Kody Paul Mansfield, Tamara Mestvirishvili, Bibi Sheleeza Subhan, Valeria Mezzano-Robinson, Dianny A Almanzar, Sydney Hanson, Jimin Tan, Cynthia A Loomis, David Fenyo, Aristotelis Tsirigos, Piul S Rabbani: "Non-segmented unsupervised learning of multispectral whole slide images for robust analysis of tissue repair and regeneration", bioRxiv 2025.08.19.671136.

Jimin Tan, Xi Fu, Xinyu Ling, Shentong Mo, Jiangshan Bai, Raúl Rabadán, David Fenyö, Jef D. Boeke, Aristotelis Tsirigos, Bo Xia: "Multimodal learning decodes the global binding landscape of chromatin-associated proteins", bioRxiv 2025.08.17.670761.

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.

Julie Trolle, Sofia Sessa, Tori Rodrick, Drew R. Jones, David Fenyo, Sudarshan Pinglay, Jef D. Boeke: "A shotgun approach for highly multiplexed mammalian metabolic engineering", bioRxiv 2025.07.08.663766.

Joseph C Mays, Sally Mei, Manjunatha Kogenaru, Helberth Quysbertf, Nazario Bosco, Xin Zhao, Joy J Bianchi, Aleah Goldberg, Gururaj Rao Kidiyoor, Liam J Holt, David Fenyö, Teresa Davoli: "KaryoTap Enables Aneuploidy Detection in Thousands of Single Human Cells", bioRxiv 2023.09.08.555746.

Hussey G, Valeriano J, Zhang C, Sullivan A, Fenyö D, Schluter J: "The MTIST platform: a microbiome time series inference standardized test", Res Sq [Preprint]. 2024 May 8:rs.3.rs-4343683.

Sarah Keegan, David Fenyö, Liam J. Holt: "GEMspa: a Napari plugin for analysis of single particle tracking data", bioRxiv 2023.06.26.546612.

Jiehui Deng, David H. Peng, David Fenyo, Hao Yuan, Alfonso Lopez, Daniel S. Levin, Mary Meynardie, Mari Quinteros, Michela Ranieri, Soumyadip Sahu, Sally C. M. Lau, Elaine Shum, Vamsidhar Velcheti, Salman R. Punekar, Natasha Rekhtman, Catríona M. Dowling, Vajira Weerasekara, Yun Xue, Hongbin Ji, Yik Siu, Drew Jones, Aaron N. Hata, Takeshi Shimamura, John T. Poirier, Charles M Rudin, Takamitsu Hattori, Shohei Koide, Thales Papagiannakopoulos, Benjamin G. Neel, Nabeel Bardeesy, Kwok-kin Wong: "In vivo metabolomics identifies CD38 as an emergent vulnerability in LKB1-mutant lung cancer", bioRxiv 2023.04.18.537350.

Satpathy S, Clark NM, Chen YJ, Hosseini N, Chang YH, Hsiao Y, Lei JT, Petralia F, Chen JS, Geffen Y, Heiman DI, Paul I, Cho H, Hollenberg M, Marino GB, Lin KT, Mannan R, White CJ, Allen J, Avanessian SC, Kane MH, Wolfe A, Kinarivala M, Liu W, Anand S, Lin MW, Haines M, Bergstrom EJ, Hussey G, Li GX, Mani DC, Fang H, Jaehnig EJ, Keshishian H, Miller B, Su KY, Hsiao YJ, Hsu HH, Hsieh MS, Hsu KH, Monovoukas A, Gohsman S, Thorup JR, Deng Y, Akiyama Y, Deng E, Sheng-Wen Chen E, Krek A, Espinoza R, Ma W, Charytonowicz D, Sebra R, Lin JH, Chen YS, Hsu YC, Lin ZS, Chen KC, Yeh CW, Wang YT, Lazar AJ, Mesri M, An E, Zhang X, Clauser KR, Fenyö D, Chinnaiyan AM, Zhang B, Ding L, Ruggles K, Newton C, Zhang H, Wang P, Hostetter G, Omenn GS, Kumar-Sinha C, Thiagarajan M, Govindan R, Paik P, Parolia A, Li QK, Ma'ayan A, Getz GA, Dhanasekaran SM, Robles AI, Chang GC, Yang PC, Yu SL, Chen HY, Nesvizhskii AI, Carr SA, Mani DR, Cieslik MP, Chen YJ, Gillette MA; Taiwan Cancer Moonshot Program; Clinical Proteomic Tumor Analysis Consortium: "Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures", Cancer Cell 2025:S1535-6108(25)00317-4.

Silverman GJ, Amarnani AN, Armini AA, Kim A, Kopinsky H, Fenyo D, Kister I: "B cell-extrinsic and intrinsic factors linked to early immune repletion after anti-CD20 therapy in patients with multiple sclerosis of African ancestry", Front Immunol. 2025 16:1590165.

Kim Y, Doma V, Çakır U, Kuras M, Betancourt LH, Pla I, Sanchez A, Sugihara Y, Appelqvist R, Oskolas H, Lee B, Guedes J, Monnerat G, Carneiro GRA, Nogueira FCS, Domont GB, Malm J, Baldetorp B, Wieslander E, Németh IB, Szász AM, Hong R, Pawłowski K, Rezeli M, Kwon HJ, Timar J, Fenyö D, Kárpáti S, Marko-Varga G, Gil J: "Mitochondrial proteome landscape unveils key insights into melanoma severity and treatment strategies", Cancer 2025 131(13):e35897.

Bartha Á, Weltz B, Betancourt LH, Gil J, Pinto de Almeida N, Bianchini G, Szeitz B, Szadai L, Pla I, Kemény LV, Jánosi ÁJ, Hong R, Rajeh A, Nogueira F, Doma V, Woldmar N, Guedes J, Újfaludi Z, Kim Y, Szarvas T, Pahi Z, Pankotai T, Szasz AM, Sanchez A, Baldetorp B, Tímár J, Németh IB, Kárpáti S, Appelqvist R, Domont GB, Pawlowski K, Wieslander E, Malm J, Fenyo D, Horvatovich P, Marko-Varga G, Győrffy B: "Melanoma Proteomics Unveiled: Harmonizing Diverse Data Sets for Biomarker Discovery and Clinical Insights via MEL-PLOT", J Proteome Res. 2025.

Kołodziejczak-Guglas I, Simões RLS, de Souza Santos E, Demicco EG, Lazcano Segura RN, Ma W, Wang P, Geffen Y, Storrs E, Petralia F, Colaprico A, da Veiga Leprevost F, Pugliese P, Ceccarelli M, Noushmehr H, Nesvizhskii AI, Kamińska B, Priebe W, Lubiński J, Zhang B, Lazar AJ, Kurzawa P, Mesri M, Robles AI; Clinical Proteomic Tumor Analysis Consortium; Ding L, Malta TM, Wiznerowicz M: "Proteomic-based stemness score measures oncogenic dedifferentiation and enables the identification of druggable targets", Cell Genom. 2025:100851.

Oskolas H, Nogueira FCN, Domont GB, Yu KH, Semenov YR, Sorger P, Steinfelder E, Corps L, Schulz L, Wieslander E, Fenyö D, Kárpáti S, Holló P, Kemény LV, Döme B, Megyesfalvi Z, Pawłowski K, Nishimura T, Kwon H, Encarnación-Guevara S, Szasz AM, Veréb Z, Gyulai R, Németh IB, Appelqvist R, Rezeli M, Baldetorp B, Horvatovich P, Malmström J, Pla I, Sanchez A, Knudsen B, Kiss A, Malm J, Marko-Varga G, Gil J: "Comprehensive biobanking strategy with clinical impact at the European Cancer Moonshot Lund Center", J Proteomics 2025:105442.

Martins Rodrigues F, Terekhanova NV, Imbach KJ, Clauser KR, Esai Selvan M, Mendizabal I, Geffen Y, Akiyama Y, Maynard M, Yaron TM, Li Y, Cao S, Storrs EP, Gonda OS, Gaite-Reguero A, Govindan A, Kawaler EA, Wyczalkowski MA, Klein RJ, Turhan B, Krug K, Mani DR, Leprevost FDV, Nesvizhskii AI, Carr SA, Fenyö D, Gillette MA, Colaprico A, Iavarone A, Robles AI, Huang KL, Kumar-Sinha C, Aguet F, Lazar AJ, Cantley LC, Marigorta UM, Gümüş ZH, Bailey MH, Getz G, Porta-Pardo E, Ding L; Clinical Proteomic Tumor Analysis Consortium: "Precision proteogenomics reveals pan-cancer impact of germline variants", Cell 2025:S0092-8674(25)00344-7..

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.

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.

Gleason C, Terry SN, Hernandez MM, Jacob S, Fenyo D, Johnson JR, Deikus G, Francoeur N, Hahn A, Sebra R, Zamarin D, Molina H, Simon V, Mulder LCF: "An integrated approach for the accurate detection of HERV-K HML-2 transcription and protein synthesis", Nucleic Acids Res. 2025 Jan 11;53(2):gkaf011.

Pla I, Szabolcs BL, Péter PN, Ujfaludi Z, Kim Y, Horvatovich P, Sanchez A, Pawlowski K, Wieslander E, Kuras M, Murillo JR, Guedes J, Pál DMP, Ascsillán AA, Betancourt LH, Németh IB, Gil J, de Almeida NP, Szeitz B, Szadai L, Doma V, Woldmar N, Bartha Á, Pahi Z, Pankotai T, Győrffy B, Szasz AM, Domont G, Nogueira F, Kwon HJ, Appelqvist R, Kárpáti S, Fenyö D, Malm J, Marko-Varga G, Kemény LV: "Unbiased Drug Target Prediction Reveals Sensitivity to Ferroptosis Inducers, HDAC and RTK Inhibitors in Melanoma Subtypes", Int J Dermatol. 2024.

Goldberg GW, Kogenaru M, Keegan S, Haase MAB, Kagermazova L, Arias MA, Onyebeke K, Adams S, Beyer DK, Fenyö D, Noyes MB, Boeke JD: "Engineered transcription-associated Cas9 targeting in eukaryotic cells", Nat Commun. 2024 Nov 27;15(1):10287.

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.

Pinto de Almeida N, Jánosi ÁJ, Hong R, Rajeh A, Nogueira F, Szadai L, Szeitz B, Pla Parada I, Doma V, Woldmar N, Guedes J, Újfaludi Z, Bartha A, Kim Y, Welinder C, Baldetorp B, Kemény LV, Pahi Z, Wan G, Nguyen N, Pankotai T, Győrffy B, Pawłowski K, Horvatovich P, Szasz AM, Sanchez A, Kuras M, Rodriguez Murillo J, Betancourt L, Domont GB, Semenov YR, Yu KH, Kwon HJ, Németh IB, Fenyő D, Wieslander E, Marko-Varga G, Gil J: "Mitochondrial dysfunction and immune suppression in BRAF V600E-mutated metastatic melanoma", Clin Transl Med 2024; 14(7):e1773.

Szadai L, Bartha A, Parada IP, Lakatos AIT, Pál DMP, Lengyel AS, de Almeida NP, Jánosi ÁJ, Nogueira F, Szeitz B, Doma V, Woldmar N, Guedes J, Ujfaludi Z, Pahi ZG, Pankotai T, Kim Y, Győrffy B, Baldetorp B, Welinder C, Szasz AM, Betancourt L, Gil J, Appelqvist R, Kwon HJ, Kárpáti S, Kuras M, Murillo JR, Németh IB, Malm J, Fenyö D, Pawłowski K, Horvatovich P, Wieslander E, Kemény LV, Domont G, Marko-Varga G, Sanchez A: "Predicting immune checkpoint therapy response in three independent metastatic melanoma cohorts", Front Oncol 2024; 14:1428182.

