Human pol II promoter prediction: time series descriptors and machine learning

Although several in silico promoter prediction methods have been developed to date, they are still limited in predictive performance. The limitations are due to the challenge of selecting appropriate features of promoters that distinguish them from non-promoters and the generalization or predictive ability of the machine-learning algorithms. In this paper we attempt to define a novel approach by using unique descriptors and machine-learning methods for the recognition of eukaryotic polymerase II promoters. In this study, non-linear time series descriptors along with non-linear machine-learning algorithms, such as support vector machine (SVM), are used to discriminate between promoter and non-promoter regions. The basic idea here is to use descriptors that do not depend on the primary DNA sequence and provide a clear distinction between promoter and non-promoter regions. The classification model built on a set of 1000 promoter and 1500 non-promoter sequences, showed a 10-fold cross-validation accuracy of 87% and an independent test set had an accuracy >85% in both promoter and non-promoter identification. This approach correctly identified all 20 experimentally verified promoters of human chromosome 22. The high sensitivity and selectivity indicates that n-mer frequencies along with non-linear time series descriptors, such as Lyapunov component stability and Tsallis entropy, and supervised machine-learning methods, such as SVMs, can be useful in the identification of pol II promoters

KIRMES: kernel-based identification of regulatory modules in euchromatic sequences

Motivation: Understanding transcriptional regulation is one of the main challenges in computational biology. An important problem is the identification of transcription factor (TF) binding sites in promoter regions of potential TF target genes. It is typically approached by position weight matrix-based motif identification algorithms using Gibbs sampling, or heuristics to extend seed oligos. Such algorithms succeed in identifying single, relatively well-conserved binding sites, but tend to fail when it comes to the identification of combinations of several degenerate binding sites, as those often found in cis-regulatory modules

PhagePro: prophage finding tool

Dissertação de mestrado em BioinformáticaBacteriophages are viruses that infect bacteria and use them to reproduce. Their reproductive cycle can be lytic or lysogenic. The lytic cycle leads to the bacteria death, given that the bacteriophage hijacks hosts machinery to produce phage parts necessary to assemble a new complete bacteriophage, until cell wall lyse occurs. On the other hand, the lysogenic reproductive cycle comprises the bacteriophage genetic material in the bacterial genome, becoming a prophage. Sometimes, due to external stimuli, these prophages can be induced to perform a lytic cycle. Moreover, the lysogenic cycle can lead to significant modifications in bacteria, for example, antibiotic resistance. To that end, PhagePro was created. This tool finds and characterises prophages inserted in the bacterial genome. Using 42 features, three datasets were created and five machine learning algorithms were tested. All models were evaluated in two phases, during testing and with real bacterial cases. During testing, all three datasets reached the 98 % F1 score mark in their best result. In the second phase, the results of the models were used to predict real bacterial cases and the results compared to the results of two tools, Prophage Hunter and PHASTER. The best model found 110 zones out of 154 and the model with the best result in dataset 3 had 94 in common. As a final test, Agrobacterium fabrum strC68 was extensively analysed. The results show that PhagePro was capable of detecting more regions with proteins associated with phages than the other two tools. In the ligth of the results obtained, PhagePro has shown great potential in the discovery and characterisation of bacterial alterations caused by prophages.Bacteriófagos são vírus que infetam bactérias usando-as para garantir a manutenção do seu genoma. Este processo pode ser realizado por ciclo lítico ou lipogénico. O ciclo lítico consiste em usar a célula para seu proveito, criar bacteriófagos e lisar a célula. Por outro lado, no ciclo lipogénico o bacteriófago insere o seu código genético no genoma da bactéria, o que pode levar à transferência de genes de interesse, tornando-se importante uma monitorização dos profagos. Assim foi desenvolvido o PhagePro, uma ferramenta capaz de encontrar e caracterizar bacteriófagos em genomas bactérias. Foram criadas features para distinguir profagos de bactérias, criando três datasets e usando algoritmos de aprendizagem de máquina. Os modelos foram avaliados durante duas fases, a fase de teste e a fase de casos reais. Na primeira fase de testes, o melhor modelo do dataset 1 teve 98% de F1 score, dataset 2 teve 98% e do dataset 3 também teve 98%. Todos os modelos, para teste em casos reais, foram comparados com previsões de duas ferramentas Prophage Hunter e PHASTER. O modelo com os melhores resultados obteve 110 de 154 zonas em comum com as duas ferramentas e o modelo do dataset 3 teve 94 zonas. Por fim, foi feita a análise dos resultados da bactéria Agrobacterium fabrum strC68. Os resultados obtidos mostram resultados diferentes, mas válidos, as ferramentas comparadas, visto que o PhagePro consegue detectar zonas com proteínas associadas a fagos que as outras tools não conseguem. Em virtude dos resultados obtidos, PhagePro mostrou que é capaz de encontrar e caracterizar profagos em bactérias.Este estudo contou com o apoio da Fundação para a Ciência e Tecnologia (FCT) portuguesa no âmbito do financiamento estratégico da unidade UIDB/04469/2020. A obra também foi parcialmente financiada pelo Projeto PTDC/SAU-PUB/29182/2017 [POCI-01-0145-FEDER-029182]

