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List of works by Søren Brunak

A Brief History of Protein Sorting Prediction

scientific article published on 01 June 2019

A DNA structural atlas for Escherichia coli

scientific article (publication date: June 2000)

A Large-Cohort, Longitudinal Study Determines Precancer Disease Routes across Different Cancer Types

scientific article published on 27 December 2018

A Neural Network Method for Identification of Prokaryotic and Eukaryotic Signal Peptides and Prediction of their Cleavage Sites

article published in 1997

A Nondegenerate Code of Deleterious Variants in Mendelian Loci Contributes to Complex Disease Risk

scientific article (publication date: September 2013)

A Novel Approach to Prediction of the 3-Dimensional Structures of Protein Backbones by Neural Networks ⬇️

scholarly article by Henrik Fredholm et al published 1991 in Advances in Neural Information Processing Systems 3

A Novel Familial Cardiac Arrhythmia Syndrome with Widespread ST-Segment Depression

scientific article published on 01 November 2018

A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites

scientific article

A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts

scientific article published on 15 February 2018

A computational approach to chemical etiologies of diabetes

scientific article published on January 2013

A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links

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

scientific article published on 01 April 2019

A genome-wide association study of men with symptoms of testicular dysgenesis syndrome and its network biology interpretation

scientific article published on 3 December 2011

A genome-wide meta-analysis identifies 50 genetic loci associated with carpal tunnel syndrome

scientific article published on 24 March 2022

A genomic history of Aboriginal Australia

scientific article (publication date: 21 September 2016)

A human gut microbial gene catalogue established by metagenomic sequencing

scientific article

A human phenome-interactome network of protein complexes implicated in genetic disorders

scientific article (publication date: March 2007)

A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes

scholarly article

A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites

scientific article published in October 1997

A new non-linear normalization method for reducing variability in DNA microarray experiments

scientific article

A novel approach to prediction of the 3-dimensional structures of protein backbones by neural networks

scientific article published in February 1990

A proteomic study of the regulatory role for STAT-1 in cytokine-induced beta-cell death.

scientific article

A scored human protein-protein interaction network to catalyze genomic interpretation.

scientific article published on 28 November 2016

A systematic study of site-specific GalNAc-type O-glycosylation modulating proprotein convertase processing

scientific article

A wiring of the human nucleolus.

scientific article

Age-stratified longitudinal study of Alzheimer's and vascular dementia patients

scientific article published on 27 April 2020

Alcoholic liver disease: A registry view on comorbidities and disease prediction

scientific article published on 22 September 2020

Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis

scientific article

An Aboriginal Australian genome reveals separate human dispersals into Asia

scientific article (publication date: 7 October 2011)

An integrated catalog of reference genes in the human gut microbiome

scientific article

An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions

scientific article published in August 2005

Analysis and prediction of gene splice sites in four Aspergillus genomes

scientific article published on 10 October 2008

Analysis and prediction of leucine-rich nuclear export signals

scientific article (publication date: June 2004)

Analysis and prediction of mammalian protein glycation

scientific article

Analysis and recognition of 5' UTR intron splice sites in human pre-mRNA.

scientific article published on 11 February 2004

Analysis of Time-Series Gene Expression Data to Explore Mechanisms of Chemical-Induced Hepatic Steatosis Toxicity

article

Analysis of a gene panel for targeted sequencing of colorectal cancer samples

scientific article published on 10 January 2018

Analysis of cell death inducing compounds

article published in 2007

Analysis of eukaryotic promoter sequences reveals a systematically occurring CT-signal

scientific article

Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci

scientific article

Analysis of gene expression profiles of microdissected cell populations indicates that testicular carcinoma in situ is an arrested gonocyte

scientific article

Analysis of the secondary structure of the human immunodeficiency virus (HIV) proteins p17, gp120, and gp41 by computer modeling based on neural network methods.

scientific article published in January 1990

Ancient human genome sequence of an extinct Palaeo-Eskimo

scientific article

Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics

scientific article

Assessing the accuracy of prediction algorithms for classification: an overview

scientific article (publication date: May 2000)

