List of works - Joke Reumers

A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays

scientific article

An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins

scientific article

Assessing interactions between the associations of common genetic susceptibility variants, reproductive history and body mass index with breast cancer risk in the breast cancer association consortium: a combined case-control study

scientific article

Erratum: Corrigendum: Exploring the sequence determinants of amyloid structure using position-specific scoring matrices

scholarly article published in Nature Methods

Exploring the sequence determinants of amyloid structure using position-specific scoring matrices

scientific article published on 14 February 2010

Gain of function of mutant p53 by coaggregation with multiple tumor suppressors

Genetic variability in the mitochondrial serine protease HTRA2 contributes to risk for Parkinson disease

scientific article published in June 2008

Genetically Engineered iPSC-Derived FTDP-17 MAPT Neurons Display Mutation-Specific Neurodegenerative and Neurodevelopmental Phenotypes.

scientific article published on 26 July 2018

Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations

scientific article

Halvade-RNA: Parallel variant calling from transcriptomic data using MapReduce.

scientific article

Halvade: scalable sequence analysis with MapReduce

scientific article published on 26 March 2015

Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks

scientific article published on 30 August 2017

Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases

scientific article published on 17 December 2007

Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks

scientific article

Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing.

scientific article published on 18 December 2011

PepX: a structural database of non-redundant protein-peptide complexes

scientific article published on 30 October 2009

Performance assessment of the Illumina massively parallel sequencing platform for deep sequencing analysis of viral minority variants.

scientific article

Pipit: visualizing functional impacts of structural variations

scientific article

Protein sequences encode safeguards against aggregation.

scientific article

PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes

scientific article

QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles

scientific article published on 10 November 2015

Reconstruction of protein backbones from the BriX collection of canonical protein fragments

scientific article

SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants

scientific article

SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs

scientific article published on 29 June 2006

SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs

scientific article

Sequencing of DISC1 pathway genes reveals increased burden of rare missense variants in schizophrenia patients from a northern Swedish population.

scientific article

Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations

scientific article

VEGF pathway genetic variants as biomarkers of treatment outcome with bevacizumab: an analysis of data from the AViTA and AVOREN randomised trials

scientific article

ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering

scientific article

VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering

scientific article published on 31 August 2014

Whole-genome sequencing reveals a coding non-pathogenic variant tagging a non-coding pathogenic hexanucleotide repeat expansion in C9orf72 as cause of amyotrophic lateral sclerosis

scientific article

elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling

scientific article published on 16 July 2015

α-Galactosidase aggregation is a determinant of pharmacological chaperone efficacy on Fabry disease mutants

scientific article published on 6 July 2012

List of works by Joke Reumers

A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays

An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins

Assessing interactions between the associations of common genetic susceptibility variants, reproductive history and body mass index with breast cancer risk in the breast cancer association consortium: a combined case-control study

Erratum: Corrigendum: Exploring the sequence determinants of amyloid structure using position-specific scoring matrices

Exploring the sequence determinants of amyloid structure using position-specific scoring matrices

Gain of function of mutant p53 by coaggregation with multiple tumor suppressors

Genetic variability in the mitochondrial serine protease HTRA2 contributes to risk for Parkinson disease

Genetically Engineered iPSC-Derived FTDP-17 MAPT Neurons Display Mutation-Specific Neurodegenerative and Neurodevelopmental Phenotypes.

Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations

Halvade-RNA: Parallel variant calling from transcriptomic data using MapReduce.

Halvade: scalable sequence analysis with MapReduce

Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks

Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases

Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks

Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing.

PepX: a structural database of non-redundant protein-peptide complexes

Performance assessment of the Illumina massively parallel sequencing platform for deep sequencing analysis of viral minority variants.

Pipit: visualizing functional impacts of structural variations

Protein sequences encode safeguards against aggregation.

PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes

QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles

Reconstruction of protein backbones from the BriX collection of canonical protein fragments

SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants

SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs

SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs

Sequencing of DISC1 pathway genes reveals increased burden of rare missense variants in schizophrenia patients from a northern Swedish population.

Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations

VEGF pathway genetic variants as biomarkers of treatment outcome with bevacizumab: an analysis of data from the AViTA and AVOREN randomised trials

ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering

VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering

Whole-genome sequencing reveals a coding non-pathogenic variant tagging a non-coding pathogenic hexanucleotide repeat expansion in C9orf72 as cause of amyotrophic lateral sclerosis

elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling

α-Galactosidase aggregation is a determinant of pharmacological chaperone efficacy on Fabry disease mutants