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7 results on '"Weging, Silvio [0000-0002-8484-4352]"'

1. Enhancing European capabilities for application of multi-omics studies in biology and biomedicine space research

Author

European Space Agency, NASA Astrobiology Institute (US), University of Nottingham, Medical Research Council (UK), Comunidad de Madrid, Manzano, Aranzazu [0000-0002-0150-0803], Weging, Silvio [0000-0002-8484-4352], Bezdan, Daniela [0000-0002-1203-8239], Cahill, Thomas [0000-0003-3607-6069], Carnero-Díaz, Eugénie [0000-0002-3771-3106], Cope, Henry [0000-0002-4984-0567], Deane, Colleen S. [0000-0002-2281-6479], Etheridge,Timothy [0000-0002-3588-8711], Giacomello, Stefania [0000-0003-0738-1574], Hardiman, Gary [0000-0003-4558-0400], Leys, Natalie [0000-0002-4556-5211], Madrigal, Pedro [0000-0003-1959-8199], Mastroleo, Felice [0000-0002-9815-8038], Medina, F. Javier [0000-0002-0866-7710], Mieczkowski, Jakub [0000-0002-2091-012X], Fernández-Rojo, Manuel A. [0000-0002-2240-1951], Siew, Keith [0000-0002-6502-5095], Szewczyk, Nathaniel [0000-0003-4425-9746], Walsh, Stephen B. [0000-0002-8693-1353], Da Silveira, William A. [0000-0001-6370-2884], Herranz, Raúl [0000-0002-0246-9449], Manzano, Aranzazu, Weging, Silvio, Bezdan, Daniela, Borg, Joseph, Cahill, Thomas, Carnero-Díaz, Eugénie, Cope, Henry, Deane, Colleen S., Etheridge,Timothy, Giacomello, Stefania, Hardiman, Gary, Leys, Natalie, Madrigal, Pedro, Mastroleo, Felice, Medina, F. Javier, Mieczkowski, Jakub, Fernández-Rojo, Manuel A., Siew, Keith, Szewczyk, Nathaniel, Walsh, Stephen B., Da Silveira, William A., Herranz, Raúl, European Space Agency, NASA Astrobiology Institute (US), University of Nottingham, Medical Research Council (UK), Comunidad de Madrid, Manzano, Aranzazu [0000-0002-0150-0803], Weging, Silvio [0000-0002-8484-4352], Bezdan, Daniela [0000-0002-1203-8239], Cahill, Thomas [0000-0003-3607-6069], Carnero-Díaz, Eugénie [0000-0002-3771-3106], Cope, Henry [0000-0002-4984-0567], Deane, Colleen S. [0000-0002-2281-6479], Etheridge,Timothy [0000-0002-3588-8711], Giacomello, Stefania [0000-0003-0738-1574], Hardiman, Gary [0000-0003-4558-0400], Leys, Natalie [0000-0002-4556-5211], Madrigal, Pedro [0000-0003-1959-8199], Mastroleo, Felice [0000-0002-9815-8038], Medina, F. Javier [0000-0002-0866-7710], Mieczkowski, Jakub [0000-0002-2091-012X], Fernández-Rojo, Manuel A. [0000-0002-2240-1951], Siew, Keith [0000-0002-6502-5095], Szewczyk, Nathaniel [0000-0003-4425-9746], Walsh, Stephen B. [0000-0002-8693-1353], Da Silveira, William A. [0000-0001-6370-2884], Herranz, Raúl [0000-0002-0246-9449], Manzano, Aranzazu, Weging, Silvio, Bezdan, Daniela, Borg, Joseph, Cahill, Thomas, Carnero-Díaz, Eugénie, Cope, Henry, Deane, Colleen S., Etheridge,Timothy, Giacomello, Stefania, Hardiman, Gary, Leys, Natalie, Madrigal, Pedro, Mastroleo, Felice, Medina, F. Javier, Mieczkowski, Jakub, Fernández-Rojo, Manuel A., Siew, Keith, Szewczyk, Nathaniel, Walsh, Stephen B., Da Silveira, William A., and Herranz, Raúl

Abstract

Following on from the NASA twins’ study there has been a tremendous interest in the use of omics techniques in spaceflight. The individual space agency’s, NASA’s GeneLab, JAXA´s ibSLS and ESA-funded Space Omics Topical Team and the International Standards for Space Omics Processing (ISSOP) group have established several initiatives to support this growth. Here, we present recommendations from the Space Omics Topical Team to promote standard application of space omics in Europe. We focus on four main themes: i) continued participation in and co-ordination with international omics endeavours; ii) strengthening of the European space omics infrastructure including workforce and facilities; iii) capitalizing on the emerging opportunities in the commercial space sector, and iv) capitalizing on the emerging opportunities in human subjects research.

