Søren Brunak | Academic Influence

Søren Brunak's AcademicInfluence.com Rankings

Søren Brunak

Biology

#1218

World Rank

#2074

Historical Rank

Bioinformatics

#20

World Rank

#20

Historical Rank

biology Degrees

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Biology

Søren Brunak's Degrees

PhD Bioinformatics Technical University of Denmark

Why Is Søren Brunak Influential?

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According to Wikipedia, Søren Brunak is a Danish biological and physical scientist working in bioinformatics, systems biology, and medical informatics. He is a professor of Disease Systems Biology at the University of Copenhagen and professor of bioinformatics at the Technical University of Denmark. As Research Director at the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen Medical School, he leads a research effort where molecular-level systems biology data are combined with phenotypic data from the healthcare sector, such as electronic patient records, registry information, and biobank questionnaires. A major aim is to understand the network biology basis for time-ordered comorbidities and discriminate between treatment-related disease correlations and other comorbidities in disease trajectories. Søren Brunak also holds a position as a Medical Informatics Officer at Rigshospitalet, the Capital Region of Denmark.

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Søren Brunak's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

A human gut microbial gene catalogue established by metagenomic sequencing (2010) (9177)
SignalP 4.0: discriminating signal peptides from transmembrane regions (2011) (8414)
Improved prediction of signal peptides: SignalP 3.0. (2004) (6574)
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. (1997) (5624)
Enterotypes of the human gut microbiome (2011) (4920)
Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. (2000) (4307)
Richness of human gut microbiome correlates with metabolic markers (2013) (3351)
Locating proteins in the cell using TargetP, SignalP and related tools (2007) (3216)
Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. (1999) (2980)
SignalP 5.0 improves signal peptide predictions using deep neural networks (2019) (2398)
Assessing the accuracy of prediction algorithms for classification: an overview (2000) (1938)
Prediction of post‐translational glycosylation and phosphorylation of proteins from the amino acid sequence (2004) (1785)
An integrated catalog of reference genes in the human gut microbiome (2014) (1431)
Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis (2010) (1425)
Mining electronic health records: towards better research applications and clinical care (2012) (1356)
Human gut microbes impact host serum metabolome and insulin sensitivity (2016) (1257)
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota (2015) (1243)
Prediction of lipoprotein signal peptides in Gram‐negative bacteria (2003) (1090)
Feature-based prediction of non-classical and leaderless protein secretion. (2004) (1073)
Population genomics of Bronze Age Eurasia (2015) (1059)
Precision mapping of the human O‐GalNAc glycoproteome through SimpleCell technology (2013) (1043)
Reliable prediction of T‐cell epitopes using neural networks with novel sequence representations (2003) (996)
A human phenome-interactome network of protein complexes implicated in genetic disorders (2007) (955)
Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. (2005) (905)
Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. (1996) (822)
Prediction of human mRNA donor and acceptor sites from the DNA sequence. (1991) (819)
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes (2014) (812)
Analysis and prediction of leucine-rich nuclear export signals. (2004) (793)
A Neural Network Method for Identification of Prokaryotic and Eukaryotic Signal Peptides and Prediction of their Cleavage Sites (1997) (783)
Ancient human genome sequence of an extinct Palaeo-Eskimo (2010) (754)
Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans (2013) (744)
Enterotypes of the human gut microbiome (2011) (713)
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse (2013) (706)
An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia (2011) (675)
Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function (2001) (662)
Machine learning approaches for the prediction of signal peptides and other protein sorting signals. (1999) (628)
Non-classical protein secretion in bacteria (2005) (620)
Bioinformatics: the machine learning approach (2002) (599)
A new non-linear normalization method for reducing variability in DNA microarray experiments (2002) (570)
Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci (2016) (549)
Prediction of twin-arginine signal peptides (2005) (510)
Exploiting the past and the future in protein secondary structure prediction (1999) (503)
Prediction of proprotein convertase cleavage sites. (2004) (497)
The genome of a Late Pleistocene human from a Clovis burial site in western Montana (2014) (464)
Mapping the human genetic architecture of COVID-19 (2021) (455)
Linear Motif Atlas for Phosphorylation-Dependent Signaling (2008) (442)
Metagenomic species profiling using universal phylogenetic marker genes (2013) (421)
A scored human protein–protein interaction network to catalyze genomic interpretation (2017) (416)
NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility (1998) (411)
Dynamic Complex Formation During the Yeast Cell Cycle (2005) (407)
Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago (2015) (385)
Disentangling the effects of type 2 diabetes and metformin on the human gut microbiota (2015) (383)
Patterns of somatic structural variation in human cancer genomes (2020) (377)
A genomic history of Aboriginal Australia (2016) (355)
Prediction of human protein function from post-translational modifications and localization features. (2002) (333)
Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. (2003) (332)
Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients (2014) (301)
Definition of supertypes for HLA molecules using clustering of specificity matrices (2004) (300)
Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts (2011) (299)
SignalP 6.0 predicts all five types of signal peptides using protein language models (2022) (297)
Prediction of proteasome cleavage motifs by neural networks. (2002) (295)
An integrative approach to CTL epitope prediction: A combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions (2005) (293)
Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing (2005) (292)
A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes (2008) (285)
PhosphoBase, a database of phosphorylation sites: release 2.0 (1999) (283)
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach (2004) (277)
Clustering Patterns of Cytotoxic T-Lymphocyte Epitopes in Human Immunodeficiency Virus Type 1 (HIV-1) Proteins Reveal Imprints of Immune Evasion on HIV-1 Global Variation (2002) (271)
Prediction of human protein function according to Gene Ontology categories (2003) (266)
O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins (1999) (265)
Network biology concepts in complex disease comorbidities (2016) (247)
Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae (2006) (246)
NESbase version 1.0: a database of nuclear export signals (2003) (243)
Intrauterine exposure to mild analgesics is a risk factor for development of male reproductive disorders in human and rat. (2011) (240)
Unexplored therapeutic opportunities in the human genome (2018) (238)
The Biology of Eukaryotic Promoter Prediction - A Review (1999) (237)
A DNA structural atlas for Escherichia coli. (2000) (237)
Alternative Splicing in Colon, Bladder, and Prostate Cancer Identified by Exon Array Analysis*S (2008) (233)
Cleavage site analysis in picornaviral polyproteins: Discovering cellular targets by neural networks (1996) (228)
The implications of alternative splicing in the ENCODE protein complement (2007) (227)
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes (2020) (220)
Comparison of computational methods for the identification of cell cycle-regulated genes (2005) (217)
Co-evolution of transcriptional and post-translational cell-cycle regulation (2006) (204)
Pharos: Collating protein information to shed light on the druggable genome (2016) (202)
Comprehensive molecular characterization of mitochondrial genomes in human cancers (2017) (197)
A Nondegenerate Code of Deleterious Variants in Mendelian Loci Contributes to Complex Disease Risk (2013) (197)
On the total number of genes and their length distribution in complete microbial genomes. (2001) (194)
env Sequences of Simian Immunodeficiency Viruses from Chimpanzees in Cameroon Are Strongly Related to Those of Human Immunodeficiency Virus Group N from the Same Geographic Area (2000) (185)
Displaying the information contents of structural RNA alignments: the structure logos (1997) (184)
Analysis of gene expression profiles of microdissected cell populations indicates that testicular carcinoma in situ is an arrested gonocyte. (2009) (170)
Modules, networks and systems medicine for understanding disease and aiding diagnosis (2014) (170)
Protein secondary structure and homology by neural networks The α‐helices in rhodopsin (1988) (167)
Analysis and prediction of mammalian protein glycation. (2006) (167)
Protein distance constraints predicted by neural networks and probability density functions. (1997) (155)
Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease (2017) (153)
Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios (2015) (148)
Statistical analysis of protein kinase specificity determinants (1998) (145)
Continuum secondary structure captures protein flexibility. (2002) (141)
Prediction of protein secondary structure at 80% accuracy (2000) (141)
Bacterial natural transformation by highly fragmented and damaged DNA (2013) (135)
Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes. (2013) (134)
Modeling the adaptive immune system: predictions and simulations (2007) (131)
Dynamic and explainable machine learning prediction of mortality in patients in the intensive care unit: a retrospective study of high-frequency data in electronic patient records. (2020) (131)
Prediction of N-terminal protein sorting signals. (1997) (121)
Genetic and environmental risk factors in congenital heart disease functionally converge in protein networks driving heart development (2012) (120)
Tools and data services registry: a community effort to document bioinformatics resources (2015) (120)
A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts (2018) (119)
A novel approach to prediction of the 3‐dimensional structures of protein backbones by neural networks (1990) (118)
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference (2017) (118)
The SH2 domain interaction landscape. (2013) (114)
A Brief History of Protein Sorting Prediction (2019) (114)
Improving the Odds in Discriminating "Drug-like" from "Non Drug-like" Compounds (2000) (114)
Acute and persistent symptoms in non-hospitalized PCR-confirmed COVID-19 patients (2021) (111)
Scanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks. (1999) (104)
DNA structure in human RNA polymerase II promoters. (1998) (99)
A genome-wide association study of men with symptoms of testicular dysgenesis syndrome and its network biology interpretation (2011) (98)
Integrative pathway enrichment analysis of multivariate omics data (2018) (96)
Many Putative Endocrine Disruptors Inhibit Prostaglandin Synthesis (2010) (95)
Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima. (2000) (95)
Population-wide analysis of differences in disease progression patterns in men and women (2019) (95)
Genome organisation and chromatin structure in Escherichia coli. (2001) (94)
A Systematic Study of Site-specific GalNAc-type O-Glycosylation Modulating Proprotein Convertase Processing* (2011) (93)
