MGH Center for Systems Biology

Ziller MJ, Müller F, Liao J, Zhang Y, Gu H, Bock C, Boyle P, Epstein CB, Bernstein BE, Lengauer T, Gnirke A, Meissner A

Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types.

PLoS Genet. 2011;7(12):e1002389 - PMID: 22174693 - PMCID: PMC3234221 - DOI: 10.1371/journal.pgen.1002389

Endoh M, Endo TA, Endoh T, Isono K, Sharif J, Ohara O, Toyoda T, Ito T, Eskeland R, Bickmore WA, Vidal M, Bernstein BE, Koseki H

Histone H2A Mono-Ubiquitination Is a Crucial Step to Mediate PRC1-Dependent Repression of Developmental Genes to Maintain ES Cell Identity.

PLoS Genet. 2012;8(7):e1002774 - PMID: 22844243 - PMCID: PMC3405999 - DOI: 10.1371/journal.pgen.1002774

Viaud S, Daillère R, Boneca IG, Lepage P, Langella P, Chamaillard M, Pittet MJ, Ghiringhelli F, Trinchieri G, Goldszmid R, Zitvogel L

Gut microbiome and anticancer immune response: really hot Sh*t!

Cell Death Differ. 2014;22(2):199-214 - PMID: 24832470 - PMCID: PMC4291500 - DOI: 10.1038/cdd.2014.56

Shtatland T, Gill S, Javornik B, Johansson H, Singer B, Uhlenbeck O, Zichi D, Gold L

Interactions of Escherichia coli RNA with bacteriophage MS2 coat protein: genomic SELEX.

Nucleic Acids Res. 2000;28:E93 - PMID: 11058143 - PMCID: PMC113162 - DOI: 10.1093/nar/28.21.e93

Singer B, Shtatland T, Brown D, Gold L

Libraries for genomic SELEX.

Nucleic Acids Res. 1997;25:781-6 - PMID: 9016629 - PMCID: PMC146522 - DOI: 10.1093/nar/25.4.781

Abrams E, Shtatland T, Lerman L

PCR assay for a polymorphic TaqI site in the human K-ras-2 gene on chromosome 12p (KRAS2).

Nucleic Acids Res. 1991;19:4795 - PMID: 1679926 - PMCID: PMC328755 - DOI: 10.1093/nar/19.17.4795

Sander JD, Ramirez CL, Linder SJ, Pattanayak V, Shoresh N, Ku M, Foden JA, Reyon D, Bernstein BE, Liu DR, Joung JK

In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites.

Nucleic Acids Res. 2013;41(19):e181 - PMID: 23945932 - PMCID: PMC3799455 - DOI: 10.1093/nar/gkt716

Babitt JL, Lin HY

The molecular pathogenesis of hereditary hemochromatosis.

Semin Liver Dis. 2011;31(3):280-92 - PMID: 21901658 - DOI: 10.1055/s-0031-1286059

Etzrodt M, Cortez-Retamozo V, Newton A, Zhao J, Ng A, Wildgruber M, Romero P, Wurdinger T, Xavier RJ, Geissmann F, Meylan E, Nahrendorf M, Swirski FK, Baltimore D, Weissleder R, Pittet MJ

Regulation of Monocyte Functional Heterogeneity by miR-146a and Relb

Cell Rep. 2012;1(4):1-8 - PMID: 22545247 - PMCID: PMC3334310 - DOI: 10.1016/j.celrep.2012.02.009

Fan X, Li Q, Pisarek-Horowitz A, Rasouly HM, Wang X, Bonegio RG, Wang H, McLaughlin M, Mangos S, Kalluri R, Holzman LB, Drummond IA, Brown D, Salant DJ, Lu W

Inhibitory Effects of Robo2 on Nephrin: A Crosstalk between Positive and Negative Signals Regulating Podocyte Structure.

Cell Rep. 2012;2(1):52-61 - PMID: 22840396 - PMCID: PMC3627357 - DOI: 10.1016/j.celrep.2012.06.002

Mak AB, Nixon AM, Kittanakom S, Stewart JM, Chen GI, Curak J, Gingras AC, Mazitschek R, Neel BG, Stagljar I, Moffat J

Regulation of CD133 by HDAC6 Promotes β-Catenin Signaling to Suppress Cancer Cell Differentiation.

