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Bianchi A, De Castro Silva I, Deshpande NU, Singh S, Mehra S, Garrido VT, Guo X, Nivelo LA, Kolonias DS, Saigh SJ, Wieder E, Rafie CI, Dosch AR, Zhou Z, Umland O, Amirian H, Ogobuiro IC, Zhang J, Ban Y, Shiau C, Nagathihalli NS, Montgomery EA, Hwang WL, Brambilla R, Komanduri K, Villarino AV, Toska E, Stanger BZ, Gabrilovich DI, Merchant NB, Datta J

Cell-autonomous Cxcl1 sustains tolerogenic circuitries and stromal inflammation via neutrophil-derived TNF in pancreatic cancer.
Cancer Discov. 2023;13(6):1428-1453 - PMID: 36946782 - PMCID: PMC10259764 - DOI: 10.1158/2159-8290.CD-22-1046

Weissleder R, Nahrendorf M, Pittet MJ

Imaging macrophages with nanoparticles.
Nat Mater. 2014;13(2):125-38 - PMID: 24452356 - DOI: 10.1038/nmat3780

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

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

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

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

Drier Y, Cotton MJ, Williamson KE, Gillespie SM, Ryan RJ, Kluk MJ, Carey CD, Rodig SJ, Sholl LM, Afrogheh AH, Faquin WC, Queimado L, Qi J, Wick MJ, El-Naggar AK, Bradner JE, Moskaluk CA, Aster JC, Knoechel B, Bernstein BE

An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma.
Nat Genet. 2016;48(3):265-72 - PMID: 26829750 - PMCID: PMC4767593 - DOI: 10.1038/ng.3502

Wang X, Lee RS, Alver BH, Haswell JR, Wang S, Mieczkowski J, Drier Y, Gillespie SM, Archer TC, Wu JN, Tzvetkov EP, Troisi EC, Pomeroy SL, Biegel JA, Tolstorukov MY, Bernstein BE, Park PJ, Roberts CW

SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation.
Nat Genet. 2016;49(2):289-295 - PMID: 27941797 - PMCID: PMC5285474 - DOI: 10.1038/ng.3746

Knoechel B, Roderick JE, Williamson KE, Zhu J, Lohr JG, Cotton MJ, Gillespie SM, Fernandez D, Ku M, Wang H, Piccioni F, Silver SJ, Jain M, Pearson D, Kluk MJ, Ott CJ, Shultz LD, Brehm MA, Greiner DL, Gutierrez A, Stegmaier K, Kung AL, Root DE, Bradner JE, Aster JC, Kelliher MA, Bernstein BE

An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia.
Nat Genet. 2014;46(4):364-70 - PMID: 24584072 - PMCID: PMC4086945 - DOI: 10.1038/ng.2913

Hwang WL, Jagadeesh KA, Guo JA, Hoffman HI, Yadollahpour P, Reeves JW, Mohan R, Drokhlyansky E, Van Wittenberghe N, Ashenberg O, Farhi SL, Schapiro D, Divakar P, Miller E, Zollinger DR, Eng G, Schenkel JM, Su J, Shiau C, Yu P, Freed-Pastor WA, Abbondanza D, Mehta A, Gould J, Lambden C, Porter CBM, Tsankov A, Dionne D, Waldman J, Cuoco MS, Nguyen L, Delorey T, Phillips D, Barth JL, Kem M, Rodrigues C, Ciprani D, Roldan J, Zelga P, Jorgji V, Chen JH, Ely Z, Zhao D, Fuhrman K, Fropf R, Beechem JM, Loeffler JS, Ryan DP, Weekes CD, Ferrone CR, Qadan M, Aryee MJ, Jain RK, Neuberg DS, Wo JY, Hong TS, Xavier R, Aguirre AJ, Rozenblatt-Rosen O, Mino-Kenudson M, Castillo CF, Liss AS, Ting DT, Jacks T, Regev A

Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment.
Nat Genet. 2022;54(8):1178-1191 - PMID: 35902743 - PMCID: PMC10290535 - DOI: 10.1038/s41588-022-01134-8 - Cover

Shiau C, Cao J, Gong D, Gregory MT, Caldwell NJ, Yin X, Cho JW, Wang PL, Su J, Wang S, Reeves JW, Kim TK, Kim Y, Guo JA, Lester NA, Bae JW, Zhao R, Schurman N, Barth JL, Ganci ML, Weissleder R, Jacks T, Qadan M, Hong TS, Wo JY, Roberts H, Beechem JM, Castillo CF, Mino-Kenudson M, Ting DT, Hemberg M, Hwang WL

