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Søren Brunak
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2020 – today
- 2024
- [j69]Victorine P. Muse
, Davide Placido, Amalie Dahl Haue
Seasonally adjusted laboratory reference intervals to improve the performance of machine learning models for classification of cardiovascular diseases. BMC Medical Informatics Decis. Mak. 24(1): 62 (2024) - 2023
- [j68]Jessica Xin Hjaltelin, Hannah Currant
Visualising disease trajectories from population-wide data. Frontiers Bioinform. 3 (2023) - [j67]Victorine P. Muse
Population-wide analysis of hospital laboratory tests to assess seasonal variation and temporal reference interval modification. Patterns 4(8): 100778 (2023) - [j66]Agnete T. Lundgaard
BALDR: A Web-based platform for informed comparison and prioritization of biomarker candidates for type 2 diabetes mellitus. PLoS Comput. Biol. 19(8) (2023) - 2022
- [j65]Laust Hvas Mortensen
Reply to: Immortal time bias in the analysis of drug prescription trajectories. npj Digit. Medicine 5 (2022) - [j64]Hans-Christian Thorsen-Meyer, Davide Placido
Discrete-time survival analysis in the critically ill: a deep learning approach using heterogeneous data. npj Digit. Medicine 5 (2022) - 2021
- [j63]Alejandro Aguayo-Orozco
Optimizing drug selection from a prescription trajectory of one patient. npj Digit. Medicine 4 (2021) - [j62]Isabella Friis Jørgensen
Time-ordered comorbidity correlations identify patients at risk of mis- and overdiagnosis. npj Digit. Medicine 4 (2021) - 2020
- [j61]Søren Brunak, Catherine Bjerre Collin, Katharina Eva Ó Cathaoir
Towards standardization guidelines for in silico approaches in personalized medicine. J. Integr. Bioinform. 17(2-3) (2020) - [j60]Nadine Kadi Eskildsen, Robert Eriksson
Implementation and comparison of two text mining methods with a standard pharmacovigilance method for signal detection of medication errors. BMC Medical Informatics Decis. Mak. 20(1): 94 (2020) - [j59]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, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020) - [j58]Dhouha Grissa
Alcoholic liver disease: A registry view on comorbidities and disease prediction. PLoS Comput. Biol. 16(9) (2020) - [c23]Dhouha Grissa
Using National Electronic Health Care Registries to Analyse and Predict Alcoholic Liver Disease. EGC 2020: 389-390
2010 – 2019
- 2019
- [j57]Emilio Fenoy
A generic deep convolutional neural network framework for prediction of receptor-ligand interactions - NetPhosPan: application to kinase phosphorylation prediction. Bioinform. 35(7): 1098-1107 (2019) - [j56]Alejandro Aguayo-Orozco
sAOP: linking chemical stressors to adverse outcomes pathway networks. Bioinform. 35(24): 5391-5392 (2019) - [j55]Martin Lademann, Mette Lademann
Incorporating symptom data in longitudinal disease trajectories for more detailed patient stratification. Int. J. Medical Informatics 129: 107-113 (2019) - 2018
- [j54]Maria Luisa Matey-Hernandez
Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios. BMC Bioinform. 19(1): 239:1-239:12 (2018) - [j53]Francesco Russo
miRandola 2017: a curated knowledge base of non-invasive biomarkers. Nucleic Acids Res. 46(Database-Issue): D354-D359 (2018) - [j52]David Westergaard
A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts. PLoS Comput. Biol. 14(2) (2018) - 2017
- [j51]Dac-Trung Nguyen
Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Res. 45(Database-Issue): D995-D1002 (2017) - [j50]Lasse Maretty