Cell Rep. 2012;2(4):951-63 - PMID: 23084749 - PMCID: PMC3590846 - DOI: 10.1016/j.celrep.2012.09.016

Rheinbay E, Suvà ML, Gillespie SM, Wakimoto H, Patel AP, Shahid M, Oksuz O, Rabkin SD, Martuza RL, Rivera MN, Louis DN, Kasif S, Chi AS, Bernstein BE

An Aberrant Transcription Factor Network Essential for Wnt Signaling and Stem Cell Maintenance in Glioblastoma.

Cell Rep. 2013;3(5):1567-1579 - PMID: 23707066 - PMCID: PMC3774301 - DOI: 10.1016/j.celrep.2013.04.021

Lan YY, Londoño D, Bouley R, Rooney MS, Hacohen N

Dnase2a Deficiency Uncovers Lysosomal Clearance of Damaged Nuclear DNA via Autophagy.

Cell Rep. 2014;9(1):180-92 - PMID: 25284779 - PMCID: PMC4555847 - DOI: 10.1016/j.celrep.2014.08.074

Levy O, Mortensen LJ, Boquet G, Tong Z, Perrault C, Benhamou B, Zhang J, Stratton T, Han E, Safaee H, Musabeyezu J, Yang Z, Multon MC, Rothblatt J, Deleuze JF, Lin CP, Karp JM

A Small-Molecule Screen for Enhanced Homing of Systemically Infused Cells.

Cell Rep. 2015;10(8):1261-1268 - PMID: 25732817 - PMCID: PMC4361231 - DOI: 10.1016/j.celrep.2015.01.057

Pucci F, Rickelt S, Newton AP, Garris C, Nunes E, Evavold C, Pfirschke C, Engblom C, Mino-Kenudson M, Hynes RO, Weissleder R, Pittet MJ

PF4 Promotes Platelet Production and Lung Cancer Growth.

Cell Rep. 2016;17(7):1764-1772 - PMID: 27829148 - PMCID: PMC5108525 - DOI: 10.1016/j.celrep.2016.10.031

Pittet M, Swirski F, Reynolds F, Josephson L, Weissleder R.

Labeling of immune cells for in vivo imaging using magnetofluorescent nanoparticles

Nat Protoc. 2006;1(1):73-79 - PMID: 17406214 - DOI: 10.1038/nprot.2006.11

Lo Celso C, Lin CP, Scadden DT

In vivo imaging of transplanted hematopoietic stem and progenitor cells in mouse calvarium bone marrow.

Nat Protoc. 2010;6(1):1-14 - PMID: 21212779 - PMCID: PMC3382040 - DOI: 10.1038/nprot.2010.168

Adli M, Bernstein BE

Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq.

Nat Protoc. 2011;6(10):1656-68 - PMID: 21959244 - PMCID: PMC4493313 - DOI: 10.1038/nprot.2011.402

Vinegoni C, Aguirre AD, Lee S, Weissleder R

Imaging the beating heart in the mouse using intravital microscopy techniques.

Nat Protoc. 2015;10(11):1802-1819 - PMID: 26492138 - PMCID: PMC5380003 - DOI: 10.1038/nprot.2015.119

Bremer C, Mustafa M, Bogdanov A Jr, Ntziachristos V, Petrovsky A, Weissleder R

Steady-state blood volume measurements in experimental tumors with different angiogenic burdens a study in mice

Radiology. 2003;226:214-20 - PMID: 12511693 - DOI: 10.1148/radiol.2261012140

Mahmood U, Tung CH, Tang Y, Weissleder R

Feasibility of in vivo multichannel optical imaging of gene expression: experimental study in mice

Radiology. 2002;224:446-51 - PMID: 12147841 - DOI: 10.1148/radiol.2242011589

Bremer C, Tung CH, Bogdanov A Jr, Weissleder R

Imaging of differential protease expression in breast cancers for detection of aggressive tumor phenotypes

Radiology. 2002;222:814-8 - PMID: 11867806 - DOI: 10.1148/radiol.2223010812

Weissleder R, Mahmood U

Molecular imaging

Radiology. 2001;219:316-33 - PMID: 11323453 - DOI: 10.1148/radiology.219.2.r01ma19316

