text:
%% Journal articles
@article{brown2021libceed,
  title={{libCEED}: Fast algebra for high-order element-based discretizations},
  author={Jed Brown and Ahmad Abdelfattah and Valeria Barra* and Natalie Beams and Jean-Sylvain Camier and Veselin Dobrev and Yohann Dudouit and Leila Ghaffari* and Tzanio Kolev and David Medina and Will Pazner and Thilina Rathnayake and Jeremy Thompson* and Stan Tomov},
  journal={Journal of Open Source Software},
  year={2021 (submitted)},
  doi={10.21105/joss.02945}
}
@article{zhang2021petscsf,
  title={The {PetscSF} Scalable Communication Layer},
  author={Zhang, Junchao and Brown, Jed and Balay, Satish and Faibussowitsch, Jacob and Knepley, Matthew and Marin, Oana and Mills, Richard Tran and Munson, Todd and Smith, Barry F and Zampini, Stefano},
  journal={International Journal of High Performance Computing Applications},
  archivePrefix={arXiv},
  eprint={2102.13018},
  year={2021 (submitted)}
}
@article{kolev2021ecpceed,
  title={Efficient Exascale Discretizations: High-Order Finite Element Methods},
  author={Tzanio Kolev and Paul Fischer and Misun Min and Jack Dongarra and Jed Brown and Veselin Dobrev and Tim Warburton and Stanimire Tomov and Mark S. Shephard and Ahmad Abdelfattah and Valeria Barra* and Natalie Beams and Jean-Sylvain Camier and Noel Chalmers and Yohann Dudouit and Ali Karakus and Ian Karlin and Stefan Kerkemeier and Yu-Hsiang Lan and David Medina and Elia Merzari and Aleksandr Obabko and Will Pazner and Thilina Rathnayake and Cameron W. Smith and Lukas Spies and Kasia Swirydowicz and Jeremy Thompson* and Ananias Tomboulides and Vladimir Tomov},
  journal={International Journal of High Performance Computing Applications},
  year={2020 (submitted)}
}
@article{mills2021ecppetsc,
  title={Toward Performance-Portable {PETSc} for {GPU}-based Exascale Systems},
  author={Richard Tran Mills and Mark F. Adams and Satish Balay and Jed Brown and Alp Dener and Matthew Knepley and Scott E. Kruger and Hannah Morgan and Todd Munson and Karl Rupp and Barry F. Smith and Stefano Zampini and Hong Zhang and Junchao Zhang},
  journal={International Journal of High Performance Computing Applications},
  year={2020 (submitted)}
}
@misc{abhyankar2018petscts,
  title={{PETSc/TS}: {A} Modern Scalable {ODE/DAE} Solver Library},
  author={Shrirang Abhyankar and Jed Brown and Emil M. Constantinescu and Debojyoti Ghosh and
Barry F. Smith and Hong Zhang},
  year={2018}
}
@article{brown2021tuning,
  title={Tuning Multigrid Methods with Robust Optimization},
  author={Brown, Jed and He, Yunhui and MacLachlan, Scott and Menickelly, Matt and Wild, Stefan M},
  journal={SIAM Journal on Scientific Computing},
  volume={43},
  issue=1,
  pages={A109--A138},
  archivePrefix={arXiv},
  eprint={2001.00887},
  year={2021},
  doi={10.1137/19M1308669}
}
@article{fischer2020scalability,
  title={Scalability of High-Performance {PDE} Solvers},
  author={Fischer, Paul and Min, Misun and Rathnayake, Thilina and Dutta, Som and Kolev, Tzanio and Dobrev, Veselin and Camier, Jean-Sylvain and Kronbichler, Martin and Warburton, Tim and Świrydowicz, Kasia and Brown, Jed},
  journal={International Journal of High Performance Computing Applications},
  publisher={SAGE Publications},
  year={2020},
  volume={34},
  issue=5,
  pages={562--586},
  doi={10.1177/1094342020915762},
  archivePrefix={arXiv},
  eprint={2004.06722}
}
@article{brown2019lfabddc,
  title={Local {F}ourier analysis of {BDDC}-like algorithms},
  author={Jed Brown and Yunhui He and Scott MacLachlan},
  journal={SIAM Journal on Scientific Computing},
  volume={41},
  issue=5,
  pages={S346--S369},
  publisher={SIAM},
  year={2019},
  doi={10.1137/18M1191373},
  pdf={https://jedbrown.org/files/BrownHeMacLachlan-LocalFourierAnalysisOfBDDCAlgorithms-2019.pdf},
}
@article{AdamsHirvijokiKnepleyBrownIsaacMills2017,
  title={Landau Collision Integral Solver with Adaptive Mesh Refinement on Emerging Architectures},
  author={Adams, Mark F and Hirvijoki, Eero and Knepley, Matthew G and Brown, Jed and Isaac, Tobin and Mills, Richard},
  journal={SIAM Journal on Scientific Computing},
  volume={39},
  number={6},
  pages={C452--C465},
  year={2017},
  publisher={SIAM},
  doi={10.1137/17M1118828},
  archivePrefix={arXiv},
  eprint={1702.08880},
  pdf={https://jedbrown.org/files/AdamsHirvijokiKnepleyBrownIsaacMills-LandauCollisionIntegralSolverAMR-2017.pdf}
}
@article{AdamsBrownKnepleySamtaney2016,
  title   = {Segmental Refinement: A Multigrid Technique for Data Locality},
  author  = {Mark F. Adams and Jed Brown and Matthew G. Knepley and Ravi Samtaney},
  journal = {SIAM Journal on Scientific Computing},
  archivePrefix={arXiv},
  eprint  = {1406.7808},
  volume  = {38},
  number  = {4},
  pages={C426--C440},
  doi     = {10.1137/140975127},
  year    = {2016}
}
@article{ghosh2015efficient,
  title={Efficient Implementation of Nonlinear Compact Schemes on Massively Parallel Platforms},
  author = {Debojyoti Ghosh and Emil M. Constantinescu and Jed Brown},
  journal={SIAM Journal on Scientific Computing},
  volume=37,
  number=3,
  pages={C354--C383},
  doi={10.1137/140989261},
  note={Also preprint ANL/MCS-P5121-0414},
  pdf={http://www.mcs.anl.gov/~emconsta/Repository/Papers/Ghosh_S2014a-preprint.pdf},
  year = {2015}
}
@article{may2015scalable,
  title = "A scalable, matrix-free multigrid preconditioner for finite element discretizations of heterogeneous {S}tokes flow ",
  journal = "Computer Methods in Applied Mechanics and Engineering ",
  volume = "290",
  number = "0",
  pages = "496--523",
  year = "2015",
  issn = "0045-7825",
  doi = "10.1016/j.cma.2015.03.014",
  pdf={https://jedbrown.org/files/MayBrownLePourhiet-ScalableMatrixFreeMultigridPreconditionerFEHeterogeneousStokes-2015.pdf},
  author = "David A. May and Jed Brown and Laetitia Le Pourhiet",
}
@article{brown2015runtime,
  title={Run-time extensibility and librarization of simulation software},
  author={Jed Brown and Matthew G. Knepley and Barry F. Smith},
  journal={IEEE Computing in Science and Engineering},
  volume={17},
  number={1},
  pages={38--45},
  year={2015},
  doi={10.1109/MCSE.2014.95},
  pdf={https://jedbrown.org/files/BrownKnepleySmith-RuntimeExtensibilityAndLibrarizationOfSimulationSoftware-2014.pdf}
}
@article{brown2013tmeice,
  title={Achieving textbook multigrid efficiency for hydrostatic ice flow},
  author={Jed Brown and Barry F. Smith and Aron Ahmadia},
  journal={SIAM Journal on Scientific Computing},
  volume=35,
  number=2,
  year={2013},
  pages={359--375},
  doi={10.1137/110834512},
  note={Also preprint ANL/MCS-P743-1298}
}
@article{KeyesMcInnesWoodwardEtAl13,
 title    = {Multiphysics Simulations: Challenges and Opportunities},
 author   = {David E. Keyes and Lois Curfman McInnes and Carol Woodward and
             William Gropp and Eric Myra and Michael Pernice and
             John Bell and Jed Brown and Alain Clo and Jeffrey Connors and
             Emil Constantinescu and Don Estep and Kate Evans and Charbel Farhat and
             Ammar Hakim and Glenn Hammond and Glen Hansen and Judith Hill and
             Tobin Isaac and Xiangmin Jiao and Kirk Jordan and Dinesh Kaushik and
             Efthimios Kaxiras and Alice Koniges and Kihwan Lee and Aaron Lott and
             Qiming Lu and John Magerlein and Reed Maxwell and Michael McCourt and
             Miriam Mehl and Roger Pawlowski and Amanda Peters Randles and Daniel Reynolds and
             Beatrice Rivi\`{e}re and Ulrich R\"{u}de and Tim Scheibe and John Shadid and
             Brendan Sheehan and Mark Shephard and Andrew Siegel and
             Barry Smith and Xianzhu Tang and Cian Wilson and Barbara Wohlmuth},
 journal  = {International Journal of High Performance Computing Applications},
 month    = {Feb},
 year     = {2013},
 volume   = {27},
 number   = {1},
 pages    = {4--83},
 doi      = {10.1177/1094342012468181},
 note     = {Special issue},
 abstract = {We consider multiphysics applications from algorithmic and
architectural perspectives, where ``algorithmic'' includes both
mathematical analysis and computational complexity and
``architectural'' includes both software and hardware environments.
Many diverse multiphysics applications can be reduced, en route to
their computational simulation, to a common algebraic coupling
paradigm. Mathematical analysis of multiphysics coupling in this form
is not always practical for realistic applications, but model problems
representative of applications discussed herein can provide insight.
A variety of software frameworks for multiphysics applications have
been constructed and refined within disciplinary communities and
executed on leading-edge computer systems.  We examine several of
these, expose some commonalities among them, and attempt to
extrapolate best practices to future systems. From our study, we
summarize challenges and forecast opportunities.}
}
@article{malas2012streaming,
  title={Optimizing the Performance of Streaming Numerical Kernels on the {IBM BlueGene/P PowerPC} 450 Processor},
  author={Tareq M. Malas and Aron J. Ahmadia and Jed Brown and John A. Gunnels and David E. Keyes},
  journal={International Journal of High Performance Computing Applications},
  volume={27},
  number={2},
  pages={193--209},
  year={2013},
  publisher={SAGE Publications},
  doi={10.1177/1094342012444795}
}
@article {biezuner2012computing,
   author = {Biezuner, Rodney and Brown, Jed and Ercole, Grey and Martins, Eder},
   affiliation = {Departamento de Matem\'atica—ICEx, Universidade Federal de Minas Gerais, Av. Ant\^onio Carlos 6627, Caixa Postal 702, 30161-970 Belo Horizonte, MG, Brazil},
   title = {Computing the First Eigenpair of the $p$-{L}aplacian via Inverse Iteration of Sublinear Supersolutions},
   journal = {Journal of Scientific Computing},
   publisher = {Springer Netherlands},
   issn = {0885-7474},
   keyword = {Mathematics and Statistics},
   pages = {180--201},
   volume = 52,
   issue = 1,
   year = 2012,
   doi = {10.1007/s10915-011-9540-0}
}
@article {brown2010dohp,
  author = {Brown, Jed},
  affiliation = {Versuchsanstalt f\"ur Wasserbau, Hydrologie und Glaziologie (VAW), ETH Z\"urich, Z\"urich, Switzerland},
  title = {Efficient Nonlinear Solvers for Nodal High-Order Finite Elements in {3D}},
  journal = {Journal of Scientific Computing},
  publisher = {Springer Netherlands},
  issn = {0885-7474},
  keyword = {Mathematics and Statistics},
  pages = {48-63},
  volume = {45},
  issue = {1},
  doi = {10.1007/s10915-010-9396-8},
  abstract = {Conventional high-order finite element methods are rarely used for industrial problems because the Jacobian rapidly loses sparsity as the order is increased, leading to unaffordable solve times and memory requirements. This effect typically limits order to at most quadratic, despite the favorable accuracy and stability properties offered by quadratic and higher order discretizations. We present a method in which the action of the Jacobian is applied matrix-free exploiting a tensor product basis on hexahedral elements, while much sparser matrices based on Q 1 sub-elements on the nodes of the high-order basis are assembled for preconditioning. With this  dual-order  scheme, storage is independent of spectral order and a natural taping scheme is available to update a full-accuracy matrix-free Jacobian during residual evaluation. Matrix-free Jacobian application circumvents the memory bandwidth bottleneck typical of sparse matrix operations, providing several times greater floating point performance and better use of multiple cores with shared memory bus. Computational results for the p-Laplacian and Stokes problem, using block preconditioners and AMG, demonstrate mesh-independent convergence rates and weak (bounded) dependence on order, even for highly deformed meshes and nonlinear systems with several orders of magnitude dynamic range in coefficients. For spectral orders around 5, the dual-order scheme requires half the memory and similar time to assembled quadratic (Q 2) elements, making it very affordable for general use.},
  year = {2010},
  pdf = {https://jedbrown.org/files/Brown-EfficientNonlinearSolversNodalHighOrder3D-2010.pdf}
}
@article{amundson2010ice,
  title={{Ice m{\'e}lange dynamics and implications for terminus stability, Jakobshavn Isbr{\ae}, Greenland}},
  author={Jason M. Amundson and Mark Fahnestock and Martin Truffer and Jed Brown and Martin P. L{\"u}thi and Roman J. Motyka},
  journal={J. Geophys. Res},
  volume={115},
  pages={F01005},
  year={2010},
  doi={10.1029/2009JF001405}
}
@article{bueler2009shallow,
  title={{Shallow shelf approximation as a ``sliding law'' in a thermomechanically coupled ice sheet model}},
  author={Bueler, E. and Brown, J.},
  journal={Journal of Geophysical Research-Earth Surface},
  volume={114},
  number={F3},
  pages={F03008},
  year={2009},
  publisher={American Geophysical Union},
  doi={10.1029/2008JF001179},
  archivePrefix={arXiv},
  eprint={0810.3449}
}
@article{bueler2007est,
  title={{Exact solutions to the thermomechanically coupled shallow ice approximation: effective tools for verification}},
  author={Bueler, E. and Brown, J. and Lingle, C.},
  journal={J. Glaciol},
  volume={53},
  pages={499--516},
  year={2007},
  doi={10.3189/002214307783258396}
}
@article{bueler2007fcv,
  title={Fast computation of a viscoelastic deformable {Earth} model for ice-sheet simulations},
  author={Bueler, E. and Lingle, C.S. and Brown, J.},
  journal={Ann. Glaciol},
  volume={46},
  pages={97--105},
  year={2007},
  doi={10.3189/172756407782871567},
}
@article {bueler2005iso,
  author = {E. Bueler and C. S. Lingle and J. A. Kallen-Brown and D. N. Covey and L. N. Bowman},
  title = {Exact solutions and numerical verification for isothermal ice sheets},
  journal = {J. Glaciol.},
  volume = {51},
  number = {173},
  pages = {291--306},
  year = {2005},
  doi = {10.3189/172756505781829449}
}

