Posted by: genomescience | December 20, 2011

Anthrax investigation

Researchers at IGS had a pivotal role in the 2001 anthrax investigation, and their work helped pioneer the new
field known as microbial forensics.

PNAS article Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation

Medical News – Institute for Genome Sciences Plays Key Role

CNN coverage (TV) – “The Anthrax Mystery: Death By Mail”

Frontline coverage (TV) – “The Anthrax Files”

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Posted by: genomescience | December 20, 2011

E. coli

E. coli

IGS Cracks Genome Code of Deadly German E. Coli Outbreak

In May of 2011 a large outbreak of E. coli, that was later demonstrated to be associated with food products, was rapidly expanding across Europe. Greater than 300 people were sickened, over 900 were hospitalized for the syndrome known as hemolytic uremic syndrome (HUS) and 34 people were fatally infected. An international group of scientists from the United States and Denmark worked together to use third-generation single-molecule real-time DNA sequencing to determine the complete genome sequence of the German outbreak….

IGS Press release

YouTube interview with Dr. David Rasko, PI at IGS

Pacific Biosciences press release about their work with E. coli research

New England Journal of Medicine article on the Origins of the E. coli Strain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany

Posted by: genomescience | July 13, 2011

Introduction to Bioinformatics video

Posted by: genomescience | July 13, 2011

The benefits of being mentored in science….

The Fine Art of Being Mentored (Part 1)

No doubt about it, there’s an art to building an effective mentor-mentee relationship.  Seeking out a good mentor for your career growth and actively engaging as a “mentee” are integral to initiating a connection.

research is a collaborative process

Since this process is so important to the development of life scientists’ careers, I’ve decided to make this two posts and interview different faculty here at our Institute.

My first interview is with Lynn Schriml, PhD, an Assistant Professor, Epidemiology and Public Health at the University of Maryland School of Medicine, and a scientist in the Bioinformatics Department at the Institute for Genome Sciences.

Lynn graduated as a Biology major in 1989 from Wells College (Aurora, New York), an all female undergraduate college and then received her doctorate in 1997 from the University of Ottawa.

When you talk with Lynn, it’s immediately apparent that her career development has been positively affected through the cultivation of effective mentors in a process she describes as ‘organic’ rather than finding mentors through formal programs.

 “When I was a post-doc at NIH, they had a structured, mandated mentoring program,” she explains. “Your PI would schedule ‘mentoring meetings’ and they was a ‘formulaic’ feel to it. Their intention was good, but the process didn’t work to have relationships ‘forced’.”

As she progressed with her post-doctorate work and attended workshops in specific scientific specialty areas, she found opportunities to get targeted career advice and to build long-lasting relationships with key scientists.

“One presenter at Cold Spring Harbor spoke about the growth of bioinformatics research and about where the field was evolving,” she said.  Lynn was curious about the emerging field of bioinformatics and approached him with a few related questions.  Over the years, she regularly sought and received good career advice from colleagues. Hallway discussions discussing research ideas, conferences to attend and new directions for grant proposals have fostered ongoing career development.

Another mentor relationship grew out of her participation in the OBO Foundry and meeting a colleague in the ontology space. Lynn admired this particular scientist’s style – how he organizes projects, how he interacts with other scientists, and found that he was open to periodically giving her helpful advice about managing her academic careers.

“I’ve gotten great advice from various mentors about specific issues – how to write a good grant, how to develop a good story about your research and how important that story is to your continued success. Mentors can affect you generally, too, and their style can influence your style.”

Lynn’s most successful mentoring relationships happened because she sought out particular scientists and knew a little about their work.

 “You can’t be passive about developing mentors or it just won’t happen,” she explained. “It isn’t necessary to be aggressive but you have to approach the scientists you admire or who are doing research that interests you.”

Expending the energy and being open to seeking out the help you need at each point in your career is critical to ongoing growth, synergizing of ideas, and fostering the collaborative relationships that are integral to a science career. 

