The Boss

Douglas L. Theobald

Professor and Chair
Department of Biochemistry
Brandeis University
Kosow-Wolfson 308

MS 009
415 South St
Waltham, MA 02454
(781) 736-2303

Lab 2013 with Brandeis Castle

The lab, with the lovely historic Brandeis Usen Castle in background, August 2, 2013.

Left to right: Rick Roy, Erin Devine, Brian Beckett, Joe Jacobowitz, Kristine Mackin, Jeff Boucher, Phil Steindel, Douglas Theobald.

Lab 2017 at Monadnock, NH

Beginning the White Dot trail up Mt. Monadnock, NH, June 8, 2017.

Left to right: Charles Xu, Miriam Hood, Molly Lorenz, Jacob Wirth, Rick Roy, Douglas Theobald, Christine Minor.

Lab 2018 Blue Hills hike

Lab hike at the Blue Hills, MA, July 20, 2018.

Back, left to right: Jacob Wirth, Noa Don, Chloe Morales, Mike Sennett.
Front, left to right: Douglas Theobald, Christine Minor, Nora Perlmutter.

Lab 2021 hike to Monadnock

Lab covid hike up Monadnock, NH, May 13, 2021.

Left to right: Douglas Theobald, Mike Sennett, Jonah Theobald, Brandon Black, Chris Sharma, Yerdos Ordabayev.

Lab 2022 Novemeber 20, at Purgatory Chasm, MA

Yerdos' going-away party and hike at Purgatory Chasm, MA, November 20, 2022.

Left to right: Neerja Garikipati, Tara Azam, Cris Sharma, Yerdos Ordabayev, Douglas Theobald.

Graduate students

Cris Sharma

Cris Sharma (2020)


Neerja Garikipati

Neerja Garikipati (2022)


Alex MacNeil

Alex MacNeil (2023)



Lab Alumni

Post docs

Yerdos Ordabayev

Yerdos Ordabayev (2019 – 2022)


Graduate Students

Brandon Black

Brandon Black, PhD (2019 – 2023)

Thesis: "An Evolutionary and Structural Analysis of Type I Terpene Synthases"
Committee: Dan Oprian (co-mentor, Brandeis), Timothy O. Street (Biochemistry), Isaac Krauss (Chemistry), C. Brandon Ogbunugafor (Yale University)


Michael Sennett

Michael Sennett, PhD (2018 – 2023)

Thesis: "Application and Evaluation of Probabilistic Sequence Reconstructions and Resurrections for Protein Evolution"
Committee: Timothy Street (Biochemistry), Maria-Eirini Pandeli (Biochemistry), C. Brandon Ogbunugafor (Yale University)


Tara Azam

Tara Azam (2022 – 2023)


Jacob Wirth

Jacob Wirth, PhD (2014 – 2019)

Thesis: "Functional convergence and epistasis in apicomplexan lactate dehydrogenases"
Committee: Niels Bradshaw (Biochemistry), Lizbeth Hedstrom (Biology), Jing-Ke Wang (Whitehead/MIT)

Jacob is interested in the evolution of allostery and other cryptic long-range interactions in proteins.

He now works for Double Rainbow Biosciences!

Brian Beckett

Brian C. Beckett, PhD (2013 – 2019)

Thesis: "Biophysical properties of ancestrally resurrected proteins are unbiased"
Committee: Dorothee Kern (Biochemistry), Chris Miller (Biochemistry), Greg Fournier (MIT)
2014 Graduate School of Arts and Sciences Outstanding Teaching Fellow
2012 Kukin Moskowitz Fellowship for Outstanding Graduate Student in the Medical Sciences (Brandeis)

Brian graduated from McGill in 2012 with a M.Sc. in Structural Cell Biology and in 2010 with a B.Sc. in Anatomy and Cell Biology, and Theater. He is studying protein evolution and the dynamics of strong evolutionary epistasis. He is passionate about conquering scientific apathy, the education of young scientists, and donuts.

Currently a Research Integrity Associate at University Health Network, Toronto, Canada.

Rick Roy

Rick Roy, PhD (2012 – 2017)

Thesis: "Bayesian optimization of structure-based multiple alignment and superposition"
Committee: Jeff Gelles (Biochemistry), Jané Kondev (Physics), Pengyu Hong (Computer Science)

Rick also worked on understanding the functional and structural constraints on universally conserved residues in Type I rhodopsins.

Founder of Stryx Biotech.

