Canzar Lab Faculty of Informatics and Data Science

Publications

For the development of accurate and efficient computational methods we combine techniques from combinatorial optimization and machine learning. For instance, we have developed exact and approximate algorithms for a graph coloring problem to increase the resolution of experimental protein structure data, used neural networks to project high-dimensional cellular measurments to an interpretable low-dimensional space, and extended dynamic time warping to the comparison of complex trajectories of, e.g., differentiating immune cells.

The software tools we develop address important biological and medical questions. In close collaborations with biologists and clinicians we have contributed, for example, to the discovery of the embryonic origin of adult neural progenitors, and to linking TIM-3 expression to increased relapse risk in pediatric patients with acute lymphoblastic leukemia.

Highlighted

The link between advances in algorithmic theory and new insights into fundamental problems in biology and human disease is a central characteristic of the research in our lab. The following two publications span the fields of approximation algorithms, wet lab experiments, and applications in neurobiology.

Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data
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, ..., Maria L. Spletter, Ki-Jun Yoon, Guo-li Ming, Hongjun Song, Stefan Canzar
Nature Biotechnology   ·   10 Jan 2022   ·   doi:10.1038/s41587-021-01136-7
On Tree-Constrained Matchings and Generalizations
On Tree-Constrained Matchings and Generalizations
Stefan Canzar, Khaled Elbassioni, Gunnar W. Klau, Julián Mestre
Algorithmica   ·   24 Apr 2013   ·   doi:10.1007/s00453-013-9785-0

All

2025

Optimal marker genes for <i>c</i>-separated cell types with SepSolve
Optimal marker genes for c-separated cell types with SepSolve
Bartol Borozan, Tomislav Prusina, Luka Borozan, Domagoj Severdija, Francisca Rojas Ringeling, Domagoj Matijevic, Stefan Canzar
Genome Research   ·   09 Oct 2025   ·   doi:10.1101/gr.280637.125
Coreset-based logistic regression for atlas-scale cell type annotation
Coreset-based logistic regression for atlas-scale cell type annotation
Danrong Li, Young Kun Ko, Stefan Canzar
Cold Spring Harbor Laboratory   ·   06 Jun 2025   ·   doi:10.1101/2025.06.04.655742
UMIche: A UMI-centric analysis platform for enhancing molecular quantification accuracy in bulk and single-cell sequencing
UMIche: A UMI-centric analysis platform for enhancing molecular quantification accuracy in bulk and single-cell sequencing
Jianfeng Sun, Shuang Li, Stefan Canzar, Adam P. Cribbs
Springer Science and Business Media LLC   ·   02 May 2025   ·   doi:10.21203/rs.3.rs-6523497/v1
mclUMI: Markov clustering of unique molecular identifiers enables dynamic removal of PCR duplicates
mclUMI: Markov clustering of unique molecular identifiers enables dynamic removal of PCR duplicates
Jianfeng Sun, Shuang Li, Stefan Canzar, Adam P. Cribbs
Cold Spring Harbor Laboratory   ·   16 Mar 2025   ·   doi:10.1101/2025.03.15.643033
UMIche: A platform for robust UMI-centric simulation and analysis in bulk and single-cell sequencing
UMIche: A platform for robust UMI-centric simulation and analysis in bulk and single-cell sequencing
Jianfeng Sun, Shuang Li, Stefan Canzar, Adam P. Cribbs
Cold Spring Harbor Laboratory   ·   16 Mar 2025   ·   doi:10.1101/2025.03.15.643072
Optimal marker genes for <i>c</i>-separated cell types
Optimal marker genes for c-separated cell types
Bartol Borozan, Luka Borozan, Domagoj Ševerdija, Domagoj Matijević, Stefan Canzar
Cold Spring Harbor Laboratory   ·   17 Feb 2025   ·   doi:10.1101/2025.02.12.637849

