prot references

[Bernstein1977Protein] F. C. Bernstein, T. F. Koetzle, G. J. Williams, E. F. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi. The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112(3):535-542, May 1977. [ bib ]
[Pepperrell1991Techniques] C. A. Pepperrell and P. Willett. Techniques for the calculation of three-dimensional structural similarity using inter-atomic distances. J Comput Aided Mol Des, 5(5):455-474, Oct 1991. [ bib | Abstract ]
[Russell1992Multiple] R. B. Russell and G. J. Barton. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins, 14(2):309-323, Oct 1992. [ bib | DOI | http | Abstract ]
[Henikoff1992Amino] S. Henikoff and J. G. Henikoff. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA, 89(22):10915-10919, Nov 1992. [ bib | Abstract ]
[Sette1994relationship] A. Sette, A. Vitiello, B. Reherman, P. Fowler, R. Nayersina, W. M. Kast, C. J. Melief, C. Oseroff, L. Yuan, J. Ruppert, J. Sidney, M. F. del Guercio, S. Southwood, R. T. Kubo, R. W. Chesnut, H. M. Grey, and F. V. Chisari. The relationship between class i binding affinity and immunogenicity of potential cytotoxic t cell epitopes. J. Immunol., 153(12):5586-5592, Dec 1994. [ bib | Abstract ]
[Sidney1995Several] J. Sidney, M. F. del Guercio, S. Southwood, V. H. Engelhard, E. Appella, H. G. Rammensee, K. Falk, O. Rötzschke, M. Takiguchi, and R. T. Kubo. Several HLA alleles share overlapping peptide specificities. J. Immunol., 154(1):247-259, Jan 1995. [ bib | Abstract ]
[Wilkins1996From] M. R. Wilkins, C. Pasquali, R. D. Appel, K. Ou, O. Golaz, J. C. Sanchez, J. X. Yan, A. A. Gooley, G. Hughes, I. Humphery-Smith, K. L. Williams, and D. F. Hochstrasser. From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology (N Y), 14(1):61-65, Jan 1996. [ bib | Abstract ]
[Sidney1996Definition] J. Sidney, H. M. Grey, S. Southwood, E. Celis, P. A. Wentworth, M. F. del Guercio, R. T. Kubo, R. W. Chesnut, and A. Sette. Definition of an HLA-A3-like supermotif demonstrates the overlapping peptide-binding repertoires of common HLA molecules. Hum Immunol, 45(2):79-93, Feb 1996. [ bib | Abstract ]
[Rarey1996Placement] M. Rarey, S. Wefing, and T. Lengauer. Placement of medium-sized molecular fragments into active sites of proteins. J Comput Aided Mol Des, 10(1):41-54, Feb 1996. [ bib | Abstract ]
[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 ]
[Nielsen1997Identification] H. Nielsen, J. Engelbrecht, S. Brunak, and G. von Heijne. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng., 10(1):1-6, 1997. [ bib | http | .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 ]
[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 ]
[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 ]
[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 ]
[Girosi1998Equivalence] Girosi. An Equivalence Between Sparse Approximation and Support Vector Machines. Neural Comput, 10(6):1455-80, Jul 1998. [ bib | Abstract ]
[Early1998Polychemotherapy] Early Breast Cancer Trialists’ Collaborative Group. Polychemotherapy for early breast cancer: an overview of the randomised trials. early breast cancer trialists' collaborative group. Lancet, 352(9132):930-942, Sep 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 ]
[Rigaut1999generic] G. Rigaut, A. Shevchenko, B. Rutz, M. Wilm, M. Mann, and B. Séraphin. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol, 17(10):1030-1032, Oct 1999. [ bib | DOI | http | Abstract ]
[Gygi1999Quantitative] S. P. Gygi, B. Rist, S. A. Gerber, F. Turecek, M. H. Gelb, and R. Aebersold. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol, 17(10):994-999, Oct 1999. [ bib | DOI | http | Abstract ]
[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 ]
