MGH Center for Systems Biology

Publications

Tawakol A, Ishai A, Takx RA, Figueroa AL, Ali A, Kaiser Y, Truong QA, Solomon CJ, Calcagno C, Mani V, Tang CY, Mulder WJ, Murrough JW, Hoffmann U, Nahrendorf M, Shin LM, Fayad ZA, Pitman RK

Relation between resting amygdalar activity and cardiovascular events: a longitudinal and cohort study.

Lancet. 2017;389(10071):834-845 - PMID: 28088338

Miller TE, Liau BB, Wallace LC, Morton AR, Xie Q, Dixit D, Factor DC, Kim LJY, Morrow JJ, Wu Q, Mack SC, Hubert CG, Gillespie SM, Flavahan WA, Hoffmann T, Thummalapalli R, Hemann MT, Paddison PJ, Horbinski CM, Zuber J, Scacheri PC, Bernstein BE, Tesar PJ, Rich JN

Transcription elongation factors represent in vivo cancer dependencies in glioblastoma.

Nature. 2017;547(7663):355-359 - PMID: 28678782

Miller MA, Weissleder R

Imaging of anticancer drug action in single cells

Nat Rev Cancer. 2017;17:399–414

Behzadi S, Serpooshan V, Tao W, Hamaly MA, Alkawareek MY, Dreaden EC, Brown D, Alkilany AM, Farokhzad OC, Mahmoudi M

Cellular uptake of nanoparticles: journey inside the cell.

Chem Soc Rev. 2017;46(14):4218-4244 - PMID: 28585944

Hulsmans M, Clauss S, Xiao L, Aguirre AD, King KR, Hanley A, Hucker WJ, Wülfers EM, Seemann G, Courties G, Iwamoto Y, Sun Y, Savol AJ, Sager HB, Lavine KJ, Fishbein GA, Capen DE, Da Silva N, Miquerol L, Wakimoto H, Seidman CE, Seidman JG, Sadreyev RI, Naxerova K, Mitchell RN, Brown D, Libby P, Weissleder R, Swirski FK, Kohl P, Vinegoni C, Milan DJ, Ellinor PT, Nahrendorf M

Macrophages Facilitate Electrical Conduction in the Heart

Cell. 2017;169:510-522 - PMID: 28431249 - PMCID: PMC5474950

Naxerova K, Reiter JG, Brachtel E, Lennerz JK, van de Wetering M, Rowan A, Cai T, Clevers H, Swanton C, Nowak MA, Elledge SJ, Jain RK

Origins of lymphatic and distant metastases in human colorectal cancer.

Science. 2017;357(6346):55-60 - PMID: 28684519

Flavahan WA, Gaskell E, Bernstein BE

Epigenetic plasticity and the hallmarks of cancer.

Science. 2017;357(6348):ePub - PMID: 28729483

Venteicher AS, Tirosh I, Hebert C, Yizhak K, Neftel C, Filbin MG, Hovestadt V, Escalante LE, Shaw ML, Rodman C, Gillespie SM, Dionne D, Luo CC, Ravichandran H, Mylvaganam R, Mount C, Onozato ML, Nahed BV, Wakimoto H, Curry WT, Iafrate AJ, Rivera MN, Frosch MP, Golub TR, Brastianos PK, Getz G, Patel AP, Monje M, Cahill DP, Rozenblatt-Rosen O, Louis DN, Bernstein BE, Regev A, Suvà ML

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq.

Science. 2017;355(6332):ePub - PMID: 28360267 - PMCID: PMC5519096

Pfirschke C, Siwicki M, Liao HW, Pittet MJ

Tumor Microenvironment: No Effector T Cells without Dendritic Cells.

Cancer Cell. 2017;31(5):614-615 - PMID: 28486102

Castro CM

Good to the last "emulsified" drop.

Sci Transl Med. 2017;9(373):ePub - PMID: 28100835

King KR

Squeeze-E squeeze-E.

Sci Transl Med. 2017;9(382):ePub - PMID: 28330860

Miller MA

Nanoparticles improve economic mileage for CARs.