2024

Complete sequencing of ape genomes
Complete sequencing of ape genomes
DongAhn Yoo, Arang Rhie, Prajna Hebbar, Francesca Antonacci, Glennis A. Logsdon, ..., Rachel J. O’Neill, Sergey Koren, Kateryna D. Makova, Adam M. Phillippy, Evan E. Eichler
Cold Spring Harbor Laboratory   ·   31 Jul 2024   ·   doi:10.1101/2024.07.31.605654
Metric multidimensional scaling for large single-cell datasets using neural networks
Metric multidimensional scaling for large single-cell datasets using neural networks
Stefan Canzar, Van Hoan Do, Slobodan Jelić, Sören Laue, Domagoj Matijević, Tomislav Prusina
Algorithms for Molecular Biology   ·   11 Jun 2024   ·   doi:10.1186/s13015-024-00265-3
Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
Dhanur P. Iyer, Lambert Moyon, Lars Wittler, Chieh-Yu Cheng, Francisca R. Ringeling, Stefan Canzar, Annalisa Marsico, Aydan Bulut-Karslioğlu
Genome Research   ·   06 May 2024   ·   doi:10.1101/gr.278662.123
Transcript Isoform Diversity of Y Chromosome Ampliconic Genes of Great Apes Uncovered Using Long Reads and Telomere-to-Telomere Reference Genome Assemblies
Transcript Isoform Diversity of Y Chromosome Ampliconic Genes of Great Apes Uncovered Using Long Reads and Telomere-to-Telomere Reference Genome Assemblies
Aleksandra Greshnova, Karol Pál, Juan Francisco Iturralde Martinez, Stefan Canzar, Kateryna D. Makova
Cold Spring Harbor Laboratory   ·   03 Apr 2024   ·   doi:10.1101/2024.04.02.587783
Anti Tai mapping for unordered labeled trees
Anti Tai mapping for unordered labeled trees
Mislav Blažević, Stefan Canzar, Khaled Elbassioni, Domagoj Matijević
Information Processing Letters   ·   01 Mar 2024   ·   doi:10.1016/j.ipl.2023.106454
Correcting PCR amplification errors in unique molecular identifiers to generate accurate numbers of sequencing molecules
Correcting PCR amplification errors in unique molecular identifiers to generate accurate numbers of sequencing molecules
Jianfeng Sun, Martin Philpott, Danson Loi, Shuang Li, Pablo Monteagudo-Mesas, ..., Tom Brown, Tom Brown, Stefan Canzar, Udo Oppermann, Adam P. Cribbs
Nature Methods   ·   05 Feb 2024   ·   doi:10.1038/s41592-024-02168-y

2023

Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
Dhanur P. Iyer, Lambert Moyon, Francisca R. Ringeling, Chieh-Yu Cheng, Lars Wittler, Stefan Canzar, Annalisa Marsico, Aydan Bulut-Karslioglu
Cold Spring Harbor Laboratory   ·   21 Dec 2023   ·   doi:10.1101/2023.12.20.572612
Identifying Cell Types in Single-Cell Multimodal Omics Data via Joint Embedding Learning
Identifying Cell Types in Single-Cell Multimodal Omics Data via Joint Embedding Learning
Van Hoan Do, Stefan Canzar
KSE   ·   18 Oct 2023   ·   doi:10.1109/kse59128.2023.10299517
Counting pseudoalignments to novel splicing events
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
Bioinformatics   ·   01 Jul 2023   ·   doi:10.1093/bioinformatics/btad419
Fortuna Detects Novel Splicing in Drosophila scRNASeq Data
Fortuna Detects Novel Splicing in Drosophila scRNASeq Data
B. Borozan, L. Borozan, D. Ševerdija, D. Matijević, S. Canzar
MIPRO   ·   22 May 2023   ·   doi:10.23919/mipro57284.2023.10159716

