Alexander Lucaci

Ancient genomics and the origin, dispersal, and development of domestic sheep The origins and prehistory of domestic sheep (Ovis aries) are incompletely understood; to address this, we generated data from 118 ancient genomes spanning 12,000 years sampled from across Eurasia. Ge...

www.science.org/doi/10.1126/...

Viroid-like colonists of human microbiomes Obelisks are widespread RNA-based agents found in diverse environmental and human-associated microbiomes. These apparently unbranched and circular RNAs represent a previously uncharacterized class of ...

www.cell.com/cell/abstrac...

VirusT5: Harnessing Large Language Models to Predicting SARS-CoV-2 Evolution During a virus's evolution,various regions of the genome are subjected to distinct levels of functional constraints.Combined with factors like codon bias and DNA repair efficiency,these constraints co...

arxiv.org/abs/2412.16262

www.nature.com/articles/s41...

Pathogen genomic surveillance and the AI revolution | Journal of Virology Genomic pathogen sequencing during the COVID-19 pandemic highlighted the critical role of surveillance in understanding the persistence of SARS-CoV-2 in the human population despite high levels of protective immunity and the effect of the changing circulating variants on public health, advising policymakers and informing vaccine design. With nearly 20 million SARS-CoV-2 genomes currently available in the GISAID database, the sequencing effort since 2020 has surpassed those of other viruses, followed by less than half a million influenza virus genomes (GISAID) and less than 50,000 HIV-1 genomes (GenBank) all collected over several decades. The almost real-time resolution of circulating SARS-CoV-2 variants allowed scientists to readily detect and characterize genome changes corresponding to the virus’s functional and antigenic evolution in humans and anthroponosis events to other animals. This phenotypic change was apparent from the outset of the pandemic, with genomic surveillance revealing the first “functional” substitution, D614G (1, 2), and first significant antigenic substitution, N439K (3), both changes in the virus’s Spike entry glycoprotein. In addition to such point mutations creating variants with altered phenotypic properties, the global sequencing effort uncovered several mechanisms this new human virus used to maintain its circulation in the population: recurring indel mutations generating new variants, e.g., deletion H69/V70 (4); independent occurrence of the same amino acid substitutions at the same site in different variants (convergence) (5, 6); the emergence of variants of concern associated with multiple beneficial mutations through saltation-like evolution linked to chronic infections (7, 8); and bringing novel sets of mutations together in one variant (recombination) (9, 10), which can have a combinatory beneficial effect for the virus (positive epistasis) (11).

journals.asm.org/doi/10.1128/...

Quantifying cell divisions along evolutionary lineages in cancer - Nature Genetics This work presents a framework for estimating cell division numbers using DNA replication-associated polyguanine tract mutations, with applications for understanding tumor natural histories and origin...

www.nature.com/articles/s41...

A Bioinformatician, Computer Scientist, and Geneticist lead bioinformatic tool development—which one is better? Abstract. The development of accurate bioinformatic software tools is crucial for the effective analysis of complex biological data. This study examines th

academic.oup.com/bioinformati...

C-terminal amides mark proteins for degradation via SCF–FBXO31 - Nature SCF–FBXO31 scans proteins for C-terminal amidation and marks them for subsequent proteasomal degradation.

www.nature.com/articles/s41...

Global meta-analysis shows action is needed to halt genetic diversity loss - Nature A comprehensive meta-analysis of global terrestrial and marine genetic diversity covering more than three decades of research demonstrates rapid loss of genetic diversity and identifies conservation i...

www.nature.com/articles/s41...

Association of poultry vaccination with interspecies transmission and molecular evolution of H5 subtype avian influenza virus Mass poultry vaccination affects H5 avian influenza virus transmission and evolution, revealing complex host-virus dynamics.

www.science.org/doi/10.1126/...

Functional innovation through new genes as a general evolutionary process - Nature Genetics This Review discusses the various molecular mechanisms underlying the generation of new genes and highlights their important functions and phenotypes with an emphasis on the evolutionary forces underl...

www.nature.com/articles/s41...

Recovery of nearly 3,000 archaeal genomes from 152 terrestrial geothermal spring metagenomes - Scientific Data Scientific Data - Recovery of nearly 3,000 archaeal genomes from 152 terrestrial geothermal spring metagenomes

www.nature.com/articles/s41...

Rapid in silico directed evolution by a protein language model with EVOLVEpro Directed protein evolution is central to biomedical applications but faces challenges such as experimental complexity, inefficient multiproperty optimization, and local maxima traps. Although in silic...

www.science.org/doi/10.1126/...

CASTER: Direct species tree inference from whole-genome alignments Genomes contain mosaics of discordant evolutionary histories, challenging the accurate inference of the tree of life. While genome-wide data are routinely used for discordance-aware phylogenomic analy...

www.science.org/doi/10.1126/...

Site-saturation mutagenesis of 500 human protein domains - Nature Large-scale experimental analysis of Human Domainome 1, a library containing more than 500,000 missense mutation variants across more than 500 human protein domains, reveals that 60% of pathogenic mis...

www.nature.com/articles/s41...

The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure RNA viruses like SARS-CoV-2 have a high mutation rate, which contributes to their rapid evolution. The rate of mutations depends on the mutation type (e.g., A→C, A→G, etc.) and can vary between sites ...

Building on the UShER tree of millions of SARS-CoV-2 genomes maintained by Angie Hinrichs, Hugh Haddox and Georg Angehrn (and others in @matsen.bsky.social lab and @jbloomlab.bsky.social) have looked into how the neutral mutation rate varies along the genome:

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www.biorxiv.org/content/10.1...

Phylogenetic substitution rate estimates from millions-deep SARS-CoV-2 alignments

Workshop on Molecular Evolution | Marine Biological Laboratory The workshop serves graduate students, postdocs, and established faculty from around the world seeking to apply the principles of molecular evolution to questions of anthropology, conservation genetic...

Applications are now open for the 2025 Workshop on Molecular Evolution (MOLE) at the Marine Biological Laboratory in *beautiful* Woods Hole, MA!

More info here: molevolworkshop.github.io

Apply here: www.mbl.edu/education/ad...

Application deadline: Jan. 29th

Workshop dates: May 22nd - June 1st