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Institute for Systems Genetics NYU Langone logo NIH logo NIH logo

FENYO LAB

Selected Publications

  • Overview
  • People
  • Research
  • Education
  • Publications
  • Contact
Institute for Systems Genetics NYU Langone logo NIH logo NIH logo
  • Spatial Biology
    • Michelle Hollenberg, Catherine Hermann, Aliza Siegman, Wenke Liu, Cynthia Loomis, Valeria Mezzano, Shanmugapriya Selvaraj, Jimin Tan, Tianxiao Zhao, Joshua M. Wang, Lizabeth Katsnelson, Linda Procell, Esther Adler, Leslie Boyd, David Fenyö: "The Spatial Immune Landscape of Mismatch Repair Deficient Endometrial Cancer: Implications for Clinical Outcomes", medRxiv 2026.03.12.26348249.
    • Tianxiao Zhao, Katherine Zhang, Michelle Hollenberg, Wen Zhou, David Fenyö: "SimSpace: a comprehensive in-silico spatial omics data simulation framework", bioRxiv 2025.07.18.665587.
    • Storrs E, Mo CK, Chou WH, Bhatt G, Chen S, Wei X, Houston A, Karpova A, Jayasinghe RG, Lal P, Bayguinov P, Herndon JM, Li X, Anjum Simin F, Fang X, Wendl MC, Liu X, Zheng H, Davies SR, Wang JT, Shinkle A, Fulton RS, Ponce J, Heinz M, Head R, Chen D, Zhao Y, Fenyo D, Li YE, Ma CX, Aft R, Reimers MA, Kim AH, Puram SV, Fitzpatrick JAJ, Shoghi KI, Figenshau RS, Ademuyiwa FO, Ju T, Colditz GA, Drake BF, Patti GJ, Oh ST, Kim EH, Gillanders WE, Olson JA, Chheda MG, Weimholt C, Veis DJ, Raphael BJ, Fields RC, Pachynski RK, Chen F, Ding L: "Spatial Mapping of the Precancer-to-Cancer Transition in Breast and Prostate", Cancer Discov. 2026.
    • Tan J, Le H, Deng J, Liu Y, Hao Y, Hollenberg M, Liu W, Wang JM, Xia B, Ramaswami S, Mezzano V, Loomis C, Murrell N, Moreira AL, Cho K, Pass HI, Wong KK, Ban Y, Neel BG, Tsirigos A, Fenyö D: "Characterization of tumour heterogeneity through segmentation-free representation learning on multiplexed imaging data", Nat Biomed Eng. 2025 Feb 20.
    • Wang JM, Hong R, Demicco EG, Tan J, Lazcano R, Moreira AL, Li Y, Calinawan A, Razavian N, Schraink T, Gillette MA, Omenn GS, An E, Rodriguez H, Tsirigos A, Ruggles KV, Ding L, Robles AI, Mani DR, Rodland KD, Lazar AJ, Liu W, Fenyö D; Clinical Proteomic Tumor Analysis Consortium: "Deep learning integrates histopathology and proteogenomics at a pan-cancer level", Cell Rep Med. 2023 Aug 11:101173.
    • Runyu Hong, Wenke Liu, Deborah DeLair, Narges Razavian, David Fenyö: "Predicting endometrial cancer subtypes and molecular features from histopathology images using multi-resolution deep learning models", Cell Reports Medicine 2 (2021) 100400.
      NCI announcement
    • Coudray N, Ocampo PS, Sakellaropoulos T, Narula N, Snuderl M, Fenyö D, Moreira AL, Razavian N, Tsirigos A: "Classification and mutation prediction from non-small cell lung cancer histopathology images using deep learning", Nat Med. 2018 Sep 17.
    • Bermudez-Hernandez K, Keegan S, Whelan DR, Reid DA, Zagelbaum J, Yin Y, Ma S, Rothenberg E, Fenyö D: "A Method for Quantifying Molecular Interactions Using Stochastic Modelling and Super-Resolution Microscopy", Scientific Reports (2017).
