Data Science Specialist Michael Franklin to Lead Computer Science at UChicago

Michael Franklin UChicagoThe University of Chicago announced today that prominent data science scholar Michael Franklin will chair its Department of Computer Science and serve as senior advisor to the provost on computation and data science.

Franklin will provide leadership for a major expansion in faculty, education programs, and scientific directions of the computer science department, building upon ongoing UChicago data science projects, and the expanding research area of data science among the University’s affiliated institutions, including the MBL.

Research at the MBL depends increasingly on the generation of large amounts of data of many different types, ranging from to imaging, to genome sequences, to longitudinal environmental surveys.  As such, one of the key areas of strategic focus at the MBL is the use of cutting-edge imaging and computation to illuminate cellular function and previously unknown biology.

“We are delighted with the appointment of Professor Franklin and look forward to engaging him fully in the work of the MBL,” said Jonathan Gitlin, Director of the Division of Research at the MBL. “His appointment will greatly enrich our ongoing partnerships in computational sciences with UChicago and Argonne National Laboratory that are vital to our collective research vision.”

Read UChicago announcement

MBL Celebration of Discovery to Focus on Research and Education Partnerships and Opportunities

Whale Course Among UChicago-MBL Programs to be Held in Woods Hole

whale-and-calfThe first undergraduate course cultivated from the UChicago-partnership is set for the Fall of 2015.  Twelve UChicago undergraduates will spend the 10 weeks at the MBL for “The Whale: Biology, Culture and Evolution on Nantucket Sound,” a four course program that targets undergraduate, non-science majors interested in the maritime culture and entwined histories of whales and America.

Students will be exposed to New England maritime history and culture, and provided a comprehensive overview of biology that includes evolution, environmental science, biodiversity, physiology, and cell and developmental biology.

The lead instructors will be Karl Matlin, University of Chicago Professor of Surgery, teaching “Experimental Biology by the Sea,” Michael Rossi, University of Chicago Assistant Professor of the History of Medicine teaching, “Whales, Whaling, and American History,” and Robert Richards, University of Chicago Distinguished Professor in History of Science and Medicine teaching, “Darwin’s The Origin of Species and The Descent of Man.”

Guest lecturers include Mitch Sogin, MBL Distinguished Scientist and Professor in Molecular Biology, Cell and Biochemistry at Brown University, and Nathaniel Philbrick, noted author of In the Heart of the Sea and other works on whaling and the maritime history of New England.

The program will run from September 25 to November 25, 2015.

A “Quantitative Biology Boot Camp” targeted for all incoming graduate students from all programs in UChicago’s Biological Sciences Division is also scheduled for September 2015 at the MBL.

Co-directed by Stefano Allesina, an Assistant Professor, UChicago Department of Ecology & Evolution and Stephanie Palmer, an Assistant Professor, UChicago Department of Organismal Biology and Anatomy, the course will provide students with a working knowledge of computational and statistical approaches through their application to analysis of real world data sets.  Organizers also hope to foster future MBL-UChicago collaborations by exposing students to the full range of MBL’s research opportunities and resources .

The program will run from September 5 to 11, 2015.

In late August, 12 students from the University of Chicago Lab Schools will spend a week at the MBL engaged in intense biology experiences that both enhance and relate to the current High School curriculum. Experiences will include a trip on the MBL’s R/V Gemma to collect samples and gather data on the local marine intertidal ecosystem, visits to the salt marshes to study restoration ecology, learning about and utilizing cutting-edge microscopes made exclusively available to the MBL community as well as a community service project.

The program will run from August 23– August 30.

UChicago Metcalf Students to Conduct Summer Research at MBL the summer of 2015, twelve undergraduates from the University of Chicago will gain substantive, project-based professional research experience at the Marine Biological Laboratory through the MBL/Jeff Metcalf Summer for Undergraduate Research Fellows program (SURF). The goal of the SURF Program is to introduce students to scientific research under the guidance and direction of MBL’s leading scientists.

“The Metcalf SURF Program represents the best of the MBL/UC partnership as it reflects the enthusiasm of both institutions for research and educational advancement,” says Beth Simmons, MBL-University of Chicago Assistant Director for Education Programs.

