Publications 2023

Motor nerves direct the development of the sympathetic nervous system

Erickson A, Motta A, Kastriti ME, ..., Bonanomi D, Adameyko I

- - (-) - [2023-03-18; online 2023-03-18]

Integrated Microscopy Technologies Stockholm [Service]

Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis.

Majumdar S, Emmerich A, Krakovka S, ..., Svärd SG, Sanyal S

Nucleic Acids Res. - (-) - [2023-03-13; online 2023-03-13]

Identification of phenotypically, functionally, and anatomically distinct stromal niche populations in human bone marrow based on single-cell RNA sequencing.

Li H, Bräunig S, Dhapolar P, ..., Lang S, Scheding S

Elife 12 (-) - [2023-03-06; online 2023-03-06]

Subtyping of cardiac amyloidosis by mass spectrometry-based proteomics of endomyocardial biopsies.

Noborn F, Thomsen C, Vorontsov E, ..., Oldfors A, Larson G

Amyloid 30 (1) 96-108 [2023-03-00; online 2022-10-09]

Glycoproteomics [Collaborative]

Occupational inhalable agents constitute major risk factors for rheumatoid arthritis, particularly in the context of genetic predisposition and smoking.

Tang B, Liu Q, Ilar A, ..., Alfredsson L, Jiang X

Ann. Rheum. Dis. 82 (3) 316-323 [2023-03-00; online 2022-12-06]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Isobaric labeling-based quantitative proteomics of FACS-purified immune cells and epithelial cells from the intestine of Crohn's disease patients reveals proteome changes of potential importance in disease pathogenesis.

Alfredsson J, Fabrik I, Gorreja F, ..., Lindskog EB, Wick MJ

Proteomics 23 (5) e2200366 [2023-03-00; online 2022-12-25]

Glycoproteomics [Collaborative]

NCF1-dependent production of ROS protects against lupus by regulating plasmacytoid dendritic cell development and functions.

Luo H, Urbonaviciute V, Saei AA, ..., Zubarev RA, Holmdahl R

JCI Insight - (-) - [2023-02-28; online 2023-02-28]

Chemical Proteomics [Service]

Insights into the structure-function relationship of the NorQ/NorD chaperones from Paracoccus denitrificans reveal shared principles of interacting MoxR AAA+/VWA domain proteins.

Kahle M, Appelgren S, Elofsson A, Carroni M, Ädelroth P

BMC Biol. 21 (1) 47 [2023-02-28; online 2023-02-28]

Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.

Jun S, Toosi H, Mold J, ..., Roth A, Lagergren J

Nat Commun 14 (1) 982 [2023-02-22; online 2023-02-22]

NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Accelerated epigenetic aging in women with emotionally unstable personality disorder and a history of suicide attempts.

Boström ADE, Andersson P, Jamshidi E, ..., Åsberg M, Jokinen J

Transl Psychiatry 13 (1) 66 [2023-02-22; online 2023-02-22]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Multi-organ single-cell analysis reveals an on/off switch system with potential for personalized treatment of immunological diseases.

Lilja S, Li X, Smelik M, ..., Wang H, Benson M

Cell Reports Medicine - (-) 100956 [2023-02-17; online 2023-02-17]

Affinity Proteomics Stockholm [Service]

Antibiotic thermorubin tethers ribosomal subunits and impedes A-site interactions to perturb protein synthesis in bacteria.

Parajuli NP, Emmerich A, Mandava CS, Pavlov MY, Sanyal S

Nat Commun 14 (1) 918 [2023-02-17; online 2023-02-17]

Cryo-EM structure and function of S. pombe complex IV with bound respiratory supercomplex factor.

Moe A, Ädelroth P, Brzezinski P, Näsvik Öjemyr L

Commun Chem 6 (1) 32 [2023-02-16; online 2023-02-16]

Associations of DNA Methylation With Behavioral Problems, Gray Matter Volumes, and Negative Life Events Across Adolescence: Evidence From the Longitudinal IMAGEN Study.

Sun Y, Jia T, Barker ED, ..., Schumann G, Desrivières S

Biol. Psychiatry 93 (4) 342-351 [2023-02-15; online 2022-06-22]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Array-Based Multiplex and High-Throughput Serology Assays.

