net references

[Chavel1984Eigenvalues] I. Chavel. Eigenvalues in Riemannian geometry. Academic Press, Orlando, Fl., 1984. [ bib ]
[Aoyama1990Neural] T. Aoyama, Y. Suzuki, and H. Ichikawa. Neural networks applied to quantitative structure-activity relationship analysis. J. Med. Chem., 33(9):2583-2590, Sep 1990. [ bib | Abstract ]
[Mohar1991Laplacian] B. Mohar. The Laplacian spectrum of graphs. In Y. Alavi, G. Chartrand, O. Ollermann, and A. Schwenk, editors, Graph theory, combinatorics, and applications, pages 871-898, New-York, 1991. John Wiley and Sons, Inc. [ bib | .pdf | .pdf ]
[de1993Multiplicites] Y. C. de Verdière. Multiplicités des valeurs propres Laplaciens discrets et Laplaciens continus. Rendiconti di Matematica, 13:433-460, 1993. [ bib ]
[Friedman1993Some] J. Friedman. Some geometric aspects of graphs and their eigenfunctions. Duke Math. J., 69:487-525, March 1993. [ bib ]
[Molloy1995critical] M. Molloy and B. Reed. A critical point for random graphs with a given degree sequence. Random Struct. Algorithm., 6:161-179, 1995. [ bib | .ps | .pdf ]
[Stadler1996Landscapes] P. F. Stadler. Landscapes and Their Correlation Functions. J. Math. Chem., 20:1-45, 1996. [ bib | .html | .pdf ]
[Rarey1996fast] M. Rarey, B. Kramer, T. Lengauer, and G. Klebe. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol., 261(3):470-489, Aug 1996. [ bib | DOI | http | Abstract ]
[Kristiansen1996database] K. Kristiansen, S. G. Dahl, and O. Edvardsen. A database of mutants and effects of site-directed mutagenesis experiments on G protein-coupled receptors. Proteins, 26(1):81-94, Sep 1996. [ bib | DOI | http | Abstract ]
[Holst1996Topological] H. van der Holst. Topological and spectral graph characterizations. PhD thesis, Universiteit van Amsterdam, 1996. [ bib ]
[Bauknecht1996Locating] H. Bauknecht, A. Zell, H. Bayer, P. Levi, M. Wagener, J. Sadowski, and J. Gasteiger. Locating biologically active compounds in medium-sized heterogeneous datasets by topological autocorrelation vectors: dopamine and benzodiazepine agonists. J Chem Inf Comput Sci, 36(6):1205-1213, 1996. [ bib | Abstract ]
[Mohar1997Some] B. Mohar. Some applications of Laplace eigenvalues of graphs. In G. Hahn and G. Sabidussi, editors, Graph Symmetry: Algebraic Methods and Applications, volume 497 of NATO ASI Series C, pages 227-275. Kluwer, Dordrecht, 1997. [ bib | .html | .pdf ]
[Luo1997Mammalian] Y. Luo, A. Batalao, H. Zhou, and L. Zhu. Mammalian two-hybrid system: a complementary approach to the yeast two-hybrid system. Biotechniques, 22(2):350-352, Feb 1997. [ bib | Abstract ]
[Kanehisa1997database] M. Kanehisa. A database for post-genome analysis. Trends Genet., 13:375-376, 1997. [ bib | DOI | http | .pdf ]
[Jones1997Development] G. Jones, P. Willett, R. C. Glen, A. R. Leach, and R. Taylor. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol., 267(3):727-748, Apr 1997. [ bib | DOI | http | Abstract ]
[Gulukota1997Two] K. Gulukota, J. Sidney, A. Sette, and C. DeLisi. Two complementary methods for predicting peptides binding major histocompatibility complex molecules. J. Mol. Biol., 267(5):1258-1267, Apr 1997. [ bib | DOI | http | Abstract ]
[Chung1997Spectral] F. R. K. Chung. Spectral graph theory, volume 92 of CBMS Regional Conference Series. American Mathematical Society, Providence, 1997. [ bib ]
[Arkin1997test] A. Arkin, P. Shen, and J. Ross. A test case of correlation metric construction of a reaction pathway from measurements. Science, 277(5330):1275-1279, 1997. [ bib | .pdf | Abstract ]
[Watts1998Collective] D. J. Watts and S. H. Strogatz. Collective dynamics of 'small-world' networks. Nature, 393:440-442, 1998. [ bib | http | .pdf ]
[Sette1998HLA] A. Sette and J. Sidney. HLA supertypes and supermotifs: a functional perspective on HLA polymorphism. Curr. Opin. Immunol., 10(4):478-482, Aug 1998. [ bib | Abstract ]
[Schneider1998Artificial] G. Schneider and P. Wrede. Artificial neural networks for computer-based molecular design. Prog Biophys Mol Biol, 70(3):175-222, 1998. [ bib | Abstract ]
[Poggio1998Sparse] Poggio and Girosi. A Sparse Representation for Function Approximation. Neural Comput, 10(6):1445-54, Jul 1998. [ bib | Abstract ]
[Molloy1998size] M. Molloy and B. Reed. The size of the giant component of a random graph with a given degree sequence. Combinator. Probab. Comput., 7:295-305, 1998. [ bib | .ps | .pdf ]
[Kononen1998Tissue] J. Kononen, L. Bubendorf, A. Kallioniemi, M. Bärlund, P. Schraml, S. Leighton, J. Torhorst, M. J. Mihatsch, G. Sauter, and O. P. Kallioniemi. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med, 4(7):844-847, Jul 1998. [ bib | Abstract ]
[Goto1998LIGAND:] S. Goto, T. Nishioka, and M. Kanehisa. LIGAND: chemical database for enzyme reactions. Bioinformatics, 14:591-599, 1998. [ bib | http | .pdf ]
[Girosi1998Equivalence] Girosi. An Equivalence Between Sparse Approximation and Support Vector Machines. Neural Comput, 10(6):1455-80, Jul 1998. [ bib | Abstract ]
[Pontil1998Properties] M. Pontil and A. Verri. Properties of support vector machines. Neural Comput, 10(4):955-74, May 1998. [ bib | Abstract ]
[Strahl1999Methylation] B. D. Strahl, R. Ohba, R. G. Cook, and C. D. Allis. Methylation of histone h3 at lysine 4 is highly conserved and correlates with transcriptionally active nuclei in tetrahymena. Proc Natl Acad Sci U S A, 96(26):14967-14972, Dec 1999. [ bib | Abstract ]
[Sette1999Nine] A. Sette and J. Sidney. Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism. Immunogenetics, 50(3-4):201-212, Nov 1999. [ bib | Abstract ]
[Rammensee1999SYFPEITHI] H. Rammensee, J. Bachmann, N. P. Emmerich, O. A. Bachor, and S. Stevanović. Syfpeithi: database for MHC ligands and peptide motifs. Immunogenetics, 50(3-4):213-219, Nov 1999. [ bib | Abstract ]
[Lander1999Array] E. S. Lander. Array of hope. Nat Genet, 21(1 Suppl):3-4, Jan 1999. [ bib | DOI | http ]
[Faloutsos1999On] M. Faloutsos, P. Faloutsos, and C. Faloutsos. On power-law relationships of the internet topology. Comput. Comm. Rev., 29:251-262, 1999. [ bib | .html | .pdf ]
[Debouck1999DNA] C. Debouck and P. N. Goodfellow. DNA microarrays in drug discovery and development. Nat. Genet., 21(1 Suppl):48-50, Jan 1999. [ bib | DOI | http | Abstract ]
[Barabasi1999Emergence] A.-L. Barabási and R. Albert. Emergence of scaling in random networks. Science, 286:509-512, 1999. [ bib | .pdf | .pdf | Abstract ]
[Albert1999Diameter] R. Albert, H. Jeong, and A.-L. Barabási. Diameter of the World-Wide Web. Nature, 401:130-131, 1999. [ bib | .pdf | .pdf ]
[Mathews1999Expandeda] D. H. Mathews, J. Sabina, M. Zuker, and D. H. Turner. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288(5):911-940, May 1999. [ bib | DOI | http | Abstract ]
[Wilbur2000Boosting] W. J. Wilbur. Boosting naive Bayesian learning on a large subset of MEDLINE. Proc AMIA Symp, pages 918-22, 2000. [ bib | Abstract ]
[Vapnik2000Bounds] V. Vapnik and O. Chapelle. Bounds on error expectation for support vector machines. Neural Comput, 12(9):2013-36, Sep 2000. [ bib | Abstract ]
[Uetz2000comprehensive] P. Uetz, L. Giot, G. Cagney, T. A. Mansfield, R. S. Judson, J. R. Knight, D. Lockshon, V. Narayan, M. Srinivasan, P. Pochart, A. Qureshi-Emili, Y. Li, B. Godwin, D. Conover, T. Kalbfleish, G. Vijayadamodar, M. Yang, M. Johnston, S. Fields, and J. M. Rothberg. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403:623-627, 2000. [ bib | http | .pdf ]
[Slanina2000Random] F. Slanina and M. Kotrla. Random networks created by biological evolution. Phys. Rev. E, 62(5):6170-6177, 2000. [ bib | http | .pdf ]
[Risau-Gusman2000Generalization] Risau-Gusman and Gordon. Generalization properties of finite-size polynomial support vector machines. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics, 62(5 Pt B):7092-9, Nov 2000. [ bib | Abstract ]
[Rice2000EMBOSS] P. Rice, I. Longden, and A. Bleasby. Emboss: the european molecular biology open software suite. Trends Genet., 16(6):276-277, Jun 2000. [ bib ]
[Rea2000Regulation] S. Rea, F. Eisenhaber, D. O'Carroll, B. D. Strahl, Z. W. Sun, M. Schmid, S. Opravil, K. Mechtler, C. P. Ponting, C. D. Allis, and T. Jenuwein. Regulation of chromatin structure by site-specific histone h3 methyltransferases. Nature, 406(6796):593-599, Aug 2000. [ bib | DOI | http | Abstract ]
[Raudys2000How] S. Raudys. How good are support vector machines? Neural Netw, 13(1):17-9, Jan 2000. [ bib | Abstract ]
[Opper2000Gaussian] M. Opper and O. Winther. Gaussian processes for classification: mean-field algorithms. Neural Comput, 12(11):2655-84, Nov 2000. [ bib | Abstract ]
[Lazo2000Combinatorial] J. S. Lazo and P. Wipf. Combinatorial chemistry and contemporary pharmacology. J. Pharmacol. Exp. Ther., 293(3):705-709, Jun 2000. [ bib | Abstract ]
[Kwon2000candidate] J. M. Kwon and A. M. Goate. The candidate gene approach. Alcohol Res Health, 24(3):164-168, 2000. [ bib | Abstract ]
[Jeong2000large-scale] H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai, and A.-L. Barabási. The large-scale organization of metabolic networks. Nature, 407:651-654, 2000. [ bib | http | .pdf ]
