Adam Ameur

T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population

Schmitz, Daniel; Ameur, Adam; Johansson, Åsa

Part of Genome Research, p. 2377-2388, 2025

• DOI for T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population

A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities

Eisfeldt, Jesper; Ameur, Adam; Lenner, Felix; Ten Berk de Boer, Esmee et al.

Part of Genome Research, p. 1774-1784, 2024

• DOI for A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities

Long-read whole-genome analysis of human single cells

Hård, Joanna; Mold, Jeff E; Eisfeldt, Jesper; Tellgren-Roth, Christian et al.

Part of Nature Communications, 2023

• DOI for Long-read whole-genome analysis of human single cells
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CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations

Höijer, Ida; Emmanouilidou, Anastasia; Östlund, Rebecka; van Schendel, Robin et al.

Part of Nature Communications, 2022

• DOI for CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations
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Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts

Zaghlool, Ammar; Niazi, Adnan; Björklund, Åsa K.; Orzechowski Westholm, Jakub et al.

Part of Scientific Reports, 2021

• DOI for Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts
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Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity

Höijer, Ida; Johansson, Josefin; Gudmundsson, Sanna; Chin, Chen-Shan et al.

Part of Genome Biology, 2020

• DOI for Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity
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CRISPR and Long-Read Sequencing: A Perfect Match.

Ameur, Adam

Part of The CRISPR journal, p. 425-427, 2020

• DOI for CRISPR and Long-Read Sequencing: A Perfect Match.

Single-Molecule Sequencing: Towards Clinical Applications

Ameur, Adam; Kloosterman, Wigard P.; Hestand, Matthew S.

Part of Trends in Biotechnology, p. 72-85, 2019

• DOI for Single-Molecule Sequencing: Towards Clinical Applications

Goodbye reference, hello genome graphs

Ameur, Adam

Part of Nature Biotechnology, p. 866-868, 2019

• DOI for Goodbye reference, hello genome graphs

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

Ardui, Simon; Ameur, Adam; Vermeesch, Joris R.; Hestand, Matthew S.

Part of Nucleic Acids Research, p. 2159-2168, 2018

• DOI for Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics
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Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing

Höijer, Ida; Tsai, Yu-Chih; Clark, Tyson A.; Kotturi, Paul et al.

Part of Human Mutation, p. 1262-1272, 2018

• DOI for Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing
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De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data

Ameur, Adam; Che, Huiwen; Martin, Marcel; Bunikis, Ignas et al.

Part of Genes, 2018

• DOI for De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data
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SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population

Ameur, Adam; Dahlberg, Johan; Olason, Pall; Vezzi, Francesco et al.

Part of European Journal of Human Genetics, p. 1253-1260, 2017

• DOI for SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population
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PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c

Pan, Gang; Ameur, Adam; Enroth, Stefan; Bysani, Madhusudhan et al.

Part of Nucleic Acids Research, p. 2408-2422, 2017

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

Identification of novel genetic causes of Rett syndrome-like phenotypes

Lopes, Fatima; Barbosa, Mafalda; Ameur, Adam; Soares, Gabriela et al.

Part of Journal of Medical Genetics, p. 190-199, 2016

• DOI for Identification of novel genetic causes of Rett syndrome-like phenotypes

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

Cavelier, Lucia; Ameur, Adam; Häggqvist, Susana; Höijer, Ida et al.

Part of BMC Cancer, 2015

• DOI for Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing
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CanvasDB: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects

Ameur, Adam; Bunikis, Ignas; Enroth, Stefan; Gyllensten, Ulf

Part of Database, 2014

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

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

Ameur, Adam; Meiring, Tracy L.; Bunikis, Ignas; Häggqvist, Susana et al.

Part of Scientific Reports, p. 4398, 2014

• DOI for Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing
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Genetic Adaptation of Fatty-Acid Metabolism: A Human-Specific Haplotype Increasing the Biosynthesis of Long-Chain Omega-3 and Omega-6 Fatty Acids

Ameur, Adam; Enroth, Stefan; Johansson, Åsa; Zaboli, Ghazal et al.

Part of American Journal of Human Genetics, p. 809-820, 2012

• DOI for Genetic Adaptation of Fatty-Acid Metabolism: A Human-Specific Haplotype Increasing the Biosynthesis of Long-Chain Omega-3 and Omega-6 Fatty Acids

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

Ameur, Adam; Zaghlool, Ammar; Halvardson, Jonatan; Wetterbom, Anna et al.

