Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M, Durham T, Zhang X, Donaghey J, Epstein CB, Regev A, Bernstein BE

Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells.
Cell. 2011;147(7):1628-39 - PMID: 22196736 - PMCID: PMC3312319 - DOI: 10.1016/j.cell.2011.09.057

Pittet MJ, Weissleder R

Intravital imaging.
Cell. 2011;147(5):983-91 - PMID: 22118457 - PMCID: PMC3824153 - DOI: 10.1016/j.cell.2011.11.004

Rao SSP, Huang SC, Glenn St Hilaire B, Engreitz JM, Perez EM, Kieffer-Kwon KR, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID, Huang X, Shamim MS, Shin J, Turner D, Ye Z, Omer AD, Robinson JT, Schlick T, Bernstein BE, Casellas R, Lander ES, Aiden EL

Cohesin Loss Eliminates All Loop Domains.
Cell. 2017;171(2):305-320.e24 - PMID: 28985562 - PMCID: PMC5846482 - DOI: 10.1016/j.cell.2017.09.026

Cheek DM, Naxerova K

Mapping the long road to cancer.
Cell. 2022;185(6):939-940 - PMID: 35263624 - DOI: 10.1016/j.cell.2022.02.020

Neftel C, Laffy J, Filbin MG, Hara T, Shore ME, Rahme GJ, Richman AR, Silverbush D, Shaw ML, Hebert CM, Dewitt J, Gritsch S, Perez EM, Gonzalez Castro LN, Lan X, Druck N, Rodman C, Dionne D, Kaplan A, Bertalan MS, Small J, Pelton K, Becker S, Bonal D, Nguyen QD, Servis RL, Fung JM, Mylvaganam R, Mayr L, Gojo J, Haberler C, Geyeregger R, Czech T, Slavc I, Nahed BV, Curry WT, Carter BS, Wakimoto H, Brastianos PK, Batchelor TT, Stemmer-Rachamimov A, Martinez-Lage M, Frosch MP, Stamenkovic I, Riggi N, Rheinbay E, Monje M, Rozenblatt-Rosen O, Cahill DP, Patel AP, Hunter T, Verma IM, Ligon KL, Louis DN, Regev A, Bernstein BE, Tirosh I, Suvà ML

An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma.
Cell. 2019;178(4):835-849.e21 - PMID: 31327527 - PMCID: PMC6703186 - DOI: 10.1016/j.cell.2019.06.024

van Galen P, Hovestadt V, Wadsworth Ii MH, Hughes TK, Griffin GK, Battaglia S, Verga JA, Stephansky J, Pastika TJ, Lombardi Story J, Pinkus GS, Pozdnyakova O, Galinsky I, Stone RM, Graubert TA, Shalek AK, Aster JC, Lane AA, Bernstein BE

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity.
Cell. 2019;176(6):1265-1281.e24 - PMID: 30827681 - PMCID: PMC6515904 - DOI: 10.1016/j.cell.2019.01.031

Deindl S, Hwang WL, Hota SK, Blosser TR, Prasad P, Bartholomew B, Zhuang X

ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps.
Cell. 2013;152(3):442-52 - PMID: 23374341 - PMCID: PMC3647478 - DOI: 10.1016/j.cell.2012.12.040

Heyde A, Rohde D, McAlpine CS, Zhang S, Hoyer FF, Gerold JM, Cheek D, Iwamoto Y, Schloss MJ, Vandoorne K, Iborra-Egea O, Muñoz-Guijosa C, Bayes-Genis A, Reiter JG, Craig M, Swirski FK, Nahrendorf M, Nowak MA, Naxerova K

Increased stem cell proliferation in atherosclerosis accelerates clonal hematopoiesis
Cell. 2021;184(5):1348-1361.e22 - PMID: 33636128 - PMCID: PMC8109274 - DOI: 10.1016/j.cell.2021.01.049

McBrayer SK, Mayers JR, DiNatale GJ, Shi DD, Khanal J, Chakraborty AA, Sarosiek KA, Briggs KJ, Robbins AK, Sewastianik T, Shareef SJ, Olenchock BA, Parker SJ, Tateishi K, Spinelli JB, Islam M, Haigis MC, Looper RE, Ligon KL, Bernstein BE, Carrasco RD, Cahill DP, Asara JM, Metallo CM, Yennawar NH, Vander Heiden MG, Kaelin WG

