List of works - Adam Ameur

1.12 Transcriptome Sequencing Reveals Novel Mutations and Differential Gene Expression in Stereotyped Subsets of Chronic Lymphocytic Leukemia

article

A nonsense mutation in CEP55 defines a new locus for a Meckel-like syndrome, an autosomal recessive lethal fetal ciliopathy.

scientific article published on 14 March 2017

A novel approach using long-read sequencing and ddPCR to investigate gonadal mosaicism and estimate recurrence risk in two families with developmental disorders

scientific article published on 16 September 2017

A novel variant in MYLK causes thoracic aortic dissections: genotypic and phenotypic description.

scientific article

Abolished InsP3R2 function inhibits sweat secretion in both humans and mice.

scientific article

Analysis of hepatitis C NS5A resistance associated polymorphisms using ultra deep single molecule real time (SMRT) sequencing

scientific article published on 18 December 2015

Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays

scientific article

Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes

scientific article published in June 2007

CanvasDB: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects

scientific article

Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing

scientific article

Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3

scientific article

Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing

scientific article

Data-driven unbiased curation of the TP53 tumor suppressor gene mutation database and validation by ultradeep sequencing of human tumors

scientific article

De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data

scientific article published on 09 October 2018

De novoassembly of two Swedish genomes reveals missing segments from the human GRCh38 reference and improves variant calling of population-scale sequencing data

Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing

scientific article published on 12 July 2018

Determination of obesity associated gene variants related to TMEM18 through ultra-deep targeted re-sequencing in a case-control cohort for pediatric obesity.

scientific article published on 14 September 2015

Determination of the obesity-associated gene variants within the entire FTO gene by ultra-deep targeted sequencing in obese and lean children

scientific article

Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems

scientific article

Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq

scientific article published in 2009

Discovery of Novel Sequences in 1,000 Swedish Genomes

scientific article published on 01 January 2020

Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues

scientific article

Endocan is a VEGF-A and PI3K regulated gene with increased expression in human renal cancer.

scientific article published on 6 February 2007

Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes

scientific article published on 30 November 2020

Expression profiling and in situ screening of circular RNAs in human tissues

scientific article published in Scientific Reports

Genetic adaptation of fatty-acid metabolism: a human-specific haplotype increasing the biosynthesis of long-chain omega-3 and omega-6 fatty acids

scientific article published on 12 April 2012

Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention ⬇️

scientific article published on 7 September 2022

Global and unbiased detection of splice junctions from RNA-seq data

scientific article (publication date: 2010)

Global gene expression analysis by combinatorial optimization

scientific article published in January 2004

Goodbye reference, hello genome graphs

scientific article published on 01 August 2019

High throughput expression profiling and in situ screening of circular RNAs in tissues

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP

scientific article

Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing

scientific article

Identification of novel genetic causes of Rett syndrome-like phenotypes

scientific article published on 6 January 2016

Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia

scientific article published on 15 April 2020

Intratumoral genome diversity parallels progression and predicts outcome in pediatric cancer

scientific article published on 27 January 2015

Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies

scientific article

Molecular characterization of a large unselected cohort of metastatic colorectal cancers in relation to primary tumor location, rare metastatic sites and prognosis

scientific article published on 10 January 2020

MuSK: a new target for lethal fetal akinesia deformation sequence (FADS).

scientific article published on 22 January 2015

Mutation in CEP63 co-segregating with developmental dyslexia in a Swedish family

scientific article

Next generation RNA-sequencing in prognostic subsets of chronic lymphocytic leukemia

scientific article published on 3 June 2012

Novel genes in cell cycle control and lipid metabolism with dynamically regulated binding sites for sterol regulatory element-binding protein 1 and RNA polymerase II in HepG2 cells detected by chromatin immunoprecipitation with microarray detection.

scientific article

PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c

scientific article

Phenotypic expansion of visceral myopathy associated with ACTG2 tandem base substitution.

scientific article published on 18 March 2015

Revertant mosaicism repairs skin lesions in a patient with keratitis-ichthyosis-deafness syndrome by second-site mutations in connexin 26.

scientific article

Role of the AMP kinase in cytokine-induced human EndoC-βH1 cell death

scientific article published on 23 July 2015

SNX10 gene mutation leading to osteopetrosis with dysfunctional osteoclasts

scientific article

Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits

scientific article published on 3 August 2011

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

scientific article published in February 2018

Single-Molecule Sequencing: Towards Clinical Applications

scientific article published on 13 August 2018

Somatic cells with a heavy mitochondrial DNA mutational load render induced pluripotent stem cells with distinct differentiation defects.

scientific article published in May 2014

Splicing in the human brain

scientific article

SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.