[Ito2000Toward] T. Ito, K. Tashiro, S. Muta, R. Ozawa, T. Chiba, M. Nishizawa, K. Yamamoto, S. Kuhara, and Y. Sakaki. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl. Acad. Sci. USA, 93(3):1143-1147, 2000. [ bib | http | .pdf ]
[Butte2000Mutual] A. J. Butte and I. S. Kohane. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput, pages 418-429, 2000. [ bib | Abstract ]
[Amaral2000Classes] L. A. N. Amaral, A. Scala, M. Barthélémy, and H. E. Stanley. Classes of small-world networks. Proc. Natl. Acad. Sci. USA, 97(21):11149-11152, 2000. [ bib | http | .pdf ]
[Albert2000Attack] R. Albert, H. Jeong, and A.-L. Barabási. Attack and error tolerance in complex networks. Nature, 406:378-381, 2000. [ bib | .pdf | .pdf ]
[Akutsu2000Inferring] T. Akutsu, S. Miyano, and S. Kuhara. Inferring qualitative relations in genetic networks and metabolic pathways. Bioinformatics, 16(8):727-734, 2000. [ bib | http | .pdf ]
[Ashburner2000Gene] M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, G. M. Rubin, and G. Sherlock. Gene ontology: tool for the unification of biology. the gene ontology consortium. Nat Genet, 25(1):25-29, May 2000. [ bib | DOI | http ]
[Yook2001Weighted] S. H. Yook, H. Jeong, Y. Tu, and A.-L. Barabási. Weighted evolution networks. Phys. Rev. Lett., 86(25):5835-5838, 2001. [ bib | .pdf | .pdf ]
[Wang2001Methylation] H. Wang, Z. Q. Huang, L. Xia, Q. Feng, H. Erdjument-Bromage, B. D. Strahl, S. D. Briggs, C. D. Allis, J. Wong, P. Tempst, and Y. Zhang. Methylation of histone h4 at arginine 3 facilitating transcriptional activation by nuclear hormone receptor. Science, 293(5531):853-857, Aug 2001. [ bib | DOI | http | Abstract ]
[Wagner2001Yeast] A. Wagner. The Yeast Protein Interaction Network Evolves Rapidly and Contains Few Redundant Duplicate Genes. Mol. Biol. Evol., 18:1283-1292, 2001. [ bib | .html | .pdf ]
[Vercoutere2001Rapid] W. Vercoutere, S. Winters-Hilt, H. Olsen, D. Deamer, D. Haussler, and M. Akeson. Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nat Biotechnol, 19(3):248-52, Mar 2001. [ bib | DOI | http | .pdf | Abstract ]
[Vazquez2001Modeling] A. Vazquez, A. Flammini, A. Maritan, and A. Vespignani. Modeling of protein interaction networks. E-print cond-mat/0108043, Aug 2001. [ bib | http | .pdf ]
[Suykens2001Optimal] J. A. Suykens, J. Vandewalle, and B. De Moor. Optimal control by least squares support vector machines. Neural Netw, 14(1):23-35, Jan 2001. [ bib | Abstract ]
[Strogatz2001Exploring] S. S. Strogatz. Exploring complex networks. Nature, 410:268-276, 2001. [ bib | http | .pdf ]
[Strahl2001Methylation] B. D. Strahl, S. D. Briggs, C. J. Brame, J. A. Caldwell, S. S. Koh, H. Ma, R. G. Cook, J. Shabanowitz, D. F. Hunt, M. R. Stallcup, and C. D. Allis. Methylation of histone h4 at arginine 3 occurs in vivo and is mediated by the nuclear receptor coactivator prmt1. Curr Biol, 11(12):996-1000, Jun 2001. [ bib | Abstract ]
[Sole2001Model] R. V. Solé, R. Pastor-Satorras, E. D. Smith, and T. Kepler. A Model of Large-Scale Proteome Evolution. Technical report, Santa Fe Institute, 2001. Working paper 01-08-041. [ bib | .html | .pdf ]
[Sherry2001dbSNP] S. T. Sherry, M. H. Ward, M. Kholodov, J. Baker, L. Phan, E. M. Smigielski, and K. Sirotkin. dbsnp: the ncbi database of genetic variation. Nucleic Acids Res, 29(1):308-311, Jan 2001. [ bib | Abstract ]
[Seol2001Skp1] J. H. Seol, A. Shevchenko, A. Shevchenko, and R. J. Deshaies. Skp1 forms multiple protein complexes, including RAVE, a regulator of V-ATPase assembly. Nat Cell Biol, 3(4):384-91, Apr 2001. [ bib | DOI | http | .pdf | Abstract ]
[Sachidanandam2001Map] R. Sachidanandam, D. Weissman, S. C. Schmidt, J. M. Kakol, L. D. Stein, G. Marth, S. Sherry, J. C. Mullikin, B. J. Mortimore, D. L. Willey, S. E. Hunt, C. G. Cole, P. C. Coggill, C. M. Rice, Z. Ning, J. Rogers, D. R. Bentley, P. Y. Kwok, E. R. Mardis, R. T. Yeh, B. Schultz, L. Cook, R. Davenport, M. Dante, L. Fulton, L. Hillier, R. H. Waterston, J. D. McPherson, B. Gilman, S. Schaffner, W. J. Van Etten, D. Reich, J. Higgins, M. J. Daly, B. Blumenstiel, J. Baldwin, N. Stange-Thomann, M. C. Zody, L. Linton, E. S. Lander, D. Altshuler, and International SNP Map Working Group. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature, 409(6822):928-933, Feb 2001. [ bib | Abstract ]
[Rain2001protein-protein] J.-C. Rain, L. Selig, H. De Reuse, V. Battaglia, C. Reverdy, S. Simon, G. Lenzen, F. Petel, J. Wojcik, V. Schächter, Y. Chemama, A. Labigne, and P. Legrain. The protein-protein interaction map of Helicobacter pylori. Nature, 409:211-215, 2001. [ bib | http | .pdf ]
[Qian2001Protein] J. Qian, N. M. Luscombe, and M. Gerstein. Protein Fold and Family Occurrence in Genomes: Power-Law Behaviour and Evolutionary Model. J. Mol. Biol., 313:673-681, 2001. [ bib | http | .pdf ]
[Puig2001tandem] O. Puig, F. Caspary, G. Rigaut, B. Rutz, E. Bouveret, E. Bragado-Nilsson, M. Wilm, and B. Séraphin. The tandem affinity purification (tap) method: a general procedure of protein complex purification. Methods, 24(3):218-229, Jul 2001. [ bib | DOI | http | Abstract ]
[Podani2001Comparable] J. Podani, Z.N. Oltvai, H. Jeong, B. Tombor, A.-L. Barabási, and E. Szathmáry. Comparable system-level organization of Archaea and Eukaryotes. Nat. Genet., 29:54-56, 2001. [ bib | http | .pdf ]
[Newman2001Random] M. E. J. Newman, S. H. Strogatz, and D. J. Watts. Random graphs with arbitrary degree distributions and their applications. Phys. Rev. E, 64:26118, 2001. [ bib | http | .pdf ]
[Nakayama2001Role] J. Nakayama, J. C. Rice, B. D. Strahl, C. D. Allis, and S. I. Grewal. Role of histone h3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science, 292(5514):110-113, Apr 2001. [ bib | DOI | http | Abstract ]
[Miwakeichi2001comparison] F. Miwakeichi, R. Ramirez-Padron, P. A. Valdes-Sosa, and T. Ozaki. A comparison of non-linear non-parametric models for epilepsy data. Comput. Biol. Med., 31(1):41-57, Jan 2001. [ bib | Abstract ]
[Ma2001Hormone-dependent] H. Ma, C. T. Baumann, H. Li, B. D. Strahl, R. Rice, M. A. Jelinek, D. W. Aswad, C. D. Allis, G. L. Hager, and M. R. Stallcup. Hormone-dependent, carm1-directed, arginine-specific methylation of histone h3 on a steroid-regulated promoter. Curr Biol, 11(24):1981-1985, Dec 2001. [ bib | Abstract ]
[Kim2001Evolving] J. Kim, P.L. Krapivsky, B. Kahng, and S. Redner. Evolving protein interaction networks. E-print cond-mat/0203167, 2001. [ bib | http | .pdf ]
[Kallioniemi2001Tissue] O. P. Kallioniemi, U. Wagner, J. Kononen, and G. Sauter. Tissue microarray technology for high-throughput molecular profiling of cancer. Hum Mol Genet, 10(7):657-662, Apr 2001. [ bib | Abstract ]
[Jeong2001Lethality] H. Jeong, S. P. Mason, A.-L. Barabási, and Z. N. Oltvai. Lethality and centrality in protein networks. Nature, 411:41-42, 2001. [ bib | http | .pdf ]
[Ito2001comprehensive] T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, and Y. Sakaki. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA, 98(8):4569-4574, 2001. [ bib | http | .pdf ]
[Dreiseitl2001comparison] S. Dreiseitl, L. Ohno-Machado, H. Kittler, S. Vinterbo, H. Billhardt, and M. Binder. A comparison of machine learning methods for the diagnosis of pigmented skin lesions. J Biomed Inform, 34(1):28-36, Feb 2001. [ bib | DOI | http | .pdf | Abstract ]
[Davies2001Discrete] E. B. Davies, G. M. L. Gladwell, J. Leydold, and P. F. Stadler. Discrete Nodal Domain Theorems. Lin. Alg. Appl., 336:51-60, 2001. [ bib | .html | .pdf ]
[Briggs2001Histone] S. D. Briggs, M. Bryk, B. D. Strahl, W. L. Cheung, J. K. Davie, S. Y. Dent, F. Winston, and C. D. Allis. Histone h3 lysine 4 methylation is mediated by set1 and required for cell growth and rdna silencing in saccharomyces cerevisiae. Genes Dev, 15(24):3286-3295, Dec 2001. [ bib | DOI | http | Abstract ]
[Barabasi2001Deterministic] A.-L. Barabási and E. Ravasz. Deterministic scale-free networks. E-print cond-mat/0107419, 2001. [ bib | http | .pdf ]
[Achard2001XML] F. Achard, G. Vaysseix, and E. Barillot. Xml, bioinformatics and data integration. Bioinformatics, 17(2):115-125, Feb 2001. [ bib | Abstract ]
[Opper2001Universal] M. Opper and R. Urbanczik. Universal learning curves of support vector machines. Phys Rev Lett, 86(19):4410-3, May 2001. [ bib | Abstract ]
[Liang2001Detection] H. Liang and Z. Lin. Detection of delayed gastric emptying from electrogastrograms with support vector machine. IEEE Trans Biomed Eng, 48(5):601-4, May 2001. [ bib | Abstract ]
[Jeong2001] H. Jeong, S. P. Mason, A. L. Barabási, and Z. N. Oltvai. Lethality and centrality in protein networks. Nature, 411(6833):41-42, May 2001. [ bib | DOI | http ]
[Weber2002Building] Griffin Weber, Staal Vinterbo, and Lucila Ohno-Machado. Building an asynchronous web-based tool for machine learning classification. Proc AMIA Symp, pages 869-73, 2002. [ bib | Abstract ]
[Wahba2002Soft] Grace Wahba. Soft and hard classification by reproducing kernel Hilbert space methods. Proc Natl Acad Sci U S A, 99(26):16524-30, Dec 2002. [ bib | DOI | http | .pdf | Abstract ]
