A Travelling Salesman Approach to Protein Conformation. - Henrik Bohr; Søren Brunak (Complex Syst., 1989)

A Novel Approach to Prediction of the 3-Dimensional Structures. - Henrik Fredholm; Henrik Bohr; Jakob Bohr; Søren Brunak; Rodney M. J. Cotterill; Benny Lautrup; Steffen B. Petersen (NIPS, 1990)

Hidden Markov Models for Human Genes. - Pierre Baldi; Søren Brunak; Yves Chauvin; Jacob Engelbrecht; Anders Krogh (NIPS, 1993)

Periodic Sequence Patterns in Human Exons. - Pierre Baldi; Søren Brunak; Yves Chauvin; Jacob Engelbrecht; Anders Krogh (ISMB, 1995)

Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models. - Anders Gorm Pedersen; Pierre Baldi; Søren Brunak; Yves Chauvin (ISMB, 1996)

O-GLYCBASE: a revised database of O-glycosylated proteins. - Jan E. Hansen; Ole Lund; Jens O. Nielsen; John-E. S. Hansen; Søren Brunak (Nucleic Acids Res., 1996)

Displaying the information contents of structural RNA alignments: the structure logos. - Jan Gorodkin; Laurie J. Heyer; Søren Brunak; Gary D. Stormo (Comput. Appl. Biosci., 1997)

A Neural Network Method for Identification of Prokaryotic and Eukaryotic Signal Peptides and Prediction of their Cleavage Sites. - Henrik Nielsen; Jacob Engelbrecht; Søren Brunak; Gunnar von Heijne (Int. J. Neural Syst., 1997)

O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins. - Jan E. Hansen; Ole Lund; Kristoffer Rapacki; Søren Brunak (Nucleic Acids Res., 1997)

Computational Applications of DNA Structural Scales. - Pierre Baldi; Søren Brunak; Yves Chauvin; Anders Gorm Pedersen (ISMB, 1998)

PhosphoBase: a database of phosphorylation sites. - Nikolaj Blom; Andres Kreegipuu; Søren Brunak (Nucleic Acids Res., 1998)

O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins. - Jan E. Hansen; Ole Lund; Jette Nilsson; Kristoffer Rapacki; Søren Brunak (Nucleic Acids Res., 1998)

Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints. - Jan Gorodkin; Ole Lund; Claus A. F. Andersen; Søren Brunak (ISMB, 1999)

Structural basis for triplet repeat disorders: a computational analysis. - Pierre Baldi; Søren Brunak; Yves Chauvin; Anders Gorm Pedersen (Bioinform., 1999)

Exploiting the past and the future in protein secondary structure prediction. - Pierre Baldi; Søren Brunak; Paolo Frasconi; Giovanni Soda; Gianluca Pollastri (Bioinform., 1999)

MatrixPlot: visualizing sequence constraints. - Jan Gorodkin; Hans Henrik Stærfeldt; Ole Lund; Søren Brunak (Bioinform., 1999)

The Biology of Eukaryotic Promoter Prediction - A Review. - Anders Gorm Pedersen; Pierre Baldi; Yves Chauvin; Søren Brunak (Comput. Chem., 1999)

O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins. - Ramneek Gupta; Hanne Birch; Kristoffer Rapacki; Søren Brunak; Jan E. Hansen (Nucleic Acids Res., 1999)

PhosphoBase, a database of phosphorylation sites: release 2.0. - Andres Kreegipuu; Nikolaj Blom; Søren Brunak (Nucleic Acids Res., 1999)

Bioinformatics - the machine learning approach. - Pierre Baldi; Søren Brunak (MIT Press, 2000)

Protein β-Sheet Partner Prediction by Neural Networks. - Pierre Baldi; Gianluca Pollastri; Claus A. F. Andersen; Søren Brunak (ANNIMAB, 2000)

Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks. - Pierre Baldi; Gianluca Pollastri; Claus A. F. Andersen; Søren Brunak (ISMB, 2000)