2022

CYFIP1 Dosages Exhibit Divergent Behavioral Impact via Diametric Regulation of NMDA Receptor Complex Translation in Mouse Models of Psychiatric Disorders
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, ..., Paul Worley, Kimberly M. Christian, Ki-Jun Yoon, Hongjun Song, Guo-li Ming
Biological Psychiatry   ·   01 Nov 2022   ·   doi:10.1016/j.biopsych.2021.04.023
The function of Wtap in N6-adenosine methylation of mRNAs controls T cell receptor signaling and survival of T cells
The function of Wtap in N6-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, ..., Stefan Canzar, Stefan Feske, Silvia Monticelli, Julian König, Vigo Heissmeyer
Nature Immunology   ·   25 Jul 2022   ·   doi:10.1038/s41590-022-01268-1
Ccr4–Not complex reduces transcription efficiency in heterochromatin
Ccr4–Not complex reduces transcription efficiency in heterochromatin
Pablo Monteagudo-Mesas, Cornelia Brönner, Parastou Kohvaei, Haris Amedi, Stefan Canzar, Mario Halic
Nucleic Acids Research   ·   30 May 2022   ·   doi:10.1093/nar/gkac403
Predicting RNA splicing branchpoints
Predicting RNA splicing branchpoints
Antonio Jovanovic, Israa Alqassem, Nathan Chappell, Stefan Canzar, Domagoj Matijevic
MIPRO   ·   23 May 2022   ·   doi:10.23919/mipro55190.2022.9803685
Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data
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, ..., Maria L. Spletter, Ki-Jun Yoon, Guo-li Ming, Hongjun Song, Stefan Canzar
Nature Biotechnology   ·   10 Jan 2022   ·   doi:10.1038/s41587-021-01136-7
Genome‐wide off‐target analyses of CRISPR/Cas9‐mediated T‐cell receptor engineering in primary human T cells
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, ..., Paulina Ferrada‐Ernst, Nicola Habjan, Annika E Peters, Dirk H Busch, Tobias Feuchtinger
Clinical & Translational Immunology   ·   01 Jan 2022   ·   doi:10.1002/cti2.1372

2021

Ccr4-Not complex reduces transcription efficiency in heterochromatin
Ccr4-Not complex reduces transcription efficiency in heterochromatin
Pablo Monteagudo, Cornelia Brönner, Parastou Kohvaei, Haris Amedi, Stefan Canzar, Mario Halic
Cold Spring Harbor Laboratory   ·   08 Aug 2021   ·   doi:10.1101/2021.08.08.455218
Metric Multidimensional Scaling for Large Single-Cell Data Sets using Neural Networks
Metric Multidimensional Scaling for Large Single-Cell Data Sets using Neural Networks
Stefan Canzar, Van Hoan Do, Slobodan Jelić, Sören Laue, Domagoj Matijević, Tomislav Prusina
Cold Spring Harbor Laboratory   ·   25 Jun 2021   ·   doi:10.1101/2021.06.24.449725
A generalization of t-SNE and UMAP to single-cell multimodal omics
A generalization of t-SNE and UMAP to single-cell multimodal omics
Van Hoan Do, Stefan Canzar
Genome Biology   ·   03 May 2021   ·   doi:10.1186/s13059-021-02356-5
Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data
Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data
Van Hoan Do, Francisca Rojas Ringeling, Stefan Canzar
Genome Research   ·   24 Feb 2021   ·   doi:10.1101/gr.267906.120
McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data
McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data
Israa Alqassem, Yash Sonthalia, Erika Klitzke-Feser, Heejung Shim, Stefan Canzar
Bioinformatics   ·   30 Jan 2021   ·   doi:10.1093/bioinformatics/btab050
A generalization of t-SNE and UMAP to single-cell multimodal omics
A generalization of t-SNE and UMAP to single-cell multimodal omics
Van Hoan Do, Stefan Canzar
Cold Spring Harbor Laboratory   ·   10 Jan 2021   ·   doi:10.1101/2021.01.10.426098