Dissecting spatio-temporal protein networks driving human heart development and related disorders (2010) (92)
Large-scale study of Toxoplasma and Cytomegalovirus shows an association between infection and serious psychiatric disorders (2019) (92)
ChemProt: a disease chemical biology database (2010) (91)
hERG classification model based on a combination of support vector machine method and GRIND descriptors. (2008) (90)
Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries. (2019) (88)
Coronavirus 3CLpro proteinase cleavage sites: Possible relevance to SARS virus pathology (2004) (88)
Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates (2005) (87)
Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry. (2004) (87)
Predicting proteasomal cleavage sites: a comparison of available methods. (2003) (85)
Blood cell gene expression profiling in rheumatoid arthritis. Discriminative genes and effect of rheumatoid factor. (2004) (85)
Defining a similarity threshold for a functional protein sequence pattern: The signal peptide cleavage site (1996) (82)
Ibuprofen alters human testicular physiology to produce a state of compensated hypogonadism (2018) (82)
Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing (2016) (81)
Sigma A recognition sites in the Bacillus subtilis genome. (2001) (80)
A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites. (1997) (80)
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis (2020) (80)
Naturally occurring nucleosome positioning signals in human exons and introns. (1996) (79)
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags (2007) (79)
PhosphoBase: a database of phosphorylation sites (1998) (78)
Familial Atrial Septal Defect and Sudden Cardiac Death: Identification of a Novel NKX2‐5 Mutation and a Review of the Literature (2015) (77)
Nucleotide Sequence Database Policies (2002) (77)
Prediction of pH-Dependent Aqueous Solubility of Druglike Molecules (2006) (77)
Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer (2017) (76)
Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text (2013) (76)
Modeling of waning immunity after SARS-CoV-2 vaccination and influencing factors (2022) (75)
Survival prediction in intensive-care units based on aggregation of long-term disease history and acute physiology: a retrospective study of the Danish National Patient Registry and electronic patient records. (2019) (75)
Generating Genome‐Scale Candidate Gene Lists for Pharmacogenomics (2009) (75)
The sequences of 150,119 genomes in the UK Biobank (2021) (72)
A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links (2018) (71)
Diagnosis trajectories of prior multi-morbidity predict sepsis mortality (2016) (71)
Bidirectional Dynamics for Protein Secondary Structure Prediction (2001) (71)
Cyclebase.org—a comprehensive multi-organism online database of cell-cycle experiments (2007) (65)
Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics (2014) (65)
Prediction of Glycosylation Sites in Proteins (2009) (65)
New weakly expressed cell cycle‐regulated genes in yeast (2005) (65)
Immune Profiling of Human Gut-Associated Lymphoid Tissue Identifies a Role for Isolated Lymphoid Follicles in Priming of Region-Specific Immunity. (2020) (65)
Immunological bioinformatics (2005) (64)
A wiring of the human nucleolus. (2006) (64)
Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil (2014) (64)
Protein Interaction-Based Genome-Wide Analysis of Incident Coronary Heart Disease (2011) (63)
Neural network detects errors in the assignment of mRNA splice sites. (1990) (63)
Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models (1996) (63)
Klinefelter syndrome comorbidities linked to increased X chromosome gene dosage and altered protein interactome activity (2016) (62)
Multiple alignment using simulated annealing: branch point definition in human mRNA splicing. (1992) (62)
O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins (1997) (62)
Pathway and network analysis of more than 2500 whole cancer genomes (2018) (62)
Complete Genes May Pass from Food to Human Blood (2013) (61)
Leveraging European infrastructures to access 1 million human genomes by 2022 (2019) (60)
Sequence-based feature prediction and annotation of proteins (2009) (59)
Country-specific chemical signatures of persistent environmental compounds in breast milk. (2010) (58)
Huntingtin-interacting protein 14 is a type 1 diabetes candidate protein regulating insulin secretion and β-cell apoptosis (2011) (58)
The Type 2 Diabetes Associated Minor Allele of rs2237895 KCNQ1 Associates with Reduced Insulin Release Following an Oral Glucose Load (2009) (56)
Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results (2009) (56)
Cleaning the GenBank Arabidopsis thaliana data set. (1996) (56)
Protein Folds: A Distance-Based Approach (1995) (56)
ChemProt-2.0: visual navigation in a disease chemical biology database (2012) (54)
Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks (2010) (52)
ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale† (2010) (52)
Integrative analysis for finding genes and networks involved in diabetes and other complex diseases (2007) (52)
Legacy data sharing to improve drug safety assessment: the eTOX project (2017) (52)
Cometin is a novel neurotrophic factor that promotes neurite outgrowth and neuroblast migration in vitro and supports survival of spiral ganglion neurons in vivo (2012) (51)
SARS CTL Vaccine Candidates — HLA Supertype, Genome‐Wide Scanning and Biochemical Validation (2004) (50)
Protein structures from distance inequalities. (1993) (50)
Discovery of biomarkers for glycaemic deterioration before and after the onset of type 2 diabetes: rationale and design of the epidemiological studies within the IMI DIRECT Consortium (2014) (49)
Transcriptional interactions suggest niche segregation among microorganisms in the human gut (2016) (48)
miRandola 2017: a curated knowledge base of non-invasive biomarkers (2017) (48)
Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks (2000) (48)
G+C-rich tract in 5' end of human introns. (1992) (48)
Protein structure and the sequential structure of mRNA: α‐Helix and β‐sheet signals at the nucleotide level (1996) (47)
DBDS Genomic Cohort, a prospective and comprehensive resource for integrative and temporal analysis of genetic, environmental and lifestyle factors affecting health of blood donors (2019) (47)
Genetic variability in the absorption of dietary sterols affects the risk of coronary artery disease (2020) (45)
Disease trajectory browser for exploring temporal, population-wide disease progression patterns in 7.2 million Danish patients (2020) (45)
Cleaning up gene databases (1990) (45)
Improving data and knowledge management to better integrate health care and research (2013) (45)
Analysis of the secondary structure of the human immunodeficiency virus (HIV) proteins p17, gp120, and gp41 by computer modeling based on neural network methods. (1990) (45)
Identification and Design of p53‐Derived HLA‐A2‐Binding Peptides with Increased CTL Immunogenicity * (2001) (44)
Meta‐analysis of heterogeneous data sources for genome‐scale identification of risk genes in complex phenotypes (2011) (44)
Association between chemical pattern in breast milk and congenital cryptorchidism: modelling of complex human exposures. (2012) (44)
Unexplored therapeutic opportunities in the human genome (2018) (44)
Dose-Specific Adverse Drug Reaction Identification in Electronic Patient Records: Temporal Data Mining in an Inpatient Psychiatric Population (2014) (44)
Protein structure by distance analysis (1994) (43)
Report on EU–USA Workshop: How Systems Biology Can Advance Cancer Research (27 October 2008) (2009) (43)
ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization (2008) (43)
Identification of Odorant-Receptor Interactions by Global Mapping of the Human Odorome (2014) (43)
Large-scale genome-wide association meta-analysis of endometriosis reveals 13 novel loci and genetically-associated comorbidity with other pain conditions (2018) (42)
ChemProt-3.0: a global chemical biology diseases mapping (2016) (42)
Optimization and immune recognition of multiple novel conserved HLA-A2, human immunodeficiency virus type 1-specific CTL epitopes. (2003) (42)
Bioinformatics - the machine learning approach (2. ed.) (2001) (42)
Computational analyses and annotations of the Arabidopsis peroxidase gene family (1998) (42)
Sex differences in oncogenic mutational processes (2019) (41)
MatrixPlot: visualizing sequence constraints (1999) (40)
Cofactory: Sequence‐based prediction of cofactor specificity of Rossmann folds (2014) (40)
Predicting and elucidating the etiology of fatty liver disease: A machine learning modeling and validation study in the IMI DIRECT cohorts (2020) (40)
Prediction of novel archaeal enzymes from sequence‐derived features (2002) (40)
A genome-wide meta-analysis yields 46 new loci associating with biomarkers of iron homeostasis (2021) (40)
O-GLYCBASE: a revised database of O-glycosylated proteins (1996) (40)
Functionality of system components: conservation of protein function in protein feature space. (2003) (39)
Identifying cytotoxic T cell epitopes from genomic and proteomic information: "The human MHC project.". (2000) (39)
Integration of Known DNA, RNA and Protein Biomarkers Provides Prediction of Anti-TNF Response in Rheumatoid Arthritis: Results from the COMBINE Study (2016) (39)
Neural network model of the genetic code is strongly correlated to the GES scale of amino acid transfer free energies. (1994) (38)
Corrigendum: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota (2017) (37)
Analysis of eukaryotic promoter sequences reveals a systematically occurring CT-signal. (1995) (37)
Bias of Purine Stretches in Sequenced Chromosomes (2002) (37)
Integrative network analysis highlights biological processes underlying GLP-1 stimulated insulin secretion: A DIRECT study (2018) (36)
Analysis and recognition of 5' UTR intron splice sites in human pre-mRNA. (2004) (36)
Prenatal exposure to paracetamol/acetaminophen and precursor aniline impairs masculinisation of male brain and behaviour. (2017) (36)
Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing (2015) (35)
Computational Applications of DNA Structural Scales (1998) (34)
SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation (2007) (34)
Prediction of the secondary structure of HIV‐1 gp120 (1996) (33)
MetaRanker 2.0: a web server for prioritization of genetic variation data (2013) (33)
Matching protein beta-sheet partners by feedforward and recurrent neural networks. (2000) (32)
Immunological Bioinformatics (Computational Molecular Biology) (2005) (32)
Protein feature based identification of cell cycle regulated proteins in yeast. (2003) (32)
SARS CTL vaccine candidates; HLA supertype‐, genome‐wide scanning and biochemical validation (2004) (31)
Knowledge engineering for health: A new discipline required to bridge the “ICT gap” between research and healthcare (2012) (31)
Combined burden and functional impact tests for cancer driver discovery using DriverPower (2020) (31)
Evolution of Cell Cycle Control: Same Molecular Machines, Different Regulation (2007) (31)
Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging (2017) (30)
A computational approach to chemical etiologies of diabetes (2013) (30)
Transcriptome analysis of the adult human Klinefelter testis and cellularity-matched controls reveals disturbed differentiation of Sertoli- and Leydig cells (2018) (30)
Systematic Characterisation of Cellular Localisation and Expression Profiles of Proteins Containing MHC Ligands (2009) (30)
Metabolite ratios as potential biomarkers for type 2 diabetes: a DIRECT study (2017) (29)
Quantitative predictions of peptide binding to MHC class I molecules using specificity matrices and anchor-stratified calibrations. (2001) (29)