Liu J, Cao S, Imbach KJ, Gritsenko MA, Lih TM, Kyle JE, Yaron-Barir TM, Binder ZA, Li Y, Strunilin I, Wang YT, Tsai CF, Ma W, Chen L, Clark NM, Shinkle A, Naser Al Deen N, Caravan W, Houston A, Simin FA, Wyczalkowski MA, Wang LB, Storrs E, Chen S, Illindala R, Li YD, Jayasinghe RG, Rykunov D, Cottingham SL, Chu RK, Weitz KK, Moore RJ, Sagendorf T, Petyuk VA, Nestor M, Bramer LM, Stratton KG, Schepmoes AA, Couvillion SP, Eder J, Kim YM, Gao Y, Fillmore TL, Zhao R, Monroe ME, Southard-Smith AN, Li YE, Jui-Hsien Lu R, Johnson JL, Wiznerowicz M, Hostetter G, Newton CJ, Ketchum KA, Thangudu RR, Barnholtz-Sloan JS, Wang P, Fenyö D, An E, Thiagarajan M, Robles AI, Mani DR, Smith RD, Porta-Pardo E, Cantley LC, Iavarone A, Chen F, Mesri M, Nasrallah MP, Zhang H, Resnick AC, Chheda MG, Rodland KD, Liu T, Ding L: "Philadelphia Coalition for a Cure; Clinical Proteomic Tumor Analysis Consortium. Multi-scale signaling and tumor evolution in high-grade gliomas", Cancer Cell 2024; 42(7):1217-1238.e19.

Kohlrausch FB, Wang F, McKerrow W, Grivainis M, Fenyo D, Keefe DL: "Mapping of long interspersed element-1 (L1) insertions by TIPseq provides information about sub chromosomal genetic variation in human embryos", J Assist Reprod Genet 2024.

Goehring L, Keegan S, Lahiri S, Xia W, Kong M, Jimenez-Sainz J, Gupta D, Drapkin R, Jensen RB, Smith DJ, Rothenberg E, Fenyö D, Huang TT: "Dormant origin firing promotes head-on transcription-replication conflicts at transcription termination sites in response to BRCA2 deficiency", Nat Commun. 2024 Jun 3;15(1):4716.

Stephan G, Haddock S, Wang S, Erdjument-Bromage H, Liu W, Ravn-Boess N, Frenster JD, Bready D, Cai J, Ronnen R, Sabio-Ortiz J, Fenyo D, Neubert TA, Placantonakis DG: "Modulation of GPR133 (ADGRD1) signaling by its intracellular interaction partner extended synaptotagmin 1", Cell Rep. 2024 May 28;43(5):114229.

Rona G, Miwatani-Minter B, Zhang Q, Goldberg HV, Kerzhnerman MA, Howard JB, Simoneschi D, Lane E, Hobbs JW, Sassani E, Wang AA, Keegan S, Laverty DJ, Piett CG, Pongor LS, Xu ML, Andrade J, Thomas A, Sicinski P, Askenazi M, Ueberheide B, Fenyö D, Nagel ZD, Pagano M: "CDK-independent role of D-type cyclins in regulating DNA mismatch repair", Mol Cell 2024 S1097-2765(24)00129-1.

Okimoto LYS, Mendonca-Neto R, Nakamura FG, Nakamura EF, Fenyö D, Silva CT: "Few-shot genes selection: subset of PAM50 genes for breast cancer subtypes classification", BMC Bioinformatics 25 (2024) 92.

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.

María Xóchitl Benítez-Jones, Sarah Keegan, Sebastian Jamshahi, David Fenyö: "Machine Learning Classification of 53BP1 Foci", bioRxiv 2024.02.28.582150.

Dou Y, Katsnelson L, Zhang B, Fenyö D, Liu T: "Proteogenomics unveils mechanistic insights to precision oncology", Clin Transl Med. 13 (2023) e1477.

Szadai L, Guedes JS, Woldmar N, de Almeida NP, Jánosi ÁJ, Rajeh A, Kovács F, Kriston A, Migh E, Wan G, Nguyen N, Oskolás H, Appelqvist R, Nogueira FC, Domont GB, Yu KH, Semenov ER, Malm J, Rezeli M, Wieslander E, Fenyö D, Kemény L, Horvath P, Németh IB, Marko-Varga G, Gil J: "Mitochondrial and immune response dysregulation in melanoma recurrence", Clin Transl Med. 13 (2023) e1495.

Ravn-Boess N, Roy N, Hattori T, Bready D, Donaldson H, Lawson C, Lapierre C, Korman A, Rodrick T, Liu E, Frenster JD, Stephan G, Wilcox J, Corrado AD, Cai J, Ronnen R, Wang S, Haddock S, Sabio Ortiz J, Mishkit O, Khodadadi-Jamayran A, Tsirigos A, Fenyö D, Zagzag D, Drube J, Hoffmann C, Perna F, Jones DR, Possemato R, Koide A, Koide S, Park CY, Placantonakis DG: "The expression profile and tumorigenic mechanisms of CD97 (ADGRE5) in glioblastoma render it a targetable vulnerability", Cell Rep. 42 (2023) 113374.

Ruoff R, Weber H, Wang Y, Huang H, Shapiro E, Fenyö D, Garabedian MJ: "MED19 encodes two unique protein isoforms that confer prostate cancer growth under low androgen through distinct gene expression programs", Sci Rep. 13 (2023) 18227.

Wang Y, Fenyö D: "Proteogenomics Reveal the Overexpression of HLA-I in Cancer", J Proteome Res. 22 (2023) 3625-3639.

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.

Liang WW, Lu RJ, Jayasinghe RG, Foltz SM, Porta-Pardo E, Geffen Y, Wendl MC, Lazcano R, Kolodziejczak I, Song Y, Govindan A, Demicco EG, Li X, Li Y, Sethuraman S, Payne SH, Fenyö D, Rodriguez H, Wiznerowicz M, Shen H, Mani DR, Rodland KD, Lazar AJ, Robles AI, Ding L; Clinical Proteomic Tumor Analysis Consortium: "Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin", Cancer Cell 2023 Aug 13:S1535-6108(23)00253-2.

Li Y, Porta-Pardo E, Tokheim C, Bailey MH, Yaron TM, Stathias V, Geffen Y, Imbach KJ, Cao S, Anand S, Akiyama Y, Liu W, Wyczalkowski MA, Song Y, Storrs EP, Wendl MC, Zhang W, Sibai M, Ruiz-Serra V, Liang WW, Terekhanova NV, Rodrigues FM, Clauser KR, Heiman DI, Zhang Q, Aguet F, Calinawan AP, Dhanasekaran SM, Birger C, Satpathy S, Zhou DC, Wang LB, Baral J, Johnson JL, Huntsman EM, Pugliese P, Colaprico A, Iavarone A, Chheda MG, Ricketts CJ, Fenyö D, Payne SH, Rodriguez H, Robles AI, Gillette MA, Kumar-Sinha C, Lazar AJ, Cantley LC, Getz G, Ding L; Clinical Proteomic Tumor Analysis Consortium: "Pan-cancer proteogenomics connects oncogenic drivers to functional states", Cell 2023 Aug 14:S0092-8674(23)00780-8.

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.

Chowdhury S, Kennedy JJ, Ivey RG, Murillo OD, Hosseini N, Song X, Petralia F, Calinawan A, Savage SR, Berry AB, Reva B, Ozbek U, Krek A, Ma W, da Veiga Leprevost F, Ji J, Yoo S, Lin C, Voytovich UJ, Huang Y, Lee SH, Bergan L, Lorentzen TD, Mesri M, Rodriguez H, Hoofnagle AN, Herbert ZT, Nesvizhskii AI, Zhang B, Whiteaker JR, Fenyo D, McKerrow W, Wang J, Schürer SC, Stathias V, Chen XS, Barcellos-Hoff MH, Starr TK, Winterhoff BJ, Nelson AC, Mok SC, Kaufmann SH, Drescher C, Cieslik M, Wang P, Birrer MJ, Paulovich AG: "Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer", Cell 186 (2023) 3476-3498.e35.

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.

Srinivasan Rajsri K, McRae MP, Christodoulides NJ, Dapkins I, Simmons GW, Matz H, Dooley H, Fenyö D, McDevitt JT: "Simultaneous Quantitative SARS-CoV-2 Antigen and Host Antibody Detection and Pre-Screening Strategy at the Point of Care", Bioengineering (Basel) 10 (2023) 670.

Azzouz DF, Chen Z, Izmirly PM, Chen LA, Li Z, Zhang C, Mieles D, Trujillo K, Heguy A, Pironti A, Putzel GG, Schwudke D, Fenyo D, Buyon JP, Alekseyenko AV, Gisch N, Silverman GJ: "Longitudinal gut microbiome analyses and blooms of pathogenic strains during lupus disease flares", Ann Rheum Dis. 2023 ard-2023-223929.

Frenster JD, Erdjument-Bromage H, Stephan G, Ravn-Boess N, Wang S, Liu W, Bready D, Wilcox J, Kieslich B, Jankovic M, Wilde C, Horn S, Sträter N, Liebscher I, Schöneberg T, Fenyo D, Neubert TA, Placantonakis DG: "TK7 is a positive allosteric modulator of GPR133 signaling in glioblastoma", Cell Rep. 42 (2023) 112679.

Berteli TS, Wang F, McKerrow W, Navarro PA, Fenyo D, Boeke JD, Kohlrausch FB, Keefe DL: "Transposon insertion profiling by sequencing (TIPseq) identifies novel LINE-1 insertions in human sperm", J Assist Reprod Genet. 2023.

Bosco N, Goldberg A, Zhao X, Mays JC, Cheng P, Johnson AF, Bianchi JJ, Toscani C, Di Tommaso E, Katsnelson L, Annuar D, Mei S, Faitelson RE, Pesselev IY, Mohamed KS, Mermerian A, Camacho-Hernandez EM, Gionco CA, Manikas J, Tseng YS, Sun Z, Fani S, Keegan S, Lippman SM, Fenyö D, Giunta S, Santaguida S, Davoli T: "KaryoCreate: A CRISPR-based technology to study chromosome-specific aneuploidy by targeting human centromeres", Cell 186 (2023) 1985-2001.e19.

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.

Tan J, Shenker-Tauris N, Rodriguez-Hernaez J, Wang E, Sakellaropoulos T, Boccalatte F, Thandapani P, Skok J, Aifantis I, Fenyö D, Xia B, Tsirigos A: "Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening", Nat Biotechnol 2023 Jan 9.

Li Y, Lih TM, Dhanasekaran SM, Mannan R, Chen L, Cieslik M, Wu Y, Lu RJ, Clark DJ, Kolodziejczak I, Hong R, Chen S, Zhao Y, Chugh S, Caravan W, Naser Al Deen N, Hosseini N, Newton CJ, Krug K, Xu Y, Cho KC, Hu Y, Zhang Y, Kumar-Sinha C, Ma W, Calinawan A, Wyczalkowski MA, Wendl MC, Wang Y, Guo S, Zhang C, Le A, Dagar A, Hopkins A, Cho H, Leprevost FDV, Jing X, Teo GC, Liu W, Reimers MA, Pachynski R, Lazar AJ, Chinnaiyan AM, Van Tine BA, Zhang B, Rodland KD, Getz G, Mani DR, Wang P, Chen F, Hostetter G, Thiagarajan M, Linehan WM, Fenyö D, Jewell SD, Omenn GS, Mehra R, Wiznerowicz M, Robles AI, Mesri M, Hiltke T, An E, Rodriguez H, Chan DW, Ricketts CJ, Nesvizhskii AI, Zhang H, Ding L; Clinical Proteomic Tumor Analysis Consortium: "Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness", Cancer Cell. 2022 Dec 20:S1535-6108(22)00565-7.

