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Molecular Medicine Partnership Unit

The MMPU is a joint venture between the Medical Faculty of the University of Heidelberg and the European Molecular Biology Laboratory (EMBL).

Cancer Early Detection

Peer Bork and Magnus von Knebel Doeberitz

MMPU Group 2006 – 2020

Project Summary

Molecular Pathogenesis of Colorectal Cancer and Development of Novel Approaches for Early Detection, Diagnosis and Prevention

This MMPU team, comprising of a computational biology and a clinical group, aims at utilizing novel, large-scale data by innovative computational approaches in tight conjunction with preclinical and clinical research to translate basic scientific concepts into clinically relevant modalities for cancer diagnostics, prevention, or treatment. The major aim is to achieve true practical relevance by most efficient ways to develop basic research into new globally accepted clinical paradigms.

The research structure of the team is designed to foster innovation in molecular medicine by iterating between ‘dry’ and ‘wet’ experiments in longer lasting research themes. This synergy is used to identify key events responsible for the very first steps of cancer transformation, to identify model cancer types for clinical proof of principle, and to channel newly established modalities into the health care system, all in the context of this MMPU team.

Background

Cancer is a disease, which is caused by genomic instability and accumulation of mutations. One specific subtype of cancers is caused by DNA mismatch repair deficiency. These tumors are characterized by an excessive mutational load, particularly at regions harboring repetitive DNA sequences (microsatellite instability, MSI). Mutations of coding microsatellites results in the translation of proteins with mutation-induced frameshift peptides (neoantigens) rendering MSI cancers highly immunogenic. MSI cancers express a defined set of shared neoantigens resulting from functionally relevant driver mutations. Patients with MSI cancers and individuals affected by Lynch syndrome, an inherited predisposition for MSI cancers, develop specific immune responses against these neoantigens.

Goals

The main goal of the project is the development of novel approaches for early detection, diagnosis and prevention using state-of-the-art bioinformatics tools for the prediction of novel target structures.

Research Focus 1: Identification and utilization of novel target genes 

Utilization of neo-antigens in cancers caused by deficient DNA mismatch repair mechanisms resulting from the accumulation of mutations particularly in repetitive sequence elements (microsatellite-unstable or MSI-H cancers). These tumors constitute a substantial part of colorectal cancers, but also a wide variety of cancers outside the colorectum. Due to the excessive number of genetic alterations and the predictability of resulting neo-antigens, MSI-H cancers are an ideal cancer type for developing immune intervention and prevention strategies against cancer and for evaluating them in the clinical setting.

Our MMPU group has pioneered research on the immune biology of MSI cancers for many years. In immunological studies we identified several frameshift derived immunogenic peptides and subsequently showed that MSI tumor cells can be lysed in vitro by cytotoxic T-cells in a peptide specific manner. A Phase I/II study has been successfully completed, demonstrating that vaccination with MSI-specific frameshift peptide neoantigens in patients with MSI colorectal cancer of stage III and IV consistently induces specific T cell-based and humoral immune responses.

Research Focus 2: The microbiome for cancer diagnosis and treatment

Utilization of changed microbial communities as biomarkers for early stages of cancer and possibly as targets for potential treatment. The group has been involved in major breakthroughs in microbiomics and is actively pursuing gut microbiome biomarker validation for colorectal cancer. The concept is being broadened to include oral samples and to also involve other cancers.

Important publications

Correction to ‘The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets’.
Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C.
Nucleic Acids Res. 2021 Sep 16:gkab835. doi: 10.1093/nar/gkab835. Online ahead of print. PMID: 34530444

Coupling proteomics and metabolomics for the unsupervised identification of protein-metabolite interactions in Chaetomium thermophilum.
Li Y, Kuhn M, Zukowska-Kasprzyk J, Hennrich ML, Kastritis PL, O’Reilly FJ, Phapale P, Beck M, Gavin AC, Bork P.
PLoS One. 2021 Jul 9;16(7):e0254429. doi: 10.1371/journal.pone.0254429. eCollection 2021. PMID: 34242379 Free PMC article.

Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.
Wirbel J, Zych K, Essex M, Karcher N, Kartal E, Salazar G, Bork P, Sunagawa S, Zeller G.
Genome Biol. 2021 Mar 30;22(1):93. doi: 10.1186/s13059-021-02306-1. PMID: 33785070 Free PMC article.

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C.
Nucleic Acids Res. 2021 Jan 8;49(D1):D605-D612. doi: 10.1093/nar/gkaa1074. PMID: 33237311 Free PMC article.

OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.
Gurumayum S, Jiang P, Hao X, Campos TL, Young ND, Korhonen PK, Gasser RB, Bork P, Zhao XM, He LJ, Chen WH.
Nucleic Acids Res. 2021 Jan 8;49(D1):D998-D1003. doi: 10.1093/nar/gkaa884. PMID: 33084874 Free PMC article.

Primary mismatch repair deficient IDH-mutant astrocytoma (PMMRDIA) is a distinct type with a poor prognosis.
Suwala AK, Stichel D, Schrimpf D, Kloor M, Wefers AK, Reinhardt A, Maas SLN, Kratz CP, Schweizer L, Hasselblatt M, Snuderl M, Abedalthagafi MSJ, Abdullaev Z, Monoranu CM, Bergmann M, Pekrun A, Freyschlag C, Aronica E, Kramm CM, Hinz F, Sievers P, Korshunov A, Kool M, Pfister SM, Sturm D, Jones DTW, Wick W, Unterberg A, Hartmann C, Dodgshun A, Tabori U, Wesseling P, Sahm F, von Deimling A, Reuss DE.
Acta Neuropathol. 2021 Jan;141(1):85-100. doi: 10.1007/s00401-020-02243-6. Epub 2020 Nov 20. PMID: 33216206

Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.
Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, Bastard JP, Forslund S, Le Chatelier E, Falony G, Pons N, Prifti E, Quinquis B, Roume H, Vieira-Silva S, Hansen TH, Pedersen HK, Lewinter C, Sønderskov NB; MetaCardis Consortium, Køber L, Vestergaard H, Hansen T, Zucker JD, Galan P, Dumas ME, Raes J, Oppert JM, Letunic I, Nielsen J, Bork P, Ehrlich SD, Stumvoll M, Pedersen O, Aron-Wisnewsky J, Clément K, Bäckhed F.
Nat Commun. 2020 Dec 21;11(1):6448. doi: 10.1038/s41467-020-20412-9. PMID: 33349634 Free PMC article.