%% Conference
@InProceedings{mehraban2021nearlyincompressible,
  author = {A. Mehraban* and J. Thompson* and J. Brown and R. Regueiro and V. Barra* and H. Tufo},
  title = {Simulating Compressible and Nearly-Incompressible Linear Elasticity Using an Efficient Parallel Scalable Matrix-Free High-Order Finite Element Method},
  booktitle = {Proceedings of {WCCM-ECCOMAS2020}},
  pages = {1--15},
  year = 2021,
  doi = {10.23967/wccm-eccomas.2020.302},
  pdf={//files/MehrabanAO-CompressibleNearlyIncompressibleLinearElasticity-2021.pdf}
}
@proceedings{mehraban2020neohookean,
    author = {Mehraban*, Arash and Brown, Jed and Barra*, Valeria and Tufo, Henry and Thompson*, Jeremy and Regueiro, Richard},
    title = "{Efficient Residual and Matrix-Free Jacobian Evaluation for Three-Dimensional Tri-Quadratic Hexahedral Finite Elements With Nearly-Incompressible Neo-Hookean Hyperelasticity Applied to Soft Materials on Unstructured Meshes in Parallel, With PETSc and libCEED}",
    volume = {Volume 12: Mechanics of Solids, Structures, and Fluids},
    series = {ASME International Mechanical Engineering Congress and Exposition},
    year = {2020},
    month = {11},
    abstract = "{Soft materials such as rubber, elastomers, and soft biological tissues mechanically deform at large strain isochorically for all time, or during their initial transient (when a pore fluid, typically incompressible such as water, does not have time to flow out of the deforming polymer or soft tissue porous skeleton). Simulating these large isochoric deformations computationally, such as with the Finite Element Method (FEM), requires higher order (typically quadratic) interpolation functions and/or enhancements through hybrid/mixed methods to maintain stability. Lower order (linear) finite elements with hybrid/mixed formulation may not perform stably for all mechanical loading scenarios involving large isochoric deformations, whereas quadratic finite elements with or without hybrid/mixed formulation typically perform stably, especially when large bending or folding deformations are being simulated. For topology-optimization design of soft robotics, for instance, the FEM solid mechanics solver must run efficiently and stably. Stability is ensured by the higher order finite element formulation (with possible enhancement), but efficiency for higher order FEM remains a challenge. Thus, this paper addresses efficiency from the perspective of computer science algorithms and programming. The proposed efficient algorithm utilizes the Portable, Extensible Toolkit for Scientific Computation (PETSc), along with the libCEED library for efficient compiler optimized tensor-product-basis computation to demonstrate an efficient nonlinear solution algorithm. For preconditioning, a scalable p-multigrid method is presented whereby a hierarchy of levels is constructed. In contrast to classical geometric multigrid, also known as h-multigrid, each level in p-multigrid is related to a different approximation polynomial order, p, instead of the element size, h. A Chebyshev polynomial smoother is used on each multigrid level. Algebraic MultiGrid (AMG) is then applied to the assembled Q1 (linear) coarse mesh on the nodes of the quadratic Q2 (quadratic) mesh. This allows low storage that can be efficiently used to accelerate the convergence to solution. For a Neo-Hookean hyperelastic problem, we examine a residual and matrix-free Jacobian formulation of a tri-quadratic hexahedral finite element with enhancement. Efficiency estimates on AVX-2 architecture based on CPU time are provided as a comparison to similar simulation (and mesh) of isochoric large deformation hyperelasticity as applied to soft materials conducted with the commercially-available FEM software program ABAQUS. The particular problem in consideration is the simulation of an assistive device in the form of finger-bending in 3D.}",
    doi = {10.1115/IMECE2020-24522},
    note = {V012T12A027},
    url = {https://asmedigitalcollection.asme.org/IMECE/proceedings-pdf/IMECE2020/84607/V012T12A027/6638664/v012t12a027-imece2020-24522.pdf},
}
@InProceedings{ libceed-paper-proc-scipy-2020,
  author    = { {V}aleria {B}arra* and {J}ed {B}rown and {J}eremy {T}hompson* and {Y}ohann {D}udouit },
  title     = { {H}igh-performance operator evaluations with ease of use: lib{C}{E}{E}{D}'s {P}ython interface },
  booktitle = { {P}roceedings of the 19th {P}ython in {S}cience {C}onference },
  pages     = { 85 - 90 },
  year      = { 2020 },
  editor    = { {M}eghann {A}garwal and {C}hris {C}alloway and {D}illon {N}iederhut and {D}avid {S}hupe },
  doi       = { 10.25080/Majora-342d178e-00c }
}
@inproceedings{konolige2018parallel,
  title={A Parallel Solver for Graph {L}aplacians},
  author={Tristan Konolige* and Jed Brown},
  booktitle={Proceedings of the Platform for Advanced Scientific Computing (PASC)},
  doi={10.1145/3218176.3218227},
  note={Best Paper Award},
  archivePrefix={arXiv},
  eprint={1705.06266},
  year={2018},
  pdf={https://arxiv.org/pdf/1705.06266.pdf}
}
@inproceedings{duplyakin2018memory,
  title={Evaluating Active Learning with Cost and Memory Awareness},
  author={Dmitry Duplyakin* and Jed Brown and Donna Calhoun},
  booktitle={2018 IEEE International Parallel and Distributed Processing Symposium (IPDPS)},
  doi={10.1109/IPDPS.2018.00031},
  pages={214--223},
  year={2018},
  organization={IEEE},
  note={Acceptance Rate 24.4\%},
  pdf={https://jedbrown.org/files/DuplyakinBrownCalhoun-ActiveLearningCostMemoryAware-2018.pdf}
}
@InProceedings{duplyakin2016active,
    author      = "Dmitry Duplyakin* and Jed Brown and Robert Ricci",
    title       = "Active Learning in Performance Analysis",
    booktitle   = "Proceedings of the IEEE Cluster Conference",
    doi         = {10.1109/CLUSTER.2016.63},
    year        = 2016,
    month       = Sep,
    url         = "http://www.flux.utah.edu/paper/duplyakin-cluster16",
    note={Acceptance Rate 24.1\%},
    pdf         = {https://jedbrown.org/files/DuplyakinBrownRicci-ActiveLearningPerformanceAnalysis-2016.pdf}
}
@inproceedings{may2014ptatin,
  author={Dave A. May and Jed Brown and Laetitia Le Pourhiet},
  title={{pTatin3D}: {H}igh-Performance Methods for Long-Term Lithospheric Dynamics},
  booktitle={Proceedings of SC14: International Conference for High Performance Computing, Networking, Storage and Analysis},
  year={2014},
  organization={ACM},
  note={Acceptance Rate 21\%},
  pdf = {https://jedbrown.org/files/MayBrownLePourhiet-pTatin3d-2014.pdf},
  doi = {10.1109/SC.2014.28},
}
@inproceedings{knepley2013citations,
  title={Accurately Citing Software and Algorithms Used in Publications},
  author={Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry F. Smith},
  booktitle={Workshop towards Sustainable Software for Science: Practice and Experiences (WSSSPE)},
  doi={10.6084/m9.figshare.785731},
  year={2013}
}
@inproceedings{brown2013runtime,
  title={Run-time extensibility: anything less is unsustainable},
  author={Jed Brown, Matthew G. Knepley, Barry F. Smith},
  booktitle={Workshop towards Sustainable Software for Science: Practice and Experiences (WSSSPE)},
  doi={10.6084/m9.figshare.791571},
  year={2013}
}
@inproceedings{brown2013quasinewton,
  author    = {Jed Brown and Peter Brune},
  title     = {Low-rank quasi-{N}ewton updates for robust {J}acobian lagging in {N}ewton-type methods},
  year      = {2013},
  booktitle = {International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering},
  pages     = {2554--2565},
  pdf       = {https://jedbrown.org/files/BrownBrune-LowRankQuasiNewtonRobustJacobianLagging-2013.pdf}
}
@inproceedings{bkmms2012,
  author    = {J. Brown and M. G. Knepley and D. A. May and L. C. McInnes and B. F. Smith},
  title     = {Composable Linear Solvers for Multiphysics},
  booktitle = {Proceeedings of the 11th International Symposium on Parallel and Distributed Computing (ISPDC 2012)},
  year      = {2012},
  doi       = {10.1109/ISPDC.2012.16},
  publisher = {IEEE Computer Society},
  pages     = {55--62},
}
@InProceedings{eth_biwi_00721,
  author = {K. Burckhardt and D. Szczerba and J. Brown and K. Muralidhar and and G. Székely},
  title = {Fast Implicit Simulation of Oscillatory Flow in Human Abdominal Bifurcation using a Schur Complement Preconditioner},
  booktitle = {Euro-Par 2009 Parallel Processing},
  year = {2009},
  month = {August},
  pages = {747-759},
  volume = {5704},
  editor = {H. Sips and D. Epema and and H.-X. Lin},
  series = {Lecture Notes in Computer Science},
  publisher = {Springer},
  keywords = {Aortic aneurysm, flow simulation, streamline diffusion FEM, indefinite matrix, parallel Krylov solver},
  doi = {10.1007/978-3-642-03869-3_70}
}

