Outreach and research communication
This is a work in progress. Whenever possible, I’ll add materials from recent oral presentations in here. Over time, I will also add older materials from older talks.
Talks
2025
- July 24, 2025: “Beetles, bytes, and branches: integrating artificial intelligence into the taxonomy and phylogenetics of Passalidae” by Larry Jiménez-Ferbans, Cristian Beza-Beza, Anastasiia Duchenko, Aram Mikaelyan, and Denis Jacob Machado. This talk was given at the XLII Annual Meeting of the Willi Hennig Society (The Chinese University of Hong Kong, HKSAR, China). Click here for the Conference Website.
- July 23, 2025: “Advancing phylogenetics for health threats: lessons from the COVID-19 pandemic and beyond” by Omkar Marne and Denis Jacob Machado. This talk was presented as part of Symposium 1: Phylogenetics & Public Health at the XLII Annual Meeting of the Willi Hennig Society (The Chinese University of Hong Kong, HKSAR, China). Click here for the Conference Website.
- July 9, 2025: “AI-driven predictions of phylogenetic trees from zoogeographical data in dactylogyrids (Platyhelminthes: Monogenea): a novel strategy for external phylogenetic support” by Aline Acosta, Anastasiia Duchenko, and Denis Jacob Machado. This talk was given at The 100th Annual Meeting of the American Society of Parasitologists (Winstom-Salem, NC, USA). Click here for the Conference Website.
- May 29, 2025: “Simplifying specimen loans: Ten simple rules for researchers” by Giovanni Yumi Scorsim Omura and Denis Jacob Machado. This talk was given at the SPNHC (Society for the Preservation of Natural History Collections) 2025 Annual Meeting (Lawrence, KS, USA). Click here for the Conference Website.
- April 17, 2025: “FLAVi 2: Increasing Efficiency and Accessibility of Flaviviridae Genome Annotation” by Cayden Jacobsen and Denis Jacob Machado. This talk was given at the UNC Charlotte Undergraduate Research Conference (URC) 2025 (Charlotte, NC, USA). Click here for the YouTube video.
- January 5, 2025: “Unveiling the modulators of mutable collagenous tissue in the brittle star Ophiomastix wendtii: an RNA-Seq analysis” by Reyhaneh Nouri, Vladimir Mashanov, and Denis Jacob Machado. This talk was given by Reyhaneh Nouri at the 2025 Annual Meeting of the Society for Integrative and Comparative Biology (SICB) (Atlanta, GA, USA). Click here for the slide deck.
2024
- October 21, 2024: “How much should we worry about SARS-CoV-2 mutations according to AI?” by Anastasiia Duchenko, under the supervision of Dr. Jun-tao Guo and Dr. Denis Jacob Machado. This talk was given by Anastasiia Duchenko at the 10th Annual Biological Sciences Research Symposium (UNC Charlotte, NC, USA). Additional information is available upon request.
- September 9, 2024: “Unveiling the Modulators of Mutable Collagenous Tissue in the Brittle Star Ophiomastix wendtii: An RNA-Seq Analysis” by Reyhaneh Nouri, Vladimir Mashanov, and Denis Jacob Machado. This talk was given by Reyhaneh Nouri at the 2024 Biomedical Sciences Symposium (Charlotte, NC, USA). Contact us for more details.
- July 30, 2024: “Twenty years after: What larval characters are still telling us about the phylogeny of frogs (Amphibia: Anura)” by Pedro Henrique dos Santos Dias, Alexander Haas, and Denis Jacob Machado. This talk was given by Dr. Jacob Machado at the XLI Annual Meeting of the Willi Hennig Society (Mexico City, Mexico) and is available in Zenodo.
- June 14-17, 2024: “Mitogenome organization, diversity, and evolutionary relationships of proteocephalidean tapeworms (Cestoda, Onchoproteocephalidea) unveiled by a genome skimming approach” by Philippe V. Alves, Reinaldo J. da Silva, Daniel Janies, Willian Taylor, April Harris, Gari New, and Denis Jacob Machado. A presentation for the 99th Annual Meeting of the American Association of Parasitology (ASP) (Zenodo)
- June 14-17, 2024: “Machine learning models accurately predict clades of proteocephalidean tapeworms (Onchoproteocephalidea) based on host and zoogeographical data” by Philippe Vieira Alves, Reinaldo J. da Silva, Alain de Chambrier, José L. Luque, Anastasiia Duchenko, Daniel Janies, and Denis Jacob Machado. A presentation for the 99th Annual Meeting of the American Association of Parasitology (ASP) (Zenodo)
- June 11-14, 2024: “Evidence of recombination in dengue virus (DENV)” by by Hugo de Paula Oliveira, Paula Prieto Oliveira, Denis Jacob Machado, and Kary Ocaña. A presentation for the X-Meeting 2024 (Brazilian Bioinformatics Conference, Salvador–BA, Brazil). The presentation is available upon request (contact Dr. Kary Ocaña)
- March 22, 2024: “How can we reversibly control collagen pliability? An investigation of mutable collagenous tissues in the brittle star Ophiomastix wendtii” by Reyhaneh Nouri, Vladimir Mashanov, and Denis Jacob Machado. This talk was given by Reyhaneh Nouri at the UNC Charlotte’s 23rd Annual Graduate Research Symposium (Charlotte, NC, USA). Contact us for more details.
