Páll Melsted

Selected publications. For a complete list see Google Scholar.

Highlighted

1. RNA-seq analysis in seconds using GPUs

   P Melsted, E M Guðnýjarson, J Nordal

   bioRxiv, 2026

   RNA-seqsoftware
2. Modular, efficient and constant-memory single-cell RNA-seq preprocessing

   P Melsted, A S Booeshaghi, L Liu, F Gao, L Lu, K H Min, E da Veiga Beltrame, K E Hjörleifsson, J Gehring, L Pachter

   Nature Biotechnology, 2021

   single-cellsoftwareRNA-seq
3. Near-optimal probabilistic RNA-seq quantification

   N L Bray, H Pimentel, P Melsted, L Pachter

   Nature Biotechnology, 2016

   RNA-seqsoftware

All publications

No publications match the selected filters.

1. BloodVariome: a high-resolution atlas of inherited genetic effects in human immune cells

   A Lopez de Lapuente Portilla, L Ekdahl, G Thorleifsson, Z Ali, et al.

   bioRxiv, 2026

   geneticsdeCODE Genetics
2. Genetic Architecture and Myocardial Fibrotic Remodeling in Mitral Valve Prolapse

   A M Small, M Yu, T E Berrandou, A Georges, M Huff, et al.

   medRxiv, 2026

   geneticsdeCODE Genetics
3. Population-scale immunoglobulin genetics resolves the human B-cell system

   Z Ali, A Lopez de Lapuente Portilla, G Thorleifsson, et al.

   bioRxiv, 2026

   geneticsdeCODE Genetics
4. Resistant hypertension variants link to hyperaldosteronism and potassium levels

   V Tragante, P Sulem, G Thorleifsson, M L Frigge, J G Arthur, et al.

   Hypertension, 2026

   geneticsdeCODE Genetics
5. RNA-seq analysis in seconds using GPUs

   P Melsted, E M Guðnýjarson, J Nordal

   bioRxiv, 2026

   RNA-seqsoftware
6. Sequence variants affecting fetal globin expression pointing to potential drug targets

   M Magnusson, G Oskarsson, S Mwende, K Kristjansdottir, A Sigurdsson, et al.

   Research Square, 2026

   geneticsdeCODE Genetics
7. The impact of package selection and versioning on single-cell RNA-seq analysis

   J M Rich, L Moses, P H Einarsson, K Jackson, L Luebbert, et al.

   Cell Systems, 2026

   single-cellRNA-seqsoftware
8. A genome-wide association meta-analysis links hidradenitis suppurativa to common and rare sequence variants causing disruption of the Notch and Wnt/β-catenin signaling pathways

   R K Andersen, L Stefansdottir, P T Riis, G Halldorsson, E Ferkingstad, et al.

   Journal of the American Academy of Dermatology, 2025

   geneticsdeCODE Genetics
9. A partial loss-of-function variant in STAT6 protects against type 2 asthma

   K Kristjansdottir, G L Norddahl, E V Ivarsdottir, G H Halldorsson, et al.

   Journal of Allergy and Clinical Immunology, 2025

   geneticsdeCODE Genetics
10. Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq

    D K Sullivan, K E Hjörleifsson, N Swarna, C Oakes, G Holley, P Melsted, L Pachter

    Nucleic Acids Research, 2025

    single-cellRNA-seq
11. Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated

    S E Antonsson, P Melsted

    Genome Research, 2025

    single-cellRNA-seq
12. Bi-allelic variants in BRF2 are associated with perinatal death and craniofacial anomalies

    F Mattioli, R Friðriksdóttir, A Hebert, S Bassani, N Ibrahim, et al.

    Genome Medicine, 2025

    geneticsdeCODE Genetics
13. kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq

    D K Sullivan, K H Min, K E Hjörleifsson, L Luebbert, G Holley, L Moses, J Gustafsson, N L Bray, H Pimentel, A S Booeshaghi, P Melsted, L Pachter

    Nature Protocols, 2025

    RNA-seqsingle-cellsoftware
14. Long-read sequencing transcriptome quantification with lr-kallisto

    R K Loving, D K Sullivan, F Reese, E Rebboah, J Sakr, N Rezaie, et al.

    PLOS Computational Biology, 2025

    RNA-seqlong-read
15. Missense variants in FRS3 affect body mass index in populations of diverse ancestries

    A B Jonsdottir, G Sveinbjornsson, R B Thorolfsdottir, M Tamlander, et al.

    Nature Communications, 2025

    geneticsdeCODE Genetics
16. Gene-based burden tests of rare germline variants identify six cancer susceptibility genes

    E V Ivarsdottir, J Gudmundsson, V Tragante, G Sveinbjornsson, et al.