Identification of MLH2/hPMS1 dominant mutations that prevent DNA mismatch repair function.
Reyes GX, Zhao B, Schmidt TT, Gries K, Kloor M, Hombauer H.
Commun Biol. 2020 Dec 10;3(1):751. doi: 10.1038/s42003-020-01481-4.
PMID: 33303966

Correction to: The majority of β-catenin mutations in colorectal cancer is homozygous.
Arnold A, Tronser M, Sers C, Ahadova A, Endris V, Mamlouk S, Horst D, Möbs M, Bischoff P, Kloor M, Bläker H.
BMC Cancer. 2020 Nov 26;20(1):1151. doi: 10.1186/s12885-020-07645-z. PMID: 33243186

Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.
Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, Bastard JP, Forslund S, Le Chatelier E, Falony G, Pons N, Prifti E, Quinquis B, Roume H, Vieira-Silva S, Hansen TH, Pedersen HK, Lewinter C, Sønderskov NB; MetaCardis Consortium, Køber L, Vestergaard H, Hansen T, Zucker JD, Galan P, Dumas ME, Raes J, Oppert JM, Letunic I, Nielsen J, Bork P, Ehrlich SD, Stumvoll M, Pedersen O, Aron-Wisnewsky J, Clément K, Bäckhed F.
Nat Commun. 2020 Nov 18;11(1):5881. doi: 10.1038/s41467-020-19589-w. PMID: 33208748 Free PMC article. Clinical Trial.

Age-dependent performance of BRAF mutation testing in Lynch syndrome diagnostics.
Bläker H, Haupt S, Morak M, Holinski-Feder E, Arnold A, Horst D, Sieber-Frank J, Seidler F, von Winterfeld M, Alwers E, Chang-Claude J, Brenner H, Roth W, Engel C, Löffler M, Möslein G, Schackert HK, Weitz J, Perne C, Aretz S, Hüneburg R, Schmiegel W, Vangala D, Rahner N, Steinke-Lange V, Heuveline V, von Knebel Doeberitz M, Ahadova A, Hoffmeister M, Kloor M; German Consortium for Familial Intestinal Cancer.
Int J Cancer. 2020 Nov 15;147(10):2801-2810. doi: 10.1002/ijc.33273. Epub 2020 Sep 14. PMID: 32875553

The majority of β-catenin mutations in colorectal cancer is homozygous.
Arnold A, Tronser M, Sers C, Ahadova A, Endris V, Mamlouk S, Horst D, Möbs M, Bischoff P, Kloor M, Bläker H.
BMC Cancer. 2020 Oct 28;20(1):1038. doi: 10.1186/s12885-020-07537-2. PMID: 33115416

The shared frameshift mutation landscape of microsatellite-unstable cancers suggests immunoediting during tumor evolution.
Ballhausen A, Przybilla MJ, Jendrusch M, Haupt S, Pfaffendorf E, Seidler F, Witt J, Hernandez Sanchez A, Urban K, Draxlbauer M, Krausert S, Ahadova A, Kalteis MS, Pfuderer PL, Heid D, Stichel D, Gebert J, Bonsack M, Schott S, Bläker H, Seppälä T, Mecklin JP, Ten Broeke S, Nielsen M, Heuveline V, Krzykalla J, Benner A, Riemer AB, von Knebel Doeberitz M, Kloor M.
Nat Commun. 2020 Sep 21;11(1):4740. doi: 10.1038/s41467-020-18514-5. PMID: 32958755

Value of upper GI endoscopy for gastric cancer surveillance in patients with Lynch syndrome.
Ladigan-Badura S, Vangala DB, Engel C, Bucksch K, Hueneburg R, Perne C, Nattermann J, Steinke-Lange V, Rahner N, Schackert HK, Weitz J, Kloor M, Kuhlkamp J, Nguyen HP, Moeslein G, Strassburg C, Morak M, Holinski-Feder E, Buettner R, Aretz S, Loeffler M, Schmiegel W, Pox C, Schulmann K; German Consortium for Familial Intestinal Cancer.
Int J Cancer. 2020 Sep 15. doi: 10.1002/ijc.33294. Online ahead of print. PMID: 32930401

A Frameshift Peptide Neoantigen-Based Vaccine for Mismatch Repair-Deficient Cancers: A Phase I/IIa Clinical Trial.
Kloor M, Reuschenbach M, Pauligk C, Karbach J, Rafiyan MR, Al-Batran SE, Tariverdian M, Jäger E, von Knebel Doeberitz M.
Clin Cancer Res. 2020 Sep 1;26(17):4503-4510. doi: 10.1158/1078-0432.CCR-19-3517. Epub 2020 Jun 15. PMID: 32540851

Diversity within species: interpreting strains in microbiomes.
Van Rossum T, Ferretti P, Maistrenko OM, Bork P.
Nat Rev Microbiol. 2020 Sep;18(9):491-506. doi: 10.1038/s41579-020-0368-1. Epub 2020 Jun 4. PMID: 32499497 Free PMC article. Review.