Published
2023

2. Space omics research in Europe: contributions, geographical distribution and ESA member state funding schemes

Author

European Space Agency, National Aeronautics and Space Administration (US), Medical Research Council (UK), Comunidad de Madrid, Ministerio de Ciencia e Innovación (España), Swedish Research Council, Centre National D'Etudes Spatiales (France), Wellcome Trust, Deane, Colleen S. [0000-0002-2281-6479], Carnero-Díaz, Eugénie [0000-0002-3771-3106], Etheridge,Timothy [0000-0002-3588-8711], Hardiman, Gary [0000-0003-4558-0400], Leys, Natalie [0000-0002-4556-5211], Madrigal, Pedro [0000-0003-1959-8199], Manzano, Aranzazu [0000-0002-0150-0803], Mastroleo, Felice [0000-0002-9815-8038], Medina, F. Javier [0000-0002-0866-7710], Fernández-Rojo, Manuel A. [0000-0002-2240-1951], Siew, Keith [0000-0002-6502-5095], Szewczyk, Nathaniel [0000-0003-4425-9746], Villacampa, Alicia [0000-0002-7398-8545], Walsh, Stephen B. [0000-0002-8693-1353], Weging, Silvio [0000-0002-8484-4352], Bezdan, Daniela [0000-0002-1203-8239], Giacomello, Stefania [0000-0003-0738-1574], Da Silveira, William A. [0000-0001-6370-2884], Herranz, Raúl [0000-0002-0246-9449], Deane, Colleen S., Borg, Joseph, Cahill, Thomas, Carnero-Díaz, Eugénie, Etheridge,Timothy, Hardiman, Gary, Leys, Natalie, Madrigal, Pedro, Manzano, Aranzazu, Mastroleo, Felice, Medina, F. Javier, Fernández-Rojo, Manuel A., Siew, Keith, Szewczyk, Nathaniel, Villacampa, Alicia, Walsh, Stephen B., Weging, Silvio, Bezdan, Daniela, Giacomello, Stefania, Da Silveira, William A., Herranz, Raúl, European Space Agency, National Aeronautics and Space Administration (US), Medical Research Council (UK), Comunidad de Madrid, Ministerio de Ciencia e Innovación (España), Swedish Research Council, Centre National D'Etudes Spatiales (France), Wellcome Trust, Deane, Colleen S. [0000-0002-2281-6479], Carnero-Díaz, Eugénie [0000-0002-3771-3106], Etheridge,Timothy [0000-0002-3588-8711], Hardiman, Gary [0000-0003-4558-0400], Leys, Natalie [0000-0002-4556-5211], Madrigal, Pedro [0000-0003-1959-8199], Manzano, Aranzazu [0000-0002-0150-0803], Mastroleo, Felice [0000-0002-9815-8038], Medina, F. Javier [0000-0002-0866-7710], Fernández-Rojo, Manuel A. [0000-0002-2240-1951], Siew, Keith [0000-0002-6502-5095], Szewczyk, Nathaniel [0000-0003-4425-9746], Villacampa, Alicia [0000-0002-7398-8545], Walsh, Stephen B. [0000-0002-8693-1353], Weging, Silvio [0000-0002-8484-4352], Bezdan, Daniela [0000-0002-1203-8239], Giacomello, Stefania [0000-0003-0738-1574], Da Silveira, William A. [0000-0001-6370-2884], Herranz, Raúl [0000-0002-0246-9449], Deane, Colleen S., Borg, Joseph, Cahill, Thomas, Carnero-Díaz, Eugénie, Etheridge,Timothy, Hardiman, Gary, Leys, Natalie, Madrigal, Pedro, Manzano, Aranzazu, Mastroleo, Felice, Medina, F. Javier, Fernández-Rojo, Manuel A., Siew, Keith, Szewczyk, Nathaniel, Villacampa, Alicia, Walsh, Stephen B., Weging, Silvio, Bezdan, Daniela, Giacomello, Stefania, Da Silveira, William A., and Herranz, Raúl