Association between antipsychotic drug dose and length of clinical notes: a proxy of disease severity?

scientific article published on 07 May 2020

Association between chemical pattern in breast milk and congenital cryptorchidism: modelling of complex human exposures.

scientific article published on 23 April 2012

Author Correction: Leveraging European infrastructures to access 1 million human genomes by 2022

scientific article published on 01 November 2019

Bacterial diversity in snow on North Pole ice floes.

scientific article

Bacterial natural transformation by highly fragmented and damaged DNA ⬇️

scientific article (publication date: 3 December 2013)

Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios.

scientific article published on 25 June 2018

Bias of purine stretches in sequenced chromosomes

scientific article published in July 2002

Bioinformatics-driven identification and examination of candidate genes for non-alcoholic fatty liver disease ⬇️

scientific article

Blood cell gene expression profiling in rheumatoid arthritis. Discriminative genes and effect of rheumatoid factor

scientific article

Characterization of prokaryotic and eukaryotic promoters using hidden Markov models

scientific article published on January 1996

ChemProt-2.0: visual navigation in a disease chemical biology database

scientific article

ChemProt-3.0: a global chemical biology diseases mapping

scientific article published on 13 February 2016

ChemProt: a disease chemical biology database

scientific article

Chromosome-wise Protein Interaction Patterns and Their Impact on Functional Implications of Large-Scale Genomic Aberrations

scientific article published on 14 February 2017

Circular reasoning rather than cyclic expression

scientific article (publication date: 2008)

Cleaning the GenBank Arabidopsis thaliana data set.

scientific article

Cleaning up gene databases.

scientific article

Cleavage site analysis in picornaviral polyproteins: discovering cellular targets by neural networks

scientific article

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

scientific article

Co-evolution of transcriptional and post-translational cell-cycle regulation

scientific article (publication date: 27 September 2006)

Cofactory: sequence-based prediction of cofactor specificity of Rossmann folds

scientific article published on 20 March 2014

Coherent topological phenomena in protein folding ⬇️

scientific article published on 01 January 1997

Combinatorial Drug Screening Identifies Ewing Sarcoma-specific Sensitivities

scientific article published on 15 November 2016

Combined Ensemble Docking and Machine Learning in Identification of Therapeutic Agents with Potential Inhibitory Effect on Human CES1

scientific article published on 29 July 2019

Combing the Hairball: Improving Visualization of miRNA-Target Interaction Networks

scientific article published on 01 January 2019

Cometin is a novel neurotrophic factor that promotes neurite outgrowth and neuroblast migration in vitro and supports survival of spiral ganglion neurons in vivo

scientific article published on 2 October 2011

Comorbidity landscape of the Danish patient population affected by chromosome abnormalities

scientific article published on 25 April 2019

Comparison of computational methods for the identification of cell cycle-regulated genes

scientific article (publication date: 28 October 2004)

Comparison of global gene expression profiles of microdissected human foetal Leydig cells with their normal and hyperplastic adult equivalents

scientific article

Comparison of quantitative trait loci methods: Total expression and allelic imbalance method in brain RNA-seq

scientific article published on 17 June 2019

Compass: a hybrid method for clinical and biobank data mining.

scientific article

Complete Topological Mapping of a Cellular Protein Interactome Reveals Bow-Tie Motifs as Ubiquitous Connectors of Protein Complexes

scientific article published on 01 June 2020

Complete genes may pass from food to human blood.

scientific article

Computational analyses and annotations of theArabidopsisperoxidase gene family

article

Computational applications of DNA structural scales

scientific article published in January 1998

Concordance of gene expression in human protein complexes reveals tissue specificity and pathology

scientific article published on 05 August 2013

Conflicting associations between dietary patterns and changes of anthropometric traits across subgroups of middle-aged women and men

scientific article published on 14 February 2019

Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response

scientific article

Continuum secondary structure captures protein flexibility

scientific article (publication date: February 2002)

Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology

scientific article

Corrigendum: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

scientific article published in Nature

Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia

Country-specific chemical signatures of persistent environmental compounds in breast milk

scientific article published on 24 September 2009

Cross-tissue transcriptome-wide association studies identify susceptibility genes shared between schizophrenia and inflammatory bowel disease

scientific article published on 20 January 2022

Cutavirus in Cutaneous Malignant Melanoma

scientific article published on February 2017

Cyclebase.org a comprehensive multi-organism online database of cell-cycle experiments

scientific article (publication date: 23 December 2007)

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

scientific article (publication date: 24 November 2009)

DBDS Genomic Cohort, a prospective and comprehensive resource for integrative and temporal analysis of genetic, environmental and lifestyle factors affecting health of blood donors

scientific article published on 09 June 2019

DNA Bendability and Nucleosome Positioning in Transcriptional Regulation

DNA structure in human RNA polymerase II promoters

scientific article published on August 1998

Deciphering diseases and biological targets for environmental chemicals using toxicogenomics networks

scientific article

Defining a similarity threshold for a functional protein sequence pattern: the signal peptide cleavage site

scientific article

Definition of supertypes for HLA molecules using clustering of specificity matrices

scientific article published on 13 February 2004

Diagnosis trajectories of prior multi-morbidity predict sepsis mortality

scientific article

Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text

scientific article (publication date: September 2013)

Dietary metabolite profiling brings new insight into the relationship between nutrition and metabolic risk: An IMI DIRECT study

scientific article published on 04 August 2020

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

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

scientific article published on 15 June 2019

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

scientific article

Discrepancies in listed adverse drug reactions in pharmaceutical product information supplied by the regulatory authorities in Denmark and the USA

scientific article (publication date: 22 April 2014)

Disease Trajectories for Hidradenitis Suppurativa in the Danish Population

scientific article published on 20 May 2020

Disease trajectory browser for exploring temporal, population-wide disease progression patterns in 7.2 million Danish patients

scientific article published on 02 October 2020

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

scientific article published on 2 December 2015

Displaying the information contents of structural RNA alignments: the structure logos.

scientific article

Dissecting spatio-temporal protein networks driving human heart development and related disorders

scientific article

Distance distributions in proteins: a six-parameter representation

scientific article published on 01 September 1996

Dose-Specific Adverse Drug Reaction Identification in Electronic Patient Records: Temporal Data Mining in an Inpatient Psychiatric Population

scientific article (publication date: 15 March 2014)

Early differences in islets from prediabetic NOD mice: combined microarray and proteomic analysis

scientific article published on 12 January 2017

Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago

scientific article

Effects of active farnesoid X receptor on GLUTag enteroendocrine L cells

scientific article published on 20 July 2020

Enterotypes of the human gut microbiome

scientific article

Enterotypes of the human gut microbiome

scientific article published in Nature

Erratum to: Dose-Specific Adverse Drug Reaction Identification in Electronic Patient Records: Temporal Data Mining in an Inpatient Psychiatric Population

scientific article (publication date: 9 April 2014)

Erratum: Addendum: Enterotypes of the human gut microbiome

scientific article published in Nature

Estimating heritability and genetic correlations from large health datasets in the absence of genetic data

scientific article published on 03 December 2019

Evolution of Cell Cycle Control: Same Molecular Machines, Different Regulation

scientific article (publication date: August 2007)

Exploiting the past and the future in protein secondary structure prediction

scientific article

Expression profiling of human genetic and protein interaction networks in type 1 diabetes

scientific article published on 17 July 2009

Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics

scientific article

Familial Atrial Septal Defect and Sudden Cardiac Death: Identification of a Novel NKX2-5 Mutation and a Review of the Literature

scientific article published on 18 December 2015

Feature-based prediction of non-classical and leaderless protein secretion

scientific article

Finding Cervical Cancer Symptoms in Swedish Clinical Text using a Machine Learning Approach and NegEx

scientific article published on 5 November 2015

Flexibility of the genetic code with respect to DNA structure

scientific article

Functionality of System Components: Conservation of Protein Function in Protein Feature Space

scientific article (publication date: November 2003)

