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Daofeng Li et al.
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Brenda Pardo et al.
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Erick Armingol et al.
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Ankit Naik et al.
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C. Goble et al.
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Rose Oughtred et al.
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Adam Frankish et al.
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Seth Carbon et al.
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Damian Szklarczyk et al.
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Anqiang Jia et al.
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Luke Zappia et al.
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Phuc-Loi Luu et al.
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James T. Robinson et al.
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