A ROADMAP TO SAFE AND RELIABLE ENGINEERED BIOLOGICAL NANO-COMMUNICATION NETWORKS

Synthetic biology has the potential to benefit society with novel applications that can improve soil quality, produce biofuels, grow customized biological tissue, and perform intelligent drug delivery, among many other possibilities. Engineers are creating techniques to program living cells, inserting new logic, and leveraging cell-to-cell communication, which result in changes to a cell\u27s core functionality. Using these techniques, we can now create synthetic biological organisms (SBOs) with entirely new (potentially unseen) behaviors, which, similar to silicon devices, can sense, actuate, perform computation, and interconnect with other networks at the nanoscale level. SBOs are programmable evolving entities, and can be likened to self-adaptive programs that read inputs, process them, and produce outputs, reacting differently to different environmental conditions. With the increasing complexity of potential programs for SBOs, as in any new technology, there will be both beneficial as well as malicious uses. Although there has been much discussion about the potential safety and security risks of SBOs, and some research on predicting whether engineered life will be harmful, there has been little research on how to validate or verify safety of SBOs. In this thesis, we lay a foundation for validating and verifying safety for SBOs. We first present two case studies where we give insight into the difficulties of determining whether novel SBOs will be harmful given the vast combinatorial search space available for their engineering. Second, we explain how the current U.S. regulatory environment is fragmented with respect to the multiple dimensions of SBOs. Finally, we present a way forward for formalizing the architecture of SBOs and present a case study to show how we might utilize assurance cases to reason about SBO safety. Advisors: Myra Cohen and Massimiliano Pierobo

An iterative strategy combining biophysical criteria and duration hidden Markov) models for structural predictions of Chlamydia trachomatis s66 promoters

Background: Promoter identification is a first step in the quest to explain gene regulation in bacteria. It has been demonstrated that the initiation of bacterial transcription depends upon the stability and topology of DNA in the promoter region as well as the binding affinity between the RNA polymerase σ-factor and promoter. However, promoter prediction algorithms to date have not explicitly used an ensemble of these factors as predictors. In addition, most promoter models have been trained on data from Escherichia coli. Although it has been shown that transcriptional mechanisms are similar among various bacteria, it is quite possible that the differences between Escherichia coli and Chlamydia trachomatis are large enough to recommend an organism-specific modeling effort. Results: Here we present an iterative stochastic model building procedure that combines such biophysical metrics as DNA stability, curvature, twist and stress-induced DNA duplex destabilization along with duration hidden Markov model parameters to model Chlamydia trachomatis σ66 promoters from 29 experimentally verified sequences. Initially, iterative duration hidden Markov modeling of the training set sequences provides a scoring algorithm for Chlamydia trachomatis RNA polymerase σ66/DNA binding. Subsequently, an iterative application of Stepwise Binary Logistic Regression selects multiple promoter predictors and deletes/replaces training set sequences to determine an optimal training set. The resulting model predicts the final training set with a high degree of accuracy and provides insights into the structure of the promoter region. Model based genome-wide predictions are provided so that optimal promoter candidates can be experimentally evaluated, and refined models developed. Co-predictions with three other algorithms are also supplied to enhance reliability. Conclusion: This strategy and resulting model support the conjecture that DNA biophysical properties, along with RNA polymerase σ-factor/DNA binding collaboratively, contribute to a sequence\u27s ability to promote transcription. This work provides a baseline model that can evolve as new Chlamydia trachomatis σ66 promoters are identified with assistance from the provided genome-wide predictions. The proposed methodology is ideal for organisms with few identified promoters and relatively small genomes

