Biology subjects

Gordon, C. M.

Publications and source records attributed to Gordon, C. M..

2 recordsLinked to original sources

bioRxiv2026

PPGLomics: An Interactive Platform for Pheochromocytoma and Paraganglioma Transcriptomics

Pheochromocytoma and paraganglioma (PPGL) are rare neuroendocrine tumors with unique biological behavior and remarkably high heritability, yet dedicated bioinformatics resources for these diagnoses remain limited. Existing cancer multi-omics platforms are pan-cancer in scope, often lacking the disease-specific annotations, granularity, and cross-database harmonization required for meaningful stratification and hypothesis generation. Here we introduce PPGLomics, an interactive web-based platform designed for comprehensive PPGL transcriptomics analysis. PPGLomics v1.0 integrates two major datasets, the TCGA-PCPG cohort (n=160) spanning multiple molecular subtypes, and the A5 consortium SDHB cohort (n=91) with detailed clinicopathological and molecular annotations. The platform provides basic and clinical scientists, as well as a broad range of healthcare professionals, with tools for differential expression analysis, correlation analysis, survival analysis, and visualization, including boxplots, heatmaps, volcano plots, and Kaplan-Meier survival plots, enabling exploration of gene expression patterns across PPGL subtypes without requiring bioinformatics expertise. PPGLomics v1.0 is freely available at https://alkaissilab.shinyapps.io/PPGLomics. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=51 SRC="FIGDIR/small/702561v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@3b98daorg.highwire.dtl.DTLVardef@b050f4org.highwire.dtl.DTLVardef@1930219org.highwire.dtl.DTLVardef@6edf18_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Limb proportions predict aquatic habits and soft-tissue flippers in extinct amniotes

IN BRIEFGordon et al. use a phylogenetic machine-learning approach incorporating linear and geometric morphometric analyses (including >11,000 original linear measurements) to characterize osteological correlates of interdigital webbing, soft-tissue flippers, and aquatic habits in amniotes. They find that relative hand length can reconstruct soft-tissue phenotypes and aquatic habits in extinct amniotes with >90% accuracy, enabling a more phylogenetically comprehensive investigation of limb evolution among bona fide aquatic and terrestrial species. This investigation reveals distinct morphometric landscapes for limb evolution in mammals and reptiles and clarifies the aquatic habits of multiple extinct groups with historically ambiguous ecologies. In addition, it debuts a versatile supervised machine-learning approach for reconstructing cryptic phenotypes from fossil material. O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/661573v1_ufig1.gif" ALT="Figure 1"> View larger version (83K): org.highwire.dtl.DTLVardef@38ca68org.highwire.dtl.DTLVardef@708fb4org.highwire.dtl.DTLVardef@1eaa6f6org.highwire.dtl.DTLVardef@7795c6_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIForelimb proportions reliably predict soft-tissue flippers and highly/fully aquatic habits with >90% accuracy across amniotes. C_LIO_LIInterdigital webbing cannot be predicted from the bones alone using previously suggested correlates. C_LIO_LIAll Paleozoic marine reptiles known to date lived at most an amphibious lifestyle, regularly voyaging onto land. C_LIO_LIPhylogenetic Receiver-Operating Characteristic (ROC) analysis effectively reconstructs cryptic phenotypes in extinct species. C_LI

paleontology↗