| At line 3 changed one line |
| * Altman, R.B. A Probabilistic Approach to Determining Biological Structure: Integrating Uncertain Data Sources. Int. J. Human-Computer Studies, 42, pp. 593-616, 1995. |
| * Altman, R.B. A Probabilistic Approach to Determining Biological Structure: Integrating Uncertain Data Sources. Int. J. Human-Computer Studies, 42, pp. 593-616, 1995. [getPDF |altman1995.pdf] |
| At line 5 changed one line |
| * Altschul, S.F. Amino Acid Substitution Matrices from an Information Theoretic Perspective. J. Mol. Bio. , 219, pp. 555-565, 1991. |
| * Altschul, S.F. Amino Acid Substitution Matrices from an Information Theoretic Perspective. J. Mol. Bio. , 219, pp. 555-565, 1991. [getPDF |altschul1991.pdf] |
| At line 7 changed one line |
| * Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. Basic Local Alignment Search Tool. J. Mol. Biol., 215, pp. 403-410, 1990. |
| * Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. Basic Local Alignment Search Tool. J. Mol. Biol., 215, pp. 403-410, 1990. [getPDF |altschuletal1990.pdf] |
| At line 9 changed one line |
| * Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs. Nucleic Acids Research, 25(17), pp. 3389-3402, 1997., pp. 698-700, 1987. |
| * Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs. Nucleic Acids Research, 25(17), pp. 3389-3402, 1997., pp. 698-700, 1987. [getPDF |altschuletal1997.pdf] |
| At line 11 changed one line |
| * Bagley, S.C. and Altman, R.B. Characterizing the Microenvironment Surrounding Protein Sites. Protein Science, 4, pp. 622 -635, 1995. |
| * Bagley, S.C. and Altman, R.B. Characterizing the Microenvironment Surrounding Protein Sites. Protein Science, 4, pp. 622 -635, 1995. [getPDF | bagleyandaltman1995.pdf] |
| At line 13 changed one line |
| * Bork, P., Dandekar, T., Diaz -Lazcoz, Y., Eisenhaber, F., Huynen, M., and Yuan, Y. Predicting Function: From Genes to Genomes and Back. J. Mol. Biol., 283, pp. 707-725, 1998. |
| * Bork, P., Dandekar, T., Diaz -Lazcoz, Y., Eisenhaber, F., Huynen, M., and Yuan, Y. Predicting Function: From Genes to Genomes and Back. J. Mol. Biol., 283, pp. 707-725, 1998. [getPDF | borketal1998.pdf] |
| At line 15 changed one line |
| * Bowie, J.U., Luthy, R., and Eisenberg, D. A Method to Identify Protein Sequences that Fold into a Known Three-Dimensional Structure. Science, 253, pp. 164 -170, 1991. |
| * Bowie, J.U., Luthy, R., and Eisenberg, D. A Method to Identify Protein Sequences that Fold into a Known Three-Dimensional Structure. Science, 253, pp. 164 -170, 1991. [getPDF | bowieetal1991.pdf] |
| At line 17 changed one line |
| * Brown, M.P.S., Grundy, W.N., Lin, D., Cristianini, N., Sugent, C.W., Furey, T.S., Ares Jr., M., and Haussler, D. Knowledge-based Analysis of Microarray Gene Expression Data by Using Support Vector Machines. PNAS, 97(1), pp. 262-267, 2000. |
| * Brown, M.P.S., Grundy, W.N., Lin, D., Cristianini, N., Sugent, C.W., Furey, T.S., Ares Jr., M., and Haussler, D. Knowledge-based Analysis of Microarray Gene Expression Data by Using Support Vector Machines. PNAS, 97(1), pp. 262-267, 2000. [getPDF | brownetal2000.pdf] |
| At line 19 changed one line |
| * Bryant, S.H. and Altschul, S.F. Statistics of Sequence-structure Threading. Current Opinion in Structural Biology, 5, pp. 236-244, 1995. |
| * Bryant, S.H. and Altschul, S.F. Statistics of Sequence-structure Threading. Current Opinion in Structural Biology, 5, pp. 236-244, 1995. [getPDF | bryantandaltschul1995.pdf] |
