Proc. Natl. Acad. Sci. U.S.A.

Inhibition mechanism of potential antituberculosis compound lansoprazole sulfide.

Kovalova T, Król S, Gamiz-Hernandez AP, ..., Brzezinski P, Högbom M

Proc. Natl. Acad. Sci. U.S.A. 121 (47) e2412780121 [2024-11-19; online 2024-11-12]

Inherited human RelB deficiency impairs innate and adaptive immunity to infection.

Le Voyer T, Maglorius Renkilaraj MRL, Moriya K, ..., Tangye SG, Puel A

Proc. Natl. Acad. Sci. U.S.A. 121 (37) e2321794121 [2024-09-10; online 2024-09-04]

Autoimmunity and Serology Profiling [Service]

A chemical inhibitor of IST1-CHMP1B interaction impairs endosomal recycling and induces noncanonical LC3 lipidation.

Knyazeva A, Li S, Corkery DP, ..., Waldmann H, Wu YW

Proc. Natl. Acad. Sci. U.S.A. 121 (17) e2317680121 [2024-04-23; online 2024-04-18]

Chemical Proteomics [Collaborative] Cryo-EM [Service]

Antibiotic class with potent in vivo activity targeting lipopolysaccharide synthesis in Gram-negative bacteria.

Huseby DL, Cao S, Zamaratski E, ..., Hughes D, Karlén A

Proc. Natl. Acad. Sci. U.S.A. 121 (15) e2317274121 [2024-04-09; online 2024-04-05]

Drug Discovery and Development (DDD) [Collaborative]

Deletion of the TMEM30A gene enables leukemic cell evasion of NK cell cytotoxicity.

Kristenson L, Badami C, Ljungberg A, ..., Tang KW, Thorén FB

Proc. Natl. Acad. Sci. U.S.A. 121 (15) e2316447121 [2024-04-09; online 2024-04-01]

Bioinformatics Support for Computational Resources [Service] CRISPR Functional Genomics [Service]

Ligand-induced protein transition state stabilization switches the binding pathway from conformational selection to induced fit.

Stenström O, Diehl C, Modig K, Akke M

Proc. Natl. Acad. Sci. U.S.A. 121 (14) e2317747121 [2024-04-02; online 2024-03-25]

Swedish NMR Centre (SNC) [Service]

Genomic ancestry and social dynamics of the last hunter-gatherers of Atlantic France.

Simões LG, Peyroteo-Stjerna R, Marchand G, ..., Günther T, Jakobsson M

Proc. Natl. Acad. Sci. U.S.A. 121 (10) e2310545121 [2024-03-05; online 2024-02-26]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Molecular basis for human aquaporin inhibition.

Huang P, Åbacka H, Wilson CJ, ..., Venskutonytė R, Lindkvist-Petersson K

Proc. Natl. Acad. Sci. U.S.A. 121 (7) e2319682121 [2024-02-13; online 2024-02-06]

A macrophage-collagen fragment axis mediates subcutaneous adipose tissue remodeling in mice.

Vujičić M, Broderick I, Salmantabar P, ..., Sihlbom Wallem C, Wernstedt Asterholm I

Proc. Natl. Acad. Sci. U.S.A. 121 (6) e2313185121 [2024-02-06; online 2024-02-01]

Glycoproteomics and MS Proteomics [Collaborative]

Structure and function of the S. pombe III-IV-cyt c supercomplex.

Moe A, Dimogkioka AR, Rapaport D, Öjemyr LN, Brzezinski P

Proc. Natl. Acad. Sci. U.S.A. 120 (46) e2307697120 [2023-11-14; online 2023-11-08]

Ablation of ZC3H11A causes early embryonic lethality and dysregulation of metabolic processes.

Younis S, Jouneau A, Larsson M, ..., Brochard V, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 120 (23) e2216799120 [2023-06-06; online 2023-05-30]

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

Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle.

Knöppel A, Broström O, Gras K, Elf J, Fange D

Proc. Natl. Acad. Sci. U.S.A. 120 (22) e2213795120 [2023-05-30; online 2023-05-23]

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Reply to Pandey: IgG3 allotypes, modulation of antigen binding by constant domain changes, and therapeutic applications of Fc engineering.

