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Building Science at the Intersection of Everything: Three Years of the Phyloinformatics Lab
When I joined UNC Charlotte’s CIPHER center as an Assistant Professor in August 2022, I arrived with a laptop, a set of ideas, and a deep conviction that the best science happens at the intersection of disciplines, borders, and generations of researchers. Three years later, the Phyloinformatics Lab has grown into something I am genuinely proud of: a research group that has secured competitive funding at the national and international levels, published peer-reviewed work in high-impact journals, trained a cohort of students who are winning their own awards, and built a collaboration network spanning four continents.
This post is an honest account of that journey — the wins, the near-misses, and the proposals still in flight — because I believe that transparency about the full arc of scientific effort matters just as much as celebrating the successes.
The Lab’s Philosophy: Science as a Team Sport
The Phyloinformatics Lab sits at the crossroads of evolutionary biology, machine learning, and public health. We use phylogenetics — the science of reconstructing evolutionary trees — as a lens through which to understand how pathogens emerge, how genomes are organized, and how biodiversity can be harnessed for biomedical innovation. Our work is computational at its core, but it is motivated by real-world urgency: the next pandemic, the next antibiotic-resistant parasite, the next biomaterial that could revolutionize regenerative medicine.
None of this work happens alone. From the beginning, I made a deliberate choice to build the lab around collaboration — with colleagues at UNC Charlotte and across the world, and above all, with students at every career stage. The results of that philosophy are now visible in our funding record, our publications, and the independent achievements of our trainees.
Federal and International Funding: A Diversified Portfolio
Joining the National Biodefense Response
In 2023, our lab became part of one of the most ambitious antiviral research initiatives in the United States. Through a subaward from the Rapidly Emerging Antiviral Drug Development Initiative – Antiviral Drug Discovery (READDI-AViDD) Center, led by the University of North Carolina at Chapel Hill and funded by the National Institutes of Health (NIH/NIAID), the Phyloinformatics Lab received $462,000 to lead a computational component focused on large-scale virtual screening of candidate antiviral compounds.
The project — running from May 2023 through April 2025 — brings together machine learning and high-performance computing to predict, at scale, which molecules are most likely to bind to viral protein targets, including those of alphaviruses such as Chikungunya, Eastern equine encephalitis virus, and Venezuelan equine encephalitis virus. In a world still recovering from COVID-19 and bracing for the next outbreak, this kind of work is not abstract: it is the computational infrastructure of pandemic preparedness.
Being part of a U19 center grant at this stage of my career is a rare opportunity, and I did not take it lightly. The READDI-AViDD collaboration brought rigorous timelines, strict reporting requirements, and the experience of doing science at the scale of national health security. It also confirmed something I had long suspected: computational labs like ours, when properly resourced, can contribute disproportionately to large consortia.
Building Bridges to Brazil
Long before I arrived at UNC Charlotte, I had deep roots in Brazilian science. My Ph.D. was earned at the University of São Paulo; my postdoctoral fellowship was conducted at UNC Charlotte, but my collaborators in Brazil never stopped being partners. Sustaining and formalizing those relationships has been one of my proudest accomplishments as a faculty member.
In 2023, I co-wrote a proposal with the Brazilian National Laboratory for Scientific Computing (LNCC) — an entity of the Brazilian Ministry of Science, Technology, and Innovation — that brought together eight institutions from four countries. The proposal aimed to apply artificial intelligence and phylogenetics to the detection of viral genome recombination events, a critical challenge in understanding and responding to emerging diseases such as Dengue, Zika, and Chikungunya. The Brazilian National Council for Scientific and Technological Development (CNPq) positively reviewed the proposal in its first submission, and after refinement, the project was officially funded in late 2024 under the CNPq/MCTI/FNDCT Conhecimento Brasil program.
The funded project, “ARISE in HPC: Artificial Intelligence for Recombination Identification and Surveillance in Epidemiology in a CAD Environment,” runs from December 2024 through December 2026 and supports international researcher mobility, technical exchanges, and conference participation. It represents exactly the kind of science I set out to do: methodologically ambitious, internationally connected, and directly relevant to public health challenges in the Global South.
