Classification and interaction in random forests von Denisko, Danielle, Hoffman, Michael M.

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Variable-Centered, Person-Centered, and Person-Specific Approaches: Where Theory Meets the Method von Howard, Matt C., Hoffman, Michael E.

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Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities von Zitnik, Marinka, Nguyen, Francis, Wang, Bo, Leskovec, Jure, Goldenberg, Anna, Hoffman, Michael M.

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Umap and Bismap: quantifying genome and methylome mappability von Karimzadeh, Mehran, Ernst, Carl, Kundaje, Anshul, Hoffman, Michael M

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Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome von Karimzadeh, Mehran, Hoffman, Michael M

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Unsupervised pattern discovery in human chromatin structure through genomic segmentation von Hoffman, Michael M, Buske, Orion J, Wang, Jie, Weng, Zhiping, Bilmes, Jeff A, Noble, William Stafford

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QUASI-SYMMETRIC FUNCTIONS AND MOD p MULTIPLE HARMONIC SUMS von HOFFMAN, Michael E.

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Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns von Libbrecht, Maxwell W., Chan, Rachel C. W., Hoffman, Michael M.

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Reproducibility standards for machine learning in the life sciences von Heil, Benjamin J., Hoffman, Michael M., Markowetz, Florian, Lee, Su-In, Greene, Casey S., Hicks, Stephanie C.

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Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet von Viner, Coby, Ishak, Charles A, Johnson, James, Walker, Nicolas J, Shi, Hui, Sjöberg-Herrera, Marcela K, Shen, Shu Yi, Lardo, Santana M, Adams, David J, Ferguson-Smith, Anne C, De Carvalho, Daniel D, Hainer, Sarah J, Bailey, Timothy L, Hoffman, Michael M

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Matrix metalloproteinase (MMP)-degradable tissue engineered periosteum coordinates allograft healing via early stage recruitment and support of host neurovasculature von Li, Yiming, Hoffman, Michael D., Benoit, Danielle S.W.

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Sensitive tumour detection and classification using plasma cell-free DNA methylomes von Shen, Shu Yi, Singhania, Rajat, Fehringer, Gordon, Chakravarthy, Ankur, Roehrl, Michael H. A., Chadwick, Dianne, Zuzarte, Philip C., Borgida, Ayelet, Wang, Ting Ting, Li, Tiantian, Kis, Olena, Zhao, Zhen, Spreafico, Anna, Medina, Tiago da Silva, Wang, Yadon, Roulois, David, Ettayebi, Ilias, Chen, Zhuo, Chow, Signy, Murphy, Tracy, Arruda, Andrea, O’Kane, Grainne M., Liu, Jessica, Mansour, Mark, McPherson, John D., O’Brien, Catherine, Leighl, Natasha, Bedard, Philippe L., Fleshner, Neil, Liu, Geoffrey, Minden, Mark D., Gallinger, Steven, Goldenberg, Anna, Pugh, Trevor J., Hoffman, Michael M., Bratman, Scott V., Hung, Rayjean J., De Carvalho, Daniel D.

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DNAmod: the DNA modification database von Sood, Ankur Jai, Viner, Coby, Hoffman, Michael M.

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Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma von Abatti, Luis E, Lado-Fernández, Patricia, Huynh, Linh, Collado, Manuel, Hoffman, Michael M, Mitchell, Jennifer A

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Top considerations for creating bioinformatics software documentation von Karimzadeh, Mehran, Hoffman, Michael M

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Transparency and reproducibility in artificial intelligence von Haibe-Kains, Benjamin, Adam, George Alexandru, Hosny, Ahmed, Khodakarami, Farnoosh, Waldron, Levi, Wang, Bo, McIntosh, Chris, Goldenberg, Anna, Kundaje, Anshul, Greene, Casey S., Broderick, Tamara, Hoffman, Michael M., Leek, Jeffrey T., Korthauer, Keegan, Huber, Wolfgang, Brazma, Alvis, Pineau, Joelle, Tibshirani, Robert, Hastie, Trevor, Ioannidis, John P. A., Quackenbush, John, Aerts, Hugo J. W. L.

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Human papillomavirus integration transforms chromatin to drive oncogenesis von Karimzadeh, Mehran, Arlidge, Christopher, Rostami, Ariana, Lupien, Mathieu, Bratman, Scott V, Hoffman, Michael M

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Integrative annotation of chromatin elements from ENCODE data von Hoffman, Michael M, Ernst, Jason, Wilder, Steven P, Kundaje, Anshul, Harris, Robert S, Libbrecht, Max, Giardine, Belinda, Ellenbogen, Paul M, Bilmes, Jeffrey A, Birney, Ewan, Hardison, Ross C, Dunham, Ian, Kellis, Manolis, Noble, William Stafford

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Epidemiology of COVID-19 vs. influenza: Differential failure of COVID-19 mitigation among Hispanics, Cook County Health, Illinois von Trick, William E., Badri, Sheila, Doshi, Kruti, Zhang, Huiyuan, Rezai, Katayoun, Hoffman, Michael J., Weinstein, Robert A.

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The effect of mesenchymal stem cells delivered via hydrogel-based tissue engineered periosteum on bone allograft healing von Hoffman, Michael D, Xie, Chao, Zhang, Xinping, Benoit, Danielle S.W

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