Sci Transl Med. 2017;9(387):ePub - PMID: 28446684

Miller MA, Chandra R, Cuccarese MF, Pfirschke C, Engblom C, Stapleton S, Adhikary U, Kohler RH, Mohan JF, Pittet MJ, Weissleder R

Radiation therapy primes tumors for nanotherapeutic delivery via macrophage-mediated vascular bursts

Sci Transl Med. 2017;9(392):eaal0225 - PMID: 28566423

King KR

Stunning neutrophils changes the forecast: No more showers.

Sci Transl Med. 2017;9(388):ePub - PMID: 28469035

Miller MA

Driver mutations take the wheel in invasive yet nonmalignant disease.

Sci Transl Med. 2017;9(393):ePub - PMID: 28592567

Miller MA

Richer data with personalized GEMs.

Sci Transl Med. 2017;9(381):ePub - PMID: 28298424

Arlauckas SP*, Garris CS*, Kohler RH, Kitaoka M, Cuccarese MF, Yang KS, Miller MA, Carlson JC, Freeman GJ, Anthony RM, Weissleder R, Pittet MJ

In vivo imaging reveals a tumor-associated macrophage–mediated resistance pathway in anti–PD-1 therapy

Sci Transl Med. 2017;9(389):eaal3604 - PMID: 28490665 - Cover

Yang KS*, Im H*, Hong S, Pergolini I, Del Castillo AF, Wang R, Clardy S, Huang CH, Pille C, Ferrone S, Yang R, Castro CM, Lee H, Del Castillo CF, Weissleder R

Multiparametric plasma EV profiling facilitates diagnosis of pancreatic malignancy

Sci Transl Med. 2017;9(391):eaal3226 - PMID: 28539469

Nahrendorf M, Swirski FK

Cholesterol, CCR2, and monocyte phenotypes in atherosclerosis.

Eur Heart J. 2017;38(20):1594-1596 - PMID: 28329093

Frodermann V, Nahrendorf M

Neutrophil-macrophage cross-talk in acute myocardial infarction.

Eur Heart J. 2017;38(3):198-200 - PMID: 28158564

Hoyer FF, Nahrendorf M

Neutrophil contributions to ischaemic heart disease.

Eur Heart J. 2017;38(7):465-472 - PMID: 28363210

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

Alaarg A, Pérez-Medina C, Metselaar JM, Nahrendorf M, Fayad ZA, Storm G, Mulder WJM

Applying nanomedicine in maladaptive inflammation and angiogenesis.

Adv Drug Deliv Rev. 2017;:ePub - PMID: 28506745

Lee J, Dykstra B, Spencer JA, Kenney LL, Greiner DL, Shultz LD, Brehm MA, Lin CP, Sackstein R, Rossi DJ

mRNA-mediated glycoengineering ameliorates deficient homing of human stem cell-derived hematopoietic progenitors.

J Clin Invest. 2017;127(6):2433-2437 - PMID: 28481220 - PMCID: PMC5451245

Seo KJ, Qiang Y, Bilgin I, Kar S, Vinegoni C, Weissleder R, Fang H

Transparent Electrophysiology Microelectrodes and Interconnects from Metal Nanomesh.

ACS Nano. 2017;11(4):4365-4372 - PMID: 28391679

Swirski FK, Nahrendorf M

Inflammation: Old, caffeinated, and healthy.

Nat Rev Cardiol. 2017;14(4):194-196 - PMID: 28250451

Harada T, Ohguchi H, Grondin Y, Kikuchi S, Sagawa M, Tai YT, Mazitschek R, Hideshima T, Anderson KC

HDAC3 regulates DNMT1 expression in multiple myeloma: Therapeutic implications.

Leukemia. 2017;:ePub - PMID: 28490812

Cuccarese MF, Dubach JM, Pfirschke C, Engblom C, Garris C, Miller MA, Pittet MJ, Weissleder R

Heterogeneity of macrophage infiltration and therapeutic response in lung carcinoma revealed by 3D organ imaging.

Nat Commun. 2017;8:14293 - PMID: 28176769 - PMCID: PMC5309815

Keliher EJ, Ye YX, Wojtkiewicz GR, Aguirre AD, Tricot B, Senders ML, Groenen H, Fay F, Perez-Medina C, Calcagno C, Carlucci G, Reiner T, Sun Y, Courties G, Iwamoto Y, Kim HY, Wang C, Chen JW, Swirski FK, Wey HY, Hooker J, Fayad ZA, Mulder WJ, Weissleder R, Nahrendorf M

Polyglucose nanoparticles with renal elimination and macrophage avidity facilitate PET imaging in ischaemic heart disease.

