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Jochems J, Boulden J, Lee BG, Blendy JA, Jarpe M, Mazitschek R, Van Duzer JH, Berton O

Antidepressant-Like Properties of Novel HDAC6 Selective Inhibitors with Improved Brain Bioavailability.
Neuropsychopharmacology. 2013;39(2):389-400 - PMID: 23954848 - PMCID: PMC3870780 - DOI: 10.1038/npp.2013.207

Gerosa L, Chidley C, Fröhlich F, Sanchez G, Lim SK, Muhlich J, Chen JY, Vallabhaneni S, Baker GJ, Schapiro D, Atanasova MI, Chylek LA, Shi T, Yi L, Nicora CD, Claas A, Ng TSC, Kohler RH, Lauffenburger DA, Weissleder R, Miller MA, Qian WJ, Wiley HS, Sorger PK

Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells.
Cell Syst. 2020;11(5):478-494.e9 - PMID: 33113355 - PMCID: PMC8009031 - DOI: 10.1016/j.cels.2020.10.002

Arlauckas S, Oh N, Li R, Weissleder R, Miller MA

Macrophage imaging and subset analysis using single-cell RNA sequencing.
Nanotheranostics. 2021;5(1):36-56 - PMID: 33391974 - PMCID: PMC7738942 - DOI: 10.7150/ntno.50185

Miller MA, Arlauckas S, Weissleder R

Prediction of Anti-cancer Nanotherapy Efficacy by Imaging
Nanotheranostics. 2017;1(3):296-312 - PMID: 29071194 - PMCID: PMC5646731 - DOI: 10.7150/ntno.20564

Ferder IC, Fung L, Ohguchi Y, Zhang X, Lassen KG, Capen D, Brown D, Xavier RJ, Wang N

Meiotic gatekeeper STRA8 suppresses autophagy by repressing Nr1d1 expression during spermatogenesis in mice.
PLoS Genet. 2019;15(5):e1008084 - PMID: 31059511 - PMCID: PMC6502318 - DOI: 10.1371/journal.pgen.1008084

Ku M, Koche R, Rheinbay E, Mendenhall E, Endoh M, Mikkelsen T, Presser A, Nusbaum C, Xie X, Chi A, Adli M, Kasif S, Ptaszek L, Cowan C, Lander E, Koseki H, Bernstein B

Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains.
PLoS Genet. 2008;4(10):e1000242 - PMID: 18974828 - PMCID: PMC2567431 - DOI: 10.1371/journal.pgen.1000242

Mendenhall EM, Koche RP, Truong T, Zhou VW, Issac B, Chi AS, Ku M, Bernstein BE

GC-Rich Sequence Elements Recruit PRC2 in Mammalian ES Cells.
PLoS Genet. 2010;6(12):e1001244 - PMID: 21170310 - PMCID: PMC3000368 - DOI: 10.1371/journal.pgen.1001244

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

Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, De Jager PL, Shaw SY, Wolfish CS, Slavik JM, Cotsapas C, Rivas M, Dermitzakis ET, Cahir-McFarland E, Kieff E, Hafler D, Daly MJ, Altshuler D

Genetic Analysis of Human Traits In Vitro: Drug Response and Gene Expression in Lymphoblastoid Cell Lines
PLoS Genet. 2008;4(11):e1000287 - PMID: 19043577 - PMCID: PMC2583954 - DOI: 10.1371/journal.pgen.1000287

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

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

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

Brown CR, Gupta S, Qin J, Racie T, He G, Lentini S, Malone R, Yu M, Matsuda S, Shulga-Morskaya S, Nair AV, Theile CS, Schmidt K, Shahraz A, Goel V, Parmar RG, Zlatev I, Schlegel MK, Nair JK, Jayaraman M, Manoharan M, Brown D, Maier MA, Jadhav V

Investigating the pharmacodynamic durability of GalNAc-siRNA conjugates.
Nucleic Acids Res. 2020;48(21):11827-11844 - PMID: 32808038 - PMCID: PMC7708070 - DOI: 10.1093/nar/gkaa670

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

Pittet MJ, Garris CS, Arlauckas SP, Weissleder R

Recording the wild lives of immune cells.
Sci Immunol. 2018;3(27):ePub - PMID: 30194240 - PMCID: PMC6771424 - DOI: 10.1126/sciimmunol.aaq0491

