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Dayanne M. Castro et al.
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Robert A. Beagrie et al.
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Xi Chen et al.
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Zhana Duren et al.
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David Lamparter et al.
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Ricardo N. Ramirez et al.
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Katarzyna Karwacz et al.
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Tarmo Aeijoe et al.
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Olivia Wilkins et al.
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The maternal interleukin-17a pathway in mice promotes autism-like phenotypes in offspring
Gloria B. Choi et al.
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Andre F. Rendeiro et al.
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Hamed S. Najafabadi et al.
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Charles Blatti et al.
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Mika Gustafsson et al.
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TRRUST: a reference database of human transcriptional regulatory interactions
Heonjong Han et al.
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Zachary D. Kurtz et al.
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Simon Anders et al.
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Edgar Wingender et al.
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AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors
Hong-Mei Zhang et al.
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Lian En Chai et al.
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Isaac T. W. Harley et al.
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Conservation of trans-acting circuitry during mammalian regulatory evolution
Andrew B. Stergachis et al.
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Jing Qin et al.
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Michael I. Love et al.
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STAR: ultrafast universal RNA-seq aligner
Alexander Dobin et al.
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Maria Ciofani et al.
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Shane Neph et al.
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Roger Pique-Regi et al.
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Pathway Commons, a web resource for biological pathway data
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BEDTools: a flexible suite of utilities for comparing genomic features
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Stability selection
Nicolai Meinshausen et al.
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Aviv Madar et al.
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The Sequence Alignment/Map format and SAMtools
Heng Li et al.
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Michael Hecker et al.
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S. A. Khader et al.
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ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells
Zhengqing Ouyang et al.
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Erez Lieberman-Aiden et al.
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