  • Multiomics Integration
    • Szeitz B, Hagemeijer YP, Pahi ZG, Ujfaludi Z, Kuras M, Rodriguez J, Doma V, Mohacsi R, Herold M, Herold Z, Horvath Z, Pla I, Sugihara Y, Baldetorp B, Lindberg H, Oskolas H, Rezeli M, Gil J, Appelqvist R, Kemeny LV, Guedes J, Malm J, Sanchez A, Boros IM, Nemeth IB, Guryev V, Pankotai T, Pawłowski K, Wieslander E, Szasz AM, Fenyö D, Horvatovich P, Timar J, Marko-Varga G, Betancourt LH: "Distant metastases of melanoma exhibit varying extent of intrapatient proteogenomic heterogeneity", Clin Transl Med. 2025 Oct;15(10):e70477.
    • Kuras M, Betancourt LH, Hong R, Szadai L, Rodriguez J, Horvatovich P, Pla I, Eriksson J, Szeitz B, Deszcz B, Welinder C, Sugihara Y, Ekedahl H, Baldetorp B, Ingvar C, Lundgren L, Lindberg H, Oskolas H, Horvath Z, Rezeli M, Gil J, Appelqvist R, Kemény LV, Malm J, Sanchez A, Szasz AM, Pawłowski K, Wieslander E, Fenyö D, Nemeth IB, Marko-Varga G: "Proteogenomic Profiling of Treatment-Naïve Metastatic Malignant Melanoma", Cancers (Basel). 2025 Feb 27;17(5):832.
    • Petralia F, Ma W, Yaron TM, Caruso FP, Tignor N, Wang JM, Charytonowicz D, Johnson JL, Huntsman EM, Marino GB, Calinawan A, Evangelista JE, Selvan ME, Chowdhury S, Rykunov D, Krek A, Song X, Turhan B, Christianson KE, Lewis DA, Deng EZ, Clarke DJB, Whiteaker JR, Kennedy JJ, Zhao L, Segura RL, Batra H, Raso MG, Parra ER, Soundararajan R, Tang X, Li Y, Yi X, Satpathy S, Wang Y, Wiznerowicz M, González-Robles TJ, Iavarone A, Gosline SJC, Reva B, Robles AI, Nesvizhskii AI, Mani DR, Gillette MA, Klein RJ, Cieslik M, Zhang B, Paulovich AG, Sebra R, Gümüs ZH, Hostetter G, Fenyö D, Omenn GS, Cantley LC, Ma'ayan A, Lazar AJ, Ceccarelli M, Wang P, Clinical Proteomic Tumor Analysis Consortium: "Pan-cancer proteogenomics characterization of tumor immunity", Cell 2024 S0092-8674(24)00064-3.
    • Fridy PC, Farrell RJ, Molloy KR, Keegan S, Wang J, Jacobs EY, Li Y, Trivedi J, Sehgal V, Fenyö D, Wu Z, Chait BT, Rout MP: "A new generation of nanobody research tools using improved mass spectrometry-based discovery methods", J Biol Chem. 2024 Aug 2:107623.
    • Wang Y, Fenyö D: "Proteogenomics Reveal the Overexpression of HLA-I in Cancer", J Proteome Res. 22 (2023) 3625-3639.
    • Li Y, Dou Y, Da Veiga Leprevost F, Geffen Y, Calinawan AP, Aguet F, Akiyama Y, Anand S, Birger C, Cao S, Chaudhary R, Chilappagari P, Cieslik M, Colaprico A, Zhou DC, Day C, Domagalski MJ, Esai Selvan M, Fenyö D, Foltz SM, Francis A, Gonzalez-Robles T, Gümüs ZH, Heiman D, Holck M, Hong R, Hu Y, Jaehnig EJ, Ji J, Jiang W, Katsnelson L, Ketchum KA, Klein RJ, Lei JT, Liang WW, Liao Y, Lindgren CM, Ma W, Ma L, MacCoss MJ, Martins Rodrigues F, McKerrow W, Nguyen N, Oldroyd R, Pilozzi A, Pugliese P, Reva B, Rudnick P, Ruggles KV, Rykunov D, Savage SR, Schnaubelt M, Schraink T, Shi Z, Singhal D, Song X, Storrs E, Terekhanova NV, Thangudu RR, Thiagarajan M, Wang LB, Wang JM, Wang Y, Wen B, Wu Y, Wyczalkowski MA, Xin Y, Yao L, Yi X, Zhang H, Zhang Q, Zuhl M, Getz G, Ding L, Nesvizhskii AI, Wang P, Robles AI, Zhang B, Payne SH; Clinical Proteomic Tumor Analysis Consortium: "Proteogenomic data and resources for pan-cancer analysis", Cancer Cell 2023 Aug 14;41(8):1397-1406.
