Biologically informed deep neural network for prostate cancer discovery
Elmarakeby, Haitham A, Hwang, Justin, Arafeh, Rand, Crowdis, Jett, Gang, Sydney, Liu, David, AlDubayan, Saud H, Salari, Keyan, Kregel, Steven, Richter, Camden, Arnoff, Taylor E, Park, Jihye, Hahn, William C, Van Allen, Eliezer M
Published in Nature (London) (14.10.2021)
Published in Nature (London) (14.10.2021)
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Journal Article
Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma
Liu, David, Schilling, Bastian, Liu, Derek, Sucker, Antje, Livingstone, Elisabeth, Jerby-Arnon, Livnat, Zimmer, Lisa, Gutzmer, Ralf, Satzger, Imke, Loquai, Carmen, Grabbe, Stephan, Vokes, Natalie, Margolis, Claire A, Conway, Jake, He, Meng Xiao, Elmarakeby, Haitham, Dietlein, Felix, Miao, Diana, Tracy, Adam, Gogas, Helen, Goldinger, Simone M, Utikal, Jochen, Blank, Christian U, Rauschenberg, Ricarda, von Bubnoff, Dagmar, Krackhardt, Angela, Weide, Benjamin, Haferkamp, Sebastian, Kiecker, Felix, Izar, Ben, Garraway, Levi, Regev, Aviv, Flaherty, Keith, Paschen, Annette, Van Allen, Eliezer M, Schadendorf, Dirk
Published in Nature medicine (01.12.2019)
Published in Nature medicine (01.12.2019)
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Journal Article
ATM Loss Confers Greater Sensitivity to ATR Inhibition than PARP Inhibition in Prostate Cancer
Rafiei, Shahrzad, Fitzpatrick, Kenyon, Liu, David, Cai, Mu-Yan, Elmarakeby, Haitham A, Park, Jihye, Ricker, Cora, Kochupurakkal, Bose S, Choudhury, Atish D, Hahn, William C, Balk, Steven P, Hwang, Justin H, Van Allen, Eliezer M, Mouw, Kent W
Published in Cancer research (Chicago, Ill.) (01.06.2020)
Published in Cancer research (Chicago, Ill.) (01.06.2020)
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Journal Article
Artificial intelligence-aided clinical annotation of a large multi-cancer genomic dataset
Kehl, Kenneth L, Xu, Wenxin, Gusev, Alexander, Bakouny, Ziad, Choueiri, Toni K, Riaz, Irbaz Bin, Elmarakeby, Haitham, Van Allen, Eliezer M, Schrag, Deborah
Published in Nature communications (15.12.2021)
Published in Nature communications (15.12.2021)
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Journal Article
Genomics of response to immune checkpoint therapies for cancer: implications for precision medicine
Conway, Jake R, Kofman, Eric, Mo, Shirley S, Elmarakeby, Haitham, Van Allen, Eliezer
Published in Genome medicine (29.11.2018)
Published in Genome medicine (29.11.2018)
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Journal Article
Empirical evaluation of language modeling to ascertain cancer outcomes from clinical text reports
Elmarakeby, Haitham A, Trukhanov, Pavel S, Arroyo, Vidal M, Riaz, Irbaz Bin, Schrag, Deborah, Van Allen, Eliezer M, Kehl, Kenneth L
Published in BMC bioinformatics (02.09.2023)
Published in BMC bioinformatics (02.09.2023)
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Journal Article
Assessment of Deep Natural Language Processing in Ascertaining Oncologic Outcomes From Radiology Reports
Kehl, Kenneth L, Elmarakeby, Haitham, Nishino, Mizuki, Van Allen, Eliezer M, Lepisto, Eva M, Hassett, Michael J, Johnson, Bruce E, Schrag, Deborah
Published in JAMA oncology (01.10.2019)
Published in JAMA oncology (01.10.2019)
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Journal Article
A Proposal for a Genome Similarity-Based Taxonomy for Plant-Pathogenic Bacteria that Is Sufficiently Precise to Reflect Phylogeny, Host Range, and Outbreak Affiliation Applied to Pseudomonas syringae sensu lato as a Proof of Concept
Vinatzer, Boris A, Weisberg, Alexandra J, Monteil, Caroline L, Elmarakeby, Haitham A, Sheppard, Samuel K, Heath, Lenwood S
Published in Phytopathology (01.01.2017)