Erin Devine

Erin Devine, PhD (2011 – 2015)

co-mentor with Daniel D. Oprian, Brandeis University

Thesis: "Evolution of retinylidene proteins: Relocating the active-site lysine in rhodopsin"
Committee: Christopher Miller (Biochemistry), Jeff Gelles (Biochemistry), Daniel Oprian (Biochemistry), Elena Oancea (Brown University)
2013 Poster Award, Biology and Chemistry of Vision Conference, Steamboat Springs, CO
2012 Jay Pepose '75 Vision Sciences Fellowship
2012 Rose Simon Endowed Fellowship (Brandeis)

Erin studies the evolution of visual cone opsins in metazoans. She's also interested in the physical constraints on rhodopsin and GPCR structure and evolution, and the implications for discerning homology from convergence.

Erin did a post-doc with Bob Sauer at MIT.
Presently Scientist I at Bristol-Myers Squibb.


Kristine Mackin

Kristine Mackin, PhD (2010 – 2014)

Thesis: "An empirical test of convergent evolution in rhodopsins by examination of novel mutant folds."
Committee: Daniel Oprian (Biochemistry), Timo Street (Biochemistry), Don Engelman (Yale)
2013 Mechanisms of Protein Evolution II Travel Award

Kristine successfully defended her PhD, March 20, 2014.

Kristine's thesis project explored the biophysical constraints on the evolution of bacteriorhodopsin and the implications for convergence of the GPCR protein fold in rhodopsins from bacteria, arachaea, and eumetazoans.

Now making all the dollars as a Senior Business Insights Analyst at Decision Resources Group.

Phil Steindel

Phillip Steindel, PhD (2008 – 2013)

Thesis: "Structural and functional evolution of the trichomonad lactate and malate dehydrogenases."
Committee: Jeff Gelles (chair), Daniel Pomeranz Krummel, Karen Allen (Boston University)

Phil successfully defended his PhD, September 23, 2013.

Phillip Steindel was a graduate student in the Biophysics and Structural Biology program. He has a BS in Chemistry from UNC-Chapel Hill. Phil developed Bayesian and likelihood methods for analyzing macromolecular structures, in addition to the evolution of substrate specificity in parabasalid malate and lactate dehydrogenases.

Phil did a post-doc with Sean Elliott at Boston University.
He is presently a review editor at JoVE, Cambridge.

Jeff Boucher

Jeff Boucher, PhD (2008 – 2013)

Jeff successfully defended his PhD, August 7, 2013.

Thesis: "Evolution of apicomplexan lactate dehydrogenases by saltation and neofunctionalization."
Committee: Daniel Oprian (chair), Lizbeth Hedstrom, Karen Allen (Boston University)
2013 Selected Attendee — St. Jude National Graduate Student Symposium
2013 Mechanisms of Protein Evolution II Darwin-Wallace Speaker Award
2013 Mechanisms of Protein Evolution II Travel Award
2012 HHMI Interfaces Scholar Award
2011 Selected Attendee — Molecular Evolution Workshop, MBL, Woods Hole, MA

Jeff also holds a BS in Biochemistry from Worcester Polytechnic Institute, and he was a graduate student in the Biochemistry program here at Brandeis. In his former life, Jeff spent over four years slaving for biotechnology companies in the Boston area, including Pierce Biotechnology, Phylogix, and Epitome Biosystems. Jeff's PhD thesis research investigated the evolution of substrate specificity in apicomplexan malate and lactate dehydrogenases.

Jeff did a post-doc in Dan Bolon's lab at UMass Medical School, Worcester.
He now is a Senior Protein Engineer at Gingko Bioworks, Boston.


Undergraduates, Senior Theses

Karen Phuong

Karen Phuong (2022)

Nora Perlmutter

Nora Perlmutter (2018 – 2020)

BS MS (2020) Biochemistry and Chemical Biology, High Honors

2018 Provost’s Undergraduate Research Fund (Brandeis), Summer Fellowship

Christine Minor

Christine Minor (2017 – 2019)

BS (2019) Biochemistry, Chemical Biology, Mathematics minor, High honors

Presently a technical assistant with Christopher Burge at MIT.

Miriam Hood

Miriam Hood (2015 – 2018)

BS MS (2018) Biochemistry, Highest honors

2018 Professor Dagmar Ringe Biochemistry Award
2016 Division of Science Summer Undergraduate Research Fellowship (Brandeis)
2015 Provost’s Undergraduate Research Fund (Brandeis), Summer Fellowship

Presently a graduate student at UC Berkeley with Susan Marqusee.

Charles Xu

Charles Xu (2015 – 2017)

BS MS (2017) Biochemistry, High honors

Presently a medical student at Australian National University.

Michelle Fry

Michelle Y. Fry (2013 – 2015)

BS Biological Physics, BA Mathematics (2015), High honors

Michelle made a constitutive dimer from tetrameric Apicomplexan lactate dehydrogenases.

