| Project Title: | A SYSTEMS APPROACH TO MAPPING THE DNA DAMAGE RESPONSE |
|---|---|
| PI: | Ideker, Trey |
| Institution: | University Of California, San Diego |
| Grant Number: | R01ES014811 |
These search results have not been confirmed by NIEHS and are therefore, not official. They are to be used only for general information and to inform the public and grantees on the breadth of research funded by NIEHS.
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| Publication Title | Authors | Grant Number(s) | Journal (Pub date) | PubMed Link | Pub Year |
|---|---|---|---|---|---|
| A census of pathway maps in cancer systems biology. | Kuenzi, Brent M; Ideker, Trey | R01ES014811 | Nat Rev Cancer (2020 04) |
32066900
|
2020 |
| A genetic interaction map centered on cohesin reveals auxiliary factors involved in sister chromatid ... | Ming Sun, Su; Batté, Amandine; Elmer, Mireille; van der Horst, Sophie C; van Welsem, Tibor; Bea ... | R01ES014811 | J Cell Sci (2020 05 22) |
32299836
|
2020 |
| De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. | Vakirlis, Nikolaos; Acar, Omer; Hsu, Brian; Castilho Coelho, Nelson; Van Oss, S Branden; Wachol ... | R01ES014811 | Nat Commun (2020 02 07) |
32034123
|
2020 |
| Epigenetic Markers of Aging Predict the Neural Oscillations Serving Selective Attention. | Wiesman, Alex I; Rezich, Michael T; O'Neill, Jennifer; Morsey, Brenda; Wang, Tina; Ideker, Tre ... | R01ES014811 | Cereb Cortex (2020 03 14) |
31504270
|
2020 |
| Extracellular NAD+ enhances PARP-dependent DNA repair capacity independently of CD73 activity. | Wilk, Anna; Hayat, Faisal; Cunningham, Richard; Li, Jianfeng; Garavaglia, Silvia; Zamani, Leil ... | R01ES014811, U01ES029518, U01ES029518 | Sci Rep (2020 01 20) |
31959836
|
2020 |
| Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response. | Silva, Erica; Michaca, Manuel; Munson, Brenton; Bean, Gordon J; Jaeger, Philipp A; Licon, Kath ... | R01ES014811 | G3 (Bethesda) (2020 Sep 02) |
32732306
|
2020 |
| NAD+-mediated regulation of mammalian base excision repair. | Saville, Kate M; Clark, Jennifer; Wilk, Anna; Rogers, Gresyn D; Andrews, Joel F; Koczor, Chris ... | P01ES028949, R01ES014811, U01ES029518, U01ES029518 | DNA Repair (Amst) (2020 09) |
33087267
|
2020 |
| Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells. | Kuenzi, Brent M; Park, Jisoo; Fong, Samson H; Sanchez, Kyle S; Lee, John; Kreisberg, Jason F; ... | R01ES014811 | Cancer Cell (2020 Nov 09) |
33096023
|
2020 |
| Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome. | Wang, Tina; Ma, Jianzhu; Hogan, Andrew N; Fong, Samson; Licon, Katherine; Tsui, Brian; Kreisbe ... | R01ES014811 | Cell Syst (2020 Aug 26) |
32619550
|
2020 |
| Regulation of ALT-associated homology-directed repair by polyADP-ribosylation. | Hoang, Song My; Kaminski, Nicole; Bhargava, Ragini; Barroso-González, Jonathan; Lynskey, Michel ... | R01ES014811 | Nat Struct Mol Biol (2020 12) |
33046907
|
2020 |
| DNA methylation aging clocks: challenges and recommendations. | Bell, Christopher G; Lowe, Robert; Adams, Peter D; Baccarelli, Andrea A; Beck, Stephan; Bell, ... | P30ES009089, R01ES014811, R01ES025225, R01ES027747 | Genome Biol (2019 11 25) |
31767039
|
2019 |
| Mechanisms of MTH1 inhibition-induced DNA strand breaks: The slippery slope from the oxidized nucleo ... | Rai, Priyamvada; Sobol, Robert W | P01ES028949, R01ES014811, U01ES029518, U01ES029518 | DNA Repair (Amst) (2019 05) |
30852368
|
2019 |
| Stability and sub-cellular localization of DNA polymerase β is regulated by interactions with NQO1 a ... | Fang, Qingming; Andrews, Joel; Sharma, Nidhi; Wilk, Anna; Clark, Jennifer; Slyskova, Jana; Koc ... | R01ES014811 | Nucleic Acids Res (2019 07 09) |
