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Canzar Lab - Publications

2018   |   2017   |   2016   |   2013   |   2012   |  2011   |   2010   |   2009   |   2008  |   2007   |   2006    

 

2018




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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

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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. M─ândoiu and A. Zelikovsky). 2016. doi: 10.1002/9781119272182.ch11. Link

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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

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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

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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

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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

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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

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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

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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

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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

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2006

Shape Distributions and Protein Similarity.
Canzar S, Remy J.
German Conference on Bioinformatics. GCB 2006. Lecture Notes in Informatics. 2006;1-10. Link