[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 ]
[Strahl2000language] B. D. Strahl and C. D. Allis. The language of covalent histone modifications. Nature, 403(6765):41-45, Jan 2000. [ bib | DOI | http | Abstract ]
[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 ]
[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 ]
[Pandey2000Proteomics] A. Pandey and M. Mann. Proteomics to study genes and genomes. Nature, 405:837-846, 2000. [ bib | http | .pdf ]
[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 ]
[Klebe2000Recent] G. Klebe. Recent developments in structure-based drug design. J Mol Med, 78(5):269-281, 2000. [ bib | Abstract ]
[Gether2000Uncovering] U. Gether. Uncovering molecular mechanisms involved in activation of g protein-coupled receptors. Endocr Rev, 21(1):90-113, Feb 2000. [ bib | Abstract ]
[Zhu2001Global] H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, N. Lan, R. Jansen, S. Bidlingmaier, T. Houfek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Snyder. Global analysis of protein activities using proteome chips. Science, 293(5537):2101-5, Sep 2001. [ bib | DOI | http | .pdf | Abstract ]
[Xue2001Mini-fingerprints] L. Xue, F. L. Stahura, J. W. Godden, and J. Bajorath. Mini-fingerprints detect similar activity of receptor ligands previously recognized only by three-dimensional pharmacophore-based methods. J Chem Inf Comput Sci, 41(2):394-401, 2001. [ bib | Abstract ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[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 ]
[Chou2001Using] K.-C. Chou. Using subsite coupling to predict signal peptides. Protein Eng., 14(2):75-79, 2001. [ bib | http | .pdf ]
[Chou2001Prediction] K.-C. Chou. Prediction of protein signal sequences and their cleavage sites. Protein. Struct. Funct. Genet., 42:136-139, 2001. [ bib | http | .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 ]
[Bostroem2001Reproducing] J. Boström. Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools. J Comput Aided Mol Des, 15(12):1137-1152, Dec 2001. [ bib | Abstract ]
[Ballesteros2001G] J. Ballesteros and K. Palczewski. G protein-coupled receptor drug discovery: implications from the crystal structure of rhodopsin. Curr. Opin. Drug Discov. Devel., 4(5):561-574, Sep 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 ]
[Yu2002Methods] Kun Yu, Nikolai Petrovsky, Christian Schönbach, Judice Y L Koh, and Vladimir Brusic. Methods for prediction of peptide binding to MHC molecules: a comparative study. Mol Med, 8(3):137-148, Mar 2002. [ bib | Abstract ]
[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 ]
[Tucker2002Gene] D. L. Tucker, N. Tucker, and T. Conway. Gene expression profiling of the ph response in escherichia coli. J Bacteriol., 184(23):6551-6558, Dec 2002. [ bib | 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 ]
[Schmitt2002New] Stefan Schmitt, Daniel Kuhn, and Gerhard Klebe. A new method to detect related function among proteins independent of sequence and fold homology. J. Mol. Biol., 323(2):387-406, Oct 2002. [ bib | 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 ]
[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 ]
[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 ]
[MacBeath2002Protein] Gavin MacBeath. Protein microarrays and proteomics. Nat Genet, 32 Suppl:526-532, Dec 2002. [ bib | DOI | http | 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 ]
[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 ]
[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 ]
[Dekker2002Capturing] Job Dekker, Karsten Rippe, Martijn Dekker, and Nancy Kleckner. Capturing chromosome conformation. Science, 295(5558):1306-1311, Feb 2002. [ bib | DOI | http | Abstract ]
