Evidence for dual roles of histone H3 lysine 4 in antagonizing Polycomb group function and promoting target gene expression.

Tight control over cell identity gene expression is necessary for proper adult form and function. The opposing activities of Polycomb and trithorax complexes determine the on/off state of cell identity genes such as the Hox factors. Polycomb group complexes repress target genes, whereas trithorax group complexes are required for their expression.

Dual roles of histone H3 lysine-4 in antagonizing Polycomb group function and promoting target gene expression.

Tight control over cell identity gene expression is necessary for proper adult form and function. The opposing activities of Polycomb and trithorax complexes determine the ON/OFF state of targets like the Hox genes. Trithorax encodes a methyltransferase specific to histone H3 lysine-4 (H3K4).

Histone H3K18 & H3K23 acetylation directs establishment of MLL-mediated H3K4 methylation.

In an unmodified state, positively charged histone N-terminal tails engage nucleosomal DNA in a manner which restricts access to not only the underlying DNA but also key tail residues subject to binding and/or modification. Charge-neutralizing modifications, such as histone acetylation, serve to disrupt this DNA-tail interaction, facilitating access to such residues. We previously showed that a polyacetylation-mediated chromatin "switch" governs the read-write capability of H3K4me3 by the MLL1 methyltransferase complex.

H3K18 & H3K23 acetylation directs establishment of MLL-mediated H3K4 methylation.

In an unmodified state, positively charged histone N-terminal tails engage nucleosomal DNA in a manner which restricts access to not only the underlying DNA, but also key tail residues subject to binding and/or modification. Charge-neutralizing modifications, such as histone acetylation, serve to disrupt this DNA-tail interaction, facilitating access to such residues. We previously showed that a polyacetylation-mediated chromatin "switch" governs the read-write capability of H3K4me3 by the MLL1 methyltransferase complex.

FAIR for AI: An interdisciplinary and international community building perspective.

A foundational set of findable, accessible, interoperable, and reusable (FAIR) principles were proposed in 2016 as prerequisites for proper data management and stewardship, with the goal of enabling the reusability of scholarly data. The principles were also meant to apply to other digital assets, at a high level, and over time, the FAIR guiding principles have been re-interpreted or extended to include the software, tools, algorithms, and workflows that produce data. FAIR principles are now being adapted in the context of AI models and datasets.

An acetylation-mediated chromatin switch governs H3K4 methylation read-write capability.

In nucleosomes, histone N-terminal tails exist in dynamic equilibrium between free/accessible and collapsed/DNA-bound states. The latter state is expected to impact histone N-termini availability to the epigenetic machinery. Notably, H3 tail acetylation (e.

Optimizing Earthquake Nowcasting With Machine Learning: The Role of Strain Hardening in the Earthquake Cycle.

Nowcasting is a term originating from economics, finance, and meteorology. It refers to the process of determining the uncertain state of the economy, markets or the weather at the current time by indirect means. In this paper, we describe a simple two-parameter data analysis that reveals hidden order in otherwise seemingly chaotic earthquake seismicity.

Parallel Operators for High Performance Data Science and Data Engineering.

Data-intensive applications are becoming commonplace in all science disciplines. They are comprised of a rich set of sub-domains such as data engineering, deep learning, and machine learning. These applications are built around efficient data abstractions and operators that suit the applications of different domains.

Deep Learning Approaches to Surrogates for Solving the Diffusion Equation for Mechanistic Real-World Simulations.

In many mechanistic medical, biological, physical, and engineered spatiotemporal dynamic models the numerical solution of partial differential equations (PDEs), especially for diffusion, fluid flow and mechanical relaxation, can make simulations impractically slow. Biological models of tissues and organs often require the simultaneous calculation of the spatial variation of concentration of dozens of diffusing chemical species. One clinical example where rapid calculation of a diffusing field is of use is the estimation of oxygen gradients in the retina, based on imaging of the retinal vasculature, to guide surgical interventions in diabetic retinopathy.

Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical exams.

Background: In this work, we aimed to demonstrate how to utilize the lab test results and other clinical information to support precision medicine research and clinical decisions on complex diseases, with the support of electronic medical record facilities. We defined "clinotypes" as clinical information that could be observed and measured objectively using biomedical instruments. From well-known 'omic' problem definitions, we defined problems using clinotype information, including stratifying patients-identifying interested sub cohorts for future studies, mining significant associations between clinotypes and specific phenotypes-diseases, and discovering potential linkages between clinotype and genomic information.

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering.

