Mary Jo Ondrechen

Ondrechen received an American Chemical Society certified bachelor's degree in chemistry from Reed College, Portland, Oregon, in 1974. She pursued doctoral studies in chemistry and chemical physics at Northwestern University, Evanston, Illinois, and earned the Ph.D. degree in 1978 under the direction of Mark A. Ratner.{{cite web|url=http://chemgroups.northwestern.edu/ratner/|title=Ratner Group – Home of the Ratner Research Group|website=chemgroups.northwestern.edu}} 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 in 1980.Pollastri, M.P. [http://www.northeastern.edu/cos/chemistry/faculty-4/] (2017)

Her earlier research achievements include the design of molecules and materials with desirable spectroscopic and conductive properties, prediction of electric field effects in molecules and proteins, the optimization of energy conversion devices, and the design and characterization of ionic conductor materials for rechargeable batteries. Her current research activities include modeling of biological macromoleculesFinley, A., [http://www.sdsc.edu/pub/envision/v15.4/ondrechen.html Investigating Enzyme-Substrate Interactions with Vitamin B6]. (1999). and predictive calculations for functional genomics.

She co-developed THEMATICS[https://www.sciencedaily.com/releases/2001/10/011030225809.htm Protein Function Predicted With New "THEMATICS" Method Developed By Northeastern University & Brandeis Scientists]. ScienceDaily, (2001).Borman, S., From sequence to consequence. Chemical and Engineering News, 79(48): p. 31-33 (2001).Ball, P., [http://www.nature.com/news/2001/011019/full/news011025-1.html Computers spot shape clues]. Nature, (2001). (Theoretical Microscopic Anomalous Titration Curve Shapes), a computational predictor of functional information about proteins from their three-dimensional structure alone. THEMATICS predicts catalytic and binding sites in proteins with high sensitivity and good selectivity. A unique feature of THEMATICS is that it requires neither sequence nor structural comparisons and hence applies to novel folds, orphan sequences, and also to engineered polypeptide systems.

She is also the co-developer, with Wenxu Tong and Ronald J. Williams, of a machine learning technology called Partial Order Optimum Likelihood (POOL).{{Cite journal|last1=Tong|first1=Wenxu|last2=Wei|first2=Ying|last3=Murga|first3=Leonel F.|last4=Ondrechen|first4=Mary Jo|last5=Williams|first5=Ronald J.|date=2009-01-16|title=Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties|url= |journal=PLOS Computational Biology|volume=5|issue=1|pages=e1000266|doi=10.1371/journal.pcbi.1000266|pmid=19148270|pmc=2612599|bibcode=2009PLSCB...5E0266T|issn=1553-7358 |doi-access=free }}{{Cite journal|last1=Somarowthu|first1=Srinivas|last2=Yang|first2=Huyuan|last3=Hildebrand|first3=David G. C.|last4=Ondrechen|first4=Mary Jo|date=2011-06-01|title=High-performance prediction of functional residues in proteins with machine learning and computed input features|journal=Biopolymers|volume=95|issue=6|pages=390–400|doi=10.1002/bip.21589|issn=0006-3525|pmid=21254002}} POOL is a monotonicity-constrained maximum likelihood method for the prediction of properties that depend monotonically on the input features. This method, coupled with THEMATICS input features, is a top-performing active site predictor for protein structures.{{cn|date=March 2025}}

These methods are also being used for the successful annotation of structural genomics proteins, i.e. for the discovery of the function of gene products whose function is currently unknown. Her Structurally Aligned Local Sites of Activity (SALSA) method uses local sets of amino acid residues that are computationally predicted to be active in catalysis to identify the biochemical function of enzyme structures of unknown function.

These computational methods are also currently used to understand how enzymes affect catalysis.{{Cite journal|last1=Ondrechen|first1=Mary Jo|last2=Clifton|first2=James G.|last3=Ringe|first3=Dagmar|date=2001-10-23|title=THEMATICS: A simple computational predictor of enzyme function from structure|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=98|issue=22|pages=12473–12478|doi=10.1073/pnas.211436698|issn=0027-8424|pmc=60078|pmid=11606719|bibcode=2001PNAS...9812473O|doi-access=free}} Ondrechen has emphasized and developed the concept of spatially extended enzyme active sites, and that the participation of amino acids, even if they are distant from the site of the catalyzed reaction, may be predicted with a relatively simple calculation.Herring, A., [http://phys.org/news/2012-04-function-enzyme.html Form and function in enzyme activity]. (2012).

