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Colwell Continues Groundbreaking Research to Battle Cholera

Tue Sep 11, 2018

Research by a renowned University of Maryland microbiologist is enabling an international aid effort to predict and stop potential epidemics of cholera.

Rita Colwell, a Distinguished University Professor in the University of Maryland Institute for Advanced Computer Studies (UMIACS), is collaborating with the United Nations and the British government to help curb the waterborne bacterium Vibrio cholerae in Yemen and other affected regions.

The World Health Organization estimates that the disease–which can be deadly if left untreated–infects 1.3 million to 4 million people annually.

The team is using data from NASA satellites to create risk maps based on several factors including air and water temperatures, precipitation, severity of natural disasters, sanitation and hygiene infrastructure, and population density.

Colwell first realized that satellite data could be used to forecast potential cholera outbreaks in 1995. Seeing her research put into action to save lives “is the greatest satisfaction any scientist, mathematician, or engineer could possibly have … essentially a dream fulfilled,” she says.

Anwar Huq, a research professor at the University of Maryland’s Pathogen Research Institute, is also one of the lead scientists on the project.

Last spring, aid workers distributed sterilization and medical supplies in Yemen based on the team’s model that predicted the locations and timing of cholera outbreaks.

The country is currently experiencing a civil war and the worst humanitarian aid crisis in the world, says the UN.

The team’s model will be applied to other impoverished regions to prevent and assist with more cholera outbreaks.

“It is truly satisfying to be able to see one’s research, including that done here at the University over the past forty plus years, incorporated into an effective public health success on a global scale,” says Colwell. “I certainly hope other governments, NGOs, and the United Nations will incorporate our model into their ongoing work.”

Go here to see a video of the latest work by Colwell and others involved in this project.

-Story by Maria Herd

Pop Gives Keynote Talk on Use of Algorithms in Microbial Research

Wed Aug 22, 2018

Mihai Pop, a professor of computer science in the Center for Bioinformatics and Computational Biology, recently gave a keynote talk on the use of algorithms in bioinformatics.

Pop spoke at ALGO 2018, an annual meeting combining the premier algorithmic conference, European Symposium on Algorithms, and a number of other specialized conferences and workshops, all related to algorithms and their applications.

The symposium was held from Aug. 20–24 in Helsinki.

Pop’s talk, “From Clustering to Variant Discovery: Algorithmics Opportunities in Microbiome Research,” covered the emergence of metagenomics—the sequencing-based exploration of the genomic content of microbial communities.

Pop says that metagenomics has made it possible to characterize the genomes, and even functions of microbes, that cannot currently be grown in a laboratory. As a result, new microbes and new microbial functions have been discovered in recent years.

In addition to this transformative effect on biology, the analysis of metagenomic data has created new opportunities for computational research. Pop focused his talk on algorithmic challenges related to sequence clustering, functional annotation and structural variant discovery. He also described recent results from his lab in these areas, and discussed several challenges in metagenomics that his group is currently working on.

“Millions of good and bad intestinal bacteria have a very complicated, and partly unknown, way of interacting with each other,” Pop says. “We have focused particularly on studying the intestinal bacteria of children in developing countries, but our algorithmic tools can also be used in cancer research.”

Rita Colwell Awarded Prestigious Lee Kuan Yew Water Prize

Thu Mar 22, 2018

Rita Colwell, a Distinguished University Professor in the University of Maryland Institute for Advanced Computer Studies (UMIACS), has been awarded the prestigious Lee Kuan Yew Water Prize.

The award, now in its 10th year, honors outstanding contributions by individuals or organizations that work toward solving global water challenges with innovative technologies, policies or programs. It is named for Singapore's first Prime Minister, Lee Kuan Yew, whose foresight and leadership enabled Singapore to attain a sustainable water supply.

Colwell was recognized for her pioneering insights into microbial water quality surveillance and life-saving work in fighting waterborne diseases.

The impact of Colwell's research and scholarship has been especially felt in cholera-endemic countries—the result of a key discovery she made in the 1970s involving cholera-causing bacteria, known as Vibrio cholera. Previously thought to be incapable of surviving more than a few hours outside a human host, she discovered that the bacteria occur naturally in the aquatic environment associated with plankton.

This highlighted the critical link between the environment and cholera and led to Colwell's subsequent application of satellite imagery and modelling to predict cholera outbreaks, as well as her innovative use of sari cloths as filters to greatly reduce contamination in drinking water.

Colwell will travel to Singapore in July to receive the award-which includes $300,000 and a gold medallion-as part of a series of events tied to Singapore International Water Week.

