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Haase C, Gustafsson K, Mei S, Yeh SC, Richter D, Milosevic J, Turcotte R, Kharchenko PV, Sykes DB, Scadden DT, Lin CP

Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging.
Nat Methods. 2022;19(12):1622-1633 - PMID: 36424441 - PMCID: PMC9718684 - DOI: 10.1038/s41592-022-01673-2

Chittajallu DR, Florian S, Kohler RH, Iwamoto Y, Orth JD, Weissleder R*, Danuser G*, Mitchison TJ*

In vivo cell-cycle profiling in xenograft tumors by quantitative intravital microscopy
Nat Methods. 2015;12(6):577-585 - PMID: 25867850 - PMCID: PMC4579269 - DOI: 10.1038/nmeth.3363

Glenn DR#, Lee K#, Park H, Weissleder R, Yacoby A, Lukin MD, Lee H*, Walsworth RL*, Connolly CB*

Single-cell magnetic imaging using a quantum diamond microscope.
Nat Methods. 2015;12(8):736-738 - PMID: 26098019 - PMCID: PMC4521973 - DOI: 10.1038/nmeth.3449

Kong L, Tang J, Little JP, Yu Y, Lämmermann T, Lin CP, Germain RN, Cui M

Continuous volumetric imaging via an optical phase-locked ultrasound lens.
Nat Methods. 2015;12(8):759-762 - PMID: 26167641 - PMCID: PMC4551496 - DOI: 10.1038/nmeth.3476

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

Herrmann K, Schwaiger M, Lewis JS, Solomon SB, McNeil BJ, Baumann M, Gambhir SS, Hricak H, Weissleder R

Radiotheranostics: a roadmap for future development
Lancet Oncol. 2020;21(3):e146–56 - PMID: 32135118 - PMCID: PMC7367151 - DOI: 10.1016/S1470-2045(19)30821-6 - Cover

Shi DD, Guo JA, Hoffman HI, Su J, Mino-Kenudson M, Barth JL, Schenkel JM, Loeffler JS, Shih HA, Hong TS, Wo JY, Aguirre AJ, Jacks T, Zheng L, Wen PY, Wang TC, Hwang WL

Therapeutic avenues for cancer neuroscience: translational frontiers and clinical opportunities.
Lancet Oncol. 2022;23(2):e62-e74 - PMID: 35114133 - PMCID: PMC9516432 - DOI: 10.1016/S1470-2045(21)00596-9

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

Hricak H, Mayerhoefer ME, Herrmann K, Lewis JS, Pomper MG, Hess CP, Riklund K , Scott AM, Weissleder R

Advances and challenges in precision imaging
Lancet Oncol. 2025;26:e34-e45 - PMID: 39756454 - PMCID: PMC12117531 - DOI: 10.1016/S1470-2045(24)00395-4

Bernstock JD, Ling A, Chiocca EA

Combined gene therapies for high-grade glioma.
Lancet Oncol. 2023;24(9):949-950 - PMID: 37657467 - DOI: 10.1016/S1470-2045(23)00389-3

Song J, Cho MH, Cho H, Song Y, Lee SW, Nam HC, Yoon TH, Shin JC, Hong JS, Kim Y, Ekanayake E, Jeon J, You DG, Im SG, Choi GS, Park JS, Carter BC, Balaj L, Seo AN, Miller MA, Park SY, Kang T, Castro CM, Lee H

Amplifying mutational profiling of extracellular vesicle mRNA with SCOPE.
Nat Biotechnol. 2024;43(9):1485-1495 - PMID: 39375445 - PMCID: PMC12747296 - DOI: 10.1038/s41587-024-02426-6

Gustafsson K, Isaev S, Mirsanaye K, Hofmann J, Kooshesh KA, Baryawno N, Kiem A, Severe N, Zhao T, Scadden EW, Spencer JA, Burns C, Akilan K, Barkas N, Gessessew H, Kokkaliaris KD, Lin CP, Kharchenko PV, Scadden DT

Mesenchymal thymic niche cells enable regeneration of the adult thymus and T cell immunity.
Nat Biotechnol. 2025;:ePub - PMID: 41168496 - PMCID: PMC13229158 - DOI: 10.1038/s41587-025-02864-w

Gupta A, Das R, Reed K, Jeon T, Nguyen QTC, Rudra A, Ge X, Trongjit S, Vanrobaeys YS, Langer R, Weissleder R, Garris C, Anderson DG

