Publications - Algorithms for Computational Genomics

Current Preprints

  1. M. J. P. Chaisson*, A. D. Sanders*, X. Zhao*, A. Malhotra, D. Porubsky, T. Rausch, E. J. Gardner, O. Rodriguez, L. Guo, R. L. Collins, X. Fan, J. Wen, R. E. Handsaker, S. Fairley, Z. N. Kronenberg, X. Kong, F. Hormozdiari, D. Lee, A. M. Wenger, A. Hastie, D. Antaki, P. Audano, H. Brand, S. Cantsilieris, H. Cao, E. Cerveira, C. Chen, X. Chen, C. Chin, Z. Chong, N. T. Chuang, D. M. Church, L. Clarke, A. Farrell, J. Flores, T. Galeev, G. David, M. Gujral, V. Guryev, W. Haynes-Heaton, J. Korlach, S. Kumar, J. Y. Kwon, J. E. Lee, J. Lee, W. Lee, S. P. Lee, P. Marks, K. Valud-Martinez, S. Meiers, K. M. Munson, F. Navarro, B. J. Nelson, C. Nodzak, A. Noor, S. Kyriazopoulou-Panagiotopoulou, A. Pang, Y. Qiu, G. Rosanio, M. Ryan, A. Stutz, D. C. J. Spierings, A. Ward, A. E. Welsch, M. Xiao, W. Xu, C. Zhang, Q. Zhu, X. Zheng-Bradley, G. Jun, L. Ding, C. L. Koh, B. Ren, P. Flicek, K. Chen, M. B. Gerstein, P. Kwok, P. M. Lansdorp, G. Marth, J. Sebat, X. Shi, A. Bashir, K. Ye, S. E. Devine, M. Talkowski, R. E. Mills, T. Marschall, J. Korbel, E. E. Eichler, C. Lee.
    Multi-platform discovery of haplotype-resolved structural variation in human genomes.
    bioRxiv, 2017.
    DOI: 10.1101/193144

  2. L. J. Dijkstra, J. Köster, T. Marschall, A. Schönhuth.
    Enhancing Sensitivity And Controlling False Discovery Rate In Somatic Indel Discovery Using A Latent Variable Model.
    bioRxiv, 2017.
    DOI: 10.1101/121954

  3. M. Martin*, M. Patterson*, S. Garg, S. O. Fischer, N. Pisanti, G. W. Klau, A. Schönhuth, T. Marschall.
    WhatsHap: fast and accurate read-based phasing.
    bioRxiv, 2016.
    DOI: 10.1101/085050

  4. T. Marschall, N. E. Passing.
    Representing Pattern Matching Algorithms by Polynomial-Size Automata.
    arXiv, 1607.00138, 2016.

Peer-Reviewed Publications

  1. M. Ghareghani*, D. Porubsky*, A. D. Sanders, S. Meiers, E. E. Eichler, J. O. Korbel, T. Marschall.
    Strand-seq Enables Reliable Separation of Long Reads by Chromosome via Expectation Maximization.
    Bioinformatics (Proceedings of ISMB), 2018.

  2. S. Garg, M. Rautiainen, A. M. Novak, E. Garrison, R. Durbin, T. Marschall.
    A graph-based approach to diploid genome assembly.
    Bioinformatics (Proceedings of ISMB), 2018.

  3. S. Chakraborty, S. Canzar, T. Marschall, M. H. Schulz.
    Chromatyping: Reconstructing nucleosome profiles from NOMe sequencing data.
    Proceedings of the 22nd Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2018.

  4. D. Porubsk\'y, S. Garg, A. D. Sanders, J. O. Korbel, V. Guryev, P. M. Lansdorp, T. Marschall.
    Dense and accurate whole-chromosome haplotyping of individual genomes.
    Nature Communications, 8(1), pp. 1293, 2017.

  5. J. Ebler, A. Schönhuth, T. Marschall.
    Genotyping Inversions and Tandem Duplications.
    Bioinformatics, 33(24), pp. 4015-4023, 2017.

  6. M. C. Stancu, M. J. Roosmalen, I. Renkens, M. M. Nieboer, S. Middelkamp, J. Ligt, G. Pregno, D. Giachino, G. Mandrile, J. E. Valle-Inclan, J. Korzelius, E. Bruijn, E. Cuppen, M. E. Talkowski, T. Marschall, J. Ridder, W. P. Kloosterman.
    Mapping and phasing of structural variation in patient genomes using nanopore sequencing.
    Nature Communications, 8(1), pp. 1326, 2017.