That same network produced another funded partnership. In collaboration with Dr. Philippe Vieira Alves — a postdoctoral researcher from Brazil — we prepared and submitted a proposal to the São Paulo Research Foundation (FAPESP) for a Research Internship Abroad grant. FAPESP funded the proposal, supporting a 12-month postdoctoral stay at the Phyloinformatics Lab within UNC Charlotte’s CIPHER center. During that year, Dr. Vieira Alves and our team sequenced the mitochondrial genomes of fish tapeworms using genome skimming, and together we reviewed the phylogenetic relationships of all proteocephalid tapeworms. That work has since resulted in peer-reviewed publications in Cladistics and the International Journal for Parasitology.
Contributing to NSF-Funded Education
I also serve as Senior Personnel and Mentor on the NSF REU Site: Smart and Secure Future Computing, a $362,520 award that brings undergraduate researchers to UNC Charlotte for a nine-week summer experience. My role in this program has allowed me to connect the next generation of computing students with “omics” research and host-pathogen biology — fields they might otherwise never encounter. This is science education as recruitment: showing talented undergraduates that the boundaries between computer science and life science are, in the best labs, completely artificial.
From Seed Grant to Patent to Pipeline
Not all good science starts with a federal grant. In 2022–2023, UNC Charlotte’s internal Faculty Research Grant (FRG) program awarded our lab $8,000 to pursue a seemingly niche question: what genes control the remarkable mechanical properties of mutable collagenous tissue (MCT) in echinoderms — the sea stars, sea urchins, and brittle stars whose bodies can shift from rigid to fluid-like in seconds?
That seed grant turned out to be one of the highest-return investments of my career so far. The work led to a peer-reviewed publication in BMC Genomics, a provisional patent application with the U.S. Patent and Trademark Office, and the foundation for a pending proposal to the National Science Foundation’s Division of Integrative Organismal Systems. It also funded the first major research project of Ph.D. student Reyhaneh Nouri, who has since built an independent funding record that any early-career researcher would be proud of.
Recognizing the computational demands of this and other projects, I also co-led a successful $80,000 request to UNC Charlotte’s Academic Affairs for one-time infrastructure funding, acquiring 64 compute cores and 4 GPUs for the CIPHER center’s research cluster. Good science requires good tools, and securing that infrastructure for the entire center — not just my lab — was a deliberate act of institutional investment.
The Proposals That Did Not Work Out (And Why They Still Matter)
A tenure dossier that only lists successes is an incomplete picture of a scientist’s ambition and productivity. I believe in being honest about the full scope of my grant activity.
Our lab has contributed to — and in some cases led — several large-scale proposals that were not funded. I served as Co-Investigator and Aim 1 Lead on an approximately $18 million NSF PIPP Phase II proposal on preventing the pre-emergence of zoonotic pathogens, and as Senior Personnel on a roughly $3 million NSF NRT (Research Traineeship) proposal for an interdisciplinary training program. We also prepared, but did not ultimately submit or fund, an NIH R15 AREA proposal on echinoderm tissue regeneration genomics and an NIH/NIAID Mentored Pilot Award through the READDI-AViDD center.
These efforts were not failures. They were evidence of my standing within a community of researchers who sought me out as a credible partner on the most ambitious proposals in our field. They also generated substantial preliminary work, deepened my collaborative relationships, and sharpened my grant-writing skills in ways that directly contributed to the proposals that were ultimately funded. In grant-writing, as in evolution, the variants that don’t survive still matter for what comes next.
Student Success: The Metric I Am Most Proud Of
The most important number in our lab’s funding record is not the total dollars raised. It is this: every Ph.D. student in the Phyloinformatics Lab who has applied for an internal fellowship at UNC Charlotte has been awarded one. That is not a coincidence. It is the result of a deliberate mentorship philosophy that treats student funding as a core responsibility of the lab’s principal investigator.