Immune-remodeling mRNAs expressing IRF8 or NIK generate durable antitumor immunity in multiple cancer models.
Nat Biotechnol. 2026;:ePub - PMID: 42129506 - PMCID: PMC13242704 - DOI: 10.1038/s41587-026-03115-2

Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk RP, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A

Evaluation of SARS-CoV-2 serology assays reveals a range of test performance.
Nat Biotechnol. 2020;38(10):1174-1183 - PMID: 32855547 - PMCID: PMC7740072 - DOI: 10.1038/s41587-020-0659-0

Ko J, Wilkovitsch M, Oh J, Kohler RH, Bolli E, Pittet MJ, Vinegoni C, Sykes DB, Mikula H, Weissleder R, Carlson JCT

Spatiotemporal multiplexed immunofluorescence imaging of living cells and tissues with bioorthogonal cycling of fluorescent probes
Nat Biotechnol. 2022;40(11):1654-1662 - PMID: 35654978 - PMCID: PMC9669087 - DOI: 10.1038/s41587-022-01339-6

Najm FJ, Strand C, Donovan KF, Hegde M, Sanson KR, Vaimberg EW, Sullender ME, Hartenian E, Kalani Z, Fusi N, Listgarten J, Younger ST, Bernstein BE, Root DE, Doench JG

Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens.
Nat Biotechnol. 2017;36(2):179-189 - PMID: 29251726 - PMCID: PMC5800952 - DOI: 10.1038/nbt.4048

Shareef SJ, Bevill SM, Raman AT, Aryee MJ, van Galen P, Hovestadt V, Bernstein BE

Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells.
Nat Biotechnol. 2021;39(9):1086-1094 - PMID: 33958785 - PMCID: PMC8434949 - DOI: 10.1038/s41587-021-00910-x

Millar DG, Ramjiawan RR, Kawaguchi K, Gupta N, Chen J, Zhang S, Nojiri T, Ho WW, Aoki S, Jung K, Chen I, Shi F, Heather JM, Shigeta K, Morton LT, Sepulveda S, Wan L, Joseph R, Minogue E, Khatri A, Bardia A, Ellisen LW, Corcoran RB, Hata AN, Pai SI, Jain RK, Fukumura D, Duda DG, Cobbold M

Antibody-mediated delivery of viral epitopes to tumors harnesses CMV-specific T cells for cancer therapy.
Nat Biotechnol. 2020;38(4):420-425 - PMID: 32042168 - PMCID: PMC7456461 - DOI: 10.1038/s41587-019-0404-8

Im H*, Shao H*, Park YI, Peterson VM, Castro CM, Weissleder R*, Lee H*

Label-free detection and molecular profiling of exosomes with a nano-plasmonic sensor
Nat Biotechnol. 2014;32(5):490-5 - PMID: 24752081 - PMCID: PMC4356947 - DOI: 10.1038/nbt.2886

Maeder ML, Angstman JF, Richardson ME, Linder SJ, Cascio VM, Tsai SQ, Ho QH, Sander JD, Reyon D, Bernstein BE, Costello JF, Wilkinson MF, Joung JK

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins.
Nat Biotechnol. 2013;31(12):1137-42 - PMID: 24108092 - PMCID: PMC3858462 - DOI: 10.1038/nbt.2726

Zangi L, Lui KO, von Gise A, Ma Q, Ebina W, Ptaszek LM, Später D, Xu H, Tabebordbar M, Gorbatov R, Sena B, Nahrendorf M, Briscoe DM, Li RA, Wagers AJ, Rossi DJ, Pu WT, Chien KR

Modified mRNA directs the fate of heart progenitor cells and induces vascular regeneration after myocardial infarction.
Nat Biotechnol. 2013;31(10):898-907 - PMID: 24013197 - PMCID: PMC4058317 - DOI: 10.1038/nbt.2682

Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE

Locus-specific editing of histone modifications at endogenous enhancers.
Nat Biotechnol. 2013;31(12):1133-6 - PMID: 24013198 - PMCID: PMC3858395 - DOI: 10.1038/nbt.2701

Rotem A, Ram O, Shoresh N, Sperling RA, Goren A, Weitz DA, Bernstein BE

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state.
Nat Biotechnol. 2015;33(11):1165-72 - PMID: 26458175 - PMCID: PMC4636926 - DOI: 10.1038/nbt.3383

Perez JM, Josephson L, O'Loughlin T, Hogemann D, Weissleder R

Magnetic relaxation switches capable of sensing molecular interactions
Nat Biotechnol. 2002;20:816-20 - PMID: 12134166 - DOI: 10.1038/nbt720

Weissleder R

A clearer vision for in vivo imaging
Nat Biotechnol. 2001;19:316-7 - PMID: 11283581 - DOI: 10.1038/86684

Weissleder R, Kelly K, Sun E, Shtatland T, Josephson L.

