MGH Center for Systems Biology

Rami A, Zhong C, Muniz M, Xie W, Khorasanchi A, Gallagher J, Mohammadi S, Fein D, Voter AF, Stoltenberg H, Gopalakrishan D, Yang Y, Ng TSC, Gafita A, Childs DS, Jacene H, Ravi P

Race and Outcomes to [¹⁷⁷Lu]Lu-PSMA-617 in Advanced Prostate Cancer.

Cancers (Basel). 2025;17(12):ePub - PMID: 40563610 - PMCID: PMC12191161 - DOI: 10.3390/cancers17121960

Ruan YC, Shum WW, Belleannée C, Da Silva N, Breton S

ATP secretion in the male reproductive tract: essential role of CFTR.

J Physiol. 2012;590(Pt 17):4209-22 - PMID: 22711960 - PMCID: PMC3473280 - DOI: 10.1113/jphysiol.2012.230581

Cheung PW, Terlouw A, Janssen SA, Brown D, Bouley R

Inhibition of non-receptor tyrosine kinase Src induces phosphoserine 256-independent aquaporin-2 membrane accumulation.

J Physiol. 2018;597(6):1627-1642 - PMID: 30488437 - PMCID: PMC6418769 - DOI: 10.1113/JP277024

Battistone MA, Merkulova M, Park YJ, Peralta MA, Gombar F, Brown D, Breton S

Unraveling purinergic regulation in the epididymis: Activation of V-ATPase-dependent acidification by luminal ATP and adenosine.

J Physiol. 2019;597(7):1957-1973 - PMID: 30746715 - PMCID: PMC6441927 - DOI: 10.1113/JP277565

Koch PD, Ahmed MS, Kohler RH, Li R, Weissleder R

Imaging of Tie2 with a fluorescently labeled small molecule affinity ligand.

ACS Chem Biol. 2019;15(1):151-157 - PMID: 31809013 - PMCID: PMC7808335 - DOI: 10.1021/acschembio.9b00724

Badr CE, da Hora CC, Kirov AB, Tabet E, Amante R, Maksoud S, Nibbs AE, Fitzsimons E, Boukhali M, Chen JW, Chiu NHL, Nakano I, Haas W, Mazitschek R, Tannous BA

Obtusaquinone is a cysteine modifying compound that targets Keap1 for degradation.

ACS Chem Biol. 2020;15(6):1445-1454 - PMID: 32338864 - PMCID: PMC7995447 - DOI: 10.1021/acschembio.0c00104

Shaw SY, Tran K, Castoreno AB, Peloquin JM, Lassen KG, Khor B, Aldrich LN, Tan PH, Graham DB, Kuballa P, Goel G, Daly MJ, Shamji AF, Schreiber SL, Xavier RJ

Selective Modulation of Autophagy, Innate Immunity, and Adaptive Immunity by Small Molecules.

ACS Chem Biol. 2013;8(12):2724-33 - PMID: 24168452 - PMCID: PMC3951132 - DOI: 10.1021/cb400352d

McLellan CA, Whitesell L, King OD, Lancaster AK, Mazitschek R, Lindquist S

Correction to Inhibiting GPI Anchor Biosynthesis in Fungi Stresses the Endoplasmic Reticulum and Enhances Immunogenicity.

ACS Chem Biol. 2012;9(4):1061 - PMID: 22724584 - DOI: 10.1021/cb300235m

Iaconelli J, Huang JH, Berkovitch SS, Chattopadhyay S, Mazitschek R, Schreiber SL, Haggarty SJ, Karmacharya R

HDAC6 Inhibitors Modulate Lys49 Acetylation and Membrane Localization of β-Catenin in Human iPSC-Derived Neuronal Cells.

ACS Chem Biol. 2015;10(3):883-90 - PMID: 25546293 - PMCID: PMC4372110 - DOI: 10.1021/cb500838r

Iaconelli J, Lalonde J, Watmuff B, Liu B, Mazitschek R, Haggarty SJ, Karmacharya R

Lysine Deacetylation by HDAC6 Regulates the Kinase Activity of AKT in Human Neural Progenitor Cells.