[Doennes2002Prediction] Pierre Dönnes and Arne Elofsson. Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics, 3:25, Sep 2002. [ bib | 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 ]
[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 ]
[Vickers2003Efficient] T. A. Vickers, S. Koo, C. F. Bennett, S. T. Crooke, N. M. Dean, and B. F. Baker. Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis. J. Biol. Chem., 278(9):7108-18, Feb 2003. [ bib | DOI | http | 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 ]
[Sheinerman2003Sequence] Felix B Sheinerman, Bissan Al-Lazikani, and Barry Honig. Sequence, structure and energetic determinants of phosphopeptide selectivity of SH2 domains. J. Mol. Biol., 334(4):823-841, Dec 2003. [ bib | Abstract ]
[Salim2003Combination] N. Salim, J. Holliday, and P. Willett. Combination of fingerprint-based similarity coefficients using data fusion. J Chem Inf Comput Sci, 43(2):435-442, 2003. [ bib | DOI | http | 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 ]
[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 ]
[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 ]
[Formosa2003Changing] T. Formosa. Changing the dna landscape: putting a spn on chromatin. Curr Top Microbiol Immunol, 274:171-201, 2003. [ bib | 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 ]
[Bhasin2003MHCBN] Manoj Bhasin, Harpreet Singh, and G. P S Raghava. MHCBN: a comprehensive database of MHC binding and non-binding peptides. Bioinformatics, 19(5):665-666, Mar 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 ]
[Attwood2003PRINTS] T. K. Attwood, P. Bradley, D. R. Flower, A. Gaulton, N. Maudling, A. L. Mitchell, G. Moulton, A. Nordle, K. Paine, P. Taylor, A. Uddin, and C. Zygouri. Prints and its automatic supplement, preprints. Nucleic Acids Res., 31(1):400-402, Jan 2003. [ bib | 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 ]
[Anderson2003new] D.C. Anderson, W. Li, D.G. Payan, and W.S. Noble. A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J Proteome Res, 2(2):137-146, 2003. [ bib | .pdf | Abstract ]
[Bleicher2003Hit] K. H. Bleicher, H.-J. Böhm, K. Müller, and A. I. Alanine. Hit and lead generation: beyond high-throughput screening. Nat Rev Drug Discov, 2(5):369-378, May 2003. [ 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 ]
[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 ]
[Vallabhaneni2004Motor] Anirudh Vallabhaneni and Bin He. Motor imagery task classification for brain computer interface applications using spatiotemporal principle component analysis. Neurol Res, 26(3):282-7, Apr 2004. [ bib | DOI | http | 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 ]
[Sun2004protein] Zhenghong Sun, Xiaoli Fu, Lu Zhang, Xiaoli Yang, Feizhou Liu, and Gengxi Hu. A protein chip system for parallel analysis of multi-tumor markers and its application in cancer detection. Anticancer Res, 24(2C):1159-65, 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 ]
[Shulman-Peleg2004Recognition] Alexandra Shulman-Peleg, Ruth Nussinov, and Haim J Wolfson. Recognition of functional sites in protein structures. J Mol Biol, 339(3):607-633, Jun 2004. [ bib | DOI | http | 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 ]
[Ross2004Multiplexed] Philip L Ross, Yulin N Huang, Jason N Marchese, Brian Williamson, Kenneth Parker, Stephen Hattan, Nikita Khainovski, Sasi Pillai, Subhakar Dey, Scott Daniels, Subhasish Purkayastha, Peter Juhasz, Stephen Martin, Michael Bartlet-Jones, Feng He, Allan Jacobson, and Darryl J Pappin. Multiplexed protein quantitation in saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics, 3(12):1154-1169, Dec 2004. [ bib | DOI | http | 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 ]
