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Your Environment. Your Health.

Who We Fund: Publications associated with Application Of Technology To Disease - Computational Biology / Computational Methods for Exposure Assessment

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 113 publications
Export to Excel (http://www.niehs.nih.gov//portfolio/index.cfm?do=portfolio.sciencecodepubs&&sc=75&topic=75&format=excel)
Publication Title Authors Grant Number(s) Journal (Pub date) PubMed Link Pub Year
A computational system for Bayesian benchmark dose estimation of genomic data in BBMD.   Ji, Chao; Weissmann, Andrew; Shao, Kan R42ES032642 Environ Int (2022 03) 35151117 Exiting the NIEHS site 2022 
Adverse childhood experiences, diabetes and associated conditions, preventive care practices and hea ...   Schüssler-Fiorenza Rose, Sophia Miryam; Snyder, Michael P; Slavich, George M K08ES028825 Prev Med (2022 07) 35398366 Exiting the NIEHS site 2022 
Double-strand breaks: When DNA repair events accidentally meet.   Fujii, Shingo; Sobol, Robert W; Fuchs, Robert P P01ES028949, R01ES014811, U01ES029518, U01ES029518 DNA Repair (Amst) (2022 04) 35219626 Exiting the NIEHS site 2022 
In Silico Structure Predictions for Non-targeted Analysis: From Physicochemical Properties to Molecu ...   Abrahamsson, Dimitri; Siddharth, Adi; Young, Thomas M; Sirota, Marina; Park, June-Soo; Martin, ... K99ES032892, P30ES030284, R01ES027051 J Am Soc Mass Spectrom (2022 Jul 06) 35649165 Exiting the NIEHS site 2022 
Mechanism-driven modeling of chemical hepatotoxicity using structural alerts and an in vitro screeni ...   Jia, Xuelian; Wen, Xia; Russo, Daniel P; Aleksunes, Lauren M; Zhu, Hao P30ES005022, R01ES031080, R35ES031709 J Hazard Mater (2022 08 15) 35739723 Exiting the NIEHS site 2022 
Precision environmental health monitoring by longitudinal exposome and multi-omics profiling.   Gao, Peng; Shen, Xiaotao; Zhang, Xinyue; Jiang, Chao; Zhang, Sai; Zhou, Xin; Schüssler-Fiorenz ... K08ES028825 Genome Res (2022 06) 35667843 Exiting the NIEHS site 2022 
Predicting Prenatal Developmental Toxicity Based On the Combination of Chemical Structures and Biolo ...   Ciallella, Heather L; Russo, Daniel P; Sharma, Swati; Li, Yafan; Sloter, Eddie; Sweet, Len; Hu ... R01ES031080, R35ES031709 Environ Sci Technol (2022 05 03) 35451820 Exiting the NIEHS site 2022 
Replacement per- and polyfluoroalkyl substances (PFAS) are potent modulators of lipogenic and drug m ...   Marques, Emily; Pfohl, Marisa; Wei, Wei; Tarantola, Giuseppe; Ford, Lucie; Amaeze, Ogochukwu; ... P42ES027706, R01ES031080, R35ES031709 Toxicol Appl Pharmacol (2022 05 01) 35337807 Exiting the NIEHS site 2022 
Secular Trends in Prevalence of Heart Failure Diagnosis over 20 Years (from the US NHANES).   Siontis, George Cm; Bhatt, Deepak L; Patel, Chirag J R01ES032470 Am J Cardiol (2022 06 01) 35361480 Exiting the NIEHS site 2022 
Shared exposure liability of type 2 diabetes and other chronic conditions in the UK Biobank.   He, Yixuan; Patel, Chirag J R01ES032470 Acta Diabetol (2022 Jun) 35348899 Exiting the NIEHS site 2022 
Statistical implications of endogeneity induced by residential segregation in small-area modelling o ...   Nethery, Rachel C; Chen, Jarvis T; Krieger, Nancy; Waterman, Pamela D; Peterson, Emily; Waller, ... K01ES032458, P30ES000002 Am Stat (2022) 35531350 Exiting the NIEHS site 2022 
Systematically assessing microbiome-disease associations identifies drivers of inconsistency in meta ...   Tierney, Braden T; Tan, Yingxuan; Yang, Zhen; Shui, Bing; Walker, Michaela J; Kent, Benjamin M ... R01ES032470 PLoS Biol (2022 03) 35235560 Exiting the NIEHS site 2022 
Using deep learning to predict abdominal age from liver and pancreas magnetic resonance images.   Le Goallec, Alan; Diai, Samuel; Collin, Sasha; Prost, Jean-Baptiste; Vincent, Théo; Patel, Chi ... R01ES032470 Nat Commun (2022 04 13) 35418184 Exiting the NIEHS site 2022 
