text:
% statistics

@article{karpievitch2009statistical,
  title={A statistical framework for protein quantitation in bottom-up
{MS}-based proteomics},
  author={Karpievitch, Yuliya and Stanley, Jeff and Taverner, Thomas
and Huang, Jianhua and Adkins, Joshua N and Ansong, Charles and
Heffron, Fred and Metz, Thomas O and Qian, Wei-Jun and Yoon, Hyunjin
and others},
  journal={Bioinformatics},
  volume={25},
  number={16},
  pages={2028--2034},
  year={2009},
  publisher={Oxford University Press}
}
@article {the2018integrated,
  author = {The, Matthew and K{\"a}ll, Lukas},
  title = {Integrated identification and quantification error
probabilities for shotgun proteomics},
  year = {2018},
  doi = {10.1101/357285},
  publisher = {Cold Spring Harbor Laboratory},
  URL = {https://www.biorxiv.org/content/early/2018/06/28/357285},
  eprint =
{https://www.biorxiv.org/content/early/2018/06/28/357285.full.pdf},
  journal = {bio{R}xiv}
}
@article{tyanova2016perseus,
  title={The {P}erseus computational platform for comprehensive analysis of
(prote) omics data},
  author={Tyanova, Stefka and Temu, Tikira and Sinitcyn, Pavel and Carlson,
Arthur and Hein, Marco Y and Geiger, Tamar and Mann, Matthias and Cox,
J{\"u}rgen},
  journal={Nature {M}ethods},
  volume={13},
  number={9},
  pages={731},
  year={2016},
  publisher={Nature Publishing Group}
}

% matches between runs

@article{cox2014accurate,
  title={Accurate proteome-wide label-free quantification by delayed
normalization and maximal peptide ratio extraction, termed {MaxLFQ}},
  author={Cox, J{\"u}rgen and Hein, Marco Y and Luber, Christian A and
Paron, Igor and Nagaraj, Nagarjuna and Mann, Matthias},
  journal={Molecular \& {C}ellular {P}roteomics},
  volume={13},
  number={9},
  pages={2513--2526},
  year={2014},
  publisher={ASBMB}
}
@article{zhang2016demix,
  title={{DeMix-Q}: {Q}uantification-centered data processing workflow},
  author={Zhang, Bo and K{\"a}ll, Lukas and Zubarev, Roman A},
  journal={Molecular \& {C}ellular {P}roteomics},
  volume={15},
  number={4},
  pages={1467--1478},
  year={2016},
  publisher={ASBMB}
}
@article{argentini2016moff,
  title={{moFF}: {A} robust and automated approach to extract peptide ion
intensities},
  author={Argentini, Andrea and Goeminne, Ludger JE and Verheggen,
Kenneth and Hulstaert, Niels and Staes, An and Clement, Lieven and
Martens, Lennart},
  journal={Nature {M}ethods},
  volume={13},
  number={12},
  pages={964--966},
  year={2016},
  publisher={Nature Research}
}

% missing value imputation

@article{webb2015review,
  title={Review, evaluation, and discussion of the challenges of missing value
imputation for mass spectrometry-based label-free global proteomics},
  author={Webb-Robertson, Bobbie-Jo M and Wiberg, Holli K and Matzke, Melissa M
and Brown, Joseph N and Wang, Jing and McDermott, Jason E and Smith, Richard D
and Rodland, Karin D and Metz, Thomas O and Pounds, Joel G and Waters, Katrina
M},
  journal={Journal of {P}roteome {R}esearch},
  volume={14},
  number={5},
  pages={1993--2001},
  year={2015},
  publisher={ACS Publications}
}
@article{lazar2016accounting,
  title={Accounting for the multiple natures of missing values in
label-free quantitative proteomics data sets to compare imputation
strategies},
  author={Lazar, Cosmin and Gatto, Laurent and Ferro, Myriam and
Bruley, Christophe and Burger, Thomas},
  journal={Journal of {P}roteome {R}esearch},
  volume={15},
  number={4},
  pages={1116--1125},
  year={2016},
  publisher={ACS Publications}
}
@article{rosenberger2017statistical,
  title={Statistical control of peptide and protein error rates in
large-scale targeted data-independent acquisition analyses},
  author={Rosenberger, George and Bludau, Isabell and Schmitt, Uwe and
Heusel, Moritz and Hunter, Christie L and Liu, Yansheng and MacCoss,
Michael J and MacLean, Brendan X and Nesvizhskii, Alexey I and
Pedrioli, Patrick GA and others},
  journal={Nature {M}ethods},
  volume={14},
  number={9},
  pages={921},
  year={2017},
  publisher={Nature Publishing Group}
}
@article{ong2005mass,
  title={Mass spectrometry--based proteomics turns quantitative},
  author={Ong, Shao-En and Mann, Matthias},
  journal={Nature {C}hemical {B}iology},
  volume={1},
  number={5},
  pages={252--262},
  year={2005},
  publisher={Nature Publishing Group}
}
@article{mueller2008assessment,
  title={An assessment of software solutions for the analysis of mass
spectrometry based quantitative proteomics data},
  author={Mueller, Lukas N and Brusniak, Mi-Youn and Mani, DR and
Aebersold, Ruedi},
  journal={Journal of {P}roteome {R}esearch},
  volume={7},
  number={01},
  pages={51--61},
  year={2008},
  publisher={ACS Publications}
}
@article{the2016talk,
  title={How to talk about protein-level false discovery rates in
shotgun proteomics},
  author={The, Matthew and Tasnim, Ayesha and K{\"a}ll, Lukas},
  journal={Proteomics},
  volume={16},
  number={18},
  pages={2461--2469},
  year={2016},
  publisher={Wiley Online Library}
}
@article{granholm2013determining,
  title={Determining the calibration of confidence estimation
procedures for unique peptides in shotgun proteomics},
  author={Granholm, Viktor and Navarro, Jos\'{e} Fern\'{a}ndez and
Noble, William Stafford and K\"{a}ll, Lukas},
  journal={Journal of {P}roteomics},
  volume={80},
  pages={123--131},
  year={2013},
  publisher={Elsevier}
}
@article{kall2008non,
  title={Non-parametric estimation of posterior error probabilities
associated with peptides identified by tandem mass spectrometry},
  author={K{\"a}ll, Lukas and Storey, John D and Noble, William
Stafford},
  journal={Bioinformatics},
  volume={24},
  number={16},
  pages={i42--i48},
  year={2008},
  publisher={Oxford University Press}
}
@article{the2016fast,
  title={Fast and Accurate Protein False Discovery Rates on
Large-Scale Proteomics Data Sets with {P}ercolator 3.0},
  author={The, Matthew and MacCoss, Michael J and Noble, William S and
K{\"a}ll, Lukas},
  journal={Journal of the {A}merican {S}ociety for {M}ass {S}pectrometry},
  volume={27},
  number={11},
  pages={1719},
  year={2016},
  publisher={Springer}
}

% datasets

@article{latosinska2015comparative,
  title={Comparative analysis of label-free and {8-Plex iTRAQ} approach for
quantitative tissue proteomic analysis},
  author={Latosinska, Agnieszka and Vougas, Konstantinos and Makridakis,
Manousos and Klein, Julie and Mullen, William and Abbas, Mahmoud and
Stravodimos, Konstantinos and Katafigiotis, Ioannis and Merseburger, Axel S and
Zoidakis, Jerome and others},
  journal={PloS one},
  volume={10},
  number={9},
  pages={e0137048},
  year={2015},
  publisher={Public Library of Science}
}
@article{bracht2015analysis,
  title={Analysis of Disease-Associated Protein Expression Using Quantitative
Proteomics---Fibulin-5 Is Expressed in Association with Hepatic Fibrosis},
  author={Bracht, Thilo and Schweinsberg, Vincent and Trippler, Martin and Kohl,
Michael and Ahrens, Maike and Padden, Juliet and Naboulsi, Wael and Barkovits,
Katalin and Megger, Dominik A and Eisenacher, Martin and others},
  journal={Journal of {P}roteome {R}esearch},
  volume={14},
  number={5},
  pages={2278--2286},
  year={2015},
  publisher={ACS Publications}
}

@article{GiaiGianetto2016,
  author = {{Giai Gianetto}, Quentin and Combes, Florence and Ramus, Claire and
Bruley, Christophe and Cout{\'{e}}, Yohann and Burger, Thomas},
  doi = {10.1002/pmic.201500189},
  issn = {16159861},
  journal = {Proteomics},
  number = {1},
  pages = {29--32},
  pmid = {26572953},
  title = {Calibration plot for proteomics: {A} graphical tool to
visually check the assumptions underlying {FDR} control in quantitative
experiments},
  volume = {16},
  year = {2016}
}
@article{Choi2017,
  author = {Choi, Meena and Eren-Dogu, Zeynep F. and Colangelo, Christopher and
Cottrell, John and Hoopmann, Michael R. and Kapp, Eugene A. and Kim, Sangtae and
Lam, Henry and Neubert, Thomas A. and Palmblad, Magnus and Phinney, Brett S. and
Weintraub, Susan T. and MacLean, Brendan and Vitek, Olga},
  doi = {10.1021/acs.jproteome.6b00881},
  issn = {15353907},
  journal = {Journal of {P}roteome {R}esearch},
  number = {2},
  pages = {945--957},
  pmid = {27990823},
  title = {{ABRF} {P}roteome {I}nformatics {R}esearch {G}roup ({iPRG}) 2015
Study: {D}etection of Differentially Abundant Proteins in Label-Free
Quantitative {LC-MS/MS} Experiments},
  volume = {16},
  year = {2017}
}
@article{the2017protein,
  title={A protein standard that emulates homology for the
characterization of protein inference algorithms},
  author={The, Matthew and Edfors, Fredrik and Perez-Riverol, Yasset
and Payne, Samuel H and Hoopmann, Michael R and Palmblad, Magnus and
Forsstr{\"o}m, Bj{\"o}rn and K{\"a}ll, Lukas and others},
  journal={bio{R}xiv},
  pages={236471},
  year={2017},
  publisher={Cold Spring Harbor Laboratory}
}