%% Reports
@misc{kolev2021ceedms36,
  title={{CEED ECP} Milestone Report: High-order algorithmic developments and optimizations for large-scale {GPU}-accelerated simulations},
  DOI={10.5281/zenodo.4672664},
  publisher={Zenodo},
  author={Kolev, Tzanio and Fischer, Paul and Austin, Anthony P. and Barker, Andrew T. and Beams, Natalie and Brown, Jed and Camier, Jean-Sylvain and Chalmers, Noel and Dobrev, Veselin and Dudouit, Yohann and et al.},
  year={2021},
  month={Mar}
}
@misc{konolige2020multigrid,
  title={Multigrid for Bundle Adjustment},
  author={Tristan Konolige and Jed Brown},
  year={2020},
  eprint={2007.01941},
  archivePrefix={arXiv},
  primaryClass={cs.CV}
}
@misc{abdelfattah_ahmad_2020_4302737,
  author       = {Abdelfattah, Ahmad and
                  Barra, Valeria and
                  Beams, Natalie and
                  Brown, Jed and
                  Camier, Jean-Sylvain and
                  Dobrev, Veselin and
                  Dudouit, Yohann and
                  Ghaffari, Leila and
                  Kolev, Tzanio and
                  Medina, David and
                  Rathnayake, Thilina and
                  Thompson, Jeremy L and
                  Tomov, Stanimire},
  title        = {libCEED User Manual},
  month        = sep,
  year         = 2020,
  publisher    = {Zenodo},
  version      = {0.7},
  doi          = {10.5281/zenodo.4302737},
  url          = {https://doi.org/10.5281/zenodo.4302737}
}
@misc{kolev_tzanio_2020_4146401,
  author       = {Kolev, Tzanio and
                  Fischer, Paul and
                  Abdelfattah, Ahmad and
                  Barra, Valeria and
                  Beams, Natalie and
                  Brown, Jed and
                  Camier, Jean-Sylvain and
                  Chalmers, Noel and
                  Dobrev, Veselin and
                  Kerkemeier, Stefan and
                  Lan, Yu-Hsiang and
                  Merzari, Elia and
                  Min, Misun and
                  Phillips, Malachi and
                  Ratnayaka, Thilina and
                  Rowe, Kris and
                  Thompson, Jeremy and
                  Tomboulides, Ananias and
                  Tomov, Stanimire and
                  Tomov, Vladimir and
                  Warburton, Tim},
  title        = {{CEED ECP Milestone Report: Support CEED-enabled
                   ECP applications in their preparation for
                   Aurora/Frontier}},
  month        = sep,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.4146401},
  url          = {https://doi.org/10.5281/zenodo.4146401}
}
@misc{kolev_tzanio_2020_3860804,
  author       = {Kolev, Tzanio and
                  Fischer, Paul and
                  Abdelfattah, Ahmad and
                  Ananthan, Shreyas and
                  Barra, Valeria and
                  Beams, Natalie and
                  Bleile, Ryan and
                  Brown, Jed and
                  Carson, Robert and
                  Camier, Jean-Sylvain and
                  Churchfield, Matthew and
                  Dobrev, Veselin and
                  Dongarra, Jack and
                  Dudouit, Yohann and
                  Karakus, Ali and
                  Kerkemeier, Stefan and
                  Lan, YuHsiang and
                  Medina, David and
                  Merzari, Elia and
                  Min, Misun and
                  Parker, Scott and
                  Ratnayaka, Thilina and
                  Smith, Cameron and
                  Sprague, Michael and
                  Stitt, Thomas and
                  Thompson, Jeremy and
                  Tomboulides, Ananias and
                  Tomov, Stanimire and
                  Tomov, Vladimir and
                  Vargas, Arturo and
                  Warburton, Tim and
                  Weiss, Kenneth},
  title        = {{CEED ECP Milestone Report: Improve performance and
                   capabilities of CEED-enabled ECP applications on
                   Summit/Sierra}},
  month        = may,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3860804},
  url          = {https://doi.org/10.5281/zenodo.3860804}
}
@misc{tomov_stanimire_2019_3477618,
  author       = {Tomov, Stanimire and
                  Abdelfattah, Ahmad and
                  Barra, Valeria and
                  Beams, Natalie and
                  Brown, Jed and
                  Camier, Jean-Sylvain and
                  Dobrev, Veselin and
                  Dongarra, Jack and
                  Dudouit, Yohann and
                  Fischer, Paul and
                  Karakus, Ali and
                  Kerkemeier, Stefan and
                  Kolev, Tzanio and
                  Lan, YuHsiang and
                  Merzari, Elia and
                  Min, Misun and
                  Obabko, Aleks and
                  Parker, Scott and
                  Ratnayaka, Thilina and
                  Thompson, Jeremy and
                  Tomboulides, Ananias and
                  Tomov, Vladimir and
                  Warburton, Tim},
  title        = {{CEED ECP Milestone Report: Performance tuning of
                   CEED software and 1st and 2nd wave apps}},
  month        = oct,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3477618},
  url          = {https://doi.org/10.5281/zenodo.3477618}
}
@misc{shephard_mark_2019_3336420,
  author       = {Shephard, Mark and
                  Barra, Valeria and
                  Brown, Jed and
                  Camier, Jean-Sylvain and
                  Dudouit, Yohan and
                  Fischer, Paul and
                  Kolev, Tzanio and
                  Medina, David and
                  Min, Misun and
                  Smith, Cameron and
                  Siboni, Morteza H. and
                  Thompson, Jeremy and
                  Warburton, Tim},
  title        = {{CEED ECP Milestone Report: Improved Support for
                   Parallel Adaptive Simulation in CEED}},
  month        = jul,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3336420},
  url          = {https://doi.org/10.5281/zenodo.3336420}
}
@misc{brown_jed_2019_2641316,
  author       = {Brown, Jed and
                  Abdelfattah, Ahmad and
                  Barra, Valeria and
                  Dobrev, Veselin and
                  Dudouit, Yohann and
                  Fischer, Paul and
                  Kolev, Tzanio and
                  Medina, David and
                  Min, Misun and
                  Ratnayaka, Thilina and
                  Smith, Cameron and
                  Thompson, Jeremy and
                  Tomov, Stanimire and
                  Tomov, Vladimir and
                  Warburton, Tim},
  title        = {{CEED ECP Milestone Report: Public release of CEED
                   2.0}},
  month        = mar,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.2641316},
  url          = {https://doi.org/10.5281/zenodo.2641316}
}
@misc{camier_jean_sylvain_2019_2542359,
  author       = {Camier, Jean-Sylvain and
                  Fischer, Paul and
                  Ali Karakus and
                  Kerkemeier, Stefan and
                  Kolev, Tzanio and
                  Lan, Yu-Hsiang and
                  Medina, David and
                  Merzari, Elia and
                  Min, Misun and
                  Obabko, Aleks and
                  Ratnayaka, Thilina and
                  Shaver, Dillon and
                  Tomboulides, Ananias and
                  Tomov, Vladimir and
                  Warburton, Tim},
  title        = {{CEED ECP Milestone Report: Engage second wave
                   ECP/CEED applications}},
  month        = mar,
  year         = 2019,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.2542359},
  url          = {https://doi.org/10.5281/zenodo.2542359}
}
@misc{barba2019softwaredue,
 title={Giving software its due through community-driven review and publication},
 url={osf.io/f4vx6},
 publisher={OSF Preprints},
 author={Barba, Lorena and Bazán, Juanjo and Brown, Jed and Guimera, Roman V and Gymrek, Melissa and Hanna, Alex and Heagy, Lindsey J and Huff, Kathryn D and Katz, Daniel S and Madan, Christopher R and et al.},
 year={2019},
 month={Apr},
 doi={10.31219/osf.io/f4vx6}
}
@book{jupyter4edu,
  author = {Lorena A. Barba and
    Lecia J. Barker and
    Douglas S. Blank and
    Jed Brown and
    Allen B. Downey and
    Timothy George and
    Lindsey J. Heagy and
    Kyle T. Mandli and
    Jason K. Moore and
    David Lippert and
    Kyle E. Niemeyer and
    Ryan R. Watkins and
    Richard H. West and
    Elizabeth Wickes and
    Carol Willing and
    Michael Zingale},
  title={Teaching and Learning with Jupyter},
  year={2019},
  publisher={GitHub},
  url={https://jupyter4edu.github.io/jupyter-edu-book/},
}
@techreport{barnhart2018ctsp,
  author={Katherine Barnhart and Thorsten Becker and Mark Behn and Jed Brown and Eunseo Choi and Catherine Cooper and Juliane Dannberg and Nicole Gasparini and Rene Gassmoeller and Lorraine Hwang and Boris Kaus and Louise Kellogg and Luc Lavier and Eric Mittelstaedt and Louis Moresi and Adina Pusok and Greg Tucker and Phaedra Upton and Pedro Va},
  title={{CTSP}: Coupling of Tectonic and Surface Processes},
  subtitle={Whitepaper Reporting Outcomes from NSF-Sponsored Workshop},
  institution={University of Colorado},
  year={2018},
  pdf={https://jedbrown.org/files/CTSP-Report-2018.pdf}
}
@article{williams2018hpgmg,
  author = {Samuel Williams and Mark F. Adams and Jed Brown},
  title = {High-Performance Geometric Multigrid: {A}n {HPC} Performance Benchmark},
  journal = {SIAM News},
  volume = 51,
  number = 3,
  year = 2018,
  url={https://sinews.siam.org/Details-Page/the-high-performance-geometric-multigrid-an-hpc-performance-benchmark}
}
@misc{tomov_stanimire_2018_2542350,
  author       = {Tomov, Stanimire and
                  Bello-Maldonado, Pedro and
                  Brown, Jed and
                  Camier, Jean-Sylvain and
                  Dobrev, Veselin and
                  Dongarr, Jack and
                  Fischer, Paul and
                  Haidar, Azzam and
                  Kolev, Tzanio and
                  Merzari, Elia and
                  Min, Misun and
                  Obabko, Aleks and
                  Parker, Scott and
                  Ratnayaka, Thilina and
                  Thompson, Jeremy and
                  Abdelfattah, Ahmad and
                  Tomov, Vladimir and
                  Warburton, Tim},
  title        = {{CEED ECP Milestone Report: Performance tuning of CEED software and first wave apps}},
  month        = sep,
  year         = 2018,
  doi          = {10.5281/zenodo.2542350},
}
@misc{brown_jed_2018_2542346,
  author       = {Brown, Jed and
                  Dobrev, Veselin and
                  Dutta, Som and
                  Fischer, Paul and
                  Kamran, Kazem and
                  Kolev, Tzanio and
                  Medina, David and
                  Min, Misun' and
                  Ratnayaka, Thilina and
                  Shephard, Mark and
                  Smith, Cameron and
                  Thompson, Jeremy},
  title        = {{CEED ECP Milestone Report: Propose high-order mesh/data format}},
  month        = jun,
  year         = 2018,
  doi          = {10.5281/zenodo.2542346},
}
@misc{brown_jed_2018_2542343,
  author       = {Brown, Jed and
                  Abdelfata, Ahmad and
                  Camier, Jean-Sylvain and
                  Dobrev, Veselin and
                  Dongarra, Jack and
                  Fischer, Paul and
                  Fisher, Aaron and
                  Dudouit, Yohann and
                  Haidar, Azzam and
                  Kamran, Kazem and
                  Kalev, Tzanio and
                  Min, Misun and
                  Ratnayaka, Thilina and
                  Shephard, Mark and
                  Smith, Cameron and
                  Tomov, Stanimire and
                  Tomov, Vladimir and
                  Warburton, Tim},
  title        = {{CEED ECP Milestone Report: Public release of CEED 1.0}},
  month        = mar,
  year         = 2018,
  doi          = {10.5281/zenodo.2542343},
}
@misc{brown_jed_2017_2542340,
  author       = {Brown, Jed and
                  Camier, Jean-Sylvain and
                  Dobrev, Veselin and
                  Fischer, Paul and
                  Kolev, Tzanio and
                  Ratnayaka, Thilina' and
                  Shephard, Mark and
                  Thompson, Jeremy and
                  Tomov, Vladimir},
  title        = {CEED ECP Milestone Report: Initial CEED API},
  month        = dec,
  year         = 2017,
  doi          = {10.5281/zenodo.2542340},
}
@misc{min_misun_2017_2542338,
  author       = {Min, Misun and
                  Brown, Jed and
                  Dobrev, Veselin and
                  Fischer, Paul and
                  Kolev, Tzanio and
                  Medina, David and
                  Merzari, Elia and
                  Obabko, Aleks and
                  Parker, Scott and
                  Rahaman, Ron and
                  Tomov, Stanimire and
                  Tomov, Vladimir and
                  Warburton, Tim},
  title        = {{CEED ECP Milestone Report: Initial Integration of CEED Software in ECP Applications}},
  month        = oct,
  year         = 2017,
  doi          = {10.5281/zenodo.2542338},
}
@misc{dobrev_veselin_2017_2542333,
  author       = {Dobrev, Veselin and
                  Dongarra, Jack and
                  Brown, Jed and
                  Fischer, Paul and
                  Haidar, Azzam and
                  Karlin, Ian and
                  Kolev, Tzanio and
                  Min, Misun and
                  Moon, Tim and
                  Ratnayaka, Thilina and
                  Tomov, Stanimire and
                  Tomov, Vladimir},
  title        = {{CEED ECP Milestone Report: Identify initial kernels, bake-off problems (benchmarks) and miniapps}},
  month        = jul,
  year         = 2017,
  doi          = {10.5281/zenodo.2542333},
}
@misc{brown2016standards,
  title = {Higher Standards on the Control of Numerical Accuracy},
  author = {Jed Brown},
  pdf = {https://jedbrown.org/files/Brown-HigherStandardsNumericalAccuracy-2015.pdf},
  note = {Whitepaper accepted to the DOE Advancing X-cutting Ideas for Computational Climate Science (AXICCS)},
  year = 2016
}
@article{petsc-extensibility2016,
  author = {M. Knepley and D. A. May and J. Brown and B. Smith},
  title = {Extensibility in {PETSc}},
  journal = {SIAM News},
  volume=49,
  number=9,
  year=2016,
  url = {https://sinews.siam.org/Details-Page/extensibility-in-petsc}
}
@misc{KnepleyBrownMcInnesSmithRuppAdams2015,
  title  = {Exascale Computing without Threads},
  author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and Karl Rupp and Mark Adams},
  pdf    = {http://www.orau.gov/hpcor2015/whitepapers/Exascale_Computing_without_Threads-Barry_Smith.pdf},
  note   = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on Scientific Software Architecture for Portability and Performance},
  year   = {2015}
}
@misc{KnepleyBrownMcInnesSmithRuppAdams2015b,
  title  = {Overview of the {PETSc} Library},
  author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and Karl Rupp and Mark Adams},
  pdf    = {http://www.orau.gov/hpcor2015/whitepapers/Overview_of_the_PETSc_Library-Lois_McInnes.pdf},
  note   = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on Scientific Software Architecture for Portability and Performance},
  year   = {2015}
}
@inbook{BalayBrownKnepleyMcInnesSmith2015,
  author     = {Satish Balay and Jed Brown and Matthew G. Knepley and Lois McInnes and Barry Smith},
  bookeditor = {J. Carver},
  title      = {Software Engineering for Science},
  chapter    = {Providing Mixed Language and Legacy Support within a Library},
  publisher  = {Taylor \& Francis},
  year       = {2015}
}
@article{RuppBalayBrownKnepleyMcInnesSmith2015,
  title   = {On The Evolution Of User Support Topics in Computational Science and Engineering Software},
  author  = {Karl Rupp and Satish Balay and Jed Brown and Matthew G. Knepley and Lois Curfman McInnes and Barry F. Smith},
  note    = {Whitepaper for Computational Science \& Engineering Software Sustainability and Productivity Challenges},
  journal = {ArXiv e-prints},
  archivePrefix = {arXiv},
  eprint = {1510.01122},
  year   = {2015}
}

