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| *Publications page - numbered in journal, book chapter sections | = Peer-reviewed Journals = == 2006 == == 2004 == 1. '''Global Mapping of the Yeast Genetic Interaction Network'''[[BR]]Tong AH, Lesage G, '''Bader GD''', Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C[[BR]][http://www.sciencemag.org/cgi/content/full/303/5659/808 Science 2004 Feb 6;303(5659):808-813][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14764870 PubMed Abstract] - [attachment:2004_GlobalMappingoftheYeastGeneticInteractionNetwork_TongEtAl_Science_Feb.pdf PDF][[BR]][attachment:2004_SGA_Hartwell_comment.pdf Science Perspective PDF] 1. '''The HUPO PSI Molecular Interaction Format - a community standard for the representation of protein interaction data'''[[BR]]Hermjakob H, Montecchi-Palazzi L, '''Bader G''', Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, Von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R[[BR]][http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n2/abs/nbt926.html&dynoptions=doi1079900147 Nature Biotechnology 2004 Feb;22(2):177-83][[BR]][http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n2/abs/nbt926.html&dynoptions=doi1079900147 PubMed Abstract] - [attachment:2004_TheHUPOPSIsMolecularInteractionFormat_HermjakobMontecchiBaderEtAl_NatBiotech_Feb.pdf PDF] == 2003 == 1. '''Playing tag with the yeast proteome'''[[BR]] Andrews BJ, '''Bader GD''', Boone C[[BR]] [ Nature Biotechnology Nov;21(11):1297-1299][[BR]] [PubMed Abstract] - [PDF] 1. '''Functional Genomics and Proteomics: Charting a Multidimensional Map of the Cell'''[[BR]] '''Bader GD''', Heilbut A, Andrews B, Tyers M, Hughes T, Boone C[[BR]] [ Trends in Cell Biology Jul, 2003 13(7):344-56][[BR]] [PubMed Abstract] - [PDF] 1. '''PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine'''[[BR]] Donaldson I, Martin J, De Bruijn B, Wolting C, Lay V, Tuekam B, Zhang S, Baskin B, '''Bader GD''', Michalickova K, Pawson T, Hogue CW[[BR]] [ BMC Bioinformatics Mar 27, 2003 4(1):11][[BR]] [PubMed Abstract] - [PDF] 1. '''Functional genomics of intracellular peptide recognition domains with combinatorial biology methods'''[[BR]] Sidhu SS, '''Bader GD''', Boone C[[BR]] [ Current Opinion in Chemical Biology 2003 Feb;7(1):97-102][[BR]] [PubMed Abstract] - [PDF] 1. '''An automated method for finding molecular complexes in large protein interaction networks'''[[BR]] '''Bader GD''', Hogue CWV[[BR]] [ BMC Bioinformatics'' 2003 Jan 13;4(1):2][[BR]] [PubMed Abstract] - [PDF] 1. '''BIND-The Biomolecular Interaction Network Database'''[[BR]] '''Bader GD''', Betel D, Hogue CWV[[BR]] [ Nucleic Acids Research Jan 1, 2003 31(1):248-250][[BR]] [PubMed Abstract] - [PDF] == 2002 == 1. '''!SeqHound: biological sequence and structure database as a platform for bioinformatics research'''[[BR]] Michalickova K, '''Bader GD''', Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW[[BR]] [ BMC Bioinformatics 2002, 3:32 (25 October 2002)][[BR]] [PubMed Abstract] - [PDF] 1. '''Analyzing yeast protein–protein interaction data obtained from different sources'''[[BR]] '''Bader GD''', Hogue CW[[BR]] [ Nature Biotechnology 2002 Oct;20(10):991-997][[BR]] [PubMed Abstract] - [PDF] 1. '''A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules'''[[BR]] Tong AH, Drees B, Nardelli G, '''Bader GD''', Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, Cesareni G[[BR]] [Science 2002 Jan 11;295(5553):321-324][[BR]] [PubMed Abstract] - [PDF][[BR]] [Science Perspective PDF] 1. '''Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry'''[[BR]] Ho Y, Gruhler A, Heilbut A, '''Bader GD''', Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M[[BR]] [ Nature 2002 Jan 10;415(6868): 180-183][[BR]] [PubMed Abstract] - [PDF] - [Supplementary website][[BR]] [Nature News and Views PDF] == 2001 == 1. '''Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants'''[[BR]] Tong AH, Evangelista M, Parsons AB, Xu H, '''Bader GD''', Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C. [Science 2001 Dec 14;294(5550):2364-8][[BR]] [PubMed Abstract - PubMed] - [PDF] 1. '''BIND - The Biomolecular Interaction Network Database'''[[BR]] '''Bader GD''', Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW[[BR]] [ Nucleic Acids Research Jan 1, 2001 29(1):242-245][[BR]] [PubMed Abstract] - [PDF] == 2000 == 1. '''BIND - A data specification for storing and describing biomolecular interactions, molecular complexes and pathways'''[[BR]] '''Bader GD''', Hogue CW[[BR]] [ Bioinformatics. 