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Contemporary Prognostic Signatures and Refined Risk Stratification of Gliomas: An Analysis of 4,400 Tumors. Neuro Oncol. 2024 Aug 21.
Ghosh HS, Patel RV, Woodward E, Greenwald NF, Bhave VM, Maury EA, Cello G, Hoffman SE, Li Y, Gupta H, Youssef G, Spurr LF, Vogelzang J, Touat M, Dubois F, Cherniack AD, Guo X, Tavakol S, Cioffi G, Lindeman NI, Ligon AH, Chiocca EA, Reardon DA, Wen PY, Meredith D, Santagata S, Barnholtz-Sloan JS, Ligon KL, Beroukhim R, Bi WL. PMID: 39164213.
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Automated classification of cellular expression in multiplexed imaging data with Nimbus. bioRxiv. 2024 Jun 03.
Rumberger JL, Greenwald NF, Ranek JS, Boonrat P, Walker C, Franzen J, Varra SR, Kong A, Sowers C, Liu CC, Averbukh I, Piyadasa H, Vanguri R, Nederlof I, Wang XJ, Van Valen D, Kok M, Hollmann TJ, Kainmueller D, Angelo M. PMID: 38895405; PMCID: PMC11185540.
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Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity. Science. 2024 May 31; 384(6699):eadh8697.
Houlahan KE, Khan A, Greenwald NF, Vivas CS, West RB, Angelo M, Curtis C. PMID: 38815010.
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HumansCells
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The multimodality cell segmentation challenge: toward universal solutions. Nat Methods. 2024 Jun; 21(6):1103-1113.
Ma J, Xie R, Ayyadhury S, Ge C, Gupta A, Gupta R, Gu S, Zhang Y, Lee G, Kim J, Lou W, Li H, Upschulte E, Dickscheid T, de Almeida JG, Wang Y, Han L, Yang X, Labagnara M, Gligorovski V, Scheder M, Rahi SJ, Kempster C, Pollitt A, Espinosa L, Mignot T, Middeke JM, Eckardt JN, Li W, Li Z, Cai X, Bai B, Greenwald NF, Van Valen D, Weisbart E, Cimini BA, Cheung T, Brück O, Bader GD, Wang B. PMID: 38532015; PMCID: PMC11210294.
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PubMed Mentions:
8 Fields:
Translation:
HumansAnimals
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Single-Cell Imaging Maps Inflammatory Cell Subsets to Pulmonary Arterial Hypertension Vasculopathy. Am J Respir Crit Care Med. 2024 01 15; 209(2):206-218.
Ferrian S, Cao A, McCaffrey EF, Saito T, Greenwald NF, Nicolls MR, Bruce T, Zamanian RT, Del Rosario P, Rabinovitch M, Angelo M. PMID: 37934691; PMCID: PMC10806425.
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PubMed Mentions:
7 Fields:
Translation:
HumansCells
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Loss-of-function mutations in Dnmt3a and Tet2 lead to accelerated atherosclerosis and concordant macrophage phenotypes. Nat Cardiovasc Res. 2023 Sep; 2(9):805-818.
Rauch PJ, Gopakumar J, Silver AJ, Nachun D, Ahmad H, McConkey M, Nakao T, Bosse M, Rentz T, Vivanco Gonzalez N, Greenwald NF, McCaffrey EF, Khair Z, Gopakumar M, Rodrigues KB, Lin AE, Sinha E, Fefer M, Cohen DN, Vromman A, Shvartz E, Sukhova G, Bendall S, Angelo M, Libby P, Ebert BL, Jaiswal S. PMID: 39196062.
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13 Translation:
AnimalsCells
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Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering. Nat Commun. 2023 08 01; 14(1):4618.
Liu CC, Greenwald NF, Kong A, McCaffrey EF, Leow KX, Mrdjen D, Cannon BJ, Rumberger JL, Varra SR, Angelo M. PMID: 37528072; PMCID: PMC10393943.
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28 Fields:
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A spatially resolved timeline of the human maternal-fetal interface. Nature. 2023 Jul; 619(7970):595-605.
Greenbaum S, Averbukh I, Soon E, Rizzuto G, Baranski A, Greenwald NF, Kagel A, Bosse M, Jaswa EG, Khair Z, Kwok S, Warshawsky S, Piyadasa H, Goldston M, Spence A, Miller G, Schwartz M, Graf W, Van Valen D, Winn VD, Hollmann T, Keren L, van de Rijn M, Angelo M. PMID: 37468587; PMCID: PMC10356615.
