Noah Greenwald, PhD
Postdoctoral Scholar
Bioengineering
School of Pharmacy

Noah received his Bachelor’s in Biophysics from Harvard University. He then worked at the Broad Institute, where he analyzed DNA sequencing data to identify the genomic drivers that separate low-grade and high-grade brain cancers. Following his work at the Broad, he received his Ph.D in Cancer Biology from Stanford University, where he was co-advised by Mike Angelo and Christina Curtis.

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While at Stanford, Noah developed machine learning tools to profile highly-multiplexed imaging data. He then used these tools to characterize the tumor microenvironment in breast cancer patient samples, combining this spatial information with paired DNA and RNA sequencing data to predict patient response to immunotherapy. In the Coyote-Maestas lab, Noah is using deep mutational scanning to understand the cross talk between cancer and immune cells.

Awards

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• F99/K00 Fellow, National Institutes of Health, National Cancer Institute, 2021-2028
• F31 Fellow, National Institutes of Health, National Cancer Institute, 2020-2021
• Lucille P. Markey Biomedical Research Fellow, Stanford University, 2017-2020

Education & Training

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• PhD Cancer Biology Stanford University 2024
• BA Biophysics Harvard University 2015

Websites

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• Personal website (ngreenwald.github.io)

Publications (40)

Top publication keywords:
Protein Phosphatase 2CHydralazineSingle-Cell AnalysisPublishingLoss of Function MutationImmunohistochemistryDNA Copy Number VariationsMeningiomaMeningeal NeoplasmsClonal EvolutionGliomaDioxygenasesPituitary NeoplasmsPublicationsImage Processing, Computer-Assisted

• Automated classification of cellular expression in multiplexed imaging data with Nimbus.
  bioRxiv : the preprint server for biology 2024 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, …
• Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning.
  Nature biotechnology 2021 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, …
• Temporal and spatial composition of the tumor microenvironment predicts response to immune checkpoint inhibition.
  bioRxiv : the preprint server for biology 2025 Greenwald NF, Nederlof I, Sowers C, Ding DY, Park S, Kong A, Houlahan KE, Varra SR, de Graaf M, Geurts V, Liu CC, Ranek JS, Voorwerk L, de Maaker M, Kagel A, McCaffrey E, Khan A, Yeh CY, Fullaway CC, …
• Contemporary prognostic signatures and refined risk stratification of gliomas: An analysis of 4400 tumors.
  Neuro-oncology 2025 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, …
• Society for Immunotherapy of Cancer: updates and best practices for multiplex immunohistochemistry (IHC) and immunofluorescence (IF) image analysis and data sharing.
  Journal for immunotherapy of cancer 2025 Taube JM, Sunshine JC, Angelo M, Akturk G, Eminizer M, Engle LL, Ferreira CS, Gnjatic S, Green B, Greenbaum S, Greenwald NF, Hedvat CV, Hollmann TJ, Jiménez-Sánchez D, Korski K, Lako A, Parra ER, …

