MGH Center for Systems Biology

Pfirschke C, Garris C, Pittet MJ

Common TLR5 Mutations Control Cancer Progression.

Cancer Cell. 2015;27(1):1-3 - PMID: 25584886 - DOI: 10.1016/j.ccell.2014.12.008

Aiden AP, Rivera MN, Rheinbay E, Ku M, Coffman EJ, Truong TT, Vargas SO, Lander ES, Haber DA, Bernstein BE

Wilms Tumor Chromatin Profiles Highlight Stem Cell Properties and a Renal Developmental Network.

Cell Stem Cell. 2010;6(6):591-602 - PMID: 20569696 - PMCID: PMC2897075 - DOI: 10.1016/j.stem.2010.03.016

Koche RP, Smith ZD, Adli M, Gu H, Ku M, Gnirke A, Bernstein BE, Meissner A

Reprogramming factor expression initiates widespread targeted chromatin remodeling.

Cell Stem Cell. 2011;8(1):96-105 - PMID: 21211784 - PMCID: PMC3220622 - DOI: 10.1016/j.stem.2010.12.001

Park D, Spencer JA, Koh BI, Kobayashi T, Fujisaki J, Clemens TL, Lin CP, Kronenberg HM, Scadden DT

Endogenous Bone Marrow MSCs Are Dynamic, Fate-Restricted Participants in Bone Maintenance and Regeneration.

Cell Stem Cell. 2012;10(3):259-72 - PMID: 22385654 - PMCID: PMC3652251 - DOI: 10.1016/j.stem.2012.02.003

Silberstein LE, Lin CP

A new image of the hematopoietic stem cell vascular niche.

Cell Stem Cell. 2013;13(5):514-6 - PMID: 24209758 - PMCID: PMC4148778 - DOI: 10.1016/j.stem.2013.10.012

Dutta P, Sager HB, Stengel KR, Naxerova K, Courties G, Saez B, Silberstein L, Heidt T, Sebas M, Sun Y, Wojtkiewicz G, Feruglio PF, King K, Baker JN, van der Laan AM, Borodovsky A, Fitzgerald K, Hulsmans M, Hoyer F, Iwamoto Y, Vinegoni C, Brown D, Di Carli M, Libby P, Hiebert SW, Scadden DT, Swirski FK, Weissleder R, Nahrendorf M

Myocardial Infarction Activates CCR2(+) Hematopoietic Stem and Progenitor Cells

Cell Stem Cell. 2015;16 (5):477-487 - PMID: 25957903 - PMCID: PMC4426344 - DOI: 10.1016/j.stem.2015.04.008

Silberstein L, Goncalves KA, Kharchenko PV, Turcotte R, Kfoury Y, Mercier F, Baryawno N, Severe N, Bachand J, Spencer JA, Papazian A, Lee D, Chitteti BR, Srour EF, Hoggatt J, Tate T, Lo Celso C, Ono N, Nutt S, Heino J, Sipilä K, Shioda T, Osawa M, Lin CP, Hu GF, Scadden DT

Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem/Progenitor Cell Regulators.

Cell Stem Cell. 2016;19(4):530-543 - PMID: 27524439 - PMCID: PMC5402355 - DOI: 10.1016/j.stem.2016.07.004

Liau BB, Sievers C, Donohue LK, Gillespie SM, Flavahan WA, Miller TE, Venteicher AS, Hebert CH, Carey CD, Rodig SJ, Shareef SJ, Najm FJ, van Galen P, Wakimoto H, Cahill DP, Rich JN, Aster JC, Suvà ML, Patel AP, Bernstein BE

Adaptive Chromatin Remodeling Drives Glioblastoma Stem Cell Plasticity and Drug Tolerance.

