Thomas Lengauer

According to our database1, Thomas Lengauer
  • authored at least 191 papers between 1979 and 2017.
  • has a "Dijkstra number"2 of three.

Timeline

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Bibliography

2017
Selecting optimal minimum spanning trees that share a topological correspondence with phylogenetic trees.
CoRR, 2017

2016
ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing.
PLoS Computational Biology, 2016

DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets.
Nucleic Acids Research, 2016

2015
How to Write a Presubmission Inquiry.
PLoS Computational Biology, 2015

ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.
PLoS Computational Biology, 2015

Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus.
Bioinformatics, 2015

A general concept for consistent documentation of computational analyses.
Database, 2015

2014
BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives.
Nucleic Acids Research, 2014

Correction to On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking.
Journal of Chemical Information and Modeling, 2014

Entropy gain due to water release upon ligand binding.
J. Cheminformatics, 2014

Efficient computation of root mean square deviations under rigid transformations.
Journal of Computational Chemistry, 2014

2013
Sensitive Detection of Viral Transcripts in Human Tumor Transcriptomes.
PLoS Computational Biology, 2013

New Methods Section in PLOS Computational Biology.
PLoS Computational Biology, 2013

Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage.
PLoS Computational Biology, 2013

A method for finding consensus breakpoints in the cancer genome from copy number data.
Bioinformatics, 2013

2012
History-alignment models for bias-aware prediction of virological response to HIV combination therapy.
Proceedings of the Fifteenth International Conference on Artificial Intelligence and Statistics, 2012

On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking.
Journal of Chemical Information and Modeling, 2012

Paving the future: finding suitable ISMB venues.
Bioinformatics, 2012

Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data.
Bioinformatics, 2012

2011
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing.
Nucleic Acids Research, 2011

Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis.
BMC Med. Inf. & Decision Making, 2011

Classification with correlated features: unreliability of feature ranking and solutions.
Bioinformatics, 2011

2010
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.
Nucleic Acids Research, 2010

Chasing the AIDS virus.
Commun. ACM, 2010

Predicting MHC class I epitopes in large datasets.
BMC Bioinformatics, 2010

Improving disease gene prioritization using the semantic similarity of Gene Ontology terms.
Bioinformatics, 2010

Dealing with sparse data in predicting outcomes of HIV combination therapies.
Bioinformatics, 2010

Permutation importance: a corrected feature importance measure.
Bioinformatics, 2010

2009
Bioinformatische Unterstützung der Auswahl von HIV-Therapien.
Informatik Spektrum, 2009

DASMI: exchanging, annotating and assessing molecular interaction data.
Bioinformatics, 2009

Semi-Supervised Learning for Improving Prediction of HIV Drug Resistance.
Proceedings of the German Conference on Bioinformatics 2009, 2009

2008
Local Function Conservation in Sequence and Structure Space.
PLoS Computational Biology, 2008

Integrative Visual Analysis of the Effects of Alternative Splicing on Protein Domain Interaction Networks.
J. Integrative Bioinformatics, 2008

Stability analysis of mixtures of mutagenetic trees.
BMC Bioinformatics, 2008

Integrating expression data with domain interaction networks.
Bioinformatics, 2008

Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores.
Bioinformatics, 2008

Computational epigenetics.
Bioinformatics, 2008

Computing topological parameters of biological networks.
Bioinformatics, 2008

Selecting anti-HIV therapies based on a variety of genomic and clinical factors.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

Multi-task learning for HIV therapy screening.
Proceedings of the Machine Learning, 2008

An integrative approach for predicting interactions of protein regions.
Proceedings of the ECCB'08 Proceedings, 2008

Applications of semantic similarity measures.
Proceedings of the Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives, 24.03., 2008

Structural Descriptors of Protein-Protein Binding Sites.
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

2007
Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage.
PLoS Computational Biology, 2007

ISMB/ECCB 2007: The Premier Conference on Computational Biology.
PLoS Computational Biology, 2007

CpG Island Mapping by Epigenome Prediction.
PLoS Computational Biology, 2007

Moment invariants as shape recognition technique for comparing protein binding sites.
Bioinformatics, 2007