A Comprehensive Non-targeted Analysis Study of the Prenatal Exposome.   Panagopoulos Abrahamsson, Dimitri; Wang, Aolin; Jiang, Ting; Wang, Miaomiao; Siddharth, Adi; Mo ... K99ES032892, P30ES030284, R01ES027051 Environ Sci Technol (2021 08 03) 34260856 Exiting the NIEHS site 2021 
CATMoS: Collaborative Acute Toxicity Modeling Suite.   Mansouri, Kamel; Karmaus, Agnes L; Fitzpatrick, Jeremy; Patlewicz, Grace; Pradeep, Prachi; Albe ... P42ES016465, R01ES031080 Environ Health Perspect (2021 04) 33929906 Exiting the NIEHS site 2021 
Characterising the relationships between physiological indicators and all-cause mortality (NHANES): ...   Nguyen, Vy Kim; Colacino, Justin; Chung, Ming Kei; Goallec, Alan Le; Jolliet, Olivier; Patel, ... P30ES017885, R01ES028802, R01ES028802, R01ES028802, R01ES028802, R01ES032470 Lancet Healthy Longev (2021 10) 34825242 Exiting the NIEHS site 2021 
Construction of a Virtual Opioid Bioprofile: A Data-Driven QSAR Modeling Study to Identify New Analg ...   Jia, Xuelian; Ciallella, Heather L; Russo, Daniel P; Zhao, Linlin; James, Morgan H; Zhu, Hao P30ES005022, R01ES031080 ACS Sustain Chem Eng (2021 Mar 15) 34239782 Exiting the NIEHS site 2021 
Depression, health comorbidities, cognitive symptoms and their functional impact: Not just a geriatr ...   Schüssler-Fiorenza Rose, Sophia Miryam; Bott, Nicholas T; Heinemeyer, Erin E; Hantke, Nathan C; ... K08ES028825 J Psychiatr Res (2021 07) 34087515 Exiting the NIEHS site 2021 
Differential impacts of COVID-19 lockdowns on PM across the United States.   Chen, Kevin L; Henneman, Lucas R F; Nethery, Rachel C K01ES032458, T32ES007142 Environ Adv (2021 Dec) 34642672 Exiting the NIEHS site 2021 
Exploiting DNA Endonucleases to Advance Mechanisms of DNA Repair.   Thompson, Marlo K; Sobol, Robert W; Prakash, Aishwarya P01ES028949, R01ES014811, R01ES030084, R01ES030084, R35ES031708, R35ES031708, R44ES032522, U01ES029518, U01ES029518 Biology (Basel) (2021 Jun 14) 34198612 Exiting the NIEHS site 2021 
Large-Scale Implementation and Flaw Investigation of Human Serum Suspect Screening Analysis for Indu ...   Jiang, Ting; Wang, Miaomiao; Wang, Aolin; Abrahamsson, Dimitri; Kuang, Weixin; Morello-Frosch, ... K99ES032892, P30ES030284, R01ES027051 J Am Soc Mass Spectrom (2021 Sep 01) 34409840 Exiting the NIEHS site 2021 
Leveraging vibration of effects analysis for robust discovery in observational biomedical data scien ...   Tierney, Braden T; Anderson, Elizabeth; Tan, Yingxuan; Claypool, Kajal; Tangirala, Sivateja; Ko ... R01ES032470 PLoS Biol (2021 09) 34555021 Exiting the NIEHS site 2021 
Mapping the multiscale structure of biological systems.   Schaffer, Leah V; Ideker, Trey R01ES014811 Cell Syst (2021 06 16) 34139169 Exiting the NIEHS site 2021 
Optimization of 1,4-bis(arylsulfonamido)naphthalene-N,N'-diacetic acids as inhibitors of Keap1-Nrf2 ...   Abed, Dhulfiqar Ali; Lee, Sumi; Wen, Xia; Ali, Ahmed R; Mangipudy, Vaibhav; Aleksunes, Lauren ... P30ES005022, R01ES031080 Bioorg Med Chem (2021 08 15) 34252790 Exiting the NIEHS site 2021 
Plasma metabolomics of autism spectrum disorder and influence of shared components in proband famili ...   Chung, Ming Kei; Smith, Matthew Ryan; Lin, Yufei; Walker, Douglas I; Jones, Dean; Patel, Chira ... R01ES032470 Exposome (2021) 35028569 Exiting the NIEHS site 2021 
Predictive modeling of estrogen receptor agonism, antagonism, and binding activities using machine- ...   Ciallella, Heather L; Russo, Daniel P; Aleksunes, Lauren M; Grimm, Fabian A; Zhu, Hao P30ES005022, R01ES031080 Lab Invest (2021 04) 32778734 Exiting the NIEHS site 2021 
Revealing Adverse Outcome Pathways from Public High-Throughput Screening Data to Evaluate New Toxica ...   Ciallella, Heather L; Russo, Daniel P; Aleksunes, Lauren M; Grimm, Fabian A; Zhu, Hao P30ES005022, R01ES031080 Environ Sci Technol (2021 08 03) 34304572 Exiting the NIEHS site 2021 
Temporal dynamics of base excision/single-strand break repair protein complex assembly/disassembly a ...   Koczor, Christopher A; Saville, Kate M; Andrews, Joel F; Clark, Jennifer; Fang, Qingming; Li, ... P01ES028949, R01ES014811, U01ES029518, U01ES029518 Cell Rep (2021 11 02) 34731617 Exiting the NIEHS site 2021 