2020

BiCoN: network-constrained biclustering of patients and omics data
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
Bioinformatics   ·   26 Dec 2020   ·   doi:10.1093/bioinformatics/btaa1076
McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data
McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data
Israa Alqassem, Yash Sonthalia, Erika Klitzke-Feser, Heejung Shim, Stefan Canzar
Cold Spring Harbor Laboratory   ·   11 Aug 2020   ·   doi:10.1101/2020.08.10.243097
Validation strategies for antibodies targeting modified ribonucleotides
Validation strategies for antibodies targeting modified ribonucleotides
Franziska Weichmann, Robert Hett, Aloys Schepers, Taku Ito-Kureha, Andrew Flatley, ..., Stefan Canzar, Mark Helm, Vigo Heissmeyer, Regina Feederle, Gunter Meister
RNA   ·   07 Jul 2020   ·   doi:10.1261/rna.076026.120
Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data
Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data
Van Hoan Do, Francisca Rojas Ringeling, Stefan Canzar
Cold Spring Harbor Laboratory   ·   15 Jun 2020   ·   doi:10.1101/2020.06.15.151910
Sphetcher: Spherical Thresholding Improves Sketching of Single-Cell Transcriptomic Heterogeneity
Sphetcher: Spherical Thresholding Improves Sketching of Single-Cell Transcriptomic Heterogeneity
Van Hoan Do, Khaled Elbassioni, Stefan Canzar
iScience   ·   01 Jun 2020   ·   doi:10.1016/j.isci.2020.101126
Clinical presentation and differential splicing of SRSF2, U2AF1 and SF3B1 mutations in patients with acute myeloid leukemia
Clinical presentation and differential splicing of SRSF2, U2AF1 and SF3B1 mutations in patients with acute myeloid leukemia
Stefanos A. Bamopoulos, Aarif M. N. Batcha, Vindi Jurinovic, Maja Rothenberg-Thurley, Hanna Janke, ..., Wolfgang Hiddemann, Jan Braess, Karsten Spiekermann, Klaus H. Metzeler, Tobias Herold
Leukemia   ·   01 May 2020   ·   doi:10.1038/s41375-020-0839-4
Leukemia-induced dysfunctional TIM-3+CD4+ bone marrow T cells increase risk of relapse in pediatric B-precursor ALL patients
Leukemia-induced dysfunctional TIM-3+CD4+ bone marrow T cells increase risk of relapse in pediatric B-precursor ALL patients
Franziska Blaeschke, Semjon Willier, Dana Stenger, Mareike Lepenies, Martin A. Horstmann, ..., Theresa Kaeuferle, Meino Rohlfs, Vera Binder, Christoph Klein, Tobias Feuchtinger
Leukemia   ·   13 Mar 2020   ·   doi:10.1038/s41375-020-0793-1
Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data
Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data
Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz
Journal of Computational Biology   ·   01 Mar 2020   ·   doi:10.1089/cmb.2019.0457
BiCoN: Network-constrained biclustering of patients and omics data
BiCoN: Network-constrained biclustering of patients and omics data
Olga Lazareva, Hoan Van Do, Stefan Canzar, Kevin Yuan, Jan Baumbach, David B. Blumenthal, Paolo Tieri, Tim Kacprowski, Markus List
Cold Spring Harbor Laboratory   ·   03 Feb 2020   ·   doi:10.1101/2020.01.31.926345
Protein-Protein Interaction Networks
Protein-Protein Interaction Networks
[no author info]
Methods in Molecular Biology   ·   01 Jan 2020   ·   doi:10.1007/978-1-4939-9873-9

2019

Alternative splicing regulates stochastic NLRP3 activity
Alternative splicing regulates stochastic NLRP3 activity
Florian Hoss, James L. Mueller, Francisca Rojas Ringeling, Juan F. Rodriguez-Alcazar, Rebecca Brinkschulte, ..., Richard D. Kolodner, Stefan Canzar, Matthias Geyer, Hal M. Hoffman, Eicke Latz
Nature Communications   ·   19 Jul 2019   ·   doi:10.1038/s41467-019-11076-1
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources
Dinanath Sulakhe, Mark D’Souza, Sheng Wang, Sandhya Balasubramanian, Prashanth Athri, Bingqing Xie, Stefan Canzar, Gady Agam, T Conrad Gilliam, Natalia Maltsev
Briefings in Bioinformatics   ·   03 Jun 2019   ·   doi:10.1093/bib/bby047
Properties of the generalized Robinson-Foulds metric
Properties of the generalized Robinson-Foulds metric
L. Borozan, D. Matijevic, S. Canzar
2019 42nd International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO)   ·   01 May 2019   ·   doi:10.23919/mipro.2019.8756638
Proteome Analysis of Human Neutrophil Granulocytes From Patients With Monogenic Disease Using Data-independent Acquisition
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, ..., Türkan Patıroğlu, Stefan Canzar, Jutte van der Werff Ten Bosch, Christoph Klein, Juri Rappsilber
Molecular & Cellular Proteomics   ·   01 Apr 2019   ·   doi:10.1074/mcp.ra118.001141
A Common Embryonic Origin of Stem Cells Drives Developmental and Adult Neurogenesis
A Common Embryonic Origin of Stem Cells Drives Developmental and Adult Neurogenesis
Daniel A. Berg, Yijing Su, Dennisse Jimenez-Cyrus, Aneek Patel, Nancy Huang, ..., Qing-Feng Wu, Stefan Canzar, Guo-Li Ming, Hongjun Song, Allison M. Bond
Cell   ·   01 Apr 2019   ·   doi:10.1016/j.cell.2019.02.010
Dynamic pseudo-time warping of complex single-cell trajectories
Dynamic pseudo-time warping of complex single-cell trajectories
Van Hoan Do, Mislav Blažević, Pablo Monteagudo, Luka Borozan, Khaled Elbassioni, Sören Laue, Francisca Rojas Ringeling, Domagoj Matijević, Stefan Canzar
RECOMB   ·   17 Jan 2019   ·   doi:10.1101/522672
Preprint

