NCEMS working groups to answer molecular and cellular bioscience questions
The U.S. National Science Foundation National Synthesis Center for Emergence in the Molecular and Cellular Sciences at Penn State aims to drive multidisciplinary collaboration utilizing publicly available research data.
The U.S. National Science Foundation (NSF) National Synthesis Center for Emergence in the Molecular and Cellular Sciences (NCEMS) at Penn State recently formed 10 initial working groups, according to Justin Petucci, NCEMS associate director. The groups will conduct research in accordance with open science principles, producing peer-reviewed articles, public datasets, reproducible workflows and other forms of openly shared knowledge to advance molecular sciences.
The working groups, which span 43 institutions across 18 states — including Washington, D.C. — and six countries, are supported with NCEMS resources for up to two years. After the two years, working groups will pursue external funding and leverage their novel research findings into long-term research opportunities.
The working groups were selected from an open request for proposals focused on fundamental research questions in the molecular and cellular biosciences to drive multidisciplinary collaboration and produce publicly available derivative data products.
“Our goals as a center are increasing broad data use and data re-use, as well as integrating diverse datasets and theories to gain deeper insights about emergent properties that could lead to fundamental discoveries such as identifying new protein interactions that influence cellular function, support environmental adaptation and enable advances in areas like bioengineering, agriculture and synthetic biology,” said Petucci, Penn State Institute for Computational and Data Sciences (ICDS) Research Innovations with Scientists and Engineers (RISE) artificial intelligence and machine learning team lead and Penn State Clinical and Translational Scientific Institute informatics core scientist.
NCEMS will provide the cohort of 87 researchers, comprised of faculty principal investigators, postdoctoral scholars and graduate students with access to staff scientist time and support, computational resources, data storage, research project management, publication and travel costs.
"I'm most excited by the new connections across disciplines that NCEMS has catalyzed. Most working groups bring together researchers from different fields who haven't collaborated before, which highlights how NCEMS is lowering barriers to enable boundary-crossing synthesis research,” said Daniel Nissley, NCEMS chief science officer and ICDS RISE bioinformatician and computational biologist.
Each working group will convene at Penn State for their first meeting and continue their work at their home institutions with regular virtual meetings. The project leads will also participate in leadership training to refine the skills needed to guide the groups.
“These groups are working on community-scale problems that aren’t something a typical lab has the capacity or diverse expertise to take on,” Petucci said, explaining that community-scale problems require a team science approach to reuse diverse and publicly available datasets to gain insights into unanswered scientific questions. “It really takes a community effort to come together and make discoveries.”
The working groups are:
Transposable Elements and the Emergence of Genomic Innovation
Project leads: Shaun Mahony, associate professor of biochemistry and molecular biology at Penn State; and Miriam Konkel, assistant professor in the Department of Genetics and Biochemistry at Clemson University
Energetic Origins of Connectivity Within Protein Interaction Networks
Project leads: Jonathan Schlebach, associate professor in the Department of Biochemistry at Purdue University; Shahid Mukhtar, professor in the Department of Genetics and Biochemistry at Clemson University; and Adrian Serohijos, associate professor at the University of Montreal
Intelligent Metadata Compilation to Enhance Synthesis of Mass Spectrometry-Based Proteomics
Project Leads: Wout Bittremieux, assistant professor at the University of Antwerp in Belgium; Iddo Friedberg, associate professor in the Department of Veterinary Microbiology and Preventative Medicine at Iowa State University; and Shomir Wilson, associate professor in the College of Information Sciences and Technology at Penn State
Discovering New Protein-Protein Interactions Within Crosslinking Mass Spectrometry Data
Project Leads: Stephen Fried, assistant professor in the Department of Chemistry at Johns Hopkins University; Yasset Perez-Riverol, proteomics team coordinator at the European Bioinformatics Institute in Cambridge, United Kingdom; and Henning Hermjakob, head of molecular systems at the European Bioinformatics Institute
Identifying the Molecular Origins of Heat Resistance in Plants
Project Leads: Andrei Smertenko, associate professor in the Department of Molecular Plant Sciences at Washington State University; Carolyn Rasmussen, associate professor in the Department of Botany and Plant Sciences at University of California, Riverside; Dawn Nagel, associate professor of genetics and genomics at University of California, Riverside; Georgia Drakakaki, professor in the Department of Plant Sciences at University of California, Davis; and Stephen Ficklin, professor in the Department of Horticulture, Washington State University
Oceans of Disorder: Elucidating the Role of Disordered Proteins in Cellular Adaptation
Project Leads: Keren Lasker, assistant professor in the Department of Integrative Structural and Computational Biology at Scripps Research; Jerelle Joseph, assistant professor of chemical and biological engineering at Princeton University; and Alex Holehouse, assistant professor in the Department of Biochemistry and Molecular Biophysics at Washington State University School of Medicine
Mapping Bacterial Cell States Across Environments and Evolution
Project Leads: Jeffrey Barrick, professor in the Department of Molecular Biosciences and Benjamin Clayton Centennial Professor in Biochemistry at the University of Texas at Austin, co-lead and technical liaison; and Jeremy Schmit, ancillary associate professor in the Department of Biochemistry and Molecular Biophysics, co-lead in data interpretation
The Epigenetic Drivers of Neurodegenerative Processes in Human Brain Cells
Project Leads: Bin Zhang, associate professor of chemistry at the Massachusetts Institute of Technology; Longzhi Tan, assistant professor of neurobiology at Stanford University; Tamar Schlick, professor of chemistry, mathematics and computer science at New York University; Dave Thirumalai, professor in the Department of Chemistry at the University of Texas at Austin; and Justin Whalley, assistant professor at Rosalind Franklin University of Medicine and Science
Data-Driven Discovery of Regulatory Mechanisms and Cellular Resource Allocation via Multi-Modal Data Integration
Project Leads: Elizabeth Brunk, assistant professor of pharmacology and of chemistry at University of NorthCarolina School of Medicine; Ferhat Ay, associate professor at the La Jolla Institute for Immunology and associate adjunct professor in the Department of Pediatrics at the University of California, San Diego; Vasant Honavar, Dorothy Foehr Huck and J. Lloyd Huck Chair in biomedical data sciences and artificial intelligence and professor of data sciences at Penn State; William Noble, professor in the Departments of Genome Sciences and Computer Science and Engineering at the University of Washington; and Hyebin Song, assistant professor of statistics at Penn State
Protein Misfolding, Mutations and the Emergence of Disease Phenotypes
Project Leads: Hyebin Song, assistant professor of statistics at Penn State; and James Stephenson, lead data scientist at the European Bioinformatics Institute in Cambridge, United Kingdom
“We expect the diverse perspectives of the researchers will lead to transformative discoveries. It’s exciting research that we are bringing together,” said Ed O’Brien, NCEMS director, ICDS co-hire and professor of chemistry in the Eberly College of Science.
NCEMS is supported by the NSF, as well as ICDS and the Huck Institutes of the Life Sciences, both at Penn State.
To find a full list of the working groups’ projects, visit the NCEMS website.