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.

Johannet P, Liu W, Fenyo D, Wind-Rotolo M, Krogsgaard M, Mehnert JM, Weber JS, Zhong J, Osman I: "Baseline Serum Autoantibody Signatures Predict Recurrence and Toxicity in Melanoma Patients Receiving Adjuvant Immune Checkpoint Blockade", Clin Cancer Res 28 (2022) 4121-4130.

Zwack EE, Chen Z, Devlin JC, Li Z, Zheng X, Weinstock A, Lacey KA, Fisher EA, Fenyö D, Ruggles KV, Loke P, Torres VJ: "Staphylococcus aureus induces a muted host response in human blood that blunts the recruitment of neutrophils", Proc Natl Acad Sci U S A 119 (2022) e2123017119.

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.

Zhao CC, Bjurlin MA, Wysock JS, Taneja SS, Huang WC, Fenyo D, Matulewicz RS: "Machine learning decision support model for radical cystectomy discharge planning", Urol Oncol. 2022 Jun 21:S1078-1439(22)00195-8.

Runyu Hong & David Fenyö: When blockchain meets artificial intelligence: "An application to cancer histopathology", Cell Reports Medicine 3 (2022) 100666.

Coleman KE, Yin Y, Lui SKL, Keegan S, Fenyo D, Smith DJ, Rothenberg E, Huang TT: "USP1-trapping lesions as a source of DNA replication stress and genomic instability", Nat Commun. 2022 Apr 1;13(1):1740.

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.

Hong, R.; Liu, W.; Fenyö, D: "Predicting and Visualizing STK11 Mutation in Lung Adenocarcinoma Histopathology Slides Using Deep Learning", BioMedInformatics 2022, 2, 101-105.

Hong, R.; Fenyö, D: "Deep Learning and Its Applications in Computational Pathology", BioMedInformatics 2022, 2, 159-168.

Sergei German, Leslie Mitchell, Antonio Vela Gartner, David Fenyo, Jef D. Boeke: "MenDEL: PCR Primer Design as Constrained Optimization Process", bioRxiv 2022.06.26.496474.

Sergei German, Sudarshan Pinglay, Brendan Camellato, David Fenyo, Jef D. Boeke: "MenDEL: automated search of BAC sets covering long DNA regions of interest", bioRxiv 2022.06.26.496179.

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.

Mendoncaneto R, Fenyo D, Li Z, Nakamura EF, Nakamura FG, Silva CT: "A Gene Selection Method Based On Outliers for Breast Cancer Subtype Classification", IEEE/ACM Trans Comput Biol Bioinform. 2021 Dec 3;PP.

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.

Cao L, Huang C, Cui Zhou D, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJ, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L, Zhang B, Zhang H: "Clinical Proteomic Tumor Analysis Consortium. Proteogenomic characterization of pancreatic ductal adenocarcinoma", Cell, 2021 Sep 16;184(19):5031-5052.e26.

Gorbunova V, Seluanov A, Mita P, McKerrow W, Fenyö D, Boeke JD, Linker SB, Gage FH, Kreiling JA, Petrashen AP, Woodham TA, Taylor JR, Helfand SL, Sedivy JM: "The role of retrotransposable elements in ageing and age-associated diseases", Nature, 2021 Aug;596(7870):43-53. doi: 10.1038/s41586-021-03542-y.

Satpathy S, Krug K, Jean Beltran PM, Savage SR, Petralia F, Kumar-Sinha C, Dou Y, Reva B, Kane MH, Avanessian SC, Vasaikar SV, Krek A, Lei JT, Jaehnig EJ, Omelchenko T, Geffen Y, Bergstrom EJ, Stathias V, Christianson KE, Heiman DI, Cieslik MP, Cao S, Song X, Ji J, Liu W, Li K, Wen B, Li Y, Gümüs ZH, Selvan ME, Soundararajan R, Visal TH, Raso MG, Parra ER, Babur Ö, Vats P, Anand S, Schraink T, Cornwell M, Rodrigues FM, Zhu H, Mo CK, Zhang Y, da Veiga Leprevost F, Huang C, Chinnaiyan AM, Wyczalkowski MA, Omenn GS, Newton CJ, Schurer S, Ruggles KV, Fenyö D, Jewell SD, Thiagarajan M, Mesri M, Rodriguez H, Mani SA, Udeshi ND, Getz G, Suh J, Li QK, Hostetter G, Paik PK, Dhanasekaran SM, Govindan R, Ding L, Robles AI, Clauser KR, Nesvizhskii AI, Wang P, Carr SA, Zhang B, Mani DR, Gillette MA; Clinical Proteomic Tumor Analysis Consortium: "A proteogenomic portrait of lung squamous cell carcinoma", Cell, 2021 Aug 5;184(16):4348-4371.e40.

Lazaro Hiram Betancourt, Jeovanis Gil, Aniel Sanchez, Viktória Doma, Magdalena Kuras, Jimmy Rodriguez Murillo, Erika Velasquez, Ugur Çakir, Yonghyo Kim, Yutaka Sugihara, Indira Pla Parada, Beáta Szeitz, Roger Appelqvist, Elisabet Wieslander, Charlotte Welinder, Natália Pinto de Almeida, Nicole Woldmar, Matilda Marko-Varga, Jonatan Eriksson, Krzysztof Pawlowski, Bo Baldetorp, Christian Ingvar, Håkan Olsson, Lotta Lundgren, Henrik Lindberg, Henriett Oskolas, Boram Lee, Ethan Berge, Marie Sjögren, Carina Eriksson, Dasol Kim, Ho Jeong Kwon, Beatrice Knudsen, Melinda Rezeli, Johan Malm, Runyu Hong, Peter Horvath, A. Marcell Szász, József Tímár, Sarolta Kárpáti, Peter Horvatovich, Tasso Miliotis, Toshihide Nishimura, Harubumi Kato, Erik Steinfelder, Madalina Oppermann, Ken Miller, Francesco Florindi, Quimin Zhou, Gilberto B. Domont, Luciana Pizzatti, Fábio C. S. Nogueira, Leticia Szadai, István Balázs Németh, Henrik Ekedahl, David Fenyö, György Marko-Varga: "The Human Melanoma Proteome Atlas—Complementing the melanoma transcriptome", Clin Transl Med. 2021; 11:e451.

Lazaro Hiram Betancourt, Jeovanis Gil, Yonghyo Kim, Viktória Doma, Ugur Çakir, Aniel Sanchez, Jimmy Rodriguez Murillo, Magdalena Kuras, Indira Pla Parada, Yutaka Sugihara, Roger Appelqvist, Elisabet Wieslander, Charlotte Welinder, Erika Velasquez, Natália Pinto de Almeida, Nicole Woldmar, Matilda Marko-Varga, Krzysztof Pawlowski, Jonatan Eriksson, Beáta Szeitz, Bo Baldetorp, Christian Ingvar, Håkan Olsson, Lotta Lundgren, Henrik Lindberg, Henriett Oskolas, Boram Lee, Ethan Berge, Marie Sjögren, Carina Eriksson, Dasol Kim, Ho Jeong Kwon, Beatrice Knudsen, Melinda Rezeli, Runyu Hong, Peter Horvatovich, Tasso Miliotis, Toshihide Nishimura, Harubumi Kato, Erik Steinfelder, Madalina Oppermann, Ken Miller, Francesco Florindi, Qimin Zhou, Gilberto B. Domont, Luiciana Pizzatti, Fábio C. S. Nogueira, Peter Horvath, Leticia Szadai, József Tímár, Sarolta Kárpáti, A. Marcell Szász, Johan Malm, David Fenyö, Henrik Ekedahl, István Balázs Németh, György Marko-Varga: "The human melanoma proteome atlas—Defining the molecular pathology", Clin Transl Med. 2021; 11:e473.

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.

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.

Yang H, Butler ER, Monier SA, Teubl J, Fenyö D, Ueberheide B, Siegel D: "A predictive model for vertebrate bone identification from collagen using proteomic mass spectrometry", Sci Rep. 2021 May 25;11(1):10900.

Radke Emily E., Li Zhi, Hernandez David N., El Bannoudi Hanane, Kosakovsky Pond Sergei L., Shopsin Bo, Lopez Peter, Fenyö David, Silverman Gregg J.: "Diversity of Functionally Distinct Clonal Sets of Human Conventional Memory B Cells That Bind Staphylococcal Protein A", Frontiers in Immunology 12 (2021) 1400.

Castro CM, Corciulo C, Friedman B, Li Z, Jacob S, Fenyo D, Cronstein BN: "Adenosine A2A receptor null chondrocyte transcriptome resembles that of human osteoarthritic chondrocytes", Purinergic Signal. 2021 May 11.

Huang KL, Scott AD, Zhou DC, Wang LB, Weerasinghe A, Elmas A, Liu R, Wu Y, Wendl MC, Wyczalkowski MA, Baral J, Sengupta S, Lai CW, Ruggles K, Payne SH, Raphael B, Fenyö D, Chen K, Mills G, Ding L: "Spatially interacting phosphorylation sites and mutations in cancer", Nat Commun. 2021 Apr 19;12(1):2313.

Simoneschi D, Rona G, Zhou N, Jeong YT, Jiang S, Milletti G, Arbini AA, O'Sullivan A, Wang AA, Nithikasem S, Keegan S, Siu Y, Cianfanelli V, Maiani E, Nazio F, Cecconi F, Boccalatte F, Fenyö D, Jones DR, Busino L, Pagano M: "CRL4^AMBRA1 is a master regulator of D-type cyclins", Nature 2021, 10.1038/s41586-021-03445-y.

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.

Wang LB, Karpova A, Gritsenko MA, Kyle JE, Cao S, Li Y, Rykunov D, Colaprico A, Rothstein JH, Hong R, Stathias V, Cornwell M, Petralia F, Wu Y, Reva B, Krug K, Pugliese P, Kawaler E, Olsen LK, Liang WW, Song X, Dou Y, Wendl MC, Caravan W, Liu W, Cui Zhou D, Ji J, Tsai CF, Petyuk VA, Moon J, Ma W, Chu RK, Weitz KK, Moore RJ, Monroe ME, Zhao R, Yang X, Yoo S, Krek A, Demopoulos A, Zhu H, Wyczalkowski MA, McMichael JF, Henderson BL, Lindgren CM, Boekweg H, Lu S, Baral J, Yao L, Stratton KG, Bramer LM, Zink E, Couvillion SP, Bloodsworth KJ, Satpathy S, Sieh W, Boca SM, Schürer S, Chen F, Wiznerowicz M, Ketchum KA, Boja ES, Kinsinger CR, Robles AI, Hiltke T, Thiagarajan M, Nesvizhskii AI, Zhang B, Mani DR, Ceccarelli M, Chen XS, Cottingham SL, Li QK, Kim AH, Fenyö D, Ruggles KV, Rodriguez H, Mesri M, Payne SH, Resnick AC, Wang P, Smith RD, Iavarone A, Chheda MG, Barnholtz-Sloan JS, Rodland KD, Liu T, Ding L, Clinical Proteomic Tumor Analysis Consortium: "Proteogenomic and metabolomic characterization of human glioblastoma", Cancer Cell 2021 Feb 2:S1535-6108(21)00050-7.

