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Documents authored by Lengauer, Thomas

Document
DOI: 10.4230/DagSemProc.08131.2
Applications of semantic similarity measures

Authors: Andreas Schlicker, Fidel Ramírez, Jörg Rahnenführer, Carola Huthmacher, Alejandro Pironti, Francisco S. Domingues, Thomas Lengauer, and Mario Albrecht

Published in: Dagstuhl Seminar Proceedings, Volume 8131, Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives (2008)

Abstract
There has been much interest in uncovering protein-protein interactions and their underlying domain-domain interactions. Many experimental techniques have been developed, for example yeast-two-hybrid screening and tandem affinity purification. Since it is time consuming and expensive to perform exhaustive experimental screens, in silico methods are used for predicting interactions. However, all experimental and computational methods have considerable false positive and false negative rates. Therefore, it is necessary to validate experimentally determined and predicted interactions. One possibility for the validation of interactions is the comparison of the functions of the proteins or domains. Gene Ontology (GO) is widely accepted as a standard vocabulary for functional terms, and is used for annotating proteins and protein families with biological processes and their molecular functions. This annotation can be used for a functional comparison of interacting proteins or domains using semantic similarity measures. Another application of semantic similarity measures is the prioritization of disease genes. It is know that functionally similar proteins are often involved in the same or similar diseases. Therefore, functional similarity is used for predicting disease associations of proteins. In the first part of my talk, I will introduce some semantic and functional similarity measures that can be used for comparison of GO terms and proteins or protein families. Then, I will show their application for determining a confidence threshold for domain-domain interaction predictions. Additionally, I will present FunSimMat (http://www.funsimmat.de/), a comprehensive resource of functional similarity values available on the web. In the last part, I will introduce the problem of comparing diseases, and a first attempt to apply functional similarity measures based on GO to this problem.
Cite as

Andreas Schlicker, Fidel Ramírez, Jörg Rahnenführer, Carola Huthmacher, Alejandro Pironti, Francisco S. Domingues, Thomas Lengauer, and Mario Albrecht. Applications of semantic similarity measures. In Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives. Dagstuhl Seminar Proceedings, Volume 8131, p. 1, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

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@InProceedings{schlicker_et_al:DagSemProc.08131.2,
  author =	{Schlicker, Andreas and Ram{\'\i}rez, Fidel and Rahnenf\"{u}hrer, J\"{o}rg and Huthmacher, Carola and Pironti, Alejandro and Domingues, Francisco S. and Lengauer, Thomas and Albrecht, Mario},
  title =	{{Applications of semantic similarity measures}},
  booktitle =	{Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
  pages =	{1--1},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8131},
  editor =	{Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.2},
  URN =		{urn:nbn:de:0030-drops-15198},
  doi =		{10.4230/DagSemProc.08131.2},
  annote =	{Keywords: Semantic similarity, functional similarity, Gene Ontology, domain-domain interactions}
}
Document
DOI: 10.4230/DagSemRep.360
Computational Biology (Dagstuhl Seminar 02471)

Authors: Ross B. Altman, David Gilbert, and Thomas Lengauer

Published in: Dagstuhl Seminar Reports. Dagstuhl Seminar Reports, Volume 1 (2021)

Abstract
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Ross B. Altman, David Gilbert, and Thomas Lengauer. Computational Biology (Dagstuhl Seminar 02471). Dagstuhl Seminar Report 360, pp. 1-30, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2003)

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@TechReport{altman_et_al:DagSemRep.360,
  author =	{Altman, Ross B. and Gilbert, David and Lengauer, Thomas},
  title =	{{Computational Biology (Dagstuhl Seminar 02471)}},
  pages =	{1--30},
  ISSN =	{1619-0203},
  year =	{2003},
  type = 	{Dagstuhl Seminar Report},
  number =	{360},
  institution =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemRep.360},
  URN =		{urn:nbn:de:0030-drops-152405},
  doi =		{10.4230/DagSemRep.360},
}
Document
DOI: 10.4230/DagSemRep.293
Bioinformatics (Dagstuhl Seminar 00491)

Authors: Douglas Brutlag, Thomas Lengauer, and Martin Vingron

Published in: Dagstuhl Seminar Reports. Dagstuhl Seminar Reports, Volume 1 (2021)

Abstract
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Douglas Brutlag, Thomas Lengauer, and Martin Vingron. Bioinformatics (Dagstuhl Seminar 00491). Dagstuhl Seminar Report 293, pp. 1-29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2001)

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@TechReport{brutlag_et_al:DagSemRep.293,
  author =	{Brutlag, Douglas and Lengauer, Thomas and Vingron, Martin},
  title =	{{Bioinformatics (Dagstuhl Seminar 00491)}},
  pages =	{1--29},
  ISSN =	{1619-0203},
  year =	{2001},
  type = 	{Dagstuhl Seminar Report},
  number =	{293},
  institution =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemRep.293},
  URN =		{urn:nbn:de:0030-drops-151773},
  doi =		{10.4230/DagSemRep.293},
}
Document
DOI: 10.4230/DagSemRep.120
Molecular Bioinformatics (Dagstuhl Seminar 9528)

