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1.
"Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling.
EMBO J
; 42(23): e115008, 2023 Dec 01.
Article
in English
| MEDLINE | ID: mdl-37964598
2.
The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond.
Genome Res
; 33(2): 261-268, 2023 02.
Article
in English
| MEDLINE | ID: mdl-36828587
3.
DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data.
Bioinformatics
; 40(5)2024 May 02.
Article
in English
| MEDLINE | ID: mdl-38656970
4.
PLANTdataHUB: a collaborative platform for continuous FAIR data sharing in plant research.
Plant J
; 116(4): 974-988, 2023 Nov.
Article
in English
| MEDLINE | ID: mdl-37818860
5.
Galaxy Training: A powerful framework for teaching!
PLoS Comput Biol
; 19(1): e1010752, 2023 01.
Article
in English
| MEDLINE | ID: mdl-36622853
6.
Transformer-based tool recommendation system in Galaxy.
BMC Bioinformatics
; 24(1): 446, 2023 Nov 27.
Article
in English
| MEDLINE | ID: mdl-38012574
7.
Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function.
Mol Biol Evol
; 39(4)2022 04 11.
Article
in English
| MEDLINE | ID: mdl-35325204
8.
MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone.
J Proteome Res
; 21(6): 1558-1565, 2022 06 03.
Article
in English
| MEDLINE | ID: mdl-35503992
9.
Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation.
Genome Res
; 29(3): 383-395, 2019 03.
Article
in English
| MEDLINE | ID: mdl-30674556
10.
Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs.
Bioinformatics
; 37(22): 4006-4013, 2021 11 18.
Article
in English
| MEDLINE | ID: mdl-34021764
11.
Scool: a new data storage format for single-cell Hi-C data.
Bioinformatics
; 37(14): 2053-2054, 2021 08 04.
Article
in English
| MEDLINE | ID: mdl-33135074
12.
pyGenomeTracks: reproducible plots for multivariate genomic datasets.
Bioinformatics
; 37(3): 422-423, 2021 04 20.
Article
in English
| MEDLINE | ID: mdl-32745185
13.
A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive.
Bioinformatics
; 37(21): 3983-3985, 2021 11 05.
Article
in English
| MEDLINE | ID: mdl-34096994
14.
No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics.
PLoS Pathog
; 16(8): e1008643, 2020 08.
Article
in English
| MEDLINE | ID: mdl-32790776
15.
A constructivist-based proposal for bioinformatics teaching practices during lockdown.
PLoS Comput Biol
; 17(5): e1008922, 2021 05.
Article
in English
| MEDLINE | ID: mdl-33983931
16.
Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine.
PLoS Comput Biol
; 17(6): e1009014, 2021 06.
Article
in English
| MEDLINE | ID: mdl-34061826
17.
Fostering accessible online education using Galaxy as an e-learning platform.
PLoS Comput Biol
; 17(5): e1008923, 2021 05.
Article
in English
| MEDLINE | ID: mdl-33983944
18.
Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization.
Nucleic Acids Res
; 48(W1): W177-W184, 2020 07 02.
Article
in English
| MEDLINE | ID: mdl-32301980
19.
The omics discovery REST interface.
Nucleic Acids Res
; 48(W1): W380-W384, 2020 07 02.
Article
in English
| MEDLINE | ID: mdl-32374843
20.
BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers.
J Proteome Res
; 20(4): 2056-2061, 2021 04 02.
Article
in English
| MEDLINE | ID: mdl-33625229