Part of Nature Structural & Molecular Biology, p. 1435-1440, 2011

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

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

Ameur, Adam; Wetterbom, Anna; Feuk, Lars; Gyllensten, Ulf

Part of Genome Biology, 2010

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

Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing

Wetterbom, Anna; Ameur, Adam; Feuk, Lars; Gyllensten, Ulf et al.

Part of Genome Biology, 2010

• DOI for Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing

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

Birney, Ewan; Stamatoyannopoulos, John A.; Dutta, Anindya; Guigó, Roderic et al.

Part of Nature, p. 799-816, 2007

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

Accurate characterization of CRISPR-Cas9 genome editing outcomes and mosaicism with near-perfect long reads

Höijer, Ida; van Schendel, Robin; Emmanouilidou, Anastasia; Östlund, Rebecka et al.

Part of Genome Medicine, 2026

• DOI for Accurate characterization of CRISPR-Cas9 genome editing outcomes and mosaicism with near-perfect long reads
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Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis

Lenner, Felix; Jemt, Anders; Pena Perez, Lucia; Neethiraj, Ramprasad et al.

Part of Bioinformatics, 2026

• DOI for Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis
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Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases

Höjer, Pontus; Alneberg, Johannes; Lundin, Pär; Martin, Tom et al.

Part of NAR Genomics and Bioinformatics, 2026

• DOI for Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases
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T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population

Schmitz, Daniel; Ameur, Adam; Johansson, Åsa

Part of Genome Research, p. 2377-2388, 2025

• DOI for T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population

Single cell long read whole genome sequencing reveals somatic transposon activity in human brain

Izydorczyk, Michal B.; Kalef-Ezra, Ester; Horner, Dominic W.; Zheng, Xinchang et al.

Part of Communications Biology, 2025

• DOI for Single cell long read whole genome sequencing reveals somatic transposon activity in human brain
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Accurate characterization of CRISPR-Cas9 genome editing outcomes and mosaicism with near-perfect long reads

Höijer, Ida; van Schendel, Robin; Emmanouilidou, Anastasia; Östlund, Rebecka et al.

Part of Genome Medicine, 2026

• DOI for Accurate characterization of CRISPR-Cas9 genome editing outcomes and mosaicism with near-perfect long reads
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Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis

Lenner, Felix; Jemt, Anders; Pena Perez, Lucia; Neethiraj, Ramprasad et al.

Part of Bioinformatics, 2026

• DOI for Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis
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Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases

Höjer, Pontus; Alneberg, Johannes; Lundin, Pär; Martin, Tom et al.

Part of NAR Genomics and Bioinformatics, 2026

• DOI for Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases
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T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population

Schmitz, Daniel; Ameur, Adam; Johansson, Åsa

Part of Genome Research, p. 2377-2388, 2025

• DOI for T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population

Single cell long read whole genome sequencing reveals somatic transposon activity in human brain

Izydorczyk, Michal B.; Kalef-Ezra, Ester; Horner, Dominic W.; Zheng, Xinchang et al.

Part of Communications Biology, 2025

• DOI for Single cell long read whole genome sequencing reveals somatic transposon activity in human brain
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UYSD: a novel data repository accessible via public website for worldwide population frequencies of Y-SNP haplogroups

Ralf, Arwin; Zandstra, Dion; van Wersch, Bram; Köksal, Zehra et al.

Part of European Journal of Human Genetics, p. 904-912, 2025

• DOI for UYSD: a novel data repository accessible via public website for worldwide population frequencies of Y-SNP haplogroups
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A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

Lysenkova, Mariya; Arvidsson, Gustav; Bunikis, Ignas; Lundmark, Anders et al.

Part of Life Science Alliance, 2024

• DOI for A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing
• Download full text (pdf) of A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities

Eisfeldt, Jesper; Ameur, Adam; Lenner, Felix; Ten Berk de Boer, Esmee et al.

Part of Genome Research, p. 1774-1784, 2024

• DOI for A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities

Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR

De Coster, Wouter; Höijer, Ida; Bruggeman, Inge; D'Hert, Svenn et al.

