Søren Brunak

Sonny Kim Kjærulff, Louis Wich, Jens Kringelum, Ulrik Plesner Jacobsen, Irene Kouskoumvekaki, Karine Audouze, Ole Lund, Søren Brunak, Tudor I. Oprea, Olivier Taboureau: ChemProt-2.0: visual navigation in a disease chemical biology database. Nucleic Acids Research 41(Database-Issue): 464-469 (2013)

Kai Wang, Rasmus Wernersson, Søren Brunak: The strength of intron donor splice sites in human genes displays a bell-shaped pattern. Bioinformatics 27(22): 3079-3084 (2011)

Qiyuan Li, Aron C. Eklund, Nicolai J. Birkbak, Christine Desmedt, Benjamin Haibe-Kains, Christos Sotiriou, W. Fraser Symmans, Lajos Pusztai, Søren Brunak, Andrea L. Richardson, Zoltan Szallasi: Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response. BMC Bioinformatics 12: 310 (2011)

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: ChemProt: a disease chemical biology database. Nucleic Acids Research 39(Database-Issue): 367-372 (2011)

Francisco S. Roque, Peter B. Jensen, Henriette Schmock, Marlene Dalgaard, Massimo Andreatta, Thomas Hansen, Karen Søeby, Søren Bredkjær, Anders Juul, Thomas Werge, Lars Juhl Jensen, Søren Brunak: Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts. PLoS Computational Biology 7(8) (2011)

Nicholas Paul Gauthier, Lars Juhl Jensen, Rasmus Wernersson, Søren Brunak, Thomas Skøt Jensen: Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. Nucleic Acids Research 38(Database-Issue): 699-702 (2010)

Karine Audouze, Agnieszka Sierakowska Juncker, Francisco S. Roque, Konrad Krysiak-Baltyn, Nils Weinhold, Olivier Taboureau, Thomas Skøt Jensen, Søren Brunak: Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks. PLoS Computational Biology 6(5) (2010)

Francesco Pappalardo, Mark D. Halling-Brown, Nicolas Rapin, Ping Zhang, Davide Alemani, Andrew Emerson, Paola Paci, Patrice Duroux, Marzio Pennisi, Arianna Palladini, Olivo Miotto, Daniel Churchill, Elda Rossi, Adrian J. Shepherd, David S. Moss, Filippo Castiglione, Massimo Bernaschi, Marie-Paule Lefranc, Søren Brunak, Santo Motta, Pierluigi Lollini, Kaye E. Basford, Vladimir Brusic: ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization. Briefings in Bioinformatics 10(3): 330-340 (2009)

Nicholas Paul Gauthier, Malene Erup Larsen, Rasmus Wernersson, Ulrik de Lichtenberg, Lars Juhl Jensen, Søren Brunak, Thomas Skøt Jensen: Cyclebase.org - a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Research 36(Database-Issue): 854-859 (2008)

Claus Lundegaard, Ole Lund, Can Kesmir, Søren Brunak, Morten Nielsen: Modeling the adaptive immune system: predictions and simulations. Bioinformatics 23(24): 3265-3275 (2007)

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, Xuefei Wang, Rasmus Wernersson, Claus B. Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J. Nielsen, Jakob Hull Havgaard, Søren Brunak, Merete Fredholm, Christian Bendixen: SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. ISMB/ECCB (Supplement of Bioinformatics) 2007: 387-391

Goran Neshich, Philip E. Bourne, Søren Brunak: ISMB 2006. PLoS Computational Biology 2(2) (2006)

Philip E. Bourne, Søren Brunak: ISMB 2006. ISMB (Supplement of Bioinformatics) 2006: 1-2

Ulrik de Lichtenberg, Lars Juhl Jensen, Anders Fausbøll, Thomas Skøt Jensen, Peer Bork, Søren Brunak: Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics 21(7): 1164-1171 (2005)

Svava Ósk Jónsdóttir, Flemming Steen Jørgensen, Søren Brunak: Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates. Bioinformatics 21(10): 2145-2160 (2005)

