Canzar Lab - Publications
2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006
Preprints
Anti Tai Mapping for Unordered Labeled Trees
Blažević M, Canzar S, Elbassioni K, Matijević D.
arXiv. 2021. arXiv:2107.08292 Link
Metric Multidimensional Scaling for Large Single-Cell Data Sets using Neural Networks
Canzar S, Van Do H, Jelić S, Laue S, Matijević D, Prusina T.
bioRxiv. 2021. doi: 10.1101/2021.06.24.449725 Link
Dynamic pseudo-time warping of complex single-cell trajectories
Van Do H, Blažević M, Monteagudo P, Borozan L, Elbassioni K, Laue S, Rojas Ringeling F, Matijević D, Canzar S
bioRxiv. 2019. doi: 10.1101/2020.01.31.926345 Link
The function of Wtap in N6-adenosine methylation of mRNAs controls T cell receptor signaling and survival of T cells
Ito-Kureha T, Leoni C, Borland K, Cantini G, Bataclan M, Metzger R, Ammann G, Krug A, Marsico A, Kellner S, Canzar S, Feske S, Monticelli S, König J, Heissmeyer V
Nature Immunology. 2022. In press. (preprint Research Square)
Ccr4-Not complex reduces transcription efficiency in heterochromatin
Monteagudo P, Broenner C, Kohvaei P, Amedi H, Canzar S, Halic M
Nucleic Acid Research. 2022. doi:10.1093/nar/gkac403 (preprint bioRxiv)
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
Genome-wide off-target analyses of CRISPR/Cas9-mediated T-cell receptor engineering in primary human T cells
Kaeuferle T, Stief TA, Canzar S, Kutlu NN, Willier S, Stenger D, Ferrada-Ernst P, Habjan N, Peters AE, Busch DH, Feuchtinger T
Clinical & Translational Immunology. 2022;11(1):e1372. doi: 10.1002/cti2.1372.
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 Link
CYFIP1 dosages exhibit divergent behavioral impact via diametric regulation of NMDAR complex translation in mouse models of psychiatric disorders
Kim NS, Rojas Ringeling F, Zhou Y, Nguyen HN, Temme SJ, Lin YT, Eacker S, Dawson VL, Dawson TM, Xiao B, Hsu KS, Canzar S, Li W, Worley P, Christian KM, Yoon KJ , Song H, Ming GL
Biological Psychiatry. 2021. in press. doi: 10.1016/j.biopsych.2021.04.023 Link
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 Link (preprint bioRxiv)
McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data
Alqassem I, Sonthalia Y, Klitzke-Feser E, Shim H , Canzar S
Bioinformatics. 2021. doi: 10.1093/bioinformatics/btab050 Link (preprint bioRxiv)
BiCoN: Network-constrained biclustering of patients and omics data
Lazareva O , Canzar S, Yuan K, Baumbach J, Tieri P, Kacprowski T , List M
Bioinformatics. 2020. doi: 10.1093/bioinformatics/btaa1076 Link (preprint bioRxiv)
Validation strategies for antibodies targeting modified ribonucleotides
Weichmann F, Hett R, Schepers A, Ito-Kureha T, Flatley A, Slama K, Hastert F, Angstman N, Cardoso CM, König J, Huettelmaier S, Dieterich C, Canzar S, Helm M, Heissmeyer V, Feederle R, Meister G
RNA. 2020. doi: 10.1261/rna.076026.120 Link
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 Link
Leukemia-induced dysfunctional TIM-3+CD4+ bone marrow T cells increase risk of relapse in pediatric B-precursor ALL patients
Blaeschke F, Willier S, Stenger D, Lepenies M, Horstmann M, Escherich G, Zimmermann M, Rojas Ringeling F, Canzar S, Kaeuferle T, Rohlfs M, Binder V, Klein C, Feuchtinger T
Leukemia. 2020. doi: 10.1038/s41375-020-0793-1 Link
Clinical presentation and differential splicing of SRSF2, U2AF1 and SF3B1 mutations in patients with Acute Myeloid Leukaemia
Bamopoulos S , Batcha A, Jurinovic V, Rothenberg-Thurley M, Janke H, Ksienzyk B, Philippou-Massier J, Graf A, Krebs S, Blum H, Schneider S, Konstandin N, Sauerland MC, Goerlich D, Berdel WE, Woermann BJ, Bohlander SK, Canzar S, Mansmann U, Hiddemann W, Braess J, Spiekermann K, Metzeler KH, Herold T