[Prados2004Mining] J. Prados, A. Kalousis, J.C. Sanchez, L. Allard, O. Carrette, and M. Hilario. Mining mass spectra for diagnosis and biomarker discovery of cerebral accidents. Proteomics, 4(8):2320-2332, 2004. [ bib | DOI | http | .pdf | 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 ]
[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 ]
[Hizukuri2004Extraction] Yoshiyuki Hizukuri, Yoshihiro Yamanishi, Kosuke Hashimoto, and Minoru Kanehisa. Extraction of species-specific glycan substructures. Genome Inform Ser Workshop Genome Inform, 15(1):69-81, 2004. [ bib | .html | .pdf | 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 ]
[Glotsos2004Computer-based] Dimitris Glotsos, Panagiota Spyridonos, Panagiotis Petalas, Dionisis Cavouras, Panagiota Ravazoula, Petroula-Arampatoni Dadioti, Ioanna Lekka, and George Nikiforidis. Computer-based malignancy grading of astrocytomas employing a support vector machine classifier, the WHO grading system and the regular hematoxylin-eosin diagnostic staining procedure. Anal Quant Cytol Histol, 26(2):77-83, Apr 2004. [ bib | 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 ]
[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 ]
[Doytchinova2004Identifying] Irini A Doytchinova, Pingping Guan, and Darren R Flower. Identifying human MHC supertypes using bioinformatic methods. J. Immunol., 172(7):4314-4323, Apr 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 ]
[Causier2004Studying] Barry Causier. Studying the interactome with the yeast two-hybrid system and mass spectrometry. Mass Spectrom Rev, 23(5):350-367, 2004. [ bib | DOI | http | 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 ]
[Bern2004Automatic] M. Bern, D. Goldberg, W. H. McDonald, and III Yates, J. R. Automatic Quality Assessment of Peptide Tandem Mass Spectra. Bioinformatics, 20(Suppl. 1):i49-i54, 2004. [ bib | http | .pdf | Abstract ]
[Baumgartner2004Supervised] C. Baumgartner, C. Bohm, D. Baumgartner, G. Marini, K. Weinberger, B. Olgemoller, B. Liebl, and A. A. Roscher. Supervised machine learning techniques for the classification of metabolic disorders in newborns. Bioinformatics, 20(17):2985-2996, 2004. [ bib | DOI | http | .pdf | Abstract ]
[Perola2004Conformational] Emanuele Perola and Paul S Charifson. Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. J. Med. Chem., 47(10):2499-2510, May 2004. [ bib | DOI | http | Abstract ]
[Mestres2004Computational] Jordi Mestres. Computational chemogenomics approaches to systematic knowledge-based drug discovery. Curr Opin Drug Discov Devel, 7(3):304-313, 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 ]
[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 ]
[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 ]
[Stelzl2005human] Ulrich Stelzl, Uwe Worm, Maciej Lalowski, Christian Haenig, Felix H Brembeck, Heike Goehler, Martin Stroedicke, Martina Zenkner, Anke Schoenherr, Susanne Koeppen, Jan Timm, Sascha Mintzlaff, Claudia Abraham, Nicole Bock, Silvia Kietzmann, Astrid Goedde, Engin Toksöz, Anja Droege, Sylvia Krobitsch, Bernhard Korn, Walter Birchmeier, Hans Lehrach, and Erich E Wanker. A human protein-protein interaction network: a resource for annotating the proteome. Cell, 122(6):957-968, Sep 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 ]
[Sheinerman2005High] Felix B Sheinerman, Elie Giraud, and Abdelazize Laoui. High affinity targets of protein kinase inhibitors have similar residues at the positions energetically important for binding. J. Mol. Biol., 352(5):1134-1156, Oct 2005. [ bib | DOI | http | 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 ]