scientific article

SweHLA: the high confidence HLA typing bio-resource drawn from 1000 Swedish genomes

scientific article published on 16 December 2019

The LCB Data Warehouse

scientific article published on 2 February 2006

The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly

scientific article published on 23 January 2020

The TGFB2-AS1 lncRNA Regulates TGF-β Signaling by Modulating Corepressor Activity

scientific article published on 01 September 2019

The Versatility of SMRT Sequencing

article

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

scientific article published on 6 November 2011

Transcription factor ZBED6 affects gene expression, proliferation, and cell death in pancreatic beta cells

scientific article published on 16 September 2013

Transcriptional profiling reveals a critical role for tyrosine phosphatase VE-PTP in regulation of VEGFR2 activity and endothelial cell morphogenesis

scientific article

Transcriptome Profiling Reveals Degree of Variability in Induced Pluripotent Stem Cell Lines: Impact for Human Disease Modeling

scientific article published on 8 September 2015

Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach

scientific article published on 16 July 2020

Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins

scientific article

Welander distal myopathy caused by an ancient founder mutation in TIA1 associated with perturbed splicing.

scientific article

Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders

scientific article

Xdrop: Targeted sequencing of long DNA molecules from low input samples using droplet sorting

scientific article published on 09 June 2020

List of works by Adam Ameur

1.12 Transcriptome Sequencing Reveals Novel Mutations and Differential Gene Expression in Stereotyped Subsets of Chronic Lymphocytic Leukemia

A nonsense mutation in CEP55 defines a new locus for a Meckel-like syndrome, an autosomal recessive lethal fetal ciliopathy.

A novel approach using long-read sequencing and ddPCR to investigate gonadal mosaicism and estimate recurrence risk in two families with developmental disorders

A novel variant in MYLK causes thoracic aortic dissections: genotypic and phenotypic description.

Abolished InsP3R2 function inhibits sweat secretion in both humans and mice.

Analysis of hepatitis C NS5A resistance associated polymorphisms using ultra deep single molecule real time (SMRT) sequencing

Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays

Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes

CanvasDB: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects

Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing

Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3

Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing

Data-driven unbiased curation of the TP53 tumor suppressor gene mutation database and validation by ultradeep sequencing of human tumors

De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data

De novoassembly of two Swedish genomes reveals missing segments from the human GRCh38 reference and improves variant calling of population-scale sequencing data

Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing

Determination of obesity associated gene variants related to TMEM18 through ultra-deep targeted re-sequencing in a case-control cohort for pediatric obesity.

Determination of the obesity-associated gene variants within the entire FTO gene by ultra-deep targeted sequencing in obese and lean children

Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems

Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq

Discovery of Novel Sequences in 1,000 Swedish Genomes

Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues

Endocan is a VEGF-A and PI3K regulated gene with increased expression in human renal cancer.

Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes

Expression profiling and in situ screening of circular RNAs in human tissues

Genetic adaptation of fatty-acid metabolism: a human-specific haplotype increasing the biosynthesis of long-chain omega-3 and omega-6 fatty acids

Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention ⬇️

Global and unbiased detection of splice junctions from RNA-seq data

Global gene expression analysis by combinatorial optimization

Goodbye reference, hello genome graphs

High throughput expression profiling and in situ screening of circular RNAs in tissues

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP

Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing

Identification of novel genetic causes of Rett syndrome-like phenotypes

Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia

Intratumoral genome diversity parallels progression and predicts outcome in pediatric cancer

Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies

Molecular characterization of a large unselected cohort of metastatic colorectal cancers in relation to primary tumor location, rare metastatic sites and prognosis

MuSK: a new target for lethal fetal akinesia deformation sequence (FADS).

Mutation in CEP63 co-segregating with developmental dyslexia in a Swedish family

Next generation RNA-sequencing in prognostic subsets of chronic lymphocytic leukemia

Novel genes in cell cycle control and lipid metabolism with dynamically regulated binding sites for sterol regulatory element-binding protein 1 and RNA polymerase II in HepG2 cells detected by chromatin immunoprecipitation with microarray detection.

PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c

Phenotypic expansion of visceral myopathy associated with ACTG2 tandem base substitution.

Revertant mosaicism repairs skin lesions in a patient with keratitis-ichthyosis-deafness syndrome by second-site mutations in connexin 26.

Role of the AMP kinase in cytokine-induced human EndoC-βH1 cell death

SNX10 gene mutation leading to osteopetrosis with dysfunctional osteoclasts

Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

Single-Molecule Sequencing: Towards Clinical Applications

Somatic cells with a heavy mitochondrial DNA mutational load render induced pluripotent stem cells with distinct differentiation defects.

Splicing in the human brain

SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.

SweHLA: the high confidence HLA typing bio-resource drawn from 1000 Swedish genomes

The LCB Data Warehouse

The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly

The TGFB2-AS1 lncRNA Regulates TGF-β Signaling by Modulating Corepressor Activity

The Versatility of SMRT Sequencing

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

Transcription factor ZBED6 affects gene expression, proliferation, and cell death in pancreatic beta cells

Transcriptional profiling reveals a critical role for tyrosine phosphatase VE-PTP in regulation of VEGFR2 activity and endothelial cell morphogenesis

Transcriptome Profiling Reveals Degree of Variability in Induced Pluripotent Stem Cell Lines: Impact for Human Disease Modeling

Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach

Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins

Welander distal myopathy caused by an ancient founder mutation in TIA1 associated with perturbed splicing.

Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders

Xdrop: Targeted sequencing of long DNA molecules from low input samples using droplet sorting