31287140
|
2019 |
| Transcriptional responses to DNA damage. | Silva, Erica; Ideker, Trey | R01ES014811 | DNA Repair (Amst) (2019 07) |
31102970
|
2019 |
| Ultrahigh-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate. | Licon, Katherine; Shen, John Paul; Munson, Brenton P; Michaca, Manuel; Fassino, Cole; Fassino, ... | R01ES014811 | Methods Mol Biol (2019) |
31602605
|
2019 |
| Disruption of NSD1 in Head and Neck Cancer Promotes Favorable Chemotherapeutic Responses Linked to H ... | Bui, Nam; Huang, Justin K; Bojorquez-Gomez, Ana; Licon, Katherine; Sanchez, Kyle S; Tang, Sean ... | R01ES014811 | Mol Cancer Ther (2018 07) |
29636367
|
2018 |
| DNA Methylation Clocks in Aging: Categories, Causes, and Consequences. | Field, Adam E; Robertson, Neil A; Wang, Tina; Havas, Aaron; Ideker, Trey; Adams, Peter D | R01ES014811 | Mol Cell (2018 09 20) |
30241605
|
2018 |
| Mapping Cellular Reprogramming via Pooled Overexpression Screens with Paired Fitness and Single-Cell ... | Parekh, Udit; Wu, Yan; Zhao, Dongxin; Worlikar, Atharv; Shah, Neha; Zhang, Kun; Mali, Prashan ... | R01ES014811 | Cell Syst (2018 11 28) |
30448000
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2018 |
| Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls. | Shen, John Paul; Ideker, Trey | R01ES014811 | J Mol Biol (2018 09 14) |
29932943
|
2018 |
| Systematic Gene-to-Phenotype Arrays: A High-Throughput Technique for Molecular Phenotyping. | Jaeger, Philipp A; Ornelas, Lilia; McElfresh, Cameron; Wong, Lily R; Hampton, Randolph Y; Ideke ... | R01ES014811 | Mol Cell (2018 01 18) |
29351850
|
2018 |
| The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins. | Neal, Sonya; Jaeger, Philipp A; Duttke, Sascha H; Benner, Christopher; Glass, Christopher K; Id ... | R01ES014811 | Mol Cell (2018 03 01) |
29499140
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2018 |
| The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins. | Neal, Sonya; Jaeger, Philipp A; Duttke, Sascha H; Benner, Christopher; K Glass, Christopher; Id ... | R01ES014811 | Mol Cell (2018 01 18) |
29351849
|
2018 |
| Using deep learning to model the hierarchical structure and function of a cell. | Ma, Jianzhu; Yu, Michael Ku; Fong, Samson; Ono, Keiichiro; Sage, Eric; Demchak, Barry; Sharan, ... | R01ES014811 | Nat Methods (2018 04) |
29505029
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2018 |
| Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. | Kramer, Michael H; Farré, Jean-Claude; Mitra, Koyel; Yu, Michael Ku; Ono, Keiichiro; Demchak, ... | R01ES014811 | Mol Cell (2017 Feb 16) |
28132844
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2017 |
| Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. | Shen, John Paul; Zhao, Dongxin; Sasik, Roman; Luebeck, Jens; Birmingham, Amanda; Bojorquez-Gome ... | R01ES014811 | Nat Methods (2017 Jun) |
28319113
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2017 |
| Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex ... | Moder, Martin; Velimezi, Georgia; Owusu, Michel; Mazouzi, Abdelghani; Wiedner, Marc; Ferreira d ... | R01ES014811 | Nat Commun (2017 11 01) |
29089570
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2017 |
| A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy. | Srivas, Rohith; Shen, John Paul; Yang, Chih Cheng; Sun, Su Ming; Li, Jianfeng; Gross, Andrew M ... | R01ES014811 | Mol Cell (2016 08 04) |
27453043
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2016 |
| Challenges in identifying cancer genes by analysis of exome sequencing data. | Hofree, Matan; Carter, Hannah; Kreisberg, Jason F; Bandyopadhyay, Sourav; Mischel, Paul S; Frie ... | R01ES014811 | Nat Commun (2016 07 15) |
