Adam Ameur
Bioinformatician at Institutionen för immunologi, genetik och patologi; Faciliteter; Uppsala genomcenter
- Telephone:
- +46 18 471 48 41
- Mobile phone:
- +46 70 425 02 79
- E-mail:
- adam.ameur@igp.uu.se
- Visiting address:
- BMC, Husargatan 3
75122 Uppsala - Postal address:
- Box 815
75108 Uppsala
- ORCID:
- 0000-0001-6085-6749
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Short presentation
Associate professor and senior bioinformatician at the SciLifeLab National Genomics Infrastructure, Uppsala University, Sweden. My work is focused on technology development and novel sequencing applications for the study of human health and disease. Ongoing activities include the construction of a whole-genome reference dataset for genetic variation in the Swedish population, as well as new long-read sequencing based solutions for biomedical research.
Keywords
- bioinformatics
- genomics
- sequencing
Publications
Selection of publications
- Long-read whole-genome analysis of human single cells (2023)
- CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations (2022)
- Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts (2021)
- CRISPR and Long-Read Sequencing (2020)
- Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity (2020)
- Goodbye reference, hello genome graphs (2019)
- Single-Molecule Sequencing (2019)
- De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data (2018)
- Single molecule real-time (SMRT) sequencing comes of age (2018)
- Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing (2018)
- SweGen (2017)
- PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c (2017)
- Identification of novel genetic causes of Rett syndrome-like phenotypes (2016)
- Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing (2015)
- CanvasDB (2014)
- Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing (2014)
- Genetic Adaptation of Fatty-Acid Metabolism (2012)
- Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain (2011)
- Global and unbiased detection of splice junctions from RNA-seq data (2010)
- Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing (2010)
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project (2007)
Recent publications
- Exonic trinucleotide repeat expansions in ZFHX3 cause spinocerebellar ataxia type 4 (2024)
- Complete Mitochondrial DNA Genome Variation in the Swedish Population (2023)
- Long-read whole-genome analysis of human single cells (2023)
- A novel quantitative targeted analysis of X-chromosome Inactivation (XCI) using Nanopore sequencing (2023)
- The Broad Spectrum of TP53 Mutations in CLL (2023)
All publications
Articles
- Exonic trinucleotide repeat expansions in ZFHX3 cause spinocerebellar ataxia type 4 (2024)
- Complete Mitochondrial DNA Genome Variation in the Swedish Population (2023)
- Long-read whole-genome analysis of human single cells (2023)
- A novel quantitative targeted analysis of X-chromosome Inactivation (XCI) using Nanopore sequencing (2023)
- The Broad Spectrum of TP53 Mutations in CLL (2023)
- Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH (2023)
- Transposable element insertions in 1000 Swedish individuals (2023)
- Copy number variations and their effect on the plasma proteome. (2023)
- Novel cancer gene discovery using a forward genetic screen in RCAS-PDGFB-driven gliomas (2023)
- CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations (2022)
- Loss of Nexilin function leads to a recessive lethal fetal cardiomyopathy characterized by cardiomegaly and endocardial fibroelastosis (2022)
- Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening (2022)
- The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies (2022)
- Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention (2022)
- Immune cells lacking Y chromosome show dysregulation of autosomal gene expression (2021)
- Phylogenetic history of patrilineages rare in northern and eastern Europe from large-scale re-sequencing of human Y-chromosomes (2021)
- A polygenic risk score predicts mosaic loss of chromosome Y in circulating blood cells (2021)
- Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts (2021)
- CRISPR and Long-Read Sequencing (2020)
- Discovery of Novel Sequences in 1,000 Swedish Genomes (2020)
- Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes (2020)
- Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia (2020)
- Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity (2020)
- SweHLA (2020)
- Molecular characterization of a large unselected cohort of metastatic colorectal cancers in relation to primary tumor location, rare metastatic sites and prognosis (2020)
- The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly (2020)
- Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach (2020)
- Goodbye reference, hello genome graphs (2019)
- Single-Molecule Sequencing (2019)
- Invasive cervical tumors with high and low HPV titer represent molecular subgroups with different disease etiology (2019)
