Publications:

1. ‣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. (Web Server Issue) (2011), accepted
   

2. ‣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.
   

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

4. ‣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
   

5. ‣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.
   

6. ‣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
   

7. ‣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
   

8. ‣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
   

9. ‣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
   

10. ‣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.
    

11. ‣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.
    

12. ‣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.
    

13. ‣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.
    

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

15. ‣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