Publications

"A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads". Bioinformatics (Accepted for publication), 2009.

"Statistical Quality Assessment and Outlier Detection for Liquid Chromatography-Mass Spectrometry Experiments". BioDataMining (accepted for publication), 2009.

"The problem solving handbook for computational biology and bioinformatics". In Heath, L. S., Ramakrishnan, N., editors, chapter Practical multiple sequence alignment, 2009. Springer (Accepted for publication).

"A parallel genetic algorithm to discover patterns in genetic markers that indicate predisposition to multifactorial disease". Comput. Biol. Med., volume 38, pages 826-836, Jul 2008.

"An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment.". Algorithmic Operations Research, 2008. to appear.

"Computational Quantification of Peptides from LC-MS data". Journal of Computational Biology, number 7, volume 15, pages 685-704, 2008.
[computational mass spectrometry, liquid chromatography - massspectrometry, quantification, wavelets]

"Critical assessment of alignment procedures for LC-MS proteomics and metabolomic measurements". BMC Bioinformatics, volume 9, 2008.

"Efficient String Mining under Constraints via the Deferred Frequency Index". In Petra Perner, editors, "Proceedings of the 8th Industrial Conference on Data Mining (ICDM'08)", pages 374-388, LNAI 5077, Jul 2008. Springer Verlag.

"Fast and Adaptive Variable Order Markov Chain Construction". In "Proceedings of the 8th International Workshop in Algorithms in Bioinformatics (WABI'08)", pages 306-317, LNBI 5251, 2008. Springer Verlag.

"Generating unlabeled connected cubic planar graphs uniformly at random". Random Structures and Algorithms, number 2, volume 32, pages 157-180, 2008.

"LC-MSsim - a simulation software for liquid chromatography mass spectrometry data". BMC Bioinformatics, number 423, volume 9, 2008.
[algorithm, benchmark, lc-ms-ms, massspec, metabolomics, proteomics]

"OpenMS - An open-source software framework for mass spectrometry". BMC Bioinformatics, number 163, volume 9, 2008.
[lc-ms-ms, massspec, proteomics]

"Robust consensus computation". BMC Bioinformatics, number Suppl 10, volume 9, pages P4, 2008.

"Segment-based multiple sequence alignment". Bioinformatics, number 16, volume 24, pages i187-192, 2008.

"SeqAn an efficient, generic C++ library for sequence analysis.". BMC Bioinformatics, volume 9, pages 11, Jan 2008.
[Algorithms; Database Management Systems; Databases, Genetic; Programming Languages; Sequence Alignment; Sequence Analysis; Software; User-Computer Interface]

"A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry data". In "Proceedings of the Eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB 2007)", pages 473-487, 2007.

"A Geometric Approach for the Alignment of Liquid Chromatography-Mass Spectrometry Data". In "Proceedings of the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB)", pages i273-i281, 2007.

"A direct decomposition of 3-connected planar graphs". In "Proceedings of the 17th Annual International Conference on Formal Power Series and Algebraic Combinatorics (FPSAC05)", S'eminaire Lotharingien de Combinatoire, volume B54Ak, pages 15 pages, Taormina, 2007.
[Three-Connected Planar Graph, Cnet, Planar Graph, Enumeration, Random graphs, Random Generation, Dynamic Programming, Graph Theory]

"A general paradigm for fast and adaptive clustering of biological sequences". In "German Conference on Bioinformatics (GCB 2007)", pages 15-29, 2007.

"Accelerated microRNA Precursor Detection Using the Smith-Waterman Algorithm on FPGAs". In "Proc. of GCCB 2006", LNBI, volume 4360, pages 19-32, 2007.

"Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.". BMC Bioinformatics, number 1, volume 8, pages 271, Jul 2007.

"Alignment of Mass Spectrometry Data by Clique Finding and Optimization". In "Systems Biology and Computational Proteomics", Lecture Notes in Computer Science, volume 4532, pages 119-129, 2007. Springer Verlag.