An iterative strategy combining biophysical criteria and duration hidden Markov models for structural predictions of Chlamydia trachomatis σ66 promoters

<p>Abstract</p> <p>Background</p> <p>Promoter identification is a first step in the quest to explain gene regulation in bacteria. It has been demonstrated that the initiation of bacterial transcription depends upon the stability and topology of DNA in the promoter region as well as the binding affinity between the RNA polymerase σ-factor and promoter. However, promoter prediction algorithms to date have not explicitly used an ensemble of these factors as predictors. In addition, most promoter models have been trained on data from <it>Escherichia coli</it>. Although it has been shown that transcriptional mechanisms are similar among various bacteria, it is quite possible that the differences between <it>Escherichia coli </it>and <it>Chlamydia trachomatis </it>are large enough to recommend an organism-specific modeling effort.</p> <p>Results</p> <p>Here we present an iterative stochastic model building procedure that combines such biophysical metrics as DNA stability, curvature, twist and stress-induced DNA duplex destabilization along with duration hidden Markov model parameters to model <it>Chlamydia trachomatis </it>σ⁶⁶promoters from 29 experimentally verified sequences. Initially, iterative duration hidden Markov modeling of the training set sequences provides a scoring algorithm for <it>Chlamydia trachomatis </it>RNA polymerase σ⁶⁶/DNA binding. Subsequently, an iterative application of Stepwise Binary Logistic Regression selects multiple promoter predictors and deletes/replaces training set sequences to determine an optimal training set. The resulting model predicts the final training set with a high degree of accuracy and provides insights into the structure of the promoter region. Model based genome-wide predictions are provided so that optimal promoter candidates can be experimentally evaluated, and refined models developed. Co-predictions with three other algorithms are also supplied to enhance reliability.</p> <p>Conclusion</p> <p>This strategy and resulting model support the conjecture that DNA biophysical properties, along with RNA polymerase σ-factor/DNA binding collaboratively, contribute to a sequence's ability to promote transcription. This work provides a baseline model that can evolve as new <it>Chlamydia trachomatis </it>σ⁶⁶promoters are identified with assistance from the provided genome-wide predictions. The proposed methodology is ideal for organisms with few identified promoters and relatively small genomes.</p

Integrating Diverse Datasets Improves Developmental Enhancer Prediction

Gene-regulatory enhancers have been identified using various approaches, including evolutionary conservation, regulatory protein binding, chromatin modifications, and DNA sequence motifs. To integrate these different approaches, we developed EnhancerFinder, a two-step method for distinguishing developmental enhancers from the genomic background and then predicting their tissue specificity. EnhancerFinder uses a multiple kernel learning approach to integrate DNA sequence motifs, evolutionary patterns, and diverse functional genomics datasets from a variety of cell types. In contrast with prediction approaches that define enhancers based on histone marks or p300 sites from a single cell line, we trained EnhancerFinder on hundreds of experimentally verified human developmental enhancers from the VISTA Enhancer Browser. We comprehensively evaluated EnhancerFinder using cross validation and found that our integrative method improves the identification of enhancers over approaches that consider a single type of data, such as sequence motifs, evolutionary conservation, or the binding of enhancer-associated proteins. We find that VISTA enhancers active in embryonic heart are easier to identify than enhancers active in several other embryonic tissues, likely due to their uniquely high GC content. We applied EnhancerFinder to the entire human genome and predicted 84,301 developmental enhancers and their tissue specificity. These predictions provide specific functional annotations for large amounts of human non-coding DNA, and are significantly enriched near genes with annotated roles in their predicted tissues and lead SNPs from genome-wide association studies. We demonstrate the utility of EnhancerFinder predictions through in vivo validation of novel embryonic gene regulatory enhancers from three developmental transcription factor loci. Our genome-wide developmental enhancer predictions are freely available as a UCSC Genome Browser track, which we hope will enable researchers to further investigate questions in developmental biology. © 2014 Erwin et al

Exploiting gene expression and protein data for predicting remote homology and tissue specificity