Plant nutrient-acquisition strategies drive topsoil microbiome structure and function.
Bahram M, Netherway T, Hildebrand F, Pritsch K, Drenkhan R, Loit K, Anslan S, Bork P, Tedersoo L.
New Phytol. 2020 Aug;227(4):1189-1199. doi: 10.1111/nph.16598. Epub 2020 May 6. PMID: 32279325

(Phospho)proteomic Profiling of Microsatellite Unstable CRC Cells Reveals Alterations in Nuclear Signaling and Cholesterol Metabolism Caused by Frameshift Mutation of NMD Regulator UPF3A.
Michalak M, Katzenmaier EM, Roeckel N, Woerner SM, Fuchs V, Warnken U, Yuan YP, Bork P, Neu-Yilik G, Kulozik A, von Knebel Doeberitz M, Kloor M, Kopitz J, Gebert
J. Int J Mol Sci. 2020 Jul 23;21(15):5234. doi: 10.3390/ijms21155234. PMID: 32718059

The “unnatural” history of colorectal cancer in Lynch syndrome: Lessons from colonoscopy surveillance.
Ahadova A, Seppälä TT, Engel C, Gallon R, Burn J, Holinski-Feder E, Steinke-Lange V, Möslein G, Nielsen M, Ten Broeke SW, Laghi L, Dominguez-Valentin M, Capella G, Macrae F, Scott R, Hüneburg R, Nattermann J, Hoffmeister M, Brenner H, Bläker H, von Knebel Doeberitz M, Sampson JR, Vasen H, Mecklin JP, Møller P, Kloor M.
Int J Cancer. 2020 Jul 19. doi: 10.1002/ijc.33224. Online ahead of print. PMID: 32683684

Implications of Hereditary Origin on the Immune Phenotype of Mismatch Repair-Deficient Cancers: Systematic Literature Review.
Bohaumilitzky L, von Knebel Doeberitz M, Kloor M, Ahadova A.
J Clin Med. 2020 Jun 4;9(6):1741. doi: 10.3390/jcm9061741. PMID: 32512823

Glycogen accumulation, central carbon metabolism, and aging of hematopoietic stem and progenitor cells
Laura poisa‑Beiro, Judith Thoma, Jonathan Landry, Sven Sauer, Akihisa Yamamoto, Volker Eckstein, Natalie Romanov, Simon Raffel, Georg F. Hoffmann, Peer Bork, Vladimir Benes, Anne‑claude Gavin, Motomu Tanaka & Anthony D. Ho
Scientific Reports | (2020) 10:11597 | https://doi.org/10.1038/s41598-020-68396-2www.nature.com/scientificreports

Statin therapy is associated with lower prevalence of gut microbiota dysbiosis.
Vieira-Silva S, Falony G, Belda E, Nielsen T, Aron-Wisnewsky J, Chakaroun R, Forslund SK, Assmann K, Valles-Colomer M, Nguyen TTD, Proost S, Prifti E, Tremaroli V, Pons N, Le Chatelier E, Andreelli F, Bastard JP, Coelho LP, Galleron N, Hansen TH, Hulot JS, Lewinter C, Pedersen HK, Quinquis B, Rouault C, Roume H, Salem JE, Søndertoft NB, Touch S; MetaCardis Consortium, Dumas ME, Ehrlich SD, Galan P, Gøtze JP, Hansen T, Holst JJ, Køber L, Letunic I, Nielsen J, Oppert JM, Stumvoll M, Vestergaard H, Zucker JD, Bork P, Pedersen O, Bäckhed F, Clément K, Raes J.
Nature. 2020 May;581(7808):310-315. doi: 10.1038/s41586-020-2269-x. Epub 2020 May 6. PMID: 32433607

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.
Maistrenko OM, Mende DR, Luetge M, Hildebrand F, Schmidt TSB, Li SS, Rodrigues JFM, von Mering C, Pedro Coelho L, Huerta-Cepas J, Sunagawa S, Bork P.
ISME J. 2020 May;14(5):1247-1259. doi: 10.1038/s41396-020-0600-z. Epub 2020 Feb 11. PMID: 32047279 Free PMC article.

Associations of Pathogenic Variants in MLH1, MSH2, and MSH6 With Risk of Colorectal Adenomas and Tumors and With Somatic Mutations in Patients With Lynch Syndrome.
Engel C, Ahadova A, Seppälä TT, Aretz S, Bigirwamungu-Bargeman M, Bläker H, Bucksch K, Büttner R, de Vos Tot Nederveen Cappel WT, Endris V, Holinski-Feder E, Holzapfel S, Hüneburg R, Jacobs MAJM, Koornstra JJ, Langers AM, Lepistö A, Morak M, Möslein G, Peltomäki P, Pylvänäinen K, Rahner N, Renkonen-Sinisalo L, Schulmann K, Steinke-Lange V, Stenzinger A, Strassburg CP, van de Meeberg PC, van Kouwen M, van Leerdam M, Vangala DB, Vecht J, Verhulst ML, von Knebel Doeberitz M, Weitz J, Zachariae S, Loeffler M, Mecklin JP, Kloor M, Vasen HF; German HNPCC Consortium, the Dutch Lynch Syndrome Collaborative Group; Finnish Lynch Syndrome Registry.
Gastroenterology. 2020 Apr;158(5):1326-1333. doi: 10.1053/j.gastro.2019.12.032. Epub 2020 Jan 8. PMID: 31926173

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.
Li Y, Kuhn M, Gavin AC, Bork P.
Bioinformatics. 2020 Feb 15;36(4):1213-1218. doi: 10.1093/bioinformatics/btz736. PMID: 31605112

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
Mende DR, Letunic I, Maistrenko OM, Schmidt TSB, Milanese A, Paoli L, Hernández-Plaza A, Orakov AN, Forslund SK, Sunagawa S, Zeller G, Huerta-Cepas J, Coelho LP, Bork P.
Nucleic Acids Res. 2020 Jan 8;48(D1):D621-D625. doi: 10.1093/nar/gkz1002. PMID: 31647096 Free PMC article.