[Seike2005Proteomic] M. Seike, T. Kondo, K. Fujii, T. Okano, T. Yamada, Y. Matsuno, A. Gemma, S. Kudoh, and S. Hirohashi. Proteomic signatures for histological types of lung cancer. Proteomics, Jul 2005. [ bib | DOI | http | .pdf | 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 ]
[Rual2005Towards] Jean-François Rual, Kavitha Venkatesan, Tong Hao, Tomoko Hirozane-Kishikawa, Amélie Dricot, Ning Li, Gabriel F Berriz, Francis D Gibbons, Matija Dreze, Nono Ayivi-Guedehoussou, Niels Klitgord, Christophe Simon, Mike Boxem, Stuart Milstein, Jennifer Rosenberg, Debra S Goldberg, Lan V Zhang, Sharyl L Wong, Giovanni Franklin, Siming Li, Joanna S Albala, Janghoo Lim, Carlene Fraughton, Estelle Llamosas, Sebiha Cevik, Camille Bex, Philippe Lamesch, Robert S Sikorski, Jean Vandenhaute, Huda Y Zoghbi, Alex Smolyar, Stephanie Bosak, Reynaldo Sequerra, Lynn Doucette-Stamm, Michael E Cusick, David E Hill, Frederick P Roth, and Marc Vidal. Towards a proteome-scale map of the human protein-protein interaction network. Nature, 437(7062):1173-1178, Oct 2005. [ bib | DOI | http | Abstract ]
[Rice2005Reconstructing] J.J. Rice, Y. Tu, and G. Stolovitzky. Reconstructing biological networks using conditional correlation analysis. Bioinformatics, 21(6):765-773, Mar 2005. [ bib | DOI | http | 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 ]
[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 ]
[Papadopoulos2005Characterization] A. Papadopoulos, D. I. Fotiadis, and A. Likas. Characterization of clustered microcalcifications in digitized mammograms using neural networks and support vector machines. Artif. Intell. Med., 34(2):141-50, Jun 2005. [ bib | DOI | http | .pdf | Abstract ]
[Nabieva2005Whole-proteome] Elena Nabieva, Kam Jim, Amit Agarwal, Bernard Chazelle, and Mona Singh. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics, 21 Suppl 1:i302-i310, Jun 2005. [ bib | DOI | http | Abstract ]
[Miteva2005Fast] M. A. Miteva, W. H. Lee, M. O. Montes, and B. O. Villoutreix. Fast structure-based virtual ligand screening combining FRED, DOCK, and Surflex. J. Med. Chem., 48(19):6012-6022, Sep 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 ]
[Lasso2005Vessel] András Lassó and Emanuele Trucco. Vessel enhancement in digital X-ray angiographic sequences by temporal statistical learning. Comput Med Imaging Graph, 29(5):343-55, Jul 2005. [ bib | DOI | http ]
[Larsen2005integrative] Mette Voldby Larsen, Claus Lundegaard, Kasper Lamberth, Søren Buus, Søren Brunak, Ole Lund, and Morten Nielsen. An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. Eur. J. Immunol., 35(8):2295-2303, Aug 2005. [ bib | DOI | http | Abstract ]
[LaBaer2005Protein] Joshua LaBaer and Niroshan Ramachandran. Protein microarrays as tools for functional proteomics. Curr Opin Chem Biol, 9(1):14-19, Feb 2005. [ bib | DOI | http | Abstract ]
[Ikeda2005asymptotic] Kazushi Ikeda and Tsutomu Aoishi. An asymptotic statistical analysis of support vector machines with soft margins. Neural Netw, 18(3):251-9, Apr 2005. [ bib | DOI | http | .pdf | 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 ]
[Dong2005Prediction] Hai-Long Dong and Yan-Fang Sui. Prediction of HLA-A2-restricted CTL epitope specific to HCC by SYFPEITHI combined with polynomial method. World J Gastroenterol, 11(2):208-211, Jan 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 ]
[Dhingra2005Substantial] Vikas Dhingra, Mukta Gupta, Tracy Andacht, and Zhen F Fu. New frontiers in proteomics research: a perspective. Int. J. Pharm., 299(1-2):1-18, Aug 2005. [ bib | DOI | http | Abstract ]
[Cole2005Comparing] Jason C Cole, Christopher W Murray, J. Willem M Nissink, Richard D Taylor, and Robin Taylor. Comparing protein-ligand docking programs is difficult. Proteins, 60(3):325-332, Aug 2005. [ bib | DOI | http | Abstract ]
