MGH Center for Systems Biology

Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE

Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.

Nat Methods. 2009;7(1):47-9 - PMID: 19946276 - PMCID: PMC2862482 - DOI: 10.1038/nmeth.1404

Adli M, Zhu J, Bernstein BE

Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors.

Nat Methods. 2010;7(8):615-8 - PMID: 20622861 - PMCID: PMC2924612 - DOI: 10.1038/nmeth.1478

Chittajallu DR, Florian S, Kohler RH, Iwamoto Y, Orth JD, Weissleder R*, Danuser G*, Mitchison TJ*

In vivo cell-cycle profiling in xenograft tumors by quantitative intravital microscopy

Nat Methods. 2015;12(6):577-585 - PMID: 25867850 - PMCID: PMC4579269 - DOI: 10.1038/nmeth.3363

Glenn DR#, Lee K#, Park H, Weissleder R, Yacoby A, Lukin MD, Lee H*, Walsworth RL*, Connolly CB*

Single-cell magnetic imaging using a quantum diamond microscope.

Nat Methods. 2015;12(8):736-738 - PMID: 26098019 - PMCID: PMC4521973 - DOI: 10.1038/nmeth.3449

Kong L, Tang J, Little JP, Yu Y, Lämmermann T, Lin CP, Germain RN, Cui M

Continuous volumetric imaging via an optical phase-locked ultrasound lens.

Nat Methods. 2015;12(8):759-762 - PMID: 26167641 - PMCID: PMC4551496 - DOI: 10.1038/nmeth.3476

Haase C, Gustafsson K, Mei S, Yeh SC, Richter D, Milosevic J, Turcotte R, Kharchenko PV, Sykes DB, Scadden DT, Lin CP

Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging.

Nat Methods. 2022;19(12):1622-1633 - PMID: 36424441 - PMCID: PMC9718684 - DOI: 10.1038/s41592-022-01673-2

Liu JF, Herold C, Gray KP, Penson RT, Horowitz N, Konstantinopoulos PA, Castro CM, Hill SJ, Curtis J, Luo W, Matulonis UA, Cannistra SA, Dizon DS

Assessment of Combined Nivolumab and Bevacizumab in Relapsed Ovarian Cancer: A Phase 2 Clinical Trial.

JAMA Oncol. 2019;5(12):1731-1738 - PMID: 31600397 - PMCID: PMC6802049 - DOI: 10.1001/jamaoncol.2019.3343

Hwang WL, Niemierko A, Efstathiou JA

Comparing Adjuvant vs Early-Salvage Radiotherapy After Radical Prostatectomy-Reply.

JAMA Oncol. 2018;4(11):1620-1621 - PMID: 30422248 - DOI: 10.1001/jamaoncol.2018.3552

Hwang WL, Tendulkar RD, Niemierko A, Agrawal S, Stephans KL, Spratt DE, Hearn JW, Koontz BF, Lee WR, Michalski JM, Pisansky TM, Liauw SL, Abramowitz MC, Pollack A, Moghanaki D, Anscher MS, Den RB, Zietman AL, Stephenson AJ, Efstathiou JA

Comparison Between Adjuvant and Early-Salvage Postprostatectomy Radiotherapy for Prostate Cancer With Adverse Pathological Features.

JAMA Oncol. 2018;4(5):e175230 - PMID: 29372236 - PMCID: PMC5885162 - DOI: 10.1001/jamaoncol.2017.5230

Hwang WL, Niemierko A, Hwang KL, Hubbeling H, Schapira E, Gainor JF, Keane FK

Clinical Outcomes in Patients With Metastatic Lung Cancer Treated With PD-1/PD-L1 Inhibitors and Thoracic Radiotherapy.

JAMA Oncol. 2018;4(2):253-255 - PMID: 28973343 - PMCID: PMC5838581 - DOI: 10.1001/jamaoncol.2017.3808

Lee CY, Degani I, Cheong J, Weissleder R, Lee JH, Cheon J, Lee H

Development of Integrated Systems for On-Site Infection Detection.

Acc Chem Res. 2021;54(21):3991-4000 - PMID: 34677927 - PMCID: PMC9099220 - DOI: 10.1021/acs.accounts.1c00498

Cheon J, Qin J, Lee LP, Lee H

Advances in Biosensor Technologies for Infection Diagnostics.