2018

Guided Reconstruction of Full-Length Isoforms from Short Reads by CIDANE
Guided Reconstruction of Full-Length Isoforms from Short Reads by CIDANE
Sandro Andreotti, Stefan Canzar
Methods in Molecular Biology   ·   12 Dec 2018   ·   doi:10.1007/978-1-4939-8808-2_15
Genome wide association analysis in a mouse advanced intercross line
Genome wide association analysis in a mouse advanced intercross line
Natalia M. Gonzales, Jungkyun Seo, Ana I. Hernandez Cordero, Celine L. St. Pierre, Jennifer S. Gregory, Margaret G. Distler, Mark Abney, Stefan Canzar, Arimantas Lionikas, Abraham A. Palmer
Nature Communications   ·   04 Dec 2018   ·   doi:10.1038/s41467-018-07642-8
On the approximability of the maximum interval constrained coloring problem
On the approximability of the maximum interval constrained coloring problem
Stefan Canzar, Khaled Elbassioni, Amr Elmasry, Rajiv Raman
Discrete Optimization   ·   01 Feb 2018   ·   doi:10.1016/j.disopt.2017.09.002
Tracking Alternatively Spliced Isoforms from Long Reads by SpliceHunter
Tracking Alternatively Spliced Isoforms from Long Reads by SpliceHunter
Zheng Kuang, Stefan Canzar
Methods in Molecular Biology   ·   01 Jan 2018   ·   doi:10.1007/978-1-4939-7710-9_5
Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data
Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data
Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz
RECOMB   ·   01 Jan 2018   ·   doi:10.1007/978-3-319-89929-9_2

2017

Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation
Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation
Ki-Jun Yoon, Francisca Rojas Ringeling, Caroline Vissers, Fadi Jacob, Michael Pokrass, ..., Xiaoxi Zhuang, Stefan Canzar, Chuan He, Guo-li Ming, Hongjun Song
Cell   ·   01 Nov 2017   ·   doi:10.1016/j.cell.2017.09.003
Short Read Mapping: An Algorithmic Tour
Short Read Mapping: An Algorithmic Tour
Stefan Canzar, Steven L. Salzberg
Proceedings of the IEEE   ·   01 Mar 2017   ·   doi:10.1109/jproc.2015.2455551

2016

The dynamic landscape of fission yeast meiosis alternative-splice isoforms
The dynamic landscape of fission yeast meiosis alternative-splice isoforms
Zheng Kuang, Jef D. Boeke, Stefan Canzar
Genome Research   ·   17 Nov 2016   ·   doi:10.1101/gr.208041.116
BASIC: BCR assembly from single cells
BASIC: BCR assembly from single cells
Stefan Canzar, Karlynn E Neu, Qingming Tang, Patrick C Wilson, Aly A Khan
Bioinformatics   ·   02 Oct 2016   ·   doi:10.1093/bioinformatics/btw631
ModuleAlign: module-based global alignment of protein–protein interaction networks
ModuleAlign: module-based global alignment of protein–protein interaction networks
Somaye Hashemifar, Jianzhu Ma, Hammad Naveed, Stefan Canzar, Jinbo Xu
Bioinformatics   ·   29 Aug 2016   ·   doi:10.1093/bioinformatics/btw447
Computational Methods for Transcript Assembly from RNA‐SEQ Reads
Computational Methods for Transcript Assembly from RNA‐SEQ Reads
Stefan Canzar, Liliana Florea
Computational Methods for Next Generation Sequencing Data Analysis   ·   26 Aug 2016   ·   doi:10.1002/9781119272182.ch11
The dynamic landscape of fission yeast meiosis alternative-splice isoforms
The dynamic landscape of fission yeast meiosis alternative-splice isoforms
Zheng Kuang, Jef D. Boeke, Stefan Canzar
Cold Spring Harbor Laboratory   ·   29 Mar 2016   ·   doi:10.1101/045922
Resolving Conflicting Predictions from Multimapping Reads
Resolving Conflicting Predictions from Multimapping Reads
Stefan Canzar, Khaled Elbassioni, Mitchell Jones, Julián Mestre
Journal of Computational Biology   ·   01 Mar 2016   ·   doi:10.1089/cmb.2015.0164
CIDANE: comprehensive isoform discovery and abundance estimation
CIDANE: comprehensive isoform discovery and abundance estimation
Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau
Genome Biology   ·   30 Jan 2016   ·   doi:10.1186/s13059-015-0865-0