2023
- December 27-29, 2023: “Replicating Ford et al.’s investigation on the immune consequences and antibody binding affinity of SARS-CoV-2 variant XBB.1.5 using an in silico approach” by Hannah Zeru, Cameron Jones, and Denis Jacob Machado, a presentation for the 7th International Conference on Interdisciplinary Research on Computer Science, Psychology, and Education (ICICPE’ 2023) (Zenodo)
- November 17, 2023: “How can we reversibly control collagen pliability? An investigation of mutable collagenous tissue in the brittle star Ophiomastix wendtii” by Reyhaneh Nouri, Vladimir Mashanov, and Denis Jacob Machado, presented at UNC Charlotte’s 9th Annual Biological Sciences Research Symposium Program (click here)
- November 17, 2023: “A phylogenomic and machine learning framework for discriminating SARS-CoV-2 variants” by Omkar Marne and Denis Jacob Machado, presented at UNC Charlotte’s 9th Annual Biological Sciences Research Symposium Program (click here)
- July 11, 2023: “Combining phylogenetic and artificial intelligence to unravel viral recombination,” a talk given at the XL Annual Meeting of the Willi Hennig Society – Cornell University, Ithaca, N.Y., U.S.A. (click here)
- June 15, 2023: “What is phyloinformatics and how can it help us respond faster to health emergencies?,” a talk prepared as response to an invitation from Dr. Jhon Ospina-Sarria – Calima Foundation, Cali, Valle del Cauca, Colombia (click here)
2022
- September 16, 2022: “What is phyloinformatics and how can it help us respond faster to health emergencies?,” a talk given by Dr. Denis Jacob Machado at CCI’s Academic Research Seminar – Charlotte, NC, USA.
Posters
2025
- April 23, 2025: “Automated Protocol for Testing Crucial Mutations in Coronaviruses Using AI: Insights into Immune Escape and Resistance,” by Anastasiia Duchenko, Daniel Janies, and Denis Jacob Machado at Mutations in Time and Space 2025 Conference – Broad Institute of MIT and Harvard, Cambridge, MA, USA (click here to go to the GitLab project)
Fall 2024 Bioinformatics Poster Showcase
The Bioinformatics Graduate Student Poster Presentation happened Friday, November 22nd at 3:30pm (immediately following our Bioinformatics Seminar series) on the 2nd floor of the bioinformatics building (9331 Robert D. Snyder Rd, Charlotte, NC 28262, USA). Below, we list each of our students, their poster titles, and the link for the poster and digital materials:
- Anastasiia Duchenko (Ph.D. student): “SARS-CoV-2 mutations in Spike RBD and its impact on the docking to antibodies and ACE2”. Click here to go to GitLab.
- Prudvi Ragi (Master’s student): “Investigating sodium voltage-gated channel alpha subunit 4 (SCN4A) mutations in poison frogs”. Available at Click here to go to GitLab.
- Shivam Patel (Master’s student): “Docking analyses to identify mutations in the sodium channels of poison dart frogs that may confer resistance against lipophilic alkaloids”. Available at Click here to go to GitLab.
- Tulasi Arla (Master’s student): “New software for recombination simulation and phylogenomic character categorization”. Available at Click here to go to GitLab.
- Vedika Judyani (Master’s student): “Viral recombination detection using machine learning”. Available at Click here to go to GitLab.
Additional Poster Presentations of 2024
- July 26, 2024: “Training a natural language processing tool to parse and standardize species descriptions and create searchable databases to assist taxonomists on Passalidae (bess beetles) identification: preliminary data using chatGPT” by Amariah Robinson and Denis Jacob Machado. This student project and presentation was funded by CCI’s REU program “Smart and Secure Future Computing” (NSF #2244424). See the poster and supplementary materials in GitLab.
- July 26, 2024: “Leveraging Convolutional Neural Networks (CNNs) for Accurate Identification of Passalidae Species to Aid Ecological Research and Global Warming” by Manish Kota and Denis Jacob Machado. This student project and presentation was funded by CCI’s REU program “Smart and Secure Future Computing” (NSF #2244424). See the poster and supplementary materials in GitLab.