Abstract

The European research community, via European Space Agency (ESA) spaceflight opportunities, has significantly contributed towards our current understanding of spaceflight biology. Recent molecular biology experiments include “omic” analysis, which provides a holistic and systems level understanding of the mechanisms underlying phenotypic adaptation. Despite vast interest in, and the immense quantity of biological information gained from space omics research, the knowledge of ESA-related space omics works as a collective remains poorly defined due to the recent exponential application of omics approaches in space and the limited search capabilities of pre-existing records. Thus, a review of such contributions is necessary to clarify and promote the development of space omics among ESA and ESA state members. To address this gap, in this review we: i) identified and summarised omics works led by European researchers, ii) geographically described these omics works, and iii) highlighted potential caveats in complex funding scenarios among ESA member states.

Published
2022

3. NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data

Author

National Aeronautics and Space Administration (US), Biotechnology and Biological Sciences Research Council (UK), Centre for Musculoskeletal Ageing Research (UK), Agencia Estatal de Investigación (España), Nottingham Biomedical Research Centre (UK), Overbey, Eliah G. [0000-0002-2866-8294], Fogle, Homer [0000-0002-5579-5432], Beheshti, Afshin [0000-0003-4643-531X], Berrios, Daniel C. [0000-0003-4312-9552], Cekanaviciute, Egle [0000-0003-3306-1806], Davin, Laurence B. [0000-0002-3248-6485], Gebre, Samrawit [0000-0002-8963-4856], Geniza, Matthew [0000-0003-4828-7891], Gilroy, Simon [0000-0001-9597-6839], Hardiman, Gary [0000-0003-4558-0400], Herranz, Raúl [0000-0002-0246-9449], Kruse, Colin P. S. [0000-0001-7070-8889], Mishra, Tejaswini [0000-0001-9931-1260], Perera, Imara Y. [0000-0001-9421-1420], Ray, Shayoni [0000-0003-1911-7738], Reinsch, Sigrid [0000-0002-6484-7521], Rosenthal, Sara Brin [0000-0002-6548-9658], Strong, Michael [0000-0002-3247-6260], Szewczyk, Nathaniel [0000-0003-4425-9746], Tahimic, Candice G. T. [0000-0001-5862-2652], Taylor, Deanne M. [0000-0002-3302-4610], Villacampa, Alicia [0000-0002-7398-8545], Weging, Silvio [0000-0002-8484-4352], Wolverton, Chris [0000-0003-2248-474X], Wyatt, Sarah E. [0000-0001-7874-0509], Costes, Sylvain V. [0000-0002-8542-2389], Galazka, Jonathan M. [0000-0002-4153-0249], Overbey, Eliah G., Saravia-Butler, Amanda M., Zhang, Zhe, Rathi, Komal S., Fogle, Homer, da Silveira, William A., Barker, Richard, Bass, Joseph J., Beheshti, Afshin, Berrios, Daniel C., Blaber, Elizabeth A., Cekanaviciute, Egle, Costa, Helio A., Davin, Laurence B., Fisch, Kathleen M., Gebre, Samrawit, Geniza, Matthew, Gilbert, Rachel, Gilroy, Simon, Hardiman, Gary, Herranz, Raúl, Kidane, Yared H., Kruse, Colin P. S., Lee, Michael D., Liefeld, Ted, Lewis, Norman G., McDonald, J. Tyson, Meller, Robert, Mishra, Tejaswini, Perera, Imara Y., Ray, Shayoni, Reinsch, Sigrid, Rosenthal, Sara Brin, Strong, MichaelSzewczyk, Nathaniel, Tahimic, Candice G. T., Taylor, Deanne M., Vandenbrink, Joshua P., Villacampa, Alicia, Weging, Silvio, Wolverton, Chris, Wyatt, Sarah E., Zea, Luis, Costes, Sylvain V., Galazka, Jonathan M., National Aeronautics and Space Administration (US), Biotechnology and Biological Sciences Research Council (UK), Centre for Musculoskeletal Ageing Research (UK), Agencia Estatal de Investigación (España), Nottingham Biomedical Research Centre (UK), Overbey, Eliah G. [0000-0002-2866-8294], Fogle, Homer [0000-0002-5579-5432], Beheshti, Afshin [0000-0003-4643-531X], Berrios, Daniel C. [0000-0003-4312-9552], Cekanaviciute, Egle [0000-0003-3306-1806], Davin, Laurence B. [0000-0002-3248-6485], Gebre, Samrawit [0000-0002-8963-4856], Geniza, Matthew [0000-0003-4828-7891], Gilroy, Simon [0000-0001-9597-6839], Hardiman, Gary [0000-0003-4558-0400], Herranz, Raúl [0000-0002-0246-9449], Kruse, Colin P. S. [0000-0001-7070-8889], Mishra, Tejaswini [0000-0001-9931-1260], Perera, Imara Y. [0000-0001-9421-1420], Ray, Shayoni [0000-0003-1911-7738], Reinsch, Sigrid [0000-0002-6484-7521], Rosenthal, Sara Brin [0000-0002-6548-9658], Strong, Michael [0000-0002-3247-6260], Szewczyk, Nathaniel [0000-0003-4425-9746], Tahimic, Candice G. T. [0000-0001-5862-2652], Taylor, Deanne M. [0000-0002-3302-4610], Villacampa, Alicia [0000-0002-7398-8545], Weging, Silvio [0000-0002-8484-4352], Wolverton, Chris [0000-0003-2248-474X], Wyatt, Sarah E. [0000-0001-7874-0509], Costes, Sylvain V. [0000-0002-8542-2389], Galazka, Jonathan M. [0000-0002-4153-0249], Overbey, Eliah G., Saravia-Butler, Amanda M., Zhang, Zhe, Rathi, Komal S., Fogle, Homer, da Silveira, William A., Barker, Richard, Bass, Joseph J., Beheshti, Afshin, Berrios, Daniel C., Blaber, Elizabeth A., Cekanaviciute, Egle, Costa, Helio A., Davin, Laurence B., Fisch, Kathleen M., Gebre, Samrawit, Geniza, Matthew, Gilbert, Rachel, Gilroy, Simon, Hardiman, Gary, Herranz, Raúl, Kidane, Yared H., Kruse, Colin P. S., Lee, Michael D., Liefeld, Ted, Lewis, Norman G., McDonald, J. Tyson, Meller, Robert, Mishra, Tejaswini, Perera, Imara Y., Ray, Shayoni, Reinsch, Sigrid, Rosenthal, Sara Brin, Strong, MichaelSzewczyk, Nathaniel, Tahimic, Candice G. T., Taylor, Deanne M., Vandenbrink, Joshua P., Villacampa, Alicia, Weging, Silvio, Wolverton, Chris, Wyatt, Sarah E., Zea, Luis, Costes, Sylvain V., and Galazka, Jonathan M.