Jannick Dyrløv Bendtsen, Henrik Nielsen, David Widdick, Tracy Palmer, Søren Brunak: Prediction of twin-arginine signal peptides. BMC Bioinformatics 6: 167 (2005)

Claus A. F. Andersen, Søren Brunak: Representation of Protein-Sequence Information by Amino Acid Subalphabets. AI Magazine 25(1): 97-104 (2004)

Morten Nielsen, Claus Lundegaard, Peder Worning, Christina Sylvester-Hvid, Kasper Lamberth, Søren Buus, Søren Brunak, Ole Lund: Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics 20(9): 1388-1397 (2004)

Lars Kiemer, Ole Lund, Søren Brunak, Nikolaj Blom: Coronavirus 3CL^pro proteinase cleavage sites: Possible relevance to SARS virus pathology. BMC Bioinformatics 5: 72 (2004)

Claus Lundegaard, Morten Nielsen, Kasper Lamberth, Peder Worning, Christina Sylvester-Hvid, Søren Buus, Søren Brunak, Ole Lund: MHC Class I Epitope Binding Prediction Trained on Small Data Sets. ICARIS 2004: 217-225

Lars Juhl Jensen, Ramneek Gupta, Hans Henrik Stærfeldt, Søren Brunak: Prediction of human protein function according to Gene Ontology categories. Bioinformatics 19(5): 635-642 (2003)

Tanja la Cour, Ramneek Gupta, Kristoffer Rapacki, Karen Skriver, Flemming M. Poulsen, Søren Brunak: NESbase version 1.0: a database of nuclear export signals. Nucleic Acids Research 31(1): 393-396 (2003)

Jens Kaae Christensen, Kasper Lamberth, Morten Nielsen, Claus Lundegaard, Peder Worning, Sanne Lise Lauemøller, Søren Buus, Søren Brunak, Ole Lund: Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach. Neural Computation 15(12): 2931-2942 (2003)

Claus Lundegaard, Thomas Nordahl Petersen, Morten Nielsen, Henrik Bohr, Jakob Bohr, Søren Brunak, Garry Gippert, Ole Lund: Prediction of Protein Secondary Structure at High Accuracy Using a Combination of Many Neural Networks. Mathematical Methods for Protein Structure Analysis and Design 2003: 117-122

Jeppe S. Spicker, Friedrik Wikman, Ming-Lan Lu, Carlos Cordon-Cardo, Christopher T. Workman, Torben F. Ørntoft, Søren Brunak, Steen Knudsen: Neural network predicts sequence of TP53 gene based on DNA chip. Bioinformatics 18(8): 1133-1134 (2002)

David Ussery, Dikeos Mario Soumpasis, Søren Brunak, Hans Henrik Stærfeldt, Peder Worning, Anders Krogh: Bias of Purine Stretches in Sequenced Chromosomes. Computers & Chemistry 26(5): 531-541 (2002)

Ramneek Gupta, Søren Brunak: Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function. Pacific Symposium on Biocomputing 2002: 310-322

Pierre Baldi, Søren Brunak: Bioinformatics - the machine learning approach (2. ed.). MIT Press 2001, isbn 978-0-262-02506-5, pp. I-XXI, 1-452

Pierre-François Baisnée, Pierre Baldi, Søren Brunak, Anders Gorm Pedersen: Flexibility of the genetic code with respect to DNA structure. Bioinformatics 17(3): 237-248 (2001)

Jan Gorodkin, Bodil Søgaard, Hanne Bay, Hans Doll, Per Kølster, Søren Brunak: Recognition of Environmental and Genetic Effects on Barley Phenolic Fingerprints by Neural Networks. Computers & Chemistry 25(3): 301-307 (2001)

Søren Brunak, Anders Krogh: ISMB 2001. ISMB (Supplement of Bioinformatics) 2001: 1-4

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

Pierre Baldi, Søren Brunak, Paolo Frasconi, Gianluca Pollastri, Giovanni Soda: Bidirectional Dynamics for Protein Secondary Structure Prediction. Sequence Learning 2001: 80-104

