Skip Navigation
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Internet Explorer is no longer a supported browser.

This website may not display properly with Internet Explorer. For the best experience, please use a more recent browser such as the latest versions of Google Chrome, Microsoft Edge, and/or Mozilla Firefox. Thank you.

COVID-19 is an emerging, rapidly evolving situation.

Get the latest public health information from CDC. Get the latest research information from NIH.

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 133 publications
Export to Excel (http://www.niehs.nih.gov//portfolio/index.cfm/portfolio/sciencecodepubs/sc/75/topic/75/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 May 22) 32299836 Exiting the NIEHS site 2020 
Analysis of model PM2.5-induced inflammation and cytotoxicity by the combination of a virtual carbon ...   Liu, Guohong; Yan, Xiliang; Sedykh, Alexander; Pan, Xiujiao; Zhao, Xiaoli; Yan, Bing; Zhu, Ha ... R15ES023148, R15ES023148 Ecotoxicol Environ Saf (2020 Mar 15) 31972454 Exiting the NIEHS site 2020 
Analysis of stimulus-induced brain dynamics during naturalistic paradigms.   Simony, Erez; Chang, Catie K22ES028048 Neuroimage (2020 Aug 01) 31843711 Exiting the NIEHS site 2020 
Big Data and Artificial Intelligence Modeling for Drug Discovery.   Zhu, Hao R15ES023148, R15ES023148 Annu Rev Pharmacol Toxicol (2020 01 06) 31518513 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, R15ES023148, R15ES023148 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 
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 
Harnessing big 'omics' data and AI for drug discovery in hepatocellular carcinoma.   Chen, Bin; Garmire, Lana; Calvisi, Diego F; Chua, Mei-Sze; Kelley, Robin K; Chen, Xin K01ES028047 Nat Rev Gastroenterol Hepatol (2020 04) 31900465 Exiting the NIEHS site 2020 
Impaired vigilance networks in temporal lobe epilepsy: Mechanisms and clinical implications.   Englot, Dario J; Morgan, Victoria L; Chang, Catie K22ES028048 Epilepsia (2020 02) 31901182 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, R15ES023148, R15ES023148 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 May 28) 32470399 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 
Physiological changes in sleep that affect fMRI inference.   Duyn, Jeff H; Ozbay, Pinar S; Chang, Catie; Picchioni, Dante K22ES028048 Curr Opin Behav Sci (2020 Jun) 32613032 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 Jul 01) 32619550 Exiting the NIEHS site 2020 
Resting-state "physiological networks".   Chen, Jingyuan E; Lewis, Laura D; Chang, Catie; Tian, Qiyuan; Fultz, Nina E; Ohringer, Ned A; ... K22ES028048 Neuroimage (2020 Jun) 32145437 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 May 13) 32400901 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 
A single H/ACA small nucleolar RNA mediates tumor suppression downstream of oncogenic RAS.   McMahon, Mary; Contreras, Adrian; Holm, Mikael; Uechi, Tamayo; Forester, Craig M; Pang, Xiamin ... K01ES028047 Elife (2019 09 03) 31478838 Exiting the NIEHS site 2019 
Advancing Computational Toxicology in the Big Data Era by Artificial Intelligence: Data-Driven and M ...   Ciallella, Heather L; Zhu, Hao R15ES023148, R15ES023148 Chem Res Toxicol (2019 04 15) 30907586 Exiting the NIEHS site 2019 
AICM: A Genuine Framework for Correcting Inconsistency Between Large Pharmacogenomics Datasets.   Hu, Zhiyue Tom; Ye, Yuting; Newbury, Patrick A; Huang, Haiyan; Chen, Bin K01ES028047 Pac Symp Biocomput (2019) 30864327 Exiting the NIEHS site 2019 
All-night functional magnetic resonance imaging sleep studies.   Moehlman, Thomas M; de Zwart, Jacco A; Chappel-Farley, Miranda G; Liu, Xiao; McClain, Irene B; ... K22ES028048 J Neurosci Methods (2019 03 15) 30243817 Exiting the NIEHS site 2019 
Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor type ...   Yu, K; Chen, B; Aran, D; Charalel, J; Yau, C; Wolf, D M; van 't Veer, L J; Butte, A J; Golds ... K01ES028047 Nat Commun (2019 08 08) 31395879 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, R01ES025225, R01ES027747 Genome Biol (2019 11 25) 31767039 Exiting the NIEHS site 2019 
Evaluating cell lines as models for metastatic breast cancer through integrative analysis of genomic ...   Liu, Ke; Newbury, Patrick A; Glicksberg, Benjamin S; Zeng, William Z D; Paithankar, Shreya; And ... K01ES028047 Nat Commun (2019 05 15) 31092827 Exiting the NIEHS site 2019 
Leveraging Big Data to Transform Drug Discovery.   Glicksberg, Benjamin S; Li, Li; Chen, Rong; Dudley, Joel; Chen, Bin K01ES028047 Methods Mol Biol (2019) 30848458 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 
Nonanimal Models for Acute Toxicity Evaluations: Applying Data-Driven Profiling and Read-Across.   Russo, Daniel P; Strickland, Judy; Karmaus, Agnes L; Wang, Wenyi; Shende, Sunil; Hartung, Thom ... R15ES023148, R15ES023148 Environ Health Perspect (2019 04) 30933541 Exiting the NIEHS site 2019 
Selecting precise reference normal tissue samples for cancer research using a deep learning approach ...   Zeng, William Z D; Glicksberg, Benjamin S; Li, Yangyan; Chen, Bin K01ES028047 BMC Med Genomics (2019 01 31) 30704474 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 
Sympathetic activity contributes to the fMRI signal.   Özbay, Pinar Senay; Chang, Catie; Picchioni, Dante; Mandelkow, Hendrik; Chappel-Farley, Miranda ... K22ES028048 Commun Biol (2019) 31754651 Exiting the NIEHS site 2019 
Sympathetic activity contributes to the fMRI signal.   Özbay, Pinar Senay; Chang, Catie; Picchioni, Dante; Mandelkow, Hendrik; Chappel-Farley, Miranda ... K22ES028048 Commun Biol (2019 Nov 18) 31925226 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 
Using a hybrid read-across method to evaluate chemical toxicity based on chemical structure and biol ...   Guo, Yajie; Zhao, Linlin; Zhang, Xiaoyi; Zhu, Hao R15ES023148, R15ES023148 Ecotoxicol Environ Saf (2019 Aug 30) 31004930 Exiting the NIEHS site 2019 
Co-activation patterns in resting-state fMRI signals.   Liu, Xiao; Zhang, Nanyin; Chang, Catie; Duyn, Jeff H K22ES028048 Neuroimage (2018 10 15) 29355767 Exiting the NIEHS site 2018 
Comparing Multiple Machine Learning Algorithms and Metrics for Estrogen Receptor Binding Prediction.   Russo, Daniel P; Zorn, Kimberley M; Clark, Alex M; Zhu, Hao; Ekins, Sean R15ES023148, R15ES023148 Mol Pharm (2018 10 01) 30114914 Exiting the NIEHS site 2018 
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 
Hippo Cascade Controls Lineage Commitment of Liver Tumors in Mice and Humans.   Zhang, Shanshan; Wang, Jingxiao; Wang, Haichuan; Fan, Lingling; Fan, Biao; Zeng, Billy; Tao, ... K01ES028047 Am J Pathol (2018 04) 29378174 Exiting the NIEHS site 2018 
Mapping and interpreting the dynamic connectivity of the brain.   Chang, Catie; Keilholz, Shella; Miller, Robyn; Woolrich, Mark K22ES028048 Neuroimage (2018 10 15) 30075278 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; 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 
Alternative approaches for identifying acute systemic toxicity: Moving from research to regulatory t ...   Hamm, Jon; Sullivan, Kristie; Clippinger, Amy J; Strickland, Judy; Bell, Shannon; Bhhatarai, B ... P30ES005022, R15ES023148, R15ES023148 Toxicol In Vitro (2017 Jun) 28069485 Exiting the NIEHS site 2017 
CIIPro: a new read-across portal to fill data gaps using public large-scale chemical and biological ...   Russo, Daniel P; Kim, Marlene T; Wang, Wenyi; Pinolini, Daniel; Shende, Sunil; Strickland, Jud ... P30ES005022, R15ES023148, R15ES023148 Bioinformatics (2017 02 01) 28172359 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 
Elucidation of the Molecular Determinants for Optimal Perfluorooctanesulfonate Adsorption Using a Co ...   Liu, Yin; Su, Gaoxing; Wang, Fei; Jia, Jianbo; Li, Shuhuan; Zhao, Linlin; Shi, Yali; Cai, Ya ... R15ES023148, R15ES023148 Environ Sci Technol (2017 Jun 20) 28537376 Exiting the NIEHS site 2017 