Olofsson J, Hellström C, Andersson E, ..., Nilsson P, Pin E

Methods Mol. Biol. 2628 (-) 535-553 [2023-02-14; online 2023-02-14]

Autoimmunity and Serology Profiling [Technology development]

Genomic architecture of migration timing in a long-distance migratory songbird.

de Greef E, Suh A, Thorstensen MJ, Delmore KE, Fraser KC

Sci Rep 13 (1) 2437 [2023-02-10; online 2023-02-10]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Microneedle Patch for Painless Intradermal Collection of Interstitial Fluid Enabling Multi-analyte Measurement of Small Molecules, SARS-CoV-2 Antibodies, and Protein Profiling.

Ribet F, Bendes A, Fredolini C, ..., Stemme G, Roxhed N

Adv Healthc Mater - (-) e2202564 [2023-02-07; online 2023-02-07]

Affinity Proteomics Stockholm [Collaborative]

Proteomic Analysis of Mucosal and Systemic Responses to SARS-CoV-2 Antigen.

Martinson N, Gordhan B, Petkov S, ..., Kana B, Herrera C

Vaccines (Basel) 11 (2) - [2023-02-02; online 2023-02-02]

Affinity Proteomics Stockholm [Service]

Proteogenomics decodes the evolution of human ipsilateral breast cancer.

De Marchi T, Pyl PT, Sjöström M, ..., Malmstöm J, Niméus E

Commun Biol 6 (1) 139 [2023-02-02; online 2023-02-02]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Ten years of marine evolutionary biology-Challenges and achievements of a multidisciplinary research initiative.

Johannesson K, Leder EH, André C, ..., Thorndyke M, Blomberg A

Evol Appl 16 (2) 530-541 [2023-02-00; online 2023-01-07]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Migratory behaviour is positively associated with genetic diversity in butterflies.

García-Berro A, Talla V, Vila R, ..., Backström N, Talavera G

Mol. Ecol. 32 (3) 560-574 [2023-02-00; online 2022-11-23]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Inactivation of RB1, CDKN2A, and TP53 have distinct effects on genomic stability at side-by-side comparison in karyotypically normal cells.

Andersson N, Saba KH, Magnusson L, ..., Nord KH, Gisselsson D

Genes Chromosomes Cancer 62 (2) 93-100 [2023-02-00; online 2022-09-30]

Hypercomplex Low Rank Reconstruction for NMR Spectroscopy

Guo Y, Zhan J, Tu Z, ..., Qu X, Guo D

Signal Processing 203 (-) 108809 [2023-02-00; online 2023-02-00]

Swedish NMR Centre (SNC) [Collaborative]

Evaluation of kraft and hydrolysis lignin hydroconversion over unsupported NiMoS catalyst

Achour A, Bernin D, Creaser D, Olsson L

Chemical Engineering Journal 453 (-) 139829 [2023-02-00; online 2023-02-00]

Swedish NMR Centre (SNC) [Service]

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]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.

Sountoulidis A, Marco Salas S, Braun E, ..., Nilsson M, Samakovlis C

Nat Cell Biol 25 (2) 351-365 [2023-02-00; online 2023-01-16]

NGI Short read [Service] NGI Single cell [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Inversions maintain differences between migratory phenotypes of a songbird.

Lundberg M, Mackintosh A, Petri A, Bensch S

Nat Commun 14 (1) 452 [2023-01-27; online 2023-01-27]

NGI Single cell [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.).

Höök L, Näsvall K, Vila R, Wiklund C, Backström N

Chromosome Res. 31 (1) 2 [2023-01-20; online 2023-01-20]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Single-cell analysis of myeloid cells in HPV+ tonsillar cancer.

Jimenez DG, Altunbulakli C, Swoboda S, ..., Greiff L, Lindstedt M

Front Immunol 13 (-) 1087843 [2023-01-19; online 2023-01-19]

Microbial communities mediating net methylmercury formation along a trophic gradient in a peatland chronosequence.

Wang B, Hu H, Bishop K, ..., Bertilsson S, Bravo AG

J Hazard Mater 442 (-) 130057 [2023-01-15; online 2022-09-23]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A hypomorphic variant in the translocase of the outer mitochondrial membrane complex subunit TOMM7 causes short stature and developmental delay.

