Publications

Thank you to all my coauthors! 😍

2023

E. Zaunseder, U. MĂŒtze, S. Garbade, S. Haupt, S. Kölker, V. Heuveline: Deep Learning and Explainable Artificial Intelligence for Improving Specificity and Detecting Metabolic Patterns in Newborn Screening. 2023 IEEE Symposium Series on Computational Intelligence (SSCI), December 2023
DOI: 10.1109/ssci52147.2023.10371991
P. MĂžller, T. SeppĂ€lĂ€, A. Ahadova, E. Crosbie, E. Holinski-Feder, R. Scott, S. Haupt, G. Möslein, I. Winship, S. Broeke, K. Kohut, N. Ryan, P. Bauerfeind, L. Thomas, D. Evans, S. Aretz, R. Sijmons, E. Half, K. Heinimann, K. Horisberger, K. Monahan, C. Engel, G. Cavestro, R. Fruscio, N. Abu-Freha, L. Zohar, L. Laghi, L. Bertario, B. Bonanni, M. Tibiletti, L. Lino-Silva, C. Vaccaro, A. Valle, B. Rossi, L. da Silva, I. de Oliveira Nascimento, N. Rossi, T. Dębniak, J. Mecklin, I. Bernstein, A. Lindblom, L. Sunde, S. Nakken, V. Heuveline, J. Burn, E. Hovig, M. Kloor, J. Sampson, M. Dominguez-Valentin, On behalf of the Prospective Lynch Syndrome Database (www.plsd.eu) and The European Hereditary Tumour Group (www.ehtg.org): Dominantly inherited micro-satellite instable cancer – the four Lynch syndromes - an EHTG, PLSD position statement. Hereditary Cancer in Clinical Practice, October 2023
DOI: 10.1186/s13053-023-00263-3
S. Haupt: Mathematical modeling of Lynch syndrome carcinogenesis. Dissertation. Heidelberg University Library, April 2023
DOI: 10.11588/HEIDOK.00033194
M. Dominguez-Valentin, S. Haupt, T. SeppĂ€lĂ€, J. Sampson, L. Sunde, I. Bernstein, M. Jenkins, C. Engel, S. Aretz, M. Nielsen, G. Capella, F. Balaguer, D. Evans, J. Burn, E. Holinski-Feder, L. Bertario, B. Bonanni, A. Lindblom, Z. Levi, F. Macrae, I. Winship, J. Plazzer, R. Sijmons, L. Laghi, A. Della Valle, K. Heinimann, T. Dębniak, R. Fruscio, F. Lopez-Koestner, K. Alvarez-Valenzuela, L. Katz, I. Laish, E. Vainer, C. Vaccaro, D. Carraro, K. Monahan, E. Half, A. Stakelum, D. Winter, R. Kennelly, N. Gluck, H. Sheth, N. Abu-Freha, M. Greenblatt, B. Rossi, M. Bohorquez, G. Cavestro, L. Lino-Silva, K. Horisberger, M. Tibiletti, I. Nascimento, H. Thomas, N. Rossi, L. ApolinĂĄrio da Silva, A. ZarĂĄnd, J. Ruiz-Bañobre, V. Heuveline, J. Mecklin, K. PylvĂ€nĂ€inen, L. Renkonen-Sinisalo, A. Lepistö, P. PeltomĂ€ki, C. Therkildsen, M. Madsen, S. Burgdorf, J. Hopper, A. Win, R. Haile, N. Lindor, S. Gallinger, L. Le Marchand, P. Newcomb, J. Figueiredo, D. Buchanan, S. Thibodeau, M. von Knebel Doeberitz, M. Loeffler, N. Rahner, E. Schröck, V. Steinke-Lange, W. Schmiegel, D. Vangala, C. Perne, R. HĂŒneburg, S. Redler, R. BĂŒttner, J. Weitz, M. Pineda, N. Duenas, J. Vidal, L. Moreira, A. SĂĄnchez, E. Hovig, S. Nakken, K. Green, F. Lalloo, J. Hill, E. Crosbie, M. Mints, Y. Goldberg, D. Tjandra, S. ten Broeke, R. Kariv, G. Rosner, S. Advani, L. Thomas, P. Shah, M. Shah, F. Neffa, P. Esperon, W. Pavicic, G. Torrezan, T. Bassaneze, C. Martin, G. Moslein, P. Moller: Mortality by age, gene and gender in carriers of pathogenic mismatch repair gene variants receiving surveillance for early cancer diagnosis and treatment: a report from the prospective Lynch syndrome database. eClinicalMedicine, March 2023
DOI: 10.1016/j.eclinm.2023.101909
A. Ahadova, A. Stenzinger, T. SeppĂ€lĂ€, R. HĂŒneburg, M. Kloor, H. BlĂ€ker, J. Wittemann, V. Endris, L. Gerling, V. Bertram, M. Neumuth, J. Witt, S. Graf, G. Kristiansen, O. Hommerding, S. Haupt, A. Zeilmann, V. Heuveline, D. Kazdal, J. Gebert, M. von Knebel Doeberitz, J. Mecklin, J. Nattermann: A “two-in-one hit” model of shortcut carcinogenesis in MLH1 Lynch syndrome carriers. Gastroenterology, March 2023
DOI: 10.1053/j.gastro.2023.03.007
E. Zaunseder, U. MĂŒtze, S. Garbade, S. Haupt, P. Feyh, G. Hoffmann, V. Heuveline, S. Kölker: Machine Learning Methods Improve Specificity in Newborn Screening for Isovaleric Aciduria. Metabolites, February 2023
DOI: 10.3390/metabo13020304

