Site Director

Adam Hall

Adam HallDr. Adam Hall is the Director of the Core Mass Spectrometry Facility within the Barnett Institute of Chemical and Biological Analysis – Department of Chemistry and Chemical Biology at Northeastern University. He received a Bachelor’s degree in Chemistry from Stonehill College, a Master’s degree in Chemistry and a PhD in Analytical Chemistry, from Northeastern University. Prior to his academic career, he was employed by the Massachusetts State Police Crime Laboratory as a forensic chemist. His expertise in forensic analytical chemistry is derived from a combination of casework experience, education, research, and consulting opportunities. Over time, the formation of strong collaborations with industry partners has helped to advance forensic research initiatives within the areas of drugs of abuse, toxicology, and ignitable liquid analysis as well as the analysis of energetic materials. Dr. Hall is a board member of the Northeastern Association of Forensic Scientists and a member of the Fire Debris and Explosives subcommittee within the Organization of Scientific Area Committees (OSAC) through the National Institute of Standards and Technology (NIST).

Faculty

Penny Beuning

Penny BeuningPenny Beuning is an Associate Professor of Chemistry and Chemical Biology at Northeastern University. She earned a B.A. in Chemistry from Macalester College in St. Paul, MN, and a Ph.D. from the University of Minnesota in the field of RNA-protein interactions and RNA biochemistry. She completed postdoctoral research at MIT focused on the protein-protein interactions that regulate cellular responses to DNA damage. Her research on DNA damage tolerance and protein engineering has been recognized with a Cottrell Scholar Award, an NSF CAREER Award, and an American Cancer Society Research Scholar Grant. Prof. Beuning has been active in efforts to enhance the recruitment and retention of groups traditionally underrepresented in the sciences. She is a leader in the Boston chapter of Graduate Women in Science, a Councilor for the American Chemical Society and is on the Scientific Advisory Committee of Research Corporation for Science Advancement.

Yun Raymond Fu

Yun Raymond FuProf. Y. Raymond Fu is an interdisciplinary Associate Professor affiliated with College of Engineering and the College of Computer and Information Science at Northeastern University. He received the Ph.D. degree in electrical and computer engineering from the University of Illinois at Urbana-Champaign. Dr. Fu’s research interests are interdisciplinary research in Machine Learning, Computational Intelligence, Data Mining, and Computer Vision. In particular, he creates machine learning algorithms to deal with data under uncertainties, such as high dimensionality, noise, multiple view, multiple modality, outliers, missing data, etc. He received seven Prestigious Young Investigator Awards from NAE, ONR, ARO, IEEE, INNS, UIUC, Grainger Foundation; and seven Best Paper Awards from IEEE, IAPR, SPIE, SIAM.

Proposed Title: Multimodal and Multimodality Data Analytics under Uncertainty

Roger Giese

roger-gieseRoger Giese is a Professor of Chemistry and Biomedical Science; Director, Environmental Cancer Research Program within the Department of Pharmaceutical Sciences, School of Pharmacy at Northeastern University. He received a B.S. from Hamline University and a Ph.D. from MIT. Professor Giese is a Diplomate of the American Board of Clinical Chemistry and specializes in Analytical Chemistry, Environmental Analysis and Mass spectrometry. The research projects in Dr. Giese’s laboratory combine aspects of analytical chemistry, organic chemistry and biochemistry to make advances in the reagents and techniques available for trace organic analysis. Emphasis is placed on the development of new methodology for high sensitivity and multi-analyte detection, applied especially to human samples. The principle detection technique being used for high sensitivity is mass spectrometry. Examples of analytes of interest are DNA adducts (damage to genes by carcinogens) and metabolites/xenobiotics (metabolomics).