She's now a grad student at CalTech working on her PhD in Biochemistry and Molecular Biophysics with Bill Clemons.

Joe Jacobowitz

Joe Jacobowitz (2012 – 2014)

BS MS (2014) Biochemistry, Highest honors

2014 William P. Jencks Award in Biochemistry
2013 Division of Science Summer Undergraduate Research Fellowship
2013 Division of Science Prize for Outstanding Research Accomplishment

Joe helped figure out how Plasmodium falsciparum lactate dehydrogenase has such strong specificity for its substrate. He's good at crystallizing proteins, especially ancestral 2-hydroxyacid dehydrogenases.

Presently a graduate student at MIT with Jing-Ke Weng.

Mackenzie Gallegos

Mackenzie Gallegos (2009 – 2011)

and the Lab's Research Technician (2011 – 2013)

BS (2011) Biochemistry

2010 Division of Science Summer Undergraduate Research Fellowship
Mackenzie kept the world turning :(.

Mackenzie got her DVM in 2018 from Michigan State University College of Veterinary Medicine with Linda Mansfield. Now pursuing her dream as a vet!

Adam Drake

Adam Drake (2010 – 2013)

BS MS (2013) Biochemistry, Highest honors

Adam's thesis research developed better phylogenetic methods for modeling the evolution of transmembrane proteins by explicitly incorporating structural information. Adam spent the summer of 2013 in the Adirondack woods.

Presently Computational Biologist at Freenome.

Emily Chen

Emily Chen (2011 – 2013)

BS (2013) Biochemistry

Emily helped determine the crystal structures of both ancestral and modern malate/lactate dehydrogenases.

Emily presently works at Brown University in Rebecca Page's lab.

Amy Eisenberg

Amy Eisenberg (2011 – 2012)

BS (2012) Biology, Highest honors

Amy's senior thesis was on the physical requirements on the position and identity of the conserved "counterion" aspartate residue in bacteriorhodopsin, including its evolutionary implications.

She's now a graduate student in MCB at UC Berkeley with Gloria Brar.

Mark Kelly

Marcus Kelly (2009 – 2011)

BS MS (2011) Biochemistry, Highest honors

2011 William P. Jencks Award in Biochemistry

While in the lab, Mark's senior thesis involved the development of membrane protein specific substitution matrices for modeling transmembrane proteins.

In 2019 Mark defended his PhD in Cancer Biology from Stanford University with Peter K. Jackson.

Nat Lazar, Halloween 2008

Nathaniel Lazar (2008 – 2010)

BS (2010) Biochemistry, High honors

2009 Division of Science Summer Undergraduate Research Fellowship

During his tenure in the lab, Nat's thesis research involved developing structural methods for analyzing and determining rates of evolution specific to particular protein families.

Nat received his PhD in 2017 in Immunology and Microbial Pathogenesis from Cornell University with Michael S. Glickman at the Gerstner Sloan Kettering Graduate School of Biomedical Science.

Nat is now a Biology teacher at Pequannock Township High School in NJ.

High School Students

Chloe Morales

Chloe Morales (summer 2018), high school student

Currently attending Brandeis (2023)!

Noa Don

Noa Don (summer 2018), high school student


Meredith Roaten (summer 2015), high school student

Currently an Editorial Researcher at NPR.


Megan Peck (summer 2011), high school student

Currently Factory Support Team Lead at Boeing.


Marion Estelle Peyrega (summer 2008), French high school student

What is Marion doing now?


Masha Rosenberg

Masha Rosenberg (2017 – 2019), research assistant


Molly Lorenz

Molly Lorenz (2017 – 2018), research technician

Molly kept the world turning.

Marco Viera

Marco Viera (2007 – 2010), research assistant

Marco was the lab's Research Assistant from 2007 to 2010. Marco used to keep the world turning.

Marco is currently the Associate Director of Alumni Technology and External Relations at Harvard Business School.

Other Lab Minions

Katie Ferguson

Katie Ferguson (2022)

Catherine Ackley

Catherine Ackley (summer 2016), undergraduate

Catherine was a Chem-E major at Notre Dame. She spent the summer of 2014 with us, studying the tetramerization of Plasmodium falsciparum LDH.

Presently a Manufacturing Engineer II at Saint-Gobain Life Sciences.

Bojan Rajkovic

Bojan Rajkovic (2010), undergraduate

Bojan Rajkovic. The j is pronounced like a y and the c is pronounced like a tch.

Presently a Senior Software Engineering Manager at Microsoft.


Hannah Kirsch (summer 2009), undergraduate

Hannah got an MD (2014) in Neurology from New York University School of Medicine and UCSF.