In this thesis I describe my investigations of applying machine learning methods to high throughput experimental and predicted biological data. The importance of such analysis as a means of making inferences about biological functions is widely acknowledged in the bioinformatics community. Specifically, this work makes three novel contributions based on the systematic analysis of publicly archived data of protein sequences, three dimensional structures, gene expression and functional annotations: (a) remote homology detection based on amino acid sequences and secondary structures; (b) the analysis of tissue-specific gene expression for predictive signals in the sequence and secondary structure of the resulting protein product; and (c) a study of ageing in the fruit fly, a commonly used model organism, in which tissue specific and whole-organism gene expression changes are contrasted. In the problem of remote homology detection, a kernel-based method that combines pairwise alignment scores of amino acid sequences and secondary structures is shown to improve the prediction accuracies in a benchmark task defined using the Structural Classification of Proteins (SCOP) database. While the task of predicting SCOP superfamilies should be regarded as an easy one, with not much room for performance improvement, it is still widely accepted as the gold standard due to careful manual annotation by experts in the subject of protein evolution.A similar method is introduced to investigate whether tissue specificity of gene expression is correlated with the sequence and secondary structure of the resulting protein product. An information theoretic approach is adopted for sorting fruit fly and mouse genes according to their tissue specificity based on gene expression data. A classifier is then trained to predict the degree of specificity for these genes. The study concludes that the tissue specificity of gene expression is correlated with the sequence, and to a certain extent, with the secondary structure of the gene’s protein product.The sorted list of genes introduced in the previous chapter is used to investigate the tissue specificity of transcript profiles obtained from a study of ageing in the fruit fly. The same list is utilised to investigate how filtering tissue-restricted genes affects gene set enrichment analysis in the ageing study, and to examine the specificity of age-associated genes identified in the literature. The conclusion drawn in this chapter is that categorisation of genes according to their tissue specificity using Shannon’s information theory is useful for the interpretation of whole-fly gene expression data

Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor

Streptomyces spp. produce a variety of valuable secondary metabolites, which are regulated in a spatio-temporal manner by a complex network of inter-connected gene products. Using a compilation of genome-scale temporal transcriptome data for the model organism, Streptomyces coelicolor, under different environmental and genetic perturbations, we have developed a supervised machine-learning method for operon prediction in this microorganism. We demonstrate that, using features dependent on transcriptome dynamics and genome sequence, a support vector machines (SVM)-based classification algorithm can accurately classify >90% of gene pairs in a set of known operons. Based on model predictions for the entire genome, we verified the co-transcription of more than 250 gene pairs by RT-PCR. These results vastly increase the database of known operons in S. coelicolor and provide valuable information for exploring gene function and regulation to harness the potential of this differentiating microorganism for synthesis of natural products

Automatic detection of exonic splicing enhancers (ESEs) using SVMs

<p>Abstract</p> <p>Background</p> <p>Exonic splicing enhancers (ESEs) activate nearby splice sites and promote the inclusion (vs. exclusion) of exons in which they reside, while being a binding site for SR proteins. To study the impact of ESEs on alternative splicing it would be useful to have a possibility to detect them in exons. Identifying SR protein-binding sites in human DNA sequences by machine learning techniques is a formidable task, since the exon sequences are also constrained by their functional role in coding for proteins.</p> <p>Results</p> <p>The choice of training examples needed for machine learning approaches is difficult since there are only few exact locations of human ESEs described in the literature which could be considered as positive examples. Additionally, it is unclear which sequences are suitable as negative examples. Therefore, we developed a motif-oriented data-extraction method that extracts exon sequences around experimentally or theoretically determined ESE patterns. Positive examples are restricted by heuristics based on known properties of ESEs, e.g. location in the vicinity of a splice site, whereas negative examples are taken in the same way from the middle of long exons. We show that a suitably chosen SVM using optimized sequence kernels (e.g., combined oligo kernel) can extract meaningful properties from these training examples. Once the classifier is trained, every potential ESE sequence can be passed to the SVM for verification. Using SVMs with the combined oligo kernel yields a high accuracy of about 90 percent and well interpretable parameters.</p> <p>Conclusion</p> <p>The motif-oriented data-extraction method seems to produce consistent training and test data leading to good classification rates and thus allows verification of potential ESE motifs. The best results were obtained using an SVM with the combined oligo kernel, while oligo kernels with oligomers of a certain length could be used to extract relevant features.</p