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19 Fields:
Translation:
HumansCells
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Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology. Nat Commun. 2023 07 07; 14(1):4013.
Bai Y, Zhu B, Oliveria JP, Cannon BJ, Feyaerts D, Bosse M, Vijayaragavan K, Greenwald NF, Phillips D, Schürch CM, Naik SM, Ganio EA, Gaudilliere B, Rodig SJ, Miller MB, Angelo M, Bendall SC, Rovira-Clavé X, Nolan GP, Jiang S. PMID: 37419873; PMCID: PMC10329015.
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PubMed Mentions:
7 Fields:
Translation:
Humans
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Single-cell spatial proteomic imaging for human neuropathology. Acta Neuropathol Commun. 2022 11 04; 10(1):158.
Vijayaragavan K, Cannon BJ, Tebaykin D, Bossé M, Baranski A, Oliveria JP, Bukhari SA, Mrdjen D, Corces MR, McCaffrey EF, Greenwald NF, Sigal Y, Marquez D, Khair Z, Bruce T, Goldston M, Bharadwaj A, Montine KS, Angelo RM, Montine TJ, Bendall SC. PMID: 36333818; PMCID: PMC9636771.
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PubMed Mentions:
7 Fields:
Translation:
HumansAnimalsCells
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Spatial epitope barcoding reveals clonal tumor patch behaviors. Cancer Cell. 2022 11 14; 40(11):1423-1439.e11.
Rovira-Clavé X, Drainas AP, Jiang S, Bai Y, Baron M, Zhu B, Dallas AE, Lee MC, Chu TP, Holzem A, Ayyagari R, Bhattacharya D, McCaffrey EF, Greenwald NF, Markovic M, Coles GL, Angelo M, Bassik MC, Sage J, Nolan GP. PMID: 36240778; PMCID: PMC9673683.
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PubMed Mentions:
15 Fields:
Translation:
HumansCells
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Structural variants shape driver combinations and outcomes in pediatric high-grade glioma. Nat Cancer. 2022 08; 3(8):994-1011.
Dubois FPB, Shapira O, Greenwald NF, Zack T, Wala J, Tsai JW, Crane A, Baguette A, Hadjadj D, Harutyunyan AS, Kumar KH, Blattner-Johnson M, Vogelzang J, Sousa C, Kang KS, Sinai C, Wang DK, Khadka P, Lewis K, Nguyen L, Malkin H, Ho P, O'Rourke R, Zhang S, Gold R, Deng D, Serrano J, Snuderl M, Jones C, Wright KD, Chi SN, Grill J, Kleinman CL, Goumnerova LC, Jabado N, Jones DTW, Kieran MW, Ligon KL, Beroukhim R, Bandopadhayay P. PMID: 35788723; PMCID: PMC10365847.
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PubMed Mentions:
15 Fields:
Translation:
Humans
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A molecularly integrated grade for meningioma. Neuro Oncol. 2022 05 04; 24(5):796-808.
Driver J, Hoffman SE, Tavakol S, Woodward E, Maury EA, Bhave V, Greenwald NF, Nassiri F, Aldape K, Zadeh G, Choudhury A, Vasudevan HN, Magill ST, Raleigh DR, Abedalthagafi M, Aizer AA, Alexander BM, Ligon KL, Reardon DA, Wen PY, Al-Mefty O, Ligon AH, Dubuc AM, Beroukhim R, Claus EB, Dunn IF, Santagata S, Bi WL. PMID: 34508644; PMCID: PMC9071299.
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PubMed Mentions:
70 Fields:
Translation:
Humans
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Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments. Immunity. 2022 06 14; 55(6):1118-1134.e8.
Jiang S, Chan CN, Rovira-Clavé X, Chen H, Bai Y, Zhu B, McCaffrey E, Greenwald NF, Liu C, Barlow GL, Weirather JL, Oliveria JP, Nakayama T, Lee IT, Matter MS, Carlisle AE, Philips D, Vazquez G, Mukherjee N, Busman-Sahay K, Nekorchuk M, Terry M, Younger S, Bosse M, Demeter J, Rodig SJ, Tzankov A, Goltsev Y, McIlwain DR, Angelo M, Estes JD, Nolan GP. PMID: 35447093; PMCID: PMC9220319.
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36 Fields:
Translation:
AnimalsCells
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Deep Learning-Inferred Multiplex ImmunoFluorescence for Immunohistochemical Image Quantification. Nat Mach Intell. 2022 Apr; 4(4):401-412.
Ghahremani P, Li Y, Kaufman A, Vanguri R, Greenwald N, Angelo M, Hollmann TJ, Nadeem S. PMID: 36118303; PMCID: PMC9477216.
