Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation

K.-J. YOON, F. ROJAS RINGELING, C. VISSERS, … , S. CANZAR, C. HE, G. MING, H. SONG,

Cell, 2017.

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On the Approximability of the Maximum Interval Constrained Coloring Problem

S. CANZAR , K. ELBASSIONI , A. ELMASRY , R. RAMAN

Discrete Optimization, 2017

Tracking alternatively spliced isoforms from long reads by SpliceHunter

Z. KUANG, S. CANZAR,

Method in Molecular Biology, in press.

The dynamic landscape of fission yeast meiosis alternative-splice isoforms

Z. KUANG, J. D. BOEKE, S. CANZAR,

Genome Research, 27:145-156, 2017.

BASIC: BCR assembly from single cells

S. CANZAR, K. E. NEU, Q. TANG, P. C. WILSON, A. A. KHAN,

Bioinformatics, 33(3):425-427, 2016.

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

S. HASHEMIFAR, J. MA, H. NAVEED, S. CANZAR , J. XU

Bioinformatics (Proceedings of ECCB'16), 32(17):i658-i664, 2016.

CIDANE: Comprehensive isoform discovery and abundance estimation

S. CANZAR , S. ANDREOTTI, D. WEESE, K. REINERT, G. W. KLAU

Genome Biology, 17(1):1-18, 2016. (preprint: bioRxiv, April 2015.)

Resolving conflicting predictions from multi-mapping reads

S. CANZAR , K. ELBASSIONI, M. JONES, J. MESTRE

Journal of Computational Biology, 23(3):203-17, 2016.

Short Read Mapping: An Algorithmic Tour

S. CANZAR and S. L. Salzberg

Proceedings of the IEEE, advance publication, 7 Sep 2015.

Computational Methods for Transcript Assembly from RNA-seq Reads (book chapter)

S. CANZAR and L. Florea

Computational Methods for Next Generation Sequencing Data Analysis (Wiley Series in Bioinformatics), in press.

CIDANE: Comprehensive isoform discovery and abundance estimation

S. CANZAR , S. ANDREOTTI, D. WEESE, K. REINERT, G. W. KLAU

In Proceedings of the 19th Annual International Conference on Research in Computational Molecular Biology (RECOMB),
Lecture Notes in Computer Science, Springer, 2015.

The Duplication-Loss Small Phylogeny Problem: From Cherries to Trees

S. ANDREOTTI, K. REINERT, S. CANZAR

Journal of Computational Biology, 20(9):643-59, 2013.
preprint: arXiv:1208.2698

GAGE-B: An Evaluation of Genome Assemblers for Bacterial Organisms

T. MAGOC, S. PABINGER, S. CANZAR , X. LIU, Q. SU D. PUIU, L. J. TALLON, S. L. SALZBERG

Bioinformatics, 29:1718-1725, 2013.

A Polynomial Delay Algorithm for Enumerating Approximate Solutions to the Interval Constrained Coloring Problem

S. CANZAR , K. ELBASSIONI, J. MESTRE

ACM Journal on Experimental Algorithmics, 18:2.2:2.1-2.2:2.19, 2013.

On Tree-Constrained Matchings and Generalizations

S. CANZAR , K. ELBASSIONI, G. W. KLAU, J. MESTRE

Algorithmica, 1-22, 2013.

Charge Group Partitioning in Biomolecular Simulation

S. CANZAR , M. El-KEBIR, R. POOL, K. ELBASSIONI, A. K. MALDE, A. E. MARK, D. P. GEERKE, L. STOUGIE, G. W. KLAU

Journal of Computational Biology, 2013, volume 20(3), pages 167-187.

The generalized Robinson-Foulds metric

S. BÖCKER, S. CANZAR , G. W. KLAU

In Proceedings of the 13th Workshop on Algorithms in Bioinformatics (WABI),
Lecture Notes in Bioinformatics, Springer, 2013.

CLEVER: Clique-Enumerating Variant Finder

T. MARSCHALL, I. COSTA, S. CANZAR , M. BAUER, G. W. KLAU , A. SCHLIEP, A. SCHÖNHUTH

Bioinformatics, 2012, volume 28(22), pages 2875-2882.

Charge Group Partitioning in Biomolecular Simulation

S. CANZAR , M. El-KEBIR, R. POOL, K. ELBASSIONI, A. K. MALDE, A. E. MARK, D. P. GEERKE, L. STOUGIE, G. W. KLAU

In Proceedings of the 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB),
Lecture Notes in Computer Science, Springer, 2012.

Solving the Minimum String Cover Problem

S. CANZAR , T. MARSCHALL, S. RAHMANN, C. SCHWIEGELSHOHN

In Proceedings of the 14th Meeting on Algorithm Engineering and Experiments (ALENEX), SIAM 2012.

CLEVER: Clique-Enumerating Variant Finder

T. MARSCHALL, I. COSTA, S. CANZAR, M. BAUER, G. KLAU, A. SCHLIEP, A. SCHOENHUTH

RECOMB-seq and ISMB-HitSeq, 2012.