Carlos Hidrovo

carlos hidrovoDr. Carlos Hidrovo is an assistant professor in the Mechanical and Industrial Engineering Department at Northeastern University. He earned his Ph.D. in Mechanical Engineering from the Massachusetts Institute of Technology in 2001. Prior to joining Northeastern, Dr. Hidrovo held professional appointments at MIT, Stanford University, and The University of Texas at Austin. He is the recipient of an NSF CAREER Award from the Fluid Dynamics program, a DARPA Young Faculty Award from the Microsystems Technology Office (MTO), and an ASME Robert T. Knapp Award. Dr. Hidrovo research interests lie at the intersection of multiscale and multiphase flow and transport phenomena, surface tension interactions in micro/nanoengineered structures, and electrokinetic ion transport in porous media for applications in energy storage, portable biochemical diagnostics, thermal management, and water treatment systems. He is also actively involved in developing novel imaging and diagnostic tools in these areas.

Alexander R. Ivanov

Alexander IvanovProfessor Ivanov is an expert in the area of mass spectrometry-based proteomic research. Prof. Ivanov earned his Ph.D. in Bioorganic Chemistry at the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Science, Moscow in 2000. He performed his postdoctoral training at Northeastern University prior to joining the Harvard School of Public Health at Harvard University, where he served as Director of the HSPH Proteomics Resource in 2003-2011. Dr. Ivanov re-joined Northeastern as Research Associate Professor at the Barnett Institute in 2011. He has been actively involved in national and international initiatives enabled under the umbrella of the ABRF to develop standards for proteomics research and standardize proteomic practices. For his work in the field of high sensitivity proteomics, Prof. Ivanov was recognized with an ASMS Research Award in 2015.

Prof. Ivanov has a long-standing interest in developing and applying analytical technologies to answer questions and generate new knowledge in biological and clinical studies. Prof. Ivanov’s current research focuses on the following areas: (1) development of techniques for ultra-high sensitivity deep proteomic profiling of limited biological samples; (2) comprehensive characterization of protein isoforms, proteoforms, and modifications (e.g. post-translational modifications, chemical modifications, sequence variants, charge variants), including detailed characterization of biopharmaceuticals; (3) analysis of proteins and protein complexes in their native non-denatured states; (4) isolation and characterization of extracellular vesicles, including circulating exosomes and microparticles, as potential sources of disease biomarkers and vehicles for targeted therapy delivery; (5) large-scale metabolomic, lipidomic, and systems biology studies of complex biological systems.

Proposed Title:
Technology Development for Ultra-High Sensitivity Deep Characterization of Proteins, Protein Complexes, and Proteomes

Carolyn W.T. Lee-Parsons

Carolyn Lee-Parsons, Associate Professor of Chemical Engineering.  Carolyn W.T. Lee-Parsons is an Associate Professor jointly appointed in the Departments of Chemical Engineering and Chemistry & Chemical Biology at Northeastern University. Prior to joining Northeastern in 1999, she was an Assistant Professor of Chemical Engineering at Rose-Hulman Institute of Technology. She received her B.S. from the University of Kansas and her Ph.D. from Cornell University. Her research interests are in biochemical engineering, specifically the production of pharmaceutical compounds and biofuels from plant tissue cultures and microalgae cultures.

Research interests: The research vision of her laboratory is

  1. to enhance the production of valuable, biologically active compounds (i.e. anti-cancer, anti-infectives, and anti-microbials) from plant cell and tissue cultures to meet the need for critical plant-derived pharmaceuticals or therapies and
  2. to improve the oil productivity of microalgae to provide a secure, renewable, and environmentally sustainable source of biofuels.

Towards that vision, my research investigates bottlenecks to production and elucidates fundamental mechanisms underlying the regulation of biosynthesis. Using this fundamental knowledge, we apply genetic engineering and bioprocess engineering strategies to increase the production of these valuable metabolites in a reproducible and scalable tissue culture system.