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nat. 548(7665): 87-91 (2017) - [c22]Mette Beck, David Westergaard, Leif Groop, Søren Brunak:
Temporal Order of Disease Pairs Affects Subsequent Disease Trajectories: The Case of Diabetes and Sleep Apnea. PSB 2017: 380-389 - 2016
- [j49]Jens Kringelum, Sonny Kim Kjærulff, Søren Brunak
ChemProt-3.0: a global chemical biology diseases mapping. Database J. Biol. Databases Curation 2016 (2016) - [j48]Jon C. Ison
Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 44(Database-Issue): 38-47 (2016) - [j47]Anna-Sapfo Malaspinas
A genomic history of Aboriginal Australia. Nat. 538(7624): 207-214 (2016) - 2015
- [j46]Kristoffer Forslund
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nat. 528(7582): 262-266 (2015) - [c21]Rebecka Weegar, Maria Kvist, Karin Sundström, Søren Brunak, Hercules Dalianis:
Finding Cervical Cancer Symptoms in Swedish Clinical Text using a Machine Learning Approach and NegEx. AMIA 2015 - [c20]Søren Brunak, Francisco M. de la Vega, Adam A. Margolin, Benjamin J. Raphael, Gunnar Rätsch, Joshua M. Stuart:
Session Introduction. Pacific Symposium on Biocomputing 2015: 8-9 - 2014
- [j45]Irene Kouskoumvekaki
Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics. Briefings Bioinform. 15(6): 942-952 (2014) - [j44]Konrad Krysiak-Baltyn, Thomas Nordahl Petersen
Compass: A hybrid method for clinical and biobank data mining. J. Biomed. Informatics 47: 160-170 (2014) - [j43]Manimozhiyan Arumugam, Jeroen Raes
Addendum: Enterotypes of the human gut microbiome. Nat. 506(7489): 516 (2014) - [c19]Cecilia Engel Thomas
Negation scope and spelling variation for text-mining of Danish electronic patient records. Louhi@EACL 2014: 64-68 - [c18]Søren Brunak, Francisco M. de la Vega, Gunnar Rätsch, Joshua M. Stuart:
Session Introduction. Pacific Symposium on Biocomputing 2014: 1-2 - 2013
- [j42]Robert Eriksson, Peter Bjødstrup Jensen
Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text. J. Am. Medical Informatics Assoc. 20(5): 947-953 (2013) - [j41]Sonny Kim Kjærulff, Louis Wich, Jens Kringelum, Ulrik Plesner Jacobsen, Irene Kouskoumvekaki
ChemProt-2.0: visual navigation in a disease chemical biology database. Nucleic Acids Res. 41(Database-Issue): 464-469 (2013) - [j40]Tune H. Pers
MetaRanker 2.0: a web server for prioritization of genetic variation data. Nucleic Acids Res. 41(Webserver-Issue): 104-108 (2013) - [c17]Bente Maegaard, Udo Hahn, Søren Brunak, Stefan Schulz, Ulrich Andersen, Sebastian Welter:
Question Answering for Health Professionals and Laypersons. MedInfo 2013: 1244 - 2011
- [j39]Kai Wang, Rasmus Wernersson
The strength of intron donor splice sites in human genes displays a bell-shaped pattern. Bioinform. 27(22): 3079-3084 (2011) - [j38]Qiyuan Li, Aron C. Eklund
Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response. BMC Bioinform. 12: 310 (2011) - [j37]Olivier Taboureau
ChemProt: a disease chemical biology database. Nucleic Acids Res. 39(Database-Issue): 367-372 (2011) - [j36]Francisco S. Roque, Peter Bjødstrup Jensen
Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts. PLoS Comput. Biol. 7(8) (2011) - 2010
- [j35]Nicholas Paul Gauthier, Lars Juhl Jensen
Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. Nucleic Acids Res. 38(Database-Issue): 699-702 (2010) - [j34]Karine Audouze
Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks. PLoS Comput. Biol. 6(5) (2010)
2000 – 2009
- 2009
- [j33]Francesco Pappalardo
ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization. Briefings Bioinform. 10(3): 330-340 (2009) - 2008