Transaminase Inhibition by 2-Hydroxyglutarate Impairs Glutamate Biosynthesis and Redox Homeostasis in Glioma.
Cell. 2018;175(1):101-116.e25 - PMID: 30220459 - PMCID: PMC6219629 - DOI: 10.1016/j.cell.2018.08.038

Puram SV, Tirosh I, Parikh AS, Patel AP, Yizhak K, Gillespie S, Rodman C, Luo CL, Mroz EA, Emerick KS, Deschler DG, Varvares MA, Mylvaganam R, Rozenblatt-Rosen O, Rocco JW, Faquin WC, Lin DT, Regev A, Bernstein BE

Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer.
Cell. 2017;171(7):1611-1624.e24 - PMID: 29198524 - PMCID: PMC5878932 - DOI: 10.1016/j.cell.2017.10.044

Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi Q, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, Kampmann M, Bernstein BE, Hovestadt V, Gilbert LA, Weissman JS

Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing.
Cell. 2021;184(9):2503-2519.e17 - PMID: 33838111 - PMCID: PMC8376083 - DOI: 10.1016/j.cell.2021.03.025

Johnstone SE, Reyes A, Qi Y, Adriaens C, Hegazi E, Pelka K, Chen JH, Zou LS, Drier Y, Hecht V, Shoresh N, Selig MK, Lareau CA, Iyer S, Nguyen SC, Joyce EF, Hacohen N, Irizarry RA, Zhang B, Aryee MJ, Bernstein BE

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer.
Cell. 2020;182(6):1474-1489.e23 - PMID: 32841603 - PMCID: PMC7575124 - DOI: 10.1016/j.cell.2020.07.030

Burger ML, Cruz AM, Crossland GE, Gaglia G, Ritch CC, Blatt SE, Bhutkar A, Canner D, Kienka T, Tavana SZ, Barandiaran AL, Garmilla A, Schenkel JM, Hillman M, de Los Rios Kobara I, Li A, Jaeger AM, Hwang WL, Westcott PMK, Manos MP, Holovatska MM, Hodi FS, Regev A, Santagata S, Jacks T

Antigen dominance hierarchies shape TCF1+ progenitor CD8 T cell phenotypes in tumors.
Cell. 2021;184(19):4996-5014.e26 - PMID: 34534464 - PMCID: PMC8522630 - DOI: 10.1016/j.cell.2021.08.020

Sack LM, Davoli T, Li MZ, Li Y, Xu Q, Naxerova K, Wooten EC, Bernardi RJ, Martin TD, Chen T, Leng Y, Liang AC, Scorsone KA, Westbrook TF, Wong KK, Elledge SJ

Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns.
Cell. 2018;173(2):499-514.e23 - PMID: 29576454 - PMCID: PMC6643283 - DOI: 10.1016/j.cell.2018.02.037

Gungabeesoon J, Gort-Freitas NA, Kiss M, Bolli E, Messemaker M, Siwicki M, Hicham M, Bill R, Koch P, Cianciaruso C, Duval F, Pfirschke C, Mazzola M, Peters S, Homicsko K, Garris C, Weissleder R, Klein AM, Pittet MJ

A neutrophil response linked to tumor control in immunotherapy.
Cell. 2023;186(7):1448-1464.e20 - PMID: 37001504 - PMCID: PMC10132778 - DOI: 10.1016/j.cell.2023.02.032

Chen S, Sanjana NE, Zheng K, Shalem O, Lee K, Shi X, Scott DA, Song J, Pan JQ, Weissleder R, Lee H, Zhang F, Sharp PA

Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis.
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Aceto N, Bardia A, Miyamoto DT, Donaldson MC, Wittner BS, Spencer JA, Yu M, Pely A, Engstrom A, Zhu H, Brannigan BW, Kapur R, Stott SL, Shioda T, Ramaswamy S, Ting DT, Lin CP, Toner M, Haber DA, Maheswaran S

Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis.
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Liu J, Lee J, Salazar Hernandez MA, Mazitschek R, Ozcan U

Treatment of obesity with celastrol.
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Yu VW, Yusuf RZ, Oki T, Wu J, Saez B, Wang X, Cook C, Baryawno N, Ziller MJ, Lee E, Gu H, Meissner A, Lin CP, Kharchenko PV, Scadden DT

Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells.
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Suvà ML, Rheinbay E, Gillespie SM, Patel AP, Wakimoto H, Rabkin SD, Riggi N, Chi AS, Cahill DP, Nahed BV, Curry WT, Martuza RL, Rivera MN, Rossetti N, Kasif S, Beik S, Kadri S, Tirosh I, Wortman I, Shalek AK, Rozenblatt-Rosen O, Regev A, Louis DN, Bernstein BE

Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells.
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Garris CS, Pittet MJ

ER Stress in Dendritic Cells Promotes Cancer.
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Sebastián C, Zwaans BM, Silberman DM, Gymrek M, Goren A, Zhong L, Ram O, Truelove J, Guimaraes AR, Toiber D, Cosentino C, Greenson JK, Macdonald AI, McGlynn L, Maxwell F, Edwards J, Giacosa S, Guccione E, Weissleder R, Bernstein BE, Regev A, Shiels PG, Lombard DB, Mostoslavsky R

The Histone Deacetylase SIRT6 Is a Tumor Suppressor that Controls Cancer Metabolism.
Cell. 2012;151(6):1185-99 - PMID: 23217706 - PMCID: PMC3526953 - DOI: 10.1016/j.cell.2012.10.047

Hulsmans M, Clauss S, Xiao L, Aguirre AD, King KR, Hanley A, Hucker WJ, Wülfers EM, Seemann G, Courties G, Iwamoto Y, Sun Y, Savol AJ, Sager HB, Lavine KJ, Fishbein GA, Capen DE, Da Silva N, Miquerol L, Wakimoto H, Seidman CE, Seidman JG, Sadreyev RI, Naxerova K, Mitchell RN, Brown D, Libby P, Weissleder R, Swirski FK, Kohl P, Vinegoni C, Milan DJ, Ellinor PT, Nahrendorf M

Macrophages Facilitate Electrical Conduction in the Heart
Cell. 2017;169:510-522 - PMID: 28431249 - PMCID: PMC5474950 - DOI: 10.1016/j.cell.2017.03.050

Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, Zhang X, Durham T, Miri M, Deshpande V, De Jager PL, Bennett DA, Houmard JA, Muoio DM, Onder TT, Camahort R, Cowan CA, Meissner A, Epstein CB, Shoresh N, Bernstein BE

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues.
Cell. 2013;152(3):642-54 - PMID: 23333102 - PMCID: PMC3563935 - DOI: 10.1016/j.cell.2012.12.033

Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells.
Cell. 2013;153(5):1149-1163 - PMID: 23664763 - PMCID: PMC3709577 - DOI: 10.1016/j.cell.2013.04.037

Shum WW, Da Silva N, McKee M, Smith PJ, Brown D, Breton S

Transepithelial Projections from Basal Cells are Luminal Sensors in Pseudostratified Epithelia
Cell. 2008;135:1108-17 - PMID: 19070580 - PMCID: PMC2646085 - DOI: 10.1016/j.cell.2008.10.020

Ventura A, Young A, Winslow M, Lintault L, Meissner A, Erkeland S, Newman J, Bronson R, Crowley D, Stone J, Jaenisch R, Sharp P, Jacks T

Targeted deletion reveals essential and overlapping functions of the miR-17 through 92 family of miRNA clusters.
Cell. 2008;132(5):875-86 - PMID: 18329372 - PMCID: PMC2323338 - DOI: 10.1016/j.cell.2008.02.019

Ji H, Li D, Chen L, Shimamura T, Kobayashi S, McNamara K, Mahmood U, Mitchell A, Sun Y, Al-Hashem R, Chirieac LR, Padera R, Bronson RT, Kim W, Janne PA, Shapiro GI, Tenen D, Johnson BE, Weissleder R, Sharpless NE, Wong KK

The impact of human EGFR kinase domain mutations on lung tumorigenesis and in vivo sensitivity to EGFR-targeted therapies.
Cancer Cell. 2006;9(6):485-95 - PMID: 16730237 - DOI: 10.1016/j.ccr.2006.04.022

