David Langenberger

 

phd student

David Langenberger

Junior Research Group

Transcriptome Bioinformatics

LIFE - Leipzig Research Center

for Civilization Diseases

University Leipzig

Haertelstrasse 16-18

04107 Leipzig


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

Phone: +49 341 97 16 698

Background:


  1. I studied bioinformatics at the University of Applied Sciences Weihenstephan in Freising, Germany. During my studies I spent 6 month in Nikolaus Rajewsky‘s group at the NYU in New York and another 6 month in Guochun Liao‘s group at the Roche Palo Alto research facility in Palo Alto. In 2008 I wrote my diploma thesis in Dimitrij Frishman‘s group at the Department of Genome-Oriented Bioinformatics of the Technical University of Munich, entitled ,Reduced RNAi off-target effects by artifically designed siRNAs in mammals‘.

  2. Since January 2009 I work as a PhD student in Peter Stadler‘s group in Leipzig and since 2010 I am part of Steve Hoffmann‘s junior research group which is part of the Leipzig Research Center for Civilization Diseases (LIFE).



Research interests:


  1. Analyzing High Throughput Sequencing Data and small non-coding RNAs

  2. Small RNAs, including microRNAs, snoRNAs and tRNAs, are a diverse collection of molecules with several important biological functions. High Throughput Sequencing (HTS) has the ability to rapidly sequence millions of individual small RNA molecules. This, for the first time, offers the opportunity to identify known and classify new small RNAs based on unbiased data. Exploring small RNA biology or characterizing differential expression profiles by sequencing and comparing small RNA transcriptomes is also an exciting possibility to get more and deeper information about the world of non-coding RNAs (ncRNAs).

Publications:


  2. •Findeiß S, Langenberger D, Stadler PF, Hoffmann S: "Traces of Post-Transcriptional RNA Modifications in Deep Sequencing Data", 62. Mosbacher Colloquium, April 7-9. 2011, Mosbach, Baden, Germany, (2011) in press.

  3. •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.

  4. •Sturm M, Hackenberg M, Langenberger D, Frishman D: "TargetSpy: a supervised machine learning approach for microRNA target prediction", BMC Bioinformatics (2010) 11(1):292. 

  5. •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

  6. •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

  7. •Hackenberg M, Sturm M, Falcon J, Langenberger D, Aransay A: "miRanalyzer: A microRNA detection and analysis tool for next-generation sequencing experiments", Nucleic Acids Res. (2009) 37 (Web Server Issue):W68-76

  8. •Gruen D, Wang YL, Langenberger D, Gunsalus KC, Rajewsky N: "microRNA Target predictions across seven Drosophial species and comparison to mammalian targets", PLoS Comp. Biol (2005) 1:e13