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

Corsten MF, Shah K

Therapeutic stem-cells for cancer treatment: hopes and hurdles in tactical warfare.

Lancet Oncol. 2008;9(4):376-84 - PMID: 18374291 - DOI: 10.1016/S1470-2045(08)70099-8

Harisinghani M

Nanoparticle-enhanced MRI: are we there yet?

Lancet Oncol. 2008;9(9):814-815 - PMID: 18760237 - DOI: 10.1016/S1470-2045(08)70215-8

Khosroshahi A, Stone JR, Pratt DS, Deshpande V, Stone JH

Painless jaundice with serial multi-organ dysfunction.

Lancet Oncol. 2009;373(9673):1494 - PMID: 19394539 - DOI: 10.1016/S0140-6736(09)60615-2

Ji H, Ohmura K, Mahmood U, Lee DM, Hofhuis FM, Boackle SA, Takahashi K, Holers VM, Walport M, Gerard C, Ezekowitz A, Carroll MC, Brenner M, Weissleder R, Verbeek JS, Duchatelle V, Degott C, Benoist C, Mathis D

Arthritis critically dependent on innate immune system players

Immunity. 2002;16:157-68 - PMID: 11869678 - DOI: 10.1016/s1074-7613(02)00275-3

Mempel T, Pittet M, Khazaie K, Weninger W, Weissleder R, von Boehmer H, von Adrian U.

Regulatory T cells reversibly suppress cytotoxic T cell function independent of effector differentiation

Immunity. 2006;25(1):129-41 - PMID: 16860762 - DOI: 10.1016/j.immuni.2006.04.015

Reiser J, Polu KR, Moller CC, Kenlan P, Altintas MM, Wei C, Faul C, Herbert S, Villegas I, Avila-Casado C, McGee M, Sugimoto H, Brown D, Kalluri R, Mundel P, Smith PL, Clapham DE, Pollak MR

TRPC6 is a glomerular slit diaphragm-associated channel required for normal renal function.

Nat Genet. 2005;37(7):739-44 - PMID: 15924139 - PMCID: PMC1360984 - DOI: 10.1038/ng1592

Babitt JL, Huang FW, Wrighting DM, Xia Y, Sidis Y, Samad TA, Campagna JA, Chung RT, Schneyer AL, Woolf CJ, Andrews NC, Lin HY

Bone morphogenetic protein signaling by hemojuvelin regulates hepcidin expression.

Nat Genet. 2006;38(5):531-9 - PMID: 16604073 - DOI: 10.1038/ng1777

Andriopoulos Jr B, Corradini E, Xia Y, Faasse SA, Chen S, Grgurevic L, Knutson MD, Pietrangelo A, Vukicevic S, Lin HY, Babitt JL

BMP6 is a key endogenous regulator of hepcidin expression and iron metabolism.

Nat Genet. 2009;41(4):482-7 - PMID: 19252486 - PMCID: PMC2810136 - DOI: 10.1038/ng.335

Reich DE, Schaffner SF, Daly MJ, McVean G, Mullikin JC, Higgins JM, Richter DJ, Lander ES, Altshuler D

Human genome sequence variation and the influence of gene history, mutation and recombination.

Nat Genet. 2002;32(1):135-42 - PMID: 12161752 - DOI: 10.1038/ng947

Zhou VW, Goren A, Bernstein BE

Charting histone modifications and the functional organization of mammalian genomes.

Nat Rev Genet. 2010;12(1):7-18 - PMID: 21116306 - DOI: 10.1038/nrg2905

Rabin O, Manuel Perez J, Grimm J, Wojtkiewicz G, Weissleder R

An X-ray computed tomography imaging agent based on long-circulating bismuth sulphide nanoparticles.

Nat Mater. 2006;5(2):118-22 - PMID: 16444262 - DOI: 10.1038/nmat1571

Marten K, Bremer C, Khazaie K, Sameni M, Sloane B, Tung CH, Weissleder R

Detection of dysplastic intestinal adenomas using enzyme-sensing molecular beacons in mice

Gastroenterology. 2002;122:406-14 - PMID: 11832455 - DOI: 10.1053/gast.2002.30990

Mahmood U, Wallace MB

Molecular imaging in gastrointestinal disease.