Part of Genome Research, p. 2074-2080, 2024

• DOI for Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR
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Exonic trinucleotide repeat expansions in ZFHX3 cause spinocerebellar ataxia type 4: A poly-glycine disease

Wallenius, Joel; Kafantari, Efthymia; Jhaveri, Emma; Gorcenco, Sorina et al.

Part of American Journal of Human Genetics, p. 82-95, 2024

• DOI for Exonic trinucleotide repeat expansions in ZFHX3 cause spinocerebellar ataxia type 4: A poly-glycine disease
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Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps

Bilgrav Saether, Kristine; Eisfeldt, Jesper; Bengtsson, Jesse D.; Lun, Ming Yin et al.

Part of Genome Research, p. 1785-1797, 2024

• DOI for Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps

Long-read sequencing and optical mapping generates near T2T assemblies that resolves a centromeric translocation

ten Berk de Boer, Esmee; Ameur, Adam; Bunikis, Ignas; Ek, Marlene et al.

Part of Scientific Reports, 2024

• DOI for Long-read sequencing and optical mapping generates near T2T assemblies that resolves a centromeric translocation
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Gustavson syndrome is caused by an in-frame deletion in RBMX associated with potentially disturbed SH3 domain interactions

Johansson, Josefin; Lidéus, Sarah; Frykholm, Carina; Gunnarsson, Cecilia et al.

Part of European Journal of Human Genetics, 2024

• DOI for Gustavson syndrome is caused by an in-frame deletion in RBMX associated with potentially disturbed SH3 domain interactions
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MDM2 amplification in rod-shaped chromosomes provides clues to early stages of circularized gene amplification in liposarcoma

Sydow, Saskia; Piccinelli, Paul; Mitra, Shamik; Tsagkozis, Panagiotis et al.

Part of Communications Biology, 2024

• DOI for MDM2 amplification in rod-shaped chromosomes provides clues to early stages of circularized gene amplification in liposarcoma
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The long non-coding RNA LINC00707 interacts with Smad proteins to regulate TGFβ signaling and cancer cell invasion

Gélabert, Caroline; Papoutsoglou, Panagiotis; Cancela Golan, Irene; Ahlström, Eric et al.

Part of Cell Communication and Signaling, 2023

• DOI for The long non-coding RNA LINC00707 interacts with Smad proteins to regulate TGFβ signaling and cancer cell invasion
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Copy number variations and their effect on the plasma proteome

Schmitz, Daniel; Li, Zhiwei; Lo Faro, Valeria; Rask-Andersen, Mathias et al.

Part of Genetics, 2023

• DOI for Copy number variations and their effect on the plasma proteome
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A novel quantitative targeted analysis of X-chromosome Inactivation (XCI) using Nanopore sequencing

Johansson, Josefin; Lidéus, Sarah; Höijer, Ida; Ameur, Adam et al.

Part of Scientific Reports, 2023

• DOI for A novel quantitative targeted analysis of X-chromosome Inactivation (XCI) using Nanopore sequencing
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The Broad Spectrum of TP53 Mutations in CLL: Evidence of Multiclonality and Novel Mutation Hotspots

Lazarian, Gregory; Leroy, Bernard; Theves, Floriane; Hormi, Myriam et al.

Part of Human Mutation, 2023

• DOI for The Broad Spectrum of TP53 Mutations in CLL: Evidence of Multiclonality and Novel Mutation Hotspots

Transposable element insertions in 1000 Swedish individuals

Saether, Kristine Bilgrav; Nilsson, Daniel; Thonberg, Håkan; Tham, Emma et al.

Part of PLOS ONE, 2023

• DOI for Transposable element insertions in 1000 Swedish individuals
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Long-read whole-genome analysis of human single cells

Hård, Joanna; Mold, Jeff E; Eisfeldt, Jesper; Tellgren-Roth, Christian et al.

Part of Nature Communications, 2023

• DOI for Long-read whole-genome analysis of human single cells
• Download full text (pdf) of Long-read whole-genome analysis of human single cells

Complete Mitochondrial DNA Genome Variation in the Swedish Population

Andreaggi, Kimberly; Bodner, Martin; Ring, Joseph D.; Ameur, Adam et al.

Part of Genes, p. 1989-1989, 2023

• DOI for Complete Mitochondrial DNA Genome Variation in the Swedish Population
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Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH

Lysenkova Wiklander, Mariya; Övernäs, Elin; Lagensjö, Johanna; Raine, Amanda et al.