G+C-rich tract in 5' end of human introns

scientific article published in September 1992

Generating genome-scale candidate gene lists for pharmacogenomics

scientific article published on 15 April 2009

Genetic and environmental risk factors in congenital heart disease functionally converge in protein networks driving heart development

scientific article

Genetic variability in the absorption of dietary sterols affects the risk of coronary artery disease

scientific article published on 01 July 2020

Genome organisation and chromatin structure in Escherichia coli

scientific article published on February 2001

Genome-wide assessment of the association of rare and common copy number variations to testicular germ cell cancer

scientific article published on 29 January 2013

Genomic profiling of thousands of candidate polymorphisms predicts risk of relapse in 778 Danish and German childhood acute lymphoblastic leukemia patients

scientific article

Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae

scientific article

Herpes Simplex Virus Type 1 infection is associated with suicidal behavior and first registered psychiatric diagnosis in a healthy population

scientific article published on 28 June 2019

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

scientific article published on 22 June 2011

Hidden Markov Models for Human Genes ⬇️

scientific article published in January 1994

High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach

scientific article published on 01 September 2019

How Suitable Are Registry Data for Recurrence Risk Calculations? Validation of Diagnoses on 1,593 Families With Congenital Heart Disease

scientific article

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

scientific article

Human gut microbes impact host serum metabolome and insulin sensitivity

scientific article

Huntingtin-interacting protein 14 is a type 1 diabetes candidate protein regulating insulin secretion and beta-cell apoptosis

scientific article

ISMB 2001

scientific article (publication date: June 2001)

ISMB 2006

scientific article

ISMB 2006

scientific article published in 2006

Ibuprofen alters human testicular physiology to produce a state of compensated hypogonadism

scientific article published on 8 January 2018

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

scientific article published on 6 July 2014

Identification and design of p53-derived HLA-A2-binding peptides with increased CTL immunogenicity.

scientific article published on April 2001

Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers

scientific article

Identification of T1D susceptibility genes within the MHC region by combining protein interaction networks and SNP genotyping data

scientific article

Identification of a new hTERT-derived HLA-A*0201 restricted, naturally processed CTL epitope.

scientific article published on 27 April 2007

Identification of biomarkers for glycaemic deterioration in type 2 diabetes

scientific article published in 2023

Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types

scientific article published on 07 August 2019

Identification of odorant-receptor interactions by global mapping of the human odorome

scientific article

Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry

scientific article

Identification of possible adverse drug reactions in clinical notes: The case of glucose-lowering medicines

scientific article (publication date: 2015)

Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites

scientific article (publication date: 1997)

Identifying Sepsis Phenotypes

Identifying the druggable interactome of EWS-FLI1 reveals MCL-1 dependent differential sensitivities of Ewing sarcoma cells to apoptosis inducers

Immune Profiling of Human Gut-Associated Lymphoid Tissue Identifies a Role for Isolated Lymphoid Follicles in Priming of Region-Specific Immunity

scientific article published on 10 March 2020

ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization

scientific article published on May 2009

ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale

scientific article published on June 2010

Implementation and comparison of two text mining methods with a standard pharmacovigilance method for signal detection of medication errors

scientific article published on 24 May 2020

Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach

scientific article published on 12 February 2004

Improved prediction of signal peptides: SignalP 3.0

scientific article (publication date: 16 July 2004)

Improving data and knowledge management to better integrate health care and research.

scientific article

Improving the odds in discriminating "drug-like" from "non drug-like" compounds

scientific article published in November 2000

In Silico Systems Pharmacology to Assess Drug's Therapeutic and Toxic Effects.

scientific article published on 6 September 2016

Incorporating symptom data in longitudinal disease trajectories for more detailed patient stratification

scientific article published on 04 June 2019

Increase in clinically recorded type 2 diabetes after colectomy

scientific article published on 30 October 2018

Individualization of treatments with drugs metabolized by CES1: combining genetics and metabolomics.