Young C, Batkovskyte D, Kitamura M, ..., Grigelioniene G, Kobayashi T

HGG Adv 4 (1) 100148 [2023-01-12; online 2022-10-04]

Clinical Genomics Stockholm [Service]

Single-cell transcriptomics reveals correct developmental dynamics and high-quality midbrain cell types by improved hESC differentiation.

Nishimura K, Yang S, Lee KW, ..., Linnarsson S, Arenas E

Stem Cell Reports 18 (1) 337-353 [2023-01-10; online 2022-11-17]

NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Persistence of salivary antibody responses after COVID-19 vaccination is associated with oral microbiome variation in both healthy and people living with HIV

Ghorbani M, Al-Manei K, Naud S, ..., Aleman S, Sällberg Chen M

Front Immunol 13 (-) - [2023-01-10; online 2023-01-10]

Autoimmunity and Serology Profiling [Service]

Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.

Koptekin D, Yüncü E, Rodríguez-Varela R, ..., Götherström A, Somel M

Curr. Biol. 33 (1) 41-57.e15 [2023-01-09; online 2022-12-08]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The effect of side chain variations on quinazoline-pyrimidine G-quadruplex DNA ligands.

Bhuma N, Chand K, Andréasson M, ..., Öhlund D, Chorell E

Eur J Med Chem 248 (-) 115103 [2023-01-08; online 2023-01-08]

Swedish NMR Centre (SNC) [Service]

The genetic history of Scandinavia from the Roman Iron Age to the present.

Rodríguez-Varela R, Moore KHS, Ebenesersdóttir SS, ..., Helgason A, Götherström A

Cell 186 (1) 32-46.e19 [2023-01-05; online 2023-01-08]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Solid-phase capture and profiling of open chromatin by spatial ATAC.

Llorens-Bobadilla E, Zamboni M, Marklund M, ..., Frisén J, Ståhl PL

Nat. Biotechnol. - (-) - [2023-01-05; online 2023-01-05]

NGI Short read [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Xylan glucuronic acid side chains fix suberin-like aliphatic compounds to wood cell walls.

Derba-Maceluch M, Mitra M, Hedenström M, ..., Master ER, Mellerowicz EJ

New Phytol. - (-) - [2023-01-04; online 2023-01-04]

Swedish NMR Centre (SNC) [Collaborative]

Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression.

Sokolov AV, Manu DM, Nordberg DOT, ..., Jokinen J, Schiöth HB

Clin Epigenetics 15 (1) 1 [2023-01-04; online 2023-01-04]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats.

Alaei Kakhki N, Schweizer M, Lutgen D, ..., Schielzeth H, Burri R

Mol. Biol. Evol. 40 (1) - [2023-01-04; online 2022-12-30]

NGI Short read [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models.

Allesøe RL, Lundgaard AT, Hernández Medina R, ..., Brunak S, IMI DIRECT Consortium

Nat. Biotechnol. - (-) - [2023-01-02; online 2023-01-02]

Affinity Proteomics Stockholm [Collaborative]

The path to immortalization of cells starts by managing stress through gene duplications.

Lewerentz J, Johansson AM, Stenberg P

Exp. Cell Res. 422 (1) 113431 [2023-01-01; online 2022-11-21]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The injury-induced transcription factor SOX9 alters the expression of LBR, HMGA2, and HIPK3 in the human kidney.

Kha M, Krawczyk K, Choong OK, ..., Swärd K, Johansson ME

Am. J. Physiol. Renal Physiol. 324 (1) F75-F90 [2023-01-01; online 2022-12-01]

Rare tandem repeat expansions associate with genes involved in synaptic and neuronal signaling functions in schizophrenia.

Wen J, Trost B, Engchuan W, ..., Yuen RKC, Szatkiewicz JP

Mol. Psychiatry 28 (1) 475-482 [2023-01-00; online 2022-11-16]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Graphene oxide elicits microbiome-dependent type 2 immune responses via the aryl hydrocarbon receptor.

Peng G, Sinkko HM, Alenius H, ..., Bräutigam L, Fadeel B

Nat Nanotechnol 18 (1) 42-48 [2023-01-00; online 2022-12-12]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]