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  1. Mesirov JP. Perturbation Theory for the Existence of Critical Points in the Calculus of Variations. Dissertation, Brandeis University. 1974.
  2. Mesirov JP. Calculus of Variations: Perturbations Preserving Condition (C). Bulletins of the American Mathematical Society. 1974; 80:1260-1264.
  3. Mesirov JP. Necessary Condition for Existence of Minima in the Calculus of Variations. Notices of the American Mathematical Society. 1977; 24.
  4. Mesirov JP. Perturbations Theory for Condition (C) in the Calculus of Variations. Journal of Differential Geometry. 1977; 12:523-553.
  5. Mesirov JP. A Classification of Polynomial Lagrangians. Indiana University Mathematical Journal. 1978; 28:99-117.
  6. Mesirov JP. The IDAL Primer. IDA working paper #734. 1983 June;
  7. Lieserson C, Mesirov JP, Nekludova L, Omohundro S, Reif J, Taylor W. Solving Sparse Systems of Linear Equations on the Connection Machine. Annual SIAM Conference. 1986; Boston, MA.
  8. Mesirov JP, Sweet M. Continued Fraction Expansions of Rational Expressions with Irreducible Denominators in Characteristic 2. Journal of Number Theory. 1987; 27:144-148.
  9. Zhang X, Waltz D, Mesirov JP. Protein Structure Prediction by Memory-based Reasoning. Thinking Machines Technical Report RL88-3. 1988;
  10. Lander ES, Mesirov JP, Taylor W. Study of Protein Sequence Comparison Metrics on the Connection Machine CM-2. Proceedings of Supercomputing '88: Volume II, Science and Applications. The Journal of Supercomputing. 1988; 3:255-269.
  11. Lander ES, Mesirov JP, Taylor W. Protein Sequence Comparison on a Data Parallel Computer. Proceedings of 1988 International Conference on Parallel Processing. Penn State Press: Thinking Machines Technical Report CB88-1. 1988;
  12. Zhang X, Waltz D, Mesirov JP. Protein Structure Prediction by a Data-level Parallel Algorithm. Proceedings of Supercomputing '89. Thinking Machines Technical Report CB90-1. 1989;
  13. Jones R, Taylor W, Zhang X, Mesirov JP, Lander ES. Protein Sequence Comparison on the Connection Machine CM-2. Computers and DNA, SFI Studies in the Sciences of Complexity, vol. VII. Thinking Machines Technical Report CB90-2. 1989;
  14. Zhang X, McKenna M, Mesirov JP, Waltz D. The Back Propagation Algorithm on Grid and Hypercube Architectures. Thinking Machines Technical Report RL90-3. 1990;
  15. Brunet JP, Mesirov JP, Edelman A. An Optimal Hypercube Direct N-body Solver on the Connection Machine. Proceedings of Supercomputing '90. Thinking Machines Technical Report NA90-2. 1990;
  16. Mesirov JP. Very Large Scale Computation in the 21st Century. Society for Industrial and Applied Mathematics. 1991;
  17. Sethian J, Brunet J, Greenberg A, Mesirov JP. Computing Turbulent Flow in Complex Geometries on a Massively Parallel Processor . In: Proceedings of Supercomputing '91. Los Alamitas, CA: IEEE Computer Society Press; 1991. p.230-241.
  18. Sethian J, Brunet J, Greenberg A, Mesirov JP. Vortex Methods and Massively Parallel Processors. Vortex Dynamics and Vortex Methods. American Mathematical Society. 1991; 28:597-611.
  19. Sethian J, Brunet J, Greenberg A, Mesirov JP. A Parallel Implementation of the Random Vortex Method. Computer Physics Communications. 1991; 65:231-237.
  20. Tamayo P, Mesirov JP, Boghosian B. Parallel Approaches to Short Range Molecular Dynamics Simulations . In: Proceedings of Supercomputing '91. Los Alamitas, CA: IEEE Computer Society Press; 1991. p.462-470.
  21. Sethian JA, Brunet J, Greenberg A, Mesirov JP. Two-Dimensional, Viscous, Incompressible Flow in Complex Geometries on a Massively Parallel Processor. Journal of Computational Physics. 1992; 101:185-206.
  22. Zhang X, Mesirov JP, Waltz DL. Hybrid system for protein secondary structure prediction. J Mol Biol. 1992 Jun 20;225(4):1049-63. doi: 10.1016/0022-2836(92)90104-r. PubMed PMID: 1613789.
  23. Greenberg A, Sethian J, Mesirov JP. Programming Direct N-body Solvers on Connection Machines. Thinking Machines Technical Report. 1993;
  24. Brunet J, Mesirov JP, Edelman A. A. Hypercube Algorithms for Direct N-body Solvers for Different Granularities. Society for Industrial and Applied Mathematics. 1993; 15(1):238.
  25. Taylor W, Boghosian B, Mesirov JP. Optmized Local Data Distribution on Lattice Graphs. Thinking Machines Technical Report. 1995;
  26. Mesirov JP. Mathematical Theory in Parallel Algorithms. Notices of the AMS. 1995; 42:36-37.
  27. Bartrouni G, Godzik A, Mesirov JP, Macke T, Skolnick J, Tamayo P. A Parallel Approach to the Topology Fingerprint Method for Inverse Protein Folding. Thinking Machines Technical Report. 1995;
  28. McKenna M, Mesirov JP, Zenios S. Massively Parallel Quadradic Programming with Box-Constrained Problems. SIAM journal on optimization : a publication of the Society for Industrial and Applied Mathematics. 1995; 5:570-589.
  29. Mesirov JP, Tamayo P, Nagle R. On the Parallelization of CHARMm on the CM5/5E . In: Mathematical Approaches to Biomolecular Structure and Dynamics. New York, NY: Springer-Verlag; 1996. p.187-194.
