39 Publications (Page 1 of 2)
2014
A large scale Huntingtin protein interaction network implicates Rho GTPase signaling pathways in Huntington disease.
Tourette, Cendrine⋅Li, Biao⋅Bell, Russell⋅O'Hare, Shannon⋅Kaltenbach, Linda S⋅Mooney, Sean D and Hughes, Robert E
The Journal of biological chemistry, vol. 289, (no. 10), pp. 6709-26, 2014/Mar/7. | Journal Article
 
The automated function prediction SIG looks back at 2013 and prepares for 2014.
Wass, Mark N⋅Friedberg, Iddo⋅Mooney, Sean D⋅Linial, Michal⋅Radivojac, Predrag and Friedberg, Iddo
Bioinformatics (Oxford, England), vol. 30, (no. 14), pp. 2091-2, 2014/Jul/15. | Journal Article
2013
A large-scale evaluation of computational protein function prediction
Radivojac, Predrag⋅Radivojac, Predrag⋅Friedberg, Iddo⋅Radivojac, Predrag⋅Clark, Wyatt T⋅Clark, Wyatt T⋅Clark, Wyatt T⋅Oron, Tal R⋅Oron, Tal R⋅Oron, Tal R⋅Schnoes, Alexandra M⋅Schnoes, Alexandra M⋅Schnoes, Alexandra M⋅Wittkop, Tobias⋅Wittkop, Tobias⋅Wittkop, Tobias⋅Sokolov, Artem⋅Sokolov, Artem⋅Sokolov, Artem⋅Graim, Kiley⋅Graim, Kiley⋅Graim, Kiley⋅Funk, Christopher⋅Funk, Christopher⋅Funk, Christopher⋅Verspoor, Karin⋅Verspoor, Karin⋅Verspoor, Karin M⋅Ben-hur, Asa⋅Ben Hur, Asa⋅Ben-hur, Asa⋅Pandey, Gaurav⋅Pandey, Gaurav⋅Pandey, Gaurav⋅Yunes, Jeffrey M⋅Yunes, Jeffrey M⋅Yunes, Jeffrey M⋅Talwalkar, Ameet S⋅Talwalkar, Ameet S⋅Talwalkar, Ameet S⋅Repo, Susanna⋅Repo, Susanna⋅Repo, Susanna⋅Souza, Michael L⋅Souza, Michael L⋅Souza, Michael L⋅Piovesan, Damiano⋅Piovesan, Damiano⋅Piovesan, Damiano⋅Casadio, Rita⋅Casadio, Rita⋅Casadio, Rita⋅Wang, Zheng⋅Wang, Zheng⋅Wang, Zheng⋅Cheng, Jianlin⋅Cheng, Jianlin⋅Cheng, Jianlin⋅Fang, Hai⋅Fang, Hai⋅Fang, Hai⋅Gough, Julian⋅Gough, Julian⋅Gough, Julian⋅Koskinen, Patrik⋅Koskinen, Patrik⋅Koskinen, Patrik⋅Törönen, Petri⋅Törönen, Petri⋅Törönen, Petri⋅Nokso-koivisto, Jussi⋅Nokso-koivisto, Jussi⋅Nokso-Koivisto, Jussi⋅Nokso-koivisto, Jussi⋅Holm, Liisa⋅Holm, Liisa⋅Holm, Liisa⋅Cozzetto, Domenico⋅Cozzetto, Domenico⋅Cozzetto, Domenico⋅Buchan, Daniel W A⋅Buchan, Daniel⋅Buchan, Daniel W A⋅Bryson, Kevin⋅Bryson, Kevin⋅Bryson, Kevin⋅Jones, David T⋅Jones, David⋅Jones, David T⋅Limaye, Bhakti⋅Limaye, Bhakti⋅Limaye, Bhakti⋅Inamdar, Harshal⋅Inamdar, Harshal⋅Inamdar, Harshal⋅Datta, Avik⋅Datta, Avik⋅Datta, Avik⋅Manjari, Sunitha K⋅Manjari, Sunitha K⋅Manjari, Sunitha K⋅Joshi, Rajendra⋅Joshi, Rajendra⋅Joshi, Rajendra⋅Chitale, Meghana⋅Chitale, Meghana⋅Chitale, Meghana⋅Kihara, Daisuke⋅Kihara, Daisuke⋅Kihara, Daisuke⋅Lisewski, Andreas⋅Lisewski, Andreas M⋅Lisewski, Andreas M⋅Erdin, Serkan⋅Erdin, Serkan⋅Erdin, Serkan⋅Venner, Eric⋅Venner, Eric⋅Venner, Eric⋅Lichtarge, Olivier⋅Lichtarge, Olivier⋅Lichtarge, Olivier⋅Rentzsch, Robert⋅Rentzsch, Robert⋅Rentzsch, Robert⋅Yang, Haixuan⋅Yang, Haixuan⋅Yang, Haixuan⋅Romero, Alfonso E⋅Romero, Alfonso E⋅Romero, Alfonso