GENE-IS: Time-Efficient and Accurate Analysis of Viral Integration Events in Large-Scale Gene Therapy Data.
Afzal S, Wilkening S, von Kalle C, Schmidt M, Fronza R.
Mol Ther Nucleic Acids. 2017 Mar 17;6:133-139. doi: 10.1016/j.omtn.2016.12.001. Epub 2016 Dec 10.

High-resolution analysis of the human T-cell receptor repertoire.
Ruggiero E, Nicolay JP, Fronza R, Arens A, Paruzynski A, Nowrouzi A, Ürenden G, Lulay C, Schneider S, Goerdt S, Glimm H, Krammer PH, Schmidt M, von Kalle C.
Nat Commun. 2015 Sep 1;6:8081. doi: 10.1038/ncomms9081.

High-throughput monitoring of integration site clonality in preclinical and clinical gene therapy studies.
Giordano FA, Appelt JU, Link B, Gerdes S, Lehrer C, Scholz S, Paruzynski A, Roeder I, Wenz F, Glimm H, von Kalle C, Grez M, Schmidt M, Laufs S.
Mol Ther Methods Clin Dev. 2015 Apr 1;2:14061. doi: 10.1038/mtm.2014.61. eCollection 2015.

Mapping the precision of genome editing.
Gabriel R, von Kalle C, Schmidt M.
Nat Biotechnol. 2015 Feb;33(2):150-2. doi: 10.1038/nbt.3142.

Gene therapy for Wiskott-Aldrich syndrome--long-term efficacy and genotoxicity.
Braun CJ, Boztug K, Paruzynski A, Witzel M, Schwarzer A, Rothe M, Modlich U, Beier R, Göhring G, Steinemann D, Fronza R, Ball CR, Haemmerle R, Naundorf S, Kühlcke K, Rose M, Fraser C, Mathias L, Ferrari R, Abboud MR, Al-Herz W, Kondratenko I, Maródi L, Glimm H, Schlegelberger B, Schambach A, Albert MH, Schmidt M*, von Kalle C*, Klein C*.
Sci Transl Med. 2014 Mar 12;6(227):227ra33. doi: 10.1126/scitranslmed.3007280.
* Shared authorship

Lentiviral hematopoietic stem cell gene therapy benefits metachromatic leukodystrophy.
Biffi A, Montini E, Lorioli L, Cesani M, Fumagalli F, Plati T, Baldoli C, Martino S, Calabria A, Canale S, Benedicenti F, Vallanti G, Biasco L, Leo S, Kabbara N, Zanetti G, Rizzo WB, Mehta NA, Cicalese MP, Casiraghi M, Boelens JJ, Del Carro U, Dow DJ, Schmidt M, Assanelli A, Neduva V, Di Serio C, Stupka E, Gardner J, von Kalle C, Bordignon C, Ciceri F, Rovelli A, Roncarolo MG, Aiuti A, Sessa M, Naldini L.
Science. 2013 Aug 23;341(6148):1233158. doi: 10.1126/science.1233158. Epub 2013 Jul 11.

Lentiviral hematopoietic stem cell gene therapy in patients with Wiskott-Aldrich syndrome.
Aiuti A, Biasco L, Scaramuzza S, Ferrua F, Cicalese MP, Baricordi C, Dionisio F, Calabria A, Giannelli S, Castiello MC, Bosticardo M, Evangelio C, Assanelli A, Casiraghi M, Di Nunzio S, Callegaro L, Benati C, Rizzardi P, Pellin D, Di Serio C, Schmidt M, Von Kalle C, Gardner J, Mehta N, Neduva V, Dow DJ, Galy A, Miniero R, Finocchi A, Metin A, Banerjee PP, Orange JS, Galimberti S, Valsecchi MG, Biffi A, Montini E, Villa A, Ciceri F, Roncarolo MG, Naldini L.
Science. 2013 Aug 23;341(6148):1233151. doi: 10.1126/science.1233151. Epub 2013 Jul 11.

A largely random AAV integration profile after LPLD gene therapy.
Kaeppel C, Beattie SG, Fronza R, van Logtenstein R, Salmon F, Schmidt S, Wolf S, Nowrouzi A, Glimm H, von Kalle C, Petry H, Gaudet D, Schmidt M.
Nat Med. 2013 Jul;19(7):889-91. doi: 10.1038/nm.3230. Epub 2013 Jun 16.

An unbiased genome-wide analysis of zinc-finger nuclease specificity.
Gabriel R, Lombardo A, Arens A, Miller JC, Genovese P, Kaeppel C, Nowrouzi A, Bartholomae CC, Wang J, Friedman G, Holmes MC, Gregory PD, Glimm H, Schmidt M, Naldini L, von Kalle C.
Nat Biotechnol. 2011 Aug 7;29(9):816-23. doi: 10.1038/nbt.1948.

Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing.
Paruzynski A, Arens A, Gabriel R, Bartholomae CC, Scholz S, Wang W, Wolf S, Glimm H, Schmidt M, von Kalle C.
Nat Protoc. 2010 Aug;5(8):1379-95. doi: 10.1038/nprot.2010.87. Epub 2010 Jul 8.

Comprehensive genomic access to vector integration in clinical gene therapy.
Gabriel R, Eckenberg R, Paruzynski A, Bartholomae CC, Nowrouzi A, Arens A, Howe SJ, Recchia A, Cattoglio C, Wang W, Faber K, Schwarzwaelder K, Kirsten R, Deichmann A, Ball CR, Balaggan KS, Yáñez-Muñoz RJ, Ali RR, Gaspar HB, Biasco L, Aiuti A, Cesana D, Montini E, Naldini L, Cohen-Haguenauer O, Mavilio F, Thrasher AJ, Glimm H, von Kalle C, Saurin W, Schmidt M.
Nat Med. 2009 Dec;15(12):1431-6. doi: 10.1038/nm.2057. Epub 2009 Nov 22.