Published in Phytopathology (01.01.2017)
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Journal Article
Harmonization of Tumor Mutational Burden Quantification and Association With Response to Immune Checkpoint Blockade in Non-Small-Cell Lung Cancer
Vokes, Natalie I, Liu, David, Ricciuti, Biagio, Jimenez-Aguilar, Elizabeth, Rizvi, Hira, Dietlein, Felix, He, Meng Xiao, Margolis, Claire A, Elmarakeby, Haitham A, Girshman, Jeffrey, Adeni, Anika, Sanchez-Vega, Francisco, Schultz, Nikolaus, Dahlberg, Suzanne, Zehir, Ahmet, Jänne, Pasi A, Nishino, Mizuki, Umeton, Renato, Sholl, Lynette M, Van Allen, Eliezer M, Hellmann, Matthew D, Awad, Mark M
Published in JCO precision oncology (2019)
Published in JCO precision oncology (2019)
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Journal Article
Systematic auditing is essential to debiasing machine learning in biology
Eid, Fatma-Elzahraa, Elmarakeby, Haitham A, Chan, Yujia Alina, Fornelos, Nadine, ElHefnawi, Mahmoud, Van Allen, Eliezer M, Heath, Lenwood S, Lage, Kasper
Published in Communications biology (10.02.2021)
Published in Communications biology (10.02.2021)
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Journal Article
Author Correction: Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma
Liu, David, Schilling, Bastian, Liu, Derek, Sucker, Antje, Livingstone, Elisabeth, Jerby-Arnon, Livnat, Zimmer, Lisa, Gutzmer, Ralf, Satzger, Imke, Loquai, Carmen, Grabbe, Stephan, Vokes, Natalie, Margolis, Claire A, Conway, Jake, He, Meng Xiao, Elmarakeby, Haitham, Dietlein, Felix, Miao, Diana, Tracy, Adam, Gogas, Helen, Goldinger, Simone M, Utikal, Jochen, Blank, Christian U, Rauschenberg, Ricarda, von Bubnoff, Dagmar, Krackhardt, Angela, Weide, Benjamin, Haferkamp, Sebastian, Kiecker, Felix, Izar, Ben, Garraway, Levi, Regev, Aviv, Flaherty, Keith, Paschen, Annette, Van Allen, Eliezer M, Schadendorf, Dirk
Published in Nature medicine (01.07.2020)
Published in Nature medicine (01.07.2020)
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Journal Article
A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines
Weir, Barbara A., Cowley, Glenn S., Vazquez, Francisca, Guan, Yuanfang, Jaiswal, Alok, Karasuyama, Masayuki, Uzunangelov, Vladislav, Wang, Tao, Tsherniak, Aviad, Howell, Sara, Marbach, Daniel, Hoff, Bruce, Norman, Thea C., Bivol, Adrian, Bunte, Kerstin, Carlin, Daniel, Chopra, Sahil, Deran, Alden, Ellrott, Kyle, Gopalacharyulu, Peddinti, Graim, Kiley, Kaski, Samuel, Khan, Suleiman A., Newton, Yulia, Ng, Sam, Pahikkala, Tapio, Paull, Evan, Sokolov, Artem, Tang, Hao, Tang, Jing, Wennerberg, Krister, Xie, Yang, Zhan, Xiaowei, Zhu, Fan, Afsari, Bahman, Airola, Antti, Bivol, Adrian, Boehm, Jesse S., Bunte, Kerstin, Carlin, Daniel, Chang, Yu-Chuan, Chopra, Sahil, Cowley, Glenn S., Deran, Alden, Ellrott, Kyle, Elmarakeby, Haitham, Fertig, Elana J., Gonçalves, Emanuel, Gönen, Mehmet, Gopalacharyulu, Peddinti, Guan, Yuanfang, Hafemeister, Christoph, Hahn, William C., Heath, Lenwood, Howell, Sara, Jaiswal, Alok, Karasuyama, Masayuki, Kaski, Samuel, Kędziorski, Łukasz, Khan, Suleiman A., Khemka, Niraj, King, Erh-kan, Lauria, Mario, Liu, Mark, Mamitsuka, Hiroshi, Marbach, Daniel, Margolin, Adam A., Mazurkiewicz, Mateusz, Menden, Michael P., Migacz, Szymon, Newton, Yulia, Ng, Sam, Nie, Zhi, Norman, Thea C., Pahikkala, Tapio, Paull, Evan, Priami, Corrado, Root, David E., Saez-Rodriguez, Julio, Sokolov, Artem, Song, Lei, Stuart, Joshua M., Tang, Jing, Uzunangelov, Vladislav, Vazquez, Francisca, Weir, Barbara A., Wu, Ling-yun, Xiao, Guanghua, Ye, Jieping, Ye, Yuting, Zhan, Xiaowei, Aittokallio, Tero, Mamitsuka, Hiroshi, Stuart, Joshua M., Boehm, Jesse S., Root, David E., Xiao, Guanghua, Stolovitzky, Gustavo, Hahn, William C., Margolin, Adam A.
