BMC Bioinformatics

ISSN	1471-2105
ISSN-L	1471-2105
IUID	edc8172872c64882b5b47a101d65a6f8
Modified	2020-11-27T13:14:03.615Z
Created	2017-05-09T09:12:21.285Z

Year 2024

PubMed DOI Crossref

CircNetVis: an interactive web application for visualizing interaction networks of circular RNAs.

Nguyen TH, Nguyen HN, Vu TN

BMC Bioinformatics 25 (1) 31 [2024-01-17; online 2024-01-17]

Bioinformatics Support for Computational Resources [Service]

Year 2023

PubMed DOI Crossref

Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network.

Xu X, Bhalla N, Ståhl P, Jaldén J

BMC Bioinformatics 24 (1) 461 [2023-12-07; online 2023-12-07]

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

PubMed DOI Crossref

Fast and sensitive validation of fusion transcripts in whole-genome sequencing data.

Hafstað V, Häkkinen J, Persson H

BMC Bioinformatics 24 (1) 359 [2023-09-23; online 2023-09-23]

Bioinformatics Support for Computational Resources [Service]

PubMed DOI Crossref

RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy.

Øvrebø Ø, Ojansivu M, Kartasalo K, ..., Holme MN, Stevens MM

BMC Bioinformatics 24 (1) 237 [2023-06-05; online 2023-06-05]

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

PubMed DOI Crossref

ASV portal: an interface to DNA-based biodiversity data in the Living Atlas.

Prager M, Lundin D, Ronquist F, Andersson AF

BMC Bioinformatics 24 (1) 6 [2023-01-05; online 2023-01-05]

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

Year 2022

PubMed DOI Crossref

Practical application of a Bayesian network approach to poultry epigenetics and stress.

Videla Rodriguez EA, Pértille F, Guerrero-Bosagna C, ..., Jensen P, Smith VA

BMC Bioinformatics 23 (1) 261 [2022-07-01; online 2022-07-01]

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

PubMed DOI Crossref

GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species.

Kutschera VE, Kierczak M, van der Valk T, ..., Dalén L, Díez-Del-Molino D

BMC Bioinformatics 23 (1) 228 [2022-06-13; online 2022-06-13]

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

PubMed DOI Crossref

PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data.

Abrahamsson S, Eiengård F, Rohlin A, Dávila López M

BMC Bioinformatics 23 (1) 59 [2022-02-03; online 2022-02-03]

Clinical Genomics [Technology development] Clinical Genomics Gothenburg [Technology development]

Year 2021

PubMed DOI Crossref

Comparison of sequencing data processing pipelines and application to underrepresented African human populations.

Breton G, Johansson ACV, Sjödin P, Schlebusch CM, Jakobsson M

BMC Bioinformatics 22 (1) 488 [2021-10-09; online 2021-10-09]

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

PubMed DOI Crossref

Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps.

Marco Salas S, Gyllborg D, Mattsson Langseth C, Nilsson M

BMC Bioinformatics 22 (1) 391 [2021-07-31; online 2021-07-31]

In Situ Sequencing (ISS) [Technology development]

PubMed DOI Crossref

OmicLoupe: facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons.

Willforss J, Siino V, Levander F

BMC Bioinformatics 22 (1) 107 [2021-03-04; online 2021-03-04]

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

Year 2020

PubMed DOI Crossref

GeneSetCluster: a tool for summarizing and integrating gene-set analysis results.

Ewing E, Planell-Picola N, Jagodic M, Gomez-Cabrero D

BMC Bioinformatics 21 (1) 443 [2020-10-07; online 2020-10-07]

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

PubMed DOI Crossref

Loqusdb: added value of an observations database of local genomic variation.

Magnusson M, Eisfeldt J, Nilsson D, ..., Wedell A, Stranneheim H

BMC Bioinformatics 21 (1) 273 [2020-07-01; online 2020-07-01]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Technology development] Clinical Genomics Stockholm [Technology development]

PubMed DOI Crossref

Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations.

Buetti-Dinh A, Herold M, Christel S, ..., Friedman R, Dopson M

BMC Bioinformatics 21 (1) 23 [2020-01-21; online 2020-01-21]

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

Year 2019

PubMed DOI Crossref

doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows.

Svensson D, Sjögren R, Sundell D, Sjödin A, Trygg J

BMC Bioinformatics 20 (1) 498 [2019-10-15; online 2019-10-15]

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

PubMed DOI Crossref

Greedy de novo motif discovery to construct motif repositories for bacterial proteomes.

Khakzad H, Malmström J, Malmström L

BMC Bioinformatics 20 (Suppl 4) 141 [2019-04-18; online 2019-04-18]

Structural Proteomics [Technology development]

Year 2017

PubMed DOI Crossref

NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis.

Jeggari A, Alexeyenko A

BMC Bioinformatics 18 (Suppl 5) 118 [2017-03-23; online 2017-03-23]

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

Year 2016

PubMed DOI Crossref

Combinatorial identification of DNA methylation patterns over age in the human brain.

Torabi Moghadam B, Dabrowski M, Kaminska B, Grabherr MG, Komorowski J

BMC Bioinformatics 17 (1) 393 [2016-09-23; online 2016-09-23]

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

PubMed DOI Crossref

PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics.

Fernandez-Ricaud L, Kourtchenko O, Zackrisson M, Warringer J, Blomberg A

BMC Bioinformatics 17 (-) 249 [2016-06-23; online 2016-06-23]

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

PubMed DOI Crossref

Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2.

Prezza N, Vezzi F, Käller M, Policriti A

BMC Bioinformatics 17 Suppl 4 (-) 69 [2016-03-02; online 2016-03-02]

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

Year 2015

PubMed DOI Crossref

MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics.

Kushwaha SK, Manoharan L, Meerupati T, Hedlund K, Ahrén D

BMC Bioinformatics 16 (-) 65 [2015-02-28; online 2015-02-28]

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

Year 2014

PubMed DOI Crossref

Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis.

Merid SK, Goranskaya D, Alexeyenko A

BMC Bioinformatics 15 (-) 308 [2014-09-19; online 2014-09-19]

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

PubMed DOI Crossref

BESST--efficient scaffolding of large fragmented assemblies.

Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L

BMC Bioinformatics 15 (-) 281 [2014-08-15; online 2014-08-15]

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

PubMed DOI Crossref

A universal genomic coordinate translator for comparative genomics.

Zamani N, Sundström G, Meadows JR, ..., Haas BJ, Grabherr MG

BMC Bioinformatics 15 (-) 227 [2014-06-30; online 2014-06-30]

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

Year 2013

PubMed DOI Crossref

FANTOM: Functional and taxonomic analysis of metagenomes.

Sanli K, Karlsson FH, Nookaew I, Nielsen J

BMC Bioinformatics 14 (-) 38 [2013-02-01; online 2013-02-01]

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

Year 2010

PubMed DOI Crossref

A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins.

Ensterö M, Akerborg O, Lundin D, ..., Ohman M, Lagergren J

BMC Bioinformatics 11 (-) 6 [2010-01-04; online 2010-01-04]

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