2022

J. Witt, S. Haupt, A. Ahadova, L. Bohaumilitzky, V. Fuchs, A. Ballhausen, M. Przybilla, M. Jendrusch, T. SeppĂ€lĂ€, D. FĂŒrst, T. Walle, E. Busch, G. Haag, R. HĂŒneburg, J. Nattermann, M. von Knebel Doeberitz, V. Heuveline, M. Kloor: A simple approach for detecting HLA‐A *02 alleles in archival formalin‐fixed paraffin‐embedded tissue samples and an application example for studying cancer immunoediting. HLA, October 2022
DOI: 10.1111/tan.14846
A. Ahadova, J. Witt, S. Haupt, R. Gallon, R. HĂŒneburg, J. Nattermann, S. ten Broeke, L. Bohaumilitzky, A. Hernandez‐Sanchez, M. Santibanez‐Koref, M. Jackson, M. Ahtiainen, K. PylvĂ€nĂ€inen, K. Andini, V. Grolmusz, G. Möslein, M. Dominguez‐Valentin, P. MĂžller, D. FĂŒrst, R. Sijmons, G. Borthwick, J. Burn, J. Mecklin, V. Heuveline, M. von Knebel Doeberitz, T. SeppĂ€lĂ€, M. Kloor: Is HLA type a possible cancer risk modifier in Lynch syndrome?. International Journal of Cancer, October 2022
DOI: 10.1002/ijc.34312
P. MĂžller, T. SeppĂ€lĂ€, J. Dowty, S. Haupt, M. Dominguez-Valentin, L. Sunde, I. Bernstein, C. Engel, S. Aretz, M. Nielsen, G. Capella, D. Evans, J. Burn, E. Holinski-Feder, L. Bertario, B. Bonanni, A. Lindblom, Z. Levi, F. Macrae, I. Winship, J. Plazzer, R. Sijmons, L. Laghi, A. Valle, K. Heinimann, E. Half, F. Lopez-Koestner, K. Alvarez-Valenzuela, R. Scott, L. Katz, I. Laish, E. Vainer, C. Vaccaro, D. Carraro, N. Gluck, N. Abu-Freha, A. Stakelum, R. Kennelly, D. Winter, B. Rossi, M. Greenblatt, M. Bohorquez, H. Sheth, M. Tibiletti, L. Lino-Silva, K. Horisberger, C. Portenkirchner, I. Nascimento, N. Rossi, L. da Silva, H. Thomas, A. ZarĂĄnd, J. Mecklin, K. PylvĂ€nĂ€inen, L. Renkonen-Sinisalo, A. Lepisto, P. PeltomĂ€ki, C. Therkildsen, L. Lindberg, O. Thorlacius-Ussing, M. von Knebel Doeberitz, M. Loeffler, N. Rahner, V. Steinke-Lange, W. Schmiegel, D. Vangala, C. Perne, R. HĂŒneburg, A. de Vargas, A. Latchford, A. Gerdes, A. Backman, C. GuillĂ©n-Ponce, C. Snyder, C. Lautrup, D. Amor, E. Palmero, E. Stoffel, F. Duijkers, M. Hall, H. Hampel, H. Williams, H. Okkels, J. LubiƄski, J. Reece, J. Ngeow, J. Guillem, J. Arnold, K. Wadt, K. Monahan, L. Senter, L. Rasmussen, L. van