Nucleic Acids Res.

ISSN	1362-4962
ISSN-L	0305-1048
IUID	907b082c3ec9463eaf22de5341ba39cc
Modified	2020-11-27T13:14:01.979Z
Created	2017-05-09T09:12:47.541Z

Year 2023

PubMed DOI Crossref

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]

Cryo-EM [Service]

Year 2022

PubMed DOI Crossref

Monitoring drug-target interactions through target engagement-mediated amplification on arrays and in situ.

Al-Amin RA, Johansson L, Abdurakhmanov E, ..., Lundbäck T, Landegren U

Nucleic Acids Res. 50 (22) e129 [2022-12-09; online 2022-10-04]

Autoimmunity and Serology Profiling [Service] Drug Discovery and Development (DDD) [Service]

PubMed DOI Crossref

GotEnzymes: an extensive database of enzyme parameter predictions.

Li F, Chen Y, Anton M, Nielsen J

Nucleic Acids Res. - (-) - [2022-09-28; online 2022-09-28]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

Staphylococcal self-loading helicases couple the staircase mechanism with inter domain high flexibility.

Qiao C, Debiasi-Anders G, Mir-Sanchis I

Nucleic Acids Res. 50 (14) 8349-8362 [2022-08-12; online 2022-07-25]

Cryo-EM [Service]

PubMed DOI Crossref

Ultrastructure and nuclear architecture of telomeric chromatin revealed by correlative light and electron microscopy.

Hübner B, von Otter E, Ahsan B, ..., Ludwig A, Sandin S

Nucleic Acids Res. 50 (9) 5047-5063 [2022-05-20; online 2022-05-01]

Integrated Microscopy Technologies Umeå [Technology development]

PubMed DOI Crossref

Modulation of RNA stability regulates gene expression in two opposite ways: through buffering of RNA levels upon global perturbations and by supporting adapted differential expression.

Faucillion M, Johansson A, Larsson J

Nucleic Acids Res. 50 (8) 4372-4388 [2022-05-06; online 2022-04-08]

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

Year 2021

PubMed DOI Crossref

Saturation mutagenesis charts the functional landscape of Salmonella ProQ and reveals a gene regulatory function of its C-terminal domain.

Rizvanovic A, Kjellin J, Söderbom F, Holmqvist E

Nucleic Acids Res. 49 (17) 9992-10006 [2021-09-27; online 2021-08-28]

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

PubMed DOI Crossref

RqcH and RqcP catalyze processive poly-alanine synthesis in a reconstituted ribosome-associated quality control system.

Takada H, Crowe-McAuliffe C, Polte C, ..., Wilson DN, Hauryliuk V

Nucleic Acids Res. 49 (14) 8355-8369 [2021-08-20; online 2021-07-14]

Cryo-EM [Service]

PubMed DOI Crossref

INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues of Arabidopsis.

Yadav VK, Santos-González J, Köhler C

Nucleic Acids Res. 49 (8) 4371-4385 [2021-05-07; online 2021-03-22]

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

PubMed DOI Crossref

Dynamics of Ku and bacterial non-homologous end-joining characterized using single DNA molecule analysis.

Öz R, Wang JL, Guerois R, ..., Strick TR, Westerlund F

Nucleic Acids Res. 49 (5) 2629-2641 [2021-03-18; online 2021-02-17]

Integrated Microscopy Technologies Gothenburg [Service]

Year 2020

PubMed DOI Crossref

Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue.

Gyllborg D, Langseth CM, Qian X, ..., Lein ES, Nilsson M

Nucleic Acids Res. 48 (19) e112 [2020-11-04; online 2020-09-30]

Bioinformatics Compute and Storage [Service] In Situ Sequencing (ISS) [Technology development]

PubMed DOI Crossref

MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells.

Sumida N, Sifakis EG, Kiani NA, ..., Göndör A, Ohlsson R

Nucleic Acids Res. 48 (19) 10867-10876 [2020-11-04; online 2020-10-15]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Subtle structural alterations in G-quadruplex DNA regulate site specificity of fluorescence light-up probes.

Kumar R, Chand K, Bhowmik S, ..., Hedenström M, Chorell E

Nucleic Acids Res. 48 (3) 1108-1119 [2020-02-20; online 2020-01-09]

Swedish NMR Centre (SNC) [Collaborative]

Year 2019

PubMed DOI Crossref

μLAS technology for DNA isolation coupled to Cas9-assisted targeting for sequencing and assembly of a 30 kb region in plant genome.

Milon N, Chantry-Darmon C, Satge C, ..., Bergès H, Bancaud A

Nucleic Acids Res. 47 (15) 8050-8060 [2019-09-05; online 2019-09-11]

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

PubMed DOI Crossref

EnsembleCNV: an ensemble machine learning algorithm to identify and genotype copy number variation using SNP array data.