Unlabelled: Arbuscular mycorrhizal (AM) fungi form mutualisms with plant roots that increase plant growth and shape plant communities. Each AM fungal cell contains a large amount of genetic diversity, but it is unclear if this diversity varies across evolutionary lineages. We found that sequence variation in the nuclear large-subunit (LSU) rRNA gene from 29 isolates representing 21 AM fungal species generally assorted into genus- and species-level clades, with the exception of species of the genera Claroideoglomus and Entrophospora However, there were significant differences in the levels of sequence variation across the phylogeny and between genera, indicating that it is an evolutionarily constrained trait in AM fungi.

MGEScan: a Galaxy-based system for identifying retrotransposons in genomes.

Unlabelled: : MGEScan-long terminal repeat (LTR) and MGEScan-non-LTR are successfully used programs for identifying LTRs and non-LTR retrotransposons in eukaryotic genome sequences. However, these programs are not supported by easy-to-use interfaces nor well suited for data visualization in general data formats. Here, we present MGEScan, a user-friendly system that combines these two programs with a Galaxy workflow system accelerated with MPI and Python threading on compute clusters.

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications.

Biological processes are fundamentally driven by complex interactions between biomolecules. Integrated high-throughput omics studies enable multifaceted views of cells, organisms, or their communities. With the advent of new post-genomics technologies, omics studies are becoming increasingly prevalent; yet the full impact of these studies can only be realized through data harmonization, sharing, meta-analysis, and integrated research.

Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications.

Biological processes are fundamentally driven by complex interactions between biomolecules. Integrated high-throughput omics studies enable multifaceted views of cells, organisms, or their communities. With the advent of new post-genomics technologies, omics studies are becoming increasingly prevalent; yet the full impact of these studies can only be realized through data harmonization, sharing, meta-analysis, and integrated research.

Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets.

Background: Modern pyrosequencing techniques make it possible to study complex bacterial populations, such as 16S rRNA, directly from environmental or clinical samples without the need for laboratory purification. Alignment of sequences across the resultant large data sets (100,000+ sequences) is of particular interest for the purpose of identifying potential gene clusters and families, but such analysis represents a daunting computational task. The aim of this work is the development of an efficient pipeline for the clustering of large sequence read sets.

Hybrid cloud and cluster computing paradigms for life science applications.

Background: Clouds and MapReduce have shown themselves to be a broadly useful approach to scientific computing especially for parallel data intensive applications. However they have limited applicability to some areas such as data mining because MapReduce has poor performance on problems with an iterative structure present in the linear algebra that underlies much data analysis. Such problems can be run efficiently on clusters using MPI leading to a hybrid cloud and cluster environment.

Improving usability and accessibility of cheminformatics tools for chemists through cyberinfrastructure and education.

Some of the latest trends in cheminformatics, computation, and the world wide web are reviewed with predictions of how these are likely to impact the field of cheminformatics in the next five years. The vision and some of the work of the Chemical Informatics and Cyberinfrastructure Collaboratory at Indiana University are described, which we base around the core concepts of e-Science and cyberinfrastructure that have proven successful in other fields. Our chemical informatics cyberinfrastructure is realized by building a flexible, generic infrastructure for cheminformatics tools and databases, exporting "best of breed" methods as easily-accessible web APIs for cheminformaticians, scientists, and researchers in other disciplines, and hosting a unique chemical informatics education program aimed at scientists and cheminformatics practitioners in academia and industry.

Advances in cheminformatics methodologies and infrastructure to support the data mining of large, heterogeneous chemical datasets.

In recent years, there has been an explosion in the availability of publicly accessible chemical information, including chemical structures of small molecules, structure-derived properties and associated biological activities in a variety of assays. These data sources present us with a significant opportunity to develop and apply computational tools to extract and understand the underlying structure-activity relationships. Furthermore, by integrating chemical data sources with biological information (protein structure, gene expression and so on), we can attempt to build up a holistic view of the effects of small molecules in biological systems.

Web service infrastructure for chemoinformatics.

The vast increase of pertinent information available to drug discovery scientists means that there is a strong demand for tools and techniques for organizing and intelligently mining this information for manageable human consumption. At Indiana University, we have developed an infrastructure of chemoinformatics Web services that simplifies the access to this information and the computational techniques that can be applied to it. In this paper, we describe this infrastructure, give some examples of its use, and then discuss our plans to use it as a platform for chemoinformatics application development in the future.

Building messaging substrates for Web and Grid applications.

Grid application frameworks have increasingly aligned themselves with the developments in Web services. Web services are currently the most popular infrastructure based on service-oriented architecture (SOA) paradigm. There are three core areas within the SOA framework: (i) a set of capabilities that are remotely accessible, (ii) communications using messages and (iii) metadata pertaining to the aforementioned capabilities.