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TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors.
Hoffmann M, Trummer N, Schwartz L, Jankowski J, Lee HK, Willruth LL, Lazareva O, Yuan K, Baumgarten N, Schmidt F, Baumbach J, Schulz MH, Blumenthal DB, Hennighausen L, List M. Hoffmann M, et al. Among authors: baumbach j. Gigascience. 2022 Dec 28;12:giad026. doi: 10.1093/gigascience/giad026. Gigascience. 2022. PMID: 37132521 Free PMC article.
Efficient sample tracking with OpenLabFramework.
List M, Schmidt S, Trojnar J, Thomas J, Thomassen M, Kruse TA, Tan Q, Baumbach J, Mollenhauer J. List M, et al. Among authors: baumbach j. Sci Rep. 2014 Mar 4;4:4278. doi: 10.1038/srep04278. Sci Rep. 2014. PMID: 24589879 Free PMC article.
KeyPathwayMinerWeb: online multi-omics network enrichment.
List M, Alcaraz N, Dissing-Hansen M, Ditzel HJ, Mollenhauer J, Baumbach J. List M, et al. Among authors: baumbach j. Nucleic Acids Res. 2016 Jul 8;44(W1):W98-W104. doi: 10.1093/nar/gkw373. Epub 2016 May 5. Nucleic Acids Res. 2016. PMID: 27150809 Free PMC article.
Comprehensive analysis of high-throughput screens with HiTSeekR.
List M, Schmidt S, Christiansen H, Rehmsmeier M, Tan Q, Mollenhauer J, Baumbach J. List M, et al. Among authors: baumbach j. Nucleic Acids Res. 2016 Aug 19;44(14):6639-48. doi: 10.1093/nar/gkw554. Epub 2016 Jun 21. Nucleic Acids Res. 2016. PMID: 27330136 Free PMC article.
Interactive microbial distribution analysis using BioAtlas.
Lund JB, List M, Baumbach J. Lund JB, et al. Among authors: baumbach j. Nucleic Acids Res. 2017 Jul 3;45(W1):W509-W513. doi: 10.1093/nar/gkx304. Nucleic Acids Res. 2017. PMID: 28460071 Free PMC article.
On the performance of de novo pathway enrichment.
Batra R, Alcaraz N, Gitzhofer K, Pauling J, Ditzel HJ, Hellmuth M, Baumbach J, List M. Batra R, et al. Among authors: baumbach j. NPJ Syst Biol Appl. 2017 Mar 3;3:6. doi: 10.1038/s41540-017-0007-2. eCollection 2017. NPJ Syst Biol Appl. 2017. PMID: 28649433 Free PMC article.
De novo pathway-based biomarker identification.
Alcaraz N, List M, Batra R, Vandin F, Ditzel HJ, Baumbach J. Alcaraz N, et al. Among authors: baumbach j. Nucleic Acids Res. 2017 Sep 19;45(16):e151. doi: 10.1093/nar/gkx642. Nucleic Acids Res. 2017. PMID: 28934488 Free PMC article.
EpiGEN: an epistasis simulation pipeline.
Blumenthal DB, Viola L, List M, Baumbach J, Tieri P, Kacprowski T. Blumenthal DB, et al. Among authors: baumbach j. Bioinformatics. 2020 Dec 8;36(19):4957-4959. doi: 10.1093/bioinformatics/btaa245. Bioinformatics. 2020. PMID: 32289146
378 results