[Su2002Large-scale] A.I. Su, M.P. Cooke, K.A. Ching, Y. Hakak, J.R. Walker, T. Wiltshire, A.P. Orth, R.Q. Vega, L.M. Sapinoso, A. Moqrich, A. Patapoutian, G.M. Hampton, P.G. Schultz, and J.B. Hogenesch. Large-scale analysis of the human and mouse transcriptomes. Proc. Natl. Acad. Sci. U. S. A., 99(7):4465-4470, Apr 2002. [ bib | DOI | http | Abstract ]
[Sturn2002Genesis:] Alexander Sturn, John Quackenbush, and Zlatko Trajanoski. Genesis: cluster analysis of microarray data. Bioinformatics, 18(1):207-8, Jan 2002. [ bib | Abstract ]
[Strahl2002Set2] Brian D Strahl, Patrick A Grant, Scott D Briggs, Zu-Wen Sun, James R Bone, Jennifer A Caldwell, Sahana Mollah, Richard G Cook, Jeffrey Shabanowitz, Donald F Hunt, and C. David Allis. Set2 is a nucleosomal histone h3-selective methyltransferase that mediates transcriptional repression. Mol Cell Biol, 22(5):1298-1306, Mar 2002. [ bib | Abstract ]
[Song2002Prediction] Minghu Song, Curt M Breneman, Jinbo Bi, N. Sukumar, Kristin P Bennett, Steven Cramer, and Nihal Tugcu. Prediction of protein retention times in anion-exchange chromatography systems using support vector regression. J Chem Inf Comput Sci, 42(6):1347-57, 2002. [ bib | Abstract ]
[Pollack2002Microarray] Jonathan R Pollack, Therese Sørlie, Charles M Perou, Christian A Rees, Stefanie S Jeffrey, Per E Lonning, Robert Tibshirani, David Botstein, Anne-Lise Børresen-Dale, and Patrick O Brown. Microarray analysis reveals a major direct role of dna copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A, 99(20):12963-12968, Oct 2002. [ bib | DOI | http | Abstract ]
[Pastor-Satorras2002Evolving] R. Pastor-Satorras, E. D. Smith, and R. V. Solé. Evolving protein interaction networks through gene duplication. Technical report, Santa Fe Institute, 2002. Working paper 02-02-008. [ bib | .html | .pdf ]
[Newman2002Random] M. E. J. Newman. Random graphs as models of networks. In S. Bornholdt and H. G. Schuster, editors, Handbook of Graphs and Networks. Wiley-VCH, Berlin, 2002. To appear. [ bib | http | .pdf ]
[Mateos2002Systematic] Alvaro Mateos, Joaquín Dopazo, Ronald Jansen, Yuhai Tu, Mark Gerstein, and Gustavo Stolovitzky. Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons. Genome Res., 12(11):1703-15, Nov 2002. [ bib | DOI | http | .pdf | Abstract ]
[Maslov2002Specificity] S. Maslov and K. Sneppen. Specificity and stability in topology of protein networks. Science, 296:910-913, 2002. [ bib | .pdf | .pdf ]
[Martoglio2002decomposition] Ann-Marie Martoglio, James W Miskin, Stephen K Smith, and David J C MacKay. A decomposition model to track gene expression signatures: preview on observer-independent classification of ovarian cancer. Bioinformatics, 18(12):1617-24, Dec 2002. [ bib | Abstract ]
[Marsland2002self-organising] Stephen Marsland, Jonathan Shapiro, and Ulrich Nehmzow. A self-organising network that grows when required. Neural Netw, 15(8-9):1041-58, 2002. [ bib | Abstract ]
[Li2002Involvement] Jiwen Li, Qiushi Lin, Ho-Geun Yoon, Zhi-Qing Huang, Brian D Strahl, C. David Allis, and Jiemin Wong. Involvement of histone methylation and phosphorylation in regulation of transcription by thyroid hormone receptor. Mol Cell Biol, 22(16):5688-5697, Aug 2002. [ bib | Abstract ]
[Kondor2002Diffusion] R. I. Kondor and J. Lafferty. Diffusion kernels on graphs and other discrete input. In Proceedings of the Nineteenth International Conference on Machine Learning, pages 315-322, San Francisco, CA, USA, 2002. Morgan Kaufmann Publishers Inc. [ bib | .pdf ]
[Kanehisa2002KEGG] M. Kanehisa, S. Goto, S. Kawashima, and A. Nakaya. The KEGG databases at GenomeNet. Nucleic Acids Res., 30:42-46, 2002. [ bib | http | .pdf ]
[Jones2002DNA] Peter A Jones. Dna methylation and cancer. Oncogene, 21(35):5358-5360, Aug 2002. [ bib | DOI | http | Abstract ]
[Ho2002Systematic] Yuen Ho, Albrecht Gruhler, Adrian Heilbut, Gary D Bader, Lynda Moore, Sally-Lin Adams, Anna Millar, Paul Taylor, Keiryn Bennett, Kelly Boutilier, Lingyun Yang, Cheryl Wolting, Ian Donaldson, Søren Schandorff, Juanita Shewnarane, Mai Vo, Joanne Taggart, Marilyn Goudreault, Brenda Muskat, Cris Alfarano, Danielle Dewar, Zhen Lin, Katerina Michalickova, Andrew R Willems, Holly Sassi, Peter A Nielsen, Karina J Rasmussen, Jens R Andersen, Lene E Johansen, Lykke H Hansen, Hans Jespersen, Alexandre Podtelejnikov, Eva Nielsen, Janne Crawford, Vibeke Poulsen, Birgitte D Sørensen, Jesper Matthiesen, Ronald C Hendrickson, Frank Gleeson, Tony Pawson, Michael F Moran, Daniel Durocher, Matthias Mann, Christopher W V Hogue, Daniel Figeys, and Mike Tyers. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415(6868):180-3, Jan 2002. [ bib | DOI | http | .pdf | Abstract ]
[Hanisch2002Co-clustering] D. Hanisch, A. Zien, R. Zimmer, and T. Lengauer. Co-clustering of biological networks and gene expression data. Bioinformatics, 2002. [ bib | .pdf ]
[Guelzim2002Topological] N. Guelzim, S. Bottani, P. Bourgine, and F. Képès. Topological and causal structure of the yeast transcriptional regulatory network. Nat. Genet., 31:60-63, 2002. [ bib | .html | .pdf ]
[Goto2002LIGAND:] S. Goto, Y. Okuno, M. Hattori, T. Nishioka, and M. Kanehisa. LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res., 30:402-404, 2002. [ bib | http | .pdf ]
[Gavin2002Functionala] Anne-Claude Gavin, Markus Bösche, Roland Krause, Paola Grandi, Martina Marzioch, Andreas Bauer, Jörg Schultz, Jens M Rick, Anne-Marie Michon, Cristina-Maria Cruciat, Marita Remor, Christian Höfert, Malgorzata Schelder, Miro Brajenovic, Heinz Ruffner, Alejandro Merino, Karin Klein, Manuela Hudak, David Dickson, Tatjana Rudi, Volker Gnau, Angela Bauch, Sonja Bastuck, Bettina Huhse, Christina Leutwein, Marie-Anne Heurtier, Richard R Copley, Angela Edelmann, Erich Querfurth, Vladimir Rybin, Gerard Drewes, Manfred Raida, Tewis Bouwmeester, Peer Bork, Bertrand Seraphin, Bernhard Kuster, Gitte Neubauer, and Giulio Superti-Furga. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415(6868):141-7, Jan 2002. [ bib | DOI | http | .pdf | Abstract ]
[Ekins2002Towards] S. Ekins, B. Boulanger, P. W. Swaan, and M. A. Z. Hupcey. Towards a new age of virtual ADME/TOX and multidimensional drug discovery. J Comput Aided Mol Des, 16(5-6):381-401, 2002. [ bib | Abstract ]
[Dover2002Methylation] Jim Dover, Jessica Schneider, Mary Anne Tawiah-Boateng, Adam Wood, Kimberly Dean, Mark Johnston, and Ali Shilatifard. Methylation of histone h3 by compass requires ubiquitination of histone h2b by rad6. J Biol Chem, 277(32):28368-28371, Aug 2002. [ bib | DOI | http | Abstract ]
[Chan2002Comparison] Kwokleung Chan, Te-Won Lee, Pamela A Sample, Michael H Goldbaum, Robert N Weinreb, and Terrence J Sejnowski. Comparison of machine learning and traditional classifiers in glaucoma diagnosis. IEEE Trans Biomed Eng, 49(9):963-74, Sep 2002. [ bib | DOI | http | .pdf | Abstract ]
[Bryk2002Evidence] Mary Bryk, Scott D Briggs, Brian D Strahl, M. Joan Curcio, C. David Allis, and Fred Winston. Evidence that set1, a factor required for methylation of histone h3, regulates rdna silencing in s. cerevisiae by a sir2-independent mechanism. Curr Biol, 12(2):165-170, Jan 2002. [ bib | Abstract ]
[Brusic2002Prediction] V. Brusic, N. Petrovsky, G. Zhang, and V. B. Bajic. Prediction of promiscuous peptides that bind HLA class I molecules. Immunol. Cell Biol., 80(3):280-285, Jun 2002. [ bib | Abstract ]
[Briggs2002Gene] Scott D Briggs, Tiaojiang Xiao, Zu-Wen Sun, Jennifer A Caldwell, Jeffrey Shabanowitz, Donald F Hunt, C. David Allis, and Brian D Strahl. Gene silencing: trans-histone regulatory pathway in chromatin. Nature, 418(6897):498, Aug 2002. [ bib | DOI | http | Abstract ]
[Bowd2002Comparing] Christopher Bowd, Kwokleung Chan, Linda M Zangwill, Michael H Goldbaum, Te-Won Lee, Terrence J Sejnowski, and Robert N Weinreb. Comparing neural networks and linear discriminant functions for glaucoma detection using confocal scanning laser ophthalmoscopy of the optic disc. Invest Ophthalmol Vis Sci, 43(11):3444-54, Nov 2002. [ bib | http | .pdf | Abstract ]
[Albert2002Statistical] R. Albert and A.L. Barabási. Statistical mechanics of complex networks. Rev. Mod. Phys., 74:47-97, 2002. [ bib | .pdf | .pdf ]
[Ong2002Stable] Shao-En Ong, Blagoy Blagoev, Irina Kratchmarova, Dan Bach Kristensen, Hanno Steen, Akhilesh Pandey, and Matthias Mann. Stable isotope labeling by amino acids in cell culture, silac, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics, 1(5):376-386, May 2002. [ bib | Abstract ]
[Zhu2003Introduction] Lingyun Zhu, Baoming Wu, and Changxiu Cao. Introduction to medical data mining. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi, 20(3):559-62, Sep 2003. [ bib | Abstract ]
[Zhao2003Applicationa] Y. Zhao, C. Pinilla, D. Valmori, R. Martin, and R. Simon. Application of support vector machines for T-cell epitopes prediction. Bioinformatics, 19(15):1978-1984, Oct 2003. [ bib | Abstract ]
