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Nilah M. Ioannidis

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14H-index
64Paper Count
3.7KCitation Count
Published Papers 14
Publication Date
Fine-tuning sequence-to-expression models on personal genome and transcriptome data
err2026-05-25
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errOAAI
errRuchir Rastogi; Aniketh Janardhan Reddy; Ryan Chung; Nilah M. Ioannidis
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Critical assessment of missense variant effect predictors on disease-relevant variant data
err2025-03-01
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errRastogi, Ruchir; Chung, Ryan; Li, Sindy; Li, Chang; Lee, Kyoungyeul; Woo, Junwoo; Kim, Dong-Wook; Keum, Changwon; Babbi, Giulia; Martelli, Pier Luigi; Savojardo, Castrense; Casadio, Rita; Chennen, Kirsley; Weber, Thomas; Poch, Olivier; Ancien, Francois; Cia, Gabriel; Pucci, Fabrizio; Raimondi, Daniele; Vranken, Wim; Rooman, Marianne; Marquet, Celine; Olenyi, Tobias; Rost, Burkhard; Andreoletti, Gaia; Kamandula, Akash; Peng, Yisu; Bakolitsa, Constantina; Mort, Matthew; Cooper, David N.; Bergquist, Timothy; Pejaver, Vikas; Liu, Xiaoming; Radivojac, Predrag; Brenner, Steven E.; Ioannidis, Nilah M.
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Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function
err2024-09-10
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PREAI
errLoeb, Gabriel B.; Kathail, Pooja; Shuai, Richard W.; Chung, Ryan; Grona, Reinier J.; Peddada, Sailaja; Sevim, Volkan; Federman, Scot; Mader, Karl; Chu, Audrey Y.; Davitte, Jonathan; Du, Juan; Gupta, Alexander R.; Ye, Chun Jimmie; Shafer, Shawn; Przybyla, Laralynne; Rapiteanu, Radu; Ioannidis, Nilah M.; Reiter, Jeremy F.
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Current genomic deep learning models display decreased performance in cell type-specific accessible regions
err2024-08-01
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errOAAI
errKathail, Pooja; Shuai, Richard W.; Chung, Ryan; Ye, Chun Jimmie; Loeb, Gabriel B.; Ioannidis, Nilah M.
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Personal transcriptome variation is poorly explained by current genomic deep learning models
err2023-11-30
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errOAAI
errHuang, Connie; Shuai, Richard W.; Baokar, Parth; Chung, Ryan; Rastogi, Ruchir; Kathail, Pooja; Ioannidis, Nilah M.
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Cross-protein transfer learning substantially improves disease variant prediction
err2023-08-07
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errOAAI
errJagota, Milind; Ye, Chengzhong; Albors, Carlos; Rastogi, Ruchir; Koehl, Antoine; Ioannidis, Nilah; Song, Yun S.
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Tissue-specific impacts of aging and genetics on gene expression patterns in humans
err2022-10-03
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errOAAI
errYamamoto, Ryo; Chung, Ryan; Vazquez, Juan Manuel; Sheng, Huanjie; Steinberg, Philippa L.; Ioannidis, Nilah M.; Sudmant, Peter H.
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Two-stage Study of Familial Prostate Cancer by Whole-exome Sequencing and Custom Capture Identifies 10 Novel Genes Associated with the Risk of Prostate Cancer
err2021-03-01
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errOAAI
errSchaid, Daniel J.; McDonnell, Shannon K.; FitzGerald, Liesel M.; DeRycke, Lissa; Fogarty, Zachary; Giles, Graham G.; MacInnis, Robert J.; Southey, Melissa C.; Nguyen-Dumont, Tu; Cancel-Tassin, Geraldine; Cussenot, Oliver; Whittemore, Alice S.; Sieh, Weiva; Ioannidis, Nilah Monnier; Hsieh, Chih-Lin; Stanford, Janet L.; Schleutker, Johanna; Cropp, Cheryl D.; Carpten, John; Hoegel, Josef; Eeles, Rosalind; Kote-Jarai, Zsofia; Ackerman, Michael J.; Klein, Christopher J.; Mandal, Diptasri; Cooney, Kathleen A.; Bailey-Wilson, Joan E.; Helfand, Brian; Catalona, William J.; Wiklund, Fredrick; Riska, Shaun; Bahetti, Saurabh; Larson, Melissa C.; Albright, Lisa Cannon; Teerlink, Craig; Xu, Jianfeng; Isaacs, William; Ostrander, Elaine A.; Thibodeau, Stephen N.
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Estimating prevalence for limb-girdle muscular dystrophy based on public sequencing databases
err2019-11-01
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errOAAI
errLiu, Wei; Pajusalu, Sander; Lake, Nicole J.; Zhou, Geyu; Ioannidis, Nilah; Mittal, Plavi; Johnson, Nicholas E.; Weihl, Conrad C.; Williams, Bradley A.; Albrecht, Douglas E.; Rufibach, Laura E.; Lek, Monkol
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A Prediction Tool to Facilitate Risk-Stratified Screening for Squamous Cell Skin Cancer
err2018-12-01
err11
errOAAI
errWang, Wei; Jorgenson, Eric; Ioannidis, Nilah M.; Asgari, Maryam M.; Whittemore, Alice S.
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Gene expression imputation identifies candidate genes and susceptibility loci associated with cutaneous squamous cell carcinoma
err2018-10-15
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errIoannidis, Nilah M.; Wang, Wei; Furlotte, Nicholas A.; Hinds, David A.; Bustamante, Carlos D.; Jorgenson, Eric; Asgari, Maryam M.; Whittemore, Alice S.
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Cutaneous squamous cell cancer (cSCC) risk and the human leukocyte antigen (HLA) system
err2017-04-01
err25
errOAAI
errYesantharao, Pooja; Wang, Wei; Ioannidis, Nilah M.; Demehri, Shadmehr; Whittemore, Alice S.; Asgari, Maryam M.
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REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants
err2016-10-01
err1.7K
errOAAI
errIoannidis, Nilah M.; Rothstein, Joseph H.; Pejaver, Vikas; Middha, Sumit; McDonnell, Shannon K.; Baheti, Saurabh; Musolf, Anthony; Li, Qing; Holzinger, Emily; Karyadi, Danielle; Cannon-Albright, Lisa A.; Teerlink, Craig C.; Stanford, Janet L.; Isaacs, William B.; Xu, Jianfeng; Cooney, Kathleen A.; Lange, Ethan M.; Schleutker, Johanna; Carpten, John D.; Powell, Isaac J.; Cussenot, Olivier; Cancel-Tassin, Geraldine; Giles, Graham G.; MacInnis, Robert J.; Maier, Christiane; Hsieh, Chih-Lin; Wiklund, Fredrik; Catalona, William J.; Foulkes, William D.; Mandal, Diptasri; Eeles, Rosalind A.; Kote-Jarai, Zsofia; Bustamante, Carlos D.; Schaid, Daniel J.; Hastie, Trevor; Ostrander, Elaine A.; Bailey-Wilson, Joan E.; Radivojac, Predrag; Thibodeau, Stephen N.; Whittemore, Alice S.; Sieh, Weiva
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Identification of Susceptibility Loci for Cutaneous Squamous Cell Carcinoma
err2016-05-01
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errOAAI
errAsgari, Maryam M.; Wang, Wei; Ioannidis, Nilah M.; Itnyre, Jacqueline; Hoffmann, Thomas; Jorgenson, Eric; Whittemore, Alice S.
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