All Stories

  1. Genome sequencing with comprehensive variant calling identifies structural variants and repeat expansions in a large fraction of individuals with ataxia and/or neuromuscular disorders

    Article • Frontiers in Neurology, May 2023, Frontiers

    Daniel Nilsson

  2. Genome sequencing is a sensitive first-line test to diagnose individuals with intellectual disability

    Article • Genetics in Medicine, November 2022, Elsevier

    Daniel Nilsson

  3. PatientMatcher: A customizable Python‐based open‐source tool for matching undiagnosed rare disease patients via the Matchmaker Exchange network

    Article • Human Mutation, March 2022, Hindawi Publishing Corporation

    Daniel Nilsson

  4. Partial Monosomy 21 Mirrors Gene Expression of Trisomy 21 in a Patient-Derived Neuroepithelial Stem Cell Model

    Article • Frontiers in Genetics, February 2022, Frontiers

    Daniel Nilsson

  5. Massive parallel sequencing in individuals with multiple primary tumours reveals the benefit of re-analysis

    Article • Hereditary Cancer in Clinical Practice, October 2021, Springer Science + Business Media

    Daniel Nilsson

  6. Adult-Onset Ataxia With Neuropathy and White Matter Abnormalities Due to a Novel SAMD9L Variant

    Article • Neurology Genetics, October 2021, Wolters Kluwer Health

    Daniel Nilsson

  7. High diagnostic yield in skeletal ciliopathies using massively parallel genome sequencing, structural variant screening and RNA analyses

    Article • Journal of Human Genetics, April 2021, Springer Science + Business Media

    Daniel Nilsson

  8. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients

    Article • Genome Medicine, March 2021, Springer Science + Business Media

    Daniel Nilsson

  9. Cell-free tumour DNA analysis detects copy number alterations in gastro-oesophageal cancer patients

    Article • PLoS ONE, February 2021, PLOS

    Daniel Nilsson

  10. Increasing involvement of CAPN1 variants in spastic ataxias and phenotype-genotype correlations

    Article • Neurogenetics, January 2021, Springer Science + Business Media

    Daniel Nilsson

  11. V374A KCND3 Pathogenic Variant Associated With Paroxysmal Ataxia Exacerbations

    Article • Neurology Genetics, January 2021, Wolters Kluwer Health

    Daniel Nilsson

  12. Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier

    Article • Human Genetics, December 2020, Springer Science + Business Media

    Daniel Nilsson

  13. Severe congenital neutropenia‐associated JAGN1 mutations unleash a calpain‐dependent cell death programme in myeloid cells

    Article • British Journal of Haematology, November 2020, Wiley

    Daniel Nilsson

  14. Heterozygous variants in DCC

    Article • Neurology Genetics, October 2020, Wolters Kluwer Health

    Daniel Nilsson

  15. Cytogenetically visible inversions are formed by multiple molecular mechanisms

    Article • Human Mutation, October 2020, Hindawi Publishing Corporation

    Daniel Nilsson

  16. Loqusdb: added value of an observations database of local genomic variation

    Article • BMC Bioinformatics, July 2020, Springer Science + Business Media

    Daniel Nilsson

  17. pyCancerSig: subclassifying human cancer with comprehensive single nucleotide, structural and microsatellite mutational signature deconstruction from whole genome sequencing

    Article • BMC Bioinformatics, April 2020, Springer Science + Business Media

    Daniel Nilsson

  18. From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability

    Article • Genome Medicine, November 2019, Springer Science + Business Media

    Daniel Nilsson

  19. Overexpression of chromatin remodeling and tyrosine kinase genes in iAMP21-positive acute lymphoblastic leukemia

    Article • Leukemia & Lymphoma, October 2019, Taylor & Francis

    Daniel Nilsson

  20. Discovery of Novel Sequences in 1,000 Swedish Genomes

    Article • Molecular Biology and Evolution, September 2019, Oxford University Press (OUP)