- [j32]Nicholas Paul Gauthier, Malene Erup Larsen, Rasmus Wernersson
Cyclebase.org - a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Res. 36(Database-Issue): 854-859 (2008) - 2007
- [j31]Claus Lundegaard, Ole Lund
Modeling the adaptive immune system: predictions and simulations. Bioinform. 23(24): 3265-3275 (2007) - [c16]Frank Panitz
SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. ISMB/ECCB (Supplement of Bioinformatics) 2007: 387-391 - 2006
- [j30]Niclas Tue Hansen, Irene Kouskoumvekaki
Prediction of pH-Dependent Aqueous Solubility of Druglike Molecules. J. Chem. Inf. Model. 46(6): 2601-2609 (2006) - [j29]Goran Neshich, Philip E. Bourne, Søren Brunak:
ISMB 2006. PLoS Comput. Biol. 2(2) (2006) - [c15]Philip E. Bourne, Søren Brunak
ISMB 2006. ISMB (Supplement of Bioinformatics) 2006: 1-2 - 2005
- [b3]Ole Lund, Morten Nielsen, Claus Lundegaard, Can Kesmir, Søren Brunak:
Immunological bioinformatics. Computational molecular biology, AAAI Press 2005, ISBN 978-0-262-12280-1, pp. I-XII, 1-296 - [j28]Ulrik de Lichtenberg
Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinform. 21(7): 1164-1171 (2005) - [j27]Svava Ósk Jónsdóttir, Flemming Steen Jørgensen
Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates. Bioinform. 21(10): 2145-2160 (2005) - [j26]Jannick Dyrløv Bendtsen, Henrik Nielsen
Prediction of twin-arginine signal peptides. BMC Bioinform. 6: 167 (2005) - 2004
- [j25]Claus A. F. Andersen, Søren Brunak:
Representation of Protein-Sequence Information by Amino Acid Subalphabets. AI Mag. 25(1): 97-104 (2004) - [j24]Morten Nielsen
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinform. 20(9): 1388-1397 (2004) - [j23]Lars Kiemer, Ole Lund
Coronavirus 3CLpro proteinase cleavage sites: Possible relevance to SARS virus pathology. BMC Bioinform. 5: 72 (2004) - [c14]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 - 2003
- [j22]Lars Juhl Jensen
Prediction of human protein function according to Gene Ontology categories. Bioinform. 19(5): 635-642 (2003) - [j21]Tanja la Cour, Ramneek Gupta
NESbase version 1.0: a database of nuclear export signals. Nucleic Acids Res. 31(1): 393-396 (2003) - [j20]Jens Kaae Christensen, Kasper Lamberth, Morten Nielsen
Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach. Neural Comput. 15(12): 2931-2942 (2003) - [c13]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 - 2002
- [j19]Jeppe S. Spicker, Friedrik Wikman, Ming-Lan Lu, Carlos Cordon-Cardo, Christopher T. Workman
Neural network predicts sequence of TP53 gene based on DNA chip. Bioinform. 18(8): 1133-1134 (2002) - [j18]David Ussery
Bias of Purine Stretches in Sequenced Chromosomes. Comput. Chem. 26(5): 531-541 (2002) - [c12]Ramneek Gupta, Søren Brunak:
Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function. Pacific Symposium on Biocomputing 2002: 310-322 - 2001
- [b2]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 - [j17]Pierre-François Baisnée, Pierre Baldi, Søren Brunak, Anders Gorm Pedersen
Flexibility of the genetic code with respect to DNA structure. Bioinform. 17(3): 237-248 (2001) - [j16]Jan Gorodkin
Recognition of Environmental and Genetic Effects on Barley Phenolic Fingerprints by Neural Networks. Comput. Chem. 25(3): 301-307 (2001) - [c11]Søren Brunak, Anders Krogh:
ISMB 2001. ISMB (Supplement of Bioinformatics) 2001: 1-4 - [c10]Pierre Baldi, Søren Brunak:
Bioethics, Fiction Science, and the Future of Mankind - Session Introduction. Pacific Symposium on Biocomputing 2001 - [c9]Pierre Baldi, Søren Brunak, Paolo Frasconi, Gianluca Pollastri
