biostudies-literatureCarstensen LEuropean Research Council456https://www.ebi.ac.uk/biostudies/studies/S-EPMC2949889biostudies-literatureUnknown11<h4>Background</h4>A central question in molecular biology is how transcriptional regulatory elements (TREs) act in combination. Recent high-throughput data provide us with the location of multiple regulatory regions for multiple regulators, and thus with the possibility of analyzing the multivariate distribution of the occurrences of these TREs along the genome.<h4>Results</h4>We present a model of TRE occurrences known as the Hawkes process. We illustrate the use of this model by analyzing two different publically available data sets. We are able to model, in detail, how the occurrence of one TRE is affected by the occurrences of others, and we can test a range of natural hypotheses about the dependencies among the TRE occurrences. In contrast to earlier efforts, pre-processing steps sucBMC bioinformaticsMultivariate Hawkes process models of the occurrence of regulatory elements.PMC2949889204135Hansen NRCarstensen LWinther OSandelin AfalseMultivariate Hawkes process models of the occurrence of regulatory elements.<h4>Background</h4>A central question in molecular biology is how transcriptional regulatory elements (TREs) act in combination. Recent high-throughput data provide us with the location of multiple regulatory regions for multiple regulators, and thus with the possibility of analyzing the multivariate distribution of the occurrences of these TREs along the genome.<h4>Results</h4>We present a model of TRE occurrences known as the Hawkes process. We illustrate the use of this model by analyzing two different publically available data sets. We are able to model, in detail, how the occurrence of one TRE is affected by the occurrences of others, and we can test a range of natural hypotheses about the dependencies among the TRE occurrences. In contrast to earlier efforts, pre-processing steps suc2010-01-01T00:00:00Z2010 Sep2025-04-19T09:53:00.1Z2019-03-27T00:34:37ZS-EPMC29498892082841310.1186/1471-2105-11-456