TY - JOUR AU - Torkamani, A. AU - Andersen, K. G. AU - Steinhubl, S. R. AU - Topol, E. J. PY - 2017 DA - 2017// TI - High-definition medicine JO - Cell VL - 170 UR - https://doi.org/10.1016/j.cell.2017.08.007 DO - 10.1016/j.cell.2017.08.007 ID - Torkamani2017 ER - TY - JOUR AU - Riba, M. AU - Sala, C. AU - Toniolo, D. AU - Tonon, G. PY - 2019 DA - 2019// TI - Big data in medicine, the present and hopefully the future JO - Front Med VL - 6 UR - https://doi.org/10.3389/fmed.2019.00263 DO - 10.3389/fmed.2019.00263 ID - Riba2019 ER - TY - JOUR AU - Topol, E. J. PY - 2019 DA - 2019// TI - High-performance medicine: the convergence of human and artificial intelligence JO - Nat Med VL - 25 UR - https://doi.org/10.1038/s41591-018-0300-7 DO - 10.1038/s41591-018-0300-7 ID - Topol2019 ER - TY - JOUR AU - Filipp, F. V. PY - 2019 DA - 2019// TI - Opportunities for artificial intelligence in advancing precision medicine JO - Curr Genet Med Rep VL - 7 UR - https://doi.org/10.1007/s40142-019-00177-4 DO - 10.1007/s40142-019-00177-4 ID - Filipp2019 ER - TY - JOUR AU - Griffith, M. PY - 2015 DA - 2015// TI - Genome modeling system: a knowledge management platform for genomics JO - PLoS Comput Biol VL - 11 UR - https://doi.org/10.1371/journal.pcbi.1004274 DO - 10.1371/journal.pcbi.1004274 ID - Griffith2015 ER - TY - JOUR AU - Wagle, P. AU - Nikolić, M. AU - Frommolt, P. PY - 2015 DA - 2015// TI - QuickNGS elevates next-generation sequencing data analysis to a new level of automation JO - BMC Genom VL - 16 UR - https://doi.org/10.1186/s12864-015-1695-x DO - 10.1186/s12864-015-1695-x ID - Wagle2015 ER - TY - JOUR AU - Quilez, J. PY - 2017 DA - 2017// TI - Parallel sequencing lives, or what makes large sequencing projects successful JO - bioRxiv UR - https://doi.org/10.1101/136358 DO - 10.1101/136358 ID - Quilez2017 ER - TY - JOUR AU - Reisinger, E. PY - 2017 DA - 2017// TI - OTP: an automatized system for managing and processing NGS data JO - J Biotechnol VL - 261 UR - https://doi.org/10.1016/j.jbiotec.2017.08.006 DO - 10.1016/j.jbiotec.2017.08.006 ID - Reisinger2017 ER - TY - JOUR AU - Bianchi, V. PY - 2016 DA - 2016// TI - Integrated systems for NGS data management and analysis: open issues and available solutions JO - Front Genet VL - 7 UR - https://doi.org/10.3389/fgene.2016.00075 DO - 10.3389/fgene.2016.00075 ID - Bianchi2016 ER - TY - JOUR AU - Leipzig, J. PY - 2017 DA - 2017// TI - A review of bioinformatic pipeline frameworks JO - Brief Bioinform VL - 18 ID - Leipzig2017 ER - TY - JOUR AU - Cohen-Boulakia, S. PY - 2017 DA - 2017// TI - Scientific workflows for computational reproducibility in the life sciences: status, challenges and opportunities JO - Future Gener Comput Syst VL - 75 UR - https://doi.org/10.1016/j.future.2017.01.012 DO - 10.1016/j.future.2017.01.012 ID - Cohen-Boulakia2017 ER - TY - JOUR AU - Kulkarni, P. AU - Frommolt, P. PY - 2017 DA - 2017// TI - Challenges in the setup of large-scale next-generation sequencing analysis workflows JO - Comput Struct Biotechnol J VL - 15 UR - https://doi.org/10.1016/j.csbj.2017.10.001 DO - 10.1016/j.csbj.2017.10.001 ID - Kulkarni2017 ER - TY - JOUR AU - Wilkinson, M. D. PY - 2016 DA - 2016// TI - The FAIR guiding principles for scientific data management and stewardship JO - Sci Data VL - 3 UR - https://doi.org/10.1038/sdata.2016.18 DO - 10.1038/sdata.2016.18 ID - Wilkinson2016 ER - TY - JOUR AU - Pittard, W. S. AU - Li, S. PY - 2020 DA - 2020// TI - The essential toolbox of data science: Python, R, Git, and Docker JO - Methods Mol Biol VL - 2104 UR - https://doi.org/10.1007/978-1-0716-0239-3_15 DO - 10.1007/978-1-0716-0239-3_15 ID - Pittard2020 ER - TY - STD TI - Chen, L. Microservices: architecting for continuous delivery and DevOps. In: 2018 IEEE International conference on software architecture (ICSA) (2018). https://doi.org/10.1109/icsa.2018.00013. ID - ref15 ER - TY - JOUR AU - Perez, F. AU - Granger, B. E. PY - 2007 DA - 2007// TI - IPython: a system for interactive scientific computing JO - Comput Sci Eng VL - 9 UR - https://doi.org/10.1109/MCSE.2007.53 DO - 10.1109/MCSE.2007.53 ID - Perez2007 ER - TY - JOUR AU - Ye, K. AU - Schulz, M. H. AU - Long, Q. AU - Apweiler, R. AU - Ning, Z. PY - 2009 DA - 2009// TI - Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp394 DO - 10.1093/bioinformatics/btp394 ID - Ye2009 ER - TY - JOUR AU - Saunders, C. T. PY - 2012 DA - 2012// TI - Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts271 DO - 10.1093/bioinformatics/bts271 ID - Saunders2012 ER - TY - JOUR AU - Sadedin, S. P. AU - Pope, B. AU - Oshlack, A. PY - 2012 DA - 2012// TI - Bpipe: a tool for running and managing bioinformatics pipelines JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts167 DO - 10.1093/bioinformatics/bts167 ID - Sadedin2012 ER - TY - JOUR AU - Vivian, J. PY - 2017 DA - 2017// TI - Toil enables reproducible, open source, big biomedical data analyses JO - Nat Biotechnol VL - 35 UR - https://doi.org/10.1038/nbt.3772 DO - 10.1038/nbt.3772 ID - Vivian2017 ER - TY - JOUR AU - Kurtzer, G. M. AU - Sochat, V. AU - Bauer, M. W. PY - 2017 DA - 2017// TI - Singularity: scientific containers for mobility of compute JO - PLoS ONE VL - 12 UR - https://doi.org/10.1371/journal.pone.0177459 DO - 10.1371/journal.pone.0177459 ID - Kurtzer2017 ER - TY - JOUR AU - Rustad, E. H. PY - 2019 DA - 2019// TI - Stability and uniqueness of clonal immunoglobulin CDR3 sequences for MRD tracking in multiple myeloma JO - Am J Hematol UR - https://doi.org/10.1002/ajh.25641 DO - 10.1002/ajh.25641 ID - Rustad2019 ER - TY - JOUR AU - Rustad, E. H. PY - 2019 DA - 2019// TI - Baseline identification of clonal V(D)J sequences for DNA-based minimal residual disease detection in multiple myeloma JO - PLoS ONE VL - 14 UR - https://doi.org/10.1371/journal.pone.0211600 DO - 10.1371/journal.pone.0211600 ID - Rustad2019 ER - TY - JOUR AU - Slotkin, E. K. PY - 2019 DA - 2019// TI - Patient-driven discovery, therapeutic targeting, and post-clinical validation of a novel fusion-driven cancer JO - Cancer Discov VL - 9 UR - https://doi.org/10.1158/2159-8290.CD-18-0953 DO - 10.1158/2159-8290.CD-18-0953 ID - Slotkin2019 ER - TY - JOUR AU - Kazandjian, D. PY - 2019 DA - 2019// TI - Molecular underpinnings of clinical disparity patterns in African American vs. Caucasian American multiple myeloma patients JO - Blood Cancer J VL - 9 UR - https://doi.org/10.1038/s41408-019-0177-9 DO - 10.1038/s41408-019-0177-9 ID - Kazandjian2019 ER - TY - JOUR AU - Diolaiti, D. PY - 2018 DA - 2018// TI - A recurrent novel fusion identifies a new subtype of high-grade spindle cell sarcoma JO - Cold Spring Harb Mol Case Stud VL - 4 UR - https://doi.org/10.1101/mcs.a003194 DO - 10.1101/mcs.a003194 ID - Diolaiti2018 ER - TY - JOUR AU - Ledergor, G. PY - 2018 DA - 2018// TI - Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma JO - Nat Med VL - 24 UR - https://doi.org/10.1038/s41591-018-0269-2 DO - 10.1038/s41591-018-0269-2 ID - Ledergor2018 ER - TY - JOUR AU - Xiao, W. PY - 2018 DA - 2018// TI - Mutations are enriched in distinct subgroups of mixed phenotype acute leukemia with T-lineage differentiation JO - Blood Adv VL - 2 UR - https://doi.org/10.1182/bloodadvances.2018023531 DO - 10.1182/bloodadvances.2018023531 ID - Xiao2018 ER - TY - JOUR AU - Bolton, K. L. PY - 2019 DA - 2019// TI - Oncologic therapy shapes the fitness landscape of clonal hematopoiesis JO - bioRxiv UR - https://doi.org/10.1101/848739 DO - 10.1101/848739 ID - Bolton2019 ER - TY - JOUR AU - Bernard, E. PY - 2019 DA - 2019// TI - Implications of TP53 allelic state for genome stability, clinical presentation and outcomes in myelodysplastic syndromes JO - bioRxiv UR - https://doi.org/10.1101/2019.12.19.868844 DO - 10.1101/2019.12.19.868844 ID - Bernard2019 ER - TY - JOUR AU - Zehir, A. PY - 2017 DA - 2017// TI - Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients JO - Nat Med VL - 23 UR - https://doi.org/10.1038/nm.4333 DO - 10.1038/nm.4333 ID - Zehir2017 ER - TY - JOUR AU - Niu, B. PY - 2014 DA - 2014// TI - MSIsensor: microsatellite instability detection using paired tumor-normal sequence data JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btt755 DO - 10.1093/bioinformatics/btt755 ID - Niu2014 ER - TY - JOUR AU - Davies, H. PY - 2017 DA - 2017// TI - HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures JO - Nat Med VL - 23 UR - https://doi.org/10.1038/nm.4292 DO - 10.1038/nm.4292 ID - Davies2017 ER - TY - JOUR AU - Fu, Y. PY - 2020 DA - 2020// TI - Pan-cancer computational histopathology reveals mutations, tumor composition and prognosis JO - Nat Cancer UR - https://doi.org/10.1101/813543 DO - 10.1101/813543 ID - Fu2020 ER - TY - JOUR AU - Barker, J. AU - Hoogi, A. AU - Depeursinge, A. AU - Rubin, D. L. PY - 2016 DA - 2016// TI - Automated classification of brain tumor type in whole-slide digital pathology images using local representative tiles JO - Med Image Anal VL - 30 UR - https://doi.org/10.1016/j.media.2015.12.002 DO - 10.1016/j.media.2015.12.002 ID - Barker2016 ER - TY - JOUR AU - O’Connor, B. D. AU - Merriman, B. AU - Nelson, S. F. PY - 2010 DA - 2010// TI - SeqWare query engine: storing and searching sequence data in the cloud JO - BMC Bioinform VL - 11 UR - https://doi.org/10.1186/1471-2105-11-S12-S2 DO - 10.1186/1471-2105-11-S12-S2 ID - O’Connor2010 ER - TY - STD TI - Correction: The cancer genomics cloud: collaborative, reproducible, and democratized-a new paradigm in large-scale computational research. Cancer Res. 2018;78:5179. ID - ref37 ER - TY - JOUR AU - Birger, C. PY - 2017 DA - 2017// TI - FireCloud, a scalable cloud-based platform for collaborative genome analysis: strategies for reducing and controlling costs JO - bioRxiv UR - https://doi.org/10.1101/209494 DO - 10.1101/209494 ID - Birger2017 ER - TY - JOUR AU - Fisch, K. M. PY - 2015 DA - 2015// TI - Omics Pipe: a community-based framework for reproducible multi-omics data analysis JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv061 DO - 10.1093/bioinformatics/btv061 ID - Fisch2015 ER - TY - JOUR AU - Kallio, M. A. PY - 2011 DA - 2011// TI - Chipster: user-friendly analysis software for microarray and other high-throughput data JO - BMC Genom VL - 12 UR - https://doi.org/10.1186/1471-2164-12-507 DO - 10.1186/1471-2164-12-507 ID - Kallio2011 ER - TY - JOUR AU - Reich, M. PY - 2006 DA - 2006// TI - GenePattern 2.0 JO - Nat Genet VL - 38 UR - https://doi.org/10.1038/ng0506-500 DO - 10.1038/ng0506-500 ID - Reich2006 ER -