27417679
|
2016 |
| Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal s ... | Guo, Theresa; Gaykalova, Daria A; Considine, Michael; Wheelan, Sarah; Pallavajjala, Aparna; Bis ... | R01ES014811 | Int J Cancer (2016 07 15) |
26949921
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2016 |
| Leveraging premalignant biology for immune-based cancer prevention. | Spira, Avrum; Disis, Mary L; Schiller, John T; Vilar, Eduardo; Rebbeck, Timothy R; Bejar, Rafa ... | R01ES014811 | Proc Natl Acad Sci U S A (2016 09 27) |
27638202
|
2016 |
| Parenchymal Volumetric Assessment as a Predictive Tool to Determine Renal Function Benefit of Nephro ... | Liss, Michael A; DeConde, Robert; Caovan, Dominique; Hofler, Joseph; Gabe, Michael; Palazzi, K ... | R01ES014811 | J Endourol (2016 Jan) |
26192380
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2016 |
| Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems. | Yu, Michael Ku; Kramer, Michael; Dutkowski, Janusz; Srivas, Rohith; Licon, Katherine; Kreisberg ... | R01ES014811 | Cell Syst (2016 Feb 24) |
26949740
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2016 |
| Advanced Applications of RNA Sequencing and Challenges. | Han, Yixing; Gao, Shouguo; Muegge, Kathrin; Zhang, Wei; Zhou, Bing | R01ES014811 | Bioinform Biol Insights (2015) |
26609224
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2015 |
| Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluore ... | Jaeger, Philipp A; McElfresh, Cameron; Wong, Lily R; Ideker, Trey | R01ES014811 | Appl Environ Microbiol (2015 Aug 15) |
26070672
|
2015 |
| Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition. | Shen, John Paul; Srivas, Rohith; Gross, Andrew; Li, Jianfeng; Jaehnig, Eric J; Sun, Su Ming; B ... | R01ES014811 | Oncotarget (2015 Nov 3) |
26437225
|
2015 |
| Combined TP53 mutation/3p loss correlates with decreased radiosensitivity and increased matrix-metal ... | Raju, Sharat C; Hauff, Samantha J; Lemieux, Aaron J; Orosco, Ryan K; Gross, Andrew M; Nguyen, ... | R01ES014811 | Oral Oncol (2015 May) |
25735654
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2015 |
| ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer. | Choueiri, Michel B; Shen, John Paul; Gross, Andrew M; Huang, Justin K; Ideker, Trey; Fanta, Pa ... | R01ES014811 | PLoS One (2015) |
26083491
|
2015 |
| Evolutionary trends and functional anatomy of the human expanded autophagy network. | Till, Andreas; Saito, Rintaro; Merkurjev, Daria; Liu, Jing-Jing; Syed, Gulam Hussain; Kolnik, ... | R01ES014811 | Autophagy (2015) |
26103419
|
2015 |
| Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues. | Yan, Julia Fangfei; Kim, Hoguen; Jeong, Seul-Ki; Lee, Hyoung-Joo; Sethi, Manveen K; Lee, Ling ... | R01ES014811 | J Proteome Res (2015 Dec 04) |
26435392
|
2015 |
| Transcriptional repression of IFNβ1 by ATF2 confers melanoma resistance to therapy. | Lau, E; Sedy, J; Sander, C; Shaw, M A; Feng, Y; Scortegagna, M; Claps, G; Robinson, S; Cheng ... | R01ES014811 | Oncogene (2015 Nov 12) |
25728676
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2015 |
| Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling. | Hustedt, Nicole; Seeber, Andrew; Sack, Ragna; Tsai-Pflugfelder, Monika; Bhullar, Bhupinder; Vla ... | R01ES014811 | Mol Cell (2015 Jan 22) |
25533186
|
2015 |
| Proteome-wide remodeling of protein location and function by stress. | Lee, KiYoung; Sung, Min-Kyung; Kim, Jihyun; Kim, Kyung; Byun, Junghyun; Paik, Hyojung; Kim, B ... | R01ES014811 | Proc Natl Acad Sci U S A (2014 Jul 29) |
25028499
|
2014 |
| A gene ontology inferred from molecular networks. | Dutkowski, Janusz; Kramer, Michael; Surma, Michal A; Balakrishnan, Rama; Cherry, J Michael; Kro ... | R01ES014811 | Nat Biotechnol (2013 Jan) |