@techreport{ghosh2014scalable,
  title = {Scalable Nonlinear Compact Schemes},
  number = {ANL/MCS-TM-340},
  institution={Argonne National Laboratory},
  year = {2014},
  abstract = {Solutions to hyperbolic conservation laws are often characterized by a large range of length scales as well as discontinuities. Standard nonlinear finite-difference schemes, such as the WENO schemes, yield non- oscillatory solutions but lack the spectral resolution required to model the relevant length scales. Linear compact schemes have a high spectral resolution; however, they suffer from spurious oscillations across discontinuities and sharp gradients. Weighted nonlinear compact schemes, such as the CRWENO scheme and the hybrid compact-WENO schemes, combine the non-oscillatory nature of the WENO schemes with the high spectral resolution of the compact schemes and are thus ideal for solutions with multiple length scales and discontinuities. One example of an application area is compressible, turbulent flows. The CRWENO scheme and the hybrid compact-WENO schemes have a nonlinear, solution-dependent left-hand side and therefore require the solution of banded systems of equations at each time-integration step or stage. Application of these schemes to multiprocessor simulations requires an efficient, scalable algorithm for the solution to the banded systems. Past efforts at implementing nonlinear compact schemes for parallel simulations suffer from one or more of the following drawbacks: parallelization-induced approximations and errors, complicated and inefficient scheduling of communication and computation, significant increase in the mathematical complexity of the banded systems solver, and high communication overhead. Therefore, these algorithms do not scale well for massively parallel simulations and are inefficient compared with the corresponding standard finite-difference schemes.},
  author = {Debojyoti Ghosh and Emil M. Constantinescu and Jed Brown},
  pdf={http://www.mcs.anl.gov/papers/ANL/MCS-TM-340.pdf}
}
@techreport{arrigo2013earthcube,
  title={{EarthCube} Modeling Workshop Results},
  author={Jennifer Arrigo and Jed Brown and Louise Kellogg and Lorraine Hwang and Scott Peckham and David Tarboton},
  institution={Computational Infrastructure for Geodynamics},
  url={http://geodynamics.org/cig/community/workshops/Earthcube13/ExecSummary},
  year={2013}
}
@inproceedings{brown2013dimension,
  title={Vectorization, communication aggregation, and reuse in stochastic and temporal dimensions},
  author={Jed Brown},
  booktitle={Exascale Mathematics Workshop, Aug 21--22, Washington, DC},
  year={2013},
  organization={DOE Office of Advanced Scientific Computing Research}
}
@inproceedings{AdamsBrownKnepley2013,
    author       = {Mark F. Adams and Jed Brown and Matthew G. Knepley},
    title        = {Low-communication techniques for extreme-scale multilevel solvers},
    booktitle    = {Exascale Mathematics Workshop, Aug 21--22, Washington, DC},
    organization = {DOE Office of Advanced Scientific Computing Research},
    year         = {2013}
}
@article{KnepleyBrownRuppSmith13,
  author   = {{Knepley}, M.~G. and {Brown}, J. and {Rupp}, K. and {Smith}, B.~F.},
  title    = {Achieving High Performance with Unified Residual Evaluation},
  journal  = {ArXiv e-prints},
  eprint   = {1309.1204},
  archivePrefix = "arXiv",
  primaryClass  = "cs.MS",
  keywords = {Computer Science - Mathematical Software, Computer Science - Computational Engineering, Finance, and Science},
  year     = 2013,
  month    = sep,
  adsurl   = {http://adsabs.harvard.edu/abs/2013arXiv1309.1204K},
  adsnote  = {Provided by the SAO/NASA Astrophysics Data System}
}
@misc{brown2013repo,
  author = {J. Brown},
  title = {Scalable Repository Workflows},
  note = {Whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}},
  year = 2013,
  pdf = {https://jedbrown.org/files/Brown-ScalableRepositoryWorkflows-2013.pdf}
}
@article{brown2012nonblockingieee,
  author={Jed Brown},
  title = {User-Defined Non-Blocking Collectives Must Make Progress},
  journal = {IEEE Technical Committee on Scalable Computing},
  type = {Blog},
  url = {https://www.ieeetcsc.org/activities/blog/user_defined_nonblocking_collectives_must_make_progress},
  year = 2012
}
@inproceedings{adams2012exascalelibraries,
  author = {Mark Adams and Jed Brown and Barry F. Smith},
  title = {Exascale Programming Models Must Vigorously Enable Libraries},
  booktitle = {DOE Exascale Research Conference},
  year = 2012
}
@techreport{smcabbkz2012,
  author = "Barry Smith and Lois Curfman McInnes and Emil Constantinescu and Mark Adams and
            Satish Balay and Jed Brown and Matthew Knepley and Hong Zhang",
  title = "{PETSc's} software strategy for the design space of composable extreme-scale solvers",
  institution = "Argonne National Laboratory",
  type = "Preprint",
  note = "{DOE} Exascale Research Conference, April 16-18, 2012, Portland, OR",
  year = 2012,
  number = "ANL/MCS-P2059-0312"
}
@inproceedings{anitescu2012exascale,
  author = {Mihai Anitescu and Jed Brown and Paul Fischer and Sven Leyffer and Lois Curfman McInnes and Todd Munson and Barry F. Smith},
  title = {Exascale Co-design Opportunities: {M}ultilevel Approaches for Hierarchical Models, Architectures, Algorithms, and Software},
  booktitle = {DOE Exascale Research Conference},
  year = 2012
}
@techreport{scott2012fosteringgeo,
  title={Fostering Interactions Between the Geosciences and Mathematics, Statistics, and Computer Science},
  author={L. Ridgway Scott and Jed Brown and George W. Bergantz and Dan Cooley and Clint Dawson and Maarten de Hoop and Donald Estep and Natasha Flyer and Efi Foufoula-Georgiou and Michael Ghil and Matthew Knepley and Randall J. LeVeque and Lek-Heng Lim and Serge Prudhomme and Adrian Sandu and Frederik J. Simons and Philip B. Stark and Michael Stein and Seth Stein and Toshiro Tanimoto and Daniel Tartakovsky and Jonathan Weare and Robert Weiss and Grady B. Wright and Dave Yuen},
  institution={University of Chicago},
  number={2012-02},
  year=2012,
  pdf={http://cs.uchicago.edu/files/tr_authentic/TR-2012-02.pdf}
}
@TechReport{petsc-user-ref,
  author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Jed Brown and Peter Brune
            and Kris Buschelman and Lisandro Dalcin and Alp Dener and Victor Eijkhout and William~D. Gropp
            and Dinesh Kaushik and Matthew~G. Knepley and Dave~A. May and Lois Curfman McInnes
            and Richard Tran Mills and Todd Munson and Karl Rupp and Patrick Sanan
            and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang},
  title  = {{PETS}c Users Manual: Revision 3.15},
  institution = {Argonne National Laboratory},
  year   = 2021,
  Number = {ANL-95/11 - Rev 3.15},
  url    = {https://mcs.anl.gov/petsc}
}
@techreport{HPGMGv1,
  author =      "M. F. Adams  and J. Brown and J. Shalf and B. Van Straalen
and E. Strohmaier and S. Williams",
  title =       "{HPGMG} 1.0: A Benchmark for Ranking High Performance
Computing Systems",
  institution = "LBNL",
  address =     "Berkeley",
  year =        "2014",
  NUMBER =        {LBNL-6630E},
  doi={10.2172/1131029}
}
@techreport{cyr2015assembly,
  title={Algorithms and Abstractions for Assembly in {PDE} Codes: Workshop Report},
  author={Cyr, Eric C and Phipps, Eric and Heroux, Michael A and Brown, Jed and Coon, Ethan T and Hoemmen, Mark and Kirby, Robert C and Kolev, Tzanio V and Sutherland, James C and Trott, Christian R},
  number={SAND2015-1379},
  institution={Sandia National Laboratory},
  year=2015,
  pdf={http://www.sandia.gov/~eccyr/pubs/assembly-wksp-report-2015.pdf}
}


text:
@ARTICLE{skip1,
  OPTIONS     = {skipbib},
  AUTHOR	    = {John Doe},
  SHORTHAND   = {AFS},
  TITLE		    = {Algorithms For Sorting},
  PUBLISHER	  = {A press},
  LOCATION	  = {Cambridge},
  YEAR		    = {1994},
}

@ARTICLE{skip2,
  OPTIONS     = {skipbiblist},
  SHORTHAND   = {SA},
  AUTHOR	    = {John Doe},
  TITLE		    = {Sorting Algorithms},
  PUBLISHER	  = {A press},
  LOCATION	  = {Cambridge},
  YEAR		    = {1995},
}

@ARTICLE{skip3,
  OPTIONS     = {skipbiblist,skiplab},
  SHORTHAND   = {SWA},
  AUTHOR	    = {John Doe},
  TITLE		    = {Sorting With Algorithms},
  PUBLISHER	  = {A press},
  LOCATION	  = {Cambridge},
  YEAR		    = {1934},
}

@ARTICLE{skip4,
  OPTIONS     = {dataonly},
  SHORTHAND   = {AWS},
  AUTHOR	    = {John Doe},
  TITLE		    = {Algorithms Which Sort},
  PUBLISHER	  = {A press},
  LOCATION	  = {Cambridge},
  YEAR		    = {1932},
}

@SET{seta,
  ENTRYSET	  = {set:membera,set:memberb,set:memberc}
}

@BOOK{set:membera,
  KEYWORDS    = {key1, key2},
  AUTHOR	    = {Doe, John},
  TITLE	      = {Set Member A},
  DATE		    = {2010},
}

@BOOK{set:memberb,
  AUTHOR	    = {Doe, John},
  TITLE       = {Set Member B},
  DATE		    = {2010},
}

@BOOK{set:memberc,
  AUTHOR	    = {Doe, John},
  TITLE		    = {Set Member C},
  DATE		    = {2010},
}

@BOOK{noseta,
  AUTHOR	    = {Doe, John},
  TITLE		    = {Stand-Alone A},
  DATE		    = {2010},
}

@BOOK{nosetb,
  AUTHOR	    = {Doe, John},
  TITLE       = {Stand-Alone B},
  DATE		    = {2010},
}

@BOOK{nosetc,
  AUTHOR	    = {Doe, John},
  TITLE       = {Stand-Alone C},
  DATE		    = {2010},
}

license: MIT

repository: FlamingTempura/bibtex-tidy

license_type: permissive

repo_name: FlamingTempura/bibtex-tidy

branch_name: refs/heads/master

gha_license_id: MIT

gha_language: TeX

extension: bib


text:
@misc{data,
  title = {Music Genres task from ISMIS 2011 Contest: Music Information Retrieval/Music Genres},
  author = {prof. Bozena Kostek, dr Pawel Zwan, Andrzej Sitek and prof. Andrzej Czyzewski},
  howpublished = {\url{http://tunedit.org/challenge/music-retrieval/genres}},
  note = {Available: 2016-06-19}
}
@misc{gztan,
	title = {Musical genre classification of audio signals},
	author = {G. Tzanetakis and P. Cook},
	howpublished = {IEEE Transactions on Audio and Speech Processing 2002},
	note = {Available: 2002}
}

repository: SoundSourceAnalyzer/Report

repo_name: SoundSourceAnalyzer/Report


text:
inherit qt4e
require python-pyside.inc

PR = "${INC_PR}.2"
SRC_URI += " \
 file://no-accessibility-support.patch \
 file://support-qws.patch \
"