Cancer risks by gene, age, and gender in 6350 carriers of pathogenic mismatch repair variants: findings from the Prospective Lynch Syndrome Database.
Dominguez-Valentin M, Sampson JR, Seppälä TT, Ten Broeke SW, Plazzer JP, Nakken S, Engel C, Aretz S, Jenkins MA, Sunde L, Bernstein I, Capella G, Balaguer F, Thomas H, Evans DG, Burn J, Greenblatt M, Hovig E, de Vos Tot Nederveen Cappel WH, Sijmons RH, Bertario L, Tibiletti MG, Cavestro GM, Lindblom A, Della Valle A, Lopez-Köstner F, Gluck N, Katz LH, Heinimann K, Vaccaro CA, Büttner R, Görgens H, Holinski-Feder E, Morak M, Holzapfel S, Hüneburg R, Knebel Doeberitz MV, Loeffler M, Rahner N, Schackert HK, Steinke-Lange V, Schmiegel W, Vangala D, Pylvänäinen K, Renkonen-Sinisalo L, Hopper JL, Win AK, Haile RW, Lindor NM, Gallinger S, Le Marchand L, Newcomb PA, Figueiredo JC, Thibodeau SN, Wadt K, Therkildsen C, Okkels H, Ketabi Z, Moreira L, Sánchez A, Serra-Burriel M, Pineda M, Navarro M, Blanco I, Green K, Lalloo F, Crosbie EJ, Hill J, Denton OG, Frayling IM, Rødland EA, Vasen H, Mints M, Neffa F, Esperon P, Alvarez K, Kariv R, Rosner G, Pinero TA, Gonzalez ML, Kalfayan P, Tjandra D, Winship IM, Macrae F, Möslein G, Mecklin JP, Nielsen M, Møller P.
Genet Med. 2020 Jan;22(1):15-25. doi: 10.1038/s41436-019-0596-9. Epub 2019 Jul 24. PMID: 31337882

[Current recommendations for surveillance, risk reduction and therapy in Lynch syndrome patients].
Hüneburg R, Aretz S, Büttner R, Daum S, Engel C, Fechner G, Habermann JK, Heling D, Hoffmann K, Holinski-Feder E, Kloor M, von Knebel-Döberitz M, Loeffler M, Möslein G, Perne C, Redler S, Rieß O, Schmiegel W, Seufferlein T, Siebers-Renelt U, Steinke-Lange V, Tecklenburg J, Vangala D, Vilz T, Weitz J, Wiedenmann B, Strassburg CP, Nattermann J. Z
Gastroenterol. 2019 Nov;57(11):1309-1320. doi: 10.1055/a-1008-9827. Epub 2019 Nov 18. PMID: 31739377

Resistance of the stable-towards more precise prediction of response to immune checkpoint blockade in microsatellite-unstable cancer patients.
Kloor M.
Ann Transl Med. 2019 Nov;7(21):603. doi: 10.21037/atm.2019.10.29. PMID: 32047764

Survival by colon cancer stage and screening interval in Lynch syndrome: a prospective Lynch syndrome database report.
Dominguez-Valentin M, Seppälä TT, Sampson JR, Macrae F, Winship I, Evans DG, Scott RJ, Burn J, Möslein G, Bernstein I, Pylvänäinen K, Renkonen-Sinisalo L, Lepistö A, Lindblom A, Plazzer JP, Tjandra D, Thomas H, Green K, Lalloo F, Crosbie EJ, Hill J, Capella G, Pineda M, Navarro M, Vidal JB, Rønlund K, Nielsen RT, Yilmaz M, Elvang LL, Katz L, Nielsen M, Ten Broeke SW, Nakken S, Hovig E, Sunde L, Kloor M, Knebel Doeberitz MV, Ahadova A, Lindor N, Steinke-Lange V, Holinski-Feder E, Mecklin JP, Møller P. Hered
Cancer Clin Pract. 2019 Oct 14;17:28. doi: 10.1186/s13053-019-0127-3. eCollection 2019. PMID: 31636762

TGFBR2‑dependent alterations of microRNA profiles in extracellular vesicles and parental colorectal cancer cells.
Fricke F, Mussack V, Buschmann D, Hausser I, Pfaffl MW, Kopitz J, Gebert J.
Int J Oncol. 2019 Oct;55(4):925-937. doi: 10.3892/ijo.2019.4859. Epub 2019 Aug 19. PMID: 31432155

SILAC-Based Quantification of TGFBR2-Regulated Protein Expression in Extracellular Vesicles of Microsatellite Unstable Colorectal Cancers.
Fricke F, Michalak M, Warnken U, Hausser I, Schnölzer M, Kopitz J, Gebert J.
Int J Mol Sci. 2019 Aug 26;20(17):4162. doi: 10.3390/ijms20174162. PMID: 31454892

High endothelial venules are associated with microsatellite instability, hereditary background and immune evasion in colorectal cancer.
Pfuderer PL, Ballhausen A, Seidler F, Stark HJ, Grabe N, Frayling IM, Ager A, von Knebel Doeberitz M, Kloor M, Ahadova A.
Br J Cancer. 2019 Aug;121(5):395-404. doi: 10.1038/s41416-019-0514-6. Epub 2019 Jul 30. PMID:31358939

Effects of Weight-Loss Interventions on Short-Chain Fatty Acid Concentrations in Blood and Feces of Adults: A Systematic Review.
Sowah SA, Riedl L, Damms-Machado A, Johnson TS, Schübel R, Graf M, Kartal E, Zeller G, Schwingshackl L, Stangl GI, Kaaks R, Kühn T.
Adv Nutr. 2019 Jul 1;10(4):673-684. doi: 10.1093/advances/nmy125. PMID:31075175

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.
Coelho LP, Alves R, Monteiro P, Huerta-Cepas J, Freitas AT, Bork P.
Microbiome. 2019 Jun 3;7(1):84. doi: 10.1186/s40168-019-0684-8. PMID:31159881

Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity.
Gossmann TI, Shanmugasundram A, Börno S, Duvaux L, Lemaire C, Kuhl H, Klages S, Roberts LD, Schade S, Gostner JM, Hildebrand F, Vowinckel J, Bichet C, Mülleder M, Calvani E, Zelezniak A, Griffin JL, Bork P, Allaine D, Cohas A, Welch JJ, Timmermann B, Ralser M.
Curr Biol. 2019 May 20;29(10):1712-1720.e7. doi: 10.1016/j.cub.2019.04.020. Epub 2019 May 9. PMID:31080084

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.
Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N.
Nat Med. 2019 Apr;25(4):667-678. doi: 10.1038/s41591-019-0405-7. Epub 2019 Apr 1.

