Publications 2018

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow

Zhu Y, Orre LM, ..., Branca RMM, Lehtiö J

Nat Commun 9 (1) - [2018-12-00; online 2018-03-02]

Bioinformatics Long-term Support WABI [Collaborative]

Somatic mutagenesis in satellite cells associates with human skeletal muscle aging

Franco I, Johansson A, ..., Fischer H, Eriksson M

Nat Commun 9 (1) - [2018-12-00; online 2018-02-23]

Bioinformatics Long-term Support WABI [Collaborative]

A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage

Ladds MJGW, van Leeuwen IMM, ..., McCormack E, Laín S

Nat Commun 9 (1) - [2018-12-00; online 2018-03-16]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Effects of predation stress and food ration on perch gut microbiota

Zha Y, Eiler A, Johansson F, Svanbäck R

Microbiome 6 (1) - [2018-12-00; online 2018-02-06]

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

Targeted NUDT5 inhibitors block hormone signaling in breast cancer cells

Page BDG, Valerie NCK, ..., Beato M, Helleday T

Nat Commun 9 (1) - [2018-12-00; online 2018-01-17]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Protein Science Facility (PSF) [Service]

Linking FOXO3, NCOA3, and TCF7L2 to Ras pathway phenotypes through a genome-wide forward genetic screen in human colorectal cancer cells

Kundu S, Ali MA, ..., Hellström M, Sjöblom T

Genome Med 10 (1) - [2018-12-00; online 2018-01-04]

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

Topology of membrane proteins — predictions, limitations and variations

Tsirigos KD, Govindarajan S, ..., Shu N, Elofsson A

Current Opinion in Structural Biology 50 (-) 9-17 [2018-06-00; online 2018-06-00]

Bioinformatics Support and Infrastructure [Collaborative]

Bioinformatics Support and Infrastructure [Service]

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

Proc. Natl. Acad. Sci. U.S.A. - (-) - [2018-04-17; online 2018-04-17]

Active and inactive β1 integrins segregate into distinct nanoclusters in focal adhesions

Spiess M, Hernandez-Varas P, ..., Lakadamyali M, Strömblad S

J. Cell Biol. - (-) jcb.201707075 [2018-04-09; online 2018-04-09]

Advanced Light Microscopy (ALM) [Collaborative]

Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor

Boerema AP, Aibara S, ..., Lindahl E, Amunts A

NPLANTS 4 (4) 212-217 [2018-04-00; online 2018-04-02]

Cryo-EM [Service]

Identification of Poly(ADP-Ribose) Polymerase Macrodomain Inhibitors Using an AlphaScreen Protocol

Ekblad T, Verheugd P, ..., Elofsson M, Schüler H

SLAS DISCOVERY: Advancing Life Sciences R&D 23 (4) 353-362 [2018-04-00; online 2018-01-09]

Chemical Biology Consortium Sweden (CBCS) [Service] Protein Science Facility (PSF) [Collaborative]

Protein Expression in Tonsillar and Base of Tongue Cancer and in Relation to Human Papillomavirus (HPV) and Clinical Outcome

Ramqvist T, Näsman A, ..., Dalianis T, Munck-Wikland E

Int J Mol Sci 19 (4) 978 [2018-03-25; online 2018-03-25]

Bioinformatics Support and Infrastructure [Collaborative]

Increased thermal stability of nanocellulose composites by functionalization of the sulfate groups on cellulose nanocrystals with azetidinium ions

Börjesson M, Sahlin K, Bernin D, Westman G

J. Appl. Polym. Sci. 135 (10) 45963 [2018-03-10; online 2017-11-08]

Swedish NMR Centre (SNC) [Service]

The Immunogenicity of a Proline-Substituted Altered Peptide Ligand toward the Cancer-Associated TEIPP Neoepitope Trh4 Is Unrelated to Complex Stability.

