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Architecture of the Escherichia coli nucleoid
Subhash C. Verma et al.
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Monica S. Guo et al.
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Geoffrey Fudenberg et al.
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William C. Hacker et al.
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Samuel Corless et al.
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HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
Nicolas Servant et al.
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Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
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Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization
Iain Williamson et al.
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Functional implications of genome topology
Giacomo Cavalli et al.
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Tung B. K. Le et al.
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Maxim Imakaev et al.
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Ben Langmead et al.
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The Sequence Alignment/Map format and SAMtools
Heng Li et al.
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Max Kuhn
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Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
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Macrodomain organization of the Escherichia coli chromosome
M Valens et al.
EMBO JOURNAL (2004)