ACS Chem Biol. 2017;12(8):2139-2148 - PMID: 28628306 - PMCID: PMC6747705 - DOI: 10.1021/acschembio.6b01014

Moy TI, Conery AL, Larkins-Ford J, Wu G, Mazitschek R, Casadei G, Lewis K, Carpenter AE, Ausubel FM

High-Throughput Screen for Novel Antimicrobials using a Whole Animal Infection Model.

ACS Chem Biol. 2009;4(7):527-33 - PMID: 19572548 - PMCID: PMC2745594 - DOI: 10.1021/cb900084v

McLellan CA, Whitesell L, King OD, Lancaster AK, Mazitschek R, Lindquist S

Inhibiting GPI Anchor Biosynthesis in Fungi Stresses the Endoplasmic Reticulum and Enhances Immunogenicity.

ACS Chem Biol. 2012;7(9):1520-8 - PMID: 22724584 - DOI: 10.1021/cb300235m

Pittet MJ, Nahrendorf M, Swirski FK

The journey from stem cell to macrophage.

Ann N Y Acad Sci. 2014;1319(1):1-18 - PMID: 24673186 - PMCID: PMC4074243 - DOI: 10.1111/nyas.12393

Srinivasulu V, Srikanth G, Khanfar MA, Abu-Yousef IA, Majdalawieh AF, Mazitschek R, Setty SC, Sebastian A, Al-Tel TH

Stereodivergent Complexity-to-Diversity Strategy en Route to the Synthesis of Nature-Inspired Skeleta.

J Org Chem. 2022;87(2):1377-1397 - PMID: 35014258 - DOI: 10.1021/acs.joc.1c02698

Bhaumik J, Weissleder R, McCarthy JR

Synthesis and Photophysical Properties of Sulfonamidophenyl Porphyrins as Models for Activatable Photosensitizers.

J Org Chem. 2009;74(16):5894-901 - PMID: 19610602 - PMCID: PMC2888918 - DOI: 10.1021/jo900832y

Brueckner C, Ogikubo J, McCarthy JR, Akhigbe J, Hyland MA, Daddario P, Worlinsky JL, Zeller M, Engle JT, Ziegler CJ, Ranaghan MJ, Sandberg MN, Birge RR

meso-Arylporpholactones and their Reduction Products.

J Org Chem. 2012;77(15):6480-94 - PMID: 22734444 - PMCID: PMC3411881 - DOI: 10.1021/jo300963m

Bogdanov AA, Lin CP, Kang HW

Optical imaging of the adoptive transfer of human endothelial cells in mice using anti-human CD31 monoclonal antibody.

Pharmacol Res. 2007;24:1186-92 - PMID: 17373582 - PMCID: PMC2795329 - DOI: 10.1007/s11095-006-9219-7

Kim KM, Cambria RP, Isselbacher EM, Baker JN, LaMuraglia GM, Stone JR, MacGillivray TE

Contemporary Surgical Approaches and Outcomes in Adults With Kommerell Diverticulum.

Ann Thorac Surg. 2014;98(4):1347-1354 - PMID: 25134861 - DOI: 10.1016/j.athoracsur.2014.05.045

Heng E, Stone JR, Kim JB, Lee H, MacGillivray TE, Sundt TM

Comparative Histology of Aortic Dilatation Associated With Bileaflet Versus Trileaflet Aortic Valves.

Ann Thorac Surg. 2015;100(6):2095-2101 - PMID: 26338050 - DOI: 10.1016/j.athoracsur.2015.05.105

Roedl JB, Harisinghani MG, Colen RR, Fischman AJ, Blake MA, Mathisen DJ, Mueller PR

Assessment of treatment response and recurrence in esophageal carcinoma based on tumor length and standardized uptake value on positron emission tomography-computed tomography.