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.
Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G.
Nat Med. 2019 Apr;25(4):679-689. doi: 10.1038/s41591-019-0406-6. Epub 2019 Apr 1.PMID:30936547

Microbial abundance, activity and population genomic profiling with mOTUs2.
Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G, Sunagawa S.
Nat Commun. 2019 Mar 4;10(1):1014. doi: 10.1038/s41467-019-08844-4. PMID:30833550

Extensive transmission of microbes along the gastrointestinal tract.
Schmidt TS, Hayward MR, Coelho LP, Li SS, Costea PI, Voigt AY, Wirbel J, Maistrenko OM, Alves RJ, Bergsten E, de Beaufort C, Sobhani I, Heintz-Buschart A, Sunagawa S, Zeller G, Wilmes P, Bork P.
Elife. 2019 Feb 12;8. pii: e42693. doi: 10.7554/eLife.42693. PMID:30747106

Antibiotics-induced monodominance of a novel gut bacterial order.
Hildebrand F, Moitinho-Silva L, Blasche S, Jahn MT, Gossmann TI, Heuerta-Cepas J, Hercog R, Luetge M, Bahram M, Pryszlak A, Alves RJ, Waszak SM, Zhu A, Ye L, Costea PI, Aalvink S, Belzer C, Forslund SK, Sunagawa S, Hentschel U, Merten C, Patil KR, Benes V, Bork P.
Gut. 2019 Jan 18. pii: gutjnl-2018-317715. doi: 10.1136/gutjnl-2018-317715. [Epub ahead of print] PMID:30658995

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering CV.
Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613. doi: 10.1093/nar/gky1131. PMID:30476243

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P.
Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314. doi: 10.1093/nar/gky1085. PMID:30418610

Cancer Risks for PMS2-Associated Lynch Syndrome.
Ten Broeke SW, van der Klift HM, Tops CMJ, Aretz S, Bernstein I, Buchanan DD, de la Chapelle A, Capella G, Clendenning M, Engel C, Gallinger S, Gomez Garcia E, Figueiredo JC, Haile R, Hampel HL, Hopper JL, Hoogerbrugge N, von Knebel Doeberitz M, Le Marchand L, Letteboer TGW, Jenkins MA, Lindblom A, Lindor NM, Mensenkamp AR, Møller P, Newcomb PA, van Os TAM, Pearlman R, Pineda M, Rahner N, Redeker EJW, Olderode-Berends MJW, Rosty C, Schackert HK, Scott R, Senter L, Spruijt L, Steinke-Lange V, Suerink M, Thibodeau S, Vos YJ, Wagner A, Winship I, Hes FJ, Vasen HFA, Wijnen JT, Nielsen M, Win AK.
J Clin Oncol. 2018 Oct 10;36(29):2961-2968. doi:10.1200/JCO.2018.78.4777.  Epub 2018 Aug 30.

Integrated analysis of the immunological and genetic status in and across cancer types: impact of mutational signatures beyond tumor mutational burden.
Budczies J, Seidel A, Christopoulos P, Endris V, Kloor M, Győrffy B, Seliger B, Schirmacher P, Stenzinger A, Denkert C.
Oncoimmunology. 2018 Oct 19;7(12):e1526613. doi: 10.1080/2162402X.2018.1526613. eCollection 2018. PMID:30524909

No Difference in Colorectal Cancer Incidence or Stage at Detection by Colonoscopy Among 3 Countries With Different Lynch Syndrome Surveillance Policies.
Engel C, Vasen HF, Seppälä T, Aretz S, Bigirwamungu-Bargeman M, de Boer SY, Bucksch K, Büttner R, Feder EH, Holzapfel S, Hüneburg R, Jacobs MAJM, Järvinen H, Kloor M, von Knebel Doeberitz M, Koornstra JJ, van Kouwen M, Langers AM, van de Meeberg PC, Morak M, Möslein G, Nagengast FM, Pylvanainen K, Rahner N, Renkonen-Sinisalo L, Sanduleanu S, Schackert HK, Schmiegel W, Schulmann K, Steinke-Lange V, Strassburg CP, Vecht J, Verhulst ML, de Vos Tot Nederveen Cappel W, Zachariae S, Mecklin JP, Loeffler M; German HNPCC Consortium, the Dutch Lynch Syndrome Collaborative Group, and the Finnish Lynch Syndrome Registry.
Gastroenterology. 2018 Jul 28. pii: S0016-5085(18)34818-2. doi: 10.1053/j.gastro.2018.07.030.

Three molecular pathways model colorectal carcinogenesis in Lynch syndrome. Ahadova A, Gallon R, Gebert J, Ballhausen A, Endris V, Kirchner M, Stenzinger A, Burn J, von Knebel Doeberitz M, Bläker H, Kloor M.
Int J Cancer. 2018 Jul 1;143(1):139-150. doi: 10.1002/ijc.31300. Epub 2018 Feb 23.

Copy number variation analysis and targeted NGS in 77 families with suspected Lynch syndrome reveals novel potential causative genes.
Kayser K, Degenhardt F, Holzapfel S, Horpaopan S, Peters S, Spier I, Morak M, Vangala D, Rahner N, von Knebel-Doeberitz M, Schackert HK, Engel C, Büttner R, Wijnen J, Doerks T, Bork P, Moebus S, Herms S, Fischer S, Hoffmann P, Aretz S, Steinke-Lange V.
Int J Cancer. 2018 Jul 10. doi: 10.1002/ijc.31725

Complex pattern of immune evasion in MSI colorectal cancer.
Ozcan M, Janikovits J, von Knebel Doeberitz M, Kloor M.
Oncoimmunology. 2018 Mar 26;7(7):e1445453. doi: 10.1080/2162402X.2018.1445453. eCollection 2018

Reply to ‘Comment on ‘Human papillomavirus association is the most important predictor for surgically treated patients with oropharyngeal cancer”.
Wagner S, Wittekindt C, Sharma SJ, Wuerdemann N, Jüttner T, Reuschenbach M, Prigge ES, von Knebel Doeberitz M, Gattenlöhner S, Burkhardt E, Pons-Kühnemann J, Klussmann JP.
Br J Cancer. 2018 Feb 6;118(3):e6. doi: 10.1038/bjc.2017.464. Epub 2018 Jan 23. No abstract available.