scientific article

Integration of clinical chemistry, expression, and metabolite data leads to better toxicological class separation

scientific article

Integration of known DNA, RNA and protein biomarkers provides prediction of anti-TNF response in rheumatoid arthritis: results from the COMBINE study

scientific article published on 15 August 2016

Integrative analysis for finding genes and networks involved in diabetes and other complex diseases

scientific article (publication date: 2007)

Intrauterine exposure to mild analgesics is a risk factor for development of male reproductive disorders in human and rat.

scientific article

Investigating the impact of missense mutations in hCES1 by in silico structure-based approaches

scientific article published on 19 February 2016

Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing

scientific article published on 19 August 2015

KinMutRF: a random forest classifier of sequence variants in the human protein kinase superfamily

scientific article

Kissing loops hide premature termination codons in pre-mRNA of selenoprotein genes and in genes containing programmed ribosomal frameshifts ⬇️

scientific article published on July 1, 1997

Klinefelter syndrome comorbidities linked to increased X chromosome gene dosage and altered protein interactome activity

scientific article

Knowledge engineering for health: a new discipline required to bridge the "ICT gap" between research and healthcare

scientific article published on 04 April 2012

Lapatinib potentiates cytotoxicity of  YM155 in neuroblastoma via inhibition of the ABCB1 efflux transporter

scientific article published on 8 June 2017

Large-scale study of Toxoplasma and Cytomegalovirus shows an association between infection and serious psychiatric disorders

scientific article published on 29 January 2019

Legacy data sharing to improve drug safety assessment: the eTOX project

scientific article published on 13 October 2017

Leveraging European infrastructures to access 1 million human genomes by 2022

scientific article published on 27 August 2019

Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells

scientific article published on 4 August 2014

Linear Motif Atlas for Phosphorylation-Dependent Signaling

scientific article (publication date: 2 September 2008)

Linjedeling med TEX

scientific article (publication date: 1988)

Linjedeling med et neuralt netværk

scientific article (publication date: 1989)

Linking glycemic dysregulation in diabetes to symptoms, comorbidities, and genetics through EHR data mining

scientific article published on 10 December 2019

Lipidomic profiles, lipid trajectories and clinical biomarkers in female elite endurance athletes

scientific article published on 11 February 2020

Locating proteins in the cell using TargetP, SignalP and related tools

scientific article (publication date: 2007)

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.

scientific article published on 15 December 2015

Machine learning approaches for the prediction of signal peptides and other protein sorting signals

scientific article

Many putative endocrine disruptors inhibit prostaglandin synthesis

scientific article

Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease

scientific article

Matching protein beta-sheet partners by feedforward and recurrent neural networks.

scientific article published on January 2000

MatrixPlot: visualizing sequence constraints

scientific article published in September 1999

Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes

scientific article

MetaRanker 2.0: a web server for prioritization of genetic variation data

scientific article (publication date: 22 May 2013)

Metabolite ratios as potential biomarkers for type 2 diabetes: a DIRECT study.

scientific article published on 21 September 2017

Metagenomic species profiling using universal phylogenetic marker genes

scientific article

MicroRNAs, Regulatory Networks, and Comorbidities: Decoding Complex Systems.

scientific article published on January 2017

Mining electronic health records: towards better research applications and clinical care

scientific article (publication date: 2 May 2012)

Modeling the adaptive immune system: predictions and simulations

scientific article published on 28 November 2007

Modelling the human immune system by combining bioinformatics and systems biology approaches

scientific article published on 27 October 2006

Modules, networks and systems medicine for understanding disease and aiding diagnosis.

scientific article

Molecular wring resonances in chain molecules

scientific article published on 01 January 1997

Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2.

scientific article

Multiple alignment using simulated annealing: branch point definition in human mRNA splicing

scientific article published in May 1992

NESbase version 1.0: a database of nuclear export signals

scientific article

Naturally occurring nucleosome positioning signals in human exons and introns

scientific article published in November 1996

Negation scope and spelling variation for text-mining of Danish electronic patient records ⬇️

scientific article (publication date: April 2014)

