NGI Long read

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Started: -

Ended: Current

Year 2024

PubMed DOI Crossref
DMI fungicide resistance in Zymoseptoria tritici is unlinked to geographical origin and genetic background: a case study in Europe.
Oreiro EG, Samils B, Kildea S, ..., Zhan J, Andersson B
Pest Manag Sci - (-) - [2024-11-06; online 2024-11-06]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Urban Pigeons as Reservoirs of Critical Pathogens: Improved protocol for sequencing pigeon faeces in disease monitoring
Hermann E, Van Damme R, Bongcam-Rudloff E, Nasirzadeh L
EMBnet j. 30 (-) e1059 [2024-11-04; online 2024-11-04]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps.
Bilgrav Saether K, Eisfeldt J, Bengtsson JD, ..., Carvalho CMB, Lindstrand A
Genome Res. - (-) - [2024-11-01; online 2024-11-01]
NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Pushing the boundaries of rare disease diagnostics with the help of the first Undiagnosed Hackathon.
Delgado-Vega AM, Cederroth H, Taylan F, ..., Cederroth M, Nordgren A
Nat. Genet. 56 (11) 2287-2294 [2024-11-00; online 2024-10-22]
Clinical Genomics Gothenburg [Service] Clinical Genomics Stockholm [Collaborative] NGI Long read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes.
Jayaprasad S, Peona V, Ellerstrand SJ, ..., Schielzeth H, Palacios-Gimenez OM
Mol. Ecol. - (-) e17567 [2024-10-30; online 2024-10-30]
NGI Long read [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing.
Eisfeldt J, Higginbotham EJ, Lenner F, ..., Scherer SW, Feuk L
Genome Res. - (-) - [2024-10-29; online 2024-10-29]
NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities.
Eisfeldt J, Ameur A, Lenner F, ..., Feuk L, Lindstrand A
Genome Res. - (-) - [2024-10-29; online 2024-10-29]
NGI Long read [Technology development] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
PubMed DOI Crossref
Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctorium (Cheiracanthiidae).
Schöneberg Y, Audisio TL, Ben Hamadou A, ..., Prost S, Kennedy S
Mol Ecol Resour - (-) e14038 [2024-10-22; online 2024-10-22]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.
Mc Cartney AM, Formenti G, Mouton A, ..., Waterhouse RM, Mazzoni CJ
NPJ Biodivers 3 (1) 31 [2024-10-15; online 2024-10-15]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
The genome sequence of the white-tailed eagle, Haliaeetus albicilla (Linnaeus, 1758)
Pálsson S, Skarphéðinsson KH, Heintz J, ..., Bunikis I, Pettersson OV
Wellcome Open Res 9 (-) 575 [2024-10-09; online 2024-10-09]
NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Mini-heterochromatin domains constrain the cis-regulatory impact of SVA transposons in human brain development and disease.
Horváth V, Garza R, Jönsson ME, ..., Douse CH, Jakobsson J
Nat. Struct. Mol. Biol. 31 (10) 1543-1556 [2024-10-00; online 2024-06-04]
Clinical Genomics Lund [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes.
Overgaard CK, Jamy M, Radutoiu S, Burki F, Dueholm MKD
Mol Ecol Resour 24 (7) e13991 [2024-10-00; online 2024-07-09]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
CDK4 is co-amplified with either TP53 promoter gene fusions or MDM2 through distinct mechanisms in osteosarcoma.
Saba KH, Difilippo V, Styring E, ..., Baumhoer D, Nord KH
npj Genom. Med. 9 (1) 42 [2024-09-25; online 2024-09-25]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.
Mc Cartney AM, Formenti G, Mouton A, ..., Waterhouse RM, Mazzoni CJ
NPJ Biodivers 3 (1) 28 [2024-09-17; online 2024-09-17]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
An Improved Chromosome-scale Genome Assembly and Population Genetics resource for Populus tremula.
Robinson KM, Schiffthaler B, Liu H, ..., Ingvarsson PK, Street NR
Physiol Plantarum 176 (5) e14511 [2024-09-16; online 2024-09-16]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Chromosome-level genome assembly of the morabine grasshopper Vandiemenella viatica19.
