Richard Quintana Feliciano, PhD

nature.com/articles/s4146… Our paper is out in Nat. Commun.! 🎉 An amazing collab between the Aggarwal, Fang, Filizola, and Shapiro labs. We show a mechanism of #DNAbinding wherein each monomer of M.BceJIV #methyltransferase helps to recognize two #DNAs! #epigenetics #methylation

@AyaOsman @ualbany Congratulations, Aya! Lots of blessings and success always! 😊

Official announcement: this September 1, the Osman laboratory will be opening its doors in the biological sciences department at SUNY, Albany! Anyone interested in joining the lab, please contact me. aosman@albany.edu Lab website coming soon! @ualbany

Amazing work by Dr. Rechkoblit et al. from the Aggarwal and @gangfang_1 Labs on CBASS Cap5 endonuclease showing bacterial self-destruction by digesting its own DNA! Congratulations! 👏 #bacteria #cbass #cap5 #proteinstructure #immunology #virology nature.com/articles/s4146…

Would you like to discover low-efficacy ligands or biased ligands for GPCRs? Our fine-tuned deep learning models using transfer learning and protein language processing make it possible! | bioRxiv biorxiv.org/content/10.110…

Glad to share our preprint 🏃**LongTrack**: long read metagenomics-based precise tracking of bacterial strains (and their genomic changes!) after fecal microbiota transplantation. A 4+ years journey and tour de force by ** @fanyu48696214 ** and team. A long 🧵 💩Fecal microbiota transplantation (FMT) has revolutionized the treatment of recurrent Clostridioides difficile infection (rCDI) and is being evaluated across other diseases, including inflammatory bowel disease (IBD) and cancer immunotherapy. Accurate tracking of bacterial strains, the functional units of the microbiota, that stably engraft in recipients is critical for understanding the determinants of strain engraftment, evaluating their correlation with clinical outcomes, and guiding the development of therapeutic bacterial cocktails. Several previous FMT strain tracking studies, powered by metagenomic shotgun sequencing, have provided valuable insights. These studies relied on short-read sequencing, which faces challenges in strain-level de novo metagenomic assembly, especially when multiple strains co-exist in a single microbiome sample, which is very common in a FMT setting. Comprehensive bacterial isolation effectively addressed this challenge: once the genomes of individual bacterial isolates from donor and pre-FMT recipient samples are assembled (high-purity and high-completeness), downstream tracking (post-FMT) can be reliably achieved based on the unique k-mers of each strain using short-read metagenomic sequencing even with modest-to-low depth. However, it is hard (labor intensive and time consuming) to perform comprehensive bacterial culture for large FMT cohorts. In this context, long-read metagenomic sequencing could empower bacterial strain tracking in FMT with efficiency and scalability. Specifically, long-read sequencing is much more effective at de novo genome assembly, constructing metagenome-assembled genomes (MAGs) at strain resolution. However, how to reliably use long-read MAGs for strain tracking?? This is not trivial because long read MAGs are not always 100% complete, which needs to be handled carefully to ensure precise strain tracking. This motivated us to develop a new framework, **LongTrack**, that uses tailored informatics to overcome some unique challenges in order to reliably use long-read MAGs for precision strain tracking. For rigorous evaluation of LongTrack, we built upon a recent study by @ jeremiahfaith1’s team that conducted a systematic culture of bacterial strains from FMT donors and recipients for rCDI with 5-year follow-ups, which serve as a reliable, complex and realistic ground truth. We systematically evaluated LongTrack in comparison with short-read MAGs and alternative methods and observed superior performance of LongTrack over short-read based approaches, especially in distinguishing co-existing bacterial strains within a microbiome sample for reliable FMT strain tracking. We applied LongTrack to four FMT cases for rCDI patients and two FMT cases for IBD patients to demonstrate the reliability and scalability of LongTrack. Next, we wondered **how stable** are the genomes of the engrafted strains (before vs. after FMT)? We asked this question to expand beyond the standard scope of strain tracking building on the FMT cohort with longitudinal sample collections across five years! Quantitative analysis building on the unique advantage of long reads for reliable strain-level mapping uncovered complex structural genomic variations and epigenetic variations (DNA methylation) within the same strains that differ between donor and post-FMT samples. These in-depth genomic and epigenomic analyses suggest the versatile capacity of individual strains during FMT and long-term adaptation. Combined, this study introduces **LongTrack**, a novel framework that advocates the incorporation of long-read sequencing to improve the tracking of bacterial strains and their genomic dynamics in future FMT studies, paving the way towards better understanding FMT and the development of more effective defined therapeutic bacterial cocktails! Superb work by @fanyu48696214 over the past 4+ years! Also thanks to lab members and collaborators, especially Mi Ni, Varun Aggarwala, Edward Mead, @MagdalenaKsi, and importantly, the great collaboration with @jeremiahfaith1 lab!, and also thanks to @grinsa01 and @NOKaakoush! Preprint link: LongTrack: long read metagenomics-based precise tracking of bacterial strains and their genomic changes after fecal microbiota transplantation biorxiv.org/content/10.110…