Assessing the accuracy of prediction algorithms for classification: an overview. - Pierre Baldi; Søren Brunak; Yves Chauvin; Claus A. F. Andersen; Henrik Nielsen (Bioinform., 2000)

Improving the Odds in Discriminating "Drug-like" from "Non Drug-like" Compounds. - Thomas M. Frimurer; Robert Bywater; Lars Nærum; Leif Nørskov Lauritsen; Søren Brunak (J. Chem. Inf. Comput. Sci., 2000)

Bioinformatics - the machine learning approach (2. ed.). - Pierre Baldi; Søren Brunak (MIT Press, 2001)

ISMB 2001. - Søren Brunak; Anders Krogh (ISMB (Supplement of Bioinformatics), 2001)

Bioethics, Fiction Science, and the Future of Mankind - Session Introduction. - Pierre Baldi; Søren Brunak (Pacific Symposium on Biocomputing, 2001)

Bidirectional Dynamics for Protein Secondary Structure Prediction. - Pierre Baldi; Søren Brunak; Paolo Frasconi; Gianluca Pollastri; Giovanni Soda (Sequence Learning, 2001)

Flexibility of the genetic code with respect to DNA structure. - Pierre-François Baisnée; Pierre Baldi; Søren Brunak; Anders Gorm Pedersen (Bioinform., 2001)

Recognition of Environmental and Genetic Effects on Barley Phenolic Fingerprints by Neural Networks. - Jan Gorodkin; Bodil Søgaard; Hanne Bay; Hans Doll; Per Kølster; Søren Brunak (Comput. Chem., 2001)

Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function. - Ramneek Gupta; Søren Brunak (Pacific Symposium on Biocomputing, 2002)

Neural network predicts sequence of TP53 gene based on DNA chip. - Jeppe S. Spicker; Friedrik Wikman; Ming-Lan Lu; Carlos Cordon-Cardo; Christopher T. Workman; Torben F. Ørntoft; Søren Brunak; Steen Knudsen (Bioinform., 2002)

Bias of Purine Stretches in Sequenced Chromosomes. - David Ussery; Dikeos Mario Soumpasis; Søren Brunak; Hans Henrik Stærfeldt; Peder Worning; Anders Krogh (Comput. Chem., 2002)

Prediction of Protein Secondary Structure at High Accuracy Using a Combination of Many Neural Networks. - Claus Lundegaard; Thomas Nordahl Petersen; Morten Nielsen 001; Henrik Bohr; Jakob Bohr; Søren Brunak; Garry Gippert; Ole Lund (Mathematical Methods for Protein Structure Analysis and Design, 2003)

Prediction of human protein function according to Gene Ontology categories. - Lars Juhl Jensen; Ramneek Gupta; Hans Henrik Stærfeldt; Søren Brunak (Bioinform., 2003)

NESbase version 1.0: a database of nuclear export signals. - Tanja la Cour; Ramneek Gupta; Kristoffer Rapacki; Karen Skriver; Flemming M. Poulsen; Søren Brunak (Nucleic Acids Res., 2003)

Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach. - Jens Kaae Christensen; Kasper Lamberth; Morten Nielsen 001; Claus Lundegaard; Peder Worning; Sanne Lise Lauemøller; Søren Buus; Søren Brunak; Ole Lund (Neural Comput., 2003)

MHC Class I Epitope Binding Prediction Trained on Small Data Sets. - Claus Lundegaard; Morten Nielsen 001; Kasper Lamberth; Peder Worning; Christina Sylvester-Hvid; Søren Buus; Søren Brunak; Ole Lund (ICARIS, 2004)

Representation of Protein-Sequence Information by Amino Acid Subalphabets. - Claus A. F. Andersen; Søren Brunak (AI Mag., 2004)

Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. - Morten Nielsen 001; Claus Lundegaard; Peder Worning; Christina Sylvester-Hvid; Kasper Lamberth; Søren Buus; Søren Brunak; Ole Lund (Bioinform., 2004)