Integration of clinical chemistry, expression, and metabolite data leads to better toxicological class separation. (2008) (29)
Artificial Intelligence and Early Detection of Pancreatic Cancer: 2020 Summative Review. (2021) (29)
Lapatinib potentiates cytotoxicity of YM155 in neuroblastoma via inhibition of the ABCB1 efflux transporter (2017) (29)
Relationship between protein structure and geometrical constraints (1996) (28)
The bio.tools registry of software tools and data resources for the life sciences (2019) (28)
Modelling the Human Immune System by Combining Bioinformatics and Systems Biology Approaches (2006) (28)
Polychlorinated dibenzo-p-dioxins, furans, and biphenyls (PCDDs/PCDFs and PCBs) in breast milk and early childhood growth and IGF1. (2014) (28)
Addendum: Enterotypes of the human gut microbiome (2014) (28)
Bacterial diversity in snow on North Pole ice floes (2014) (28)
Lipidomic profiles, lipid trajectories and clinical biomarkers in female elite endurance athletes (2020) (27)
Analysis and prediction of gene splice sites in four Aspergillus genomes. (2009) (27)
Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia (2011) (26)
Discovery of biomarkers for glycaemic deterioration before and after the onset of type 2 diabetes: descriptive characteristics of the epidemiological studies within the IMI DIRECT Consortium (2019) (26)
Structural basis for triplet repeat disorders: a computational analysis (1999) (26)
OCT4 and downstream factors are expressed in human somatic urogenital epithelia and in culture of epididymal spheres. (2010) (26)
Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics (2014) (25)
ARDD 2020: from aging mechanisms to interventions (2020) (25)
Representation of Protein-Sequence Information by Amino Acid Subalphabets (2004) (25)
Identification of a new hTERT-derived HLA-A*0201 restricted, naturally processed CTL epitope (2007) (24)
Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level. (1996) (24)
Training neural networks to analyse biological sequences. (1990) (24)
Genomic profiling of thousands of candidate polymorphisms predicts risk of relapse in 778 Danish and German childhood acute lymphoblastic leukemia patients (2014) (24)
Neural Networks: Computers With Intuition (1990) (23)
Concordance of gene expression in human protein complexes reveals tissue specificity and pathology (2013) (23)
Individualization of treatments with drugs metabolized by CES1: combining genetics and metabolomics. (2015) (23)
The Type 1 Diabetes - HLA Susceptibility Interactome - Identification of HLA Genotype-Specific Disease Genes for Type 1 Diabetes (2010) (23)
Early differences in islets from prediabetic NOD mice: combined microarray and proteomic analysis (2017) (23)
Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints (1999) (22)
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (2020) (22)
Identification of T1D susceptibility genes within the MHC region by combining protein interaction networks and SNP genotyping data (2009) (22)
Protein secondary structure and homology by neural networks. The alpha-helices in rhodopsin. (1988) (22)
Bioinformatics-Driven Identification and Examination of Candidate Genes for Non-Alcoholic Fatty Liver Disease (2011) (22)
The Formation of Protein Structure (1996) (22)
Four groups of type 2 diabetes contribute to the etiological and clinical heterogeneity in newly diagnosed individuals: An IMI DIRECT study (2022) (22)
Genetic insight into sick sinus syndrome (2021) (21)
Discrepancies in listed adverse drug reactions in pharmaceutical product information supplied by the regulatory authorities in Denmark and the USA (2014) (21)
Prediction of Disease Causing Non-Synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP (2013) (21)
Ranking factors involved in diabetes remission after bariatric surgery using machine-learning integrating clinical and genomic biomarkers (2016) (20)
Cutavirus in Cutaneous Malignant Melanoma (2017) (20)
Protein secondary structure: category assignment and predictability (2001) (20)
Traces of ATCV-1 associated with laboratory component contamination (2015) (20)
The Cancer Exome Generated by Alternative mRNA Splicing Dilutes Predicted HLA Class I Epitope Density (2012) (19)
Viscous trees and Voronoi-structure formation in expanding systems (1994) (19)
Finding Cervical Cancer Symptoms in Swedish Clinical Text using a Machine Learning Approach and NegEx (2015) (19)
Genetic studies of abdominal MRI data identify genes regulating hepcidin as major determinants of liver iron concentration (2019) (19)
Text mining of 15 million full-text scientific articles (2017) (19)
Chance of live birth: a nationwide, registry-based cohort study. (2021) (18)
Combinatorial Drug Screening Identifies Ewing Sarcoma–specific Sensitivities (2016) (18)
Familial co-occurrence of congenital heart defects follows distinct patterns (2017) (18)
Patient stratification and identification of adverse event correlations in the space of 1190 drug related adverse events (2014) (17)
RNA secondary structure and squence conservation in C1 region of human immunodeficiency virus type 1 env gene. (2002) (17)
Motif Decomposition of the Phosphotyrosine Proteome Reveals a New N-terminal Binding Motif for SHIP2*S (2008) (17)
Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios (2018) (17)
Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach (2003) (17)
Temporal Order of Disease Pairs Affects Subsequent Disease Trajectories: The Case of Diabetes and Sleep Apnea (2017) (17)
Flexibility of the genetic code with respect to DNA structure (2001) (17)
Molecular wring resonances in chain molecules. (1997) (16)
Estimating heritability and genetic correlations from large health datasets in the absence of genetic data (2019) (16)
Pancreatic Islet Protein Complexes and Their Dysregulation in Type 2 Diabetes (2017) (16)
SignalP 6.0 achieves signal peptide prediction across all types using protein language models (2021) (16)
