MGH Center for Systems Biology

Wang JS, Kamath T, Mazur CM, Mirzamohammadi F, Rotter D, Hojo H, Castro CD, Tokavanich N, Patel R, Govea N, Enishi T, Wu Y, da Silva Martins J, Bruce M, Brooks DJ, Bouxsein ML, Tokarz D, Lin CP, Abdul A, Macosko EZ, Fiscaletti M, Munns CF, Ryder P, Kost-Alimova M, Byrne P, Cimini B, Fujiwara M, Kronenberg HM, Wein MN

Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin.

Nat Commun. 2021;12(1):6271 - PMID: 34725346 - PMCID: PMC8560803 - DOI: 10.1038/s41467-021-26571-7

Yeh SA, Hou J, Wu JW, Yu S, Zhang Y, Belfield KD, Camargo FD, Lin CP

Quantification of bone marrow interstitial pH and calcium concentration by intravital ratiometric imaging.

Nat Commun. 2022;13(1):393 - PMID: 35046411 - PMCID: PMC8770570 - DOI: 10.1038/s41467-022-27973-x

Foy BH, Sundt TM, Carlson JCT, Aguirre AD, Higgins JM

Human acute inflammatory recovery is defined by co-regulatory dynamics of white blood cell and platelet populations.

Nat Commun. 2022;13(1):4705 - PMID: 35995789 - PMCID: PMC9395541 - DOI: 10.1038/s41467-022-32222-2

Tye MA, Payne NC, Johansson C, Singh K, Santos SA, Fagbami L, Pant A, Sylvester K, Luth MR, Marques S, Whitman M, Mota MM, Winzeler EA, Lukens AK, Derbyshire ER, Oppermann U, Wirth DF, Mazitschek R

Elucidating the path to Plasmodium prolyl-tRNA synthetase inhibitors that overcome halofuginone resistance.

Nat Commun. 2022;13(1):4976 - PMID: 36008486 - PMCID: PMC9403976 - DOI: 10.1038/s41467-022-32630-4

Che M, Chaturvedi A, Munro SA, Pitzen SP, Ling A, Zhang W, Mentzer J, Ku SY, Puca L, Zhu Y, Bergman AM, Severson TM, Forster C, Liu Y, Hildebrand J, Daniel M, Wang TY, Selth LA, Hickey T, Zoubeidi A, Gleave M, Bareja R, Sboner A, Tilley W, Carroll JS, Tan W, Kohli M, Yang R, Hsieh AC, Murugan P, Zwart W, Beltran H, Huang RS, Dehm SM

Opposing transcriptional programs of KLF5 and AR emerge during therapy for advanced prostate cancer.

Nat Commun. 2021;12(1):6377 - PMID: 34737261 - PMCID: PMC8568894 - DOI: 10.1038/s41467-021-26612-1

Momin N, Palmeri JR, Lutz EA, Jailkhani N, Mak H, Tabet A, Chinn MM, Kang BH, Spanoudaki V, Hynes RO, Wittrup KD

Maximizing response to intratumoral immunotherapy in mice by tuning local retention.

Nat Commun. 2022;13(1):109 - PMID: 35013154 - PMCID: PMC8748612 - DOI: 10.1038/s41467-021-27390-6

Turco V, Pfleiderer K, Hunger J, Horvat NK, Karimian-Jazi K, Schregel K, Fischer M, Brugnara G, Jähne K, Sturm V, Streibel Y, Nguyen D, Altamura S, Agardy DA, Soni SS, Alsasa A, Bunse T, Schlesner M, Muckenthaler MU, Weissleder R, Wick W, Heiland S, Vollmuth P, Bendszus M, Rodell CB, Breckwoldt MO, Platten M

T cell-independent eradication of experimental glioma by intravenous TLR7/8-agonist-loaded nanoparticles.

Nat Commun. 2023;14(1):771 - PMID: 36774352 - PMCID: PMC9922247 - DOI: 10.1038/s41467-023-36321-6

Spitzberg JD, Ferguson S, Yang KS, Peterson HM, Carlson JCT, Weissleder R

Multiplexed analysis of EV reveals specific biomarker composition with diagnostic impact.