Bidirectional Dynamics for Protein Secondary Structure Prediction. Sequence Learning 2001: 80-104 - 2000
- [b1]Pierre Baldi, Søren Brunak:
Bioinformatics - the machine learning approach. MIT Press 2000, ISBN 978-0-262-02442-6, pp. 1-44 - [j15]Pierre Baldi, Søren Brunak, Yves Chauvin, Claus A. F. Andersen, Henrik Nielsen
Assessing the accuracy of prediction algorithms for classification: an overview. Bioinform. 16(5): 412-424 (2000) - [j14]Thomas M. Frimurer
Improving the Odds in Discriminating "Drug-like" from "Non Drug-like" Compounds. J. Chem. Inf. Comput. Sci. 40(6): 1315-1324 (2000) - [c8]Pierre Baldi, Gianluca Pollastri
Protein β-Sheet Partner Prediction by Neural Networks. ANNIMAB 2000: 3-9 - [c7]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
1990 – 1999
- 1999
- [j13]Jan Gorodkin
MatrixPlot: visualizing sequence constraints. Bioinform. 15(9): 769-770 (1999) - [j12]Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen
Structural basis for triplet repeat disorders: a computational analysis. Bioinform. 15(11): 918-929 (1999) - [j11]Pierre Baldi, Søren Brunak, Paolo Frasconi, Giovanni Soda, Gianluca Pollastri
Exploiting the past and the future in protein secondary structure prediction. Bioinform. 15(11): 937-946 (1999) - [j10]Anders Gorm Pedersen
The Biology of Eukaryotic Promoter Prediction - A Review. Comput. Chem. 23(3-4): 191-207 (1999) - [j9]Andres Kreegipuu, Nikolaj Blom
PhosphoBase, a database of phosphorylation sites: release 2.0. Nucleic Acids Res. 27(1): 237-239 (1999) - [j8]Ramneek Gupta
O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins. Nucleic Acids Res. 27(1): 370-372 (1999) - [c6]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 - 1998
- [j7]Nikolaj Blom
PhosphoBase: a database of phosphorylation sites. Nucleic Acids Res. 26(1): 382-386 (1998) - [j6]Jan E. Hansen, Ole Lund
O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins. Nucleic Acids Res. 26(1): 387-389 (1998) - [c5]Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen:
Computational Applications of DNA Structural Scales. ISMB 1998: 35-42 - 1997
- [j5]Jan Gorodkin, Laurie J. Heyer, Søren Brunak, Gary D. Stormo:
Displaying the information contents of structural RNA alignments: the structure logos. Comput. Appl. Biosci. 13(6): 583-586 (1997) - [j4]Henrik Nielsen
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) - [j3]Jan E. Hansen, Ole Lund
O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins. Nucleic Acids Res. 25(1): 278-282 (1997) - 1996
- [j2]Jan E. Hansen, Ole Lund
O-GLYCBASE: a revised database of O-glycosylated proteins. Nucleic Acids Res. 24(1): 248-252 (1996) - [c4]Anders Gorm Pedersen, Pierre Baldi, Søren Brunak, Yves Chauvin:
Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models. ISMB 1996: 182-191 - 1995
- [c3]Pierre Baldi, Søren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh:
Periodic Sequence Patterns in Human Exons. ISMB 1995: 30-38 - 1993
- [c2]Pierre Baldi, Søren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh:
Hidden Markov Models for Human Genes. NIPS 1993: 761-768 - 1990
- [c1]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
1980 – 1989
- 1989
- [j1]Henrik Bohr, Søren Brunak:
A Travelling Salesman Approach to Protein Conformation. Complex Syst. 3(1) (1989)
Coauthor Index
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last updated on 2024-11-07 20:36 CET by the dblp team
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