Moore A, Josephson L, Bhorade RM, Basilion JP, Weissleder R

Human transferrin receptor gene as a marker gene for MR imaging

Radiology. 2001;221:244-50 - PMID: 11568347 - DOI: 10.1148/radiol.2211001784

Bremer C, Bredow S, Mahmood U, Weissleder R, Tung CH

Optical imaging of matrix metalloproteinase-2 activity in tumors: feasibility study in a mouse model

Radiology. 2001;221:523-9 - PMID: 11687699 - DOI: 10.1148/radiol.2212010368

Moore A, Marecos E, Bogdanov A Jr, Weissleder R

Tumoral distribution of long-circulating dextran-coated iron oxide nanoparticles in a rodent model

Radiology. 2000;214:568-74 - PMID: 10671613 - DOI: 10.1148/radiology.214.2.r00fe19568

Weissleder R

Molecular imaging: exploring the next frontier

Radiology. 1999;212:609-14 - PMID: 10478223 - DOI: 10.1148/radiology.212.3.r99se18609

Mahmood U, Tung CH, Bogdanov A Jr, Weissleder R

Near-infrared optical imaging of protease activity for tumor detection

Radiology. 1999;213:866-70 - PMID: 10580968 - DOI: 10.1148/radiology.213.3.r99dc14866

Funovics MA, Weissleder R, Mahmood U

Catheter-based in vivo imaging of enzyme activity and gene expression: feasibility study in mice.

Radiology. 2004;231(3):659-66 - PMID: 15163807 - DOI: 10.1148/radiol.2313030831

Mahmood U

Can MR Imaging Be Used to Track Delivery of Intravascularly Administered Stem Cells?

Radiology. 2004;233(3):625-6 - PMID: 15564396 - DOI: 10.1148/radiol.2333041190

Chen JW, Querol Sans M, Bogdanov Jr A, Weissleder R

Imaging of myeloperoxidase in mice by using novel amplifiable paramagnetic substrates

Radiology. 2006;240 (2):473-81 - PMID: 16864673 - DOI: 10.1148/radiol.2402050994

Mahmood U

Can a clinically used chemoembolization vehicle improve transgene delivery?

Radiology. 2006;240(3):619-20 - PMID: 16926318 - DOI: 10.1148/radiol.2403060761

Kim DE, Tsuji K, Kim YR, Mueller FJ, Eom HS, Snyder EY, Lo EH, Weissleder R, Schellingerhout D

Neural Stem Cell Transplant Survival in Brains of Mice: Assessing the Effect of Immunity and Ischemia by using Real-time Bioluminescent Imaging.

Radiology. 2006;241(3):822-830 - PMID: 17114629 - DOI: 10.1148/radiol.2413050466

Montet X, Figueiredo JL, Alencar H, Ntziachristos V, Mahmood U, Weissleder R.

Tomographic fluorescence imaging of tumor vascular volume in mice.

Radiology. 2007;242 (3):751-758 - PMID: 17325064 - DOI: 10.1148/radiol.2423052065

Alencar H, Funovics MA, Figueiredo J, Sawaya H, Weissleder R, Mahmood U

Colonic Adenocarcinomas: Near-Infrared Microcatheter Imaging of Smart Probes for Early Detection.

Radiology. 2007;244(1):232-8 - PMID: 17507718 - DOI: 10.1148/radiol.2441052114

Upadhyay R, Sheth RA, Weissleder R, Mahmood U

Quantitative Real-time Catheter-based Fluorescence Molecular Imaging in Mice.

Radiology. 2007;245(2):523-31 - PMID: 17940307 - DOI: 10.1148/radiol.2452061613

Nahrendorf M, Hiller K, Theisen D, Hu K, Waller C, Kaiser R, Haase A, Ertl G, Brinkmann R, Bauer W

Effect of transmyocardial laser revascularization on myocardial perfusion and left ventricular remodeling after myocardial infarction in rats.

Radiology. 2002;225(2):487-93 - PMID: 12409584 - DOI: 10.1148/radiol.2252011325

Goldberg M, Gazelle G, Boland G, Hahn P, Mayo-Smith W, Pivovarov M, Halpern E, Wittenberg J

Focal hepatic lesions: effect of three-dimensional wavelet compression on detection at CT.

