Source: https://compgen.mpi-inf.mpg.de/publications.php
Timestamp: 2019-04-24 16:56:10+00:00

Document:
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‡.
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.
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.
T. Marschall, N. E. Passing.
M. Ghareghani*, D. Porubsky*, A. D. Sanders, S. Meiers, E. E. Eichler, J. O. Korbel, T. Marschall.
Bioinformatics (Proceedings of ISMB), 2018.
S. Garg, M. Rautiainen, A. M. Novak, E. Garrison, R. Durbin, T. Marschall.
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.
D. Porubsk\'y, S. Garg, A. D. Sanders, J. O. Korbel, V. Guryev, P. M. Lansdorp, T. Marschall.
Nature Communications, 8(1), pp. 1293, 2017.
J. Ebler, A. Schönhuth, T. Marschall.
Genotyping Inversions and Tandem Duplications.
Bioinformatics, 33(24), pp. 4015-4023, 2017.
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.
G. W. Klau, T. Marschall.
Proceedings of Computability in Europe (CiE), pp. 50-63, 2017.
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.
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.
S. Garg, M. Martin, T. Marschall.
Bioinformatics (Proceedings of ISMB), 32, pp. i234-i242, 2016.
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.
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.
R. Wittler*, T. Marschall*, A. Schönhuth, V. Mäkinen.
Repeat- and Error-Aware Comparison of Deletions.
Bioinformatics, 31(18), pp. 2947-2954, 2015.
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.
R. Cijvat, S. Manegold, M. Kersten, G. W. Klau, A. Schönhuth, T. Marschall, Y. Zhang.
Datenbank-Spektrum, 15(3), pp. 185-191, 2015.
T. Bellitto, T. Marschall, A. Schönhuth, G. W. Klau.
Proceeding of the German Conference on Bioinformatics (GCB) in PeerJ Preprints, 2015.
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.
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.
M. Aldinucci, A. Bracciali, T. Marschall, M. Patterson, N. Pisanti, M. Torquati.
Proceedings of the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB), pp. 245-258, 2015.
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.
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.
M. Patterson*, T. Marschall*, N. Pisanti, L. van Iersel, L. Stougie, G. W. Klau, A. Schönhuth.
Journal of Computational Biology, 22(6), pp. 498-509, 2015.
Proceedings of the Workshop on Data Management for Life Sciences at DTW, pp. 143-150, 2015.
The Genome of the Netherlands Consortium (including T.Marschall).
Nature Genetics, 46, pp. 818-825, 2014.
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.
A. Töpfer, T. Marschall, R. A. Bull, F. Luciani, A. Schönhuth, N. Beerenwinkel.
Proceedings of the 18th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp. 309-310, 2014.
PLoS Computational Biology, 10(3), pp. e1003515, 2014.
M. Patterson*, T. Marschall*, N. Pisanti, L. v. Iersel, L. Stougie, G. W. Klau, A. Schönhuth.
Proceedings of the 18th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp. 237-249, 2014.
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.
M. El-Kebir*, T. Marschall*, I. Wohlers*, M. Patterson, J. Heringa, A. Schönhuth, G. W. Klau.
BMC Bioinformatics (Proceedings of RECOMB-CG), 14(Suppl 15), pp. S18, 2013.
M. Allhoff, A. Schönhuth, M. Martin, I. G. Costa, S. Rahmann, T. Marschall.
BMC Bioinformatics (Proceedings of RECOMB-seq), 14(Suppl 5), pp. S1, 2013.
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.
International Journal of Cancer, 132(3), pp. E106-E115, 2013.
S. Rahmann, M. Martin, J. H. Schulte, J. Köster, T. Marschall, A. Schramm.
Methods, 59(1), pp. 154-163, 2013.
T. Marschall*, I. G. Costa*, S. Canzar, M. Bauer, G. W. Klau, A. Schliep, A. Schönhuth.
Bioinformatics, 28(22), pp. 2875-2882, 2012.
T. Marschall, I. Herms, H. Kaltenbach, S. Rahmann.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(6), pp. 1737-1750, 2012.
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.
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.
An Algorithm to Compute the Character Access Count Distribution for Pattern Matching Algorithms.
Algorithms, 4, pp. 285-306, 2011.
Construction of minimal deterministic finite automata from biological motifs.
Theoretical Computer Science, 412, pp. 922-930, 2011.
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.
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.
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.
Nucleic Acids Research, 38(17), pp. 5919-5928, 2010.
Bioinformatics (Proceedings of ISMB), 25(12), pp. i356-364, 2009.
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.
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.
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.
Sensitive Long-Indel-Aware Alignment of Sequencing Reads.

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