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]
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]
<b>2004</b><P> <ul> <LI><b>Gary D. Bader</b>, Amy Tong, Lan V. Zhang, Frederick P. Roth, Brenda Andrews and Charles Boone<BR> <b>Exploiting Synthetic Genetic Interactions to Predict Pathways and Complexes</b><BR> in Protein-Protein Interactions: A Molecular Cloning Manual, 2nd Edition.<BR> Ed. Erica Golemis, Cold Spring Harbor Laboratory Press, New York, USA (in press)</LI><P> <LI><b>Gary D. Bader</b>, Christopher W.V. Hogue<BR> <b>Interaction Databases, in Genomics and Bioinformatics, 2nd Edition</b><BR> in <a href="http://www.wiley-vch.de/books/biotech/con_v05b.html">Volume 5B of the Series: Biotechnology, 2nd Edition.</a><BR> Eds Rehm, H.-J., Reed, G., P�hler, A., Stadler, P. Wiley-VCH, Germany (in press)</LI><P> <LI><b>Gary D. Bader</b>, Anton J. Enright<BR> <b>Intermolecular Interactions and Biological Pathways</b><BR> in <a href="http://jws-edcv.wiley.com/college/bcs/redesign/student/0,,_0471478784_BKS_2102____,00.html">Bioinformatics 3E<BR> Eds. Andreas D. Baxevanis and B.F.Francis Ouellette. John Wiley and Sons, New Jersey</a></LI><P> <LI>Anton J. Enright, Lucy Skrabanek, <b>Gary D. Bader</b><BR> <b>Computational Prediction of Protein-Protein Interactions</b><BR> in <a href="http://www.humanapress.com/ProductDetail.pasp?txtCatalog=HumanaBooks&txtProductID=1-58829-593-1">The Proteomics Handbook<BR> Ed. John Walker. (Humana Press, New Jersey)</a></LI><P> </ul> <b>2003</b><P> <ul> <b>Gary D. Bader</b>, Amy Hin Yan Tong, Gianni Cesareni, Christopher W.V. Hogue, Stanley Fields, Charles Boone<BR> <b>Peptide Recognition Module Networks: Combining Phage Display with Two-hybrid Analysis to Define Protein-Protein Interactions</b><BR> in <a href="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)</a></LI><P> </ul> <b>2002</b><P> <ul> <LI><b>Gary D. Bader</b>, Christopher W.V. Hogue<BR> <b>Interaction Databases</b><BR> Chapter 18, in <a href="http://www.wiley-vch.de/books/biotech/vol_05b.html">Genomics and Bioinformatics (Volume 5B of the Series: Biotechnology, 2nd Edition.)</a><BR> Eds. Rehm, H.-J., Reed, G., P�hler, A., Stadler, P.<BR> Wiley-VCH, Germany</LI> <P> 2002
2001
2000
Textbook Chapters