Part of BMC Research Notes, 2023

• DOI for Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH
• Download full text (pdf) of Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH

Novel cancer gene discovery using a forward genetic screen in RCAS-PDGFB-driven gliomas

Weishaupt, Holger; Čančer, Matko; Rosén, Gabriela; Holmberg, Karl O. et al.

Part of Neuro-Oncology, p. 97-107, 2023

• DOI for Novel cancer gene discovery using a forward genetic screen in RCAS-PDGFB-driven gliomas
• Download full text (pdf) of Novel cancer gene discovery using a forward genetic screen in RCAS-PDGFB-driven gliomas

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

Wang, Zhe; Emmerich, Andrew; Pillon, Nicolas J; Moore, Tim et al.

Part of Nature Genetics, p. 1332-1344, 2022

• DOI for Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention
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Loss of Nexilin function leads to a recessive lethal fetal cardiomyopathy characterized by cardiomegaly and endocardial fibroelastosis

Johansson, Josefin; Frykholm, Carina; Ericson, Katharina; Kazamia, Kalliopi et al.

Part of American Journal of Medical Genetics. Part A, p. 1676-1687, 2022

• DOI for Loss of Nexilin function leads to a recessive lethal fetal cardiomyopathy characterized by cardiomegaly and endocardial fibroelastosis
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CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations

Höijer, Ida; Emmanouilidou, Anastasia; Östlund, Rebecka; van Schendel, Robin et al.

Part of Nature Communications, 2022

• DOI for CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations
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The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes

Sturk-Andreaggi, Kimberly; Ring, Joseph D.; Ameur, Adam; Gyllensten, Ulf et al.

Part of International Journal of Molecular Sciences, 2022

• DOI for The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes
• Download full text (pdf) of The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes

Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening

Schaal, Wesley; Ameur, Adam; Olsson-Strömberg, Ulla; Hermansson, Monica et al.

Part of Cancer Informatics, p. 1-8, 2022

• DOI for Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening
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A polygenic risk score predicts mosaic loss of chromosome Y in circulating blood cells

Riaz, Moeen; Mattisson, Jonas; Polekhina, Galina; Bakshi, Andrew et al.

Part of Cell & Bioscience, 2021

• DOI for A polygenic risk score predicts mosaic loss of chromosome Y in circulating blood cells
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Immune cells lacking Y chromosome show dysregulation of autosomal gene expression

Dumanski, Jan P.; Halvardson, Jonatan; Davies, Hanna; Rychlicka-Buniowska, Edyta et al.

Part of Cellular and Molecular Life Sciences (CMLS), p. 4019-4033, 2021

• DOI for Immune cells lacking Y chromosome show dysregulation of autosomal gene expression
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Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts

Zaghlool, Ammar; Niazi, Adnan; Björklund, Åsa K.; Orzechowski Westholm, Jakub et al.

Part of Scientific Reports, 2021

• DOI for Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts
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Phylogenetic history of patrilineages rare in northern and eastern Europe from large-scale re-sequencing of human Y-chromosomes

Ilumae, Anne-Mai; Post, Helen; Flores, Rodrigo; Karmin, Monika et al.

Part of European Journal of Human Genetics, p. 1510-1519, 2021

• DOI for Phylogenetic history of patrilineages rare in northern and eastern Europe from large-scale re-sequencing of human Y-chromosomes

Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity

Höijer, Ida; Johansson, Josefin; Gudmundsson, Sanna; Chin, Chen-Shan et al.

Part of Genome Biology, 2020

• DOI for Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity
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Molecular characterization of a large unselected cohort of metastatic colorectal cancers in relation to primary tumor location, rare metastatic sites and prognosis

Nunes, Luís; Aasebø, Kristine; Mathot, Lucy; Ljungström, Viktor et al.

Part of Acta Oncologica, p. 417-426, 2020

• DOI for Molecular characterization of a large unselected cohort of metastatic colorectal cancers in relation to primary tumor location, rare metastatic sites and prognosis
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Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia

Halvorsen, Matthew; Huh, Ruth; Oskolkov, Nikolay; Wen, Jia et al.

Part of Nature Communications, 2020

• DOI for Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia
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The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly

Pinese, Mark; Lacaze, Paul; Rath, Emma M.; Stone, Andrew et al.