Bachoo RM, Maher EA, Ligon KL, Sharpless NE, Chan SS, You MJ, Tang Y, DeFrances J, Stover E, Weissleder R, Rowitch DH, Louis DN, DePinho RA

Epidermal growth factor receptor and Ink4a/Arf: convergent mechanisms governing terminal differentiation and transformation along the neural stem cell to astrocyte axis
Cancer Cell. 2002;1:269-77 - PMID: 12086863 - DOI: 10.1016/s1535-6108(02)00046-6

Wurdinger T, Tannous BA, Saydam O, Skog J, Grau S, Soutschek J, Weissleder R, Breakefield XO, Krichevsky AM

miR-296 Regulates Growth Factor Receptor Overexpression in Angiogenic Endothelial Cells.
Cancer Cell. 2008;14(5):382-393 - PMID: 18977327 - PMCID: PMC2597164 - DOI: 10.1016/j.ccr.2008.10.005

Gong D, Arbesfeld-Qiu JM, Perrault E, Bae JW, Hwang WL

Spatial oncology: Translating contextual biology to the clinic.
Cancer Cell. 2024;42(10):1653-1675 - PMID: 39366372 - PMCID: PMC12051486 - DOI: 10.1016/j.ccell.2024.09.001

Bolli E, Wirapati P, Hicham M, Xie Y, Siwicki M, Duval F, Goubet AG, Kiss M, Zitti B, Zwahlen T, Mcdowell S, Bill R, Angerani S, Engblom C, Anderson S, Jiang A, Hartley O, Sykes DB, Jankovic M, Fournier N, Gunzer M, Tarussio D, Tissot S, Sadow PM, Faquin WC, Sade-Feldman M, Weissleder R, Pai S, Mercier F, Manguso R, Pittet MJ

CCL3 is produced by aged neutrophils across cancers and promotes tumor growth.
Cancer Cell. 2026;44(3):624-640.e12 - PMID: 41650972 - PMCID: PMC13179570 - DOI: 10.1016/j.ccell.2026.01.006

Hwang WL, Perrault EN, Birbrair A, Mattson BJ, Gutmann DH, Mabbott DJ, Cukierman E, Repasky EA, Sloan EK, Zong H, Demir IE, Saloman JL, Borniger JC, Hu J, Dietrich J, Breunig JJ, Kaan Cifcibası,, K, Ahmad Kasm KA, Valiente M, Wintermark M, Acharya MM, Scheff NN, D'Silva NJ, Vermeer PD, Wong RJ, Talbot S, Hervey-Jumper SL, Wang TC, Ye Y, Pan Y, Bunimovich YL, Amit M

Integrating priorities at the intersection of cancer and neuroscience.
Cancer Cell. 2024;43(1):1-5 - PMID: 39423816 - PMCID: PMC11732710 - DOI: 10.1016/j.ccell.2024.09.014

Abdel-Wahab O, Adli M, Lafave LM, Gao J, Hricik T, Shih AH, Pandey S, Patel JP, Chung YR, Koche R, Perna F, Zhao X, Taylor JE, Park CY, Carroll M, Melnick A, Nimer SD, Jaffe JD, Aifantis I, Bernstein BE, Levine RL

ASXL1 Mutations Promote Myeloid Transformation through Loss of PRC2-Mediated Gene Repression.
Cancer Cell. 2012;22(2):180-93 - PMID: 22897849 - PMCID: PMC3422511 - DOI: 10.1016/j.ccr.2012.06.032

Rheinbay E, Louis DN, Bernstein BE, Suvà ML

A Tell-Tail Sign of Chromatin: Histone Mutations Drive Pediatric Glioblastoma.
Cancer Cell. 2012;21(3):329-331 - PMID: 22439930 - DOI: 10.1016/j.ccr.2012.03.001

Anastas JN, Zee BM, Kalin JH, Kim M, Guo R, Alexandrescu S, Blanco MA, Giera S, Gillespie SM, Das J, Wu M, Nocco S, Bonal DM, Nguyen QD, Suva ML, Bernstein BE, Alani R, Golub TR, Cole PA, Filbin MG, Shi Y

Re-programing Chromatin with a Bifunctional LSD1/HDAC Inhibitor Induces Therapeutic Differentiation in DIPG.
Cancer Cell. 2019;36(5):528-544.e10 - PMID: 31631026 - DOI: 10.1016/j.ccell.2019.09.005