NetOglyc: prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility

scientific article published in February 1998

Network biology concepts in complex disease comorbidities

scientific article (publication date: October 2016)

Neural network detects errors in the assignment of mRNA splice sites

scientific article

Neural network model of the genetic code is strongly correlated to the GES scale of amino acid transfer free energies

scientific article published in November 1994

Neural network predicts sequence of TP53 gene based on DNA chip

scientific article published in August 2002

Neurale netværk : computere med intuition

New weakly expressed cell cycle-regulated genes in yeast.

scientific article published in November 2005

Non-classical protein secretion in bacteria ⬇️

scientific article

Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios ⬇️

scientific article

Nucleotide sequence database policies

scientific article published in November 2002

O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins

scientific article

O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins

scientific article

O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins

scientific article published on January 1999

O-GLYCBASE: a revised database of O-glycosylated proteins

scientific article

OCT4 and downstream factors are expressed in human somatic urogenital epithelia and in culture of epididymal spheres

scientific article published on 31 January 2010

On the total number of genes and their length distribution in complete microbial genomes

scientific article published in August 2001

Optimization and immune recognition of multiple novel conserved HLA-A2, human immunodeficiency virus type 1-specific CTL epitopes

scientific article published in September 2003

Orphan protein function and its relation to glycosylation.

scientific article

Pancreatic Islet Protein Complexes and Their Dysregulation in Type 2 Diabetes

scientific article published on 20 April 2017

Pathway and network analysis of more than 2,500 whole cancer genomes

Pathway and network analysis of more than 2500 whole cancer genomes

scientific article published on 05 February 2020

Patient stratification and identification of adverse event correlations in the space of 1190 drug related adverse events

scientific article

Periodic sequence patterns in human exons

scientific article published on January 1, 1995

Pharos: Collating protein information to shed light on the druggable genome

scientific article

Phenome-Wide Analysis of Short- and Long-Run Disease Incidence Following Recurrent Pregnancy Loss Using Data From a 39-Year Period

scientific article published on 17 April 2020

PhosphoBase, a database of phosphorylation sites: release 2.0.

scientific article published on January 1999

PhosphoBase: a database of phosphorylation sites

scientific article published in January 1998

Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer

scientific article published on March 2017

Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing

scientific article

Polychlorinated dibenzo-p-dioxins, furans, and biphenyls (PCDDs/PCDFs and PCBs) in breast milk and early childhood growth and IGF1

scientific article published on 02 March 2014

Population genomics of Bronze Age Eurasia

scientific article published on June 2015

Population-wide analysis of differences in disease progression patterns in men and women

scientific article published in Nature Communications

Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags

scientific article

Precision cardiology ⬇️

Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology

scientific article published on 12 April 2013

Precision medicine in complex diseases—Molecular subgrouping for improved prediction and treatment stratification

scientific article published in 2023

Predicting and elucidating the etiology of fatty liver disease: A machine learning modeling and validation study in the IMI DIRECT cohorts

scientific article published on 19 June 2020

Predicting proteasomal cleavage sites: a comparison of available methods

scientific article

Predicting subcellular localization of proteins based on their N-terminal amino acid sequence

scientific article (publication date: 21 July 2000)

Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates

scientific article

Prediction of Human Protein Function from Post-translational Modifications and Localization Features

scientific article (publication date: June 2002)

Prediction of N-terminal protein sorting signals

scientific article

Prediction of disease causing non-synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP.

scientific article

Prediction of glycosylation across the human proteome and the correlation to protein function.

scientific article

Prediction of human mRNA donor and acceptor sites from the DNA sequence

scientific article published in July 1991

Prediction of human protein function according to Gene Ontology categories

scientific article (publication date: 22 March 2003)

Prediction of lipoprotein signal peptides in Gram-negative bacteria

scientific article published on August 2003

Prediction of novel archaeal enzymes from sequence-derived features

scientific article (publication date: 13 April 2009)

Prediction of pH-dependent aqueous solubility of druglike molecules

scientific article

Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence

scientific article (publication date: June 2004)