Functional evaluation of domain-domain interactions and human protein interaction networks.
Bioinformatics, 2007

Conformational analysis of alternative protein structures.
Bioinformatics, 2007

2006
Flexible Docking of Ligands into Synthetic Receptors Using a Two-Sided Incremental Construction Algorithm.
Journal of Chemical Information and Modeling, 2006

A Fully Computational Model for Predicting Percutaneous Drug Absorption.
Journal of Chemical Information and Modeling, 2006

Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies.
Journal of Chemical Information and Modeling, 2006

NOXclass: prediction of protein-protein interaction types.
BMC Bioinformatics, 2006

Improving the quality of protein structure models by selecting from alignment alternatives.
BMC Bioinformatics, 2006

A new measure for functional similarity of gene products based on Gene Ontology.
BMC Bioinformatics, 2006

Local protein structure prediction using discriminative models.
BMC Bioinformatics, 2006

Editorial.
Bioinformatics, 2006

Recco: recombination analysis using cost optimization.
Bioinformatics, 2006

Computational recognition of potassium channel sequences.
Bioinformatics, 2006

Improved scoring of functional groups from gene expression data by decorrelating GO graph structure.
Bioinformatics, 2006

DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

Functional Evaluation of Domain-Domain Interactions and Human Protein Interaction Networks.
Proceedings of the German Conference on Bioinformatics GCB 2006, 19.09. 2006, 2006

Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV.
Proceedings of the Data Integration in the Life Sciences, Third International Workshop, 2006

2005
Automatic Generation of Complementary Descriptors with Molecular Graph Networks.
Journal of Chemical Information and Modeling, 2005

POEM: Parameter Optimization Using Ensemble Methods: Application to Target Specific Scoring Functions.
Journal of Chemical Information and Modeling, 2005

Learning Multiple Evolutionary Pathways from Cross-Sectional Data.
Journal of Computational Biology, 2005

The DFG Priority Program "Informatics Methods for the Analysis and Interpretation of Large Genomic Datasets".
it - Information Technology, 2005

Confirmation of human protein interaction data by human expression data.
BMC Bioinformatics, 2005

ROCR: visualizing classifier performance in R.
Bioinformatics, 2005

Estimating cancer survival and clinical outcome based on genetic tumor progression scores.
Bioinformatics, 2005

BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing.
Bioinformatics, 2005

Computational methods for the design of effective therapies against drug resistant HIV strains.
Bioinformatics, 2005

Mtreemix: a software package for learning and using mixture models of mutagenetic trees.
Bioinformatics, 2005

Characterization of Novel HIV Drug Resistance Mutations Using Clustering, Multidimensional Scaling and SVM-Based Feature Ranking.
Proceedings of the Knowledge Discovery in Databases: PKDD 2005, 2005

Supervised and Unsupervised Approaches for Analyzing Covariation and Phenotypic Impact of HIV Drug Resistance Mutations.
Proceedings of the Lernen, 2005

Decomposing protein networks into domain-domain interactions.
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005

2004
Ensemble Methods for Classification in Cheminformatics.
Journal of Chemical Information and Modeling, 2004

Predicting protein structure classes from function predictions.
Bioinformatics, 2004

Arby: automatic protein structure prediction using profile-profile alignment and confidence measures.
Bioinformatics, 2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.
Bioinformatics, 2004

Learning Mixtures of Localized Rules by Maximizing the Area Under the ROC Curve.
Proceedings of the ROC Analysis in Artificial Intelligence, 1st International Workshop, 2004

Learning multiple evolutionary pathways from cross-sectional data.
Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004

2003
Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes.
Nucleic Acids Research, 2003

Parallel 'go with the winners' algorithms in distributed memory models.
J. Parallel Distrib. Comput., 2003

Microarrays: How Many Do You Need?
Journal of Computational Biology, 2003

Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence.
Bioinformatics, 2003

Pyranose Oxidase Identified as A Member of the GMC Oxidoreductase Family.
Bioinformatics, 2003

