Genome Informatics 2016

por Chicco, Davide, Hoffman, Michael M.
Publicado 2017

Top considerations for creating bioinformatics software documentation

por Karimzadeh, Mehran, Hoffman, Michael M
Publicado 2017

Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome

por Karimzadeh, Mehran, Hoffman, Michael M.
Publicado 2022

Motif elucidation in ChIP-seq datasets with a knockout control

por Denisko, Danielle, Viner, Coby, Hoffman, Michael M
Publicado 2023

DNAmod: the DNA modification database

por Sood, Ankur Jai, Viner, Coby, Hoffman, Michael M.
Publicado 2019

The Genomedata format for storing large-scale functional genomics data

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

Umap and Bismap: quantifying genome and methylome mappability

por Karimzadeh, Mehran, Ernst, Carl, Kundaje, Anshul, Hoffman, Michael M
Publicado 2018

Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns

por Libbrecht, Maxwell W., Chan, Rachel C. W., Hoffman, Michael M.
Publicado 2021

Assessing and assuring interoperability of a genomics file format

por Niu, Yi Nian, Roberts, Eric G, Denisko, Danielle, Hoffman, Michael M
Publicado 2022

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 2010

Human papillomavirus integration transforms chromatin to drive oncogenesis

por Karimzadeh, Mehran, Arlidge, Christopher, Rostami, Ariana, Lupien, Mathieu, Bratman, Scott V., Hoffman, Michael M.
Publicado 2023

Exploratory analysis of genomic segmentations with Segtools

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

Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma

por Abatti, Luis E, Lado-Fernández, Patricia, Huynh, Linh, Collado, Manuel, Hoffman, Michael M, Mitchell, Jennifer A
Publicado 2023

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 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 2015

A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types

por Libbrecht, Maxwell W., Rodriguez, Oscar L., Weng, Zhiping, Bilmes, Jeffrey A., Hoffman, Michael M., Noble, William Stafford
Publicado 2019

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 2018

Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls

por Wilson, Samantha L., Shen, Shu Yi, Harmon, Lauren, Burgener, Justin M., Triche, Tim, Bratman, Scott V., De Carvalho, Daniel D., Hoffman, Michael M.
Publicado 2022

Exploring the merits of research performance measures that comply with the San Francisco Declaration on Research Assessment and strategies to overcome barriers of adoption: qualita...

por Boury, Himani, Albert, Mathieu, Chen, Robert H. C., Chow, James C. L., DaCosta, Ralph, Hoffman, Michael M., Keshavarz, Behrang, Kontos, Pia, McAndrews, Mary Pat, Protze, Stephanie, Gagliardi, Anna R.
Publicado 2023

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 2013