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Jacob D. Washburn et al.
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Awais Athar et al.
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Alan L. Hutchison et al.
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Nicole Wittenbrink et al.
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Junhyun Lim et al.
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Rosemary Braun et al.
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Chen Li et al.
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Alexander Graf et al.
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McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes
Dina Hafez et al.
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Forest Agostinelli et al.
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Gang Wu et al.
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DeepChrome: deep-learning for predicting gene expression from histone modifications
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Jacob J. Hughey et al.
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DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences
Daniel Quang et al.
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Positional distribution of transcription factor binding sites in Arabidopsis thaliana
Chun-Ping Yu et al.
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MicroRNA activity in the Arabidopsis male germline
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Reetika Rawat et al.
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Anireddy S. N. Reddy et al.
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JTK_CYCLE: An Efficient Nonparametric Algorithm for Detecting Rhythmic Components in Genome-Scale Data Sets
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Gang Wu et al.
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WGCNA: an R package for weighted correlation network analysis
Peter Langfelder et al.
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Todd P. Michael et al.
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Michael F. Covington et al.
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Zhaojun Ding et al.
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EF Glynn et al.
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AN Dodd et al.
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MA Beer et al.
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ST Jensen et al.
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W Thompson et al.
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TP Michael et al.
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A Hall et al.
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RM Green et al.
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G Thijs et al.
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Photoperiodism: The consistent use of CONSTANS
A Samach et al.
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Orchestrated transcription of key pathways in Arabidopsis by the circadian clock
SL Harmer et al.
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Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
S Kaul et al.
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