Izadi A, Bahnan W, Ohlin M, Nordenfelt P

Proc. Natl. Acad. Sci. U.S.A. 120 (22) e2306562120 [2023-05-30; online 2023-05-22]

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Subclass-switched anti-spike IgG3 oligoclonal cocktails strongly enhance Fc-mediated opsonization.

Izadi A, Hailu A, Godzwon M, ..., Bahnan W, Nordenfelt P

Proc. Natl. Acad. Sci. U.S.A. 120 (15) e2217590120 [2023-04-11; online 2023-04-03]

Drug Discovery and Development (DDD) [Service]

Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data.

Gustafsson J, Anton M, Roshanzamir F, ..., Robinson JL, Nielsen J

Proc. Natl. Acad. Sci. U.S.A. 120 (6) e2217868120 [2023-02-07; online 2023-01-31]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Antibiotic perseverance increases the risk of resistance development.

Brandis G, Larsson J, Elf J

Proc. Natl. Acad. Sci. U.S.A. 120 (2) e2216216120 [2023-01-10; online 2023-01-03]

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Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction.

Chen X, Sifakis EG, Robertson S, ..., Ma R, Hartman J

Proc. Natl. Acad. Sci. U.S.A. 120 (1) e2209856120 [2023-01-03; online 2022-12-27]

Bioinformatics Support for Computational Resources [Service] Chemical Biology Consortium Sweden (CBCS) [Service]

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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SPACA9 is a lumenal protein of human ciliary singlet and doublet microtubules.

Gui M, Croft JT, Zabeo D, ..., Höög JL, Brown A

Proc. Natl. Acad. Sci. U.S.A. 119 (41) e2207605119 [2022-10-11; online 2022-10-03]

Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests.

Law SR, Serrano AR, Daguerre Y, ..., Street NR, Hurry V

Proc. Natl. Acad. Sci. U.S.A. 119 (26) e2118852119 [2022-06-28; online 2022-06-21]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] National Genomics Infrastructure [Service]

Membrane insertion mechanism of the caveola coat protein Cavin1.

Liu KC, Pace H, Larsson E, ..., Hubert M, Lundmark R

Proc. Natl. Acad. Sci. U.S.A. 119 (25) e2202295119 [2022-06-21; online 2022-06-13]

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Occasional paternal inheritance of the germline-restricted chromosome in songbirds.

Pei Y, Forstmeier W, Ruiz-Ruano FJ, ..., Suh A, Kempenaers B

Proc. Natl. Acad. Sci. U.S.A. 119 (4) - [2022-01-25; online 2022-01-22]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast.

Malina C, Yu R, Björkeroth J, Kerkhoven EJ, Nielsen J

Proc. Natl. Acad. Sci. U.S.A. 118 (51) - [2021-12-21; online 2021-12-15]

Glycoproteomics and MS Proteomics [Service]

THCz: Small molecules with antimicrobial activity that block cell wall lipid intermediates.

Reithuber E, Wixe T, Ludwig KC, ..., Almqvist F, Mellroth P

Proc. Natl. Acad. Sci. U.S.A. 118 (47) - [2021-11-23; online 2021-11-18]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A tripartite cytolytic toxin formed by Vibrio cholerae proteins with flagellum-facilitated secretion.

Nadeem A, Nagampalli R, Toh E, ..., Wai SN, Persson K

Proc. Natl. Acad. Sci. U.S.A. 118 (47) - [2021-11-23; online 2021-11-21]

Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens.

Li J, Lee MO, Chen J, ..., Chuong CM, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 118 (41) - [2021-10-12; online 2021-10-06]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genome-scale metabolic network reconstruction of model animals as a platform for translational research.

Wang H, Robinson JL, Kocabas P, ..., Zetterberg H, Nielsen J

Proc. Natl. Acad. Sci. U.S.A. 118 (30) e2102344118 [2021-07-27; online 2021-07-21]

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Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives.

Bohutínská M, Vlček J, Yair S, ..., Slotte T, Kolář F

Proc. Natl. Acad. Sci. U.S.A. 118 (21) - [2021-05-25; online 2021-05-19]

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

Small noncoding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology.

Zheleznyakova GY, Piket E, Needhamsen M, ..., Piehl F, Jagodic M

Proc. Natl. Acad. Sci. U.S.A. 118 (17) e2011574118 [2021-04-27; online 2021-04-22]

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An introgressed gene causes meiotic drive in Neurospora sitophila.

