Differences between revisions 2 and 4 (spanning 2 versions)

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]

2002

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]

2001

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]

2000

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]

Textbook Chapters

2004
<ul>
<LI>Gary D. Bader, Amy Tong, Lan V. Zhang, Frederick P. Roth, Brenda Andrews and Charles Boone Exploiting Synthetic Genetic Interactions to Predict Pathways and Complexes in Protein-Protein Interactions: A Molecular Cloning Manual, 2nd Edition. Ed. Erica Golemis, Cold Spring Harbor Laboratory Press, New York, USA (in press)</LI>
<LI>Gary D. Bader, Christopher W.V. Hogue 
Interaction Databases, in Genomics and Bioinformatics, 2nd Edition in <a href="http://www.wiley-vch.de/books/biotech/con_v05b.html">Volume 5B of the Series: Biotechnology, 2nd Edition.</a> Eds Rehm, H.-J., Reed, G., P�hler, A., Stadler, P. Wiley-VCH, Germany (in press)</LI>
<LI>Gary D. Bader, Anton J. Enright Intermolecular Interactions and Biological Pathways in <a href="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</a></LI>
<LI>Anton J. Enright, Lucy Skrabanek, Gary D. Bader Computational Prediction of Protein-Protein Interactions in <a href="http://www.humanapress.com/ProductDetail.pasp?txtCatalog=HumanaBooks&txtProductID=1-58829-593-1">The Proteomics Handbook Ed. John Walker. (Humana Press, New Jersey)</a></LI>
</ul>
2003
<ul> Gary D. Bader, Amy Hin Yan Tong, Gianni Cesareni, Christopher W.V. Hogue, Stanley Fields, Charles Boone Peptide Recognition Module Networks: Combining Phage Display with Two-hybrid Analysis to Define Protein-Protein Interactions in <a href="http://books.elsevier.com/us//apcatalog/us/subindex.asp?maintarget=&isbn=0121245462">Handbook of Cell Signaling Eds. Ralph Bradshaw and Edward Dennis. (San Diego: Academic/Elsevier Press)</a></LI>
</ul>
2002
<ul>
<LI>Gary D. Bader, Christopher W.V. Hogue Interaction Databases 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> Eds. Rehm, H.-J., Reed, G., P�hler, A., Stadler, P. Wiley-VCH, Germany</LI>

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== 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 =

<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>