Coronavirus 3CLpro proteinase cleavage sites: Possible relevance to SARS virus pathology. - Lars Kiemer; Ole Lund; Søren Brunak; Nikolaj Blom (BMC Bioinform., 2004)

Immunological bioinformatics. - Ole Lund; Morten Nielsen 001; Claus Lundegaard; Can Kesmir; Søren Brunak (AAAI Press, 2005)

Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates. - Svava Ósk Jónsdóttir; Flemming Steen Jørgensen; Søren Brunak (Bioinform., 2005)

Comparison of computational methods for the identification of cell cycle-regulated genes. - Ulrik de Lichtenberg; Lars Juhl Jensen; Anders Fausbøll; Thomas Skøt Jensen; Peer Bork; Søren Brunak (Bioinform., 2005)

Prediction of twin-arginine signal peptides. - Jannick Dyrløv Bendtsen; Henrik Nielsen; David Widdick; Tracy Palmer; Søren Brunak (BMC Bioinform., 2005)

ISMB 2006. - Philip E. Bourne; Søren Brunak (ISMB (Supplement of Bioinformatics), 2006)

Prediction of pH-Dependent Aqueous Solubility of Druglike Molecules. - Niclas Tue Hansen; Irene Kouskoumvekaki; Flemming Steen Jørgensen; Søren Brunak; Svava Ósk Jónsdóttir (J. Chem. Inf. Model., 2006)

ISMB 2006. - Goran Neshich; Philip E. Bourne; Søren Brunak (PLoS Comput. Biol., 2006)

SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. - Frank Panitz; Henrik Stengaard; Henrik Hornshøj; Jan Gorodkin; Jakob Hedegaard; Susanna Cirera; Bo Thomsen; Lone B. Madsen; Anette Høj; Rikke K. Vingborg; Bujie Zahn; Xuegang Wang; et al. (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Modeling the adaptive immune system: predictions and simulations. - Claus Lundegaard; Ole Lund; Can Kesmir; Søren Brunak; Morten Nielsen 001 (Bioinform., 2007)

Cyclebase.org - a comprehensive multi-organism online database of cell-cycle experiments. - Nicholas Paul Gauthier; Malene Erup Larsen; Rasmus Wernersson; Ulrik de Lichtenberg; Lars Juhl Jensen; Søren Brunak; Thomas Skøt Jensen (Nucleic Acids Res., 2008)

ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization. - Francesco Pappalardo 001; Mark D. Halling-Brown; Nicolas Rapin; Ping Zhang 008; Davide Alemani; Andrew P. J. Emerson; Paola Paci; Patrice Duroux; Marzio Pennisi; Arianna Palladini; Olivo Miotto; Daniel Churchill; et al. (Briefings Bioinform., 2009)

Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. - Nicholas Paul Gauthier; Lars Juhl Jensen; Rasmus Wernersson; Søren Brunak; Thomas Skøt Jensen (Nucleic Acids Res., 2010)

Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks. - Karine Audouze; Agnieszka Sierakowska Juncker; Francisco S. Roque; Konrad Krysiak-Baltyn; Nils Weinhold; Olivier Taboureau; Thomas Skøt Jensen; Søren Brunak (PLoS Comput. Biol., 2010)

The strength of intron donor splice sites in human genes displays a bell-shaped pattern. - Kai Wang; Rasmus Wernersson; Søren Brunak (Bioinform., 2011)

Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response. - Qiyuan Li; Aron C. Eklund; Nicolai J. Birkbak; Christine Desmedt; Benjamin Haibe-Kains; Christos P. Sotiriou; W. Fraser Symmans; Lajos Pusztai; Søren Brunak; Andrea L. Richardson; Zoltan Szallasi (BMC Bioinform., 2011)