SRC_URI[code.md5sum] = "62d718a81fc7e7d19919f17fff5b43a6"
SRC_URI[code.sha256sum] = "a74db2de659009364f61ec2f2751cbef0dd59410673795880ec3cc9f0f810960"

repository: balister/openembedded

repo_name: balister/openembedded

extension: bb


text:
@inproceedings{de2010practical,
  title={Practical private set intersection protocols with linear complexity},
  author={De Cristofaro, Emiliano and Tsudik, Gene},
  booktitle={Financial Cryptography and Data Security},
  pages={143--159},
  year={2010},
  organization={http://eprint.iacr.org/2009/491.pdf}
}

@inproceedings{de2009privacy,
  title={Privacy-preserving policy-based information transfer},
  author={De Cristofaro, Emiliano and Jarecki, Stanislaw and Kim, Jihye and Tsudik, Gene},
  booktitle={International Symposium on Privacy Enhancing Technologies Symposium},
  pages={164--184},
  year={2009},
  organization={Springer Berlin Heidelberg}
}

repository: emidec/academic-kickstart

repo_name: emidec/academic-kickstart


text:
@article{aubin2019spiked,
  title={The spiked matrix model with generative priors},
  author={Aubin, Benjamin and Loureiro, Bruno and Maillard, Antoine and Krzakala, Florent and Zdeborov{\'a}, Lenka},
  journal={arXiv preprint arXiv:1905.12385},
   booktitle = {Advances in Neural Information Processing Systems 32},
  year={2019}
}

repository: krzakala/academic-kickstart

repo_name: krzakala/academic-kickstart


text:
@article{Kobilarov2009,
    abstract = {In this paper, we describe how the BBC is working to integrate data and linking documents across BBC domains by using Semantic Web technology, in particular Linked Data, MusicBrainz and DBpedia. We cover the work of BBC Programmes and BBC Music building Linked Data sites for all music and programmes related brands, and we describe existing projects, ongoing development, and further research we are doing in a joint collaboration between the BBC, Freie Universitat Berlin and Rattle Research in order to use DBpedia as the controlled vocabulary and semantic backbone for the whole BBC.},
    author = {Kobilarov, Georgi and Scott, Tom and Raimond, Yves and Oliver, Silver and Sizemore, Chris and Smethurst, Michael and Bizer, Christian and Lee, Robert},
    doi = {10.1007/978-3-642-02121-3_53},
    file = {:C$\backslash$:/Users/Andreas/Downloads/eswc2009-bbc-dbpedia-2.pdf:pdf},
    isbn = {3642021204},
    issn = {03029743},
    journal = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
    pages = {723--737},
    title = {{Media meets semantic web - How the bbc uses dbpedia and linked data to make connections}},
    volume = {5554 LNCS},
    year = {2009}
}

repository: devmount/SemanticWeb

repo_name: devmount/SemanticWeb


text:
DESCRIPTION = "SamyGO Extensions ${PN}"
LICENSE = "GPL"
SECTION = "Gallery/Games"
MAINTAINER = "Ser Lev Arris <arris@ZsoltTech.Com>"
HOMEPAGE = "http://samygo.sourceforge.net"

PR = "r05"

# dev info T-CHEAUSC -> no games in gallery
# T-SPHAUSC -> no games work in SEC_GAMES and must be named lib<something> + need
# SamyGO.dat

RECOMMENDS = ""
RRECOMMENDS = "CoreScript InitScripts"
DEPENDS = "virtual/libsdl libsdl-image libsdl-mixer samsung-firmware"
RDEPENDS = ""

INHIBIT_PACKAGE_STRIP = "1"

# Enable this to generate package per MACHINE / MACHINE_ARCH
# PACKAGE_ARCH = ${MACHINE_ARCH}
PACKAGE_ARCH = ${MACHINE}

SRC_URI = "file://SamyGOE.c \
		file://SamyGO.png \
		file://SGexeDSP.c \
		file://savesurf.h \
"

PACKAGES = "${PN}-dbg ${PN} ${PN}-bin ${PN}-dev ${PN}-doc ${PN}-locale"

S = ${WORKDIR}

do_compile(){
 	# oe_runmake
 	${CC} ${TARGET_CFLAGS} -O2 -Wall `sdl-config-${HOST_SYS} --cflags --libs` -fPIC -shared -o libSamyGO.so SamyGOE.c
 	# ${CC} ${TARGET_CFLAGS} -O2 -Wall -Wl,--unresolved-symbols=ignore-all `sdl-config-${HOST_SYS} --cflags --libs` ${TARGET_LDFLAGS} -o SGexeDSP SGexeDSP.c -lGPlayerPorting
	${CC} ${TARGET_CFLAGS} -O2 -Wall -Wl,--unresolved-symbols=ignore-all `sdl-config-${HOST_SYS} --cflags --libs` -I. -Itrunk ${TARGET_LDFLAGS} -lSDL_mixer -lpngGP -lSDL_image -lGPlayerPorting -Wl,-rpath,/mtd_cmmlib/YWidget_LIB -Wl,-rpath,/mtd_cmmlib/GAME_LIB -lYahooSDLHWAcceleration -o SGexeDSP SGexeDSP.c ${STAGING_LIBDIR}/libjpeg.a
}

do_install () {
        mkdir -p ${D}/mtd_tlib/SamyGO/
        mkdir -p ${D}/usr/bin/
        install -m 0755 SGexeDSP ${D}/usr/bin/SGexeDSP
#        install -m 0755 SamyGOE.so ${D}/mtd_tlib/SamyGO/
        install -m 0755 libSamyGO.so ${D}/mtd_tlib/SamyGO/
        install -m 0644 SamyGO.png ${D}/mtd_tlib/SamyGO/

        # Create .dat file
        for i in Name Category Size Vendor Release_Date Description ; do
                # printf "SamyGO\0" | xxd -i
                # Size -> 01 MB
                # date "+%Y/%m/%d" | xxd -i | tr A 0
                echo "[$i]" >> ${D}/mtd_tlib/SamyGO/SamyGO.dat
                        for j in 1 2 3 4 ; do
                                if [ "$i" == "Release_Date" ] ; then
                                        echo "$(date "+%Y/%m/%d" | xxd -i | tr a 0 | tr -d " ")" >> ${D}/mtd_tlib/SamyGO/SamyGO.dat
                                elif [ "$i" == "Size" ] ; then
                                        echo "$(printf "01 MB\0" | xxd -i | tr -d " ")" >> ${D}/mtd_tlib/SamyGO/SamyGO.dat
                                else
                                        echo "$(printf "SamyGO\0" | xxd -i | tr -d " ")" >> ${D}/mtd_tlib/SamyGO/SamyGO.dat
                                fi
                        done
        done
        echo '[JoyStick_Support]
0' >> ${D}/mtd_tlib/SamyGO/SamyGO.dat
        echo '[icon_path]
SamyGO.png

// End of Generated Text Resource Source File
' >> ${D}/mtd_tlib/SamyGO/SamyGO.dat

# fixup .dat file
# perl -pi -e "s/^\s+//g" ${D}/mtd_tlib/SamyGO/SamyGO.dat
perl -pi -e "s/0x/0x00/g" ${D}/mtd_tlib/SamyGO/SamyGO.dat
perl -pi -e "s/0x0000\n/0x0000,\n/g" ${D}/mtd_tlib/SamyGO/SamyGO.dat
perl -pi -e "s/\n/\r\n/g" ${D}/mtd_tlib/SamyGO/SamyGO.dat

	# Create clmeta.dat file
echo '<?xml version="1.0" encoding="utf-8"?>
<contentlibrary>
  <contentpack id="SamyGO">
    <category>Game</category>
    <title language_id="German">SamyGO Erweiterungen</title>
    <startpoint language_id="German">./libSamyGO.so</startpoint>
    <title language_id="English">SamyGO Extensions</title>
    <startpoint language_id="English">./libSamyGO.so</startpoint>
    <thumbnailpath>./SamyGO.png</thumbnailpath>
    <totalsize>1</totalsize>
  </contentpack>
</contentlibrary>' > ${D}/mtd_tlib/SamyGO/clmeta.dat

        mkdir -p ${D}/usr/share/doc/${PN}
        cp -a doc/* ${D}/usr/share/doc/${PN}/ || true
}

do_stage(){
	install -m 0755 SGexeDSP ${STAGING_DIR}/${TARGET_SYS}/bin/
}

FILES_${PN}-bin = "/usr/bin/SGexeDSP"
FILES_${PN}-dbg = "/mtd_tlib/SamyGO/.debug"
FILES_${PN} = "/mtd_tlib"
FILES_${PN}-doc = "/usr/share/doc/${PN}"

repository: metalsky/SamyGO

repo_name: metalsky/SamyGO


text:
# Copyright (c) 2018 ASWF Build Util Project and contributors
# SPDX-License-Identifier: MIT

#
# This file is contains a set of functions / macros
# that make writing VFX platform compliant cmake files
# easier.
#
# Additionally, it defines common options that are considered
# to be common / considerate options to provide in all projects
# this makes it easier to script the building of an entire
# suite of software by using common names for common variables

# common options to expose to the configure tool/script

# this has all the logic to construct gnu-compatible install folders
# and seems to be what modern projects are using, where the cmake config
# ends up in /usr/lib64/cmake/ProjectName/*.cmake
# rather than using the old FindProjectName.cmake mechanisms
#
# Given that these are just folder names, they are fine under windows
# etc.
include(GNUInstallDirs)

include(ASWF_Utilities)

include(ASWF_VFX_Checks)
include(ASWF_FindMacros)
include(ASWF_LibrarySupport)

# if the testing is enabled, we turn that on
option(ASWF_ENABLE_TESTS "Enable the tests" ON)
if(ASWF_ENABLE_TESTS)
  include(CTest)
  enable_testing()
  # we add a custom command "check" that will compile all the tests
  # first (if we add dependencies)
  add_custom_target(check COMMAND ${CMAKE_CTEST_COMMAND})
endif(ASWF_ENABLE_TESTS)

# MacOS & linux rpathing, meaning things can be run in-place,
# and are correctly re-linked upon install to pull any DSO
# from the install location, eliminating the need for any
# LD_LIBRARY_PATH shenanigans
if(APPLE)
  set(CMAKE_MACOSX_RPATH 1)
endif(APPLE)
set(BUILD_WITH_INSTALL_RPATH 1)

# Set position independent code (mostly for static builds, but not a bad idea regardless)
set(CMAKE_POSITION_INDEPENDENT_CODE ON)

# set a postfix on output names to handle debug vs. opt naming
# if that is necessary
IF(WIN32)
  SET(CMAKE_DEBUG_POSTFIX "_d")
ENDIF()

include(ASWF_AddMacros)
include(ASWF_DocMacros)
include(ASWF_InstallMacros)

extension: cmake


text:
FILE(REMOVE_RECURSE
  "CMakeFiles/opencv_test_cuda.dir/test/test_opengl.cpp.o"
  "CMakeFiles/opencv_test_cuda.dir/test/test_gpumat.cpp.o"
  "CMakeFiles/opencv_test_cuda.dir/test/test_labeling.cpp.o"
  "CMakeFiles/opencv_test_cuda.dir/test/test_calib3d.cpp.o"
  "CMakeFiles/opencv_test_cuda.dir/test/test_main.cpp.o"
  "CMakeFiles/opencv_test_cuda.dir/test/test_buffer_pool.cpp.o"
  "CMakeFiles/opencv_test_cuda.dir/test/test_stream.cpp.o"
  "CMakeFiles/opencv_test_cuda.dir/test/test_global_motion.cpp.o"
  "CMakeFiles/opencv_test_cuda.dir/test/test_objdetect.cpp.o"
  "../../bin/opencv_test_cuda.pdb"
  "../../bin/opencv_test_cuda"
)

# Per-language clean rules from dependency scanning.
FOREACH(lang CXX)
  INCLUDE(CMakeFiles/opencv_test_cuda.dir/cmake_clean_${lang}.cmake OPTIONAL)
ENDFOREACH(lang)


text:
require libgpg-error.inc

PR = "r5"

SRC_URI = "ftp://ftp.gnupg.org/gcrypt/alpha/libgpg-error/libgpg-error-${PV}.tar.gz \
	   file://pkgconfig.patch;patch=1"


text:
SUMMARY = "HTTP::Cookies - HTTP cookie jars"
AUTHOR = "Gisle Aas <gisle@activestate.com>"
HOMEPAGE = "https://metacpan.org/module/HTTP::Cookies"
SECTION = "libs"
LICENSE = "Artistic-1.0+ | GPL-1.0+"
LIC_FILES_CHKSUM = "file://README;md5=d601f2e0bf56c067a5c4d70f20e3b118"

SRC_URI = "http://cpan.metacpan.org/authors/id/G/GA/GAAS/HTTP-Cookies-${PV}.tar.gz"
SRC_URI[md5sum] = "ecfd0eeb88512033352c2f13c9580f03"
SRC_URI[sha256sum] = "f5d3ade383ce6389d80cb0d0356b643af80435bb036afd8edce335215ec5eb20"