Hafstrand I, Doorduijn EM, ..., van Hall T, Achour A

J. Immunol. - (-) - [2018-03-05; online 2018-03-05]

Sexual dimorphism in the width of the mouse synaptonemal complex

Agostinho A, Kouznetsova A, ..., Brismar H, Höög C

J Cell Sci 131 (5) jcs212548 [2018-03-01; online 2018-02-02]

Advanced Light Microscopy (ALM) [Collaborative]

The fungus that came in from the cold: dry rot’s pre-adapted ability to invade buildings

Balasundaram SV, Hess J, ..., Eastwood DC, Skrede I

ISME J 12 (3) 791-801 [2018-03-00; online 2018-01-05]

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

Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste

Marathe NP, Janzon A, ..., Kristiansson E, Larsson DGJ

Environment International 112 (-) 279-286 [2018-03-00; online 2018-03-00]

Cleaner fish escape salmon farms and hybridize with local wrasse populations

Faust E, Halvorsen KT, ..., Knutsen H, André C

R. Soc. open sci. 5 (3) 171752 [2018-03-00; online 2018-03-21]

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

The ZBED6–IGF2 axis has a major effect on growth of skeletal muscle and internal organs in placental mammals

Younis S, Schönke M, ..., Zierath JR, Andersson L

Proc Natl Acad Sci USA 115 (9) E2048-E2057 [2018-02-27; online 2018-02-12]

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

Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella

Bachmann JA, Tedder A, ..., Steige KA, Slotte T

G3 (Bethesda) - (-) g3.300467.2017 [2018-02-23; online 2018-02-23]

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

In Situ Target Engagement Studies in Adherent Cells

Axelsson H, Almqvist H, ..., Lundbäck T, Seashore-Ludlow B

ACS Chem. Biol. - (-) - [2018-02-21; online 2018-02-21]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

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

Thutkawkorapin J, Mahdessian H, ..., Jiao X, Lindblom A

Oncotarget 9 (13) - [2018-02-16; online 2018-01-30]

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

Irreversible inhibition of cytosolic thioredoxin reductase 1 as a mechanistic basis for anticancer therapy.

Stafford WC, Peng X, ..., Linder S, Arnér ESJ

Sci Transl Med 10 (428) - [2018-02-14; online 2018-02-16]

Educated natural killer cells show dynamic movement of the activating receptor NKp46 and confinement of the inhibitory receptor Ly49A

Staaf E, Hedde PN, ..., Gratton E, Johansson S

Sci. Signal. 11 (517) eaai9200 [2018-02-13; online 2018-02-13]

Advanced Light Microscopy (ALM) [Service]

Kynurenic Acid and Gpr35 Regulate Adipose Tissue Energy Homeostasis and Inflammation.

Agudelo LZ, Ferreira DMS, ..., Berggren P, Ruas JL

Cell Metab. 27 (2) 378-392.e5 [2018-02-06; online 2018-02-08]

Mass Cytometry [Collaborative]

Ten steps to get started in Genome Assembly and Annotation

Dominguez Del Angel V, Hjerde E, ..., Binzer-Panchal M, Lantz H

F1000Res 7 (-) 148 [2018-02-05; online 2018-02-05]

NGI Uppsala (Uppsala Genome Center) [Collaborative]

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

Ardui S, Ameur A, Vermeesch JR, Hestand MS

Nucleic Acids Res - (-) - [2018-02-01; online 2018-02-01]

NGI Uppsala (Uppsala Genome Center) [Collaborative]

Small molecule PGC-1α1 protein stabilizers induce adipocyte Ucp1 expression and uncoupled mitochondrial respiration

Pettersson-Klein AT, Izadi M, ..., Griffin PR, Ruas JL

Mol Metab - (-) - [2018-02-00; online 2018-02-00]

Drug Discovery and Development (DDD) [Service]

Life after tree death: Does restored dead wood host different fungal communities to natural woody substrates?

Pasanen H, Junninen K, ..., Stenlid J, Kouki J

Forest Ecology and Management 409 (-) 863-871 [2018-02-00; online 2018-02-00]

Red meat intake in chronic kidney disease patients: Two sides of the coin

Mafra D, Borges NA, ..., Lindholm B, Stenvinkel P

Nutrition 46 (-) 26-32 [2018-02-00; online 2018-02-00]

Swedish Metabolomics Centre (SMC) [Service]

Human NUDT22 Is a UDP-Glucose/Galactose Hydrolase Exhibiting a Unique Structural Fold

