Søren Brunak

According to our database1, Søren Brunak authored at least 81 papers between 1989 and 2019.

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Bibliography

2019
Incorporating symptom data in longitudinal disease trajectories for more detailed patient stratification.
Int. J. Medical Informatics, 2019

A generic deep convolutional neural network framework for prediction of receptor-ligand interactions - NetPhosPan: application to kinase phosphorylation prediction.
Bioinformatics, 2019

sAOP: linking chemical stressors to adverse outcomes pathway networks.
Bioinformatics, 2019

2018
A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts.
PLoS Computational Biology, 2018

miRandola 2017: a curated knowledge base of non-invasive biomarkers.
Nucleic Acids Research, 2018

Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios.
BMC Bioinformatics, 2018

2017
Pharos: Collating protein information to shed light on the druggable genome.
Nucleic Acids Research, 2017

Temporal Order of Disease Pairs Affects Subsequent Disease Trajectories: The Case of Diabetes and Sleep Apnea.
Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

2016
A genomic history of Aboriginal Australia.
Nature, 2016

Tools and data services registry: a community effort to document bioinformatics resources.
Nucleic Acids Research, 2016

ChemProt-3.0: a global chemical biology diseases mapping.
Database, 2016

2015
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.
Nature, 2015

Session Introduction.
Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

Finding Cervical Cancer Symptoms in Swedish Clinical Text using a Machine Learning Approach and NegEx.
Proceedings of the AMIA 2015, 2015

2014
Addendum: Enterotypes of the human gut microbiome.
Nature, 2014

Compass: A hybrid method for clinical and biobank data mining.
J. Biomed. Informatics, 2014

Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics.
Briefings in Bioinformatics, 2014

Session Introduction.
Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014

Negation scope and spelling variation for text-mining of Danish electronic patient records.
Proceedings of the 5th International Workshop on Health Text Mining and Information Analysis, 2014

2013
MetaRanker 2.0: a web server for prioritization of genetic variation data.
Nucleic Acids Research, 2013

ChemProt-2.0: visual navigation in a disease chemical biology database.
Nucleic Acids Research, 2013

Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text.
JAMIA, 2013

Question Answering for Health Professionals and Laypersons.
Proceedings of the MEDINFO 2013, 2013

2011
Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts.
PLoS Computational Biology, 2011

ChemProt: a disease chemical biology database.
Nucleic Acids Research, 2011

Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response.
BMC Bioinformatics, 2011

The strength of intron donor splice sites in human genes displays a bell-shaped pattern.
Bioinformatics, 2011

2010
Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks.
PLoS Computational Biology, 2010

Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results.
Nucleic Acids Research, 2010

2009
ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization.
Briefings in Bioinformatics, 2009

2008
Cyclebase.org - a comprehensive multi-organism online database of cell-cycle experiments.
Nucleic Acids Research, 2008

2007
Modeling the adaptive immune system: predictions and simulations.
Bioinformatics, 2007

SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation.
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006
ISMB 2006.
PLoS Computational Biology, 2006

Prediction of pH-Dependent Aqueous Solubility of Druglike Molecules.
Journal of Chemical Information and Modeling, 2006

ISMB 2006.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005
Prediction of twin-arginine signal peptides.
BMC Bioinformatics, 2005

Comparison of computational methods for the identification of cell cycle-regulated genes.
Bioinformatics, 2005

Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates.
Bioinformatics, 2005

Immunological bioinformatics.
Computational molecular biology, AAAI Press, ISBN: 978-0-262-12280-1, 2005

2004
Coronavirus 3CLpro proteinase cleavage sites: Possible relevance to SARS virus pathology.
BMC Bioinformatics, 2004

Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach.
Bioinformatics, 2004

Representation of Protein-Sequence Information by Amino Acid Subalphabets.
AI Magazine, 2004

MHC Class I Epitope Binding Prediction Trained on Small Data Sets.
Proceedings of the Artificial Immune Systems, Third International Conference, 2004

2003
Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach.
Neural Computation, 2003

NESbase version 1.0: a database of nuclear export signals.
Nucleic Acids Research, 2003

Prediction of human protein function according to Gene Ontology categories.
Bioinformatics, 2003

Prediction of Protein Secondary Structure at High Accuracy Using a Combination of Many Neural Networks.
Proceedings of the Mathematical Methods for Protein Structure Analysis and Design, 2003

2002
Bias of Purine Stretches in Sequenced Chromosomes.
Computers & Chemistry, 2002

Neural network predicts sequence of TP53 gene based on DNA chip.
Bioinformatics, 2002

Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

2001
Recognition of Environmental and Genetic Effects on Barley Phenolic Fingerprints by Neural Networks.
Computers & Chemistry, 2001

Flexibility of the genetic code with respect to DNA structure.
Bioinformatics, 2001

Bidirectional Dynamics for Protein Secondary Structure Prediction.
Proceedings of the Sequence Learning - Paradigms, Algorithms, and Applications, 2001

Bioethics, Fiction Science, and the Future of Mankind - Session Introduction.
Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

ISMB 2001.
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

Bioinformatics - the machine learning approach (2. ed.).
MIT Press, ISBN: 978-0-262-02506-5, 2001

2000
Improving the Odds in Discriminating "Drug-like" from "Non Drug-like" Compounds.
Journal of Chemical Information and Computer Sciences, 2000

Assessing the accuracy of prediction algorithms for classification: an overview.
Bioinformatics, 2000

Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks.
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

Protein β-Sheet Partner Prediction by Neural Networks.
Proceedings of the Artificial Neural Networks in Medicine and Biology, 2000

Bioinformatics - the machine learning approach.
MIT Press, ISBN: 978-0-262-02442-6, 2000

1999
PhosphoBase, a database of phosphorylation sites: release 2.0.
Nucleic Acids Research, 1999

O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins.
Nucleic Acids Research, 1999

The Biology of Eukaryotic Promoter Prediction - A Review.
Computers & Chemistry, 1999

MatrixPlot: visualizing sequence constraints.
Bioinformatics, 1999

Exploiting the past and the future in protein secondary structure prediction.
Bioinformatics, 1999

Structural basis for triplet repeat disorders: a computational analysis.
Bioinformatics, 1999

Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints.
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, 1999

1998
O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins.
Nucleic Acids Research, 1998

PhosphoBase: a database of phosphorylation sites.
Nucleic Acids Research, 1998

Computational Applications of DNA Structural Scales.
Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology (ISMB-98), Montréal, Québec, Canada, June 28, 1998

1997
O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins.
Nucleic Acids Research, 1997

A Neural Network Method for Identification of Prokaryotic and Eukaryotic Signal Peptides and Prediction of their Cleavage Sites.
Int. J. Neural Syst., 1997

Displaying the information contents of structural RNA alignments: the structure logos.
Computer Applications in the Biosciences, 1997

1996
O-GLYCBASE: a revised database of O-glycosylated proteins.
Nucleic Acids Research, 1996

Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models.
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, 1996

1995
Periodic Sequence Patterns in Human Exons.
Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 1995

1993
Hidden Markov Models for Human Genes.
Proceedings of the Advances in Neural Information Processing Systems 6, 1993

1990
A Novel Approach to Prediction of the 3-Dimensional Structures.
Proceedings of the Advances in Neural Information Processing Systems 3, 1990

1989
A Travelling Salesman Approach to Protein Conformation.
Complex Systems, 1989


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