gobics.de [ Thomas Lingner ]

Address: Universität Göttingen Institut für Mikrobiologie und Genetik Abteilung für Bioinformatik Goldschmidtstr. 1 37077 Göttingen Germany eMail: thomas [at] gobics [dot] de Phone: +49 551 39 13993 FAX: +49 551 39 14929

Short CV

• from 1999 to 2005 I studied "Naturwissenschaftliche Informatik" at the University of Bielefeld
• in October 2005 I joined the Department of Bioinformatics at the University of Göttingen as a PhD student.
• Note: since March 2009 I'm PostDoc at the CRG in Barcelona

Research Interests:

• Protein classification, function prediction, subcellular localization prediction and remote homology detection
• Machine learning and data mining on biological sequences

Download:

• Word Correlation kernel matrices for SCOP benchmark setup (tared and gzipped tab-delimited ASCII-Format, sequence order as in label file, 443 MB)
  
• Oligomer Distance Histogram kernel matrices gzipped (tab-delimited ASCII-Format, sequence order as in label file): monomers / dimers / trimers
• ODH toolbox for MATLAB^®

Publications:

• K. J. Hoff, T. Lingner, P. Meinicke, M. Tech
  Orphelia: predicting genes in metagenomic sequencing reads
  Nucleic Acids Research 37, W101-W105, 2009.
• A. Kaever, T. Lingner, K. Feussner, C. Gobel, I. Feussner, P. Meinicke
  MarVis: a tool for clustering and visualization of metabolic biomarkers
  BMC Bioinformatics 10, 92, 2009.
• Thomas Lingner and Peter Meinicke
  Fast Target Set Reduction for Large-Scale Protein Function Prediction: A Multi-class Multi-label Machine Learning Approach
  WABI 2008, Lecture Notes in Computer Science, 5251 (Algorithms in Bioinformatics), 198-209.
• P. Meinicke, T. Lingner, A. Kaever, K. Feussner, C. Goebel, I. Feussner, P. Karlovsky, and B. Morgenstern.
  Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps.
  Algorithms for Molecular Biology, 3:9, 2008.
• T. Lingner and P. Meinicke
  Word correlation matrices for protein sequence analysis and remote homology detection
  BMC Bioinformatics, 9:259, 2008.
• D. Krefting, J. Bart, K. Beronow, O. Dzhimova, J. Falkner, M. Hartung, A. Hoheisel, T. Knoch, T. Lingner, Y. Mohammed, K. Peter, E. Rahm, U. Sax, D. Sommerfeld, T. Steinke, T. Tolxdorff, F. Viezens, M, Vossberg, A. Weisbecker
  MediGRID - A User Friendly Secured Grid Infrastructure
  Future Generation Computer Systems, in press.
• D. Sommerfeld, T. Lingner, M. Stanke, B. Morgenstern, H. Richter
  AUGUSTUS at MediGRID: Adaption of a Bioinformatics Application to Grid Computing for Efficient Genome Analysis
  Future Generation Computer Systems, in press.
• K. J. Hoff, M. Tech, T. Lingner, R. Daniel, B. Morgenstern, P. Meinicke
  Gene prediction in metagenomic fragments: a large scale machine learning approach
  BMC Bioinformatics, 9:217, 2008.
• Dietmar Sommerfeld, Thomas Lingner, and Harald Richter
  Stepwise Enabling of AUGUSTUS for MediGRID
  IfI-07-12, November 2007, 26 pp., Technical Report.
• T. Lingner and P. Meinicke
  Remote homology detection based on oligomer distances
  Bioinformatics 22, 2224-2231, 2006.
  Supplementary data (normalized kernel matrices in gzipped tab-delimited ASCII-Format): monomers / dimers / trimers
• Kaper M, Meinicke P, Großekathöfer U, Lingner T, Ritter H.
  BCI Competition 2003--Data set IIb: support vector machines for the P300 speller paradigm
  IEEE Trans Biomed Eng. 2004 Jun; 51(6):1073-6.

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• PhD thesis:
  Alignmentfreie Analyse von Proteinsequenzen mit Verfahren des maschinellen Lernens
  (german, with english abstract and articles)

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• Diploma thesis:
  Neue Ansätze zum maschinellen Lernen von Alignments
  (german, with Ulf Großekathöfer)