  7. G. W. Klau, T. Marschall.
    A Guided Tour to Computational Haplotyping.
    Proceedings of Computability in Europe (CiE), pp. 50-63, 2017.

  8. J. Y. Hehir-Kwa*, T. Marschall*, W. P. Kloosterman*, L. C. Francioli, J. A. Baaijens, L. J. Dijkstra, A. Abdellaoui, V. Koval, D. T. Thung, R. Wardenaar, I. Renkens, B. P. Coe, P. Deelen, J. d. Ligt, E. Lameijer, F. v. Dijk, F. Hormozdiari, A. G. Uitterlinden, C. M. v. Duijn, E. E. Eichler, P. I. W. d. Bakker, M. A. Swertz, C. Wijmenga, G. B. v. Ommen, P. E. Slagboom, D. I. Boomsma, A. Schönhuth, K. Ye, V. Guryev.
    A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.
    Nature Communications, 7, pp. 12989, 2016.
    DOI: 10.1038/ncomms12989

  9. T. Marschall, M. Marz, T. Abeel, L. Dijkstra, B. E. Dutilh, A. Ghaffaari, P. Kersey, W. P. Kloosterman, V. Mäkinen, A. M. Novak, B. Paten, D. Porubsky, E. Rivals, C. Alkan, J. Baaijens, P. I. W. de Bakker, V. Boeva, R. J. P. Bonnal, F. Chiaromonte, R. Chikhi, F. D. Ciccarelli, R. Cijvat, E. Datema, C. M. V. Duijn, E. E. Eichler, C. Ernst, E. Eskin, E. Garrison, M. El-Kebir, G. W. Klau, J. O. Korbel, E. Lameijer, B. Langmead, M. Martin, P. Medvedev, J. C. Mu, P. Neerincx, K. Ouwens, P. Peterlongo, N. Pisanti, S. Rahmann, B. Raphael, K. Reinert, D. de Ridder, J. de Ridder, M. Schlesner, O. Schulz-Trieglaff, A. Sanders, S. Sheikhizadeh, C. Shneider, S. Smit, D. Valenzuela, J. Wang, L. Wessels, Y. Zhang, V. Guryev, F. Vandin, K. Ye, A. Schönhuth.
    Computational pan-genomics: status, promises and challenges.
    Briefings in Bioinformatics, 2016.
    DOI: 10.1093/bib/bbw089

  10. S. Garg, M. Martin, T. Marschall.
    Read-Based Phasing of Related Individuals.
    Bioinformatics (Proceedings of ISMB), 32, pp. i234-i242, 2016.
    DOI: 10.1093/bioinformatics/btw276

  11. K. Trappe, T. Marschall, B. Y. Renard.
    Detecting Horizontal Gene Transfer by Mapping Sequencing Reads Across Species Boundaries.
    Bioinformatics (Proceedings of ECCB), 32(17), pp. i595-i604, 2016.
    DOI: 10.1093/bioinformatics/btw423

  12. A. Bracciali, M. Aldinucci, M. Patterson, T. Marschall, N. Pisanti, I. Merelli, M. Torquati.
    pWhatsHap: efficient haplotyping for future generation sequencing.
    BMC Bioinformatics, 17(Suppl. 11), pp. 342, 2016.
    DOI: 10.1186/s12859-016-1170-y

  13. R. Wittler*, T. Marschall*, A. Schönhuth, V. Mäkinen.
    Repeat- and Error-Aware Comparison of Deletions.
    Bioinformatics, 31(18), pp. 2947-2954, 2015.
    DOI: 10.1093/bioinformatics/btv304

  14. W. P. Kloosterman, L. C. Francioli, F. Hormozdiari, T. Marschall, J. Y. Hehir-Kwa, A. Abdellaoui, E. Lameijer, M. H. Moed, V. Koval, I. Renkens, M. J. v. Roosmalen, P. Arp, L. C. Karssen, B. P. Coe, R. E. Handsaker, E. D. Suchiman, E. Cuppen, D. T. Thung, M. McVey, M. C. Wendl, Genome of the Netherlands Consortium, A. Uitterlinden, C. M. v. Duijn, M. Swertz, C. Wijmenga, G. v. Ommen, E. Slagboom, D. I. Boomsma, A. Schönhuth, E. E. Eichler, P. I. W. d. Bakker, K. Ye, V. Guryev.
    Origin, frequency and functional impact of de novo structural changes in the human genome.
    Genome Research, 25, pp. 792-801, 2015.
    DOI: 10.1101/gr.185041.114