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PubMed Mentions:
27
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PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation. Nat Commun. 2022 02 01; 13(1):604.
Khadka P, Reitman ZJ, Lu S, Buchan G, Gionet G, Dubois F, Carvalho DM, Shih J, Zhang S, Greenwald NF, Zack T, Shapira O, Pelton K, Hartley R, Bear H, Georgis Y, Jarmale S, Melanson R, Bonanno K, Schoolcraft K, Miller PG, Condurat AL, Gonzalez EM, Qian K, Morin E, Langhnoja J, Lupien LE, Rendo V, Digiacomo J, Wang D, Zhou K, Kumbhani R, Guerra Garcia ME, Sinai CE, Becker S, Schneider R, Vogelzang J, Krug K, Goodale A, Abid T, Kalani Z, Piccioni F, Beroukhim R, Persky NS, Root DE, Carcaboso AM, Ebert BL, Fuller C, Babur O, Kieran MW, Jones C, Keshishian H, Ligon KL, Carr SA, Phoenix TN, Bandopadhayay P. PMID: 35105861; PMCID: PMC8807747.
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PubMed Mentions:
19 Fields:
Translation:
HumansAnimalsCells
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Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma. Cell. 2022 01 20; 185(2):299-310.e18.
Risom T, Glass DR, Averbukh I, Liu CC, Baranski A, Kagel A, McCaffrey EF, Greenwald NF, Rivero-Gutiérrez B, Strand SH, Varma S, Kong A, Keren L, Srivastava S, Zhu C, Khair Z, Veis DJ, Deschryver K, Vennam S, Maley C, Hwang ES, Marks JR, Bendall SC, Colditz GA, West RB, Angelo M. PMID: 35063072; PMCID: PMC8792442.
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PubMed Mentions:
115 Fields:
Translation:
HumansCells
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The immunoregulatory landscape of human tuberculosis granulomas. Nat Immunol. 2022 02; 23(2):318-329.
McCaffrey EF, Donato M, Keren L, Chen Z, Delmastro A, Fitzpatrick MB, Gupta S, Greenwald NF, Baranski A, Graf W, Kumar R, Bosse M, Fullaway CC, Ramdial PK, Forgó E, Jojic V, Van Valen D, Mehra S, Khader SA, Bendall SC, van de Rijn M, Kalman D, Kaushal D, Hunter RL, Banaei N, Steyn AJC, Khatri P, Angelo M. PMID: 35058616; PMCID: PMC8810384.
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PubMed Mentions:
82 Fields:
Translation:
HumansCells
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Evaluation of Geuenich et al.: Targeting a crucial bottleneck for analyzing single-cell multiplexed imaging data. Cell Syst. 2021 12 15; 12(12):1121-1123.
Averbukh I, Greenwald NF, Liu CC, Angelo M. PMID: 34914901.
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Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning. Nat Biotechnol. 2022 04; 40(4):555-565.
Greenwald NF, Miller G, Moen E, Kong A, Kagel A, Dougherty T, Fullaway CC, McIntosh BJ, Leow KX, Schwartz MS, Pavelchek C, Cui S, Camplisson I, Bar-Tal O, Singh J, Fong M, Chaudhry G, Abraham Z, Moseley J, Warshawsky S, Soon E, Greenbaum S, Risom T, Hollmann T, Bendall SC, Keren L, Graf W, Angelo M, Van Valen D. PMID: 34795433; PMCID: PMC9010346.
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PubMed Mentions:
228 Fields:
Translation:
Humans
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Multiplexed Ion Beam Imaging: Insights into Pathobiology. Annu Rev Pathol. 2022 01 24; 17:403-423.
Liu CC, McCaffrey EF, Greenwald NF, Soon E, Risom T, Vijayaragavan K, Oliveria JP, Mrdjen D, Bosse M, Tebaykin D, Bendall SC, Angelo M. PMID: 34752710.
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PubMed Mentions:
15 Fields:
Translation:
Humans
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DeepCell Kiosk: scaling deep learning-enabled cellular image analysis with Kubernetes. Nat Methods. 2021 01; 18(1):43-45.
Bannon D, Moen E, Schwartz M, Borba E, Kudo T, Greenwald N, Vijayakumar V, Chang B, Pao E, Osterman E, Graf W, Van Valen D. PMID: 33398191; PMCID: PMC8759612.
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PubMed Mentions:
46 Fields:
Translation:
HumansCells
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Single-cell metabolic profiling of human cytotoxic T cells. Nat Biotechnol. 2021 02; 39(2):186-197.