Go here to see an overview of the work that Colwell is doing in the fight against cholera.

Mihai Pop Named Interim Director of UMIACS, Effective March 1

Tue Feb 06, 2018

Mihai Pop, a professor of computer science with appointments in the Center for Bioinformatics and Computational Biology and the University of Maryland Institute for Advanced Computer Studies (UMIACS), has been named interim director of UMIACS, effective March 1.

As interim director, Pop will provide leadership to 70-plus faculty and research scientists, 150 graduate students, and almost two-dozen administrative and technical staff working in the institute.

He succeeds current director Amitabh Varshney, who begins a new role as dean of the College of Computer, Mathematical, and Natural Sciences on March 1.

“Mihai has proven to be a strong advocate for enhancing the strength and visibility of UMIACS both on and off campus, and I expect he will continue to seek out new research and academic collaborations that will benefit from our expertise,” says Varshney.

Pop says he is honored to step back into a leadership role in UMIACS, having already served as interim director for a year while Varshney was the university’s interim vice president for research.

“I look forward to working closely with our faculty, postdocs, students and staff to bring the power of modern computing to bear on many of the challenges faced by our society today,” he says.

A strong advocate for bringing more diversity to the field of computer science, Pop says he will continue to support for the Maryland Center for Women in Computing and other initiatives that enhance participation in the discipline by people from diverse backgrounds.

Pop is a noted researcher and educator active in numerous interdisciplinary, cross-institutional projects. His research interests cover several areas of bioinformatics, primarily related to the development of computational algorithms for analyzing biological data generated through high-throughput experimental techniques, such as sequencing technologies.

Part of Pop’s research focuses on the computational analysis of the microbial communities inhabiting our world and our bodies—a scientific field called metagenomics. His lab has developed a number of software tools that are now widely used in the field. He has also been an active participant in a number of large projects, including the Human Microbiome Project, and the GEMS study of diarrheal disease in children from the developing world.

He recently took on the role of co-director for the Center for Health-related Informatics and Bioimaging, a partnership between the University of Maryland, College Park and the University of Maryland, Baltimore that is funded by the MPowering the State initiative.

Pop received his doctorate in computer science from Johns Hopkins University in 2000 and has been at the University of Maryland since 2005.

Ruppin Part of International Team Studying Interaction Between Aging Diseases and Cancer

Tue Jan 30, 2018

Eytan Ruppin, a professor of computer science in the Center for Bioinformatics and Computational Biology (CBCB), is co-lead of an international study on the molecular interactions between neurodegenerative diseases and cancer during aging.

Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly”—published today in Nature Communications—examines molecular alterations that occur as people get older.

Studies have shown that while death due to cancer is most prevalent among people in their 60s, cancer’s contribution to the total mortality rate declines at more advanced ages. Degenerative diseases such as heart failure, dementia or diabetes are on the rise for those over 70.

Ruppin, working with researchers from the Jena Centre for Systems Biology of Ageing (JenAge) and a second team at Kiel University led by Professor Christoph Kaleta, studied the molecular alterations that occur as people get older, comparing them to the molecular signatures of cancer and degenerative diseases.

The study involved the most comprehensive comparison of aging across species and tissues that has been undertaken to date. The scientists compared age-related changes in the activity of genes in humans, mice, the zebrafish Danio rerio and the short-lived killifish Nothobranchius furzeri across several organs. The researchers found many similarities in the molecular signatures of age-associated changes across all species.

Subsequently, the researchers compared the changes in gene activity with the signatures of age-specific diseases. Age-related changes in gene activity were aligned with changes observed in degenerative diseases. Strikingly, the aging-related changes showed a reverse trend compared to the changes observed with cancer.

“As the molecular signatures of cancer and degenerative disorders oppose each other in key cellular processes, it logically follows that the molecular alterations occurring later in life are not able to drive away both cancer and degenerative disorders at the same time,” Ruppin says. “Indeed, our results show that they are likely to be aligned to counteract the increased risk of cancer but, probably inevitably, the price might be an increased risk of a degenerative disease.”

Ruppin, a former professor of computer science and medicine at Tel-Aviv University, was director of CBCB from July 2014 to January 2018. He recently started a new position as chief of the newly founded Cancer Data Science Lab at the National Cancer Institute.

Varshney Named Dean of the College of Computer, Mathematical, and Natural Sciences

Wed Jan 24, 2018

Computer scientist Amitabh Varshney has been named dean of the University of Maryland’s College of Computer, Mathematical, and Natural Sciences (CMNS), effective March 1, 2018.