Ann Thorac Surg. 2008;86:1131-8 - PMID: 18805147 - DOI: 10.1016/j.athoracsur.2008.05.019

Raghu VK, Moonsamy P, Sundt TM, Ong CS, Singh S, Cheng A, Hou M, Denning L, Gleason TG, Aguirre AD, Lu MT

Deep learning to predict mortality after cardiothoracic surgery using preoperative chest radiographs.

Ann Thorac Surg. 2022;115(1):257-264 - PMID: 35609650 - PMCID: PMC11373441 - DOI: 10.1016/j.athoracsur.2022.04.056

Fagbami L, Deik AA, Herman JD, Singh K, Santos SA, Bopp S, Lukens AK, Clish CB, Wirth DF, Mazitschek R

The adaptive proline response in P. falciparum is independent of PfeIK1 and eIF2α signaling.

ACS Infect Dis. 2019;5(4):515-520 - PMID: 30773881 - PMCID: PMC6747701 - DOI: 10.1021/acsinfecdis.8b00363

Michot C, Le Goff C, Mahaut C, Afenjar A, Brooks AS, Campeau PM, Destree A, Di Rocco M, Donnai D, Hennekam R, Heron D, Jacquemont S, Kannu P, Lin AE, Manouvrier-Hanu S, Mansour S, Marlin S, McGowan R, Murphy H, Raas-Rothschild A, Rio M, Simon M, Stolte-Dijkstra I, Stone JR, Sznajer Y, Tolmie J, Touraine R, van den Ende J, Van der Aa N, van Essen T, Verloes A, Munnich A, Cormier-Daire V

Myhre and LAPS syndromes: clinical and molecular review of 32 patients.

Eur J Hum Genet. 2014;22(11):1272-7 - PMID: 24424121 - PMCID: PMC4200423 - DOI: 10.1038/ejhg.2013.288

Rao SM, Auger JL, Gaillard P, Weissleder R, Wada E, Torres R, Kojima M, Benoist C, Mathis D, Binstadt BA

The neuropeptide neuromedin U promotes autoantibody-mediated arthritis.

Arthritis Res Ther. 2012;14(1):R29 - PMID: 22314006 - PMCID: PMC3392824 - DOI: 10.1186/ar3732

Chen WT, Mahmood U, Weissleder R, Tung CH

Arthritis imaging using a near-infrared fluorescence folate-targeted probe

Arthritis Res Ther. 2005;7:R310-R317 - PMID: 15743478 - PMCID: PMC1065321 - DOI: 10.1186/ar1483

Lee S, Vinegoni C, Sebas M, Weissleder R

Automated motion artifact removal for intravital microscopy, without a priori information.

Sci Rep. 2014;4:4507 - PMID: 24676021 - PMCID: PMC3968488 - DOI: 10.1038/srep04507

Turetsky A, Kim E, Kohler RH, Miller MA, Weissleder R

Single cell imaging of Bruton's tyrosine kinase using an irreversible inhibitor.

Sci Rep. 2014;4:4782 - PMID: 24759210 - PMCID: PMC3998017 - DOI: 10.1038/srep04782

Yang KS, Kohler RH, Landon M, Giedt R, Weissleder R

Single cell resolution in vivo imaging of DNA damage following PARP inhibition

Sci Rep. 2015;5:10129 - PMID: 25984718 - PMCID: PMC4434991 - DOI: 10.1038/srep10129

Tacke R, Hilgendorf I, Garner H, Waterborg C, Park K, Nowyhed H, Hanna RN, Wu R, Swirski FK, Geissmann F, Hedrick CC

The transcription factor NR4A1 is essential for the development of a novel macrophage subset in the thymus.