Part of Nature Communications, 2020

• DOI for The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly
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Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach

von der Heyde, Benedikt; Emmanouilidou, Anastasia; Mazzaferro, Eugenia; Vicenzi, Silvia et al.

Part of Scientific Reports, 2020

• DOI for Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach
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Xdrop: Targeted sequencing of long DNA molecules from low input samples using droplet sorting

Madsen, Esben B; Höijer, Ida; Kvist, Thomas; Ameur, Adam et al.

Part of Human Mutation, p. 1671-1679, 2020

• DOI for Xdrop: Targeted sequencing of long DNA molecules from low input samples using droplet sorting
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SweHLA: the high confidence HLA typing bio-resource drawn from 1000 Swedish genomes

Nordin, Jessika; Ameur, Adam; Lindblad-Toh, Kerstin; Gyllensten, Ulf et al.

Part of European Journal of Human Genetics, p. 627-635, 2020

• DOI for SweHLA: the high confidence HLA typing bio-resource drawn from 1000 Swedish genomes
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CRISPR and Long-Read Sequencing: A Perfect Match.

Ameur, Adam

Part of The CRISPR journal, p. 425-427, 2020

• DOI for CRISPR and Long-Read Sequencing: A Perfect Match.

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

Fatima, Nazeefa; Petri, Anna; Gyllensten, Ulf; Feuk, Lars et al.

Part of Genes, 2020

• DOI for Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes
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Discovery of Novel Sequences in 1,000 Swedish Genomes

Eisfeldt, Jesper; Mårtensson, Gustaf; Ameur, Adam; Nilsson, Daniel et al.

Part of Molecular biology and evolution, p. 18-30, 2020

• DOI for Discovery of Novel Sequences in 1,000 Swedish Genomes
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The TGFB2-AS1 lncRNA regulates TGFβ signaling by modulating corepressor activity

Papoutsoglou, Panagiotis; Tsubakihara, Yutaro; Caja, Laia; Pallis, Paris et al.

Part of Cell Reports, p. 3182-319800000000000, 2019

• DOI for The TGFB2-AS1 lncRNA regulates TGFβ signaling by modulating corepressor activity
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The Versatility of SMRT Sequencing

Hestand, Matthew S.; Ameur, Adam

Part of Genes, 2019

• DOI for The Versatility of SMRT Sequencing
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Goodbye reference, hello genome graphs

Ameur, Adam

Part of Nature Biotechnology, p. 866-868, 2019

• DOI for Goodbye reference, hello genome graphs

Invasive cervical tumors with high and low HPV titer represent molecular subgroups with different disease etiology

Cui, Tao; Enroth, Stefan; Ameur, Adam; Gustavsson, Inger et al.

Part of Carcinogenesis, p. 269-278, 2019

• DOI for Invasive cervical tumors with high and low HPV titer represent molecular subgroups with different disease etiology

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

Zaghlool, Ammar; Ameur, Adam; Wu, Chenglin; Westholm, Jakub Orzechowski et al.

Part of Scientific Reports, 2018

• DOI for Expression profiling and in situ screening of circular RNAs in human tissues
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Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

Ardui, Simon; Ameur, Adam; Vermeesch, Joris R.; Hestand, Matthew S.

Part of Nucleic Acids Research, p. 2159-2168, 2018

• DOI for Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics
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Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing

Höijer, Ida; Tsai, Yu-Chih; Clark, Tyson A.; Kotturi, Paul et al.

Part of Human Mutation, p. 1262-1272, 2018

• DOI for Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing
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A novel ECEL1 mutation expands the phenotype of distal arthrogryposis multiplex congenita type 5D to include pretibial vertical skin crease

Stattin, Eva-Lena; Johansson, Josefin; Gudmundsson, Sanna; Ameur, Adam et al.

Part of American Journal of Medical Genetics. Part A, p. 1405-1410, 2018

• DOI for A novel ECEL1 mutation expands the phenotype of distal arthrogryposis multiplex congenita type 5D to include pretibial vertical skin crease

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

Ameur, Adam; Che, Huiwen; Martin, Marcel; Bunikis, Ignas et al.

Part of Genes, 2018

• DOI for De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data
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Single-molecule DNA sequencing of acute myeloid leukemia and myelodysplastic syndromes with multiple TP53 alterations

Lode, Laurence; Ameur, Adam; Coste, Thibault; Menard, Audrey et al.

