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19 results on '"Mehta, Subina P."'

3. Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome

Author

Edwinson, Adam L., Yang, Lu, Peters, Stephanie, Hanning, Nikita, Jeraldo, Patricio, Jagtap, Pratik, Simpson, Joshua B., Yang, Tzu-Yi, Kumar, Praveen, Mehta, Subina, Nair, Asha, Breen-Lyles, Margaret, Chikkamenahalli, Lakshmikanth, Graham, Rondell P., De Winter, Benedicte, Patel, Robin, Dasari, Surendra, Kashyap, Purna, Griffin, Timothy, Chen, Jun, Farrugia, Gianrico, Redinbo, Matthew R., and Grover, Madhusudan

Published
2022
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5. Quantitative Metaproteomics in Microbiomes of Diverse Complexity via Data-dependent and Data-independent Acquisition Mass Spectrometry

Author

Mehta, Subina P and Pratik Jagtap

Abstract

While many taxonomic members of microbiomes are mostly known, there are still some undetected taxa.Functional unknowns: Almost 40% of genes are without a match in functional databases. There is a need for the quantitation of taxonomy and functions expressed by the microbiome. With the metaproteomics datasets we have analyzed here, DIA analysis provides a deeper quantitative insight into the taxonomy and functional features of the microbiome. The DIA approach is reproducible with fewer missing values as compared to the DDA approach. However, there is a need to assess the accuracy of DIA estimations in the context of metaproteomics studies by using benchmarked datasets (such as with known amounts of taxonomy and functions).

Published
2023
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7. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses:2022 update

Author

Afgan, Enis, Nekrutenko, Anton, Grüning, Bjórn A., Blankenberg, Daniel, Goecks, Jeremy, Schatz, Michael C., Ostrovsky, Alexander E., Mahmoud, Alexandru, Lonie, Andrew J., Syme, Anna, Fouilloux, Anne, Bretaudeau, Anthony, Kumar, Anup, Eschenlauer, Arthur C., Desanto, Assunta D., Guerler, Aysam, Serrano-Solano, Beatriz, Batut, Bérénice, Grüning, Björn A., Langhorst, Bradley W., Carr, Bridget, Raubenolt, Bryan A., Hyde, Cameron J., Bromhead, Catherine J., Barnett, Christopher B., Royaux, Coline, Gallardo, Cristóbal, Fornika, Daniel J., Baker, Dannon, Bouvier, Dave, Clements, Dave, De Lima Morais, David A., Tabernero, D. L., Lariviere, Delphine, Nasr, Engy, Zambelli, Federico, Heyl, Florian, Psomopoulos, Fotis, Coppens, Frederik, Price, Gareth R., Cuccuru, Gianmauro, Corguillé, Gildas Le, Von Kuster, Greg, Akbulut, Gulsum Gudukbay, Rasche, Helena, Hans-Rudolf, Hotz, Eguinoa, Ignacio, Makunin, Igor, Ranawaka, Isuru J., Taylor, James P., Joshi, Jayadev, Hillman-Jackson, Jennifer, Chilton, John