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Who We Fund: Publication Detail

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.

Viewing 70 publications
Export to Excel (http://www.niehs.nih.gov//portfolio/index.cfm/portfolio/grantpubdetail/grant_number/R01ES014811/format/excel)
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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 2019 
Transcriptional responses to DNA damage.   Silva, Erica; Ideker, Trey R01ES014811 DNA Repair (Amst) (2019 07) 31102970 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 2018 
Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls.   Shen, John Paul; Ideker, Trey R01ES014811 J Mol Biol (2018 09 14) 29932943 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 2016 
Advanced Applications of RNA Sequencing and Challenges.   Han, Yixing; Gao, Shouguo; Muegge, Kathrin; Zhang, Wei; Zhou, Bing R01ES014811 Bioinform Biol Insights (2015) 26609224 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 2013 
Differential analysis of high-throughput quantitative genetic interaction data.   Bean, Gordon J; Ideker, Trey R01ES014811 Genome Biol (2012 Dec 26) 23268787 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 2010 
Dynamic reprogramming of transcription factors to and from the subtelomere.   Mak, H Craig; Pillus, Lorraine; Ideker, Trey R01ES014811 Genome Res (2009 Jun) 19372386 Exiting the NIEHS site 2009 
Genome-wide fitness and expression profiling implicate Mga2 in adaptation to hydrogen peroxide.   Kelley, Ryan; Ideker, Trey R01ES014811 PLoS Genet (2009 May) 19503593 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 2008 
Forging new ties between E. coli genes.   Ideker, Trey R01ES014811 Cell (2008 Jun 27) 18585345 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 2008 
Protein networks in disease.   Ideker, Trey; Sharan, Roded R01ES014811 Genome Res (2008 Apr) 18381899 Exiting the NIEHS site 2008 
Integrating physical and genetic maps: from genomes to interaction networks.   Beyer, Andreas; Bandyopadhyay, Sourav; Ideker, Trey R01ES014811 Nat Rev Genet (2007 Sep) 17703239 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 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 Exiting the NIEHS site 2006 
The Plasmodium protein network diverges from those of other eukaryotes.   Suthram, Silpa; Sittler, Taylor; Ideker, Trey R01ES014811 Nature (2005 Nov 3) 16267557 Exiting the NIEHS site 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 Exiting the NIEHS site 2004 
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