"Bioinformatik: Aktuelle Proteinausstattung erlaubt Aussagen über den Gesundheitszustand. Software hilft Ärzten künftig bei der Diagnose.". 22. Juni 2007. VDI Nachrichten. Der Artikel eines freien Medienjournalisten beschreibt den Einsatz von OpenMS in der Proteomik.

"Generating labeled planar graphs uniformly at random". Theoretical Computer Science, number 3, volume 379, pages 377-386, 2007.
[Labeled planar graph, Enumeration, Decomposition, Sampling algorithm, Dynamic programming, Graph theory]

"Integer Linear Programming Approaches for Non-unique Probe Selection". Discrete Applied Mathematics, volume 155, pages 840-856, 2007.

"Sequence Assembly". Bioinformatics - From Genomes to Therapies, volume 1, chapter 2, pages 25-55, First edition, Dec 2007. Wiley-VCH" address = "Weinheim.

"A Branch-and-Cut Algorithm for Multiple Sequence Alignment". Mathematical Programming, number 105, pages 387-425, 2006.

"Absolute Myoglobin Quantitation in Serum by Combining Two-Dimensional Liquid Chromatography-Electrospray Ionization Mass Spectrometry and Novel Data Analysis Algorithms". Journal of Proteome Research, volume 5, pages 414-421, 2006.

"Analytical model of peptide mass cluster centres with applications". Proteome Science, number 18, volume 4, pages doi:10.1186/1477-5956-4-18, 2006.

"Bioinformatik - Ein ideales Fach, um mathematisch-naturwissenschaftliche Fächer (Biologie, Chemie, Mathematik) mit der Informatik zu verbinden". 2006. Talk given at 5. Berliner MNU-Kongress, TU Berlin, http://www.mnu-berlin.de/.

"Discovering causes of multifactorial diseases". Hasso-Plattner-Institut für Softwaresystemtechnik GmbH, Universität Potsdam, September 2006.

"Entwurf und Implementierung eines generischen Substring-Index". Humboldt University Berlin, May 2006. http://www.seqan.de/publications/weese06.pdf.

"High Accuracy Peak-Picking of Proteomics Data using Wavelet Techniques". In "Proceedings of the 11th Pacific Symposium on Biocomputing (PSB-06)", pages 243-254, 2006.

"OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics". In Christian G. Huber, Oliver Kohlbacher, Knut Reinert, editors, "Computational Proteomics", Dagstuhl Seminar Proceedings, number 05471, 2006. Internationales Begegnungs- und Forschungszentrum für Informatik (IBFI), Schloss Dagstuhl, Germany. [date of citation: 2006-01-01].

 ReiKohGro06.pdf (240 KB)  BibTeX

"Peptide Biomarker Discovery for the Diagnosis of Renal Allograft Rejection". 2006. Poster presented at the European Conference on Computational Biology (ECCB 2006), Eilat, Israel.

"Peptide Quantification for the Early Diagnosis of Renal Allograft Rejection". 2006. Poster at the German Conference on Computational Biology (GCB 2006), Tübingen, Germany. http://www.gcb2006.de/.

"TOPP - The OpenMS Proteomics Pipeline". In "Proceedings of the 5th European Conference on Computational Biology (ECCB 2006)", 2006.

"A direct decomposition of 3-connected planar graphs". In "Proceedings of the 17th Annual International Conference on Formal Power Series and Algebraic Combinatorics (FPSAC05)", Taormina, 2005.
[Three-Connected Planar Graph, Cnet, Planar Graph, Enumeration, Random graphs, Random Generation, Dynamic Programming, Graph Theory]

"Absolute quantification of the myoglobin content in blood serum using HPLC/MS through automatic bioinformatics analysis". 2005. Poster presented at the Fourth Annual World Congress of the Human Proteome Organization (HUPO05), Munich . http://www.hupo2005.com/.
[mass spectrometry, proteomics, open source software]

"Algorithms for the automated absolute quantification of diagnostic markers in complex proteomics samples". In "Proceedings of the 1st International Symposium on Computational Life Science (CompLife05)", pages 151-163, 2005.