Nat Commun. 2017;8:14064 - PMID: 28091604 - PMCID: PMC5241815

Walsh RM, Shen EY, Bagot RC, Anselmo A, Jiang Y, Javidfar B, Wojtkiewicz GJ, Cloutier J, Chen JW, Sadreyev R, Nestler EJ, Akbarian S, Hochedlinger K

Phf8 loss confers resistance to depression-like and anxiety-like behaviors in mice.

Nat Commun. 2017;8:15142 - PMID: 28485378 - PMCID: PMC5436068

Miller MA, Askevold B, Mikula H, Kohler RH, Pirovich D, Weissleder R

Nano-palladium is a cellular catalyst for in vivo chemistry

Nat Commun. 2017;8:15906 - PMID: 28699627 - PMCID: PMC5510178

Grossman SR, Zhang X, Wang L, Engreitz J, Melnikov A, Rogov P, Tewhey R, Isakova A, Deplancke B, Bernstein BE, Mikkelsen TS, Lander ES

Systematic dissection of genomic features determining transcription factor binding and enhancer function.

Proc Natl Acad Sci U S A. 2017;114(7):E1291-E1300 - PMID: 28137873 - PMCID: PMC5321001

Wang CY, Core AB, Canali S, Zumbrennen-Bullough KB, Ozer S, Umans L, Zwijsen A, Babitt JL

Smad1/5 is required for erythropoietin-mediated suppression of hepcidin in mice.

Blood. 2017;130(1):73-83 - PMID: 28438754 - PMCID: PMC5501149

Mikula H, Stapleton S, Kohler RH, Vinegoni C, Weissleder R

Design and Development of Fluorescent Vemurafenib Analogs for In Vivo Imaging.

Theranostics. 2017;7(5):1257-1265 - PMID: 28435463 - PMCID: PMC5399591

Vinegoni C, Fumene Feruglio P, Brand C, Lee S, Nibbs AE, Stapleton S, Shah S, Gryczynski I, Reiner T, Mazitschek R, Weissleder R

Measurement of drug-target engagement in live cells by two-photon fluorescence anisotropy imaging.

Nat Protoc. 2017;12(7):1472-1497 - PMID: 28686582

Wilk K, Yeh SA, Mortensen LJ, Ghaffarigarakani S, Lombardo CM, Bassir SH, Aldawood ZA, Lin CP, Intini G

Postnatal Calvarial Skeletal Stem Cells Expressing PRX1 Reside Exclusively in the Calvarial Sutures and Are Required for Bone Regeneration.

Stem Cell Reports. 2017;8(4):933-946 - PMID: 28366454 - PMCID: PMC5390237

Godlewski J, Ferrer-Luna R, Rooj AK, Mineo M, Ricklefs F, Takeda YS, Nowicki MO, Salińska E, Nakano I, Lee H, Weissleder R, Beroukhim R, Chiocca EA, Bronisz A

MicroRNA Signatures and Molecular Subtypes of Glioblastoma: The Role of Extracellular Transfer.

Stem Cell Reports. 2017;8(6):1497-1505 - PMID: 28528698 - PMCID: PMC5470095

She A, Kurtser I, Reis SA, Hennig K, Lai J, Lang A, Zhao WN, Mazitschek R, Dickerson BC, Herz J, Haggarty SJ

Selectivity and Kinetic Requirements of HDAC Inhibitors as Progranulin Enhancers for Treating Frontotemporal Dementia.

Cell Chem Biol. 2017;24(7):892-906.e5 - PMID: 28712747

Hong S, Park KS, Weissleder R, Castro CM, Lee H

Facile silicification of plastic surface for bioassays.

Chem Commun. 2017;53(13):2134-2137 - PMID: 28134385 - PMCID: PMC5327824

Hideshima T, Mazitschek R, Qi J, Mimura N, Tseng JC, Kung AL, Bradner JE, Anderson KC

HDAC6 inhibitor WT161 downregulates growth factor receptors in breast cancer.

