Sabina Stefan, PhD
Lee Lab

Optical coherence tomography for quantifying cortical tissue and vascular properties

• Stefan S, Kim A, Marchand PJ, Lesage F, Lee J. Deep Learning and Simulation for the Estimation of Red Blood Cell Flux With Optical Coherence Tomography. Front Neurosci. 2022 Feb 17;16:835773. doi: 10.3389/fnins.2022.835773. PMID: 35250467; PMCID: PMC8891630.
• Stefan S, Lee J. Deep learning toolbox for automated enhancement, segmentation, and graphing of cortical optical coherence tomography microangiograms. Biomed Opt Express. 2020 Nov 24;11(12):7325-7342. doi: 10.1364/BOE.405763. PMID: 33409000; PMCID: PMC7747889.
• Stefan S, Jeong KS, Polucha C, Tapinos N, Toms SA, Lee J. Determination of confocal profile and curved focal plane for OCT mapping of the attenuation coefficient. Biomed Opt Express. 2018 Oct 1;9(10):5084-5099. doi: 10.1364/BOE.9.005084. PMID: 30319923; PMCID: PMC6179411.

Sabina has been such a great person to work with and share ideas for healthy discussions. Her research involved developing computational tools to analyze cortex imaged by Optical Coherence Tomography, specializing in deep learning approaches. Her inclination to take on new challenges, passionate leadership, and skillful mentorship have been invaluable to the Lee Lab during her time at Brown. Working with Sabina has been a pleasure. She will be greatly missed. Best of luck in your next adventure!  - Jang-Hoon Lee and Joshua Assi 

 

Sean Flannery, PhD
Fleming Lab

An End-to-End Pipeline for Quantitative MRI Analysis of Ligament/Graft Healing

• Flannery SW, Walsh EG, Sanborn RM, Chrostek CA, Costa MQ, Kaushal SG, Murray MM, Fleming BC, Kiapour AM. Reproducibility and postacquisition correction methods for quantitative magnetic resonance imaging of the anterior cruciate ligament (ACL). J Orthop Res. 2022 Mar 10. doi: 10.1002/jor.25319. PMID: 35266588.
• Flannery SW, Kiapour AM, Edgar DJ, Murray MM, Beveridge JE, Fleming BC. A transfer learning approach for automatic segmentation of the surgically treated anterior cruciate ligament. J Orthop Res. 2022 Jan;40(1):277-284. doi: 10.1002/jor.24984. PMID: 33458865; PMCID: PMC8285460.
• Barnett SC, Murray MM, Flannery SW; BEAR Trial Team, Menghini D, Fleming BC, Kiapour AM, Proffen B, Sant N, Portilla G, Sanborn R, Freiberger C, Henderson R, Ecklund K, Yen YM, Kramer D, Micheli L. ACL Size, but Not Signal Intensity, Is Influenced by Sex, Body Size, and Knee Anatomy. Orthop J Sports Med. 2021 Dec 17;9(12):23259671211063836. doi: 10.1177/23259671211063836. PMID: 34988237; PMCID: PMC8721387.
• Kiapour AM, Flannery SW, Murray MM, Miller PE; BEAR Trial Team, Proffen BL, Sant N, Portilla G, Sanborn R, Freiberger C, Henderson R, Barnett S, Ecklund K, Yen YM, Kramer DE, Micheli LJ, Fleming BC. Regional Differences in Anterior Cruciate Ligament Signal Intensity After Surgical Treatment. Am J Sports Med. 2021 Dec;49(14):3833-3841. doi: 10.1177/03635465211047554. PMID: 34668789; PMCID: PMC8829819.
• Flannery SW, Kiapour AM, Edgar DJ, Murray MM, Fleming BC. Automated magnetic resonance image segmentation of the anterior cruciate ligament. J Orthop Res. 2021 Apr;39(4):831-840. doi: 10.1002/jor.24926. PMID: 33241856; PMCID: PMC8005419.

It has been a great pleasure to work with Sean over the past few years. Sean was responsible for advancing our MRI-based methods to document ligament and tendon healing using machine learning. Furthermore, he has put together these algorithms in a user-friendly package that will facilitate future research and clinical care. He is pursuing a job in industry where his expertise in big data, machine learning and imaging will clearly be an asset. Congrats and thank you Sean! – Braden Fleming, Team ACL-RI.

Sean is a mentor and friend to all. Lending a hand in a moment’s notice and continuously encouraging others to work hard to achieve their goals. He is always willing to take his time to brainstorm ideas or critically think of ways to solve problems. He has been a great leader in the lab and a driving force propelling the projects forward. We wish you the best Sean! – Dominique Barnes, Doctoral Student, Team ACL-RI.