Calcagno DM, Ng RP, Toomu A, Zhang C, Huang K, Aguirre AD, Weissleder R, Daniels LB, Fu Z, King KR

Type I interferon responses to ischemic injury begin in the bone marrow of mice and humans and depend on Tet2, Nrf2, and Irf3
Sci Immunol. 2020;5(51):ePub - PMID: 32978242 - PMCID: PMC7808338 - DOI: 10.1126/sciimmunol.aaz1974

Siwicki M, Gort-Freitas NA, Messemaker M, Bill R, Gungabeesoon J, Engblom C, Zilionis R, Garris C, Gerhard GM, Kohl A, Lin Y, Zou AE, Cianciaruso C, Bolli E, Pfirschke C, Lin YJ, Piot C, Mindur JE, Talele N, Kohler RH, Iwamoto Y, Mino-Kenudson M, Pai SI, deVito C, Koessler T, Merkler D, Coukos A, Wicky A, Fraga M, Sempoux C, Jain RK, Dietrich PY, Michielin O, Weissleder R, Klein AM, Pittet MJ

Resident Kupffer cells and neutrophils drive liver toxicity in cancer immunotherapy.
Sci Immunol. 2021;6(61):eabi7083 - PMID: 34215680 - PMCID: PMC8845079 - DOI: 10.1126/sciimmunol.abi7083

Adamson RJ, Payne NC, Bartual SG, Mazitschek R, Bullock AN

Structural and biochemical characterization establishes a detailed understanding of KEAP1-CUL3 complex assembly.
Free Radic Biol Med. 2023;204:215-225 - PMID: 37156295 - PMCID: PMC10564622 - DOI: 10.1016/j.freeradbiomed.2023.04.021

Malka R, Brugnara C, Cialic R, Higgins JM

Non-Parametric Combined Reference Regions and Prediction of Clinical Risk.
Clin Chem. 2020;66(2):363-372 - PMID: 32040586 - PMCID: PMC7055670 - DOI: 10.1093/clinchem/hvz020

Chen J, Landegger LD, Sun Y, Ren J, Maimon N, Wu L, Ng MR, Chen JW, Zhang N, Zhao Y, Gao X, Fujita T, Roberge S, Huang P, Jain RK, Plotkin SR, Stankovic KM, Xu L

A cerebellopontine angle mouse model for the investigation of tumor biology, hearing, and neurological function in NF2-related vestibular schwannoma.
Nat Protoc. 2019;14(2):541-555 - PMID: 30617350 - PMCID: PMC6571021 - DOI: 10.1038/s41596-018-0105-7

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

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

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

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 - PMCID: PMC5928516 - DOI: 10.1038/nprot.2017.043

Pulli B, Bure L, Wojtkiewicz GR, Iwamoto Y, Ali M, Li D, Schob S, Li-Chun Hsieh K, Jacobs AH, Chen JW

Multiple Sclerosis: Myeloperoxidase Immunoradiology Improves Detection of Acute and Chronic Disease in Experimental Model.
Radiology. 2014;275(2):480-9 - PMID: 25494298 - PMCID: PMC4455671 - DOI: 10.1148/radiol.14141495

Zhang Y, Seeburg DP, Pulli B, Wojtkiewicz GR, Bure L, Atkinson W, Schob S, Iwamoto Y, Ali M, Zhang W, Rodriguez E, Milewski A, Keliher EJ, Wang C, Pan Y, Swirski FK, Chen JW

Myeloperoxidase Nuclear Imaging for Epileptogenesis.
Radiology. 2015;278(3):822-30 - PMID: 26397127 - PMCID: PMC4770943 - DOI: 10.1148/radiol.2015141922

Albadawi H, Chen JW, Oklu R, Wu Y, Wojtkiewicz G, Pulli B, Milner JD, Cambria RP, Watkins MT

Spinal Cord Inflammation: Molecular Imaging after Thoracic Aortic Ischemia Reperfusion Injury.
Radiology. 2016;282(1):202-211 - PMID: 27509542 - PMCID: PMC5207124 - DOI: 10.1148/radiol.2016152222

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;284(2):390-400 - PMID: 28358240 - PMCID: PMC5548451 - DOI: 10.1148/radiol.2017160588

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
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