Roadmap for a precision-medicine initiative in the Nordic region (2019) (16)
Increase in clinically recorded type 2 diabetes after colectomy (2018) (16)
Neural Networks: Applications (2001) (15)
A Large-Cohort, Longitudinal Study Determines Precancer Disease Routes across Different Cancer Types. (2019) (15)
A Travelling Salesman Approach to Protein Conformation (1989) (14)
Retinoic Acid Signaling in Thymic Epithelial Cells Regulates Thymopoiesis. (2018) (14)
A generic deep convolutional neural network framework for prediction of receptor–ligand interactions—NetPhosPan: application to kinase phosphorylation prediction (2018) (14)
The Atlas visualization of genomewide information (2002) (14)
Compass: A hybrid method for clinical and biobank data mining (2014) (14)
Expression Profiling of Human Genetic and Protein Interaction Networks in Type 1 Diabetes (2009) (14)
O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins (1998) (14)
A Novel Familial Cardiac Arrhythmia Syndrome with Widespread ST-Segment Depression. (2018) (14)
Analysis of Time-Series Gene Expression Data to Explore Mechanisms of Chemical-Induced Hepatic Steatosis Toxicity (2018) (14)
Genome-Wide Assessment of the Association of Rare and Common Copy Number Variations to Testicular Germ Cell Cancer (2013) (13)
New susceptibility loci for severe COVID-19 by detailed GWAS analysis in European populations (2021) (13)
Distance distributions in proteins: a six-parameter representation. (1996) (13)
Detailed stratified GWAS analysis for severe COVID-19 in four European populations (2022) (13)
Neural network predicts sequence of TP53 gene based on DNA chip (2002) (13)
Comorbidity landscape of the Danish patient population affected by chromosome abnormalities (2019) (12)
Periodic Sequence Patterns in Human Exons (1995) (12)
Eleven genomic loci affect plasma levels of chronic inflammation marker soluble urokinase-type plasminogen activator receptor (2021) (12)
Identifying the druggable interactome of EWS-FLI1 reveals MCL-1 dependent differential sensitivities of Ewing sarcoma cells to apoptosis inducers (2018) (12)
DNA Bendability and Nucleosome Positioning in Transcriptional Regulation (2005) (12)
Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers (2016) (12)
Secreted breast tumor interstitial fluid microRNAs and their target genes are associated with triple-negative breast cancer, tumor grade, and immune infiltration (2020) (12)
Understanding inherent image features in CNN-based assessment of diabetic retinopathy (2021) (12)
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Uncovering the Molecular Machinery of the Human Spindle—An Integration of Wet and Dry Systems Biology (2012) (11)
Randomized Phase II Study of Nivolumab With or Without Ipilimumab Combined With Stereotactic Body Radiotherapy for Refractory Metastatic Pancreatic Cancer (CheckPAC) (2022) (11)
Chromosome-wise Protein Interaction Patterns and Their Impact on Functional Implications of Large-Scale Genomic Aberrations. (2017) (11)
Identification of a Synthetic Lethal Relationship between Nucleotide Excision Repair Deficiency and Irofulven Sensitivity in Urothelial Cancer (2020) (11)
Age‐stratified longitudinal study of Alzheimer's and vascular dementia patients (2020) (11)
Detection of Molecular Signatures of Homologous Recombination Deficiency in Bladder Cancer (2021) (11)
Comparison of global gene expression profiles of microdissected human foetal Leydig cells with their normal and hyperplastic adult equivalents (2017) (11)
Genome-wide analysis of 944 133 individuals provides insights into the etiology of haemorrhoidal disease (2021) (11)
Web-based Tools for Vaccine Design (2002) (11)
Transcriptome profiling of mice testes following low dose irradiation (2013) (10)
sAOP: linking chemical stressors to adverse outcomes pathway networks (2019) (10)
Rare SLC13A1 variants associate with intervertebral disc disorder highlighting role of sulfate in disc pathology (2022) (10)
Long-term risk of cardiovascular and cerebrovascular disease after removal of the colonic microbiota by colectomy: a cohort study based on the Danish National Patient Register from 1996 to 2014 (2015) (10)
Improved prediction of MHC class I and II epitopes using a novel Gibbs sampling approach (2003) (10)
Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells. (2014) (10)
High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach (2019) (9)
Herpes Simplex Virus Type 1 infection is associated with suicidal behavior and first registered psychiatric diagnosis in a healthy population (2019) (9)
Pancreatic cancer risk predicted from disease trajectories using deep learning (2021) (9)
Alcoholic liver disease: A registry view on comorbidities and disease prediction (2020) (9)
Profiles of Glucose Metabolism in Different Prediabetes Phenotypes, Classified by Fasting Glycemia, 2-Hour OGTT, Glycated Hemoglobin, and 1-Hour OGTT: An IMI DIRECT Study (2021) (9)
wKinMut‐2: Identification and Interpretation of Pathogenic Variants in Human Protein Kinases (2016) (9)
Endotrophin is associated with chronic multimorbidity and all-cause mortality in a cohort of elderly women (2021) (9)
Heterozygous deletion at the RLN1 locus in a family with testicular germ cell cancer identified by integrating copy number variation data with phenome and interactome information. (2011) (8)
Hidden Markov Models for Human Genes (1993) (8)
Identification of possible adverse drug reactions in clinical notes: The case of glucose-lowering medicines (2015) (8)
The use of systems biology in chemical risk assessment (2019) (8)
The role of physical activity in metabolic homeostasis before and after the onset of type 2 diabetes: an IMI DIRECT study (2020) (8)
Analysis of cell death inducing compounds (2007) (8)
Systems genetics analysis identifies calcium-signaling defects as novel cause of congenital heart disease (2019) (8)
Towards standardization guidelines for in silico approaches in personalized medicine (2020) (8)