S = "${WORKDIR}/HTTP-Cookies-${PV}"

inherit cpan

RDEPENDS_${PN} += "libhttp-date-perl \
                   libhttp-headers-util-perl \
                   libtime-local-perl \
                   "

BBCLASSEXTEND = "native"


text:
require efitools.inc

# The generated native binaries are used during native and target build
DEPENDS += "${BPN}-native gnu-efi openssl"

SRC_URI:append = " \
    file://LockDown-enable-the-enrollment-for-DBX.patch \
    file://LockDown-show-the-error-message-with-3-sec-timeout.patch \
    file://Makefile-do-not-build-signed-efi-image.patch \
    file://Build-DBX-by-default.patch \
    file://LockDown-disable-the-entrance-into-BIOS-setup-to-re-.patch \
    file://Fix-help2man-error.patch \
"

COMPATIBLE_HOST = '(i.86|x86_64).*-linux'

inherit user-key-store deploy

EXTRA_OEMAKE:append = " \
    INCDIR_PREFIX='${STAGING_DIR_TARGET}' \
    CRTPATH_PREFIX='${STAGING_DIR_TARGET}' \
    SIGN_EFI_SIG_LIST='${STAGING_BINDIR_NATIVE}/sign-efi-sig-list' \
    CERT_TO_EFI_SIG_LIST='${STAGING_BINDIR_NATIVE}/cert-to-efi-sig-list' \
    CERT_TO_EFI_HASH_LIST='${STAGING_BINDIR_NATIVE}/cert-to-efi-hash-list' \
    HASH_TO_EFI_SIG_LIST='${STAGING_BINDIR_NATIVE}/hash-to-efi-sig-list' \
    MYGUID='${UEFI_SIG_OWNER_GUID}' \
    HELP2MAN_PROG_PREFIX='${STAGING_BINDIR_NATIVE}' \
"

python do_prepare_signing_keys() {
    if d.expand('${UEFI_SB}') != '1':
        return

    # Prepare PK, KEK and DB for LockDown.efi.
    if uks_signing_model(d) in ('sample', 'user'):
        dir = uefi_sb_keys_dir(d)
    else:
        dir = d.expand('${SAMPLE_UEFI_SB_KEYS_DIR}/')

    import shutil

    for _ in ('PK', 'KEK', 'DB'):
        shutil.copyfile(dir + _ + '.crt', d.expand('${S}/') + _ + '.crt')
        shutil.copyfile(dir + _ + '.key', d.expand('${S}/') + _ + '.key')

    # Make sure LockDown.efi contains the DB and KEK from Microsoft.
    if "${@bb.utils.contains('DISTRO_FEATURES', 'msft', '1', '0', d)}" == '1':
        shutil.copyfile(d.expand('${MSFT_DB_CERT}'), d.expand('${S}/DB.crt'))
        shutil.copyfile(d.expand('${MSFT_KEK_CERT}'), d.expand('${S}/KEK.crt'))

    path = create_uefi_dbx(d)
    if path:
        with open(d.expand('${S}/DBX.crt'), 'w') as f:
            pass

        shutil.copyfile(path, d.expand('${S}/DBX.esl'))

        # Cheat the Makefile to avoid running this rule:
        # %.esl: %.crt cert-to-efi-sig-list
        #        $(CERT_TO_EFI_SIG_LIST) -g $(MYGUID) $< $@
        import time, os
        tm = time.strptime('2038-01-01 00:00:00', \
                           '%Y-%m-%d %H:%M:%S')
        time_stamp = time.mktime(tm)
        os.utime(d.expand('${S}/DBX.esl'), (time_stamp, time_stamp))
}
addtask prepare_signing_keys after do_configure before do_compile
do_prepare_signing_keys[prefuncs] += "check_deploy_keys"

do_install:append() {
    install -d ${D}${EFI_BOOT_PATH}
    install -m 0755 ${D}${datadir}/efitools/efi/LockDown.efi ${D}${EFI_BOOT_PATH}
}

do_deploy() {
    install -d ${DEPLOYDIR}

    install -m 0600 ${D}${EFI_BOOT_PATH}/LockDown.efi "${DEPLOYDIR}"
    if [ -e ${D}${EFI_BOOT_PATH}/LockDown.efi.sig ] ; then
        install -m 0600 ${D}${EFI_BOOT_PATH}/LockDown.efi.sig "${DEPLOYDIR}"
    fi
}
addtask deploy after do_install before do_build

RDEPENDS:${PN}:append = " \
    parted mtools coreutils util-linux openssl libcrypto \
"

gha_language: BitBake


text:
@InProceedings{las14cloudmeshmultiple,
  title =	 {{Accessing Multiple Clouds with Cloudmesh}},
  author =	 {von Laszewski, Gregor and Wang, Fugang and Lee,
                  Hyungro and Chen, Heng and Fox, Geoffrey C.},
  booktitle =	 {Proceedings of the 2014 ACM International Workshop
                  on Software-defined Ecosystems},
  year =	 2014,
  address =	 {New York, NY, USA},
  pages =	 {21--28},
  publisher =	 {ACM},
  series =	 {BigSystem '14},
  acmid =	 2609638,
  doi =		 {10.1145/2609441.2609638},
  isbn =	 {978-1-4503-2909-5},
  keywords =	 {cloud computing},
  location =	 {Vancouver, BC, Canada},
  numpages =	 8,
  url =		 {http://doi.acm.org/10.1145/2609441.2609638}
}

@InProceedings{chem14cdms,
  title =	 {{Detection of Late Intermediates in Virus Capsid
                  Assembly by Charge Detection Mass Spectrometry}},
  author =	 {Pierson, Elizabeth E. and Keifer, David Z. and
                  Selzer, Lisa and Le, Lye Siang and Contino, Nathan
                  C. and Wang, Joseph C.-Y. and Zlotnick, Adam and
                  Jarrold, Martin F.},
  booktitle =	 {J. Am. Chem. Soc.},
  year =	 2014,
  address =	 {Department of Chemistry and Department of Molecular
                  and Cellular Biochemistry, Indiana University,
                  Bloomington, Indiana 47405,United States},
  pages =	 {3536–-3541},
  publisher =	 {ACS},
  doi =		 {10.1021/ja411460w},
  location =	 {Bloomington, IN, United States},
  numpages =	 6,
  url =		 {http://pubs.acs.org/doi/pdf/10.1021/ja411460w}
}

@misc{www-i524,
  author =	 {{Gregor von Laszewski and Badi Abdul-Wahid}},
  title =	 {{Big Data Classes}},
  url =		 {https://cloudmesh.github.io/classes/},
  howpublished = {Web Page},
  address =	 {Indiana University},
  year =	 2017,
  month =	 jan
}

@misc{www-karst,
  author =	 {{Indiana University}},
  title =	 {{Karst at Indiana University}},
  url =		 {https://kb.iu.edu/d/bezu},
  howpublished = {Web Page},
  address =	 {Indiana University},
  year =	 2017,
  month =	 mar
}

@misc{www-br2,
  author =	 {{Indiana University}},
  title =	 {{Big Red II at Indiana University}},
  url =		 {https://kb.iu.edu/d/bcqt},
  howpublished = {Web Page},
  address =	 {Indiana University},
  year =	 2017,
  month =	 mar
}

@misc{www-chameleon,
  author =	 {{National Science Foundation}},
  title =	 {{Home | Chameleon Cloud}},
  url =		 {https://www.chameleoncloud.org},
  howpublished = {Web Page}
}

@misc{www-matplotlib,
  author =	 {{The MathWorks, Inc.}},
  title =	 {{Matplotlib: Python plotting - Matplotlib 2.0.0 documentation}},
  url =		 {https://matplotlib.org},
  howpublished = {Web Page},
  year =	 2017,
  month =	 feb
}

@misc{www-mpi,
  author =	 {{Software in the Public Interest}},
  title =	 {{Open MPI: Open Source High Performance Computing}},
  url =		 {https://www.open-mpi.org},
  howpublished = {Web Page},
  address =	 {Houston, TX, USA},
  year =	 2017,
  month =	 mar
}

@misc{www-iu-vpn,
  author =	 {{Indiana University}},
  title =	 {{About the IU VPN}},
  url =		 {https://kb.iu.edu/d/ajrq},
  howpublished = {Web Page},
  address =	 {Indiana University},
  year =	 2017,
  month =	 mar
}

@misc{www-iu-duo,
  author =	 {{Indiana University}},
  title =	 {{What is Two-Step Login (Duo) and how does it work?}},
  url =		 {https://kb.iu.edu/d/beum},
  howpublished = {Web Page},
  address =	 {Indiana University},
  year =	 2017,
  month =	 mar
}

@misc{www-hadoop,
  author =	 {{The Apache Software Foundation}},
  title =	 {{Welcome to Apache Hadoop!}},
  url =		 {https://cloudmesh.github.io/classes/},
  howpublished = {Web Page},
  year =	 2017,
  month =	 mar
}

@misc{www-hadoop-streaming,
  author =	 {{The Apache Software Foundation}},
  title =	 {{Hadoop Streaming}},
  url =		 {https://hadoop.apache.org/docs/r1.2.1/streaming.html},
  howpublished = {Web Page},
  year =	 2013,
  month =	 aug
}

@misc{www-github,
  author =	 {{GitHub, Inc.}},
  title =	 {{The world's leading software development platform · GitHub}},
  url =		 {https://github.com},
  howpublished = {Web Page},
  year =	 2017
}

@misc{www-github-i524,
  author =	 {{GitHub, Inc.}},
  title =	 {{Class submissions for Spring 2017 i524}},
  url =		 {https://github.com/cloudmesh/sp17-i524},
  howpublished = {Web Page},
  year =	 2017
}

@misc{www-apache-lic,
  author =	 {{The Apache Software Foundation}},
  title =	 {{Apache License}},
  url =		 {https://www.apache.org/licenses/LICENSE-2.0.html},
  howpublished = {Web Page},
  year =	 2017
}

@misc{www-intel-lic,
  author =	 {{Intel Corporation}},
  title =	 {{Product Licensing FAQ}},
  url =		 {https://software.intel.com/en-us/faq/licensing},
  howpublished = {Web Page},
  year =	 2017
}

@misc{www-intel-reg,
  author =	 {{Intel Corporation}},
  title =	 {{Manage License}},
  url =		 {https://registrationcenter.intel.com/en/products/license/2hws-f758wjvr/},
  howpublished = {Web Page},
  year =	 2017,
}

@misc{www-openmp,
  author =	 {{OpenMP}},
  title =	 {{Home - OpenMP}},
  url =		 {http://www.openmp.org},
  howpublished = {Web Page},
  year =	 2016
}

@misc{www-intel-mkl,
  author =	 {{md-rezaur-rahman (Intel) and Gennady F. (Intel)}},
  title =	 {{The Intel Math Kernel Library and its Fast Fourier
                  Transform Routines}},
  url =
                  {https://software.intel.com/en-us/articles/the-intel-math-kernel-library-and-its-fast-fourier-transform-routines},
  howpublished = {Web Page},
  year =	 2011,
  month =	 jun
}

@misc{www-intel,
  author =	 {{Intel Corporation}},
  title =	 {{Intel Fortran Compiler}},
  url =          {https://software.intel.com/en-us/fortran-compilers},
  howpublished = {Web Page},
  year =	 2017
}

@misc{www-cloudmesh,
  author =	 {{Gregor von Laszewski}},
  title =	 {{Cloudmesh Client Toolkit}},
  url =		 {http://cloudmesh-client.readthedocs.io/en/latest/},
  howpublished = {Web Page},
  address =	 {Indiana University},
  year =	 2015,
}

@misc{www-ansible-galaxy,
  author =	 {{Red Hat, Inc.}},
  title =	 {{Ansible Galaxy | Find, reuse, and share the best Ansible content}},
  url =		 {https://galaxy.ansible.com},
  howpublished = {Web Page},
  year =	 2016,
}

@misc{www-ansible,
  author =	 {{Red Hat, Inc.}},
  title =	 {{Ansible is Simple IT Automation}},
  url =		 {https://www.ansible.com},
  howpublished = {Web Page},
  year =	 2017,
}

@misc{www-mfj,
  author =	 {{Benjamin Draper}},
  title =	 {{MFJ Research Group}},
  url =		 {http://www.indiana.edu/~nano/},
  howpublished = {Web Page},
  address =	 {Indiana University},
  year =	 2017
}

@misc{www-mfjgroup,
  author =	 {{Benjamin Draper}},
  title =	 {{MFJ Research Group}},
  url =		 {http://www.indiana.edu/~nano/group/},
  howpublished = {Web Page},
  address =	 {Indiana University},
  year =	 2017
}

@Misc {www-underscore,
  key =		 {google},
  howpublished = {Web Page},
  url =		 {http://www.google.com/some_underscore}
}


text:
@online{Shuyi_Wang2018,
author = {Shuyi Wang},
title = {wei_lda_debate: },
year = 2018,
howpublished = {GitHub},
url = {https://github.com/wshuyi/wei_lda_debate},
urldate = {2020-02-09}
}

gha_license_id: NOASSERTION

gha_language: Jupyter Notebook


text:
% bmc_article.bib
%
%  An example of bibtex entries.
%  Entries taken from BMC instructions for authors page.