Cell-specific targeting of nanoparticles by multivalent attachment of small molecules
Nat Biotechnol. 2005;23:1418-1423 - PMID: 16244656 - DOI: 10.1038/nbt1159

Peterson R, Shaw S, Peterson T, Milan D, Zhong T, Schreiber S, MacRae C, Fishman M

Chemical suppression of a genetic mutation in a zebrafish model of aortic coarctation.
Nat Biotechnol. 2004;22(5):595-9 - PMID: 15097998 - DOI: 10.1038/nbt963

Ntziachristos V, Ripoll J, Wang L, Weissleder R

Looking and Listening to light: the evolution of whole-body photonic imaging
Nat Biotechnol. 2005;23:313-320 - PMID: 15765087 - DOI: 10.1038/nbt1074

Lewin M, Carlesso N, Tung CH, Tang XW, Cory D, Scadden DT, Weissleder R

Tat peptide-derivatized magnetic nanoparticles allow in vivo tracking and recovery of progenitor cells
Nat Biotechnol. 2000;18:410-4 - PMID: 10748521 - DOI: 10.1038/74464

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

In vivo imaging of tumors with protease-activated near-infrared fluorescent probes
Nat Biotechnol. 1999;17:375-8 - PMID: 10207887 - DOI: 10.1038/7933

Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
Nat Biotechnol. 2010;28(10):1097-105 - PMID: 20852635 - PMCID: PMC2955169 - DOI: 10.1038/nbt.1682

Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA

The NIH Roadmap Epigenomics Mapping Consortium.
Nat Biotechnol. 2010;28(10):1045-8 - PMID: 20944595 - PMCID: PMC3607281 - DOI: 10.1038/nbt1010-1045

Leuschner F, Dutta P, Gorbatov R, Novobrantseva TI, Donahoe JS, Courties G, Lee KM, Kim JI, Markmann JF, Marinelli B, Panizzi P, Lee WW, Iwamoto Y, Milstein S, Epstein-Barash H, Cantley W, Wong J, Cortez-Retamozo V, Newton A, Love K, Libby P, Pittet MJ, Swirski FK, Koteliansky V, Langer R, Weissleder R, Anderson DG, Nahrendorf M

Therapeutic siRNA silencing in inflammatory monocytes in mice
Nat Biotechnol. 2011;29(11):1005-10 - PMID: 21983520 - PMCID: PMC3212614 - DOI: 10.1038/nbt.1989

Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D

The structure of haplotype blocks in the human genome.
Science. 2002;296(5576):2225-9 - PMID: 12029063 - DOI: 10.1126/science.1069424

Ryan RJ, Bernstein BE

Molecular biology. Genetic events that shape the cancer epigenome.
Science. 2012;336(6088):1513-4 - PMID: 22723401 - DOI: 10.1126/science.1223730

Sundrud MS, Koralov SB, Feuerer M, Calado DP, Kozhaya AE, Rhule-Smith A, Lefebvre RE, Unutmaz D, Mazitschek R, Waldner H, Whitman M, Keller T, Rao A

Halofuginone Inhibits TH17 Cell Differentiation by Activating the Amino Acid Starvation Response.
Science. 2009;324(5932):1334-1338 - PMID: 19498172 - PMCID: PMC2803727 - DOI: 10.1126/science.1172638

Swirski* FK, Nahrendorf* M, Etzrodt M, Wildgruber M, Cortez-Retamozo V, Panizzi P, Figueiredo JL, Kohler RH, Chudnovskiy A, Waterman P, Aikawa E, Mempel TR, Libby P, Weissleder R, Pittet MJ

