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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.

University of Maryland Joins International Phytobiomes Alliance

Oct 31, 2017

The International Alliance for Phytobiomes Research is pleased to announce that the University of Maryland (UMD) has joined the organization as a sponsoring partner.

The Alliance is an international, nonprofit consortium of academic institutions, private companies, and government agencies. Launched in 2016, it is building a foundation for exploitation of the phytobiome for food security. “Phytobiomes” refers to a plant growing within a particular biome, enabling a holistic view of the production of crops, trees, and grasslands that includes the plant itself, all micro- and macro-organisms living in, on, or around the plant—such as microbes, animals, insects, and other plants—as well as the environment, which includes soil, air, water, weather, and climate.

The University of Maryland is one of the nation’s preeminent public research universities. Researchers in the University of Maryland Institute for Advanced Computer Studies (UMIACS), will bring extensive knowledge of genomic sequencing and bioinformatics to the Alliance, allowing for a detailed analysis of soil, water and air samples, as well as the organisms and other elements that inhabit those environments.

The university, located just outside of Washington, D.C., also has close research and educational ties to U.S. government labs and agencies like the U.S. Department of Agriculture, U.S. Food and Drug Administration, the National Institutes of Health, earth and climate specialists and the nearby NASA Goddard Space Flight Center, and more.

“The Phytobiomes Alliance proposes a holistic approach to solving one of the critical challenges facing our world—the sustainable production of food for the growing world population,” says Mihai Pop, a computational biologist at UMD who will be leading collaborative efforts with the Alliance. “We expect to contribute by bringing to bear unique expertise in machine learning and data science, high-performance computing, and metagenomics.”

Representatives of Phytobiomes Alliance sponsors serve on the organization’s coordinating committee, which identifies research projects, resource and technology gaps, establishes priorities, and develops strategic plans to achieve the Alliance’s goals.

“The University of Maryland brings to the Alliance a broad range of expertise in agricultural sciences including genetics, genomics, breeding, metagenomics, earth, climate, bioinformatics, and new technologies in high-performance computing,” says Kellye Eversole, the Phytobiomes Alliance executive director. “Mihai Pop’s background, experience, and knowledge will be extremely beneficial to the Alliance as we develop not only databases of disparate biological and geophysical information but also predictive and prescriptive analytics that could help growers increase the sustainable production of food, feed, and fiber.”

Over the next decades, the United Nations predicts that the world population will grow by 83 million every year, to reach 9.8 billion by 2050 and 11.2 billion by 2100. Producing enough food for this growing population—in a sustainable way, while preserving biodiversity and natural resources—requires a major paradigm shift in agricultural production of food, feed and fiber. By establishing a foundation of knowledge on how phytobiome components interact and affect each other, the Phytobiomes Alliance aims at addressing these challenges.

By 2050, the Alliance envisions that all farmers, ranchers, growers, and foresters will have at their disposal predictive and prescriptive tools that empower them to choose the best combination of crops, management practices, and inputs for a specific field in a given year.

About the Phytobiomes Alliance The Phytobiomes Alliance is an international, nonprofit alliance of industry, academic, and governmental partners created in 2016. The goal of the Alliance is to understand, predict and control emergent phenotypes for sustainable production of food, feed and fiber on any given farm. The Phytobiomes Alliance is sponsored by Bayer CropScience, Eversole Associates, Monsanto, The Climate Corporation, INRA, Indigo, the Noble Research Institute, NewLeaf Symbiotics, Colorado State University, the University of Maryland, Penn State College of Agricultural Sciences, the American Phytopathological Society, the University of Nebraska-Lincoln, and BioConsortia.

About the University of Maryland The University of Maryland, the state’s flagship institution of higher education, is one of the nation’s preeminent public research universities. A global leader in scientific discovery, entrepreneurship and innovation, UMD is home to nearly 38,000 students, 9,500 faculty and staff, and 250 academic programs. The institution secures more than $500M in external research funding each year.

About the Institute for Advanced Computer Studies The University of Maryland Institute for Advanced Computer Studies (UMIACS) provides a unique multidisciplinary computing environment to address some of today’s most pressing scientific and societal challenges in areas like cybersecurity, bioinformatics, computer vision, data science, and quantum information science.

CBCB Doctoral Student Uses Powerful Computing to Unlock the Mysteries of Microbes

Sun Oct 15, 2017

Nidhi Shah loves a good challenge and is inquisitive by nature, so it’s only fitting that she’s involved in an expanding scientific field where curiosity and determination are essential: metagenomics.

Shah, a second-year computer science doctoral student in the Center for Bioinformatics and Computational Biology (CBCB), is developing algorithms and software tools to unlock the mysteries of microbes, the tiny microorganisms that make up the majority of our planet’s living material.

Until the last decade or so, there were many unanswered questions surrounding microbes, mostly due to the fact that only a small percentage of them could be isolated and studied in a controlled lab environment.

Now, with advances in high-throughput DNA sequencing and other tools, scientists are able to take an environmental sample—whether from a hydrothermal vent or the gut of a sheep—sequence the DNA in it, and then piece together the genomes of any microbes that are present.

One of the biggest challenges in metagenomics is to annotate, or identify, which microorganism or gene that a specific DNA sequence originates from, which is where the research by Shah and other computational biologists comes into play.

“Annotating the sequences found in these samples is complicated work, but it’s important because it helps us not only understand the diversity of our environment, but also lets us better characterize a microbe’s functional capabilities,” Shah says. “This, in turn, can help us understand and have a positive impact on human health, agricultural yield, the environment, and more, by exploring these types of microbial dynamics.”

Helping Shah in her work are the vast computing resources available in CBCB, one the dozen-plus labs and centers in the University of Maryland Institute for Advanced Computer Studies (UMIACS).

“I use UMIACS’ computational resources extensively,” she says. “It’s practically impossible to run and test our algorithms and ideas for large-scale study samples on our [desktop] computers. So being able to quickly migrate workloads to the large-scale UMIACS data center lets me quickly make informed decisions about the capabilities of our sampling methods.”

Shah says that prior to coming to the University of Maryland, she had very little experience with computational biology. As an undergraduate majoring in information technology at the Veermata Jijabai Technological Institute in Mumbai, she studied computer science theory. When it came time to apply to graduate school, Shah searched for something that would be a “good mix” of both theory and application.

The cutting-edge research in metagenomics underway in CBCB seemed to be a good pathway to explore, she says.

At Maryland, Shah is working closely with her adviser, Mihai Pop, a professor of computer science who has a joint appointment in UMIACS.

Pop, an expert in metagenomics, says that Shah has made tremendous progress in her research over the past year, publishing her initial results in the recent Workshop on Algorithms in Bioinformatics (WABI 2017) held in Boston.

“We are already using the new approaches she has developed to study microbial communities from the guts of children from the developing world, as well as to study the impact of brain injury on the gastrointestinal track of mice,” Pop says. “Nidhi has strong technical skills, and an amazingly positive and thoughtful attitude—attributes that foretell an outstanding scientific career in graduate school and beyond.”

Although Shah doesn’t know exactly where her path will lead once her doctoral program is complete, she says that working in CBCB is not only teaching her computational biology, but is also providing the academic tools needed to become an independent researcher.

“Whatever field I end up working in, I want to be able to ask the right questions, and have the intuitive knowledge needed to answer those questions effectively,” she says. “Equally important is being able to communicate one’s research findings to the public. Working with all of the amazing research scientists, postdocs and other graduate students in CBCB is definitely helping me master these important skills.”

—Story by Melissa Brachfeld


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