| Project Title: | A SYSTEMS APPROACH TO MAPPING THE DNA DAMAGE RESPONSE |
|---|---|
| PI: | Ideker, Trey |
| Institution: | University Of California, San Diego |
| Grant Number: | R01ES014811 |
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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 09 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 |
| 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 08 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
|
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
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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; Glass, Christopher K; Id ... | R01ES014811 | Mol Cell (2018 03 01) |
29499140
|
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
|
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
|
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
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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
|
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
|
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
|
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
|
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
|
2013 |
| Differential analysis of high-throughput quantitative genetic interaction data. | Bean, Gordon J; Ideker, Trey | R01ES014811 | Genome Biol (2012 Dec 26) |
23268787
|
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
|
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
|
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 |