M., Kamali, Kaivan, Suderman, Keith, Poterlowicz, Krzysztof, Yvan, Le Bras, Lopez-Delisle, Lucille, Sargent, Luke, Bassetti, Madeline E., Tangaro, Marco Antonio, Van Den Beek, Marius, Cech, Martin, Bernt, Matthias, Fahrner, Matthias, Tekman, Mehmet, Föll, Melanie C., Crusoe, Michael R., Roncoroni, Miguel, Kucher, Natalie, Coraor, Nate, Stoler, Nicholas, Rhodes, Nick, Soranzo, Nicola, Pinter, Niko, Goonasekera, Nuwan A., Moreno, Pablo A., Videm, Pavankumar, Melanie, Petera, Mandreoli, Pietro, Jagtap, Pratik D., Gu, Qiang, Weber, Ralf J.M., Lazarus, Ross, Vorderman, Ruben H.P., Hiltemann, Saskia, Golitsynskiy, Sergey, Garg, Shilpa, Bray, Simon A., Gladman, Simon L., Leo, Simone, Mehta, Subina P., Griffin, Timothy J., Jalili, Vahid, Yves, Vandenbrouck, Wen, Victor, Nagampalli, Vijay K., Bacon, Wendi A., De Koning, Willem, Maier, Wolfgang, Briggs, Peter J., Afgan, Enis, Nekrutenko, Anton, Grüning, Bjórn A., Blankenberg, Daniel, Goecks, Jeremy, Schatz, Michael C., Ostrovsky, Alexander E., Mahmoud, Alexandru, Lonie, Andrew J., Syme, Anna, Fouilloux, Anne, Bretaudeau, Anthony, Kumar, Anup, Eschenlauer, Arthur C., Desanto, Assunta D., Guerler, Aysam, Serrano-Solano, Beatriz, Batut, Bérénice, Grüning, Björn A., Langhorst, Bradley W., Carr, Bridget, Raubenolt, Bryan A., Hyde, Cameron J., Bromhead, Catherine J., Barnett, Christopher B., Royaux, Coline, Gallardo, Cristóbal, Fornika, Daniel J., Baker, Dannon, Bouvier, Dave, Clements, Dave, De Lima Morais, David A., Tabernero, D. L., Lariviere, Delphine, Nasr, Engy, Zambelli, Federico, Heyl, Florian, Psomopoulos, Fotis, Coppens, Frederik, Price, Gareth R., Cuccuru, Gianmauro, Corguillé, Gildas Le, Von Kuster, Greg, Akbulut, Gulsum Gudukbay, Rasche, Helena, Hans-Rudolf, Hotz, Eguinoa, Ignacio, Makunin, Igor, Ranawaka, Isuru J., Taylor, James P., Joshi, Jayadev, Hillman-Jackson, Jennifer, Chilton, John M., Kamali, Kaivan, Suderman, Keith, Poterlowicz, Krzysztof, Yvan, Le Bras, Lopez-Delisle, Lucille, Sargent, Luke, Bassetti, Madeline E., Tangaro, Marco Antonio, Van Den Beek, Marius, Cech, Martin, Bernt, Matthias, Fahrner, Matthias, Tekman, Mehmet, Föll, Melanie C., Crusoe, Michael R., Roncoroni, Miguel, Kucher, Natalie, Coraor, Nate, Stoler, Nicholas, Rhodes, Nick, Soranzo, Nicola, Pinter, Niko, Goonasekera, Nuwan A., Moreno, Pablo A., Videm, Pavankumar, Melanie, Petera, Mandreoli, Pietro, Jagtap, Pratik D., Gu, Qiang, Weber, Ralf J.M., Lazarus, Ross, Vorderman, Ruben H.P., Hiltemann, Saskia, Golitsynskiy, Sergey, Garg, Shilpa, Bray, Simon A., Gladman, Simon L., Leo, Simone, Mehta, Subina P., Griffin, Timothy J., Jalili, Vahid, Yves, Vandenbrouck, Wen, Victor, Nagampalli, Vijay K., Bacon, Wendi A., De Koning, Willem, Maier, Wolfgang, and Briggs, Peter J.