Nat Commun. 2023;14(1):1239 - PMID: 36870999 - PMCID: PMC9985597 - DOI: 10.1038/s41467-023-36932-z

De Souza DC, Hebert N, Esrick EB, Ciuculescu MF, Archer NM, Armant M, Audureau, Brendel C, Di Caprio G, Galactéros F, Liu D, McCabe A, Morris E, Schonbrun E, Williams D, Wood DK, Williams DA, Bartolucci P, Higgins JM

Genetic reversal of the globin switch concurrently modulates both fetal and sickle hemoglobin and reduces red cell sickling.

Nat Commun. 2023;14(1):5850 - PMID: 37730674 - PMCID: PMC10511721 - DOI: 10.1038/s41467-023-40923-5

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

Wang Y, Cao T, Ko J, Shen Y, Zong W, Sheng K, Cao W, Sun S, Cai L, Zhou YL, Zhang XX, Zong C, Weissleder R, Weitz D

Dissolvable Polyacrylamide Beads for High-Throughput Droplet DNA Barcoding.

Adv Sci. 2020;7(8):1903463 - PMID: 32328429 - PMCID: PMC7175265 - DOI: 10.1002/advs.201903463

Haun JB*, Castro CM*, Wang R, Peterson VM, Marinelli BS, Lee H, Weissleder R.

Micro-NMR for Rapid Molecular Analysis of Human Tumor Samples

Sci Transl Med. 2011;3(71):71ra16 - PMID: 21346169 - PMCID: PMC3086073 - DOI: 10.1126/scitranslmed.3002048

Vinegoni C, Botnaru I, Aikawa E, Calfon MA, Iwamoto Y, Folco EJ, Ntziachristos V, Weissleder R, Libby P, Jaffer FA

Indocyanine Green Enables Near-Infrared Fluorescence Imaging of Lipid-Rich, Inflamed Atherosclerotic Plaques

Sci Transl Med. 2011;3 (84) ra45):84ra45 - PMID: 21613624 - PMCID: PMC3112179 - DOI: 10.1126/scitranslmed.3001577

Ferraro F, Lymperi S, Méndez-Ferrer S, Saez B, Spencer JA, Yeap BY, Masselli E, Graiani G, Prezioso L, Rizzini EL, Mangoni M, Rizzoli V, Sykes SM, Lin CP, Frenette PS, Quaini F, Scadden DT

Diabetes impairs hematopoietic stem cell mobilization by altering niche function.

Sci Transl Med. 2011;3(104):104ra101 - PMID: 21998408 - PMCID: PMC3754876 - DOI: 10.1126/scitranslmed.3002191

Wood DK, Soriano A, Mahadevan L, Higgins JM, Bhatia SN

A Biophysical Indicator of Vaso-occlusive Risk in Sickle Cell Disease.

Sci Transl Med. 2012;4(123):123ra26 - PMID: 22378926 - PMCID: PMC3633235 - DOI: 10.1126/scitranslmed.3002738

Issadore D, Chung J*, Shao H*, Liong M, Ghazani AA, Castro CM, Weissleder R*, Lee H*

Ultrasensitive Clinical Enumeration of Rare Cells ex Vivo Using a Micro-Hall Detector

Sci Transl Med. 2012;4 (141):141ra92 - PMID: 22764208 - PMCID: PMC3603277 - DOI: 10.1126/scitranslmed.3003747

Ullal AV*, Peterson V*, Agasti SS, Tuang S, Juric D, Castro CM, Weissleder R

Cancer Cell Profiling by Barcoding Allows Multiplexed Protein Analysis in Fine-Needle Aspirates

Sci Transl Med. 2014;6(219):219ra9 - PMID: 24431113 - PMCID: PMC4063286 - DOI: 10.1126/scitranslmed.3007361

Kobzik L, Swirski FK

MARCOing Monocytes for Elimination.

Sci Transl Med. 2014;6(219):219fs4 - PMID: 24431109 - PMCID: PMC4374341 - DOI: 10.1126/scitranslmed.3008448

Mulder WJ, Jaffer FA, Fayad ZA, Nahrendorf M

Imaging and Nanomedicine in Inflammatory Atherosclerosis.

