An integrated Encyclopedia of DNA Elements in the human genome ENCODE Project Consortium Nature 489 (7414), 57-74, 2012 | 16793 | 2012 |
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution International Chicken Genome Sequencing Consortium Nature 432 (7018), 695-716, 2004 | 2929* | 2004 |
ChIP-seq guidelines and practices used by the ENCODE and modENCODE consortia SG Landt, GK Marinov, A Kundaje, P Kheradpour, F Pauli, S Batzoglou, ... Genome Research 22 (9), 1813-31, 2012 | 2243 | 2012 |
Opportunities and obstacles for deep learning in biology and medicine T Ching, DS Himmelstein, BK Beaulieu-Jones, AA Kalinin, BT Do, ... Journal of the royal society interface 15 (141), 20170387, 2018 | 2015 | 2018 |
A user's guide to the encyclopedia of DNA elements (ENCODE) ENCODE Project Consortium PLoS biology 9 (4), e1001046, 2011 | 854 | 2011 |
Sensitive tumour detection and classification using plasma cell-free DNA methylomes SY Shen, R Singhania, G Fehringer, A Chakravarthy, MHA Roehrl, ... Nature 563 (7732), 579-583, 2018 | 726 | 2018 |
Unsupervised pattern discovery in human chromatin structure through genomic segmentation MM Hoffman, OJ Buske, J Wang, Z Weng, JA Bilmes, WS Noble Nature Methods 9 (5), 473, 2012 | 725 | 2012 |
A user's guide to the encyclopedia of DNA elements (ENCODE) RM Myers, J Stamatoyannopoulos, M Snyder, I Dunham, RC Hardison, ... PLoS biology 9 (4), 2011 | 675 | 2011 |
Integrative annotation of chromatin elements from ENCODE data MM Hoffman, J Ernst, SP Wilder, A Kundaje, RS Harris, M Libbrecht, ... Nucleic Acids Res 41 (2), 827-841, 2013 | 606 | 2013 |
Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities M Zitnik, F Nguyen, B Wang, J Leskovec, A Goldenberg, MM Hoffman Information Fusion 50, 71-91, 2019 | 523 | 2019 |
Comparative analysis of metazoan chromatin organization JWK Ho, YL Jung, T Liu, BH Alver, S Lee, K Ikegami, KA Sohn, A Minoda, ... Nature 512 (7515), 449-452, 2014 | 419 | 2014 |
Transparency and reproducibility in artificial intelligence B Haibe-Kains, GA Adam, A Hosny, F Khodakarami, ... Nature 586 (7829), E14-E16, 2020 | 351 | 2020 |
Classification and interaction in random forests D Denisko, MM Hoffman Proceedings of the National Academy of Sciences 115 (8), 1690-1692, 2018 | 244 | 2018 |
Extending reference assembly models DM Church, VA Schneider, KM Steinberg, MC Schatz, AR Quinlan, ... Genome Biol 16, 13, 2015 | 189 | 2015 |
Metrics reloaded: Pitfalls and recommendations for image analysis validation L Maier-Hein, B Menze arXiv. org, 2022 | 165* | 2022 |
AANT: the Amino Acid–Nucleotide Interaction Database MM Hoffman, MA Khrapov, JC Cox, J Yao, L Tong, AD Ellington Nucleic Acids Research 32 (Database issue), D174-D181, 2004 | 165 | 2004 |
Reproducibility standards for machine learning in the life sciences BJ Heil, MM Hoffman, F Markowetz, SI Lee, CS Greene, SC Hicks Nature Methods 18 (10), 1132-1135, 2021 | 161 | 2021 |
Common limitations of image processing metrics: A picture story A Reinke, MD Tizabi, CH Sudre, M Eisenmann, T Rädsch, M Baumgartner, ... arXiv preprint arXiv:2104.05642, 2021 | 157 | 2021 |
GA4GH: International policies and standards for data sharing across genomic research and healthcare HL Rehm, AJH Page, L Smith, JB Adams, G Alterovitz, LJ Babb, ... Cell genomics 1 (2), 2021 | 148 | 2021 |
Umap and Bismap: quantifying genome and methylome mappability M Karimzadeh, C Ernst, A Kundaje, MM Hoffman Nucleic acids research 46 (20), e120-e120, 2018 | 145 | 2018 |