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132 results on '"Kouril, Michal"'

1. An immunophenotype-coupled transcriptomic atlas of human hematopoietic progenitors

Author

Zhang, Xuan, Song, Baobao, Carlino, Maximillian J., Li, Guangyuan, Ferchen, Kyle, Chen, Mi, Thompson, Evrett N., Kain, Bailee N., Schnell, Dan, Thakkar, Kairavee, Kouril, Michal, Jin, Kang, Hay, Stuart B., Sen, Sidharth, Bernardicius, David, Ma, Siyuan, Bennett, Sierra N., Croteau, Josh, Salvatori, Ornella, Lye, Melvin H., Gillen, Austin E., Jordan, Craig T., Singh, Harinder, Krause, Diane S., Salomonis, Nathan, and Grimes, H. Leighton

Published
2024
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2. Guided construction of single cell reference for human and mouse lung

Author

Guo, Minzhe, Morley, Michael P., Jiang, Cheng, Wu, Yixin, Li, Guangyuan, Du, Yina, Zhao, Shuyang, Wagner, Andrew, Cakar, Adnan Cihan, Kouril, Michal, Jin, Kang, Gaddis, Nathan, Kitzmiller, Joseph A., Stewart, Kathleen, Basil, Maria C., Lin, Susan M., Ying, Yun, Babu, Apoorva, Wikenheiser-Brokamp, Kathryn A., Mun, Kyu Shik, Naren, Anjaparavanda P., Clair, Geremy, Adkins, Joshua N., Pryhuber, Gloria S., Misra, Ravi S., Aronow, Bruce J., Tickle, Timothy L., Salomonis, Nathan, Sun, Xin, Morrisey, Edward E., Whitsett, Jeffrey A., and Xu, Yan

Published
2023
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3. Connecting omics signatures and revealing biological mechanisms with iLINCS

Author

Pilarczyk, Marcin, Fazel-Najafabadi, Mehdi, Kouril, Michal, Shamsaei, Behrouz, Vasiliauskas, Juozas, Niu, Wen, Mahi, Naim, Zhang, Lixia, Clark, Nicholas A., Ren, Yan, White, Shana, Karim, Rashid, Xu, Huan, Biesiada, Jacek, Bennett, Mark F., Davidson, Sarah E., Reichard, John F., Roberts, Kurt, Stathias, Vasileios, Koleti, Amar, Vidovic, Dusica, Clarke, Daniel J. B., Schürer, Stephan C., Ma’ayan, Avi, Meller, Jarek, and Medvedovic, Mario

Published
2022
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6. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

Author

Keenan, Alexandra B, Jenkins, Sherry L, Jagodnik, Kathleen M, Koplev, Simon, He, Edward, Torre, Denis, Wang, Zichen, Dohlman, Anders B, Silverstein, Moshe C, Lachmann, Alexander, Kuleshov, Maxim V, Ma'ayan, Avi, Stathias, Vasileios, Terryn, Raymond, Cooper, Daniel, Forlin, Michele, Koleti, Amar, Vidovic, Dusica, Chung, Caty, Schürer, Stephan C, Vasiliauskas, Jouzas, Pilarczyk, Marcin, Shamsaei, Behrouz, Fazel, Mehdi, Ren, Yan, Niu, Wen, Clark, Nicholas A, White, Shana, Mahi, Naim, Zhang, Lixia, Kouril, Michal, Reichard, John F, Sivaganesan, Siva, Medvedovic, Mario, Meller, Jaroslaw, Koch, Rick J, Birtwistle, Marc R, Iyengar, Ravi, Sobie, Eric A, Azeloglu, Evren U, Kaye, Julia, Osterloh, Jeannette, Haston, Kelly, Kalra, Jaslin, Finkbiener, Steve, Li, Jonathan, Milani, Pamela, Adam, Miriam, Escalante-Chong, Renan, Sachs, Karen, Lenail, Alex, Ramamoorthy, Divya, Fraenkel, Ernest, Daigle, Gavin, Hussain, Uzma, Coye, Alyssa, Rothstein, Jeffrey, Sareen, Dhruv, Ornelas, Loren, Banuelos, Maria, Mandefro, Berhan, Ho, Ritchie, Svendsen, Clive N, Lim, Ryan G, Stocksdale, Jennifer, Casale, Malcolm S, Thompson, Terri G, Wu, Jie, Thompson, Leslie M, Dardov, Victoria, Venkatraman, Vidya, Matlock, Andrea, Van Eyk, Jennifer E, Jaffe, Jacob D, Papanastasiou, Malvina, Subramanian, Aravind, Golub, Todd R, Erickson, Sean D, Fallahi-Sichani, Mohammad, Hafner, Marc, Gray, Nathanael S, Lin, Jia-Ren, Mills, Caitlin E, Muhlich, Jeremy L, Niepel, Mario, Shamu, Caroline E, Williams, Elizabeth H, Wrobel, David, Sorger, Peter K, Heiser, Laura M, Gray, Joe W, Korkola, James E, Mills, Gordon B, LaBarge, Mark, Feiler, Heidi S, Dane, Mark A, Bucher, Elmar, Nederlof, Michel, Sudar, Damir, and Gross, Sean

