Rusnak, A. | Search bioRxiv

bioRxiv2026

Temporal Biodynamics: An AI Platform for Identification of Stage-Relevant Targets and Biomarkers

Temporal modeling of disease progression is poised to revolutionize the process of target identification, leading to better characterization of and intervention at the critical early stages of chronic conditions. Temporal Biodynamics is an artificial intelligence-driven platform that leverages within-tissue heterogeneity in cross-sectional cohorts to assemble a single, continuous trajectory of transcriptomic changes between health and disease. We demonstrate that the platform enriches for known disease-associated genes and proteins by more than 50% over the conventional case-control comparisons. When compared to other published pseudotime methods, our models were better at extracting disease-relevant signals in the presence of confounders and co-morbidities. The Temporal Biodynamics platform enables rich profiling of a disease continuum, providing temporal insights that are otherwise hidden by the traditional discrete staging of chronic diseases. This includes detecting cascades of molecular events, providing clues regarding causality, and increasing confidence in blood-based protein biomarkers using tissue-based context.

bioinformatics↗

bioRxiv2023

Endangered Przewalski's horse, Equus pzrewalskii, cloned from historically cryopreserved cells

Two endangered Przewalskis horse stallions were cloned from fibroblast cells cultured and cryopreserved in 1980. These stallions are clones of a male that lived from 1975-1998 that pedigree analyses identified as a genetically valuable male for present-day conservation breeding. This is the first time that multiple healthy clones have been produced for an endangered species.

zoology↗

bioRxiv2021

The early embryonic transcriptome of a Hawaiian Drosophila picture-wing fly shows evidence of altered gene expression and novel gene evolution

A massive adaptive radiation on the Hawaiian archipelago has produced approximately one quarter of the fly species in the family Drosophilidae. The Hawaiian Drosophila clade has long been recognized as a model system for the study of both the ecology of island endemics and the evolution of developmental mechanisms, but relatively few genomic and transcriptomic datasets are available for this group. We present here a differential expression analysis of the transcriptional profiles of two highly conserved embryonic stages in the Hawaiian picture-wing fly Drosophila grimshawi. When we compared our results to previously published datasets across the family Drosophilidae, we identified cases of both gains and losses of gene representation in D. grimshawi, including an apparent delay in Hox gene activation. We also found high expression of unannotated genes. Most transcripts of unannotated genes with open reading frames do not have homologs in non-Hawaiian Drosophila species, although the vast majority have sequence matches in other genomes of the Hawaiian picture-wing flies. Some of these genes may have arisen from non-coding sequence in the ancestor of Hawaiian flies or during the evolution of the clade. Our results suggests that both the modified use of ancestral genes and the evolution of new ones may occur in rapid radiations. RESEARCH HIGHLIGHTSThe early embryonic transcriptome of the Hawaiian fly Drosophila grimshawi shows a loss of expression of conserved Stage 5 genes, including the Hox genes The de novo evolution of embryonically expressed genes may be occurring in the Hawaiian Drosophila lineage AUTHORS STATEMENTThis paper is not being considered for publication elsewhere. This study formed part of Madeline Cheneverts M.S. thesis.

developmental biology↗