Li X, Jayaprasad S, Einarsdottir E, ..., Kawakami T, Palacios-Gimenez OM
Sci Data 11 (1) 997 [2024-09-12; online 2024-09-12]
NGI Long read [Service] NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressor.
Pandiloski N, Horváth V, Karlsson O, ..., Jakobsson J, Douse CH
Nat Commun 15 (1) 7534 [2024-08-30; online 2024-08-30]
Clinical Genomics Lund [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR.
De Coster W, Hoijer I, Bruggeman I, ..., Ameur A, Rademakers R
Genome Res. - (-) - [2024-08-15; online 2024-08-15]
NGI Long read [Technology development] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
DOI Crossref
Fungal communities associated with Picea abiesPinus sylvestris and Larix sp. seeds of different geographic origin: Implications for disease management
Larsson R, Menkis A, Olson Å
For. Path. 54 (4) - [2024-08-00; online 2024-08-05]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing.
Lysenkova Wiklander M, Arvidsson G, Bunikis I, ..., Ameur A, Nordlund J
Life Sci. Alliance 7 (8) - [2024-08-00; online 2024-05-22]
NGI Long read [Collaborative] NGI Short read [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Spinocerebellar ataxia type 4 is caused by a GGC expansion in the ZFHX3 gene and is associated with prominent dysautonomia and motor neuron signs.
Paucar M, Nilsson D, Engvall M, ..., Wedell A, Svenningsson P
J. Intern. Med. - (-) - [2024-07-07; online 2024-07-07]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring.
Pettersson ME, Quintela M, Besnier F, ..., Glover KA, Andersson L
Genome Biol Evol 16 (7) - [2024-07-03; online 2024-06-26]
NGI Long read [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
DOI Crossref
A combination of long and short read genomics reveals frequent p-arm breakpoints within chromosome 21 complex genomic rearrangements
Schuy J, Sæther KB, Lisfeld J, ..., Eisfeldt J, Lindstrand A
Genetics in Medicine Open - (-) 101863 [2024-06-00; online 2024-06-00]
NGI Long read [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
MDM2 amplification in rod-shaped chromosomes provides clues to early stages of circularized gene amplification in liposarcoma.
Sydow S, Piccinelli P, Mitra S, ..., Spierings D, Mertens F
Commun Biol 7 (1) 606 [2024-05-20; online 2024-05-20]
Clinical Genomics Lund [Service] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Copy number variation and elevated genetic diversity at immune trait loci in Atlantic and Pacific herring.
Mohamadnejad Sangdehi F, Jamsandekar MS, Enbody ED, Pettersson ME, Andersson L
BMC Genomics 25 (1) 459 [2024-05-10; online 2024-05-10]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum.
Gutiérrez-Valencia J, Zervakis P, Postel Z, ..., Arroyo J, Slotte T
Mol. Biol. Evol. 41 (5) - [2024-05-03; online 2024-05-06]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Ectomycorrhizal fungi are more sensitive to high soil nitrogen levels in forests exposed to nitrogen deposition.
Jörgensen K, Clemmensen KE, Wallander H, Lindahl BD
New Phytol. 242 (4) 1725-1738 [2024-05-00; online 2024-01-11]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Long-read sequencing and optical mapping generates near T2T assemblies that resolves a centromeric translocation.
Ten Berk de Boer E, Ameur A, Bunikis I, ..., Eisfeldt J, Lindstrand A
Sci Rep 14 (1) 9000 [2024-04-18; online 2024-04-18]
NGI Long read [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Adaptive introgression reveals the genetic basis of a sexually selected syndrome in wall lizards.
Feiner N, Yang W, Bunikis I, While GM, Uller T
Sci Adv 10 (14) eadk9315 [2024-04-05; online 2024-04-03]
NGI Long read [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Habitat is more important than climate for structuring soil fungal communities associated in truffle sites.
Piñuela Y, Alday JG, Oliach D, ..., Peter M, Bonet JA
Fungal Biol 128 (2) 1724-1734 [2024-04-00; online 2024-02-24]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees.
Shi T, Zhang X, Hou Y, ..., Yin T, Wang J
Mol Plant - (-) - [2024-03-13; online 2024-03-13]
NGI Long read [Service] NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern.