[Bui2005Automated] Huynh-Hoa Bui, John Sidney, Bjoern Peters, Muthuraman Sathiamurthy, Asabe Sinichi, Kelly-Anne Purton, Bianca R Mothé, Francis V Chisari, David I Watkins, and Alessandro Sette. Automated generation and evaluation of specific mhc binding predictive tools: Arb matrix applications. Immunogenetics, 57(5):304-314, Jun 2005. [ bib | DOI | http | Abstract ]
[Bernardo2005Chemogenomica] D. di Bernardo, M.J. Thompson, T.S. Gardner, S.E. Chobot, E.L. Eastwood, A.P. Wojtovich, S.J. Elliott, S.E. Schaus, and J.J. Collins. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat Biotechnol, 23(3):377-383, Mar 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 ]
[Asefa2005Support] Tirusew Asefa, Mariush Kemblowski, Gilberto Urroz, and Mac McKee. Support vector machines (SVMs) for monitoring network design. Ground Water, 43(3):413-22, 2005. [ bib | DOI | http | .pdf | Abstract ]
[Yu2005Ovarian] J. S. Yu, S. Ongarello, R. Fiedler, X. W. Chen, G. Toffolo, C. Cobelli, and Z. Trajanoski. Ovarian cancer identification based on dimensionality reduction for high-throughput mass spectrometry data. Bioinformatics, 21(10):2200-9, May 2005. [ bib | DOI | http | .pdf | Abstract ]
[Begg2005Support] Rezaul K Begg, Marimuthu Palaniswami, and Brendan Owen. Support vector machines for automated gait classification. IEEE Trans Biomed Eng, 52(5):828-38, May 2005. [ bib | DOI | http | .pdf | Abstract ]
[Surgand2006chemogenomic] Jean-Sebastien Surgand, Jordi Rodrigo, Esther Kellenberger, and Didier Rognan. A chemogenomic analysis of the transmembrane binding cavity of human g-protein-coupled receptors. Proteins, 62(2):509-538, 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 ]
[Paik2006Gene] Soonmyung Paik, Gong Tang, Steven Shak, Chungyeul Kim, Joffre Baker, Wanseop Kim, Maureen Cronin, Frederick L. Baehner, Drew Watson, John Bryant, Joseph P. Costantino, Charles E Geyer, Jr, D Lawrence Wickerham, and Norman Wolmark. Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer. J Clin Oncol, 24(23):3726-3734, Aug 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 ]
[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 ]
[Ma2006MSB] Wenzhe Ma, Luhua Lai, Qi Ouyang, and Chao Tang. Robustness and modular design of the drosophila segment polarity network. Mol Syst Biol, 2:70, 2006. [ bib | DOI | http | Abstract ]
[Leach2006Prediction] A. R. Leach, B. K. Shoichet, and C. E. Peishoff. Prediction of protein-ligand interactions. docking and scoring: successes and gaps. J. Med. Chem., 49(20):5851-5855, Oct 2006. [ bib | DOI | http ]
[Kurata2006PlosCompBio] Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A Gross, and Mustafa Khammash. Module-based analysis of robustness tradeoffs in the heat shock response system. PLoS Comput Biol, 2(7):e59, Jul 2006. [ bib | DOI | http | Abstract ]
[Kubinyi2006Chemogenomics] H. Kubinyi. Chemogenomics in drug discovery. Ernst Schering Res Found Workshop, 58:1-19, 2006. [ bib | Abstract ]
[Huebert2006Genome-wide] Dana J Huebert, Michael Kamal, Aisling O'Donovan, and Bradley E Bernstein. Genome-wide analysis of histone modifications by chip-on-chip. Methods, 40(4):365-369, Dec 2006. [ bib | DOI | http | Abstract ]
[Huang2006Ligsite] Bingding Huang and Michael Schroeder. Ligsitecsc: predicting ligand binding sites using the connolly surface and degree of conservation. BMC Struct Biol, 6:19, 2006. [ bib | DOI | http | Abstract ]
[Theres2006Structural] Theres Fagerberg, Jean-Charles Cerottini, and Olivier Michielin. Structural prediction of peptides bound to MHC class I. J. Mol. Biol., 356(2):521-546, Feb 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 ]