% uncomment next line to make author-year bibliography
% @settings{label, options="nameyear"}

% 27419868

@article{zhang2020improved,
  title={Improved genetic prediction of complex traits from individual-level data or summary statistics},
  author={Zhang, Qianqian and Prive, Florian and Vilhjalmsson, Bjarni J and Speed, Doug},
  journal={bioRxiv},
  year={2020},
  publisher={Cold Spring Harbor Laboratory}
}

@article{speed2012improved,
  title={Improved heritability estimation from genome-wide SNPs},
  author={Speed, Doug and Hemani, Gibran and Johnson, Michael R and Balding, David J},
  journal={The American Journal of Human Genetics},
  volume={91},
  number={6},
  pages={1011--1021},
  year={2012},
  publisher={Elsevier}
}

@article{LDpred2,
    author = {Privé, Florian and Arbel, Julyan and Vilhjálmsson, Bjarni J},
    title = "{LDpred2: better, faster, stronger}",
    journal = {Bioinformatics},
    volume = {36},
    number = {22-23},
    pages = {5424-5431},
    year = {2020},
    month = {12},
    abstract = "{Polygenic scores have become a central tool in human genetics research. LDpred is a popular method for deriving polygenic scores based on summary statistics and a matrix of correlation between genetic variants. However, LDpred has limitations that may reduce its predictive performance.Here, we present LDpred2, a new version of LDpred that addresses these issues. We also provide two new options in LDpred2: a ‘sparse’ option that can learn effects that are exactly 0, and an ‘auto’ option that directly learns the two LDpred parameters from data. We benchmark predictive performance of LDpred2 against the previous version on simulated and real data, demonstrating substantial improvements in robustness and predictive accuracy compared to LDpred1. We then show that LDpred2 also outperforms other polygenic score methods recently developed, with a mean AUC over the 8 real traits analyzed here of 65.1\\%, compared to 63.8\\% for lassosum, 62.9\\% for PRS-CS and 61.5\\% for SBayesR. Note that LDpred2 provides more accurate polygenic scores when run genome-wide, instead of per chromosome.LDpred2 is implemented in R package bigsnpr.Supplementary data are available at Bioinformatics online.}",
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btaa1029},
    url = {https://doi.org/10.1093/bioinformatics/btaa1029},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/36/22-23/5424/36855825/btaa1029.pdf},
}

@article{manichaikul2010robust,
  title={Robust relationship inference in genome-wide association studies},
  author={Manichaikul, Ani and Mychaleckyj, Josyf C and Rich, Stephen S and Daly, Kathy and Sale, Mich{\`e}le and Chen, Wei-Min},
  journal={Bioinformatics},
  volume={26},
  number={22},
  pages={2867--2873},
  year={2010},
  publisher={Oxford University Press}
}

@article{bycroft2018uk,
  title={The UK Biobank resource with deep phenotyping and genomic data},
  author={Bycroft, Clare and Freeman, Colin and Petkova, Desislava and Band, Gavin and Elliott, Lloyd T and Sharp, Kevin and Motyer, Allan and Vukcevic, Damjan and Delaneau, Olivier and O’Connell, Jared and others},
  journal={Nature},
  volume={562},
  number={7726},
  pages={203--209},
  year={2018},
  publisher={Nature Publishing Group}
}

@Article{sackton2016genotypic,
   Author="Sackton, T. B.  and Hartl, D. L. ",
   Title="{{G}enotypic {C}ontext and {E}pistasis in {I}ndividuals and {P}opulations}",
   Journal="Cell",
   Year="2016",
   Volume="166",
   Number="2",
   Pages="279--287",
   Month="Jul"
}

@Article{jakobsdottir2013mastor,
   Author="Jakobsdottir, J.  and McPeek, M. S. ",
   Title="{{M}{A}{S}{T}{O}{R}: mixed-model association mapping of quantitative traits in samples with related individuals}",
   Journal="Am J Hum Genet",
   Year="2013",
   Volume="92",
   Number="5",
   Pages="652--666",
   Month="May"
}

% 22983301
@Article{svishcheva2012rapid,
   Author="Svishcheva, G. R.  and Axenovich, T. I.  and Belonogova, N. M.  and van Duijn, C. M.  and Aulchenko, Y. S. ",
   Title="{{R}apid variance components-based method for whole-genome association analysis}",
   Journal="Nat Genet",
   Year="2012",
   Volume="44",
   Number="10",
   Pages="1166--1170",
   Month="Oct"
}

@Book{fisher1935,
  author    = "Fisher, R. A.",
  title     = "The Design of Experiments",
  publisher = "Oliver and Boyd",
  year      = "1935"
}

% 21892150
@Article{lippert2011fast,
   Author="Lippert, C.  and Listgarten, J.  and Liu, Y.  and Kadie, C. M.  and Davidson, R. I.  and Heckerman, D. ",
   Title="{{F}a{S}{T} linear mixed models for genome-wide association studies}",
   Journal="Nat Methods",
   Year="2011",
   Volume="8",
   Number="10",
   Pages="833--835",
   Month="Sep"
}

% 11315092
@Article{devlin1999genomic,
   Author="Devlin, B.  and Roeder, K. ",
   Title="{{G}enomic control for association studies}",
   Journal="Biometrics",
   Year="1999",
   Volume="55",
   Number="4",
   Pages="997--1004",
   Month="Dec"
}

% 25033443
@Article{eu2014comparison,
   Author="Eu-Ahsunthornwattana, J.  and Miller, E. N.  and Fakiola, M.  and Jeronimo, S. M.  and Blackwell, J. M.  and Cordell, H. J. ",
   Title="{{C}omparison of methods to account for relatedness in genome-wide association studies with family-based data}",
   Journal="PLoS Genet",
   Year="2014",
   Volume="10",
   Number="7",
   Pages="e1004445",
   Month="Jul"
}

% 17924335
@Article{chen2007family,
   Author="Chen, W. M.  and Abecasis, G. R. ",
   Title="{{F}amily-based association tests for genomewide association scans}",
   Journal="Am J Hum Genet",
   Year="2007",
   Volume="81",
   Number="5",
   Pages="913--926",
   Month="Nov"
}

% 20208535
@Article{zhang2010mixed,
   Author="Zhang, Z.  and Ersoz, E.  and Lai, C. Q.  and Todhunter, R. J.  and Tiwari, H. K.  and Gore, M. A.  and Bradbury, P. J.  and Yu, J.  and Arnett, D. K.  and Ordovas, J. M.  and Buckler, E. S. ",
   Title="{{M}ixed linear model approach adapted for genome-wide association studies}",
   Journal="Nat Genet",
   Year="2010",
   Volume="42",
   Number="4",
   Pages="355--360",
   Month="Apr"
}

%Regenie from bibtex
@article {mbatchou2020computationally,
        author = {Mbatchou, Joelle and Barnard, Leland and Backman, Joshua and Marcketta, Anthony and Kosmicki, Jack A. and Ziyatdinov, Andrey and Benner, Christian and O{\textquoteright}Dushlaine, Colm and Barber, Mathew and Boutkov, Boris and Habegger, Lukas and Ferreira, Manuel and Baras, Aris and Reid, Jeffrey and Abecasis, Gon{\c c}alo and Maxwell, Evan and Marchini, Jonathan},
        title = {Computationally efficient whole genome regression for quantitative and binary traits},
        elocation-id = {2020.06.19.162354},
        year = {2020},
        doi = {10.1101/2020.06.19.162354},
        publisher = {Cold Spring Harbor Laboratory},
        abstract = {Genome-wide association analysis of cohorts with thousands of phenotypes is computationally expensive, particularly when accounting for sample relatedness or population structure. Here we present a novel machine learning method called REGENIE for fitting a whole genome regression model that is orders of magnitude faster than alternatives, while maintaining statistical efficiency. The method naturally accommodates parallel analysis of multiple phenotypes, and only requires local segments of the genotype matrix to be loaded in memory, in contrast to existing alternatives which must load genomewide matrices into memory. This results in substantial savings in compute time and memory usage. The method is applicable to both quantitative and binary phenotypes, including rare variant analysis of binary traits with unbalanced case-control ratios where we introduce a fast, approximate Firth logistic regression test. The method is ideally suited to take advantage of distributed computing frameworks. We demonstrate the accuracy and computational benefits of this approach compared to several existing methods using quantitative and binary traits from the UK Biobank dataset with up to 407,746 individuals.Competing Interest StatementAll of the authors are current employees and/or stockholders of Regeneron Pharmaceuticals},
        URL = {https://www.biorxiv.org/content/early/2020/06/22/2020.06.19.162354},
        eprint = {https://www.biorxiv.org/content/early/2020/06/22/2020.06.19.162354.full.pdf},
        journal = {bioRxiv}
}

% 17701901
@Article{purcell2007plink,
   Author="Purcell, S.  and Neale, B.  and Todd-Brown, K.  and Thomas, L.  and Ferreira, M. A.  and Bender, D.  and Maller, J.  and Sklar, P.  and de Bakker, P. I.  and Daly, M. J.  and Sham, P. C. ",
   Title="{{P}{L}{I}{N}{K}: a tool set for whole-genome association and population-based linkage analyses}",
   Journal="Am J Hum Genet",
   Year="2007",
   Volume="81",
   Number="3",
   Pages="559--575",
   Month="Sep"
}

@ARTICLE{yu2006unified,
  title={A unified mixed-model method for association mapping that accounts for multiple levels of relatedness},
  author={Yu, Jianming and Pressoir, Gael and Briggs, William H and Bi, Irie Vroh and Yamasaki, Masanori and Doebley, John F and McMullen, Michael D and Gaut, Brandon S and Nielsen, Dahlia M and Holland, James B and others},
  journal={Nature genetics},
  volume={38},
  number={2},
  pages={203--208},
  year={2006},
  publisher={Nature Publishing Group}
}

@article{EMMA,
  title={Efficient control of population structure in model organism association mapping},
  author={Kang, Hyun Min and Zaitlen, Noah A and Wade, Claire M and Kirby, Andrew and Heckerman, David and Daly, Mark J and Eskin, Eleazar},
  journal={Genetics},
  volume={178},
  number={3},
  pages={1709--1723},
  year={2008},
  publisher={Genetics Soc America}
}

@article{emmax,
  title={Variance component model to account for sample structure in genome-wide association studies},
  author={Kang, Hyun Min and Sul, Jae Hoon and Service, Susan K and Zaitlen, Noah A and Kong, Sit-yee and Freimer, Nelson B and Sabatti, Chiara and Eskin, Eleazar and others},
  journal={Nature genetics},
  volume={42},
  number={4},
  pages={348},
  year={2010},
  publisher={Nature Publishing Group}
}

@article{gemma,
  title={Genome-wide efficient mixed-model analysis for association studies},
  author={Zhou, Xiang and Stephens, Matthew},
  journal={Nature genetics},
  volume={44},
  number={7},
  pages={821--824},
  year={2012},
  publisher={Nature Publishing Group}
}

@article{fastlmm,
  title={FaST-LMM-Select for addressing confounding from spatial structure and rare variants},
  author={Listgarten, Jennifer and Lippert, Christoph and Heckerman, David},
  journal={Nature genetics},
  volume={45},
  number={5},
  pages={470--471},
  year={2013},
  publisher={Nature Publishing Group}
}

@article{BOLT,
  title={Efficient Bayesian mixed-model analysis increases association power in large cohorts},
  author={Loh, Po-Ru and Tucker, George and Bulik-Sullivan, Brendan K and Vilhjalmsson, Bjarni J and Finucane, Hilary K and Salem, Rany M and Chasman, Daniel I and Ridker, Paul M and Neale, Benjamin M and Berger, Bonnie and others},
  journal={Nature genetics},
  volume={47},
  number={3},
  pages={284},
  year={2015},
  publisher={Nature Publishing Group}
}

@article{boltukb,
  title={Mixed-model association for biobank-scale datasets},
  author={Loh, Po-Ru and Kichaev, Gleb and Gazal, Steven and Schoech, Armin P and Price, Alkes L},
  journal={Nature genetics},
  volume={50},
  number={7},
  pages={906--908},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{price2010new,
  title={New approaches to population stratification in genome-wide association studies},
  author={Price, Alkes L and Zaitlen, Noah A and Reich, David and Patterson, Nick},
  journal={Nature Reviews Genetics},
  volume={11},
  number={7},
  pages={459--463},
  year={2010},
  publisher={Nature Publishing Group}
}
@article{yang2014advantages,
  title={Advantages and pitfalls in the application of mixed-model association methods},
  author={Yang, Jian and Zaitlen, Noah A and Goddard, Michael E and Visscher, Peter M and Price, Alkes L},
  journal={Nature genetics},
  volume={46},
  number={2},
  pages={100},
  year={2014},
  publisher={Nature Publishing Group}
}

