Biology subjects

Harbert, R.

Publications and source records attributed to Harbert, R..

4 recordsLinked to original sources

bioRxiv2026

SALRR: Scalable Analysis of Long-Read RNA-Seq Enables Comprehensive Transcriptome Profiling in Human Brain

Isoform-resolved transcriptomics is fundamental to decoding the molecular complexity of the human brain, yet population-scale long-read RNA sequencing has remained inaccessible due to labor-intensive library preparation, sensitivity to RNA degradation in postmortem tissue, and the absence of integrated, reproducible analysis pipelines. Here we present SALRR (Scalable Analysis of Long-Read RNA-seq), an integrated wet-lab and computational platform designed to overcome these barriers. Automated ONT long-read cDNA library preparation on the Hamilton Microlab NGS STAR platform reduces hands-on time by 67% and enables 24 libraries per operator per day while maintaining performance across RNA integrity values. A modular, Snakemake-based pipeline performs end-to-end processing from ONT signal data to isoform-level quantification, incorporating SIRV spike-in calibration, multi-stage quality control, and stringent isoform validation. Applied to 10 postmortem frontal cortex samples from the North American Brain Expression Consortium, SALRR identified 31,607 high-confidence isoforms from 10,075 genes, including 8,532 novel splice variants absent from GENCODE v49, and complex splicing events systematically missed by short-read sequencing at neurodegeneration-relevant loci, including GBA1, CCNF, CHCHD10, and TREM2. All protocols and code are openly available, providing a scalable, community-ready framework for isoform-resolved transcriptomics in neurodegeneration, aging, and complex brain disease.

genomics↗

bioRxiv2025

Rapid Derivation of Cloning-Competent Cells from Peripheral Blood Advances Conservation Biobanking

I.Establishing viable cell lines from endangered species is essential for conservation, yet traditional fibroblast derivation from skin biopsies faces challenges including variable success rates, contamination risk, and extended culture timelines. We demonstrate that endothelial progenitor cells (EPCs) and pericytes isolated from peripheral blood represent superior alternatives for biobanking across three mammalian genera (Canis, Bison, and Equus). Blood-derived cells exhibited 2-3 fold faster doubling rates (15-20 hours versus >35 hours for fibroblasts) and reduced time to generate banked lines from 3-4 weeks to 1.5-2 weeks. Proteomic profiling of 32 canonical markers confirmed EPCs and pericytes represent distinct populations with lineage-specific molecular signatures. Optical genome mapping demonstrated equivalent genomic stability across all cell types with no detectable structural variants or aneuploidies. Critically, interspecific somatic cell nuclear transfer (iSCNT) experiments confirmed both EPCs and pericytes generate viable embryos with efficiency meeting or exceeding fibroblasts. Gray wolf blood-derived cells produced six viable fetuses with 15% implantation rate, while bison EPCs showed higher blastocyst formation (7%) than fibroblasts (3%) from the same individual. Blood collection during routine veterinary procedures offers minimally invasive sampling with reduced contamination compared to skin biopsies. These findings support integrating blood-derived cell banking into conservation programs, enabling opportunistic genetic preservation during standard management activities and expanding options for genetic rescue through assisted reproductive technologies.

cell biology↗

bioRxiv2019

cRacle: R Tools for Estimating Climate from Vegetation

Premise of the studyThe Climate Reconstruction Analysis using Coexistence Likelihood Estimation (CRACLE) method for the estimation of climate from vegetation is a robust set of modeling tools for estimating climate and paleoclimate that makes use of large repositories of biodiversity data and open-access R software. MethodsHere we implement a new R library for the estimation of climate from vegetation. The cRacle library implements functions for data access, aggregation, and models to estimate climate from plant community composition. cRacle is modular and features many best-practice features. ResultsPerformance tests using modern vegetation survey data from North and South America shows that CRACLE outperforms alternative methods. CRACLE estimates of mean annual temperature (MAT) are usually within 1{degrees}C of the actual when optimal model parameters are used. Generalized Boosted Regression (GBR) model correction is also shown here to improve on CRACLE models by reducing bias. DiscussionCRACLE provides accurate estimates of climate from modern plant communities. Non-parametric CRACLE modeling coupled to GBR model correction produces the most accurate results to date. The cRacle R library streamlines the estimation of climate from plant community data, and will make this modeling more accessible to a wider range of users.

bioinformatics↗

bioRxiv2018

Quantitative Late Quaternary climate reconstruction from plant macrofossil proxy in Western North America

The Late Quaternary packrat (Neotoma spp.) midden plant macrofossil record in western North America is an exceptional record of biotic change that provides strong evidence of past climate. In this study we generate quantitative estimates of climate from plant community composition of more than 600 individual paleomiddens over the past 50,000 years. This is the first large-scale application of CRACLE, a quantitative climate inference method that uses plant community composition as a climatic proxy under and individualistic concept of plant community assembly. The results are spatiotemporally specific estimates of temperature, precipitation, available moisture, and seasonal patterns that are consistent with well understood global climate patterns, but provide previously unavailable detail and precision of the regional paleoclimate in western North America. Rapid warming is estimated at the Pleistocene-Holocene transition, at a conservative estimate of ca. 1{degrees}C per millennium. Previously projected future temperature increases suggest a rate of increase of more than 2{degrees}C over the next century, an astonishing 10X the rate experienced at any point during the past 50,000 years in Western North America. These analyses form a baseline demonstration of how the growing paleoecological record of packrat midden plant macrofossils is able to provide quantitative estimates of paleoclimate that aid in understanding the complexities of, and biotic responses to the regional climate system.

paleontology↗