Proposed Title: Engineering the Biosynthesis of Medicinal Natural Products from Plant Cell Cultures

Mary Jo Ondrechen

Enzyme ResearchersMary Jo Ondrechen‘s expertise is in the areas of theoretical chemistry, computational biology, and bioinformatics. She received the ACS-certified Bachelor’s degree in Chemistry from Reed College and the Ph.D. degree in Chemistry and Chemical Physics from Northwestern University in Illinois. After postdoctoral research appointments at the University of Chicago and at Tel-Aviv University in Israel, the latter as a NATO Postdoctoral Fellow, she joined the faculty at Northeastern University in Boston, Massachusetts. Currently she serves as Professor of Chemistry and Chemical Biology. She is the Principal Investigator of the Computational Biology Research Group at Northeastern University. Her research deals with understanding enzyme catalysis, genomics, predicting the function of proteins, protein design, and the computational aspects of drug discovery.

Olga Vitek

olga vitekProfessor Vitek was named the Sy and Laurie Sternberg Interdisciplinary Associate Professor at Northeastern University, and University Faculty Scholar at Purdue University. While at Purdue, she was recognized with an Outstanding Assistant Professor Teaching Award, a Graduate Student Mentoring Award, and a Teaching for Tomorrow Award. She is a recipient of the National Science Foundation CAREER Award. She serves on the Board of Directors of the US Human Proteome Organization.

She holds a BS degree from the University of Geneva, Switzerland, and a MS in Mathematical Statistics and a PhD in Statistics from Purdue University. She interned at Eli Lilly & Company in Indianapolis and held a position of post-doctoral associate in the Aebersold Lab at the Institute for Systems Biology in Seattle. Between 2006-2014 she was an assistant professor, and then an associate professor with tenure at Purdue University, with a joint appointment in the Department of Statistics and Department of Computer Science. In the summer of 2014 she joined Northeastern University, with a joint appointment in the College of Science and the College of Computer and Information Science.

Professor Olga Vitek’s group develops statistical and computational methods for systems-wide molecular investigations of biological organisms. The group works with high-throughput large-scale investigations in quantitative genomics, proteomics, metabolomics and ionomics, which rely on mass spectrometry and other complementary technologies to characterize the components of the biological systems, their functional interactions, and their relevance to disease. The research goal is to provide statistical and computational methods and open-source software for design of these experiments, and for accurate and objective interpretation of the resulting large and complex datasets. The methods build on the insight that the biological systems, and their large-scale measurements, contain redundancy. We therefore use measurements known to share sources of variation in single or multiple datasets, or discover these groups empirically from the data, to best represent their stochastic structure. The software, typically based on the environment R, introduces novel design features that ensure the scalability and the reproducibility of the results.

Zhaohui Sunny Zhou

Zhaohui Sunny ZhouProfessor Sunny Zhou’s laboratory (a.k.a. SunnyLand) has an abiding interest in protein chemistry and modifications, including methylation, crosslinking, isoaspartic acid (asparagine deamidation) and others involved in aging and stress. One major focus is to devise analytical methodologies that combine chemo-enzymatic approaches with instrumental analysis. Moreover, my group strives to devise robust and practical techniques, so they can tackle complex and complicated biological problems and clinical challenges. For instance, our methyltransferase activity assays have been used all over the world, patented and commercialized. Last but not least, we have successfully teamed up with chemists, biologists and physicians alike, on and off campus in both academic institutions and industrial companies; this experience will ensure that the ongoing multidisciplinary collaboration will be productive and fruitful.

Project Summary: All proteins are subjected to myriad modifications. In particular, their combinations (i.e., codes or markers) are highly specific to their biological context. Moreover, the modifications are also dynamic in response to both internal and external factors. For example, deamidations of asparagine and glutamine residues are time-dependent, so have been used to date biological samples. Another example is recombinant proteins (such as growth hormones) often bear modifications that are unique to their production cells—and importantly—are different than those endogenous to humans, thereby providing telltale signs on non-human origin. All together, patterns of protein modifications can serve as highly specific and informative markers for a broad range of applications, such as forensic analysis and tracing.