    • Dou Y, Katsnelson L, Gritsenko MA, Hu Y, Reva B, Hong R, Wang YT, Kolodziejczak I, Lu RJ, Tsai CF, Bu W, Liu W, Guo X, An E, Arend RC, Bavarva J, Chen L, Chu RK, Czekanski A, Davoli T, Demicco EG, DeLair D, Devereaux K, Dhanasekaran SM, Dottino P, Dover B, Fillmore TL, Foxall M, Hermann CE, Hiltke T, Hostetter G, Jedryka M, Jewell SD, Johnson I, Kahn AG, Ku AT, Kumar-Sinha C, Kurzawa P, Lazar AJ, Lazcano R, Lei JT, Li Y, Liao Y, Lih TM, Lin TT, Martignetti JA, Masand RP, Matkowski R, McKerrow W, Mesri M, Monroe ME, Moon J, Moore RJ, Nestor MD, Newton C, Omelchenko T, Omenn GS, Payne SH, Petyuk VA, Robles AI, Rodriguez H, Ruggles KV, Rykunov D, Savage SR, Schepmoes AA, Shi T, Shi Z, Tan J, Taylor M, Thiagarajan M, Wang JM, Weitz KK, Wen B, Williams CM, Wu Y, Wyczalkowski MA, Yi X, Zhang X, Zhao R, Mutch D, Chinnaiyan AM, Smith RD, Nesvizhskii AI, Wang P, Wiznerowicz M, Ding L, Mani DR, Zhang H, Anderson ML, Rodland KD, Zhang B, Liu T, Fenyö D; Clinical Proteomic Tumor Analysis Consortium: "Proteogenomic insights suggest druggable pathways in endometrial carcinoma", Cancer Cell S1535-6108 (2023) 00247-7.
    • Schraink T, Blumenberg L, Hussey G, George S, Miller B, Mathew N, González-Robles TJ, Sviderskiy V, Papagiannakopoulos T, Possemato R, Fenyö D, Ruggles KV: "PhosphoDisco: a toolkit for co-regulated phosphorylation module discovery in phosphoproteomic data", Mol Cell Proteomics. 2023:100596.
    • Cheng P, Zhao X, Katsnelson L, Camacho-Hernandez EM, Mermerian A, Mays JC, Lippman SM, Rosales-Alvarez RE, Moya R, Shwetar J, Grun D, Fenyo D, Davoli T: "Proteogenomic analysis of cancer aneuploidy and normal tissues reveals divergent modes of gene regulation across cellular pathways", Elife 11 (2022) e75227.
    • Blumenberg L, Kawaler EA, Cornwell M, Smith S, Ruggles KV, Fenyö D: "BlackSheep: A Bioconductor and Bioconda Package for Differential Extreme Value Analysis", J Proteome Res. 20 (2021) 3767-3773.
    • Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, Keegan S, Jiler JB, Stein ME, Olinares PDB, Herlands L, Hatziioannou T, Sather DN, Debley JS, Fenyö D, Sali A, Bieniasz PD, Aitchison JD, Chait BT, Rout MP: "Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape", Elife. 2021 Dec 7;10:e73027.
    • Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekanski A, Jedryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Fenyö D; Clinical Proteomic Tumor Analysis Consortium: "Proteogenomic Characterization of Endometrial Carcinoma", Cell 180 (2020) 729-748.e26.
    • Krug K, Jaehnig EJ, Satpathy S, Blumenberg L, Karpova A, Anurag M, Miles G, Mertins P, Geffen Y, Tang LC, Heiman DI, Cao S, Maruvka YE, Lei JT, Huang C, Kothadia RB, Colaprico A, Birger C, Wang J, Dou Y, Wen B, Shi Z, Liao Y, Wiznerowicz M, Wyczalkowski MA, Chen XS, Kennedy JJ, Paulovich AG, Thiagarajan M, Kinsinger CR, Hiltke T, Boja ES, Mesri M, Robles AI, Rodriguez H, Westbrook TF, Ding L, Getz G, Clauser KR, Fenyö D, Ruggles KV, Zhang B, Mani DR, Carr SA, Ellis MJ, Gillette MA; Clinical Proteomic Tumor Analysis Consortium: "Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy", Cell. 2020 Nov 16:S0092-8674(20)31400-8.