@article{zhu2018nanodroplet,
  title={Nanodroplet processing platform for deep and quantitative proteome
profiling of 10--100 mammalian cells},
  author={Zhu, Ying and Piehowski, Paul D and Zhao, Rui and Chen, Jing and Shen,
Yufeng and Moore, Ronald J and Shukla, Anil K and Petyuk, Vladislav A and
Campbell-Thompson, Martha and Mathews, Clayton E and others},
  journal={Nature {C}ommunications},
  volume={9},
  number={1},
  pages={882},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{geyer2016bartric,
  title={Proteomics reveals the effects of sustained weight loss on the human
  plasma proteome},
  author={Geyer PE, Wewer Albrechtsen NJ, Tyanova S, Grassl N, Iepsen EW,
  Lundgren J, Madsbad S, Holst JJ, Torekov SS, Mann M},
  journal={Molecular Systems Biology },
  volume={12},
  number={12},
  pages={901},
  year={2016},
}

% quantitative proteomics

@article{bantscheff2007quantitative,
  title={Quantitative mass spectrometry in proteomics: {A} critical review},
  author={Bantscheff, Marcus and Schirle, Markus and Sweetman, Gavain and Rick,
Jens and Kuster, Bernhard},
  journal={Analytical and {B}ioanalytical {C}hemistry},
  volume={389},
  number={4},
  pages={1017--1031},
  year={2007},
  publisher={Springer}
}
@article{bantscheff2012quantitative,
  title={Quantitative mass spectrometry in proteomics: {C}ritical review
update from 2007 to the present},
  author={Bantscheff, Marcus and Lemeer, Simone and Savitski, Mikhail M and
Kuster, Bernhard},
  journal={Analytical and {B}ioanalytical {C}hemistry},
  volume={404},
  number={4},
  pages={939--965},
  year={2012},
  publisher={Springer}
}
@article{pascovici2016multiple,
  title={Multiple testing corrections in quantitative proteomics: {A} useful
but blunt tool},
  author={Pascovici, Dana and Handler, David CL and Wu, Jemma X and Haynes, Paul
A},
  journal={Proteomics},
  volume={16},
  number={18},
  pages={2448--2453},
  year={2016},
  publisher={Wiley Online Library}
}
@article{tusher2001significance,
  title={Significance analysis of microarrays applied to the ionizing radiation
response},
  author={Tusher, Virginia Goss and Tibshirani, Robert and Chu, Gilbert},
  journal={Proceedings of the {N}ational {A}cademy of {S}ciences},
  volume={98},
  number={9},
  pages={5116--5121},
  year={2001},
  publisher={National Acad Sciences}
}

% search engines

@article{kong2017msfragger,
  title={{MSFragger}: {U}ltrafast and comprehensive peptide identification in
mass spectrometry--based proteomics},
  author={Kong, Andy T and Leprevost, Felipe V and Avtonomov, Dmitry M and
Mellacheruvu, Dattatreya and Nesvizhskii, Alexey I},
  journal={Nature {M}ethods},
  volume={14},
  number={5},
  pages={513},
  year={2017},
  publisher={Nature Publishing Group}
}
@article{kertesz2015tandem,
  title={Tandem mass spectrum identification via cascaded search},
  author={Kertesz-Farkas, Attila and Keich, Uri and Noble, William Stafford},
  journal={Journal of {P}roteome {R}esearch},
  volume={14},
  number={8},
  pages={3027--3038},
  year={2015},
  publisher={ACS Publications}
}
@article{dorfer2018charmert,
  title={{CharmeRT}: {B}oosting peptide identifications by chimeric spectra
identification and retention time prediction},
  author={Dorfer, Viktoria and Maltsev, Sergey and Winkler, Stephan and
Mechtler, Karl},
  journal={Journal of {P}roteome {R}esearch},
  year={2018},
  publisher={ACS Publications}
}
@article{diament2011faster,
  title={Faster {SEQUEST} searching for peptide identification from tandem mass
spectra},
  author={Diament, Benjamin J and Noble, William Stafford},
  journal={Journal of {P}roteome {R}esearch},
  volume={10},
  number={9},
  pages={3871--3879},
  year={2011},
  publisher={ACS Publications}
}
@article{na2011fast,
  title={Fast multi-blind modification search through tandem mass spectrometry},
  author={Na, Seungjin and Bandeira, Nuno and Paek, Eunok},
  journal={Molecular \& {C}ellular {P}roteomics},
  pages={mcp--M111},
  year={2011},
  publisher={ASBMB}
}
@article{ma2015novor,
  title={Novor: {R}eal-time peptide de novo sequencing software},
  author={Ma, Bin},
  journal={Journal of the {A}merican {S}ociety for {M}ass {S}pectrometry},
  volume={26},
  number={11},
  pages={1885--1894},
  year={2015},
  publisher={Springer}
}
@article{eng2008,
  title={A fast {SEQUEST} cross correlation algorithm},
  author={Eng, Jimmy K and Fischer, Bernd and Grossmann, Jonas and MacCoss,
Michael J},
  journal={Journal of {P}roteome {R}esearch},
  volume={7},
  number={10},
  pages={4598--4602},
  year={2008},
  publisher={ACS Publications}
}
@article{kim2008,
  title={Spectral probabilities and generating functions of tandem mass spectra:
{A} strike against decoy databases},
  author={Kim, Sangtae and Gupta, Nitin and Pevzner, Pavel A},
  journal={Journal of {P}roteome {R}esearch},
  volume={7},
  number={8},
  pages={3354--3363},
  year={2008},
  publisher={ACS Publications}
}
@article{park2008rapid,
  title={Rapid and accurate peptide identification from tandem mass spectra},
  author={Park, Christopher Y and Klammer, Aaron A and K\"{a}ll, Lukas and
MacCoss, Michael J and Noble, William S},
  journal={Journal of {P}roteome {R}esearch},
  volume={7},
  number={7},
  pages={3022--3027},
  year={2008},
  publisher={ACS Publications}
}
@article{mcilwain2014,
  title={Crux: {R}apid open source protein tandem mass spectrometry analysis},
  author={McIlwain, Sean and Tamura, Kaipo and Kertesz-Farkas, Attila and Grant,
Charles E and Diament, Benjamin and Frewen, Barbara and Howbert, J Jeffry and
Hoopmann, Michael R and K\"all, Lukas and Eng, Jimmy K and others},
  journal={Journal of {P}roteome {R}esearch},
  volume={13},
  number={10},
  pages={4488--4491},
  year={2014},
  publisher={ACS Publications}
}
@article{cottrell1999,
  title={Probability-based protein identification by searching sequence
databases using mass spectrometry data},
  author={Cottrell, John S and London, U},
  journal={Electrophoresis},
  volume={20},
  number={18},
  pages={3551--3567},
  year={1999}
}
@article{lam2007,
  title={Development and validation of a spectral library searching method for
peptide identification from {MS/MS}},
  author={Lam, Henry and Deutsch, Eric W and Eddes, James S and Eng, Jimmy K and
King, Nichole and Stein, Stephen E and Aebersold, Ruedi},
  journal={Proteomics},
  volume={7},
  number={5},
  pages={655--667},
  year={2007},
  publisher={Wiley Online Library}
}
@article{frewen2006,
  title={Analysis of peptide {MS/MS} spectra from large-scale proteomics
experiments using spectrum libraries},
  author={Frewen, Barbara E and Merrihew, Gennifer E and Wu, Christine C and
Noble, William Stafford and MacCoss, Michael J},
  journal={Analytical {C}hemistry},
  volume={78},
  number={16},
  pages={5678--5684},
  year={2006},
  publisher={ACS Publications}
}
@article{griss2016recognizing,
  title={Recognizing millions of consistently unidentified spectra across
hundreds of shotgun proteomics datasets},
  author={Griss, Johannes and Perez-Riverol, Yasset and Lewis, Steve and Tabb,
David L and Dianes, Jos{\'e} A and del-Toro, Noemi and Rurik, Marc and Walzer,
Mathias and Kohlbacher, Oliver and Hermjakob, Henning and others},
  journal={Nature {M}ethods},
  volume={13},
  number={8},
  pages={651},
  year={2016},
  publisher={Nature Publishing Group}
}
@article{kall2007,
  title={Semi-supervised learning for peptide identification from shotgun
proteomics datasets},
  author={K\"{a}ll, Lukas and Canterbury, Jesse D and Weston, Jason
and Noble,
William Stafford and MacCoss, Michael J},
  journal={Nature {M}ethods},
  volume={4},
  number={11},
  pages={923--925},
  year={2007},
  publisher={Nature Publishing Group}
}
@article{lundstrom2017spotlight,
  title={{SpotLight Proteomics}: {U}ncovering the hidden blood proteome improves
diagnostic power of proteomics},
  author={Lundstr{\"o}m, Susanna L and Zhang, Bo and Rutishauser, Dorothea and
Aarsland, Dag and Zubarev, Roman A},
  journal={Scientific {R}eports},
  volume={7},
  pages={41929},
  year={2017},
  publisher={Nature Publishing Group}
}
@article{kertesz2015tandem,
  title={Tandem mass spectrum identification via cascaded search},
  author={Kertesz-Farkas, Attila and Keich, Uri and Noble, William Stafford},
  journal={Journal of {P}roteome {R}esearch},
  volume={14},
  number={8},
  pages={3027--3038},
  year={2015},
  publisher={ACS Publications}
}