    Daniel Nilsson

  21. Ataxia in Patients With Bi-Allelic NFASC Mutations and Absence of Full-Length NF186

    Article • Frontiers in Genetics, September 2019, Frontiers

    Daniel Nilsson

  22. Further support linking the 22q11.2 microduplication to an increased risk of bladder exstrophy and highlighting LZTR1 as a candidate gene

    Article • Molecular Genetics & Genomic Medicine, May 2019, Wiley

    Daniel Nilsson

  23. Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements

    Article • PLoS Genetics, February 2019, PLOS

    Daniel Nilsson

  24. Identification of putative pathogenic single nucleotide variants (SNVs) in genes associated with heart disease in 290 cases of stillbirth

    Article • PLoS ONE, January 2019, PLOS

    Daniel Nilsson

  25. Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization

    Article • PLoS Genetics, November 2018, PLOS

    Daniel Nilsson

  26. Genomic screening in rare disorders: New mutations and phenotypes, highlighting ALG14 as a novel cause of severe intellectual disability

    Article • Clinical Genetics, October 2018, Wiley

    Daniel Nilsson

  27. Alu-Alu mediated intragenic duplications in IFT81 and MATN3 are associated with skeletal dysplasias

    Article • Human Mutation, August 2018, Wiley

    Daniel Nilsson

  28. Evaluation of the ISL1 gene in the pathogenesis of bladder exstrophy in a Swedish cohort

    Article • Human Genome Variation, March 2018, Springer Science + Business Media

    Daniel Nilsson

  29. AMYCNE: Confident copy number assessment using whole genome sequencing data

    Article • PLoS ONE, March 2018, PLOS

    Daniel Nilsson

  30. High-resolution detection of chromosomal rearrangements in leukemias through mate pair whole genome sequencing

    Article • PLoS ONE, March 2018, PLOS

    Daniel Nilsson

  31. Two novel colorectal cancer risk loci in the region on chromosome 9q22.32

    Article • Oncotarget, January 2018, Impact Journals, LLC

    Daniel Nilsson

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

    Article • European Journal of Human Genetics, August 2017, Springer Science + Business Media

    Daniel Nilsson

  33. Correction for Ekanayake et al., “Epigenetic Regulation of Transcription and Virulence in Trypanosoma cruzi by O-Linked Thymine Glucosylation of DNA”

    Article • Molecular and Cellular Biology, July 2017, ASM Journals

    Daniel Nilsson, Dr Rick L Tarleton

  34. TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data

    Article • F1000Research, June 2017, Faculty of 1000, Ltd.

    Daniel Nilsson

  35. Structural variant calling from whole genome sequencing data.

    Article • F1000Research, May 2017, Faculty of 1000, Ltd.

    Daniel Nilsson

  36. Further evidence for specific IFIH1 mutation as a cause of Singleton-Merten syndrome with phenotypic heterogeneity

    Article • American Journal of Medical Genetics Part A, March 2017, Wiley

    Daniel Nilsson

  37. A Large Inversion InvolvingGNASExon A/B and All Exons Encoding Gsα Is Associated With Autosomal Dominant Pseudohypoparathyroidism Type Ib (PHP1B)

    Article • Journal of Bone and Mineral Research, February 2017, Wiley

    marie-laure kottler, Daniel Nilsson

  38. Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation

    Article • Human Mutation, December 2016, Wiley

    Daniel Nilsson

  39. Identification of new TRIP12 variants and detailed clinical evaluation of individuals with non-syndromic intellectual disability with or without autism