Abstract

With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility, and reusability of pipeline data; to provide a template for data processing of future spaceflight-relevant datasets; and to encourage cross-analysis of data from other databases with the data available in GeneLab.

Published
2021

4. Revamping Space-omics in Europe

Author

National Aeronautics and Space Administration (US), Madrigal, Pedro [0000-0003-1959-8199], Manzano, Aranzazu [0000-0002-0150-0803], Deane, Colleen S. [0000-0002-2281-6479], Bezdan, Daniela [0000-0002-1203-8239], Carnero-Díaz, Eugénie [0000-0002-3771-3106], Medina, F. Javier [0000-0002-0866-7710], Hardiman, Gary [0000-0003-4558-0400], Grosse, Ivo [0000-0001-5318-4825], Szewczyk, Nathaniel [0000-0003-4425-9746], Weging, Silvio [0000-0002-8484-4352], Giacomello, Stefania [0000-0003-0738-1574], Harridge, Stephen D.R. [0000-0002-8203-0769], Da Silveira, William A. [0000-0001-6370-2884], Herranz, Raúl [0000-0002-0246-9449], Madrigal, Pedro, Gabel, Alexander, Villacampa, Alicia, Manzano, Aranzazu, Deane, Colleen S., Bezdan, Daniela, Carnero-Díaz, Eugénie, Medina, F. Javier, Hardiman, Gary, Grosse, Ivo, Szewczyk, Nathaniel, Weging, Silvio, Giacomello, Stefania, Harridge, Stephen D.R., Morris-Paterson, Tessa, Cahill, Thomas, Da Silveira, William A., Herranz, Raúl, National Aeronautics and Space Administration (US), Madrigal, Pedro [0000-0003-1959-8199], Manzano, Aranzazu [0000-0002-0150-0803], Deane, Colleen S. [0000-0002-2281-6479], Bezdan, Daniela [0000-0002-1203-8239], Carnero-Díaz, Eugénie [0000-0002-3771-3106], Medina, F. Javier [0000-0002-0866-7710], Hardiman, Gary [0000-0003-4558-0400], Grosse, Ivo [0000-0001-5318-4825], Szewczyk, Nathaniel [0000-0003-4425-9746], Weging, Silvio [0000-0002-8484-4352], Giacomello, Stefania [0000-0003-0738-1574], Harridge, Stephen D.R. [0000-0002-8203-0769], Da Silveira, William A. [0000-0001-6370-2884], Herranz, Raúl [0000-0002-0246-9449], Madrigal, Pedro, Gabel, Alexander, Villacampa, Alicia, Manzano, Aranzazu, Deane, Colleen S., Bezdan, Daniela, Carnero-Díaz, Eugénie, Medina, F. Javier, Hardiman, Gary, Grosse, Ivo, Szewczyk, Nathaniel, Weging, Silvio, Giacomello, Stefania, Harridge, Stephen D.R., Morris-Paterson, Tessa, Cahill, Thomas, Da Silveira, William A., and Herranz, Raúl