Cell Stem Cell. 2016;20(2):233-246.e7 - PMID: 27989769 - PMCID: PMC5291795 - DOI: 10.1016/j.stem.2016.11.003

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

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

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

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

Lee S, Vinegoni C, Feruglio PF, Fexon L, Gorbatov R, Pivovarov M, Sbarbati A, Nahrendorf M, Weissleder R

Real-time in vivo imaging of the beating mouse heart at microscopic resolution

Nat Commun. 2012;3:1054 - PMID: 22968700 - PMCID: PMC3622400 - DOI: 10.1038/ncomms2060

Thurber GM, Yang KS, Reiner T, Kohler RH, Sorger P, Mitchison T, Weissleder R

Single-cell and subcellular pharmacokinetic imaging allows insight into drug action in vivo.

Nat Commun. 2013;4:1504 - PMID: 23422672 - PMCID: PMC3579506 - DOI: 10.1038/ncomms2506

Liong M, Hoang AN, Chung J, Gural N, Ford CB, Min C, Shah RR, Ahmad R, Fernandez-Suarez M, Fortune SM, Toner M, Lee H*, Weissleder R*

Magnetic barcode assay for genetic detection of pathogens

Nat Commun. 2013;4:1752 - PMID: 23612293 - PMCID: PMC3635151 - DOI: 10.1038/ncomms2745

Gurkar AU, Chu K, Raj L, Bouley R, Lee SH, Kim YB, Dunn SE, Mandinova A, Lee SW

Identification of ROCK1 kinase as a critical regulator of Beclin1-mediated autophagy during metabolic stress.

Nat Commun. 2013;4:2189 - PMID: 23877263 - PMCID: PMC3740589 - DOI: 10.1038/ncomms3189

Ageta-Ishihara N, Miyata T, Ohshima C, Watanabe M, Sato Y, Hamamura Y, Higashiyama T, Mazitschek R, Bito H, Kinoshita M

Septins promote dendrite and axon development by negatively regulating microtubule stability via HDAC6-mediated deacetylation.

Nat Commun. 2013;4:2532 - PMID: 24113571 - PMCID: PMC3826633 - DOI: 10.1038/ncomms3532

Duivenvoorden R, Tang J, Cormode DP, Mieszawska AJ, Izquierdo-Garcia D, Ozcan C, Otten MJ, Zaidi N, Lobatto ME, van Rijs SM, Priem B, Kuan EL, Martel C, Hewing B, Sager H, Nahrendorf M, Randolph GJ, Stroes ES, Fuster V, Fisher EA, Fayad ZA, Mulder WJ

A statin-loaded reconstituted high-density lipoprotein nanoparticle inhibits atherosclerotic plaque inflammation.

Nat Commun. 2014;5:3065 - PMID: 24445279 - PMCID: PMC4001802 - DOI: 10.1038/ncomms4065

Dubach JM, Vinegoni C, Mazitschek R, Fumene Feruglio P, Cameron LA, Weissleder R

In vivo imaging of specific drug-target binding at subcellular resolution.

Nat Commun. 2014;5:3946 - PMID: 24867710 - PMCID: PMC4362617 - DOI: 10.1038/ncomms4946

Lee SK, Mortensen LJ, Lin CP, Tung CH

An authentic imaging probe to track cell fate from beginning to end.

Nat Commun. 2014;5:5216 - PMID: 25323442 - PMCID: PMC4852472 - DOI: 10.1038/ncomms6216

Shen K, Luk S, Hicks DF, Elman JS, Bohr S, Iwamoto Y, Murray R, Pena K, Wang F, Seker E, Weissleder R, Yarmush ML, Toner M, Sgroi D, Parekkadan B

Resolving cancer-stroma interfacial signalling and interventions with micropatterned tumour-stromal assays.

Nat Commun. 2014;5:5662 - PMID: 25489927 - PMCID: PMC4261930 - DOI: 10.1038/ncomms6662

Shao H, Chung J, Lee K, Balaj L, Min C, Carter BS, Hochberg FH, Breakefield XO, Lee H*, Weissleder R*

Chip-based analysis of exosomal mRNA mediating drug resistance in glioblastoma

Nat Commun. 2015;6:6999 - PMID: 25959588 - PMCID: PMC4430127 - DOI: 10.1038/ncomms7999

Lai CP, Kim EY, Badr CE, Weissleder R, Mempel TR, Tannous BA, Breakefield XO

Visualization and tracking of tumour extracellular vesicle delivery and RNA translation using multiplexed reporters.