| At line 21 changed one line |
| * Burge, C. and Karlin, S. Prediction of Complete Gene Structures in Human Genomic DNA. J. Mol. Biol., 268, pp. 78-94, 1997. |
| * Burge, C. and Karlin, S. Prediction of Complete Gene Structures in Human Genomic DNA. J. Mol. Biol., 268, pp. 78-94, 1997. [getPDF | burgeandkarlin1997.pdf] |
| At line 23 changed one line |
| * Dayhoff, M.O., Schwartz, R.M., and Orcutt, B.C. A Model of Evolutionary Change in Proteins. Atlas of Protein Sequence and Structure, v. 5 suppl. 3, pp. 345-352, 1978. |
| * Dayhoff, M.O., Schwartz, R.M., and Orcutt, B.C. A Model of Evolutionary Change in Proteins. Atlas of Protein Sequence and Structure, v. 5 suppl. 3, pp. 345-352, 1978. [getPDF | dayhoffetal1978.pdf] |
| At line 25 changed one line |
| * Doolittle, R.F., Feng, D-F, Tsang, S., Cho, G., and Little, E. Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock. Science, 271, pp. 470-477, 1996. |
| * Doolittle, R.F., Feng, D-F, Tsang, S., Cho, G., and Little, E. Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock. Science, 271, pp. 470-477, 1996. [getPDF | doolittleetal1996.pdf] |
| At line 27 changed 2 lines |
| * Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. Cluster Analysis and Display of |
| Genome-wide Expression Patterns. Proc. Natl. Acad. Sci. USA, 95, pp. 12863-14868, 1998. |
| * Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. Cluster Analysis and Display of Genome-wide Expression Patterns. Proc. Natl. Acad. Sci. USA, 95, pp. 12863-14868, 1998. [getPDF | eisenetal1998.pdf] |
| At line 30 changed one line |
| * Gerstein, M. and Levitt, M. Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures. Proc. of ISMB-96, pp. 59-67, 1996. |
| * Gerstein, M. and Levitt, M. Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures. Proc. of ISMB-96, pp. 59-67, 1996. [getPDF | gersteinandlevitt1996.pdf] |
| At line 32 changed 2 lines |
| * Gotoh, O. An Improved Algorithm for Matching Biological Sequences. J. Mol. Biol., 162, pp. |
| 705-708, 1982. |
| * Gotoh, O. An Improved Algorithm for Matching Biological Sequences. J. Mol. Biol., 162, pp. 705-708, 1982. [getPDF | gotoh1982.pdf] |
| At line 35 changed one line |
| * Gribskov, M., McLachlan, A.D., and Eisenberg, D. Prot ein Analysis: Detection of Distantly Related Proteins. Proc. Natl. Acad. Sci. USA, 84, pp. 4355-4358, 1987. |
| * Gribskov, M., McLachlan, A.D., and Eisenberg, D. Prot ein Analysis: Detection of Distantly Related Proteins. Proc. Natl. Acad. Sci. USA, 84, pp. 4355-4358, 1987. [getPDF | gribshovetal1987.pdf] |
| At line 37 changed 2 lines |
| * Gribskov, M. and Devereux, J. Dynamic Programming Methods. In Sequence Analysis Primer. |
| W.H. Freeman and Company, NY, pp. 123 -137, 1994. |
| * Gribskov, M. and Devereux, J. Dynamic Programming Methods. In Sequence Analysis Primer. W.H. Freeman and Company, NY, pp. 123 -137, 1994. [getPDF | gribskovanddevereux1994.pdf] |
| At line 40 changed one line |
| * Henikoff, S. and Henikoff, Jorja G. Amino Acid Substitution Matrices from Protein Blocks. Proc. Natl. Acad. Sci. USA, 89, pp. 10915-10919, 1992. |
| * Henikoff, S. and Henikoff, Jorja G. Amino Acid Substitution Matrices from Protein Blocks. Proc. Natl. Acad. Sci. USA, 89, pp. 10915-10919, 1992. [getPDF | henikoffandhenikoff1992.pdf] |
| At line 42 changed one line |
| * Karlin, S. and Altshcul, S.F. Methods for Assessing the Statistical Significance of Molecular Sequence Features by Using General Scoring Schemes. Proc. Natl. Acad. Sci. USA, 87, pp. 2264-2268, 1990. |