Varshney is a professor of computer science at UMD and director of the University of Maryland Institute for Advanced Computer Studies (UMIACS). He recently completed a one-year term as the university’s interim vice president for research.

In his new role, Varshney will lead the university’s largest college, which educates more than 9,000 students each year in its undergraduate and graduate programs. He will also provide strategic leadership to expand the magnitude and impact of the college’s education and research programs, which have a combined annual budget of $250 million.

“I am deeply honored to be chosen to lead this college and bring its excellence in research and academics to new levels of visibility and recognition,” Varshney said. “I look forward to championing the efforts of our talented faculty, staff and students who are advancing new frontiers of scientific knowledge every day.”

Varshney’s appointment comes after a six-month national search.

“[Dr. Varshney] has a wealth of knowledge in research and interdisciplinary work,” said Mary Ann Rankin, UMD’s senior vice president and provost. “His clear vision for the college and natural leadership style will allow CMNS to continue to be recognized nationally and globally.”

Go here to read the full CMNS news release.

Cummings Named Interim Director of CBCB

Mon Jan 22, 2018

A noted expert in computational biology and molecular evolutionary genetics has just been named interim director of the Center for Bioinformatics and Computational Biology (CBCB).

Michael Cummings, a professor of biology with an appointment in the University of Maryland Institute for Advanced Computer Studies (UMIACS), assumed leadership of CBCB on January 22.

He succeeds Eytan Ruppin, who started a new position as chief scientist of a cancer data science lab at the National Cancer Institute.

As interim director of CBCB, Cummings will help guide a diverse community of faculty, research scientists, postdocs, students and staff who are focused on research and scholarship arising from the genome revolution.

"I am privileged to collaborate with such a talented group of people, all of whom share a common interest of using powerful computational resources to gain a better understanding of how life works," says Cummings. "The work we do in CBCB—whether stemming the spread of cholera or other infectious diseases, helping curtail the use of harmful tobacco products, or analyzing synthetic DNA for possible biological threats—has a positive impact on the world we inhabit."

Cummings own research is focused on innovative experimental design and data analysis methods. This includes examining DNA sequence data for evolutionary inference, sampling of genetic diversity in relationship to conservation reserve design, hypothesis testing using tree-based statistical models, genetic differentiation, and more.

Cummings—working closely with doctoral student Daniel Ayres—was recognized last year by technology leader NVIDIA with a Global Impact Award for the development of innovative software that provides a rapid analysis of biological sequence data.

Known as BEAGLE, for Broad-platform Evolutionary Analysis General Likelihood Evaluator, the open-source software is an essential component in the software workflow of many scientists studying the evolutionary history of organisms, including the viruses that cause AIDS, influenza and Ebola.

Cummings came to the University of Maryland in 2003 as a visiting associate professor. He accepted full-time appointments in the Department of Biology and UMIACS in 2005.

Cummings received his doctorate in organismic and evolutionary biology from Harvard University in 1992, and completed postdoctoral research at the University of California, Berkeley, as an Alfred P. Sloan Foundation Postdoctoral Fellow. He also did postdoctoral work at the University of California, Riverside.

Hannenhalli and CBCB Doctoral Student Release New Study Examining Protein Networks and Breast Cancer

Wed Dec 06, 2017

Researchers in the Center for Bioinformatics and Computational Biology (CBCB) have published a new study on how any given gene may perform a different function in breast cancer cells—as opposed to healthy cells—due to changes in networks of interacting proteins.

Previous research has shown that a protein produced by a single gene can potentially have different functions in a cell depending on the proteins with which it interacts.

Building on this concept, Sridhar Hannenhalli, a professor of cell biology and molecular genetics, and Sushant Patkar, a second-year doctoral student in computer science, hypothesized that alterations in protein interaction networks in breast cancer cells may change the function of individual genes.

To test this idea, they analyzed protein expression in 1,047 breast cancer tumors and 110 healthy breast tissue samples, using data from The Cancer Genome Atlas project.

Paktar was lead author on the research paper, which was just published in PLOS Computational Biology. Assaf Magen, a fourth-year doctoral student in CBCB, and Roded Sharan, a professor of computer science and a member of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University, also contributed to the paper.

Go here to read the full news release.

Colwell Receives Prestigious Appointment to France’s Legion of Honor

Wed Nov 22, 2017

Rita Colwell, a Distinguished University Professor in the University of Maryland Institute for Advanced Computer Studies (UMIACS), has been awarded the rank of Chevalier (Knight) in the Legion of Honor by decree of the President of the French Republic. Colwell was presented the Insignia of Chevalier de la Légion d’Honneur by Gérard Araud, Ambassador of France to the United States, in a ceremony on November 20 at the ambassador’s residence in Washington, D.C.