Sci Transl Med. 2014;6(239):239sr1 - PMID: 24898749 - PMCID: PMC4110972 - DOI: 10.1126/scitranslmed.3005101

Laughney AM, Kim E, Sprachman MM, Miller MA, Kohler RH, Yang KS, Orth JD, Mitchison TJ, Weissleder R

Single-cell pharmacokinetic imaging reveals a therapeutic strategy to overcome drug resistance to the microtubule inhibitor eribulin

Sci Transl Med. 2014;6 (261):261ra152 - PMID: 25378644 - PMCID: PMC4330962 - DOI: 10.1126/scitranslmed.3009318

Herman JD, Pepper LR, Cortese JF, Estiu G, Galinsky K, Zuzarte-Luis V, Derbyshire ER, Ribacke U, Lukens AK, Santos SA, Patel V, Clish CB, Sullivan WJ, Zhou H, Bopp SE, Schimmel P, Lindquist S, Clardy J, Mota MM, Keller TL, Whitman M, Wiest O, Wirth DF, Mazitschek R

The cytoplasmic prolyl-tRNA synthetase of the malaria parasite is a dual-stage target of febrifugine and its analogs.

Sci Transl Med. 2015;7(288):288ra77 - PMID: 25995223 - PMCID: PMC4675670 - DOI: 10.1126/scitranslmed.aaa3575

Miller MA, Gadde S, Pfirschke C, Engblom C, Sprachman MM, Kohler RH, Yang KS, Laughney AM, Wojtkiewicz G, Kamal N, Bhonagiri S, Pittet MJ, Farokhzad OC, Weissleder R

Predicting therapeutic nano-medicine efficacy using a companion MR imaging nanoparticle.

Sci Transl Med. 2015;7:314 - PMID: 26582898 - PMCID: PMC5462466 - DOI: 10.1126/scitranslmed.aac6522

Sager HB, Dutta P, Dahlman JE, Hulsmans M, Courties G, Sun Y, Heidt T, Vinegoni C, Borodovsky A, Fitzgerald K, Wojtkiewicz GR, Iwamoto Y, Tricot B, Khan OF, Kauffman KJ, Xing Y, Shaw TE, Libby P, Langer R, Weissleder R, Swirski FK, Anderson DG, Nahrendorf M

RNAi targeting multiple cell adhesion molecules reduces immune cell recruitment and vascular inflammation after myocardial infarction

Sci Transl Med. 2016;8:342 - PMID: 27280687 - PMCID: PMC5125383 - DOI: 10.1126/scitranslmed.aaf1435

Weissleder R, Schwaiger MC, Gambhir SS, Hricak H

Imaging approaches to optimize molecular therapies

Sci Transl Med. 2016;8(355):355ps16 - PMID: 27605550 - DOI: 10.1126/scitranslmed.aaf3936

Malka R, Nathan DM, Higgins JM

Mechanistic modeling of hemoglobin glycation and red blood cell kinetics enables personalized diabetes monitoring

Sci Transl Med. 2016;8:359ra130 - PMID: 27708063 - PMCID: PMC5714656 - DOI: 10.1126/scitranslmed.aaf9304

Castro CM

Taking cancer drug screening very personally.

Sci Transl Med. 2016;8(367):367ec190 - PMID: 27903858 - DOI: 10.1126/scitranslmed.aal2799

Castro CM

Good to the last "emulsified" drop.

Sci Transl Med. 2017;9(373):ePub - PMID: 28100835 - DOI: 10.1126/scitranslmed.aal4993

Miller MA

Richer data with personalized GEMs.

Sci Transl Med. 2017;9(381):ePub - PMID: 28298424 - DOI: 10.1126/scitranslmed.aam9865

King KR

Squeeze-E squeeze-E.

Sci Transl Med. 2017;9(382):ePub - PMID: 28330860 - DOI: 10.1126/scitranslmed.aan0766

Miller MA

Nanoparticles improve economic mileage for CARs.

Sci Transl Med. 2017;9(387):ePub - PMID: 28446684 - DOI: 10.1126/scitranslmed.aan2784

King KR

Stunning neutrophils changes the forecast: No more showers.

Sci Transl Med. 2017;9(388):ePub - PMID: 28469035 - DOI: 10.1126/scitranslmed.aan3775

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 - PMCID: PMC5734617 - DOI: 10.1126/scitranslmed.aal3604

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 - PMCID: PMC5846089 - DOI: 10.1126/scitranslmed.aal3226

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 - PMCID: PMC6681815 - DOI: 10.1126/scitranslmed.aal0225

Miller MA

Driver mutations take the wheel in invasive yet nonmalignant disease.