Hest, L. Ricciardiello, M. Kohonen-Corish, M. Ligtenberg, M. Southey, M. Aronson, M. Zahary, N. Samadder, N. Poplawski, N. Hoogerbrugge, P. Morrison, P. James, G. Lee, R. Chen-Shtoyerman, R. Ankathil, R. Pai, R. Ward, S. Parry, T. Dębniak, T. John, T. van Overeem Hansen, T. CaldĂ©s, T. Yamaguchi, V. Barca-Tierno, P. Garre, G. Cavestro, J. Weitz, S. Redler, R. BĂŒttner, V. Heuveline, J. Hopper, A. Win, N. Lindor, S. Gallinger, L. Le Marchand, P. Newcomb, J. Figueiredo, D. Buchanan, S. Thibodeau, S. ten Broeke, E. Hovig, S. Nakken, M. Pineda, N. Dueñas, J. Brunet, K. Green, F. Lalloo, K. Newton, E. Crosbie, M. Mints, D. Tjandra, F. Neffa, P. Esperon, R. Kariv, G. Rosner, W. Pavicic, P. Kalfayan, G. Torrezan, T. Bassaneze, C. Martin, G. Moslein, A. Ahadova, M. Kloor, J. Sampson, M. Jenkins, The European Hereditary Tumour Group (EHTG) and the International Mismatch Repair Consortium (IMRC): Colorectal cancer incidences in Lynch syndrome: a comparison of results from the prospective lynch syndrome database and the international mismatch repair consortium. Hereditary Cancer in Clinical Practice, October 2022
DOI: 10.1186/s13053-022-00241-1
E. Zaunseder, S. Haupt, U. MĂŒtze, S. Garbade, S. Kölker, V. Heuveline: Opportunities and challenges in machine learning‐based newborn screening—A systematic literature review. JIMD Reports, March 2022
DOI: 10.1002/jmd2.12285
Podcast

2021

S. Haupt, N. Gleim, A. Ahadova, H. BlÀker, M. Knebel Doeberitz, M. Kloor, V. Heuveline: A computational model for investigating the evolution of colonic crypts during Lynch syndrome carcinogenesis. Computational and Systems Oncology, June 2021
DOI: 10.1002/cso2.1020
CodebioRxiv
S. Haupt, A. Zeilmann, A. Ahadova, H. BlÀker, M. von Knebel Doeberitz, M. Kloor, V. Heuveline: Mathematical modeling of multiple pathways in colorectal carcinogenesis using dynamical systems with Kronecker structure. PLOS Computational Biology, May 2021
DOI: 10.1371/journal.pcbi.1008970
Blog PostPubMedbioRxiv