Reflective of the program’s past success, this year saw an increase in the number of applications from first to fourth-year students whom expressed interest in a variety of research areas including medicine, developmental biology, genetic diseases, neurology and immunology, oceanography, and ecology.

The twelve-week program encourages students to initiate a project proposal which couples the student with an MBL faculty scientist whose expertise mirrors the student’s research interests and career goals. Each advising scientist mentors and guides the student toward successful project completion. Student experiences vary with each discipline, providing both hands-on field and laboratory-based training in an effort to allow a comprehensive research experience.

The Program is enriched by weekly lunch-seminars with MBL faculty, networking opportunities with other undergraduates on campus, evening lectures, and a variety of cultural and social activities throughout the summer. Additional professional development series workshops are also offered to assist in navigating career and graduate school admissions processes.

SURF students culminate their experience with an undergraduate student symposium through which they have the opportunity to present their projects to their peers and the MBL community prior to submission of a final paper detailing the project, its goals and related successes.

The 2015 Metcalf SURF students are:

Ruby An
“Optimizing the Performance of an Algae-to-Methane Coupled Bioreactor System Through Experimental and Modeling Approaches”
Mentors:  Zoe Cardon /Joe Vallino, Ecosystems Center

Caroline Owens  
“Atmospheric Delivery of Nitrogen to Ecosystem as a Stimulant of Harmful Algal Blooms (HABs)”
Mentor: Ivan Valiela, Ecosystems Center

Petra Byl    
“Microbial Influence on the Transformation of Ferrous and Ferric Iron in Siders Pond”
Mentors: Julie Huber, Bay Paul Center / Joe Vallino, Ecosystems Center

Clara Kao
“Zebrafish Cytoskeleton Architecture: Actin Filaments and Reconstruction”
Mentor: Jonathan Gitlin, Bell Center

Eva Kinnebrew    
Impact of Soil Nitrogen Levels on Species Diversity in Northeastern Grasslands and the Role of Grazing in Mediating the Nitrogen-Diversity Relationship”
Mentor: Chris Neill, Ecosystems Center

Corey Okinaka  
“Visual Function in Pupil Shape in Skates”
Mentor: Lydia Mathger, Bell Center

Leonard Shaw    
“Phosphorous Phase Associations as Indicators for Particle Cycling in the Water Column”
Mentor: Maureen Conte, Ecosystems Center

Hanna Weller    
“Shifting Perspectives: Quantifying Color Camouflage by Flounder in the Eyes of Different Predators”
Mentor: Roger Hanlon, Bell Center

Yangtian Yi
“Parkinson Disease Synoptic Nerves in Lamprey”
Mentor: Jennifer Morgan, Bell Center

Irene Zhang  
“Lifestyles and Hosts of Unknown Acidophilic Legionella  in the Rio Tinto”
Mentor: Linda Zettler, Bay Paul Center

MBL Announces New Recipients of MBL-UChicago-Argonne Collaboration Awards

mbl-uc-argonne.award.recipients.15The Marine Biological Laboratory (MBL) has announced new recipients of the MBL-UChicago-Argonne Collaboration Awards.

These awards support innovative scientific collaborations among faculty at the MBL and UChicago/Argonne, in service of laying the foundation for long-term interactions between the institutions. Teams of at least one UChicago/Argonne and one MBL resident scientist are eligible to receive the awards. The following projects were awarded:

“Structural investigations of a protein-primed reverse transcriptase”

Irina Arkhipova, Bay Paul Center, and collaborator Phoebe Rice, Department of Biochemistry & Molecular Biology, University of Chicago

“Color visual perception: advancing sensory ecology with innovative neural modeling and hyperspectral imaging”
Roger Hanlon, Bell Center, and collaborators Stephanie Palmer and Mark Westneat, Department of Organismal Biology and Anatomy, University of Chicago

“The molecular evolution of a neuron”
Jennifer Morgan, Bell Center, and collaborators Melina Hale, Department of Organismal Biology and Anatomy, University of Chicago, and Jeramiah Smith, Biology Department, University of Kentucky

“Can biodiversity and ecological function be restored to the residential landscape? A MBL-University of Chicago-Nature Conservancy workshop to develop science for testing the efficacy of backyard management”
Christopher Neill, Ecosystems Center, and collaborators Charles Catlett, Urban Center for Computation and Data, University of Chicago; Andrew Chien, Department of Computer Science, University of Chicago; and Tom Chase, The Nature Conservancy

UChicago and MBL Announce Recipients of Lillie Awards for Collaborative Research

research.awardees.feature.imgMBL, WOODS HOLE, MA—The University of Chicago and the Marine Biological Laboratory (MBL) have announced the 2015 recipients of the Frank R. Lillie Research Innovation Awards.