Gastroenterology. 2007;132(1):11-4 - PMID: 17241854 - DOI: 10.1053/j.gastro.2006.12.013

Magnusson FC, Liblau RS, von Boehmer H, Pittet MJ, Lee JW, Turley SJ, Khazaie K

Direct presentation of antigen by lymph node stromal cells protects against CD8 T-cell-mediated intestinal autoimmunity.

Gastroenterology. 2008;134(4):1028-37 - PMID: 18395084 - DOI: 10.1053/j.gastro.2008.01.070

Corradini E, Garuti C, Montosi G, Ventura P, Andriopoulos B, Lin HY, Pietrangelo A, Babitt JL

Bone morphogenetic protein signaling is impaired in an Hfe knockout mouse model of hemochromatosis.

Gastroenterology. 2009;137(4):1489-97 - PMID: 19591830 - PMCID: PMC2757523 - DOI: 10.1053/j.gastro.2009.06.057

Corradini E, Schmidt PJ, Meynard D, Garuti C, Montosi G, Chen S, Vukicevic S, Pietrangelo A, Lin HY, Babitt JL

BMP6 treatment compensates for the molecular defect and ameliorates hemochromatosis in Hfe knockout mice.

Gastroenterology. 2010;139(5):1721-9 - PMID: 20682319 - PMCID: PMC3295242 - DOI: 10.1053/j.gastro.2010.07.044

Parekkadan B, Upadhyay R, Dunham J, Iwamoto Y, Mizoguchi E, Mizoguchi A, Weissleder R, Yarmush ML

Bone Marrow Stromal Cell Transplants Prevent Experimental Enterocolitis and Require Host CD11b+ Splenocytes.

Gastroenterology. 2010;140(3):966-975.e4 - PMID: 20955701 - PMCID: PMC3033974 - DOI: 10.1053/j.gastro.2010.10.013

Rudin M, Weissleder R

Molecular imaging in drug discovery and development

Nat Rev Drug Discov. 2003;2:123-31 - PMID: 12563303 - DOI: 10.1038/nrd1007

Haun JB, Devaraj NK, Hilderbrand SA, Lee H, Weissleder R

Bioorthogonal chemistry amplifies nanoparticle binding and enhances the sensitivity of cell detection

Nat Nanotechnol. 2010;5(9):660-5 - PMID: 20676091 - PMCID: PMC2934903 - DOI: 10.1038/nnano.2010.148

Im H, Huang XJ, Gu B, Choi YK

A dielectric-modulated field-effect transistor for biosensing.

Nat Nanotechnol. 2007;2(7):430-4 - PMID: 18654328 - DOI: 10.1038/nnano.2007.180

Maglia G, Heron AJ, Hwang WL, Holden MA, Mikhailova E, Li Q, Cheley S, Bayley H

Droplet networks with incorporated protein diodes show collective properties.

Nat Nanotechnol. 2009;4(7):437-40 - PMID: 19581896 - DOI: 10.1038/nnano.2009.121

Jaffer F, Weissleder R

Molecular Imaging in the Clinical Arena

JAMA. 2005;293(7):855-62 - PMID: 15713776 - DOI: 10.1001/jama.293.7.855

Nahrendorf M, Aikawa E, Figueiredo JL, Stangenberg L, van den Borne S, Blankesteijn M, Sosnovik D, Jaffer F, Tung CH, Weissleder R

Transglutaminase activity in acute infarcts predicts healing outcome and let ventricular remodelling : implications for FXIII therapy and antithrombin use in myocardial infarction

Eur Heart J. 2008;29:445-454 - PMID: 18276618 - DOI: 10.1093/eurheartj/ehm558

Matter CM, Stuber M, Nahrendorf M

Imaging of the unstable plaque: how far have we got?

Eur Heart J. 2009;30(21):2566-74 - PMID: 19833636 - PMCID: PMC2771148 - DOI: 10.1093/eurheartj/ehp419

Hjortnaes J, Butcher J, Figueiredo JL, Riccio M, Kohler RH, Kozloff KM, Weissleder R, Aikawa E

Arterial and aortic valve calcification inversely correlates with osteoporotic bone remodelling: a role for inflammation.