Methods for optimizing antiviral combination therapies.
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

Analyzing resistance phenomena in HIV with bioinformatics methods.
Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003

2002
Preface: Special RECOMB 2001 Issue.
Journal of Computational Biology, 2002

Flexible docking under pharmacophore type constraints.
Journal of Computer-Aided Molecular Design, 2002

ProML - the Protein Markup Language for specification of protein sequences, structures and families.
In Silico Biology, 2002

A hypergraph-based method for unification of existing protein structure- and sequence-families.
In Silico Biology, 2002

Improving fold recognition of protein threading by experimental distance constraints.
In Silico Biology, 2002

Confidence measures for protein fold recognition.
Bioinformatics, 2002

Microarrays: how many do you need?
Proceedings of the Sixth Annual International Conference on Computational Biology, 2002

Co-clustering of biological networks and gene expression data.
Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

ECCB 2002 Organization.
Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002

Editorial.
Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002

2001
Geno2pheno: Interpreting Genotypic HIV Drug Resistance Tests.
IEEE Intelligent Systems, 2001

Centralization: a new method for the normalization of gene expression data.
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

Confidence Measures for Fold Recognition.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001

ProML - the Protein Markup Language for specification of protein sequences, structures and families.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001

A new Method for Unification of Existing Protein Structure- and Sequence-Families.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001

Identifying drug resistance-associated patterns in HIV genotypes.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001

Improving Fold Recognition of Protein Threading by Experimental Distance Constraints.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001

Computational Biology at the Beginning of the Post-genomic Era.
Proceedings of the Informatics - 10 Years Back. 10 Years Ahead., 2001

2000
Provably Good Global Routing of Integrated Circuits.
SIAM Journal on Optimization, 2000

A Simple Iterative Approach to Parameter Optimization.
Journal of Computational Biology, 2000

Computational methods for the structural alignment of molecules.
Journal of Computer-Aided Molecular Design, 2000

Engineering support vector machine kernels that recognize translation initiation sites.
Bioinformatics, 2000

Pathway analysis in metabolic databases via differential metabolic display (DMD).
Bioinformatics, 2000

Protein Structure Prediction Methods for Drug Design.
Briefings in Bioinformatics, 2000

A simple iterative approach to parameter optimization.
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000

Analysis of Gene Expression Data with Pathway Scores.
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

Bioinformatics Problems Along the Process Line from Genomic Data to New Drugs.
Proceedings of the German Conference on Bioinformatics (GCB 2000), 2000

Computational Biology - Algorithms and More.
Proceedings of the Algorithms, 2000

1999
Decision tree-based formation of consensus protein secondary structure prediction.
Bioinformatics, 1999

Docking of hydrophobic ligands with interaction-based matching algorithms.
Bioinformatics, 1999

Editorial. The Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB'99).
Bioinformatics, 1999

Invited Lecture: Discrete Optimization Methods for Packing Problems in Two and Three Dimensions - With Applications in the Textile and Car Manufacturing Industries.
Proceedings of the Graph-Theoretic Concepts in Computer Science, 1999

Application of Parameter Optimization to Molecular Comparison Problems.
Proceedings of the 4th Pacific Symposium on Biocomputing, 1999

Engineering Support Vector Machine Kerneis That Recognize Translation Initialion Sites.
German Conference on Bioinformatics, 1999

Pathway analysis in metabolic databases via differetial metabolic display (DMD).
German Conference on Bioinformatics, 1999

1998
RigFit: A new approach to superimposing ligand molecules.
Journal of Computer-Aided Molecular Design, 1998

Computing closely matching upper and lower bounds on textile nesting problems.
European Journal of Operational Research, 1998

Random Generation of Embedded Graphs and an Extension to Dobrushin Uniqueness (Extended Abstract).
Proceedings of the Thirtieth Annual ACM Symposium on the Theory of Computing, 1998

Docking of hydrophobic ligands with interaction-based matching algorithms.
German Conference on Bioinformatics, 1998

1997
Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention.
Journal of Computer-Aided Molecular Design, 1997