We are proud to partner with @IcahnMountSinai to offer a joint Ph.D. program in health sciences engineering. Beginning in the fall semester of 2025, the program will focus on reparative and regenerative medicine, immunoengineering, and neuroengineering. bit.ly/3CD2mB3

Check out this amazing resource! High quality illustrations for free! bioart.niaid.nih.gov HT @LuciaScience

Paper of the week: Our new @PsychopharmEBPS paper, led by Jennifer Bossert, on the effect of nociceptin receptor partial agonist & antagonist on heroin relapse in our rat model of opioid maintenance. Neither drug mimicked buprenorphine effect in the model pubmed.ncbi.nlm.nih.gov/39269500/

Paper of the week: Our collaborative study with Yihong Yang's imaging lab, published in @npp_journal (first author: Zilu Ma), on the role of the dorsal striatum in incubation of opioid craving after voluntary abstinence in rats pubmed.ncbi.nlm.nih.gov/39300270/

Very important read!

We are pleased to share a collaboration of the Aggarwal, Fang, @filizolalab1, and Shapiro Labs publication in @NatureComms! nature.com/articles/s4146…

@KailashBP10 @jitheshkottur @rikhiag @gangfang_1 @martafilizola @filizolalab1 @NatureComms @DPS_ISMMS @SinaiGenetics @IcahnMountSinai @GradSchoolSinai Thanks, Kailash! 😊

@richardsp621 @jitheshkottur @rikhiag @gangfang_1 @martafilizola @filizolalab1 @NatureComms @DPS_ISMMS @SinaiGenetics @IcahnMountSinai @GradSchoolSinai Congratulations! Great work!

nature.com/articles/s4146… Our paper is out in Nat. Commun.! 🎉 An amazing collab between the Aggarwal, Fang, Filizola, and Shapiro labs. We show a mechanism of #DNAbinding wherein each monomer of M.BceJIV #methyltransferase helps to recognize two #DNAs! #epigenetics #methylation

@SinaiBrain @MountSinaiAlum Thank you very much! 😊🎉

Congratulations @richardsp621!🎉✨ @MountSinaiAlum

@martafilizola @GradSchoolSinai @filizolalab1 Thank you very much, Marta! It was a pleasure to interact and work with you and your lab members. Your feedback during our committee meetings was very helpful throughout my PhD and I’m very thankful for that. 😊 I hope to visit in the near future!

AND an amazing accomplishment by another talented, newly minted PhD graduate from @GradSchoolSinai, who just started as Assistant Professor of Biology at Kennesaw State University. Double congrats, Richard! @filizolalab1 was thrilled to collaborate with you and the others.

@FreddysonJ @jitheshkottur @rikhiag @gangfang_1 @martafilizola @filizolalab1 @NatureComms @DPS_ISMMS @SinaiGenetics @IcahnMountSinai @GradSchoolSinai 🕺🎉😊

@richardsp621 @jitheshkottur @rikhiag @gangfang_1 @martafilizola @filizolalab1 @NatureComms @DPS_ISMMS @SinaiGenetics @IcahnMountSinai @GradSchoolSinai Eso! 🎉

@ovanoekelen @jitheshkottur @rikhiag @gangfang_1 @martafilizola @filizolalab1 @NatureComms @DPS_ISMMS @SinaiGenetics @IcahnMountSinai @GradSchoolSinai Thanks, Oliver!!

@richardsp621 @jitheshkottur @rikhiag @gangfang_1 @martafilizola @filizolalab1 @NatureComms @DPS_ISMMS @SinaiGenetics @IcahnMountSinai @GradSchoolSinai Congrats!

@ANeurogirl @jitheshkottur @rikhiag @gangfang_1 @martafilizola @filizolalab1 @NatureComms @DPS_ISMMS @SinaiGenetics @IcahnMountSinai @GradSchoolSinai Thank you, Ashley! 😊

@richardsp621 @jitheshkottur @rikhiag @gangfang_1 @martafilizola @filizolalab1 @NatureComms @DPS_ISMMS @SinaiGenetics @IcahnMountSinai @GradSchoolSinai Congrats Richard!! 👏🏽🤗

So excited to have my first project in the @DrChristineAnnD lab finally online! doi.org/10.1101/2024.0…! Tl;dr: we made an R software package for scalable mapping and (most importantly) analysis and visualization of 𝘮𝘶𝘭𝘵𝘪𝘱𝘭𝘦 brain-wide ensembles.

First Reaction with colleague @WackerLab "Can Targeting the Sodium Site via Water Molecules Lead to the Development of Safer Opioids?" @sushmajumdarlab , we hope you'll enjoy reading our opinion | ACS Central Science pubs.acs.org/doi/10.1021/ac…