2000 May;16(5):465-77][[BR]] [PubMed Abstract] - [PDF] = Textbook Chapters = == 2004 == 1. '''Exploiting Synthetic Genetic Interactions to Predict Pathways and Complexes'''[[BR]]'''Gary D. Bader''', Amy Tong, Lan V. Zhang, Frederick P. Roth, Brenda Andrews and Charles Boone[[BR]]in [http://www.amazon.com/gp/product/0879697237/qid=1147320880/sr=1-1/ref=sr_1_1/102-2952413-6681722?s=books&v=glance&n=283155 Protein-Protein Interactions: A Molecular Cloning Manual, 2nd Edition.][[BR]]Ed. Erica Golemis, Cold Spring Harbor Laboratory Press, New York, USA 1. '''Interaction Databases, in Genomics and Bioinformatics, 2nd Edition'''[[BR]]'''Gary D. Bader''', Christopher W.V. Hogue[[BR]]in [http://www.wiley-vch.de/books/biotech/con_v05b.html Volume 5B of the Series: Biotechnology, 2nd Edition.][[BR]]Eds Rehm, H.-J., Reed, G., Pühler, A., Stadler, P. Wiley-VCH, Germany 1. '''Intermolecular Interactions and Biological Pathways'''[[BR]]'''Gary D. Bader''', Anton J. Enright[[BR]]in [http://jws-edcv.wiley.com/college/bcs/redesign/student/0,,_0471478784_BKS_2102____,00.html Bioinformatics 3E Eds. Andreas D. Baxevanis and B.F.Francis Ouellette. John Wiley and Sons, New Jersey] 1. '''Computational Prediction of Protein-Protein Interactions'''[[BR]]Anton J. Enright, Lucy Skrabanek, '''Gary D. Bader'''[[BR]]in [http://www.humanapress.com/ProductDetail.pasp?txtCatalog=HumanaBooks&txtProductID=1-58829-593-1 The Proteomics Handbook Ed. John Walker. (Humana Press, New Jersey)] == 2003 == 1. '''Peptide Recognition Module Networks: Combining Phage Display with Two-hybrid Analysis to Define Protein-Protein Interactions'''[[BR]]'''Gary D. Bader''', Amy Hin Yan Tong, Gianni Cesareni, Christopher W.V. Hogue, Stanley Fields, Charles Boone[[BR]]in [http://books.elsevier.com/us//apcatalog/us/subindex.asp?maintarget=&isbn=0121245462 Handbook of Cell Signaling][[BR]]Eds. Ralph Bradshaw and Edward Dennis. (San Diego: Academic/Elsevier Press) == 2002 == 1. '''Interaction Databases'''[[BR]]'''Gary D. Bader''', Christopher W.V. Hogue[[BR]]Chapter 18, in [http://www.wiley-vch.de/books/biotech/vol_05b.html Genomics and Bioinformatics (Volume 5B of the Series: Biotechnology, 2nd Edition.)][[BR]]Eds. Rehm, H.-J., Reed, G., Pühler, A., Stadler, P.[[BR]]Wiley-VCH, Germany |
Under construction
Peer-reviewed Journals
2006
2004
Global Mapping of the Yeast Genetic Interaction NetworkBRTong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone CBR[http://www.sciencemag.org/cgi/content/full/303/5659/808 Science 2004 Feb 6;303(5659):808-813]BR[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14764870 PubMed Abstract] - [attachment:2004_GlobalMappingoftheYeastGeneticInteractionNetwork_TongEtAl_Science_Feb.pdf PDF]BR[attachment:2004_SGA_Hartwell_comment.pdf Science Perspective PDF]
The HUPO PSI Molecular Interaction Format - a community standard for the representation of protein interaction dataBRHermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, Von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler RBR[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n2/abs/nbt926.html&dynoptions=doi1079900147 Nature Biotechnology 2004 Feb;22(2):177-83]BR[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n2/abs/nbt926.html&dynoptions=doi1079900147 PubMed Abstract] - [attachment:2004_TheHUPOPSIsMolecularInteractionFormat_HermjakobMontecchiBaderEtAl_NatBiotech_Feb.pdf PDF]
2003
Playing tag with the yeast proteomeBR
Andrews BJ, Bader GD, Boone CBR [ Nature Biotechnology Nov;21(11):1297-1299]BR [PubMed Abstract] - [PDF]
Functional Genomics and Proteomics: Charting a Multidimensional Map of the CellBR
Bader GD, Heilbut A, Andrews B, Tyers M, Hughes T, Boone CBR [ Trends in Cell Biology Jul, 2003 13(7):344-56]BR [PubMed Abstract] - [PDF]
PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machineBR
Donaldson I, Martin J, De Bruijn B, Wolting C, Lay V, Tuekam B, Zhang S, Baskin B, Bader GD, Michalickova K, Pawson T, Hogue CWBR [ BMC Bioinformatics Mar 27, 2003 4(1):11]BR [PubMed Abstract] - [PDF]