| * Karlin, S. and Altshcul, S.F. Methods for Assessing the Statistical Significance of Molecular Sequence Features by Using General Scoring Schemes. Proc. Natl. Acad. Sci. USA, 87, pp. 2264-2268, 1990. [getPDF | karlinandatlschul1990.pdf] |
| At line 44 changed 2 lines |
| * Karp, P.D. and Riley, M. EcoCyc: The Resource and the Lessons Learned. SRI Report, January |
| 21, 1999. |
| * Karp, P.D. and Riley, M. EcoCyc: The Resource and the Lessons Learned. SRI Report, January 21, 1999. [getPDF | karpandriley1999.pdf] |
| At line 47 changed one line |
| * Koza, J.R. Evolution of a Computer Program for Classifying Protein Segments as Transmembrane Domains Using Genetic Programming. Proc. of ISMB-94, pp. 244-252, 1994. |
| * Koza, J.R. Evolution of a Computer Program for Classifying Protein Segments as Transmembrane Domains Using Genetic Programming. Proc. of ISMB-94, pp. 244-252, 1994. [getPDF | koza1994.pdf] |
| At line 49 changed 2 lines |
| * Krogh, A., Brown, M., Mian, I.S., Sjolander, K., and Haussler, D. Hidden Markov Models in |
| Computational Biology. J. Mol. Biol., 235. pp. 1501-1531, 1994. |
| * Krogh, A., Brown, M., Mian, I.S., Sjolander, K., and Haussler, D. Hidden Markov Models in Computational Biology. J. Mol. Biol., 235. pp. 1501-1531, 1994. [getPDF | kroghetal1994.pdf] |
| At line 52 changed one line |
| * Lathrop, R.H. The Protein Threading Problem with Sequence Amino Acid Interaction Preferences is NP -Complete. Protein Engineering, 7:9, pp. 1059-1068, 1994. |
| * Lathrop, R.H. The Protein Threading Problem with Sequence Amino Acid Interaction Preferences is NP -Complete. Protein Engineering, 7:9, pp. 1059-1068, 1994. [getPDF |lathrop1994.pdf ] |
| At line 54 changed one line |
| * Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F., Wootton, J.C. Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment. Science, 262, pp. 208-214, 1993. |
| * Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F., Wootton, J.C. Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment. Science, 262, pp. 208-214, 1993. [getPDF | lawrence1993.pdf] |
| At line 56 changed one line |
| * Lipman, D.J., Altschul, S.F., and Kececioglu, J.D. A Tool for Multiple Sequence Alignment. Proc. Natl. Acad. Sci. USA, Vol. 86, pp. 4412-4415, 1989. |
| * Lipman, D.J., Altschul, S.F., and Kececioglu, J.D. A Tool for Multiple Sequence Alignment. Proc. Natl. Acad. Sci. USA, Vol. 86, pp. 4412-4415, 1989. [getPDF | lipmanetal1989.pdf] |
| At line 58 changed 2 lines |
| * Marcotte, E.M., Pellegrini, M., Thompson, M.J., Yeates, T.O., and Eisenberg, D. A Combined |
| Algorithm for Genome-wide Prediction of Protein Function. Nature, Vol. 402, pp. 83-86, 1999. |
| * Marcotte, E.M., Pellegrini, M., Thompson, M.J., Yeates, T.O., and Eisenberg, D. A Combined Algorithm for Genome-wide Prediction of Protein Function. Nature, Vol. 402, pp. 83-86, 1999. [getPDF | marcotteetal1999.pdf] |
| At line 61 changed one line |
| * McClure, M.A., Vasi, T.K., and Fitch, W.M. Comparative Analysis of Multiple Protein-Sequence Alignment Methods. Mol. Biol. Evol., 11:4, pp. 571-592, 1994. |
| * McClure, M.A., Vasi, T.K., and Fitch, W.M. Comparative Analysis of Multiple Protein-Sequence Alignment Methods. Mol. Biol. Evol., 11:4, pp. 571-592, 1994. [getPDF | mcclureetal1994.pdf] |
| At line 63 changed one line |