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.

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.

Wenke Liu, Xuya Wang, D R Mani, David Fenyo: "Modeling transcriptional profiles of gene perturbation with deep neural network", bioRxiv 2021.07.15.452534.

Tamas Szoradi, Tong Shu, Gururaj R Kidiyoor, Ying Xie, Nora L Herzog, Andrew Bazley, Martina Bonucci, Sarah Keegan, Shivanjali Saxena, Farida Ettefa, Gregory P Brittingham, Joel Lemiere, David Fenyo, Fred Chang, Morgan Delarue, Liam J Holt: "nucGEMs probe the biophysical properties of the nucleoplasm", bioRxiv 2021.11.18.469159.

Jeovanis Gil, Yonghyo Kim, Beáta Szeitz, Viktória Doma, Ugur Çakir, Natália Pinto de Almeida, Yanick Paco Hagemeijer, Victor Guryev, Jenny G Johansson, Yogita Sharma, Indira Pla Parada, Zsolt Horvath, Jéssica de Siqueira Guedes, Gustavo Monnerat, Fábio CS Nogueira, Boram Lee, Henriett Oskolas, Enikö Kuroli, Judit Hársing, Yutaka Sugihara, Magdalena Kuras, Roger Appelqvist, Elisabet Wieslander, Gilberto B Domont, Bo Baldetorp, Runyu Hong, Gergely Huszty, Laura Vizkeleti, József Tímár, David Fenyö, Lazaro Hiram Betancourt, Johan Jakobsson, Johan Malm, Aniel Sanchez, A. Marcell Szász, Peter Horvatovich, Melinda Rezeli, Sarolta Kárpáti, György Marko-Varga: "Proteogenomics Reveals how Metastatic Melanoma Modulates the Immune System to Allow Immune Evasion", bioRxiv 2021.04.10.439245.

Weiping Ma, Sunkyu Kim, Shrabanti Chowdhury, Zhi Li, Mi Yang, Seungyeul Yoo, Francesca Petralia, Jeremy Jacobsen, Jingyi Jessica Li, Xinzhou Ge, Kexin Li, Thomas Yu, Nathan Edwards, Samuel Payne, Paul C. Boutros, Henry Rodriguez, Gustavo Stolovitzky, Jun Zhu, Jaewoo Kang, David Fenyo, Julio Saez-Rodriguez, Pei Wang: "DreamAI: algorithm for the imputation of proteomics data", bioRxiv 2020.07.21.214205.

Pérez-Hernández Duran M, Leo-Macias A, Keegan S, Jouni M, Kim JC, Agullo-Pascual E, Vermij SH, Zhang M, Liang FX, Burridge P, Fenyo D, Rothenberg E, Delmar M: "Structural and Functional Characterization of A Nav1.5-Mitochondrial Couplon", Circ Res. 2020 Dec 21.

Hakhverdyan Z, Molloy KR, Keegan S, Herricks T, Lepore DM, Munson M, Subbotin RI, Fenyö D, Aitchison JD, Fernandez-Martinez J, Chait BT, Rout MP: "Dissecting the Structural Dynamics of the Nuclear Pore Complex", Mol Cell. 2021 Jan 7;81(1):153-165.e7.

Petralia F, Tignor N, Reva B, Koptyra M, Chowdhury S, Rykunov D, Krek A, Ma W, Zhu Y, Ji J, Calinawan A, Whiteaker JR, Colaprico A, Stathias V, Omelchenko T, Song X, Raman P, Guo Y, Brown MA, Ivey RG, Szpyt J, Guha Thakurta S, Gritsenko MA, Weitz KK, Lopez G, Kalayci S, Gümüs ZH, Yoo S, da Veiga Leprevost F, Chang HY, Krug K, Katsnelson L, Wang Y, Kennedy JJ, Voytovich UJ, Zhao L, Gaonkar KS, Ennis BM, Zhang B, Baubet V, Tauhid L, Lilly JV, Mason JL, Farrow B, Young N, Leary S, Moon J, Petyuk VA, Nazarian J, Adappa ND, Palmer JN, Lober RM, Rivero-Hinojosa S, Wang LB, Wang JM, Broberg M, Chu RK, Moore RJ, Monroe ME, Zhao R, Smith RD, Zhu J, Robles AI, Mesri M, Boja E, Hiltke T, Rodriguez H, Zhang B, Schadt EE, Mani DR, Ding L, Iavarone A, Wiznerowicz M, Schürer S, Chen XS, Heath AP, Rokita JL, Nesvizhskii AI, Fenyö D, Rodland KD, Liu T, Gygi SP, Paulovich AG, Resnick AC, Storm PB, Rood BR, Wang P; Children’s Brain Tumor Network; Clinical Proteomic Tumor Analysis Consortium: "Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer", Cell. 2020 Nov 25:S0092-8674(20)31451-3.

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.

Dou Y, Kalmykova S, Pashkova M, Oghbaie M, Jiang H, Molloy KR, Chait BT, Rout MP, Fenyö D, Jensen TH, Altukhov I, LaCava J: "Affinity proteomic dissection of the human nuclear cap-binding complex interactome", Nucleic Acids Res. 2020 Sep 22:gkaa743.

Corciulo C, Castro CM, Coughlin T, Jacob S, Li Z, Fenyö D, Rifkin DB, Kennedy OD, Cronstein BN: "Intraarticular injection of liposomal adenosine reduces cartilage damage in established murine and rat models of osteoarthritis", Sci Rep. 2020 Aug 10;10(1):13477.

McRae MP, Dapkins IP, Sharif I, Anderson J, Fenyo D, Sinokrot O, Kang SK, Christodoulides NJ, Vurmaz D, Simmons GW, Alcorn TM, Daoura MJ, Gisburne S, Zar D, McDevitt JT: "Managing COVID-19 with a Clinical Decision Support Tool in a Community Health Network: Algorithm Development and Validation", J Med Internet Res. 2020 Jul 23.

Yang M, Petralia F, Li Z, Li H, Ma W, Song X, Kim S, Lee H, Yu H, Lee B, Bae S, Heo E, Kaczmarczyk J, Stepniak P, Warchol M, Yu T, Calinawan AP, Boutros PC, Payne SH, Reva B; NCI-CPTAC-DREAM Consortium, Boja E, Rodriguez H, Stolovitzky G, Guan Y, Kang J, Wang P, Fenyö D, Saez-Rodriguez J: "Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics", Cell Syst. 2020 Jul 24:S2405-4712(20)30242-8.

Gillette MA, Satpathy S, Cao S, Dhanasekaran SM, Vasaikar SV, Krug K, Petralia F, Li Y, Liang WW, Reva B, Krek A, Ji J, Song X, Liu W, Hong R, Yao L, Blumenberg L, Savage SR, Wendl MC, Wen B, Li K, Tang LC, MacMullan MA, Avanessian SC, Kane MH, Newton CJ, Cornwell M, Kothadia RB, Ma W, Yoo S, Mannan R, Vats P, Kumar-Sinha C, Kawaler EA, Omelchenko T, Colaprico A, Geffen Y, Maruvka YE, da Veiga Leprevost F, Wiznerowicz M, Gümüs ZH, Veluswamy RR, Hostetter G, Heiman DI, Wyczalkowski MA, Hiltke T, Mesri M, Kinsinger CR, Boja ES, Omenn GS, Chinnaiyan AM, Rodriguez H, Li QK, Jewell SD, Thiagarajan M, Getz G, Zhang B, Fenyö D, Ruggles KV, Cieslik MP, Robles AI, Clauser KR, Govindan R, Wang P, Nesvizhskii AI, Ding L, Mani DR, Carr SA: "Clinical Proteomic Tumor Analysis Consortium. Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma", Cell. 2020 Jul 9;182(1):200-225.e35.

Frenster JD, Kader M, Kamen S, Sun J, Chiriboga L, Serrano J, Bready D, Golub D, Ravn-Boess N, Stephan G, Chi AS, Kurz SC, Jain R, Park CY, Fenyo D, Liebscher I, Schöneberg T, Wiggin G, Newman R, Barnes M, Dickson JK, MacNeil DJ, Huang X, Shohdy N, Snuderl M, Zagzag D, Placantonakis DG: "Expression profiling of the adhesion G protein-coupled receptor GPR133 (ADGRD1) in glioma subtypes", Neurooncol Adv. 2020 Apr 28;2(1):vdaa053.

McRae MP, Simmons GW, Christodoulides NJ, Lu Z, Kang SK, Fenyo D, Alcorn T, Dapkins IP, Sharif I, Vurmaz D, Modak SS, Srinivasan K, Warhadpande S, Shrivastav R, McDevitt JT: "Clinical decision support tool and rapid point-of-care platform for determining disease severity in patients with COVID-19", Lab Chip. 2020.

Devlin JC, Zwack EE, Tang MS, Li Z, Fenyo D, Torres VJ, Ruggles KV, Loke P: "Distinct Features of Human Myeloid Cell Cytokine Response Profiles Identify Neutrophil Activation by Cytokines as a Prognostic Feature during Tuberculosis and Cancer", J Immunol. 2020 ji1901133.

Grivainis M, Tang Z, Fenyö D: "TranspoScope - Interactive Visualization of Retrotransposon Insertions", Bioinformatics 2020 btaa244.

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.

Trasande L, Ghassabian A, Kahn LG, Jacobson MH, Afanasyeva Y, Liu M, Chen Y, Naidu M, Alcedo G, Gilbert J, Koshy TT; NYU Children’s Health and Environment Study Team: "The NYU Children's Health and Environment Study", Eur J Epidemiol. 35 (2020) 305-320.

Mita P, Sun X, Fenyö D, Kahler DJ, Li D, Agmon N, Wudzinska A, Keegan S, BaderJS, Yun C, Boeke JD: "BRCA1 and S phase DNA repair pathways restrict LINE-1 retrotransposition in human cells", Nat Struct Mol Biol. 27 (2020) 179-191.

Ardeljan D, Steranka JP, Liu C, Li Z, Taylor MS, Payer LM, Gorbounov M, Sarnecki JS, Deshpande V, Hruban RH, Boeke JD, Fenyö D, Wu PH, Smogorzewska A, Holland AJ, Burns KH: "Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication", Nat Struct Mol Biol. 27 (2020) 168-178.

McKerrow W, Tang Z, Steranka JP, Payer LM, Boeke JD, Keefe D, Fenyö D, Burns KH, Liu C: "Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells", Phil. Trans. R. Soc. B 375 (2019) 20190335.

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.

Betancourt LH, Szasz AM, Kuras M, Rodriguez Murillo J, Sugihara Y, Pla I, Horvath Z, Pawlowski K, Rezeli M, Miharada K, Gil J, Eriksson J, Appelqvist R, Miliotis T, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Horvatovich P, Welinder C, Wieslander E, Kwon HJ, Malm J, Nemeth IB, Jönsson G, Fenyö D, Sanchez A, Marko-Varga G: "The Hidden Story of Heterogeneous B-raf V600E Mutation Quantitative Protein Expression in Metastatic Melanoma-Association with Clinical Outcome and Tumor Phenotypes", Cancers (Basel). 2019 pii: E1981.

Agmon N, Temple J, Tang Z, Schraink T, Baron M, Chen J, Mita P, Martin JA, Tu BP, Yanai I, Fenyö D, Boeke JD: "Phylogenetic debugging of a complete human biosynthetic pathway transplanted into yeast", Nucleic Acids Res. 2019 pii: gkz1098.

