People

The Current OEP Team:

Former OEP Team Members:

From the research community:

 

Alexander G. Shearer (PI)

Coming from a mixed background in both computational and bench biology, Alex searches for opportunities to solve the orphan enzyme problem through hybrid approaches that draw on both areas of research. His current focus is on tapping the wealth of data collected in the project’s first phase to predict candidate sequences for orphan enzymes. The hypothesis is that prediction followed by lab testing will prove far more cost- and effort-effective than trying to redo old purification protocols.

Alex comes to the project from Clover Collective.

Find Alex’s papers via PubMed
Alex’s LinkedIn
Alex’s personal website

 

Tomer Altman

Tomer generated the original list of orphan EC activities, wrapping in data from all the major sequence databases. Tomer has also developed additional data-checking mechanisms for the list of collected orphans that coincidentally caught over a hundred large-scale, systematic errors in several major genome sequence annotations. He is an author of our paper describing the combined literature, patent, and database search that netted us over 270 orphan sequences.

Tomer is currently a grad student in the Biomedical Informatics program at Stanford.

Find Tomer’s papers via PubMed

 

Sunil Ojha

Sunil focuses on the purification and assay of orphan enzymes, and on the relationship between sequence and enzyme function. He led our previous to purify orphans using modernized versions of older protocols. Sunil’s current project focus is on applying computational methods linking sequence with function to the goal of predicting candidate sequences for orphan enzymes.

Sunil is senior research scientist in the DuBois lab at Montana State University.

Find Sunil’s papers via PubMed

 

Christine Rhee

Christine’s work includes designing and developing new ways to drive sequence identification of orphan enzymes. She is researching novel approaches to identify sequences for orphans based on the data collected in the literature, patent and database search and on publicly available genomes. Christine was a key developer of the new “best practices” procedure we recommend in our paper on finding sequences for over 270 orphan enzymes.

Christine also created, designed and developed the OEP website.

Christine is a researcher and designer at Clover Collective.

Christine’s LinkedIn

 

Alexander Yakunin

Alexander is the group leader of the Enzyme Genomics group at the Center for Structural Proteomics in Toronto (SPiT). In our upcoming research, Alexander’s group will be applying an array of generalized and specific enzyme assays to candidate proteins that we predict to catalyze orphan enzyme activities.

Alexander leads the Enzyme Genomics Group at the University of Toronto.

Find Alexander’s papers via PubMed

 

Former team members

 

Martha Bomar

Martha was a postdoctoral fellow who worked on the purification and assay of several orphan enzymes.

Martha is now at Merck.

 

Amit K. Galande

Amit led the mass spec sequencing of orphan enzymes as the final stage in orphan identification from our lab efforts and community collaborations.

 

Anamika Kothari

Anamika Kothari is a biocurator who reviewed several hundred orphan enzymes as part of the literature, patent and database search portion of the project.

Anamika is a Scientific Database Curator at SRI International.

 

Jennifer K. Miller

Jennifer worked on modernizing older purification and assay methods for orphan enzymes to speed their identification. Jennifer’s extensive troubleshooting efforts in this area pointed out the need to take an alternate approach to make the goal of OEP truly achievable.

Jennifer presented about the experimental work on finding sequences for orphan enzymes at Experimental Biology 2011 in Washington, D.C.

 

Christian Ngo

Christian was an undergrad researcher who reviewed hundreds of orphan enzymes as part of the literature, patent and database search portion of the project.

 

Kevin Ramkissoon

Kevin was a postdoctoral fellow who took the lead in the laboratory identification of three distinct orphan enzymes (see our Publications page for the paper describing this research.

Kevin is now a postdoc in the Systems Biology Group at NHLBI.

 

Shahrzad Zarafshar

Shahrzad was an undergrad researcher who reviewed hundreds of orphan enzymes as part of the literature, patent and database search portion of the project.

She is now a production lead at Heartflow.

 

From the research community:

 

Kristian B. Axelsen from Swiss-Prot

Kristian provided tremendously valuable reviews of our draft data about “resolved” orphans – those cases where we thought we’d found the sequence for an orphan enzyme. Kristian’s enzyme expertise helped us clarify our data to truly reflect what information we have (or haven’t) found about each orphan activity.