2020

S. Haupt, N. Gleim, A. Ahadova, H. BlÀker, M. von Knebel Doeberitz, M. Kloor, V. Heuveline: A computational model for investigating the evolution of colonic crypts during Lynch syndrome carcinogenesis. bioRxiv, December 2020. Preprint
DOI: 10.1101/2020.12.29.424555
CodePublished Version
A. Ballhausen, M. Przybilla, M. Jendrusch, S. Haupt, E. Pfaffendorf, F. Seidler, J. Witt, A. Hernandez Sanchez, K. Urban, M. Draxlbauer, S. Krausert, A. Ahadova, M. Kalteis, P. Pfuderer, D. Heid, D. Stichel, J. Gebert, M. Bonsack, S. Schott, H. BlÀker, T. SeppÀlÀ, J. Mecklin, S. Ten Broeke, M. Nielsen, V. Heuveline, J. Krzykalla, A. Benner, A. Riemer, M. von Knebel Doeberitz, M. Kloor: The shared frameshift mutation landscape of microsatellite-unstable cancers suggests immunoediting during tumor evolution. Nature Communications, September 2020
DOI: 10.1038/s41467-020-18514-5
PubMedbioRxiv
H. BlĂ€ker, S. Haupt, M. Morak, E. Holinski‐Feder, A. Arnold, D. Horst, J. Sieber‐Frank, F. Seidler, M. Winterfeld, E. Alwers, J. Chang‐Claude, H. Brenner, W. Roth, C. Engel, M. Löffler, G. Möslein, H. Schackert, J. Weitz, C. Perne, S. Aretz, R. HĂŒneburg, W. Schmiegel, D. Vangala, N. Rahner, V. Steinke‐Lange, V. Heuveline, M. von Knebel Doeberitz, A. Ahadova, M. Hoffmeister, M. Kloor, The German Consortium for Familial Intestinal Cancer: Age-dependent performance of BRAF mutation testing in Lynch syndrome diagnostics. International Journal of Cancer, September 2020
DOI: 10.1002/ijc.33273
PubMedmedRxiv
S. Haupt, A. Zeilmann, A. Ahadova, M. von Knebel Doeberitz, M. Kloor, V. Heuveline: Mathematical Modeling of Multiple Pathways in Colorectal Carcinogenesis using Dynamical Systems with Kronecker Structure. bioRxiv, August 2020. Preprint
DOI: 10.1101/2020.08.14.250175
Published Version

2019

H. BlĂ€ker, S. Haupt, M. Morak, E. Holinski-Feder, A. Arnold, D. Horst, J. Sieber-Frank, F. Seidler, M. von Winterfeld, E. Alwers, J. Chang-Claude, H. Brenner, W. Roth, C. Engel, M. Löffler, G. Möslein, H. Schackert, J. Weitz, C. Perne, S. Aretz, R. HĂŒneburg, W. Schmiegel, D. Vangala, N. Rahner, V. Steinke-Lange, V. Heuveline, M. von Knebel Doeberitz, A. Ahadova, M. Hoffmeister, M. Kloor, the German Consortium for Familial Intestinal Cancer: BRAF mutation testing of MSI CRCs in Lynch syndrome diagnostics: performance and efficiency according to patient's age. medRxiv, October 2019. Preprint
DOI: 10.1101/19009274
Published Version
A. Ballhausen, M. Przybilla, M. Jendrusch, S. Haupt, E. Pfaffendorf, M. Draxlbauer, F. Seidler, S. Krausert, A. Ahadova, M. Kalteis, D. Heid, J. Gebert, M. Bonsack, S. Schott, H. BlÀker, T. SeppÀlÀ, J. Mecklin, S. Broeke, M. Nielsen, V. Heuveline, J. Krzykalla, A. Benner, A. Riemer, M. von Knebel Doeberitz, M. Kloor: The shared neoantigen landscape of MSI cancers reflects immunoediting during tumor evolution. bioRxiv, July 2019. Preprint
DOI: 10.1101/691469
Published Version

2017

S. Gawlok, P. Gerstner, S. Haupt, V. Heuveline, J. Kratzke, P. Lösel, K. Mang, M. Schmidtobreick, N. Schoch, N. Schween, J. Schwegler, C. Song, M. Wlotzka: HiFlow3 – Technical Report on Release 2.0. Preprint Series of the Engineering Mathematics and Computing Lab, November 2017
DOI: 10.11588/EMCLPP.2017.06.42879