Browse by Authors

2016

Canzar, S. and Andreotti, S. and Weese, D. and Reinert, K. and Klau, G. W. (2016) CIDANE: comprehensive isoform discovery and abundance estimation. Genome Biology, 17 (1). ISSN 1474-760X

2015

Reinert, K. and Langmead, B. and Weese, D. and Evers, D.J. (2015) Alignment of Next-Generation Sequencing Reads. Annual Review of Genomics and Human Genetics, 16 (1). pp. 133-151. ISSN 1527-8204

2014

Rahn, R. and Weese, D. and Reinert, K. (2014) Journaled string tree--a scalable data structure for analyzing thousands of similar genomes on your laptop. Bioinformatics . ISSN Online ISSN 1460-2059 - Print ISSN 1367-4803

Schulz, M. H. and Weese, D. and Holtgrewe, M. and Dimitrova, V. and Niu, S. and Reinert, K. and Richard, H. (2014) Fiona: a parallel and automatic strategy for read error correction. Bioinformatics, 30 (17). i356-i363.

2013

Steijger, T. and Abril, J. F. and Engström, P. G. and Kokocinski, F. and The RGASP Consortium and Richard, H. and Schulz, M. H. and Weese, D. and Hubbard, T. and Guigó, R. and Harrow, J. and Bertone, P. (2013) Assessment of transcript reconstruction methods for RNA-seq. Nature Methods, 10 (12). pp. 1177-1184.

Weese, D. (2013) Indices and Applications in High-Throughput Sequencing. PhD thesis, Freie Universität Berlin.

Siragusa, E. and Weese, D. and Reinert, K. (2013) Fast and accurate read mapping with approximate seeds and multiple backtracking. Oxford Journals, 41 (7). e78. ISSN Print ISSN 0305-1048; Online ISSN 1362-4962

Siragusa, E. and Weese, D. and Reinert, K. (2013) Scalable string similarity search/join with approximate seeds and multiple backtracking. In: Proceedings of the Joint EDBT/ICDT 2013 Workshops, Genoa, Italy.

2012

Weese, D. and Holtgrewe, M. and Reinert, K. (2012) RazerS 3: Faster, fully sensitive read mapping. Bioinformatics, 28 (20). pp. 2592-2599.

Emde, A.-K. and Schulz, M. H. and Weese, D. and Sun, R. and Vingron, M. and Kalscheuer, V. M. and Haas, S. A. and Reinert, K. (2012) Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics, 28 (5). pp. 619-627.

2011

Kehr, B. and Weese, D. and Reinert, K. (2011) STELLAR: fast and exact local alignments. BMC Bioinformatics, 12 (S9). S15. ISSN 1471-2105

Holtgrewe, M. and Emde, A.-K. and Weese, D. and Reinert, K. (2011) A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping. BMC Bioinformatics, 12 (120). ISSN 1471-2105

2010

Emde, A.-K. and Grunert, M. and Weese, D. and Reinert, K. and Sperling, S. R. (2010) MicroRazerS: Rapid alignment of small RNA reads. Bioinformatics, 26 (1). pp. 123-124. ISSN 1367-4803

2009

Weese, D. and Emde, A.-K. and Rausch, T. and Döring, A. and Reinert, K. (2009) RazerS - Fast Read Mapping with Sensitivity Control. Genome Research, 19 (9). pp. 1646-1654.

Rausch, T. and Koren, S. and Denisov, G. and Weese, D. and Emde, A.-K. and Döring, A. and Reinert, K. (2009) A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinformatics, 25 (9). pp. 1118-1124.

2008

Weese, D. and Schulz, M. H. (2008) Efficient String Mining under Constraints via the Deferred Frequency Index. In: Proceedings of the 8th Industrial Conference on Data Mining (ICDM'08).

Schulz, M. H. and Weese, D. and Rausch, T. and Döring, A. and Reinert, K. and Vingron, M. (2008) Fast and Adaptive Variable Order Markov Chain Construction. In: Proceedings of the 8th International Workshop in Algorithms in Bioinformatics (WABI'08).

Rausch, T. and Emde, A.-K. and Weese, D. and Notredame, C. and Reinert, K. (2008) Segment-based multiple sequence alignment. Bioinformatics, 24 (16). i187-192.

Döring, A. and Weese, D. and Rausch, T. and Reinert, K. (2008) SeqAn -- An efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9 (1). p. 11.

2006

Weese, D. (2006) Entwurf und Implementierung eines generischen Substring-Index. Other thesis, Humboldt-University.

2000

von Klinski, S. and Derz, C. and Weese, D. and Tolxdorff, T. (2000) Model-based image processing using snakes and mutual information. In: Society of Photo-Optical Instrumentation Engineers (SPIE).