France's Legion of Honor, which was created by Napoleon Bonaparte in 1802, rewards both military and civilian merit. According to the Légion d'Honneur website: “The Legion of Honor brings together, around the criterion of personal merit in the service of the nation [France], famous personalities as well as citizens unknown to the broader public.”

“It gives me great pleasure to extend my warmest congratulations to you on being recently appointed to the rank of Chevalier in the Legion of Honor by decree of the President of the French Republic,” wrote Ambassador Araud in the official award letter.

“This high honor reflects France’s profound gratitude as expressed by the President of the French Republic and acknowledges your exemplary personal commitment to trans-Atlantic collaboration with several French universities in the fields of environment, water and global infectious diseases,” continued Araud, who also cited Colwell’s major role in the promotion of science and in inspiring many students around the world to pursue scientific careers.

Colwell's career bridges many areas, including microbiology, ecology, infectious disease, public health and computer and satellite technology. She continues to be a world leader in the fight against water-borne diseases, particularly cholera, and in bioinformatics, especially for understanding microbiomes and applying this knowledge to human health and to the diagnosis and treatment of disease.

Colwell’s many achievements and firsts include:

• establishing the taxonomy of vibrio bacteria, which includes Vibrio cholerae and identifying a previously unknown survival strategy of dormant vibrio cells;

• showing how climate change has expanded the habitat range of vibrios, and the occurrence of cholera;

• helping prevent the spread of cholera in developing countries by discovering and demonstrating an effective way to use the sari, the traditional dress of women on the Indian subcontinent, as a filter to remove vibrio-carrying plankton from drinking water drawn from ponds, rivers and other surface waters;

• receiving a dozen U.S. patents, most involving computational biology;

• founding the company CosmosID, which uses next-generation DNA sequencing to advance new discoveries in microbiome research; and

• leading numerous science organizations, including the National Science Foundation (NSF) from 1998–2004 as NSF’s first woman director.

The Legion of Honor is the latest of Colwell’s many recognitions and awards, which also include the 2017 International Prize for Biology, recognized as one of the most prestigious honors for a natural scientist; the 2006 U.S. National Medal of Science; the 2010 Stockholm Water Prize; “The Order of the Rising Sun, Gold and Silver Star,” awarded by the Emperor of Japan; and membership in the U.S. National Academy of Sciences, Royal Society of Canada, Swedish Royal Academy of Science, Irish Royal Academy of Science, the Bangladesh and Indian academies of Science, the American Academy of Arts and Sciences, American Philosophical Society and the National Academy of Inventors.

CHIB to Co-Host Microbiome Workshop on Biodefense and Pathogen Detection

Wed Nov 01, 2017

The Center for Health-related Informatics and Bioimaging (CHIB) is co-hosting a one-day workshop next January focused on biodefense and pathogen detection.

The 2018 Winter Mid-Atlantic Microbiome Meet-up (M3), set for January 10, 2018 at the University of Maryland, is designed to create synergistic connections between academia, federal experts and others involved in pathogen detection, antibiotic resistance and biodefense matters.

Keynote speakers for the event are Tara O'Toole, executive vice president of In-Q-Tel (IQT), and Rita Colwell, a Distinguished University Professor in the University of Maryland Institute for Advanced Computer Studies.

O’Toole is currently leading B.Next, an IQT lab dedicated to exploring opportunities and risks likely to arise as a result of advances in the biological sciences and biotechnologies, with a particular focus on detecting and preventing biological attacks.

Colwell is recognized as an international leader in the field of bioinformatics—most notably in understanding microbiomes and the application of this knowledge to human health and the diagnosis and treatment of disease. She is founder and chairman of CosmosID Inc., a microbial genomics company focused on molecular diagnostics of human pathogens and antimicrobial resistance.

Other featured speakers are Nicholas Bergman, a senior principal investigator in genomics at the National Biodefense Analysis and Countermeasures Center, and Stephanie Rogers, a deputy director of B.Next.

This is the second Mid-Atlantic Microbiome Meet-up held on the Maryland campus. The inaugural M3 in Fall 2016 brought together more than 60 researchers and scientists who discussed topics such as human skin microbiomes and tracking the spread of hospital infections.

“M3 has served as a conduit for the Mid-Atlantic scientific community interested in microbiome research, enabling researchers at all levels to coalesce around the main challenges in the field,” says Todd Treangen, the assistant director of CHIB who is coordinating much of the M3 activities.

To register for the January 2018 workshop, go here.


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