Zhang Z, Cheng H, Hong X, ..., Wang X, Hao K

Nucleic Acids Res. 47 (7) e39 [2019-04-23; online 2019-02-06]

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

PubMed DOI Crossref

SAMURAI (Solid-phase Assisted Mutagenesis by Uracil Restriction for Accurate Integration) for antibody affinity maturation and paratope mapping.

Hu FJ, Lundqvist M, Uhlén M, Rockberg J

Nucleic Acids Res. 47 (6) e34 [2019-04-08; online 2019-02-05]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2018

PubMed DOI Crossref

MutT homologue 1 (MTH1) catalyzes the hydrolysis of mutagenic O6-methyl-dGTP.

Jemth AS, Gustafsson R, Bräutigam L, ..., Stenmark P, Helleday T

Nucleic Acids Res. 46 (20) 10888-10904 [2018-11-16; online 2018-10-12]

Protein Science Facility (PSF) [Service]

PubMed DOI Crossref

SWI/SNF interacts with cleavage and polyadenylation factors and facilitates pre-mRNA 3' end processing.

Yu S, Jordán-Pla A, Gañez-Zapater A, ..., Östlund Farrants AK, Visa N

Nucleic Acids Res. 46 (16) 8557-8573 [2018-09-19; online 2018-06-04]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.

Jeggari A, Alekseenko Z, Petrov I, ..., Ericson J, Alexeyenko A

Nucleic Acids Res. 46 (W1) W163-W170 [2018-07-02; online 2018-06-13]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Simultaneous determination of ribonucleoside and deoxyribonucleoside triphosphates in biological samples by hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry.

Kong Z, Jia S, Chabes AL, ..., Moritz T, Chabes A

Nucleic Acids Res. 46 (11) e66 [2018-06-20; online 2018-03-20]

Swedish Metabolomics Centre (SMC) [Service]

PubMed DOI Crossref

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. 46 (5) 2159-2168 [2018-03-16; online 2018-02-06]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Year 2017

PubMed DOI Crossref

Polysome-profiling in small tissue samples.

Liang S, Bellato HM, Lorent J, ..., Hajj GNM, Larsson O

Nucleic Acids Res. - (-) - [2017-10-23; online 2017-10-23]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules.

Redin D, Borgström E, He M, ..., Käller M, Ahmadian A

Nucleic Acids Res. 45 (13) e125 [2017-07-27; online 2017-05-20]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing.

Raine A, Manlig E, Wahlberg P, Syvänen AC, Nordlund J

Nucleic Acids Res. 45 (6) e36 [2017-04-07; online 2016-12-03]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]

PubMed DOI Crossref

Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.

Zhu Y, Engström PG, Tellgren-Roth C, ..., Scheynius A, Lehtiö J

Nucleic Acids Res. 45 (5) 2629-2643 [2017-03-17; online 2017-01-20]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Proteomics Mass spectrometry [Technology development] Global Proteomics and Proteogenomics [Technology development] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

PubMed DOI Crossref

PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c.

Pan G, Ameur A, Enroth S, ..., Gyllensten U, Wadelius C

Nucleic Acids Res. 45 (5) 2408-2422 [2017-03-17; online 2016-12-10]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Technology development]

Year 2016

PubMed DOI Crossref

Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression.

Ivanov M, Kals M, Lauschke V, ..., Milani L, Ingelman-Sundberg M

Nucleic Acids Res. 44 (14) 6756-6769 [2016-08-19; online 2016-04-29]

Bioinformatics Compute and Storage [Service] Clinical Proteomics Mass spectrometry [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

PubMed DOI Crossref

Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis.

Lee S, Mardinoglu A, Zhang C, Lee D, Nielsen J

Nucleic Acids Res. 44 (12) 5529-5539 [2016-07-08; online 2016-05-25]

Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

PubMed DOI Crossref

CRISPRz: a database of zebrafish validated sgRNAs.

Varshney GK, Zhang S, Pei W, ..., Sood R, Burgess SM

Nucleic Acids Res. 44 (D1) D822-D826 [2016-01-04; online 2015-10-04]

Genome Engineering Zebrafish [Technology development]

PubMed DOI Crossref

PGSB PlantsDB: updates to the database framework for comparative plant genome research.

Spannagl M, Nussbaumer T, Bader KC, ..., Gundlach H, Mayer KF

Nucleic Acids Res. 44 (D1) D1141-D1147 [2016-01-04; online 2015-11-04]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Year 2015

PubMed DOI Crossref

Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans.