Svedberg J, Vogan AA, Rhoades NA, ..., Hammond TM, Johannesson H

Proc. Natl. Acad. Sci. U.S.A. 118 (17) e2026605118 [2021-04-27; online 2021-04-21]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Multiple migrations to the Philippines during the last 50,000 years.

Larena M, Sanchez-Quinto F, Sjödin P, ..., Endicott P, Jakobsson M

Proc. Natl. Acad. Sci. U.S.A. 118 (13) - [2021-03-30; online 2021-03-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau.

Qu Y, Chen C, Chen X, ..., Zhang YE, Lei F

Proc. Natl. Acad. Sci. U.S.A. 118 (13) e2012398118 [2021-03-30; online 2021-03-24]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Expansions of adaptive-like NK cells with a tissue-resident phenotype in human lung and blood.

Brownlie D, Scharenberg M, Mold JE, ..., Marquardt N, Michaëlsson J

Proc. Natl. Acad. Sci. U.S.A. 118 (11) e2016580118 [2021-03-16; online 2021-04-11]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Major alterations in the mononuclear phagocyte landscape associated with COVID-19 severity.

Kvedaraite E, Hertwig L, Sinha I, ..., Svensson M, Karolinska KI/K COVID-19 Study Group

Proc. Natl. Acad. Sci. U.S.A. 118 (6) e2018587118 [2021-02-09; online 2021-01-23]

Affinity Proteomics Stockholm [Service]

Ecological adaptation in European eels is based on phenotypic plasticity.

Enbody ED, Pettersson ME, Sprehn CG, ..., Wickström H, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 118 (4) e2022620118 [2021-01-26; online 2021-01-23]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Human species D adenovirus hexon capsid protein mediates cell entry through a direct interaction with CD46.

Persson BD, John L, Rafie K, ..., Carlson LA, Arnberg N

Proc. Natl. Acad. Sci. U.S.A. 118 (3) - [2021-01-19; online 2021-01-02]

Capillary leakage provides nutrients and antioxidants for rapid pneumococcal proliferation in influenza-infected lower airways.

Sender V, Hentrich K, Pathak A, ..., Normark S, Henriques-Normark B

Proc. Natl. Acad. Sci. U.S.A. 117 (49) 31386-31397 [2020-12-08; online 2020-11-23]

Bioinformatics Support for Computational Resources [Service] Chemical Proteomics [Collaborative]

Coupling stabilizers open KV1-type potassium channels.

Silverå Ejneby M, Wallner B, Elinder F

Proc. Natl. Acad. Sci. U.S.A. 117 (43) 27016-27021 [2020-10-27; online 2020-10-13]

Chemical Biology Consortium Sweden (CBCS) [Service]

Reconstruction of the birth of a male sex chromosome present in Atlantic herring.

Rafati N, Chen J, Herpin A, ..., Schartl M, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 117 (39) 24359-24368 [2020-09-29; online 2020-09-16]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Prototypical pacemaker neurons interact with the resident microbiota.

Klimovich A, Giacomello S, Björklund Å, ..., Adameyko I, Bosch TCG

Proc. Natl. Acad. Sci. U.S.A. 117 (30) 17854-17863 [2020-07-28; online 2020-07-09]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]

Trade-off between somatic and germline repair in a vertebrate supports the expensive germ line hypothesis.

Chen HY, Jolly C, Bublys K, Marcu D, Immler S

Proc. Natl. Acad. Sci. U.S.A. 117 (16) 8973-8979 [2020-04-21; online 2020-04-03]

Bioinformatics Support for Computational Resources [Service] Genome Engineering Zebrafish [Service]

Building blocks are synthesized on demand during the yeast cell cycle.

Campbell K, Westholm J, Kasvandik S, ..., Mormino M, Nielsen J

Proc. Natl. Acad. Sci. U.S.A. 117 (14) 7575-7583 [2020-04-07; online 2020-03-25]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Footprints of natural selection at the mannose-6-phosphate isomerase locus in barnacles.