Wenke Liu, Erin Butler, Heyi Yang, David Fenyö, Donald Siegel: "Informatics Approaches to Forensic Body Fluid Identification by Proteomic Mass Spectrometry", in Applications in Forensic Proteomics: Protein Identification and Profiling, ACS Symposium Series #133 (Ed. Eric D. Merkley), Chapter 5, 81-90.

Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gümüs ZH, Geizler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H; Clinical Proteomic Tumor Analysis Consortium: "Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma", Cell. 2019 Oct 31;179(4):964-983.e31.

Adney EM, Ochmann MT, Sil S, Truong DM, Mita P, Wang X, Kahler DJ, Fenyö D, Holt LJ, Boeke JD: "Comprehensive Scanning Mutagenesis of Human Retrotransposon LINE-1 Identifies Motifs Essential for Function", Genetics. 2019 Oct 30. pii:genetics.302601.2019.

McKerrow W, Fenyö D: "L1EM: A tool for accurate locus specific LINE-1 RNA quantification", Bioinformatics. 2019 Oct 4. pii: btz724.

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.

Huang KL, Wu Y, Primeau T, Wang YT, Gao Y, McMichael JF, Scott AD, Cao, Wendl MC, Johnson KJ, Ruggles K, Held J, Payne SH, Davies SR, Dar A, Kinsinger CR, Mesri M, Rodriguez H, Ellis MJ, Townsend RR, Chen F, Fenyo D, Li S, Liu T, Carr SA, Ding L: "Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability", Mol Cell Proteomics 2019 pii: mcp.RA118.001243.

Steranka JP, Tang Z, Grivainis M, Huang CRL, Payer LM, Rego FOR, Araujo Miller TL, Galante PAF, Ramaswami S, Heguy A, Fenyö D, Boeke JD, Burns KH: "Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome", Mobile DNA 2019 10:8.

Zhang X, Nguyen KD, Rudnick P, Roper N, Kawaler E, Maity TK, Awasthi S, Gao S, Biswas R, Venugopalan A, Cultraro CM, Fenyö D, Guha U: "Quantitative mass spectrometry to interrogate proteomic heterogeneity in metastatic lung adenocarcinoma and validate a novel somatic mutation CDK12-G879V", Mol Cell Proteomics. 2019 Jan 7. pii: mcp.RA118.001266.

Mehrnoosh Oghbaie, Petr Sulc, David Fenyo, Michael Pennock, John LaCava: "Complex+: Aided Decision-Making for the Study of Protein Complexes", bioRxiv 744656.

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.

Jeong YT, Simoneschi D, Keegan S, Melville D, Adler NS, Saraf A, Florens L, Washburn MP, Cavasotto CN, Fenyö D, Cuervo AM, Rossi M, Pagano M: "The ULK1-FBXW5-SEC23B nexus controls autophagy", Elife. 2018 Dec 31;7. pii: e42253.

Hadi T, Boytard L, Silvestro M, Alebrahim D, Jacob S, Feinstein J, Barone K, Spiro W, Hutchison S, Simon R, Rateri D, Pinet F, Fenyo D, Adelman M, Moore KJ, Eltzschig HK, Daugherty A, Ramkhelawon B: "Macrophage-derived netrin-1 promotes abdominal aortic aneurysm formation by activating MMP3 in vascular smooth muscle cells", Nat Commun. 2018 Nov 27;9(1):5022.

Whelan DR, Lee WTC, Yin Y, Ofri DM, Bermudez-Hernandez K, Keegan S, Fenyo D, Rothenberg E: "Spatiotemporal dynamics of homologous recombination repair at single collapsed replication forks", Nat Commun. 2018 Sep 24;9(1):3882.

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.

Sengupta S, Sun SQ, Huang KL, Oh C, Bailey MH, Varghese R, Wyczalkowski MA, Ning J, Tripathi P, McMichael JF, Johnson KJ, Kandoth C, Welch J, Ma C, Wendl MC, Payne SH, Fenyö D, Townsend RR, Dipersio JF, Chen F, Ding L: "Integrative omics analyses broaden treatment targets in human cancer", Genome Med. 2018 Jul 27;10(1):60.

Derk J, Bermudez Hernandez K, Rodriguez M, He M, Koh H, Abedini A, Li H, Fenyö D, Schmidt AM: "Diaphanous 1 (DIAPH1) is Highly Expressed in the Aged Human Medial Temporal Cortex and Upregulated in Myeloid Cells During Alzheimer's Disease", J Alzheimers Dis. 2018 Jun 23.

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.

Schafler ED, Thomas PA, Ha S, Wang Y, Bermudez-Hernandez K, Tang Z, Fenyö D, Vigodner M, Logan SK: "UXT is required for spermatogenesis in mice", PLoS One. 13 (2018) e0195747.

Venkataraman A, Yang K, Irizarry J, Mackiewicz M, Mita P, Kuang Z, Xue L, Ghosh D, Liu S, Ramos P, Hu S, Bayron Kain D, Keegan S, Saul R, Colantonio S, Zhang H, Behn FP, Song G, Albino E, Asencio L, Ramos L, Lugo L, Morell G, Rivera J, Ruiz K, Almodovar R, Nazario L, Murphy K, Vargas I, Rivera-Pacheco ZA, Rosa C, Vargas M, McDade J, Clark BS, Yoo S, Khambadkone SG, de Melo J, Stevanovic M, Jiang L, Li Y, Yap WY, Jones B, Tandon A, Campbell E, Montelione GT, Anderson S, Myers RM, Boeke JD, Fenyö D, Whiteley G, Bader JS, Pino I, Eichinger DJ, Zhu H, Blackshaw S: "A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors", Nat Methods. 2018 Mar 19.

Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ; Cancer Genome Atlas Research Network, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L: "Systematic Analysis of Splice-Site-Creating Mutations in Cancer", Cell Rep. 23 (2018) 270-281.e3.

Pelzek AJ, Shopsin B, Radke EE, Tam K, Ueberheide BM, Fenyö D, Brown SM, Li Q, Rubin A, Fulmer Y, Chiang WK, Hernandez DN, El Bannoudi H, Sause WE, Sommerfield A, Thomsen IP, Miller AO, Torres VJ, Silverman GJ: "Human Memory B Cells Targeting Staphylococcus aureus Exotoxins Are Prevalent with Skin and Soft Tissue Infection", MBio. 2018.

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.

Menschaert G, Wang X, Jones AR, Ghali F, Fenyö D, Olexiouk V, Zhang B, Deutsch EW, Ternent T, Vizcaíno JA: "The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data", Genome Biol. 19 (2018) 12.

Mita P, Wudzinska A, Sun X, Andrade J, Nayak S, Kahler DJ, Badri S, LaCava J, Ueberheide B, Yun CY, Fenyö D, Boeke JD: "LINE-1 protein localization and functional dynamics during the cell cycle", Elife. 2018 Jan 8;7. pii: e30058.

Taylor MS, Altukhov I, Molloy KR, Mita P, Jiang H, Adney EM, Wudzinska A, Badri S, Ischenko D, Eng G, Burns KH, Fenyö D, Chait BT, Alexeev D, Rout MP, Boeke JD, LaCava J: "Dissection of affinity captured LINE-1 macromolecular complexes", Elife. 2018 Jan 8;7. pii: e30094.

Juan Ignacio Gutierrez, Gregory Brittingham, Xuya Wang, David Fenyo, Liam J Holt: "The largest SWI/SNF polyglutamine domain is a pH sensor", bioRxiv 165043.

Mostovenko E, Vegvari A, Rezeli M, Lichti C, Fenyo D, Wang Q, Lang FF, Sulman E, Sahlin KB, Marko-Varga G, Nilsson CL: "Large scale identification of variant proteins in glioma stem cells", ACS Chem Neurosci. 2017 Dec 18.

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).

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.

Ray B, Liu W, Fenyö D: "Adaptive Multiview Nonnegative Matrix Factorization Algorithm for Integration of Multimodal Biomedical Data", Cancer Inform. 16 (2017) 1176935117725727.

Snuderl M, Zhang G, Wu P, Jennings TS, Shroff S, Ortenzi V, Jain R, Cohen B, Reidy JJ, Dushay MS, Wisoff JH, Harter DH, Karajannis MA, Fenyo D, Neubert TA, Zagzag D: "Endothelium-Independent Primitive Myxoid Vascularization Creates Invertebrate-Like Channels to Maintain Blood Supply in Optic Gliomas", Am J Pathol. 2017 Jun 9. pii: S0002-9440(17)30075-5.

Agrawal P, Fontanals-Cirera B, Sokolova E, Jacob S, Vaiana CA, Argibay D, Davalos V, McDermott M, Nayak S, Darvishian F, Castillo M, Ueberheide B, Osman I, Fenyö D, Mahal LK, Hernando E: "A Systems Biology Approach Identifies FUT8 as a Driver of Melanoma Metastasis", Cancer Cell. 2017 Jun 12;31(6):804-819.e7.

Mashl RJ, Scott AD, Huang KL, Wyczalkowski MA, Yoon CJ, Niu B, DeNardo E, Yellapantula VD, Handsaker RE, Chen K, Koboldt DC, Ye K, Fenyö D, Raphael B, Wendl MC, Ding L: "GenomeVIP: a cloud platform for genomic variant discovery and interpretation", Genome Res. 2017.

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.

Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Fenyö D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Reid Townsend R, Chen X, Carr SA, Ellis MJ, Ding L: "Proteogenomic integration reveals therapeutic targets in breast cancer xenografts", Nat Commun. 8 (2017) 14864.

Mitchell LA, Wang A, Stracquadanio G, Kuang Z, Wang X, Yang K, Richardson S, Martin JA, Zhao Y, Walker R, Luo Y, Dai H, Dong K, Tang Z, Yang Y, Cai Y, Heguy A, Ueberheide B, Fenyö D, Dai J, Bader JS, Boeke JD: "Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond", Science 355 (2017) 6329.

Agmon N, Tang Z, Yang K, Sutter B, Ikushima S, Cai Y, Caravelli K, Martin JA, Sun X, Choi WJ, Zhang A, Stracquadanio G, Hao H, Tu BP, Fenyö D, Bader JS, Boeke JD: "Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae", Proc Natl Acad Sci U S A. 2017 Feb 7. pii: 201621250.

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.

Achanta P, Steranka JP, Tang Z, Rodic N, Sharma R, Yang WR, Ma S, Grivainis M, Huang CR, Schneider AM, Gallia GL, Riggins GJ, Quinones-Hinojosa A, Fenyö D, Boeke JD, Burns KH: "Somatic retrotransposition is infrequent in glioblastomas", Mob DNA. 2016.

Dankert JF, Rona G, Geter P, Clijsters L, Skaar JR, Bermudez-Hernandez K, Fenyö D, Ueberheide B, Schneider R, Pagano M: "Cyclin F-mediated degradation of SLBP limits H2A.X accumulation and apoptosis upon genotoxic stress in G2", Molecular Cell 2016.

Ruggles KV, Fenyö D: "Next Generation Sequencing Data and Proteogenomics", Adv. Exp. Med. Biol. 926 (2016) 11-19.

Mita P, Lhakhang T, Li D, Eichinger DJ, Fenyö D, Boeke JD: "Fluorescence ImmunoPrecipitation (FLIP): a novel assay for high-throughput IP", Biological Procedures Online (2016) 18:16.

Askenazi M & Fenyö D: "OpenSlice: Quantitative Data Sharing from HyperPeaks to Global Ion Chromatograms (GICs)", Proteomics 2016 July 19.