  15. R. Cijvat, S. Manegold, M. Kersten, G. W. Klau, A. Schönhuth, T. Marschall, Y. Zhang.
    Genome sequence analysis with MonetDB: a case study on Ebola virus diversity.
    Datenbank-Spektrum, 15(3), pp. 185-191, 2015.
    DOI: 10.1007/s13222-015-0198-x

  16. T. Bellitto, T. Marschall, A. Schönhuth, G. W. Klau.
    Next Generation Cluster Editing.
    Proceeding of the German Conference on Bioinformatics (GCB) in PeerJ Preprints, 2015.
    DOI: 10.7287/peerj.preprints.1301v1

  17. E. M. van Leeuwen, A. Kanterakis, P. Deelen, M. V. Kattenberg, The Genome of the Netherlands Consortium (including T.Marschall), P. E. Slagboom, P. I. W. de Bakker, C. Wijmenga, M. A. Swertz, D. I. Boomsma, C. M. van Duijn, L. C. Karssen, J. J. Hottenga.
    Population-specific genotype imputations using minimac or IMPUTE2.
    Nature Protocols, 10(9), pp. 1285-1296, 2015.
    DOI: 10.1038/nprot.2015.077

  18. L. C. Francioli, P. P. Polak, A. Koren, A. Menelaou, S. Chun, I. Renkens, Genome of the Netherlands Consortium (including T.Marschall), C. M. van Duijn, M. Swertz, C. Wijmenga, G. van Ommen, P. E. Slagboom, D. I. Boomsma, K. Ye, V. Guryev, P. F. Arndt, W. P. Kloosterman, P. I. W. de Bakker, S. R. Sunyaev.
    Genome-wide patterns and properties of de novo mutations in humans.
    Nature Genetics, 47(7), pp. 822-826, 2015.
    DOI: 10.1038/ng.3292

  19. M. Aldinucci, A. Bracciali, T. Marschall, M. Patterson, N. Pisanti, M. Torquati.
    High-Performance Haplotype Assembly.
    Proceedings of the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB), pp. 245-258, 2015.
    DOI: 10.1007/978-3-319-24462-4_21

  20. E. M. van Leeuwen, L. C. Karssen, J. Deelen, A. Isaacs, C. Medina-Gomez, H. Mbarek, A. Kanterakis, S. Trompet, I. Postmus, N. Verweij, D. J. van Enckevort, J. E. Huffman, C. C. White, M. F. Feitosa, T. M. Bartz, A. Manichaikul, P. K. Joshi, G. M. Peloso, P. Deelen, F. van Dijk, G. Willemsen, E. J. de Geus, Y. Milaneschi, B. W. J. H. Penninx, L. C. Francioli, A. Menelaou, S. L. Pulit, F. Rivadeneira, A. Hofman, B. A. Oostra, O. H. Franco, I. M. Leach, M. Beekman, A. J. M. de Craen, H. Uh, H. Trochet, L. J. Hocking, D. J. Porteous, N. Sattar, C. J. Packard, B. M. Buckley, J. A. Brody, J. C. Bis, J. I. Rotter, J. C. Mychaleckyj, H. Campbell, Q. Duan, L. A. Lange, J. F. Wilson, C. Hayward, O. Polasek, V. Vitart, I. Rudan, A. F. Wright, S. S. Rich, B. M. Psaty, I. B. Borecki, P. M. Kearney, D. J. Stott, L. Adrienne Cupples, The Genome of the Netherlands Consortium (including T.Marschall), J. W. Jukema, P. van der Harst, E. J. Sijbrands, J. Hottenga, A. G. Uitterlinden, M. A. Swertz, G. B. van Ommen, P. I. W. de Bakker, P. Eline Slagboom, D. I. Boomsma, C. Wijmenga, C. M. van Duijn.
    Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels.
    Nature Communications, 6, 2015.
    DOI: 10.1038/ncomms7065

  21. W. Y. Leung, T. Marschall, Y. Paudel, L. Falquet, H. Mei, A. Schönhuth, T. Y. Maoz.
    SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines.
    BMC Genomics, 16(1), pp. 238, 2015.
    DOI: 10.1186/s12864-015-1376-9

  22. M. Patterson*, T. Marschall*, N. Pisanti, L. van Iersel, L. Stougie, G. W. Klau, A. Schönhuth.
    WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.
    Journal of Computational Biology, 22(6), pp. 498-509, 2015.
    DOI: 10.1089/cmb.2014.0157

  23. R. Cijvat, S. Manegold, M. Kersten, G. W. Klau, A. Schönhuth, T. Marschall, Y. Zhang.
    Genome sequence analysis with MonetDB: a case study on Ebola virus diversity.
    Proceedings of the Workshop on Data Management for Life Sciences at DTW, pp. 143-150, 2015.