Leukemia. 2020. doi: 10.1038/s41375-020-0839-4 Link (preprint medRxiv)
Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data
Chakraborty S, Canzar S, Marschall T, Schulz MH
J Comput Biol. 2020 Mar;27(3):330-341. doi: 10.1089/cmb.2019.0457 Link
Alternative splicing regulates stochastic NLRP3 activity
Hoss F, Mueller JL, Rojas Ringeling F, Rodriguez-Alcazar JF, Brinkschulte R, Seifert G, Stahl R, Broderick L, Putnam CD, Kolodner RD, Canzar S, Geyer M, Hoffman HM, Latz E
Nature Communications. 2019. doi: 10.1038/s41467-019-11076-1 Link
A Common Embryonic Origin of Stem Cells Drives Developmental and Adult Neurogenesis
Berg DA, Su Y, Jimenez-Cyrus D, Patel A, Huang N, Morizet D, Lee S, Shah R, Ringeling FR, Jain R, Epstein JA, Wu QF, Canzar S, Ming GL , Song H , Bond AM
Cell. 2019 Mar 28; In press. doi: 10.1016/j.cell.2019.02.010 Link
Properties of the generalized Robinson-Foulds metric
Borozan L, Matijević D, Canzar S
Distributed Computing in Data Science and Biomedical Engineering. 2019; In press.
Dynamic pseudo-time warping of complex single-cell trajectories
Van Do H, Blažević M, Monteagudo P, Borozan L, Elbassioni K, Laue S, Rojas Ringeling F, Matijević D, Canzar S
Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science. bioRxiv
Guided Reconstruction of Full-Length Isoforms from Short Reads by CIDANE
Andreotti S, Canzar S
Methods Mol Biol. 2019;1870:199-208. doi: 10.1007/978-1-4939-8808-2_15. PubMed
Proteome analysis of human neutrophil granulocytes from patients with monogenic disease using data-independent acquisition
Grabowski P, Hesse S, Hollizeck S, Rohlfs M, Behrends U, Sherkat R, Tamary H, Ünal E, Somech R, Patıroğlu T, Canzar S, van der Werff Ten Bosch J, Klein C, Rappsilber J
Mol Cell Proteomics. 2019. doi: 10.1074/mcp.RA118.001141 PubMed
2018
Genome wide association analysis in a mouse advanced intercross line
Gonzales NM, Seo J, Hernandez-Cordero AI, St. Pierre CL, Gregory JS, Distler MG, Abney M, Canzar S, Lionikas A, Palmer AA
Nature Communications. 2018. doi: 10.1038/s41467-018-07642-8. PubMed
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources
Sulakhe D , D’Souza M , Wang S, Balasubramanian S, Athri P, Xie B, Canzar S, Agam G, Gilliam TC, Maltsev N
Briefings in Bioinformatics. 2018. doi: 10.1093/bib/bby047. PubMed
Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data
Chakraborty S, Canzar S, Marschall T , Schulz MH
Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science. 2018;10812:60-61. doi: 10.1007/978-3-319-16706-0_8. Link
Tracking Alternatively Spliced Isoforms from Long Reads by SpliceHunter.
Kuang Z, Canzar S
Methods Mol Biol. 2018;1751:73-88. doi: 10.1007/978-1-4939-7710-9_5. PubMed
2017
Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation.
Yoon KJ, Ringeling FR, Vissers C, Jacob F, Pokrass M, Jimenez-Cyrus D, Su Y, Kim NS, Zhu Y, Zheng L, Kim S, Wang X, Doré LC, Jin P, Regot S, Zhuang X, Canzar S, He C, Ming GL , Song H
Cell. 2017 Nov 2;171(4):877-889.e17. doi: 10.1016/j.cell.2017.09.003. PubMed
On the Approximability of the Maximum Interval Constrained Coloring Problem.
Canzar S , Elbassioni KM , Elmasry A , Raman R .
Discrete Optimization, https://doi.org/10.1016/j.disopt.2017.09.002. Epub 2017.
The dynamic landscape of fission yeast meiosis alternative-splice isoforms.
Kuang Z, Boeke JD , Canzar S .
Genome Res. 2017 Jan;27(1):145-156. doi: 10.1101/gr.208041.116. PubMed
BASIC: BCR assembly from single cells.