    Nature Genetics, 2024

    geneticsdeCODE Genetics
17. Homozygosity for a stop-gain variant in CCDC201 causes primary ovarian insufficiency

    A Oddsson, V Steinthorsdottir, G R Oskarsson, U Styrkarsdottir, et al.

    Nature Genetics, 2024

    geneticsdeCODE Genetics
18. Sequence variants influencing the regulation of serum IgG subclass levels

    T A Olafsdottir, G Thorleifsson, A Lopez de Lapuente Portilla, S Jonsson, et al.

    Nature Communications, 2024

    geneticsdeCODE Genetics
19. Start codon variant in LAG3 is associated with decreased LAG-3 expression and increased risk of autoimmune thyroid disease

    S Saevarsdottir, K Bjarnadottir, T Markusson, J Berglund, T A Olafsdottir, et al.

    Nature Communications, 2024

    geneticsdeCODE Genetics
20. Transformers significantly improve splice site prediction

    B A Jónsson, G H Halldórsson, S Árdal, S Rögnvaldsson, E Einarsson, et al.

    Communications Biology, 2024

    genomicssoftwaredeCODE Genetics
21. A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta)

    T E Squires, P Rödin-Mörch, G Formenti, A Tracey, L Abueg, et al.

    G3: Genes, Genomes, Genetics, 2023

    genomics
22. BUSZ: compressed BUS files

    P H Einarsson, P Melsted

    Bioinformatics, 2023

    single-cellsoftware
23. Deficit of homozygosity among 1.52 million individuals and genetic causes of recessive lethality

    A Oddsson, P Sulem, G Sveinbjornsson, G A Arnadottir, V Steinthorsdottir, et al.

    Nature Communications, 2023

    geneticsdeCODE Genetics
24. Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis

    S N Stacey, F Zink, G H Halldorsson, L Stefansdottir, S A Gudjonsson, et al.

    Nature Genetics, 2023

    geneticsgenomicsdeCODE Genetics
25. Large-scale plasma proteomics comparisons through genetics and disease associations

    G H Eldjárn, E Ferkingstad, S H Lund, H Helgason, O T Magnusson, et al.

    Nature, 2023

    proteomicsgeneticsdeCODE Genetics
26. Rare variants with large effects provide functional insights into the pathology of migraine subtypes, with and without aura

    G Bjornsdottir, M A Chalmer, L Stefansdottir, A T Skuladottir, G Einarsson, et al.

    Nature Genetics, 2023

    geneticsdeCODE Genetics
27. Sequence variant affects GCSAML splicing, mast cell specific proteins, and risk of urticaria

    R P Kristjansson, G R Oskarsson, A Skuladottir, A Oddsson, et al.

    Communications Biology, 2023

    geneticsdeCODE Genetics
28. Voyager: exploratory single-cell genomics data analysis with geospatial statistics

    L Moses, P H Einarsson, K Jackson, L Luebbert, A S Booeshaghi, et al.

    bioRxiv, 2023

    single-cellsoftware
29. Annotation-agnostic discovery of associations between novel gene isoforms and phenotypes

    K E Hjörleifsson, L Pachter, P Melsted

    bioRxiv, 2022

    RNA-seqgenetics
30. Effect of booster vaccination against Delta and Omicron SARS-CoV-2 variants in Iceland

    G L Norddahl, P Melsted, K Gunnarsdottir, G H Halldorsson, T A Olafsdottir, et al.

    Nature Communications, 2022

    COVID-19deCODE Genetics
31. HLA alleles, disease severity, and age associate with T-cell responses following infection with SARS-CoV-2

    T A Olafsdottir, K Bjarnadottir, G L Norddahl, G H Halldorsson, P Melsted, et al.

    Communications Biology, 2022

    COVID-19geneticsdeCODE Genetics
32. Multiomics analysis of rheumatoid arthritis yields sequence variants that have large effects on risk of the seropositive subset

    S Saevarsdottir, L Stefansdottir, P Sulem, G Thorleifsson, E Ferkingstad, et al.

    Annals of the Rheumatic Diseases, 2022

    geneticsdeCODE Genetics
33. Multiomics study of nonalcoholic fatty liver disease

    G Sveinbjörnsson, M O Ulfarsson, R B Thorolfsdottir, B A Jonsson, et al.

    Nature Genetics, 2022

    geneticsgenomics
34. Reconstruction of a large-scale outbreak of SARS-CoV-2 infection in Iceland informs vaccination strategies

    K E Hjorleifsson, S Rognvaldsson, H Jonsson, A B Agustsdottir, et al.

    Clinical Microbiology and Infection, 2022

    COVID-19genomicsdeCODE Genetics
35. The sequences of 150,119 genomes in the UK Biobank

    B V Halldórsson, H P Eggertsson, K H S Moore, H Hauswedell, O Eiriksson, et al.