| * Needleman, S.B. and Wunsch, C.D. A General Method Applicable to the Search for Similarities in Amino Acid Sequence of Two Proteins. J. Mol. Biol., 48, pp. 443 -453, 1970. |
| * Needleman, S.B. and Wunsch, C.D. A General Method Applicable to the Search for Similarities in Amino Acid Sequence of Two Proteins. J. Mol. Biol., 48, pp. 443 -453, 1970. [getPDF | needlemanandwunsch1970.pdf] |
| At line 65 changed one line |
| * Nei, M. Phylogenetic Analysis in Molecular Evolutionary Genetics. Annu. Rev. Genet., 30, pp. 371-403, 1996. |
| * Nei, M. Phylogenetic Analysis in Molecular Evolutionary Genetics. Annu. Rev. Genet., 30, pp. 371-403, 1996. [getPDF | nei1996.pdf] |
| At line 67 changed one line |
| * Nussinov, R. and Wolfson, H.J. Efficient Detection of Three -dimensional Structural Motifs in Biological Macromolecules by Computer Vision Techniques. Proc. Natl. Acad. Sci. USA, 88, pp. 10495-10499, 1991. |
| * Nussinov, R. and Wolfson, H.J. Efficient Detection of Three -dimensional Structural Motifs in Biological Macromolecules by Computer Vision Techniques. Proc. Natl. Acad. Sci. USA, 88, pp. 10495-10499, 1991. [getPDF |nussinovandwolfson1991.pdf ] |
| At line 69 changed 2 lines |
| * Orengo, C.A. and Taylor, W.R. SSAP: Sequential Structure Alignment Program for Protein |
| Structure Comparison. Methods in Enzymology, 266, pp. 617-635, 1996. |
| * Orengo, C.A. and Taylor, W.R. SSAP: Sequential Structure Alignment Program for Protein Structure Comparison. Methods in Enzymology, 266, pp. 617-635, 1996. [getPDF | orengoandtaylor1996.pdf] |
| At line 72 changed one line |
| * Pedersen, J.T. and Moult, J. Protein Folding Simulations with Genetic Algorithms and a Detailed Molecular * Description. J. Mol. Biol., 269, pp. 240 -259, 1997. |
| * Pedersen, J.T. and Moult, J. Protein Folding Simulations with Genetic Algorithms and a Detailed Molecular Description. J. Mol. Biol., 269, pp. 240 -259, 1997. [getPDF | pendersenandmoult1997.pdf] |
| At line 74 changed one line |
| * Prevelige, P. and Fasman, G.D. Chou-Fasman Prediction of the Secondary Structure of Proteins: The Chou-Fasman-Prevelige Algorithm. In Prediction of Protein Structure and the Principles of Protein Conformation (G.D. Fasman, ed.) Plenum Publishing, N.Y., pp. 391 -416, 1989. |
| * Prevelige, P. and Fasman, G.D. Chou-Fasman Prediction of the Secondary Structure of Proteins: The Chou-Fasman-Prevelige Algorithm. In Prediction of Protein Structure and the Principles of Protein Conformation (G.D. Fasman, ed.) Plenum Publishing, N.Y., pp. 391 -416, 1989. [getPDF | preveligeandfasman1989.pdf] |
| At line 76 changed one line |
| * Richards, F.M. Calculation of Molecular Volumes and Areas for Structures of Known Geometry. Methods in Enzymology, 115, pp. 440 -464, 1996. |
| * Richards, F.M. Calculation of Molecular Volumes and Areas for Structures of Known Geometry. Methods in Enzymology, 115, pp. 440 -464, 1996. [getPDF | richards1985.pdf] |
| At line 78 changed 2 lines |
| * Richards, F.M. The Protein Folding Problem. Scientific American, pp. 54-63, January 1991. |
| Sippl, M.J. Knowledge-based Potentials for Proteins. Current Opinion in Structural Biology, 5, pp. 229-235, 1995. |
| * Richards, F.M. The Protein Folding Problem. Scientific American, pp. 54-63, January 1991. [getPDF | richards1991.pdf] |
| At line 81 changed 2 lines |
| * Smith, T.F. The History of the Genetic Sequence Databases. Genomics, 6, pp. 701-707, 1990. |
| Smith, T.F. and Waterman, M.S. Identification of Common Molecular Subsequences. J. Mol. Biol., 147, pp. 195-197, 1981. |