% unidentified spectra

@article{skinner2015illuminating,
  title={Illuminating the dark matter of shotgun proteomics},
  author={Skinner, Owen S and Kelleher, Neil L},
  journal={Nature {B}iotechnology},
  volume={33},
  number={7},
  pages={717},
  year={2015},
  publisher={Nature Publishing Group}
}

@article{matzke2013comparative,
  title={A comparative analysis of computational approaches to
relative protein quantification using peptide peak intensities in
label-free {LC-MS} proteomics experiments},
  author={Matzke, Melissa M and Brown, Joseph N and Gritsenko, Marina
A and Metz, Thomas O and Pounds, Joel G and Rodland, Karin D and
Shukla, Anil K and Smith, Richard D and Waters, Katrina M and
McDermott, Jason E and others},
  journal={Proteomics},
  volume={13},
  number={3-4},
  pages={493--503},
  year={2013},
  publisher={Wiley Online Library}
}

% MS2 clustering

@article{the2016maracluster,
  title={{MaRaCluster}: {A} Fragment Rarity Metric for Clustering Fragment
Spectra in Shotgun Proteomics},
  author={The, Matthew and K\"{a}ll, Lukas},
  journal={Journal of {P}roteome {R}esearch},
  volume={15},
  number={3},
  pages={713--720},
  year={2016},
  publisher={ACS Publications}
}
@article{frank2011,
  title={Spectral archives: {E}xtending spectral libraries to analyze both
identified and unidentified spectra},
  author={Frank, Ari M and Monroe, Matthew E and Shah, Anuj R and Carver, Jeremy
J and Bandeira, Nuno and Moore, Ronald J and Anderson, Gordon A and Smith,
Richard D and Pevzner, Pavel A},
  journal={Nature {M}ethods},
  volume={8},
  number={7},
  pages={587--591},
  year={2011},
  publisher={Nature Publishing Group}
}
@article{griss2013,
  title={{PRIDE Cluster}: {B}uilding a consensus of proteomics data},
  author={Griss, Johannes and Foster, Joseph M and Hermjakob, Henning and
Vizca{\'\i}no, Juan Antonio},
  journal={Nature {M}ethods},
  volume={10},
  number={2},
  pages={95--96},
  year={2013},
  publisher={Nature Publishing Group}
}

% retention time alignment

@article{rost2016tric,
  title={{TRIC}: {A}n automated alignment strategy for reproducible protein
quantification in targeted proteomics},
  author={R{\"o}st, Hannes L and Liu, Yansheng and D'Agostino, Giuseppe and
Zanella, Matteo and Navarro, Pedro and Rosenberger, George and Collins, Ben C
and Gillet, Ludovic and Testa, Giuseppe and Malmstr{\"o}m, Lars and others},
  journal={Nature {M}ethods},
  volume={13},
  number={9},
  pages={777},
  year={2016},
  publisher={Nature Publishing Group}
}

% feature detection

@article{teleman2016dinosaur,
  author = {Teleman, Johan and Chawade, Aakash and Sandin, Marianne and
  Levander, Fredrik and Malmstr{\"{o}}m, Johan},
  journal = {Journal of {P}roteome {R}esearch},
  number = {7},
  pages = {2143--2151},
  title = {Dinosaur: {A} Refined Open-Source Peptide {MS} Feature Detector},
  volume = {15},
  year = {2016}
}
@article{michalski2011more,
  title={More than 100,000 detectable peptide species elute in single
shotgun proteomics runs but the majority is inaccessible to
data-dependent {LC-MS/MS}},
  author={Michalski, Annette and Cox, Juergen and Mann, Matthias},
  journal={Journal of {P}roteome {R}esearch},
  volume={10},
  number={4},
  pages={1785--1793},
  year={2011},
  publisher={ACS Publications}
}

% chimeric spectra

@article{wang2011peptide,
  title={Peptide identification by database search of mixture tandem mass
spectra},
  author={Wang, Jian and Bourne, Philip E and Bandeira, Nuno},
  journal={Molecular \& {C}ellular {P}roteomics},
  volume={10},
  number={12},
  pages={M111--010017},
  year={2011},
  publisher={ASBMB}
}
@article{houel2010quantifying,
  title={Quantifying the impact of chimera {MS/MS} spectra on peptide
identification in large-scale proteomics studies},
  author={Houel, Stephane and Abernathy, Robert and Renganathan, Kutralanathan
and Meyer-Arendt, Karen and Ahn, Natalie G and Old, William M},
  journal={Journal of {P}roteome {R}esearch},
  volume={9},
  number={8},
  pages={4152--4160},
  year={2010},
  publisher={ACS Publications}
}

@article{kessner2008,
  title={{ProteoWizard}: {O}pen source software for rapid proteomics tools
development},
  author={Kessner, Darren and Chambers, Matt and Burke, Robert and Agus, David
and Mallick, Parag},
  journal={Bioinformatics},
  volume={24},
  number={21},
  pages={2534--2536},
  year={2008},
  publisher={Oxford Univ Press}
}

% functional annotation

@article{huang2008systematic,
  title={Systematic and integrative analysis of large gene lists using {DAVID}
bioinformatics resources},
  author={Huang, Da Wei and Sherman, Brad T and Lempicki, Richard A},
  journal={Nature {P}rotocols},
  volume={4},
  number={1},
  pages={44},
  year={2008},
  publisher={Nature Publishing Group}
}
@article{di2017nextflow,
  title={Nextflow enables reproducible computational workflows},
  author={Di Tommaso, Paolo and Chatzou, Maria and Floden, Evan W and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric},
  journal={Nature biotechnology},
  volume={35},
  number={4},
  pages={316},
  year={2017},
  publisher={Nature Publishing Group}
}

% MISC

@ARTICLE{biocontainers,
    autohor = "Leprevost F V. et al",
    title = "BioContainers: an open-source and community-driven framework for software standardization",
    journal = "Bioinformatics",
    volume = "33",
    number = "16",
    pages = "2580-2582",
    DOI = "10.1093/bioinformatics/btx192",
    year = "2017"
}

@MISC{pyside2,
    title = "Qt for Python",
    howpublished = "\url{https://wiki.qt.io/Qt_for_Python}",
    note = "Accessed: 2019-03-28"
}

@ARTICLE{boxcar,
    author = "Meier F. et al.",
    title = "BoxCar acquisition method enables single-shot proteomics at a depth
    of 10,000 proteins in 100 minutes",
    DOI = "10.1038/s41592-018-0003-5",
    volume = "15",
    year = "2017"
}

@ARTICLE{boxcar-data,
    author = "Albrechtsen N. et al",
    title = "Plasma Proteome Profiling Reveals Dynamics of Inflammatory and
     Lipid Homeostasis Markers after Roux-En-Y Gastric Bypass Surgery",
    journal = "Cell Systems",
    volume = "7",
    number = "6",
    pages = "601-612",
    DOI = "10.1016/j.cels.2018.10.012",
    year = "2018"
}

@ARTICLE{docker,
  author = "Merkel, Dirk",
  year = "2014",
  month = "03",
  pages = "",
  title = "Docker: lightweight Linux containers for consistent development and deployment",
  volume = "2014",
  journal = "Linux Journal"
}

@ARTICLE{singularity-hub,
    author = "Sochat V. Prybol CJ. Kurtzer GM",
    title = "Enhancing reproducibility in scientific computing: Metrics and registry for Singularity containers",
    journal = "PLoS ONE",
    volume = "12",
    number = "11",
    DOI = "10.1371/journal.pone.0188511",
    year = "2017"
}

@MISC{singularity-uppmax,
    title = "Singularity User Guide",
    howpublished = "\url{https://www.uppmax.uu.se/support/user-guides/singularity-user-guide/}",
    note = "Accessed: 2019-03-27"
}

@ARTICLE{crux,
    author = "McIlwain S. et al",
    title = "Crux: rapid open source protein tandem mass spectrometry analysis",
    journal = "Journal of Proteome Research",
    volume = "13",
    number = "10",
    pages = "4488-4491",
    year = "2014"
}

@ARTICLE{tide-search,
    author = "Diament J. B. and Noble S. W.",
    title = "Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra",
    journal = "Journal of Proteome Research",
    volume = "10",
    number = "9",
    pages = "3871-3879",
    year = "2010"
}