"An Algorithm for Feature Finding in LC/MS Raw Data". In "Computational Proteomics", IBFI, 2005. Dagstuhl Online Publication Server (DROPS). Extended abstract for talk given at Dagstuhl Seminar 05471 on Computational Proteomics, 20.-25. November 2005.

"Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants". BMC Bioinformatics, number 203, volume 6, pages http://www.biomedcentral.com/1471-2105/6/203, 2005.

"Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Relaxation". In "Proceedings of the 1st International Symposium on Computational Life Science (CompLife-05)", pages 217-228, 2005.

"High-accuracy peak picking of proteomics data". In "Computational Proteomics", IBFI, 2005. Dagstuhl Online Publication Server (DROPS). Extended abstract for talk given at Dagstuhl Seminar 05471 on Computational Proteomics, 20.-25. November 2005.

"Mass Spectrometry and Computational Proteomics". In "Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics", 2005. Wiley-Eastern.

"Modelling the Randomness in Biological Systems". 2005. Poster presented at the BioSysBio Workshop 2005, Edinburgh, Scotland.
[petri nets, Gillespie algorithm]

"Multiple Structural RNA Alignment with Lagrangian Relaxation". In "Proceedings of the 5th Workshop on Algorithms Bioinformatics (WABI-05)", pages 303-314, 2005.

"OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics". In "Computational Proteomics", IBFI, 2005. Dagstuhl Online Publication Server (DROPS). Extended abstract for talk given at Dagstuhl Seminar 05471 on Computational Proteomics, 20.-25. November 2005.

"OpenMS - Software for Mass Spectrometry". 2005. Poster presented at the MBI Workshop on Computational Proteomics and Mass Spectrometry, January 11-14, Mathematical Biosciences Institute, Ohio State University, Columbus, Ohio. http://mbi.osu.edu/2004/workshops2004.html.
[mass spectrometry, proteomics, open source software]

"OpenMS - a generic open source framework for HPLC/MS-based proteomics". 2005. Poster presented at the Fourth Annual World Congress of the Human Proteome Organization, Munich. http://www.hupo2005.com/.
[mass spectrometry, proteomics, open source software]

"Reference methods and materials in standardisation and quality assurance (abstract)". FEBS Journal, number Supplement 1, volume 272, pages 490-504, 2005.

"Sampling Unlabeled Biconnected Planar Graphs". In "Proceedings of the 16th Annual International Symposium on Algorithms and Computation (ISAAC05)", 2005.
[Planar Graph, Enumeration, Random graphs, Random Generation, Graph Theory]

"Software Platforms for Computational Proteomics". In "Computational Proteomics", IBFI, 2005. Dagstuhl Online Publication Server (DROPS). Extended abstract for talk given at Dagstuhl Seminar 05471 on Computational Proteomics, 20.-25. November 2005.

"Transformation and other factors of the peptide mass spectormetry pairwise peaklist comparison process". BMC Bioinformatics, number 285, volume 6, pages http://www.biomedcentral.com/1471-2105/6/285, 2005.

"Differenzielle Proteomanalyse - Experimentelle Methoden, Algorithmische Herausforderungen". it - Information technology, volume 46, pages 31-38, 2004.

"Optimal Robust Non-Unique Probe Selection Using Integer Linear Programming". In "Proceedings of the Twelfth International Conference on Intelligent Systems for Molecular Biology (ISMB-04)", pages 186-193, 2004.

"Ordered binary decision diagrams and the Shannon effect". Discrete Applied Mathematics, volume 142, pages 67-85, 2004.

"Peak picking in mass spectra". 2004. Poster presented at the German Conference on Bioinformatics.

"Structural Alignment of Two RNA Sequences with Lagrangian Relaxation". In "Proceedings of the 15th International Symposium, ISAAC 2004, Hong Kong", LNCS 3341, pages 113-125, 2004. Springer Verlag.