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• Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity.
  Science (New York, N.Y.) 2024 Houlahan KE, Khan A, Greenwald NF, Vivas CS, West RB, Angelo M, Curtis C
• The multimodality cell segmentation challenge: toward universal solutions.
  Nature methods 2024 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…
• Single-Cell Imaging Maps Inflammatory Cell Subsets to Pulmonary Arterial Hypertension Vasculopathy.
  American journal of respiratory and critical care medicine 2024 Ferrian S, Cao A, McCaffrey EF, Saito T, Greenwald NF, Nicolls MR, Bruce T, Zamanian RT, Del Rosario P, Rabinovitch M, Angelo M
• Loss-of-function mutations in Dnmt3a and Tet2 lead to accelerated atherosclerosis and concordant macrophage phenotypes.
  Nature cardiovascular research 2023 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…
• Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering.
  Nature communications 2023 Liu CC, Greenwald NF, Kong A, McCaffrey EF, Leow KX, Mrdjen D, Cannon BJ, Rumberger JL, Varra SR, Angelo M
• A spatially resolved timeline of the human maternal-fetal interface.
  Nature 2023 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 …
• Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology.
  Nature communications 2023 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-…
• Single-cell spatial proteomic imaging for human neuropathology.
  Acta neuropathologica communications 2022 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, …
• Spatial epitope barcoding reveals clonal tumor patch behaviors.
  Cancer cell 2022 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…
• Structural variants shape driver combinations and outcomes in pediatric high-grade glioma.
  Nature cancer 2022 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, …
• A molecularly integrated grade for meningioma.
  Neuro-oncology 2022 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, …
• Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments.
  Immunity 2022 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, …
• Deep Learning-Inferred Multiplex ImmunoFluorescence for Immunohistochemical Image Quantification.
  Nature machine intelligence 2022 Ghahremani P, Li Y, Kaufman A, Vanguri R, Greenwald N, Angelo M, Hollmann TJ, Nadeem S
• PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation.
  Nature communications 2022 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, …
• The immunoregulatory landscape of human tuberculosis granulomas.
  Nature immunology 2022 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, …
• Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma.
  Cell 2022 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, …
• Evaluation of Geuenich et al.: Targeting a crucial bottleneck for analyzing single-cell multiplexed imaging data.
  Cell systems 2021 Averbukh I, Greenwald NF, Liu CC, Angelo M
• Multiplexed Ion Beam Imaging: Insights into Pathobiology.
  Annual review of pathology 2021 Liu CC, McCaffrey EF, Greenwald NF, Soon E, Risom T, Vijayaragavan K, Oliveria JP, Mrdjen D, Bosse M, Tebaykin D, Bendall SC, Angelo M
• DeepCell Kiosk: scaling deep learning-enabled cellular image analysis with Kubernetes.
  Nature methods 2021 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
• Single-cell metabolic profiling of human cytotoxic T cells.
  Nature biotechnology 2020 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
• The Society for Immunotherapy of Cancer statement on best practices for multiplex immunohistochemistry (IHC) and immunofluorescence (IF) staining and validation.
  Journal for immunotherapy of cancer 2020 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, …
• MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure.
  Science advances 2019 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…
• Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma.
  Nature communications 2019 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…
• SvABA: genome-wide detection of structural variants and indels by local assembly.
  Genome research 2018 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
• Radiographic prediction of meningioma grade by semantic and radiomic features.
  PloS one 2017 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, …
• Open data: Spot data glitches before publication.
  Nature 2017 Greenwald NF, Bandopadhayay P, Beroukhim R
• Patient-derived xenografts undergo mouse-specific tumor evolution.
  Nature genetics 2017 Ben-David U, Ha G, Tseng YY, Greenwald NF, Oh C, Shih J, McFarland JM, Wong B, Boehm JS, Beroukhim R, Golub TR
• Osteoglycin promotes meningioma development through downregulation of NF2 and activation of mTOR signaling.
  Cell communication and signaling : CCS 2017 Mei Y, Du Z, Hu C, Greenwald NF, Abedalthagafi M, Agar NYR, Dunn GP, Bi WL, Santagata S, Dunn IF
• Artificial intelligence in research.
  Science (New York, N.Y.) 2017 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
• Clinical Identification of Oncogenic Drivers and Copy-Number Alterations in Pituitary Tumors.
  Endocrinology 2017 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
• Clinical targeted exome-based sequencing in combination with genome-wide copy number profiling: precision medicine analysis of 203 pediatric brain tumors.
  Neuro-oncology 2017 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, …
• Genomic profile of human meningioma cell lines.
  PloS one 2017 Mei Y, Bi WL, Greenwald NF, Agar NY, Beroukhim R, Dunn GP, Dunn IF
• Genomic landscape of high-grade meningiomas.
  NPJ genomic medicine 2017 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,…
• Increased expression of programmed death ligand 1 (PD-L1) in human pituitary tumors.
  Oncotarget 2016 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
• Landscape of Genomic Alterations in Pituitary Adenomas.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2016 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, …