Part of Haematologica, 2018

• DOI for Single-molecule DNA sequencing of acute myeloid leukemia and myelodysplastic syndromes with multiple TP53 alterations

Stereocilin gene variants associated with episodic vertigo: expansion of the DFNB16 phenotype

Frykholm, Carina; Klar, Joakim; Tomanovic, Tatjana; Ameur, Adam et al.

Part of European Journal of Human Genetics, p. 1871-1874, 2018

• DOI for Stereocilin gene variants associated with episodic vertigo: expansion of the DFNB16 phenotype

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

Wilbe, Maria; Gudmundsson, Sanna; Johansson, Josefin; Ameur, Adam et al.

Part of Prenatal Diagnosis, p. 1146-1154, 2017

• DOI for A novel approach using long-read sequencing and ddPCR to investigate gonadal mosaicism and estimate recurrence risk in two families with developmental disorders
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SNX10 gene mutation leading to osteopetrosis with dysfunctional osteoclasts.

Stattin, Evalena; Henning, Petra; Klar, Joakim; McDermott, Emma et al.

Part of Scientific Reports, 2017

• DOI for SNX10 gene mutation leading to osteopetrosis with dysfunctional osteoclasts.
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SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population

Ameur, Adam; Dahlberg, Johan; Olason, Pall; Vezzi, Francesco et al.

Part of European Journal of Human Genetics, p. 1253-1260, 2017

• DOI for SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population
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Revertant mosaicism repairs skin lesions in a patient with keratitis-ichthyosis-deafness syndrome by second-site mutations in connexin 26

Gudmundsson, Sanna; Wilbe, Maria; Ekvall, Sara; Ameur, Adam et al.

Part of Human Molecular Genetics, p. 1070-1077, 2017

• DOI for Revertant mosaicism repairs skin lesions in a patient with keratitis-ichthyosis-deafness syndrome by second-site mutations in connexin 26
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A nonsense mutation in CEP55 defines a new locus for a Meckel-like syndrome, an autosomal recessive lethal fetal ciliopathy.

Bondeson, Marie-Louise; Ericson, Katharina; Gudmundsson, Sanna; Ameur, Adam et al.

Part of Clinical Genetics, p. 510-516, 2017

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

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

Pan, Gang; Ameur, Adam; Enroth, Stefan; Bysani, Madhusudhan et al.

Part of Nucleic Acids Research, p. 2408-2422, 2017

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

Identification of novel genetic causes of Rett syndrome-like phenotypes

Lopes, Fatima; Barbosa, Mafalda; Ameur, Adam; Soares, Gabriela et al.

Part of Journal of Medical Genetics, p. 190-199, 2016

• DOI for Identification of novel genetic causes of Rett syndrome-like phenotypes

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

Rafati, Nima; Andersson, Lisa S.; Mikko, Sofia; Feng, Chungang et al.

Part of G3, p. 2213-2223, 2016

• DOI for Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies
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A novel variant in MYLK causes thoracic aortic dissections: genotypic and phenotypic description

Hannuksela, Matias; Stattin, Eva-Lena; Klar, Joakim; Ameur, Adam et al.

Part of BMC Medical Genetics, 2016

• DOI for A novel variant in MYLK causes thoracic aortic dissections: genotypic and phenotypic description
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Analysis of hepatitis C NS5A resistance associated polymorphisms using ultra deep single molecule real time (SMRT) sequencing

Bergfors, Assar; Leenheer, Daniel; Bergqvist, Anders; Ameur, Adam et al.

Part of Antiviral Research, p. 81-89, 2016

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

Intratumoral genome diversity parallels progression and predicts outcome in pediatric cancer

Mengelbier, Linda Holmquist; Karlsson, Jenny; Lindgren, David; Valind, Anders et al.

Part of Nature Communications, 2015

• DOI for Intratumoral genome diversity parallels progression and predicts outcome in pediatric cancer

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

Rask-Andersen, Mathias; Sällman Almén, Markus; Jacobsson, Josefin A; Ameur, Adam et al.

Part of Genetical Research, 2015

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

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

Einarsdottir, Elisabet; Svensson, Idor; Darki, Fahimeh; Peyrard-Janvid, Myriam et al.