Nunez JCB, Flight PA, Neil KB, ..., Blomberg A, Rand DM

Proc. Natl. Acad. Sci. U.S.A. 117 (10) 5376-5385 [2020-03-10; online 2020-02-25]

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HISTONE DEACETYLASE 9 stimulates auxin-dependent thermomorphogenesis in Arabidopsis thaliana by mediating H2A.Z depletion.

van der Woude LC, Perrella G, Snoek BL, ..., Kaiserli E, van Zanten M

Proc. Natl. Acad. Sci. U.S.A. 116 (50) 25343-25354 [2019-12-10; online 2019-11-25]

A MYC2/MYC3/MYC4-dependent transcription factor network regulates water spray-responsive gene expression and jasmonate levels.

Van Moerkercke A, Duncan O, Zander M, ..., Millar AH, Van Aken O

Proc. Natl. Acad. Sci. U.S.A. 116 (46) 23345-23356 [2019-11-12; online 2019-10-29]

Interaction between VPS35 and RABG3f is necessary as a checkpoint to control fusion of late compartments with the vacuole.

Rodriguez-Furlan C, Domozych D, Qian W, ..., Raikhel NV, Hicks GR

Proc. Natl. Acad. Sci. U.S.A. - (-) - [2019-09-30; online 2019-09-30]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Recurrent convergent evolution at amino acid residue 261 in fish rhodopsin.

Hill J, Enbody ED, Pettersson ME, ..., Scheerer P, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 116 (37) 18473-18478 [2019-09-10; online 2019-08-26]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Molecular mimicry between Anoctamin 2 and Epstein-Barr virus nuclear antigen 1 associates with multiple sclerosis risk.

Tengvall K, Huang J, Hellström C, ..., Olsson T, Kockum I

Proc. Natl. Acad. Sci. U.S.A. 116 (34) 16955-16960 [2019-08-20; online 2019-08-02]

Autoimmunity and Serology Profiling [Collaborative]

α-synuclein-lipoprotein interactions and elevated ApoE level in cerebrospinal fluid from Parkinson's disease patients.

Paslawski W, Zareba-Paslawska J, Zhang X, ..., Andrén PE, Svenningsson P

Proc. Natl. Acad. Sci. U.S.A. 116 (30) 15226-15235 [2019-07-23; online 2019-07-03]

Spatial Mass Spectrometry [Collaborative]

Mic60 exhibits a coordinated clustered distribution along and across yeast and mammalian mitochondria.

Stoldt S, Stephan T, Jans DC, ..., Hell SW, Jakobs S

Proc. Natl. Acad. Sci. U.S.A. 116 (20) 9853-9858 [2019-05-14; online 2019-04-26]

Integrated Microscopy Technologies Stockholm [Collaborative]

Selective auxin agonists induce specific AUX/IAA protein degradation to modulate plant development.

Vain T, Raggi S, Ferro N, ..., Pauwels L, Robert S

Proc. Natl. Acad. Sci. U.S.A. 116 (13) 6463-6472 [2019-03-26; online 2019-03-08]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Swedish Metabolomics Centre (SMC) [Service]

Zinc depletion does not necessarily induce ribosome hibernation in mycobacteria.

Tobiasson V, Dow A, Prisic S, Amunts A

Proc. Natl. Acad. Sci. U.S.A. 116 (7) 2395-2397 [2019-02-12; online 2019-01-25]

Transcriptional landscape of B cell precursor acute lymphoblastic leukemia based on an international study of 1,223 cases.

Li JF, Dai YT, Lilljebjörn H, ..., Chen SJ, Huang JY

Proc. Natl. Acad. Sci. U.S.A. 115 (50) E11711-E11720 [2018-12-11; online 2018-11-28]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Folding pathway of an Ig domain is conserved on and off the ribosome.

Tian P, Steward A, Kudva R, ..., Clarke J, Best RB

Proc. Natl. Acad. Sci. U.S.A. 115 (48) E11284-E11293 [2018-11-27; online 2018-11-09]

Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks.

De Vadder F, Grasset E, Mannerås Holm L, ..., Olofsson LE, Bäckhed F

Proc. Natl. Acad. Sci. U.S.A. 115 (25) 6458-6463 [2018-06-19; online 2018-06-04]

Integrated Microscopy Technologies Gothenburg [Service]

O6-methylguanine–induced transcriptional mutagenesis reduces p53 tumor-suppressor function

Ezerskyte M, Paredes JA, Malvezzi S, ..., Scicchitano DA, Dreij K

Proc. Natl. Acad. Sci. U.S.A. 115 (18) 4731-4736 [2018-05-01; online 2018-04-17]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia.