Ma S, Galatzer-Levy IR, Wang X, Fenyö D, Shalev AY: "A First Step towards a Clinical Decision Support System for Post-traumatic Stress Disorders", AMIA Annu Symp Proc. (2016) 837-843.

Whelan DR, Yin Y, Bermudez-Hernandez K, Keegan S, Fenyö D, Rothenberg E: "Single Molecule Localization Microscopy of DNA Damage Response Pathways in Cancer", Microsc Microanal. 22 (2016) 1016-1017.

Zhang H, Liu T, Zhang Z, Payne S, Zhang B, McDermott J, Zhou JY, Petyuk V, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha S, Aiyetan P, Woo S, Tian Y, Gritsenko M, Choi C, Monroe M, Thomas S, Moore R, Yu KH, Tabb D, Fenyö D, Bafna V, Wang Y, Rodriguez H, Boja E, Hiltke T, Rivers R, Sokoll L, Zhu H, Shih IM, Pandey A, Zhang B, Snyder M, Levine D, Smith R, Chan D, Rodland K: "Deep proteogenomic characterization of human ovarian cancer", Cell 2016.

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.

Luo Y, Jacobs EY, Greco TM, Mohammed KD, Tong T, Keegan S, Binley JM, Cristea IM, Fenyö D, Rout MP, Chait BT, Muesing MA: "Probing the HIV-Host Interactome in Infected Cells", Nature Microbiology 2016 May 23.

Ma S, Ren J, Fenyö D: "Breast Cancer Prognostics Using Multi-Omics Data", AMIA Jt Summits Transl Sci Proc. 2016.

Saxe G, Statnikov A, Fenyö D, Ren J, Li Z, Prasad M, Wall D, Bergman N, Briggs E, Aliferis C: "A Complex Systems Approach to Causal Discovery in Psychiatry", PLOS ONE 2016 March 30.

Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Boja E, Carr SA, Chan DW, Chen X, Chen J, Davies SR, Ellis MJ, Fenyö D, Hiltke T, Ketchum KA, Kinsinger C, Kuhn E, Liebler DC, Liu T, Loss M, MacCoss MJ, Qian WJ, Rivers R, Rodland KD, Ruggles KV, Scott MG, Smith RD, Thomas S, Townsend RR, Whiteley G, Wu C, Zhang H, Zhang Z, Rodriguez H, Paulovich AG.: "Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays", Methods Mol Biol. 1410 (2016) 223-236.

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.

Leo-Macias A, Agullo-Pascual E, Sanchez-Alonso JL, Keegan S, Lin X, Fengxia-Liang, Korchev YE, Gorelik J, Fenyö D, Rothenberg E, Delmar M: "Nanoscale Visualization of a Functional Adhesion/Excitability Node at the Cardiac Intercalated Disc", Nature Communications 2016 Jan 20.

Thompson MK, Fridy PC, Sarah Keegan S, Chait BT, Fenyö D, Rout MP: "Optimizing Selection of Large Animals for Antibody Production by Screening Immune Response to Standard Vaccines", Journal of Immunological Methods 2016 Jan 9.

Tufariello JM, Chapman JR, Kerantzas CA, Wong KW, Vilcheze C, Jones CM, Cole LE, Tinaztepe E, Thompson V, Fenyö D, Niederweis M, Ueberheide B, Philips JA, Jacobs WR Jr.: "Separable Roles for Mycobacterium tuberculosis ESX-3 Effectors in Iron Acquisition and Virulence", PNAS 2016.

Fenyo D, Beavis RC: "Selenocysteine: Wherefore art thou?", J Proteome Res. 2015. PMID: 26680273.

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.

Ntai I, LeDuc RD, Fellers RT, Erdmann-Gilmore P, Davies SR, Rumsey J, Early BP, Thomas PM, Li S, Compton PD, Ellis MJ, Ruggles KV, Fenyo D, Boja ES, Rodriguez H, Townsend RR, Kelleher NL.: "Integrated Bottom-up and Top-down Proteomics of Patient-derived Breast Tumor Xenografts", Mol Cell Proteomics. 2015 Oct 26.

Boeke JD, Fenyo D: "Much Ado about Zero", Cell. 163 (2015) 534-5.

Ruggles K, Fenyö D: "Proteogenomics", Next-generation DNA sequencing Informatics, 2nd Edition, Ed. Stuart Brown, Cold Spring Harbor Laboratory Press 2015, Cold Spring Harbor, New York.

Hakhverdyan Z, Domanski M, Hough L, Oroskar AA, Oroskar AR, Keegan S, Dilworth DJ, Molloy K, Sherman V, Aitchison JD, Fenyö D, Chait BT, Jensen TH, Rout MP, LaCava J: "Rapid Optimized Interactomic Screening", Nature Methods 2015 May 4. PMID 25938370.

Fenyö D, Beavis R: "The GPMDB REST Interface", Bioinformatics 2015. PMID: 25697819.

Reid D, Keegan S, Leo-Macias A, Watanabe G, Strande NT, Oksuz BA, Fenyö D, Lieber MR, Ramsden DA, Rothenberg E: "Organization and dynamics of the nonhomologous end-joining machinery during DNA double-strand break repair", PNAS 2015 May 4 PMID 25941401.

P.C. Fridy, Y. Li, S. Keegan, M.K. Thompson, I. Nudelman, J.F. Scheid, M. Oeffinger, M.C. Nussenzweig, D. Fenyö, B.T. Chait, M.P. Rout: "A robust pipeline for rapid production of versatile nanobody repertoires", Nature Methods 11 (2014) 1253-1260.

Sun J, Zhang G, Li S, Ivanov AR, Fenyö D, Lisacek F, Murthy SK, Karger BL, Brusic V: "Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells - a benchmarking study", BMC Genomics 2014.

Nilsson CL, Mostovenko E, Lichti CF, Ruggles K, Fenyö D, Rosenbloom KR, Hancock WS, Paik YK, Omenn GS, LaBaer J, Kroes RA, Uhlén M, Hober S, Végvári A, Andrén PE, Sulman EP, Lang FF, Fuentes M, Carlsohn E, Emmett MR, Moskal JR, Berven FS, Fehniger TE, Marko-Varga G.: "Use of ENCODE Resources to Characterize Novel Proteoforms and Missing Proteins in the Human Proteome", J Proteome Res. 2014.

Agullo-Pascual E, Lin X, Leo-Macias A, Zhang M, Liang FX, Li Z, Pfenniger A, Lübkemeier I, Keegan S, Fenyö D, Willecke K, Rothenberg E, Delmar M.: "Super-resolution imaging reveals that loss of the C-terminus of Connexin43 limits microtubule plus-end capture and NaV1.5 localization at the intercalated disc", Cardiovasc Res. 2014 Aug 18. pii: cvu195.

Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC; National Cancer Institute Clinical Proteomics Tumor Analysis Consortium (NCI CPTAC): "Proteogenomic characterization of human colon and rectal cancer", Nature 2014 Jul 20.

Mertins P, Yang F, Liu T, Mani DR, Petyuk VA, Gillette MA, Clauser KR, Qiao JW, Gritsenko MA, Moore RJ, Levine DA, Townsend R, Erdmann-Gilmore P, Snider JE, Davies SA, Ruggles KV, Fenyö D, Kitchens RT, Li S, Olvera N, Dao F, Rodriguez H, Chan DW, Liebler D, White F, Rodland KD, Mills GB, Smith RD, Paulovich AG, Ellis M, Carr SA: "Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels", Mol Cell Proteomics. 2014.

Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Rodriguez H; Clinical Proteomic Tumor Analysis Consortium (CPTAC), Paulovich AG.: "CPTAC Assay Portal: a repository of targeted proteomic assays", Nat Methods 11 (2014) 703-4.

Lichti CF, Liu H, Shavkunov AS, Mostovenko E, Sulman EP, Ezhilarasan R, Wang Q, Kroes R, Moskal JR, Fenyö D, Oksuz BA, Conrad CA, Lang FF, Berven FS, Végvári A, Rezeli M, Marko-Varga G, Hober S, Nilsson CL: "Integrated Chromosome 19 Transcriptomic and Proteomic Datasets Derived from Glioma Cancer Stem Cell Lines", J Proteome Res. 2013.

Agullo-Pascual E, Reid DA, Keegan S, Sidhu M, Fenyö D, Rothenberg E, Delmar M.: "Super-resolution fluorescence microscopy of the cardiac connexome reveals plakophilin-2 inside the connexin43 plaque", Cardiovasc Res. 2013.

J. Malm, T.E. Fehniger, P. Danmyr, A. Végvári, C. Welinder, H. Lindberg, R. Appelqvist, K. Sjödin, E. Wieslander, T. Laurell, S. Hober, F. Berven, D. Fenyö D, X. Wang, P.E. Andrén, G. Edula, E. Carlsohn, M. Fuentes, C. Nilsson C, M. Dahlbäck, M. Rezeli, D. Erlinge, G. Marko-Varga: "Developments in biobanking workflow standardization providing sample integrity and stability", J Proteomics 2013.

Y. Bao, S. Waldemarson, G. Zhang, A. Wahlander, B. Ueberheide, S. Myung, B. Reed, K. Molloy, J.C. Padovan, J. Eriksson, T.A. Neubert, B.T. Chait, D. Fenyö: "Detection and Correction of Interference in SRM Analysis", Methods 61(2013) 299-303.

M.F. Muellenbeck, B. Ueberheide, B. Amulic, A. Epp, D Fenyö, C.E. Busse, M. Esen, M. Theisen, B. Mordmüller, H. Wardemann: "Atypical and classical memory B cells produce Plasmodium falciparum neutralizing antibodies", J Exp Med. 210 (2013) 389-99.

S. Liu, H. Im, A. Bairoch, M. Cristofanilli, R. Chen, E.W. Deutsch, S. Dalton, D. Fenyö, S. Fanayan, C. Gates, P. Gaudet, M. Hincapie, S. Hanash, H. Kim, S.-K. Jeong, E. Lundberg, G. Mias, R. Menon, Z. Mu, E. Nice, Y.-K. Paik, M. Uhlen, L. Wells, S.-L. Wu, F.Yan, F.Zhang, Y.Zhang, M.Snyder, G.S. Omenn, R.C. Beavis, W.S. Hancock: "A Chromosome-centric Human Proteome Project (C-HPP) to Characterize the Sets of Proteins Encoded in Chromosome 17", J. Proteome Res. 12 (2013) 45-57.

C.L. Nilsson, F. Berven, F. Selheim, H. Liu, J.R. Moskal, R.A. Kroes, E.P. Sulman, C.A. Conrad, F.F. Lang, P.E. Andrén, A. Nilsson, E. Carlsohn, H. Lilja, J. Malm, D. Fenyö, D. Subramaniyam, X. Wang, M. Gonzales-Gonzales, N. Dasilva, P. Diez, M. Fuentes, Á. Végvári, K. Sjödin, C. Welinder, T. Laurell, T.E. Fehniger, H. Lindberg, M. Rezeli, G. Edula, S. Hober, G. Marko-Varga: "Chromosome 19 Annotations with Disease Speciation: A First Report from the Global Research Consortium", J. Proteome Res. 12 (2013) 135-150.

E. Kefaloyianni, J.S. Lyssand, C. Moreno, D. Delaroche, M. Hong, D. Fenyö, C.V. Mobbs, T.A. Neubert, W.A. Coetzee: "A comparative proteomic analysis of the KATP channel complex in different tissue types", Proteomics 13 (2013) 368-78.