- June 11, 2024: “Recombinant analyses in dengue virus type 1 with RDP5” by Hugo de Paula Oliveira, Paula Prieto Oliveira, Denis Jacob Machado, and Kary Ocaña. A presentation for the X-Meeting 2024 (Brazilian Bioinformatics Conference, Salvador–BA, Brazil) (click here)
2023
- July 28, 2023: “Replicating Ford et al.’s investigation on the immune consequences and SARS-CoV-2 antibody’s binding affinity using an in silico approach” by C. Jones, H. Zeru, and D. Jacob Machado (click here)
- April 28, 2023: “Are there alkaloid-resistance mutations in Phyllobates terribilis’ sodium channels?” by R. Nouri and D. Jacob Machado. Poster presenter at the Spring graduate poster session of UNC Charlotte’s Dept. of Bioinformatics and Genomics – Charlotte, NC, USA (click here)
- April 28, 2023: “A phylogenomics and machine learning framework for discriminating SARS-CoV-2 variants” by O. Marne and D. Jacob Machado. Poster presenter at the Spring graduate poster session of UNC Charlotte’s Dept. of Bioinformatics and Genomics – Charlotte, NC, USA (click here)
Event organization
Symposium on “Phylogenetics & Public Health: Lessons From COVID19 and Emerging Threats” at the XLII Hennig Meeting (July 22-25, 2025)
Description
How can evolutionary trees help us respond to pandemics? This symposium brings together scientists from across the globe to explore the power—and limits—of phylogenetics in public health. We will examine how researchers have used evolutionary methods to trace outbreaks, detect zoonotic spillovers, monitor variants, and inform policy. From SARS-CoV-2 to emerging viruses, join us to rethink what phylogenetics can do in a time of global health uncertainty.
Program
July 23, 2025:
- 9:00 AM:Symposium welcome & introduction, by Denis Jacob Machado (University of North Carolina at Charlotte)
- 9:10 AM: “H5N1 Influenza A is now promiscuous in host range and has improved replication in mammals,” by Sayal Guirales-Medrano (University of North Carolina at Charlotte) et al.
- 9:40 AM: “Evolutionary adaptations of papillomaviruses: understanding carcinogenicity through host-virus coevolution,” by Dr. Zigui Chen (The Chinese University of Hong Kong)
- 10:10 AM: “Evolutionary trait of the mpox virus in its recent epidemics and clinical association,” by Dr. Maggie Wang & Jingzhi Lou (The Chinese University of Hong Kong)
- 11:00 AM: “Genomic surveillance and molecular epidemiology of SARS-CoV-2 in Hong Kong,” by Dr. Haoga Gu (The University of Hong Kong)
- 11:30 PM: Symposium 1 conclusion, with the talk “Advancing phylogenetics for health threats: lessons from the COVID-19 pandemic and beyond,” by Dr. Denis Jacob Machado & Omkar Marne (University of North Carolina at Charlotte)
XLII Meeting of the Willi Hennig Society
The “Phylogenetics as Applied to Infectious Diseases” Symposium at the XL Hennig Meeting
This symposium was organized by Drs. Daniel Janies and Denis Jacob Machado at the The XL Annual Meeting of the Willi Hennig Society (Cornell University, Ithaca, NY July 9th -13th, 2023). The symposium took place on July 11, 2023.
Program
- 1:30-2:10 pm, Janies: “Phylogenetics as applied to infectious diseases”
- 2:10-3 pm, Czech & Stamatakis: “Leveraging phylogenetic placement to understand the environmental drivers of microbial community composition”
- 3-3:40pm, Dornburg, Hassler, and Townsend: “An evolving future for pandemic preparedness: evolutionary medicine and phylogenetic comparative methods inform the durability of SARS-CoV-2 immunity”
- 4:10-4:50 pm, Ocaña, Silva, Coelho, Terra, & Osthoff: “Phylogenetic and evolutionary analysis of dengue virus serotypes in Brazil: User-steering in large-scale phylogenomic workflows”
- 4:50-5:30 pm, Jacob Machado: “Combining phylogenetic and artificial intelligence to unravel viral recombination”
SBE meetings (2020-22)
In response to the COVID-19 pandemic, our lab has co-founded and co-organized Virtual Meetings in Systematics, Biogeography, and Evolution (SBE), also known as the SBE meetings.
The main goals of the Virtual Meetings of Systematics, Biogeography, and Evolution are:
- First, provide a high-quality international scientific meeting on systematics, biogeography, and evolution.
- Second, make the event accessible to people that could have difficulty attending other international scientific events due to financial constraints or the COVID-19 pandemic.
- Third, promote diversity and gender equality in science, technology, agronomy, mathematics, and medicine (STEAMM).
For those reasons, the first three editions (2020, 2021, and 2022) of the SBE meeting were 100% online and 100% free for all attendees.