Abstract

Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations., Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.

Published
2022

16. metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes*

Author

Easterly, Caleb W., Sajulga, Ray, Mehta, Subina, Johnson, James, Kumar, Praveen, Hubler, Shane, Mesuere, Bart, Rudney, Joel, Griffin, Timothy J., and Jagtap, Pratik D.

Abstract

metaQuantome enables quantitative analysis of the taxonomic and functional state of a microbiome. Leveraging quantitative mass spectrometry data generated from metaproteomic samples along with taxonomic and functional annotations, metaQuantome unravels the complex and hierarchical data structure of taxonomic and functional ontologies. As a result, metaQuantome enables data exploration, tests hypotheses, and generates high-quality visualizations. metaQuantome deciphers the contribution of taxa to a functional process and vice versa. Its accessibility will pave the way for advanced multi-omic analysis of diverse microbiomes.

Published
2019
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17. QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics

Author

Kumar, Praveen, Panigrahi, Priyabrata, Johnson, James, Weber, Wanda J., Mehta, Subina, Sajulga, Ray, Easterly, Caleb, Crooker, Brian A., Heydarian, Mohammad, Anamika, Krishanpal, Griffin, Timothy J., and Jagtap, Pratik D.

Abstract

Next-generation sequencing technologies, coupled to advances in mass-spectrometry-based proteomics, have facilitated system-wide quantitative profiling of expressed mRNA transcripts and proteins. Proteo-transcriptomic analysis compares the relative abundance levels of transcripts and their corresponding proteins, illuminating discordant gene product responses to perturbations. These results reveal potential post-transcriptional regulation, providing researchers with important new insights into underlying biological and pathological disease mechanisms. To carry out proteo-transcriptomic analysis, researchers require software that statistically determines transcript–protein abundance correlation levels and provides results visualization and interpretation functionality, ideally within a flexible, user-friendly platform. As a solution, we have developed the QuanTP software within the Galaxy platform. The software offers a suite of tools and functionalities critical for proteo-transcriptomics, including statistical algorithms for assessing the correlation between single transcript–protein pairs as well as across two cohorts, outlier identification and clustering, along with a diverse set of results visualizations. It is compatible with analyses of results from single experiment data or from a two-cohort comparison of aggregated replicate experiments. The tool is available in the Galaxy Tool Shed through a cloud-based instance and a Docker container. In all, QuanTP provides an accessible and effective software resource, which should enable new multiomic discoveries from quantitative proteo-transcriptomic data sets.

Published
2018
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18. Update on the moFF Algorithm for Label-Free Quantitative Proteomics

Author

Argentini, Andrea, Staes, An, Grüning, Björn, Mehta, Subina, Easterly, Caleb, Griffin, Timothy J., Jagtap, Pratik, Impens, Francis, and Martens, Lennart

Abstract

moFF is a modular and operating-system-independent tool for quantitative analysis of label-free mass-spectrometry-based proteomics data. The moFF workflow, comprising matching-between-runs and apex quantification, can be applied to any upstream search engine’s output, along with the corresponding Thermo or mzML raw file. We here present moFF 2.0, with improvements in speed through multithreading, the use of a new raw file access library, and a novel filtering approach in the matching-between-runs module. This filter allows moFF to correctly identify features that are present in one run but not in another, as demonstrated using spiked-in iRT peptides. Moreover, moFF 2.0 also provides a new peptide summary export that can be used in downstream statistical analysis. moFF is open source and freely available and can be downloaded from https://github.com/compomics/moFF

Published
2018
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19. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Author

Ostrovsky, Alexander E., Mahmoud, Alexandru, Lonie, Andrew J., Syme, Anna, Fouilloux, Anne, Bretaudeau, Anthony, Nekrutenko, Anton, Kumar, Anup, Eschenlauer, Arthur C., DeSanto, Assunta D., Guerler, Aysam, Serrano-Solano, Beatriz, Batut, Berenice, Gruening, Bjoern A., Langhorst, Bradley W., Carr, Bridget, Raubenolt, Bryan A., Hyde, Cameron J., Bromhead, Catherine J., Barnett, Christopher B., Royaux, Coline, Gallardo, Cristobal, Blankenberg, Daniel, Fornika, Daniel J., Baker, Dannon, Bouvier, Dave, Clements, Dave, Morais, David A. de Lima, Tabernero, David Lopez, Lariviere, Delphine, Nasr, Engy, Afgan, Enis, Zambelli, Federico, Heyl, Florian, Psomopoulos, Fotis, Coppens, Frederik, Price, Gareth R., Cuccuru, Gianmauro, Le Corguille, Gildas, Von Kuster, Greg, Akbulut, Gulsum Gudukbay, Rasche, Helena, Hans-Rudolf, Hotz, Eguinoa, Ignacio, Makunin, Igor, Ranawaka, Isuru J., Taylor, James P., Joshi, Jayadev, Hillman-Jackson, Jennifer, Goecks, Jeremy, Chilton, John M., Kamali, Kaivan, Suderman, Keith, Poterlowicz, Krzysztof, Yvan, Le Bras, Lopez-Delisle, Lucille, Sargent, Luke, Bassetti, Madeline E., Tangaro, Marco Antonio, van den Beek, Marius, Cech, Martin, Bernt, Matthias, Fahrner, Matthias, Tekman, Mehmet, Foell, Melanie C., Schatz, Michael C., Crusoe, Michael R., Roncoroni, Miguel, Kucher, Natalie, Coraor, Nate, Stoler, Nicholas, Rhodes, Nick, Soranzo, Nicola, Pinter, Niko, Goonasekera, Nuwan A., Moreno, Pablo A., Videm, Pavankumar, Melanie, Petera, Mandreoli, Pietro, Jagtap, Pratik D., Gu, Qiang, Weber, Ralf J. M., Lazarus, Ross, Vorderman, Ruben H. P., Hiltemann, Saskia, Golitsynskiy, Sergey, Garg, Shilpa, Bray, Simon A., Gladman, Simon L., Leo, Simone, Mehta, Subina P., Griffin, Timothy J., Jalili, Vahid, Yves, Vandenbrouck, Wen, Victor, Nagampalli, Vijay K., Bacon, Wendi A., de Koning, Willem, Maier, Wolfgang, and Briggs, Peter J.

Abstract

Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.

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