In the news / Bioinformatics

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The use of new technologies and automation raises questions about the impact on the job market and their respective hacking vulnerabilities. Dr. Larry Head, BIO5 faculty member and professor of Systems and Industrial Engineering at UA, discusses the importance of consumers doing research about the safety of autonomous vehicles before using them. 
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Scientists lead by The BIO5 Institute's Dr. Michael Worobey at the University of Arizona were able to extract from the tissue a nearly complete genetic sequence of an HIV virus — the oldest nearly full-length genetic code for an HIV-1 virus recovered thus far, and one that supports the theory that the virus that causes AIDS began to transmit among people within the first decade or two of the 20th century.
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Thrombocytopenia, or HIT, is a deficiency of blood platelets, the cells that help blood clot. A team of UA College of Medicine-Tucson researchers including Associate Vice President and Director of the Center for Biomedical Informatics and Biostatistics at UA Health Sciences, Dr. Yves Lussier, is working in support of a new grant with the aim to identify predictive and early biomarkers for HIT.
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Struggling to make sense of a large amount of student evaluations from her UA introductory biology course, Associate Vice Provost in the Office of Instruction and Assessment and BIO5 member, Dr. Lisa Elfring, developed a way to visualize the feedback. This kind of presentation provides her with the ability to create and test hypotheses of what students thought of a course.
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Testing a long-held hypothesis of a late UA professor, fellow UA Ecology and Evolutionary Biology professor and BIO5 faculty, Dr. Alexander Badyaev, has led a team to show that evolution is driven by species interaction within a community. Studying nearly 300 bird species, Dr. Badyaev’s team built and tested their carotenoid biochemical pathways to explore how the populations changed over the last 50 million years.
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UA researchers are building a quantum hub known as Inquire, which will be the world's first shared research and training instrument to help researchers in diverse fields benefit from quantum resources. The interdisicplinary research team includes Dr. Jennifer Barton, Director of the BIO5 Institute and UA Professor of Biomedical Engineering, Biosystems Engineering, Electrical and Computer Engineering, and Dr. Marek Romanowski, BIO5 member and Associate Professor of Biomedical Engineering, and Materials Science and Engineering.
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The Translational Genomics Research Institute (TGen), an affiliate of City of Hope, has identified a polio-like virus as a potential cause of an outbreak of a disease known as Acute Flaccid Myelitis (AFM), a crippling condition that causes muscle weakness and paralysis usually among children. Dr. Bonnie LaFleur, UA Professor of Biostatistics and BIO5 member, aided in data analysis for the study.
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Imaging and genomic technologies have dramatically increased the amount of information generated and used to make clinical decisions for diseases like Alzheimer's. “There is an untapped opportunity to leverage existing data from longitudinal cohorts, from the postmortem human brain, and from clinical trials to help the field advance our shared goals more effectively than we otherwise could,” said BIO5 member Dr. Eric Reiman, Executive Director of the Banner Alzheimer’s Institute.
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The BIO5 Institute's Dr. Michael Worobey has reconstructed the genome of the Spanish Flu from century old blood samples. The University of Arizona scientist had connected with a man named Jim Cox. And Cox just so happened to have in his possession a collection of human tissue slides had handed down through the generations. Those slides, it turns out, could now help rewrite the history of the 1918 Spanish flu — altering our understanding of when it began and how it spread.
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The UA's Data Science Institute, known as Data7, a unit of the Office of Research, Discovery and Innovation, is focused on connecting researchers, fostering collaboration and promoting literacy across campus. UA-TRIPODS, an integrated research and educational institute funded by the National Science Foundation, shares these goals and also is focused on developing new algorithms and foundational approaches necessary for large-scale data-driven research.
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UA ecologist and member of the BIO5 Institute, Dr. Ramona Walls is co-author on a recent Nature Ecology and Evolution paper, "Measuring species traits for biodiversity policy goals". This new research is part of collaboration with scientists around the world in an effort to study how species are responding to global changes in habitat, environment and climate.
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The KEYS Summer Research Internship Program lets high school students work alongside university faculty in top research labs. “Our interns learned to use tools that data scientists use every day...Their contributions will be used by many of the researchers that take advantage of our open access platform,” said Nirav Merchant, BIO5 member, CyVerse Co-Principal Investigator and Director of Data7.
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Drug interactions can pose a serious risk to patients when they are not identified and addressed. That is why a team of UA researchers, including BIO5's Dr. Vignesh Subbian, Assistant Professor in the Department of Biomedical Engineering and the Department of Systems & Industrial Engineering, are developing a drug interaction knowledge database, combined with clinically validated algorithms, which is expected to increase the specificity of warnings concerning dangerous drug combinations.
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A team led by the UA Cancer Center’s Dr. Melissa M. Herbst-Kralovetz, BIO5 member and associate professor at the UA College of Medicine – Phoenix, studied 100 premenopausal women to find links between vaginal bacteria and cervical cancer. They found that there is a distinct difference between the vaginal microbiome in those who develop cervical cancer and those who do not.
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A UA team, headed by Dr. Michael S. Barker, BIO5 member and assistant professor and director of bioinformatics in the UA Department of Ecology and Evolutionary Biology, has found that polyploidy, the duplication of whole genomes, has occurred many times during the evolution of insects, the most diverse group of animals.
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The recent revolution in artificial intelligence won’t be spawning computers hell-bent on doing in the human race. Instead, artificial intelligence, or AI, will be working with us and not against us, in what BIO5's Mihai Surdeanu, UA associate professor of computer science, terms “intelligence augmentation,” or IA.
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BIO5 Institute member and Director of the Division of Population Genetics at the UA Center for Applied Genetics and Genomic Medicine, Dr. Rick Kittles probes African-American genetic ancestry for data that could help resolve health disparities in communities of color.
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The year you were born might predict how you’ll respond to this year’s flu—and how well you’d fair in a flu pandemic. Scientists, including BIO5 researcher researcher Dr. Michael Worobey, have found a clear link between flu susceptibility and bird flu viruses; that connection has been easier to trace because humans aren't regularly exposed to them.
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The BIO5 Institute is home to The KEYS Research Internship, a program that facilitates research internships for 378 Arizona teens in the areas of in bioscience, biomedicine, engineering, environmental health or biostatistics and contribute to ongoing research projects across The University of Arizona.
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BIO5 Institute and iPlant Collaborative have teamed up to host a series of Software Carpentry workshops, offering instruction to researchers, students and educators across Arizona that will help them to hone their computing skills. These skills are necessary to efficiently and reliably process data sets and analyses.
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Scientists have made major strides toward creating new breeds of rice that could be more sustainable, as well as more resilient to environmental stresses. "This dataset provides access to millions of genetic markers that can be used to design sustainable crops for the future" says Dr. Rod Wing, director of the Arizona Genomics Institute at the UA and member of The BIO5 Institute.
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Dr. Eric Lyons, iPlant Collaborative co-principal investigator and BIO5 member, is one of three scientists using big data management tools to better understand the mysterious inner-workings of RNA molecules.