Eur Heart J. 2010;31(16):1975-84 - PMID: 20601388 - PMCID: PMC2921509 - DOI: 10.1093/eurheartj/ehq237

Weissleder R, Ntziachristos V

Shedding light onto live molecular targets

Nature Med. 2003;9:123-8 - PMID: 12514725 - DOI: 10.1038/nm0103-123

Ntziachristos V, Tung CH, Bremer C, Weissleder R

Fluorescence molecular tomography resolves protease activity in vivo

Nature Med. 2002;8:757-60 - PMID: 12091907 - DOI: 10.1038/nm729

Bremer C, Tung CH, Weissleder R

In vivo molecular target assessment of matrix metalloproteinase inhibition

Nature Med. 2001;7:743-8 - PMID: 11385514 - DOI: 10.1038/89126

Weissleder R, Moore A, Mahmood U, Bhorade R, Benveniste H, Chiocca EA, Basilion JP

In vivo magnetic resonance imaging of transgene expression

Nature Med. 2000;6:351-5 - PMID: 10700241 - DOI: 10.1038/73219

Kirsch DG, Dinulescu DM, Miller JB, Grimm J, Santiago PM, Young NP, Nielsen GP, Quade BJ, Chaber CJ, Schultz CP, Takeuchi O, Bronson RT, Crowley D, Korsmeyer SJ, Yoon SS, Hornicek FJ, Weissleder R, Jacks T

A spatially and temporally restricted mouse model of soft tissue sarcoma.

Nature Med. 2007;13(8):992-997 - PMID: 17676052 - DOI: 10.1038/nm1602

Sackstein R, Merzaban JS, Cain DW, Dagia NM, Spencer JA, Lin CP, Wohlgemuth R

Ex vivo glycan engineering of CD44 programs human multipotent mesenchymal stromal cell trafficking to bone.

Nature Med. 2008;14(2):181-7 - PMID: 18193058 - DOI: 10.1038/nm1703

Kaushal S, Amiel G, Guleserian K, Shapira O, Perry T, Sutherland F, Rabkin E, Moran A, Schoen F, Atala A, Soker S, Bischoff J, Mayer J

Functional small-diameter neovessels created using endothelial progenitor cells expanded ex vivo.

Nature Med. 2001;7:1035-40 - PMID: 11533707 - PMCID: PMC2818999 - DOI: 10.1038/nm0901-1035

Shimizu K, Sugiyama S, Aikawa M, Fukumoto Y, Rabkin E, Libby P, Mitchell R

Host bone-marrow cells are a source of donor intimal smooth- muscle-like cells in murine aortic transplant arteriopathy.

Nature Med. 2001;7:738-41 - PMID: 11385513 - DOI: 10.1038/89121

Lee H, Sun E, Ham D, Weissleder R

Chip-NMR biosensor for detection and molecular analysis of cells.

Nature Med. 2008;14(8):869-74 - PMID: 18607350 - PMCID: PMC2729055 - DOI: 10.1038/nm.1711

Engelman JA, Chen L, Tan X, Crosby K, Guimaraes AR, Upadhyay R, Maira M, McNamara K, Perera SA, Song Y, Chirieac LR, Kaur R, Lightbown A, Simendinger J, Li T, Padera RF, Garcia-Echeverria C, Weissleder R, Mahmood U, Cantley LC, Wong KK

Effective use of PI3K and MEK inhibitors to treat mutant Kras G12D and PIK3CA H1047R murine lung cancers.

Nature Med. 2008;14(12)::1351-1356 - PMID: 19029981 - PMCID: PMC2683415 - DOI: 10.1038/nm.1890

Dagia N, Gadhoum S, Knoblauch C, Spencer J, Zamiri P, Lin CP, Sackstein R

G-CSF induces E-selectin ligand expression on human myeloid cells.

Nature Med. 2006;12:1185-90 - PMID: 16980970 - DOI: 10.1038/nm1470

Fan Z, Spencer JA, Lu Y, Pitsillides CM, Singh G, Kim P, Yun SH, Toxavidis V, Strom TB, Lin CP, Koulmanda M

In vivo tracking of 'color-coded' effector, natural and induced regulatory T cells in the allograft response.

Nature Med. 2010;16(6):718-22 - PMID: 20495571 - PMCID: PMC2894571 - DOI: 10.1038/nm.2155

Breton S, Smith PJ, Lui B, Brown D

Acidification of the male reproductive tract by a proton pumping (H+)-ATPase.

