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Pavankumar Videm
Pavankumar Videm
Verified email at informatik.uni-freiburg.de
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Year
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update
AE Ostrovsky, A Mahmoud, AJ Lonie, A Syme, A Fouilloux, A Bretaudeau, ...
Nucleic Acids Research, 2022
300*2022
Community-driven data analysis training for biology
B Batut, S Hiltemann, A Bagnacani, D Baker, V Bhardwaj, C Blank, ...
Cell systems 6 (6), 752-758. e1, 2018
1822018
MOF-associated complexes ensure stem cell identity and Xist repression
T Chelmicki, F Dündar, MJ Turley, T Khanam, T Aktas, F Ramírez, ...
Elife 3, e02024, 2014
902014
DOT1L promotes progenitor proliferation and primes neuronal layer identity in the developing cerebral cortex
H Franz, A Villarreal, S Heidrich, P Videm, F Kilpert, I Mestres, F Calegari, ...
Nucleic acids research 47 (1), 168-183, 2019
542019
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
BA Grüning, J Fallmann, D Yusuf, S Will, A Erxleben, F Eggenhofer, ...
Nucleic acids research 45 (W1), W560-W566, 2017
492017
BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles
P Videm, D Rose, F Costa, R Backofen
Bioinformatics 30 (12), i274-i282, 2014
242014
FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus
SC Weise, G Arumugam, A Villarreal, P Videm, S Heidrich, N Nebel, ...
Molecular neurobiology 56 (7), 5188-5201, 2019
192019
Galaxy Training Network, Taylor J, Backofen R, Nekrutenko A, Grüning B
B Batut, S Hiltemann, A Bagnacani, D Baker, V Bhardwaj, C Blank, ...
Community-driven data analysis training for biology. Cell Syst 6 (6), 752-758, 2018
162018
The RNA workbench 2.0: next generation RNA data analysis
J Fallmann, P Videm, A Bagnacani, B Batut, MA Doyle, T Klingstrom, ...
Nucleic acids research 47 (W1), W511-W515, 2019
122019
Reference-based RNA-Seq data analysis (galaxy training materials)
B Batut, M Freeberg, M Heydarian, A Erxleben, P Videm, C Blank, ...
102022
Automated peptide mapping and protein-topographical annotation of proteomics data
P Videm, D Gunasekaran, B Schröder, B Mayer, ML Biniossek, O Schilling
BMC bioinformatics 15 (1), 1-7, 2014
92014
Hands-on: Hands-on: Reference-based RNA-Seq data analysis
B Batut, M Freeberg, M Heydarian, A Erxleben, P Videm, C Blank, ...
Galaxy Training Network, 2024
72024
ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data
P Videm, A Kumar, O Zharkov, BA Grüning, R Backofen
GigaScience 10 (2), giaa158, 2021
62021
Reference-Based RNA-Seq Data Analysis (Galaxy Training Materials).” 2020
B Batut, MA Freeberg, M Heydarian, A Erxleben, P Videm, C Blank, ...
62020
Community-Driven Data Analysis Training for Biology. Cell Syst. 2018; 6 (6): 752–758. e1
B Batut, S Hiltemann, A Bagnacani, D Baker, V Bhardwaj, C Blank, ...
5
Community-driven ELIXIR activities in single-cell omics
P Czarnewski, A Mahfouz, RA Calogero, PM Palagi, L Portell-Silva, ...
F1000Research 11 (869), 869, 2022
22022
The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update
Nucleic Acids Research, gkae410, 2024
12024
Analysis of plant scRNA-Seq Data with Scanpy
M Tekman, B Serrano-Solano, C Gallardo, P Videm
Galaxy Training Network, 2022
12022
CheRRI—Accurate classification of the biological relevance of putative RNA–RNA interaction sites
T Müller, S Mautner, P Videm, F Eggenhofer, M Raden, R Backofen
GigaScience 13, giae022, 2024
2024
Hands-on: Hands-on: Clustering 3K PBMCs with Scanpy
B Batut, HR Hotz, M Tekman, P Videm
Galaxy Training Network, 2023
2023
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