Acc Chem Res. 2022;55(2):121-122 - PMID: 35038867 - DOI: 10.1021/acs.accounts.1c00647

Villalba JA, Hilburn CF, Garlin MA, Elliott GA, Li Y, Kunitoki K, Poli S, Alba GA, Madrigal E, Taso M, Price MC, Aviles AJ, Araujo-Medina M, Bonanno L, Boyraz B, Champion SN, Harris CK, Helland TL, Hutchison B, Jobbagy S, Marshall MS, Shepherd DJ, Barth JL, Hung YP, Ly A, Hariri LP, Turbett SE, Pierce VM, Branda JA, Rosenberg ES, Mendez-Pena J, Chebib I, Rosales IA, Smith RN, Miller MA, Rosas IO, Hardin CC, Baden LR, Medoff BD, Colvin RB, Little BP, Stone JR, Mino-Kenudson M, Shih AR

Vasculopathy and Increased Vascular Congestion in Fatal COVID-19 and ARDS.

Am J Respir Crit Care Med. 2022;206(7):857-873 - PMID: 35671465 - PMCID: PMC9799276 - DOI: 10.1164/rccm.202109-2150OC

Devaraj NK, Weissleder R

Biomedical Applications of Tetrazine Cycloadditions.

Accounts Chem Res. 2011;44(9):816-27 - PMID: 21627112 - PMCID: PMC3166440 - DOI: 10.1021/ar200037t

Tassa C, Shaw SY, Weissleder R

Dextran-Coated Iron Oxide Nanoparticles: A Versatile Platform for Targeted Molecular Imaging, Molecular Diagnostics, and Therapy.

Accounts Chem Res. 2011;44(10):842-52 - PMID: 21661727 - PMCID: PMC3182289 - DOI: 10.1021/ar200084x

Hurtado-Lorenzo A, Skinner M, El Annan J, Futai M, Sun-Wada GH, Bourgoin S, Casanova J, Wildeman A, Bechoua S, Ausiello DA, Brown D, Marshansky V

V-ATPase interacts with ARNO and Arf6 in early endosomes and regulates the protein degradative pathway.

Nat Cell Biol. 2006;8(2):124-36 - PMID: 16415858 - DOI: 10.1038/ncb1348

Ahfeldt T, Schinzel RT, Lee YK, Hendrickson D, Kaplan A, Lum DH, Camahort R, Xia F, Shay J, Rhee EP, Clish CB, Deo RC, Shen T, Lau FH, Cowley A, Mowrer G, Al-Siddiqi H, Nahrendorf M, Musunuru K, Gerszten RE, Rinn JL, Cowan CA

Programming human pluripotent stem cells into white and brown adipocytes.

Nat Cell Biol. 2012;14(2):209-19 - PMID: 22246346 - PMCID: PMC3385947 - DOI: 10.1038/ncb2411

Brumbaugh J, Kim IS, Ji F, Huebner AJ, Di Stefano B, Schwarz BA, Charlton J, Coffey A, Choi J, Walsh RM, Schindler JW, Anselmo A, Meissner A, Sadreyev RI, Bernstein BE, Hock H, Hochedlinger K

Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo.

Nat Cell Biol. 2019;21(11):1449-1461 - PMID: 31659274 - PMCID: PMC6858577 - DOI: 10.1038/s41556-019-0403-5

Lim PJ, Duarte TL, Arezes J, Garcia-Santos D, Hamdi A, Pasricha SR, Armitage AE, Mehta H, Wideman S, Santos AG, Santos-Gonçalves A, Morovat A, Hughes JR, Soilleux E, Wang CY, Bayer AL, Klenerman P, Willberg CB, Hartley RC, Murphy MP, Babitt JL, Ponka P, Porto G, Drakesmith H

Nrf2 controls iron homeostasis in haemochromatosis and thalassaemia via Bmp6 and hepcidin.

Nat Metab. 2019;1(5):519-531 - PMID: 31276102 - PMCID: PMC6609153 - DOI: 10.1038/s42255-019-0063-6

Kakkar A, Traverso G, Farokhzad OC, Weissleder R, Langer R

Evolution of macromolecular complexity in drug delivery systems.

Nat Rev Chem. 2017;1(8):ePub - PMID: 31286060 - PMCID: PMC6613785 - DOI: 10.1038/s41570-017-0063

Jaffer F, Libby P, Weissleder R.