2015

CIDANE: Comprehensive isoform discovery and abundance estimation
CIDANE: Comprehensive isoform discovery and abundance estimation
Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau
RECOMB   ·   12 Apr 2015   ·   doi:10.1101/017939
Preprint

2013

The Duplication-Loss Small Phylogeny Problem: From Cherries to Trees
The Duplication-Loss Small Phylogeny Problem: From Cherries to Trees
Sandro Andreotti, Knut Reinert, Stefan Canzar
Journal of Computational Biology   ·   01 Sep 2013   ·   doi:10.1089/cmb.2013.0057
A polynomial-delay algorithm for enumerating approximate solutions to the interval constrained coloring problem
A polynomial-delay algorithm for enumerating approximate solutions to the interval constrained coloring problem
Stefan Canzar, Khaled Elbassioni, Julián Mestre
Algorithm Engineering and Experiments (ALENEX)   ·   30 Jul 2013   ·   doi:10.1145/2444016.2493372
GAGE-B: an evaluation of genome assemblers for bacterial organisms
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
Bioinformatics   ·   10 May 2013   ·   doi:10.1093/bioinformatics/btt273
On Tree-Constrained Matchings and Generalizations
On Tree-Constrained Matchings and Generalizations
Stefan Canzar, Khaled Elbassioni, Gunnar W. Klau, Julián Mestre
Algorithmica   ·   24 Apr 2013   ·   doi:10.1007/s00453-013-9785-0
Charge Group Partitioning in Biomolecular Simulation
Charge Group Partitioning in Biomolecular Simulation
Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
Journal of Computational Biology   ·   01 Mar 2013   ·   doi:10.1089/cmb.2012.0239
The Generalized Robinson-Foulds Metric
The Generalized Robinson-Foulds Metric
Sebastian Böcker, Stefan Canzar, Gunnar W. Klau
Algorithms in Bioinformatics (WABI)   ·   01 Jan 2013   ·   doi:10.1007/978-3-642-40453-5_13

2012

CLEVER: clique-enumerating variant finder
CLEVER: clique-enumerating variant finder
Tobias Marschall, Ivan G. Costa, Stefan Canzar, Markus Bauer, Gunnar W. Klau, Alexander Schliep, Alexander Schönhuth
Bioinformatics   ·   11 Oct 2012   ·   doi:10.1093/bioinformatics/bts566
Solving the Minimum String Cover Problem
Solving the Minimum String Cover Problem
Stefan Canzar, Tobias Marschall, Sven Rahmann, Chris Schwiegelshohn
Algorithm Engineering and Experiments (ALENEX)   ·   16 Jan 2012   ·   doi:10.1137/1.9781611972924.8
Charge Group Partitioning in Biomolecular Simulation
Charge Group Partitioning in Biomolecular Simulation
Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled Elbassioni, Alpesh K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
RECOMB   ·   01 Jan 2012   ·   doi:10.1007/978-3-642-29627-7_3

2011

An exact algorithm for side-chain placement in protein design
An exact algorithm for side-chain placement in protein design
Stefan Canzar, Nora C. Toussaint, Gunnar W. Klau
Optimization Letters   ·   25 Mar 2011   ·   doi:10.1007/s11590-011-0308-0
On Tree-Constrained Matchings and Generalizations
On Tree-Constrained Matchings and Generalizations
Stefan Canzar, Khaled Elbassioni, Gunnar W. Klau, Julián Mestre
Automata, Languages and Programming (ICALP)   ·   01 Jan 2011   ·   doi:10.1007/978-3-642-22006-7_9
A Mathematical Programming Approach to Marker-Assisted Gene Pyramiding
A Mathematical Programming Approach to Marker-Assisted Gene Pyramiding
Stefan Canzar, Mohammed El-Kebir
Algorithms in Bioinformatics (WABI)   ·   01 Jan 2011   ·   doi:10.1007/978-3-642-23038-7_3