For Lynn, her mentor relationships have happened ‘organically’ rather than through more formal steps. In general, she has found that approaching specific scientists who were further in their careers with very specific career questions to be an effective strategy.

 “There are many people (colleagues, PIs, collaborators at external institutions) who are generous with their time and take a genuine interest in you as a person. These mentors have been invaluable to my growth, and, in fact, they’ve helped me become a better mentor to my students.”

 

 

Posted by: genomescience | July 12, 2011

Transitioning From Biological Research to Bioinformatics

What is bioinformatics?

Bioinformatics is a field of study that combines two important disciplines – computer science and biological research. People who work in bioinformatics (e.g. bioinformatics analysts and engineers) apply computational tools to biological data in order to answer complex biological questions. This field has arisen due to the advent of biological experiments that produce extremely large quantities of data requiring interpretation and analysis. Such experiments include: whole genome sequencing, microarrays, genome-wide association studies, proteomics, transcriptomics, metabolomics, and more.

discussion about bioinformatics project

Dr. Owen White, Director of Bioinformatics here at the Institute for Genome Sciences at the University of Maryland School of Medicine, gives an overview of bioinformatics in this video.

Perhaps the most visible area of biological data explosion is that of DNA sequencing. Continuing improvements in sequencing technology produce larger and larger data sets for less and less cost.  Fifteen years ago, few microbiologists would have believed that they could obtain the complete genome sequence for their bacterium of interest within a few weeks and at a cost of only a few thousand dollars, but that has become a reality. Sequencing projects that used to take months and years can now be accomplished in days or even hours. The result is that DNA sequencing is becoming just one more item in the laboratory toolkit and is being applied to more and more types of biological questions.

Virtually all fields of biology are embracing the use of bioinformatics tools in their work: from infectious disease research to environmental studies to personalized medicine, bioinformatics is playing a huge role. Since producing large datasets is increasingly quick and easy, the bottleneck has shifted from data production to downstream analysis. This is where the challenges arise for those in the field of bioinformatics who are charged with creating tools that can aid in the interpretation of huge datasets. For sequencing data, the first challenge is annotation – turning the string of bases into meaningful predictions for the locations and functions of genes and other genomic features. The development of pipelines for genome annotation and analysis requires the combined efforts of biologists, who understand the data and the questions that need to be answered, and computer scientists, who can create the software tools to accomplish the desired task.

Working in bioinformatics

Typically, people come into bioinformatics work primarily from two different backgrounds – either they have statistics or programming expertise and then develop familiarity with biological systems or they have biological backgrounds and then learn programming skills. This creates a continuum with programming experts at one end and “pure” microbiology researchers at the other end. People working in bioinformatics can find themselves anywhere along this continuum combining different amounts of biology and computer science depending on their interests and skill sets.

Today’s microbiology graduate students are typically exposed to some bioinformatics at least in their coursework and likely in their thesis work as well. They may use various software tools such as BLAST or make use of online resources. Those microbiology students who think they might be interested in pursuing a career in bioinformatics should seek out opportunities to learn more about it. They should consider taking bioinformatics electives and exploring programming languages such as Perl. This will allow them to find out whether they like programming and help them better decide where on the bioinformatics continuum they would most be comfortable. Here’s a short video about careers in bioinformatics.

At our research center, the Institute for Genome Sciences (IGS) at the University of Maryland School of Medicine, we have an ever-expanding bioinformatics department, with researchers and faculty who have multidisciplinary backgrounds. There are multiple opportunities for bioinformatics work at all locations on the biology/computer science continuum. At the heart of all of our work are the biological questions we are hoping to answer, thus all of our faculty and much of the bioinformatics staff have advanced degrees in biology.

What are some examples of bioinformatics research projects and what advice do we give to scientists who would like a career in bioinformatics?

to be continued….