[Waterman2003Transcriptional] S.R. Waterman and P.L.C. Small. Transcriptional expression of escherichia coli glutamate-dependent acid resistance genes gada and gadbc in an hns rpos mutant. J. Bacteriol., 185(15):4644-4647, Aug 2003. [ bib | Abstract ]
[Takahashi2003Proteomic] Nobuhiro Takahashi, Mitsuaki Yanagida, Sally Fujiyama, Toshiya Hayano, and Toshiaki Isobe. Proteomic snapshot analyses of preribosomal ribonucleoprotein complexes formed at various stages of ribosome biogenesis in yeast and mammalian cells. Mass Spectrom Rev, 22(5):287-317, 2003. [ bib | DOI | http | .pdf | Abstract ]
[Shannon2003Analyzing] William Shannon, Robert Culverhouse, and Jill Duncan. Analyzing microarray data using cluster analysis. Pharmacogenomics, 4(1):41-52, Jan 2003. [ bib | Abstract ]
[Roschke2003Karyotypic] Anna V Roschke, Giovanni Tonon, Kristen S Gehlhaus, Nicolas McTyre, Kimberly J Bussey, Samir Lababidi, Dominic A Scudiero, John N Weinstein, and Ilan R Kirsch. Karyotypic complexity of the nci-60 drug-screening panel. Cancer Res, 63(24):8634-8647, Dec 2003. [ bib | Abstract ]
[Patterson2003Proteomics] Scott D Patterson and Ruedi H Aebersold. Proteomics: the first decade and beyond. Nat Genet, 33 Suppl:311-323, Mar 2003. [ bib | DOI | http | Abstract ]
[Mayr2003Cross-reactive] Torsten Mayr, Christian Igel, Gregor Liebsch, Ingo Klimant, and Otto S Wolfbeis. Cross-reactive metal ion sensor array in a micro titer plate format. Anal Chem, 75(17):4389-96, Sep 2003. [ bib | Abstract ]
[Li2003Simple] Jinyan Li, Huiqing Liu, James R Downing, Allen Eng-Juh Yeoh, and Limsoon Wong. Simple rules underlying gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients. Bioinformatics, 19(1):71-8, Jan 2003. [ bib | Abstract ]
[Jambon2003New] Martin Jambon, Anne Imberty, Gilbert Deléage, and Christophe Geourjon. A new bioinformatic approach to detect common 3d sites in protein structures. Proteins, 52(2):137-145, Aug 2003. [ bib | DOI | http | Abstract ]
[Jaenisch2003Epigenetic] Rudolf Jaenisch and Adrian Bird. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet., 33 Suppl:245-254, Mar 2003. [ bib | DOI | http | Abstract ]
[Consortium2003International] International HapMap Consortium. The international hapmap project. Nature, 426(6968):789-796, Dec 2003. [ bib | Abstract ]
[Ifantis2003nonlinear] A. Ifantis and S. Papadimitriou. The nonlinear predictability of the electrotelluric field variations data analyzed with support vector machines as an earthquake precursor. Int J Neural Syst, 13(5):315-32, Oct 2003. [ bib | Abstract ]
[Bild2003] E. Huang, S. Ishida, J. Pittman, H. Dressman, A. Bild, M. Kloos, M. D'Amico, R. G. Pestell, M. West, and J. R. Nevins. Gene expression phenotypic models that predict the activity of oncogenic pathways. Nat Genet, 34(2):226-30, 2003. [ bib | Abstract ]
[Harborth2003Sequence] J. Harborth, S. M. Elbashir, K. Vandenburgh, H. Manninga, S. A. Scaringe, K. Weber, and T. Tuschl. Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing. Antisense Nucleic Acid. Drug. Dev., 13(2):83-105, Apr 2003. [ bib | DOI | http | Abstract ]
[Ge2003Reducing] Xijin Ge, Shuichi Tsutsumi, Hiroyuki Aburatani, and Shuichi Iwata. Reducing false positives in molecular pattern recognition. Genome Inform Ser Workshop Genome Inform, 14:34-43, 2003. [ bib | Abstract ]
[Garrett2003Comparison] D. Garrett, D. A Peterson, C. Anderson, and M. Thaut. Comparison of linear, nonlinear, and feature selection methods for EEG signal classification. IEEE Trans Neural Syst Rehabil Eng, 11(2):141-4, Jun 2003. [ bib | Abstract ]
[Formosa2003Changing] T. Formosa. Changing the dna landscape: putting a spn on chromatin. Curr Top Microbiol Immunol, 274:171-201, 2003. [ bib | Abstract ]
[Driel2003new] M. van Driel, K. Cuelenaere, P.P.C.W. Kemmeren, J.A.M. Leunissen, and H.G. Brunner. A new web-based data mining tool for the identification of candidate genes for human genetic disorders. Eur. J. Hum. Genet., 11(1):57-63, Jan 2003. [ bib | DOI | http | Abstract ]
[Dieterle2003Urinary] Frank Dieterle, Silvia Müller-Hagedorn, Hartmut M Liebich, and Günter Gauglitz. Urinary nucleosides as potential tumor markers evaluated by learning vector quantization. Artif. Intell. Med., 28(3):265-79, Jul 2003. [ bib | DOI | http | .pdf | Abstract ]
[Diekman2003Hybrid] Casey Diekman, Wei He, Nagabhushana Prabhu, and Harvey Cramer. Hybrid methods for automated diagnosis of breast tumors. Anal Quant Cytol Histol, 25(4):183-90, Aug 2003. [ bib | Abstract ]
[Chenna2003Multiple] R. Chenna, H. Sugawara, T. Koike, R. Lopez, T. J. Gibson, D. G. Higgins, and J. D. Thompson. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res., 31(13):3497-3500, Jul 2003. [ bib | Abstract ]
[Chan2003Detection] Ian Chan, William Wells, Robert V Mulkern, Steven Haker, Jianqing Zhang, Kelly H Zou, Stephan E Maier, and Clare M C Tempany. Detection of prostate cancer by integration of line-scan diffusion, T2-mapping and T2-weighted magnetic resonance imaging; a multichannel statistical classifier. Med Phys, 30(9):2390-8, Sep 2003. [ bib | .pdf | Abstract ]
[Buus2003Sensitive] S. Buus, S. L. Lauemøller, P. Worning, C. Kesmir, T. Frimurer, S. Corbet, A. Fomsgaard, J. Hilden, A. Holm, and S. Brunak. Sensitive quantitative predictions of peptide-MHC binding by a 'query by committee' artificial neural network approach. Tissue Antigens, 62(5):378-384, Nov 2003. [ bib | Abstract ]
[Bagirov2003New] A. M. Bagirov, B. Ferguson, S. Ivkovic, G. Saunders, and J. Yearwood. New algorithms for multi-class cancer diagnosis using tumor gene expression signatures. Bioinformatics, 19(14):1800-7, Sep 2003. [ bib | http | .pdf | Abstract ]
[Arakawa2003Application] M. Arakawa, K. Hasegawa, and K. Funatsu. Application of the novel molecular alignment method using the Hopfield Neural Network to 3D-QSAR. J Chem Inf Comput Sci, 43(5):1396-1402, 2003. [ bib | DOI | http | Abstract ]
[Zomer2004Toxicological] Simeone Zomer, Christelle Guillo, Richard G Brereton, and Melissa Hanna-Brown. Toxicological classification of urine samples using pattern recognition techniques and capillary electrophoresis. Anal Bioanal Chem, 378(8):2008-20, Apr 2004. [ bib | DOI | http | .pdf | Abstract ]
[Yu2004Advances] J. Yu, V.A. Smith, P.P. Wang, A.J. Hartemink, and E.D. Jarvis. Advances to bayesian network inference for generating causal networks from observational biological data. Bioinformatics, 20(18):3594-3603, Dec 2004. [ bib | DOI | http | Abstract ]
[Xia2004RNAi] H. Xia, Q. Mao, S. L. Eliason, S. Q. Harper, I. H. Martins, H. T. Orr, H. L. Paulson, L. Yang, R. M. Kotin, and B. L. Davidson. RNAi suppresses polyglutamine-induced neurodegeneration in a model of spinocerebellar ataxia. Nat. Med., 10(8):816-820, Aug 2004. [ bib | DOI | http | Abstract ]
[Winters-Hilt2004Nanopore] Stephen Winters-Hilt and Mark Akeson. Nanopore cheminformatics. DNA Cell Biol, 23(10):675-83, Oct 2004. [ bib | DOI | http | Abstract ]
[Wang2004Simple] Kai Wang, Ekachai Jenwitheesuk, Ram Samudrala, and John E Mittler. Simple linear model provides highly accurate genotypic predictions of HIV-1 drug resistance. Antivir Ther, 9(3):343-52, Jun 2004. [ bib | Abstract ]
[Tzeng2004Predicting] Huey-Ming Tzeng, Jer-Guang Hsieh, and Yih-Lon Lin. Predicting nurses' intention to quit with a support vector machine: a new approach to set up an early warning mechanism in human resource management. Comput Inform Nurs, 22(4):232-42, 2004. [ bib | Abstract ]
[Stahura2004Virtual] Florence L Stahura and Jürgen Bajorath. Virtual screening methods that complement HTS. Comb Chem High Throughput Screen, 7(4):259-69, Jun 2004. [ bib | Abstract ]
[Song2004Comparison] Xiaowei Song, Arnold Mitnitski, Jafna Cox, and Kenneth Rockwood. Comparison of machine learning techniques with classical statistical models in predicting health outcomes. Medinfo, 11(Pt 1):736-40, 2004. [ bib | Abstract ]
[Smith2004Towards] P. A. Smith, M. J. Sorich, L. S C Low, R. A. McKinnon, and J. O. Miners. Towards integrated ADME prediction: past, present and future directions for modelling metabolism by UDP-glucuronosyltransferases. J Mol Graph Model, 22(6):507-17, Jul 2004. [ bib | DOI | http | .pdf | Abstract ]
[Shoeb2004Patient-specific] Ali Shoeb, Herman Edwards, Jack Connolly, Blaise Bourgeois, S. Ted Treves, and John Guttag. Patient-specific seizure onset detection. Epilepsy Behav, 5(4):483-98, Aug 2004. [ bib | DOI | http | .pdf | Abstract ]
[Seeger2004Gaussian] Matthias Seeger. Gaussian processes for machine learning. Int J Neural Syst, 14(2):69-106, Apr 2004. [ bib | Abstract ]
[Roth2004generalized] Volker Roth. The generalized LASSO. IEEE Trans Neural Netw, 15(1):16-28, Jan 2004. [ bib | DOI | http | .pdf | Abstract ]
[Qin2004[Automated] Dong mei Qin, Zhan yi Hu, and Yong heng Zhao. Automated classification of celestial spectra based on support vector machines. Guang Pu Xue Yu Guang Pu Fen Xi, 24(4):507-11, Apr 2004. [ bib | Abstract ]
[Pavlidis2004Support] Paul Pavlidis, Ilan Wapinski, and William Stafford Noble. Support vector machine classification on the web. Bioinformatics, 20(4):586-7, Mar 2004. [ bib | DOI | http | .pdf | Abstract ]