Part of Human Genetics, p. 1239-1248, 2015

• DOI for Mutation in CEP63 co-segregating with developmental dyslexia in a Swedish family
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Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems

Osman, Abdimajid; Hitzler, Walter E.; Ameur, Adam; Provost, Patrick

Part of PLOS ONE, 2015

• DOI for Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems
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MuSK: a new target for lethal fetal akinesia deformation sequence (FADS).

Wilbe, Maria; Ekvall, Sara; Eurenius, Karin; Ericson, Katharina et al.

Part of Journal of Medical Genetics, p. 195-202, 2015

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

Phenotypic expansion of visceral myopathy associated with ACTG2 tandem base substitution

Klar, Joakim; Raykova, Doroteya; Gustafson, Elisabet; Tóthová, Iveta et al.

Part of European Journal of Human Genetics, p. 1679-1683, 2015

• DOI for Phenotypic expansion of visceral myopathy associated with ACTG2 tandem base substitution

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

Cavelier, Lucia; Ameur, Adam; Häggqvist, Susana; Höijer, Ida et al.

Part of BMC Cancer, 2015

• DOI for Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing
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Role of the AMP kinase in cytokine-induced human EndoC-beta H1 cell death

Fred, Rikard G.; Kappe, Camilla; Ameur, Adam; Cen, Jing et al.

Part of Molecular and Cellular Endocrinology, p. 53-63, 2015

• DOI for Role of the AMP kinase in cytokine-induced human EndoC-beta H1 cell death
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Transcriptome Profiling Reveals Degree of Variability in Induced Pluripotent Stem Cell Lines: Impact for Human Disease Modeling

Schuster, Jens; Halvardson, Jonatan; Lorenzo, Laureanne Pilar; Ameur, Adam et al.

Part of Cellular Reprogramming, p. 327-337, 2015

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

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

Ameur, Adam; Bunikis, Ignas; Enroth, Stefan; Gyllensten, Ulf

Part of Database, 2014

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

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

Ameur, Adam; Meiring, Tracy L.; Bunikis, Ignas; Häggqvist, Susana et al.

Part of Scientific Reports, p. 4398, 2014

• DOI for Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing
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Abolished InsP₃R2 function inhibits sweat secretion in both humans and mice

Klar, Joakim; Hisatsune, Chihiro; Baig, Shahid M.; Tariq, Muhammad et al.

Part of Journal of Clinical Investigation, p. 4773-4780, 2014

• DOI for Abolished InsP₃R2 function inhibits sweat secretion in both humans and mice

Somatic Cells with a Heavy Mitochondrial DNA Mutational Load Render Induced Pluripotent Stem Cells with Distinct Differentiation Defects

Wahlestedt, Martin; Ameur, Adam; Moraghebi, Roksana; Norddahl, Gudmundur L. et al.

Part of Stem Cells, p. 1173-1182, 2014

• DOI for Somatic Cells with a Heavy Mitochondrial DNA Mutational Load Render Induced Pluripotent Stem Cells with Distinct Differentiation Defects

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

Zaghlool, Ammar; Ameur, Adam; Nyberg, Linnea; Halvardson, Jonatan et al.

Part of BMC Biotechnology, p. 99, 2013

• DOI for Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues
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Transcription factor ZBED6 affects gene expression, proliferation, and cell death in pancreatic beta cells

Wang, Xuan; Jiang, Lin; Wallerman, Ola; Engström, Ulla et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 15997-16002, 2013

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

Omega-3 and omega-6 fatty acids are more efficiently synthesized in populations having a high frequency of the derived FADS-haplotype

Enroth, Stefan; Ameur, Adam; Johansson, Åsa; Gyllensten, Ulf

Part of International Journal of Circumpolar Health, p. 511-512, 2013

Welander Distal Myopathy Caused by an Ancient Founder Mutation in TIA1 Associated with Perturbed Splicing.

Klar, Joakim; Sobol, Maria; Melberg, Atle; Mäbert, Katrin et al.

Part of Human Mutation, p. 572-577, 2013

• DOI for Welander Distal Myopathy Caused by an Ancient Founder Mutation in TIA1 Associated with Perturbed Splicing.

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

Sällman Almén, Markus; Rask-Andersen, Mathias; Jacobsson, Josefin A; Ameur, Adam et al.