| * Sippl, M.J. Knowledge-based Potentials for Proteins. Current Opinion in Structural Biology, 5, pp. 229-235, 1995. [getPDF | sippl1995.pdf] |
| At line 84 changed one line |
| * Subbiah, S., Laurents, D.V., and Levitt, M. Structural Similarity of DNA -binding Domains of Bacteriophage Repressors and the Globin Core. Current Biology, 3:3, pp. 141-148, 1993. |
| * Smith, T.F. The History of the Genetic Sequence Databases. Genomics, 6, pp. 701-707, 1990. [getPDF | smith1990.pdf] |
| At line 86 changed 3 lines |
| * Thompson, J.D., Higgins, D.G., and Gibson, T.J. CLUSTAL W: Improving the Sensitivity of |
| Progressive Multiple Sequence Alignment through Sequence Weighting, Position-specific Gap |
| Penalties and Weight Matrix Choice. Nucleic Acids Research, 22(22), pp. 4673-4680, 1994. |
| * Smith, T.F. and Waterman, M.S. Identification of Common Molecular Subsequences. J. Mol. Biol., 147, pp. 195-197, 1981. [getPDF | smithandwaterman1981.pdf] |
| At line 90 changed one line |
| * Thorne, J.L., Kishino, H., and Felsenstein, J. An Evolutionary Model for Maximum Likelihood Alignment of DNA Sequences. J. Mol. Evol., 33, pp. 114-124, 1991. |
| * Subbiah, S., Laurents, D.V., and Levitt, M. Structural Similarity of DNA -binding Domains of Bacteriophage Repressors and the Globin Core. Current Biology, 3:3, pp. 141-148, 1993. [getPDF | subbiahetal1993.pdf] |
| At line 92 changed one line |
| * Unger, R. and Moult, J. Genetic Algorithms for Protein Folding Simulations. J. Mol. Biol., 231, pp. 75-81, 1993. |
| * Thompson, J.D., Higgins, D.G., and Gibson, T.J. CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-specific Gap Penalties and Weight Matrix Choice. Nucleic Acids Research, 22(22), pp. 4673-4680, 1994. [getPDF | thompsonetal1994.pdf] |
| At line 94 changed one line |
| * Zuker, M. On Finding All Suboptimal Foldings of an RNA Molecule. Science, 244, pp. 48-52, 1989. |
| * Thorne, J.L., Kishino, H., and Felsenstein, J. An Evolutionary Model for Maximum Likelihood Alignment of DNA Sequences. J. Mol. Evol., 33, pp. 114-124, 1991. [getPDF | thorneetal1991.pdf] |
| At line 85 added one line |
| * Unger, R. and Moult, J. Genetic Algorithms for Protein Folding Simulations. J. Mol. Biol., 231, pp. 75-81, 1993. [getPDF | ungerandmoult1993.pdf] |
| At line 97 changed one line |
| !! Recent papers in systems biology |
| * Zuker, M. On Finding All Suboptimal Foldings of an RNA Molecule. Science, 244, pp. 48-52, 1989. [getPDF | zuker1989.pdf] |
| At line 100 changed one line |
| * NM Luscombe, MM Babu, H Yu, M Snyder, SA Teichmann, M Gerstein (2004). Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431: 308-12. |
| !! Recent papers in systems biology |
| At line 102 removed one line |
| * H Yu, NM Luscombe, HX Lu, X Zhu, Y Xia, JD Han, N Bertin, S Chung, M Vidal, M Gerstein (2004). Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res 14: 1107-18. |
| At line 104 changed one line |
| * J Ptacek, G Devgan, G Michaud, H Zhu, X Zhu, J Fasolo, H Guo, G Jona, A Breitkreutz, R Sopko, RR McCartney, MC Schmidt, N Rachidi, SJ Lee, AS Mah, L Meng, MJ Stark, DF Stern, C De Virgilio, M Tyers, B Andrews, M Gerstein, B Schweitzer, PF Predki, M Snyder (2005). Global analysis of protein phosphorylation in yeast. Nature 438: 679-84. |
| * NM Luscombe, MM Babu, H Yu, M Snyder, SA Teichmann, M Gerstein (2004). Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431: 308-12. [getPDF | Luscombeetal2004.pdf] |