Oncotarget. 2017;:ePub - PMID: 28708596

Pulli B, Wojtkiewicz G, Iwamoto Y, Ali M, Zeller MW, Bure L, Wang C, Choi Y, Masia R, Guimaraes AR, Corey KE, Chen JW

Molecular MR Imaging of Myeloperoxidase Distinguishes Steatosis from Steatohepatitis in Nonalcoholic Fatty Liver Disease.

Radiology. 2017;:160588 - PMID: 28358240

Fenn AM, Swirski FK

Monocytosis, Hypercholesterolemia, and the Kinase That Binds Them.

Arterioscler Thromb Vasc Biol. 2017;37(2):173-175 - PMID: 28122772

Kim DE, Kim JY, Schellingerhout D, Ryu JH, Lee SK, Jeon S, Lee JS, Kim J, Jang HJ, Park JE, Kim EJ, Kwon IC, Ahn CH, Nahrendorf M, Kim K

Quantitative Imaging of Cerebral Thromboemboli In Vivo: The Effects of Tissue-Type Plasminogen Activator.

Stroke. 2017;48(5):1376-1385 - PMID: 28432262

Im H, Lee K, Weissleder R, Lee H, Castro C

Novel Nanosensing Technologies for Exosome Detection and Profiling

Lab Chip. 2017;:ePub

Vandoorne K, Nahrendorf M

Multiparametric Imaging of Organ System Interfaces.

Circ Cardiovasc Imaging. 2017;10(4):ePub - PMID: 28360260 - PMCID: PMC5419074

Stein-Merlob AF, Hara T, McCarthy JR, Mauskapf A, Hamilton JA, Ntziachristos V, Libby P, Jaffer FA

Atheroma Susceptible to Thrombosis Exhibit Impaired Endothelial Permeability In Vivo as Assessed by Nanoparticle-Based Fluorescence Molecular Imaging.

Circ Cardiovasc Imaging. 2017;10(5):ePub - PMID: 28487316 - PMCID: PMC5509162

Global Cardiovascular Magnetic Resonance Registry (GCMR) Investigators, Kwong RY, Petersen SE, Schulz-Menger J, Arai AE, Bingham SE, Chen Y, Choi YL, Cury RC, Ferreira VM, Flamm SD, Steel K, Bandettini WP, Martin ET, Nallamshetty L, Neubauer S, Raman SV, Schelbert EB, Valeti US, Cao JJ, Reichek N, Young AA, Fexon L, Pivovarov M, Ferrari VA, Simonetti OP

The global cardiovascular magnetic resonance registry (GCMR) of the society for cardiovascular magnetic resonance (SCMR): its goals, rationale, data infrastructure, and current developments.

J Cardiovasc Magn Reson. 2017;19(1):23 - PMID: 28187739 - PMCID: PMC5303267

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

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

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;:ePub - PMID: 28628306

Chousterman BG, Swirski FK, Weber GF

Cytokine storm and sepsis disease pathogenesis.

Semin Immunopathol. 2017;39(5):517-528 - PMID: 28555385

Krukowski K, Ma J, Golonzhka O, Laumet GO, Gutti T, van Duzer JH, Mazitschek R, Jarpe MB, Heijnen CJ, Kavelaars A

HDAC6 inhibition effectively reverses chemotherapy-induced peripheral neuropathy.

Pain. 2017;158(6):1126-1137 - PMID: 28267067 - PMCID: PMC5435512

Park YI, Kim E, Huang CH, Park KS, Castro CM, Lee H, Weissleder R

Facile Coating Strategy to Functionalize Inorganic Nanoparticles for Biosensing

Bioconjug Chem. 2017;28(1):33-37 - PMID: 27792877 - PMCID: PMC5474933

Nairz M, Theurl I, Swirski FK, Weiss G

"Pumping iron" - how macrophages handle iron at the systemic, microenvironmental, and cellular levels.

Pflugers Arch. 2017;469(3-4):397-418 - PMID: 28251312 - PMCID: PMC5362662

Park YJ, Battistone MA, Kim B, Breton S

Relative contribution of clear cells and principal cells to luminal pH in the mouse epididymis.

Biol Reprod. 2017;96(2):366-375 - PMID: 28203710

Cheung PW, Ueberdiek L, Day J, Bouley R, Brown D

Protein phosphatase 2C (PP2C) is responsible for VP-induced dephosphorylation of AQP2 serine 261.