    • Pamela Wu, Zachary J Heins, James Muller, Lizabeth Katsnelson, Ino de Bruijn, Adam A Abeshouse, Nikolaus Schultz, David Fenyö and Jianjiong Gao: "Integration and analysis of CPTAC proteomics data in the context of cancer genomics in the cBioPortal", Molecular & Cellular Proteomics 2019 mcp.TIR119.001673.
    • Liu W, Payne SH, Ma S, Fenyö D: "Extracting Pathway-Level Signatures from Proteogenomic data in Breast Cancer Using Independent Component Analysis", Molecular & Cellular Proteomics 2019 mcp.TIR119.001442.
    • Mundt F, Rajput S, Li S, Ruggles KV, Mooradian AD, Mertins P, Gillette MA, Krug K, Guo Z, Hoog J, Erdmann-Gilmore P, Primeau T, Huang S, Edwards DP, Wang X, Wang X, Kawaler E, Mani DR, Clauser KR, Gao F, Luo J, Davies SR, Johnson GL, Huang KL, Yoon CJ, Ding L, Fenyö D, Ellis MJ, Townsend RR, Held JM, Carr SA, Ma CX: "Mass spectrometry-based proteomics reveals potential roles of NEK9 and MAP2K4 in resistance to PI3K inhibitors in triple negative breast cancers", Cancer Res. 2018.
    • Wang X, Mooradian AD, Erdmann-Gilmore P, Zhang Q, Viner R, Davies SR, Huang KL, Bomgarden R, Van Tine BA, Shao J, Ding L, Li S, Ellis MJ, Rogers JC, Townsend RR, Fenyö D, Held JM: "Breast tumors educate the proteome of stromal tissue in an individualized but coordinated manner", Sci Signal. 10 (2017) pii:eaam8065.
    • alt
      Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR: "Methods, tools and current perspectives in proteogenomics", Mol Cell Proteomics 2017.
    • Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang K-l, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA & the NCI CPTAC: "Proteogenomics connects somatic mutations to signaling in breast cancer", Nature 534 (2016) 55-62.
    • Keegan S, Cortens JP, Beavis RC, Fenyo D: "g2pDB: A Database Mapping Protein Post-Translational Modifications to Genomic Coordinates", J Proteome Res. 2016 Feb 4.
    • Menschaert G, Fenyo D: "Proteogenomics from a bioinformatics angle: A growing field", Mass Spectrometry Reviews 2015.
    • Askenazi M, Ruggles K, Fenyo D: "PGx: Putting Peptides to BED", J Proteome Res. 2015.
    • Ruggles KV, Tang Z, Wang X, Grover H, Askenazi M, Teubl J, Cao S, McLellan MD, Clauser KR, Tabb DL, Mertins P, Slebos R, Erdmann-Gilmore P, Li S, Gunawardena HP, Xie L, Liu T, Zhou JY, Sun S, Hoadley KA, Perou CM, Chen X, Davies SR, Maher CA, Kinsinger CR, Rodland KD, Zhang H, Zhang Z, Ding L, Townsend RR, Rodriguez H, Chan D, Smith RD, Liebler DC, Carr SA, Payne S, Ellis MJ, Fenyo D: "An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer", Mol Cell Proteomics. 2015.
  • Retrotransposition
    • Efiyenia Ismini Kaparos, Wenjing Zhang, Ryusei Miyanaga, Wilson McKerrow, Jef D Boeke, Teresa Davoli, Paolo Mita, Kelly V. Ruggles, David Fenyo: "Pan-cancer analysis reveals context-dependent roles of LINE-1 ORF1p in immune regulation and copy number alterations", bioRxiv 2025.10.03.680361.
    • McKerrow W, Kagermazova L, Doudican N, Frazzette N, Kaparos EI, Evans SA, Rocha A, Sedivy JM, Neretti N, Carucci J, Boeke JD, Fenyö D: "LINE-1 retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5' single-cell RNA-Seq", Nucleic Acids Res. 2023 Feb 6:gkad049.