Spatially resolved analysis of pancreatic cancer identifies therapy-associated remodeling of the tumor microenvironment.
Nat Genet. 2024;56(11):2466-2478 - PMID: 39227743 - PMCID: PMC11816915 - DOI: 10.1038/s41588-024-01890-9

Blohmer M, Cheek DM, Hung WT, Kessler M, Chatzidimitriou F, Wang J, Hung W, Lee IH, Gorelick AN, Wassenaar EC, Yang CY, Yeh YC, Ho HL, Speiser D, Karsten MM, Lanuti M, Pai SI, Kranenburg O, Lennerz JK, Chou TY, Kloor M, Naxerova K

Quantifying cell divisions along evolutionary lineages in cancer.
Nat Genet. 2025;57(3):706-717 - PMID: 39905260 - PMCID: PMC12765479 - DOI: 10.1038/s41588-025-02078-5

Cheek D, Blohmer M, Nowak MA, Antal T, Naxerova K

Age distinguishes selection from causation in cancer genomes.
Nat Genet. 2026;58(6):1320-1330 - PMID: 42086853 - PMCID: PMC13263150 - DOI: 10.1038/s41588-026-02593-z

Shema E, Bernstein BE, Buenrostro JD

Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution.
Nat Genet. 2018;51(1):19-25 - PMID: 30559489 - DOI: 10.1038/s41588-018-0290-x

Naxerova K

Clonal competition in a confined space.
Nat Genet. 2020;52(6):553-554 - PMID: 32424354 - DOI: 10.1038/s41588-020-0638-x

Reiter JG, Hung WT, Lee IH, Nagpal S, Giunta P, Degner S, Liu G, Wassenaar ECE, Jeck WR, Taylor MS, Farahani AA, Marble HD, Knott S, Kranenburg O, Lennerz JK, Naxerova K

Lymph node metastases develop through a wider evolutionary bottleneck than distant metastases.
Nat Genet. 2020;52(7):692-700 - PMID: 32451459 - PMCID: PMC7343611 - DOI: 10.1038/s41588-020-0633-2

Finucane HK, Reshef YA, Anttila V, Slowikowski K, Gusev A, Byrnes A, Gazal S, Loh PR, Lareau C, Shoresh N, Genovese G, Saunders A, Macosko E, Pollack S, , Perry JRB, Buenrostro JD, Bernstein BE, Raychaudhuri S, McCarroll S, Neale BM, Price AL

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types.
Nat Genet. 2018;50(4):621-629 - PMID: 29632380 - PMCID: PMC5896795 - DOI: 10.1038/s41588-018-0081-4

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

Behzadi S, Serpooshan V, Tao W, Hamaly MA, Alkawareek MY, Dreaden EC, Brown D, Alkilany AM, Farokhzad OC, Mahmoudi M

Cellular uptake of nanoparticles: journey inside the cell.
Chem Soc Rev. 2017;46(14):4218-4244 - PMID: 28585944 - PMCID: PMC5593313 - DOI: 10.1039/c6cs00636a

Conway KL, Kuballa P, Song JH, Patel KK, Castoreno AB, Yilmaz OH, Jijon HB, Zhang M, Aldrich LN, Villablanca EJ, Peloquin JM, Goel G, Lee IA, Mizoguchi E, Shi HN, Bhan AK, Shaw SY, Schreiber SL, Virgin HW, Shamji AF, Stappenbeck TS, Reinecker HC, Xavier RJ

Atg16l1 is Required for Autophagy in Intestinal Epithelial Cells and Protection of Mice from Salmonella Infection.
Gastroenterology. 2013;145(6):1347-57 - PMID: 23973919 - PMCID: PMC3840157 - DOI: 10.1053/j.gastro.2013.08.035

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, Rozier M, Meynard D, Odhiambo A, Lin HY, Feng Q, Migas MC, Britton RS, Babitt JL, Fleming RE

Iron regulation of hepcidin despite attenuated Smad1,5,8 signaling in mice without transferrin receptor 2 or Hfe.
Gastroenterology. 2011;141(5):1907-14 - PMID: 21745449 - PMCID: PMC3634343 - DOI: 10.1053/j.gastro.2011.06.077

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

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

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

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

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

Küçükköse E, Laoukili J, Gorelick AN, Degner S, Lacle M, van den Bent L, Peters NA, Verheem A, Hung WT, Frenkel NC, Wassenaar E, Lansu N, Lenos KJ, Vermeulen L, Koopman M, Roodhart JML, Kops GJPL, Borel Rinkes IHM, Hagendoorn J, Naxerova K, Kranenburg O