High-resolution insertion-site analysis by linear amplification-mediated PCR (LAM-PCR).
Schmidt M, Schwarzwaelder K, Bartholomae C, Zaoui K, Ball C, Pilz I, Braun S, Glimm H, von Kalle C.
Nat Methods. 2007 Dec;4(12):1051-7.

Correction of X-linked chronic granulomatous disease by gene therapy, augmented by insertional activation of MDS1-EVI1, PRDM16 or SETBP1.
Ott MG*, Schmidt M*, Schwarzwaelder K*, Stein S*, Siler U, Koehl U, Glimm H, Kühlcke K, Schilz A, Kunkel H, Naundorf S, Brinkmann A, Deichmann A, Fischer M, Ball C, Pilz I, Dunbar C, Du Y, Jenkins NA, Copeland NG, Lüthi U, Hassan M, Thrasher AJ, Hoelzer D, von Kalle C, Seger R, Grez M.
Nat Med. 2006 Apr;12(4):401-9. Epub 2006 Apr 2.
* Shared authorship

Hematopoietic stem cell gene therapy with a lentiviral vector in X-linked adrenoleukodystrophy.
Cartier N, Hacein-Bey-Abina S, Bartholomae CC, Veres G, Schmidt M, Kutschera I, Vidaud M, Abel U, Dal-Cortivo L, Caccavelli L, Mahlaoui N, Kiermer V, Mittelstaedt D, Bellesme C, Lahlou N, Lefrère F, Blanche S, Audit M, Payen E, Leboulch P, l'Homme B, Bougnères P, von Kalle C, Fischer A, Cavazzana-Calvo M, Aubourg P.
Science. 2009 Nov 6;326(5954):818-23. doi: 10.1126/science.1171242.

LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1.
Hacein-Bey-Abina S*, von Kalle C*, Schmidt M*, McCormack MP, Wulffraat N, Leboulch P, Lim A, Osborne CS, Pawliuk R, Morillon E, Sorensen R, Forster A, Fraser P, Cohen JI, de Saint Basile G, Alexander I, Wintergerst U, Frebourg T, Aurias A, Stoppa-Lyonnet D, Romana S, Radford-Weiss I, Gross F, Valensi F, Delabesse E, Macintyre E, Sigaux F, Soulier J, Leiva LE, Wissler M, Prinz C, Rabbitts TH, Le Deist F, Fischer A, Cavazzana-Calvo M.
Science. 2003 Oct 17;302(5644):415-9. Erratum in: Science. 2003 Oct 24;302(5645):568.
* Shared authorship

Clonality analysis after retroviral-mediated gene transfer to CD34+ cells from the cord blood of ADA-deficient SCID neonates.
Schmidt M, Carbonaro DA, Speckmann C, Wissler M, Bohnsack J, Elder M, Aronow BJ, Nolta JA, Kohn DB, von Kalle C.
Nat Med. 2003 Apr;9(4):463-8. Epub 2003 Mar 17.

Polyclonal long-term repopulating stem cell clones in a primate model.
Schmidt M, Zickler P, Hoffmann G, Haas S, Wissler M, Muessig A, Tisdale JF, Kuramoto K, Andrews RG, Wu T, Kiem HP, Dunbar CE, von Kalle C.
Blood. 2002 Oct 15;100(8):2737-43.

Detection and direct genomic sequencing of multiple rare unknown flanking DNA in highly complex samples.
Schmidt M, Hoffmann G, Wissler M, Lemke N, Müssig A, Glimm H, Williams DA, Ragg S, Hesemann CU, von Kalle C.
Hum Gene Ther. 2001 May 1;12(7):743-9.

Systematic comparative study of computational methods for T-cell receptor sequencing data analysis.
Afzal S, Gil-Farina I, Gabriel R, Ahmad S, von Kalle C, Schmidt M, Fronza R.
Brief Bioinform. 2017 Sep 23. doi: 10.1093/bib/bbx111. [Epub ahead of print]

Lentiviral Vector Promoter is Decisive for Aberrant Transcript Formation.
Scholz SJ, Fronza R, Bartholomae CC, Cesana D, Montini E, von Kalle C, Gil-Farina I, Schmidt M.
Hum Gene Ther. 2017 Oct;28(10):875-885. doi: 10.1089/hum.2017.162. Epub 2017 Aug 18.

AAVvector-mediated in vivo reprogramming into pluripotency.
Senís E, Mosteiro L, Wilkening S, Wiedtke E, Nowrouzi A, Afzal S, Fronza R, Landerer H, Abad M, Niopek D, Schmidt M, Serrano M, Grimm D.
Nat Commun. 2018 Jul 9;9(1):2651. doi: 10.1038/s41467-018-05059-x.

Mapping Active Gene-Regulatory Regions in Human Repopulating Long-Term HSCs.
Wünsche P, Eckert ESP, Holland-Letz T, Paruzynski A, Hotz-Wagenblatt A, Fronza R, Rath T, Gil-Farina I, Schmidt M, von Kalle C, Klein C, Ball CR, Herbst F, Glimm H.
Cell Stem Cell. 2018 Jul 5;23(1):132-146.e9. doi: 10.1016/j.stem.2018.06.003.