An Exact Algorithm for Side-Chain Placement in Protein Design

S. CANZAR , N. C. TOUSSAINT , G. W. KLAU

Optimization Letters, special issue on 10th International Symposium on Experimental Algorithms (SEA), 2011, volume 5(3), pages 393-406.

A Mathematical Programming Approach to Marker-Assisted Gene Pyramiding

S. CANZAR , M. EL-KEBIR

In Proceedings of the 11th Workshop on Algorithms in Bioinformatics (WABI),
Lecture Notes in Bioinformatics, Springer, 2011.

Approximation Algorithms for the Interval Constrained Coloring Problem

E. ALTHAUS, S. CANZAR , K. ELBASSIONI , A. KARRENBAUER , J. MESTRE

Algorithmica, 61:342-361, 2011.

On Tree-Constrained Matchings and Generalizations

S. CANZAR , K. ELBASSIONI , G. W. KLAU , J. MESTRE

In Proceedings of the 38th International Colloquium on Automata, Languages and Programming (ICALP),
Lecture Notes in Computer Science, Springer, 2011.

Technical Report MAC1102, Centrum Wiskunde & Informatica, Science Park 123, 1098 XG Amsterdam, The Netherlands, May 2011.


Computing H/D-Exchange rates of single residues from data of proteolytic fragments

E. ALTHAUS , S. CANZAR , C. EHRLER, M. R. EMMETT , A. KARRENBAUE R , A. G. MARSHALL , A. MEYER-BAESE , J. TIPTON, H. ZHANG

BMC Bioinformatics, 2010, 11:424.

On the Approximability of the Maximum Interval Coloring Problem

S. CANZAR , K. ELBASSIONI , A. ELMASRY , R. RAMAN

In Proceedings of the 21st International Symposium on Algorithms and Computation (ISAAC),
Lecture Notes in Computer Science, Springer, 2010.

A Polynomial Delay Algorithm for Enumerating Approximate Solutions to the Interval Constrained Coloring Problem

S. CANZAR , K. ELBASSIONI , J. MESTRE

In Proceedings of the Twelfth Workshop on Algorithm Engineering and Experiments (ALENEX), SIAM 2010.

Discrete Fitting of Hydrogen-Deuterium-Exchange-data of Overlapping Fragments

E. ALTHAUS , S. CANZAR , C. EHRLER, M. R. EMMETT , A. KARRENBAUE R , A. G. MARSHALL , A. MEYER-BAESE , J. TIPTON, H. ZHANG

In Proceedings of the International Conference on Bioinformatics & Computational Biology (BIOCOMP),
CSREA Press 2009.

A Lagrangian relaxation approach for the multiple sequence alignment problem

E. ALTHAUS, S. CANZAR

Journal of Combinatorial Optimization, 2008, volume 16(2), pages 127-154.

Computing H/D-Exchange Speeds of Single Residues from Data of Peptic Fragments.

E. ALTHAUS , S. CANZAR , M. R. EMMETT , A. KARRENBAUE R , A. G. MARSHALL , A. MEYER-BAESE , H. ZHANG

In Proceedings of the 23rd Annual ACM Symposium on Applied Computing (SAC), ACM 2008.

LASA: A tool for non-heuristic alignment of multiple sequences.

E. ALTHAUS, S. CANZAR

In Proceedings of the Second International Conference on Bioinformatics Research and Development (BIRD),
Communications in Computer and Information Science, Springer, 2008, pages 489-498.

Approximating the Interval Constrained Coloring Problem.

E. ALTHAUS, S. CANZAR , K. ELBASSIONI , A. KARRENBAUER , J. MESTRE

In Proceedings of the 11th Scandinavian Workshop on Algorithm Theory (SWAT),
Lecture Notes in Computer Science, Springer, 2008, pages 210-221.

Lagrangian Relaxation - Solving NP-hard Problems in Computational Biology via Combinatorial Optimization

S. CANZAR

PhD thesis, Universität des Saarlandes, Saarbrücken, Germany, and Université Henri Poincaré, Nancy I, France, 2008.

A Lagrangian Relaxation Approach for the Multiple Sequence Alignment Problem.

E. ALTHAUS, S. CANZAR

In Proceedings of the First International Conference on Combinatorial Optimization and Applications (COCOA),
Lecture Notes in Computer Science, Springer, 2007, pages 267-278.

Solving the extended pairwise alignment problem efficiently

E. ALTHAUS, S. CANZAR

Research Report MPI-I-2007-1-002, Max-Planck-Institut für Informatik, Campus E1 4, 66123 Saarbrücken, Germany, May 2007.

Shape Distributions and Protein Similarity

S. CANZAR , J. REMY

In Proceedings of the German Conference on Bioinformatics (GCB),
Lecture Notes in Informatics, 2006, pages 1-10.

Data Mining in Protein Databases

S. CANZAR

Diploma thesis, Technische Universität München, München, Germany, 2004.