Subjects
Bioengineering, Cancer, Genetics, Biotechnology, 2.1 Biological and endogenous factors, Aetiology, Generic health relevance, Good Health and Well Being, Cataloging, Computational Biology, Databases, Chemical, Gene Expression Profiling, Gene Library, Humans, Information Storage and Retrieval, National Health Programs, National Institutes of Health (U.S.), Systems Biology, Transcriptome, United States, BD2K, L1000, MCF10A, MEMA, P100, data integration, lincsprogram, lincsproject, systems biology, systems pharmacology, Biochemistry and Cell Biology
Abstract

The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and signatures. By assembling an integrated picture of the range of responses of human cells exposed to many perturbations, the LINCS program aims to better understand human disease and to advance the development of new therapies. Perturbations under study include drugs, genetic perturbations, tissue micro-environments, antibodies, and disease-causing mutations. Responses to perturbations are measured by transcript profiling, mass spectrometry, cell imaging, and biochemical methods, among other assays. The LINCS program focuses on cellular physiology shared among tissues and cell types relevant to an array of diseases, including cancer, heart disease, and neurodegenerative disorders. This Perspective describes LINCS technologies, datasets, tools, and approaches to data accessibility and reusability.

Published
2018

7. LungMAP Portal Ecosystem: Systems-level Exploration of the Lung

Author

Gaddis, Nathan, primary, Fortriede, Joshua, additional, Guo, Minzhe, additional, Bardes, Eric E., additional, Kouril, Michal, additional, Tabar, Scott, additional, Burns, Kevin, additional, Ardini-Poleske, Maryanne E., additional, Loos, Stephanie, additional, Schnell, Daniel, additional, Jin, Kang, additional, Iyer, Balaji, additional, Du, Yina, additional, Huo, Bing-Xing, additional, Bhattacharjee, Anukana, additional, Korte, Jeff, additional, Munshi, Ruchi, additional, Smith, Victoria, additional, Herbst, Andrew, additional, Kitzmiller, Joseph A., additional, Clair, Geremy C., additional, Carson, James P., additional, Adkins, Joshua, additional, Morrisey, Edward E., additional, Pryhuber, Gloria S., additional, Misra, Ravi, additional, Whitsett, Jeffrey A., additional, Sun, Xin, additional, Heathorn, Trevor, additional, Paten, Benedict, additional, Prasath, V. B. Surya, additional, Xu, Yan, additional, Tickle, Tim, additional, Aronow, Bruce J., additional, and Salomonis, Nathan, additional

Published
2024
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21. Dynamic Interoperable Message Passing

Author

Kouril, Michal, Paul, Jerome L., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Di Martino, Beniamino, editor, Kranzlmüller, Dieter, editor, and Dongarra, Jack, editor