Molecular and Cellular Imaging of Atherosclerosis, Emerging Applications

J Am Coll Cardiol. 2006;47:1328-1338 - PMID: 16580517 - DOI: 10.1016/j.jacc.2006.01.029

Nahrendorf M, Hu K, Hiller K, Galuppo P, Fraccarollo D, Schweizer G, Haase A, Ertl G, Bauer W, Bauersachs J

Impact of hydroxymethylglutaryl coenzyme a reductase inhibition on left ventricular remodeling after myocardial infarction: an experimental serial cardiac magnetic resonance imaging study.

J Am Coll Cardiol. 2002;40(9):1695-700 - PMID: 12427425 - DOI: 10.1016/s0735-1097(02)02375-6

Korosoglou G, Weiss RG, Kedziorek DA, Walczak P, Gilson WD, Schar M, Sosnovik DE, Kraitchman DL, Boston RC, Bulte JW, Weissleder R, Stuber M

Noninvasive detection of macrophage-rich atherosclerotic plaque in hyperlipidemic rabbits using positive contrast magnetic resonance imaging.

J Am Coll Cardiol. 2008;52:483-91 - PMID: 18672170 - PMCID: PMC2628468 - DOI: 10.1016/j.jacc.2008.03.063

Jaffer FA

Assessing niacin as an atherosclerosis therapeutic agent valuable insights provided by high-resolution vascular magnetic resonance imaging.

J Am Coll Cardiol. 2009;54(19):1795-6 - PMID: 19874993 - DOI: 10.1016/j.jacc.2009.07.026

Panizzi P, Swirski FK, Figueiredo JL, Waterman P, Sosnovik DE, Aikawa E, Libby P, Pittet M, Weissleder R, Nahrendorf M

Impaired infarct healing in atherosclerotic mice with Ly-6C(hi) monocytosis.

J Am Coll Cardiol. 2010;55(15):1629-38 - PMID: 20378083 - PMCID: PMC2852892 - DOI: 10.1016/j.jacc.2009.08.089

Jaffer FA, Calfon MA, Rosenthal A, Mallas G, Razansky RN, Mauskapf A, Weissleder R, Libby P, Ntziachristos V

Two-dimensional intravascular near-infrared fluorescence molecular imaging of inflammation in atherosclerosis and stent-induced vascular injury.

J Am Coll Cardiol. 2011;57(25):2516-26 - PMID: 21679853 - PMCID: PMC3123768 - DOI: 10.1016/j.jacc.2011.02.036

Lee WW, Marinelli B, van der Laan AM, Sena BF, Gorbatov R, Leuschner F, Dutta P, Iwamoto Y, Ueno T, Begieneman MPV, Niessen HWM, Piek JJ, Vinegoni C, Pittet MJ, Swirski FK, Tawakol A, Di Carli M, Weissleder R, Nahrendorf M

PET/MRI of Inflammation in Myocardial Infarction

J Am Coll Cardiol. 2012;59:153-163 - PMID: 22222080 - PMCID: PMC3257823 - DOI: 10.1016/j.jacc.2011.08.066

Swirski FK, Nahrendorf M

Macrophage - stem cell crosstalk after myocardial infarction.

J Am Coll Cardiol. 2013;62(20):1902-4 - PMID: 23973700 - DOI: 10.1016/j.jacc.2013.07.058

Courties G, Heidt T, Sebas M, Iwamoto Y, Jeon D, Truelove J, Tricot B, Wojtkiewicz G, Dutta P, Sager HB, Borodovsky A, Novobrantseva T, Klebanov B, Fitzgerald K, Anderson DG, Libby P, Swirski FK, Weissleder R, Nahrendorf M

In vivo silencing of the transcription factor IRF5 reprograms the macrophage phenotype and improves infarct healing.

J Am Coll Cardiol. 2013;63(15):1556-66 - PMID: 24361318 - PMCID: PMC3992176 - DOI: 10.1016/j.jacc.2013.11.023

Taqueti VR, Nahrendorf M, Di Carli MF

Translational molecular imaging: repurposing an old technique to track cell migration into human atheroma.

J Am Coll Cardiol. 2014;64(10):1030-2 - PMID: 25190239 - DOI: 10.1016/j.jacc.2014.07.004

Nahrendorf M, Frantz S, Swirski FK, Mulder WJ, Randolph G, Ertl G, Ntziachristos V, Piek JJ, Stroes ES, Schwaiger M, Mann DL, Fayad ZA

Imaging Systemic Inflammatory Networks in Ischemic Heart Disease.