[Passerini2004New] Andrea Passerini, Massimiliano Pontil, and Paolo Frasconi. New results on error correcting output codes of kernel machines. IEEE Trans Neural Netw, 15(1):45-54, Jan 2004. [ bib | Abstract ]
[Madeira2004Biclustering] S. C. Madeira and A. L. Oliveira. Biclustering algorithms for biological data analysis: a survey. IEEE/ACM Trans Comput Biol Bioinform, 1(1):24-45, 2004. [ bib | DOI | http | Abstract ]
[Lin2004Adaptive] Tzu-Chao Lin and Pao-Ta Yu. Adaptive two-pass median filter based on support vector machines for image restoration. Neural Comput, 16(2):332-53, Feb 2004. [ bib | DOI | http | Abstract ]
[Li2004Fusing] Shutao Li, James Tin-Yau Kwok, Ivor Wai-Hung Tsang, and Yaonan Wang. Fusing images with different focuses using support vector machines. IEEE Trans Neural Netw, 15(6):1555-61, Nov 2004. [ bib | Abstract ]
[Lal2004Support] Thomas Navin Lal, Michael Schröder, Thilo Hinterberger, Jason Weston, Martin Bogdan, Niels Birbaumer, and Bernhard Schölkopf. Support vector channel selection in BCI. IEEE Trans Biomed Eng, 51(6):1003-10, Jun 2004. [ bib | Abstract ]
[Kharchenko2004Filling] P. Kharchenko, D. Vitkup, and G. M. Church. Filling gaps in a metabolic network using expression information. Bioinformatics, 20 Suppl 1:I178-I185, Aug 2004. [ bib | DOI | http | Abstract ]
[Kaper2004BCI] Matthias Kaper, Peter Meinicke, Ulf Grossekathoefer, Thomas Lingner, and Helge Ritter. BCI Competition 2003-Data set IIb: support vector machines for the P300 speller paradigm. IEEE Trans Biomed Eng, 51(6):1073-6, Jun 2004. [ bib | Abstract ]
[Graumann2004Applicability] Johannes Graumann, Leslie A Dunipace, Jae Hong Seol, W. Hayes McDonald, John R Yates, Barbara J Wold, and Raymond J Deshaies. Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast. Mol Cell Proteomics, 3(3):226-37, Mar 2004. [ bib | DOI | http | .pdf | Abstract ]
[Glotsos2004Automated] Dimitris Glotsos, Panagiota Spyridonos, Dionisis Cavouras, Panagiota Ravazoula, Petroula-Arampantoni Dadioti, and George Nikiforidis. Automated segmentation of routinely hematoxylin-eosin-stained microscopic images by combining support vector machine clustering and active contour models. Anal Quant Cytol Histol, 26(6):331-40, Dec 2004. [ bib | Abstract ]
[Glenisson2004TXTGate:] P. Glenisson, B. Coessens, S. Van Vooren, J. Mathys, Y. Moreau, and B. De Moor. Txtgate: profiling gene groups with text-based information. Genome Biol, 5(6):R43, 2004. [ bib | DOI | http | Abstract ]
[Faugeras2004Variational] Olivier Faugeras, Geoffray Adde, Guillaume Charpiat, Christophe Chefd'hotel, Maureen Clerc, Thomas Deneux, Rachid Deriche, Gerardo Hermosillo, Renaud Keriven, Pierre Kornprobst, Jan Kybic, Christophe Lenglet, Lucero Lopez-Perez, Théo Papadopoulo, Jean-Philippe Pons, Florent Segonne, Bertrand Thirion, David Tschumperlé, Thierry Viéville, and Nicolas Wotawa. Variational, geometric, and statistical methods for modeling brain anatomy and function. Neuroimage, 23 Suppl 1:S46-55, 2004. [ bib | DOI | http | .pdf | Abstract ]
[Eroes2004Comparison] D. Erös, G. Kéri, I. Kövesdi, C. Szántai-Kis, G. Mészáros, and L. Orfi. Comparison of predictive ability of water solubility QSPR models generated by MLR, PLS and ANN methods. Mini Rev Med Chem, 4(2):167-177, Feb 2004. [ bib | Abstract ]
[Darbellay2004Solid] Georges A Darbellay, Rebecca Duff, Jean-Marc Vesin, Paul-André Despland, Dirk W Droste, Carlos Molina, Joachim Serena, Roman Sztajzel, Patrick Ruchat, Theodoros Karapanayiotides, Afksendyios Kalangos, Julien Bogousslavsky, Erich B Ringelstein, and Gérald Devuyst. Solid or gaseous circulating brain emboli: are they separable by transcranial ultrasound? J Cereb Blood Flow Metab, 24(8):860-8, Aug 2004. [ bib | Abstract ]
[Cohen2004application] Gilles Cohen, Mélanie Hilario, Hugo Sax, Stéphane Hugonnet, Christian Pellegrini, and Antoine Geissbuhler. An application of one-class support vector machine to nosocomial infection detection. Medinfo, 11(Pt 1):716-20, 2004. [ bib | Abstract ]
[Bowd2004Confocal] Christopher Bowd, Linda M Zangwill, Felipe A Medeiros, Jiucang Hao, Kwokleung Chan, Te-Won Lee, Terrence J Sejnowski, Michael H Goldbaum, Pamela A Sample, Jonathan G Crowston, and Robert N Weinreb. Confocal scanning laser ophthalmoscopy classifiers and stereophotograph evaluation for prediction of visual field abnormalities in glaucoma-suspect eyes. Invest Ophthalmol Vis Sci, 45(7):2255-62, Jul 2004. [ bib | DOI | http | .pdf | Abstract ]
[Baumgartner2004Unsupervised] R. Baumgartner, R. Somorjai, C. Bowman, T. C. Sorrell, C. E. Mountford, and U. Himmelreich. Unsupervised feature dimension reduction for classification of MR spectra. Magn Reson Imaging, 22(2):251-6, Feb 2004. [ bib | DOI | http | .pdf | Abstract ]
[Roth2004Bayesian] Volker Roth and Tilman Lange. Bayesian class discovery in microarray datasets. IEEE Trans Biomed Eng, 51(5):707-718, May 2004. [ bib | Abstract ]
[Luo2004gene-silencing] K. Q. Luo and D. C. Chang. The gene-silencing efficiency of siRNA is strongly dependent on the local structure of mRNA at the targeted region. Biochem. Biophys. Res. Commun., 318(1):303-10, May 2004. [ bib | DOI | http | Abstract ]
[Lee2004efficient] Martin M S Lee, S. Sathiya Keerthi, Chong Jin Ong, and Dennis DeCoste. An efficient method for computing leave-one-out error in support vector machines with Gaussian kernels. IEEE Trans Neural Netw, 15(3):750-7, May 2004. [ bib | Abstract ]
[Kim2004Emotion] K. H. Kim, S. W. Bang, and S. R. Kim. Emotion recognition system using short-term monitoring of physiological signals. Med Biol Eng Comput, 42(3):419-27, May 2004. [ bib | Abstract ]
[Kapetanovic2004Overview] Izet M Kapetanovic, Simon Rosenfeld, and Grant Izmirlian. Overview of commonly used bioinformatics methods and their applications. Ann N Y Acad Sci, 1020:10-21, May 2004. [ bib | DOI | http | .pdf | Abstract ]
[Chang2004Analysis] Ming-Wei Chang, Chih-Jen Lin, and Ruby Chiu-Hsing Weng. Analysis of switching dynamics with competing support vector machines. IEEE Trans Neural Netw, 15(3):720-7, May 2004. [ bib | DOI | http | .pdf | Abstract ]
[Zou2005Regularization] H. Zou and T. Hastie. Regularization and variable selection via the Elastic Net. J. R. Stat. Soc. Ser. B, 67:301-320, 2005. [ bib | http | Abstract ]
[Zhang2005MULTIPRED] G. L. Zhang, A. M. Khan, K. N. Srinivasan, J. T. August, and V. Brusic. MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides. Nucleic Acids Res/, 33(Web Server issue):W172-W179, Jul 2005. [ bib | DOI | http | Abstract ]
[Thukral2005Prediction] Sushil K Thukral, Paul J Nordone, Rong Hu, Leah Sullivan, Eric Galambos, Vincent D Fitzpatrick, Laura Healy, Michael B Bass, Mary E Cosenza, and Cynthia A Afshari. Prediction of nephrotoxicant action and identification of candidate toxicity-related biomarkers. Toxicol Pathol, 33(3):343-55, 2005. [ bib | DOI | http | Abstract ]
[Shulman-Peleg2005SiteEngines] Alexandra Shulman-Peleg, Ruth Nussinov, and Haim J Wolfson. Siteengines: recognition and comparison of binding sites and protein-protein interfaces. Nucleic Acids Res, 33(Web Server issue):W337-W341, Jul 2005. [ bib | DOI | http | Abstract ]
[Shen2005[Detection] Li Shen, Jie Yang, and Yue Zhou. Detection of PVCs with support vector machine. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi, 22(1):78-81, Feb 2005. [ bib | Abstract ]
[Shadforth2005Protein] Ian Shadforth, Daniel Crowther, and Conrad Bessant. Protein and peptide identification algorithms using ms for use in high-throughput, automated pipelines. Proteomics, 5(16):4082-4095, Nov 2005. [ bib | DOI | http | Abstract ]
[Sassi2005automated] Alexander P Sassi, Frank Andel, Hans-Marcus L Bitter, Michael P S Brown, Robert G Chapman, Jeraldine Espiritu, Alfred C Greenquist, Isabelle Guyon, Mariana Horchi-Alegre, Kathy L Stults, Ann Wainright, Jonathan C Heller, and John T Stults. An automated, sheathless capillary electrophoresis-mass spectrometry platform for discovery of biomarkers in human serum. Electrophoresis, 26(7-8):1500-12, Apr 2005. [ bib | DOI | http | .pdf | Abstract ]
[Perez-Cruz2005Convergence] Fernando Pérez-Cruz, Carlos Bousoño-Calzón, and Antonio Artés-Rodríguez. Convergence of the IRWLS Procedure to the Support Vector Machine Solution. Neural Comput, 17(1):7-18, Jan 2005. [ bib | Abstract ]
[Prill2005PlosBiol] Robert J Prill, Pablo A Iglesias, and Andre Levchenko. Dynamic properties of network motifs contribute to biological network organization. PLoS Biol, 3(11):e343, Nov 2005. [ bib | DOI | http | Abstract ]
[Peters2005Generating] Bjoern Peters and Alessandro Sette. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics, 6:132, 2005. [ bib | DOI | http | Abstract ]
[Perez-Iratxeta2005] Carolina Perez-Iratxeta, Matthias Wjst, Peer Bork, and Miguel A Andrade. G2d: a tool for mining genes associated with disease. BMC Genet, 6:45, 2005. [ bib | DOI | http | Abstract ]
