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Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression

Camille Berthelot, Diego Villar, Julie E. Horvath, Duncan T. Odom, Paul Flicek

Nature Ecology & Evolution · 2017 · 181 citations · 65 references

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65

Differential expression analysis for sequence count data

Simon Anders, Wolfgang Huber · Genome biology · 2010 · 16.4K citations · Full text

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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Daehwan Kim, Geo Pertea, Cole Trapnell et al. · Genome biology · 2013 · 13.7K citations · Full text

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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Cole Trapnell, Adam Roberts, Loyal A. Goff et al. · Nature Protocols · 2012 · 12.9K citations · Full text

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Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Jason D. Buenrostro, Paul G. Giresi, Lisa C. Zaba et al. · Nature Methods · 2013 · 7K citations · Full text

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GREAT improves functional interpretation of cis-regulatory regions

Cory Y. McLean, Dave Bristor, Michael Hiller et al. · Nature Biotechnology · 2010 · 5K citations

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