Published in Cell systems (22.11.2017)
Published in Cell systems (22.11.2017)
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Journal Article
Similarity-based codes sequentially assigned to ebolavirus genomes are informative of species membership, associated outbreaks, and transmission chains
Weisberg, Alexandra J, Elmarakeby, Haitham A, Heath, Lenwood S, Vinatzer, Boris A
Published in Open forum infectious diseases (01.01.2015)
Published in Open forum infectious diseases (01.01.2015)
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Journal Article
Abstract 910: Clinical inference and biological dissection of tumor ploidy and heterogeneity in cutaneous melanoma for immunotherapy response using deep learning
Glettig, Marc, Tarantino, Giuseppe, Aprati, Tyler, Elmarakeby, Haitham, Liu, David
Published in Cancer research (Chicago, Ill.) (22.03.2024)
Published in Cancer research (Chicago, Ill.) (22.03.2024)
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Journal Article
Abstract 5859: Genomic correlates of response to immune checkpoint inhibitors in advanced head and neck squamous cell carcinoma
Patel, Nisarg A., Vokes, Natalie I., Elmarakeby, Haitham, Hanna, Glenn J., Van Allen, Eliezer M.
Published in Cancer research (Chicago, Ill.) (15.08.2020)
Published in Cancer research (Chicago, Ill.) (15.08.2020)
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Journal Article
Abstract 2062: Delta prognosis: A novel clinical outcome based on automated analysis of unstructured cancer EHR data
Kehl, Kenneth L., Elmarakeby, Haitham A., Hassett, Michael J., Van Allen, Eliezer M., Schrag, Deb
Published in Cancer research (Chicago, Ill.) (15.08.2020)
Published in Cancer research (Chicago, Ill.) (15.08.2020)
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Journal Article
Potential targets of VIVIPAROUS1/ABI3‐LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos
Schneider, Andrew, Aghamirzaie, Delasa, Elmarakeby, Haitham, Poudel, Arati N, Koo, Abraham J, Heath, Lenwood S, Grene, Ruth, Collakova, Eva
Published in The Plant journal : for cell and molecular biology (2016)
Published in The Plant journal : for cell and molecular biology (2016)
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Journal Article
Detection of Pathogenic Variants With Germline Genetic Testing Using Deep Learning vs Standard Methods in Patients With Prostate Cancer and Melanoma
AlDubayan, Saud H, Conway, Jake R, Camp, Sabrina Y, Witkowski, Leora, Kofman, Eric, Reardon, Brendan, Han, Seunghun, Moore, Nicholas, Elmarakeby, Haitham, Salari, Keyan, Choudhry, Hani, Al-Rubaish, Abdullah M, Al-Sulaiman, Abdulsalam A, Al-Ali, Amein K, Taylor-Weiner, Amaro, Van Allen, Eliezer M
Published in JAMA : the journal of the American Medical Association (17.11.2020)
Published in JAMA : the journal of the American Medical Association (17.11.2020)
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Journal Article