Published
2020

5. Space omics research in Europe: contributions, geographical distribution and ESA member state funding schemes

Author

Colleen S. Deane, Willian A. da Silveira, Raúl Herranz, Joseph Borg, Thomas Cahill, Eugénie Carnero-Diaz, Timothy Etheridge, Gary Hardiman, Natalie Leys, Pedro Madrigal, Aránzazu Manzano, Felice Mastroleo, F. Javier Medina, Manuel A. Fernandez-Rojo, Keith Siew, Nathaniel J. Szewczyk, Alicia Villacampa, Stephen B. Walsh, Silvio Weging, Daniela Bezdan, Stefania Giacomello, European Space Agency, National Aeronautics and Space Administration (US), Medical Research Council (UK), Comunidad de Madrid, Ministerio de Ciencia e Innovación (España), Swedish Research Council, Centre National D'Etudes Spatiales (France), Wellcome Trust, Deane, Colleen S. [0000-0002-2281-6479], Carnero-Díaz, Eugénie [0000-0002-3771-3106], Etheridge,Timothy [0000-0002-3588-8711], Hardiman, Gary [0000-0003-4558-0400], Leys, Natalie [0000-0002-4556-5211], Madrigal, Pedro [0000-0003-1959-8199], Manzano, Aranzazu [0000-0002-0150-0803], Mastroleo, Felice [0000-0002-9815-8038], Medina, F. Javier [0000-0002-0866-7710], Fernández-Rojo, Manuel A. [0000-0002-2240-1951], Siew, Keith [0000-0002-6502-5095], Szewczyk, Nathaniel [0000-0003-4425-9746], Villacampa, Alicia [0000-0002-7398-8545], Walsh, Stephen B. [0000-0002-8693-1353], Weging, Silvio [0000-0002-8484-4352], Bezdan, Daniela [0000-0002-1203-8239], Giacomello, Stefania [0000-0003-0738-1574], Da Silveira, William A. [0000-0001-6370-2884], Herranz, Raúl [0000-0002-0246-9449], Deane, Colleen S., Carnero-Díaz, Eugénie, Etheridge,Timothy, Hardiman, Gary, Leys, Natalie, Madrigal, Pedro, Manzano, Aranzazu, Mastroleo, Felice, Medina, F. Javier, Fernández-Rojo, Manuel A., Siew, Keith, Szewczyk, Nathaniel, Villacampa, Alicia, Walsh, Stephen B., Weging, Silvio, Bezdan, Daniela, Giacomello, Stefania, Da Silveira, William A., Herranz, Raúl, and Space Omics Topical Team

Subjects
Space flight, Space sciences -- International cooperation, Multidisciplinary, Outer space -- Exploration -- Europe, Space sciences, Omics, Space medicine, Astrobiology, General, European Space Agency, International Space Station, Space biology -- Research
Abstract

