The Keedy Lab


2023 New Year news roundup

Daniel Keedy
04 January 2023

Alright, time for an end of 2022 / start of 2023 news roundup – consider this a scientific Christmas card of sorts…

First off, Shivani and Ali’s paper on serial crystallography of PTP1B is now published at Acta Cryst Fcheck it out here!

Second, Tamar’s paper on protein:ligand interactions at room temp vs. cryo was published as a bioRxiv preprint and submitted to a journal! Watch this space for more once the peer review process runs its course…

I got the chance to talk about Tamar’s work to a relatively new-to-us crowd at the FASEB Phosphatases Conference in Palm Springs, where Ali, Virgil, and Shivani presented posters on (some of) their projects as well. It was great learning about the biology of phosphatases, meeting many folks whose papers we had read, and exploring collaboration possibilities. Virgil even won a poster prize, keeping the Keedy lab conference poster prize streak alive – congrats, Virgil!

Virgil at his *award-winning* FASEB poster!

Ali at his FASEB poster

Shivani at her FASEB poster

More personnel, academic milestones, projects, and papers coming soon… I’ve got a good feeling about 2023!

End of summer news roundup

Daniel Keedy
12 August 2022

Time for another news roundup…

First, Ali, Shivani, and I had a fantastic time at the Gordon Research Seminar and Gordon Research Conference in Diffraction Methods, which had been delayed since 2020. It was fun to get to see folks face-to-face – even if we did still have masks on most of the time. Thankfully, no COVID cases were reported. On the scientific side, everyone had something to show for themselves: Ali won a best poster prize for the GRS (congrats!) and was voted co-chair of the next GRS in 2024 (congrats!!), Shivani asked a veritable barrage of insightful and clarifying questions throughout the conference, and I (Daniel) got to show off Tamar’s work on protein:ligand crystallography at cryo vs. room temperature in a talk (paper coming soon…).

Ali in front of his prize-winning GRS poster

Shivani in front of her GRS/GRC poster

Speaking of papers: Shivani, Ali, and I managed to pull together a manuscript about our recent serial synchrotron crystallography (SSX) structure of apo PTP1B at room temperature. This one is short & sweet, and sets the stage for other exciting serial crystallography studies of PTPs in the future. Check out the preprint on bioRxiv!

Shivani, Ali, and DK celebrate submitting a paper at the GRC

Finally, Jackson finished his B3 REU program with a poster presentation in the quad between the ASRC and CDI. We’ll miss you, Jackson – and best of luck back at Hopkins!

Jackson shows off his REU research poster

DK visits Jackson's REU research poster

End of spring news roundup

Daniel Keedy
25 May 2022

A few updates as we wrap up the spring and head into summer 2022…

First, we said a tearful farewell to Blake, who is off to the world of biotech across the country at Replay Holdings, San Diego. We expect lots of great science – and hopefully game-changing therapeutics in our lifetimes. Good luck, Blake!

We also say hello to a couple of new faces. First, Liliana Margent is joining the lab as a PhD student from the CUNY Biochemistry Program. Second, Akshay Raju is joining as an Honors undergraduate research student. Welcome, y’all!

Finally, Daniel presented the lab’s research on probing allostery in tyrosine phosphatases with avant-garde methods in X-ray crystallography at the EMBO phosphatases meeting, which we plan to attend again in future years. We’re currently writing papers about several projects Daniel touched on in his talk, with additional internal and collaborative projects also brewing… We look forward to sharing with the world relatively soon!

Welcome Ali, and well done Tamar!

Daniel Keedy
05 May 2022

A couple of quick hitters today. First, after an arduous and harrowing odyssey, Ali finally arrived to the ASRC, where he will continue his work on serial crystallography and pick up other new and exciting projects. Great to see you in R3, Ali!

Second, Tamar gave a very well-received talk on the temperature-dependence of protein:ligand binding in X-ray crystallography at the New York Structural Biology Discussion Group (NYSBDG) meeting this week (held virtually this time). The Q&A gave us some excellent food for thought that will be useful as Tamar works toward finishing up her paper on this work.

Congrats Shivani, and welcome Nathanael

Daniel Keedy
16 March 2022

A couple of positive news items to report as we slowly but surely emerge from winter:

First, Shivani has been awarded a Doctoral Student Research Grant (DSRG) of $1,500 from the CUNY Graduate Center! These funds will allow her to obtain key supplies for her thesis research, and travel to a conference to report her latest findings. Congratulations!

Second, Nathanael Singh has joined the lab as an undergraduate researcher from CCNY. Nathanael will be working to characterize putative allosteric inhibitors of PTP enzymes, using a variety of experiments to assess their effects on function and struture, as well as other fun side projects… Welcome Nathanael!

Daniel receives a Cottrell Scholar Award

Daniel Keedy
08 February 2022

Daniel is honored to have received a 2022 Cottrell Scholar Award. These awards are given to early-career scientists with interests in both research and teaching, ideally with integration between the two. With funding from this award, Daniel’s lab at the ASRC will exploit new techniques in structural biology to reveal how atoms in phosphatase enzymes move during catalysis and allostery. At the same time, he will engage his undergraduate biochemistry students at CCNY with a new crowd-sourced research project in which students will design and advocate for bespoke phosphatase mutations, attend virtual field trips to the Keedy lab where the mutant proteins will be characterized, and assess the experimental data to internalize lessons about how amino acid sequence determines protein function.

For more details, check out the project description via the funding agency (RCSA) website, the ASRC press release, the CCNY press release, and the CCNY RICC article.

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