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J

Javier A. Alfaro

University of Victoria

19H-index
175Paper Count
1.9KCitation Count
Published Papers 22
Publication Date
Proteomic Changes in Cancer Cell Lines as a Result of Bacterial Infection
err2025-10-20
err0
errOAAI
errBo Ren; Kenneth Weke; Darryl Hardie; Mariya I. Goncheva; Ted Hupp; Javier Antonio Alfaro; Helena Pětrošová; David R. Goodlett
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Leveraging knowledge for explainable AI in personalized cancer treatment: challenges and future directions
err2025-09-29
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errOAAI
errEmilia Daghir-Wojtkowiak†; Javier Alfaro†; Michele Mastromattei; Aleksander Palkowski; Mark Stares; Ana Roca-Umbert; Andraz Krajnc; Riccardo Leoni; Anne Boland; Aria Nourbaksh; Ashwin Kallor; Camille Ducki; Davide Venditti; Carla Montesano; Chiara Cipriani; Daniel Faria; Delphine Pflieger; Elisa Zago; Etienne Bardet; Filipa Serrano; Florian Jeanneret; Damien Alouges; Liangwei Yin; Elodine Coquelet; Apolline Bacquet; Francesco Bonchi; Francesco Maiorino; Francesco Torino; Georges Bedran; Jean-Alexandre Long; Laura Balbi; Laurent Guyon; Liana Bevilacqua; Manuel Fiorelli; Marie-Catherine Wagner; Mario Reyes; Mario Roselli; Marta Contreiras Silva; Michal Waleron; Nikolas Dovrolis; Odile Filhol-Cochet; In Hwa Um; Georg Wolflein; Patrícia Eugénio; Pauline Bazelle; Pavlos Golnas; Peter Thorpe; Pierluigi Bove; Piyush Borole; Roberta Bernardini; Rohit Kumar; Rosella Cicconi; Saskia Kaltenbrunner; Saverio Gravina; Simona Brezar; Stefan Symeonides; Steven McGinn; Susana Nunes; Ted Hupp; Yuri Gordienko; Dimitrios Varvaras; Sergii Stirenko; Luciano Xumerle; Stefania Mariani; Assilah Bouzit; Stéphane Gazut; Heiko Poth; Kyriakos Souliotis; Hector Katifelis; Elena Verzoni; Giuseppe Procopio; Sarah Schoch; Francisco Lupiáñez-Villanueva; Sandra Türk; Katarzyna Barud; Dimitri Koroliouk‡; Juan Caubet‡; Yamir Moreno‡; Jean-Luc Descotes‡; Christina Golna‡; Valentina Guadalupi‡; Paolo Garagnani‡; Maria Gazouli‡; Jean-François Deleuze‡; Frans Folkvord‡; Nikolaus Forgó‡; David J. Harrison‡; Håkan Axelson‡; Armando Stellato‡; Maurizio Mattei‡; Ajitha Rajan‡; Alexander Laird‡; Christophe Battail‡; Catia Pesquita‡; Fabio Massimo Zanzotto§
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Tuning ProteinMPNN to reduce protein visibility via MHC Class I through direct preference optimization
err2025-03-18
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PREAI
errGasser, Hans-Christof; Oyarzun, Diego A.; Alfaro, Javier Antonio; Rajan, Ajitha
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Glycosyltransferase structure and function
err2024-09-11
err35
PREAI
errSchuman, Brock; Alfaro, Javier A.; Evans, Stephen V.
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The Immunopeptidomics Ontology (ImPO)
err2024-06-10
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errOAAI
errFaria, Daniel; Eugenio, Patricia; Silva, Marta Contreiras; Balbi, Laura; Bedran, Georges; Kallor, Ashwin Adrian; Nunes, Susana; Palkowski, Aleksander; Waleron, Michal; Alfaro, Javier A.; Pesquita, Catia
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Comparative characterization of two monoclonal antibodies targeting canine PD-1
err2024-05-08
err0
errOAAI
errKocikowski, Mikolaj; Dziubek, Katarzyna; Wegrzyn, Katarzyna; Hrabal, Vaclav; Zavadil-Kokas, Filip; Vojtesek, Borivoj; Alfaro, Javier Antonio; Hupp, Ted; Parys, Maciej
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Untranslated regions (UTRs) are a potential novel source of neoantigens for personalised immunotherapy
err2024-03-15
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errOAAI
errSng, Christopher C. T.; Kallor, Ashwin Adrian; Simpson, Benjamin S.; Bedran, Georges; Alfaro, Javier; Litchfield, Kevin
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Unraveling the glycosylated immunopeptidome with HLA-Glyco
err2023-06-12
err5
errOAAI
errBedran, Georges; Polasky, Daniel A.; Hsiao, Yi; Yu, Fengchao; Leprevost, Felipe da Veiga; Alfaro, Javier A.; Cieslik, Marcin; Nesvizhskii, Alexey I.
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CARMEN: A pan-HLA and pan-cancer proteogenomic database on antigen presentation to support cancer immunotherapy
err2023-04-04
err1
PREAI
errKallor, Ashwin Adrian; Waleron, Michal; Bedran, Georges; Eugenio, Patricia; Pesquita, Catia; Faria, Daniel; Zanzotto, Fabio Massimo; Battail, Christophe; Rajan, Ajitha; Alfaro, Javier