Here is what that looks like in practice:
Reyhaneh Nouri, a Ph.D. student working on echinoderm mutable collagenous tissue, has assembled a funding record that includes a UNC Charlotte Graduate School Summer Research Fellowship, an Open Access Publication Award from the Atkins Library, a Thomas L. Reynolds Center for Graduate Life & Learning (CGLL) Fellowship, a Lawrence E. Mays Fellowship in Bioinformatics, and an International Student Scholarship — totaling over $15,000 in competitive awards. She was also a Runner-Up for the Parse Biosciences Single Cell Grant and has applied — with my active collaboration and co-writing — for the Graduate Women in Science (GWIS) National Fellowship and the Google PhD Fellowship. Not every application was successful, but every application was a training experience, and the cumulative success rate is remarkable.
Omkar Marne, a Ph.D. student working at the interface of phylogenomics and machine learning, received a Graduate School Summer Research Fellowship and was recognized with an Honorable Mention for the Susumu Ohno Award from EVOLVE — an international recognition of the quality and promise of his dissertation research.
Anastasiia Duchenko received GPSG Travel Funding to present her work at the American Society of Parasitologists meeting, and Giovanna Yumi Scorsim Omura received both a travel award from the Bioinformatics Assembly of Students (for her service as the organization’s President) and the Campus Superhero Award from the Reynolds CGLL, recognizing her extraordinary commitment to her fellow graduate students.
In Summer 2024, I also secured an Office of Undergraduate Research (OUR) Scholar Award to support an undergraduate researcher in viral recombination studies — evidence that our lab’s mentorship extends beyond the Ph.D. level.
These are not peripheral achievements. They are the primary mission. Training the next generation of computational biologists, showing them how to write proposals and articulate scientific value, and connecting them to the broader funding ecosystem is exactly what a research university asks a junior faculty member to do. We are doing it.
A Network Built on Trust
The Phyloinformatics Lab’s collaborative reach is unusual for a three-year-old research group at an early-career faculty stage. Our active and recent collaborations span the READDI-AViDD Center at UNC Chapel Hill, the National Laboratory for Scientific Computing (LNCC) in Brazil, the University of São Paulo (USP), the State University of São Paulo (UNESP), and research partners in Pakistan, Germany, Colombia, and across the United States.
These relationships are not transactional. They are the product of years of shared work, mutual trust, and a genuine commitment to questions that cross national and disciplinary boundaries. When the CNPq reviewed our international proposal and found it competitive, part of what they were evaluating was the credibility of the network behind it. When FAPESP funded Dr. Vieira Alves’s visit to our lab, they were investing in an infrastructure of collaboration that our lab helped build.
Building that kind of network is slow, unglamorous work. It means answering emails at odd hours across time zones, attending meetings that don’t directly advance your own research agenda, and investing in relationships whose payoff may take years to materialize. I believe it is among the most important things a junior faculty member can do, and I am proud of the network we have assembled.
What Comes Next
The lab’s pipeline reflects both the breadth of our scientific interests and the ambition that has characterized our work from the beginning. We are preparing a proposal to NSF’s Division of Integrative Organismal Systems (IOS) that will extend our MCT research into functional morphology and organismal biology. We are pursuing a Translational Research Grant through the NC Biotechnology Center to move our patent-stage MCT discoveries toward real-world application. We have a Fulbright proposal under review that would bring an international collaborator to Charlotte to advance Dengue virus research. And we continue to pursue the ARISE in HPC international collaboration with Brazil, which is now funded and generating new results.
Each of these efforts carries forward the same core logic: ambitious science, done collaboratively, with students at the center of every project.
Closing: Why This Work Matters
Phylogenetics is not always the first thing that comes to mind when people think about pandemic preparedness, regenerative medicine, or drug discovery. That is precisely why it matters so much that there are labs like ours pushing it to the front of those conversations.
The Phyloinformatics Lab has demonstrated, over three years and under conditions that are genuinely difficult for early-career faculty, that computational evolutionary biology is not a niche pursuit. It is a platform. It connects the history of life on Earth to the most pressing biomedical challenges of the present moment. It trains students to think across disciplines and to communicate their work to audiences that span governments, foundations, and the public. And it builds the international relationships that are, increasingly, the only way to tackle problems of the scale and complexity that our moment demands.
We are three years old. We are just getting started.
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