The Keedy Lab


Daniel Keedy
Principal Investigator
dkeedy (at)
Scholar Citations

Daniel Keedy has been an Assistant Professor with the Structural Biology Initiative at the CUNY Advanced Science Research Center (ASRC) and the Department of Chemistry and Biochemistry at The City College of New York since January 2018. He is also affiliated with the PhD Programs in Biochemistry; Chemistry; and Molecular, Cellular, and Developmental Biology (MCD) at the CUNY Graduate Center.

Prior to his appointment, Daniel was an AP Giannini Postdoctoral Fellow in Bioengineering and Therapeutic Sciences at the University of California, San Francisco working with James Fraser. He earned his PhD in Biochemistry and Structural Biology & Biophysics from Duke University with Jane and David Richardson, after receiving his BA in Biochemistry & Molecular Biology from Rhodes College.

As principal investigator of the Keedy Lab, Daniel develops experimental and computational methods to control proteins by biasing toward specific conformations that underlie functions such as allostery, ligand binding, and catalysis. His work reveals new opportunities to modulate the activities of therapeutic targets such as protein tyrosine phosphatases with small molecules and protein engineering, and also offers insights into more general evolutionary processes that led to functional diversity in the human proteome. Daniel has received a Cottrell Scholar Award and CCNY CCAPP STEM Teacher of the Year Award.

Ali Ebrahim
Postdoctoral Research Associate
aebrahim (at)
Scholar Citations

Ali is a BSc (Hons) Biology and MPhil Biochemistry graduate of the University of Portsmouth, UK. His MPhil focused on the characterisation of cellulases involved in the production of second-generation biofuels, igniting an interest into the field of X-ray crystallography. He earned his PhD from the University of Essex, UK, in early 2020, under the co-supervision of Dr. Mike Hough from the University of Essex and Dr. Robin Owen from Diamond Light Source, UK. His research focused on the development of serial crystallography data collection and processing methods for both synchrotrons and X-ray free-electron lasers, used to analyse and exploit the effects of radiation damage in metalloproteins. Ali joined the Keedy lab as a postdoc in the spring of 2020 (though the pandemic had something to say about that…). He aims to bring his experience in crystallographic multi-dataset processing and analysis to the ASRC, in order to further unlock understanding within the field of phosphatase ligand binding, activity, and allostery.

Liliana Margent
PhD Student
lmargent (at)

Originally from Colombia, Liliana graduated with BS in Biological Engineering from National University of Colombia. Liliana moved to New York in 2016 to pursue a career in Biochemistry. In 2021, Liliana graduated with a Masters in Biochemistry from Hunter College, before joining the CUNY Biochemistry PhD Program. In 2022, she joined the Keedy Lab, where she hopes to focus her research on the study of allosteric networks of phosphatases with the use of computational tools.

Tamar (Skaist) Mehlman
PhD Student
tskaist (at)

Tamar graduated summa cum laude from Chatham University in Pittsburgh in 2016, where she received her Bachelor of Science in Biochemistry. After graduating, she worked with Dr. David Koes at the University of Pittsburgh on computational drug design for various therapeutic targets. Tamar is now pursuing her PhD in Biochemistry at CUNY. In 2018, she joined the Keedy Lab, where she is developing computational strategies to leverage multistate models of protein structures with large numbers of protein:ligand structures to design novel allosteric inhibitors for phosphatases.

Akshay Raju
Undergraduate Student
araju000 (at)

Akshay is an undergraduate Biotechnology major and Computer Science minor at the Macaulay Honors College at the City College of New York. He joined the Keedy Lab in the summer of 2022 with an interest in learning about ways to use computational analyses to answer questions in cell and molecular biology. Akshay hopes to use bioinformatics to look for hotspots of covarying amino acids in the protein tyrosine phosphatase family to help find hidden allosteric networks.

Shivani Sharma
PhD Student
ssharma (at)

Born and raised in Delhi, India, Shivani moved to the States when she was 18. She completed her Bachelor’s in Science from a small university in Maryville, Missouri and transitioned to working full time at Stowers Institute for Medical research in 2017. Later, to get a taste of industry, she found a position at Eurofins, working as a scientist in the protein chemistry team. She then completed her Masters in Biochemistry from Iowa State University in 2020, where she explored the mechanisms of activation of Pyk2 tyrosine kinase. After entering the CUNY Molecular, Cellular, and Developmental Biology (MCD) PhD Program in 2020, she joined the Keedy lab in 2021, where she is currently learning new computational approaches to complement her wet lab skill set as she seeks to answer outstanding questions about the structural biology of tyrosine phosphatases.

Kevin Shionarain
Undergraduate Student
kshiona000 (at)

Kevin is an undergraduate student at City College of New York majoring in Biochemistry. He joined the Keedy lab in Spring 2023 hoping to learn more about how protein structural dynamics are vital to protein function. He also hopes to immerse himself in research rooted in biochemistry and learn more about laboratory techniques used to study proteins. Kevin is currently working on designing chimeric proteins to better understand the specific structural building blocks of protein tyrosine phosphatases.

Nathanael Singh
Undergraduate Student
nsingh002 (at)

Nathanael is working on his Bachelor of Science degree at the City College of New York. In Spring 2022, he joined the Keedy lab as an undergraduate researcher, where he enjoys seeing the principles he learned in Biochemistry class being applied in the lab. Nathanael is involved in a few projects focused on PTP1B, ranging from small-molecule allosteric inhibition to characterizing the effects of mutations (derived from various sources) on enzyme function and structure.

Selina Sun
Undergraduate Student
ss13739 (at)

Simeng “Selina” Sun is studying for a dual Data Science and Math major at NYU, conducting a research internship here at the ASRC. She is enjoying learning how to connect her computational and quantitative skillset with exciting applications in scientific research, specifically structural biology. Her project centers on exploring how recent AI-based software tools for protein structure prediction and design can be combined to reveal new insights into protein evolvability and designability.

Virgil Woods
PhD Student
vwoods (at)
Scholar Citations

Virgil graduated from the University of Chicago in 2016 with a Bachelor of Arts in Biological Sciences and a minor in Physics. During his undergraduate studies he also performed research at the University of California, San Diego, using Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) experiments to study protein dynamics, protein-ligand interactions, and protein-protein interactions, including antibody-epitope mapping. After his undergraduate degree, Virgil worked as a Research Associate at Sorrento Therapeutics in La Jolla, CA, where he applied his HDX-MS and other protein analytics skills to new systems, before joining the CUNY Biochemistry PhD Program in 2019. In 2020, he joined the Keedy Lab, where he is using a combination of solution and crystallographic experiments to map (and exploit) interactions between ligands at different sites in the structures of phosphatase enzymes.

Past Lab Members

Elena “Helen” Orins - undergraduate student, Hunter College, 2018-19
Chrissy Schmidt - rotation student, CUNY Chemistry PhD Program, fall 2018
Abhipsa Shatarupa - rotation student, CUNY Biochemistry PhD Program, spring 2019
Sheenam Sheenam - rotation student, CUNY Biochemistry PhD Program, spring 2019
Minyoung “Lily” Kim - undergraduate student (Princeton), CSURP Program, summer 2019 (subsequently @ UCSF DDS-PhD Program)
Kristiana “Spring” Smith - undergraduate student (Rhodes College), B3 REU Program, summer 2019 (subsequently @ NYU MPH Program)
Andres Cabezas - rotation student, CUNY Biochemistry PhD Program, spring 2020
Syeda Maryam Azeem - Research Assistant, Keedy lab, 2018-2020 (subsequently @ CUNY Biology PhD Program)
Sergei Dzhumaev - undergraduate student, City College of New York, 2019-20
Ben Lesea-Pringle - rotation student, CUNY Biochemistry PhD Program, fall 2020
Augustine Onyema - rotation student, CUNY Biochemistry PhD Program, fall 2020
James Parziale - rotation student, CUNY Biochemistry PhD Program, spring 2021
Yingxian Tan - undergraduate student, City College of New York, 2020-21 (subsequently @ Hunter College Cytotechnology Program)
Julia Michalak - undergraduate student (Cornell), B3 REU Program, summer 2021
David Amoh-Boateng - rotation student, CUNY Biochemistry PhD Program, spring 2022
Tania Rajpersaud - rotation student, CUNY Biochemistry PhD Program, spring 2022
Blake Riley - postdoc, 2019-2022 (subsequently @ Replay Holdings, San Diego)
Jackson Morris - undergraduate student (Johns Hopkins), B3 REU Program, summer 2022
Sakib Hossain - undergraduate student, Hunter College, 2018-22 (subsequently @ Amazon Web Services AI)