Search Results - "Keenan, Alexandra B."

ChEA3: transcription factor enrichment analysis by orthogonal omics integration by Keenan, Alexandra B, Torre, Denis, Lachmann, Alexander, Leong, Ariel K, Wojciechowicz, Megan L, Utti, Vivian, Jagodnik, Kathleen M, Kropiwnicki, Eryk, Wang, Zichen, Ma'ayan, Avi

“…Identifying the transcription factors (TFs) responsible for observed changes in gene expression is an important step in understanding gene regulatory networks…”
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L1000FWD: fireworks visualization of drug-induced transcriptomic signatures by Wang, Zichen, Lachmann, Alexander, Keenan, Alexandra B, Ma’ayan, Avi

“…Abstract Motivation As part of the NIH Library of Integrated Network-based Cellular Signatures program, hundreds of thousands of transcriptomic signatures were…”
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Massive mining of publicly available RNA-seq data from human and mouse by Lachmann, Alexander, Torre, Denis, Keenan, Alexandra B., Jagodnik, Kathleen M., Lee, Hoyjin J., Wang, Lily, Silverstein, Moshe C., Ma’ayan, Avi

“…RNA sequencing (RNA-seq) is the leading technology for genome-wide transcript quantification. However, publicly available RNA-seq data is currently provided…”
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eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks by Clarke, Daniel J B, Kuleshov, Maxim V, Schilder, Brian M, Torre, Denis, Duffy, Mary E, Keenan, Alexandra B, Lachmann, Alexander, Feldmann, Axel S, Gundersen, Gregory W, Silverstein, Moshe C, Wang, Zichen, Ma’ayan, Avi

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eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks by Clarke, Daniel J B, Kuleshov, Maxim V, Schilder, Brian M, Torre, Denis, Duffy, Mary E, Keenan, Alexandra B, Lachmann, Alexander, Feldmann, Axel S, Gundersen, Gregory W, Silverstein, Moshe C, Wang, Zichen, Ma'ayan, Avi

“…Abstract While gene expression data at the mRNA level can be globally and accurately measured, profiling the activity of cell signaling pathways is currently…”
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Geneshot: search engine for ranking genes from arbitrary text queries by Lachmann, Alexander, Schilder, Brian M, Wojciechowicz, Megan L, Torre, Denis, Kuleshov, Maxim V, Keenan, Alexandra B, Ma'ayan, Avi

“…The frequency by which genes are studied correlates with the prior knowledge accumulated about them. This leads to an imbalance in research attention where…”
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modEnrichr: a suite of gene set enrichment analysis tools for model organisms by Kuleshov, Maxim V, Diaz, Jennifer E L, Flamholz, Zachary N, Keenan, Alexandra B, Lachmann, Alexander, Wojciechowicz, Megan L, Cagan, Ross L, Ma'ayan, Avi

“…High-throughput experiments produce increasingly large datasets that are difficult to analyze and integrate. While most data integration approaches focus on…”
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Connectivity Mapping: Methods and Applications by Keenan, Alexandra B, Wojciechowicz, Megan L, Wang, Zichen, Jagodnik, Kathleen M, Jenkins, Sherry L, Lachmann, Alexander, Ma'ayan, Avi

“…Connectivity mapping resources consist of signatures representing changes in cellular state following systematic small-molecule, disease, gene, or other form…”
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Leishmania infantum chagasi: A genome-based approach to identification of excreted/secreted proteins by DebRoy, Sruti, Keenan, Alexandra B., Ueno, Norikiyo, Jeronimo, Selma M.B., Donelson, John E., Wilson, Mary E.

“…The parasitic protozoan, Leishmania, survives in harsh environments within its mammalian and sand fly hosts. Secreted proteins likely play critical roles in…”
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Exponential replication of patterns in the Signal Tile Assembly Model and experimental non-deterministic assembly of lines in the Probabilistic Tile Assembly Model by Keenan, Alexandra B

“…We introduce the problem of self-replication of rectangular two-dimensional patterns in the practically motivated Signal Tile Assembly Model (STAM), which is…”
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