selected publications
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academic article
- Genome Informatics 2016. Genome Biology. 18:5. 2017
- Top considerations for creating bioinformatics software documentation. Briefings in bioinformatics. bbw134. 2017
- ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data. Genome Biology. 17:82. 2016
- Statistical Inference, Learning and Models in Big Data. International statistical review = Revue internationale de statistique. 84:371-389. 2016
- Determining the epigenome using DNA alone. Nature methods. 12:191-192. 2015
- Extending reference assembly models. Genome Biology / Adv Genome Biol. 16:13. 2015
- Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression. Genome research. 25:544-557. 2015
- Comparative analysis of metazoan chromatin organization. Nature. 512:449-452. 2014
- Integrative annotation of chromatin elements from ENCODE data. Nucleic acids research. 41:827-841. 2013
- An integrated encyclopedia of DNA elements in the human genome. Nature. 489:57-74. 2012
- ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome research. 22:1813-1831. 2012
- Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nature methods. 9:473-476. 2012
- A User's Guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biology. 9:e1001046. 2011
- Exploratory analysis of genomic segmentations with Segtools. BMC Bioinformatics. 12:415. 2011
- A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data. Bioinformatics (Oxford, England). 26:i334-i342. 2010
- An effective model for natural selection in promoters. Genome research. 20:685-692. 2010
- The Genomedata format for storing large-scale functional genomics data. Bioinformatics (Oxford, England). 26:1458-1459. 2010
- Estimating the Neutral Rate of Nucleotide Substitution Using Introns. Molecular biology and evolution. 24:522-531. 2006
- AANT: the Amino Acid-Nucleotide Interaction Database. Nucleic Acids Research. 32:174D-181. 2004
- Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 432:695-716. 2004
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article