Cross-tissue transcriptome-wide association studies identify susceptibility genes shared between schizophrenia and inflammatory bowel disease (2022) (8)
Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types (2019) (8)
The governance structure for data access in the DIRECT consortium: an innovative medicines initiative (IMI) project (2018) (7)
The impact of the protein interactome on the syntenic structure of mammalian genomes (2017) (7)
Hidden Markov Models: Applications (2001) (7)
Conflicting associations between dietary patterns and changes of anthropometric traits across subgroups of middle-aged women and men. (2019) (7)
Recognition of Environmental and Genetic Effects on Barley Phenolic Fingerprints by Neural Networks (2001) (7)
Incorporating symptom data in longitudinal disease trajectories for more detailed patient stratification (2019) (7)
Orphan protein function and its relation to glycosylation. (2002) (7)
Linking glycemic dysregulation in diabetes to symptoms, comorbidities, and genetics through EHR data mining (2019) (6)
Information Theory, Entropy, and Relative Entropy (2001) (6)
Association of Variants Near the Bradykinin Receptor B2 Gene With Angioedema in Patients Taking ACE Inhibitors. (2021) (6)
Analysis of a gene panel for targeted sequencing of colorectal cancer samples (2018) (6)
Circular reasoning rather than cyclic expression (2008) (6)
Optimizing drug selection from a prescription trajectory of one patient (2021) (6)
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Whole blood co-expression modules associate with metabolic traits and type 2 diabetes: an IMI-DIRECT study (2020) (6)
MHC Class I Epitope Binding Prediction Trained on Small Data Sets (2004) (6)
Negation scope and spelling variation for text-mining of Danish electronic patient records (2014) (6)
Multiomics analysis of rheumatoid arthritis yields sequence variants that have large effects on risk of the seropositive subset (2022) (6)
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Extrapolation of drug induced liver injury responses from cancer cell lines using machine learning approaches (2021) (5)
How Suitable Are Registry Data for Recurrence Risk Calculations? Validation of Diagnoses on 1,593 Families With Congenital Heart Disease (2016) (5)
Impaired Vitamin D Signaling in T Cells From a Family With Hereditary Vitamin D Resistant Rickets (2021) (5)
Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients (2016) (5)
Intervening on the storage time of RBC units and its effects on adverse recipient outcomes using real-world data (2022) (5)
Kissing loops hide premature termination codons in pre-mRNA of selenoprotein genes and in genes containing programmed ribosomal frameshifts. (1997) (5)
Semen quality and waiting time to pregnancy explored using association mining (2020) (5)
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Implementation and comparison of two text mining methods with a standard pharmacovigilance method for signal detection of medication errors (2020) (5)
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Complete Topological Mapping of a Cellular Protein Interactome Reveals Bow-Tie Motifs as Ubiquitous Connectors of Protein Complexes. (2020) (4)
Combined Ensemble Docking and Machine Learning in Identification of Therapeutic Agents with Potential Inhibitory Effect on Human CES1 (2019) (4)
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Relating genomic variation to drug response in childhood acute lymphoblastic leukemia by multiplexed targeted sequencing (2010) (4)
Prediction of Protein Secondary Structure at High Accuracy Using a Combination of Many Neural Networks (2003) (4)
Artificial Intelligence and Early Detection of Pancreatic Cancer (2021) (4)
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Protein features as determinants of wild‐type glycoside hydrolase thermostability (2017) (4)
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Type I Interferons Promote Germinal Centers Through B Cell Intrinsic Signaling and Dendritic Cell Dependent Th1 and Tfh Cell Lineages (2020) (3)
The burden of disease of three food-associated heavy metals in clusters in the Danish population - towards targeted public health strategies. (2021) (3)
Single-cell characterisation of mononuclear phagocytes in the human intestinal mucosa (2021) (3)
Discovery of biomarkers for glycaemic deterioration before and after the onset of type 2 diabetes: an overview of the data from the epidemiological studies within the IMI DIRECT Consortium (2018) (3)
Identification of heterogenous treatment response trajectories to anti-IL6 receptor treatment in rheumatoid arthritis (2020) (3)
Predictive utilities of lipid traits, lipoprotein subfractions and other risk factors for incident diabetes: a machine learning approach in the Diabetes Prevention Program (2021) (3)
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Using Machine Learning to Identify Patients at High Risk of Inappropriate Drug Dosing in Periods with Renal Dysfunction (2022) (3)
Toxicogenomics Investigation Under the eTOX Project (2012) (3)
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Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types. (2019) (2)
Estimating the effect of donor sex on red blood cell transfused patient mortality: A retrospective cohort study using a targeted learning and emulated trials-based approach (2022) (2)
Clinical, genetic, and experimental increase in soluble urokinase plasminogen activator receptor levels promotes atherosclerosis. (2022) (2)
Meeting abstractPrediction of protein secondary structure at 80% accuracy using a combination of many neural networks (2000) (2)
The small and large intestine contain transcriptionally related mesenchymal stromal cell subsets that derive from embryonic Gli1+ mesothelial cells (2021) (2)
Association between antipsychotic drug dose and length of clinical notes: a proxy of disease severity? (2020) (2)