"Whole-genome shotgun assembly and comparison of human genome assemblies". Proceedings of the national academy of science (PNAS), number 7, volume 101, pages 1916-1921, 2004.

"Accelerating Screening of 3D Protein Data with a Graph Theoretical Approach". 2003. Poster presented at RECOMB 2003.

"Accelerating screening of 3D protein data with a graph theoretical approach". Bioinformatics, volume 19, pages 2442-2447, 2003. Please note that this downloadable version is a preliminary version that differs from the final published version.

"Algorithmen in der Bioinformatik". 2003. Skript zu meiner Vorlesung im Wintersemester 2002/03 am Institut für Informatik der Humboldt-Universität zu Berlin.

"Decomposing, Counting, and Generating Unlabeled Cubic Planar Graphs". In "European Conference on Combinatorics, Graph Theory, and Applications EUROCOMB'03 Prague", 2003.
[Cubic Planar Graph, Planar Graph, Cubic Graph, Enumeration, Random graphs, Random Generation, Dynamic Programming, Graph Theory]

"Generating labeled planar graphs uniformly at random". In "Proceedings of ICALP 2003", Lecture Notes in Computer Science, number 2719, pages 1095-1107, 2003. Springer Verlag. Appeared 2008 in Theoretical Computer Science. The download is the journal submission
From time to time we receive requests for source code, so here it is: See the files BGK03b.README and GBK03b.tar.bz2 .
[Planar Graph, Enumeration, Random graphs, Random Generation, Dynamic Programming, Graph Theory]

"A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome". Science, volume 296, pages 1661-1671, 2002.

"Approximationsalgorithmen für das Steinerbaumproblem in Graphen". 2002. Poster.

"Multiple Sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics". In "Proceedings of the 1st European Conference on Computational Biology (ECCB 2002)", pages 4-16, 2002.

"Recent Segmental Duplications in the Human Genome". Science, volume 297, pages 1003-1007, 2002.

"Segment Match refinment and applications". In "Proceedings of the 2nd Workshop on Algorithms Bioinformatics (WABI-02)", pages 126-139, 2002.

"Steiner trees in uniformly quasi-bipartite graphs". Information Processing Letters, volume 83, pages 195-200, 2002.
[Steiner trees, Graph algorithms, Approximation algorithms]

"The Greedy Path-Merging Algorithm for Sequence Assembly". Journal of the ACM, number 5, volume 49, pages 603-615, 2002.

"Approximation Algorithms for the Steiner Tree Problem in Graphs". In Xiuzhen Cheng, Ding-Zhu Du, editors, "Steiner Trees in Industry", pages 235-279, 2001. Kluwer Academic Publishers. Survey article with new proofs.
[Approximation algorithms, Combinatorial optimization, Graph algorithms, Steiner trees]

"Comparing Assemblies using Fragments and Mate-pairs". In "Proceedings of the 1st Workshop on Algorithms Bioinformatics (WABI-01)", pages 294-306, 2001.

"Design of a compartmentalized Shotgun Assembler for the Human Genome". In "Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB-01)", pages 132-139, 2001.

"Lower bounds for approximation algorithms for the Steiner tree problem". In "Proceedings of the 27th International Workshop on Graph-Theoretic Concepts in Computer Science (2001)", LNCS, 2001. Springer Verlag.

"On the Evolution of the Worst-Case OBDD Size". Information Processing Letters, volume 77, pages 1-7, 2001.
[Binary Decision Diagrams]

"The Greedy Path-Merging Algorithm for Sequence Assembly". In "Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB-01)", pages 157-163, 2001.

"The Sequence of the Human Genome". Science, number 5507, volume 291, pages 1304-1351, 2001.
[ASSEMBLY]

"Visualization Challenges for a New Cyberpharmaceutical Computing". In "IEEE 2001 Symposium on Parallel and Large-Data Visualization and Graphics", pages 7-18, 2001. Keynote address.