Her research group has also developed computational methods to improve the design of artificial enzymes.{{cn|date=March 2025}}

In 2020 Ondrechen's research group added a new project to characterize the proteins of SARS-CoV-2, the virus that causes COVID-19, and to seek interventions to disrupt the viral life cycle https://www.metrowestdailynews.com/news/20200501/hopkinton-resident-receives-national-science-foundation-grant-to-study-coronavirus Hopkinton resident receives National Science Foundation grant to study coronavirus.https://news.northeastern.edu/2020/05/15/the-coronavirus-might-have-hidden-weak-spots-machine-learning-could-help-find-them/ The coronavirus might have hidden weak spots. Machine learning could help find them.

Ondrechen is a community leader and activist. She has recently served on the board of advisors of the Washington, D.C.–based Interstate Technology and Regulatory Council (ITRC), representing the interests of community and tribal stakeholders.Willett, A., [http://www.itrcweb.org/Documents/2012_ITRC_Board_of_Advisors1.pdf] (2012) She is the former president of the board of directors of the North American Indian Center of Boston (NAICOB)Dunn, J., [http://www.naicob.org/about-us.html About NAICOB]. (2013). and served as chair of the board of directors of the Albuquerque, New Mexico-based American Indian Science and Engineering Society (AISES) from 2011 to 2013.EchoHawk, S., [http://www.aises.org/about/board AISES Board of Directors]. (2014). An advocate for stewardship of the Earth, she previously has served on the Conservation Commission for Hopkinton, Massachusetts, and on the Community Leaders Network of the U.S. Department of Energy. She has been active in the promotion of innovative technologies to solve environmental problems.[http://redox-tech.com/doc_download/47-itrc-chemox.html In Situ Chemical Oxidation]. (2000).[http://www.orau.org/ptp/PTP%20Library/library/Subject/Decommissioning/TRIAD-T1.pdf Technical and Regulatory Guidance for the Triad Approach: A New Paradigm for Environmental Project Management]. (2003).[https://www.scribd.com/doc/46813094/Dpt-Wells-for-Gwm-Itrc The Use of Direct Push Well Technology for Long-term Environmental Monitoring in Groundwater Investigations]. (2006). She also advocates for the inclusion of public and tribal stakeholders in environmental evaluation, decision-making, and management.

She was a speaker at the March for Science in Washington, D.C. in April 2017.{{cite news |url=https://www.washingtonpost.com/news/speaking-of-science/wp/2017/04/20/why-scientists-are-marching-on-washington-and-more-than-400-other-cities/ |title=Why scientists are marching on Washington and more than 600 other cities |date=2017-04-21 |author1=Joel Achenbach |author2=Ben Guarino |author3=Sarah Kaplan |newspaper=The Washington Post |place=Washington, D.C. |issn=0190-8286 |oclc=1330888409}}{{Cite web|url=https://www.youtube.com/watch?v=mucx9adauQQ|title = Prof. Mary Jo Ondrechen at the March for Science|website = YouTube| date=23 April 2017 }}

She has given numerous presentations on diversity and inclusiveness in the science, technology, engineering, and mathematics (STEM) fields.Hernandez, R., [http://www.oxide.gatech.edu/ver1.0/index.html?ondrechen.html&2&bios&3 OXIDE Biography: Mary Jo Ondrechen]. (2014).[http://www.pathwaystoscience.org/profiles.aspx?ind=OndreMaryJ Pathways to Science, Mary Jo Ondrechen]. (2012).

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Category:1953 births

Category:Living people

Category:American women chemists

Category:Northeastern University faculty

Category:Reed College alumni

Category:American computational chemists

Category:American women academics

Category:21st-century Native American scientists

Category:20th-century Native American scientists