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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
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
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
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
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
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
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
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
Ryan RJH, Petrovic J, Rausch DM, Zhou Y, Lareau CA, Kluk MJ, Christie AL, Lee WY, Tarjan DR, Guo B, Donohue LKH, Gillespie SM, Nardi V, Hochberg EP, Blacklow SC, Weinstock DM, Faryabi RB, Bernstein BE, Aster JC, Pear WS
A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas.
Cell Rep. 2017;21(3):784-797 - PMID: 29045844 - PMCID: PMC5687286 - DOI: 10.1016/j.celrep.2017.09.066
Zaborowski MP, Lee K, Na YJ, Sammarco A, Zhang X, Iwanicki M, Cheah PS, Lin HY, Zinter M, Chou CY, Fulci G, Tannous BA, Lai CP, Birrer MJ, Weissleder R, Lee H, Breakefield XO
Methods for Systematic Identification of Membrane Proteins for Specific Capture of Cancer-Derived Extracellular Vesicles.
Cell Rep. 2019;27(1):255-268.e6 - PMID: 30943406 - PMCID: PMC6528836 - DOI: 10.1016/j.celrep.2019.03.003
Shikatani EA, Besla R, Ensan S, Upadhye A, Khyzha N, Li A, Emoto T, Chiu F, Degousee N, Moreau JM, Perry HM, Thayaparan D, Cheng HS, Pacheco S, Smyth D, Noyan H, Zavitz CCJ, Bauer CMT, Hilgendorf I, Libby P, Swirski FK, Gommerman JL, Fish JE, Stampfli MR, Cybulsky MI, Rubin BB, Paige CJ, Bender TP, McNamara CA, Husain M, Robbins CS
c-Myb Exacerbates Atherosclerosis through Regulation of Protective IgM-Producing Antibody-Secreting Cells.
Cell Rep. 2019;27(8):2304-2312.e6 - PMID: 31116977 - DOI: 10.1016/j.celrep.2019.04.090
Gyuris A, Navarrete-Perea J, Jo A, Cristea S, Zhou S, Fraser K, Wei Z, Krichevsky AM, Weissleder R, Lee H, Gygi SP, Charest A
Physical and Molecular Landscapes of Mouse Glioma Extracellular Vesicles Define Heterogeneity.
Cell Rep. 2019;27(13):3972-3987.e6 - PMID: 31242427 - PMCID: PMC6604862 - DOI: 10.1016/j.celrep.2019.05.089
Pfirschke C, Engblom C, Gungabeesoon J, Lin Y, Rickelt S, Zilionis R, Messemaker M, Siwicki M, Gerhard GM, Kohl A, Meylan E, Weissleder R, Klein AM, Pittet MJ
Tumor-Promoting Ly-6G+ SiglecFhigh Cells Are Mature and Long-Lived Neutrophils.
Cell Rep. 2020;32(12):108164 - PMID: 32966785 - PMCID: PMC7508173 - DOI: 10.1016/j.celrep.2020.108164
Kim IS, Wu J, Rahme GJ, Battaglia S, Dixit A, Gaskell E, Chen H, Pinello L, Bernstein BE
Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies.
Cell Rep. 2020;33(1):108222 - PMID: 33027665 - PMCID: PMC7646252 - DOI: 10.1016/j.celrep.2020.108222
Barrett TJ, Corr EM, van Solingen C, Schlamp F, Brown EJ, Koelwyn GJ, Lee AH, Shanley LC, Spruill TM, Bozal F, de Jong A, Newman AAC, Drenkova K, Silvestro M, Ramkhelawon B, Reynolds HR, Hochman JS, Nahrendorf M, Swirski FK, Fisher EA, Berger JS, Moore KJ
Chronic stress primes innate immune responses in mice and humans.
Cell Rep. 2021;36(10):109595 - PMID: 34496250 - PMCID: PMC8493594 - DOI: 10.1016/j.celrep.2021.109595
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
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
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
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
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
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