Steve Hoffmann

 

Group Leader

Dr. Steve Hoffmann

Junior Research Group

Transcriptome Bioinformatics

LIFE - Leipzig Research Center

for Civilization Diseases

University Leipzig

Haertelstrasse 16-18

04107 Leipzig


E-mail: steve@bioinf.uni-leipzig.de

Phone: +49 341 97 16 711

Fax: +49 341 97 16 679

Background:


  1. Doctorate (Dr. med.) in Medicine (2007)
    Heinrich-Heine-University Düsseldorf

  2. Diploma (M.Sc.) in Bioinformatics (2007)
    University Hamburg

  3. State examination in medicine (2004/05)
    Philipps-University Marburg
    Georg-August University Göttingen

  4. First Diploma in Computer science (2003/04)
    Philipps-University Marburg




Research interests:


Genome Informatics

High-throughput data analysis

Cancer Genomics

Publications:


  1. Rivarola-Duarte L, Otto C, Jühling F, Schreiber S, Bedulina D, Jakob L, Gurkov A, Axenov-Gribanov D, Sahyoun AH, Lucassen M, Hackermüller J, Hoffmann S, Sartoris F, Pörtner HO, Timofeyev M, Luckenbach T, Stadler PF. A first Glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus. J Exp Zool B Mol Dev Evol. 2014 May;322(3):177-89.

  2. ‣Otto C, Stadler PF, Hoffmann S. Lacking alignments? The next generation sequencing mapper segemehl revisited. Bioinformatics. 2014 Mar 13. [Epub ahead ofprint] PubMed PMID: 24626854.

  3. Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt L, Teupser D, Hackermüeller J, Stadler PF. A multi-split mapping algorithm for circular RNA, splicing, trans-splicing, and fusion detection. Genome Biol. 2014 Feb 10;15(2):R34.

  4. Nitsche A, Doose G, Tafer H, Robinson M, Saha NR, Gerdol M, Canapa A, Hoffmann S, Amemiya CT, Stadler PF. Atypical RNAs in the coelacanth transcriptome. J Exp Zool B Mol Dev Evol. 2013 Oct 30.

  5. Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Børresen-Dale AL, Boyault S, Burkhardt B, Butler AP, Caldas C, Davies HR, Desmedt C, Eils R, Eyfjörd JE, Foekens JA, Greaves M, Hosoda F, Hutter B, Ilicic T, Imbeaud S, Imielinski M, Jäger N, Jones DT, Jones D, Knappskog S, Kool M, Lakhani SR, López-Otín C, Martin S, Munshi NC, Nakamura H, Northcott PA, Pajic M, Papaemmanuil E, Paradiso A, Pearson JV, Puente XS, Raine K, Ramakrishna M, Richardson AL, Richter J, Rosenstiel P, Schlesner M, Schumacher TN, Span PN, Teague JW, Totoki Y, Tutt AN, Valdés-Mas R, van Buuren MM, van 't Veer L, Vincent-Salomon A, Waddell N, Yates LR; Australian Pancreatic Cancer Genome Initiative; ICGC Breast Cancer Consortium; ICGC MMML-Seq Consortium; ICGC PedBrain, Zucman-Rossi J, Futreal PA, McDermott U, Lichter P, Meyerson M, Grimmond SM, Siebert R, Campo E, Shibata T, Pfister SM, Campbell PJ, Stratton MR. Signatures of mutational processes in human cancer. Nature. 2013 Aug 22;500(7463):415-21.

  6. Holdt LM, Hoffmann S, Sass K, Langenberger D, Scholz M, Krohn K, Finstermeier K, Stahringer A, Wilfert W, Beutner F, Gielen S, Schuler G, Gäbel G, Bergert H, Bechmann I, Stadler PF, Thiery J, Teupser D. Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. PLoS Genet. 2013;9(7):e1003588.

  7. Doose G, Alexis M, Kirsch R, Findeiß S, Langenberger D, Machné R, Mörl M, Hoffmann S, Stadler PF. Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data. RNA Biol. 2013 Jul;10(7):1204-10.