Dumesic PA, Rosenblad MA, Samuelsson T, ..., Yates JR, Madhani HD

Nucleic Acids Res. 43 (18) 9017-9027 [2015-10-15; online 2015-08-16]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

PubMed DOI Crossref

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.

Yu NY, Hallström BM, Fagerberg L, ..., Uhlén M, Daub CO

Nucleic Acids Res. 43 (14) 6787-6798 [2015-08-18; online 2015-06-27]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Collaborative]

PubMed DOI Crossref

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides.

Tsirigos KD, Peters C, Shu N, Käll L, Elofsson A

Nucleic Acids Res. 43 (W1) W401-W407 [2015-07-01; online 2015-05-15]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

Structure of the nuclease subunit of human mitochondrial RNase P.

Reinhard L, Sridhara S, Hällberg BM

Nucleic Acids Res. 43 (11) 5664-5672 [2015-06-23; online 2015-05-09]

Protein Science Facility (PSF)

PubMed DOI Crossref

The Biobanking Analysis Resource Catalogue (BARCdb): a new research tool for the analysis of biobank samples.

Galli J, Oelrich J, Taussig MJ, ..., Ortega-Paino E, Landegren U

Nucleic Acids Res. 43 (Database issue) D1158-D1162 [2015-01-00; online 2014-10-23]

PLA and Single Cell Proteomics

Year 2014

PubMed DOI Crossref

Identification of a large protein network involved in epigenetic transmission in replicating DNA of embryonic stem cells.

Aranda S, Rutishauser D, Ernfors P

Nucleic Acids Res. 42 (11) 6972-6986 [2014-06-00; online 2014-05-24]

Advanced Mass Spectrometry Proteomics

PubMed DOI Crossref

Nucleosome regulatory dynamics in response to TGFβ.

Enroth S, Andersson R, Bysani M, ..., Komorowski J, Wadelius C

Nucleic Acids Res. 42 (11) 6921-6934 [2014-06-00; online 2014-04-29]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

PubMed DOI Crossref

The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals.

Wiegand S, Meier D, Seehafer C, ..., Söderbom F, Hammann C

Nucleic Acids Res. 42 (5) 3330-3345 [2014-03-00; online 2013-12-27]

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

Year 2013

PubMed DOI Crossref

Wobble decoding by the Escherichia coli selenocysteine insertion machinery.

Xu J, Croitoru V, Rutishauser D, Cheng Q, Arnér ES

Nucleic Acids Res. 41 (21) 9800-9811 [2013-11-00; online 2013-08-29]

Advanced Mass Spectrometry Proteomics

PubMed DOI Crossref

Massive functional mapping of a 5'-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing.

Holmqvist E, Reimegård J, Wagner EG

Nucleic Acids Res. 41 (12) e122 [2013-07-00; online 2013-04-24]

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

PubMed DOI Crossref

Active transcriptomic and proteomic reprogramming in the C. elegans nucleotide excision repair mutant xpa-1.

Arczewska KD, Tomazella GG, Lindvall JM, ..., Thiede B, Nilsen H

Nucleic Acids Res. 41 (10) 5368-5381 [2013-05-01; online 2013-04-13]

Bioinformatics and Expression Analysis (BEA)

PubMed DOI Crossref

The adenovirus VA RNA-derived miRNAs are not essential for lytic virus growth in tissue culture cells.

Kamel W, Segerman B, Öberg D, Punga T, Akusjärvi G

Nucleic Acids Res. 41 (9) 4802-4812 [2013-05-00; online 2013-03-26]

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

PubMed DOI Crossref

Exome RNA sequencing reveals rare and novel alternative transcripts.

Halvardson J, Zaghlool A, Feuk L

Nucleic Acids Res. 41 (1) e6 [2013-01-07; online 2012-08-31]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Year 2012

PubMed DOI Crossref

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.

Nookaew I, Papini M, Pornputtapong N, ..., Uhlén M, Nielsen J

Nucleic Acids Res. 40 (20) 10084-10097 [2012-11-01; online 2012-09-12]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Year 2011

PubMed DOI Crossref

Histone modifications influence mediator interactions with chromatin.

Zhu X, Zhang Y, Bjornsdottir G, ..., Gustafsson CM, Myers LC

Nucleic Acids Res. 39 (19) 8342-8354 [2011-10-00; online 2011-07-12]

Bioinformatics and Expression Analysis (BEA)

PubMed DOI Crossref

Targeted resequencing of candidate genes using selector probes.

Johansson H, Isaksson M, Sörqvist EF, ..., Ericsson O, Nilsson M

Nucleic Acids Res. 39 (2) e8 [2011-01-00; online 2010-11-08]

Array and Analysis Facility NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure