The Keedy Lab


Yingxian's artwork is featured on campus

Daniel Keedy
19 September 2021

Yingxian Tan recently completed her stay in the Keedy lab after two semesters of computational research as an undergraduate during the pandemic, then one partial summer in the wet lab after graduation. Although we unfortunately didn’t manage any photos before she moved on to her graduate program, Yingxian’s artistic representation of protein tyrosine phosphatase active-site loops was selected for display right at the entrance to Marshak, the main science building at CCNY (see below)… Good luck, Yingxian!

Julia completes her summer program

Daniel Keedy
08 August 2021

Julia Michalak, an undergraduate student in the B3 REU summer program, finished her project focused on structurally characterizing a new(-to-us) phosphatase, culminating in an outdoor poster session. She worked with Blake over the course of the summer, including a couple of remote synchrotron X-ray diffraction data collection sessions. Good luck this coming academic year, Julia!

More photos here.

Virgil passes his qualifying exam

Daniel Keedy
04 June 2021

Virgil Woods passed his second level exam (i.e. qualifying exam) on Friday! He made a dramatic entrance to the post-exam party, with a thunderstorm looming behind him… Congratulations, Virgil – we’re excited about the next few years of science!

The dramatic entrance of the returning champion, with a looming thunderstorm in the background

We huddled next to the building to avoid the impending rain, lightning, and hail... then abandoned ship and moved inside

Homemade carrot cake, with flower decorations on top made from real carrot shavings

Spring 2021 news roundup

Daniel Keedy
23 April 2021

Unsurprisingly, there was a long gap between news posts… but that just means there are lots of good things to discuss now!

First of all, on the personnel front: Shivani Sharma, a PhD student with CUNY Molecular, Cellular, and Developmental Biology (MCD), has joined the lab. We are excited to give her a warm welcome in person sooner than later!

Also, Sakib has started a new and exciting job with OpenTrons – manufacturers of the OT-2 robot we have here at the ASRC SBI. He’s had the rewarding opportunity to work on their Pandemic Response Lab to help NYC trace and combat the COVID-19 pandemic. (Thankfully for us, he remains affiliated with the Keedy lab on a limited basis.)

In addition, this summer we look forward to welcoming a new undergraduate researcher, Julia Michalak, from the CCNY B3 REU Program. Fortunately, due to declining COVID cases and continuing vaccinations in NYC and elsewhere, all signs point to in-person research activities in our wet lab (with the proper safety precautions, of course), which will feel nice. Welcome, Julia!

Beyond the personnel updates, we’ve had good news on the publications front. Blake’s qFit 3 paper was accepted to Protein Science. And we submitted Ali and Blake’s joint SARS-CoV-2 Mpro multitemperature paper! Huge thanks to the beamline scientists at NSLS-II FMX for their help with remote experiments during the pandemic. Ali and Blake even managed to secure consecutive PDB codes for a dozen structures – good reason to celebrate!

In terms of awards, Tamar has been on a tear: she won both a CUNY Graduate Center Dissertation Year Fellowship and a D.E. Shaw Research Graduate & Postdoc Women’s Fellowship. I struggle to think of a more deserving recipient for these competitive awards. They will nicely complement the upcoming papers in her near-term future… Congrats, Tamar!

Looking ahead, Virgil is broadening our lab’s horizons by bringing hydrogen-deuterium exchange mass spectrometry (HDX-MS) into the mix. This is a powerful solution experiment that will open many doors for Virgil’s thesis work – which he will defend at his scheduled second level (or “qualifying”) exam next month. In addition, we are eager to analyze the reams of X-ray diffraction data we have collected recently for various PTPs in various conditions across several remote synchrotron trips (“to” FMX and NYX at NSLS-II, and FlexX at MacCHESS). So: more good things coming down the pike.

I won’t promise how long it’ll be until the next news post – but keep checking!

End of summer 2020 update

Daniel Keedy
22 September 2020

It’s been a while since the last post! (I have a feeling this won’t be the last time that happens…) Let’s attempt to fill in some gaps in the timeline:

Since my last post, the COVID-19 pandemic hit. Our wet lab was shut down for months, and we shifted toward data analysis, planning future experiments, and computational projects. Thankfully we’re now back in action in a careful, socially distanced mode. Despite the challenges of the moment, we’ve managed to see each other in person from time to time:

One of those occasions was when Maryam finished her >2 year tenure with us! :cry: (See photo below – including social-distancing-friendly elbow bumps.) But she’s going on to bigger and better things with the CUNY Molecular, Cellular, and Developmental Biology (MCD) PhD Program. We’ll miss you, Maryam – but at least you won’t be too far away!

On the flip side, we’ve had some fantastic new additions to the lab. First up: Virgil Woods, a new PhD student from the CUNY Biochemistry PhD Program. Second: Yingxian Tan, an undergraduate student from The City College of New York. You can read more about both over on our Members page. Welcome, Virgil and Yingxian!

We are also very excited to begin working with Dr. Ali Ebrahim, currently at Diamond Light Source, on some avant-garde new crystallographic experiments – more to come on our projects together quite soon…

On the science side: in October, Daniel gave a “virtual” talk on our (ongoing!) efforts to develop allosteric small-molecule modulators of PTP1B at the American Chemical Society national meeting. Thanks to our collaborators at Atomwise, you can view it here.

Finally, the lab has published its first multi-author paper on which Daniel is a corresponding author, initially as a bioRxiv preprint but with a peer-reviewed journal article to come soon. Blake did an admirable job shaping this up and getting it out to the world. Check out qFit 3 on GitHub and try it yourself!

We have several other interesting stories cooking right now – so stay tuned for more in the not-too-distant future…

Tamar passes her qualifying exam

Daniel Keedy
14 August 2019

Tamar Skaist passed her second level exam (i.e. qualifying exam) today – the day before her birthday, by the way. Double celebration! Congrats, PhD candidate Tamar!

Happy birthday AND congrats on passing, Tamar!

End of summer 2019 update

Daniel Keedy
08 August 2019

A lot has happened in the Keedy Lab in the last few months…

First of all, I’m excited to report that the lab has been awarded an NIH MIRA (R35) grant, which will provide funding for 5 years! With this support from the NIH, we can continue our work to develop new methods in multistate X-ray crystallography and elucidate allosteric mechanisms in phosphatases.

Relatedly, we are hiring for multiple positions in the lab. Email Dr. Keedy and apply by clicking this link if you are interested in a postdoc position.

Finally, two excellent undergraduates have finished their summer research in the lab: Kristiana “Spring” Smith with the B^3 REU Program (from my alma mater Rhodes College!) and Minyoung “Lily” Kim with the CSURP Program, both of whom worked with Maryam Azeem as a mentor here. We wish them both the best as they return to college for the fall, and beyond!

DK, Spring Smith, and Maryam Azeem in August 2019

DK, Lily Kim, and Maryam Azeem in August 2019

Welcome to the Keedy Lab website!

Daniel Keedy
02 June 2019

Hello, world! This is the first post from the Keedy Lab. Only 1+ year late!

We’ve gotten off to an amazing start in that time. See below for a photo of the lab during the 2018 holiday season.

Looking forward to what the rest of 2019 and beyond have to bring! Watch this space…

Finally, if you are interested in a postdoc position in the lab, please apply by clicking this link.

… and email Dr. Keedy to discuss!

the Keedy Lab in December 2018