Time-efficient flexible superposition of medium-sized molecules.
Journal of Computer-Aided Molecular Design, 1997

Fast and numerically stable parametric alignment of biosequences.
Proceedings of the First Annual International Conference on Research in Computational Molecular Biology, 1997

'Go with the winners' Generators with Applications to Molecular Modeling.
Proceedings of the Randomization and Approximation Techniques in Computer Science, 1997

Detection of Distant Structural Similarities in a Set of Proteins Using a Fast Graph-Based Method.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

Parallel 'Go with the Winners' Algorithms in the LogP Model.
Proceedings of the 11th International Parallel Processing Symposium (IPPS '97), 1997

DFG-Schwerpunkt: Informatikmethoden zur Analyse und Interpretation großer genomischer Datenmengen.
GI Jahrestagung, 1997

Algorithmen zum automatischen Zeichnen von Graphen im Rahmen des DFG-Schwerpunkts Effiziente Algorithmen für diskrete Probleme und ihre Anwendungen.
Proceedings of the Informatik '97, 1997

RigFit: a new approach to superimposing ligand molecules.
German Conference on Bioinformatics, 1997

1996
An Algorithm for Finding Maximal Common Subtopologies in a Set of Protein Structures.
Journal of Computational Biology, 1996

Placement of medium-sized molecular fragments into active sites of proteins.
Journal of Computer-Aided Molecular Design, 1996

Editorial: Informatik in den Biowissenschaften.
it+ti - Informationstechnik und Technische Informatik, 1996

Time-Efficient Flexible Superposition of Medium-Sized Molecules and Molecular Fragments.
German Conference on Bioinformatics, 1996

Computing Upper and Lower Bounds on Textile Nesting Problems.
Proceedings of the Algorithms, 1996

1995
Recursive Dynamic Programming for Adaptive Sequence and Structure Alignment.
Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 1995

Time-Efficient Docking of Flexible Ligands into Active Sites of Proteins.
Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 1995

APPlaUSE: Area and performance optimization in a unified placement and synthesis environment.
Proceedings of the 1995 IEEE/ACM International Conference on Computer-Aided Design, 1995

EMC-driven midway routing on PCBs.
Proceedings of the 1995 European Design and Test Conference, 1995

1994
Robust methods for EMC-driven routing.
IEEE Trans. on CAD of Integrated Circuits and Systems, 1994

1993
Robust and accurate hierarchical floorplanning with integrated global wiring.
IEEE Trans. on CAD of Integrated Circuits and Systems, 1993

1. Fachtagung "Informatik in den Biowissenschaften".
KI, 1993

Efficient Decision Procedures for Graph Properties on Centext-Free Graph Languages.
J. ACM, 1993

Efficient Automatic Part Nesting on Irregular and Inhomogeneous Surfaces.
Proceedings of the Fourth Annual ACM/SIGACT-SIAM Symposium on Discrete Algorithms, 1993

Algorithmic Research Problems in Molecular Bioinformatics.
Proceedings of the Second Israel Symposium on Theory of Computing Systems, 1993

Informatik in den Naturwissenschaften.
Proceedings of the Informatik: Grundlagen - Amwendungen, 1993

Informatik in den technischen Disziplinen.
Proceedings of the Informatik: Grundlagen - Amwendungen, 1993

1992
The Correlation between the Complexities of the Nonhierarchical and Hierarchical Versions of Graph Problems.
J. Comput. Syst. Sci., 1992

HERO: hierarchical EMC-constrained routing.
Proceedings of the 1992 IEEE/ACM International Conference on Computer-Aided Design, 1992

Processing of Hierarchically Defined Graphs and Graph Families.
Proceedings of the Data Structures and Efficient Algorithms, 1992

1991
The efficient solution of integer programs for hierarchical global routing.
IEEE Trans. on CAD of Integrated Circuits and Systems, 1991

Unstructured Path Problems and the Making of Semirings (Preliminary Version).
Proceedings of the Algorithms and Data Structures, 1991

Efficient Algorithms for Path Problems with Gernal Cost Citeria.
Proceedings of the Automata, Languages and Programming, 18th International Colloquium, 1991