L. Bozzacco, H. Yu, J. Dengjel, C. Trumpfheller, H.A. Zebroski III, N. Zhang, V. Küttner, B.M. Ueberheide, H. Deng, B.T. Chait, R.M. Steinman, S. Mojsov, D. Fenyö: "Strategy for Identifying Dendritic Cell-Processed CD4(+) T Cell Epitopes from the HIV Gag p24 Protein", PLoS One 7 (2012):e41897.

J.F. Scheid, H. Mouquet, B. Ueberheide, R. Diskin, F. Klein, T.Y.K. Olivera, J. Pietzsch, D. Fenyö, A. Abadir, K. Velinzon, A. Hurley, S. Myung, F. Boulad, P. Poignard, D. Burton, F. Pereyra, D.D. Ho, B.D. Walker, M.S. Seaman, P.J. Bjorkman, B.T. Chait, M.C. Nussenzweig.: "Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding", Science 6049 (2011) 1633-7.

C.F. Aliferis, A.V. Alekseyenko, Y. Aphinyanaphongs, S. Brown, D. Fenyö, L. Fu, S. Shen, A. Statnikov, J. Wang: "Trends and Developments in Bioinformatics in 2010: Prospects and Perspectives", IMIA Yearbook of Medical Informatics 6 (2011) 146-155.

S. Myung, H. Cohen, D. Fenyö, J.C. Padovan, A.N. Krutchinsky, B.T. Chait: "High-capacity ion trap coupled to a time-of-flight mass spectrometer for comprehensive linked scans with no scanning losses", International Journal of Mass Spectrometry 301 (2011) 211-219.

J. Eriksson, D. Fenyö: "Modeling mass spectrometry-based protein analysis", Methods Mol Biol. 694 (2011) 109-17.

D. Fenyö,(Ed.): "Computational Biology", Methods Mol Biol 673 (2010).

J. Eriksson, D. Fenyö: "Modeling experimental design for proteomics", Methods Mol Biol 673 (2010) 223-30.

G. Zhang, B.M. Ueberheide, S. Waldemarson, S. Myung, K. Molloy, J. Eriksson, B.T. Chait, T.A. Neubert, D. Fenyö: "Protein quantitation using mass spectrometry", Methods Mol Biol 673 (2010) 211-22.

D. Fenyö, J. Eriksson, R. Beavis: "Mass spectrometric protein identification using the global proteome machine", Methods Mol Biol 673 (2010) 189-202.

L. Peng, E.A. Kapp, D. Fenyö, M.S. Kwon, P. Jiang, S. Wu, Y. Jiang, M.I. Aguilar, N. Ahmed, M.S. Baker, Z. Cai, Y.J. Chen, P. Van Chi, M.C. Chung, F. He, A.C. Len, P.C. Liao, K. Nakamura, S.M. Ngai, Y.K. Paik, T.L. Pan, T.C. Poon, G. Hosseini Salekdeh, R.J. Simpson, R. Sirdeshmukh, C. Srisomsap, J. Svasti, Y.C. Tyan, F.S. Dreyer, D. McLauchlan, P. Rawson, T.W. Jordan: "The asia oceania human proteome organisation membrane proteomics initiative. preparation and characterization of the carbonate-washed membrane standard", Proteomics 2010 May 18.

A.G. Paulovich, D. Billheimer, A.J. Ham, L. Vega-Montoto, P.A. Rudnick, D.L. Tabb, P. Wang, R.K. Blackman, D.M. Bunk, H.L. Cardasis, K.R. Clauser, C.R. Kinsinger, B. Schilling, T.J. Tegeler, A.M. Variyath, M. Wang, J.R. Whiteaker, L.J. Zimmerman, D. Fenyo, S.A. Carr, S.J. Fisher, B.W. Gibson, M. Mesri, T.A. Neubert, F.E. Regnier, H. Rodriguez, C. Spiegelman, S.E. Stein, P. Tempst, D.C. Liebler: "Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance", Mol Cell Proteomics, 9 (2010) 242-254.

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.

B.M. Ueberheide, D. Fenyö, P.F. Alewood, B.T. Chait: "Rapid sensitive analysis of cysteine rich peptide venom components", Proc Natl Acad Sci 106 (2009) 6910-6915.

T.N. Siegel, D.R. Hekstra, L.E. Kemp, L.M. Figueiredo, J.E. Lowell, D. Fenyö, X. Wang, S. Dewell, G.A. Cross: "Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei", Genes Dev. 23 (2009) 1063-1076.

G. Zhang, D. Fenyö, T.A. Neubert: "Evaluation of the Variation in Sample Preparation for Comparative Proteomics Using Stable Isotope Labeling by Amino Acids in Cell Culture", J Proteome Res 8 (2009) 1285-1292.

J. Eriksson and D. Fenyö: "Optimizing Sensitivity and Specificity in Mass Spectrometric Proteome Analysis", pp. 211-222 in: Mass Spectrometry: Instrumentation, Interpretation, and Applications, Eds. R. Ekman, J. Silberring, A.M. Brinkmalm, D.M. Desiderio, N.M. Nibbering, Wiley 2008.

G. Zhang, D. Fenyö, T.A. Neubert: "Use of DNA Ladders for Reproducible Protein Fractionation by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE) for Quantitative Proteomics", J Proteome Res 7 (2008) 678-686.

G. Zhang, D. Fenyö, T.A. Neubert: "Screening for EphB Signaling Effectors Using SILAC with a Linear Ion Trap-Orbitrap Mass Spectrometer", J Proteome Res 7 (2008) 4715-4726.

M. Falth, M. Svensson, A. Nilsson, K. Skold, D. Fenyö, P.E. Andren: "Validation of Endogenous Peptide Identifications Using a Database of Tandem Mass Spectra", J Proteome Res 7 (2008) 3049-3053.

E.M. Woo, D. Fenyö, B.H. Kwok, H. Funabiki, B.T. Chait BT: "Efficient Identification of Phosphorylation by Mass Spectrometric Phosphopeptide Fingerprinting", Anal Chem 80 (2008) 2419-2425.

L.F. Westblade, L. Minakhin, K. Kuznedelov, A.J. Tackett, E.J. Chang, R.A. Mooney, I. Vvedenskaya, Q.J. Wang, D. Fenyö, M.P. Rout, R. Landick, B.T. Chait, K. Severinov, S.A. Darst: "Rapid Isolation and Identification of Bacteriophage T4-Encoded Modifications of Escherichia coli RNA Polymerase: A Generic Method to Study Bacteriophage/Host Interactions", J Proteome Res 7 (2008) 1244-1250.

C.C. Darie, V. Shetty, D.S. Spellman, G. Zhang, C. Xu, H.L. Cardasis, S. Blais, D. Fenyö, and T.A. Neubert: "Blue Native PAGE and Mass Spectrometry Analysis of Ephrin Stimulation-Dependent Protein-Protein Interactions in NG108-EPHB2 Cells", in Applications of Mass Spectrometry in Life Safety, C. Popescu et al. (eds.), Springer 2008.

D. Fenyö, R.C. Beavis: "Informatics development: Challenges and solutions for MALDI mass spectrometry", Mass Spectrom Rev 27 (2008) 1-19.

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, Q.J. Wang, J.A. DeGrasse, J.C. Padovan, M. Cadene, B.T. Chait: "MALDI sample preparation: the ultra thin layer method", Journal of Visualized Experiments Issue 3 (2007).

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.

M. Falth, K. Sköld, M. Svensson, A. Nilsson, D. Fenyö, P.E. Andren: "Neuropeptidomics: Strategies for specific and sensitive identification of endogenous peptides", Mol Cell Proteomics 6 (2007) 1188-1197.

A. Kaplan, M. Söderström, D. Fenyö, H. Pettersen, S. Lindqvist, K. Sköld, M. Svensson, P. Svenningsson, P.E. Andren & L. Björkesten: "An automated method for scanning LC-MS data sets for significant peptides and proteins, including quantitative profiling and interactive confirmation", Journal of Proteome Research 6 (2007) 28880-2895.

R. Craig, J.C. Cortens, D. Fenyö, R.C. Beavis: "Using Annotated Peptide Mass Spectrum Libraries for Protein Identification", Journal of Proteome Research, 5 (2006) 1843-1849.

M. Fälth, K. Sköld, M. Norrman, M. Svensson, D. Fenyö, P.E. Andren: "SwePep – A Database Designed for Endogenous Peptides and Mass Spectrometry", Molecular and Cellular Proteomics 5 (2006) 998-1005.

E. Ossipova, D. Fenyö, J. Eriksson: "Optimizing Search Conditions for the Mass-Fingerprint-Based Identification of Proteins", Proteomics 6 (2006) 2079-85.

M. Berg, A. Parbel, H. Pettersen, D. Fenyö, & L. Björkesten: "Detection of Artifacts and Peptide Modifications in LC-MS data Using Two-Dimensional Signal Intensity Map Data Visualization", Rapid Communications in Mass Spectrometry 20 (2006) 1558-62.

M. Berg, A. Parbel, H. Pettersen, D. Fenyö, & L. Björkesten: "Reproducibility of LC-MS-based protein identification", Journal of Experimental Botany, 57 (2006) 1509-14.

J. Eriksson, D. Fenyö: "Protein Identification in Complex Mixtures", J Proteome Research 4 (2005) 387-93.

E. A. Kapp, F. Schutz, L. M. Connolly, J. A. Chakel, J. E. Meza, C. A. Miller, D. Fenyö, J. K. Eng, J.N. Adkins, G.S. Omenn & R.J. Simpson: "An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis", Proteomics, 5 (2005) 3475-90.

J. Eriksson & D. Fenyö: "Simulation as a Tool for Optimizing Proteome Analysis", pp. 521-532 in: Comprehensive Analytical Chemistry vol. 46, Ed. G. Marko-Varga, Elsevier 2005.

A. Thelemann, F. Petti, G. Griffin, K. Iwata, T. Hunt, T. Settinari, D. Fenyö, N. Gibson and J. D. Haley: "Phosphotyrosine signaling networks in epidermal growth factor receptor overexpressing squamous carcinoma cells", Molecular and Cellular Proteomics, 4 (2005) 356-76.

D. Fenyö: "Protein fingerprinting", Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Ed. M. Dunn, John Wiley & Sons, 2005.

D. Fenyö, J. Eriksson & R.C. Beavis: "Protein Identification by Searching Collections of Sequences with Mass Spectrometric Information", pp. 267-276 in: Informatics in Proteomics Research, Ed. S. Srivastava, CRC Press 2005.

J. Eriksson, D. Fenyö: "The Statistical Significance of Protein Identification Results as a Function of the Number of Protein Sequences Searched", J. Proteome Research 3 (2004) 979-82.

J. Eriksson, D. Fenyö: "Probity: A Protein Identification Algorithm with Accurate Assignment of the Significance of the Results", J Proteome Research 3 (2004) 32-36.

H. Nordvarg, J. Flensburg, O. Rönn, J. Öhman, R. Marouga, B. Lundgren, D. Haid, E. Malmport, J. Goscinski, L. Hörnsten, M. Scigelova, S. Bourin, P. Garberg, G. Woffendin, D. Fenyö, H. Bergling & E. Forsberg: "A Proteomics Approach to the Study of Absorption, Distribution, Metabolism, Excretion and Toxicity", Journal of Biomolecular Techniques, 15 (2004) 265-75.

R.C. Beavis & D. Fenyö: "Finding protein sequences using PROWL", Current Protocols in Bioinformatics, Ed. D. Davidson, John Wiley & Sons, 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.

