Bioinformatics

ISSN	1367-4811
ISSN-L	1367-4803
IUID	14286d8962724ff1851c0d33eef366f8
Modified	2020-11-27T13:14:02.179Z
Created	2017-05-09T09:12:10.905Z

Year 2025

PubMed DOI Crossref

PopGLen-a Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods.

Nolen ZJ

Bioinformatics 41 (3) - [2025-03-04; online 2025-03-12]

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

Year 2024

PubMed DOI Crossref

Detecting transposable elements in long read genomes using sTELLeR.

Bilgrav Saether K, Eisfeldt J

Bioinformatics - (-) - [2024-11-18; online 2024-11-18]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

PubMed DOI Crossref

DockQ v2: improved automatic quality measure for protein multimers, nucleic acids, and small molecules.

Mirabello C, Wallner B

Bioinformatics 40 (10) - [2024-10-01; online 2024-09-30]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

PubMed DOI Crossref

AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality.

Rashid U, Wu C, Shiller J, ..., Thomson S, Deng CH

Bioinformatics 40 (8) - [2024-08-02; online 2024-07-30]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

PubMed DOI Crossref

Unravelling reference bias in ancient DNA datasets.

Dolenz S, van der Valk T, Jin C, ..., Dalén L, Heintzman PD

Bioinformatics 40 (7) - [2024-07-01; online 2024-07-04]

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

PubMed DOI Crossref

Designing efficient randstrobes for sequence similarity analyses.

Karami M, Soltani Mohammadi A, Martin M, ..., Patro R, Sahlin K

Bioinformatics 40 (4) - [2024-03-29; online 2024-04-05]

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

Year 2023

PubMed DOI Crossref

methylR: a graphical interface for comprehensive DNA methylation array data analysis.

Volpe M, Das J

Bioinformatics 39 (4) - [2023-04-03; online 2023-04-12]

Clinical Genomics [Technology development] Clinical Genomics Linköping [Technology development]

Year 2022

PubMed DOI Crossref

Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides.

Umer HM, Audain E, Zhu Y, ..., Branca RM, Perez-Riverol Y

Bioinformatics 38 (5) 1470-1472 [2022-02-07; online 2021-12-15]

Global Proteomics and Proteogenomics [Technology development]

Year 2021

PubMed DOI Crossref

A comparison of rule-based and centroid single-sample multiclass predictors for transcriptomic classification.

Eriksson P, Marzouka NA, Sjödahl G, ..., Liedberg F, Höglund M

Bioinformatics - (-) - [2021-11-12; online 2021-11-12]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

PubMed DOI Crossref

Cheetah-MS: a web server to model protein complexes using tandem cross-linking mass spectrometry data.

Khakzad H, Happonen L, Malmström J, Malmström L

Bioinformatics - (-) - [2021-06-15; online 2021-06-15]

Structural Proteomics [Technology development]

PubMed DOI Crossref

multiclassPairs: An R package to train multiclass pairbased classifier.

Marzouka NA, Eriksson P

Bioinformatics - (-) - [2021-02-05; online 2021-02-05]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Year 2020

PubMed DOI Crossref

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences.

Drysdale R, Cook CE, Petryszak R, ..., Durinx C, McEntyre J

Bioinformatics 36 (8) 2636-2642 [2020-04-15; online 2020-01-18]

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

Year 2019

PubMed DOI Crossref

SynQuant: an automatic tool to quantify synapses from microscopy images

Wang Y, Wang C, Ranefall P, ..., Tian L, Yu G

Bioinformatics 36 (5) 1599-1606 [2019-10-09; online 2019-10-09]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

PubMed DOI Crossref

Interoperable and scalable data analysis with microservices: applications in metabolomics.

Emami Khoonsari P, Moreno P, Bergmann S, ..., Kultima K, Spjuth O

Bioinformatics 35 (19) 3752-3760 [2019-10-01; online 2019-03-10]

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

Year 2018

PubMed DOI Crossref

SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy

Bernhem K, Brismar H

Bioinformatics 34 (1) 137-138 [2018-01-01; online 2017-09-04]

Bioinformatics Support for Computational Resources [Service] Integrated Microscopy Technologies Stockholm [Technology development]

Year 2017

PubMed DOI Crossref

SubCons: a new ensemble method for improved human subcellular localization predictions.

Salvatore M, Warholm P, Shu N, Basile W, Elofsson A

Bioinformatics 33 (16) 2464-2470 [2017-08-15; online 2017-04-14]

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

PubMed DOI Crossref

Prediction and modeling of pre-analytical sampling errors as a strategy to improve plasma NMR metabolomics data

Brunius C, Pedersen A, Malmodin D, ..., Tybring G, Landberg R

Bioinformatics - (-) - [2017-07-14; online 2017-07-14]

Swedish NMR Centre [Collaborative]

PubMed DOI Crossref

ProQ3D: improved model quality assessments using deep learning.

Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A

Bioinformatics 33 (10) 1578-1580 [2017-05-15; online 2017-01-06]

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

PubMed DOI Crossref

Green listed—a CRISPR screen tool

Panda SK, Boddul SV, Jiménez-Andrade GY, ..., Fernandez-Ricaud L, Wermeling F

Bioinformatics 33 (7) 1099-1100 [2017-04-01; online 2016-12-19]

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

Year 2016

PubMed DOI Crossref

MultiQC: summarize analysis results for multiple tools and samples in a single report.

Ewels P, Magnusson M, Lundin S, Käller M

Bioinformatics 32 (19) 3047-3048 [2016-10-01; online 2016-06-16]

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

PubMed DOI Crossref

Read-based phasing of related individuals.

Garg S, Martin M, Marschall T

Bioinformatics 32 (12) i234-i242 [2016-06-15; online 2016-06-17]

Bioinformatics (NBIS) [Technology development] Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

PubMed DOI Crossref

Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins.

Hayat S, Peters C, Shu N, Tsirigos KD, Elofsson A

Bioinformatics 32 (10) 1571-1573 [2016-05-15; online 2016-01-23]

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

PubMed DOI Crossref

Improved topology prediction using the terminal hydrophobic helices rule.

Peters C, Tsirigos KD, Shu N, Elofsson A

Bioinformatics 32 (8) 1158-1162 [2016-04-15; online 2015-12-09]

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

PubMed DOI Crossref

CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array.

Marzouka NA, Nordlund J, Bäcklin CL, ..., Syvänen AC, Carlsson Almlöf J

Bioinformatics 32 (7) 1080-1082 [2016-04-01; online 2015-11-09]

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

Year 2015

PubMed DOI Crossref

Whiteboard: a framework for the programmatic visualization of complex biological analyses.

Sundström G, Zamani N, Grabherr MG, Mauceli E

Bioinformatics 31 (12) 2054-2055 [2015-06-15; online 2015-02-11]

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

Year 2013

PubMed DOI Crossref

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.

Teschendorff AE, Marabita F, Lechner M, ..., Gomez-Cabrero D, Beck S

Bioinformatics 29 (2) 189-196 [2013-01-15; online 2012-11-24]

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

Year 2012

PubMed DOI Crossref

Improved gap size estimation for scaffolding algorithms.

Sahlin K, Street N, Lundeberg J, Arvestad L

Bioinformatics 28 (17) 2215-2222 [2012-09-01; online 2012-08-28]

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

Year 2010

PubMed DOI Crossref

Classification of DNA sequences using Bloom filters.

Stranneheim H, Käller M, Allander T, ..., Arvestad L, Lundeberg J

Bioinformatics 26 (13) 1595-1600 [2010-07-01; online 2010-05-18]

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