18 p.-3 fig.-1 graph. abst., The European research community, via European Space Agency (ESA) spaceflight opportunities, has significantly contributed towards our current understanding of spaceflight biology. Recent molecular biology experiments include “omic” analysis, which provides a holistic and systems level understanding of the mechanisms underlying phenotypic adaptation. Despite vast interest in, and the immense quantity of biological information gained from space omics research, the knowledge of ESA-related space omics works as a collective remains poorly defined due to the recent exponential application of omics approaches in space and the limited search capabilities of pre-existing records. Thus, a review of such contributions is necessary to clarify and promote the development of space omics among ESA and ESA state members. To address this gap, in this review we: i) identified and summarised omics works led by European researchers, ii) geographically described these omics works, and iii) highlighted potential caveats in complex funding scenarios among ESA member states., All listed authors are members of the ESA Space Omics Topical Team, funded by the ESA grant/contract 4000131202/20/NL/PG/pt “Space Omics: Towards an integrated ESA/NASA –omics database for spaceflight and ground facilities experiments” awarded to RH, which was the main funding source for this work. Individual authors also acknowledge support from: the Medical Research Council part of a Skills Development Fellowship [grant number MR/T026014/1] awarded to CSD; the Spanish CAM TALENTO program project 2020-5A_BIO-19724 to MAFR; the Spanish Plan Estatal de Investigación Científica y Desarrollo Tecnológico Grant RTI2018-099309-B-I00 to FJM, the Swedish Research Council VR grant 2020-04864 to SG and the French Centre National d'Etudes Spatiales grant DAR 2020-4800001004, 2021-4800001117 to ECD. This research was also funded in part by the Wellcome Trust [110182/Z/15/Z] to KS.

Published
2022

6. NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data

Author

Komal S. Rathi, Egle Cekanaviciute, Colin P.S. Kruse, Sara Brin Rosenthal, Eliah G. Overbey, Shayoni Ray, Robert Meller, Daniel C. Berrios, Ted Liefeld, Raúl Herranz, Gary Hardiman, Sarah E. Wyatt, Richard Barker, Kathleen M. Fisch, Norman G. Lewis, Matthew Geniza, Sylvain V. Costes, Amanda M. Saravia-Butler, Michael J. Strong, Laurence B. Davin, Simon Gilroy, Tejaswini Mishra, Chris Wolverton, Joshua P. Vandenbrink, Zhe Zhang, Michael D. Lee, Silvio Weging, Alicia Villacampa, Joseph J. Bass, Homer Fogle, Sigrid Reinsch, Elizabeth A. Blaber, Luis Zea, Rachel Gilbert, Jonathan M. Galazka, Willian A. da Silveira, J. Tyson McDonald, Samrawit G. Gebre, Yared H. Kidane, Nathaniel J. Szewczyk, Imara Y. Perera, Deanne Taylor, Helio A. Costa, Afshin Beheshti, Candice Tahimic, National Aeronautics and Space Administration (US), Biotechnology and Biological Sciences Research Council (UK), Centre for Musculoskeletal Ageing Research (UK), Agencia Estatal de Investigación (España), Nottingham Biomedical Research Centre (UK), Overbey, Eliah G. [0000-0002-2866-8294], Fogle, Homer [0000-0002-5579-5432], Beheshti, Afshin [0000-0003-4643-531X], Berrios, Daniel C. [0000-0003-4312-9552], Cekanaviciute, Egle [0000-0003-3306-1806], Davin, Laurence B. [0000-0002-3248-6485], Gebre, Samrawit [0000-0002-8963-4856], Geniza, Matthew [0000-0003-4828-7891], Gilroy, Simon [0000-0001-9597-6839], Hardiman, Gary [0000-0003-4558-0400], Herranz, Raúl [0000-0002-0246-9449], Kruse, Colin P. S. [0000-0001-7070-8889], Mishra, Tejaswini [0000-0001-9931-1260], Perera, Imara Y. [0000-0001-9421-1420], Ray, Shayoni [0000-0003-1911-7738], Reinsch, Sigrid [0000-0002-6484-7521], Rosenthal, Sara Brin [0000-0002-6548-9658], Strong, Michael [0000-0002-3247-6260], Szewczyk, Nathaniel [0000-0003-4425-9746], Tahimic, Candice G. T. [0000-0001-5862-2652], Taylor, Deanne M. [0000-0002-3302-4610], Villacampa, Alicia [0000-0002-7398-8545], Weging, Silvio [0000-0002-8484-4352], Wolverton, Chris [0000-0003-2248-474X], Wyatt, Sarah E. [0000-0001-7874-0509], Costes, Sylvain V. [0000-0002-8542-2389], Galazka, Jonathan M. [0000-0002-4153-0249], Overbey, Eliah G., Fogle, Homer, Beheshti, Afshin, Berrios, Daniel C., Cekanaviciute, Egle, Davin, Laurence B., Gebre, Samrawit, Geniza, Matthew, Gilroy, Simon, Hardiman, Gary, Herranz, Raúl, Kruse, Colin P. S., Mishra, Tejaswini, Perera, Imara Y., Ray, Shayoni, Reinsch, Sigrid, Rosenthal, Sara Brin, Strong, Michael, Szewczyk, Nathaniel, Tahimic, Candice G. T., Taylor, Deanne M., Villacampa, Alicia, Weging, Silvio, Wolverton, Chris, Wyatt, Sarah E., Costes, Sylvain V., and Galazka, Jonathan M.