M. Trester-Zedlitz, K. Kamada, S.K. Burley, D. Fenyö, B.T. Chait, T.W. Muir: "A Modular Cross-Linking Approach for Exploring Protein Interactions", J Am Chem Soc 125 (2003) 2416-2425.

D. Fenyö, R.C. Beavis: "Informatics and data management in proteomics", Trends Biotechnol 20 (2002) S35-8.

J. Eriksson, D. Fenyö: "A model of random mass-matching and its use for automated significance testing in mass spectrometric proteome analysis", Proteomics. 2 (2002) 262-70.

H.I. Field, D. Fenyö, R.C. Beavis: "RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database", Proteomics 2 (2002) 36-47.

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: "Identifying the proteome: software tools", Current Opinion in Biotechnology, 11 (2000) 391-395.

R.C. Beavis & D. Fenyö: "Database searching with mass spectrometric information", In Proteomics: A Trends Guide, Eds. M. Mann and W. Blackstock, pp 23-27, Elsevier 2000.

D. Fenyö: "The Biopolymer Markup Language", Bioinformatics 15 (1999) 339-340.

D. Fenyö and R.C. Beavis: "Network-Based Bioinformatics in Protein Mass Spectrometry", in Mass spectrometry of Biological Materials, Eds. B. Larsen & C. McEwen, Marcel Dekker, 1998.

D. Fenyö, J. Qin, B.T. Chait: "Protein Identification using Mass Spectrometric Information", Electrophoresis 19 (1998) 998-1005.

Y. Wang, K. Severinov, N. Loizos, D. Fenyö, E. Heyduk, T. Heyduk, B. T. Chait, S.A. Darst: "Determinants for Escherichia coli RNA Polymerase Assembly within the β Subunit", J Mol Biol (1997) 648-662.

J. Qin, D. Fenyö, Y. Zhao, W.W. Hall, D.M. Chao, C.J. Wilson, R.A. Young and B.T. Chait: "A Strategy for Rapid, High Confidence Protein Identification", Anal Chem 69 (1997) 3995-4001.

D. Fenyö, B.T. Chait, T.E. Johnson, J.S. Lindsey: "Laser desorption Mass Spectrometry of Large Synthetic Porphyrin Arrays", J Por and Phthalocy 1 (1997) 93-99.

D. Fenyö: "A Software Tool for Analysis of Mass Spectrometric Disulfide Mapping Experiments", Computer Applications in the Biosciences (CABIOS) 13 (1997) 617-8.

E. Severinova, K. Severinov, D. Fenyö, M. Marr, E.N. Brody, J.W. Roberts, B.T. Chait, S.A. Darst: "Organization of the Escherichia coli RNA polymerase σ⁷⁰ subunit", J Mol Biol, 263 (1996) 637-647.

D. Fenyö, W. Zhang, B.T. Chait, R.C. Beavis: "Internet-based Analytical Chemistry Resources. A Model Project", Anal Chem 68 (1996) 721A-726A.

A.A. Stewart, J.D. Haley, G.-Y. Qu, K. Stam, D. Fenyö, B.T. Chait, D.R. Marshak, A.Y.-K. Ng, G. Marley, K.K. Iwata: "Unbilical Cord Transforming Growth Factor-β3. Isolation, Comparison with Recombinant TGF-β3 and Cellular Localization", Growth Factors, 13 (1996) 87-98.

K. Stam, A.A. Stewart, G.Y. Qu, K.K. Iwata, D. Fenyö, B.T. Chait, D.R. Marshak, J.D. Haley: "Physical and Biologial Characterization of a Growth-Inhibitors Activity Purified from the Neuroepithelioma cell-line A673", Biochem J 305 (1995) 87.

K. Severinov, D. Fenyö, E. Severinov, B.T. Chait, A. Goldfarb, S. Darst: "The σ-Subunit Conserved Region 3 is Part of the "5’-Face" of the active Center of E. coli RNA Polymerase", J Biol Chem 269 (1994) 20826-8.

H. Tang, K. Severinov, A. Goldfarb, D. Fenyö, B.T. Chait, R. Ebright: "Location, Structure, and Function of the Target of a Transcription Activator Protein", Gene Dev 8 (1994) 3058-67.

P. Sinnis, P. Clavijo, D. Fenyö, B.T. Chait, C. Cerami, V. Nussenzweig: "Structural and Functional Properties of Region II-Plus of the Malaria Circumsporozoite Protein", J Exp Med 180 (1994) 297-306.

T.S.R. Krishna, D. Fenyö, X–P. Kong, S. Gary, B.T. Chait, P. Burgers, J. Kuriyan: "Crystallization of Proliferating Cell Nuclear Antigen (PCNA) from Saccharomyces cerevisiae", J Mol Biol 241 (1994) 265-268.

G. Brinkmalm, P. Demirev, J. Eriksson, D. Fenyö, P. Håkansson & B. U. R. Sundqvist: "Electronic Sputtering of Fullerenes and the Influence of Primary Ion Charge-State", Nuclear Instruments and Methods in Physics Research B84 (1994) 37-42.

R.M. Papaleo, G. Brinkmalm, D. Fenyö, J. Eriksson, H.-F. Kammer, P. Demirev, P. Håkansson & B. U. R. Sundqvist: "MeV ion sputtering of polymers: correlation between secondary ion radial velocity distributions and heavy ion track structure", Nuclear Instruments and Methods in Physics Research B91 (1994) 667-671.

D. Fenyö, P. Håkansson & B. U. R. Sundqvist: "On the Ejection of Hydrogen Ions from Organic Solids Impacted by MeV Ions", Nuclear Instruments and Methods B84 (1994) 31.

G. Brinkmalm, P. Demirev, D. Fenyö, P. Håkansson, J. Kopniczky & B. U. R. Sundqvist: "Formation of Fullerenes in MeV-ion Sputtering from Organic Solids", Physical Review B47 (1993) 7560-7567.

P. Demirev, D. D. N. B. Daya, G. Brinkmalm, D. Fenyö, P. Håkansson & B. U. R. Sundqvist: "On Molecular Ion Formation by Hydride Abstraction in Plasma Desorption Mass Spectrometry", International Journal of Mass Spectrometry and Ion Processes 123 (1993) 69.

D. Fenyö: "Sputtering by a Sum of Impulses: The Effect of Finite Track Width", Physical Review B47 (1993) 8263.

D. Fenyö & R. E. Johnson: "Computer Experiments on Molecular Ejection from an Amorphous Solid: Comparison to an Analytic Continuum Mechanical Model", Physical Review B46 (1992) 5090.

G. Brinkmalm, D. Barofsky, P. Demirev, D. Fenyö, P. Håkansson, R. E. Johnson, C.T. Reimann & B. U. R. Sundqvist: "Formation of Fullerenes in MeV Ion Track Plasmas", Chemical Physics Letters 191 (1992) 345-350.

P. Demirev, G. Brinkmalm, D. Fenyö, P. Håkansson & B. U. R. Sundqvist: "Radial velocities of ejected ions: implications for the mechanism of molecular ion formation in plasma desorption mass spectrometry of biomolecules", International Journal of Mass Spectrometry and Ion Processes 111 (1991) 41.

A. Hallen, D. Fenyö, B.U.R. Sundqvist , R.E. Johnson & B.G. Svensson, Dose-Rate: "Dependence on the Defect Production in MeV Proton-Irradiated Silicon", Journal of Applied Physics 70 (1991) 3025.

D. Fenyö: "Electronic Sputtering of Organic Solids", ACTA UNIVERSITATIS UPSALIENSIS, Almqvist & Wiksell Int., Stockholm, 1991.

B. U. R. Sundqvist, P. Håkansson, A. Hedin, D. Fenyö, G. Brinkmalm, P. Roepstorff & R.E. Johnson: "Plasma Desorption Mass Spectrometry - Achievements and Frontiers, Methods and Mechanisms for Producing Ions from Large Molecules", NATO-ASI series, Eds. W. Ens & K.G. Standing, Plenum Publ. Corp., New York, 1991, p. 7.

R. E. Johnson, S. Banarjee, A. Hedin, D. Fenyö & B. U. R. Sundqvist: "Heavy-Ion and Laser Pulse-Induced Ejection of Large Organic Molecules", Methods and Mechanisms for Producing Ions from Large Molecules", NATO-ASI series, Eds. W. Ens & K.G. Standing, Plenum Publ. Corp., New York, 1991, p. 89.

P. Demirev, D. Fenyö, P. Håkansson & B. U. R. Sundqvist: "On the Mechanism of Formation of Alkali Cation Adducts in Plasma Desorption Mass Spectrometry of Biomolecules", Organic Mass Spectrometry 26 (1991), 471.

D. Fenyö, A. Hedin, P. Håkansson & B. U. R. Sundqvist: "Radial Velocity Distribution of Ions Ejected from Organic Solids by Fast Heavy Ion Bombardment", International Journal of Mass Spectrometry and Ion Processes 100 (1990) 63.

D. Fenyö, B. U. R. Sundqvist, B. Karlsson & R. E. Johnson: "A Molecular Dynamics Study of Sputtering of Large Molecules", Physical Review B42 (1990) 1895.

D. Fenyö, A. Hedin, P. Håkansson & B. U. R. Sundqvist: "Electronic Sputtering of Large Organic Molecules", Proceedings from the 3rd International Wangerooge Workshop on the Physics of Small Systems, Ed. E.R. Hilf, W. Tuszynski, World Scientific, Singapore 1990.

D. Fenyö, A. Hedin, P. Håkansson, R. E. Johnson & B. U. R. Sundqvist: "Radial Velocity Distributions in Electronic Sputtering of Large Organic Molecules", Proceedings from the 5th International Workshop on Ion Formation from Organic Solids John Wiley & Sons 1990 England.

R. E. Johnson, B. U. R. Sundqvist, A. Hedin & D. Fenyö: "Sputtering by Fast Ions Using a Sum of Impulses", Physical Review B40 (1989) 49.

A. Hedin, D. Fenyö, P. Håkansson, G. Jonsson & B. U. R. Sundqvist: "Electronic Sputtering of Biomolecules", Nuclear Instruments and Methods B40/41 (1989) 275.

B. U. R Sundqvist, D. Fenyö, A. Hedin, P. Håkansson, G. Jonsson, W. Ens & R. E. Johnson: "Directional Correlations Between Incident Particle and Secondary Ions in Electronic Sputtering of Large Organic Molecules", Radiation Effects and Defects in Solids 109 (1989) 169.

W. Ens, B. U. R Sundqvist, P. Håkansson, D. Fenyö, A. Hedin & G. Jonsson: "Radial velocity Measurements of Secondary Molecular Ions in keV and MeV bombardement", Journal de Physique 50 (1989) C2-9.

D. Fenyö, B. U. R. Sundqvist, B. Karlsson & R. E. Johnson: "A Molecular Dynamics Study of Electronic Sputtering of Large Organic Molecules", Journal de Physique 50 (1989) C2-33.

B. U. R Sundqvist, A. Ariyaratne, W. Ens, D. Fenyö, A. Hedin, P. Håkansson, G. Jonsson: "On the Upper Limit of Secondary Ions Ejected In Electronic Sputtering from Organic Solids", Proceedings from the 4th International Workshop on Ion Formation from Organic Solids, 1988.

B. U. R Sundqvist, D. Fenyö, P. Håkansson, G. Säve, S.-E. Lindqvist, E. Söderström & J. Berg: "Fast Ion Induced Desorption of Secondary Ions from Langmuir - Blodgett Films of Fatty Acids", Secondary Ion Mass Spectrometry SIMS VI, John Wiley & Sons 1988, p 615-618.