MDC-Berlin: Ohler Lab

Recent and ongoing projects address transcription control (initiation, modeling of enhancers and their evolution, regulatory site identification, decoding enhancers based on sequence and chromatin), small RNAs (identification of microRNAs and targets), expression (condition-specific microarray/sequencing data, spatial expression from microscopy), or the modeling of regulatory networks containing transcription factors and miRNAs.

Tools for download:

Prediction of coding and non-coding genes RSVP
- prediction of alternative isoforms of protein-coding genes, based on both genomic DNA evidence and aligned RNA-seq reads

PIPmiR
- identify novel plant miRNA genes from a combination of deep sequencing data and genomic features

NASTIseq
- identification of cis-Natural Antisense Transcripts (cis-NAT) using strand specific RNA-seq data Promoter and enhancer analysis

S-Peaker
- identify probable locations for single-peak TSSs in an input sequence Orthologous enhancers
- searches for orthologous enhancer region in a related species for a given known enhancer miRNA target prediction

MUMMIE
- MUltivariate Markov Modeling Inference Engine

microMUMMIE
- microRNA target-site prediction in PAR-CLIP data

TargetThermo
- compute predicted expression fold change of a gene caused by a miRNA

WaRSwap
- network motif discovery in large multi-layer networks that include Transcription Factors (TFs), microRNAs (miRNAs), and non-TF protein coding genes. 

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