Höglund J, Dias G, Olsen RA, ..., Talla V, Backström N
Genome Biol Evol 16 (2) - [2024-02-01; online 2024-02-18]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Climate acts as an environmental filter to plant pathogens.
Caballol M, Redondo MÁ, Catalán N, ..., Stenlid J, Oliva J
ISME J 18 (1) - [2024-01-08; online 2024-02-17]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Exonic trinucleotide repeat expansions in ZFHX3 cause spinocerebellar ataxia type 4: A poly-glycine disease.
Wallenius J, Kafantari E, Jhaveri E, ..., Ehrencrona H, Puschmann A
Am. J. Hum. Genet. 111 (1) 82-95 [2024-01-04; online 2023-11-29]
NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Functional annotation of a divergent genome using sequence and structure-based similarity.
Svedberg D, Winiger RR, Berg A, ..., Vossbrinck CR, Barandun J
BMC Genomics 25 (1) 6 [2024-01-02; online 2024-01-02]
Bioinformatics Support, Infrastructure and Training [Service] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Year 2023

PubMed DOI Crossref
Gastrointestinal parasite community structure in horses after the introduction of selective anthelmintic treatment strategies.
Halvarsson P, Grandi G, Hägglund S, Höglund J
Vet Parasitol 326 (-) 110111 [2023-12-25; online 2023-12-25]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta).
Landi M, Shah T, Falquet L, ..., Bongcam-Rudloff E, Gisel A
Sci Data 10 (1) 887 [2023-12-09; online 2023-12-09]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics.
Engblom C, Thrane K, Lin Q, ..., Lundeberg J, Frisén J
Science 382 (6675) eadf8486 [2023-12-08; online 2023-12-08]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Short read NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network.
Xu X, Bhalla N, Ståhl P, Jaldén J
BMC Bioinformatics 24 (1) 461 [2023-12-07; online 2023-12-07]
NGI Long read NGI Short read [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Demonstration of reduced efficacy against cyathostomins without change in species composition after pyrantel embonate treatment in Swedish equine establishments.
Hedberg Alm Y, Halvarsson P, Martin F, ..., Törngren V, Tydén E
International Journal for Parasitology: Drugs and Drug Resistance 23 (-) 78-86 [2023-11-14; online 2023-11-14]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Retrieval of long DNA reads from herbarium specimens
Quatela AS, Cangren P, Jafari F, ..., de Boer H, Oxelman B
AoB Plants - (-) - [2023-11-08; online 2023-11-08]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies.
Willink B, Tunström K, Nilén S, ..., Svensson EI, Wheat CW
Nat Ecol Evol - (-) - [2023-11-06; online 2023-11-06]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification.
Garza R, Atacho DAM, Adami A, ..., Douse CH, Jakobsson J
Sci Adv 9 (44) eadh9543 [2023-11-03; online 2023-11-01]
Clinical Genomics Lund [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
The development of foliar fungal communities of nursery-grown Pinus sylvestris seedlings
Larsson R, Menkis A, Skogström O, ..., Larsson M, Olson Å
Scandinavian Journal of Forest Research - (-) 1-16 [2023-11-02; online 2023-11-02]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
The Release and Spread of Basidiospores of Red-Listed Wood-Decay Fungus Fistulina hepatica in Oak Stands
Marčiulynas A, Menkis A
Diversity 15 (11) 1110 [2023-10-25; online 2023-10-25]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Fungi Inhabiting Stem Wounds of Quercus robur following Bark Stripping by Deer Animals
Marčiulynas A, Sirgedaitė-Šėžienė V, Menkis A
Forests 14 (10) 2077 [2023-10-17; online 2023-10-17]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Low mutation load in a supergene underpinning alternative male mating strategies in ruff (Calidris pugnax).
Hill J, Enbody ED, Bi H, ..., Widemo F, Andersson L
Mol. Biol. Evol. 40 (12) msad224 [2023-10-06; online 2023-10-06]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Copy number variations and their effect on the plasma proteome.
Schmitz D, Li Z, Lo Faro V, ..., Rafati N, Johansson Å
Genetics - (-) - [2023-10-04; online 2023-10-04]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae).
Steffen K, Proux-Wéra E, Soler L, ..., Sundh J, Cárdenas P
G3 (Bethesda) 13 (10) - [2023-09-30; online 2023-08-25]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The relative impact of parental and current environment on plant transcriptomes depends on type of stress and genotype.
Earley TS, Feiner N, Alvarez MF, Coolon JD, Sultan SE
Proc. Biol. Sci. 290 (2007) 20230824 [2023-09-27; online 2023-09-27]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The draft genome of the microscopic Nemertoderma westbladi sheds light on the evolution of Acoelomorpha genomes.
Abalde S, Tellgren-Roth C, Heintz J, Vinnere Pettersson O, Jondelius U
Front Genet 14 (-) 1244493 [2023-09-26; online 2023-09-26]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Ectomycorrhizal fungi integrate nitrogen mobilisation and mineral weathering in boreal forest soil.
Mahmood S, Fahad Z, Bolou-Bi EB, ..., Ekblad A, Finlay RD
New Phytol. - (-) - [2023-09-11; online 2023-09-11]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Long-read whole-genome analysis of human single cells.
Hård J, Mold JE, Eisfeldt J, ..., Michaëlsson J, Ameur A
Nat Commun 14 (1) 5164 [2023-08-24; online 2023-08-24]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Technology development] NGI Single cell [Technology development] NGI Stockholm (Genomics Applications) [Collaborative] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
PubMed DOI Crossref
A novel quantitative targeted analysis of X-chromosome inactivation (XCI) using nanopore sequencing.
Johansson J, Lidéus S, Höijer I, ..., Bondeson ML, Wilbe M
Sci Rep 13 (1) 12856 [2023-08-08; online 2023-08-08]
NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Biogeography of Fungal Communities Associated with Pinus sylvestris L. and Picea abies (L.) H. Karst. along the Latitudinal Gradient in Europe.
Mishcherikova V, Lynikienė J, Marčiulynas A, ..., Marčiulynienė D, Menkis A
JoF 9 (8) - [2023-08-06; online 2023-08-06]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Y-Linked Copy Number Polymorphism of Target of Rapamycin Is Associated with Sexual Size Dimorphism in Seed Beetles.
Kaufmann P, Wiberg RAW, Papachristos K, ..., Tellgren-Roth C, Immonen E
Mol. Biol. Evol. 40 (8) - [2023-08-03; online 2023-07-22]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
DOI Crossref
A genomic platform for surveillance and antigen discovery in Plasmodium spp. using long-read amplicon sequencing
Plaza DF, Zerebinski J, Broumou I, ..., Sundling C, Färnert A
Cell Reports Methods - (-) 100574 [2023-08-00; online 2023-08-00]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Vegetation, topography, and soil depth drive microbial community structure in two Swedish grasslands.
Guasconi D, Juhanson J, Clemmensen KE, ..., Roth N, Fransson P
FEMS Microbiol. Ecol. 99 (8) - [2023-07-21; online 2023-07-21]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Forest Fire Influence on Tomicus piniperda-Associated Fungal Communities and Phloem Nutrient Availability of Colonized Pinus sylvestris.
Kluting K, Strid Y, Six D, Rosling A
Microb. Ecol. 86 (1) 224-239 [2023-07-00; online 2022-07-13]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Contrasting plant-soil-microbial feedbacks stabilize vegetation types and uncouple topsoil C and N stocks across a subarctic-alpine landscape.
Castaño C, Hallin S, Egelkraut D, ..., Olofsson J, Clemmensen KE
New Phytol. 238 (6) 2621-2633 [2023-06-00; online 2022-12-29]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex.
Himmelstrand K, Brandström Durling M, Karlsson M, Stenlid J, Olson Å
Front Microbiol 14 (-) 1159811 [2023-05-18; online 2023-05-18]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Exchange of Carbapenem-Resistant Escherichia coli Sequence Type 38 Intercontinentally and among Wild Bird, Human, and Environmental Niches.
