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(Created page with "# King CH, Keeney J, Guimera N, Das S, Weber M, Fochtman B, Walderhaug MO, Talwar S, Patel JA, Mazumder R, Donaldson EF. Communicating regulatory high-throughput sequencing data using BioCompute Objects. Drug Discov Today. 2022 Jan 22; PMID: 35077912. # Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovi...")
 
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#    King CH, Keeney J, Guimera N, Das S, Weber M, Fochtman B, Walderhaug MO, Talwar S, Patel JA, Mazumder R, Donaldson EF. Communicating regulatory high-throughput sequencing data using BioCompute Objects. Drug Discov Today. 2022 Jan 22; PMID: 35077912.
#    Charles Hadley S King 4th, Jonathon Keeney, Nuria Guimera, Souvik Das, Michiel Weber, Brian Fochtman, Mark O Walderhaug, Sneh Talwar, Janisha A Patel, Raja Mazumder, Eric F Donaldson (2022): <br />'''Communicating regulatory high-throughput sequencing data using BioCompute Objects'''.   <br />''Drug Discovery Today'' '''27'''(4). PMID: [https://pubmed.ncbi.nlm.nih.gov/35077912/ 35077912] https://doi.org/10.1016/j.drudis.2022.01.007
#    Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble. Packaging research artefacts with RO-Crate. Data Science, 2022; https://doi.org/10.3233/DS-210053.
#    Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble (2022):  <br />'''Packaging research artefacts with RO-Crate'''. <br />  ''Data Science'' '''5'''(2) https://doi.org/10.3233/DS-210053.
#    Patel JA, Dean DA, King CH, Xiao N, Koc S, Minina E, Golikov A, Brooks P, Kahsay R, Navelkar R, Ray M, Roberson D, Armstrong C, Mazumder R, Keeney J. Bioinformatics tools developed to support BioCompute Objects. Database (Oxford).2021 March 31; PMID:33784373.
#    Janisha A Patel, Dennis A Dean, Charles Hadley King, Nan Xiao, Soner Koc, Ekaterina Minina, Anton Golikov, Phillip Brooks, Robel Kahsay, Rahi Navelkar, Manisha Ray, Dave Roberson, Chris Armstrong, Raja Mazumder, Jonathon Keeney (2021):  <br /> '''Bioinformatics tools developed to support BioCompute Objects'''. <br /> ''Database'' 2021:baab008 PMID:[https://pubmed.ncbi.nlm.nih.gov/33784373/ 33784373] https://doi.org/10.1093/database/baab008
#    Alterovitz G, Dean D A, Goble C, Crusoe M R, Soiland-Reyes S, Bell A, Hayes A, King, C H S, Taylor D, Johanson E, Thompson E E, Donaldson E, Morizono H, Tsang H S, Goecks J, Yao J, Almeida J S, Krampis K, Guo L, Walderhaug M, Walsh P, Kahsay R, Gottipati S, Bloom T, Lai Y, Simonyan V, Mazumder R. Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results. PLOS Biology; 16(12): e3000099.2018. https://doi.org/10.1371/journal.pbio.3000099
#    Gil Alterovitz, Dennis Dean, Carole Goble, Michael R. Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, KanakaDurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder (2018): <br /> '''Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results'''. <br />  ''PLOS Biology'' '''16'''(12):e3000099. https://doi.org/10.1371/journal.pbio.3000099
#    Simonyan V, Goecks J, Mazumder R. BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations. PDA J Pharm Sci Technol. 2017;71(2):136-146 PMID:27974626.
#    Vahan Simonyan, Jeremy Goecks and Raja Mazumder (2017):  <br /> '''BioCompute objects—a step towards evaluation and validation of bio-medical scientific computations'''. <br />  ''PDA Journal of Pharmaceutical Science and Technology'' '''71'''(2):136-146 PMID:[https://pubmed.ncbi.nlm.nih.gov/27974626/ 27974626] https://doi.org/10.5731/pdajpst.2016.006734
#    Nan Xiao, Soner Koc, David Roberson, Phillip Brooks, Manisha Ray, Dennis Dean (2020):  <br /> '''BCO App: tools for generating BioCompute Objects from next-generation sequencing workflows and computations''' [version 1; peer review: 2 approved].  <br /> ''F1000Research'' '''9''':1144 https://doi.org/10.12688/f1000research.25902.1
#    Naila Gulzar, Jonathon Keeney, Jack B. Baker, Ondrej Klempir, Geoffrey Hannigan, Danny A. Bitton, Julia M Maritz, Charles Hadley S. King IV, Janisha A. Patel, Paul Duncan, Raja Mazumder (2021):  <br /> '''BioCompute Objects to communicate a viral detection pipeline with potential for use in a regulatory environment'''.  <br /> ''bioRxiv'' https://doi.org/10.1101/2021.10.19.465010
#    Raja Mazumder, Vahan Simonyan (eds), IEEE P2791 BioCompute Working Group (BCOWG) (2020): <br />  '''IEEE Standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication'''. <br /> ''IEEE Std'' 2791-2020. IEEE SA Standards Board. <nowiki>ISBN 9781504464666</nowiki>  https://doi.org/10.1109/IEEESTD.2020.9094416 [[https://www.research.manchester.ac.uk/portal/en/publications/ieee-standard-for-bioinformatics-analyses-generated-by-highthroughput-sequencing-hts-to-facilitate-communication(936de52b-ac53-4f0e-9927-77fd7073e88d).html preprint]]