    Nature, 2022

    genomicsgenetics
36. Genetic variants associated with platelet count are predictive of human disease and physiological markers

    E Mikaelsdottir, G Thorleifsson, L Stefansdottir, G Halldorsson, et al.

    Communications Biology, 2021

    geneticsdeCODE Genetics
37. Large-scale integration of the plasma proteome with genetics and disease

    E Ferkingstad, P Sulem, B A Atlason, G Sveinbjörnsson, M I Magnusson, et al.

    Nature Genetics, 2021

    proteomicsgenetics
38. Lifelong reduction in LDL cholesterol due to a gain-of-function mutation in LDLR

    E Bjornsson, K Gunnarsdottir, G H Halldorsson, A Sigurdsson, et al.

    Circulation: Genomic and Precision Medicine, 2021

    geneticsdeCODE Genetics
39. Loss-of-function variants in the tumor-suppressor gene PTPN14 confer increased cancer risk

    T Olafsdottir, S N Stacey, G Sveinbjornsson, G Thorleifsson, K Norland, et al.

    Cancer Research, 2021

    geneticsdeCODE Genetics
40. Mapping the human genetic architecture of COVID-19

    COVID-19 Host Genetics Initiative

    Nature, 2021

    COVID-19genetics
41. Modular, efficient and constant-memory single-cell RNA-seq preprocessing

    P Melsted, A S Booeshaghi, L Liu, F Gao, L Lu, K H Min, E da Veiga Beltrame, K E Hjörleifsson, J Gehring, L Pachter

    Nature Biotechnology, 2021

    single-cellsoftwareRNA-seq
42. Molecular benchmarks of a SARS-CoV-2 epidemic

    H Jonsson, O T Magnusson, P Melsted, J Berglund, A B Agustsdottir, et al.

    Nature Communications, 2021

    COVID-19genomicsdeCODE Genetics
43. The genetic architecture of age-related hearing impairment revealed by genome-wide association analysis

    E V Ivarsdottir, H Holm, S Benonisdottir, T Olafsdottir, G Sveinbjornsson, et al.

    Communications Biology, 2021

    geneticsdeCODE Genetics
44. Algorithm 1005: Fortran subroutines for reverse mode algorithmic differentiation of BLAS matrix operations

    K Jonasson, S Sigurdsson, H F Yngvason, P O Ragnarsson, P Melsted

    ACM Transactions on Mathematical Software, 2020

    algorithmssoftware
45. Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs

    G Holley, P Melsted

    Genome Biology, 2020

    de Bruijn graphssoftwaregenomicsk-mers
46. FLT3 stop mutation increases FLT3 ligand level and risk of autoimmune thyroid disease

    S Saevarsdottir, T A Olafsdottir, E V Ivarsdottir, G H Halldorsson, et al.

    Nature, 2020

    geneticsdeCODE Genetics
47. Genome-wide association identifies seven loci for pelvic organ prolapse in Iceland and the UK Biobank

    T Olafsdottir, G Thorleifsson, P Sulem, O A Stefansson, H Medek, et al.

    Communications Biology, 2020

    geneticsdeCODE Genetics
48. Humoral immune response to SARS-CoV-2 in Iceland

    D F Guðbjartsson, G L Norddahl, P Melsted, K Gunnarsdottir, H Holm, et al.

    New England Journal of Medicine, 2020

    COVID-19genetics
49. Spread of SARS-CoV-2 in the Icelandic population

    D F Guðbjartsson, A Helgason, H Jónsson, O T Magnusson, P Melsted, et al.

    New England Journal of Medicine, 2020

    COVID-19genomics
50. A discriminative learning approach to differential expression analysis for single-cell RNA-seq

    V Ntranos, L Yi, P Melsted, L Pachter

    Nature Methods, 2019

    single-cellRNA-seq
51. A PRPH splice-donor variant associates with reduced sural nerve amplitude and risk of peripheral neuropathy

    G Bjornsdottir, E V Ivarsdottir, K Bjarnadottir, S Benonisdottir, et al.

    Nature Communications, 2019

    geneticsdeCODE Genetics
52. GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs

    H P Eggertsson, S Kristmundsdóttir, D Beyter, H Jónsson, Á Skúladóttir, M T Hardarson, D F Guðbjartsson, K Stefánsson, B V Halldórsson, P Melsted

    Nature Communications, 2019

    deCODE Geneticsgenomics
53. The barcode, UMI, set format and BUStools

    P Melsted, V Ntranos, L Pachter

    Bioinformatics, 2019

    single-cellsoftware
54. A direct comparison of genome alignment and transcriptome pseudoalignment

    L Yi, L Liu, P Melsted, L Pachter

    bioRxiv, 2018

    RNA-seq
55. Coding variants in RPL3L and MYZAP increase risk of atrial fibrillation

    R B Thorolfsdottir, G Sveinbjornsson, P Sulem, J B Nielsen, S Jonsson, et al.

