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Journal Articles

  1. Linderman MD, Paudyal C, Shakeel M, Kelley W, Bashir A, Gelb BD. NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data. Gigascience. 2021;10(7).
  2. Linderman MD, Suckiel SA, Thompson N, Weiss DJ, Roberts JS, Green RC. Development and Validation of a Comprehensive Genomics Knowledge Scale. Public Health Genomics. 2021;1–13.
  3. Linderman MD, McElroy L, Chang L. MySeq: privacy-protecting browser-based personal Genome analysis for genomics education and exploration. BMC Med Genomics. 2019;12(1):172.
  4. Linderman MD, Chia D, Wallace F, Nothaft FA. DECA: scalable XHMM exome copy-number variant calling with ADAM and Apache Spark. BMC Bioinformatics. 2019;20:493.
  5. Zoltick ES, Linderman MD, McGinniss MA, Ramos E, Ball MP, Church GM, et al. Predispositional genome sequencing in healthy adults: design, participant characteristics, and early outcomes of the PeopleSeq Consortium. Genome Med. 2019;11(1):10.
  6. Linderman MD, Sanderson SC, Bashir A, Diaz GA, Kasarskis A, Zinberg R, et al. Impacts of incorporating personal genome sequencing into graduate genomics education: a longitudinal study over three course years. BMC Med Genomics. 2018;11(1):5.
  7. Belbin GM, Odgis J, Sorokin EP, Yee M-C, Kohli S, Glicksberg BS, et al. Genetic identification of a common collagen disease in puerto ricans via identity-by-descent mapping in a health system. Elife. 2017;6.
  8. Rasmussen-Torvik LJ, Almoguera B, Doheny KF, Freimuth RR, Gordon AS, Hakonarson H, et al. Concordance between Research Sequencing and Clinical Pharmacogenetic Genotyping in the eMERGE-PGx Study. J. Mol. Diagn. 2017;19(4):561-566.
  9. Bichoupan K, Tandon N, Martel-Laferriere V, Patel NM, Sachs D, Ng M, et al. Factors associated with success of telaprevir- and boceprevir-based triple therapy for hepatitis C virus infection. World J. Hepatol. Baishideng Publishing Group Inc; 2017;9:551–61.
  10. Sanderson SC, Linderman MD, Suckiel SA, Zinberg R, Wasserstein M, Kasarskis A, et al. Psychological and behavioural impact of returning personal results from whole-genome sequencing: the HealthSeq project. Eur J Hum Genet. 2017;25(3):280-92.
  11. Anchang B, Hart TDP, Bendall SC, Qiu P, Bjornson Z, Linderman M, et al. Visualization and cellular hierarchy inference of single-cell data using SPADE. Nat Protoc. 2016;11(7):1264–79.
  12. Uzilov AV, Ding W, Fink MY, Antipin Y, Brohl AS, Davis C, et al. Development and clinical application of an integrative genomic approach to personalized cancer therapy. Genome Med. 2016;8(1):62.
  13. Scott SA, Collet J-P, Baber U, Yang Y, Peter I, Linderman M, et al. Exome Sequencing of Extreme Clopidogrel Response Phenotypes Identifies B4GALT2 as a Determinant of On-treatment Platelet Reactivity. Clin Pharmacol Ther. 2016; 100(3):287-94.
  14. Delaney SK, Hultner ML, Jacob HJ, Ledbetter DH, McCarthy JJ, Ball M, et al. Toward clinical genomics in everyday medicine: perspectives and recommendations. Expert Rev Mol Diagn. 2016 Jan 25;16(5):521–32.
  15. Linderman MD, Nielsen DE, Green RC. Personal Genome Sequencing in Ostensibly Healthy Individuals and the PeopleSeq Consortium. J Pers Med. 2016;6(2):14.
  16. Sanderson SC, Linderman MD, Suckiel SA, Diaz GA, Zinberg RE, Ferryman K, et al. Motivations, concerns and preferences of personal genome sequencing research participants: Baseline findings from the HealthSeq project. Eur J Hum Genet. 2016 Jun 3;24(1):14–20.
  17. Suckiel SA, Linderman MD, Sanderson SC, Diaz GA, Melissa Kasarskia AW, Schadt EE, et al. Impact of genomic counseling on informed decision-making among ostensibly healthy individuals seeking personal genome sequencing: The HealthSeq project. J Genet Couns. 2016;25(5):1044-1053.
  18. Gaulton KJ, Ferreira T, Lee Y, Raimondo A, Mägi R, Reschen ME, et al. Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci. Nat Genet. 2015 Nov 9;47(12):1415–25.
  19. Linderman MD, Bashir A, Diaz GA, Kasarskis A, Sanderson SC, Zinberg RE, et al. Preparing the next generation of genomicists: a laboratory-style course in medical genomics. BMC Med Genomics. 2015;8:47.
  20. Webb BD, Wheeler PG, Hagen JJ, Cohen N, Linderman MD, Diaz GA, et al. Novel, Compound Heterozygous, Single-Nucleotide Variants in MARS2 Associated with Developmental Delay, Poor Growth, and Sensorineural Hearing Loss. Hum Mutat. 2015 Mar 9.
  21. Sanderson SC, Linderman MD, Zinberg R, Bashir A, Kasarskis A, Zweig M, Suckiel S, Shah H, Mahajan M, Diaz GA, Schadt EE. How Do Students React to Analyzing Their Own Genomes in a Whole-Genome Sequencing Course?: Outcomes of a Longitudinal Cohort Study. Genet Med. 2015;17: 866–74.
  22. Bichoupan K, Martel-Laferriere V, Sachs D, Ng M, Schonfeld EA, Pappas A, Crismale J, Stivala A, Khaitova V, Gardenier D, Linderman M, Perumalswami PV, Schiano TD, Odin JA, Liu L, Moskowitz AJ, Dieterich DT, Branch AD. Costs of Telaprevir-Based Triple Therapy for Hepatitis C: $189000 per Sustained Virologic Response. Hepatology. 2014 Oct;60(4):1187-95.
  23. Linderman MD, Brandt T, Edelmann L, Jabado O, Kasai Y, Kornreich R, Mahajan M, Shah H, Kasarskis A, Schadt EE Analytical Validation of Whole Exome and Whole Genome Sequencing for Clinical Applications. BMC medical genomics. 2014 Apr;7:20.
  24. Aghaeepour N, Finak G, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH. Critical Assessment of Automated Flow Cytometry Data Analysis Techniques. Nature methods. 2013;10:228–38.
  25. Sanderson SC, Linderman MD, Kasarskis A, Bashir A, Diaz GA, Mahajan M, Shah H, Wasserstein M, Zinberg RE, Zweig M, Schadt EE. Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study. Genome Med. 2013 Dec 30;5(12):113.
  26. Webb BD, Brandt T, Liu L, Jalas C, Liao J, Fedick A, Linderman M, Diaz G, Kornreich R, Trachtman H, Mehta L, Edelmann L. A founder mutation in COL4A3 causes autosomal recessive Alport syndrome in the Ashkenazi Jewish population. Clin Genet. 2013 Aug 8.
  27. Linderman MD, Bjornson Z, Simonds EF, Qiu P, Bruggner R, Sheode K, Meng TH, Plevritis SK, Nolan GP. CytoSPADE: High-Performance Analysis and Visualization of High-Dimensional Cytometry Data. Bioinformatics. 2012;15(18):2400-1.
  28. Qiu P, Simonds EF, Bendall SC, Gibbs KD, Jr., Bruggner RV, Linderman MD, Sachs K, Nolan GP, Plevritis SK. Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nat Biotechnol. 2011;29(10):886-91.
  29. Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP. Computational solutions to large-scale data management and analysis. Nat Rev Genet. [Review]. 2010 Sep;11(9):647-57.

