COUGER-co-factors associated with uniquely-bound genomic regions

Most transcription factors (TFs) belong to protein families that share a common DNA binding domain and have very similar DNA binding preferences. However, many paralogous TFs (i.e. members of the same TF family) perform different regulatory functions and interact with different genomic regions in the cell. A potential mechanism for achieving this differential in vivo specificity is through interactions with protein co-factors. Computational tools for studying the genomic binding profiles of paralogous TFs and identifying their putative co-factors are currently lacking. Here, we present an interactive web implementation of COUGER, a classification-based framework for identifying protein co-factors that might provide specificity to paralogous TFs. COUGER takes as input two sets of genomic regions bound by paralogous TFs, and it identifies a small set of putative co-factors that best distinguish the two sets of sequences. To achieve this task, COUGER uses a classification approach, with features that reflect the DNA-binding specificities of the putative co-factors. The identified co-factors are presented in a user-friendly output page, together with information that allows the user to understand and to explore the contributions of individual co-factor features. COUGER can be run as a stand-alone tool or through a web interface: http://couger.oit.duke.edu

30th Anniversary of Applied Intelligence: A combination of bibliometrics and thematic analysis using SciMAT

Applied Intelligence is one of the most important international scientific journals in the field of artificial intelligence. From 1991, Applied Intelligence has been oriented to support research advances in new and innovative intelligent systems, methodologies, and their applications in solving real-life complex problems. In this way, Applied Intelligence hosts more than 2,400 publications and achieves around 31,800 citations. Moreover, Applied Intelligence is recognized by the industrial, academic, and scientific communities as a source of the latest innovative and advanced solutions in intelligent manufacturing, privacy-preserving systems, risk analysis, knowledge-based management, modern techniques to improve healthcare systems, methods to assist government, and solving industrial problems that are too complex to be solved through conventional approaches. Bearing in mind that Applied Intelligence celebrates its 30th anniversary in 2021, it is appropriate to analyze its bibliometric performance, conceptual structure, and thematic evolution. To do that, this paper conducts a bibliometric performance and conceptual structure analysis of Applied Intelligence from 1991 to 2020 using SciMAT. Firstly, the performance of the journal is analyzed according to the data retrieved from Scopus, putting the focus on the productivity of the authors, citations, countries, organizations, funding agencies, and most relevant publications. Finally, the conceptual structure of the journal is analyzed with the bibliometric software tool SciMAT, identifying the main thematic areas that have been the object of research and their composition, relationship, and evolution during the period analyzed

Identification of CTQs for Complex Products Based on Mutual Information and Improved Gravitational Search Algorithm

The identification of CTQs for complex products is the first step to implement quality control. To improve the efficiency and accuracy of CTQs identification, we propose a novel hybrid approach based on mutual information and improved gravitational search algorithm, which has advantages of filter and wrapper. At first, the information relevance and redundancy are measured by mutual information. Then, the improved gravitational search algorithm is used to search the CTQs. Experimentation is carried out using 2 UCI data sets, and the classification capability of CTQs is tested by SVM and tenfold cross validation. The results show that the presented method is verified to be effective and practically applicable

Entity Recognition via Multimodal Sensor Fusion with Smart Phones

This thesis serves as an exploration that takes the sensors within a cell phone beyond the current state of recognition activities. Current state of the art sensor recognition processes tend to focus on recognizing user activity. Utilizing the same sensors available for user activity classification, this thesis validates the ability to gather data about entities separate from the user carrying the smart phone. With the ability to sense entities, the ability to recognize and classify a multitude of items, situations, and phenomena opens a new realm of possibilities for how devices perceive and react to their environment

Prediction of gene transcription start sites and initiation patterns from DNA sequence content

The computational identification of gene Transcription Start Sites (TSSs) can provide insights into the regulation and function of genes without performing expensive experiments, particularly in organisms with incomplete annotations. High-resolution general-purpose TSS prediction remains a challenging problem, with little recent progress on the identification and differentiation of TSSs which are arranged in different spatial patterns along the chromosome. In this work, we present TIPR, a sequence-based machine learning model which identifies TSSs with high accuracy and resolution for multiple spatial distribution patterns along the genome, including broadly distributed TSS patterns which have previously been difficult to characterize. TIPR predicts not only the locations of TSSs, but also the expected spatial initiation pattern each TSS will form along the chromosome--a novel capability for TSS prediction algorithms. As spatial initiation patterns are associated with spatiotemporal expression patterns and gene function, this capability has the potential to improve gene annotations and our understanding of the regulation of transcription initiation. The high nucleotide-resolution of this model locates TSSs within 10 nucleotides or less on average