Sci Rep. 2015;5:10055 - PMID: 26091486 - PMCID: PMC4473761 - DOI: 10.1038/srep10055

Clardy SM, James F. Mohan JF, Vinegoni C, Keliher EJ, Iwamoto Y, Benoist C, Mathis D, Weissleder R

Rapid, high efficiency isolation of pancreatic ß-cells

Sci Rep. 2015;5:13681 - PMID: 26330153 - PMCID: PMC4557033 - DOI: 10.1038/srep13681

Merkulova M, Păunescu TG, Azroyan A, Marshansky V, Breton S, Brown D

Mapping the H(+) (V)-ATPase interactome: identification of proteins involved in trafficking, folding, assembly and phosphorylation.

Sci Rep. 2015;5:14827 - PMID: 26442671 - PMCID: PMC4595830 - DOI: 10.1038/srep14827

Kuijten MM, Hannah Degeling M, Chen JW, Wojtkiewicz G, Waterman P, Weissleder R, Azzi J, Nicolay K, Tannous BA

Multimodal targeted high relaxivity thermosensitive liposome for in vivo imaging.

Sci Rep. 2015;5:17220 - PMID: 26610702 - PMCID: PMC4661695 - DOI: 10.1038/srep17220

Wu JW, Turcotte R, Alt C, Runnels JM, Tsao H, Lin CP

Defining Clonal Color in Fluorescent Multi-Clonal Tracking

Sci Rep. 2016;6:24303 - PMID: 27073117 - PMCID: PMC4829845 - DOI: 10.1038/srep24303

Song J, Leon Swisher C, Im H, Jeong S, Pathania D, Iwamoto Y, Pivovarov M, Weissleder R, Lee H

Sparsity-Based Pixel Super Resolution for Lens-Free Digital In-line Holography.

Sci Rep. 2016;6:24681 - PMID: 27098438 - PMCID: PMC4838824 - DOI: 10.1038/srep24681

Yang Z, Concannon J, Ng KS, Seyb K, Mortensen LJ, Ranganath S, Gu F, Levy O, Tong Z, Martyn K, Zhao W, Lin CP, Glicksman MA, Karp JM

Tetrandrine identified in a small molecule screen to activate mesenchymal stem cells for enhanced immunomodulation.

Sci Rep. 2016;6:30263 - PMID: 27457881 - PMCID: PMC4960598 - DOI: 10.1038/srep30263

Park KS, Chung HJ, Khanam F, Lee H, Rashu R, Bhuiyan MT, Berger A, Harris JB, Calderwood SB, Ryan ET, Qadri F, Weissleder R, Charles RC

A magneto-DNA nanoparticle system for the rapid and sensitive diagnosis of enteric fever.

Sci Rep. 2016;6:32878 - PMID: 27605393 - PMCID: PMC5015101 - DOI: 10.1038/srep32878

Giedt RJ, Fumene Feruglio P, Pathania D, Yang KS, Kilcoyne A, Vinegoni C, Mitchison TJ, Weissleder R

Computational imaging reveals mitochondrial morphology as a biomarker of cancer phenotype and drug response

Sci Rep. 2016;6:32985 - PMID: 27609668 - PMCID: PMC5017129 - DOI: 10.1038/srep32985

Beam AL, Kartoun U, Pai JK, Chatterjee AK, Fitzgerald TP, Shaw SY, Kohane IS

Predictive Modeling of Physician-Patient Dynamics That Influence Sleep Medication Prescriptions and Clinical Decision-Making.

Sci Rep. 2017;7:42282 - PMID: 28181568 - PMCID: PMC5299453 - DOI: 10.1038/srep42282

Miller MA, Moss ML, Powell G, Petrovich R, Edwards L, Meyer AS, Griffith LG, Lauffenburger DA

Targeting autocrine HB-EGF signaling with specific ADAM12 inhibition using recombinant ADAM12 prodomain.

Sci Rep. 2015;5:15150 - PMID: 26477568 - PMCID: PMC4609913 - DOI: 10.1038/srep15150

Turcotte R, Alt C, Runnels JM, Ito K, Wu JW, Zaher W, Mortensen LJ, Silberstein L, Côté DC, Kung AL, Ito K, Lin CP

Image-guided transplantation of single cells in the bone marrow of live animals.