@article{chambers2012cross,
  title={A cross-platform toolkit for mass spectrometry and proteomics},
  author={Chambers, Matthew C and Maclean, Brendan and Burke, Robert and Amodei, Dario and Ruderman, Daniel L and Neumann, Steffen and Gatto, Laurent and Fischer, Bernd and Pratt, Brian and Egertson, Jarrett and others},
  journal={Nature biotechnology},
  volume={30},
  number={10},
  pages={918},
  year={2012},
  publisher={Nature Publishing Group}
}
@article{percolator,
  title={Semi-supervised learning for peptide identification from shotgun proteomics datasets},
  author= {K\"{a}ll, Lukas and Canterbury, Jesse D and Weston, Jason and Noble, William Stafford and MacCoss, Michael J},
  journal={Nature methods},
  volume={4},
  number={11},
  pages={923},
  year={2007},
  publisher={Nature Publishing Group}
}
@article {quandenser,
	author = {The, Matthew and K{\"a}ll, Lukas},
	title = {Focus on the spectra that matter by clustering of quantification data in shotgun proteomics},
	elocation-id = {488015},
	year = {2018},
	doi = {10.1101/488015},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2018/12/06/488015},
	eprint = {https://www.biorxiv.org/content/early/2018/12/06/488015.full.pdf},
	journal = {bioRxiv}
}


text:
{% if "citation" in current_page %}
@article{ {{id}},
    title="{{title}}",
    author="{{author | author}}",
    year={{citation.year}},
    journal="{{citation.journal}}",
    volume={{citation.volume}},
    {% if citation.number %}number="{{citation.number}}",{% endif %}
    {% if citation.pages %}pages="{{citation.pages}}"{% endif %}
}
{% endif %}

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib


text:
# set cross-compiled system type, it's better not use the type which cmake cannot recognized.
SET ( CMAKE_SYSTEM_NAME Linux )
SET ( CMAKE_SYSTEM_PROCESSOR arm )
# when hislicon SDK was installed, toolchain was installed in the path as below:
SET ( CMAKE_C_COMPILER /opt/hisi-linux/x86-arm/arm-himix200-linux/bin/arm-himix200-linux-gcc )
SET ( CMAKE_CXX_COMPILER /opt/hisi-linux/x86-arm/arm-himix200-linux/bin/arm-himix200-linux-g++ )

# set searching rules for cross-compiler
SET ( CMAKE_FIND_ROOT_PATH_MODE_PROGRAM NEVER )
SET ( CMAKE_FIND_ROOT_PATH_MODE_LIBRARY ONLY )
SET ( CMAKE_FIND_ROOT_PATH_MODE_INCLUDE ONLY )

# set ${CMAKE_C_FLAGS} and ${CMAKE_CXX_FLAGS}flag for cross-compiled process
SET ( CROSS_COMPILATION_ARM himix200 )
SET ( CROSS_COMPILATION_ARCHITECTURE armv7-a )

# set g++ param
SET ( CMAKE_CXX_FLAGS "-mcpu=cortex-a7 -mtune=cortex-a7  -mfloat-abi=softfp -mfpu=neon-vfpv4 ${CMAKE_CXX_FLAGS}" )

add_definitions(-D__ARM_NEON)

repository: taofuyu/ncnn

repo_name: taofuyu/ncnn

gha_license_id: NOASSERTION

extension: cmake


text:
DESCRIPTION = "OpenBMC mtd-util"

LICENSE = "MIT"
LIC_FILES_CHKSUM = "file://COPYING;md5=b77c43ae4eaf67bd73fb6452b2f113a3"

SRC_URI = "git://github.com/Intel-BMC/mtd-util;protocol=ssh"

PV = "1.0+git${SRCPV}"
SRCREV = "69016601a521a95732cc49a3f4c8c7fe4b0ee058"

S = "${WORKDIR}/git"

DEPENDS += "dbus systemd sdbusplus openssl zlib boost microsoft-gsl i2c-tools"

inherit cmake pkgconfig

# Specify any options you want to pass to cmake using EXTRA_OECMAKE:
EXTRA_OECMAKE = ""

EXTRA_OECMAKE += "${@bb.utils.contains('EXTRA_IMAGE_FEATURES', 'debug-tweaks', '-DDEVELOPER_OPTIONS=ON', '', d)}"

branch_name: refs/heads/intel

extension: bb


text:
file(REMOVE_RECURSE
  "CMakeFiles/cmTC_8cb8c.dir/testCXXCompiler.cxx.o"
  "cmTC_8cb8c.pdb"
  "cmTC_8cb8c"
)

# Per-language clean rules from dependency scanning.
foreach(lang CXX)
  include(CMakeFiles/cmTC_8cb8c.dir/cmake_clean_${lang}.cmake OPTIONAL)
endforeach()

repository: ililk/CUGSE

repo_name: ililk/CUGSE


text:
@article{cohen2022nowcasting,
  title={Nowcasting with signature methods},
  author={Cohen, Samuel N and Lui, Silvia and Malpass, Will and Mantoan, Giulia and Nesheim, Lars and de Paula, Aureo and Scott, Craig and Small, Emma and Yang, Lingyi},
  year={2022}
}

repository: GiuliaMantoan/GMantoan

repo_name: GiuliaMantoan/GMantoan


text:
@InProceedings{bossek2020performance,
  Author    = {Bossek, Jakob and Kerschke, Pascal and Trautmann, Heike},
  Title     = {{A Multi-Objective Perspective on Performance Assessment and Automated Selection of Single-Objective Optimization Algorithms}},
  Booktitle = {{Applied Soft Computing}},
  Pages     = {105901},
  Year      = {2020},
  Month     = {3},
  Volume    = {88},
  URL       = {https://www.sciencedirect.com/science/article/abs/pii/S1568494619306829},
  DOI       = {10.1016/j.asoc.2019.105901},
  Publisher = {Elsevier}
}

gha_license_id: MIT

gha_language: HTML


text:
@Article{bothanovel2017,
  title = {Novel GRN mutation presenting as an aphasic dementia and evolving into corticobasal syndrome},
  volume = {3},
  copyright = {All rights reserved},
  issn = {2376-7839},
  url = {http://ng.neurology.org/lookup/doi/10.1212/NXG.0000000000000201},
  doi = {10.1212/NXG.0000000000000201},
  language = {en},
  urldate = {2020-09-19},
  journal = {Neurology Genetics},
  author = {Hugo Botha and NiCole A. Finch and Ralitza H. Gavrilova and Mary M. Machulda and Julie A. Fields and Val J. Lowe and Ronald C. Petersen and Clifford R. Jack and Christina M. Dheel and Debra J. Gearhart and David S. Knopman and Rosa Rademakers and Bradley F. Boeve},
  month = {dec},
  year = {2017},
  pages = {e201},
  number = {6},
  pubtype = {2},
  date = {2017-01-01},
}

repository: HugoBothaMD/academic-kickstart

repo_name: HugoBothaMD/academic-kickstart


text:
DESCRIPTION = "File::pushd does a temporary "chdir" that is easily and automatically \
reverted, similar to "pushd" in some Unix command shells. It works by \
creating an object that caches the original working directory. When the \
object is destroyed, the destructor calls "chdir" to revert to the original \
working directory. By storing the object in a lexical variable with a \
limited scope, this happens automatically at the end of the scope."

SECTION = "libs"
LICENSE = "Apache-2.0"
PR = "r0"

MAINTAINER=	"Poky <poky@yoctoproject.org>"
HOMEPAGE=	"https://metacpan.org/release/File-pushd"

LIC_FILES_CHKSUM = "file://${COMMON_LICENSE_DIR}/Apache-2.0;md5=89aea4e17d99a7cacdbeed46a0096b10"

SRC_URI = "https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/File-pushd-1.016.tar.gz"

SRC_URI[md5sum] = "1480e0d4813a8990c003e78338f00955"
SRC_URI[sha256sum] = "d73a7f09442983b098260df3df7a832a5f660773a313ca273fa8b56665f97cdc"

S = "${WORKDIR}/File-pushd-${PV}"

inherit cpan allarch

BBCLASSEXTEND = "native"

repository: rehsack/meta-cpan

repo_name: rehsack/meta-cpan

gha_language: BitBake


text:
DESCRIPTION = "TensorFlow Lite Standalone Pip"
LICENSE = "Apache-2.0"

LIC_FILES_CHKSUM = "file://LICENSE;md5=64a34301f8e355f57ec992c2af3e5157"
SRCREV = "582c8d236cb079023657287c318ff26adb239002"

SRC_URI = " \
    git://github.com/tensorflow/tensorflow.git;branch=r2.4 \
    file://001-Change-curl-to-wget-command.patch \
    file://001-TensorFlow-Lite_Makefile.patch \
    file://001-Remove-toolchain-setup-and-pybind11.patch \
"

S = "${WORKDIR}/git"

DEPENDS += "gzip-native \
            unzip-native \
            zlib \
            python3 \
            python3-native \
            python3-numpy-native \
            python3-pip-native \
            python3-wheel-native \
            python3-pybind11 \
"

RDEPENDS_${PN} += " \
    python3 \
    python3-numpy \
    python3-pybind11 \
"

inherit python3native

export PYTHON_BIN_PATH="${PYTHON}"
export PYTHON_LIB_PATH="${STAGING_LIBDIR_NATIVE}/${PYTHON_DIR}/site-packages"

do_configure(){
	${S}/tensorflow/lite/tools/make/download_dependencies.sh
}

do_compile () {
    echo ${TARGET_ARCH}

    if [ ${TARGET_ARCH} = "aarch64" ]; then
        echo "build aarch64"
        export TENSORFLOW_TARGET=aarch64
        export TARGET=aarch64
    elif [ ${TARGET_ARCH} = "arm" ]; then
        echo "build arm"
        export TENSORFLOW_TARGET=rpi
        export TARGET=rpi
    fi