Canzar S, Neu KE, Tang Q, Wilson PC, Khan AA .
Bioinformatics. 2017 Feb 1;33(3):425-427. doi: 10.1093/bioinformatics/btw631. PubMed
2016
ModuleAlign: module-based global alignment of protein-protein interaction networks.
Hashemifar S, Ma J, Naveed H, Canzar S , Xu J .
Bioinformatics. 2016 Sep 1;32(17):i658-i664. doi: 10.1093/bioinformatics/btw447. PubMed
CIDANE: comprehensive isoform discovery and abundance estimation.
Canzar S , Andreotti S, Weese D, Reinert K, Klau GW.
Genome Biol. 2016 Jan 30;17:16. doi: 10.1186/s13059-015-0865-0. PubMed
Resolving Conflicting Predictions from Multimapping Reads.
Canzar S , Elbassioni K, Jones M, Mestre J.
J Comput Biol. 2016 Mar;23(3):203-17. doi: 10.1089/cmb.2015.0164. Epub 2016 Jan 8. PubMed
Computational Methods for Transcript Assembly from RNA-seq Reads.
Canzar S, Florea L.
Computational Methods for Next Generation Sequencing Data Analysis (eds I. Măndoiu and A. Zelikovsky). 2016. doi: 10.1002/9781119272182.ch11. Link
2015
On Tree-Constrained Matchings and Generalizations.
Canzar S, Elbassioni K, Klau GW, Mestre J.
Algorithmica. 2015;71(1):98-119. doi:10.1007/s00453-013-9785-0. Link
CIDANE: Comprehensive isoform discovery and abundance estimation.
Canzar S , Andreotti S, Weese D, Reinert K, Klau GW.
Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science. 2015;9029:60-61. doi: 10.1007/978-3-319-16706-0_8. Link
Short Read Mapping: An Algorithmic Tour.
Canzar S, Salzberg SL.
Proc IEEE Inst Electr Electron Eng. 2017 Mar;105(3):436-458. doi: 10.1109/JPROC.2015.2455551. Epub 2015 Sep 7. PubMed
2013
The duplication-loss small phylogeny problem: from cherries to trees.
Andreotti S, Reinert K, Canzar S .
J Comput Biol. 2013 Sep;20(9):643-59. doi: 10.1089/cmb.2013.0057. PubMed
GAGE-B: an evaluation of genome assemblers for bacterial organisms.
Magoc T, Pabinger S, Canzar S, Liu X, Su Q, Puiu D, Tallon LJ, Salzberg SL .
Bioinformatics. 2013 Jul 15;29(14):1718-25. doi: 10.1093/bioinformatics/btt273. Epub 2013 May 10. PubMed
Charge group partitioning in biomolecular simulation.
Canzar S, El-Kebir M, Pool R, Elbassioni K, Mark AE, Geerke DP, Stougie L, Klau GW .
J Comput Biol. 2013 Mar;20(3):188-98. doi: 10.1089/cmb.2012.0239. PubMed
A Polynomial Delay Algorithm for Enumerating Approximate Solutions to the Interval Constrained Coloring Problem.
Canzar S, Elbassioni K, Mestre J.
ACM Journal on Experimental Algorithmics. 2013;18:2.2:2.1-2.2:2.19. doi: 10.1145/2444016.2493372. Link
The generalized Robinson-Foulds metric.
Böcker S , Canzar S , Klau GW .
Algorithms in Bioinformatics. WABI 2013. Lecture Notes in Bioinformatics. 2013;8126:156-169 doi: 10.1007/978-3-642-40453-5_13. Link
2012
CLEVER: clique-enumerating variant finder.
Marschall T, Costa IG, Canzar S, Bauer M, Klau GW, Schliep A, Schönhuth A .
Bioinformatics. 2012 Nov 15;28(22):2875-82. doi: 10.1093/bioinformatics/bts566. Epub 2012 Oct 11. PubMed
Charge Group Partitioning in Biomolecular Simulation.
Canzar S, El-Kebir M, Pool R, Elbassioni K, Malde AK, Mark AE, Geerke DP, Stougie L, Klau GW .
Research in Computational Molecular Biology. RECOMB 2012.Lecture Notes in Computer Science. 2012;7262:29-43. doi: 10.1007/978-3-642-29627-7_3. Link
Solving the Minimum String Cover Problem.
Canzar S, Marschall T, Rahmann S, Schwiegelshohn C.