Prediction of proprotein convertase cleavage sites

scientific article (publication date: 2004)

Prediction of proteasome cleavage motifs by neural networks

scientific article published in April 2002

Prediction of protein secondary structure at 80% accuracy

scientific article published in October 2000

Prediction of the secondary structure of HIV-1 gp120.

scientific article published on May 1996

Prediction of twin-arginine signal peptides

scientific article

Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites

scientific article (publication date: February 2005)

Prenatal exposure to paracetamol/acetaminophen and precursor aniline impairs masculinisation of male brain and behaviour

scientific article published on 30 May 2017

Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing

scientific article published on 27 January 2016

Protective role of the vulture facial and gut microbiomes aid adaptation to scavenging

Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging

Protein annotation in the era of personal genomics

scientific article (publication date: June 2010)

Protein distance constraints predicted by neural networks and probability density functions

scientific article published in November 1997

Protein feature based identification of cell cycle regulated proteins in yeast

scientific article published in June 2003

Protein features as determinants of wild-type glycoside hydrolase thermostability

scientific article

Protein folding and wring resonances

scientific article published in January 1997

Protein interaction-based genome-wide analysis of incident coronary heart disease

scientific article

Protein secondary structure and homology by neural networks The α-helices in rhodopsin

scientific article (publication date: 5 December 1988)

Protein secondary structure: category assignment and predictability

scientific article published on 01 October 2001

Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level

scientific article

Protein structures from distance inequalities

scientific article published in June 1993

Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

scientific article

Quantitative predictions of peptide binding to MHC class I molecules using specificity matrices and anchor-stratified calibrations

scientific article

REACH and Environmental Chemicals

RNA secondary structure and sequence conservation in C1 region of human immunodeficiency virus type 1 env gene

scientific article published in August 2002

Randomized Phase II Study of Nivolumab With or Without Ipilimumab Combined With Stereotactic Body Radiotherapy for Refractory Metastatic Pancreatic Cancer (CheckPAC)

scientific article published in 2022

Ranking factors involved in diabetes remission after bariatric surgery using machine-learning integrating clinical and genomic biomarkers

scientific article published on 26 October 2016

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

scientific article

Recognition of environmental and genetic effects on barley phenolic fingerprints by neural networks

scientific article published in May 2001

Relating genomic variation to drug response in childhood acute lymphoblastic leukemia by multiplexed targeted sequencing.

scientific article published on 11 October 2010

Relationship between protein structure and geometrical constraints

scientific article

Reliable prediction of T-cell epitopes using neural networks with novel sequence representations

scientific article

Reply to 'Mining electronic health records: an additional perspective'

scientific article (publication date: 18 December 2012)

Retinoic Acid Signaling in Thymic Epithelial Cells Regulates Thymopoiesis

scientific article published on 30 May 2018

Richness of human gut microbiome correlates with metabolic markers

scientific article (publication date: 29 August 2013)

Roadmap for a precision-medicine initiative in the Nordic region

scientific article published on 01 June 2019

SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation

scientific article

SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation.

scientific article

Scanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks.

scientific article published in October 1999

Secreted breast tumor interstitial fluid microRNAs and their target genes are associated with triple-negative breast cancer, tumor grade, and immune infiltration

scientific article published on 30 June 2020

Selecting informative data for developing peptide-MHC binding predictors using a query by committee approach.

scientific article

Semen quality and waiting time to pregnancy explored using Association Mining

scientific article published on 21 October 2020

Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach.

scientific article

Sequence and structure-based prediction of eukaryotic protein phosphorylation sites

scientific article (publication date: 17 December 1999)

Sequence-based feature prediction and annotation of proteins

scientific article (publication date: 2009)

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

scientific article published in Nature

Sex differences in text-mined possible adverse drug events associated with drugs for psychosis

scientific article published on 12 February 2020

Sigma A recognition sites in the Bacillus subtilis genome

scientific article published on 01 September 2001

SignalP 4.0: discriminating signal peptides from transmembrane regions

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SignalP 5.0 improves signal peptide predictions using deep neural networks