Authors: Dan Gusfield, Thomas Lengauer, and Chris Sander

Published in: Dagstuhl Seminar Reports. Dagstuhl Seminar Reports, Volume 1 (2021)

Abstract
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Dan Gusfield, Thomas Lengauer, and Chris Sander. Molecular Bioinformatics (Dagstuhl Seminar 9528). Dagstuhl Seminar Report 120, pp. 1-25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (1995)

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@TechReport{gusfield_et_al:DagSemRep.120,
  author =	{Gusfield, Dan and Lengauer, Thomas and Sander, Chris},
  title =	{{Molecular Bioinformatics (Dagstuhl Seminar 9528)}},
  pages =	{1--25},
  ISSN =	{1619-0203},
  year =	{1995},
  type = 	{Dagstuhl Seminar Report},
  number =	{120},
  institution =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemRep.120},
  URN =		{urn:nbn:de:0030-drops-150082},
  doi =		{10.4230/DagSemRep.120},
}
Document
DOI: 10.4230/DagSemRep.76
Combinatorial Methods for Integrated Circuits Design (Dagstuhl Seminar 9342)

Authors: Thomas Lengauer, Majid Sarrafzadeh, and Dorothea Wagner

Published in: Dagstuhl Seminar Reports. Dagstuhl Seminar Reports, Volume 1 (2021)

Abstract
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Thomas Lengauer, Majid Sarrafzadeh, and Dorothea Wagner. Combinatorial Methods for Integrated Circuits Design (Dagstuhl Seminar 9342). Dagstuhl Seminar Report 76, pp. 1-20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (1994)

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@TechReport{lengauer_et_al:DagSemRep.76,
  author =	{Lengauer, Thomas and Sarrafzadeh, Majid and Wagner, Dorothea},
  title =	{{Combinatorial Methods for Integrated Circuits Design (Dagstuhl Seminar 9342)}},
  pages =	{1--20},
  ISSN =	{1619-0203},
  year =	{1994},
  type = 	{Dagstuhl Seminar Report},
  number =	{76},
  institution =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemRep.76},
  URN =		{urn:nbn:de:0030-drops-149646},
  doi =		{10.4230/DagSemRep.76},
}
Document
DOI: 10.4230/DagSemRep.46
Molecular Bioinformatics (Dagstuhl Seminar 9237)

Authors: Thomas Lengauer, Dietmar Schomburg, and Michael S. Waterman

Published in: Dagstuhl Seminar Reports. Dagstuhl Seminar Reports, Volume 1 (2021)

Abstract
Cite as

Thomas Lengauer, Dietmar Schomburg, and Michael S. Waterman. Molecular Bioinformatics (Dagstuhl Seminar 9237). Dagstuhl Seminar Report 46, pp. 1-28, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (1992)

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@TechReport{lengauer_et_al:DagSemRep.46,
  author =	{Lengauer, Thomas and Schomburg, Dietmar and Waterman, Michael S.},
  title =	{{Molecular Bioinformatics (Dagstuhl Seminar 9237)}},
  pages =	{1--28},
  ISSN =	{1619-0203},
  year =	{1992},
  type = 	{Dagstuhl Seminar Report},
  number =	{46},
  institution =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemRep.46},
  URN =		{urn:nbn:de:0030-drops-149349},
  doi =		{10.4230/DagSemRep.46},
}
Document
DOI: 10.4230/DagSemRep.20
Theory and Practice of Physical Design of VLSI Systems (Dagstuhl Seminar 9136)

Authors: Thomas Lengauer, Rolf H. Möhring, and Bryan Preas

Published in: Dagstuhl Seminar Reports. Dagstuhl Seminar Reports, Volume 1 (2021)

Abstract
Cite as

Thomas Lengauer, Rolf H. Möhring, and Bryan Preas. Theory and Practice of Physical Design of VLSI Systems (Dagstuhl Seminar 9136). Dagstuhl Seminar Report 20, pp. 1-28, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (1991)

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@TechReport{lengauer_et_al:DagSemRep.20,
  author =	{Lengauer, Thomas and M\"{o}hring, Rolf H. and Preas, Bryan},
  title =	{{Theory and Practice of Physical Design of VLSI Systems (Dagstuhl Seminar 9136)}},
  pages =	{1--28},
  ISSN =	{1619-0203},
  year =	{1991},
  type = 	{Dagstuhl Seminar Report},
  number =	{20},
  institution =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemRep.20},
  URN =		{urn:nbn:de:0030-drops-149088},
  doi =		{10.4230/DagSemRep.20},
}
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