Carter M, Jemth AS, ..., Helleday T, Stenmark P

Structure 26 (2) 295-303.e6 [2018-02-00; online 2018-02-00]

T cells are influenced by a long non-coding RNA in the autoimmune associated PTPN2 locus

Houtman M, Shchetynsky K, ..., Malmström V, Padyukov L

Journal of Autoimmunity - (-) - [2018-02-00; online 2018-02-00]

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

Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA

Ahmed E, Parducci L, ..., Slotte T, Wohlfarth B

Quaternary Science Reviews 181 (-) 19-29 [2018-02-00; online 2018-02-00]

Bioinformatics Long-term Support WABI [Collaborative]

Molecular barcoding of viral vectors enables mapping and optimization of mRNA trans-splicing

Davidsson M, Díaz-Fernández P, ..., Lundberg C, Bjorklund T

RNA - (-) rna.063925.117 [2018-01-31; online 2018-01-31]

A comprehensive model of DNA fragmentation for the preservation of High Molecular Weight DNA

Klingstrom T, Bongcam-Rudloff E, Vinnere Pettersson O

- - (-) - [2018-01-27; online 2018-01-27]

NGI Uppsala (Uppsala Genome Center) [Collaborative]

In Situ Analyses Directly in Diarrheal Stool Reveal Large Variations in Bacterial Load and Active Toxin Expression of Enterotoxigenic Escherichia coli and Vibrio cholerae

Begum YA, Rydberg HA, ..., Qadri F, Sjöling Å

mSphere 3 (1) e00517-17 [2018-01-24; online 2018-01-24]

Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing

Das S, Pettersson F, ..., Ennis DG, Kirsebom L

- - (-) - [2018-01-17; online 2018-01-17]

Crystal Structures and Inhibitor Interactions of Mouse and Dog MTH1 Reveal Species-Specific Differences in Affinity

Narwal M, Jemth AS, ..., Helleday T, Stenmark P

Biochemistry - (-) - [2018-01-16; online 2018-01-16]

Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D

Jenjaroenpun P, Wongsurawat T, ..., Nielsen J, Nookaew I

Nucleic Acids Res - (-) - [2018-01-13; online 2018-01-13]

Rapid hybrid speciation in Darwin’s finches

Lamichhaney S, Han F, ..., Grant BR, Grant PR

Science 359 (6372) 224-228 [2018-01-12; online 2017-11-23]

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

Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation

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

PLoS Biol. 16 (1) e2003703 [2018-01-09; online 2018-01-09]

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

A protein interaction network centered on leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1) regulates growth factor receptors

Faraz M, Herdenberg C, ..., Henriksson R, Hedman H

J. Biol. Chem. - (-) jbc.M117.807487 [2018-01-09; online 2018-01-09]

Bioinformatics Long-term Support WABI [Service]

Evaluating vacquinol-1 in rats carrying glioblastoma models RG2 and NS1

Ahlstedt J, Förnvik K, ..., Salford LG, Redebrandt HN

Oncotarget - (-) - [2018-01-03; online 2018-01-03]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Minimizing inequality in access to precision medicine in breast cancer by real-time population-based molecular analysis in the SCAN-B initiative.

Rydén L, Loman N, ..., Saal LH, Borg Å

Br J Surg 105 (2) e158-e168 [2018-01-00; online 2018-01-18]

Clinical Genomics Lund [Collaborative]

Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity

Turcot V, None , ..., None , None

Nat Genet 50 (1) 26-41 [2018-01-00; online 2017-12-22]

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

Genomic consequences of intensive inbreeding in an isolated wolf population

Kardos M, Åkesson M, ..., Wikenros C, Ellegren H

Nat Ecol Evol 2 (1) 124-131 [2018-01-00; online 2017-11-20]

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

The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.

Salvatore M, Shu N, Elofsson A

Protein Sci. 27 (1) 195-201 [2018-01-00; online 2017-10-24]

Bioinformatics Support and Infrastructure [Collaborative]

Single-molecule DNA sequencing of acute myeloid leukemia and myelodysplastic syndromes with multiple TP53 alterations

Lodé L, Ameur A, ..., Lavabre-Bertrand T, Soussi T

Haematologica 103 (1) e13-e16 [2018-01-00; online 2017-10-27]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service]