The need for a Bioinformatics Program became apparent after repeated requests from researchers for bioinformatics resources and the University's announcement of BioMed 21, a 300 million dollars biomedical science initiative to bring "new knowledge of the human genetic blueprint to the patient's bedside and change how illnesses are understood, diagnosed, and successfully treated." A Bioinformatics Specialist with a strong background in the fields of Molecular Biology and Biostatistics was hired. Program development started in 2003. Initially, three core courses were developed: Sequence Similarity Search, Genetic Variation, and Human Genome Resources. Each of these courses was offered twice per semester. Additionally, partnerships were established within the University Medical School Community (e.g., the Genome Sequencing Center) to license and teach Spotfire's DecisionSite for Functional Genomics, a software package used to analyze microarray data. From March to May 2005, seven Spotfire classes were taught. Each Spotfire class consisted of seven hours of classroom work. Also, in-depth consultations were scheduled with faculty and researchers to address their specific needs. These consultations led to requests for other software packages to purchase and manage, including Lasergene and CSD (Cambridge Crystal Structure Database). Efforts to reach outside of the University Community were made through the development of a Bioinformatics Web site.
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http://dx.doi.org/10.1300/J115v26n02_08 | DOI Listing |
Proc Natl Acad Sci U S A
January 2025
Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6.
Although chromatin remodelers are among the most important risk genes associated with neurodevelopmental disorders (NDDs), the roles of these complexes during brain development are in many cases unclear. Here, we focused on the recently discovered ChAHP chromatin remodeling complex. The zinc finger and homeodomain transcription factor ADNP is a core subunit of this complex, and de novo mutations lead to intellectual disability and autism spectrum disorder.
View Article and Find Full Text PDFPlanta
January 2025
Laboratory of Environmental Microbiology and Biotechnology, Universidade Vila Velha (UVV), Vila Velha, ES, Brazil.
Both, Serendipita indica and AMF, show promise as sustainable biofertilizers for reforestation, improving nutrient uptake and stress tolerance, despite contrasting effects on photosynthetic capacity and biomass allocation. Reclaiming degraded areas is essential for biodiversity conservation and enhancing ecosystem services enhancement, especially when using native species. This study investigated Schinus terebinthifolius Raddi, a native Brazilian species, and its compatibility with plant growth-promoting microorganisms (PGPM), including an endophytic fungus (Serendipita indica) and a consortium of arbuscular mycorrhizal fungi (AMF), to identify effective strategies for reforestation in nutrient-poor environments.
View Article and Find Full Text PDFJ Microbiol Biol Educ
January 2025
Department of Chemistry, Towson University, Towson, Maryland, USA.
In recent years, there has been an increase in the number of course-based undergraduate research experience (CURE) courses. These courses provide research opportunities for many more students than are typically exposed to traditional independent research experiences, including women, historically underrepresented groups in science, and non-traditional students. However, the benefits for faculty who teach CURE courses have been less well documented, potentially discouraging faculty from offering such courses.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, Texas 79968, United States.
In this work, we describe a computational tool designed to determine the local dielectric constants (ε) of charge-neutral heterogeneous systems by analyzing dipole moment fluctuations from molecular dynamics (MD) trajectories. Unlike conventional methods, our tool can calculate dielectric constants for dynamically evolving selections of molecules within a defined region of space, rather than for fixed sets of molecules. We validated our approach by computing the dielectric constants of TIP3P water nanospheres, achieving results consistent with literature values for bulk water.
View Article and Find Full Text PDFPlant Genome
March 2025
Department of Fundamental Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
The plant Polygonum capitatum (P. capitatum) contains a variety of flavonoids that are distributed differently among different parts. Nevertheless, differentially expressed genes (DEGs) associated with this heterogeneous distribution have not been identified.
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