Published
2005
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22. Resolution Tunnels for Improved SAT Solver Performance

Author

Kouril, Michal, Franco, John, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Bacchus, Fahiem, editor, and Walsh, Toby, editor

Published
2005
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23. SBSAT: a State-Based, BDD-Based Satisfiability Solver

Author

Franco, John, Kouril, Michal, Schlipf, John, Ward, Jeffrey, Weaver, Sean, Dransfield, Michael, Vanfleet, W. Mark, Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, Giunchiglia, Enrico, editor, and Tacchella, Armando, editor

Published
2004
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25. Guided construction of single cell reference for human and mouse lung

Author

Guo, Minzhe, primary, Morley, Michael P., additional, Wu, Yixin, additional, Du, Yina, additional, Zhao, Shuyang, additional, Wagner, Andrew, additional, Kouril, Michal, additional, Jin, Kang, additional, Gaddis, Nathan, additional, Kitzmiller, Joseph A., additional, Stewart, Kathleen, additional, Basil, Maria C., additional, Lin, Susan M., additional, Ying, Yun, additional, Babu, Apoorva, additional, Wikenheiser-Brokamp, Kathryn A., additional, Mun, Kyu Shik, additional, Naren, Anjaparavanda P., additional, Lin, Sara, additional, Clair, Geremy, additional, Adkins, Joshua N., additional, Pryhuber, Gloria S., additional, Misra, Ravi S., additional, Aronow, Bruce J., additional, Tickle, Timothy L., additional, Salomonis, Nathan, additional, Sun, Xin, additional, Morrisey, Edward E., additional, Whitsett, Jeffrey A., additional, and Xu, Yan, additional

Published
2022
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26. Survey of public domain software for docking simulations and virtual screening

Author

Biesiada Jacek, Porollo Aleksey, Velayutham Prakash, Kouril Michal, and Meller Jaroslaw

Subjects
drug discovery, small molecule docking, virtual screening, docking packages, visualisation of docking poses, oestrogen receptor, oestrogen activity prediction, SAR, Medicine, Genetics, QH426-470
Abstract

Abstract Progress in functional genomics and structural studies on biological macromolecules are generating a growing number of potential targets for therapeutics, adding to the importance of computational approaches for small molecule docking and virtual screening of candidate compounds. In this review, recent improvements in several public domain packages that are widely used in the context of drug development, including DOCK, AutoDock, AutoDock Vina and Screening for Ligands by Induced-fit Docking Efficiently (SLIDE) are surveyed. The authors also survey methods for the analysis and visualisation of docking simulations, as an important step in the overall assessment of the results. In order to illustrate the performance and limitations of current docking programs, the authors used the National Center for Toxicological Research (NCTR) oestrogen receptor benchmark set of 232 oestrogenic compounds with experimentally measured strength of binding to oestrogen receptor alpha. The methods tested here yielded a correlation coefficient of up to 0.6 between the predicted and observed binding affinities for active compounds in this benchmark.

Published
2011
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27. LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung

Author

Gaddis, Nathan, primary, Fortriede, Joshua, additional, Guo, Minzhe, additional, Bardes, Eric E, additional, Kouril, Michal, additional, Tabar, Scott, additional, Burns, Kevin, additional, Ardini-Poleske, Maryanne E, additional, Loos, Stephanie, additional, Schnell, Daniel, additional, Jin, Kang, additional, Iyer, Balaji, additional, Du, Yina, additional, Korte, Jeff, additional, Munshi, Ruchi, additional, Smith, Victoria, additional, Herbst, Andrew, additional, Kitzmiller, Joseph A, additional, Clair, Geremy C, additional, Carson, James, additional, Adkins, Joshua, additional, Morrisey, Edward E, additional, Pryhuber, Gloria S, additional, Misra, Ravi, additional, Whitsett, Jeffrey A, additional, Sun, Xin, additional, Heathorn, Trevor, additional, Paten, Benedict, additional, Prasath, V. B. Surya, additional, Xu, Yan, additional, Tickle, Tim, additional, Aronow, Bruce J, additional, and Salomonis, Nathan, additional