The grant program honors Frank R. Lillie, the early 20th-century embryologist who served as the MBL’s second director and as chair of UChicago’s Department of Zoology. Awards are open to collaborators from the MBL and the University of Chicago or Argonne National Laboratory.

A. Murat Eren and Eugene B. Chang will build an open-source software platform to investigate the intricate role of microbial communities in human digestive diseases.

A. Murat Eren and Eugene B. Chang will build an open-source software platform to investigate the intricate role of microbial communities in human digestive diseases.

The grants bring together interdisciplinary teams of scientists for a project that represents a new collaborative area of inquiry for the investigators. The goal is to stimulate “blue sky” thinking that has the potential to lead to significant external funding with a consortium of collaborators working together on a big problem.

One Lillie Award was given to MBL Assistant Research Scientist, A. Murat Eren and Eugene B. Chang, a Professor of Medicine at the University of Chicago, who will build a high-performance, open-source software platform to study metagenomics, a powerful tool that is used to analyze the genetic material of microbial communities extracted directly from the environment. Once built, the researchers plan to use the software to investigate the intricate role of microbial communities in human digestive diseases.

Another grant was awarded to MBL Associate Scientist Jianwu Tang and Yuki Hamada, an Associate Biophysical Remote Sensing Scientist at Argonne National Laboratory, who will develop a novel approach to measure plant photosynthesis and other ecosystem functions that can be used to quantify the impacts of environmental change on ecosystems and agricultural systems.

Jianwu Tang, Tomomi Tani, and Yuki Hamada (left to right) will develop a novel approach to measure plant photosynthesis and other ecosystem functions that can be used to quantify the impacts of environmental change on ecosystems and agricultural systems.

Jianwu Tang, Tomomi Tani, and Yuki Hamada (left to right) will develop a novel approach to measure plant photosynthesis and other ecosystem functions that can be used to quantify the impacts of environmental change on ecosystems and agricultural systems.

“The Lillie Awards are important to support and stimulate new collaborations between the MBL and the University of Chicago,” said MBL President and Director Huntington Willard. “The two projects that have been awarded have great potential for impacting both the science and its implications for the world we live in. This program is even more far-reaching, since it catalyzes interactions between our campuses at many different levels, which will have numerous payoffs down the line.”

Eren, a computer scientist by training, builds novel algorithms to make sense of complex datasets. As part of the MBL’s Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, he recently developed oligotyping, a computational method that can help microbial ecologists investigate closely related bacterial groups with unprecedented sensitivity. At the University of Chicago, Chang leads a research program that aims to elucidate the role of microbial communities in the development and progression of human digestive diseases.

Eren and Chang’s project will contribute to the fields of microbiology and microbial ecology by tackling processing and visualization challenges that currently prevent researchers from having full control of their metagenomic data. Their software platform has the potential to transform how scientists interpret metagenomic data, which may have tremendous long-term implications on our understanding of the microbial world.

Understanding the response of natural ecosystems, agriculture, and urban ecosystems to the changing environment is critically important to guide sustainable development and protect the human environment. However, the ability to measure complex ecosystem functions (such as photosynthesis, respiration, water uptake, and nutrient cycling) and understand their processes on an ecosystem scale is limited.

Tang and Hamada’s project will address these challenges by building on Tang’s work in the MBL’s Ecosystems Center and developing a novel system to automatically measure plant fluorescence and its link to photosynthesis. This system will be integrated with Hamada’s work collecting ecosystem function data using Argonne’s EcoSpec tower-based hyperspectral remote sensing system, which explores the power of optical information to predict the dynamics of ecosystem functions. The team will further refine their approach by adding pixel-based fluorescence data and tapping the skills of MBL Associate Scientist Tomomi Tani who has been working on instrument development of fluorescent imaging for studying sub-cellular dynamics in living cells. Tang and Hamada expect their project to have a broad impact on the field in ecology, environmental science, agricultural science, remote sensing, and global change research.