Nature Med. 1996;2(4):470-2 - PMID: 8597961 - DOI: 10.1038/nm0496-470

Chen J, Tung CH, Mahmood U, Ntziachristos V, Gyurko R, Fishman MC, Huang PL, Weissleder R

In vivo imaging of proteolytic activity in atherosclerosis

Circulation. 2002;105:2766-71 - PMID: 12057992 - DOI: 10.1161/01.cir.0000017860.20619.23

Jaffer FA, Tung CH, Wykrzykowska JJ, Ho NH, Houng AK, Reed GL, Weissleder R

Molecular Imaging of Factor XIIIa Activity in Thrombosis Using a Novel, Near-Infrared Fluorescent Contrast Agent That Covalently Links to Thrombi.

Circulation. 2004;110(2):170-6 - PMID: 15210587 - DOI: 10.1161/01.CIR.0000134484.11052.44

Chen J, Tung CH, Allport JR, Chen S, Weissleder R, Huang PL.

Near-Infrared Fluorescent Imaging of Matrix Metalloproteinase Activity After Myocardial Infarction

Circulation. 2005;111:1800-1805 - PMID: 15809374 - PMCID: PMC3733536 - DOI: 10.1161/01.CIR.0000160936.91849.9F

Nahrendorf M, Hu K, Frantz S, Jaffer F, Tung CH, Hiller KH, Voll S, Nordbeck P, Sosnovik D, Gattenlohner S, Novikov M, Dickneite G, Reed G, Jakob P, Rosenzweig A, Bauer W, Weissleder R, Ertl G.

Factor XIII Deficiency Causes Cardiac Rupture, Impairs Wound Healing, and Aggravates Cardiac Remodeling in Mice with Myocardial Infarction

Circulation. 2006;113(9):1196-1202 - PMID: 16505171 - PMCID: PMC4066325 - DOI: 10.1161/CIRCULATIONAHA.105.602094

Heller EA, Liu E, Tager AM, Yuan Q, Lin AY, Ahluwalia N, Jones K, Koehn SL, Lok VM, Aikawa E, Moore KJ, Luster AD, Gerszten RE

Chemokine CXCL10 Promotes Atherogenesis by Modulating the Local Balance of Effector and Regulatory T Cells.

Circulation. 2006;113(19):2301-12 - PMID: 16682613 - DOI: 10.1161/CIRCULATIONAHA.105.605121

Deguchi JO, Aikawa M, Tung CH, Aikawa E, Kim DE, Ntziachristos V, Weissleder R, Libby P

Inflammation in Atherosclerosis. Visualizing Matrix Metalloproteinase Action in Macrophages In Vivo.

Circulation. 2006;114:55-62 - PMID: 16801460 - DOI: 10.1161/CIRCULATIONAHA.106.619056

Nahrendorf M, Jaffer FA, Kelly KA, Sosnovik DE, Aikawa E, Libby P, Weissleder R

Noninvasive Vascular Cell Adhesion Molecule-1 Imaging Identifies Inflammatory Activation of Cells in Atherosclerosis.

Circulation. 2006;114:1504-1511 - PMID: 17000904 - DOI: 10.1161/CIRCULATIONAHA.106.646380

Aikawa E, Nahrendorf M, Sosnovik D, Lok VM, Jaffer FA, Aikawa M, Weissleder R

Multimodality Molecular Imaging Identifies Proteolytic and Osteogenic Activities in Early Aortic Valve Disease.

Circulation. 2007;115:377-386 - PMID: 17224478 - DOI: 10.1161/CIRCULATIONAHA.106.654913

Sosnovik DE, Nahrendorf M, Deliolanis N, Novikov M, Aikawa E, Josephson L, Rosenzweig A, Weissleder R, Ntziachristos V

Fluorescence Tomography and Magnetic Resonance Imaging of Myocardial Macrophage Infiltration in Infarcted Myocardium In Vivo.

Circulation. 2007;115:1384-1391 - PMID: 17339546 - DOI: 10.1161/CIRCULATIONAHA.106.663351

Jaffer FA, Kim DE, Quinti L, Tung CH, Aikawa E, Pande AN, Kohler RH, Shi GP, Libby P, Weissleder R

Optical Visualization of Cathepsin K Activity in Atherosclerosis With a Novel, Protease-Activatable Fluorescence Sensor.

Circulation. 2007;115(17):2292-8 - PMID: 17420353 - DOI: 10.1161/CIRCULATIONAHA.106.660340