Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay
Shigaki, Dustin, Adato, Orit, Adhikari, Aashish N., Dong, Shengcheng, Hawkins‐Hooker, Alex, Inoue, Fumitaka, Juven‐Gershon, Tamar, Kenlay, Henry, Martin, Beth, Patra, Ayoti, Penzar, Dmitry D., Schubach, Max, Xiong, Chenling, Yan, Zhongxia, Boyle, Alan P., Kreimer, Anat, Kulakovskiy, Ivan V., Reid, John, Unger, Ron, Yosef, Nir, Shendure, Jay, Ahituv, Nadav, Kircher, Martin, Beer, Michael A.
Published in Human mutation (01.09.2019)
Published in Human mutation (01.09.2019)
Get full text
Journal Article
Generating functional protein variants with variational autoencoders
Hawkins-Hooker, Alex, Depardieu, Florence, Baur, Sebastien, Couairon, Guillaume, Chen, Arthur, Bikard, David
Published in PLoS computational biology (01.02.2021)
Published in PLoS computational biology (01.02.2021)
Get full text
Journal Article
Getting personal with epigenetics: towards individual-specific epigenomic imputation with machine learning
Hawkins-Hooker, Alex, Visonà, Giovanni, Narendra, Tanmayee, Rojas-Carulla, Mateo, Schölkopf, Bernhard, Schweikert, Gabriele
Published in Nature communications (07.08.2023)
Published in Nature communications (07.08.2023)
Get full text
Journal Article
The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles
Schreiber, Jacob, Boix, Carles, Wook Lee, Jin, Li, Hongyang, Guan, Yuanfang, Chang, Chun-Chieh, Chang, Jen-Chien, Hawkins-Hooker, Alex, Schölkopf, Bernhard, Schweikert, Gabriele, Carulla, Mateo Rojas, Canakoglu, Arif, Guzzo, Francesco, Nanni, Luca, Masseroli, Marco, Carman, Mark James, Pinoli, Pietro, Hong, Chenyang, Yip, Kevin Y, Spence, Jeffrey P, Batra, Sanjit Singh, Song, Yun S, Mahony, Shaun, Zhang, Zheng, Tan, Wuwei, Shen, Yang, Sun, Yuanfei, Shi, Minyi, Adrian, Jessika, Sandstrom, Richard, Farrell, Nina, Halow, Jessica, Lee, Kristen, Jiang, Lixia, Yang, Xinqiong, Epstein, Charles, Strattan, J Seth, Bernstein, Bradley, Snyder, Michael, Kellis, Manolis, Stafford, William, Kundaje, Anshul
Published in Genome Biology (18.04.2023)
Published in Genome Biology (18.04.2023)
Get full text
Journal Article
Chainsaw: protein domain segmentation with fully convolutional neural networks
Wells, Jude, Hawkins-Hooker, Alex, Bordin, Nicola, Sillitoe, Ian, Paige, Brooks, Orengo, Christine
Published in Bioinformatics (Oxford, England) (02.05.2024)
Published in Bioinformatics (Oxford, England) (02.05.2024)
Get full text
Journal Article
Moment Matching Denoising Gibbs Sampling
Zhang, Mingtian, Hawkins-Hooker, Alex, Brooks, Paige, Barber, David
Published in arXiv.org (19.03.2024)
Get full text
Published in arXiv.org (19.03.2024)
Paper
The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles
Schreiber, Jacob Matthew, Boix, Carles A, Lee, Jin Wook, Li, Hongyang, Guan, Yuanfang, Chang, Chun-Chieh, Jen-Chien, Chang, Hawkins-Hooker, Alex, Schoelkopf, Bernhard, Schweikert, Gabriele, Mateo Rojas Carulla, Canakoglu, Arif, Guzzo, Francesco, Nanni, Luca, Masseroli, Marco, Carman, Mark James, Pinoli, Pietro, Hong, Chenyang, Yip, Kevin Y, Spence, Jeffrey P, Sanjit Singh Batra, Song, Yun S, Mahony, Shaun, Zhang, Zheng, Tan, Wuwei, Shen, Yang, Sun, Yuanfei, Shi, Minyi, Jessika Adrian, Sandstrom, Richard S, Farrell, Nina, Halow, Jessica M, Lee, Kristen, Jiang, Lixia, Yang, Xinqiong, Epstein, Charles B, Strattan, J Seth, Snyder, Michael P, Kellis, Manolis, Noble, William S, Kundaje, Anshul Bharat
Published in bioRxiv (02.08.2022)
Published in bioRxiv (02.08.2022)
Get full text
Paper