In the news / Bioinformatics

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A new study authored by Dr. Michael Worobey, UArizona Department of Ecology and Evolutionary Biology head and BIO5 member, tracks the spread of coronavirus through North America and Europe. The study investigates when, where, and how COVID-19 established itself globally, using airline passenger flow data, disease incidence rates, and genomic sequence data.
 
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Since the University of Arizona opened its doors, more than 9,000 students, faculty and staff had been tested for COVID-19 and everyone on campus was wearing a mask. The school had even begun sampling its wastewater to quickly detect a potential hot spot. But the centerpiece in the school's preemptive battle against COVID-19 was the "Covid Watch" smartphone app, which uses Bluetooth technology to send an alert to someone's phone if they are exposed to the virus.
 
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Harnessing the power of technology, the BIO5 Institute will virtually connect University of Arizona faculty and researchers with representatives from biotech, biomedical, and life science companies at the FINE event on Thursday, August 13, 2020.
 
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A study by Dr. Ali Akoglu, electrical and computer engineering associate professor, and his graduate students Nirmal Kumbhare and Joshua Mack was selected as the Featured Paper in the August issue of IEEE Transactions on Computers due to its novelty and practicality. Their paper, "DS3: A System-Level Domain-Specific System-on-Chip Simulation Framework,” presents a system-level domain-specific systems-on-chip simulation (DS3) framework.
 
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To address the critical need of local COVID-19 data, a collaboration of researchers from UArizona Health Sciences & The Data Science Institute including BIO5’s Drs. Nirav Merchant and Sriram Iyengar, launched a 2-way texting system to gather valuable info to track the virus in Arizona. The application will assist with identifying areas where resources are needed.
 
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We all do better when we work together. Using cutting edge technology and big data analysis, the newly formed Arizona COVID-19 Genomics Union (ACGU) will track the virus’ evolution and transmission. Co-founded by UArizona Department of Ecology & Evolutionary Biology head and BIO5 associate director Dr. Michael Worobey, the cross-university collaboration between NAU, TGen and UArizona is another example of how our combined strength will provide solutions to better Arizona.
 
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A collaboration between the Information School, Computer Science, and Family Studies and Human Development has been awarded a $7.5M grant to develop a theory of mind-based cognitive architecture for teams (ToMCAT). The grant is part of the DARPA Artificial Social Intelligence for Successful Teams (ASIST) program. The collaborating team includes computer science professor Dr. Jacobus Barnard. The project aims to build artificially intelligent agents that understand both the social and goal-oriented aspects of teams in mission-like scenarios and are able to reason about possible interventions. 
 
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Directed by Dr. Hsinchun Chen, a UArizona cybersecurity program aims to train the next generation of cyberspace defenders. Thanks to a $3.6 million grant renewal from the NSF, the two-year program, the AZSecure Cybersecurity Fellowship, will continue to cover tuition and fees for graduate students and provides a stipend of $34,000 per academic year. About 30 students have already taken advantage of the program since 2013, and the renewal funding will allow the program to roughly 20 more students over the next five to seven years.
 
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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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Science has the power to improve health, strengthen economies and shed light on the unknown throughout the universe, but a small and growing number of research papers are being retracted by journals for a myriad of reasons, including falsified evidence, conflicts of interest and plagiarism, speciali
 
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New DNA analysis conducted by BIO5 faculty member and University of Arizona Plant Sciences professor Dr. Judith Brown, along with researchers at the Los Alamos National Laboratory, has found genetic diversity in predatory pest, Vampirovibrio chlorellavorus. This discovery complicates efforts to protect algae ponds used in the biofuels industry from destructive algae strains and pests.
 
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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.