Rising star Iwobi

first_imgMANCHESTER, England (AP):There’s growing competition for discovery of the season in the English Premier League.Leading the way are N’Golo Kante, the box-to-box French midfielder propelling Leicester to an unlikely title triumph; Dele Alli, the Tottenham playmaker plucked from England’s third tier; and Marcus Rashford, Manchester United’s 18-year-old striker who seems born for the big time.Time to add Arsenal winger Alex Iwobi to the list.Iwobi, like Rashford, is a shy yet fearless teenager who has burst onto centre stage in the world’s most popular league in recent weeks. Arsenal’s all-star midfield is a tough department to break into, yet Iwobi has achieved it seemingly out of nowhere.He has started four of Arsenal’s last five matches, including a Champions League game away to the mighty Barcelona. He has scored and been named man of the match in the last two appearances, against Everton and Watford in the Premier League.Theo Walcott is in desperate need of game time to retain his place in England’s squad for the European Championship, but is currently playing second fiddle to Iwobi on the right wing.He may have to get used to it.Iwobi, 19, is the nephew of Nigeria great Jay-Jay Okocha and has been at Arsenal since the age of eight, having grown up in London. He is a powerful, hard-working, technically gifted attacker with an eye for goal just as Arsenal manager Arsene Wenger likes it.BIG HITIwobi, Mesut Ozil and Alexis Sanchez as the three floating forwards behind the main striker? It’s some prospect and already proving a big hit.”He is an intelligent boy who loves football, very passionate about the game, keen to learn, very humble as well,” Wenger has said of Iwobi.”It’s surprising how quickly he’s integrated into our game.”Iwobi’s accomplished display at the Camp Nou really made people sit up and take note of a player who didn’t start a game in the first half of the season. During the recent international break, Iwobi made his debut for Nigeria in a loss to Egypt – stamping his allegiance to the African country having played for England’s youth teams up to under-18 level.A call-up to Nigeria’s squad for the Olympics in Rio de Janeiro in August is in the offing – but first he might just be Arsenal’s secret weapon as the team looks to secure a 19th straight season of Champions League football.Impressive wins over Everton and Watford have consolidated third place with seven games left, and even kept Arsenal with an outside shot at the title. That, however, would require an implosion by surprise leaders Leicester, who are seven clear of second-place Tottenham and 11 ahead of Arsenal, who have a game in hand.Arsenal visit West Ham tomorrow while Leicester travel to relegation-threatened Sunderland and Tottenham host Manchester United.TITLE IN SIGHTLeicester are grinding out the wins as they close in on arguably the most stunning title success in English football history, having picked up four straight 1-0 victories ahead of the trip to Sunderland.Sunderland are proving tough to beat of late, drawing their last four games, but have slipped four points from safety. Sunderland might be in more desperate need of the points at the Stadium of Light.last_img read more

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Flood of genome data hinders efforts to ID bacteria