Hartmann FJ, Mrdjen D, McCaffrey E, Glass DR, Greenwald NF, Bharadwaj A, Khair Z, Verberk SGS, Baranski A, Baskar R, Graf W, Van Valen D, Van den Bossche J, Angelo M, Bendall SC. PMID: 32868913; PMCID: PMC7878201.
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PubMed Mentions:
115 Fields:
Translation:
HumansCells
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The Society for Immunotherapy of Cancer statement on best practices for multiplex immunohistochemistry (IHC) and immunofluorescence (IF) staining and validation. J Immunother Cancer. 2020 05; 8(1).
Taube JM, Akturk G, Angelo M, Engle EL, Gnjatic S, Greenbaum S, Greenwald NF, Hedvat CV, Hollmann TJ, Juco J, Parra ER, Rebelatto MC, Rimm DL, Rodriguez-Canales J, Schalper KA, Stack EC, Ferreira CS, Korski K, Lako A, Rodig SJ, Schenck E, Steele KE, Surace MJ, Tetzlaff MT, von Loga K, Wistuba II, Bifulco CB, Society for Immunotherapy of Cancer (SITC) Pathology Task Force.. PMID: 32414858; PMCID: PMC7239569.
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PubMed Mentions:
100 Fields:
Translation:
Humans
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MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure. Sci Adv. 2019 10; 5(10):eaax5851.
Keren L, Bosse M, Thompson S, Risom T, Vijayaragavan K, McCaffrey E, Marquez D, Angoshtari R, Greenwald NF, Fienberg H, Wang J, Kambham N, Kirkwood D, Nolan G, Montine TJ, Galli SJ, West R, Bendall SC, Angelo M. PMID: 31633026; PMCID: PMC6785247.
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PubMed Mentions:
154 Fields:
Translation:
HumansCells
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Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nat Commun. 2019 06 03; 10(1):2400.
Bandopadhayay P, Piccioni F, O'Rourke R, Ho P, Gonzalez EM, Buchan G, Qian K, Gionet G, Girard E, Coxon M, Rees MG, Brenan L, Dubois F, Shapira O, Greenwald NF, Pages M, Balboni Iniguez A, Paolella BR, Meng A, Sinai C, Roti G, Dharia NV, Creech A, Tanenbaum B, Khadka P, Tracy A, Tiv HL, Hong AL, Coy S, Rashid R, Lin JR, Cowley GS, Lam FC, Goodale A, Lee Y, Schoolcraft K, Vazquez F, Hahn WC, Tsherniak A, Bradner JE, Yaffe MB, Milde T, Pfister SM, Qi J, Schenone M, Carr SA, Ligon KL, Kieran MW, Santagata S, Olson JM, Gokhale PC, Jaffe JD, Root DE, Stegmaier K, Johannessen CM, Beroukhim R. PMID: 31160565; PMCID: PMC6546744.
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PubMed Mentions:
26 Fields:
Translation:
HumansAnimalsCells
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SvABA: genome-wide detection of structural variants and indels by local assembly. Genome Res. 2018 04; 28(4):581-591.
Wala JA, Bandopadhayay P, Greenwald NF, O'Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang CZ, Imielinski M, Beroukhim R. PMID: 29535149; PMCID: PMC5880247.
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PubMed Mentions:
189 Fields:
Translation:
Humans
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Radiographic prediction of meningioma grade by semantic and radiomic features. PLoS One. 2017; 12(11):e0187908.
Coroller TP, Bi WL, Huynh E, Abedalthagafi M, Aizer AA, Greenwald NF, Parmar C, Narayan V, Wu WW, Miranda de Moura S, Gupta S, Beroukhim R, Wen PY, Al-Mefty O, Dunn IF, Santagata S, Alexander BM, Huang RY, Aerts HJWL. PMID: 29145421; PMCID: PMC5690632.
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PubMed Mentions:
54 Fields:
Translation:
Humans
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Open data: Spot data glitches before publication. Nature. 2017 10 18; 550(7676):333.
Greenwald NF, Bandopadhayay P, Beroukhim R. PMID: 29052624.
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Translation:
Humans
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Patient-derived xenografts undergo mouse-specific tumor evolution. Nat Genet. 2017 Nov; 49(11):1567-1575.
Ben-David U, Ha G, Tseng YY, Greenwald NF, Oh C, Shih J, McFarland JM, Wong B, Boehm JS, Beroukhim R, Golub TR. PMID: 28991255; PMCID: PMC5659952.