Valdiosera C, Günther T, Vera-Rodríguez JC, ..., Smith CI, Jakobsson M

Proc. Natl. Acad. Sci. U.S.A. 115 (13) 3428-3433 [2018-03-27; online 2018-03-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

MYCN-amplified neuroblastoma maintains an aggressive and undifferentiated phenotype by deregulation of estrogen and NGF signaling.

Dzieran J, Rodriguez Garcia A, Westermark UK, ..., Lehtiö J, Arsenian-Henriksson M

Proc. Natl. Acad. Sci. U.S.A. 115 (6) E1229-E1238 [2018-02-06; online 2018-01-26]

Global Proteomics and Proteogenomics [Collaborative]

Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina.

Laenen B, Tedder A, Nowak MD, ..., Coupland G, Slotte T

Proc. Natl. Acad. Sci. U.S.A. 115 (4) 816-821 [2018-01-23; online 2018-01-04]

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

Extracellular vesicles from human pancreatic islets suppress human islet amyloid polypeptide amyloid formation.

Ribeiro D, Horvath I, Heath N, ..., Forslöw A, Wittung-Stafshede P

Proc. Natl. Acad. Sci. U.S.A. 114 (42) 11127-11132 [2017-10-17; online 2017-10-02]

Integrated Microscopy Technologies Gothenburg [Service]

Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root.

Di Mambro R, De Ruvo M, Pacifici E, ..., Grieneisen VA, Sabatini S

Proc. Natl. Acad. Sci. U.S.A. 114 (36) E7641-E7649 [2017-09-05; online 2017-08-22]

Capturing LTA 4 hydrolase in action: Insights to the chemistry and dynamics of chemotactic LTB4 synthesis.

Stsiapanava A, Samuelsson B, Haeggström JZ

Proc. Natl. Acad. Sci. U.S.A. 114 (36) 9689-9694 [2017-09-05; online 2017-08-21]

Protein Science Facility (PSF) [Service]

Rho-associated kinase is a therapeutic target in neuroblastoma.

Dyberg C, Fransson S, Andonova T, ..., Johnsen JI, Wickström M

Proc. Natl. Acad. Sci. U.S.A. 114 (32) E6603-E6612 [2017-08-08; online 2017-07-24]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Combined epigenetic and differentiation-based treatment inhibits neuroblastoma tumor growth and links HIF2α to tumor suppression.

Westerlund I, Shi Y, Toskas K, ..., Schlisio S, Holmberg J

Proc. Natl. Acad. Sci. U.S.A. 114 (30) E6137-E6146 [2017-07-25; online 2017-07-10]

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

Continuous immunotypes describe human immune variation and predict diverse responses.

Kaczorowski KJ, Shekhar K, Nkulikiyimfura D, ..., Chakraborty AK, Brodin P

Proc. Natl. Acad. Sci. U.S.A. 114 (30) E6097-E6106 [2017-07-25; online 2017-07-10]

Cellular Immunomonitoring [Technology development]

Structural basis for ligand binding to an enzyme by a conformational selection pathway.

Kovermann M, Grundström C, Sauer-Eriksson AE, Sauer UH, Wolf-Watz M

Proc. Natl. Acad. Sci. U.S.A. 114 (24) 6298-6303 [2017-06-13; online 2017-05-30]

Swedish NMR Centre (SNC) [Service]

RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo.

Alkasalias T, Alexeyenko A, Hennig K, ..., Gad AK, Pavlova T

Proc. Natl. Acad. Sci. U.S.A. 114 (8) E1413-E1421 [2017-02-21; online 2017-02-07]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Spatial Proteomics [Collaborative]

Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora.

Steige KA, Laenen B, Reimegård J, Scofield DG, Slotte T

Proc. Natl. Acad. Sci. U.S.A. 114 (5) 1087-1092 [2017-01-31; online 2017-01-17]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Dioxygenase-encoding AtDAO1 gene controls IAA oxidation and homeostasis in Arabidopsis.

Porco S, Pěnčík A, Rashed A, ..., Bennett MJ, Ljung K

Proc. Natl. Acad. Sci. U.S.A. 113 (39) 11016-11021 [2016-09-27; online 2016-09-22]

Dynamic regulation of auxin oxidase and conjugating enzymes AtDAO1 and GH3 modulates auxin homeostasis.