J Am Coll Cardiol. 2015;65(15):1583-1591 - PMID: 25881940 - PMCID: PMC4401833 - DOI: 10.1016/j.jacc.2015.02.034

Libby P, Nahrendorf M, Swirski FK

Leukocytes Link Local and Systemic Inflammation in Ischemic Cardiovascular Disease: An Expanded "Cardiovascular Continuum"

J Am Coll Cardiol. 2016;67(9):1091-103 - PMID: 26940931 - PMCID: PMC4779182 - DOI: 10.1016/j.jacc.2015.12.048

Xing L, Higuma T, Wang Z, Aguirre AD, Mizuno K, Takano M, Dauerman HL, Park SJ, Jang Y, Kim CJ, Kim SJ, Choi SY, Itoh T, Uemura S, Lowe H, Walters DL, Barlis P, Lee S, Lerman A, Toma C, Tan JWC, Yamamoto E, Bryniarski K, Dai J, Zanchin T, Zhang S, Yu B, Lee H, Fujimoto J, Fuster V, Jang IK

Clinical Significance of Lipid-Rich Plaque Detected by Optical Coherence Tomography: A 4-Year Follow-Up Study.

J Am Coll Cardiol. 2017;69(20):2502-2513 - PMID: 28521888 - DOI: 10.1016/j.jacc.2017.03.556

Teague HL, Ahlman MA, Alavi A, Wagner DD, Lichtman AH, Nahrendorf M, Swirski FK, Nestle F, Gelfand JM, Kaplan MJ, Grinspoon S, Ridker PM, Newby DE, Tawakol A, Fayad ZA, Mehta NN

Unraveling Vascular Inflammation: From Immunology to Imaging.

J Am Coll Cardiol. 2017;70(11):1403-1412 - PMID: 28882238 - PMCID: PMC5658004 - DOI: 10.1016/j.jacc.2017.07.750

Swirski FK, Nahrendorf M

Clonal Hematopoiesis Wages War on the Myocardium.

J Am Coll Cardiol. 2018;71(8):887-889 - PMID: 29471940 - DOI: 10.1016/j.jacc.2017.12.038

Fayad ZA, Swirski FK, Calcagno C, Robbins CS, Mulder W, Kovacic JC

Monocyte and Macrophage Dynamics in the Cardiovascular System: JACC Macrophage in CVD Series (Part 3).

J Am Coll Cardiol. 2018;72(18):2198-2212 - PMID: 30360828 - PMCID: PMC6258199 - DOI: 10.1016/j.jacc.2018.08.2150

Hsue PY, Li D, Ma Y, Ishai A, Manion M, Nahrendorf M, Ganz P, Ridker PM, Deeks SG, Tawakol A

IL-1β Inhibition Reduces Atherosclerotic Inflammation in HIV Infection.

J Am Coll Cardiol. 2018;72(22):2809-2811 - PMID: 30497570 - PMCID: PMC8723182 - DOI: 10.1016/j.jacc.2018.09.038

Libby P, Nahrendorf M, Swirski FK

Reply: The Networks Between the Sympathetic Nervous System and Immune System in Atherosclerosis.

J Am Coll Cardiol. 2016;68(4):432 - PMID: 27443446 - DOI: 10.1016/j.jacc.2016.05.017

Ferraro B, Leoni G, Hinkel R, Ormanns S, Paulin N, Ortega-Gomez A, Viola JR, de Jong R, Bongiovanni D, Bozoglu T, Maas SL, D'Amico M, Kessler T, Zeller T, Hristov M, Reutelingsperger C, Sager HB, Döring Y, Nahrendorf M, Kupatt C, Soehnlein O

Pro-Angiogenic Macrophage Phenotype to Promote Myocardial Repair.

J Am Coll Cardiol. 2019;73(23):2990-3002 - PMID: 31196457 - DOI: 10.1016/j.jacc.2019.03.503

Tawakol A, Osborne MT, Wang Y, Hammed B, Tung B, Patrich T, Oberfeld B, Ishai A, Shin LM, Nahrendorf M, Warner ET, Wasfy J, Fayad ZA, Koenen K, Ridker PM, Pitman RK, Armstrong KA

Stress-Associated Neurobiological Pathway Linking Socioeconomic Disparities to Cardiovascular Disease.