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PubMed Mentions:
386 Fields:
Translation:
HumansAnimalsCells
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Osteoglycin promotes meningioma development through downregulation of NF2 and activation of mTOR signaling. Cell Commun Signal. 2017 09 18; 15(1):34.
Mei Y, Du Z, Hu C, Greenwald NF, Abedalthagafi M, Agar NYR, Dunn GP, Bi WL, Santagata S, Dunn IF. PMID: 28923059; PMCID: PMC5604305.
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PubMed Mentions:
12 Fields:
Translation:
HumansCells
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Artificial intelligence in research. Science. 2017 Jul 07; 357(6346):28-30.
Musib M, Wang F, Tarselli MA, Yoho R, Yu KH, Andrés RM, Greenwald NF, Pan X, Lee CH, Zhang J, Dutton-Regester K, Johnston JW, Sharafeldin IM. PMID: 28684488.
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PubMed Mentions:
10 Fields:
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Clinical Identification of Oncogenic Drivers and Copy-Number Alterations in Pituitary Tumors. Endocrinology. 2017 07 01; 158(7):2284-2291.
Bi WL, Greenwald NF, Ramkissoon SH, Abedalthagafi M, Coy SM, Ligon KL, Mei Y, MacConaill L, Ducar M, Min L, Santagata S, Kaiser UB, Beroukhim R, Laws ER, Dunn IF. PMID: 28486603; PMCID: PMC5505210.
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PubMed Mentions:
31 Fields:
Translation:
HumansCells
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Clinical targeted exome-based sequencing in combination with genome-wide copy number profiling: precision medicine analysis of 203 pediatric brain tumors. Neuro Oncol. 2017 Jul 01; 19(7):986-996.
Ramkissoon SH, Bandopadhayay P, Hwang J, Ramkissoon LA, Greenwald NF, Schumacher SE, O'Rourke R, Pinches N, Ho P, Malkin H, Sinai C, Filbin M, Plant A, Bi WL, Chang MS, Yang E, Wright KD, Manley PE, Ducar M, Alexandrescu S, Lidov H, Delalle I, Goumnerova LC, Church AJ, Janeway KA, Harris MH, MacConaill LE, Folkerth RD, Lindeman NI, Stiles CD, Kieran MW, Ligon AH, Santagata S, Dubuc AM, Chi SN, Beroukhim R, Ligon KL. PMID: 28104717; PMCID: PMC5570190.
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PubMed Mentions:
45 Fields:
Translation:
Humans
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Genomic profile of human meningioma cell lines. PLoS One. 2017; 12(5):e0178322.
Mei Y, Bi WL, Greenwald NF, Agar NY, Beroukhim R, Dunn GP, Dunn IF. PMID: 28552950; PMCID: PMC5446134.
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PubMed Mentions:
28 Fields:
Translation:
HumansCells
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Genomic landscape of high-grade meningiomas. NPJ Genom Med. 2017; 2.
Bi WL, Greenwald NF, Abedalthagafi M, Wala J, Gibson WJ, Agarwalla PK, Horowitz P, Schumacher SE, Esaulova E, Mei Y, Chevalier A, Ducar M, Thorner AR, van Hummelen P, Stemmer-Rachamimov A, Artyomov M, Al-Mefty O, Dunn GP, Santagata S, Dunn IF, Beroukhim R. PMID: 28713588; PMCID: PMC5506858.
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PubMed Mentions:
86
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Increased expression of programmed death ligand 1 (PD-L1) in human pituitary tumors. Oncotarget. 2016 Nov 22; 7(47):76565-76576.
Mei Y, Bi WL, Greenwald NF, Du Z, Agar NY, Kaiser UB, Woodmansee WW, Reardon DA, Freeman GJ, Fecci PE, Laws ER, Santagata S, Dunn GP, Dunn IF. PMID: 27655724; PMCID: PMC5363530.
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PubMed Mentions:
63 Fields:
Translation:
Humans
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Landscape of Genomic Alterations in Pituitary Adenomas. Clin Cancer Res. 2017 Apr 01; 23(7):1841-1851.
Bi WL, Horowitz P, Greenwald NF, Abedalthagafi M, Agarwalla PK, Gibson WJ, Mei Y, Schumacher SE, Ben-David U, Chevalier A, Carter S, Tiao G, Brastianos PK, Ligon AH, Ducar M, MacConaill L, Laws ER, Santagata S, Beroukhim R, Dunn IF. PMID: 27707790; PMCID: PMC5380512.
View in:
PubMed Mentions:
55 Fields:
Translation:
HumansCells