- The Versatility of SMRT Sequencing (2019)
- The TGFB2-AS1 lncRNA Regulates TGF-beta Signaling by Modulating Corepressor Activity (2019)
- De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data (2018)
- Single molecule real-time (SMRT) sequencing comes of age (2018)
- Stereocilin gene variants associated with episodic vertigo (2018)
- Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing (2018)
- Single-molecule DNA sequencing of acute myeloid leukemia and myelodysplastic syndromes with multiple TP53 alterations (2018)
- A novel ECEL1 mutation expands the phenotype of distal arthrogryposis multiplex congenita type 5D to include pretibial vertical skin crease (2018)
- Expression profiling and in situ screening of circular RNAs in human tissues (2018)
- SweGen (2017)
- A nonsense mutation in CEP55 defines a new locus for a Meckel-like syndrome, an autosomal recessive lethal fetal ciliopathy. (2017)
- Revertant mosaicism repairs skin lesions in a patient with keratitis-ichthyosis-deafness syndrome by second-site mutations in connexin 26 (2017)
- PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c (2017)
- SNX10 gene mutation leading to osteopetrosis with dysfunctional osteoclasts. (2017)
- A novel approach using long-read sequencing and ddPCR to investigate gonadal mosaicism and estimate recurrence risk in two families with developmental disorders (2017)
- Analysis of hepatitis C NS5A resistance associated polymorphisms using ultra deep single molecule real time (SMRT) sequencing (2016)
- A novel variant in MYLK causes thoracic aortic dissections (2016)
- Identification of novel genetic causes of Rett syndrome-like phenotypes (2016)
- Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies (2016)
- Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing (2015)
- Mutation in CEP63 co-segregating with developmental dyslexia in a Swedish family (2015)
- Role of the AMP kinase in cytokine-induced human EndoC-beta H1 cell death (2015)
- Phenotypic expansion of visceral myopathy associated with ACTG2 tandem base substitution (2015)
- Intratumoral genome diversity parallels progression and predicts outcome in pediatric cancer (2015)
- Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems (2015)
- Determination of obesity associated gene variants related to TMEM18 through ultra-deep targeted re-sequencing in a case-control cohort for pediatric obesity. (2015)
- Transcriptome Profiling Reveals Degree of Variability in Induced Pluripotent Stem Cell Lines (2015)
- MuSK (2015)
- CanvasDB (2014)
- Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing (2014)
- Abolished InsP3R2 function inhibits sweat secretion in both humans and mice (2014)
- Somatic Cells with a Heavy Mitochondrial DNA Mutational Load Render Induced Pluripotent Stem Cells with Distinct Differentiation Defects (2014)
- Omega-3 and omega-6 fatty acids are more efficiently synthesized in populations having a high frequency of the derived FADS-haplotype (2013)
- Welander Distal Myopathy Caused by an Ancient Founder Mutation in TIA1 Associated with Perturbed Splicing. (2013)
- Ultra-deep targeted re-sequencing of TMEM18 in two cohorts of European children detects new genetic variants associated with obesity (2013)
- Determination of the obesity-associated gene variants within the entire FTO gene by ultra-deep targeted sequencing in obese and lean children. (2013)
- Transcription factor ZBED6 affects gene expression, proliferation, and cell death in pancreatic beta cells (2013)
- Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues (2013)
- Genetic Adaptation of Fatty-Acid Metabolism (2012)
- Data-driven unbiased curation of the TP53 tumor suppressor gene mutation database and validation by ultradeep sequencing of human tumors (2012)
- Next generation RNA-sequencing in prognostic subsets of chronic lymphocytic leukemia (2012)
- Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits (2012)
- Ultra-deep sequencing of mouse mitochondrial DNA (2011)
- Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain (2011)
- Global and unbiased detection of splice junctions from RNA-seq data (2010)
- Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing (2010)
- Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP (2009)
- Transcriptional profiling reveals a critical role for tyrosine phosphatase VE-PTP in regulation of VEGFR2 activity and endothelial cell morphogenesis (2009)
- Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq (2009)
- 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 (2009)
- Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3 (2008)
- 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 (2008)
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project (2007)
- Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes (2007)
- Endocan is a VEGF-A and PI3K regulated gene with increased expression in human renal cancer (2007)
- T2T-CHM13 improves read mapping and detection of clinically relevant variation
Books
Chapters