Latest revision as of 14:56, 25 August 2022

  1. Charles Hadley S King 4th, Jonathon Keeney, Nuria Guimera, Souvik Das, Michiel Weber, Brian Fochtman, Mark O Walderhaug, Sneh Talwar, Janisha A Patel, Raja Mazumder, Eric F Donaldson (2022):
    Communicating regulatory high-throughput sequencing data using BioCompute Objects.
    Drug Discovery Today 27(4). PMID: 35077912 https://doi.org/10.1016/j.drudis.2022.01.007
  2. Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble (2022):
    Packaging research artefacts with RO-Crate.
    Data Science 5(2) https://doi.org/10.3233/DS-210053.
  3. Janisha A Patel, Dennis A Dean, Charles Hadley King, Nan Xiao, Soner Koc, Ekaterina Minina, Anton Golikov, Phillip Brooks, Robel Kahsay, Rahi Navelkar, Manisha Ray, Dave Roberson, Chris Armstrong, Raja Mazumder, Jonathon Keeney (2021):
    Bioinformatics tools developed to support BioCompute Objects.
    Database 2021:baab008 PMID:33784373 https://doi.org/10.1093/database/baab008
  4. Gil Alterovitz, Dennis Dean, Carole Goble, Michael R. Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, KanakaDurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder (2018):
    Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results.
    PLOS Biology 16(12):e3000099. https://doi.org/10.1371/journal.pbio.3000099
  5. Vahan Simonyan, Jeremy Goecks and Raja Mazumder (2017):
    BioCompute objects—a step towards evaluation and validation of bio-medical scientific computations.
    PDA Journal of Pharmaceutical Science and Technology 71(2):136-146 PMID:27974626 https://doi.org/10.5731/pdajpst.2016.006734
  6. Nan Xiao, Soner Koc, David Roberson, Phillip Brooks, Manisha Ray, Dennis Dean (2020):
    BCO App: tools for generating BioCompute Objects from next-generation sequencing workflows and computations [version 1; peer review: 2 approved].
    F1000Research 9:1144 https://doi.org/10.12688/f1000research.25902.1
  7. Naila Gulzar, Jonathon Keeney, Jack B. Baker, Ondrej Klempir, Geoffrey Hannigan, Danny A. Bitton, Julia M Maritz, Charles Hadley S. King IV, Janisha A. Patel, Paul Duncan, Raja Mazumder (2021):
    BioCompute Objects to communicate a viral detection pipeline with potential for use in a regulatory environment.
    bioRxiv https://doi.org/10.1101/2021.10.19.465010
  8. Raja Mazumder, Vahan Simonyan (eds), IEEE P2791 BioCompute Working Group (BCOWG) (2020):
    IEEE Standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication.
    IEEE Std 2791-2020. IEEE SA Standards Board. ISBN 9781504464666 https://doi.org/10.1109/IEEESTD.2020.9094416 [preprint]
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