    Article • Human Genetics, November 2016, Springer Science + Business Media

    Daniel Nilsson

  40. Genetic Spectrum of Idiopathic Restrictive Cardiomyopathy Uncovered by Next-Generation Sequencing

    Article • PLoS ONE, September 2016, PLOS

    Daniel Nilsson

  41. Exome sequencing in one family with gastric- and rectal cancer

    Article • BMC Genetics, February 2016, Springer Science + Business Media

    Daniel Nilsson

  42. Pathogenenic variant in theCOL2A1gene is associated with Spondyloepiphyseal dysplasia type Stanescu

    Article • American Journal of Medical Genetics Part A, September 2015, Wiley

    Daniel Nilsson

  43. Whole-exome sequencing of Ethiopian patients with ichthyosis vulgaris and atopic dermatitis

    Article • Journal of Allergy and Clinical Immunology, August 2015, Elsevier

    Daniel Nilsson

  44. WNT3 involvement in human bladder exstrophy and cloaca development in zebrafish

    Article • Human Molecular Genetics, June 2015, Oxford University Press (OUP)

    Daniel Nilsson

  45. A novel phenotype in N-glycosylation disorders: Gillessen-Kaesbach–Nishimura skeletal dysplasia due to pathogenic variants in ALG9

    Article • European Journal of Human Genetics, May 2015, Springer Science + Business Media

    Daniel Nilsson

  46. Mutations in FLVCR2 associated with Fowler syndrome and survival beyond infancy

    Article • Clinical Genetics, March 2015, Wiley

    Daniel Nilsson

  47. CTNND2—a candidate gene for reading problems and mild intellectual disability

    Article • Journal of Medical Genetics, December 2014, BMJ

    Daniel Nilsson

  48. Intragenic duplication-A novel causative mechanism for SATB2-associated syndrome

    Article • American Journal of Medical Genetics Part A, September 2014, Wiley

    Daniel Nilsson

  49. Autosomal recessive mutations in theCOL2A1gene cause severe spondyloepiphyseal dysplasia

    Article • Clinical Genetics, September 2014, Wiley

    Daniel Nilsson

  50. Neu-Laxova Syndrome Is a Heterogeneous Metabolic Disorder Caused by Defects in Enzymes of the L-Serine Biosynthesis Pathway

    Article • The American Journal of Human Genetics, September 2014, Elsevier

    Daniel Nilsson

  51. Identification of three novelFGF16mutations in X‐linked recessive fusion of the fourth and fifth metacarpals and possible correlation with heart disease

    Article • Molecular Genetics & Genomic Medicine, May 2014, Wiley

    Daniel Nilsson

  52. A novel stop mutation in the EDNRB gene in a family with Hirschsprung’s disease associated with Multiple Sclerosis

    Article • Journal of Pediatric Surgery, April 2014, Elsevier

    Daniel Nilsson

  53. An N-Terminal Missense Mutation in STX11 Causative of FHL4 Abrogates Syntaxin-11 Binding to Munc18-2

    Article • Frontiers in Immunology, January 2014, Frontiers

    Daniel Nilsson

  54. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

    Article • Genome Biology, January 2014, Springer Science + Business Media

    Daniel Nilsson

  55. Different mutations inPDE4Dassociated with developmental disorders with mirror phenotypes

    Article • Journal of Medical Genetics, November 2013, BMJ

    Daniel Nilsson

  56. A novel intellectual disability syndrome caused by GPI anchor deficiency due to homozygous mutations inPIGT

    Article • Journal of Medical Genetics, May 2013, BMJ

    Daniel Nilsson

  57. The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets

    Article • The FASEB Journal, August 2012, Federation of American Societies For Experimental Biology (FASEB)