Wearable sensors enable personalized predictions of clinical laboratory measurements.   Dunn, Jessilyn; Kidzinski, Lukasz; Runge, Ryan; Witt, Daniel; Hicks, Jennifer L; Schüssler-Fior ... K08ES028825 Nat Med (2021 06) 34031607 Exiting the NIEHS site 2021 
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 
Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling ...   Zhao, Linlin; Ciallella, Heather L; Aleksunes, Lauren M; Zhu, Hao P30ES005022, R01ES031080 Drug Discov Today (2020 09) 32663517 Exiting the NIEHS site 2020 
Construction of a web-based nanomaterial database by big data curation and modeling friendly nanostr ...   Yan, Xiliang; Sedykh, Alexander; Wang, Wenyi; Yan, Bing; Zhu, Hao P30ES005022, R01ES031080 Nat Commun (2020 05 20) 32433469 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 
Deep longitudinal multiomics profiling reveals two biological seasonal patterns in California.   Sailani, M Reza; Metwally, Ahmed A; Zhou, Wenyu; Rose, Sophia Miryam Schüssler-Fiorenza; Ahadi, ... K08ES028825 Nat Commun (2020 10 01) 33004787 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 
Factors Associated with Supportive Care Service Use Among California Alzheimer's Disease Patients an ...   Newkirk, Lori A; Dao, Virginia L; Jordan, Joshua T; Alving, Loren I; Davies, Helen D; Hewett, ... K08ES028825 J Alzheimers Dis (2020) 31743997 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 
Mechanism-Driven Read-Across of Chemical Hepatotoxicants Based on Chemical Structures and Biological ...   Zhao, Linlin; Russo, Daniel P; Wang, Wenyi; Aleksunes, Lauren M; Zhu, Hao P30ES005022, R01ES031080 Toxicol Sci (2020 04 01) 32073637 Exiting the NIEHS site 2020 
Molecular Choreography of Acute Exercise.   Contrepois, Kévin; Wu, Si; Moneghetti, Kegan J; Hornburg, Daniel; Ahadi, Sara; Tsai, Ming-Shia ... K08ES028825 Cell (2020 05 28) 32470399 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 
Personal aging markers and ageotypes revealed by deep longitudinal profiling.   Ahadi, Sara; Zhou, Wenyu; Schüssler-Fiorenza Rose, Sophia Miryam; Sailani, M Reza; Contrepois, ... K08ES028825 Nat Med (2020 01) 31932806 Exiting the NIEHS site 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 11 09) 33096023 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 
The 5-HTTLPR long allele predicts two-year longitudinal increases in cortisol and declines in verbal ...   Hirst, Rayna B; Jordan, Joshua T; Schüssler-Fiorenza Rose, Sophia Miryam; Schneider, Logan; Kawa ... K08ES028825 Int J Geriatr Psychiatry (2020 09) 32400901 Exiting the NIEHS site 2020 
Using indication embeddings to represent patient health for drug safety studies.   Melamed, Rachel D K01ES028055 JAMIA Open (2020 Oct) 33376961 Exiting the NIEHS site 2020 
A longitudinal big data approach for precision health.   Schüssler-Fiorenza Rose, Sophia Miryam; Contrepois, Kévin; Moneghetti, Kegan J; Zhou, Wenyu; Mis ... K08ES028825 Nat Med (2019 05) 31068711 Exiting the NIEHS site 2019 
DNA methylation aging clocks: challenges and recommendations.   Bell, Christopher G; Lowe, Robert; Adams, Peter D; Baccarelli, Andrea A; Beck, Stephan; Bell, ... P30ES009089, R01ES014811, R01ES027747 Genome Biol (2019 11 25) 31767039 Exiting the NIEHS site 2019 
Longitudinal multi-omics of host-microbe dynamics in prediabetes.   Zhou, Wenyu; Sailani, M Reza; Contrepois, Kévin; Zhou, Yanjiao; Ahadi, Sara; Leopold, Shana R; ... K08ES028825 Nature (2019 05) 31142858 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 
Dot1 promotes H2B ubiquitination by a methyltransferase-independent mechanism.   van Welsem, Tibor; Korthout, Tessy; Ekkebus, Reggy; Morais, Dominique; Molenaar, Thom M; van Ha ... R01ES014811 Nucleic Acids Res (2018 11 30) 30203048 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 
Patchwork of contrasting medication cultures across the USA.   Melamed, Rachel D; Rzhetsky, Andrey K01ES028055 Nat Commun (2018 10 09) 30301884 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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