    ${S}/tensorflow/lite/tools/pip_package/build_pip_package.sh

}

do_install() {
    echo "Generating pip package"
    install -d ${D}/${PYTHON_SITEPACKAGES_DIR}

    ${STAGING_BINDIR_NATIVE}/pip3 install --disable-pip-version-check -v \
        -t ${D}/${PYTHON_SITEPACKAGES_DIR} --no-cache-dir --no-deps \
        ${S}/tensorflow/lite/tools/pip_package/gen/tflite_pip${WORKDIR}/recipe-sysroot-native/usr/bin/python3-native/python3/dist/tflite_runtime-2.4.0-*.whl
}

FILES_${PN}-dev = ""
INSANE_SKIP_${PN} += "dev-so \
                     "
FILES_${PN} += "${libdir}/* ${datadir}/*"


text:
@article{Oberkampf1996,
author = {Oberkampf, Denis and DeMenthon, Daniel F. and Davis, Larry S.},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Oberkampf, DeMenthon, Davis - 1996 - Iterative Pose Estimation Using Coplanar Feature Points.pdf:pdf},
journal = {Computer Vision and Image Understanding},
title = {{Iterative Pose Estimation Using Coplanar Feature Points}},
year = {1996}
}
@inproceedings{Hartley1997,
author = {Hartley, R.I.},
booktitle = {Proc. of IEEE Int. Conf. on Computer Vision},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Hartley - 1995 - In defence of the 8-point algorithm.pdf:pdf},
title = {{In defence of the 8-point algorithm}},
year = {1997}
}
@article{Lu1998,
author = {Lu, Chien-ping and Hager, Gregory D. and Mjolsness, Eric},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Lu, Hager, Mjolsness - 1998 - Fast and Globally Convergent Pose Estimation From Video Images.pdf:pdf},
journal = {IEEE Transactions on PAMI},
number = {6},
pages = {1--26},
title = {{Fast and Globally Convergent Pose Estimation From Video Images}},
volume = {22},
year = {1998}
}
@article{Zhang2000,
author = {Zhang, Zhengyou},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Zhang - 2000 - A Flexible New Technique for Camera Calibration.pdf:pdf},
journal = {IEEE Trans. Pattern Anal. Mach. Intell.},
title = {{A Flexible New Technique for Camera Calibration}},
year = {2000}
}
@article{Sturm2000,
author = {Sturm, Peter and Sturm, Peter and Estimation, Plane-based Pose and Conference, Ieee and Sturm, Peter},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Sturm et al. - 2000 - Algorithms for Plane-Based Pose Estimation To cite this version Algorithms for Plane-Based Pose Estimation.pdf:pdf},
journal = {IEEE Conf. on Computer Vision and Pattern Recognition},
title = {{Algorithms for Plane-Based Pose Estimation}},
year = {2000}
}
@article{Lu2000,
author = {Lu, Chien Ping and Hager, Gregory D. and Mjolsness, Eric},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Lu, Hager, Mjolsness - 2000 - Fast and globally convergent pose estimation from video images.pdf:pdf},
journal = {IEEE Trans. Pattern Anal. Mach. Intell.},
title = {{Fast and globally convergent pose estimation from video images}},
year = {2000}
}
@book{RichardHartley2003,
author = {{Richard Hartley}, Andrew Zisserman},
edition = {Second},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Richard Hartley - 2004 - Multiple View Geometry.pdf:pdf},
publisher = {Cambridge University Press},
title = {{Multiple View Geometry}},
year = {2004}
}
@inproceedings{Harker2005,
author = {Harker, M. J. and O'Leary, P. L.},
booktitle = {BMVC},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Harker, O'Leary - 2005 - Computation of Homographies.pdf:pdf},
title = {{Computation of Homographies}},
year = {2005}
}
@article{Schweighofer2006,
author = {Schweighofer, Gerald and Pinz, Axel},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Schweighofer, Pinz - 2006 - Robust pose estimation from a planar target.pdf:pdf},
journal = {IEEE Trans. Pattern Anal. Mach. Intell.},
title = {{Robust pose estimation from a planar target}},
year = {2006}
}
@article{Malis2007,
author = {Malis, Ezio and Vargas, Manuel},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Malis, Vargas - 2007 - Deeper understanding of the homography decomposition for vision-based control.pdf:pdf},
journal = {Sophia},
number = {6303},
pages = {90},
title = {{Deeper understanding of the homography decomposition for vision-based control}},
volume = {6303},
year = {2007}
}
@article{Lepetit2008,
author = {Lepetit, Vincent and Moreno-Noguer, Francesc and Fua, Pascal},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Lepetit, Moreno-Noguer, Fua - 2008 - EPnP An accurate O(n) solution to the PnP problem.pdf:pdf},
journal = {International Journal of Computer Vision},
title = {{EPnP: An accurate O(n) solution to the PnP problem}},
year = {2008}
}
@article{Schweighofer2008,
author = {Schweighofer, G. and Pinz, A.},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Schweighofer, Pinz - 2008 - Globally Optimal O(n) Solution to the PnP Problem for General Camera Models.pdf:pdf},
journal = {BMVC},
title = {{Globally Optimal O(n) Solution to the PnP Problem for General Camera Models}},
year = {2008}
}
@inproceedings{Rangarajan2009,
author = {Rangarajan, Prasanna and Papamichalis, Panos},
booktitle = {Proc. of Int. Conf. on Image Processing},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Rangarajan, Papamichalis - 2009 - Estimating homographies without normalization.pdf:pdf},
title = {{Estimating homographies without normalization}},
year = {2009}
}
@article{Huynh2009,
author = {Huynh, Du Q},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Huynh - 2009 - Metrics for 3D Rotations Comparison and Analysis.pdf:pdf},
journal = {Journal of Mathematical Imaging and Vision},
number = {2},
pages = {155--164},
title = {{Metrics for 3D Rotations: Comparison and Analysis}},
volume = {35},
year = {2009}
}
@article{Chen2009,
author = {Chen, Pei and Suter, David},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Chen, Suter - 2009 - Error analysis in homography estimation by first order approximation tools A general technique.pdf:pdf},
journal = {Journal of Mathematical Imaging and Vision},
title = {{Error analysis in homography estimation by first order approximation tools: A general technique}},
year = {2009}
}
@article{Shijie2010,
annote = {34 citations},
author = {Shijie, Zhang and Fenghua, Liu and Xibin, Cao and Liang, He},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Shijie et al. - 2010 - Monocular Vision-based Two-stage Iterative Algorithm for Relative Position and Attitude Estimation of Docking Spa.pdf:pdf},
journal = {Chinese Journal of Aeronautics},
number = {2},
pages = {204--210},
publisher = {Chinese Journal of Aeronautics},
title = {{Monocular Vision-based Two-stage Iterative Algorithm for Relative Position and Attitude Estimation of Docking Spacecraft}},
volume = {23},
year = {2010}
}
@inproceedings{Willert2010,
author = {Willert, Volker},
booktitle = {Proc. of the 2010 int. conf. on indoor positioning and indoor navigation},
title = {{Optical indoor positioning using a camera phone}},
year = {2010}
}
@inproceedings{Hesch2011,
author = {Hesch, Joel A and Roumeliotis, Stergios I},
booktitle = {IEEE Int. Conf. on Computer Vision},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Hesch, Roumeliotis - 2011 - A direct least-squares (DLS) method for PnP.pdf:pdf},
title = {{A direct least-squares (DLS) method for PnP}},
year = {2011}
}
@article{Sturm2011,
author = {Sturm, Peter and Pajdla, Tomas and Chum, Ondrej},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Sturm, Pajdla, Chum - 2011 - On Geometric Error for Homographies On Geometric Error for.pdf:pdf},
title = {{On Geometric Error for Homographies On Geometric Error for}},
year = {2011}
}
@article{Li2012,
author = {Li, Shiqi and Xu, Chi and Xie, Ming},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Li, Xu, Xie - 2012 - A robust O(n) solution to the perspective-n-point problem.pdf:pdf},
journal = {IEEE Trans. Pattern Anal. Mach. Intell.},
title = {{A robust O(n) solution to the perspective-n-point problem}},
year = {2012}
}
@article{Garro2012,
author = {Garro, Valeria and Crosilla, Fabio and Fusiello, Andrea},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Garro, Crosilla, Fusiello - 2012 - Solving the PnP problem with anisotropic orthogonal procrustes analysis.pdf:pdf},
journal = {3DIMPVT},
title = {{Solving the PnP problem with anisotropic orthogonal procrustes analysis}},
year = {2012}
}
@book{Golub2013,
author = {Golub, Gene H and {Van Loan}, Charles F},
booktitle = {Johns Hopkins University Press},
edition = {4},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Golub, Van Loan - 2013 - Matrix Computations.pdf:pdf},
isbn = {9781421407944},
pages = {780},
title = {{Matrix Computations}},
year = {2013}
}
@article{Penate-sanchez,
author = {Penate-sanchez, Adrian and Andrade-cetto, Juan and Moreno-noguer, Francesc},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Penate-sanchez, Andrade-cetto, Moreno-noguer - 2013 - Exhaustive Linearization for Robust Camera Pose and Focal Length Estimation.pdf:pdf},
journal = {IEEE transactions on pattern analysis and machine intelligence},
number = {10},
pages = {2387----2400},
title = {{Exhaustive Linearization for Robust Camera Pose and Focal Length Estimation}},
volume = {35},
year = {2013}
}
@inproceedings{Zheng2013,
author = {Zheng, Yinqiang and Kuang, Yubin and Sugimoto, Shigeki and Astrom, Kalle and Okutomi, Masatoshi},
booktitle = {Proc. of the IEEE Int. Conf. on Computer Vision},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Zheng et al. - 2013 - Revisiting the PnP problem A fast, general and optimal solution.pdf:pdf},
title = {{Revisiting the PnP problem: A fast, general and optimal solution}},
year = {2013}
}
@article{Collins2014,
author = {Collins, Toby and Bartoli, Adrien},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Collins, Bartoli - 2014 - Infinitesimal plane-based pose estimation.pdf:pdf},
journal = {International Journal of Computer Vision},
title = {{Infinitesimal plane-based pose estimation}},
year = {2014}
}
@inproceedings{Zheng2014,
author = {Zheng, Yinqiang and Sugimoto, Shigeki and Sato, Imari and Okutomi, Masatoshi},
booktitle = {Proc. of the IEEE Computer Society Conf. on Computer Vision and Pattern Recognition},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Zheng et al. - 2014 - A general and simple method for camera pose and focal length determination.pdf:pdf},
pages = {430--437},
title = {{A general and simple method for camera pose and focal length determination}},
volume = {4},
year = {2014}
}
@article{Chung2014,
author = {Chung, David H S and Parry, Matthew L. and Legg, Philip A. and Griffiths, Iwan W. and Laramee, Robert S. and Chen, Min},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Chung et al. - 2014 - Visualizing multiple error-sensitivity fields for single camera positioning.pdf:pdf},
journal = {Computing and Visualization in Science},
title = {{Visualizing multiple error-sensitivity fields for single camera positioning}},
year = {2014}
}
@article{Ferraz2014,
author = {Ferraz, Luis and Binefa, Xavier and Moreno-Noguer, Francesc},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Ferraz, Binefa, Moreno-Noguer - 2014 - Leveraging Feature Uncertainty in the PnP Problem.pdf:pdf},
journal = {BMVC},
pages = {1--13},
title = {{Leveraging Feature Uncertainty in the PnP Problem}},
year = {2014}
}
@inproceedings{Ferraz2014b,
author = {Ferraz, Luis and Binefa, Xavier and Moreno-Noguer, Francesc},
booktitle = {Proc. of the IEEE Computer Society Conf. on Computer Vision and Pattern Recognition},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Ferraz, Binefa, Moreno-Noguer - 2014 - Very fast solution to the PnP problem with algebraic outlier rejection(2).pdf:pdf},
pages = {501--508},
title = {{Very fast solution to the PnP problem with algebraic outlier rejection}},
year = {2014}
}
@inproceedings{Kneip2014,
author = {Kneip, Laurent and Li, Hongdong and Seo, Yongduek},
booktitle = {European Conference on Computer Vision},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Kneip, Li, Seo - 2014 - UPnP An Optimal O(n) Solution to the Absolute Pose Problem with Universal Applicability.pdf:pdf},
title = {{UPnP: An Optimal O(n) Solution to the Absolute Pose Problem with Universal Applicability}},
year = {2014}
}
@inproceedings{Nakano2015,
author = {Nakano, Gaku},
booktitle = {BMVC},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Nakano - 2015 - Globally Optimal DLS Method for PnP Problem with Cayley parameterization.pdf:pdf},
title = {{Globally Optimal DLS Method for PnP Problem with Cayley parameterization}},
year = {2015}
}
@inproceedings{Kanaeva2015,
author = {Kanaeva, Ekaterina and Vakhitov, Alexander},
booktitle = {BMVC},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Kanaeva, Vakhitov - 2015 - Camera Pose and Focal Length Estimation Using Regularized Distance Constraints.pdf:pdf},
pages = {1--12},
title = {{Camera Pose and Focal Length Estimation Using Regularized Distance Constraints}},
year = {2015}
}
@inproceedings{Changchang2015,
author = {Changchang, Wu},
booktitle = {Proc. of the IEEE Computer Society Conf. on Computer Vision and Pattern Recognition},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Changchang - 2015 - P3.5P Pose estimation with unknown focal length.pdf:pdf},
pages = {2440--2448},
title = {{P3.5P: Pose estimation with unknown focal length}},
year = {2015}
}
@article{Urban2016,
author = {Urban, Steffen and Leitloff, Jens and Hinz, Stefan},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Urban, Leitloff, Hinz - 2016 - Mlpnp-a Real-Time Maximum Likelihood Solution to the Perspective-N Problem.pdf:pdf},
journal = {ISPRS Annals of Photogrammetry, Remote Sensing and Spatial Information Sciences},
pages = {131----138},
title = {{Mlpnp-a Real-Time Maximum Likelihood Solution to the Perspective-N Problem}},
year = {2016}
}
@inproceedings{Zheng2016,
author = {Zheng, Yinqiang and Kneip, Laurent},
booktitle = {Proc. of the IEEE Computer Society Conf. on Computer Vision and Pattern Recognition},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Zheng, Kneip - 2016 - A Direct Least-Squares Solution to the PnP Problem with Unknown Focal Length.pdf:pdf},
pages = {1790--1798},
title = {{A Direct Least-Squares Solution to the PnP Problem with Unknown Focal Length}},
year = {2016}
}
@article{Marchand2016,
author = {Marchand, E and Uchiyama, H and Spindler, F},
file = {:home/lracuna/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Marchand, Uchiyama, Spindler - 2016 - Pose Estimation for Augmented Reality A Hands-On Survey.pdf:pdf},
journal = {IEEE Trans. on Vis. and Comput. Graphics},
title = {{Pose Estimation for Augmented Reality: A Hands-On Survey}},
year = {2016}
}