2010

Computing H/D-Exchange rates of single residues from data of proteolytic fragments
Computing H/D-Exchange rates of single residues from data of proteolytic fragments
Ernst Althaus, Stefan Canzar, Carsten Ehrler, Mark R Emmett, Andreas Karrenbauer, Alan G Marshall, Anke Meyer-Bäse, Jeremiah D Tipton, Hui-Min Zhang
BMC Bioinformatics   ·   11 Aug 2010   ·   doi:10.1186/1471-2105-11-424
Approximation Algorithms for the Interval Constrained Coloring Problem
Approximation Algorithms for the Interval Constrained Coloring Problem
Ernst Althaus, Stefan Canzar, Khaled Elbassioni, Andreas Karrenbauer, Julián Mestre
Algorithmica   ·   15 Apr 2010   ·   doi:10.1007/s00453-010-9406-0
A Polynomial Delay Algorithm for Enumerating Approximate Solutions to the Interval Constrained Coloring Problem
A Polynomial Delay Algorithm for Enumerating Approximate Solutions to the Interval Constrained Coloring Problem
Stefan Canzar, Khaled Elbassioni, Julián Mestre
Algorithm Engineering and Experiments (ALENEX)   ·   16 Jan 2010   ·   doi:10.1137/1.9781611972900.3
On the Approximability of the Maximum Interval Constrained Coloring Problem
On the Approximability of the Maximum Interval Constrained Coloring Problem
Stefan Canzar, Khaled Elbassioni, Amr Elmasry, Rajiv Raman
Algorithms and Computation (ISAAC)   ·   01 Jan 2010   ·   doi:10.1007/978-3-642-17514-5_15

2009

Discrete Fitting of Hydrogen-Deuterium-Exchange-data of Overlapping Fragments
Discrete Fitting of Hydrogen-Deuterium-Exchange-data of Overlapping Fragments
Ernst Althaus, Stefan Canzar, Carsten Ehrler, Mark R. Emmett, Andreas Karrenbauer, Alan G. Marshall, Anke Meyer-Bäse, Jeremiah Tiptopn, Huimin Zhang
BIOCOMP   ·   28 Oct 2009   ·   ISBN:1-60132-095-7

2008

LASA: A Tool for Non-heuristic Alignment of Multiple Sequences
LASA: A Tool for Non-heuristic Alignment of Multiple Sequences
Ernst Althaus, Stefan Canzar
BIRD   ·   07 Jul 2008   ·   doi:10.1007/978-3-540-70600-7_38
Approximating the Interval Constrained Coloring Problem
Approximating the Interval Constrained Coloring Problem
Ernst Althaus, Stefan Canzar, Khaled Elbassioni, Andreas Karrenbauer, Julián Mestre
Algorithm Theory (SWAT)   ·   02 Jul 2008   ·   doi:10.1007/978-3-540-69903-3_20
Computing H/D-exchange speeds of single residues from data of peptic fragments
Computing H/D-exchange speeds of single residues from data of peptic fragments
Ernst Althaus, Stefan Canzar, Mark R. Emmett, Andreas Karrenbauer, Alan G. Marshall, Anke Meyer-Baese, Huimin Zhang
ACM Symposium on Applied Computing (SAC)   ·   16 Mar 2008   ·   doi:10.1145/1363686.1363981
A Lagrangian relaxation approach for the multiple sequence alignment problem
A Lagrangian relaxation approach for the multiple sequence alignment problem
Ernst Althaus, Stefan Canzar
Journal of Combinatorial Optimization   ·   05 Mar 2008   ·   doi:10.1007/s10878-008-9139-z

2007

A Lagrangian Relaxation Approach for the Multiple Sequence Alignment Problem
A Lagrangian Relaxation Approach for the Multiple Sequence Alignment Problem
Ernst Althaus, Stefan Canzar
Combinatorial Optimization and Applications (COCOA)   ·   14 Aug 2007   ·   doi:10.1007/978-3-540-73556-4_29

2006

Shape distributions and protein similarity
Shape distributions and protein similarity
Stefan Canzar, Jan Remy
GCB   ·   19 Sep 2006   ·   ISBN:978-3-88579-177-5