Published
2021
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29. Accelerating Drug Discovery and Repurposing by Combining Transcriptional Signature Connectivity with Docking

Author

Thorman, Alexander W., primary, Reigle, James, additional, Chutipongtanate, Somchai, additional, Shamsaei, Behrouz, additional, Pilarczyk, Marcin, additional, Fazel-Najafabadi, Mehdi, additional, Adamczak, Rafal, additional, Kouril, Michal, additional, Morrow, Ardythe L., additional, Czyzyk-Krzeska, Maria F., additional, McCullumsmith, Robert, additional, Seibel, William, additional, Nassar, Nicolas, additional, Zheng, Yi, additional, Hildeman, David, additional, Herr, Andrew B., additional, Medvedovic, Mario, additional, and Meller, Jarek, additional

Published
2020
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31. piNET: a versatile web platform for downstream analysis and visualization of proteomics data

Author

Shamsaei, Behrouz, primary, Chojnacki, Szymon, primary, Pilarczyk, Marcin, primary, Najafabadi, Mehdi, primary, Niu, Wen, primary, Chen, Chuming, primary, Ross, Karen, primary, Matlock, Andrea, primary, Muhlich, Jeremy, primary, Chutipongtanate, Somchai, primary, Zheng, Jie, primary, Turner, John, primary, Vidović, Dušica, primary, Jaffe, Jake, primary, MacCoss, Michael, primary, Wu, Cathy, primary, Pillai, Ajay, primary, Ma’ayan, Avi, primary, Schürer, Stephan, primary, Kouril, Michal, primary, Medvedovic, Mario, primary, and Meller, Jarek, primary

Published
2020
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32. Connectivity Enhanced Structure Activity Relationship (ceSAR): A Novel Approach to Increase Accuracy and Speed of Virtual Drug Discovery

Author

Thorman, Alexander William, primary, Reigle, James, additional, Chutipongtanate, Somchai, additional, Shamsaei, Behrouz, additional, Pilarczyk, Marcin, additional, Fazel-Najafabadi, Mehdi, additional, Adamczak, Rafal, additional, Kouril, Michal, additional, Medvedovic, Mario, additional, and Meller, Jarek, additional

Published
2020
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33. The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system

Author

Mandl, Kenneth D., primary, Glauser, Tracy, additional, Krantz, Ian D., additional, Avillach, Paul, additional, Bartels, Anna, additional, Beggs, Alan H., additional, Biswas, Sawona, additional, Bourgeois, Florence T., additional, Corsmo, Jeremy, additional, Dauber, Andrew, additional, Devkota, Batsal, additional, Fleisher, Gary R., additional, Heath, Allison P., additional, Helbig, Ingo, additional, Hirschhorn, Joel N., additional, Kilbourn, Judson, additional, Kong, Sek Won, additional, Kornetsky, Susan, additional, Majzoub, Joseph A., additional, Marsolo, Keith, additional, Martin, Lisa J., additional, Nix, Jeremy, additional, Schwarzhoff, Amy, additional, Stedman, Jason, additional, Strauss, Arnold, additional, Sund, Kristen L., additional, Taylor, Deanne M., additional, White, Peter S., additional, Marsh, Eric, additional, Grimberg, Adda, additional, Hawkes, Colin, additional, Barkman, Darlene, additional, Borglund, Erin M., additional, Chakrabarty, Ramkrishna, additional, Chandel, Alka, additional, Degala, Anil Kumar, additional, DeSain, Thomas, additional, Dexheimer, Philip, additional, Divekar, Parth, additional, Ellis, Alyssa, additional, Furgason, Mike, additional, Geehan, Christopher, additional, Guidetti, Andrew Joseph, additional, Gutierrez, Alba, additional, Hallinan, Barbara, additional, Harper, Becca, additional, Jalali, Niloofar, additional, Khanna, Jaspreet, additional, Kirby, Christopher, additional, Korodi, Gabor, additional, Kouril, Michal, additional, Kratchman, Amy, additional, Kumar, Ranjay, additional, Labilloy, Guillaume, additional, Lee, In-Hee, additional, Morgan, Bria, additional, Morgan, James, additional, Muglia, Louis J, additional, Nikitin, Aleksandr, additional, Pistone, Mike, additional, Poduri, Anna, additional, Rupert, Andrew, additional, Safier, Kristen, additional, Sliz, Piotr, additional, Stevenson, Gelvina, additional, Geme, Joseph St., additional, Thaker, Vidhu, additional, Temporal, Simone, additional, Velayutham, Prakash, additional, Wijesooriya, Julie, additional, Wolf, Bryan, additional, Wooten, Andrew, additional, Yen, Alan, additional, and Zhang, Yu, additional