    • McKerrow W, Wang X, Mendez-Dorantes C, Mita P, Cao S, Grivainis M, Ding L, LaCava J, Burns KH, Boeke JD, Fenyö D: "LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint", Proc Natl Acad Sci USA, 2022 Feb 22;119(8):e2115999119.
    • Briggs EM, McKerrow W, Mita P, Boeke JD, Logan SK, Fenyö D: "RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs", Mob DNA. 12 (2021) 5.
    • Grivainis M, Tang Z, Fenyö D: "TranspoScope - Interactive Visualization of Retrotransposon Insertions", Bioinformatics 2020 btaa244.
    • Ardeljan D, Wang X, Oghbaie M, Taylor MS, Husband D, Deshpande V, Steranka JP, Gorbounov M, Yang WR, Sie B, Larman HB, Jiang H, Molloy KR, Altukhov I, Li Z, McKerrow W, Fenyö D, Burns KH, LaCava J: "LINE-1 ORF2p expression is nearly imperceptible in human cancers", Mob DNA. 2019 11:1.
    • McKerrow W, Fenyö D: "L1EM: A tool for accurate locus specific LINE-1 RNA quantification", Bioinformatics. 2019 Oct 4. pii: btz724.
    • Sun X, Wang X, Tang Z, Grivainis M, Kahler D, Yun C, Mita P, Fenyö D, Boeke JD: "Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression", Proc Natl Acad Sci U S A. 2018 May 25. pii: 201722565.
    • Tang Z, Steranka JP, Ma S, Grivainis M, Rodic N, Huang CR, Shih IM, Wang TL, Boeke JD, Fenyö D, Burns KH: "Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer", Proc Natl Acad Sci U S A. 2017 Jan 17. pii: 201619797.
  • Genomics
    • Kit Leng Lui S, Keegan S, Tonzi P, Kahli M, Chen YH, Chalhoub N, Coleman KE, Fenyo D, Smith DJ, Huang TT: "Monitoring genome-wide replication fork directionality by Okazaki fragment sequencing in mammalian cells", Nat Protoc. 2021 Jan 13.
    • Chen YH, Keegan S, Kahli M, Tonzi P, Fenyö D, Huang TT, Smith DJ: "Transcription shapes DNA replication initiation and termination in human cells", Nat Struct Mol Biol. 2018 Dec 31.
    • M.D. Sekedat, D. Fenyö, R.S. Rogers, A.J. Tackett, J.D. Aitchison, B.T. Chait: "GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome", Mol Syst Biol. 6 (2010) 353.
  • Proteomics
    • Cifani P, Li Z, Luo D, Grivainis M, Intlekofer AM, Fenyö D, Kentsis A: "Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics", J Proteome Res. 2021, 10.1021/acs.jproteome.0c00638.
    • J. Eriksson, D. Fenyö: "Improving the success rate of proteome analysis by modeling protein-abundance distributions and experimental designs", Nature Biotechnology 25 (2007) 651-655.
    • D. Fenyö, B.S.Phinney, R.C. Beavis: "Determining the Overall Merit of Protein Identification Data Sets: rho-Diagrams and rho-Scores", J Proteome Res 6 (2007) 1997-2004.
    • D. Fenyö, R.C. Beavis: "A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes", Analytical Chemistry 75 (2003) 768-74.
    • J. Eriksson, B.T. Chait, D. Fenyö: "A statistical basis for testing the significance of mass spectrometric protein identification results", Anal Chem 72 (2000) 999-1005.
    • D. Fenyö, J. Qin, B.T. Chait: "Protein Identification using Mass Spectrometric Information", Electrophoresis 19 (1998) 998-1005.
  • Clinical
    • Westcott JM, Hughes F, Liu W, Grivainis M, Hoskins I, Fenyo D: "Prediction of Maternal Hemorrhage Using Machine Learning: Retrospective Cohort Study", J Med Internet Res 24 (2022) e34108.
    • Wang JM, Liu W, Chen X, McRae MP, McDevitt JT, Fenyo D: "Predictive modeling of morbidity and mortality in COVID-19 hospitalized patients and its clinical implications", J Med Internet Res. 2021 May 26.
  • Spatial Biology
  • Multiomics Integration
  • Retrotransposition
  • Genomics
  • Proteomics
  • Clinical