Algorithm Engineering and Experiments. ALENEX 2012;75-83. doi: 10.1137/1.9781611972924.8. Link
2011
An Exact Algorithm for Side-Chain Placement in Protein Design.
Canzar S, Toussaint NC, Klau GW .
Optimization Letters, special issue on 10th International Symposium on Experimental Algorithms (SEA). 2011;5(3),393-406. doi: doi:10.1007/s11590-011-0308-0. Link
A Mathematical Programming Approach to Marker-Assisted Gene Pyramiding.
Canzar S, El-Kebir M.
Algorithms in Bioinformatics. WABI 2011. Lecture Notes in Bioinformatics. 2011;6833:26-38. doi: 10.1007/978-3-642-23038-7_3. Link
Approximation Algorithms for the Interval Constrained Coloring Problem.
Althaus E, Canzar S, Elbassioni K, Karrenbauer A, Mestre J.
Algorithmica. 2011;61:342-361. doi: 10.1007/s00453-010-9406-0. Link
On Tree-Constrained Matchings and Generalizations.
Canzar S, Elbassioni K, Klau GW, Mestre J.
International Colloquium on Automata, Languages and Programming. ICALP 2011. Lecture Notes in Computer Science. 2011;6755:98-109. doi: 10.1007/978-3-642-22006-7_9. Link
2010
Computing H/D-exchange rates of single residues from data of proteolytic fragments.
Althaus E, Canzar S, Ehrler C, Emmett MR, Karrenbauer A, Marshall AG, Meyer-Bäse A, Tipton JD, Zhang HM.
BMC Bioinformatics. 2010 Aug 11;11:424. doi: 10.1186/1471-2105-11-424. PubMed
On the Approximability of the Maximum Interval Coloring Problem.
Canzar S, Elbassioni K, Elmasry A, Raman R.
International Symposium on Algorithms and Computation. ISAAC 2010. Lecture Notes in Computer Science, 2010;6507:168-179. doi: 10.1007/978-3-642-17514-5_15. Link
A Polynomial Delay Algorithm for Enumerating Approximate Solutions to the Interval Constrained Coloring Problem.
Canzar S, Elbassioni K, Mestre J.
Algorithm Engineering and Experiments. ALENEX 2010. SIAM 2010;23-33 doi: 10.1137/1.9781611972900.3. Link
2009
Discrete Fitting of Hydrogen-Deuterium-Exchange-data of Overlapping Fragments.
Althaus E, Canzar S, Ehrler C, Emmett MR, Karrenbauer A, Marshall AG, Meyer-Baese A, Tipton J, Zhang H.
Bioinformatics & Computational Biology. BIOCOMP 2009. CSREA Press 2009;496-502. Link
2008
A Lagrangian relaxation approach for the multiple sequence alignment problem.
Althaus E, Canzar S.
Journal of Combinatorial Optimization. 2008;16(2):127-154. 10.1007/s10878-008-9139-z. Link
Computing H/D-Exchange Speeds of Single Residues from Data of Peptic Fragments.
Althaus E, Canzar S, Emmett MR, Karrenbauer A, Marshall AG, Meyer-Baese A, Zhang H.
ACM Symposium on Applied Computing. SAC 2008;1273-1277. doi: 10.1145/1363686.1363981. Link
LASA: A tool for non-heuristic alignment of multiple sequences.
Althaus E, Canzar S.
Bioinformatics Research and Development. BIRD 2008. Springer, 2008;13:489-498. doi: 10.1007/978-3-540-70600-7_38. Link
Approximating the Interval Constrained Coloring Problem.
Althaus E, Canzar S, Elbassioni K, Karrenbauer A, Mestre J.
Scandinavian Workshop on Algorithm Theory. SWAT 2008. Lecture Notes in Computer Science. 2008;5124:210-221. doi: 10.1007/978-3-540-69903-3_20. Link
2007
A Lagrangian Relaxation Approach for the Multiple Sequence Alignment Problem.
Althaus E, Canzar S.
International Conference on Combinatorial Optimization and Applications. COCOA 2007. Lecture Notes in Computer Science. 2007;4616:267-278. doi: 10.1007/978-3-540-73556-4_29. Link
2006
Shape Distributions and Protein Similarity.
Canzar S, Remy J.
German Conference on Bioinformatics. GCB 2006. Lecture Notes in Informatics. 2006;1-10. Link