23242164
|
2013 |
| A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-depe ... | Srivas, Rohith; Costelloe, Thomas; Carvunis, Anne-Ruxandra; Sarkar, Sovan; Malta, Erik; Sun, S ... | R01ES014811 | Cell Rep (2013 Dec 26) |
24360959
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2013 |
| Checkpoint kinases regulate a global network of transcription factors in response to DNA damage. | Jaehnig, Eric J; Kuo, Dwight; Hombauer, Hans; Ideker, Trey G; Kolodner, Richard D | R01ES014811 | Cell Rep (2013 Jul 11) |
23810556
|
2013 |
| Dissection of DNA damage responses using multiconditional genetic interaction maps. | Guénolé, Aude; Srivas, Rohith; Vreeken, Kees; Wang, Ze Zhong; Wang, Shuyi; Krogan, Nevan J; Id ... | R01ES014811 | Mol Cell (2013 Jan 24) |
23273983
|
2013 |
| Genome-wide methylation profiles reveal quantitative views of human aging rates. | Hannum, Gregory; Guinney, Justin; Zhao, Ling; Zhang, Li; Hughes, Guy; Sadda, SriniVas; Klotzle ... | R01ES014811 | Mol Cell (2013 Jan 24) |
23177740
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2013 |
| Differential analysis of high-throughput quantitative genetic interaction data. | Bean, Gordon J; Ideker, Trey | R01ES014811 | Genome Biol (2012 Dec 26) |
23268787
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2012 |
| Quantitative proteomics reveal ATM kinase-dependent exchange in DNA damage response complexes. | Choi, Serah; Srivas, Rohith; Fu, Katherine Y; Hood, Brian L; Dost, Banu; Gibson, Gregory A; Wa ... | R01ES014811 | J Proteome Res (2012 Oct 05) |
22909323
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2012 |
| Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with di ... | Chuang, Han-Yu; Rassenti, Laura; Salcedo, Michelle; Licon, Kate; Kohlmann, Alexander; Haferlach ... | R01ES014811 | Blood (2012 Sep 27) |
22837534
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2012 |
| A chemical-genetic screen to unravel the genetic network of CDC28/CDK1 links ubiquitin and Rad6-Bre1 ... | Zimmermann, Christine; Chymkowitch, Pierre; Eldholm, Vegard; Putnam, Christopher D; Lindvall, J ... | R01ES014811 | Proc Natl Acad Sci U S A (2011 Nov 15) |
22042866
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2011 |
| Bayesian network analysis of targeting interactions in chromatin. | van Steensel, Bas; Braunschweig, Ulrich; Filion, Guillaume J; Chen, Menzies; van Bemmel, Joke G ... | R01ES014811 | Genome Res (2010 Feb) |
20007327
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2010 |
| Coevolution within a transcriptional network by compensatory trans and cis mutations. | Kuo, Dwight; Licon, Katherine; Bandyopadhyay, Sourav; Chuang, Ryan; Luo, Colin; Catalana, Just ... | R01ES014811 | Genome Res (2010 Dec) |
20978140
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2010 |
| Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. | Kuo, Dwight; Tan, Kai; Zinman, Guy; Ravasi, Timothy; Bar-Joseph, Ziv; Ideker, Trey | R01ES014811 | Genome Biol (2010) |
20653936
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2010 |
| Rewiring of genetic networks in response to DNA damage. | Bandyopadhyay, Sourav; Mehta, Monika; Kuo, Dwight; Sung, Min-Kyung; Chuang, Ryan; Jaehnig, Eri ... | R01ES014811 | Science (2010 Dec 03) |
21127252
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2010 |
| Dynamic reprogramming of transcription factors to and from the subtelomere. | Mak, H Craig; Pillus, Lorraine; Ideker, Trey | R01ES014811 | Genome Res (2009 Jun) |
19372386
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2009 |