[Glaser2006Method] F. Glaser, R. J. Morris, R. J. Najmanovich, R. A. Laskowski, and J. M. Thornton. A method for localizing ligand binding pockets in protein structures. Proteins, 62(2):479-488, February 2006. [ bib | DOI | http | Abstract ]
[Valentini2007Mosclust:] Giorgio Valentini. Mosclust: a software library for discovering significant structures in bio-molecular data. Bioinformatics, 23(3):387-389, Feb 2007. [ bib | DOI | http | Abstract ]
[Tung2007POPI:] Chun-Wei Tung and Shinn-Ying Ho. Popi: predicting immunogenicity of mhc class i binding peptides by mining informative physicochemical properties. Bioinformatics, 23(8):942-949, Apr 2007. [ bib | DOI | http | Abstract ]
[Taylor2007minimum] Chris F Taylor, Norman W Paton, Kathryn S Lilley, Pierre-Alain Binz, Randall K Julian, Andrew R Jones, Weimin Zhu, Rolf Apweiler, Ruedi Aebersold, Eric W Deutsch, Michael J Dunn, Albert J R Heck, Alexander Leitner, Marcus Macht, Matthias Mann, Lennart Martens, Thomas A Neubert, Scott D Patterson, Peipei Ping, Sean L Seymour, Puneet Souda, Akira Tsugita, Joel Vandekerckhove, Thomas M Vondriska, Julian P Whitelegge, Marc R Wilkins, Ioannnis Xenarios, John R Yates, and Henning Hermjakob. The minimum information about a proteomics experiment (miape). Nat Biotechnol, 25(8):887-893, Aug 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 ]
[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 ]
[Kroemer2007Structure] Romano T Kroemer. Structure-based drug design: docking and scoring. Curr. Protein Pept. Sci., 8(4):312-328, Aug 2007. [ bib | Abstract ]
[Kahraman2007Shape] A. Kahraman, R. J. Morris, R. A. Laskowski, and J. M. Thornton. Shape variation in protein binding pockets and their ligands. J. Mol. Biol., 368(1):283-301, Apr 2007. [ bib | DOI | http | Abstract ]
[Garcia2007Organismal] Benjamin A Garcia, Sandra B Hake, Robert L Diaz, Monika Kauer, Stephanie A Morris, Judith Recht, Jeffrey Shabanowitz, Nilamadhab Mishra, Brian D Strahl, C. David Allis, and Donald F Hunt. Organismal differences in post-translational modifications in histones h3 and h4. J Biol Chem, 282(10):7641-7655, Mar 2007. [ bib | DOI | http | Abstract ]
[Dalton2007Evaluation] James A R Dalton and Richard M Jackson. An evaluation of automated homology modelling methods at low target template sequence similarity. Bioinformatics, 23(15):1901-1908, Aug 2007. [ bib | DOI | http | Abstract ]
[Bock2007Effective] Mary Ellen Bock, Claudio Garutti, and Conettina Guerra. Effective labeling of molecular surface points for cavity detection and location of putative binding sites. Comput Syst Bioinformatics Conf, 6:263-274, 2007. [ bib | Abstract ]
[Bantscheff2007Quantitative] Marcus Bantscheff, Markus Schirle, Gavain Sweetman, Jens Rick, and Bernhard Kuster. Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem, 389(4):1017-1031, Oct 2007. [ bib | DOI | http | Abstract ]
[Qiu2007structural] J. Qiu, J. Hue, A. Ben-Hur, J.-P. Vert, and W. S. Noble. A structural alignment kernel for protein structures. Bioinformatics, 23(9):1090-1098, May 2007. [ bib | DOI | http | Abstract ]
[Jin2007yeast] Fulai Jin, Larisa Avramova, Jing Huang, and Tony Hazbun. A yeast two-hybrid smart-pool-array system for protein-interaction mapping. Nat Methods, 4(5):405-407, May 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 ]
[Weis2008Structural] William I Weis and Brian K Kobilka. Structural insights into G-protein-coupled receptor activation. Curr Opin Struct Biol, 18(6):734-740, Dec 2008. [ bib | DOI | http | Abstract ]