| At line 106 changed one line |
| * NJ Krogan, G Cagney, H Yu, G Zhong, X Guo, A Ignatchenko, J Li, S Pu, N Datta, AP Tikuisis, T Punna, JM Peregrín-Alvarez, M Shales, X Zhang, M Davey, MD Robinson, A Paccanaro, JE Bray, A Sheung, B Beattie, DP Richards, V Canadien, A Lalev, F Mena, P Wong, A Starostine, MM Canete, J Vlasblom, S Wu, C Orsi, SR Collins, S Chandran, R Haw, JJ Rilstone, K Gandi, NJ Thompson, G Musso, P St Onge, S Ghanny, MH Lam, G Butland, AM Altaf-Ul, S Kanaya, A Shilatifard, E O'Shea, JS Weissman, CJ Ingles, TR Hughes, J Parkinson, M Gerstein, SJ Wodak, A Emili, JF Greenblatt (2006). Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-43. |
| * H Yu, NM Luscombe, HX Lu, X Zhu, Y Xia, JD Han, N Bertin, S Chung, M Vidal, M Gerstein (2004). Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res 14: 1107-18. [getPDF | Yuetal2004.pdf] |
| At line 108 changed one line |
| * Han J-DJ, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJM, Cusick ME, Roth FP, and Vidal M. Evidence for dynamically organized modularity in the yeast protein–protein interaction network. Nature 2004;430:88–93. |
| * J Ptacek, G Devgan, G Michaud, H Zhu, X Zhu, J Fasolo, H Guo, G Jona, A Breitkreutz, R Sopko, RR McCartney, MC Schmidt, N Rachidi, SJ Lee, AS Mah, L Meng, MJ Stark, DF Stern, C De Virgilio, M Tyers, B Andrews, M Gerstein, B Schweitzer, PF Predki, M Snyder (2005). Global analysis of protein phosphorylation in yeast. Nature 438: 679-84. [getPDF | Ptaceketal2005.pdf] |
| At line 110 changed 2 lines |
| * Rual J-F, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S,Rosenberg J, Goldberg DS, ZhangLV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas e,Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M. |
| Towards a proteome-scale map of the human protein-protein interaction network. Nature 437:1173-8, 2005. |
| * NJ Krogan, G Cagney, H Yu, G Zhong, X Guo, A Ignatchenko, J Li, S Pu, N Datta, AP Tikuisis, T Punna, JM Peregrín-Alvarez, M Shales, X Zhang, M Davey, MD Robinson, A Paccanaro, JE Bray, A Sheung, B Beattie, DP Richards, V Canadien, A Lalev, F Mena, P Wong, A Starostine, MM Canete, J Vlasblom, S Wu, C Orsi, SR Collins, S Chandran, R Haw, JJ Rilstone, K Gandi, NJ Thompson, G Musso, P St Onge, S Ghanny, MH Lam, G Butland, AM Altaf-Ul, S Kanaya, A Shilatifard, E O'Shea, JS Weissman, CJ Ingles, TR Hughes, J Parkinson, M Gerstein, SJ Wodak, A Emili, JF Greenblatt (2006). Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-43. [getPDF | Kroganetal2006.pdf] |
| At line 113 changed one line |
| * Yildirim MA, Goh K-I, Cusick ME, Barabási A-L, Vidal M. Drug-target network. Nat Biotechnol 2007; 25:1119-26. |
| * Han J-DJ, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJM, Cusick ME, Roth FP, and Vidal M. Evidence for dynamically organized modularity in the yeast protein–protein interaction network. Nature 2004;430:88–93. [getPDF | Hanetal2004.pdf] |
| At line 115 changed one line |
| * Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabási AL. The human disease network. Proc Natl Acad Sci USA 2007; 104:8685-90. |
| * Rual J-F, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S,Rosenberg J, Goldberg DS, ZhangLV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas e,Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437:1173-8, 2005. [getPDF | Rualetal2005.pdf] |
| At line 117 changed one line |
