Principled Methods and Models for Deep Learning Based Functional Genomics by Krismer, Konstantin

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IDR2D identifies reproducible genomic interactions by Krismer, Konstantin, Guo, Yuchun, Gifford, David K

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spatzie: an R package for identifying significant transcription factor motif co-enrichment from enhancer–promoter interactions by Hammelman, Jennifer, Krismer, Konstantin, Gifford, David K

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seqgra: principled selection of neural network architectures for genomics prediction tasks by Krismer, Konstantin, Hammelman, Jennifer, Gifford, David K

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Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay by Hammelman, Jennifer, Krismer, Konstantin, Gifford, David K, Sherwood, Richard I.

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High resolution discovery of chromatin interactions by Guo, Yuchun, Krismer, Konstantin, Closser, Michael, Wichterle, Hynek, Gifford, David K

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Transite: A Computational Motif-Based Analysis Platform That Identifies RNA-Binding Proteins Modulating Changes in Gene Expression by Krismer, Konstantin, Bird, Molly A, Varmeh, Shohreh, Handly, Erika D, Gattinger, Anna, Bernwinkler, Thomas, Anderson, Daniel A, Heinzel, Andreas, Joughin, Brian A, Kong, Yi Wen, Cannell, Ian G, Yaffe, Michael B

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Transite: A Computational Motif-Based Analysis Platform That Identifies RNA-Binding Proteins Modulating Changes in Gene Expression by Krismer, Konstantin, Bird, Molly A., Varmeh, Shohreh, Handly, Erika D., Gattinger, Anna, Bernwinkler, Thomas, Anderson, Daniel A., Heinzel, Andreas, Joughin, Brian A., Kong, Yi Wen, Cannell, Ian G., Yaffe, Michael B.

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Acidification of tumor at stromal boundaries drives transcriptome alterations associated with aggressive phenotypes by Rohani, Nazanin, Hao, Liangliang, Alexis, Maria S, Joughin, Brian A, Krismer, Konstantin, Moufarrej, Mira N, Soltis, Anthony R, Lauffenburger, Douglas A, Yaffe, Michael B, Burge, Christopher B, Bhatia, Sangeeta N, Gertler, Frank B

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