"A Polyhedral Approach to Sequence Alignment Problems". Discrete Applied Mathematics, volume 104, pages 143-186, 2000.

"A Whole-Genome Assembly of Drosophila". Science, number 5461, volume 287, pages 2196-2203, 2000.
[ASSEMBLY]

"An Iterative Methods for Faster Sum-of-Pairs Multiple Sequence Alignment". BIOINFORMATICS, number 9, volume 16, pages 808-814, 2000.

"Approximating Minimum Spanning Sets in Hypergraphs and Polymatroids". Humboldt-University Berlin, 2000. This paper was already accepted for ICALP 2000 but we did not present it since later we were informed that the main result had already been proven in a different way..
[Hypergraphs, set systems, and designs, Steiner trees, Approximation algorithms, Colouring, packing and covering, Combinatorial optimization, Graph algorithms]

"Model-based image processing using snakes and mutual information". In Kenneth M. Hanson, editors, "Proc. SPIE, Medical Imaging 2000: Image Processing", Presented at the Society of Photo-Optical Instrumentation Engineers (SPIE) Conference, volume 3979, pages 1053-1064, Jun 2000.

"The Genome Sequence of Drosophila melanogaster". Science, number 5461, volume 287, pages 2185-2195, 2000.
[ASSEMBLY]

"The Practical Use of the A* Algorithm for Exact Multiple Sequence Alignment". Journal of Computational Biology, pages 655-671, 2000.

"An exact solution for the segment-to-segment multiple sequence alignment problem". BIOINFORMATICS, number 3, volume 15, pages 203-210, 1999.

"Binary Decision Diagrams for Random Boolean Functions". Humboldt-Universität zu Berlin, 1999.

"A Polyhedral Approach to RNA Sequence Structure Alignment". Journal of Computational Biology, number 3, volume 5, pages 517-530, 1998.

"A polyhedral approach to RNA sequence structure alignment". In "Proceedings of the Second Annual International Conference on Computational Molecular Biology (RECOMB-98)", pages 153-162, 1998.

"Parallel Repetition of MIP(2, 1) Systems". In Ernst W. Mayr, Hans Jürgen Prömel, Angelika Steger, editors, "Lectures on Proof Verification and Approximation Algorithms", Lecture Notes in Computer Science, volume 1367, chapter 6, pages 161-177, 1998. Springer. The book grow out of a Dagstuhl Seminar, April 21-25, 1997.
[Theoretical computer science (other), Approximation algorithms, PCP and non-approximability]

"Size and Structure of Random Ordered Binary Decision Diagrams (Extended Abstract)". In Daniel Korb, Christoph Meinel, Michel Morvan, editors, "STACS 98", Lecture Notes in Computer Science, number 1373, pages 238-248, Berlin, Heidelberg, New York, 1998. Springer Verlag.
[VLSI-Design and layout, Hardware verification, Random graphs]

"A branch-and-Cut algorithm for multiple sequence alignment ". In "Proceedings of the First Annual International Conference on Computational Molecular Biology (RECOMB-97)", pages 241-249, 1997.

"Efficient ordering of state variables and transition relation partitions in symbolic model checking". Humboldt-Universität zu Berlin, 1997.
[Randomized algorithms and probabilistic analysis, VLSI-Design and layout, Binary Decision Diagrams, Hardware verification, Local search and metaheuristics]

"Lower Bounds for Row Minima Searching". In "Proceedings of the 23rd International Colloquium on Automata, Languages, and Programming 1996 (ICALP-96), LNCS 1099", pages 454-465, 1996.

"Über Approximationsalgorithmen zur Färbung k-färbbarer Graphen, die vektorchromatische Zahl und andere Varianten der θ-Funktion". Diplomarbeit. Rheinische Friedrich-Wilhelms-Universität Bonn, Forschungsinstitut für Diskrete Mathematik, January 1996.
[Approximation algorithms, Colouring, packing and covering]