  8. Li Y, Podlevsky JD, Marz M, Qi X, Hoffmann S, Stadler PF, Chen JJ. dentification of purple sea urchin telomerase RNA using a next-generation sequencing based approachRNA [Epub ahead of print].

  9. Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K. The African coelacanth genome provides insights into tetrapod evolution. Nature. 2013 Apr 18;496(7445):311-6.

  10. Langenberger D, Çakir MV, Hoffmann S, Stadler PF. Dicer-processed small RNAs: rules and exceptions. J Exp Zool B Mol Dev Evol. 2013 Jan;320(1):35-46.

  11. Richter J, Schlesner M, Hoffmann S*, Kreuz M, Leich E, Burkhardt B, Rosolowski M, Ammerpohl O, Wagener R, Bernhart SH, Lenze D, Szczepanowski M, Paulsen M, Lipinski S, Russell RB, Adam-Klages S, Apic G, Claviez A, Hasenclever D, Hovestadt V, Hornig N, Korbel JO, Kube D, Langenberger D, Lawerenz C, Lisfeld J,  Meyer K, Picelli S, Pischimarov J, Radlwimmer B, Rausch T, Rohde M, Schilhabel M, Scholtysik R, Spang R, Trautmann H, Zenz T, Borkhardt A, Drexler HG, Möller P, MacLeod RA, Pott C, Schreiber S, Trümper L, Loeffler M, Stadler PF, Lichter P, Eils R, Küppers R, Hummel M, Klapper W, Rosenstiel P, Rosenwald A, Brors B, Siebert R; ICGC MMML-Seq Project. Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nature Genetics 2012 Dec;44(12):1316-20. (* joint first author; transcriptome)

  12. Qi X, Li Y, Honda S, Hoffmann S, Marz M, Mosig A, Podlevsky JD, Stadler PF, Selker EU, Chen JJ. The common ancestral core of vertebrate and fungal telomerase RNAs. Nucleic Acids Res. 2013 Jan 7;41(1):450-62.

  13. Otto C, Stadler PF, Hoffmann S. Fast and sensitive mapping of bisulfite-treated sequencing data. Bioinformatics. 2012 Jul 1;28(13):1698-704.

  14. Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J, Stadler PF, Bonas U. Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res. 2012 Mar;40(5):2020-31.

  15. Langenberger D, Pundhir S, Ekstrøm CT, Stadler PF, Hoffmann S, Gorodkin J. deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. Bioinformatics. 2012 Jan 1;28(1):17-24.

  16. Fasold M, Langenberger D, Binder H, Stadler PF, Hoffmann S: "DARIO: A ncRNA detection and analysis tool for next-generation sequencing experiments", Nucleic Acids Res. Nucleic Acids Res. 2011 Jul;39:W112-7

  17. Findeiß S, Langenberger D, Stadler PF, Hoffmann S: "Traces of Post-Transcriptional RNA Modifications in Deep Sequencing Data", Biol Chem. (2011) 392(4):305-313.

  18. Hoffmann S: "Computational analysis of high throughput sequencing data", Methods Mol. Biol. (2011) 719, S. 199–217.

  19. Otto C, Hoffmann S, Gorodkin J, Stadler PF: "Fast local fragment chaining using sum-of-pair gap costs", Alg. Mol. Biol. (2011) vol. 6:4

  20. Buck D, Cepok S, Hoffmann S, Grummel V, Jochim A, Berthele A, Hartung HP, Wassmuth R, Hemmer B. Influence of the HLA-DRB1 genotype on antibody development to interferon beta in multiple sclerosis. Arch Neurol. 2011 Apr;68(4):480-7.

  21. Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg L, Burt DW, Crasta O, Crooijmans RPMA, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Flicek P, Florea L, Folkerts O, Groenen MAM, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim A, Langenberger D, Lee MK, Lee T, Mane S, Marcais S, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu Z, Van Tassell CP, Vilella AJ, Williams K, Yorke JA, Zhang L, Zhang H, Zhang X, Zhang Y, and Reed KM: "Multi-platform next generation sequencing of the domestic turkey (Meleagris gallopavo): Genome assembly and analysis", PLoS Biology (2010) 8,9: e1000475.