[Taylor2008Guidelines] Chris F Taylor, Pierre-Alain Binz, Ruedi Aebersold, Michel Affolter, Robert Barkovich, Eric W Deutsch, David M Horn, Andreas Hühmer, Martin Kussmann, Kathryn Lilley, Marcus Macht, Matthias Mann, Dieter Müller, Thomas A Neubert, Janice Nickson, Scott D Patterson, Roberto Raso, Kathryn Resing, Sean L Seymour, Akira Tsugita, Ioannis Xenarios, Rong Zeng, and Randall K Julian. Guidelines for reporting the use of mass spectrometry in proteomics. Nat Biotechnol, 26(8):860-861, Aug 2008. [ bib | DOI | http ]
[Suter2008Two-hybrid] Bernhard Suter, Saranya Kittanakom, and Igor Stagljar. Two-hybrid technologies in proteomics research. Curr Opin Biotechnol, 19(4):316-323, Aug 2008. [ bib | DOI | http | Abstract ]
[Schalon2008Simple] C. Schalon, J-S. Surgand, E. Kellenberger, and D. Rognan. A simple and fuzzy method to align and compare druggable ligand-binding sites. Proteins, 71(4):1755-1778, Jun 2008. [ bib | DOI | http | Abstract ]
[Moitessier2008Towards] N. Moitessier, P. Englebienne, D. Lee, J. Lawandi, and C. R. Corbeil. Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br. J. Pharmacol., 153 Suppl 1:S7-26, Mar 2008. [ bib | DOI | http | Abstract ]
[Launay2008Homology] G. Launay and T. Simonson. Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations. BMC Bioinformatics, 9:427, 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 ]
[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 ]
[Topiol2009X-ray] Sid Topiol and Michael Sabio. X-ray structure breakthroughs in the GPCR transmembrane region. Biochem Pharmacol, 78(1):11-20, Jul 2009. [ bib | DOI | http | Abstract ]
[Terentiev2009Dynamic] A. A. Terentiev, N. T. Moldogazieva, and K. V. Shaitan. Dynamic proteomics in modeling of the living cell. protein-protein interactions. Biochemistry (Mosc), 74(13):1586-1607, Dec 2009. [ bib | 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 ]
[Mustafi2009Topology] Debarshi Mustafi and Krzysztof Palczewski. Topology of class a g protein-coupled receptors: insights gained from crystal structures of rhodopsins, adrenergic and adenosine receptors. Mol Pharmacol, 75(1):1-12, Jan 2009. [ bib | DOI | http | Abstract ]
[Lievens2009Mammalian] Sam Lievens, Irma Lemmens, and Jan Tavernier. Mammalian two-hybrids come of age. Trends Biochem Sci, 34(11):579-588, Nov 2009. [ bib | DOI | http | Abstract ]
[LeCao2009Sparse] K.-A. Lê Cao, P. G. P. Martin, C. Robert-Granié, and P. Besse. Sparse canonical methods for biological data integration: application to a cross-platform study. BMC Bioinformatics, 10:34, 2009. [ bib | DOI | http | Abstract ]
[Jensen2009STRING] L.J. Jensen, M. Kuhn, M. Stark, S. Chaffron, C. Creevey, J. Muller, T. Doerks, P. Julien, A. Roth, M. Simonovic, P. Bork, and C. von Mering. String 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res, 37(Database issue):D412-D416, Jan 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 ]
[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 ]
[Stoddart2010Nucleobase] David Stoddart, Andrew J Heron, Jochen Klingelhoefer, Ellina Mikhailova, Giovanni Maglia, and Hagan Bayley. Nucleobase recognition in ssdna at the central constriction of the alpha-hemolysin pore. Nano Lett, 10(9):3633-3637, Sep 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 ]
[Choudhary2010Decoding] Chunaram Choudhary and Matthias Mann. Decoding signalling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol, 11(6):427-439, Jun 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 ]
[Tomizaki2010Protein] Kin-ya Tomizaki, Kenji Usui, and Hisakazu Mihara. Protein-protein interactions and selection: array-based techniques for screening disease-associated biomarkers in predictive/early diagnosis. FEBS J, 277(9):1996-2005, May 2010. [ bib | DOI | http | Abstract ]

This file was generated by bibtex2html 1.97.