Posted by: genomescience | February 23, 2011

Biosecurity Plenary Session: AAAS 2011 General Mtg

AAAS 2011 Annual Meeting News

 

News: AAAS 2011 Annual Meeting News

Research Responsibility Is Best Defense Against Biothreats, Experts Say at AAAS

 Ten years after the anthrax attacks that killed five Americans, researchers say a “culture of responsibility” among scientists may be the most effective way to prevent a future biological attack.

 Scientists welcome their collaborations with the federal government to ensure lab safety, and they say they have made strides in screening the lab workers who handle the most deadly bacteria and viruses. But a panel of prominent researchers at the 2011 AAAS Annual Meeting said there is also a danger that burdensome regulations could discourage promising young scientists from working with these biological agents.

 “The best and the brightest that you want have a lot of other opportunities,” said Anthony Fauci, head of the National Institute of Allergy and infectious Diseases. “You don’t want to give them too much of a reason to walk away from you.”

 The meeting’s plenary discussion on biosecurity came less than a week after the National Research Council released a long-awaited report evaluating the science behind the U.S. Federal Bureau of Investigation’s analyses in the 2001 anthrax attacks. The report concluded that the FBI’s analysis could not conclusively link anthrax spores from the lab flask of U.S. Army scientist Bruce E. Ivins, the FBI’s main suspect in the attacks before suicide in 2008, to the spores used in 2001.

In a video prepared for the plenary discussion, U.S. Representative Rush Holt (D-New Jersey) praised the National Research Council’s review of the FBI science, but said “a lot of questions are still unanswered.”

Holt, the recipient of the 2010 AAAS Philip Hauge Abelson Award, introduced a bill on 15 February to probe the attacks further. Modeled on the work of the 9/11 Commission, Holt said, the Anthrax Attacks Investigation Act would examine the federal government’s response to the anthrax mailings and make recommendations to prepare for future biological strikes.

The plenary panelists, along with moderator Jeanne Guillemin of the MIT Security Studies Program, agreed that the anthrax investigation—the science part, at least—would unfold much differently now than a decade ago. For instance, researchers then had only 40 pathogen genomes to compare to the anthrax strain, unlike the thousands of genomes available today. Current sequencing technology makes it possible to analyze a bacterial genome in hours or days, compared to the months it took in 2001.

 There has also been a construction boom in biocontainment labs, said Claire Fraser-Liggett, director of the Institute for Genome Sciences; 14,000 people now work in more than 1300 of these labs across the country. The labs hold about 82 bacteria and viruses that are listed as select agents—organisms considered potentially dangerous to human health.

Fraser-Liggett’s lab worked on the samples of anthrax from the 2001 attacks, and she has been a member of the National Science Advisory Board for Biosecurity since it was formed in 2004. In her work with the advisory board, she was surprised to find that there was little evidence showing whether psychological evaluations, medical exams, and similar tests are useful in screening lab workers.

The advisory board’s conversations with scientists, Fraser-Liggett said, show that “engaged leadership at the institutional level and at the laboratory level” is the most effective way to prevent a lab worker from making a careless mistake or deliberately releasing a dangerous pathogen.

“The bottom line,” Fauci agreed, “is always the development of a culture of responsibility by the scientists involved.”

The threats posed by naturally emerging pathogens such as HIV or the SARS virus, or re-emerging pathogens such as drug-resistant staph infections or malaria, “have a much greater chance of impacting society” than deliberately released pathogens, Fauci said.

The good news, he noted, is that broad investments in vaccines, medicines, and prevention programs could be used equally against natural and deliberate disease outbreaks.

 Scientists have been working safely with harmful bacteria and viruses for nearly 100 years, and theft, loss, and release of these pathogens has been “exceedingly rare,” said Rita Colwell, a Distinguished University Professor at the University of Maryland, College Park, and Johns Hopkins University Bloomberg School of Public Health.

“We have had an extraordinary record of safe research and productive items from research,” she said, “and we need to use our common sense as well as our rigor in this 21st century to address pathogens and the potential hazards they pose to the national security.”

Becky Ham, AAAS

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