ChemProt: a disease chemical biology database. - Olivier Taboureau; Sonny Kim Nielsen; Karine Audouze; Nils Weinhold; Daniel Edsgärd; Francisco S. Roque; Irene Kouskoumvekaki; Alina Bora; Ramona Curpan; Thomas Skøt Jensen; Søren Brunak; Tudor I. Oprea (Nucleic Acids Res., 2011)

Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts. - Francisco S. Roque; Peter Bjødstrup Jensen; Henriette Schmock; Marlene Dalgaard; Massimo Andreatta; Thomas Folkmann Hansen; Karen Søeby; Søren Bredkjær; Anders Juul; Thomas Werge; Lars Juhl Jensen; Søren Brunak (PLoS Comput. Biol., 2011)

Question Answering for Health Professionals and Laypersons. - Bente Maegaard; Udo Hahn; Søren Brunak; Stefan Schulz 001; Ulrich Andersen; Sebastian Welter (MedInfo, 2013)

Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text. - Robert Eriksson; Peter Bjødstrup Jensen; Sune Frankild; Lars Juhl Jensen; Søren Brunak (J. Am. Medical Informatics Assoc., 2013)

ChemProt-2.0: visual navigation in a disease chemical biology database. - Sonny Kim Kjærulff; Louis Wich; Jens Kringelum; Ulrik Plesner Jacobsen; Irene Kouskoumvekaki; Karine Audouze; Ole Lund; Søren Brunak; Tudor I. Oprea; Olivier Taboureau (Nucleic Acids Res., 2013)

MetaRanker 2.0: a web server for prioritization of genetic variation data. - Tune H. Pers; Piotr Dworzynski; Cecilia Engel Thomas; Kasper Lage; Søren Brunak (Nucleic Acids Res., 2013)

Negation scope and spelling variation for text-mining of Danish electronic patient records. - Cecilia Engel Thomas; Peter Bjødstrup Jensen; Thomas Werge; Søren Brunak (Louhi@EACL, 2014)

Session Introduction. - Søren Brunak; Francisco M. de la Vega; Gunnar Rätsch; Joshua M. Stuart (Pacific Symposium on Biocomputing, 2014)

Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics. - Irene Kouskoumvekaki; Nour Shublaq; Søren Brunak (Briefings Bioinform., 2014)

Compass: A hybrid method for clinical and biobank data mining. - Konrad Krysiak-Baltyn; Thomas Nordahl Petersen; Karine Audouze; Niels Jørgensen; Lars Ängquist; Søren Brunak (J. Biomed. Informatics, 2014)

Addendum: Enterotypes of the human gut microbiome. - Manimozhiyan Arumugam; Jeroen Raes; Eric Pelletier; Denis Le Paslier; Takuji Yamada; Daniel R. Mende; Gabriel R. Fernandes; Julien Tap; Thomas Brüls; Jean-Michel Batto; Marcelo Bertalan; Natalia Borruel; et al. (Nat., 2014)

Finding Cervical Cancer Symptoms in Swedish Clinical Text using a Machine Learning Approach and NegEx. - Rebecka Weegar; Maria Kvist; Karin Sundström; Søren Brunak; Hercules Dalianis (AMIA, 2015)

Session Introduction. - Søren Brunak; Francisco M. de la Vega; Adam A. Margolin; Benjamin J. Raphael; Gunnar Rätsch; Joshua M. Stuart (Pacific Symposium on Biocomputing, 2015)

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. - Kristoffer Forslund; Falk Hildebrand; Trine Nielsen; Gwen Falony; Emmanuelle Le Chatelier; Shinichi Sunagawa; Edi Prifti; Sara Vieira-Silva; Valborg Gudmundsdottir; Helle Krogh Pedersen; Manimozhiyan Arumugam; Karsten Kristiansen; et al. (Nat., 2015)

ChemProt-3.0: a global chemical biology diseases mapping. - Jens Kringelum; Sonny Kim Kjærulff; Søren Brunak; Ole Lund; Tudor I. Oprea; Olivier Taboureau (Database J. Biol. Databases Curation, 2016)

