An effective model for natural selection in promoters

Por Hoffman, Michael M., Birney, Ewan
Publicado em 2010

Genome Informatics 2016

Por Chicco, Davide, Hoffman, Michael M.
Publicado no Genome Biol (2017)

Classification and interaction in random forests

Por Denisko, Danielle, Hoffman, Michael M.
Publicado no Proc Natl Acad Sci U S A (2018)

Top considerations for creating bioinformatics software documentation

Por Karimzadeh, Mehran, Hoffman, Michael M
Publicado no Brief Bioinform (2017)

The Genomedata format for storing large-scale functional genomics data

Por Hoffman, Michael M., Buske, Orion J., Noble, William Stafford
Publicado em 2010

Umap and Bismap: quantifying genome and methylome mappability

Por Karimzadeh, Mehran, Ernst, Carl, Kundaje, Anshul, Hoffman, Michael M
Publicado no Nucleic Acids Res (2018)

A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data

Por Chen, Xiaoyu, Hoffman, Michael M., Bilmes, Jeff A., Hesselberth, Jay R., Noble, William S.
Publicado em 2010

Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities

Por Zitnik, Marinka, Nguyen, Francis, Wang, Bo, Leskovec, Jure, Goldenberg, Anna, Hoffman, Michael M.
Publicado no Inf Fusion (2018)

Exploratory analysis of genomic segmentations with Segtools

Por Buske Orion J, Hoffman Michael M, Ponts Nadia, Le Roch Karine G, Noble William
Publicado em 2011-10-01

Exploratory analysis of genomic segmentations with Segtools

Por Buske, Orion J, Hoffman, Michael M, Ponts, Nadia, Le Roch, Karine G, Noble, William Stafford
Publicado em 2011

AANT: the Amino Acid–Nucleotide Interaction Database

Por Hoffman, Michael M., Khrapov, Maksim A., Cox, J. Colin, Yao, Jianchao, Tong, Lingnan, Ellington, Andrew D.
Publicado em 2004

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

Por Hoffman, Michael M., Buske, Orion J., Wang, Jie, Weng, Zhiping, Bilmes, Jeff A., Noble, William Stafford
Publicado em 2012

ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data

Por Lundberg, Scott M., Tu, William B., Raught, Brian, Penn, Linda Z., Hoffman, Michael M., Lee, Su-In
Publicado no Genome Biol (2016)

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

Por Libbrecht, Maxwell W., Ay, Ferhat, Hoffman, Michael M., Gilbert, David M., Bilmes, Jeffrey A., Noble, William Stafford
Publicado no Genome Res (2015)

Segway 2.0: Gaussian mixture models and minibatch training

Por Chan, Rachel C W, Libbrecht, Maxwell W, Roberts, Eric G, Bilmes, Jeffrey A, Noble, William Stafford, Hoffman, Michael M
Publicado no Bioinformatics (2018)

Integrative annotation of chromatin elements from ENCODE data

Por 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
Publicado em 2013

Extending reference assembly models

Por Church, Deanna M, Schneider, Valerie A, Steinberg, Karyn Meltz, Schatz, Michael C, Quinlan, Aaron R, Chin, Chen-Shan, Kitts, Paul A, Aken, Bronwen, Marth, Gabor T, Hoffman, Michael M, Herrero, Javier, Mendoza, M Lisandra Zepeda, Durbin, Richard, Flicek, Paul
Publicado no Genome Biol (2015)

Opportunities and obstacles for deep learning in biology and medicine

Por Ching, Travers, Himmelstein, Daniel S., Beaulieu-Jones, Brett K., Kalinin, Alexandr A., Do, Brian T., Way, Gregory P., Ferrero, Enrico, Agapow, Paul-Michael, Zietz, Michael, Hoffman, Michael M., Xie, Wei, Rosen, Gail L., Lengerich, Benjamin J., Israeli, Johnny, Lanchantin, Jack, Woloszynek, Stephen, Carpenter, Anne E., Shrikumar, Avanti, Xu, Jinbo, Cofer, Evan M., Lavender, Christopher A., Turaga, Srinivas C., Alexandari, Amr M., Lu, Zhiyong, Harris, David J., DeCaprio, Dave, Qi, Yanjun, Kundaje, Anshul, Peng, Yifan, Wiley, Laura K., Segler, Marwin H. S., Boca, Simina M., Swamidass, S. Joshua, Huang, Austin, Gitter, Anthony, Greene, Casey S.
Publicado no J R Soc Interface (2018)