Mellor N, Band LR, Pěnčík A, ..., Bennett MJ, Owen MR

Proc. Natl. Acad. Sci. U.S.A. 113 (39) 11022-11027 [2016-09-27; online 2016-09-20]

Oxidation and cyclization of casbene in the biosynthesis of Euphorbia factors from mature seeds of Euphorbia lathyris L.

Luo D, Callari R, Hamberger B, ..., Staerk D, Hamberger B

Proc. Natl. Acad. Sci. U.S.A. 113 (34) E5082-E5089 [2016-08-23; online 2016-08-11]

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

Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc.

Jeong C, Ozga AT, Witonsky DB, ..., Di Rienzo A, Warinner C

Proc. Natl. Acad. Sci. U.S.A. 113 (27) 7485-7490 [2016-07-05; online 2016-06-20]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Conserved 33-kb haplotype in the MHC class III region regulates chronic arthritis.

Yau AC, Tuncel J, Haag S, ..., Padyukov L, Holmdahl R

Proc. Natl. Acad. Sci. U.S.A. 113 (26) E3716-E3724 [2016-06-28; online 2016-06-16]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Variants within the SP110 nuclear body protein modify risk of canine degenerative myelopathy.

Ivansson EL, Megquier K, Kozyrev SV, ..., Coates JR, Lindblad-Toh K

Proc. Natl. Acad. Sci. U.S.A. 113 (22) E3091-E3100 [2016-05-31; online 2016-05-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Divergent non-heme iron enzymes in the nogalamycin biosynthetic pathway.

Siitonen V, Selvaraj B, Niiranen L, ..., Schneider G, Metsä-Ketelä M

Proc. Natl. Acad. Sci. U.S.A. 113 (19) 5251-5256 [2016-05-10; online 2016-04-25]

Protein Science Facility (PSF) [Service]

Anoctamin 2 identified as an autoimmune target in multiple sclerosis.

Ayoglu B, Mitsios N, Kockum I, ..., Olsson T, Nilsson P

Proc. Natl. Acad. Sci. U.S.A. 113 (8) 2188-2193 [2016-02-23; online 2016-02-09]

Autoimmunity and Serology Profiling [Collaborative] Fluorescence Tissue Profiling [Collaborative]

A dynamic Asp-Arg interaction is essential for catalysis in microsomal prostaglandin E2 synthase.

Brock JS, Hamberg M, Balagunaseelan N, ..., Rinaldo-Matthis A, Haeggström JZ

Proc. Natl. Acad. Sci. U.S.A. 113 (4) 972-977 [2016-01-26; online 2016-01-11]

Protein Science Facility (PSF) [Service]

Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques.

Günther T, Valdiosera C, Malmström H, ..., Götherström A, Jakobsson M

Proc. Natl. Acad. Sci. U.S.A. 112 (38) 11917-11922 [2015-09-22; online 2015-09-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast.

Huang M, Bai Y, Sjostrom SL, ..., Andersson-Svahn H, Nielsen J

Proc. Natl. Acad. Sci. U.S.A. 112 (34) E4689-E4696 [2015-08-25; online 2015-08-12]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris.

Douglas GM, Gos G, Steige KA, ..., Slotte T, Wright SI

Proc. Natl. Acad. Sci. U.S.A. 112 (9) 2806-2811 [2015-03-03; online 2015-02-19]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Inhibition of tumor cell proliferation and motility by fibroblasts is both contact and soluble factor dependent.

Alkasalias T, Flaberg E, Kashuba V, ..., Klein G, Guven H

Proc. Natl. Acad. Sci. U.S.A. 111 (48) 17188-17193 [2014-12-02; online 2014-11-19]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.

Rietveld CA, Esko T, Davies G, ..., Cesarini D, Koellinger PD

Proc. Natl. Acad. Sci. U.S.A. 111 (38) 13790-13794 [2014-09-23; online 2014-09-08]

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

Neuronal calcium-binding proteins 1/2 localize to dorsal root ganglia and excitatory spinal neurons and are regulated by nerve injury.

Zhang MD, Tortoriello G, Hsueh B, ..., Harkany T, Hökfelt TG

Proc. Natl. Acad. Sci. U.S.A. 111 (12) E1149-E1158 [2014-03-25; online 2014-03-13]

Fluorescence Tissue Profiling

Binding of Pro-Gly-Pro at the active site of leukotriene A4 hydrolase/aminopeptidase and development of an epoxide hydrolase selective inhibitor.