Synthesis of multi-level logic with one symbolic input.
Proceedings of the conference on European design automation, 1991

1990
The Binary Network Flow Problem is Logspace Complete for P.
Theor. Comput. Sci., 1990

A Robust Framework for Hierarchical Floorplanning with Integrated Global Wiring.
Proceedings of the IEEE/ACM International Conference on Computer-Aided Design, 1990

VLSI Theory.
Handbook of Theoretical Computer Science, Volume A: Algorithms and Complexity (A), 1990

Combinatorial algorithms for integrated circuit layout.
Applicable theory in computer science, Teubner, ISBN: 978-0-471-92838-6, 1990

1989
Hierarchical planarity testing algorithms.
J. ACM, 1989

1988
Efficient Solution of Connectivity Problems on Hierarchically Defined Graphs.
SIAM J. Comput., 1988

Linear arrangement problems on recursively partitioned graphs.
ZOR - Meth. & Mod. of OR, 1988

Efficient processing of hierarchical graphs for engineering design.
Bulletin of the EATCS, 1988

Efficient Analysis of Graph Properties on Context-free Graph Languages (Extended Abstract).
Proceedings of the Automata, Languages and Programming, 15th International Colloquium, 1988

1987
Algorithmic Aspects of One-Dimensional Layout Compaction.
IEEE Trans. on CAD of Integrated Circuits and Systems, 1987

Efficient Algorithms for Finding Minimum Spanning Forests of Hierarchically Defined Graphs.
J. Algorithms, 1987

Efficient solutions of hierarchical systems of linear equations.
Computing, 1987

The Correlation Between the Complexities of the Nonhierarchical and Hierarchical Versions of Graph Problems.
Proceedings of the STACS 87, 1987

1986
An analysis of ternary simulation as a tool for race detection in digital MOS circuits.
Integration, 1986

Efficient Algorithms for Finding Minimum Spanning Forests of Hierarchically Defined Graphs.
Proceedings of the STACS 86, 1986

Hierarchical Planary Testing Algorithms.
Proceedings of the Automata, Languages and Programming, 13th International Colloquium, 1986

Hierarchische Darstellung geometrischer Objekte und ihre algorithmische Bedeutung.
Proceedings of the GI - 16. Jahrestagung I, Berlin, 6.-10. Oktober 1986, Proceedings, 1986

Linear Algorithms For Two CMOS Layout Problems.
Proceedings of the VLSI Algorithms and Architectures, 1986

Exploiting Hierarchy in VLSI Design.
Proceedings of the VLSI Algorithms and Architectures, 1986

1984
On the Solution of Inequality Systems Relevant to IC-Layout.
J. Algorithms, 1984

Algorithmische Spezifikation von symbolischen Layouts integrierter Schaltkreise.
Proceedings of the Fachgespräche auf der 14. GI-Jahrestagung, 1984

1982
Asymptotically tight bounds on time-space trade-offs in a pebble game.
J. ACM, 1982

Cube-Connected Cycles - Shuffle Exchange Graph - Das aktuelle Schlagwort.
Informatik Spektrum, 1982

The Complexity of Compacting Hierarchically Specified Layouts of Integrated Circuits (Preliminary Version)
Proceedings of the 23rd Annual Symposium on Foundations of Computer Science, 1982

1981
Black-White Pebbles and Graph Separation.
Acta Inf., 1981

1980
The Pebbling Problem is Complete in Polynomial Space.
SIAM J. Comput., 1980

The Space Complexity of Pebble Games on Trees.
Inf. Process. Lett., 1980

1979
A Fast Algorithm for Finding Dominators in a Flowgraph.
ACM Trans. Program. Lang. Syst., 1979

Upper and Lower Bounds on Time-Space Tradeoffs
Proceedings of the 11h Annual ACM Symposium on Theory of Computing, April 30, 1979

The Pebbling Problem is Complete in Polynomial Space
Proceedings of the 11h Annual ACM Symposium on Theory of Computing, April 30, 1979


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