Rahme GJ, Gaskell E, Bernstein BE

GABPβ1L Wakes Up TERT.
Cancer Cell. 2018;34(3):358-360 - PMID: 30205042 - DOI: 10.1016/j.ccell.2018.08.011

Kleppe M, Koche R, Zou L, van Galen P, Hill CE, Dong L, De Groote S, Papalexi E, Hanasoge Somasundara AV, Cordner K, Keller M, Farnoud N, Medina J, McGovern E, Reyes J, Roberts J, Witkins M, Rapaport F, Teruya-Feldstein J, Qi J, Rampal R, Bernstein BE, Bradner JE, Levine RL

Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms.
Cancer Cell. 2017;33(1):29-43.e7 - PMID: 29249691 - PMCID: PMC5760343 - DOI: 10.1016/j.ccell.2017.11.009

Freed-Pastor WA, Lambert LJ, Ely ZA, Pattada NB, Bhutkar A, Eng G, Mercer KL, Garcia AP, Lin L, Rideout WM, Hwang WL, Schenkel JM, Jaeger AM, Bronson RT, Westcott PMK, Hether TD, Divakar P, Reeves JW, Deshpande V, Delorey T, Phillips D, Yilmaz OH, Regev A, Jacks T

The CD155/TIGIT axis promotes and maintains immune evasion in neoantigen-expressing pancreatic cancer.
Cancer Cell. 2021;39(10):1342-1360.e14 - PMID: 34358448 - PMCID: PMC8511341 - DOI: 10.1016/j.ccell.2021.07.007

Pfirschke C, Garris C, Pittet MJ

Common TLR5 Mutations Control Cancer Progression.
Cancer Cell. 2015;27(1):1-3 - PMID: 25584886 - DOI: 10.1016/j.ccell.2014.12.008

Riggi N, Knoechel B, Gillespie SM, Rheinbay E, Boulay G, Suvà ML, Rossetti NE, Boonseng WE, Oksuz O, Cook EB, Formey A, Patel A, Gymrek M, Thapar V, Deshpande V, Ting DT, Hornicek FJ, Nielsen GP, Stamenkovic I, Aryee MJ, Bernstein BE, Rivera MN

EWS-FLI1 Utilizes Divergent Chromatin Remodeling Mechanisms to Directly Activate or Repress Enhancer Elements in Ewing Sarcoma.
Cancer Cell. 2014;26(5):668-81 - PMID: 25453903 - PMCID: PMC4492343 - DOI: 10.1016/j.ccell.2014.10.004

Pfirschke C, Siwicki M, Liao HW, Pittet MJ

Tumor Microenvironment: No Effector T Cells without Dendritic Cells.
Cancer Cell. 2017;31(5):614-615 - PMID: 28486102 - DOI: 10.1016/j.ccell.2017.04.007

Miller PG, Al-Shahrour F, Hartwell KA, Chu LP, Järås M, Puram RV, Puissant A, Callahan KP, Ashton J, McConkey ME, Poveromo LP, Cowley GS, Kharas MG, Labelle M, Shterental S, Fujisaki J, Silberstein L, Alexe G, Al-Hajj MA, Shelton CA, Armstrong SA, Root DE, Scadden DT, Hynes RO, Mukherjee S, Stegmaier K, Jordan CT, Ebert BL

In Vivo RNAi Screening Identifies a Leukemia-Specific Dependence on Integrin Beta 3 Signaling.
Cancer Cell. 2013;24(1):45-58 - PMID: 23770013 - PMCID: PMC3746037 - DOI: 10.1016/j.ccr.2013.05.004

Lee H, Shin TH, Cheon J, Weissleder R

Recent Developments in Magnetic Diagnostic Systems
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Shao H, Im H, Castro CM, Breakefield X, Weissleder R, Lee H

New Technologies for Analysis of Extracellular Vesicles.
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Adli M, Zhu J, Bernstein BE

Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors.
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Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE

Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.
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Wurdinger T, Badr C, Pike L, de Kleine R, Weissleder R, Breakefield XO, Tannous BA

A secreted luciferase for ex vivo monitoring of in vivo processes.
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In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography.
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Metabolic Biotinylation of Cell Surface Receptors for in vivo Imaging
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