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Por Landt, Stephen G., Marinov, Georgi K., Kundaje, Anshul, Kheradpour, Pouya, Pauli, Florencia, Batzoglou, Serafim, Bernstein, Bradley E., Bickel, Peter, Brown, James B., Cayting, Philip, Chen, Yiwen, DeSalvo, Gilberto, Epstein, Charles, Fisher-Aylor, Katherine I., Euskirchen, Ghia, Gerstein, Mark, Gertz, Jason, Hartemink, Alexander J., Hoffman, Michael M., Iyer, Vishwanath R., Jung, Youngsook L., Karmakar, Subhradip, Kellis, Manolis, Kharchenko, Peter V., Li, Qunhua, Liu, Tao, Liu, X. Shirley, Ma, Lijia, Milosavljevic, Aleksandar, Myers, Richard M., Park, Peter J., Pazin, Michael J., Perry, Marc D., Raha, Debasish, Reddy, Timothy E., Rozowsky, Joel, Shoresh, Noam, Sidow, Arend, Slattery, Matthew, Stamatoyannopoulos, John A., Tolstorukov, Michael Y., White, Kevin P., Xi, Simon, Farnham, Peggy J., Lieb, Jason D., Wold, Barbara J., Snyder, Michael
Publicado em 2012

Comparative analysis of metazoan chromatin organization

Por Ho, Joshua W. K., Jung, Youngsook L., Liu, Tao, Alver, Burak H., Lee, Soohyun, Ikegami, Kohta, Sohn, Kyung-Ah, Minoda, Aki, Tolstorukov, Michael Y., Appert, Alex, Parker, Stephen C. J., Gu, Tingting, Kundaje, Anshul, Riddle, Nicole C., Bishop, Eric, Egelhofer, Thea A., Hu, Sheng’en Shawn, Alekseyenko, Artyom A., Rechtsteiner, Andreas, Asker, Dalal, Belsky, Jason A., Bowman, Sarah K., Chen, Q. Brent, Chen, Ron A-J, Day, Daniel S., Dong, Yan, Dose, Andrea C., Duan, Xikun, Epstein, Charles B., Ercan, Sevinc, Feingold, Elise A., Ferrari, Francesco, Garrigues, Jacob M., Gehlenborg, Nils, Good, Peter J., Haseley, Psalm, He, Daniel, Herrmann, Moritz, Hoffman, Michael M., Jeffers, Tess E., Kharchenko, Peter V., Kolasinska-Zwierz, Paulina, Kotwaliwale, Chitra V., Kumar, Nischay, Langley, Sasha A., Larschan, Erica N., Latorre, Isabel, Libbrecht, Maxwell W., Lin, Xueqiu, Park, Richard, Pazin, Michael J., Pham, Hoang N., Plachetka, Annette, Qin, Bo, Schwartz, Yuri B., Shoresh, Noam, Stempor, Przemyslaw, Vielle, Anne, Wang, Chengyang, Whittle, Christina M., Xue, Huiling, Kingston, Robert E., Kim, Ju Han, Bernstein, Bradley E., Dernburg, Abby F., Pirrotta, Vincenzo, Kuroda, Mitzi I., Noble, William S., Tullius, Thomas D., Kellis, Manolis, MacAlpine, David M., Strome, Susan, Elgin, Sarah C. R., Liu, Xiaole Shirley, Lieb, Jason D., Ahringer, Julie, Karpen, Gary H., Park, Peter J.
Publicado no Nature (2014)