Am J Physiol Renal Physiol. 2017;:ajprenal.00004.2017 - PMID: 28381458

Mamuya FA, Xie D, Lei L, Huang M, Tsuji K, Capen DE, Yang B, Weissleder R, Păunescu TG, Lu HJ

Deletion of β-1 integrin in collecting duct principal cells leads to tubular injury and renal medullary fibrosis.

Am J Physiol Renal Physiol. 2017;:ajprenal.00038.2017 - PMID: 28701310

Noiret L, Slater A, Higgins JM

Determinants of red blood cell alloantibody detection duration: analysis of multiply alloimmunized patients supports peritransfusion factors.

Transfusion. 2017;:ePub - PMID: 28639314

Li YX, Gautam V, Brüstle A, Cockburn IA, Daria VR, Gillespie C, Gaus K, Alt C, Lee WM

Flexible polygon-mirror based laser scanning microscope platform for multiphoton in-vivo imaging.

J Biophotonics. 2017;:ePub - PMID: 28164461

Conrad C, Miller MA, Bartsch JW, Schlomann U, Lauffenburger DA

Simultaneous Detection of Metalloprotease Activities in Complex Biological Samples Using the PrAMA (Proteolytic Activity Matrix Assay) Method.

Methods Mol Biol. 2017;1574:243-253 - PMID: 28315256

Pera V, Tan X, Runnels J, Sardesai N, Lin CP, Niedre M

Diffuse fluorescence fiber probe for in vivo detection of circulating cells.

J Biomed Opt. 2017;22(3):37004 - PMID: 28290598 - PMCID: PMC5348644

Lee S, Courties G, Nahrendorf M, Weissleder R, Vinegoni C

Motion characterization scheme to minimize motion artifacts in intravital microscopy.

J Biomed Opt. 2017;22(3):36005 - PMID: 28253383 - PMCID: PMC5333764

Brown D

The Discovery of Water Channels (Aquaporins).

Ann Nutr Metab. 2017;70 Suppl 1:37-42 - PMID: 28614812

Lu X, Galarneau MM, Higgins JM, Wood DK

A microfluidic platform to study the effects of vascular architecture and oxygen gradients on sickle blood flow.

Microcirculation. 2017;:ePub - PMID: 28129479 - PMCID: PMC5505799

Je KH, Ryu WS, Lee SK, Kim EJ, Kim JY, Jang HJ, Park JE, Nahrendorf M, Schellingerhout D, Kim DE

Green-channel autofluorescence imaging: A novel and sensitive technique to delineate infarcts.

J Neurosci Methods. 2017;279:22-32 - PMID: 28104485

Vieson MD, Gojmerac AM, Khan D, Dai R, van Duzer JH, Mazitschek R, Caudell DL, Liao X, Luo XM, Reilly CM

Treatment with a selective histone deacetylase 6 inhibitor decreases lupus nephritis in NZB/W mice.

Histol Histopathol. 2017;:11885 - PMID: 28245046

Yamamoto E, Xing L, Higuma T, Minami Y, Bryniarski K, Zanchin T, Wang Z, Aguirre AD, Lee H, Jang IK

Dynamic neointimal pattern after drug-eluting stent implantation defined by optical coherence tomography.

Coron Artery Dis. 2017;:ePub - PMID: 28704243

Dev S, Babitt JL

Overview of iron metabolism in health and disease.

Hemodial Int. 2017;21 Suppl 1:S6-S20 - PMID: 28296010

Christensen HL, Păunescu TG, Matchkov V, Barbuskaite D, Brown D, Damkier HH, Praetorius J

The V-ATPase is expressed in the choroid plexus and mediates cAMP-induced intracellular pH alterations.

Physiol Rep. 2017;5(1):ePub - PMID: 28053225 - PMCID: PMC5256157

Miller MA, Arlauckas S, Weissleder R

Prediction of Anti-cancer Nanotherapy Efficacy by Imaging

Nanotheranostics. 2017;1(3):296-312

Jeong S, Eskandari R, Park SM, Alvarez J, Tee SS, Weissleder R, Kharas MG, Lee H, Keshari KR

Real-time quantitative analysis of metabolic flux in live cells using a hyperpolarized micromagnetic resonance spectrometer.

Sci Adv. 2017;3(6):e1700341 - PMID: 28630930 - PMCID: PMC5473678

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