text:
SECTION = "kernel"
DESCRIPTION = "Linux kernel for TI Keystone devices"
LICENSE = "GPLv2"
LIC_FILES_CHKSUM = "file://COPYING;md5=d7810fab7487fb0aad327b76f1be7cd7"

COMPATIBLE_MACHINE = "keystone"

inherit kernel

require recipes-kernel/linux/linux-dtb.inc
require recipes-kernel/linux/setup-defconfig.inc

MACHINE_KERNEL_PR_append = "e"
PR = "${MACHINE_KERNEL_PR}"

KERNEL_DEVICETREE_k2hk-evm = "k2hk-evm.dtb"
KERNEL_DEVICETREE_k2e-evm = "k2e-evm.dtb"
KERNEL_DEVICETREE_k2l-evm = "k2l-evm.dtb"

KERNEL_EXTRA_ARGS += "LOADADDR=${UBOOT_ENTRYPOINT}"

#This commit corresponds to "K2_LINUX_03.10.72_15.08"
SRCREV = "ca334dedb5c234b1602d991d9b330360a5bc97ad"
PV = "3.10.72+git${SRCPV}"

BRANCH = "v3.10.72/master"
SRC_URI = "git://git.ti.com/keystone-linux/linux.git;protocol=git;branch=${BRANCH}\
           file://defconfig\
           "

S = "${WORKDIR}/git"

RDEPENDS_kernel-base = ""

repository: joelagnel/meta-ti

repo_name: joelagnel/meta-ti


text:
@book{west_introduction_2000,
  author = {West, Douglas Brent},
  date = {2000-08-22},
  edition = {2},
  isbn = {978-0-13-014400-3},
  pagetotal = {470},
  publisher = {{Prentice Hall}},
  timestamp = {2015-02-24 12:14:36 +0100},
  title = {Introduction to {{Graph Theory}}}
}

license: Unlicense

url: https://raw.githubusercontent.com/timhowes/zotero-better-bibtex/dff963f825762cbd25c5948d5327badbe498bbec/test/fixtures/export/date and year are switched #406.bib

repository: timhowes/zotero-better-bibtex

repo_name: timhowes/zotero-better-bibtex

filename: date and year are switched #406.bib


text:
SUMMARY          = "Bitbake Variable Substitution Example"
DESCRIPTION      = "Bitbake Variable Substitution Example"
HOMEPAGE         = "https://github.com/coreycothrum/meta-bitbake-variable-substitution"
LICENSE          = "MIT"
LIC_FILES_CHKSUM = "file://${COMMON_LICENSE_DIR}/MIT;md5=0835ade698e0bcf8506ecda2f7b4f302"

SRC_URI          = "file://bb-var-sub-example.sh"
FILES_${PN}      = "${bindir}/bb-var-sub-example.sh"

inherit bitbake-variable-substitution

do_install() {
  install -d                                      ${D}${bindir}
  install -m 744 ${WORKDIR}/bb-var-sub-example.sh ${D}${bindir}
}


text:
@article{Beven-2021-A,
    title = "A history of TOPMODEL",
    author = "Beven, Keith J.  and
      Kirkby, Mike J.  and
      Freer, Jim E.  and
      Lamb, Rob",
    journal = "Hydrology and Earth System Sciences, Volume 25, Issue 2",
    volume = "25",
    number = "2",
    year = "2021",
    publisher = "Copernicus GmbH",
    url = "https://aclanthology.org/G21-72001",
    doi = "10.5194/hess-25-527-2021",
    pages = "527--549",
}

repository: gwf-uwaterloo/gwf-publications

repo_name: gwf-uwaterloo/gwf-publications

branch_name: refs/heads/main

gha_language: Python


text:
@article{pmid34450083,
 author = {NCD Risk Factor Collaboration (NCD-RisC)},
 journal = {Lancet},
 number = {10304},
 pages = {957-980},
 publisher = {Elsevier},
 title = {Worldwide trends in hypertension prevalence and progress in treatment and control from 1990 to 2019: a pooled analysis of 1201 population-representative studies with 104 million participants},
 volume = {398},
 year = {2021}
}

repository: hypertensioncenter/academic-kickstart

repo_name: hypertensioncenter/academic-kickstart

gha_language: TeX


text:
@book{bruce2017practical,
  title={Practical statistics for data scientists: 50 essential concepts},
  author={Bruce, Peter and Bruce, Andrew},
  year={2017},
  publisher={" O'Reilly Media, Inc."}
}