High numbers of PDCD1 (PD-1)-positive T cells and B2M mutations in microsatellite-unstable colorectal cancer.
Janikovits J, Müller M, Krzykalla J, Körner S, Echterdiek F, Lahrmann B, Grabe N, Schneider M, Benner A, Doeberitz MVK, Kloor M.
Oncoimmunology. 2017 Nov 6;7(2):e1390640. doi: 10.1080/2162402X.2017.1390640. eCollection 2018. PMID:29308317

CTNNB1-mutant colorectal carcinomas with immediate invasive growth: a model of interval cancers in Lynch syndrome.
Ahadova A, von Knebel Doeberitz M, Bläker H, Kloor M.
Fam Cancer. 2016 Oct;15(4):579-86. doi: 10.1007/s10689-016-9899-z.

Transcriptional interactions suggest niche segregation among microorganisms in the human gut.
Plichta DR, Juncker AS, Bertalan M, Rettedal E, Gautier L, Varela E, Manichanh C, Fouqueray C, Levenez F, Nielsen T, Doré J, Machado AM, de Evgrafov MC, Hansen T, Jørgensen T, Bork P, Guarner F, Pedersen O; Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium, Sommer MO, Ehrlich SD, Sicheritz-Pontén T, Brunak S, Nielsen HB.
Nat Microbiol. 2016 Aug 26;1:16152. doi: 10.1038/nmicrobiol.2016.152. 

MOCAT2: a metagenomic assembly, annotation and profiling framework.
Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P.
Bioinformatics. 2016 Aug 15;32(16):2520-3. doi: 10.1093/bioinformatics/btw183. Epub 2016 Apr 8.

Human gut microbes impact host serum metabolome and insulin sensitivity.
Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Doré J, Mattila I, Plichta DR, Pöhö P, Hellgren LI, Arumugam M, Sunagawa S, Vieira-Silva S, Jørgensen T, Holm JB, Trošt K; MetaHIT Consortium, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD, Pedersen O.
Nature. 2016 Jul 21;535(7612):376-81.

5-aza-2′-deoxycytidine (DAC) treatment downregulates the HPV E6 and E7 oncogene expression and blocks neoplastic growth of HPV-associated cancer cells.
Stich M, Ganss L, Puschhof J, Prigge ES, Reuschenbach M, Guiterrez A, Vinokurova S, von Knebel Doeberitz M.
Oncotarget. 2016 Jul 16. doi: 10.18632/oncotarget.10631

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing.
Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, Shi J, Bork P, Sinha R.
PLoS One. 2016 May 12;11(5):e0155362. doi: 10.1371/journal.pone.0155362. eCollection 2016.

Durable coexistence of donor and recipient strains after fecal microbiota transplantation.
Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojärvi J, Voigt AY, Zeller G, Sunagawa S, de Vos WM, Bork P.
Science. 2016 Apr 29;352(6285):586-9. doi: 10.1126/science.aad8852.

Gut Microbiota Linked to Sexual Preference and HIV Infection.
Noguera-Julian M, Rocafort M, Guillén Y, Rivera J, Casadellà M, Nowak P, Hildebrand F, Zeller G, Parera M, Bellido R, Rodríguez C, Carrillo J, Mothe B, Coll J, Bravo I, Estany C, Herrero C, Saz J, Sirera G, Torrela A, Navarro J, Crespo M, Brander C, Negredo E, Blanco J, Guarner F, Calle ML, Bork P, Sönnerborg A, Clotet B, Paredes R.
EBioMedicine. 2016 Jan 28;5:135-46. doi: 10.1016/j.ebiom.2016.01.032. eCollection 2016 Mar.

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P.
Nucleic Acids Res. 2016 Jan 4;44(D1):D286-93. doi: 10.1093/nar/gkv1248. Epub 2015 Nov 17. PMID: 26582926

Low density of FOXP3-positive T cells in normal colonic mucosa is related to the presence of beta2-microglobulin mutations in Lynch syndrome-associated colorectal cancer.
Echterdiek F, Janikovits J, Staffa L, Müller M, Lahrmann B, Frühschütz M, Hartog B, Nelius N, Benner A, Tariverdian M, von Knebel Doeberitz M, Grabe N, Kloor M.
Oncoimmunology. 2015 Nov 11;5(2):e1075692. eCollection 2016 Feb.

A new method for detection of tumor driver-dependent changes of protein sialylation in a colon cancer cell line reveals nectin-3 as TGFBR2 target.
Lee J, Warnken U, Schnölzer M, Gebert J, Kopitz J.
Protein Sci. 2015 Oct;24(10):1686-94. doi: 10.1002/pro.2741. Epub 2015 Jul 30. PMID: 26177744

Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children.
Zhang C, Yin A, Li H, Wang R, Wu G, Shen J, Zhang M, Wang L, Hou Y, Ouyang H, Zhang Y, Zheng Y, Wang J, Lv X, Wang Y, Zhang F, Zeng B, Li W, Yan F, Zhao Y, Pang X, Zhang X, Fu H, Chen F, Zhao N, Hamaker BR, Bridgewater LC, Weinkove D, Clement K, Dore J, Holmes E, Xiao H, Zhao G, Yang S, Bork P, Nicholson JK, Wei H, Tang H, Zhang X, Zhao L.
EBioMedicine. 2015 Jul 10;2(8):966-82. doi: 10.1016/j.ebiom.2015.07.007. eCollection 2015 Aug. PMID:26425705

Reconstitution of TGFBR2-Mediated Signaling Causes Upregulation of GDF-15 in HCT116 Colorectal Cancer Cells.
Lee J, Fricke F, Warnken U, Schnölzer M, Kopitz J, Gebert J.
PLoS One. 2015 Jun 26;10(6):e0131506. doi: 10.1371/journal.pone.0131506. eCollection 2015. PMID: 26114631

Metabolic dependencies drive species co-occurrence in diverse microbial communities.
Zelezniak A, Andrejev S, Ponomarova O, Mende DR, Bork P, Patil KR.
Proc Natl Acad Sci U S A. 2015 May 19;112(20):6449-54. doi: 10.1073/pnas.1421834112. Epub 2015 May 4. PMID: 25941371

Inter-individual differences in the gene content of human gut bacterial species.
Zhu A, Sunagawa S, Mende DR, Bork P.
Genome Biol. 2015 Apr 21;16:82. doi: 10.1186/s13059-015-0646-9. PMID: 25896518