Part of International Journal of Obesity, p. 424-431, 2013

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

Genetic Adaptation of Fatty-Acid Metabolism: A Human-Specific Haplotype Increasing the Biosynthesis of Long-Chain Omega-3 and Omega-6 Fatty Acids

Ameur, Adam; Enroth, Stefan; Johansson, Åsa; Zaboli, Ghazal et al.

Part of American Journal of Human Genetics, p. 809-820, 2012

• DOI for Genetic Adaptation of Fatty-Acid Metabolism: A Human-Specific Haplotype Increasing the Biosynthesis of Long-Chain Omega-3 and Omega-6 Fatty Acids

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

Zaboli, Ghazal; Ameur, Adam; Igl, Wilmar; Johansson, Åsa et al.

Part of European Journal of Human Genetics, p. 77-83, 2012

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

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

Edlund, Karolina; Larsson, Ola; Ameur, Adam; Bunikis, Ignas et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 9551-9556, 2012

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

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

Mansouri, Larry; Gunnarsson, Rebeqa; Sutton, Lesley-Ann; Ameur, Adam et al.

Part of American Journal of Hematology, p. 737-740, 2012

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

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

Ameur, Adam; Stewart, James B.; Freyer, Christoph; Hagström, Erik et al.

Part of PLoS Genetics, 2011

• DOI for Ultra-deep sequencing of mouse mitochondrial DNA: Mutational patterns and their origins

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

Ameur, Adam; Zaghlool, Ammar; Halvardson, Jonatan; Wetterbom, Anna et al.

Part of Nature Structural & Molecular Biology, p. 1435-1440, 2011

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

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

Ameur, Adam; Wetterbom, Anna; Feuk, Lars; Gyllensten, Ulf

Part of Genome Biology, 2010

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

Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing

Wetterbom, Anna; Ameur, Adam; Feuk, Lars; Gyllensten, Ulf et al.

Part of Genome Biology, 2010

• DOI for Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing

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

Ameur, Adam; Rada-Iglesias, Alvaro; Komorowski, Jan; Wadelius, Claes

Part of Nucleic Acids Research, 2009

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

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

Motallebipour, Mehdi; Ameur, Adam; Bysani, Madhusudhan Reddy; Patra, Kalicharan et al.

Part of Genome Biology, 2009

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

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

Motallebipour, Mehdi; Enroth, Stefan; Punga, Tanel; Ameur, Adam et al.

Part of The FEBS Journal, p. 1878-1890, 2009

• DOI for 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

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

Mellberg, Sofie; Dimberg, Anna; Bahram, Fuad; Hayashi, Makoto et al.

Part of The FASEB Journal, p. 1490-1502, 2009

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

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

Rada-Iglesias, Alvaro; Ameur, Adam; Kapranov, Philipp; Enroth, Stefan et al.

Part of Genome Research, p. 380-392, 2008

• DOI for 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

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

Orzechowski Westholm, Jakub; Nordberg, Niklas; Murén, Eva; Ameur, Adam et al.

Part of BMC Genomics, p. 601, 2008

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

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

Rennel, Emma; Mellberg, Sofie; Dimberg, Anna; Petersson, Ludvig et al.

Part of Experimental Cell Research, p. 1285-1294, 2007

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

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

Rada-Iglesias, Alvaro; Enroth, Stefan; Ameur, Adam; Koch, Christoph M. et al.

Part of Genome Research, p. 708-719, 2007

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

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

Birney, Ewan; Stamatoyannopoulos, John A.; Dutta, Anindya; Guigó, Roderic et al.

Part of Nature, p. 799-816, 2007

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

Single-Molecule Sequencing: Towards Clinical Applications

Ameur, Adam; Kloosterman, Wigard P.; Hestand, Matthew S.

Part of Trends in Biotechnology, p. 72-85, 2019

• DOI for Single-Molecule Sequencing: Towards Clinical Applications

Splicing in the Human Brain

Zaghlool, Ammar; Ameur, Adam; Cavelier, Lucia; Feuk, Lars

Part of Brain Transcriptome, p. 95-125, Elsevier, 2014

• DOI for Splicing in the Human Brain

A Bioinformatics Study of Human Transcriptional Regulation

Ameur, Adam

2008

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Ultra-deep targeted re-sequencing of TMEM18 in two cohorts of European children detects new genetic variants associated with obesity

Rask-Andersen, Mathias; Sällman Almén, Markus; Jacobsson, Josefin; Ameur, Adam et al.

2013