Search research articles

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Integrated flexible DNA methylation-chromatin segmentation modeling enhances epigenomic state annotation.

Nucleic acids research·2026

Same author

Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index.

Bioinformatics (Oxford, England)·2025

Same author

Swiftly identifying strongly unique k-mers.

Algorithms for molecular biology : AMB·2025

Same author

A comprehensive review and evaluation of species richness estimation.

Briefings in bioinformatics·2025

Same author

Lossless Approximate Pattern Matching: Automated Design of Efficient Search Schemes.

Journal of computational biology : a journal of computational molecular cell biology·2024

Same author

Three-Year Mortality of Older Hospitalized Patients with Osteosarcopenia: Data from the OsteoSys Study.

Nutrients·2024

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Video

Updated: Nov 10, 2025

Author Spotlight: Advancing Cancer Therapeutics Using Tumor Xenotransplantation in Zebrafish

Author Spotlight: Advancing Cancer Therapeutics Using Tumor Xenotransplantation in Zebrafish

Published on: July 12, 2024

Fast lightweight accurate xenograft sorting.

Jens Zentgraf¹, Sven Rahmann^2,3

¹Bioinformatics, Computer Science XI, TU Dortmund University, Dortmund, Germany.

Algorithms for Molecular Biology : AMB

|April 3, 2021

Summary

Alignment-free methods efficiently sort xenograft reads, offering faster processing and comparable accuracy to alignment-based tools. This approach utilizes a novel Cuckoo hashing method for improved performance in analyzing patient-derived xenograft models.

Keywords:

Alignment-free method Cuckoo hashing Xenograft sorting k-mer

More Related Videos

High-Throughput Dissociation and Orthotopic Implantation of Breast Cancer Patient-Derived Xenografts

High-Throughput Dissociation and Orthotopic Implantation of Breast Cancer Patient-Derived Xenografts

Published on: December 20, 2024

Depletion of Mouse Cells from Human Tumor Xenografts Significantly Improves Downstream Analysis of Target Cells

Depletion of Mouse Cells from Human Tumor Xenografts Significantly Improves Downstream Analysis of Target Cells

Published on: July 29, 2016

Related Experiment Videos

Last Updated: Nov 10, 2025

Author Spotlight: Advancing Cancer Therapeutics Using Tumor Xenotransplantation in Zebrafish

Author Spotlight: Advancing Cancer Therapeutics Using Tumor Xenotransplantation in Zebrafish

Published on: July 12, 2024

High-Throughput Dissociation and Orthotopic Implantation of Breast Cancer Patient-Derived Xenografts

High-Throughput Dissociation and Orthotopic Implantation of Breast Cancer Patient-Derived Xenografts

Published on: December 20, 2024

Depletion of Mouse Cells from Human Tumor Xenografts Significantly Improves Downstream Analysis of Target Cells

Depletion of Mouse Cells from Human Tumor Xenografts Significantly Improves Downstream Analysis of Target Cells

Published on: July 29, 2016

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Patient-derived xenograft (PDX) models are crucial for cancer research and therapy guidance.
Sequencing PDX models necessitates distinguishing human tumor reads from mouse host reads.
Current methods for xenograft read sorting include alignment-based and alignment-free approaches with varying performance.

Purpose of the Study:

To develop and evaluate a novel, efficient alignment-free method for xenograft read sorting.
To compare the performance of the new method against existing alignment-based and alignment-free tools.
To provide an accessible software tool for xenograft read separation.

Main Methods:

Developed a fast, lightweight alignment-free sorting approach using three-way bucketed quotiented Cuckoo hashing.
Implemented a hash table with memory requirements comparable to FM indexes.
Optimized performance through engineering steps like shortcuts and prefetching.

Main Results:

The alignment-free method demonstrates superior CPU time usage compared to other approaches.
Achieved accuracy equivalent to state-of-the-art xenograft sorting methods.
The developed hash table offers fast lookups and reduced CPU time.

Conclusions:

Alignment-free xenograft sorting using Cuckoo hashing is a highly efficient and accurate method.
The novel approach offers significant performance improvements for analyzing PDX sequencing data.
The software 'xengsort' is publicly available, facilitating its use in research.