Functional genomics of intracellular peptide recognition domains with combinatorial biology methodsBR
Sidhu SS, Bader GD, Boone CBR [ Current Opinion in Chemical Biology 2003 Feb;7(1):97-102]BR [PubMed Abstract] - [PDF]
An automated method for finding molecular complexes in large protein interaction networksBR
Bader GD, Hogue CWVBR [ BMC Bioinformatics 2003 Jan 13;4(1):2]BR [PubMed Abstract] - [PDF] BIND-The Biomolecular Interaction Network DatabaseBR Bader GD, Betel D, Hogue CWVBR [ Nucleic Acids Research Jan 1, 2003 31(1):248-250]BR [PubMed Abstract] - [PDF]
SeqHound: biological sequence and structure database as a platform for bioinformatics researchBR Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CWBR [ BMC Bioinformatics 2002, 3:32 (25 October 2002)]BR [PubMed Abstract] - [PDF] Analyzing yeast protein–protein interaction data obtained from different sourcesBR Bader GD, Hogue CWBR [ Nature Biotechnology 2002 Oct;20(10):991-997]BR [PubMed Abstract] - [PDF] A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition ModulesBR Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, Cesareni GBR [Science 2002 Jan 11;295(5553):321-324]BR [PubMed Abstract] - [PDF]BR [Science Perspective PDF] Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometryBR Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers MBR [ Nature 2002 Jan 10;415(6868): 180-183]BR [PubMed Abstract] - [PDF] - [Supplementary website]BR [Nature News and Views PDF]
Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion MutantsBR Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C. [Science 2001 Dec 14;294(5550):2364-8]BR [PubMed Abstract - PubMed] - [PDF] BIND - The Biomolecular Interaction Network DatabaseBR Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CWBR [ Nucleic Acids Research Jan 1, 2001 29(1):242-245]BR [PubMed Abstract] - [PDF]
BIND - A data specification for storing and describing biomolecular interactions, molecular complexes and pathwaysBR Bader GD, Hogue CWBR [ Bioinformatics. 2000 May;16(5):465-77]BR [PubMed Abstract] - [PDF]
Exploiting Synthetic Genetic Interactions to Predict Pathways and ComplexesBRGary D. Bader, Amy Tong, Lan V. Zhang, Frederick P. Roth, Brenda Andrews and Charles BooneBRin [http://www.amazon.com/gp/product/0879697237/qid=1147320880/sr=1-1/ref=sr_1_1/102-2952413-6681722?s=books&v=glance&n=283155 Protein-Protein Interactions: A Molecular Cloning Manual, 2nd Edition.]BREd. Erica Golemis, Cold Spring Harbor Laboratory Press, New York, USA Interaction Databases, in Genomics and Bioinformatics, 2nd EditionBRGary D. Bader, Christopher W.V. HogueBRin [http://www.wiley-vch.de/books/biotech/con_v05b.html Volume 5B of the Series: Biotechnology, 2nd Edition.]BREds Rehm, H.-J., Reed, G., Pühler, A., Stadler, P. Wiley-VCH, Germany Intermolecular Interactions and Biological PathwaysBRGary D. Bader, Anton J. EnrightBRin [http://jws-edcv.wiley.com/college/bcs/redesign/student/0,,_0471478784_BKS_2102____,00.html Bioinformatics 3E Eds. Andreas D. Baxevanis and B.F.Francis Ouellette. John Wiley and Sons, New Jersey] Computational Prediction of Protein-Protein InteractionsBRAnton J. Enright, Lucy Skrabanek, Gary D. BaderBRin [http://www.humanapress.com/ProductDetail.pasp?txtCatalog=HumanaBooks&txtProductID=1-58829-593-1 The Proteomics Handbook Ed. John Walker. (Humana Press, New Jersey)]
Peptide Recognition Module Networks: Combining Phage Display with Two-hybrid Analysis to Define Protein-Protein InteractionsBRGary D. Bader, Amy Hin Yan Tong, Gianni Cesareni, Christopher W.V. Hogue, Stanley Fields, Charles BooneBRin [http://books.elsevier.com/us//apcatalog/us/subindex.asp?maintarget=&isbn=0121245462 Handbook of Cell Signaling]BREds. Ralph Bradshaw and Edward Dennis. (San Diego: Academic/Elsevier Press)
Interaction DatabasesBRGary D. Bader, Christopher W.V. HogueBRChapter 18, in [http://www.wiley-vch.de/books/biotech/vol_05b.html Genomics and Bioinformatics (Volume 5B of the Series: Biotechnology, 2nd Edition.)]BREds. Rehm, H.-J., Reed, G., Pühler, A., Stadler, P.BRWiley-VCH, Germany 2002
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Textbook Chapters
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2002