Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

FISH - Fluorescent In-situ Hybridization02:07

FISH - Fluorescent In-situ Hybridization

21.1K
Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...
21.1K
Genomics02:02

Genomics

37.4K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
37.4K
Animal Mitochondrial Genetics02:59

Animal Mitochondrial Genetics

8.0K
Among all the organelles in an animal cell, only mitochondria have their own independent genomes. Animal mitochondrial DNA is a double-stranded, closed-circular molecule with around 20,000 base pairs. Mitochondrial DNA is unique in that one of its two strands, the heavy, or H, -strand is guanine rich, whereas the complementary strand is cytosine rich and called the light, or L, -strand. Compared to nuclear DNA, mitochondrial DNA has a very low percentage of non-coding regions and is marked by...
8.0K

You might also read

Related Articles

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

Sort by
Same author

Root cause discovery via permutations and Cholesky decomposition.

Journal of the Royal Statistical Society. Series B, Statistical methodology·2026
Same author

Intron location and sequence modulate gene expression in Yarrowia lipolytica.

Nucleic acids research·2026
Same author

Decoding sequence determinants of gene expression in diverse cellular and disease states.

Nature methods·2026
Same author

Non-destructive transcriptomics via vesicular export.

Nature communications·2026
Same author

Fibroblast Transcriptomics in Molecular Diagnostics of a Comprehensive Dystonia Cohort.

Annals of neurology·2026
Same author

Advancing regulatory variant effect prediction with AlphaGenome.

Nature·2026

Related Experiment Video

Updated: Sep 9, 2025

Rapid and Efficient Zebrafish Genotyping Using PCR with High-resolution Melt Analysis
06:30

Rapid and Efficient Zebrafish Genotyping Using PCR with High-resolution Melt Analysis

Published on: February 5, 2014

22.4K

Flashzoi: an enhanced Borzoi for accelerated genomic analysis.

Johannes C Hingerl1,2, Alexander Karollus1,2, Julien Gagneur1,2,3,4

  • 1School of Computation, Information and Technology, Technical University of Munich, Garching, 85748, Germany.

Bioinformatics (Oxford, England)
|September 4, 2025
PubMed
Summary

Flashzoi enhances the Borzoi model for genomics, using rotary positional encodings and FlashAttention-2 for faster computation. This accelerates the analysis of DNA sequence, gene regulation, and genetic variant effects.

More Related Videos

Mosaic Zebrafish Transgenesis for Functional Genomic Analysis of Candidate Cooperative Genes in Tumor Pathogenesis
09:45

Mosaic Zebrafish Transgenesis for Functional Genomic Analysis of Candidate Cooperative Genes in Tumor Pathogenesis

Published on: March 31, 2015

11.3K
Mosaic Zebrafish Transgenesis for Evaluating Enhancer Sequences
07:23

Mosaic Zebrafish Transgenesis for Evaluating Enhancer Sequences

Published on: July 16, 2010

14.0K

Related Experiment Videos

Last Updated: Sep 9, 2025

Rapid and Efficient Zebrafish Genotyping Using PCR with High-resolution Melt Analysis
06:30

Rapid and Efficient Zebrafish Genotyping Using PCR with High-resolution Melt Analysis

Published on: February 5, 2014

22.4K
Mosaic Zebrafish Transgenesis for Functional Genomic Analysis of Candidate Cooperative Genes in Tumor Pathogenesis
09:45

Mosaic Zebrafish Transgenesis for Functional Genomic Analysis of Candidate Cooperative Genes in Tumor Pathogenesis

Published on: March 31, 2015

11.3K
Mosaic Zebrafish Transgenesis for Evaluating Enhancer Sequences
07:23

Mosaic Zebrafish Transgenesis for Evaluating Enhancer Sequences

Published on: July 16, 2010

14.0K

Area of Science:

  • Genomics
  • Computational Biology
  • Bioinformatics

Background:

  • Predicting DNA sequence's role in gene regulation and variant effects is crucial in genomics.
  • The Borzoi model is a foundation for regulatory genomics, analyzing numerous genomic assays.
  • Current Borzoi's relative positional encodings hinder computational efficiency.

Purpose of the Study:

  • To improve the computational efficiency of the Borzoi model.
  • To maintain or enhance accuracy in modeling genomic assays and variant effects.
  • To facilitate large-scale genomic analyses and explore complex regulatory mechanisms.

Main Methods:

  • Developed Flashzoi, an enhanced Borzoi model.
  • Implemented rotary positional encodings.
  • Integrated FlashAttention-2 for improved computational performance.

Main Results:

  • Achieved over 3-fold faster training and inference speeds.
  • Reduced memory usage by up to 2.4-fold.
  • Maintained or improved accuracy in RNA-seq coverage modeling, variant effect prediction, and enhancer-promoter linking.

Conclusions:

  • Flashzoi significantly enhances Borzoi's efficiency for genomic analyses.
  • The model's speed and reduced memory footprint enable larger-scale studies.
  • Flashzoi supports further research into gene regulation and complex genomic modeling.