Ahlstrom CA, Woksepp H, Sandegren L, Ramey AM, Bonnedahl J
Appl. Environ. Microbiol. - (-) e0031923 [2023-05-17; online 2023-05-17]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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The Broad Spectrum of TP53 Mutations in CLL: Evidence of Multiclonality and Novel Mutation Hotspots
Lazarian G, Leroy B, Theves F, ..., Baran-Marszak F, Soussi T
Hum. Mutat. 2023 (-) 1-17 [2023-05-09; online 2023-05-09]
NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
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A Long-Standing Hybrid Population Between Pacific and Atlantic Herring in a Subarctic Fjord of Norway.
Pettersson ME, Fuentes-Pardo AP, Rochus CM, ..., Väinölä R, Andersson L
Genome Biol Evol 15 (5) - [2023-05-05; online 2023-04-30]
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PubMed DOI Crossref
Micro Germline-Restricted Chromosome in Blue Tits: Evidence for Meiotic Functions.
Mueller JC, Schlebusch SA, Pei Y, ..., Suh A, Kempenaers B
Mol. Biol. Evol. 40 (5) - [2023-05-02; online 2023-04-28]
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Seasonal and Site-Specific Patterns of Airborne Fungal Diversity Revealed Using Passive Spore Traps and High-Throughput DNA Sequencing
Marčiulynas A, Lynikienė J, Marčiulynienė D, Gedminas A, Menkis A
Diversity 15 (4) 539 [2023-04-09; online 2023-04-09]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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The genetic basis of wing spots in Pieris canidia butterflies.
Wee JLQ, Murugesan SN, Wheat CW, Monteiro A
BMC Genomics 24 (1) 169 [2023-04-04; online 2023-04-04]
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A MITE insertion abolishes the AP3-3 self-maintenance regulatory loop in apetalous flowers of Nigella damascena.
Conde E Silva N, Leguilloux M, Bellec A, ..., Berges H, Deveaux Y
J. Exp. Bot. 74 (5) 1448-1459 [2023-03-13; online 2022-12-14]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Multiple introgressions shape mitochondrial evolutionary history in Drosophila paulistorum and the Drosophila willistoni group.
Baião GC, Schneider DI, Miller WJ, Klasson L
Mol. Phylogenet. Evol. 180 (-) 107683 [2023-03-00; online 2022-12-24]
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Ectomycorrhizal fungi with hydrophobic mycelia and rhizomorphs dominate in young pine trees surviving experimental drought stress
Castaño C, Suarez-Vidal E, Zas R, ..., Oliva J, Sampedro L
Soil Biology and Biochemistry 178 (-) 108932 [2023-03-00; online 2023-03-00]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Carbon substrate selects for different lineages of N2O reducing communities in soils under anoxic conditions
Maheshwari A, Jones CM, Tiemann M, Hallin S
Soil Biology and Biochemistry 177 (-) 108909 [2023-02-00; online 2023-02-00]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Year 2022

DOI Crossref
Resistance of subarctic soil fungal and invertebrate communities to disruption of below‐ground carbon supply
Parker TC, Chomel M, Clemmensen KE, ..., Subke J, Wookey PA
J Ecol 110 (12) 2883-2897 [2022-12-00; online 2022-10-17]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Stage-specific transposon activity in the life cycle of the fairy-ring mushroom <i>Marasmius oreades</i>.
Hiltunen M, Ament-Velásquez SL, Ryberg M, Johannesson H
Proc. Natl. Acad. Sci. U.S.A. 119 (46) e2208575119 [2022-11-16; online 2022-11-07]
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Fungal Communities in Leaves and Roots of Healthy-Looking and Diseased Ulmusglabra.
Marčiulynas A, Marčiulynienė D, Lynikienė J, Bakys R, Menkis A
Microorganisms 10 (11) - [2022-11-10; online 2022-11-10]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Genome Evolution of a Symbiont Population for Pathogen Defense in Honeybees.
Dyrhage K, Garcia-Montaner A, Tamarit D, ..., Webster MT, Andersson SGE
Genome Biol Evol 14 (11) - [2022-11-04; online 2022-10-21]
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Changes in Chemical Properties and Fungal Communities of Mineral Soil after Clear-Cutting and Reforestation of Scots Pine (Pinus sylvestris L.) Sites
Povilaitienė A, Gedminas A, Varnagirytė-Kabašinskienė I, ..., Mishcherikova V, Menkis A
Forests 13 (11) 1780 [2022-10-27; online 2022-10-27]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level.