@book{hogg,
  title={Introduction to mathematical statistics},
  author={Hogg, Robert V. and McKean, Joseph and Craig, Allen T.},
  year={2005},
  publisher={Pearson Education}
}
@book{illowsky2018introductory,
  title={Introductory statistics},
  author={Illowsky, Barbara and Dean, Susan},
  year={2018},
  publisher={OpenStax}
}
@book{deisenroth,
  title={Mathematics for machine learning},
  author={Deisenroth, Marc Peter and Faisal, Aldo and Ong, Cheng Soon},
  year={2020},
  publisher={Cambridge University Press}
}
@book{montgomery2010applied,
  title={Applied statistics and probability for engineers},
  author={Montgomery, Douglas C. and Runger, George C.},
  year={2010},
  publisher={John Wiley \& Sons}
}
@misc{dawkins,
 howpublished = {\url{https://tutorial.math.lamar.edu/classes/calcii/polarcoordinates.aspx}},
 title={Calculus II - polar coordinates},
 author={Dawkins, Paul},
 note = {Accessed: 2021-07-28}
}
@book{larsen2005introduction,
  title={An introduction to mathematical statistics},
  author={Larsen, Richard J. and Marx, Morris L.},
  year={2005},
  publisher={Prentice Hall}
}
@misc{nist,
  title = {1.3.6.7.4. Critical Values of the Chi-Square Distribution},
  publisher={NIST/SEMATECH e-Handbook of Statistical Methods},
  year = {2013},
  howpublished = {\url{https://www.itl.nist.gov/div898/handbook/eda/section3/eda3674.htm}},
  note = {Accessed: 2021-07-30}
}
@MISC{freepvalue,
  title = {p-Value Calculator for a Chi-Square Test},
  author={Daniel Soper},
  year = {2021},
  howpublished = {\url{https://www.danielsoper.com/statcalc/calculator.aspx?id=11}},
  note = {Accessed: 2021-07-30}
}
@MISC{wolfalph,
  title = {Wolfram Alpha},
  howpublished = {\url{https://www.wolframalpha.com/}},
  note = {Accessed: 2021-09-05}
}
@misc{symbolab,
  title = {Symbolab math solver - step by step calculator},
  publisher={Eqsquest Ltd.},
  howpublished = {\url{https://www.symbolab.com/}},
  note = {Accessed: 2021-07-15}
}
@misc{mathcenter,
  title = {Expected Value of a Discrete Random Variable},
  publisher = {Emory~Oxford~College},
  year = {n.d.},
  howpublished = {\url{http://mathcenter.oxford.emory.edu/site/math117/expectedValueOfADiscreteRandomVariable/}},
  note = {Accessed: 2021-09-05}
  }


text:
/* MESSAGES */
.django-messages .topics .read {
    font-weight: normal;
}
.django-messages .topics .unread {
    font-weight: bold;
}

repository: emacsway/pinax

repo_name: emacsway/pinax

extension: css


text:
SUMMARY = "A Lv2 version of the old LADSPA SooperLooper plugin."
SECTION = "multimedia"

LICENSE = "GPLv2"
LIC_FILES_CHKSUM = "file://../COPYING;md5=94d55d512a9ba36caa9b7df079bae19f"

DEPENDS = "lv2"

SRCREV = "d3e80029ce4f6ef62b3758e95c5b889cab1db740"
SRC_URI = "git://github.com/moddevices/sooperlooper-lv2-plugin.git"

S = "${WORKDIR}/git/sooperlooper"

FILES_${PN} = " ${libdir}/lv2/ "

EXTRA_OEMAKE = " INSTALL_PATH=/usr/lib/lv2/ DESTDIR=${D} "

do_install() {
        oe_runmake install
}


text:
.transbox {
	opacity: 0.6;
	filter: alpha(opacity=60); /* For IE8 and earlier */
}

.transbox h1{
	font-size: 5vw;
	max-width: 100vw;
	color: white;
	display: inline-block;
	padding: 0.1125em 0.5em;
    background-color: #000000;
    box-decoration-break: clone;
	float: left;
	position: absolute;
	left: 0px;
}

.transbox h2{
    font-size: 1.7vw;
    max-width: 100vw;
	color: white;
	display: inline-block;
	padding: 0.1125em 0.5em;
    background-color: #000000;
    box-decoration-break: clone;
	float: left 0px;
	white-space: nowrap;
	text-align: left;
	position: absolute;
	left: 0px;
}


text:
.App {
    /*background-color:aliceblue ;*/
}

.menu {
    display: flex;
    position: absolute;
    margin: 7px 0px 0px 0px;
}

li a {
    text-decoration: none;
}

.link {
    padding: 0px 10px 0px 10px;
    list-style-type: none; /* Убираем маркеры */
}

.App .header {
    height: 3.5em;
    width: 100%;
}

.App .body {
    max-height: 88vh;
    display: flex;
    flex-direction: row;
    width: 100%;
    height: 100vh;
}

    .App .body .content {
        padding:10px;
        min-width: 85%;
    }

    .App .body .sidebar {
        width: auto;
    }

repository: nkiruhin/SalaryCalculatorReact

repo_name: nkiruhin/SalaryCalculatorReact


text:
@article{fourkas,
author = {John T. Fourkas},
journal = {Opt. Lett.},
keywords = {Fluorescence microscopy; Polarization},
number = {4},
pages = {211--213},
publisher = {OSA},
title = {Rapid determination of the three-dimensional orientation of single molecules},
volume = {26},
month = {Feb},
year = {2001},
url = {http://ol.osa.org/abstract.cfm?URI=ol-26-4-211},
doi = {10.1364/OL.26.000211},
}

@article{bout2008,
  title={Analysis of orientational dynamics of single fluorophore trajectories from three-angle polarization experiments.},
  author={Chun-Yaung Lu and David A Vanden Bout},
  journal={The Journal of chemical physics},
  year={2008},
  volume={128 24},
  pages={244501}
}

@book{nov,
author={Novotny,Lukas and Hecht,Bert},
year=2006,
title={Principles of nano-optics},
publisher={Cambridge University Press},
language={English},
}

@article{backer,
author = {Backer, Adam S. and Moerner, W. E.},
title = {Extending Single-Molecule Microscopy Using Optical Fourier Processing},
journal = {The Journal of Physical Chemistry B},
volume = {118},
number = {28},
pages = {8313-8329},
year = {2014},
doi = {10.1021/jp501778z},
note ={PMID: 24745862},
URL = {http://dx.doi.org/10.1021/jp501778z},
eprint = {http://dx.doi.org/10.1021/jp501778z}
}

@article{lieb,
author = {M. Andreas Lieb and James M. Zavislan and Lukas Novotny},
journal = {J. Opt. Soc. Am. B},
keywords = {Fluorescence microscopy; Fluorescence; Emission},
number = {6},
pages = {1210--1215},
publisher = {OSA},
title = {Single-molecule orientations determined by direct emission pattern imaging},
volume = {21},
month = {Jun},
year = {2004},
url = {http://josab.osa.org/abstract.cfm?URI=josab-21-6-1210},
doi = {10.1364/JOSAB.21.001210},
}

@article{lux,
author = {Chun-Yaung Lu and David A. Vanden Bout},
title = {Analysis of orientational dynamics of single fluorophore trajectories from three-angle polarization experiments},
journal = {The Journal of Chemical Physics},
volume = {128},
number = {24},
pages = {244501},
year = {2008},
doi = {10.1063/1.2937730},
}

repository: talonchandler/dipsim

repo_name: talonchandler/dipsim


text:
PR = "r0"

require radvd.inc

SRC_URI[md5sum] = "e807ad7e9a76d46b6133df391385cd31"
SRC_URI[sha256sum] = "54eb5704a2b710ba946fa30d2bca811fa23b1b3bfab322c38cb0c2a9619aa933"

repository: morganlittle/meta-oe

repo_name: morganlittle/meta-oe


text:
SUMMARY = "Module for TB6612 DC motor driver"
LICENSE = "GPLv2"
LIC_FILES_CHKSUM = "file://COPYING;md5=b234ee4d69f5fce4486a80fdaf4a4263"

inherit module

PR = "r2"

SRC_URI = "git://github.com/maciejjo/encoder.git"
SRCREV = "3378affcf43dfc8abd5a4dadf8c331abf11f4e48"

S = "${WORKDIR}/git"

# The inherit of module.bbclass will automatically name module packages with
# "kernel-module-" prefix as required by the oe-core build environment.

repository: maciejjo/meta-pavubot

repo_name: maciejjo/meta-pavubot


text:
@online{github,
  author = {Michelfeit, Jannik},
  title = {multivar_horner},
  year = 2018,
  url = {https://github.com/jannikmi/multivar_horner},
  urldate = {2020-05-28},
}