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Sampling the proteome by emerging single-molecule and mass spectrometry methods
err2023-03-10
err41
errOAAI
errMacCoss, Michael J. J.; Alfaro, Javier Antonio; Faivre, Danielle A. A.; Wu, Christine C. C.; Wanunu, Meni; Slavov, Nikolai
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The emerging landscape of single-molecule protein sequencing technologies
err2021-06-07
err214
errOAAI
errAlfaro, Javier Antonio; Bohlander, Peggy; Dai, Mingjie; Filius, Mike; Howard, Cecil J.; van Kooten, Xander F.; Ohayon, Shilo; Pomorski, Adam; Schmid, Sonja; Aksimentiev, Aleksei; Anslyn, Eric V.; Bedran, Georges; Cao, Chan; Chinappi, Mauro; Coyaud, Etienne; Dekker, Cees; Dittmar, Gunnar; Drachman, Nicholas; Eelkema, Rienk; Goodlett, David; Hentz, Sebastien; Kalathiya, Umesh; Kelleher, Neil L.; Kelly, Ryan T.; Kelman, Zvi; Kim, Sung Hyun; Kuster, Bernhard; Rodriguez-Larrea, David; Lindsay, Stuart; Maglia, Giovanni; Marcotte, Edward M.; Marino, John P.; Masselon, Christophe; Mayer, Michael; Samaras, Patroklos; Sarthak, Kumar; Sepiashvili, Lusia; Stein, Derek; Wanunu, Meni; Wilhelm, Mathias; Yin, Peng; Meller, Amit; Joo, Chirlmin
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MicroPOTS Analysis of Barrett's Esophageal Cell Line Models Identifies Proteomic Changes after Physiologic and Radiation Stress
err2021-01-25
err12
errOAAI
errWeke, Kenneth; Singh, Ashita; Uwugiaren, Naomi; Alfaro, Javier A.; Wang, Tongjie; Hupp, Ted R.; O'Neill, J. Robert; Vojtesek, Borek; Goodlett, David R.; Williams, Sarah M.; Zhou, Mowei; Kelly, Ryan T.; Zhu, Ying; Dapic, Irena
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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
err2020-05-14
err75
errOAAI
errKalathiya, Umesh; Padariya, Monikaben; Mayordomo, Marcos; Lisowska, Malgorzata; Nicholson, Judith; Singh, Ashita; Baginski, Maciej; Fahraeus, Robin; Carragher, Neil; Ball, Kathryn; Haas, Juergen; Daniels, Alison; Hupp, Ted R.; Alfaro, Javier Antonio
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Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines
err2017-07-18
err45
errOAAI
errAlfaro, Javier A.; Ignatchenko, Alexandr; Ignatchenko, Vladimir; Sinha, Ankit; Boutros, Paul C.; Kislinger, Thomas
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Onco-proteogenomics: cancer proteomics joins forces with genomics (vol 11, pg 1107, 2014)
err2015-01-29
err1
errOAAI
errAlfaro, Javier A.; Sinha, Ankit; Kislinger, Thomas; Boutros, Paul C.
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Onco-proteogenomics: cancer proteomics joins forces with genomics
err2014-10-30
err116
PREAI
errAlfaro, Javier A.; Sinha, Ankit; Kislinger, Thomas; Boutros, Paul C.
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Hotspot activating PRKD1 somatic mutations in polymorphous low-grade adeno carcinomas of the salivary glands
err2014-09-21
err166
errOAAI
errWeinreb, Ilan; Piscuoglio, Salvatore; Martelotto, Luciano G.; Waggott, Daryl; Ng, Charlotte K. Y.; Perez-Ordonez, Bayardo; Harding, Nicholas J.; Alfaro, Javier; Chu, Kenneth C.; Viale, Agnes; Fusco, Nicola; Paula, Arnaud da Cruz; Marchio, Caterina; Sakr, Rita A.; Lim, Raymond; Thompson, Lester D. R.; Chiosea, Simion I.; Seethala, Raja R.; Skalova, Alena; Stelow, Edward B.; Fonseca, Isabel; Assaad, Adel; How, Christine; Wang, Jianxin; de Borja, Richard; Chan-Seng-Yue, Michelle; Howlett, Christopher J.; Nichols, Anthony C.; Wen, Y. Hannah; Katabi, Nora; Buchner, Nicholas; Mullen, Laura; Kislinger, Thomas; Wouters, Bradly G.; Liu, Fei-Fei; Norton, Larry; McPherson, John D.; Rubin, Brian P.; Clarke, Blaise A.; Weigelt, Britta; Boutros, Paul C.; Reis-Filho, Jorge S.
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Heterogeneity between Diagnostic Tests for IgA anti-Beta2 Glycoprotein I: Explaining the Controversy in Studies of Association with Vascular Pathology
err2013-11-26
err31
PREAI
errMartinez-Flores, Jose A.; Serrano, Manuel; Alfaro, Javier; Mora, Sergio; Paz-Artal, Estela; Morales, Jose M.; Serrano, Antonio
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pH-induced conformational changes in human ABO(H) blood group glycosyltransferases confirm the importance of electrostatic interactions in the formation of the semi-closed state
err2013-11-20
err8
errOAAI
errJohal, Asha R.; Blackler, Ryan J.; Alfaro, Javier A.; Schuman, Brock; Borisova, Svetlana; Evans, Stephen V.
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