Temporal and technical variability of human gut metagenomes.
Voigt AY, Costea PI, Kultima JR, Li SS, Zeller G, Sunagawa S, Bork P.
Genome Biol. 2015 Apr 8;16:73. doi: 10.1186/s13059-015-0639-8. PMID: 25888008

Dose-dependent effect of 2-deoxy-D-glucose on glycoprotein mannosylation in cancer cells.Ahadova A, Gebert J, von Knebel Doeberitz M, Kopitz J, Kloor M.
IUBMB Life. 2015 Mar;67(3):218-26. doi: 10.1002/iub.1364. Epub 2015 Apr 9. PMID:25854316

Association of high CD4-positive T cell infiltration with mutations in HLA class II-regulatory genes in microsatellite-unstable colorectal cancer.
Surmann EM, Voigt AY, Michel S, Bauer K, Reuschenbach M, Ferrone S, von Knebel Doeberitz M, Kloor M.
Cancer Immunol Immunother. 2015 Mar;64(3):357-66. doi: 10.1007/s00262-014-1638-4. Epub 2014 Dec 2. PMID:25445815

Mismatch repair-deficient crypt foci in Lynch syndrome–molecular alterations and association with clinical parameters.
Staffa L, Echterdiek F, Nelius N, Benner A, Werft W, Lahrmann B, Grabe N, Schneider M, Tariverdian M, von Knebel Doeberitz M, Bläker H, Kloor M.
PLoS One. 2015 Mar 27;10(3):e0121980. doi: 10.1371/journal.pone.0121980. eCollection 2015.PMID:25816162

Potential of fecal microbiota for early-stage detection of colorectal cancer.Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P.
Mol Syst Biol. 2014 Nov 28;10:766.doi:10.15252/msb.20145645.PMID:25432777

Detection of coding microsatellite frameshift mutations in DNA mismatch repair-deficient mouse intestinal tumors.
Woerner SM, Tosti E, Yuan YP, Kloor M, Bork P, Edelmann W, Gebert J.
Mol Carcinog. 2014 Sep 11. doi: 10.1002/mc.22213.

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T; MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD; MetaHIT Consortium.
Nat Biotechnol. 2014 Aug;32(8):822-8. doi: 10.1038/nbt.2939. Epub 2014 Jul 6.

An integrated catalog of reference genes in the human gut microbiome.
Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S, Zhang D, Zhang Z, Chen W, Zhao H, Al-Aama JY, Edris S, Yang H, Wang J, Hansen T, Nielsen HB, Brunak S, Kristiansen K, Guarner F, Pedersen O, Doré J, Ehrlich SD; MetaHIT Consortium, Bork P, Wang J; MetaHIT Consortium.
Nat Biotechnol. 2014 Aug;32(8):834-41. doi: 10.1038/nbt.2942. Epub 2014 Jul 6.

Clinical significance of microsatellite instability in colorectal cancer.
Kloor M, Staffa L, Ahadova A, von Knebel Doeberitz M.
Langenbecks Arch Surg. 2014 Jan;399(1):23-31. doi: 10.1007/s00423-013-1112-3. Epub 2013 Sep 19.

Chromosomal gains and losses in human papillomavirus-associated neoplasia of the lower genital tract – a systematic review and meta-analysis.
Thomas LK, Bermejo JL, Vinokurova S, Jensen K, Bierkens M, Steenbergen R, Bergmann M, von Knebel Doeberitz M, Reuschenbach M.
Eur J Cancer. 2014 Jan;50(1):85-98. doi: 10.1016/j.ejca.2013.08.022. Epub 2013 Sep 17.

Metagenomic species profiling using universal phylogenetic marker genes.
Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P.
Nat Methods. 2013 Dec;10(12):1196-9. doi: 10.1038/nmeth.2693. Epub 2013 Oct 20.

Towards a vaccine to prevent cancer in Lynch syndrome patients.
von Knebel Doeberitz M, Kloor M.
Fam Cancer. 2013 Jun;12(2):307-12. doi: 10.1007/s10689-013-9662-7. Review

Accurate and universal delineation of prokaryotic species
Mende, D.R., Sunagawa, S., Zeller, G. & Bork, P.
Nat Methods. 2013 Jul 28. doi: 10.1038/nmeth.2575.

BRAF V600E-specific immunohistochemistry for the exclusion of Lynch syndrome in MSI-H colorectal cancer
Capper D, Voigt A, Bozukova G, Ahadova A, Kickingereder P, von Deimling A, von Knebel Doeberitz M, Kloor M. 
Int J Cancer. 2013 Mar 30. doi: 10.1002/ijc.28183

Differential methylation of E2 binding sites in episomal and integrated HPV 16 genomes in preinvasive and invasive cervical lesions.
Chaiwongkot A, Vinokurova S, Pientong C, Ekalaksananan T, Kongyingyoes B, Kleebkaow P, Chumworathayi B, Patarapadungkit N, Reuschenbach M, von Knebel Doeberitz M.
Int J Cancer. 2013 May 1;132(9):2087-94. doi: 10.1002/ijc.27906. Epub 2012 Nov 26

T cell responses against microsatellite instability-induced frameshift peptides and influence of regulatory T cells in colorectal cancer.
Bauer K, Nelius N, Reuschenbach M, Koch M, Weitz J, Steinert G, Kopitz J, Beckhove P, Tariverdian M, von Knebel Doeberitz M, Kloor M.
Cancer Immunol Immunother. 2013 Jan;62(1):27-37. doi: 10.1007/s00262-012-1303-8. Epub 2012 Jun 23.

Genomic variation landscape of the human gut microbiome. Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D.R., Kultima, J.R., Martin, J., Kota, K., Sunyaev, S.R., Weinstock, G.M. & Bork, P. _Nature. 2013 Jan 3;493(7430):45-50. doi: 10.1038/nature11711. Epub 2012 Dec 5_

MOCAT: a metagenomics assembly and gene prediction toolkit.
Kultima, J.R., Sunagawa, S., Li, J., Chen, W., Chen, H., Mende, D.R., Arumugam, M., Pan, Q., Liu, B., Qin, J., Wang, J. & Bork, P.
PLoS One. 2012;7(10):e47656. doi: 10.1371/journal.pone.0047656. Epub 2012 Oct 17.