[Micchelli2005On] Charles A Micchelli and Massimiliano Pontil. On learning vector-valued functions. Neural Comput, 17(1):177-204, Jan 2005. [ bib | DOI | http | Abstract ]
[Mavroforakis2005Significance] Michael Mavroforakis, Harris Georgiou, Nikos Dimitropoulos, Dionisis Cavouras, and Sergios Theodoridis. Significance analysis of qualitative mammographic features, using linear classifiers, neural networks and support vector machines. Eur J Radiol, 54(1):80-9, Apr 2005. [ bib | DOI | http | .pdf | Abstract ]
[BioCyc2005] P. D. Karp, C. A. Ouzounis, C. Moore-Kochlacs, L. Goldovsky, P. Kaipa, D. Ahren, S. Tsoka, N. Darzentas, V. Kunin, and N. Lopez-Bigas. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res, 33(19):6083-9, 2005. [ bib | Abstract ]
[Haasdonk2005Feature] Bernard Haasdonk. Feature space interpretation of SVMs with indefinite kernels. IEEE Trans Pattern Anal Mach Intell, 27(4):482-92, Apr 2005. [ bib | DOI | http | .pdf | Abstract ]
[Golland2005Detection] Polina Golland, W. Eric L Grimson, Martha E Shenton, and Ron Kikinis. Detection and analysis of statistical differences in anatomical shape. Med Image Anal, 9(1):69-86, Feb 2005. [ bib | DOI | http | Abstract ]
[Ehlers2005NBS1] Justis P Ehlers and J. William Harbour. NBS1 expression as a prognostic marker in uveal melanoma. Clin. Cancer Res., 11(5):1849-53, Mar 2005. [ bib | DOI | http | .pdf | Abstract ]
[Doyle2005PlosBiol] John Doyle and Marie Csete. Motifs, control, and stability. PLoS Biol, 3(11):e392, Nov 2005. [ bib | DOI | http ]
[Dong2005Fast] Jian xiong Dong, Adam Krzyzak, and Ching Y Suen. Fast SVM training algorithm with decomposition on very large data sets. IEEE Trans Pattern Anal Mach Intell, 27(4):603-18, Apr 2005. [ bib | Abstract ]
[Ding2005Minimum] Chris Ding and Hanchuan Peng. Minimum redundancy feature selection from microarray gene expression data. J Bioinform Comput Biol, 3(2):185-205, Apr 2005. [ bib | Abstract ]
[Curtis2005] Keira R. Curtis, Matej Oresic, and Antonio Vidal-Puig. Pathways to the analysis of microarray data. Trends in Biotechnology, 23(8):429-435, 2005. [ bib | DOI | http | Abstract ]
[Blaveri2005Bladder] E. Blaveri, J. L. Brewer, R. Roydasgupta, J. Fridlyand, S. DeVries, T. Koppie, S. Pejavar, K. Mehta, P. Carroll, J. P. Simko, and F. M. Waldman. Bladder cancer stage and outcome by array-based comparative genomic hybridization. Clin. Cancer Res., 11(19 Pt 1):7012-7022, Oct 2005. [ bib | DOI | http | Abstract ]
[Bagos2005Evaluation] Pantelis G Bagos, Theodore D Liakopoulos, and Stavros J Hamodrakas. Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method. BMC Bioinformatics, 6(1):7, Jan 2005. [ bib | DOI | http | .pdf | Abstract ]
[Bagga2005Quantitative] Harmohina Bagga, David S Greenfield, and William J Feuer. Quantitative assessment of atypical birefringence images using scanning laser polarimetry with variable corneal compensation. Am J Ophthalmol, 139(3):437-46, Mar 2005. [ bib | DOI | http | .pdf | Abstract ]
[Zhang2006Similarity] Z. Zhang and M.G. Grigorov. Similarity networks of protein binding sites. Proteins, 62(2):470-478, Feb 2006. [ bib | Abstract ]
[Sotiriou2006Gene] Christos Sotiriou, Pratyaksha Wirapati, Sherene Loi, Adrian Harris, Steve Fox, Johanna Smeds, Hans Nordgren, Pierre Farmer, Viviane Praz, Benjamin Haibe-Kains, Christine Desmedt, Denis Larsimont, Fatima Cardoso, Hans Peterse, Dimitry Nuyten, Marc Buyse, Marc J Van de Vijver, Jonas Bergh, Martine Piccart, and Mauro Delorenzi. Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst, 98(4):262-272, Feb 2006. [ bib | DOI | http | Abstract ]
[Salomon2006Predicting] J. Salomon and D. R. Flower. Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores. BMC Bioinformatics, 7:501, 2006. [ bib | DOI | http | Abstract ]
[Salgado2006RegulonDB] H. Salgado, S. Gama-Castro, M. Peralta-Gil, E. Díaz-Peredo, F. Sánchez-Solano, A. Santos-Zavaleta, I. Martínez-Flores, V. Jiménez-Jacinto, C. Bonavides-Martínez, J. Segura-Salazar, A. Martínez-Antonio, and J. Collado-Vides. RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res., 34(Database issue):D394-D397, Jan 2006. [ bib | DOI | http | Abstract ]
[Redon2006Global] Richard Redon, Shumpei Ishikawa, Karen R Fitch, Lars Feuk, George H Perry, T. Daniel Andrews, Heike Fiegler, Michael H Shapero, Andrew R Carson, Wenwei Chen, Eun Kyung Cho, Stephanie Dallaire, Jennifer L Freeman, Juan R González, Mònica Gratacòs, Jing Huang, Dimitrios Kalaitzopoulos, Daisuke Komura, Jeffrey R MacDonald, Christian R Marshall, Rui Mei, Lyndal Montgomery, Kunihiro Nishimura, Kohji Okamura, Fan Shen, Martin J Somerville, Joelle Tchinda, Armand Valsesia, Cara Woodwark, Fengtang Yang, Junjun Zhang, Tatiana Zerjal, Jane Zhang, Lluis Armengol, Donald F Conrad, Xavier Estivill, Chris Tyler-Smith, Nigel P Carter, Hiroyuki Aburatani, Charles Lee, Keith W Jones, Stephen W Scherer, and Matthew E Hurles. Global variation in copy number in the human genome. Nature, 444(7118):444-454, Nov 2006. [ bib | DOI | http | Abstract ]
[Peters2006community] Bjoern Peters, Huynh-Hoa Bui, Sune Frankild, Morten Nielson, Claus Lundegaard, Emrah Kostem, Derek Basch, Kasper Lamberth, Mikkel Harndahl, Ward Fleri, Stephen S Wilson, John Sidney, Ole Lund, Soren Buus, and Alessandro Sette. A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput. Biol., 2(6):e65, Jun 2006. [ bib | DOI | http | Abstract ]
[Oti2006Predicting] M. Oti, B. Snel, M. A. Huynen, and H. G. Brunner. Predicting disease genes using protein-protein interactions. J Med Genet, 43(8):691-698, Aug 2006. [ bib | DOI | http | Abstract ]
[Neuvial2006Spatial] Pierre Neuvial, Philippe Hupé, Isabel Brito, Stéphane Liva, Elodie Manié, Caroline Brennetot, François Radvanyi, Alain Aurias, and Emmanuel Barillot. Spatial normalization of array-cgh data. BMC Bioinformatics, 7:264, 2006. [ bib | DOI | http | Abstract ]
[Mishra2006Human] G.R. Mishra, M. Suresh, K. Kumaran, N. Kannabiran, S. Suresh, P. Bala, K. Shivakumar, N. Anuradha, R. Reddy, T.M. Raghavan, S. Menon, G. Hanumanthu, M. Gupta, S. Upendran, S. Gupta, M. Mahesh, B. Jacob, P. Mathew, P. Chatterjee, K.S. Arun, S. Sharma, K.N. Chandrika, N. Deshpande, K. Palvankar, R. Raghavnath, R. Krishnakanth, H. Karathia, B. Rekha, R. Nayak, G. Vishnupriya, H.G.M. Kumar, M. Nagini, G.S.S. Kumar, R. Jose, P. Deepthi, S.S. Mohan, GandhiT.K.B., H.C. Harsha, K.S. Deshpande, M. Sarker, T.S.K. Prasad, and A. Pandey. Human protein reference database-2006 update. Nucleic Acids Res, 34(Database issue):D411-D414, Jan 2006. [ bib | DOI | http | Abstract ]
[Kubinyi2006Chemogenomics] H. Kubinyi. Chemogenomics in drug discovery. Ernst Schering Res Found Workshop, 58:1-19, 2006. [ bib | Abstract ]
[Kapp2006Discovery] Amy V Kapp, Stefanie S Jeffrey, Anita Langerød, Anne-Lise Børresen-Dale, Wonshik Han, Dong-Young Noh, Ida R K Bukholm, Monica Nicolau, Patrick O Brown, and Robert Tibshirani. Discovery and validation of breast cancer subtypes. BMC Genomics, 7:231, 2006. [ bib | DOI | http | Abstract ]
[Hu2006molecular] Zhiyuan Hu, Cheng Fan, Daniel S Oh, J. S. Marron, Xiaping He, Bahjat F Qaqish, Chad Livasy, Lisa A Carey, Evangeline Reynolds, Lynn Dressler, Andrew Nobel, Joel Parker, Matthew G Ewend, Lynda R Sawyer, Junyuan Wu, Yudong Liu, Rita Nanda, Maria Tretiakova, Alejandra Ruiz Orrico, Donna Dreher, Juan P Palazzo, Laurent Perreard, Edward Nelson, Mary Mone, Heidi Hansen, Michael Mullins, John F Quackenbush, Matthew J Ellis, Olufunmilayo I Olopade, Philip S Bernard, and Charles M Perou. The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics, 7:96, 2006. [ bib | DOI | http | Abstract ]
[Garnis2006High] C. Garnis, W. W. Lockwood, E. Vucic, Y. Ge, L. Girard, J. D. Minna, A. F. Gazdar, S. Lam, C. MacAulay, and W. L. Lam. High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH. Int. J. Cancer, 118(6):1556-1564, 2006. [ bib | DOI | http | Abstract ]
[Citri2006MolCelBiol] Ami Citri and Yosef Yarden. Egf-erbb signalling: towards the systems level. Nat Rev Mol Cell Biol, 7(7):505-516, Jul 2006. [ bib | DOI | http | Abstract ]
[Bulyk2006DNA] Martha L Bulyk. DNA microarray technologies for measuring protein-DNA interactions. Curr Opin Biotechnol, 17(4):422-430, Aug 2006. [ bib | DOI | http | Abstract ]
[Bui2006Structural] H.-H. Bui, A. J. Schiewe, H. von Grafenstein, and I. S. Haworth. Structural prediction of peptides binding to MHC class I molecules. Proteins, 63(1):43-52, Apr 2006. [ bib | DOI | http | Abstract ]
[Bhavani2006Substructure-based] S. Bhavani, A. Nagargadde, A. Thawani, V. Sridhar, and N. Chandra. Substructure-based support vector machine classifiers for prediction of adverse effects in diverse classes of drugs. J. Chem. Inform. Model., 46(6):2478-2486, 2006. [ bib | DOI | http | Abstract ]
[Driel2006text-mining] M.A. van Driel, J. Bruggeman, G. Vriend, H.G. Brunner, and J.A.M. Leunissen. A text-mining analysis of the human phenome. Eur. J. Hum. Genet., 14(5):535-542, May 2006. [ bib | DOI | http | Abstract ]
[Simonis2007evaluation] Marieke Simonis, Jurgen Kooren, and Wouter de Laat. An evaluation of 3c-based methods to capture dna interactions. Nat Methods, 4(11):895-901, Nov 2007. [ bib | DOI | http | Abstract ]