@article{numpy,
 author = {Walt, Stefan van der and Colbert, S. Chris and Varoquaux, Gael},
 title = {The NumPy Array: A Structure for Efficient Numerical Computation},
 journal = {Computing in Science and Engg.},
 issue_date = {March 2011},
 volume = {13},
 number = {2},
 month = mar,
 year = {2011},
 issn = {1521-9615},
 pages = {22--30},
 numpages = {9},
 url = {http://dx.doi.org/10.1109/MCSE.2011.37},
 doi = {10.1109/MCSE.2011.37},
 acmid = {1957466},
 publisher = {IEEE Educational Activities Department},
 address = {Piscataway, NJ, USA},
 keywords = {NumPy, Python, Python, NumPy, scientific programming, numerical computations, programming libraries, numerical computations, programming libraries, scientific programming},
}

@inproceedings{numba,
author = {Lam, Siu Kwan and Pitrou, Antoine and Seibert, Stanley},
title = {Numba: A LLVM-Based Python JIT Compiler},
year = {2015},
isbn = {9781450340052},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
url = {https://doi.org/10.1145/2833157.2833162},
doi = {10.1145/2833157.2833162},
booktitle = {Proceedings of the Second Workshop on the LLVM Compiler Infrastructure in HPC},
articleno = {Article 7},
numpages = {6},
keywords = {compiler, LLVM, Python},
location = {Austin, Texas},
series = {LLVM ’15}
}

@article{horner1819xxi,
  title={XXI. A new method of solving numerical equations of all orders, by continuous approximation},
  author={Horner, William George},
  journal={Philosophical Transactions of the Royal Society of London},
  number={109},
  pages={308--335},
  year={1819},
   doi = {10.1098/rstl.1819.0023},
  publisher={The Royal Society London}
}

@article{hart1968formal,
  title={A formal basis for the heuristic determination of minimum cost paths},
  author={Hart, Peter E and Nilsson, Nils J and Raphael, Bertram},
  journal={IEEE transactions on Systems Science and Cybernetics},
  volume={4},
  number={2},
  pages={100--107},
  year={1968},
  publisher={IEEE}
}

@book{neumaier2001introduction,
  title={Introduction to numerical analysis},
  author={Neumaier, Arnold},
  year={2001},
  publisher={Cambridge University Press},
  doi={10.1017/CBO9780511612916},
}

@thesis{michelfeitresponse,
  title={A Response Surface Method based on Multivariate Newton Interpolation},
  author={Michelfeit, Jannik},
  year={2019},
  url = {https://mosaic.mpi-cbg.de/docs/Michelfeit2019.pdf},
  urldate = {2020-05-28},
  type={Student Thesis},
}

@article{Hecht1,
  title={Multivariate {N}ewton Interpolation},
  author={Hecht, Michael and Hoffmann, Karl B and Cheeseman, Bevan L and Sbalzarini, Ivo F},
  journal={arXiv preprint arXiv:1812.04256},
  year={2018},
}

@inproceedings{Hecht2,
	Address = {London, UK},
	Author = {Hecht, Michael and Sbalzarini, Ivo F.},
	Booktitle = {Intelligent Computing. Proc. 2018 IEEE Computing Conf., Vol. 2,},
	Date-Added = {2018-11-05 11:04:48 +0100},
	Date-Modified = {2018-11-05 11:11:10 +0100},
	Editor = {Arai, K. and Kapoor, S. and Bhatia, R.},
	Keywords = {interpolation, Fourier transform, high dimensions},
	Pages = {53--75},
	Publisher = {Springer Nature},
	Series = {Advances in Intelligent Systems and Computing},
	Title = {Fast Interpolation and {F}ourier Transform in High-Dimensional Spaces},
	Volume = {857},
	Year = {2018},
	 doi = {10.1007/978-3-030-01177-2_5},
}

@article{trefethen2017multivariate,
  title={Multivariate polynomial approximation in the hypercube},
  author={Trefethen, Lloyd},
  journal={Proceedings of the American Mathematical Society},
  volume={145},
  number={11},
  pages={4837--4844},
  year={2017}
}

@article{greedyHorner,
  author    = {Ceberio, Martine and Kreinovich, Vladik},
  title     = {Greedy algorithms for optimizing multivariate {H}orner schemes},
  year      = {2004},
  publisher = {Association for Computing Machinery (ACM)},
  doi={10.1145/980175.980179},
}

@article{pena2000multivariate,
  title={On the multivariate {H}orner scheme},
  author={Pe{\~n}a, Juan Manuel and Sauer, Thomas},
  journal={SIAM journal on numerical analysis},
  volume={37},
  number={4},
  pages={1186--1197},
  year={2000},
  publisher={SIAM},
  abstract={We present an efficient version of the Horner scheme for the evaluation of multivariate
polynomials and study its stability properties. In particular, we show that the backward error of
evaluation is bounded by a quantity that is linear in the total degree of the polynomial, which itself
is usually significantly smaller than the number of operations involved in the evaluation process.
Moreover, we show that the same type of estimates holds also for the forward error, provided that
the polynomial basis is chosen suitably.},
}

@Article{pena2000multivariate2,
  author    = {Pe{\~n}a, Juan Manuel and Sauer, Thomas},
  title     = {On the multivariate {H}orner scheme {II}: running error analysis},
  journal   = {Computing},
  year      = {2000},
  volume    = {65},
  number    = {4},
  pages     = {313--322},
  abstract  = {As an extension of our previous paper [10] which gave for-ward and backward error estimates, we perform a running error analysis ofthe multivariate Horner scheme.  This leads to a modified algorithm whichcomputes the value of the polynomial together with an error estimate.},
  publisher = {Springer},
  doi={10.1007/s006070070002},
}

@article{kojima2008efficient,
  title={Efficient evaluation of polynomials and their partial derivatives in homotopy continuation methods},
  author={Kojima, Masakazu},
  journal={Journal of the Operations Research Society of Japan},
  volume={51},
  number={1},
  pages={29--54},
  year={2008},
  publisher={The Operations Research Society of Japan},
  doi={10.15807/jorsj.51.29},
}

@article{carnicer1990evaluation,
  title={Evaluation of multivariate polynomials and their derivatives},
  author={Carnicer, J and Gasca, M},
  journal={Mathematics of Computation},
  volume={54},
  number={189},
  pages={231--243},
  year={1990},
  abstract={An extension of Homer's algorithm to the evaluation of m-variate
polynomials and their derivatives is obtained. The schemes of computation are
represented by trees because this type of graph describes exactly in which order
the computations must be done. Some examples of algorithms for one and two
variables are given.},
doi={10.1090/s0025-5718-1990-0993925-1},
}

@article{kuipers2013improving,
  title={Improving multivariate {H}orner schemes with {M}onte {C}arlo tree search},
  author={Kuipers, Jan and Plaat, Aske and Vermaseren, JAM and van den Herik, H Jaap},
  journal={Computer Physics Communications},
  volume={184},
  number={11},
  pages={2391--2395},
  year={2013},
  publisher={Elsevier},
    abstract={Optimizing the cost of evaluating a polynomial is a classic problem in computer science. For polynomials in one variable, Horner’s method provides a scheme for producing a computationally
efficient form. For multivariate polynomials it is possible to generalize Horner’s method, but this
leaves freedom in the order of the variables. Traditionally, greedy schemes like most-occurring vari-
able first are used. This simple textbook algorithm has given remarkably efficient results. Finding
better algorithms has proved difficult. In trying to improve upon the greedy scheme we have im-
plemented Monte Carlo tree search, a recent search method from the field of artificial intelligence.
This results in better Horner schemes and reduces the cost of evaluating polynomials, sometimes by
factors up to two.},
doi={10.1016/j.cpc.2013.05.008},
}

@PhdThesis{LeeFactorization2013,
  author      = {Martin Mok-Don Lee},
  title       = {Factorization of multivariate polynomials},
  institution = {Technische Universität Kaiserslautern},
  year        = {2013},
  date        = {2013-06-13},
}

@inproceedings{leiserson2010efficient,
  title={Efficient evaluation of large polynomials},
  author={Leiserson, Charles E and Li, Liyun and Maza, Marc Moreno and Xie, Yuzhen},
  booktitle={International Congress on Mathematical Software},
  pages={342--353},
  year={2010},
  organization={Springer},
  doi={10.1007/978-3-642-15582-6_55},
}

# applications polynomials

@book{prasolov2009polynomials,
  title={Polynomials},
  author={Prasolov, Victor V},
  volume={11},
  year={2009},
  publisher={Springer Science \& Business Media}
}

@phdthesis{boumova2002applications,
  title={Applications of polynomials to spherical codes and designs},
  author={Boumova, Silvia},
  year={2002},
  school={Technische Universiteit Eindhoven}
}

@article{cools2002advances,
  title={Advances in multidimensional integration},
  author={Cools, Ronald},
  journal={Journal of computational and applied mathematics},
  volume={149},
  number={1},
  pages={1--12},
  year={2002},
  publisher={Elsevier},
  doi={10.1016/s0377-0427(02)00517-4},
}

@book{akritas1989elements,
  title={Elements of computer algebra with applications},
  author={Akritas, Alkiviadis},
  year={1989},
  publisher={John Wiley \& Sons, Inc.},
}