    Communications Biology, 2018

    geneticsdeCODE Genetics
56. Insights into imprinting from parent-of-origin phased methylomes and transcriptomes

    F Zink, D N Magnusdottir, O T Magnusson, N J Walker, T J Morris, et al.

    Nature Genetics, 2018

    geneticsgenomicsdeCODE Genetics
57. Differential analysis of RNA-seq incorporating quantification uncertainty

    H Pimentel, N L Bray, S Puente, P Melsted, L Pachter

    Nature Methods, 2017

    RNA-seq
58. Fusion detection and quantification by pseudoalignment

    P Melsted, S Hateley, I C Joseph, H Pimentel, N Bray, L Pachter

    bioRxiv, 2017

    RNA-seq
59. Graphtyper enables population-scale genotyping using pangenome graphs

    H P Eggertsson, H Jónsson, S Kristmundsdóttir, E Hjartarson, B Kehr, et al.

    Nature Genetics, 2017

    deCODE Geneticsgenomics
60. Pseudoalignment for metagenomic read assignment

    L Schaeffer, H Pimentel, N L Bray, P Melsted, L Pachter

    Bioinformatics, 2017

    metagenomics
61. BamHash: a checksum program for verifying the integrity of sequence data

    A Óskarsdóttir, G Másson, P Melsted

    Bioinformatics, 2016

    hashingsoftwaredeCODE Genetics
62. chopBAI: BAM index reduction solves I/O bottlenecks in the joint analysis of large sequencing cohorts

    B Kehr, P Melsted

    Bioinformatics, 2016

    genomicssoftwaredeCODE Genetics
63. Looking into the past – the reaction of three grouse species to climate change over the last million years using whole genome sequences

    R Kozma, P Melsted, K P Magnússon, J Höglund

    Molecular Ecology, 2016

    genomics
64. Mash: fast genome and metagenome distance estimation using MinHash

    B D Ondov, T J Treangen, P Melsted, A B Mallonee, N H Bergman, S Koren, A M Phillippy

    Genome Biology, 2016

    genomicsmetagenomicssoftware
65. Near-optimal probabilistic RNA-seq quantification

    N L Bray, H Pimentel, P Melsted, L Pachter

    Nature Biotechnology, 2016

    RNA-seqsoftware
66. PopIns: population-scale detection of novel sequence insertions

    B Kehr, P Melsted, B V Halldórsson

    Bioinformatics, 2016

    genomicssoftware
67. The Lair: a resource for exploratory analysis of published RNA-Seq data

    H Pimentel, P Sturmfels, N L Bray, P Melsted, L Pachter

    BMC Bioinformatics, 2016

    RNA-seqsoftware
68. KmerStream: streaming algorithms for k-mer abundance estimation

    P Melsted, B V Halldórsson

    Bioinformatics, 2014

    k-mersalgorithmssoftware
69. A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar

    G H Perry, D Reeves, P Melsted, A Ratan, W Miller, et al.

    Genome Biology and Evolution, 2012

    genomics
70. Comparative RNA sequencing reveals substantial genetic variation in endangered primates

    G H Perry, P Melsted, J C Marioni, Y Wang, R Bainer, J K Pickrell, et al.

    Genome Research, 2012

    RNA-seqgenomics
71. Maximum matchings in random bipartite graphs and the space utilization of Cuckoo Hash tables

    A Frieze, P Melsted

    Random Structures & Algorithms, 2012

    algorithmshashingrandom graphs
72. An Analysis of Random-Walk Cuckoo Hashing

    A Frieze, P Melsted, M Mitzenmacher

    SIAM Journal on Computing, 2011

    algorithmshashingrandom graphs
73. Efficient counting of k-mers in DNA sequences using a bloom filter

    P Melsted, J K Pritchard

    BMC Bioinformatics, 2011

    k-merssoftware
74. Randomly coloring simple hypergraphs

    A Frieze, P Melsted

    Information Processing Letters, 2011

    algorithms
75. Finding a maximum matching in a sparse random graph in O(n) expected time

    P Chebolu, A Frieze, P Melsted

    Journal of the ACM, 2010

    algorithmsrandom graphs
76. Genomic-scale capture and sequencing of endogenous DNA from feces

    G H Perry, J C Marioni, P Melsted, Y Gilad

    Molecular Ecology, 2010

    genomics
77. Average-case analyses of Vickrey costs

    P Chebolu, A Frieze, P Melsted, G B Sorkin

    Approximation, Randomization, and Combinatorial Optimization (APPROX/RANDOM), 2009

    algorithms
78. PageRank and the random surfer model

    P Chebolu, P Melsted

    Proceedings of the 19th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), 2008

    algorithmsrandom graphs