Identification of Splenic Reservoir Monocytes and Their Deployment to Inflammatory Sites
Science. 2009;325 (5940):612-6 - PMID: 19644120 - PMCID: PMC2803111 - DOI: 10.1126/science.1175202

Chi A, Bernstein B

Developmental biology. Pluripotent chromatin state.
Science. 2009;323(5911):220-1 - PMID: 19131621 - PMCID: PMC4126799 - DOI: 10.1126/science.1166261

Rauch PJ*, Chudnovskiy A*, Robbins CS*, Weber GF, Etzrodt M, Hilgendorf I, Tiglao E, Figueiredo JL, Iwamoto Y, Theurl I, Gorbatov R, Waring MT, Chicoine AT, Mouded M, Pittet MJ, Nahrendorf M, Weissleder R, Swirski FK

Innate Response Activator B Cells Protect Against Microbial Sepsis
Science. 2012;335(6068):597-601 - PMID: 22245738 - PMCID: PMC3279743 - DOI: 10.1126/science.1215173

Huang D, Swanson E, Lin C, Schuman J, Stinson W, Chang W, Hee M, Flotte T, Gregory K, Puliafito C

Optical coherence tomography.
Science. 1991;254:1178-81 - PMID: 1957169 - PMCID: PMC4638169 - DOI: 10.1126/science.1957169

Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Science. 2009;326(5950):289-93 - PMID: 19815776 - PMCID: PMC2858594 - DOI: 10.1126/science.1181369

Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses.
Science. 2009;326(5950):257-63 - PMID: 19729616 - PMCID: PMC2879337 - DOI: 10.1126/science.1179050

Weber GF, Chousterman BG, He S, Fenn AM, Nairz M, Anzai A, Brenner T, Uhle F, Iwamoto Y, Robbins CS, Noiret L, Maier SL, Zönnchen T, Rahbari NN, Schölch S, Klotzsche-von Ameln A, Chavakis T, Weitz J, Hofer S, Weigand MA, Nahrendorf M, Weissleder R, Swirski FK

Interleukin-3 amplifies acute inflammation and is a potential therapeutic target in sepsis.
Science. 2015;347(6227):1260-1265 - PMID: 25766237 - PMCID: PMC4376966 - DOI: 10.1126/science.aaa4268

Ito K, Turcotte R, Cui J, Zimmerman SE, Pinho S, Mizoguchi T, Arai F, Runnels JM, Alt C, Teruya-Feldstein J, Mar JC, Singh R, Suda T, Lin CP, Frenette PS, Ito K

Self-renewal of a purified Tie2+ hematopoietic stem cell population relies on mitochondrial clearance.
Science. 2016;354(6316):1156-1160 - PMID: 27738012 - PMCID: PMC5164878 - DOI: 10.1126/science.aaf5530

Shema E, Jones D, Shoresh N, Donohue L, Ram O, Bernstein BE

Single-molecule decoding of combinatorially modified nucleosomes.
Science. 2016;352(6286):717-21 - PMID: 27151869 - PMCID: PMC4904710 - DOI: 10.1126/science.aad7701

Patel AP, Tirosh I, Trombetta JJ, Shalek AK, Gillespie SM, Wakimoto H, Cahill DP, Nahed BV, Curry WT, Martuza RL, Louis DN, Rozenblatt-Rosen O, Suvà ML, Regev A, Bernstein BE

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.
Science. 2014;344(6190):1396-401 - PMID: 24925914 - PMCID: PMC4123637 - DOI: 10.1126/science.1254257

Katsimpardi L, Litterman NK, Schein PA, Miller CM, Loffredo FS, Wojtkiewicz GR, Chen JW, Lee RT, Wagers AJ, Rubin LL

Vascular and Neurogenic Rejuvenation of the Aging Mouse Brain by Young Systemic Factors.
Science. 2014;344(6184):630-4 - PMID: 24797482 - PMCID: PMC4123747 - DOI: 10.1126/science.1251141

Flavahan WA, Gaskell E, Bernstein BE

Epigenetic plasticity and the hallmarks of cancer.
Science. 2017;357(6348):ePub - PMID: 28729483 - PMCID: PMC5940341 - DOI: 10.1126/science.aal2380

Nahrendorf M, Swirski FK

Neutrophil-macrophage communication in inflammation and atherosclerosis.
Science. 2015;349(6245):237-8 - PMID: 26185231 - DOI: 10.1126/science.aac7801
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