies of a population in response to new or shifting environmental conditions, such as a changing climate.

Pool-sequencing of several individuals at once is a cost-effective and efficient tool to obtain reliable allele frequencies from a population of thousands to hundreds of thousands of individuals, and is often used in E&R experiments. However, specialized tools to efficiently analyze these data that take sampling noise stemming from the pool-sequencing approach into account were lacking. We developed two software tools to overcome statistical and bioinformatic challenges arising in this context.

First, we present grenepipe, a workflow from raw sequencing data of individuals or pooled populations to genotypes (variant calling) and population allele frequencies. The pipeline automates trimming, mapping, variant calling, and quality control, with a selection of popular software tools in each of these steps, and produces variant calls and frequency tables. While generally applicable to individual sample data, it offers specialized steps for pool-sequencing. Our software downloads all dependencies and runs all steps automatically using a single command line call, and parallelizes processing for computer cluster environments, allowing large datasets to be analyzed efficiently.

Second, to enable inferences of evolutionary signatures from frequency data, we created grenedalf, a C++ command line tool to compute population genetic statistics. It computes unbiased statistics of Fst, Pi, Tajima’s D with pool-sequencing data, far outperforming alternative tools, and fixing long-standing issues in the existing tools. Further it offers novel data exploration tools such as windowed allele frequency spectrum visualizations based on the allele frequencies, and built-in data filters and manipulations. Apart from its speed, it offers many convenience options, such as reading all standard file formats.

These tools are designed for scalability and ease-of-use with contemporary file formats, which we showcase using the GrENE-net.org project, a large-scale Evolve-and-Resequence experiment with Arabidopsis thaliana from across the world. We will present some preliminary results form that experiment, showcasing the use of the above tools, as well as demonstrating how E&R experiments can be used to investigate rapid evolution under differing environmental conditions such as caused by climate change.

Recommended publications:

• Click here for the grenepipe paper.
• Click here for the grenedalf preprint (submitted to Bioinformatics).

IV. September 29, 2023: Dr. Cathy Moore (Biosafety Officer at UNC Charlotte’s Division of Research) gives a special presentation.

Dr. Cathy Moore provided Biosafety Training for Graduate Students.

Dr. Moore is the University contact for:

• Handling and working with biological agents on campus
• Institutional Biosafety Committee protocol review and approval process
• Risk assessment and risk mitigation for biological agents and materials
• Use of select agents
• Dual Use of Research Concern
• Biosafety training courses and requirements
• Microbiological and Biomedical facilities renovation and design

V. October 6, 2023: Dr. Viviana Monje-Galvan (University at Buffalo) talks about an atomistic view of protein-lipid interactions at the cell membrane interface.

• Talk description: My research group uses all-atom molecular dynamics to study lipid-lipid and lipid-protein interactions. One of our goals is to determine the role of specific lipid species in disease mechanisms. We specialize in developing realistic membrane models that reproduce the physical environment of a given organism or cell organelle using key lipid species for that particular membrane. In this talk, I will present a protein-membrane study in the context of hepatitis C. Specifically, the molecular signature that results upon protein binding and the associated local membrane response when different lipid species are used to model the membrane. These results help us understand the lateral reorganization of lipids around proteins and the potential impacts of chronic hepatitis C and lipid redistribution, particularly near fat storages of the cell.
• Short Bio: Dr. Monje-Galvan is originally from Bolivia; she completed her undergraduate and graduate studies in Chemical Engineering at the University of Maryland-College Park. She completed her postdoctoral training at the University of Chicago, where she continued strengthening her background in computational biophysics. She started her lab at the University at Buffalo in January 2021, where she leads a diverse group of graduate and undergraduate students. She is actively involved with AIChE and the Biophysical Society, as well as her university, in efforts to promote the participation of women and minorities in science and engineering. She is a board member of LatinXinChE, an affinity group within MAC AIChE, AIChE CoMSEF, and is an active volunteer with the Society for Biophysicists of Latinamerica (SoBLA).

VI. October 13, 2023: Dr. Muhammad Iqbal Qureshi (Public Health Reference Laboratory and Khyber Medical University) gives a talk entitled “Genetic Recombination Potentially Drives Astrovirus Diversity in Camelids.”

VII. October 20, 2023: Dr. Brian Cleary (Assistant Professor at Boston University’s College of Engineering) discusses new technologies and algorithmic experimental designs to study intracellular and intercellular circuits.

VIII. November 3, 2023: Dr. Carla Osthoff Ferreira de Barros (National Laboratory of Scientific Computing, Brazilian Ministry of Science, Technology and Innovation) gives a seminar on developing efficient scientific gateways for supercomputer environments supported by deep learning models.

Dr. Carla Osthoff Ferreira de Barros graduated in Electrical Engineering from the Pontifical Catholic University of Rio de Janeiro with a master’s and a doctorate in Computer Engineering Systems from the Federal University of Rio de Janeiro. She is currently a researcher in the area of High-Performance Computing at the National Laboratory for Scientific Computing (LNCC), a professor at the Multidisciplinary Graduate Program at LNCC, a member of the Consultative Committee of the Supercomputer Santos Dumont, coordinates the LNCC National Center for High-Performance Processing (CENAPAD), and the High-Performance Processing Sector of LNCC, which has several collaborative projects in the area of High-Performance Computing. Her research focuses on High-Performance Computing, Parallel Programming, and scientific application performance optimizations.

IX. November 17, 2023: Dr. Grace Wyngaard talks about chromatin diminution and genome stability in a talk that unravels the role of transposable elements in a remarkable adaptation in copepods

Dr. Grace Wyngaard has been working at the “fringes” of science – chromatin diminution in copepods, spending most of her career at James Madison University. This allowed her to pursue what she was most interested in… and only what she was most interested in. It allowed her to take big risks in testing and developing novel hypotheses because she did not have to keep a large lab machine operating each year. In her talk, Dr. Wyngaard will share with us the results of a career in science in which she could work slowly and steed to produce astonishing outcomes.

X. December 1, 2023: Dr. Joshua David Campbell, from Boston University, will give a talk about his work using computational biology and bioinformatics with applications ranging from identifying early drivers of lung cancer to developing therapeutics for Chronic Obstructive Pulmonary Disease (COPD)

Dr. Joshua D. Campbell is an Associate Professor at Boston University (Division of Computational Biomedicine, Department of Medicine). He is also a member of the BU-BMC Cancer Center and an affiliate member of the Broad Institute of MIT and Harvard. He has received the Boston University Ralph Edwards Career Development Professorship and LUNGevity Career Development Award. He is also a Boston University Clinical and Translational Science Institute (CTSI) KL2 Scholar.

Dr. Campbell’s research interests include computational biology and bioinformatics applied to identifying early drivers of lung cancer. He is also interested in the therapeutic development and pathogenesis of Chronic Obstructive Pulmonary Disease (COPD), the 3rd leading cause of death globally (updated in December 2023). To learn more about his research interests, the software developed by his team, and their most recent publications, please click here.

Zoom link for December 1, 2023: click here (Meeting ID: 916 4758 5746, Passcode: 0471277)