| * Zhong Q, Simonis N, Li QR, Charloteaux B, Heuze F, Klitgord N, Tam S, Yu H, Venkatesan K, Mou D, Swearingen V, Yildirim MA, Yan H, Dricot A, Szeto D, Lin C, Hao T, Fan C, Milstein S, Dupuy D, Brasseur R, Hill DE, Cusick ME, Vidal M. Edgetic perturbation models of human inherited disorders. Mol Syst Biol 2009; 3:321. |
| * Yildirim MA, Goh K-I, Cusick ME, Barabási A-L, Vidal M. Drug-target network. Nat Biotechnol 2007; 25:1119-26. [getPDF | Yildirimetal2007.pdf] |
| At line 119 changed one line |
| * Brehme M, Vidal M. A global protein-lipid interactome map. Mol Syst Biol 2010; 6:443. |
| * Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabási AL. The human disease network. Proc Natl Acad Sci USA 2007; 104:8685-90. [getPDF | Gohetal2007.pdf] |
| At line 121 changed one line |
| * Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller D, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guenole A, van Attikum H, Shokat KM, Kolodner RD, Huh WK, Aebersold R, Keogh MC, Krogan NJ, Ideker T. Rewiring of genetic networks in response to DNA damage. Science 330:1385-1389 (2010) |
| * Zhong Q, Simonis N, Li QR, Charloteaux B, Heuze F, Klitgord N, Tam S, Yu H, Venkatesan K, Mou D, Swearingen V, Yildirim MA, Yan H, Dricot A, Szeto D, Lin C, Hao T, Fan C, Milstein S, Dupuy D, Brasseur R, Hill DE, Cusick ME, Vidal M. Edgetic perturbation models of human inherited disorders. Mol Syst Biol 2009; 3:321. [getPDF | Zhongetal2009.pdf] |
| At line 123 changed one line |
| * Chuang, HY, Lee, E, Liu, YT, Lee, D, and Ideker, T. Network-based classification of breast cancer metastasis.MolSyst Biol. 3:140 (2007). |
| * Brehme M, Vidal M. A global protein-lipid interactome map. Mol Syst Biol 2010; 6:443. [getPDF | Brehmeetal2010.pdf] |
| At line 125 changed one line |
| * Konig, R., Zhou, Y., Elleder, D., Diamond, T.L., Bonamy, G.M., Irelan, J.T., Chiang, C.Y., Tu, B.P., De Jesus, P.D., Lilley, C.E., Seidel, S., Opaluch, A.M., Caldwell, J.S., Weitzman, M.D., Kuhen, K.L., Bandyopadhyay, S., Ideker, T., Orth, A.P., Miraglia, L.J., Bushman, F.D., Young, J.A., Chanda, S.K. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 135(1):49-60 (2008). |
| * Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller D, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guenole A, van Attikum H, Shokat KM, Kolodner RD, Huh WK, Aebersold R, Keogh MC, Krogan NJ, Ideker T. Rewiring of genetic networks in response to DNA damage. Science 330:1385-1389 (2010) [getPDF | Bandyopadhyayetal2010.pdf] |
| At line 127 changed one line |
| * Kelley, B. P., Sharan, R., Karp, R., Sittler, E. T., Root, D. E., Stockwell, B. R., and Ideker, T. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. ProcNatlAcadSci U S A 100, 11394-9 (2003). |
| * Chuang, HY, Lee, E, Liu, YT, Lee, D, and Ideker, T. Network-based classification of breast cancer metastasis.MolSyst Biol. 3:140 (2007). [getPDF | chuangetal2007.pdf] |
| At line 129 changed one line |
| * Workman, CT., Mak, HC.,McCuine, S., Tagne, JB., Agarwal, M., Ozier, O., Begley, TJ., Samson, LD., Ideker, T. A Systems Approach to Mapping DNA Damage Response Pathways.Science. 312 (5776):1054-1059 (2006) |
| * Konig, R., Zhou, Y., Elleder, D., Diamond, T.L., Bonamy, G.M., Irelan, J.T., Chiang, C.Y., Tu, B.P., De Jesus, P.D., Lilley, C.E., Seidel, S., Opaluch, A.M., Caldwell, J.S., Weitzman, M.D., Kuhen, K.L., Bandyopadhyay, S., Ideker, T., Orth, A.P., Miraglia, L.J., Bushman, F.D., Young, J.A., Chanda, S.K. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 135(1):49-60 (2008). [getPDF | Konigetal2008.pdf] |