[Sebat2007Major] Jonathan Sebat. Major changes in our dna lead to major changes in our thinking. Nat. Genet., 39(7 Suppl):S3-S5, Jul 2007. [ bib | DOI | http | Abstract ]
[Rhodes2007Oncomine] Daniel R. Rhodes, Shanker Kalyana-Sundaram, Vasudeva Mahavisno, Radhika Varambally, Jianjun Yu, Benjamin B. Briggs, Terrence R. Barrette, Matthew J. Anstet, Colleen Kincead-Beal, Prakash Kulkarni, Sooryanaryana Varambally, Debashis Ghosh, and Arul M. Chinnaiyan. Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia, 9(2):166-180, Feb 2007. [ bib | Abstract ]
[Perry2007Diet] George H Perry, Nathaniel J Dominy, Katrina G Claw, Arthur S Lee, Heike Fiegler, Richard Redon, John Werner, Fernando A Villanea, Joanna L Mountain, Rajeev Misra, Nigel P Carter, Charles Lee, and Anne C Stone. Diet and the evolution of human amylase gene copy number variation. Nat Genet, 39(10):1256-1260, Oct 2007. [ bib | DOI | http | Abstract ]
[Paik2007Development] Soonmyung Paik. Development and clinical utility of a 21-gene recurrence score prognostic assay in patients with early breast cancer treated with tamoxifen. Oncologist, 12(6):631-635, Jun 2007. [ bib | DOI | http | Abstract ]
[Morris2007Identification] Stephanie A Morris, Bhargavi Rao, Benjamin A Garcia, Sandra B Hake, Robert L Diaz, Jeffrey Shabanowitz, Donald F Hunt, C. David Allis, Jason D Lieb, and Brian D Strahl. Identification of histone h3 lysine 36 acetylation as a highly conserved histone modification. J Biol Chem, 282(10):7632-7640, Mar 2007. [ bib | DOI | http | Abstract ]
[McKusick2007Mendelian] V.A. McKusick. Mendelian inheritance in man and its online version, omim. Am. J. Hum. Genet., 80(4):588-604, Apr 2007. [ bib | DOI | http ]
[Levy2007Diploid] Samuel Levy, Granger Sutton, Pauline C Ng, Lars Feuk, Aaron L Halpern, Brian P Walenz, Nelson Axelrod, Jiaqi Huang, Ewen F Kirkness, Gennady Denisov, Yuan Lin, Jeffrey R MacDonald, Andy Wing Chun Pang, Mary Shago, Timothy B Stockwell, Alexia Tsiamouri, Vineet Bafna, Vikas Bansal, Saul A Kravitz, Dana A Busam, Karen Y Beeson, Tina C McIntosh, Karin A Remington, Josep F Abril, John Gill, Jon Borman, Yu-Hui Rogers, Marvin E Frazier, Stephen W Scherer, Robert L Strausberg, and J. Craig Venter. The diploid genome sequence of an individual human. PLoS Biol, 5(10):e254, Sep 2007. [ bib | DOI | http | Abstract ]
[Dostie2007Chromosome] Josée Dostie, Ye Zhan, and Job Dekker. Chromosome conformation capture carbon copy technology. Curr Protoc Mol Biol, Chapter 21:Unit 21.14, Oct 2007. [ bib | DOI | http | Abstract ]
[Calvo2007partially] B. Calvo, N. López-Bigas, S.J. Furney, P. Larrañaga, and J.A. Lozano. A partially supervised classification approach to dominant and recessive human disease gene prediction. Comput. Methods Programs Biomed., 85(3):229-237, Mar 2007. [ bib | DOI | http | Abstract ]
[Wu2008Network-based] X. Wu, R. Jiang, M.Q. Zhang, and S. Li. Network-based global inference of human disease genes. Mol. Syst. Biol., 4:189, 2008. [ bib | DOI | http | Abstract ]
[Wheeler2008Complete] David A Wheeler, Maithreyan Srinivasan, Michael Egholm, Yufeng Shen, Lei Chen, Amy McGuire, Wen He, Yi-Ju Chen, Vinod Makhijani, G. Thomas Roth, Xavier Gomes, Karrie Tartaro, Faheem Niazi, Cynthia L Turcotte, Gerard P Irzyk, James R Lupski, Craig Chinault, Xing zhi Song, Yue Liu, Ye Yuan, Lynne Nazareth, Xiang Qin, Donna M Muzny, Marcel Margulies, George M Weinstock, Richard A Gibbs, and Jonathan M Rothberg. The complete genome of an individual by massively parallel dna sequencing. Nature, 452(7189):872-876, Apr 2008. [ bib | DOI | http | Abstract ]
[Wadman2008James] Meredith Wadman. James watson's genome sequenced at high speed. Nature, 452(7189):788, Apr 2008. [ bib | DOI | http ]
[Waaijenborg2008Quantifying] S. Waaijenborg, P. C. Verselewel de Witt Hamer, and A. H. Zwinderman. Quantifying the association between gene expressions and dna-markers by penalized canonical correlation analysis. Stat Appl Genet Mol Biol, 7(1):Article3, 2008. [ bib | DOI | http | Abstract ]
[Oti2008Conserved] M. Oti, J. van Reeuwijk, M.A. Huynen, and H.G. Brunner. Conserved co-expression for candidate disease gene prioritization. BMC Bioinformatics, 9:208, 2008. [ bib | DOI | http | Abstract ]
[Leclerc2008Survival] R.D. Leclerc. Survival of the sparsest: robust gene networks are parsimonious. Mol Syst Biol, 4:213, 2008. [ bib | DOI | http | Abstract ]
[Kohler2008Walking] S. Köhler, S. Bauer, D. Horn, and P.N. Robinson. Walking the interactome for prioritization of candidate disease genes. Am. J. Hum. Genet., 82(4):949-958, Apr 2008. [ bib | DOI | http | Abstract ]
[Harris2008Single-molecule] Timothy D Harris, Phillip R Buzby, Hazen Babcock, Eric Beer, Jayson Bowers, Ido Braslavsky, Marie Causey, Jennifer Colonell, James Dimeo, J. William Efcavitch, Eldar Giladi, Jaime Gill, John Healy, Mirna Jarosz, Dan Lapen, Keith Moulton, Stephen R Quake, Kathleen Steinmann, Edward Thayer, Anastasia Tyurina, Rebecca Ward, Howard Weiss, and Zheng Xie. Single-molecule dna sequencing of a viral genome. Science, 320(5872):106-109, Apr 2008. [ bib | DOI | http | Abstract ]
[Goendoer2008High-resolution] Anita Göndör, Carole Rougier, and Rolf Ohlsson. High-resolution circular chromosome conformation capture assay. Nat Protoc, 3(2):303-313, 2008. [ bib | DOI | http | Abstract ]
[Ala2008Prediction] U. Ala, R.M. Piro, E. Grassi, C. Damasco, L. Silengo, M. Oti, P. Provero, and F. Di Cunto. Prediction of human disease genes by human-mouse conserved coexpression analysis. PLoS Comput. Biol., 4(3):e1000043, Mar 2008. [ bib | DOI | http | Abstract ]
[Xie2009Unified] Lei Xie, Li Xie, and Philip E Bourne. A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. Bioinformatics, 25(12):i305-i312, Jun 2009. [ bib | DOI | http | Abstract ]
[Sutherland2009Transcription] Heidi Sutherland and Wendy A Bickmore. Transcription factories: gene expression in unions? Nat Rev Genet, 10(7):457-466, Jul 2009. [ bib | DOI | http | Abstract ]
[Praz2009CleanEx:] Viviane Praz and Philipp Bucher. Cleanex: new data extraction and merging tools based on mesh term annotation. Nucleic Acids Res, 37(Database issue):D880-D884, Jan 2009. [ bib | DOI | http | Abstract ]
[Popova2009Genome] Tatiana Popova, Elodie Manié, Dominique Stoppa-Lyonnet, Guillem Rigaill, Emmanuel Barillot, and Marc Henri Stern. Genome alteration print (gap): a tool to visualize and mine complex cancer genomic profiles obtained by snp arrays. Genome Biol, 10(11):R128, 2009. [ bib | DOI | http | Abstract ]
[Park2009ChIP] Peter J Park. Chip-seq: advantages and challenges of a maturing technology. Nat Rev Genet, 10(10):669-680, Oct 2009. [ bib | DOI | http | Abstract ]
[Marbach2009Replaying] D. Marbach, C. Mattiussi, and D. Floreano. Replaying the evolutionary tape: biomimetic reverse engineering of gene networks. Ann N Y Acad Sci, 1158:234-245, Mar 2009. [ bib | DOI | http | Abstract ]
[Lima-Mendez2009powerful] G. Lima-Mendez and J. van Helden. The powerful law of the power law and other myths in network biology. Mol Biosyst, 5(12):1482-1493, Dec 2009. [ bib | DOI | http | Abstract ]
[Ioannidis2009Repeatability] John P A Ioannidis, David B Allison, Catherine A Ball, Issa Coulibaly, Xiangqin Cui, Aedín C Culhane, Mario Falchi, Cesare Furlanello, Laurence Game, Giuseppe Jurman, Jon Mangion, Tapan Mehta, Michael Nitzberg, Grier P Page, Enrico Petretto, and Vera van Noort. Repeatability of published microarray gene expression analyses. Nat Genet, 41(2):149-155, Feb 2009. [ bib | DOI | http | Abstract ]
[Goendoer2009Chromosome] Anita Göndör and Rolf Ohlsson. Chromosome crosstalk in three dimensions. Nature, 461(7261):212-217, Sep 2009. [ bib | DOI | http | Abstract ]
[Fullwood2009oestrogen-receptor-alpha-bound] Melissa J Fullwood, Mei Hui Liu, You Fu Pan, Jun Liu, Han Xu, Yusoff Bin Mohamed, Yuriy L Orlov, Stoyan Velkov, Andrea Ho, Poh Huay Mei, Elaine G Y Chew, Phillips Yao Hui Huang, Willem-Jan Welboren, Yuyuan Han, Hong Sain Ooi, Pramila N Ariyaratne, Vinsensius B Vega, Yanquan Luo, Peck Yean Tan, Pei Ye Choy, K. D Senali Abayratna Wansa, Bing Zhao, Kar Sian Lim, Shi Chi Leow, Jit Sin Yow, Roy Joseph, Haixia Li, Kartiki V Desai, Jane S Thomsen, Yew Kok Lee, R. Krishna Murthy Karuturi, Thoreau Herve, Guillaume Bourque, Hendrik G Stunnenberg, Xiaoan Ruan, Valere Cacheux-Rataboul, Wing-Kin Sung, Edison T Liu, Chia-Lin Wei, Edwin Cheung, and Yijun Ruan. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature, 462(7269):58-64, Nov 2009. [ bib | DOI | http | Abstract ]