The Lillie Awards will support up to two years of pilot research for a total of $125,000 per award. Recipients will be able to develop their projects over a period including two or three successive summers, working in residence as a team at the MBL, in addition to continued progress on the project during the traditional academic years in between MBL visits.

A complete list of 2015 Lillie Award recipients and their teams is listed below.

“Post-assembly metagenomics pipeline for comparative analysis of microbial populations”
Principal Investigators:
A. Murat Eren, Assistant Research Scientist, Marine Biological Laboratory
Eugene B. Chang, Professor, University of Chicago

“Using chlorophyll fluorescence and other hyperspectral reflectance signatures to investigate plant photosynthesis and other ecosystem functions”
Principal Investigators:
Jianwu Tang, Associate Scientist, Marine Biological Laboratory
Yuki Hamada, Associate Scientist, Argonne National Laboratory
Tomomi Tani, Associate Scientist Marine Biological Laboratory



The Marine Biological Laboratory (MBL) is dedicated to scientific discovery and improving the human condition through research and education in biology, biomedicine, and environmental science. Founded in Woods Hole, Massachusetts, in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.


UChicago Innovation Fund Now Accepting Applications for Spring 2015


Fund Open to Resident MBL Faculty

The University of Chicago has built an array of programs to create an entrepreneurial ecosystem that can help researchers navigate the path toward commercialization and overcome the hurdles to attracting investment. These programs include the Chicago Innovation Exchange, The New Venture Challenge, accelerator and incubator programs, and the University of Chicago Innovation Fund.

About the Innovation Fund
The Innovation Fund is a philanthropic proof-of-concept fund created to support the evolution of your ideas into products and services. The Fund has now been expanded to $20 million dollars and is open to current UChicago and affiliated lab faculty, staff, and students with technologies in a wide variety of industries.

Applications are due via electronic submission by Thursday, March 12th.

Apply Now!

The Innovation Fund is intended to provide proof-of-concept funding for technologies / concepts which:

  • are submitted by a current University of Chicago Principal Investigator, student, affiliate (including national labs), or their representative,
  • possess the potential to have a substantial commercial impact but are too early to attract commercial investment,
  • and cannot be funded through existing granting mechanisms.

It is not intended to fund research / activities that are not directly driving towards an externally validated business outcome.

If you have any questions, contact Jason Pariso, The Director of Operations (, or Wolfgang Connell, Chicago Innovation Exchange Program Manager (

— The Innovation Fund Team



New Assistant Director for Education Programs Appointed

Beth-Simmons-HeadshotBeth Simmons has been appointed Assistant Director for Education Programs. In this newly created role, Simmons will serve as an education science and program liaison between the MBL and the University of Chicago. She will work closely with both institutions’ staff and scientists to support and enable the offering of new programs in light of the MBL’s current education portfolio and commitments.

Among Simmons’ responsibilities will be to ensure new affiliation education programs run smoothly, deliver a consistently high quality educational experience to participants, and support the well-being of students. She will report directly to Dr. Neil Shubin, Senior Advisor to the President and Robert R. Bensley Distinguished Service Professor of Anatomy, University of Chicago and will be working closely with William Reznikoff, MBL Director for Education and his team. Simmons will be located in Woods Hole. Her office will be alongside MBL’s Education department.

Simmons brings a wealth of education programming experience to this role. She was previously the Education & Outreach Coordinator for the National Science Foundation’s Palmer Long Term Ecological Research (LTER) Station, the Lead Primary Investigator for the LTER Education Digital Library Project, and has been an education consultant to Woods Hole Oceanographic Institution’s Ocean Carbon & Biogeochemistry Project. Earlier in her career Simmons served as an oceanography and biology teacher in various high schools in the New England and Southern California areas.

MBL Announces First Recipients of MBL-UChicago/Argonne Collaboration Award

The Marine Biological Laboratory (MBL) has announced the first recipients of the MBL-UChicago/Argonne Collaboration Awards.