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Genetic variants associated with syncope implicate neural and autonomic processes. (2023) (2)
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Modules, networks and systems medicine for understanding disease and aiding diagnosis (2014) (2)
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Increased soluble urokinase plasminogen activator levels modulate monocyte function to promote atherosclerosis (2022) (2)
Discrete-time survival analysis in the critically ill: a deep learning approach using heterogeneous data (2022) (2)
SignalP 5.0 improves signal peptide predictions using deep neural networks (2019) (1)
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Author Correction: Combined burden and functional impact tests for cancer driver discovery using DriverPower (2020) (1)
Dietary metabolite profiling brings new insight into the relationship between nutrition and metabolic risk: An IMI DIRECT study (2020) (1)
Glycolytic repression and reduced GLP-1 secretion by active Farnesoid X Receptor in enteroendocrine L cells achieved via PKLR (2018) (1)
Systems genetics analysis identifies calcium-signaling defects as novel cause of congenital heart disease (2020) (1)
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Author Correction: Rare SLC13A1 variants associate with intervertebral disc disorder highlighting role of sulfate in disc pathology (2022) (1)
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Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios (2018) (0)
Cancer panomics: Computational methods and nfrastructure for integrative analysis of cancer highthroughput "omics" data (2014) (0)
Established risk loci for systemic lupus erythematosus at NCF2, STAT4, TNPO3, IRF5 and ITGAM associate with distinct clinical manifestations: a Danish genome-wide association study. (2022) (0)
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Reduced vitamin D-induced cathelicidin production and killing of Mycobacterium tuberculosis in macrophages from a patient with a non-functional vitamin D receptor: A case report (2022) (0)
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Using National Electronic Health Care Registries to Analyse and Predict Alcoholic Liver Disease (2020) (0)
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Predicting and elucidating the etiology of fatty liver disease using a machine learning-based approach: an IMI DIRECT study (2020) (0)
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Deciphering the clinical effect of drugs through large-scale data integration (2013) (0)
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Genome-wide analysis of 944,133 individuals provides insights into the etiology of hemorrhoidal disease (2020) (0)
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PMHnet-alpha: development and validation of a neural network based discrete-time survival model for mortality prediction in ischemic heart disease (2022) (0)
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Linking progression patterns in ischaemic heart disease to comorbidities and genetics by integrated analysis of electronic health records and population-wide registries (2020) (0)
Eleven genomic loci affect plasma levels of chronic inflammation marker soluble urokinase-type plasminogen activator receptor (2021) (0)
‘Query‐by Committee’— An Efficient Method to Select Information‐Rich Data for the Development of Peptide—HLA‐Binding Predictors (2004) (0)
Precision medicine in complex diseases-Molecular subgrouping for improved prediction and treatment stratification. (2023) (0)
Associations of ABO and Rhesus D blood groups with phenome-wide disease incidence: A 41-year retrospective cohort study of 482,914 patients (2022) (0)
A genome-wide meta-analysis yields 46 new loci associating with biomarkers of iron homeostasis (2021) (0)
Roadmap for a precision-medicine initiative in the Nordic region (2019) (0)
Author Correction: Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models. (2023) (0)
The small and large intestine contain related mesenchymal subsets that derive from embryonic Gli1+ precursors (2023) (0)
Author Correction: The evolutionary history of 2,658 cancers (2023) (0)
Identification of biomarkers for glycaemic deterioration in type 2 diabetes (2023) (0)
Multi-omics analysis reveals drivers of loss of Î²-cell function after newly diagnosed autoimmune type 1 diabetes: An INNODIA multicenter study (2023) (0)
Development and validation of a dynamic prediction model for unplanned ICU admission and mortality in hospitalized patients (2022) (0)
The role of physical activity in metabolic homeostasis before and after the onset of type 2 diabetes (2020) (0)
Genetic insight into sick sinus syndrome. (2021) (0)
Machine Learning Algorithms (2020) (0)
Author Correction: Patterns of somatic structural variation in human cancer genomes (2020) (0)
Cancer-om-atics: Multilevel interpretation of cancer genome data (2011) (0)
Stochastic Grammars and Linguistics (2001) (0)
Exploring the Danish Diseasome (2013) (0)
Fishing for new Alzheimer's drug targets in large proteomics and transcriptomics datasets using expert-curated pathways and predicted interaction networks. (2007) (0)
Integrative analyses of complex phenotypes (2009) (0)
Prediction of endotoxin variants in the human gut microbiome and their relation to metabolic disease (2017) (0)
Probabilistic Models of Evolution: Phylogenetic Trees (2001) (0)
Identifying tissue-specificity of protein-complexes based on a global map of human expression data (2012) (0)
University of Southern Denmark Antibiotic regimens for neonatal sepsis A protocol for a systematic review with meta-analysis (2019) (0)
A prototype linking ICD10/SNOMED CT concepts to Ensembl gene identifiers (2015) (0)
Improving the Odds in Discriminating “Drug‐Like” from “Non Drug‐Like” Compounds. (2001) (0)

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