    Dr Sujai Kumar, Daniel Nilsson

  58. Autoregulation of the nonsense-mediated mRNA decay pathway in human cells

    Article • RNA, October 2011, Cold Spring Harbor Laboratory Press

    Daniel Nilsson

  59. The Short Non-Coding Transcriptome of the Protozoan Parasite Trypanosoma cruzi

    Article • PLoS Neglected Tropical Diseases, August 2011, PLOS

    Piero Carninci, Daniel Nilsson

  60. Genome-Wide Identification of Molecular Mimicry Candidates in Parasites

    Article • PLoS ONE, March 2011, PLOS

    Daniel Nilsson

  61. Epigenetic Regulation of Transcription and Virulence in Trypanosoma cruzi by O-Linked Thymine Glucosylation of DNA

    Article • Molecular and Cellular Biology, February 2011, ASM Journals

    Daniel Nilsson, Dr Rick L Tarleton

  62. Phylogenomics of Ligand-Gated Ion Channels Predicts Monepantel Effect

    Article • PLoS Pathogens, September 2010, PLOS

    Daniel Nilsson

  63. Spliced Leader Trapping Reveals Widespread Alternative Splicing Patterns in the Highly Dynamic Transcriptome of Trypanosoma brucei

    Article • PLoS Pathogens, August 2010, PLOS

    Daniel Nilsson

  64. The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development

    Article • Nucleic Acids Research, July 2010, Oxford University Press (OUP)

    Daniel Nilsson

  65. var gene transcription dynamics in Plasmodium falciparum patient isolates

    Article • Molecular and Biochemical Parasitology, April 2010, Elsevier

    Daniel Nilsson

  66. Comparative genomics of metabolic networks of free-living and parasitic eukaryotes

    Article • BMC Genomics, January 2010, Springer Science + Business Media

    Daniel Nilsson

  67. Proteomics in Trypanosoma cruzi - localization of novel proteins to various organelles

    Article • PROTEOMICS, July 2008, Wiley

    Professor Roberto Docampo, Daniel Nilsson

  68. Database of Trypanosoma cruzi repeated genes: 20 000 additional gene variants

    Article • BMC Genomics, October 2007, Springer Science + Business Media

    Daniel Nilsson

  69. PfEMP1-DBL1α amino acid motifs in severe disease states of Plasmodium falciparum malaria

    Article • Proceedings of the National Academy of Sciences, October 2007, Proceedings of the National Academy of Sciences

    Daniel Nilsson

  70. Characterization of a Trypanosoma cruzi acetyltransferase: cellular location, activity and structure☆

    Article • Molecular and Biochemical Parasitology, April 2007, Elsevier

    Daniel Nilsson

  71. GRAT—genome-scale rapid alignment tool

    Article • Computer Methods and Programs in Biomedicine, April 2007, Elsevier

    Daniel Nilsson

  72. Repetitive DNA is associated with centromeric domains in Trypanosoma brucei but not Trypanosoma cruzi

    Article • Genome Biology, January 2007, Springer Science + Business Media

    Daniel Nilsson

  73. A Solanesyl-diphosphate Synthase Localizes in Glycosomes ofTrypanosoma cruzi

    Article • Journal of Biological Chemistry, October 2006, American Society for Biochemistry & Molecular Biology (ASBMB)

    Daniel Nilsson

  74. Messenger RNA processing sites in Trypanosoma brucei

    Article • Molecular and Biochemical Parasitology, October 2005, Elsevier

    Daniel Nilsson

  75. The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease

    Article • Science, July 2005, American Association for the Advancement of Science

    Professor Elodie Ghedin, Daniel Nilsson, Dr Rick L Tarleton

  76. Comparative Genomics of Trypanosomatid Parasitic Protozoa

    Article • Science, July 2005, American Association for the Advancement of Science

    Professor Elodie Ghedin, Daniel Nilsson

  77. Strand asymmetry patterns in trypanosomatid parasites

    Article • Experimental Parasitology, March 2005, Elsevier

    Daniel Nilsson

  78. A graphical tool for parasite genome annotation

    Article • Computer Methods and Programs in Biomedicine, January 2004, Elsevier

    Daniel Nilsson

  79. Expressed sequence tag analysis of Sarcoptes scabiei

    Article • Parasitology, August 2003, Cambridge University Press

    Daniel Nilsson

  80. Selective Charging of tRNA Isoacceptors Explains Patterns of Codon Usage

    Article • Science, June 2003, American Association for the Advancement of Science

    Daniel Nilsson