  30. Mesirov JP, Schulten K, Sumners D. Mathematical Approaches to Biomolecular Structure and Dynamics. New York, NY: Springer-Verlag; 1996.
  31. Mukherjee S, Tamayo P, Slonim D, Verri A, Golub T, Mesirov JP. Support Vector Machine Classification of Microarray Data. CBCL Paper #182/AI Memo #1676. 1996;
  32. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2907-12. doi: 10.1073/pnas.96.6.2907. PubMed PMID: 10077610; PubMed Central PMCID: PMC15868.
  33. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 1999 Oct 15;286(5439):531-7. doi: 10.1126/science.286.5439.531. PubMed PMID: 10521349.
  34. Batzoglou S, Berger B, Mesirov J, Lander ES. Sequencing a genome by walking with clone-end sequences: a mathematical analysis. Genome Res. 1999 Dec;9(12):1163-74. doi: 10.1101/gr.9.12.1163. PubMed PMID: 10613838.
  35. Slonim DK, Tamayo P, Mesirov JP, Golub TR, Lander ES. Class prediction and discovery using gene expression data. Procs. of the Fourth Annual International Conference on Computational Molecular Biology. 2000; Tokyo, Japan.
  36. Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES. Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res. 2000 Jul;10(7):950-8. doi: 10.1101/gr.10.7.950. PubMed PMID: 10899144; PubMed Central PMCID: PMC310911.
  37. Yeang CH, Ramaswamy S, Tamayo P, Mukherjee S, Rifkin RM, Angelo M, Reich M, Lander E, Mesirov J, Golub T. Molecular classification of multiple tumor types. Bioinformatics. 2001;17 Suppl 1:S316-22. doi: 10.1093/bioinformatics/17.suppl_1.s316. PubMed PMID: 11473023.
  38. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860-921. doi: 10.1038/35057062. PubMed PMID: 11237011.
  39. Staunton JE, Slonim DK, Coller HA, Tamayo P, Angelo MJ, Park J, Scherf U, Lee JK, Reinhold WO, Weinstein JN, Mesirov JP, Lander ES, Golub TR. Chemosensitivity prediction by transcriptional profiling. Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10787-92. doi: 10.1073/pnas.191368598. PubMed PMID: 11553813; PubMed Central PMCID: PMC58553.
  40. Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, Ladd C, Reich M, Latulippe E, Mesirov JP, Poggio T, Gerald W, Loda M, Lander ES, Golub TR. Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):15149-54. doi: 10.1073/pnas.211566398. Epub 2001 Dec 11. PubMed PMID: 11742071; PubMed Central PMCID: PMC64998.
  41. Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. ARACHNE: a whole-genome shotgun assembler. Genome Res. 2002 Jan;12(1):177-89. doi: 10.1101/gr.208902. PubMed PMID: 11779843; PubMed Central PMCID: PMC155255.
  42. Shipp MA, Ross KN, Tamayo P, Weng AP, Kutok JL, Aguiar RC, Gaasenbeek M, Angelo M, Reich M, Pinkus GS, Ray TS, Koval MA, Last KW, Norton A, Lister TA, Mesirov J, Neuberg DS, Lander ES, Aster JC, Golub TR. Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med. 2002 Jan;8(1):68-74. doi: 10.1038/nm0102-68. PubMed PMID: 11786909.
  43. Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, McLaughlin ME, Kim JY, Goumnerova LC, Black PM, Lau C, Allen JC, Zagzag D, Olson JM, Curran T, Wetmore C, Biegel JA, Poggio T, Mukherjee S, Rifkin R, Califano A, Stolovitzky G, Louis DN, Mesirov JP, Lander ES, Golub TR. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature. 2002 Jan 24;415(6870):436-42. doi: 10.1038/415436a. PubMed PMID: 11807556.
  44. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 5;420(6915):520-62. doi: 10.1038/nature01262. PubMed PMID: 12466850.
  45. Monti S, Tamayo P, Mesirov JP, Golub T. Consensus Clustering. A resampling-based method for class discovery and visualization of gene-expression microarray data. Functional Genomics special issue, Machine Learning. 2003; 52:91-118.
  46. Mukherjee S, Tamayo P, Rogers S, Rifkin R, Engle A, Campbell C, Golub TR, Mesirov JP. Estimating dataset size requirements for classifying DNA microarray data. J Comput Biol. 2003;10(2):119-42. doi: 10.1089/106652703321825928. PubMed PMID: 12804087.
  47. Rifkin, Mukherjee, Tamayo, Ramaswamy, Yeang, Angelo, Reich, Poggio, Lander, Golub, Mesirov JP. An Analytical Method for Multi-class Molecular Cancer Classification. SIAM review. Society for Industrial and Applied Mathematics. 2003; 45(4):706-723.
  48. Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res. 2003 Jan;13(1):91-6. doi: 10.1101/gr.828403. PubMed PMID: 12529310; PubMed Central PMCID: PMC430950.
  49. Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstråle M, Laurila E, Houstis N, Daly MJ, Patterson N, Mesirov JP, Golub TR, Tamayo P, Spiegelman B, Lander ES, Hirschhorn JN, Altshuler D, Groop LC. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003 Jul;34(3):267-73. doi: 10.1038/ng1180. PubMed PMID: 12808457.
  50. Brunet JP, Tamayo P, Golub TR, Mesirov JP. Metagenes and molecular pattern discovery using matrix factorization. Proc Natl Acad Sci U S A. 2004 Mar 23;101(12):4164-9. doi: 10.1073/pnas.0308531101. Epub 2004 Mar 11. PubMed PMID: 15016911; PubMed Central PMCID: PMC384712.