Radiology. 1997;202:159-65 - PMID: 8988206 - DOI: 10.1148/radiology.202.1.8988206

Gee MS, Upadhyay R, Bergquist H, Alencar H, Reynolds F, Maricevich M, Weissleder R, Josephson L, Mahmood U

Human Breast Cancer Tumor Models: Molecular Imaging of Drug Susceptibility and Dosing during HER2/neu-targeted Therapy.

Radiology. 2008;248(3):925-35 - PMID: 18647846 - PMCID: PMC2798096 - DOI: 10.1148/radiol.2482071496

Korosoglou G, Shah S, Vonken EJ, Gilson WD, Schar M, Tang L, Kraitchman DL, Boston RC, Sosnovik DE, Weiss RG, Weissleder R, Stuber M

Off-Resonance Angiography: A New Method to Depict Vessels--Phantom and Rabbit Studies.

Radiology. 2008;249(2)::501-509 - PMID: 18780823 - PMCID: PMC2657865 - DOI: 10.1148/radiol.2491071706

Sosnovik DE

Will molecular MR imaging play a role in identification and treatment of patients with vulnerable atherosclerotic plaques?

Radiology. 2009;251:309-10 - PMID: 19401565 - DOI: 10.1148/radiol.2512090268

Sheth RA, Tam JM, Maricevich MA, Josephson L, Mahmood U

Quantitative Endovascular Fluorescence-based Molecular Imaging through Blood of Arterial Wall Inflammation.

Radiology. 2009;251(3):813-21 - PMID: 19474377 - PMCID: PMC2687531 - DOI: 10.1148/radiol.2513081450

Pandharipande PV, Gervais DA, Hartman RI, Harisinghani MG, Feldman AS, Mueller PR, Gazelle GS

Renal Mass Biopsy to Guide Treatment Decisions for Small Incidental Renal Tumors: A Cost-effectiveness Analysis.

Radiology. 2010;256(3):836-46 - PMID: 20720070 - PMCID: PMC2923731 - DOI: 10.1148/radiol.10092013

de Marco G, Bogdanov A, Marecos E, Moore A, Simonova M, Weissleder R

MR imaging of gene delivery to the central nervous system with an artificial vector.

Radiology. 1998;208(1):65-71 - PMID: 9646794 - DOI: 10.1148/radiology.208.1.9646794

Weissleder R, Simonova M, Bogdanova A, Bredow S, Enochs WS, Bogdanov A

MR imaging and scintigraphy of gene expression through melanin induction.

Radiology. 1997;204(2):425-9 - PMID: 9240530 - DOI: 10.1148/radiology.204.2.9240530

Enochs WS, Petherick P, Bogdanova A, Mohr U, Weissleder R

Paramagnetic metal scavenging by melanin: MR imaging.

Radiology. 1997;204(2):417-23 - PMID: 9240529 - DOI: 10.1148/radiology.204.2.9240529

Harisinghani MG, Saini S, Weissleder R, Halpern EF, Schima W, Rubin DL, Stillman AE, Sica GT, Small WC, Hahn PF

Differentiation of liver hemangiomas from metastases and hepatocellular carcinoma at MR imaging enhanced with blood-pool contrast agent Code-7227.

Radiology. 1997;202(3):687-91 - PMID: 9051017 - DOI: 10.1148/radiology.202.3.9051017

Harika L, Weissleder R, Poss K, Papisov MI

Macromolecular intravenous contrast agent for MR lymphography: characterization and efficacy studies.

Radiology. 1996;198(2):365-70 - PMID: 8596833 - DOI: 10.1148/radiology.198.2.8596833

Gupta H, Wilkinson RA, Bogdanov AA, Callahan RJ, Weissleder R

Inflammation: imaging with methoxy poly(ethylene glycol)-poly-L-lysine-DTPA, a long-circulating graft copolymer.

Radiology. 1995;197(3):665-9 - PMID: 7480736 - DOI: 10.1148/radiology.197.3.7480736

Zimmer C, Weissleder R, Poss K, Bogdanova A, Wright SC, Enochs WS

MR imaging of phagocytosis in experimental gliomas.

Radiology. 1995;197(2):533-8 - PMID: 7480707 - DOI: 10.1148/radiology.197.2.7480707