Search Results - "Tripodi, Ignacio J."

Detecting Differential Transcription Factor Activity from ATAC-Seq Data by Tripodi, Ignacio J, Allen, Mary A, Dowell, Robin D

“…Transcription factors are managers of the cellular factory, and key components to many diseases. Many non-coding single nucleotide polymorphisms affect…”
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Combining signal and sequence to detect RNA polymerase initiation in ATAC-seq data by Tripodi, Ignacio J, Chowdhury, Murad, Gruca, Margaret, Dowell, Robin D

“…The assay for transposase-accessible chromatin followed by sequencing (ATAC-seq) is an inexpensive protocol for measuring open chromatin regions. ATAC-seq is…”
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A Tissue-Specific and Toxicology-Focused Knowledge Graph by Tripodi, Ignacio J., Schmidt, Lena, Howard, Brian E., Mav, Deepak, Shah, Ruchir

“…Molecular biology-focused knowledge graphs (KGs) are directed graphs that integrate information from heterogeneous sources of biological and biomedical data,…”
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An open source knowledge graph ecosystem for the life sciences by Callahan, Tiffany J., Tripodi, Ignacio J., Stefanski, Adrianne L., Cappelletti, Luca, Taneja, Sanya B., Wyrwa, Jordan M., Casiraghi, Elena, Matentzoglu, Nicolas A., Reese, Justin, Silverstein, Jonathan C., Hoyt, Charles Tapley, Boyce, Richard D., Malec, Scott A., Unni, Deepak R., Joachimiak, Marcin P., Robinson, Peter N., Mungall, Christopher J., Cavalleri, Emanuele, Fontana, Tommaso, Valentini, Giorgio, Mesiti, Marco, Gillenwater, Lucas A., Santangelo, Brook, Vasilevsky, Nicole A., Hoehndorf, Robert, Bennett, Tellen D., Ryan, Patrick B., Hripcsak, George, Kahn, Michael G., Bada, Michael, Baumgartner, William A., Hunter, Lawrence E.

“…Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the…”
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Knowledge-Based Biomedical Data Science by Callahan, Tiffany J, Tripodi, Ignacio J, Pielke-Lombardo, Harrison, Hunter, Lawrence E

“…Knowledge-based biomedical data science involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems…”
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Applying knowledge-driven mechanistic inference to toxicogenomics by Tripodi, Ignacio J., Callahan, Tiffany J., Westfall, Jessica T., Meitzer, Nayland S., Dowell, Robin D., Hunter, Lawrence E.

“…When considering toxic chemicals in the environment, a mechanistic, causal explanation of toxicity may be preferred over a statistical or machine…”
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Proceedings of a workshop to address animal methods bias in scientific publishing by Krebs, Catharine E, Camp, Celean, Constantino, Helder, Courtot, Lilas, Kavanagh, Owen, Leite, Sofia Batista, Madden, Judith, Paini, Alicia, Poojary, Brinda, Tripodi, Ignacio J, Trunnell, Emily R

“…Animal methods bias in scientific publishing is a newly defined type of publishing bias describing a preference for animal-based methods where they may not be…”
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Planned Suicide Methods in Crisis Conversations: Effects of Age and Gender by Tripodi, Ignacio J., Buda, Greg, Török, Lili, Meagher, Margaret, Olson, Elizabeth A.

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Setting the rhythm scene: deep learning-based drum loop generation from arbitrary language cues by Tripodi, Ignacio J

“…Generative artificial intelligence models can be a valuable aid to music composition and live performance, both to aid the professional musician and to help…”
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Knowledge-based Biomedical Data Science 2019 by Callahan, Tiffany J, Pielke-Lombardo, Harrison, Tripodi, Ignacio J, Hunter, Lawrence E

“…Annual Review of Biomedical Data Science. 2020 Jul 20;3:23-41 Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer…”
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An Open-Source Knowledge Graph Ecosystem for the Life Sciences by Callahan, Tiffany J, Tripodi, Ignacio J, Stefanski, Adrianne L, Cappelletti, Luca, Taneja, Sanya B, Wyrwa, Jordan M, Casiraghi, Elena, Matentzoglu, Nicolas A, Reese, Justin, Silverstein, Jonathan C, Hoyt, Charles Tapley, Boyce, Richard D, Malec, Scott A, Unni, Deepak R, Joachimiak, Marcin P, Robinson, Peter N, Mungall, Christopher J, Cavalleri, Emanuele, Fontana, Tommaso, Valentini, Giorgio, Mesiti, Marco, Gillenwater, Lucas A, Santangelo, Brook, Vasilevsky, Nicole A, Hoehndorf, Robert, Bennett, Tellen D, Ryan, Patrick B, Hripcsak, George, Kahn, Michael G, Bada, Michael, BaumgartnerJr, William A, Hunter, Lawrence E

“…Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the…”
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Hypernetwork Science: From Multidimensional Networks to Computational Topology by Joslyn, Cliff A, Aksoy, Sinan, Callahan, Tiffany J, Hunter, Lawrence E, Jefferson, Brett, Praggastis, Brenda, Purvine, Emilie A. H, Tripodi, Ignacio J

“…As data structures and mathematical objects used for complex systems modeling, hypergraphs sit nicely poised between on the one hand the world of network…”
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