first_imgShareNEWS RELEASEEditor’s note: A link to a high-resolution image for download appears at the end of this release.David Ruth713-348-6327david@rice.eduMike Williams713-348-6728mikewilliams@rice.eduFlood of genome data hinders efforts to ID bacteriaRice U. scientist’s study finds growth of genomic databases affects species accuracyHOUSTON – (Oct. 30, 2018) – There are many ways to slice and dice genomic data to identify a species of bacteria, or at least find its close relatives. But fast techniques to sequence genomes have flooded the public databases and in a biased fashion, containing lots of genomic data about some species and not enough about others, according to a Rice University computer scientist.Todd Treangen and his colleagues tested taxonomic classification methods that match genomic sequences from bacteria of interest with those recorded in large databases to identify species. In the process, they charted a path toward improved accuracy and sensitivity. AddThis A study led by Rice University computer scientist Todd Treangen demonstrates that recent growth in genomic databases has a negative effect on attempts to identify microbes from metagenomic samples. (Credit: Courtesy of Todd Treangen) Todd Treangen Return to article. Long Description Return to article. Long DescriptionTodd TreangenTreangen is senior author of a study published this month in Genome Biology that demonstrates how changes over time in a widely used federal database, the National Center for Biotechnology Information’s RefSeq, have influenced the accuracy of metagenomic classification methods.A primary concern for Treangen, an expert in metagenomics — the study of genetic material from environmental samples — is maintaining the ability to quickly identify bacteria that pose a threat to public health.Big data is uniquely positioned to do this — but there’s so much of it. At present, he said, low-cost and high-throughput DNA shotgun sequencing machines, which read short DNA sequences from collections of microorganisms, have resulted in the doubling of genomic data in RefSeq every two to three years.“I initially thought more data is always better for these methods,” said Treangen, who joined Rice this year from the University of Maryland Institute for Advanced Computer Studies. “You would expect that there would be no penalty, because database growth is good.” However, the researchers found that bacterial data in RefSeq has an outsized effect at the species level of the taxonomic hierarchy, which is growing at a breakneck pace.That’s a problem for researchers who combine two common techniques to identify what they find. One is called k-mer-based classification, which identifies short DNA sequences from all the organisms in a bacterial sample via exact matches.“Most of the methods that have made the problem computationally feasible rely on k-mers, which are exact matches of length ‘k,’ or a key in to the microbes contained in the database,” he said. “If a sequenced read perfectly matches something in the database, the intuition is that you can say what that is with great precision and shortcut more expensive computational approaches.”A commonly used technique with k-mer-based classification is lowest common ancestor (LCA) assignment, he said. LCA compares samples to sequences that share a match, assigning them if necessary to a higher level in the taxonomy, such as a genus rather than a species. But this may not be specific enough for researchers trying to pin down a pathogen, he said.In fact, the study found a k-mer-based classification tool called Bracken, which uses Bayesian statistics to infer the best match for a sequence, helped mitigate the imbalance. Even so, it struggled to identify genomes with close relatives, but not perfect matches, in the database.Treangen said well-funded research into particular pathogens is a necessity and has greatly aided rapid-outbreak detection and tracking, but it ultimately biases public databases like RefSeq.“For instance, there’s an immense bias toward foodborne pathogens,” he said. “Society wants to know a lot about Salmonella, and rightfully so. The FDA, and specifically GenomeTrakr, have aided in the sequencing of thousands of relevant pathogens and have added them directly to the reference database.”However, he said that skews the reference database toward particular genera and families of microbes in a way that affects the accuracy and sensitivity of fast taxonomic-classification tools like Kraken that use k-mer and LCA-based approaches.Treangen said the best recent example of a false positive identification is a study that initially reported evidence of anthrax bacteria in New York City’s subways. The study, based on sequenced genomes from samples, was later revised to reflect mismatches that falsely identified the sequences as Bacillus anthracis.While a focus on public health is a key priority, Treangen said novel techniques able to cope with database growth and noise, coupled with an increased breadth of sequenced genomes, is needed for continued improvements in the field. “For example, microorganisms from the soil and ocean are severely under-sampled,” he said. “There remain a lot of microbes that we need to continue to sequence to better fill out public databases, and that will ultimately help our ability to accurately classify microbes from complex samples.”Daniel Nasko, a postdoctoral researcher at the University of Maryland, is lead author of the study. Co-authors are staff scientist Sergey Koren and investigator Adam Phillippy of the National Human Genome Research Institute, Bethesda, Md. Treangen is an assistant professor of computer science.The research was supported by the Division of Intramural Research of the National Human Genome Research Institute, part of the National Institutes of Health, and the Intelligence Advanced Research Projects Activity via the Army Research Office.-30-Read the abstract at https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1554-6Follow Rice News and Media Relations via Twitter @RiceUNews.Related materials:Todd Treangen: https://sites.google.com/view/treangen/homeRice Department of Computer Science: https://csweb.rice.eduGeorge R. Brown School of Engineering: https://engineering.rice.eduImage for download: http://news.rice.edu/files/2018/10/1102_ANCESTOR-1-web-1sx65j2.jpgA study led by Rice University computer scientist Todd Treangen demonstrates that recent growth in genomic databases has a negative effect on attempts to identify microbes from metagenomic samples. (Credit: Courtesy of Todd Treangen)Located on a 300-acre forested campus in Houston, Rice University is consistently ranked among the nation’s top 20 universities by U.S. News & World Report. Rice has highly respected schools of Architecture, Business, Continuing Studies, Engineering, Humanities, Music, Natural Sciences and Social Sciences and is home to the Baker Institute for Public Policy. With 3,970 undergraduates and 2,934 graduate students, Rice’s undergraduate student-to-faculty ratio is just under 6-to-1. Its residential college system builds close-knit communities and lifelong friendships, just one reason why Rice is ranked No. 1 for lots of race/class interaction and No. 2 for quality of life by the Princeton Review. Rice is also rated as a best value among private universities by Kiplinger’s Personal Finance. To read “What they’re saying about Rice,” go to http://tinyurl.com/RiceUniversityoverview.last_img read more

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