These awards support innovative scientific collaborations among faculty at the MBL and UChicago/Argonne, in service of laying the foundation for long-term interactions between the institutions. Teams of at least one UChicago/Argonne and one MBL resident scientist are eligible to receive the awards. The following projects were awarded:

“High-Resolution Microbiome Informatics”— A. Murat Eren, Bay Paul Center, MBL, and collaborator Jack Gilbert, Department of Ecology & Evolution, University of Chicago, will work with co-investigators Jessica Mark Welch and Mitchell Sogin of the Bay Paul Center; Andrew Chien, Department of Computer Science, University of Chicago; and Eugene Chang, Department of Medicine, University of Chicago.

“Cytoskeletal Adaptation During Suspended Animation”Shalin Mehta, Cellular Dynamics Program, MBL and collaborator Patrick La Rivière, Department of Radiology, University of Chicago, will work with co-investigators Hari Shroff, National Institute of Biomedical Imaging and Bioengineering, and Jonathan Gitlin, Bell Center, MBL.

“Developing a Pan-Arctic Ecosystem Respiration Model”Edward Rastetter, Ecosystems Center, MBL, and collaborator Julie Jastrow, Biosciences Division, Argonne National Laboratory, will work with co-investigator Susan Natali, Woods Hole Research Center.

A second round of awards will be announced in December 2014.

New Internships Allow Eight UChicago Undergrads to Spend Summer at Marine Biological Laboratory

Dianna Douglas, University of Chicago


ight UChicago undergraduates will spend their summer at the MBL as research interns through the Metcalf program.

Eight UChicago undergraduates will spend their summer at the MBL as research interns through the Metcalf program.

Eight students in the College will spend their summer as research interns at the Marine Biological Laboratory in Massachusetts, marking a new phase in the affiliation between the lab and the University of Chicago that will allow students to pursue significant scientific projects.

“The student interns will make invaluable contributions this summer, while gaining important contacts and resources to navigate the complex process of finding a career path,” said John W. Boyer, dean of the College. “The Marine Biological Laboratory internships are an example of the faculty and laboratory collaborations that can help our students succeed in many careers.”

Funding for the internship comes through a partnership between the MBL and the College, and the interns will be part of UChicago’s Metcalf internship program in Career Advancement. Each student will live in or near the MBL campus in Woods Hole, Mass., a village on Cape Cod that attracts world-renowned scientists for intense, transformative research and advanced courses in a range of biological subjects. The MBL’s summer courses are famous for creating a distinctive environment of collaboration among instructors and students, often working with the latest technology to address research questions.

“It is a fantastic opportunity. We’re going to have a lot of exposure to the scientists, and will understand more things that are happening in the field,” said Medha Biswas, a second-year biology student, who will be part of the first group of interns. She visited the MBL during a Career Advancement trek over spring break.

This summer she will work on live imaging of synaptic proteins in the laboratory of William Green, professor of neuroscience at UChicago and a visiting fellow at the MBL.

While the MBL has hosted many scholars from UChicago during its summer programs, this is the first time that a formal internship program will bring a group of students to Woods Hole.

“Scientific discovery moves forward when bright, young, curious minds are given the opportunity to explore without limits. These outstanding undergraduates are the perfect connection of real intellectual capital between our two great institutions and I have every anticipation of extraordinary accomplishments,” said Jonathan Gitlin, deputy director for research and programs at MBL.

Biswas said she is excited by the opportunity for these inaugural interns to show what UChicago students are capable of contributing at the MBL. The other interns—Rachel Folz, Shaunae Alex, Clara Kao, Lyda Harris, Para Mehta, Caroline Owens and Andrea Rummel—will work on projects as varied as suspended animation in zebrafish and the sedimentary layers of the salt marsh ecosystem.

Each of the student interns identified a faculty member at the MBL whose area of study intersected with their own work. They wrote proposals to the faculty members, explaining a research project that they hoped to pursue in collaboration with the laboratory scientists.

“We look forward to the energy and scholarship that the Chicago students will bring to our summer programs, and to seeing the results of the research and discoveries that will come out of their work,” said Joel Smith, a biologist at the MBL who has worked closely on bringing the UChicago interns to the lab this summer. The MBL’s renowned summer programs attract more than 1,700 scientists and advanced students from around the world.

The MBL interns will be part of the College’s largest group of Metcalf interns. More than 1,000 undergraduates will travel around the world through UChicago’s paid internship program to gain on-the-job skills and explore career opportunities this year.