It has been wonderful to work with and get to know Sean over the past five years. I have always admired Sean's strong work ethic, ingenuity, and steadfast pursuit of excellence—qualities that are evident in thenew MRI-based methods that Sean has developed during his time in the Department of Orthopaedic Research. I am excited to see all that Sean will accomplish and contribute to in industry. Congratulations, Sean, and best of luck with your next chapter! – Meggin Costa, Clinical Coordinator, Team ACL-RI.

I have enjoyed my time getting to know Sean over the last year or two. He has helped to make the lab a very welcoming place!  – Megan Pinette, Research Engineer, Team ACL-RI.
Working with Sean over the past few months has been very inspirational. He is able to break down and explain complex ideas for anyone to understand, and I think that is something that will take him very far. Congratulations! – Madalyn Hague, Research Engineer, Team ACL-RI.

I have truly enjoyed working with Sean as a collaborator and to see him grow into a seasoned researcher. He is very talented and an amazing team player. He has been a key member of TEAM ACL and will be missed. I have no doubt about his future success. – Ata Kiapour, Team ACL-Boston.

It has been a privilege to watch Sean’s professional growth as a young scientist and to take the rudimentary MR image analysis work I had started and mold it into a usable and clinically-translatable product. His enthusiasm to tackle big challenges and determination to see his pipeline through to completion are intangible assets that will support his future success. All the best in your next position! –Jillian Beveridge, Team ACL-RI alumna, collaborator, and external PhD examiner.

 

Cameron Baptiste, PhD
Mathiowitz Lab

Novel Methods in Polymer Drug Delivery

• Baptista, C., Azagury, A., Baker, C. M., & Mathiowitz, E. (2021). The characterization and quantification of the induced mesophases of poly-l-lactic acid. Polymer, 226, 123822.
• Baptista, C., Azagury, A., Shin, H., Baker, C. M., Ly, E., Lee, R., & Mathiowitz, E. (2020). The effect of temperature and pressure on polycaprolactone morphology. Polymer, 191, 122227.

 

Radu Darie, PhD
Borton Lab

Toward enabling new technologies for sensorimotor restoration: Analysis of primary sensory cortex during electrical stimulation of the spinal cord

• Shaaya E, Calvert J, Wallace K, Parker S, Darie R, Syed S, Fridley J, Parthasarathy G, Duclos S, Borton DA. Intraoperative Monitoring of Spinal Cord Perfusion using Ultrasound in an Ovine Model. Annu Int Conf IEEE Eng Med Biol Soc. 2021 Nov;2021:3813-3816. 
• Dastin-van Rijn EM, Provenza NR, Calvert JS, Gilron R, Allawala AB, Darie R, Syed S, Matteson E, Vogt GS, Avendano-Ortega M, Vasquez AC, Ramakrishnan N, Oswalt DN, Bijanki KR, Wilt R, Starr PA, Sheth SA, Goodman WK, Harrison MT, Borton DA. Uncovering biomarkers during therapeutic neuromodulation with PARRM: Period-based Artifact Reconstruction and Removal Method. Cell Rep Methods. 2021 Jun 21;1(2):100010. 
• Black C, Darie R, Borton D. Organic Electronics for Artificial Touch. Trends Neurosci. 2018 Sep;41(9):568-570. doi: 10.1016/j.tins.2018.07.010. 
• Darie R, Powell M, Borton D. Delivering the Sense of Touch to the Human Brain. Neuron. 2017 Feb 22;93(4):728-730. 

 

Rajeev Kant, PhD
Coulombe Lab

Patterned arteriole-scale vessels enhance engraftment, perfusion, and maturation of engineered human myocardium for heart regeneration

• Kant RJ, Bare CF, Coulombe KLK. Tissues with Patterned Vessels or Protein Release Induce Vascular Chemotaxis in an In Vitro Platform. Tissue Eng Part A. 2021 Oct;27(19-20):1290-1304. 
• Kofron CM, Kim TY, Munarin F, Soepriatna AH, Kant RJ, Mende U, Choi BR, Coulombe KLK. A predictive in vitro risk assessment platform for pro-arrhythmic toxicity using human 3D cardiac microtissues. Sci Rep. 2021 May 13;11(1):10228. 
• Munarin F, Kant RJ, Rupert CE, Khoo A, Coulombe KLK. Engineered human myocardium with local release of angiogenic proteins improves vascularization and cardiac function in injured rat hearts. Biomaterials. 2020 Apr 12;251:120033. 
• Kaiser NJ, Bellows JA, Kant RJ, Coulombe KLK. Digital Design and Automated Fabrication of Bespoke Collagen Microfiber Scaffolds. Tissue Eng Part C Methods. 2019 Nov;25(11):687-700. 
• Kaiser NJ, Kant RJ, Minor AJ, Coulombe KLK. Optimizing Blended Collagen-Fibrin Hydrogels for Cardiac Tissue Engineering with Human iPSC-derived Cardiomyocytes. ACS Biomater Sci Eng. 2019 Feb 11;5(2):887-899. 
• Kant RJ, Coulombe KLK. Integrated approaches to spatiotemporally directing angiogenesis in host and engineered tissues. Acta Biomater. 2018 Mar 15;69:42-62. 

Jeev’s research in the Coulombe Lab focused on the fabrication of patterned, endothelialized channels in engineered heart tissue to promote inosculation (connection of blood vessels between the host and implant) to improve vascularization in vivo. During his time at Brown, he has pioneered the creation of many technologies, including a bioreactor to uniformly coat channels with endothelial cells and OCT imaging in collaboration with Dr. Lee to quantify flow in blood vessels. He is a strong leader and student advocate having served on numerous committees within the Center of BME to increase graduate student and faculty engagement. Jeev is known to embrace new challenges, whether it be perfecting the art of cardiac differentiation, 3D printing new gadgets or mixing bold flavors to create delicious (and colorful) macarons, he is truly a talented, well-rounded scientist and will be missed. Congratulations Jeev! - The Coulombe Lab 

 

Theodora Myrto Perdikari, PhD
Fawzi Lab

Biophysical studies of phase separation: RNA-binding proteins at the nexus of neurodegeneration, cancer and viral infection

• Murthy AC, Tang WS, Jovic N, Janke AM, Seo DH, Perdikari TM, Mittal J, Fawzi NL. Molecular interactions contributing to FUS SYGQ LC-RGG phase separation and co-partitioning with RNA polymerase II heptads. Nat Struct Mol Biol. 2021 Nov;28(11):923-935. 
• Owen I, Yee D, Wyne H, Perdikari TM, Johnson V, Smyth J, Kortum R, Fawzi NL, Shewmaker F. The oncogenic transcription factor FUS-CHOP can undergo nuclear liquid-liquid phase separation. J Cell Sci. 2021 Sep 1;134(17):jcs258578. 
• Perdikari TM, Jovic N, Dignon GL, Kim YC, Fawzi NL, Mittal J. A predictive coarse-grained model for position-specific effects of post-translational modifications. Biophys J. 2021 Apr 6;120(7):1187-1197. 
• Ryan VH, Perdikari TM, Naik MT, Saueressig CF, Lins J, Dignon GL, Mittal J, Hart AC, Fawzi NL. Tyrosine phosphorylation regulates hnRNPA2 granule protein partitioning and reduces neurodegeneration. EMBO J. 2021 Feb 1;40(3):e105001. 
• Perdikari TM, Murthy AC, Ryan VH, Watters S, Naik MT, Fawzi NL. SARS-CoV-2 nucleocapsid protein phase-separates with RNA and with human hnRNPs. EMBO J. 2020 Dec 15;39(24):e106478. 

Myrto’s research focuses on determining the biomolecular driving forces attributed to functional biocondensate formation in oncogenic Fused in Sarcoma and SARS-CoV2 nucelocapsid protein. She has been a fantastic leader, mentor, and friend to me as I started my Ph.D. career. She was always willing to teach me new techniques and help me troubleshoot any issues–or to simply chat about science. Myrto has made significant contributions to the lab and the field at large. She will be missed, but has a bright future ahead of her! -Noah Wake

Amy Lee, PhD
Dawson Lab

Heterogeneous Epithelial Ovarian Cancer Exosomes Mediate Microenvironment Interactions Contributing to Advanced Malignancy

• Lee AH, Mejia Peña C, Dawson MR. Comparing the Secretomes of Chemorefractory and Chemoresistant Ovarian Cancer Cell Populations. Cancers (Basel). 2022 Mar 10;14(6):1418.
• Lee AH, Ghosh D, Dawson MR. Senescence-Associated Exosome Exchange Activates Myofibroblast Phenotype in Mesenchymal Stem Cells. The FASEB Journal. 2021 May 1;35.
• Lee AH, Ghosh D, Quach N, Schroeder D, Dawson MR. Ovarian Cancer Exosomes Trigger Differential Biophysical Response in Tumor-Derived Fibroblasts. Sci Rep. 2020 May 26;10(1):8686.
• Ghosh D, Mejia Pena C, Quach N, Xuan B, Lee AH, Dawson MR. Senescent mesenchymal stem cells remodel extracellular matrix driving breast cancer cells to a more-invasive phenotype. J Cell Sci. 2020 Jan 23;133(2):jcs232470.