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Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information

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Statistical analysis of protein kinase specificity determinants

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Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima

scientific article (publication date: February 2000)

Structural basis for triplet repeat disorders: a computational analysis

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Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands

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Systems genetics analysis identifies calcium-signaling defects as novel cause of congenital heart disease

scientific article published on 28 August 2020

TEMPORAL ORDER OF DISEASE PAIRS AFFECTS SUBSEQUENT DISEASE TRAJECTORIES: THE CASE OF DIABETES AND SLEEP APNEA.

scientific article published on January 2016

Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients

scientific article (publication date: 24 June 2014)

Text mining of 15 million full-text scientific articles

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The Atlas visualization of genomewide information

scientific article (publication date: 2002)

The Interplay of Non-coding RNAs and X Chromosome Inactivation in Human Disease

The SH2 domain interaction landscape

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The bio.tools registry of software tools and data resources for the life sciences

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The biology of eukaryotic promoter prediction--a review

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The cancer exome generated by alternative mRNA splicing dilutes predicted HLA class I epitope density

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The genome of a Late Pleistocene human from a Clovis burial site in western Montana

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The governance structure for data access in the DIRECT consortium: an innovative medicines initiative (IMI) project

scholarly article by Harriet J A Teare et al published 4 September 2018 in Life sciences, society and policy

The hunt for fatal myocardial infarction biomarkers: predictive circulating microRNAs

scientific article published on October 2016

The impact of the protein interactome on the syntenic structure of mammalian genomes

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The implications of alternative splicing in the ENCODE protein complement

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The protein kinase SIK downregulates the polarity protein Par3.

scientific article published on 31 December 2017

The role of physical activity in metabolic homeostasis before and after the onset of type 2 diabetes: an IMI DIRECT study

scientific article published on 30 January 2020

The small and large intestine contain related mesenchymal subsets that derive from embryonic Gli1+ precursors

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

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The type 1 diabetes - HLA susceptibility interactome--identification of HLA genotype-specific disease genes for type 1 diabetes

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Time-ordered comorbidity correlations identify patients at risk of mis- and overdiagnosis

scientific article published on 29 January 2021

Tools and data services registry: a community effort to document bioinformatics resources

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Towards standardization guidelines for in silico approaches in personalized medicine

scientific article published on 24 July 2020

Traces of ATCV-1 associated with laboratory component contamination

scientific article published on 5 February 2015

Training neural networks to analyse biological sequences

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Transcriptional interactions suggest niche segregation among microorganisms in the human gut.

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Transcriptome analysis of the adult human Klinefelter testis and cellularity-matched controls reveals disturbed differentiation of Sertoli- and Leydig cells.

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Transcriptome profiling of mice testes following low dose irradiation

scientific article published on 28 May 2013

Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

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Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology

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Unexplored therapeutic opportunities in the human genome

scientific article published on 23 March 2018

Unexplored therapeutic opportunities in the human genome.

scientific article published on 23 February 2018

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

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Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts

scientific article (publication date: 25 August 2011)

Using sequence motifs for enhanced neural network prediction of protein distance constraints

scientific article published in January 1999

Viscous Trees and Voronoi-Structure Formation in Expanding Systems

Whole blood co-expression modules associate with metabolic traits and type 2 diabetes: an IMI-DIRECT study

scientific article published on 01 December 2020

Whole-Exome Sequencing of 2,000 Danish Individuals and the Role of Rare Coding Variants in Type 2 Diabetes

Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes

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[Infrastructure of clinical support and research in the Danish national genome centre] ⬇️

scientific article published on 01 April 2019

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

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hERG classification model based on a combination of support vector machine method and GRIND descriptors

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miRandola 2017: a curated knowledge base of non-invasive biomarkers

scientific article published on 25 September 2017

sAOP: Linking chemical stressors to Adverse Outcomes Pathway Networks

scientific article published on 19 July 2019

wKinMut-2: Identification and Interpretation of Pathogenic Variants in Human Protein Kinases.

scientific article published on 7 October 2015

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