Tools and data services registry: a community effort to document bioinformatics resources. - Jon C. Ison; Kristoffer Rapacki; Hervé Ménager; Matús Kalas; Emil Rydza; Piotr Chmura; Christian Anthon; Niall Beard; Karel Berka; Dan M. Bolser; Tim Booth; Anthony Bretaudeau; et al. (Nucleic Acids Res., 2016)

A genomic history of Aboriginal Australia. - Anna-Sapfo Malaspinas; Michael C. Westaway; Craig Muller; Vitor C. Sousa; Oscar Lao; Isabel Alves; Anders Bergström; Georgios Athanasiadis; Jade Yu Cheng; Jacob E. Crawford; Tim H. Heupink; Enrico Macholdt; et al. (Nat., 2016)

Temporal Order of Disease Pairs Affects Subsequent Disease Trajectories: The Case of Diabetes and Sleep Apnea. - Mette Beck; David Westergaard; Leif Groop; Søren Brunak (PSB, 2017)

Pharos: Collating protein information to shed light on the druggable genome. - Dac-Trung Nguyen; Stephen L. Mathias; Cristian Bologa; Søren Brunak; Nicolas F. Fernandez; Anna Gaulton; Anne Hersey; Jayme Holmes; Lars Juhl Jensen; Anneli Karlsson; Guixia Liu; Avi Ma'ayan; et al. (Nucleic Acids Res., 2017)

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. - Lasse Maretty; Jacob Malte Jensen; Bent Petersen; Jonas Andreas Sibbesen; Siyang Liu 007; Palle Villesen; Laurits Skov; Kirstine Belling; Christian Theil Have; José M. G. Izarzugaza; Marie Grosjean; Jette Bork-Jensen; et al. (Nat., 2017)

Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios. - Maria Luisa Matey-Hernandez; Lasse Maretty; Jacob Malte Jensen; Bent Petersen; Jonas Andreas Sibbesen; Siyang Liu 007; Palle Villesen; Laurits Skov; Kirstine Belling; Christian Theil Have; José M. G. Izarzugaza; Marie Grosjean; et al. (BMC Bioinform., 2018)

miRandola 2017: a curated knowledge base of non-invasive biomarkers. - Francesco Russo 004; Sebastiano Di Bella; Federica Vannini; Gabriele Berti; Flavia Scoyni; Helen Cook; Alberto Santos; Giovanni Nigita; Vincenzo Bonnici; Alessandro Laganà; Filippo Geraci; Alfredo Pulvirenti; et al. (Nucleic Acids Res., 2018)

A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts. - David Westergaard; Hans Henrik Stærfeldt; Christian Tønsberg; Lars Juhl Jensen; Søren Brunak (PLoS Comput. Biol., 2018)

sAOP: linking chemical stressors to adverse outcomes pathway networks. - Alejandro Aguayo-Orozco; Karine Audouze; Troels Siggaard; Robert Barouki; Søren Brunak; Olivier Taboureau (Bioinform., 2019)

A generic deep convolutional neural network framework for prediction of receptor-ligand interactions - NetPhosPan: application to kinase phosphorylation prediction. - Emilio Fenoy; José M. G. Izarzugaza; Vanessa Isabell Jurtz; Søren Brunak; Morten Nielsen 001 (Bioinform., 2019)

Incorporating symptom data in longitudinal disease trajectories for more detailed patient stratification. - Martin Lademann; Mette Lademann; Anders Boeck Jensen; Søren Brunak (Int. J. Medical Informatics, 2019)

Using National Electronic Health Care Registries to Analyse and Predict Alcoholic Liver Disease. - Dhouha Grissa; Ditlev Nytoft Rasmussen; Aleksander Krag; Søren Brunak; Lars Juhl Jensen (EGC, 2020)