Pierre Baldi, Søren Brunak: Bioinformatics - the machine learning approach. MIT Press 2000, isbn 978-0-262-02442-6, pp. 1-44

Pierre Baldi, Søren Brunak, Yves Chauvin, Claus A. F. Andersen, Henrik Nielsen: Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16(5): 412-424 (2000)

Thomas M. Frimurer, Robert Bywater, Lars Nærum, Leif Nørskov Lauritsen, Søren Brunak: Improving the Odds in Discriminating "Drug-like" from "Non Drug-like" Compounds. Journal of Chemical Information and Computer Sciences 40(6): 1315-1324 (2000)

Pierre Baldi, Gianluca Pollastri, Claus A. F. Andersen, Søren Brunak: Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks. ISMB 2000: 25-36

Jan Gorodkin, Hans Henrik Stærfeldt, Ole Lund, Søren Brunak: MatrixPlot: visualizing sequence constraints. Bioinformatics 15(9): 769-770 (1999)

Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen: Structural basis for triplet repeat disorders: a computational analysis. Bioinformatics 15(11): 918-929 (1999)

Pierre Baldi, Søren Brunak, Paolo Frasconi, Giovanni Soda, Gianluca Pollastri: Exploiting the past and the future in protein secondary structure prediction. Bioinformatics 15(11): 937-946 (1999)

Anders Gorm Pedersen, Pierre Baldi, Yves Chauvin, Søren Brunak: The Biology of Eukaryotic Promoter Prediction - A Review. Computers & Chemistry 23(3-4): 191-207 (1999)

Andres Kreegipuu, Nikolaj Blom, Søren Brunak: PhosphoBase, a database of phosphorylation sites: release 2.0. Nucleic Acids Research 27(1): 237-239 (1999)

Ramneek Gupta, Hanne Birch, Kristoffer Rapacki, Søren Brunak, Jan E. Hansen: O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins. Nucleic Acids Research 27(1): 370-372 (1999)

Jan Gorodkin, Ole Lund, Claus A. F. Andersen, Søren Brunak: Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints. ISMB 1999: 95-105

Nikolaj Blom, Andres Kreegipuu, Søren Brunak: PhosphoBase: a database of phosphorylation sites. Nucleic Acids Research 26(1): 382-386 (1998)

Jan E. Hansen, Ole Lund, Jette Nilsson, Kristoffer Rapacki, Søren Brunak: O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins. Nucleic Acids Research 26(1): 387-389 (1998)

Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen: Computational Applications of DNA Structural Scales. ISMB 1998: 35-42

Jan Gorodkin, Laurie J. Heyer, Søren Brunak, Gary D. Stormo: Displaying the information contents of structural RNA alignments: the structure logos. Computer Applications in the Biosciences 13(6): 583-586 (1997)

Henrik Nielsen, Jacob Engelbrecht, Søren Brunak, Gunnar von Heijne: A Neural Network Method for Identification of Prokaryotic and Eukaryotic Signal Peptides and Prediction of their Cleavage Sites. Int. J. Neural Syst. 8(5-6): 581-599 (1997)

Jan E. Hansen, Ole Lund, Kristoffer Rapacki, Søren Brunak: O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins. Nucleic Acids Research 25(1): 278-282 (1997)

Jan E. Hansen, Ole Lund, Jens O. Nielsen, John-E. S. Hansen, Søren Brunak: O-GLYCBASE: a revised database of O-glycosylated proteins. Nucleic Acids Research 24(1): 248-252 (1996)

Anders Gorm Pedersen, Pierre Baldi, Søren Brunak, Yves Chauvin: Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models. ISMB 1996: 182-191

Pierre Baldi, Søren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh: Periodic Sequence Patterns in Human Exons. ISMB 1995: 30-38

Pierre Baldi, Søren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh: Hidden Markov Models for Human Genes. NIPS 1993: 761-768

Henrik Fredholm, Henrik Bohr, Jakob Bohr, Søren Brunak, Rodney M. J. Cotterill, Benny Lautrup, Steffen B. Petersen: A Novel Approach to Prediction of the 3-Dimensional Structures. NIPS 1990: 523-529