J Am Coll Cardiol. 2019;73(25):3243-3255 - PMID: 31248544 - PMCID: PMC6767929 - DOI: 10.1016/j.jacc.2019.04.042

Libby P, Swirski FK, Nahrendorf M

The Myocardium: More Than Myocytes.

J Am Coll Cardiol. 2019;74(25):3136-3138 - PMID: 31856970 - DOI: 10.1016/j.jacc.2019.10.031

Cremer S, Schloss MJ, Vinegoni C, Foy BH, Zhang S, Rohde D, Hulsmans M, Fumene Feruglio P, Schmidt S, Wojtkiewicz G, Higgins JM, Weissleder R, Swirski FK, Nahrendorf M

Diminished Reactive Hematopoiesis and Cardiac Inflammation in a Mouse Model of Recurrent Myocardial Infarction.

J Am Coll Cardiol. 2020;75(8):901-915 - PMID: 32130926 - PMCID: PMC7254576 - DOI: 10.1016/j.jacc.2019.12.056

Nahrendorf M

Innate Lymphoid Cells Participate in Myocardial Inflammation After Ischemia.

J Am Coll Cardiol. 2021;78(11):1143-1144 - PMID: 34503683 - DOI: 10.1016/j.jacc.2021.07.013

Aguirre AD, Arbab-Zadeh A, Soeda T, Fuster V, Jang IK

Optical Coherence Tomography of Plaque Vulnerability and Rupture: JACC Focus Seminar Part 1/3.

J Am Coll Cardiol. 2021;78(12):1257-1265 - PMID: 34531027 - PMCID: PMC9851427 - DOI: 10.1016/j.jacc.2021.06.050

Atri M, Zhang Z, Marques H, Gorelick J, Harisinghani M, Sohaib A, Koh D, Raman S, Gee MS, Choi H, Landrum LM, Mannel RS, Chuang LT, Yu JQ, McCourt CK, Gold M,

Utility of preoperative ferumoxtran-10 enhanced MRI to evaluate retroperitoneal lymph node metastasis in advanced cervical cancer: Results of ACRIN 6671/GOG 0233.

J Clin Oncol. 2011;29(15_suppl):5035 - PMID: 28023716

Gold M, Zhang Z, Marques H, Gorelick J, Landrum LM, Mannel RS, Chuang LT, Yu JQ, McCourt CK, Harisinghani M, Sohaib A, Koh D, Raman S, Gee MS, Choi H, Atri M

MRI prior to systematic lymphadenectomy in patients with locally advanced cervical cancer.

J Clin Oncol. 2011;29(15_suppl):5042 - PMID: 28023697

Santo L, Hideshima T, Kung AL, Yang M, Tamang D, Jarpe M, van Duzer JH, Mazitschek R, Cirstea D, Patel K, Tseng J, Rodig S, Pozzi S, Bradner J, Anderson KC, Jones SS, Raje NS

The effect of selective inhibition of HDAC6 with ACY1215 on bortezomib activity in multiple myeloma (MM).

J Clin Oncol. 2011;29(15_suppl):e18569 - PMID: 28023028

D'Souza G, Gross ND, Pai SI, Haddad R, Anderson KS, Rajan S, Gerber J, Gillison ML, Posner MR

Oral human papillomavirus (HPV) infection in HPV-positive patients with oropharyngeal cancer and their partners.

J Clin Oncol. 2014;32(23):2408-15 - PMID: 24778397 - PMCID: PMC4263818 - DOI: 10.1200/JCO.2014.55.1341

Ashida N, Senbanerjee S, Kodama S, Foo SY, Coggins M, Spencer JA, Zamiri P, Shen D, Li L, Sciuto T, Dvorak A, Gerszten RE, Lin CP, Karin M, Rosenzweig A

IKKb regulates essential functions of the vascular endothelium through kinase-dependent and -independent pathways.

Nat Commun. 2011;2:318 - PMID: 21587235 - PMCID: PMC3113230 - DOI: 10.1038/ncomms1317

Shi P, Scott MA, Ghosh B, Wan D, Wissner-Gross Z, Mazitschek R, Haggarty SJ, Yanik MF

Synapse microarray identification of small molecules that enhance synaptogenesis.

Nat Commun. 2011;2:510 - PMID: 22027590 - PMCID: PMC3544154 - DOI: 10.1038/ncomms1518