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Canzar Lab - Algorithmic Bioinformatics

Research Topics

  • Computational Genomics & Transcriptomics
  • Algorithm Engineering
  • Single Cell Genomics
  • Combinatorial Optimization

Part of the group relocated in January 2023 to Penn State University

Dr. Stefan Canzar or

Next-generation sequencing instruments produce a huge number of short DNA 'reads', each of which carries little information by itself. These reads therefore have to be pieced together by well-engineered algorithms to reconstruct biologically meaningful measurements. The lab's goal is the development of accurate mathematical models, efficient algorithms, and usable software to solve these complex, high-dimensional puzzles. Read more...

Selected Publications

Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data.
Ringeling FR, Chakraborty S, Vissers C, Reiman D, Patel AM, Lee KH, Hong A, Park CW, Reska T, Gagneur J, Chang H, Spletter ML, Yoon KJ, Ming GL, Song H, Canzar S
Nature Biotechnology. 2022. doi:10.1038/s41587-021-01136-7

A generalization of t-SNE and UMAP to single-cell multimodal omics.
Van Do H, Canzar S.
Genome Biology. 2021;22(1):130. doi: 10.1186/s13059-021-02356-5.

Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data.
Van Do H, Rojas Ringeling F, Canzar S.
Genome Research. 2021;31(4):677-688 doi: 10.1101/gr.267906.120

Sphetcher: Spherical thresholding improves sketching of single-cell transcriptomic heterogeneity.
Van Do H, Elbassioni K, Canzar S.
iScience. 2020;23(6):101126. doi: 10.1016/j.isci.2020.101126

More publications


30.05.2022 New paper
Ccr4–Not complex reduces transcription efficiency in heterochromatin. Congrats Pablo! 

10.01.2022 Ladder-seq is out! 
Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data.

20.07.2021 - New preprint
Anti Tai Mapping for Unordered Labeled Trees

01.07.2021 - DFG funding
We are part of LETSIMMUN, a collaborative research center funded by the DFG

27.06.2021 - New preprint
Fast metric multidimensional scaling using a neural network

03.05.2021 - New paper
j-SNE and j-UMAP generalize t-SNE and UMAP to single-cell multimodal omics

19.02.2021 - New paper
Specter for (fast) multi-modal clustering of single cells accepted at Genome Research.

30.01.2021 - New paper
McSplicer infers a probabilistic model of alternative splicing

21.02.2020 - New paper

Single-cell sampling by Van Hoan Do accepted for presentation at RECOMB-seq and for publication at iScience

18.12.2019 - DAAD Project funding

Application of Generic Optimizer in Medical Imaging Classification Problems