Lymphatic invasion of plakoglobin-dependent tumor cell clusters drives formation of polyclonal lung metastases in colon cancer.
Gastroenterology. 2023;165(2):429-444.e15 - PMID: 36906044 - DOI: 10.1053/j.gastro.2023.02.047

Yang KS, Ciprani D, O'Shea A, Liss A, Yang R, Fletcher-Mercaldo S, Mino-Kenudson M, Castillo CF, Weissleder R

Extracellular Vesicle Analysis Allows for Identification of Invasive IPMN
Gastroenterology. 2020;160(4):1345-1358.e11 - PMID: 33301777 - PMCID: PMC7956058 - DOI: 10.1053/j.gastro.2020.11.046

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

Lameijer M, Binderup T, van Leent MMT, Senders ML, Fay F, Malkus J, Sanchez-Gaytan BL, Teunissen AJP, Karakatsanis N, Robson P, Zhou X, Ye Y, Wojtkiewicz G, Tang J, Seijkens TTP, Kroon J, Stroes ESG, Kjaer A, Ochando J, Reiner T, Pérez-Medina C, Calcagno C, Fisher EA, Zhang B, Temel RE, Swirski FK, Nahrendorf M, Fayad ZA, Lutgens E, Mulder WJM, Duivenvoorden R

Efficacy and safety assessment of a TRAF6-targeted nanoimmunotherapy in atherosclerotic mice and non-human primates.
Nat Biomed Eng. 2018;2(5):279-292 - PMID: 30936448 - PMCID: PMC6447057 - DOI: 10.1038/s41551-018-0221-2

Weissleder R, Pittet MJ

The expanding landscape of inflammatory cells affecting cancer therapy
Nat Biomed Eng. 2020;4(5):489-498 - PMID: 32203281 - PMCID: PMC7405944 - DOI: 10.1038/s41551-020-0524-y

Krohn-Grimberghe M, Mitchell MJ, Schloss MJ, Khan OF, Courties G, Guimaraes PPG, Rohde D, Cremer S, Kowalski PS, Sun Y, Tan M, Webster J, Wang K, Iwamoto Y, Schmidt SP, Wojtkiewicz GR, Nayar R, Frodermann V, Hulsmans M, Chung A, Hoyer FF, Swirski FK, Langer R, Anderson DG, Nahrendorf M

Nanoparticle-encapsulated siRNAs for gene silencing in the haematopoietic stem-cell niche.
Nat Biomed Eng. 2020;4(11):1076-1089 - PMID: 33020600 - PMCID: PMC7655681 - DOI: 10.1038/s41551-020-00623-7

Cheong J, Yu H, Lee CY, Lee JU, Choi HJ, Lee JH, Lee H, Cheon J

Fast detection of SARS-CoV-2 RNA via the integration of plasmonic thermocycling and fluorescence detection in a portable device.
Nat Biomed Eng. 2020;4(12):1159-1167 - PMID: 33273713 - PMCID: PMC8202505 - DOI: 10.1038/s41551-020-00654-0

Lee H, Castro CM

Thermophoretically enriched detection.
Nat Biomed Eng. 2019;3(3):163-164 - PMID: 30948812 - DOI: 10.1038/s41551-019-0364-9

Andreou C, Weissleder R, Kircher MF

Multiplexed imaging in oncology
Nat Biomed Eng. 2022;6(5):527-540 - PMID: 35624151 - DOI: 10.1038/s41551-022-00891-5

Park J, Park JS, Huang CH, Jo A, Cook K, Wang R, Lin HY, Van Deun J, Li H, Min J, Wang L, Yoon G, Carter BS, Balaj L, Choi GS, Castro CM, Weissleder R, Lee H

An integrated magneto-electrochemical device for the rapid profiling of tumour extracellular vesicles from blood plasma
Nat Biomed Eng. 2021;5(7):678-689 - PMID: 34183802 - PMCID: PMC8437135 - DOI: 10.1038/s41551-021-00752-7

Im H, Pathania D, McFarland PJ, Sohani AR, Degani I, Allen M, Coble M, Kilcoyne A, Hong S, Rohrer L, Abramson JS, Dryden-Peterson S, Fexon L, Pivovarov M, Chabner B, Lee H, Castro CM, Weissleder R

Design and clinical validation of a point-of-care device for the diagnosis of lymphoma via contrast- enhanced microholography and machine learning
Nat Biomed Eng. 2018;2(9):666-674 - PMID: 30555750 - PMCID: PMC6291220 - DOI: 10.1038/s41551-018-0265-3

Rodell CB, Arlauckas SP, Cuccarese MF, Garris CS, Li R, Ahmed MS, Kohler RH, Pittet MJ, Weissleder R