| At line 131 changed one line |
| * Lee I, Date SV, Adai AT, Marcotte EM, A probabilistic functional network of yeast genes, Science, 306(5701):1555-8 (2004) |
| * Kelley, B. P., Sharan, R., Karp, R., Sittler, E. T., Root, D. E., Stockwell, B. R., and Ideker, T. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. ProcNatlAcadSci U S A 100, 11394-9 (2003). [getPDF | kelleyetal2003.pdf] |
| At line 133 changed one line |
| * Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D, Detecting protein function and protein-protein interactions from genome sequences, Science, 285(5428):751-3 (1999) |
| * Workman, CT., Mak, HC.,McCuine, S., Tagne, JB., Agarwal, M., Ozier, O., Begley, TJ., Samson, LD., Ideker, T. A Systems Approach to Mapping DNA Damage Response Pathways.Science. 312 (5776):1054-1059 (2006) [getPDF | workmanetal2006.pdf] |
| At line 135 changed one line |
| * W. Ma, A. Trusina, H. El-Samad, W. Lim and C. Tang, "Defining Network Topologies that Can Achieve Biochemical Adaptation," Cell 138(4), 760 (2009). |
| * Lee I, Date SV, Adai AT, Marcotte EM, A probabilistic functional network of yeast genes, Science, 306(5701):1555-8 (2004) [getPDF | Leeetal2004.pdf] |
| At line 137 changed one line |
| * H. Li, R. Helling, C. Tang, and N. Wingreen, "Emergence of Preferred Structures in a Simple Model of Protein Folding," Science 273, 666 (1996). |
| * Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D, Detecting protein function and protein-protein interactions from genome sequences, Science, 285(5428):751-3 (1999) [getPDF | Marcotteetal1999.pdf] |
| At line 139 changed one line |
| * X Wu, R Jiang, MQ Zhang, S.Li - Network-based global inference of human disease genes. Molecular Systems Biology, 2008 |
| * W. Ma, A. Trusina, H. El-Samad, W. Lim and C. Tang, "Defining Network Topologies that Can Achieve Biochemical Adaptation," Cell 138(4), 760 (2009). [getPDF | maetal2009.pdf] |
| At line 141 removed one line |
| * Jothi R, Balaji S, Wuster A, Grochow JA, Gsponer J, Przytycka TM, Aravind L, et al. Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol. 2009;5:294. |
| At line 143 changed one line |
| * Gardner TS, Bernardo D, Lorenz D and Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105 (2003). |
| * X Wu, R Jiang, MQ Zhang, S.Li - Network-based global inference of human disease genes. Molecular Systems Biology, 2008 [getPDF | Wuetal2008.pdf] |
| At line 145 changed one line |
| * Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ and Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biology 5(1): e8 (2007). |
| * Jothi R, Balaji S, Wuster A, Grochow JA, Gsponer J, Przytycka TM, Aravind L, et al. Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol. 2009;5:294. [getPDF | Jothietal2009.pdf] |
| At line 147 changed one line |
| * Gardner TS, Cantor CR and Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342 (2000). |
| * Gardner TS, Bernardo D, Lorenz D and Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105 (2003). [getPDF | gardneretal2003.pdf] |
| At line 136 added 4 lines |
| * Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ and Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biology 5(1): e8 (2007). [getPDF | faithetal2007.pdf] |
| |
| * Gardner TS, Cantor CR and Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342 (2000). [getPDF | gardneretal2001.pdf] |
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