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Parallel-Processing Systems And Methods For Highly Scalable Analysis Of Biological Sequence Data - EP3221695

The patent EP3221695 was granted to The Research Institute AT Nationwide Childrens Hospital on Sep 27, 2023. The application was originally filed on Nov 20, 2015 under application number EP15860295A. The patent is currently recorded with a legal status of "Granted And Under Opposition".

EP3221695

THE RESEARCH INSTITUTE AT NATIONWIDE CHILDRENS HOSPITAL
Application Number
EP15860295A
Filing Date
Nov 20, 2015
Status
Granted And Under Opposition
Aug 25, 2023
Grant Date
Sep 27, 2023
External Links
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MARKS & CLERKJun 27, 2024-ADMISSIBLE

Patent Citations (10) New

Patent citations refer to prior patents cited during different phases such as opposition or international search.

Citation PhasePublication NumberPublication Link
INTERNATIONAL-SEARCH-REPORTUS2003194724
INTERNATIONAL-SEARCH-REPORTUS2011177517
INTERNATIONAL-SEARCH-REPORTUS2012264632
INTERNATIONAL-SEARCH-REPORTUS2013311106
INTERNATIONAL-SEARCH-REPORTUS2013345070
OPPOSITIONEP2759953
OPPOSITIONKR100681795B
OPPOSITIONUS2013311106
OPPOSITIONUS2013338934
SEARCHUS2013311106

Non-Patent Literature (NPL) Citations (12) New

NPL citations refer to non-patent references such as research papers, articles, or other publications cited during examination or opposition phases.

Citation PhaseReference TextLink
OPPOSITION- Anonymous, "Blue Collar Bioinformatics - Scaling variant detection pipelines for whole genome sequencing analysis", (20130522), URL: https://bcbio.wordpress.com/2013/05/22/scaling-variant-detection-pipelines-for-whole-genome-sequencing-analysis/, XP093195638-
OPPOSITION- Anonymous, "Mapping", (20240625), URL: https://www.genome.gov/genetics-glossary/Mapping#:~:text=Mapping%20refers%20to%20the%20process,within%20a%20chromosome%20or%20genome, XP093195641-
OPPOSITION- Massie Matt, Nothaft Frank, Hartl Christopher, Kozanitis Christos, Schumacher André, Joseph Anthony D, Patterson David A, "ADAM: Genomics Formats and Processing Patterns for Cloud Scale Computing", Technical Report UCB/EECS-2013-2017, Berkeley, (20131215), pages 1 - 24, Technical Report UCB/EECS-2013-2017, URL: https://www2.eecs.berkeley.edu/Pubs/TechRpts/2013/EECS-2013-207.pdf, XP093186134-
OPPOSITION- "IDENTIFICATION OF COMMON MOLECULAR SUBSEQUENCES.", Journal of Molecular Biology, Academic Press, United Kingdom, United Kingdom , (19810325), vol. 147., no. 01., doi:10.1016/0022-2836(81)90087-5, ISSN 0022-2836, pages 195 - 197., XP000857458
OPPOSITION- Lam Hugo Y K, Pan Cuiping, Clark Michael J, Lacroute Phil, Chen Rui, Haraksingh Rajini, O'huallachain Maeve, Gerstein Mark B, Kidd Jeffrey M, Bustamante Carlos D, Snyder Michael, "Detecting and annotating genetic variations using the HugeSeq pipeline", Nature Biotechnology, Nature Publishing Group US, New York, New York, (20120307), vol. 30, no. 3, doi:10.1038/nbt.2134, ISSN 1087-0156, pages 226 - 229, XP055070514
OPPOSITION- M. C. Schatz, "CloudBurst: highly sensitive read mapping with MapReduce", Bioinformatics, Oxford University Press, (20090601), vol. 25, no. 11, doi:10.1093/bioinformatics/btp236, ISSN 13674803, pages 1363 - 1369, XP055070043
OPPOSITION- Puckelwartz Megan J, Pesce Lorenzo L, Nelakuditi Viswateja, Dellefave-Castillo Lisa, Golbus Jessica R, Day Sharlene M, Cappola Thomas P, Dorn, Foster Ian T, Mcnally Elizabeth M, "Supercomputing for the parallelization of whole genome analysis", Bioinformatics (Oxford, England), Oxford University Press, England, England , (20140212), doi:10.1093/bioinformatics/btu071, pages 1508 - 1513, XP055831484
OPPOSITION- Tarasov Artem, Vilella Albert J., Cuppen Edwin, Nijman Isaac J., Prins Pjotr, "Sambamba: fast processing of NGS alignment formats", Bioinformatics, Oxford university press , Surrey, GB, GB , (20150615), vol. 31, no. 12, doi:10.1093/bioinformatics/btv098, ISSN 1367-4803, pages 2032 - 2034, XP093195640
OPPOSITION- Dries Decap, Reumers Joke, Herzeel Charlotte, Costanza Pascal, Fostier Jan, "Halvade: scalable sequence analysis with MapReduce", Bioinformatics, Oxford university press , Surrey, GB, GB , (20150323), vol. 31, no. 15, doi:10.1093/bioinformatics/btv179, ISSN 1367-4803, pages 2482 - 2488, XP055560889
OPPOSITION- A. Mckenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, M. Daly, M. A. Depristo, "The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data", Genome Research, Cold Spring Harbor Laboratory Press, (20100901), vol. 20, no. 9, doi:10.1101/gr.107524.110, ISSN 10889051, pages 1297 - 1303, XP055089173
OPPOSITION- Benjamin J Kelly;James R Fitch;Yangqiu Hu;Donald J Corsmeier;Huachun Zhong;Amy N Wetzel;Russell D Nordquist;David L Newsom;Peter White, "Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics", Genome Biology, BioMed Central Ltd., (20150120), vol. 16, no. 1, doi:10.1186/s13059-014-0577-x, ISSN 1465-6906, page 6, XP021210854
OPPOSITION- Pandey Ram Vinay, Schlötterer Christian, "DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster", PLOS ONE, Public Library of Science, US, US , (20130801), vol. 8, no. 8, doi:10.1371/journal.pone.0072614, ISSN 1932-6203, page e72614, XP093195639

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