    Assocciated audio slide show Computational Solutions to Large-scale Data Management and correspondence.

  30. Santhanam G, Linderman MD, Gilja V, Afshar A, Ryu SI, Meng TH, Shenoy KV. HermesB: a continuous neural recording system for freely behaving primates. IEEE Trans Biomed Eng. 2007 Nov;54(11):2037-50.

Conference Proceedings

  1. Nothaft FA, Massie M, Danford T, Zhang Z, Laserson U, Yeksigian C, et al. Rethinking Data-Intensive Science Using Scalable Analytics Systems. Proceedings of the 2015 ACM SIGMOD International Conference on Management of Data. Melbourne, Victoria, Australia: ACM; 2015. p. 631–46.
  2. Linderman MD, Bruggner R, Athalye V, Meng TH, Asadi NB, Nolan GP. High-throughput Bayesian network learning using heterogeneous multicore computers. Proc ACM Intl Conf on Supercomputing (ICS); 2010. p. 95-104.
  3. Linderman MD, Ho M, Dill DL, Meng TH, Nolan GP. Towards program optimization through automated analysis of numerical precision. Proc IEEE/ACM Intl Symp on Code Generation and Optimization (CGO); 2010. p. 230-7.
  4. Linderman MD, Balfour J, Meng TH, Dally WJ. Embracing heterogeneity: parallel programming for changing hardware. Proc USENIX Conf on Hot Topics in Parallelism (HOTPAR); 2009.
  5. Linderman MD, Collins JD, Wang H, Meng TH. Merge: a programming model for heterogeneous multi-core systems. Proc Intl Conf on Architectural Support for Programming Languages and Operating Systems (ASPLOS); 2008. p. 287-96.
  6. Linderman MD, Gilja V, Santhanam G, Afshar A, Ryu S, Meng TH, Shenoy KV. An autonomous, broadband, multi-channel neural recording system for freely behaving primates. Conf Proc IEEE Eng Med Biol Soc. 2006;1:1212-5.
  7. Linderman MD, Gilja V, Santhanam G, Afshar A, Ryu S, Meng TH, Shenoy KV. Neural recording stability of chronic electrode arrays in freely behaving primates. Conf Proc IEEE Eng Med Biol Soc. 2006;1:4387-91.
  8. Gilja V, Linderman MD, Santhanam G, Afshar A, Ryu S, Meng TH, Shenoy KV. Multiday electrophysiological recordings from freely behaving primates. Conf Proc IEEE Eng Med Biol Soc. 2006;1:5643-6.
  9. Shenoy KV, Santhanam G, Ryu SI, Afshar A, Yu BM, Gilja V, Linderman MD, Kalmar RS, Cunningham JP, Kemere CT, Batista AP, Churchland MM, Meng TH. Increasing the performance of cortically-controlled prostheses. Conf Proc IEEE Eng Med Biol Soc. 2006;Suppl:6652-6.


Linderman MD. A Programming Model and Processor Architecture for Heterogeneous Multicore Computers. Stanford, CA: Stanford University; 2009.