Sci Rep. 2017;7(1):3875 - PMID: 28634334 - PMCID: PMC5478633 - DOI: 10.1038/s41598-017-02896-6

Yang KS, O'Shea A, Zelga P, Liss AS, Del Castillo CF, Weissleder R

Extracellular vesicle analysis of plasma allows differential diagnosis of atypical pancreatic serous cystadenoma.

Sci Rep. 2023;13(1):10969 - PMID: 37414831 - PMCID: PMC10325992 - DOI: 10.1038/s41598-023-37966-5

Bagramyan A, Lin CP

Miniaturized microscope for non-invasive imaging of leukocyte-endothelial interaction in human microcirculation.

Sci Rep. 2023;13(1):17881 - PMID: 37857684 - PMCID: PMC10587353 - DOI: 10.1038/s41598-023-45018-1

Rosenthal ZC, Fass DM, Payne NC, She A, Patnaik D, Hennig KM, Tesla R, Werthmann GC, Guhl C, Reis SA, Wang X, Chen Y, Placzek M, Williams NS, Hooker J, Herz J, Mazitschek R, Haggarty SJ

Epigenetic modulation through BET bromodomain inhibitors as a novel therapeutic strategy for progranulin-deficient frontotemporal dementia.

Sci Rep. 2024;14(1):9064 - PMID: 38643236 - PMCID: PMC11032351 - DOI: 10.1038/s41598-024-59110-7

Landeros C, Oh J, Weissleder R, Lee H

Deep learning pipeline for automated cell profiling from cyclic imaging

Sci Rep. 2024;14(1):23600 - PMID: 39384907 - PMCID: PMC11464789 - DOI: 10.1038/s41598-024-74597-w

Nairz M, Haschka D, Dichtl S, Sonnweber T, Schroll A, Aßhoff M, Mindur JE, Moser PL, Wolf D, Swirski FK, Theurl I, Cerami A, Brines M, Weiss G

Cibinetide dampens innate immune cell functions thus ameliorating the course of experimental colitis.

Sci Rep. 2017;7(1):13012 - PMID: 29026145 - PMCID: PMC5638901 - DOI: 10.1038/s41598-017-13046-3

Brannen A, Eggert M, Nahrendorf M, Arnold R, Panizzi P

Correlation of 360-degree Surface Mapping In Vivo Bioluminescence with Multi-Spectral Optoacoustic Tomography in Human Xenograft Tumor Models.

Sci Rep. 2018;8(1):3321 - PMID: 29463820 - PMCID: PMC5820276 - DOI: 10.1038/s41598-018-21668-4

Yeh SA, Wilk K, Lin CP, Intini G

In Vivo 3D Histomorphometry Quantifies Bone Apposition and Skeletal Progenitor Cell Differentiation.

Sci Rep. 2018;8(1):5580 - PMID: 29615817 - PMCID: PMC5882859 - DOI: 10.1038/s41598-018-23785-6

Aganj I, Harisinghani MG, Weissleder R, Fischl B

Unsupervised medical image segmentation based on the local center of mass

Sci Rep. 2018;8:13012 - PMID: 30158534 - PMCID: PMC6115387 - DOI: 10.1038/s41598-018-31333-5

Vasaturo M, Cotugno R, Fiengo L, Vinegoni C, Dal Piaz F, De Tommasi N

The anti-tumor diterpene oridonin is a direct inhibitor of Nucleolin in cancer cells.

Sci Rep. 2018;8(1):16735 - PMID: 30425290 - PMCID: PMC6233161 - DOI: 10.1038/s41598-018-35088-x

Kim SJ*, Wang C*, Zhao B, Im H, Min J, Choi HJ, Tadros J, Choi NR, Castro CM, Weissleder R, Lee H, Lee K

Deep transfer learning-based hologram classification for molecular diagnostics.

Sci Rep. 2018;8(1):17003 - PMID: 30451953 - PMCID: PMC6242900 - DOI: 10.1038/s41598-018-35274-x