  24. The Genome of the Netherlands Consortium (including T.Marschall).
    Whole-genome sequence variation, population structure and demographic history of the Dutch population.
    Nature Genetics, 46, pp. 818-825, 2014.
    DOI: 10.1038/ng.3021

  25. P. Deelen, A. Menelaou, E. M. van Leeuwen, A. Kanterakis, F. van Dijk, C. Medina-Gomez, L. C. Francioli, J. J. Hottenga, L. C. Karssen, K. Estrada, E. Kreiner-Møller, F. Rivadeneira, J. van Setten, J. Gutierrez-Achury, H. Westra, L. Franke, D. van Enckevort, M. Dijkstra, H. Byelas, C. M. van Duijn, Genome of the Netherlands Consortium (including T.Marschall), P. I. W. d. Bakker, C. Wijmenga, M. A. Swertz.
    Improved imputation quality of low-frequency and rare variants in European samples using the `Genome of The Netherlands'.
    European Journal of Human Genetics, 22, pp. 1321-1326, 2014.
    DOI: 10.1038/ejhg.2014.19

  26. A. Töpfer, T. Marschall, R. A. Bull, F. Luciani, A. Schönhuth, N. Beerenwinkel.
    Viral Quasispecies Assembly via Maximal Clique Enumeration.
    Proceedings of the 18th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp. 309-310, 2014.

  27. A. Töpfer, T. Marschall, R. A. Bull, F. Luciani, A. Schönhuth, N. Beerenwinkel.
    Viral Quasispecies Assembly via Maximal Clique Enumeration.
    PLoS Computational Biology, 10(3), pp. e1003515, 2014.
    DOI: 10.1371/journal.pcbi.1003515

  28. M. Patterson*, T. Marschall*, N. Pisanti, L. v. Iersel, L. Stougie, G. W. Klau, A. Schönhuth.
    WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads.
    Proceedings of the 18th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp. 237-249, 2014.
    DOI: 10.1007/978-3-319-05269-4_19, self-archived version: link

  29. T. Marschall, I. Hajirasouliha, A. Schönhuth.
    MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels.
    Bioinformatics, 29(24), pp. 3143-3150, 2013.
    DOI: 10.1093/bioinformatics/btt556

  30. M. El-Kebir*, T. Marschall*, I. Wohlers*, M. Patterson, J. Heringa, A. Schönhuth, G. W. Klau.
    Mapping proteins in the presence of paralogs using units of coevolution.
    BMC Bioinformatics (Proceedings of RECOMB-CG), 14(Suppl 15), pp. S18, 2013.
    DOI: 10.1186/1471-2105-14-S15-S18

  31. M. Allhoff, A. Schönhuth, M. Martin, I. G. Costa, S. Rahmann, T. Marschall.
    Discovering motifs that induce sequencing errors.
    BMC Bioinformatics (Proceedings of RECOMB-seq), 14(Suppl 5), pp. S1, 2013.
    DOI: 10.1186/1471-2105-14-S5-S1

  32. A. Schramm, J. Köster, T. Marschall, M. Martin, M. Schwermer, K. Fielitz, G. Büchel, M. Barann, D. Esser, P. Rosenstiel, S. Rahmann, A. Eggert, J. H. Schulte.
    Next-generation RNA sequencing reveals differential expression of MYCN target genes and suggests the mTOR pathway as a promising therapy target in MYCN-amplified neuroblastoma.
    International Journal of Cancer, 132(3), pp. E106-E115, 2013.
    DOI: 10.1002/ijc.27787

  33. S. Rahmann, M. Martin, J. H. Schulte, J. Köster, T. Marschall, A. Schramm.
    Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data.
    Methods, 59(1), pp. 154-163, 2013.
    DOI: 10.1016/j.ymeth.2012.10.005