  22. Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermueller J, Reinhardt R, Stadler PF, Vogel J: "The primary transcriptome of the major human pathogen Helicobacter pylori", Nature (2010) vol. 464 (7286) pp. 250-5

  23. Langenberger D, Bermudez-Santana C, Stadler PF, Hoffmann S: "Identification and Classification of Small RNAs in Transcriptome Sequence Data", Pac Symp Biocomput (2010) pp. 80-7

  24. Langenberger D, Bermudez-Santana C, Hertel J, Hoffmann S, Khaitovitch P, Stadler PF: "Evidence for Human microRNA-Offset RNAs in Small RNA Sequencing Data", Bioinformatics (2009) vol. 25 (18) pp. 2298-301

  25. Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermueller J: "Fast mapping of short sequences with mismatches, insertions and deletions using index structures", PLoS Comput Biol (2009) vol. 5 (9) pp. e1000502

  26. Schmidt H, Taubert H, Lange H, Kriese K, Schmitt WD, Hoffmann S, Bartel F, Hauptmann S. Small polydispersed circular DNA contains strains of mobile genetic elements and occurs more frequently in permanent cell lines of malignant tumors than in normal lymphocytes. Oncol Rep. 2009 Aug;22(2):393-400.

  27. Stadler PF, Chen JJ, Hackermüller J, Hoffmann S, Horn F, Khaitovich P, Kretzschmar AK, Mosig A, Prohaska SJ, Qi X, Schutt K, Ullmann K. Evolution of vault RNAs. Mol Biol Evol. 2009 Sep;26(9):1975-91.

  28. Hoffmann S, Cepok S, Grummel V, Lehmann-Horn K, Hackermüller J, Stadler PF, Hartung HP, Berthele A, Deisenhammer F, Wassmuth R, Hemmer B. HLA-DRB1*0401 and HLA-DRB1*0408 are strongly associated with the development of antibodies against interferon-beta therapy in multiple sclerosis. Am J Hum Genet. 2008 Aug;83(2):219-27.

  29. Cepok S, Schreiber H, Hoffmann S, Zhou D, Neuhaus O, von Geldern G, Hochgesand S, Nessler S, Rothhammer V, Lang M, Hartung HP, Hemmer B. Enhancement of chemokine expression by interferon beta therapy in patients with multiple sclerosis. Arch Neurol. 2009 Oct;66(10):1216-23.

  30. Rosche B, Cepok S, Stei S, Vogel F, Grummel V, Hoffmann S, Kroner A, Maurer M, Rieckmann P, Sommer N, Hemmer B: “The role of the polio virus receptor and the herpesvirus entry mediator B genes for the development of MS“, J Neuroimmunol. (2004) 156(1-2):171-7.

  31. Hoffmann S, Becker A, Hoerle S, Metz A, Oertel WH, Sommer N, Hemmer B: „Autosomal dominant congenital nystagmus is not linked to 6p12, 7p11, and 15q11 in a German family“, Am J Ophthal. (2004) 138(3):439-43.

  32. Jacobsen M, Hoffmann S, Cepok S, Stei S, Ziegler A, Sommer N, Hemmer B: „A novel mutation in PTPRC interferes with splicing and alters the structure of the human CD45 molecule“, Immunogenetics. (2002) 54(3):158-63.

  33. Bussow K, Hoffmann S, Sievert V: „ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files“ BMC Bioinformatics. (2002) 19;3:40.

  34. Hoffmann S, Hemmer B: „Genetische Aspekte der Multiplen Sklerose“ Der Neurologe und Psychiater (DNP). (2002) Sonderheft (1):17-20.

  35. Hanauske A-R, Eismann U, Oberschmidt O, Pospisil H, Hoffmann S, Hanauske-Abel H, Ma D, Chen V, Paoletti P, Niyikiza C: „ Correlations of mRNA expression and in vitro chemosensitivity to pemetrexed in freshly explanted tumor cells“ Invest New Drugs. (2007) 25(5):417-23