Search Results - "V Kuleshov, Maxim"

KEA3: improved kinase enrichment analysis via data integration by Kuleshov, Maxim V, Xie, Zhuorui, London, Alexandra B K, Yang, Janice, Evangelista, John Erol, Lachmann, Alexander, Shu, Ingrid, Torre, Denis, Ma’ayan, Avi

“…Abstract Phosphoproteomics and proteomics experiments capture a global snapshot of the cellular signaling network, but these methods do not directly measure…”
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SigCom LINCS: data and metadata search engine for a million gene expression signatures by Evangelista, John Erol, Clarke, Daniel J B, Xie, Zhuorui, Lachmann, Alexander, Jeon, Minji, Chen, Kerwin, Jagodnik, Kathleen M, Jenkins, Sherry L, Kuleshov, Maxim V, Wojciechowicz, Megan L, Schürer, Stephan C, Medvedovic, Mario, Ma’ayan, Avi

“…Abstract Millions of transcriptome samples were generated by the Library of Integrated Network-based Cellular Signatures (LINCS) program. When these data are…”
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The COVID-19 Drug and Gene Set Library by Kuleshov, Maxim V., Stein, Daniel J., Clarke, Daniel J.B., Kropiwnicki, Eryk, Jagodnik, Kathleen M., Bartal, Alon, Evangelista, John E., Hom, Jason, Cheng, Minxuan, Bailey, Allison, Zhou, Abigail, Ferguson, Laura B., Lachmann, Alexander, Ma'ayan, Avi

“…In a short period, many research publications that report sets of experimentally validated drugs as potential COVID-19 therapies have emerged. To organize this…”
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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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Getting Started with LINCS Datasets and Tools by Xie, Zhuorui, Kropiwnicki, Eryk, Wojciechowicz, Megan L, Jagodnik, Kathleen M, Shu, Ingrid, Bailey, Allison, Clarke, Daniel J B, Jeon, Minji, Evangelista, John Erol, V Kuleshov, Maxim, Lachmann, Alexander, Parigi, Abhijna A, Sanchez, Jose M, Jenkins, Sherry L, Ma'ayan, Avi

“…The Library of Integrated Network-based Cellular Signatures (LINCS) was an NIH Common Fund program that aimed to expand our knowledge about human cellular…”
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Enrichr: a comprehensive gene set enrichment analysis web server 2016 update by Kuleshov, Maxim V, Jones, Matthew R, Rouillard, Andrew D, Fernandez, Nicolas F, Duan, Qiaonan, Wang, Zichen, Koplev, Simon, Jenkins, Sherry L, Jagodnik, Kathleen M, Lachmann, Alexander, McDermott, Michael G, Monteiro, Caroline D, Gundersen, Gregory W, Ma'ayan, Avi

“…Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools…”
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Gene Set Knowledge Discovery with Enrichr by Xie, Zhuorui, Bailey, Allison, Kuleshov, Maxim V, Clarke, Daniel J B, Evangelista, John E, Jenkins, Sherry L, Lachmann, Alexander, Wojciechowicz, Megan L, Kropiwnicki, Eryk, Jagodnik, Kathleen M, Jeon, Minji, Ma'ayan, Avi

“…Profiling samples from patients, tissues, and cells with genomics, transcriptomics, epigenomics, proteomics, and metabolomics ultimately produces lists of…”
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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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lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs by Marino, Giacomo B, Wojciechowicz, Megan L, Clarke, Daniel J B, Kuleshov, Maxim V, Xie, Zhuorui, Jeon, Minji, Lachmann, Alexander, Ma’ayan, Avi

“…Abstract Long non-coding ribonucleic acids (lncRNAs) account for the largest group of non-coding RNAs. However, knowledge about their function and regulation…”
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Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning by Kropiwnicki, Eryk, Evangelista, John E, Stein, Daniel J, Clarke, Daniel J B, Lachmann, Alexander, Kuleshov, Maxim V, Jeon, Minji, Jagodnik, Kathleen M, Ma'ayan, Avi

“…Understanding the underlying molecular and structural similarities between seemingly heterogeneous sets of drugs can aid in identifying drug repurposing…”
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Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses by Torre, Denis, Krawczuk, Patrycja, Jagodnik, Kathleen M., Lachmann, Alexander, Wang, Zichen, Wang, Lily, Kuleshov, Maxim V., Ma’ayan, Avi

“…Biomedical data repositories such as the Gene Expression Omnibus (GEO) enable the search and discovery of relevant biomedical digital data objects. Similarly,…”
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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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Gene and drug landing page aggregator by Clarke, Daniel J B, Kuleshov, Maxim V, Xie, Zhuorui, Evangelista, John E, Meyers, Marilyn R, Kropiwnicki, Eryk, Jenkins, Sherry L, Ma'ayan, Avi

“…Many biological and biomedical researchers commonly search for information about genes and drugs to gather knowledge from these resources. For the most part,…”
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