Published
2020
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37. Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS

Author

Pilarczyk, Marcin, primary, Kouril, Michal, additional, Shamsaei, Behrouz, additional, Vasiliauskas, Juozas, additional, Niu, Wen, additional, Mahi, Naim, additional, Zhang, Lixia, additional, Clark, Nicholas, additional, Ren, Yan, additional, White, Shana, additional, Karim, Rashid, additional, Xu, Huan, additional, Biesiada, Jacek, additional, Bennett, Mark F., additional, Davidson, Sarah, additional, Reichard, John F, additional, Roberts, Kurt, additional, Stathias, Vasileios, additional, Koleti, Amar, additional, Vidovic, Dusica, additional, Clarke, Daniel J.B., additional, Schurer, Stephan C., additional, Ma’ayan, Avi, additional, Meller, Jarek, additional, and Medvedovic, Mario, additional

Published
2019
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39. Project moved! Now at https://osf.io/hgy3z

Author

Chakroff, Alek, Isenberg , Naomi, Aguilar, Stephen, Labouff, Jordan, Kouril, Michal, Pullig, Chris, Pogacar, Ruth, Carpenter, Thomas, Aguilar , Stephen, and Carpenter , Thomas

Subjects
PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Intragroup Processes, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Social Cognition, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Politics, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Personality and Creativity, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Individual Differences, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Nonverbal Behavior, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Theories of Personality, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Interventions, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Narrative Research, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Diversity, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Genetic factors, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Moral Behavior, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Interpersonal Relationships, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Personality and Situations, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Personality Processes, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Impression Formation, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Testing and Assessment, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Violence and Aggression, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Disability, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Self-regulation, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Achievement and Status, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Motivational Behavior, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Prejudice and Discrimination, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Prosocial Behavior, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Well-being, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Social Influence, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Affect and Emotion Regulation, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Self-esteem, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Social Well-being, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Intergroup Processes, PsyArXiv|Social and Behavioral Sciences, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Sexuality, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Cultural Differences, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Trait Theory, bepress|Social and Behavioral Sciences, bepress|Social and Behavioral Sciences|Psychology|Social Psychology, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Self and Social Identity, bepress|Social and Behavioral Sciences|Psychology|Personality and Social Contexts, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Religion and Spirituality, PsyArXiv|Social and Behavioral Sciences|Social and Personality Psychology|Attitudes and Persuasion
Abstract

Due to an error with the Open Science Framework, this preprint was unavailable for several months. A new one was created and now exists at OSF: https://osf.io/ntd97/ with a direct link to the preprint at https://psyarxiv.com/hgy3z/.We were surprised to see that this preprint is suddenly available again. Because work is now established (with two new studies and a major rework) at the new location, please direct all citations for iatgen or survey-based IATs to the above locations.