Subjects
0301 basic medicine, Data processing, Multidisciplinary, Computer science, Science, Pipeline (computing), Analysis working, Omics, RNA-Seq, 02 engineering and technology, 021001 nanoscience & nanotechnology, Short read, computer.software_genre, Article, Transcriptome, 03 medical and health sciences, 030104 developmental biology, Differentially expressed genes, Gene expression, Data mining, 0210 nano-technology, Space Sciences, Gene, computer
Abstract

Summary With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility, and reusability of pipeline data; to provide a template for data processing of future spaceflight-relevant datasets; and to encourage cross-analysis of data from other databases with the data available in GeneLab., Graphical abstract, Highlights • Analysis of omics data from different spaceflight studies presents unique challenges • A standardized pipeline for RNA-seq analysis eliminates data processing variation • The GeneLab RNA-seq pipeline includes QC, trimming, mapping, quantification, and DGE • Space-relevant data processed with this pipeline are available at genelab.nasa.gov, Omics; Space Sciences

Published
2021

7. Revamping Space-omics in Europe

Author

Willian A. da Silveira, Alicia Villacampa, Pedro Madrigal, Daniela Bezdan, F. Javier Medina, Stefania Giacomello, Gary Hardiman, Thomas J. Cahill, Alexander Gabel, Aránzazu Manzano, Stephen D. R. Harridge, Raúl Herranz, Colleen S. Deane, Ivo Grosse, Eugénie Carnero-Diaz, Nathaniel J. Szewczyk, Tessa Eleri Morris-Paterson, Silvio Weging, Madrigal, Pedro [0000-0003-1959-8199], Apollo - University of Cambridge Repository, National Aeronautics and Space Administration (US), Madrigal, Pedro, Manzano, Aranzazu, Deane, Colleen S., Bezdan, Daniela, Carnero-Díaz, Eugénie, Medina, F. Javier, Hardiman, Gary, Grosse, Ivo, Szewczyk, Nathaniel, Weging, Silvio, Giacomello, Stefania, Harridge, Stephen D.R., Da Silveira, William A., Herranz, Raúl, Manzano, Aranzazu [0000-0002-0150-0803], Deane, Colleen S. [0000-0002-2281-6479], Bezdan, Daniela [0000-0002-1203-8239], Carnero-Díaz, Eugénie [0000-0002-3771-3106], Medina, F. Javier [0000-0002-0866-7710], Hardiman, Gary [0000-0003-4558-0400], Grosse, Ivo [0000-0001-5318-4825], Szewczyk, Nathaniel [0000-0003-4425-9746], Weging, Silvio [0000-0002-8484-4352], Giacomello, Stefania [0000-0003-0738-1574], Harridge, Stephen D.R. [0000-0002-8203-0769], Da Silveira, William A. [0000-0001-6370-2884], and Herranz, Raúl [0000-0002-0246-9449]

Subjects
Europe, Histology, SDG 3 - Good Health and Well-being, Humans, Cell Biology, Biology, Space (commercial competition), Space Research, Omics, Data science, Pathology and Forensic Medicine
Abstract

6 p., The authors belong to the ESA Space Omics Topical Team funded by the ESA grant/contract 4000131202/20/NL/PG/pt “Space Omics: Towards an integrated ESA/NASA –omics database for spaceflight and ground facilities experiments” to RH.

Published
2020

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