  34. T. Marschall*, I. G. Costa*, S. Canzar, M. Bauer, G. W. Klau, A. Schliep, A. Schönhuth.
    CLEVER: clique-enumerating variant finder.
    Bioinformatics, 28(22), pp. 2875-2882, 2012.
    DOI: 10.1093/bioinformatics/bts566

  35. T. Marschall, I. Herms, H. Kaltenbach, S. Rahmann.
    Probabilistic Arithmetic Automata and Their Applications.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(6), pp. 1737-1750, 2012.
    DOI: 10.1109/TCBB.2012.109

  36. A. Schramm, B. Schowe, K. Fielitz, M. Heilmann, M. Martin, T. Marschall, J. Köster, J. Vandesompele, J. Vermeulen, K. de Preter, J. Koster, R. Versteeg, R. Noguera, F. Speleman, S. Rahmann, A. Eggert, K. Morik, J. H. Schulte.
    Exon-level expression analyses identify MYCN and NTRK1 as major determinants of alternative exon usage and robustly predict primary neuroblastoma outcome.
    British Journal of Cancer, 107(8), pp. 1409-1417, 2012.
    DOI: 10.1038/bjc.2012.391

  37. S. Canzar, T. Marschall, S. Rahmann, C. Schwiegelshohn.
    Solving the Minimum String Cover Problem.
    Proceedings of the Meeting on Algorithm Engineering and Experiments (ALENEX), 2012.
    DOI: 10.1137/1.9781611972924.8

  38. T. Marschall, S. Rahmann.
    An Algorithm to Compute the Character Access Count Distribution for Pattern Matching Algorithms.
    Algorithms, 4, pp. 285-306, 2011.
    DOI: 10.3390/a4040285

  39. T. Marschall.
    Construction of minimal deterministic finite automata from biological motifs.
    Theoretical Computer Science, 412, pp. 922-930, 2011.
    DOI: 10.1016/j.tcs.2010.12.003

  40. T. Marschall, S. Rahmann.
    Exact Analysis of Horspool's and Sunday's Pattern Matching Algorithms with Probabilistic Arithmetic Automata.
    Proceedings of the Fourth International Conference on Language and Automata Theory and Applications (LATA), pp. 439-450, 2010.
    DOI: 10.1007/978-3-642-13089-2_37

  41. T. Marschall, S. Rahmann.
    Speeding Up Exact Motif Discovery by Bounding the Expected Clump Size.
    Proceedings of the 10th International Workshop on Algorithms in Bioinformatics (WABI), pp. 337-349, 2010.
    DOI: 10.1007/978-3-642-15294-8_28

  42. J. H. Schulte, T. Marschall, M. Martin, P. Rosenstiel, P. Mestdagh, S. Schlierf, T. Thor, J. Vandesompele, A. Eggert, S. Schreiber, S. Rahmann, A. Schramm.
    Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma.
    Nucleic Acids Research, 38(17), pp. 5919-5928, 2010.
    DOI: 10.1093/nar/gkq342

  43. T. Marschall, S. Rahmann.
    Efficient exact motif discovery.
    Bioinformatics (Proceedings of ISMB), 25(12), pp. i356-364, 2009.
    DOI: 10.1093/bioinformatics/btp188

  44. S. Rahmann, T. Marschall, F. Behler, O. Kramer.
    Modeling evolutionary fitness for DNA motif discovery.
    Proceedings of the Genetic and Evolutionary Computation Conference (GECCO), pp. 225-232, 2009.
    DOI: 10.1145/1569901.1569933

  45. T. Marschall, S. Rahmann.
    Probabilistic Arithmetic Automata and Their Application to Pattern Matching Statistics.
    Proceedings of the 19th Annual Symposium on Combinatorial Pattern Matching (CPM), pp. 95-106, 2008.
    DOI: 10.1007/978-3-540-69068-9_11

  46. T. Plötz, G. A. Fink, P. Husemann, S. Kanies, K. Lienemann, T. Marschall, M. Martin, L. Schillingmann, M. Steinrücken, H. Sudek.
    Automatic Detection of Song Changes in Music Mixes Using Stochastic Models.
    Proceedings of the 18th International Conference on Pattern Recognition (ICPR), pp. 665-668, 2006.
    DOI: 10.1109/ICPR.2006.297

Further Publications

  1. T. Marschall, A. Schönhuth.
    Sensitive Long-Indel-Aware Alignment of Sequencing Reads.
    arXiv, 1303.3520, 2013.