Gutiérrez-Valencia J, Fracassetti M, Berdan EL, ..., Arroyo J, Slotte T
Curr. Biol. 32 (20) 4360-4371.e6 [2022-10-24; online 2022-09-09]
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PubMed DOI Crossref
Principal Drivers of Fungal Communities Associated with Needles, Shoots, Roots and Adjacent Soil of Pinus sylvestris.
Marčiulynienė D, Marčiulynas A, Mischerikova V, ..., Franic I, Menkis A
JoF 8 (10) - [2022-10-21; online 2022-10-21]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Do ectomycorrhizal exploration types reflect mycelial foraging strategies?
Jörgensen K, Clemmensen KE, Wallander H, Lindahl BD
New Phytol. - (-) - [2022-10-21; online 2022-10-21]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA.
Behra PRK, Pettersson BMF, Ramesh M, ..., Dasgupta S, Kirsebom LA
BMC Genomics 23 (1) 704 [2022-10-15; online 2022-10-15]
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Mycobiota Associated with Symptomatic and Asymptomatic Fraxinus excelsior in Post-Dieback Forest Stands
Bakys R, Pliūra A, Bajerkevičienė G, ..., Lynikienė J, Menkis A
Forests 13 (10) 1609 [2022-10-01; online 2022-10-01]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Global patterns and rates of habitat transitions across the eukaryotic tree of life.
Jamy M, Biwer C, Vaulot D, ..., Massana R, Burki F
Nat Ecol Evol 6 (10) 1458-1470 [2022-10-00; online 2022-08-04]
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Endophytes dominate fungal communities in six-year-old veteranisation wounds in living oak trunks
Menkis A, Redr D, Bengtsson V, ..., Nordén B, Dahlberg A
Fungal Ecology 59 (-) 101020 [2022-10-00; online 2022-10-00]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Parasitic strongyle nemabiome communities in wild ruminants in Sweden.
Halvarsson P, Baltrušis P, Kjellander P, Höglund J
Parasit Vectors 15 (1) 341 [2022-09-27; online 2022-09-27]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Natural alleles of the abscisic acid catabolism gene ZmAbh4 modulate water use efficiency and carbon isotope discrimination in maize.
Blankenagel S, Eggels S, Frey M, ..., Schön CC, Avramova V
Plant Cell 34 (10) 3860-3872 [2022-09-27; online 2022-07-07]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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A chromosome-scale reference genome for Spironucleus salmonicida.
Xu F, Jiménez-González A, Kurt Z, ..., Andersson JO, Svärd SG
Sci Data 9 (1) 585 [2022-09-24; online 2022-09-24]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Multi-Omic Investigations of a 17-19 Translocation Links MINK1 Disruption to Autism, Epilepsy and Osteoporosis.
Eisfeldt J, Schuy J, Stattin EL, ..., Feuk L, Lindstrand A
Int J Mol Sci 23 (16) - [2022-08-20; online 2022-08-20]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Estimation of the impact of three different bioinformatic pipelines on sheep nemabiome analysis.
Baltrušis P, Halvarsson P, Höglund J
Parasit Vectors 15 (1) 290 [2022-08-11; online 2022-08-11]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing.
Dahn HA, Mountcastle J, Balacco J, ..., Jarvis ED, Fedrigo O
Gigascience 11 (-) - [2022-08-10; online 2022-08-11]
NGI Long read [Technology development] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
PubMed DOI Crossref
Detecting DNA Methylations in the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius Using SMRT Sequencing.
Tellgren-Roth C, Couturier M
Methods Mol. Biol. 2516 (-) 39-50 [2022-08-04; online 2022-08-04]
NGI Long read [Technology development] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
PubMed DOI Crossref
The genomic architecture of the passerine MHC region: High repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes.
Westerdahl H, Mellinger S, Sigeman H, ..., Wolf JBW, Strandh M
Mol Ecol Resour 22 (6) 2379-2395 [2022-08-00; online 2022-04-11]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Human adaptation to arsenic in Bolivians living in the Andes.