[Eid2009Real] John Eid, Adrian Fehr, Jeremy Gray, Khai Luong, John Lyle, Geoff Otto, Paul Peluso, David Rank, Primo Baybayan, Brad Bettman, Arkadiusz Bibillo, Keith Bjornson, Bidhan Chaudhuri, Frederick Christians, Ronald Cicero, Sonya Clark, Ravindra Dalal, Alex Dewinter, John Dixon, Mathieu Foquet, Alfred Gaertner, Paul Hardenbol, Cheryl Heiner, Kevin Hester, David Holden, Gregory Kearns, Xiangxu Kong, Ronald Kuse, Yves Lacroix, Steven Lin, Paul Lundquist, Congcong Ma, Patrick Marks, Mark Maxham, Devon Murphy, Insil Park, Thang Pham, Michael Phillips, Joy Roy, Robert Sebra, Gene Shen, Jon Sorenson, Austin Tomaney, Kevin Travers, Mark Trulson, John Vieceli, Jeffrey Wegener, Dawn Wu, Alicia Yang, Denis Zaccarin, Peter Zhao, Frank Zhong, Jonas Korlach, and Stephen Turner. Real-time dna sequencing from single polymerase molecules. Science, 323(5910):133-138, Jan 2009. [ bib | DOI | http | Abstract ]
[Bengtsson2009Single] Henrik Bengtsson, Pratyaksha Wirapati, and Terence P Speed. A single-array preprocessing method for estimating full-resolution raw copy numbers from all affymetrix genotyping arrays including genomewidesnp 5 & 6. Bioinformatics, 25(17):2149-2156, Sep 2009. [ bib | DOI | http | Abstract ]
[Tayrac2009Simultaneous] M. de Tayrac, S. Lê, M. Aubry, J. Mosser, and F. Husson. Simultaneous analysis of distinct omics data sets with integration of biological knowledge: Multiple factor analysis approach. BMC Genomics, 10:32, 2009. [ bib | DOI | http | Abstract ]
[Wallace2010Identification] Emma V B Wallace, David Stoddart, Andrew J Heron, Ellina Mikhailova, Giovanni Maglia, Timothy J Donohoe, and Hagan Bayley. Identification of epigenetic dna modifications with a protein nanopore. Chem Commun (Camb), 46(43):8195-8197, Nov 2010. [ bib | DOI | http | Abstract ]
[Vanunu2010Associating] O. Vanunu, O. Magger, E. Ruppin, T. Shlomi, and R. Sharan. Associating genes and protein complexes with disease via network propagation. PLoS Comput. Biol., 6(1):e1000641, Jan 2010. [ bib | DOI | http | Abstract ]
[Taby2010Cancer] Rodolphe Taby and Jean-Pierre J Issa. Cancer epigenetics. CA Cancer J Clin, 60(6):376-392, 2010. [ bib | DOI | http | Abstract ]
[Soneson2010Integrative] Charlotte Soneson, Henrik Lilljebjörn, Thoas Fioretos, and Magnus Fontes. Integrative analysis of gene expression and copy number alterations using canonical correlation analysis. BMC Bioinformatics, 11:191, 2010. [ bib | DOI | http | Abstract ]
[Shoval2010Cell] Oren Shoval and Uri Alon. Snapshot: network motifs. Cell, 143(2):326-3e1, Oct 2010. [ bib | DOI | http ]
[Shi2010MicroArray] Leming Shi, Gregory Campbell, Wendell D Jones, Fabien Campagne, Zhining Wen, Stephen J Walker, Zhenqiang Su, Tzu-Ming Chu, Federico M Goodsaid, Lajos Pusztai, John D Shaughnessy, André Oberthuer, Russell S Thomas, Richard S Paules, Mark Fielden, Bart Barlogie, Weijie Chen, Pan Du, Matthias Fischer, Cesare Furlanello, Brandon D Gallas, Xijin Ge, Dalila B Megherbi, W. Fraser Symmans, May D Wang, John Zhang, Hans Bitter, Benedikt Brors, Pierre R Bushel, Max Bylesjo, Minjun Chen, Jie Cheng, Jing Cheng, Jeff Chou, Timothy S Davison, Mauro Delorenzi, Youping Deng, Viswanath Devanarayan, David J Dix, Joaquin Dopazo, Kevin C Dorff, Fathi Elloumi, Jianqing Fan, Shicai Fan, Xiaohui Fan, Hong Fang, Nina Gonzaludo, Kenneth R Hess, Huixiao Hong, Jun Huan, Rafael A Irizarry, Richard Judson, Dilafruz Juraeva, Samir Lababidi, Christophe G Lambert, Li Li, Yanen Li, Zhen Li, Simon M Lin, Guozhen Liu, Edward K Lobenhofer, Jun Luo, Wen Luo, Matthew N McCall, Yuri Nikolsky, Gene A Pennello, Roger G Perkins, Reena Philip, Vlad Popovici, Nathan D Price, Feng Qian, Andreas Scherer, Tieliu Shi, Weiwei Shi, Jaeyun Sung, Danielle Thierry-Mieg, Jean Thierry-Mieg, Venkata Thodima, Johan Trygg, Lakshmi Vishnuvajjala, Sue Jane Wang, Jianping Wu, Yichao Wu, Qian Xie, Waleed A Yousef, Liang Zhang, Xuegong Zhang, Sheng Zhong, Yiming Zhou, Sheng Zhu, Dhivya Arasappan, Wenjun Bao, Anne Bergstrom Lucas, Frank Berthold, Richard J Brennan, Andreas Buness, Jennifer G Catalano, Chang Chang, Rong Chen, Yiyu Cheng, Jian Cui, Wendy Czika, Francesca Demichelis, Xutao Deng, Damir Dosymbekov, Roland Eils, Yang Feng, Jennifer Fostel, Stephanie Fulmer-Smentek, James C Fuscoe, Laurent Gatto, Weigong Ge, Darlene R Goldstein, Li Guo, Donald N Halbert, Jing Han, Stephen C Harris, Christos Hatzis, Damir Herman, Jianping Huang, Roderick V Jensen, Rui Jiang, Charles D Johnson, Giuseppe Jurman, Yvonne Kahlert, Sadik A Khuder, Matthias Kohl, Jianying Li, Li Li, Menglong Li, Quan-Zhen Li, Shao Li, Zhiguang Li, Jie Liu, Ying Liu, Zhichao Liu, Lu Meng, Manuel Madera, Francisco Martinez-Murillo, Ignacio Medina, Joseph Meehan, Kelci Miclaus, Richard A Moffitt, David Montaner, Piali Mukherjee, George J Mulligan, Padraic Neville, Tatiana Nikolskaya, Baitang Ning, Grier P Page, Joel Parker, R. Mitchell Parry, Xuejun Peng, Ron L Peterson, John H Phan, Brian Quanz, Yi Ren, Samantha Riccadonna, Alan H Roter, Frank W Samuelson, Martin M Schumacher, Joseph D Shambaugh, Qiang Shi, Richard Shippy, Shengzhu Si, Aaron Smalter, Christos Sotiriou, Mat Soukup, Frank Staedtler, Guido Steiner, Todd H Stokes, Qinglan Sun, Pei-Yi Tan, Rong Tang, Zivana Tezak, Brett Thorn, Marina Tsyganova, Yaron Turpaz, Silvia C Vega, Roberto Visintainer, Juergen von Frese, Charles Wang, Eric Wang, Junwei Wang, Wei Wang, Frank Westermann, James C Willey, Matthew Woods, Shujian Wu, Nianqing Xiao, Joshua Xu, Lei Xu, Lun Yang, Xiao Zeng, Jialu Zhang, Li Zhang, Min Zhang, Chen Zhao, Raj K Puri, Uwe Scherf, Weida Tong, Russell D Wolfinger, and M. A. Q. C. Consortium. The microarray quality control (maqc)-ii study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol, 28(8):827-838, Aug 2010. [ bib | Abstract ]
[Portela2010Epigenetic] Anna Portela and Manel Esteller. Epigenetic modifications and human disease. Nat Biotechnol, 28(10):1057-1068, Oct 2010. [ bib | DOI | http | Abstract ]
[Markowetz2010How] Florian Markowetz. How to understand the cell by breaking it: network analysis of gene perturbation screens. PLoS Comput Biol, 6(2):e1000655, 2010. [ bib | DOI | http ]
[Jovanovic2010epigenetics] Jovana Jovanovic, Jo Anders Rønneberg, Jörg Tost, and Vessela Kristensen. The epigenetics of breast cancer. Mol Oncol, 4(3):242-254, Jun 2010. [ bib | DOI | http | Abstract ]
[Gibney2010Epigenetics] E. R. Gibney and C. M. Nolan. Epigenetics and gene expression. Heredity, 105(1):4-13, Jul 2010. [ bib | DOI | http | Abstract ]
[Gehlenborg2010Visualization] Nils Gehlenborg, Seán I O'Donoghue, Nitin S Baliga, Alexander Goesmann, Matthew A Hibbs, Hiroaki Kitano, Oliver Kohlbacher, Heiko Neuweger, Reinhard Schneider, Dan Tenenbaum, and Anne-Claude Gavin. Visualization of omics data for systems biology. Nat Methods, 7(3 Suppl):S56-S68, Mar 2010. [ bib | DOI | http | Abstract ]
[Flusberg2010Direct] Benjamin A Flusberg, Dale R Webster, Jessica H Lee, Kevin J Travers, Eric C Olivares, Tyson A Clark, Jonas Korlach, and Stephen W Turner. Direct detection of dna methylation during single-molecule, real-time sequencing. Nat Methods, 7(6):461-465, Jun 2010. [ bib | DOI | http | Abstract ]
[Cook2010model] Peter R Cook. A model for all genomes: the role of transcription factories. J Mol Biol, 395(1):1-10, Jan 2010. [ bib | DOI | http | Abstract ]
[Bullard2010Evaluation] J. H. Bullard, E. Purdom, K. D. Hansen, and S. Dudoit. Evaluation of statistical methods for normalization and differential expression in mrna-seq experiments. BMC Bioinformatics, 11:94, 2010. [ bib | DOI | http | Abstract ]
[Aranda2010IntAct] B. Aranda, P. Achuthan, Y. Alam-Faruque, I. Armean, A. Bridge, C. Derow, M. Feuermann, A. T. Ghanbarian, S. Kerrien, J. Khadake, J. Kerssemakers, C. Leroy, M. Menden, M. Michaut, L. Montecchi-Palazzi, S. N. Neuhauser, S. Orchard, V. Perreau, B. Roechert, K. van Eijk, and H. Hermjakob. The intact molecular interaction database in 2010. Nucleic Acids Res, 38(Database issue):D525-D531, Jan 2010. [ bib | DOI | http | Abstract ]
[Consortium2010map] 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature, 467(7319):1061-1073, Oct 2010. [ bib | DOI | http | Abstract ]
[Barash2010Deciphering] Yoseph Barash, John A Calarco, Weijun Gao, Qun Pan, Xinchen Wang, Ofer Shai, Benjamin J Blencowe, and Brendan J Frey. Deciphering the splicing code. Nature, 465(7294):53-59, May 2010. [ bib | DOI | http | Abstract ]
[Tubio2011Cancer:] Jose M C Tubio and Xavier Estivill. Cancer: When catastrophe strikes a cell. Nature, 470(7335):476-477, Feb 2011. [ bib | DOI | http ]
[Stephens2011Massive] Philip J Stephens, Chris D Greenman, Beiyuan Fu, Fengtang Yang, Graham R Bignell, Laura J Mudie, Erin D Pleasance, King Wai Lau, David Beare, Lucy A Stebbings, Stuart McLaren, Meng-Lay Lin, David J McBride, Ignacio Varela, Serena Nik-Zainal, Catherine Leroy, Mingming Jia, Andrew Menzies, Adam P Butler, Jon W Teague, Michael A Quail, John Burton, Harold Swerdlow, Nigel P Carter, Laura A Morsberger, Christine Iacobuzio-Donahue, George A Follows, Anthony R Green, Adrienne M Flanagan, Michael R Stratton, P. Andrew Futreal, and Peter J Campbell. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell, 144(1):27-40, Jan 2011. [ bib | DOI | http | Abstract ]
[Rodriguez-Paredes2011Cancer] Manuel Rodríguez-Paredes and Manel Esteller. Cancer epigenetics reaches mainstream oncology. Nat Med, 17(3):330-339, Mar 2011. [ bib | DOI | http | Abstract ]

This file was generated by bibtex2html 1.97.