Published
2017
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41. Conducting IAT Research within Online Surveys: A Procedure, Validation, and Open Source Tool

Author

Carpenter, Thomas, Pogacar, Ruth, Pullig, Chris, Kouril, Michal, LaBouff, Jordan, Aguilar, Stephen, Isenberg, Naomi, and Chakroff, Alek

Subjects
FOS: Psychology, Social Psychology, Psychology, Social and Behavioral Sciences
Abstract

The past decade has seen the widespread proliferation of online research, both among undergraduate and community (i.e., MTurk) populations. Given this reality, researchers may wish to include the Implicit Association Test (IAT) in online surveys. However, to date, few options exist, and existing options are cumbersome. We consider whether it is possible to validly conduct IAT research using standard survey software. We propose that online survey tools can be a valid vehicle for the IAT, and we outline the necessary approach and specific considerations that should be followed for building a survey-based IAT. We then propose a specific method for conducting IATs via online surveys and test the validity of this method across studies. We also provide an open-source software tool (and R package) that automates the entire described procedure, allowing researchers to rapidly build and score IATs using our procedure. Across studies, the survey-based IAT performed comparably to commercially available software and yielded results that align well with published IAT findings. The present procedure thus increases the accessibility of the IAT, removes the need for special software, reduces cost and difficulty of conducting IAT research, and opens doors to larger-n online IAT research. Implications for the future of IAT research are discussed.

Published
2017
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45. GRcalculator: an online tool for calculating and mining drug response data

Author

Clark, Nicholas, Hafner, Marc, Kouril, Michal, Muhlich, Jeremy, Niepel, Mario, Williams, Elizabeth, Sorger, Peter, and Medvedovic, Mario

Subjects
ComputingMethodologies_PATTERNRECOGNITION
Abstract

Large-scale dose-response data and genomic datasets can be combined to discover novel drug-response biomarkers. There exist numerous online datasets of drug-response assays, but they are currently poorly accessible and their potential as a big data resource is limited due to lack of access and connection. Furthermore, it has recently been found that drug-response data often vary from one study to the next. A major reason for this variance is that traditional metrics of drug sensitivity such as IC50, Emax, and AUC values are confounded by the number of cell divisions taking place over the course of an assay. To solve this problem, we have developed GRcalculator, a suite of online tools found at www.grcalculator.org. The tools use GR metrics (proposed recently by Hafner et al. in Nature), a set of alterative drug-response metrics based on growth rate inhibition that are robust to differences in nominal division rate and assay duration. GRcalculator is a powerful, user-friendly and free tool for mining drug-response data using GR metrics. These metrics harmonize drug-response data, improving the discovery of novel drug-response biomarkers using big data as well as allowing for comparisons with patient-derived tumor cells that are generally slow growing. Direct access to LINCS drug-response datasets and, in the future, other public domain datasets is a unique functionality that will facilitate re-use of the valuable resources that these data represent. As well as mining datasets, the tool also offers calculation and visualization of GR metrics (and traditional metrics), generates publication-ready figures, and provides a unified platform for researchers analyzing drug sensitivity. For offline calculation and analysis, we have developed the GRmetrics R package (available via Bioconductor), which allows for use of larger datasets and inclusion of GR metrics calculations within existing R analysis pipelines.

Published
2016
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50. Building Gold Standard Corpora for Medical Natural Language Processing Tasks

Author

Deleger, Louise, Li, Qi, Lingren, Todd, Kaiser, Megan, Molnar, Katalin, Stoutenborough, Laura, Kouril, Michal, Marsolo, Keith, and Solti, Imre

Subjects
Clinical Trials as Topic, United States Food and Drug Administration, Articles, Medical Records, Software, United States, Drug Labeling, Natural Language Processing
Abstract

We present the construction of three annotated corpora to serve as gold standards for medical natural language processing (NLP) tasks. Clinical notes from the medical record, clinical trial announcements, and FDA drug labels are annotated. We report high inter-annotator agreements (overall F-measures between 0.8467 and 0.9176) for the annotation of Personal Health Information (PHI) elements for a de-identification task and of medications, diseases/disorders, and signs/symptoms for information extraction (IE) task. The annotated corpora of clinical trials and FDA labels will be publicly released and to facilitate translational NLP tasks that require cross-corpora interoperability (e.g. clinical trial eligibility screening) their annotation schemas are aligned with a large scale, NIH-funded clinical text annotation project.

Published
2012

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