Prevalence of mismatch repair-deficient crypt foci in Lynch syndrome: a pathological study.
Kloor M, Huth C, Voigt AY, Benner A, Schirmacher P, von Knebel Doeberitz M, Bläker H.
Lancet Oncol. 2012 Jun;13(6):598-606. Epub 2012 May 1

The molecular basis of EPCAM expression loss in Lynch syndrome-associated tumors.
Huth C, Kloor M, Voigt AY, Bozukova G, Evers C, Gaspar H, Tariverdian M, Schirmacher P, von Knebel Doeberitz M, Bläker H.
Mod Pathol. 2012 Jun;25(6):911-6. doi: 10.1038/modpathol.2012.30. Epub 2012 Mar 2

Microsatellite instability and Beta2-Microglobulin mutations as prognostic markers in colon cancer: results of the FOGT-4 trial.
Tikidzhieva A, Benner A, Michel S, Formentini A, Link KH, Dippold W, von Knebel Doeberitz M, Kornmann M, Kloor M.
Br J Cancer. 2012 Mar 13;106(6):1239-45. doi: 10.1038/bjc.2012.53. Epub 2012 Feb 21

Analysis of EPCAM protein expression in diagnostics of Lynch syndrome
Kloor M, Voigt AY, Schackert HK, Schirmacher P, von Knebel Doeberitz M, Bläker H
J Clin Oncol. 2011 Jan 10;29(2):223-7. Epub 2010 Nov 29

A network of conserved co-occurring motifs for the regulation of alternative splicing
Suyama M, Harrington ED, Vinokourova S, von Knebel Doeberitz M, Ohara O, Bork P
Nucleic Acids Res. 2010 Aug 11

SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology
Woerner SM, Yuan YP, Benner A, Korff S, von Knebel Doeberitz M, Bork P
Nucleic Acids Res. 2010 Jan; 38 (Database issue)

High frequency of LMAN1 abnormalities in colorectal tumors with microsatellite instability.
Roeckel N, Woerner SM, Kloor M, Yuan YP, Patsos G, Gromes R, Kopitz J, Gebert, J.
Cancer Res 2009; 69(1):292-9

ASTD: The Alternative Splicing and Transcript Diversity database.
Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, Harrington E, Boué S, Eyras E, Plass M, Lopez F, Ritchie W, Moucadel V, Ara T, Pospisil H, Herrmann A, G Reich J, Guigó R, Bork P, Doeberitz MK, Vilo J, Hide W,Apweiler R, Thanaraj TA, Gautheret D.
Genomics. 2009 Mar;93(3):213-20. Epub 2008 Dec 24

Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability.
Korff S, Woerner SM, Yuan YP, Bork P, von Knebel Doeberitz M, Gebert J.
BMC Cancer. 2008 Nov 10;8:329

Immune response against frameshift-induced neopeptides in HNPCC patients and healthy HNPCC mutation carriers.
Schwitalle Y, Kloor M, Eiermann S, Linnebacher M, Kienle P, Knaebel HP, Tariverdian M, Benner A, von Knebel Doeberitz M.
Gastroenterology 2008; 134(4):988-97 

All publications of the von Knebel Doeberitz Group
All publications of the Bork Group

Group Members in alphabetical order

Aysel Ahadova, Postdoc

Sebastian Aretz, PhD Student

Seda Ballikaya, PhD Student
Seda.Ballikaya@med.uni-heidelberg.de

Alexej Ballhausen, MD student

Kathrin Bauer, PhD Student

Marion Bergmann, PhD

Peer Bork, PhD, Professor of Bioinformatics, Group Leader

Gergana Bozukova, MD Student

Ece Cevirgen, PhD Student

Arkom Chaiwongkot, PhD Student

Wei-Hua Chen, PhD

Franziska Faulstich, PhD

Kristoffer Forslund, PhD

Fabia Fricke, PhD student

Lennard Ganß, PhD

Yvette Garbe, PhD
yvette.garbe@oncoray.de

Johannes Gebert, PhD, Senior Scientist / Principal Investigator

Roland Gromes, PhD
roland.gromes@med.uni-heidelberg.de

Ana Ligia Gutierrez, PhD student

Günter Hämmerling, PhD

Eoghan Harrington, PhD student

Matthew Hayward, PhD

Cathrin Huth, MD Student

Jonas Janikovits, MD student

Martin Simon Kalteis, MD, Postdoc

Eva-Maria Katzenmaier, PhD, Postdoc

Richard Köhler, MD student

Matthias Kloor, MD, PhD, Postdoc

Alexander Kolleker, PhD

Jürgen Kopitz, PhD, Professor of Pathobiochemistry

Jennifer Lee, PhD

Malwina Michalak, PhD, Postdoc

Sara Michel, PhD
michel@grundipg.com

Meike Müller, MD student

Jonathan Netivi, MD student

Jessica Oberheim

Mine Özcan, PhD student

Elisabeth Pfaffendorf, MD student

Elena Prigge, MD, Postdoc

Miriam Reuschenbach, MD, PhD

Jens Roat-Kultima, PhD Student

Nina Röckel, PhD
nina.roeckel@med.uni-heidelberg.de

Madeleine Sauer, PhD

Lara Schlegel, PhD student

Sebastian Schmidt, PhD, Postdoc

Patrick Schulz, PhD Student

Mirjam Seiz, MD student

Julia Sieber-Frank, PhD student

Maximilian Stich, MD student (JCF, HRCMM)

Shinichi Sunagawa, PhD

Julien Tap, PhD

Lorenz Thomas, PhD Student

Anna Tikidzhieva, PhD Student

Kalliopi Trachana, PhD

Katharina Urban, PhD student

Svetlana Vinokurova, PhD Postdoc

Anita Voigt, PhD Student

Magnus von Knebel Doeberitz, MD, PhD, Professor of Molecular Oncology and Tumorbiology, Group Leader

Alison Waller, PhD

Nicolas Wentzensen, PhD

Stefan Wörner, PhD

Yan Ping Yuan, PhD, Lab Manager

Peer Bork and Magnus von Knebel Doeberitz
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