Towards standardization guidelines for in silico approaches in personalized medicine. - Søren Brunak; Catherine Bjerre Collin; Katharina Eva Ó Cathaoir; Martin Golebiewski; Marc Kirschner; Ingrid Kockum; Heike Moser; Dagmar Waltemath (J. Integr. Bioinform., 2020)

Implementation and comparison of two text mining methods with a standard pharmacovigilance method for signal detection of medication errors. - Nadine Kadi Eskildsen; Robert Eriksson; Sten B. Christensen; Tamilla Stine Aghassipour; Mikael Juul Bygsø; Søren Brunak; Suzanne Lisbet Hansen (BMC Medical Informatics Decis. Mak., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

Alcoholic liver disease: A registry view on comorbidities and disease prediction. - Dhouha Grissa; Ditlev Nytoft Rasmussen; Aleksander Krag; Søren Brunak; Lars Juhl Jensen (PLoS Comput. Biol., 2020)

Optimizing drug selection from a prescription trajectory of one patient. - Alejandro Aguayo-Orozco; Amalie Dahl Haue; Isabella Friis Jørgensen; David Westergaard; Pope L. Moseley; Laust Hvas Mortensen; Søren Brunak (npj Digit. Medicine, 2021)

Time-ordered comorbidity correlations identify patients at risk of mis- and overdiagnosis. - Isabella Friis Jørgensen; Søren Brunak (npj Digit. Medicine, 2021)

Reply to: Immortal time bias in the analysis of drug prescription trajectories. - Laust Hvas Mortensen; Søren Brunak (npj Digit. Medicine, 2022)

Discrete-time survival analysis in the critically ill: a deep learning approach using heterogeneous data. - Hans-Christian Thorsen-Meyer; Davide Placido; Benjamin Skov Kaas-Hansen; Anna P. Nielsen; Theis Lange; Annelaura B. Nielsen; Palle Toft; Jens Schierbeck; Thomas Strøm; Piotr Chmura; Marc Heimann; Kirstine Belling; et al. (npj Digit. Medicine, 2022)

BALDR: A Web-based platform for informed comparison and prioritization of biomarker candidates for type 2 diabetes mellitus. - Agnete T. Lundgaard; Frédéric Burdet; Troels Siggaard; David Westergaard; Danai Vagiaki; Lisa Cantwell; Timo Röder; Dorte Vistisen; Thomas Sparsø; Giuseppe N. Giordano; Mark Ibberson; Karina Banasik; et al. (PLoS Comput. Biol., 2023)

Visualising disease trajectories from population-wide data. - Jessica Xin Hjaltelin; Hannah Currant; Isabella Friis Jørgensen; Søren Brunak (Frontiers Bioinform., 2023)

Population-wide analysis of hospital laboratory tests to assess seasonal variation and temporal reference interval modification. - Victorine P. Muse; Alejandro Aguayo-Orozco; Sedrah B. Balaganeshan; Søren Brunak (Patterns, 2023)

Implementing a Nordic-Baltic Federated Health Data Network: a case report. - Taridzo Chomutare; Aleksandar Babic; Laura-Maria Peltonen; Silja Elunurm; Peter Lundberg; Arne Jönsson; Emma Eneling; Ciprian-Virgil Gerstenberger; Troels Siggaard; Raivo Kolde; Oskar Jerdhaf; Martin Hansson; et al. (CoRR, 2024)

Seasonally adjusted laboratory reference intervals to improve the performance of machine learning models for classification of cardiovascular diseases. - Victorine P. Muse; Davide Placido; Amalie Dahl Haue; Søren Brunak (BMC Medical Informatics Decis. Mak., 2024)

LSD600: the first corpus of biomedical abstracts annotated with lifestyle-disease relations. - Esmaeil Nourani; Evangelia-Mantelena Makri; Xiqing Mao; Sampo Pyysalo; Søren Brunak; Katerina C. Nastou; Lars Juhl Jensen (Database J. Biol. Databases Curation, 2025)