ArticleNucleic acids research2018
The BaMM web server for de-novo motif discovery and regulatory sequence analysis.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
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- DMTF1 up-regulation rescues proliferation defect of telomere dysfunctional neural stem cells via the SWI/SNF-E2F axis.Science advances · 2026Article
- The essential genome ofScience (New York, N.Y.) · 2025Article
- Coactivator networks orchestrating noncanonical AR programs in enzalutamide-resistant CRPC.Frontiers in oncology · 2025Review
- MethylSeqLogo: DNA methylation smart sequence logos.BMC bioinformatics · 2024Article
- Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data.NAR genomics and bioinformatics · 2024Article
- Single cell expression and chromatin accessibility of the Toxoplasma gondii lytic cycle identifies AP2XII-8 as an essential ribosome regulon driver.Nature communications · 2024Article
- A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data.Patterns (New York, N.Y.) · 2024Article
- Less-is-more: selecting transcription factor binding regions informative for motif inference.Nucleic acids research · 2024Article
- The circadian clock circuitry modulates leukemia initiating cell activity in T-cell acute lymphoblastic leukemia.Journal of experimental & clinical cancer research : CR · 2023Article
- Deciphering transcription factors and their corresponding regulatory elements during inhibitory interneuron differentiation using deep neural networks.Frontiers in cell and developmental biology · 2023Article
- Motif and conserved module analysis in DNA (promoters, enhancers) and RNA (lncRNA, mRNA) using AlModules.Scientific reports · 2022Article
- NF-κB signaling controls H3K9me3 levels at intronic LINE-1 and hematopoietic stem cell genes in cis.The Journal of experimental medicine · 2022Article
- Z-DNA is remodelled by ZBTB43 in prospermatogonia to safeguard the germline genome and epigenome.Nature cell biology · 2022Article
- Sequence and tissue targeting specificity of ZFP36L2 reveals Elavl2 as a novel target with co-regulation potential.Nucleic acids research · 2022Article
- Fast and exact quantification of motif occurrences in biological sequences.BMC bioinformatics · 2021Article
- Bayesian Markov models improve the prediction of binding motifs beyond first order.NAR genomics and bioinformatics · 2021Article
- Significant non-existence of sequences in genomes and proteomes.Nucleic acids research · 2021Article
- Decoding the epitranscriptional landscape from native RNA sequences.Nucleic acids research · 2021Article
- GTRD: an integrated view of transcription regulation.Nucleic acids research · 2021Article
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6 authors.
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Abstract
The BaMM web server offers four tools: (i) de-novo discovery of enriched motifs in a set of nucleotide sequences, (ii) scanning a set of nucleotide sequences with motifs to find motif occurrences, (iii) searching with an input motif for similar motifs in our BaMM database with motifs for >1000 transcription factors, trained from the GTRD ChIP-seq database and (iv) browsing and keyword searching the motif database. In contrast to most other servers, we represent sequence motifs not by position weight matrices (PWMs) but by Bayesian Markov Models (BaMMs) of order 4, which we showed previously to perform substantially better in ROC analyses than PWMs or first order models. To address the inadequacy of P- and E-values as measures of motif quality, we introduce the AvRec score, the average recall over the TP-to-FP ratio between 1 and 100. The BaMM server is freely accessible without registration at https://bammmotif.mpibpc.mpg.de.
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