Stefan Canzar

Associate Professor of Computer Science and Engineering

Stefan Canzar

Research Summary

Algorithmic bioinformatics, computational genomics. We develop algorithms and software for single-cell genomics and spatial transcriptomics data. We use techniques from combinatorial optimization, linear programming, and machine learning.

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Rna Genes Proteins Genome Protein Rna Seq Messenger Rna Methylation Genomics Length Cell T Lymphocytes T Cell Antigen Receptor Neurogenesis Protein Isoforms Libraries Cells Molecules Hardness Leucine Costs Rna Sequencing Rna Sequence Analysis Gene Dna

Most Recent Publications

Counting pseudoalignments to novel splicing events

Luka Borozan, Francisca Rojas Ringeling, Shao Yen Kao, Elena Nikonova, Pablo Monteagudo-Mesas, Domagoj Matijević, Maria L. Spletter, Stefan Canzar, 2023, Bioinformatics

Fortuna Detects Novel Splicing in Drosophila scRNASeq Data

B. Borozan, L. Borozan, D. Severdija, D. Matijevic, S. Canzar, 2023, on p. 410-415

CYFIP1 Dosages Exhibit Divergent Behavioral Impact via Diametric Regulation of NMDA Receptor Complex Translation in Mouse Models of Psychiatric Disorders

Nam Shik Kim, Francisca Rojas Ringeling, Ying Zhou, Ha Nam Nguyen, Stephanie J. Temme, Yu Ting Lin, Stephen Eacker, Valina L. Dawson, Ted M. Dawson, Bo Xiao, Kuei sen Hsu, Stefan Canzar, Weidong Li, Paul Worley, Kimberly M. Christian, Ki Jun Yoon, Hongjun Song, Guo li Ming, 2022, Biological Psychiatry on p. 815-826

The function of Wtap in N <sup>6</sup>-adenosine methylation of mRNAs controls T cell receptor signaling and survival of T cells

Taku Ito-Kureha, Cristina Leoni, Kayla Borland, Giulia Cantini, Marian Bataclan, Rebecca N. Metzger, Gregor Ammann, Anne B. Krug, Annalisa Marsico, Stefanie Kaiser, Stefan Canzar, Stefan Feske, Silvia Monticelli, Julian König, Vigo Heissmeyer, 2022, Nature Immunology on p. 1208-1221

Ccr4-Not complex reduces transcription efficiency in heterochromatin

Pablo Monteagudo-Mesas, Cornelia Brönner, Parastou Kohvaei, Haris Amedi, Stefan Canzar, Mario Halic, 2022, Nucleic Acids Research on p. 5565-5576

Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data

Francisca Rojas Ringeling, Shounak Chakraborty, Caroline Vissers, Derek Reiman, Akshay M. Patel, Ki Heon Lee, Ari Hong, Chan Woo Park, Tim Reska, Julien Gagneur, Hyeshik Chang, Maria L. Spletter, Ki Jun Yoon, Guo li Ming, Hongjun Song, Stefan Canzar, 2022, Nature Biotechnology on p. 741-750

Genome-wide off-target analyses of CRISPR/Cas9-mediated T-cell receptor engineering in primary human T cells

Theresa Kaeuferle, Tanja A. Stief, Stefan Canzar, Nayad N. Kutlu, Semjon Willier, Dana Stenger, Paulina Ferrada-Ernst, Nicola Habjan, Annika E. Peters, Dirk H. Busch, Tobias Feuchtinger, 2022, Clinical and Translational Immunology

Predicting RNA splicing branchpoints

Antonio Jovanovic, Israa Alqassem, Nathan Chappell, Stefan Canzar, Domagoj Matijevic, 2022, on p. 383-388

A generalization of t-SNE and UMAP to single-cell multimodal omics

Van Hoan Do, Stefan Canzar, 2021, Genome Biology

BiCoN: Network-constrained biclustering of patients and omics data

Olga Lazareva, Stefan Canzar, Kevin Yuan, Jan Baumbach, David B. Blumenthal, Paolo Tieri, Tim Kacprowski, Markus List, 2021, Bioinformatics on p. 2398-2404

Most-Cited Papers

Temporal Control of Mammalian Cortical Neurogenesis by m<sup>6</sup>A Methylation

Ki Jun Yoon, Francisca Rojas Ringeling, Caroline Vissers, Fadi Jacob, Michael Pokrass, Dennisse Jimenez-Cyrus, Yijing Su, Nam Shik Kim, Yunhua Zhu, Lily Zheng, Sunghan Kim, Xinyuan Wang, Louis C. Doré, Peng Jin, Sergi Regot, Xiaoxi Zhuang, Stefan Canzar, Chuan He, Guo li Ming, Hongjun Song, 2017, Cell on p. 877-889.e17

Charge group partitioning in biomolecular simulation

Stefan Canzar, Mohammed El-Kebir, Reńe Pool, Khaled Elbassioni, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau, 2013, Journal of Computational Biology on p. 188-198

A Common Embryonic Origin of Stem Cells Drives Developmental and Adult Neurogenesis

Daniel A. Berg, Yijing Su, Dennisse Jimenez-Cyrus, Aneek Patel, Nancy Huang, David Morizet, Stephanie Lee, Reeti Shah, Francisca Rojas Ringeling, Rajan Jain, Jonathan A. Epstein, Qing Feng Wu, Stefan Canzar, Guo Li Ming, Hongjun Song, Allison M. Bond, 2019, Cell on p. 654-668.e15

GAGE-B: An evaluation of genome assemblers for bacterial organisms

Tanja Magoc, Stephan Pabinger, Stefan Canzar, Xinyue Liu, Qi Su, Daniela Puiu, Luke J. Tallon, Steven L. Salzberg, 2013, Bioinformatics on p. 1718-1725

BASIC: BCR assembly from single cells

Stefan Canzar, Karlynn E. Neu, Qingming Tang, Patrick C. Wilson, Aly A. Khan, 2017, Bioinformatics on p. 425-427

Short Read Mapping: An Algorithmic Tour

Stefan Canzar, Steven L. Salzberg, 2017, Proceedings of the Institute of Radio Engineers on p. 436-458

Proteome analysis of human neutrophil granulocytes from patients with monogenic disease using data-independent acquisition

Piotr Grabowski, Sebastian Hesse, Sebastian Hollizeck, Meino Rohlfs, Uta Behrends, Roya Sherkat, Hannah Tamary, Ekrem Ünal, Raz Somech, Türkan Patiroǧlu, Stefan Canzar, Jutte Van Der Werff Ten Bosch, Christoph Klein, Juri Rappsilber, 2019, Molecular and Cellular Proteomics on p. 760-772

Alternative splicing regulates stochastic NLRP3 activity

Florian Hoss, James L. Mueller, Francisca Rojas Ringeling, Juan F. Rodriguez-Alcazar, Rebecca Brinkschulte, Gerald Seifert, Rainer Stahl, Lori Broderick, Chris D. Putnam, Richard D. Kolodner, Stefan Canzar, Matthias Geyer, Hal M. Hoffman, Eicke Latz, 2019, Nature Communications

ModuleAlign: Module-based global alignment of protein-protein interaction networks

Somaye Hashemifar, Jianzhu Ma, Hammad Naveed, Stefan Canzar, Jinbo Xu, 2016, Bioinformatics on p. i658-i664

CIDANE: Comprehensive isoform discovery and abundance estimation

Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau, 2016, Genome Biology