Stsiapanava A, Olsson U, Wan M, ..., Rinaldo-Matthis A, Haeggström JZ

Proc. Natl. Acad. Sci. U.S.A. 111 (11) 4227-4232 [2014-03-18; online 2014-03-05]

Advanced Mass Spectrometry Proteomics Protein Science Facility (PSF)

Transcription factor ZBED6 affects gene expression, proliferation, and cell death in pancreatic beta cells.

Wang X, Jiang L, Wallerman O, ..., Andersson L, Welsh N

Proc. Natl. Acad. Sci. U.S.A. 110 (40) 15997-16002 [2013-10-01; online 2013-09-16]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Molecular genetics and subjective well-being.

Rietveld CA, Cesarini D, Benjamin DJ, ..., Krueger RF, Bartels M

Proc. Natl. Acad. Sci. U.S.A. 110 (24) 9692-9697 [2013-06-11; online 2013-05-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Dynamic gradients of an intermediate filament-like cytoskeleton are recruited by a polarity landmark during apical growth.

Fuchino K, Bagchi S, Cantlay S, ..., Flärdh K, Ausmees N

Proc. Natl. Acad. Sci. U.S.A. 110 (21) E1889-E1897 [2013-05-21; online 2013-05-04]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals.

Oosterveen T, Kurdija S, Ensterö M, ..., Muhr J, Ericson J

Proc. Natl. Acad. Sci. U.S.A. 110 (18) 7330-7335 [2013-04-30; online 2013-04-15]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Majority of differentially expressed genes are down-regulated during malignant transformation in a four-stage model.

Danielsson F, Skogs M, Huss M, ..., Uhlén M, Lundberg E

Proc. Natl. Acad. Sci. U.S.A. 110 (17) 6853-6858 [2013-04-23; online 2013-04-10]

Spatial Proteomics

Identification of genetic variants influencing the human plasma proteome.

Johansson Å, Enroth S, Palmblad M, ..., Bergquist J, Gyllensten U

Proc. Natl. Acad. Sci. U.S.A. 110 (12) 4673-4678 [2013-03-19; online 2013-03-15]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genomic diversity of the 2011 European outbreaks of Escherichia coli O104:H4.

Guy L, Jernberg C, Ivarsson S, ..., Engstrand L, Andersson SG

Proc. Natl. Acad. Sci. U.S.A. 109 (52) E3627-E3628 [2012-12-26; online 2012-12-19]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Strong signatures of selection in the domestic pig genome.

Rubin C, Megens H, Martinez Barrio A, ..., Groenen MAM, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 109 (48) 19529-19536 [2012-11-27; online 2012-11-16]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring.

Lamichhaney S, Martinez Barrio A, Rafati N, ..., Ryman N, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 109 (47) 19345-19350 [2012-11-20; online 2012-11-09]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

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

Edlund K, Larsson O, Ameur A, ..., Botling J, Soussi T

Proc. Natl. Acad. Sci. U.S.A. 109 (24) 9551-9556 [2012-06-12; online 2012-05-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

High-resolution structure of a BRICHOS domain and its implications for anti-amyloid chaperone activity on lung surfactant protein C.

Willander H, Askarieh G, Landreh M, ..., Knight SD, Johansson J

Proc. Natl. Acad. Sci. U.S.A. 109 (7) 2325-2329 [2012-02-14; online 2012-02-07]

Protein Science Facility (PSF)

Hypothalamic mitochondrial dysfunction associated with anorexia in the anx/anx mouse.

Lindfors C, Nilsson IA, Garcia-Roves PM, ..., Schalling M, Johansen JE

Proc. Natl. Acad. Sci. U.S.A. 108 (44) 18108-18113 [2011-11-01; online 2011-10-26]

Fluorescence Tissue Profiling

Multiple recognition assay reveals prostasomes as promising plasma biomarkers for prostate cancer.

Tavoosidana G, Ronquist G, Darmanis S, ..., Landegren UD, Kamali-Moghaddam M

Proc. Natl. Acad. Sci. U.S.A. 108 (21) 8809-8814 [2011-05-24; online 2011-05-11]

Affinity Proteomics Uppsala [Technology development] Clinical Biomarkers PLA and Single Cell Proteomics