| Genome-wide fitness and expression profiling implicate Mga2 in adaptation to hydrogen peroxide. | Kelley, Ryan; Ideker, Trey | R01ES014811 | PLoS Genet (2009 May) |
19503593
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2009 |
| Perspectives on the DNA damage and replication checkpoint responses in Saccharomyces cerevisiae. | Putnam, Christopher D; Jaehnig, Eric J; Kolodner, Richard D | R01ES014811 | DNA Repair (Amst) (2009 Sep 2) |
19477695
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2009 |
| A systems approach to delineate functions of paralogous transcription factors: role of the Yap famil ... | Tan, Kai; Feizi, Hoda; Luo, Colin; Fan, Stephanie H; Ravasi, Timothy; Ideker, Trey G | R01ES014811 | Proc Natl Acad Sci U S A (2008 Feb 26) |
18287073
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2008 |
| Forging new ties between E. coli genes. | Ideker, Trey | R01ES014811 | Cell (2008 Jun 27) |
18585345
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2008 |
| Functional maps of protein complexes from quantitative genetic interaction data. | Bandyopadhyay, Sourav; Kelley, Ryan; Krogan, Nevan J; Ideker, Trey | R01ES014811 | PLoS Comput Biol (2008 Apr 18) |
18421374
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2008 |
| Inferring pathway activity toward precise disease classification. | Lee, Eunjung; Chuang, Han-Yu; Kim, Jong-Won; Ideker, Trey; Lee, Doheon | R01ES014811 | PLoS Comput Biol (2008 Nov) |
18989396
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2008 |
| Protein networks in disease. | Ideker, Trey; Sharan, Roded | R01ES014811 | Genome Res (2008 Apr) |
18381899
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2008 |
| Integrating physical and genetic maps: from genomes to interaction networks. | Beyer, Andreas; Bandyopadhyay, Sourav; Ideker, Trey | R01ES014811 | Nat Rev Genet (2007 Sep) |
17703239
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2007 |
| Network-based classification of breast cancer metastasis. | Chuang, Han-Yu; Lee, Eunjung; Liu, Yu-Tsueng; Lee, Doheon; Ideker, Trey | R01ES014811 | Mol Syst Biol (2007) |
17940530
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2007 |
| Transcriptional regulation of protein complexes within and across species. | Tan, Kai; Shlomi, Tomer; Feizi, Hoda; Ideker, Trey; Sharan, Roded | R01ES014811 | Proc Natl Acad Sci U S A (2007 Jan 23) |
17227853
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2007 |
| A direct comparison of protein interaction confidence assignment schemes. | Suthram, Silpa; Shlomi, Tomer; Ruppin, Eytan; Sharan, Roded; Ideker, Trey | R01ES014811 | BMC Bioinformatics (2006 Jul 26) |
16872496
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2006 |
| A systems approach to mapping DNA damage response pathways. | Workman, Christopher T; Mak, H Craig; McCuine, Scott; Tagne, Jean-Bosco; Agarwal, Maya; Ozier, ... | R01ES014811 | Science (2006 May 19) |
16709784
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2006 |
| Integrated assessment and prediction of transcription factor binding. | Beyer, Andreas; Workman, Christopher; Hollunder, Jens; Radke, Dörte; Möller, Ulrich; Wilhelm, ... | R01ES014811 | PLoS Comput Biol (2006 Jun 16) |
16789814
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2006 |
| The Plasmodium protein network diverges from those of other eukaryotes. | Suthram, Silpa; Sittler, Taylor; Ideker, Trey | R01ES014811 | Nature (2005 Nov 3) |
16267557
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2005 |
| A systems approach to discovering signaling and regulatory pathways--or, how to digest large interac ... | Ideker, Trey | R01ES014811 | Adv Exp Med Biol (2004) |
15230090
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2004 |