Sci Transl Med. 2017;9(393):ePub - PMID: 28592567 - DOI: 10.1126/scitranslmed.aan8194

Miller MA

Nanotransfection brings progress that’s more than skin-deep

Sci Transl Med. 2017;9(405):eaao4216

Miller MA

Counting on carbon quantum dots to clear infection

Sci Transl Med. 2017;9(399):eaao0969

Miller MA

It’s what’s inside that counts for nanoparticle vaccines

Sci Transl Med. 2017;9(417):eaar2438 - DOI: 10.1126/scitranslmed.aar2438

Miller MA

Less is more for anticancer therapy combinations

Sci Transl Med. 2017;9 (411):aap8166 - DOI: 10.1126/scitranslmed.aap8166

Kodack DP, Askoxylakis V, Ferraro GB, Sheng Q, Badeaux M, Goel S, Qi X, Shankaraiah R, Cao ZA, Ramjiawan RR, Bezwada D, Patel B, Song Y, Costa C, Naxerova K, Wong CSF, Kloepper J, Das R, Tam A, Tanboon J, Duda DG, Miller CR, Siegel MB, Anders CK, Sanders M, Estrada MV, Schlegel R, Arteaga CL, Brachtel E, Huang A, Fukumura D, Engelman JA, Jain RK

The brain microenvironment mediates resistance in luminal breast cancer to PI3K inhibition through HER3 activation.

Sci Transl Med. 2017;9(391):ePub - PMID: 28539475 - PMCID: PMC5917603 - DOI: 10.1126/scitranslmed.aal4682

Miller MA

Gold photothermal therapy: A positive for negative margins

Sci Transl Med. 2018;10(423):eaar7512 - DOI: 10.1126/scitranslmed.aar7512

Binderup T, Duivenvoorden R, Fay F, van Leent MMT, Malkus J, Baxter S, Ishino S, Zhao Y, Sanchez-Gaytan B, Teunissen AJP, Frederico YCA, Tang J, Carlucci G, Lyashchenko S, Calcagno C, Karakatsanis N, Soultanidis G, Senders ML, Robson PM, Mani V, Ramachandran S, Lobatto ME, Hutten BA, Granada JF, Reiner T, Swirski FK, Nahrendorf M, Kjaer A, Fisher EA, Fayad ZA, Pérez-Medina C, Mulder WJM

Imaging-assisted nanoimmunotherapy for atherosclerosis in multiple species.

Sci Transl Med. 2019;11(506):ePub - PMID: 31434756 - PMCID: PMC7328283 - DOI: 10.1126/scitranslmed.aaw7736

Naxerova K

A new function for polycomb in immune evasion

Sci Transl Med. 2019;11(514):eaaz3718 - DOI: 10.1126/scitranslmed.aaz3718

Harisinghani MG, O’Shea A, Weissleder R

Advances in clinical MRI technology

Sci Transl Med. 2019;11 (523):eaba2591 - PMID: 31852796 - DOI: 10.1126/scitranslmed.aba2591

Naxerova K

Tumor mutations are not alone in the plasma

Sci Transl Med. 2019;11(522):eaaz9767 - DOI: 10.1126/scitranslmed.aaz9767

Naxerova K

Interrogating CD8+ T cell reactivity on a genome-wide scale

Sci Transl Med. 2019;11(506):eaaz0302 - DOI: 10.1126/scitranslmed.aaz0302

Naxerova K

From micrographs to microsatellites in one bold step

Sci Transl Med. 2019;11(498):eaax9570 - DOI: 10.1126/scitranslmed.aax9570

Naxerova K

Somatic mutations are improving their bad rap

Sci Transl Med. 2019;11(490):eaax4871 - DOI: 10.1126/scitranslmed.aax4871

Weissleder R, Lee H, Ko J, Pittet MJ

COVID-19 diagnostics in context

Sci Transl Med. 2020;12(546):eabc1931 - PMID: 32493791 - DOI: 10.1126/scitranslmed.abc1931

Min J*, Chin LK*, Oh J, Landeros C, Vinegoni C, Lee J, Lee SJ, Park JY, Liu AQ, Castro CM, Lee H, Im H, Weissleder R

CytoPAN—Portable cellular analyses for rapid point-of-care cancer diagnosis

Sci Transl Med. 2020;12:eaaz9746 - PMID: 32759277 - PMCID: PMC8217912 - DOI: 10.1126/scitranslmed.aaz9746