E⋅Bhat, Prajwal⋅Bhat, Prajwal⋅Bhat, Prajwal⋅Paccanaro, Alberto⋅Paccanaro, Alberto⋅Paccanaro, Alberto⋅Hamp, Tobias⋅Hamp, Tobias⋅Hamp, Tobias⋅Kaßner, Rebecca⋅Kaßner, Rebecca⋅Kaßner, Rebecca⋅Seemayer, Stefan⋅Seemayer, Stefan⋅Seemayer, Stefan⋅Vicedo, Esmeralda⋅Vicedo, Esmeralda⋅Vicedo, Esmeralda⋅Schaefer, Christian⋅Schaefer, Christian⋅Schaefer, Christian⋅Achten, Dominik⋅Achten, Dominik⋅Achten, Dominik⋅Auer, Florian⋅Auer, Florian⋅Auer, Florian⋅Boehm, Ariane⋅Boehm, Ariane⋅Boehm, Ariane⋅Braun, Tatjana⋅Braun, Tatjana⋅Braun, Tatjana⋅Hecht, Maximilian⋅Hecht, Maximilian⋅Hecht, Maximilian⋅Heron, Mark⋅Heron, Mark⋅Heron, Mark⋅Hönigschmid, Peter⋅Hönigschmid, Peter⋅Hönigschmid, Peter⋅Hopf, Thomas A⋅Hopf, Thomas A⋅Hopf, Thomas A⋅Kaufmann, Stefanie⋅Kaufmann, Stefanie⋅Kaufmann, Stefanie⋅Kiening, Michael⋅Kiening, Michael⋅Kiening, Michael⋅Krompass, Denis⋅Krompass, Denis⋅Krompass, Denis⋅Landerer, Cedric⋅Landerer, Cedric⋅Landerer, Cedric⋅Mahlich, Yannick⋅Mahlich, Yannick⋅Mahlich, Yannick⋅Roos, Manfred⋅Roos, Manfred⋅Roos, Manfred⋅Björne, Jari⋅Björne, Jari⋅Björne, Jari⋅Salakoski, Tapio⋅Salakoski, Tapio⋅Salakoski, Tapio⋅Wong, Andrew⋅Wong, Andrew⋅Wong, Andrew⋅Shatkay, Hagit⋅Shatkay, Hagit⋅Shatkay, Hagit⋅Gatzmann, Fanny⋅Gatzmann, Fanny⋅Gatzmann, Fanny⋅Sommer, Ingolf⋅Sommer, Ingolf⋅Sommer, Ingolf⋅Wass, Mark N⋅Wass, Mark N⋅Wass, Mark N⋅Sternberg, Michael J E⋅Sternberg, Michael J⋅Sternberg, Michael J E⋅Skunca, Nives⋅Škunca, Nives⋅Skunca, Nives⋅Skunca, Nives⋅Supek, Fran⋅Supek, Fran⋅Supek, Fran⋅Bošnjak, Matko⋅Bosnjak, Matko⋅Bosnjak, Matko⋅Bosnjak, Matko⋅Panov, Pance⋅Panov, Pance⋅Panov, Pance⋅Dzeroski, Saso⋅Dzeroski, Saso⋅Džeroski, Sašo⋅Dzeroski, Saso⋅Šmuc, Tomislav⋅Smuc, Tomislav⋅Smuc, Tomislav⋅Smuc, Tomislav⋅Kourmpetis, Yiannis A I⋅Kourmpetis, Yiannis A⋅Kourmpetis, Yiannis A I⋅Van Dijk, Aalt D⋅Van Dijk, Aalt D J⋅Van Dijk, Aalt D J⋅van Dijk, Aalt D J⋅ter Braak, Cajo J F⋅Braak, Cajo J⋅Braak, Cajo J F T⋅Braak, Cajo J F T⋅Zhou, Yuanpeng⋅Zhou, Yuanpeng⋅Zhou, Yuanpeng⋅Gong, Qingtian⋅Gong, Qingtian⋅Gong, Qingtian⋅Dong, Xinran⋅Dong, Xinran⋅Dong, Xinran⋅Tian, Weidong⋅Tian, Weidong⋅Tian, Weidong⋅Falda, Marco⋅Falda, Marco⋅Falda, Marco⋅Fontana, Paolo⋅Fontana, Paolo⋅Fontana, Paolo⋅Lavezzo, Enrico⋅Lavezzo, Enrico⋅Lavezzo, Enrico⋅Di Camillo, Barbara⋅Di Camillo, Barbara⋅Di Camillo, Barbara⋅Toppo, Stefano⋅Toppo, Stefano⋅Toppo, Stefano⋅Lan, Liang⋅Lan, Liang⋅Lan, Liang⋅Djuric, Nemanja⋅Djuric, Nemanja⋅Djuric, Nemanja⋅Guo, Yuhong⋅Guo, Yuhong⋅Guo, Yuhong⋅Vucetic, Slobodan⋅Vucetic, Slobodan⋅Vucetic, Slobodan⋅Bairoch, Amos⋅Bairoch, Amos⋅Bairoch, Amos⋅Linial, Michal⋅Linial, Michal⋅Linial, Michal⋅Babbitt, Patricia C⋅Babbitt, Patsy C⋅Babbitt, Patricia C⋅Brenner, Steven E⋅Brenner, Steven E⋅Brenner, Steven E⋅Orengo, Christine⋅Orengo, Christine⋅Orengo, Christine⋅Rost, Burkhard⋅Rost, Burkhard⋅Rost, Burkhard⋅Mooney, Sean D⋅Mooney, Sean D⋅Mooney, Sean D⋅Friedberg, Iddo⋅Friedberg, Iddo and Friedberg, Iddo
Nature Methods, vol. 10, (no. 3), pp. 221-7, Mar 2013. | Journal Article
 
Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions.
Thompson, Bryony A⋅Thompson, Bryony⋅Greenblatt, Marc S⋅Greenblatt, Marc⋅Vallee, Maxime P⋅Vallee, Maxime⋅Herkert, Johanna C⋅Herkert, Johanna⋅Tessereau, Chloe⋅Tessereau, Chloe⋅Young, Erin⋅Young, Erin L⋅Adzhubey, Ivan⋅Adzhubey, Ivan A⋅Li, Biao⋅Li, Biao⋅Bell, Russell⋅Bell, Russell⋅Feng, Bingjian⋅Feng, Bingjian⋅Mooney, Sean⋅Mooney, Sean D⋅Radivojac, Predrag⋅Radivojac, Preag⋅Sunyaev, Shamil R⋅Sunyaev, Shamil⋅Frebourg, Thierry⋅Frebourg, Thierry⋅Hofstra, Robert M⋅Hofstra, Robert⋅Sijmons, Rolf H⋅Sijmons, Rolf⋅Boucher, Ken⋅Boucher, Ken⋅Thomas, Alun⋅Thomas, Alun⋅Goldgar, David E⋅Goldgar, David⋅Spurdle, Amanda B⋅Spurdle, Amanda⋅Tavtigian, Sean and Tavtigian, Sean V
Human mutation, vol. 34, (no. 1), pp. 255-65, 2013/Jan. | Journal Article
 
STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation
Wittkop, Tobias⋅TerAvest, Emily⋅Evani, Uday S⋅Fleisch, K. M⋅Berman, Ari E⋅Powell, Corey⋅Shah, Nigam and Mooney, Sean D
BMC Bioinformatics, vol. 14, (no. 1), pp. 53, 2013. | Journal Article
 
STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation.
Wittkop, Tobias⋅Teravest, Emily⋅Evani, Uday S⋅Fleisch, K M⋅Berman, Ari E⋅Powell, Corey⋅Shah, Nigam and Mooney, Sean D
BMC bioinformatics, vol. 14, pp. 53, 2013. | Journal Article
2012
DEFOG: discrete enrichment of functionally organized genes.
Wittkop, Tobias⋅Berman, Ari E⋅Fleisch, K M and Mooney, Sean D
Integrative biology : quantitative biosciences from nano to macro, vol. 4, (no. 7), pp. 795-804, 2012/Jul. | Journal Article
2011
Identifying viral integration sites using SeqMap 2.0
Hawkins, Troy B⋅Dantzer, Jessica⋅Peters, Brandon⋅Dinauer, Mary C⋅Mockaitis, Keithanne⋅Mooney, Sean D and Cornetta, Kenneth G
Bioinformatics, vol. 27, (no. 5), pp. 720-722, 2011. | Journal Article
 
Prediction of functional regulatory SNPs in monogenic and complex disease
Zhao, Yiqiang⋅Clark, Wyatt T⋅Mort, Matthew⋅Cooper, David N⋅Radivojac, Predrag and Mooney, Sean D
Human Mutation, vol. 32, (no. 10), pp. 1183-1190, 2011. | Journal Article
2010
An ontology-neutral framework for enrichment analysis.
Tirrell, Rob⋅Evani, Uday⋅Berman, Ari E⋅Mooney, Sean D⋅Musen, Mark A and Shah, Nigam
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium, vol. 2010, pp. 797-801, 2010. | Journal Article
 
Bioinformatic tools for identifying disease gene and SNP candidates.
Mooney, Sean D⋅Krishnan, Vidhya G and Evani, Uday S
Methods in molecular biology (Clifton, N.J.), vol. 628, pp. 307-19, 2010. | Journal Article
 
Bioinformatic Tools for Identifying Disease Gene and SNP Candidates
Mooney, Sean D⋅Barnes, M. R⋅Krishnan, VG⋅Breen, G. and Evani, US
Methods in Molecular Biology, vol. 628, pp. 307-319, 2010. | Journal Article
 
In silico functional profiling of human disease-associated and polymorphic amino acid substitutions.
Mort, Matthew⋅Evani, Uday S⋅Krishnan, Vidhya G⋅Kamati, Kishore K⋅Baenziger, Peter H⋅Bagchi, Angshuman⋅Peters, Brandon J⋅Sathyesh, Rakesh⋅Li, Biao⋅Sun, Yanan⋅Xue, Bin⋅Shah, Nigam⋅Kann, Maricel⋅Cooper, David N⋅Radivojac, Predrag and Mooney, Sean D
Human mutation, vol. 31, (no. 3), pp. 335-46, 2010/Mar. | Journal Article
 
Loss of post-translational modification sites in disease.
Li, Shuyan⋅Iakoucheva, Lilia M⋅Mooney, Sean D and Radivojac, Predrag
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pp. 337-47, 2010. | Journal Article
 
Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease
Xin, Fuxiao⋅Myers, Steven⋅Li, Yong⋅Cooper, David⋅Mooney, Sean and Radivojac, Predrag
BMC Bioinformatics , vol. 11, (no. Suppl 10), 2010. | Journal Article
 
Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease
Xin, Fuxiao⋅Myers, Steven⋅Li, Yong F⋅Cooper, David N⋅Mooney, Sean D and Radivojac, Predrag
Bioinformatics, vol. 26, (no. 16), pp. 1975-1982, 2010. | Journal Article
2009
Automated inference of molecular mechanisms of disease from amino acid substitutions
Li, Biao⋅Krishnan, Vidhya G⋅Mort, Matthew E⋅Xin, Fuxiao⋅Kamati, Kishore K⋅Cooper, David N⋅Mooney, Sean D and Radivojac, Predrag
Bioinformatics, vol. 25, (no. 21), pp. 2744-2750, 2009. | Journal Article
 
Retroviral vector integration in post-transplant hematopoiesis in mice conditioned with either submyeloablative or ablative irradiation.
Sadat, M A⋅Dirscherl, S⋅Sastry, L⋅Dantzer, J⋅Pech, N⋅Griffin, S⋅Hawkins, T⋅Zhao, Y⋅Barese, C N⋅Cross, S⋅Orazi, Attilio⋅An, C⋅Goebel, W S⋅Yoder, Mervin C⋅Li, Xiaoman⋅Grez, M⋅Cornetta, Kenneth G⋅Mooney, Sean D and Dinauer, Mary C
Gene therapy, vol. 16, (no. 12), pp. 1452-64, 2009/Dec. | Journal Article
 
Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts.
Sanford, Jeremy⋅Wang, Xin⋅Mort, Matthew⋅Vanduyn, Natalia⋅Cooper, David N⋅Mooney, Sean D⋅Edenberg, Howard J and Liu, Yunlong
Genome research, vol. 19, (no. 3), pp. 381-94, 2009/Mar. | Journal Article
2008
An integrated approach to inferring gene-disease associations in humans.
Radivojac, Predrag⋅Peng, Kang⋅Clark, Wyatt T⋅Peters, Brandon J⋅Mohan, Amrita⋅Boyle, Sean M and Mooney, Sean D
Proteins, vol. 72, (no. 3), pp. 1030-7, 2008/Aug/15. | Journal Article
 
Automated analysis of viral integration sites in gene therapy research using the SeqMap web resource
Peters, B⋅Dirscherl, S⋅Dantzer, J⋅Nowacki, J⋅Cross, S⋅Li, Xiaoman⋅Cornetta, Kenneth G⋅Dinauer, Mary C and Mooney, Sean D
Gene Therapy, vol. 15, (no. 18), pp. 1294-1298, Sep 2008. | Journal Article
 
Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group
Mooney, Sean D and Baenziger, Peter H
Briefings in Bioinformatics, vol. 9, (no. 1), pp. 69-74, Jan 2008. | Journal Article
 
Gain and loss of phosphorylation sites in human cancer
Radivojac, Predrag⋅Baenziger, Peter H⋅Kann, Maricel⋅Mort, Matthew E⋅Hahn, Matthew and Mooney, Sean D
Bioinformatics, vol. 24, (no. 16), pp. i241-7, Aug 15, 2008. | Journal Article
 
MutDB: update on development of tools for the biochemical analysis of genetic variation
Singh, Arti⋅Olowoyeye, Adebayo⋅Baenziger, Peter H⋅Dantzer, Jessica⋅Kann, Maricel G⋅Radivojac, Predrag⋅Heiland, Randy and Mooney, Sean D
Nucleic acids research., vol. 36, pp. D815-D819, 2008. | Journal Article
 
MutDB: update on development of tools for the biochemical analysis of genetic variation
Singh, Arti⋅Olowoyeye, Adebayo⋅Baenziger, Peter H⋅Dantzer, Jessica⋅Kann, Maricel G⋅Radivojac, Predrag⋅Heiland, Randy and Mooney, Sean D
Nucleic Acids Research, vol. 36, pp. D815-D819, 2008. | Journal Article