De Loma J, Vicente M, Tirado N, ..., Schlebusch CM, Broberg K
Chemosphere 301 (-) 134764 [2022-08-00; online 2022-04-28]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Long read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Host genotype interacts with aerial spore communities and influences the needle mycobiome of Norway spruce.
Redondo MA, Oliva J, Elfstrand M, ..., Karlsson B, Berlin A
Environ. Microbiol. 24 (8) 3640-3654 [2022-08-00; online 2022-03-22]
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DOI Crossref
Ericaceous dwarf shrubs contribute a significant but drought‐sensitive fraction of soil respiration in a boreal pine forest
Mielke LA, Ekblad A, Finlay RD, ..., Lindahl BD, Clemmensen KE
J Ecol 110 (8) 1928-1941 [2022-08-00; online 2022-06-15]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening.
Schaal W, Ameur A, Olsson-Strömberg U, ..., Cavelier L, Spjuth O
Cancer Inform 21 (-) 11769351221110872 [2022-07-15; online 2022-07-15]
NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
DOI Crossref
High Variability of Fungal Communities Associated with the Functional Tissues and Rhizosphere Soil of Picea abies in the Southern Baltics
Marčiulynas A, Marčiulynienė D, Mishcherikova V, ..., Gedminas A, Menkis A
Forests 13 (7) 1103 [2022-07-13; online 2022-07-13]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The long noncoding RNA ADIPINT regulates human adipocyte metabolism via pyruvate carboxylase.
Kerr AG, Wang Z, Wang N, ..., Arner P, Gao H
Nat Commun 13 (1) 2958 [2022-05-26; online 2022-05-26]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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The Carniolan Honeybee from Slovenia-A Complete and Annotated Mitochondrial Genome with Comparisons to Closely Related Apis mellifera Subspecies.
Moškrič A, Marinč A, Ferk P, ..., Soler L, Prešern J
Insects 13 (5) 403 [2022-04-22; online 2022-04-22]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
The era of reference genomes in conservation genomics.
Formenti G, Theissinger K, Fernandes C, ..., Bálint M, European Reference Genome Atlas (ERGA) Consortium
Trends Ecol Evol 37 (3) 197-202 [2022-03-00; online 2022-01-24]
NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long-read metabarcoding.
Eshghi Sahraei S, Furneaux B, Kluting K, ..., Hytteborn H, Rosling A
Ecol Evol 12 (3) e8676 [2022-03-00; online 2022-03-08]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations.
Höijer I, Emmanouilidou A, Östlund R, ..., den Hoed M, Ameur A
Nat Commun 13 (1) 627 [2022-02-02; online 2022-02-02]
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DOI Crossref
Links between boreal forest management, soil fungal communities and below‐ground carbon sequestration
Jörgensen K, Granath G, Strengbom J, Lindahl BD
Functional Ecology 36 (2) 392-405 [2022-02-00; online 2021-12-22]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component.
Christmas MJ, Jones JC, Olsson A, ..., Miller-Struttmann NE, Webster MT
Mol. Ecol. 31 (4) 1111-1127 [2022-02-00; online 2021-12-07]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Standards recommendations for the Earth BioGenome Project.
Lawniczak MKN, Durbin R, Flicek P, ..., Lewin HA, Richards S
Proc. Natl. Acad. Sci. U.S.A. 119 (4) - [2022-01-25; online 2022-01-20]
NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Cold case: The disappearance of Egypt bee virus, a fourth distinct master strain of deformed wing virus linked to honeybee mortality in 1970's Egypt.
de Miranda JR, Brettell LE, Chejanovsky N, ..., Martin SJ, Ball BV
Virol J 19 (1) 12 [2022-01-15; online 2022-01-15]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Fungal Perspective of Pine and Oak Colonization in Mediterranean Degraded Ecosystems
Adamo I, Dashevskaya S, Alday JG
Forests 13 (1) 88 [2022-01-08; online 2022-01-08]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Year 2021

PubMed DOI Crossref
Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier.
Eisfeldt J, Pettersson M, Petri A, ..., Feuk L, Lindstrand A
Hum. Genet. 140 (5) 775-790 [2021-05-00; online 2020-12-14]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
SciLifeLab Data Centre
Publications 9.5.1