Nat Commun. 2015;6:7029 - PMID: 25967391 - PMCID: PMC4435621 - DOI: 10.1038/ncomms8029

Miller MA, Zheng YR, Gadde S, Pfirschke C, Zope H, Engblom C, Kohler RH, Iwamoto Y, Yang KS, Askevold B, Kolishetti N, Pittet M, Lippard SJ, Farokhzad OC, Weissleder R

Tumour-associated macrophages act as a slow-release reservoir of nano-therapeutic Pt(IV) pro-drug.

Nat Commun. 2015;6:8692 - PMID: 26503691 - PMCID: PMC4711745 - DOI: 10.1038/ncomms9692

Signore S, Sorrentino A, Borghetti G, Cannata A, Meo M, Zhou Y, Kannappan R, Pasqualini F, O'Malley H, Sundman M, Tsigkas N, Zhang E, Arranto C, Mangiaracina C, Isobe K, Sena BF, Kim J, Goichberg P, Nahrendorf M, Isom LL, Leri A, Anversa P, Rota M

Late Na(+) current and protracted electrical recovery are critical determinants of the aging myopathy.

Nat Commun. 2015;6:8803 - PMID: 26541940 - PMCID: PMC4638135 - DOI: 10.1038/ncomms9803

Roy J*, Kim B*, Hill E, Visconti P, Krapf D, Vinegoni C, Weissleder R, Brown D, Breton S

Tyrosine kinase-mediated axial motility of basal cells revealed by intravital imaging.

Nat Commun. 2016;7:10666 - PMID: 26868824 - PMCID: PMC4754344 - DOI: 10.1038/ncomms10666

Vinegoni C, Leon Swisher C, Fumene Feruglio P, Giedt RJ, Rousso DL, Stapleton S, Weissleder R

Real-time high dynamic range laser scanning microscopy.

Nat Commun. 2016;7:11077 - PMID: 27032979 - PMCID: PMC4821995 - DOI: 10.1038/ncomms11077

Aryal B, Rotllan N, Araldi E, Ramírez CM, He S, Chousterman BG, Fenn AM, Wanschel A, Madrigal-Matute J, Warrier N, Martín-Ventura JL, Swirski FK, Suárez Y, Fernández-Hernando C

ANGPTL4 deficiency in haematopoietic cells promotes monocyte expansion and atherosclerosis progression.

Nat Commun. 2016;7:12313 - PMID: 27460411 - PMCID: PMC4974469 - DOI: 10.1038/ncomms12313

Schlomann U, Koller G, Conrad C, Ferdous T, Golfi P, Garcia AM, Höfling S, Parsons M, Costa P, Soper R, Bossard M, Hagemann T, Roshani R, Sewald N, Ketchem RR, Moss ML, Rasmussen FH, Miller MA, Lauffenburger DA, Tuveson DA, Nimsky C, Bartsch JW

ADAM8 as a drug target in pancreatic cancer.

Nat Commun. 2015;6:6175 - PMID: 25629724 - PMCID: PMC5014123 - DOI: 10.1038/ncomms7175

Chen X, Park HR, Pelton M, Piao X, Lindquist NC, Im H, Kim YJ, Ahn JS, Ahn KJ, Park N, Kim DS, Oh SH

Atomic layer lithography of wafer-scale nanogap arrays for extreme confinement of electromagnetic waves.

Nat Commun. 2013;4:2361 - PMID: 23999053 - DOI: 10.1038/ncomms3361

Chapman S, Dobrovolskaia M, Farahani K, Goodwin A, Joshi A, Lee H, Meade T, Pomper M, Ptak K, Rao J, Singh R, Sridhar S, Stern S, Wang A, Weaver JB, Woloschak G, Yang L

Nanoparticles for cancer imaging: The good, the bad, and the promise.

Nano Today. 2013;8(5):454-460 - PMID: 25419228 - PMCID: PMC4240321 - DOI: 10.1016/j.nantod.2013.06.001