Stefan Canzar
Associate Professor of Computer Science and Engineering

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W204B Westgate
University Park, PA - skc6192@psu.edu
- 814-863-4134
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 DnaMost 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