Hello!
I’m Alexander Lucaci

Postdoctoral Associate in Systems and Computational Biomedicine / WEILL CORNELL MEDICINE.

I am a computational biologist studying how microbial communities evolve and interact across urban environments. My work combines evolutionary modeling, comparative genomics, and large-scale sequencing to map and predict microbiome dynamics in cities. I focus on building atlas-scale resources that enable the detection and anticipation of emerging biological signals, with applications in biosurveillance, public health, and urban systems biology.

About me

My current work and research interests include:

Urban microbiome atlas: Leading the development of the Urban Microbiome Atlas (UMA), a globally scalable, queryable map of city-scale microbial ecosystems integrating sequencing, environmental sensing, and geospatial data. The UMA captures how microbial communities shift across transit systems, public spaces, and peri-urban environments, linking composition to variables like climate, air quality, and human density. This enables tracking of adaptation, dispersal, and emerging biological signals, supporting biosurveillance, comparative urban microbiology, and biotechnology discovery.
Predictive biology: Developing computational frameworks that transform evolutionary analysis into a predictive science. Leveraging phylogenetics, codon models, and large-scale genomics, this work identifies real-time signals of adaptation such as positive selection and convergent evolution. By integrating these signals with epidemiological and environmental data, the goal is to forecast viral trajectories, including immune escape and transmission fitness, to inform vaccines, therapeutics, and public health strategy.
Software & infrastructure: Designing reproducible, scalable bioinformatics systems that connect raw sequencing data and environmental inputs to interpretable insights. This includes modular workflows, standardized data schemas, and API-driven architectures for integrating multi-modal datasets, enabling automated analysis, real-time data ingestion, and clear visualization for research and biosurveillance applications.

Publications

highlights

Evolutionary Shortcuts via Multinucleotide Substitutions and Their Impact on Natural Selection Analyses

MBE • 2023

Inference and interpretation of evolutionary processes, in particular of the types and targets of natural selection affecting coding sequences, are critically influenced by the assumptions built into statistical models and tests. If certain aspects of the substitution process (even when they are not of direct interest) are presumed absent or are modeled with too crude of a simplification, estimates of key model parameters can become biased, often systematically, and lead to poor statistical performance.

RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysis

PLoS ONE • 2022

An important unmet need revealed by the COVID-19 pandemic is the near-real-time identification of potentially fitness-altering mutations within rapidly growing SARS-CoV-2 lineages. Although powerful molecular sequence analysis methods are available to detect and characterize patterns of natural selection within modestly sized gene-sequence datasets, the computational complexity of these methods and their sensitivity to sequencing errors render them effectively inapplicable in large-scale genomic surveillance contexts.

Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes

PLoS ONE • 2021

Traditional codon models assume only single-nucleotide substitutions, largely dismissing multi-nucleotide changes as rare or artifactual. However, analysis of over 42,000 alignments shows strong and widespread support for multi-hit models, especially involving serine codon switching, indicating that standard models may bias estimates like dN/dS and should be reevaluated, with new tools now implemented in HyPhy and Datamonkey to assess these effects.

Public Engagement

outreach

The Subway’s Invisible Microbiome

AMNH SciCafe • Feb 4, 2026 • New York, NY

Public talk on how urban metagenomics reveals hidden microbial and viral ecosystems in the NYC subway and how localized sampling scales into global atlas-building and biosurveillance efforts.

Book chapters

Viral evolution in the cosmos

Book Chapter • Fundamentals of Space Medicine and Clinical Technology • 2026

Space travel exposes human beings to unique environmental stressors (e.g., radiation, microgravity) and induces significant physiological changes in hosts, profoundly impacting host–virus dynamics and creating conditions conducive to viral evolution.

Blogs & Media

writing

A VAST New View of Viruses

Media • Weill Cornell Medicine • 2025

A major new effort at Weill Cornell Medicine seeks to catalog the normal human virome, the immense ecosystem of viruses that lives in and on us. The work, part of a multi-institution collaboration called Viromes Across Space and Time (VAST), supported by the National Institute on Aging, part of the National Institutes of Health, will pioneer new techniques, illuminate a crucial aspect of human biology that was impossible to study before, and establish a baseline set of data that could help in preventing, diagnosing and treating disease.

Assessing evolutionary pressures on the SARS-CoV-2 Mu (B.1.621) clade

Blog post • Virological • 2021