TLR7/8-agonist-loaded nanoparticles promote the polarization of tumour-associated macrophages to enhance cancer immunotherapy.
Nat Biomed Eng. 2018;2:578-588 - PMID: 31015631 - PMCID: PMC6192054 - DOI: 10.1038/s41551-018-0236-8

Senders ML, Calcagno C, Tawakol A, Nahrendorf M, Mulder WJM, Fayad ZA

PET/MR imaging of inflammation in atherosclerosis.
Nat Biomed Eng. 2022;7(3):202-220 - PMID: 36522465 - DOI: 10.1038/s41551-022-00970-7

Janizek JD, Dincer AB, Celik S, Chen H, Chen W, Naxerova K, Lee SI

Uncovering expression signatures of synergistic drug responses via ensembles of explainable machine-learning models.
Nat Biomed Eng. 2023;7(6):811-829 - PMID: 37127711 - PMCID: PMC11149694 - DOI: 10.1038/s41551-023-01034-0

Qiu W, Dincer AB, Janizek JD, Celik S, Pittet MJ, Naxerova K, Lee SI

Deep profiling of gene expression across 18 human cancers.
Nat Biomed Eng. 2024;9(3):333-355 - PMID: 39690287 - DOI: 10.1038/s41551-024-01290-8

Kaiser Y, Garris CS, Marinari E, Kim HS, Oh J, Pedard M, Halabi EA, Choi M, Parvanian S, Kohler R, Migliorini D, Weissleder R

Targeting immunosuppressive myeloid cells via implant-mediated slow release of small molecules to prevent glioblastoma recurrence
Nat Biomed Eng. 2025;10(7):1431-1444 - PMID: 41125869 - PMCID: PMC13150848 - DOI: 10.1038/s41551-025-01533-2

Woo HK, Kim C, Choi Y, Cho YK, Do LN, Kim H, Jung DH, Allen M, Jeon J, Chung S, Park SY, Park I, Castro CM, Park JS, Lee H

Automated disc device for multiplexed extracellular vesicle isolation and labelling from liquid biopsies in cancer diagnostics.
Nat Biomed Eng. 2026;10(5):882-896 - PMID: 41606293 - PMCID: PMC13396894 - DOI: 10.1038/s41551-025-01601-7

Cephas AT, Hwang WL, Maitra A, Parnas O, DelGiorno KE

It is better to light a candle than to curse the darkness: single-cell transcriptomics sheds new light on pancreas biology and disease.
Gut. 2023;72(6):1211-1219 - PMID: 36997301 - PMCID: PMC10988578 - DOI: 10.1136/gutjnl-2022-329313

Guan D, Men Y, Bartlett A, Hernández MAS, Xu J, Yi X, Li HS, Kong D, Mazitschek R, Ozcan U

Central inhibition of HDAC6 re-sensitizes leptin signaling during obesity to induce profound weight loss.
Cell Metab. 2024;36(4):857-876.e10 - PMID: 38569472 - DOI: 10.1016/j.cmet.2024.02.007

Dai N, Zhao L, Wrighting D, Krämer D, Majithia A, Wang Y, Cracan V, Borges-Rivera D, Mootha VK, Nahrendorf M, Thorburn DR, Minichiello L, Altshuler D, Avruch J

IGF2BP2/IMP2-Deficient Mice Resist Obesity through Enhanced Translation of Ucp1 mRNA and Other mRNAs Encoding Mitochondrial Proteins.
Cell Metab. 2015;21(4):609-21 - PMID: 25863250 - PMCID: PMC4663978 - DOI: 10.1016/j.cmet.2015.03.006

Siwicki M, Engblom C, Pittet MJ

Gal3 Links Inflammation and Insulin Resistance.
Cell Metab. 2016;24(5):655-656 - PMID: 27829136 - DOI: 10.1016/j.cmet.2016.10.014

Swirski FK, Nahrendorf M, Libby P

The ins and outs of inflammatory cells in atheromata.
Cell Metab. 2012;15(2):135-6 - PMID: 22326216 - DOI: 10.1016/j.cmet.2012.01.012

Jain IH, Zazzeron L, Goldberger O, Marutani E, Wojtkiewicz GR, Ast T, Wang H, Schleifer G, Stepanova A, Brepoels K, Schoonjans L, Carmeliet P, Galkin A, Ichinose F, Zapol WM, Mootha VK

Leigh Syndrome Mouse Model Can Be Rescued by Interventions that Normalize Brain Hyperoxia, but Not HIF Activation.
Cell Metab. 2019;30(4):824-832.e3 - PMID: 31402314 - PMCID: PMC6903907 - DOI: 10.1016/j.cmet.2019.07.006
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