@article{listgarten2012improved,
  title={Improved linear mixed models for genome-wide association studies},
  author={Listgarten, Jennifer and Lippert, Christoph and Kadie, Carl M and Davidson, Robert I and Eskin, Eleazar and Heckerman, David},
  journal={Nature methods},
  volume={9},
  number={6},
  pages={525},
  year={2012},
  publisher={Nature Publishing Group}
}

@article{lippert2013benefits,
  title={The benefits of selecting phenotype-specific variants for applications of mixed models in genomics},
  author={Lippert, Christoph and Quon, Gerald and Kang, Eun Yong and Kadie, Carl M and Listgarten, Jennifer and Heckerman, David},
  journal={Scientific reports},
  volume={3},
  pages={1815},
  year={2013},
  publisher={Nature Publishing Group}
}

@article{tucker2014improving,
  title={Improving the power of GWAS and avoiding confounding from population stratification with PC-Select},
  author={Tucker, George and Price, Alkes L and Berger, Bonnie},
  journal={Genetics},
  volume={197},
  number={3},
  pages={1045--1049},
  year={2014},
  publisher={Genetics Soc America}
}

@article{canela2018atlas,
  title={An atlas of genetic associations in UK Biobank},
  author={Canela-Xandri, Oriol and Rawlik, Konrad and Tenesa, Albert},
  journal={Nature genetics},
  volume={50},
  number={11},
  pages={1593--1599},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{tam2019benefits,
  title={Benefits and limitations of genome-wide association studies},
  author={Tam, Vivian and Patel, Nikunj and Turcotte, Michelle and Boss{\'e}, Yohan and Par{\'e}, Guillaume and Meyre, David},
  journal={Nature Reviews Genetics},
  volume={20},
  number={8},
  pages={467--484},
  year={2019},
  publisher={Nature Publishing Group}
}

@article{martin2019predicting,
  title={Predicting polygenic risk of psychiatric disorders},
  author={Martin, Alicia R and Daly, Mark J and Robinson, Elise B and Hyman, Steven E and Neale, Benjamin M},
  journal={Biological psychiatry},
  volume={86},
  number={2},
  pages={97--109},
  year={2019},
  publisher={Elsevier}
}

@article{khera2018genome,
  title={Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations},
  author={Khera, Amit V and Chaffin, Mark and Aragam, Krishna G and Haas, Mary E and Roselli, Carolina and Choi, Seung Hoan and Natarajan, Pradeep and Lander, Eric S and Lubitz, Steven A and Ellinor, Patrick T and others},
  journal={Nature genetics},
  volume={50},
  number={9},
  pages={1219--1224},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{torkamani2018personal,
  title={The personal and clinical utility of polygenic risk scores},
  author={Torkamani, Ali and Wineinger, Nathan E and Topol, Eric J},
  journal={Nature Reviews Genetics},
  volume={19},
  number={9},
  pages={581},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{yanes2020clinical,
  title={Clinical applications of polygenic breast cancer risk: a critical review and perspectives of an emerging field},
  author={Yanes, Tatiane and Young, Mary-Anne and Meiser, Bettina and James, Paul A},
  journal={Breast Cancer Research},
  volume={22},
  number={1},
  pages={1--10},
  year={2020},
  publisher={Springer}
}

@article{lambert2019towards,
  title={Towards clinical utility of polygenic risk scores},
  author={Lambert, Samuel A and Abraham, Gad and Inouye, Michael},
  journal={Human molecular genetics},
  volume={28},
  number={R2},
  pages={R133--R142},
  year={2019},
  publisher={Oxford University Press}
}

@article{duncan2019analysis,
  title={Analysis of polygenic risk score usage and performance in diverse human populations},
  author={Duncan, L and Shen, H and Gelaye, B and Meijsen, J and Ressler, K and Feldman, M and Peterson, R and Domingue, B},
  journal={Nature communications},
  volume={10},
  number={1},
  pages={1--9},
  year={2019},
  publisher={Nature Publishing Group}
}

@techreport{jiang2019resource,
  title={A resource-efficient tool for mixed model association analysis of large-scale data},
  author={Jiang, Longda and Zheng, Zhili and Qi, Ting and Kemper, Kathryn E and Wray, Naomi R and Visscher, Peter M and Yang, Jian},
  year={2019},
  institution={Nature Publishing Group}
}

@article{dudbridge2013power,
  title={Power and predictive accuracy of polygenic risk scores},
  author={Dudbridge, Frank},
  journal={PLoS genetics},
  volume={9},
  number={3},
  year={2013},
  publisher={Public Library of Science}
}

@article{chang2015second,
  title={Second-generation PLINK: rising to the challenge of larger and richer datasets},
  author={Chang, Christopher C and Chow, Carson C and Tellier, Laurent CAM and Vattikuti, Shashaank and Purcell, Shaun M and Lee, James J},
  journal={Gigascience},
  volume={4},
  number={1},
  pages={s13742--015},
  year={2015},
  publisher={Oxford University Press}
}

@article{yang2011gcta,
  title={GCTA: a tool for genome-wide complex trait analysis},
  author={Yang, Jian and Lee, S Hong and Goddard, Michael E and Visscher, Peter M},
  journal={The American Journal of Human Genetics},
  volume={88},
  number={1},
  pages={76--82},
  year={2011},
  publisher={Elsevier}
}

@article{choi2019prsice,
  title={PRSice-2: Polygenic Risk Score software for biobank-scale data},
  author={Choi, Shing Wan and O'Reilly, Paul F},
  journal={Gigascience},
  volume={8},
  number={7},
  pages={giz082},
  year={2019},
  publisher={Oxford University Press}
}

@article{robin2011proc,
  title={pROC: an open-source package for R and S+ to analyze and compare ROC curves},
  author={Robin, Xavier and Turck, Natacha and Hainard, Alexandre and Tiberti, Natalia and Lisacek, Fr{\'e}d{\'e}rique and Sanchez, Jean-Charles and M{\"u}ller, Markus},
  journal={BMC bioinformatics},
  volume={12},
  number={1},
  pages={77},
  year={2011},
  publisher={BioMed Central}
}

@article{watanabe2017functional,
  title={Functional mapping and annotation of genetic associations with FUMA},
  author={Watanabe, Kyoko and Taskesen, Erdogan and Van Bochoven, Arjen and Posthuma, Danielle},
  journal={Nature communications},
  volume={8},
  number={1},
  pages={1--11},
  year={2017},
  publisher={Nature Publishing Group}
}

@article{de2015magma,
  title={MAGMA: generalized gene-set analysis of GWAS data},
  author={de Leeuw, Christiaan A and Mooij, Joris M and Heskes, Tom and Posthuma, Danielle},
  journal={PLoS computational biology},
  volume={11},
  number={4},
  year={2015},
  publisher={Public Library of Science}
}

@article{lloyd2019improved,
  title={Improved polygenic prediction by Bayesian multiple regression on summary statistics},
  author={Lloyd-Jones, Luke R and Zeng, Jian and Sidorenko, Julia and Yengo, Lo{\"\i}c and Moser, Gerhard and Kemper, Kathryn E and Wang, Huanwei and Zheng, Zhili and Magi, Reedik and Esko, Tonu and others},
  journal={Nature communications},
  volume={10},
  number={1},
  pages={1--11},
  year={2019},
  publisher={Nature Publishing Group}
}

@article{watanabe2019global,
  title={A global overview of pleiotropy and genetic architecture in complex traits},
  author={Watanabe, Kyoko and Stringer, Sven and Frei, Oleksandr and Mirkov, Ma{\v{s}}a Umi{\'c}evi{\'c} and de Leeuw, Christiaan and Polderman, Tinca JC and van der Sluis, Sophie and Andreassen, Ole A and Neale, Benjamin M and Posthuma, Danielle},
  journal={Nature genetics},
  volume={51},
  number={9},
  pages={1339--1348},
  year={2019},
  publisher={Nature Publishing Group}
}

%cloud lmm bioxriv
@article {Kadie2019ludicrous,
	author = {Kadie, Carl and Heckerman, David},
	title = {Ludicrous Speed Linear Mixed Models for Genome-Wide Association Studies},
	elocation-id = {154682},
	year = {2019},
	doi = {10.1101/154682},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {We have developed Ludicrous Speed Linear Mixed Models, a version of FaST-LMM optimized for the cloud. The approach can perform a genome-wide association analysis on a dataset of one million SNPs across one million individuals at a cost of about 868 CPU days with an elapsed time on the order of two weeks. A Python implementation is available at https://fastlmm.github.io/.Significance Identifying SNP-phenotype correlations using GWAS is difficult because effect sizes are so small for common, complex diseases. To address this issue, institutions are creating extremely large cohorts with sample sizes on the order of one million. Unfortunately, such cohorts are likely to contain confounding factors such as population structure and family/cryptic relatedness. The linear mixed model (LMM) can often correct for such confounding factors, but is too slow to use even with algebraic speedups known as FaST-LMM. We present a cloud implementation of FaST-LMM, called Ludicrous Speed LMM, that can process one million samples and one million test SNPs in a reasonable amount of time and at a reasonable cost.},
	URL = {https://www.biorxiv.org/content/early/2019/12/07/154682},
	eprint = {https://www.biorxiv.org/content/early/2019/12/07/154682.full.pdf},
	journal = {bioRxiv}
}
%%%%%%%%
% cancer pgs
@article{michailidou2017association,
  title={Association analysis identifies 65 new breast cancer risk loci},
  author={Michailidou, Kyriaki and Lindstr{\"o}m, Sara and Dennis, Joe and Beesley, Jonathan and Hui, Shirley and Kar, Siddhartha and Lema{\c{c}}on, Audrey and Soucy, Penny and Glubb, Dylan and Rostamianfar, Asha and others},
  journal={Nature},
  volume={551},
  number={7678},
  pages={92},
  year={2017},
  publisher={Nature Publishing Group}
}

@article{bahcall2013common,
  title={Common variation and heritability estimates for breast, ovarian and prostate cancers},
  author={Bahcall, Orli},
  journal={Nat Genet},
  volume={10},
  year={2013}
}

% discussion
@article{mars2020polygenic,
  title={Polygenic and clinical risk scores and their impact on age at onset and prediction of cardiometabolic diseases and common cancers},
  author={Mars, Nina and Koskela, Jukka T and Ripatti, Pietari and Kiiskinen, Tuomo TJ and Havulinna, Aki S and Lindbohm, Joni V and Ahola-Olli, Ari and Kurki, Mitja and Karjalainen, Juha and Palta, Priit and others},
  journal={Nature Medicine},
  pages={1--9},
  year={2020},
  publisher={Nature Publishing Group}
}

%discussion
@article{gibson2019utilization,
  title={On the utilization of polygenic risk scores for therapeutic targeting},
  author={Gibson, Greg},
  journal={PLoS genetics},
  volume={15},
  number={4},
  year={2019},
  publisher={Public Library of Science}
}

%Discussion
@article{nolte2017comparison,
  title={A comparison of heritability estimates by classical twin modeling and based on genome-wide genetic relatedness for cardiac conduction traits},
  author={Nolte, Ilja M and Jansweijer, Joeri A and Riese, Hariette and Asselbergs, Folkert W and Van Der Harst, Pim and Spector, Timothy D and Pinto, Yigal M and Snieder, Harold and Jamshidi, Yalda},
  journal={Twin Research and Human Genetics},
  volume={20},
  number={6},
  pages={489--498},
  year={2017},
  publisher={Cambridge University Press}
}

%height h2
@article{hou2019accurate,
  title={Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture},
  author={Hou, Kangcheng and Burch, Kathryn S and Majumdar, Arunabha and Shi, Huwenbo and Mancuso, Nicholas and Wu, Yue and Sankararaman, Sriram and Pasaniuc, Bogdan},
  journal={Nature genetics},
  pages={1},
  year={2019},
  publisher={Nature Publishing Group}
}

@article{yengo2018meta,
  title={Meta-analysis of genome-wide association studies for height and body mass index in~ 700000 individuals of European ancestry},
  author={Yengo, Loic and Sidorenko, Julia and Kemper, Kathryn E and Zheng, Zhili and Wood, Andrew R and Weedon, Michael N and Frayling, Timothy M and Hirschhorn, Joel and Yang, Jian and Visscher, Peter M and others},
  journal={Human molecular genetics},
  volume={27},
  number={20},
  pages={3641--3649},
  year={2018},
  publisher={Oxford University Press}
}

@article{neuhaus1998estimation,
  title={Estimation efficiency with omitted covariates in generalized linear models},
  author={Neuhaus, John M},
  journal={Journal of the American Statistical Association},
  volume={93},
  number={443},
  pages={1124--1129},
  year={1998},
  publisher={Taylor \& Francis Group}
}