Jensen, C. B. | Search bioRxiv

bioRxiv2026

TOPAS: phosphoproteome data analysis and decision support platform for molecular tumor boards

The molecular tumor board (MTB) is central to precision oncology, providing personalized treatment recommendations based on molecular profiles of patient tumors. Genomics is instrumental for MTBs but often fails to identify clinically actionable targets, a gap that phosphoproteomics can fill. We present the tumor proteome activity status (TOPAS) platform, an end-to-end analysis pipeline that converts terabytes of phosphoproteomic data into patient-specific reports for MTB discussions, focusing on clinically relevant signaling linked to oncogenic mechanisms and therapeutic targets. Designed to scale with growing cohorts, the platform integrates data from 1,998 tumor samples to support patient- and cohort-level hypothesis generation. A web portal handles quality control, calculates TOPAS scores, identifies tumor antigens and immune checkpoints, and offers interactive analyses of differential protein abundance and outlier detection. The TOPAS platform is open source, addresses a critical unmet need and facilitates broader adoption of phosphoproteomics in precision oncology in the future.

bioinformatics↗

bioRxiv2022

The Choice of Reference Frame Alters Interpretations of Non-Linear Gait

IntroductionHumans regularly follow non-linear trajectories, such as turning, during everyday ambulation. However, globally-defined and locally-defined reference frames fall out of alignment during non- linear locomotion, which complicates spatiotemporal and biomechanical analyses of gait. Thus, the choice of the locally-defined reference frame is an important methodological consideration. This study investigated how different definitions of reference frame change the results and interpretations of common gait measures. MethodsNine healthy adults completed two walking trials around a circular track. Kinematic data were collected via motion capture and used to calculate step length, step width, anteroposterior margin of stability, and mediolateral margin of stability using three different locally-defined reference frames: walkway-fixed, body-fixed, and trajectory-fixed. Linear-mixed effects models compared the effect of reference frame on each gait measure, and the effect of reference frame on conclusions about a known effect of turning gait - asymmetrical stepping patterns. ResultsAll four gait measures differed significantly across the three reference frames. A significant interaction of reference frame and step type (i.e. inside vs outside step) on all four gait measures (p < 0.001) indicated conclusions about asymmetry differed based on the choice of reference frame. ConclusionThe choice of reference frame will change the calculated gait measures and may alter the conclusions of studies investigating non-linear gait. Care should be taken when comparing studies that used different reference frames, as results cannot be easily harmonized. Future studies of non-linear gait need to justify and detail their choice of reference frame.

bioengineering↗