Experimental Errors in QSAR Modeling Sets: What We Can Do and What We Cannot Do.   Zhao, Linlin; Wang, Wenyi; Sedykh, Alexander; Zhu, Hao P30ES005022, R15ES023148, R15ES023148 ACS Omega (2017 Jun 30) 28691113 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 
Predicting Nano-Bio Interactions by Integrating Nanoparticle Libraries and Quantitative Nanostructur ...   Wang, Wenyi; Sedykh, Alexander; Sun, Hainan; Zhao, Linlin; Russo, Daniel P; Zhou, Hongyu; Yan, ... P30ES005022, R15ES023148, R15ES023148 ACS Nano (2017 12 26) 29149552 Exiting the NIEHS site 2017 
Toward a systematic exploration of nano-bio interactions.   Bai, Xue; Liu, Fang; Liu, Yin; Li, Cong; Wang, Shenqing; Zhou, Hongyu; Wang, Wenyi; Zhu, Hao ... P30ES005022, R15ES023148, R15ES023148 Toxicol Appl Pharmacol (2017 05 15) 28344110 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 
Accessing the High-Throughput Screening Data Landscape.   Russo, Daniel P; Zhu, Hao R15ES023148, R15ES023148 Methods Mol Biol (2016) 27518633 Exiting the NIEHS site 2016 
Analysis of Draize eye irritation testing and its prediction by mining publicly available 2008-2014 ...   Luechtefeld, Thomas; Maertens, Alexandra; Russo, Daniel P; Rovida, Costanza; Zhu, Hao; Hartung, ... R15ES023148, R15ES023148, T32ES007141 ALTEX (2016) 26863293 Exiting the NIEHS site 2016 
Analysis of public oral toxicity data from REACH registrations 2008-2014.   Luechtefeld, Thomas; Maertens, Alexandra; Russo, Daniel P; Rovida, Costanza; Zhu, Hao; Hartung, ... R15ES023148, R15ES023148, T32ES007141 ALTEX (2016) 26863198 Exiting the NIEHS site 2016 
Analysis of publically available skin sensitization data from REACH registrations 2008-2014.   Luechtefeld, Thomas; Maertens, Alexandra; Russo, Daniel P; Rovida, Costanza; Zhu, Hao; Hartung, ... R15ES023148, R15ES023148, T32ES007141 ALTEX (2016) 26863411 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 
CIIPro: a new read-across portal to fill data gaps using public large-scale chemical and biological ...   Russo, Daniel P; Kim, Marlene T; Wang, Wenyi; Pinolini, Daniel; Shende, Sunil; Strickland, Jud ... P30ES005022, R15ES023148, R15ES023148 Bioinformatics (2016 Oct 14) 27742693 Exiting the NIEHS site 2016 
Curating and Preparing High-Throughput Screening Data for Quantitative Structure-Activity Relationsh ...   Kim, Marlene T; Wang, Wenyi; Sedykh, Alexander; Zhu, Hao R15ES023148, R15ES023148 Methods Mol Biol (2016) 27518634 Exiting the NIEHS site 2016 
Discovery of Novel Tricyclic Thiazepine Derivatives as Anti-Drug-Resistant Cancer Agents by Combinin ...   Xiang, Jinbao; Zhang, Zhuoqi; Mu, Yan; Xu, Xianxiu; Guo, Sigen; Liu, Yongjin; Russo, Daniel P ... P30ES005022, R15ES023148, R15ES023148 ACS Comb Sci (2016 05 09) 27082930 Exiting the NIEHS site 2016 
From fighting depression to conquering tumors: a novel tricyclic thiazepine compound as a tubulin po ...   Mu, Y; Liu, Y; Xiang, J; Zhang, Q; Zhai, S; Russo, D P; Zhu, H; Bai, X; Yan, B R15ES023148, R15ES023148 Cell Death Dis (2016 Mar 17) 26986511 Exiting the NIEHS site 2016 
Global analysis of publicly available safety data for 9,801 substances registered under REACH from 2 ...   Luechtefeld, Thomas; Maertens, Alexandra; Russo, Daniel P; Rovida, Costanza; Zhu, Hao; Hartung, ... R15ES023148, R15ES023148, T32ES007141 ALTEX (2016) 26863090 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 
Mechanism Profiling of Hepatotoxicity Caused by Oxidative Stress Using Antioxidant Response Element ...   Kim, Marlene Thai; Huang, Ruili; Sedykh, Alexander; Wang, Wenyi; Xia, Menghang; Zhu, Hao P30ES005022, R15ES023148, R15ES023148 Environ Health Perspect (2016 05) 26383846 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 
Predictive Modeling of Estrogen Receptor Binding Agents Using Advanced Cheminformatics Tools and Mas ...   Ribay, Kathryn; Kim, Marlene T; Wang, Wenyi; Pinolini, Daniel; Zhu, Hao P30ES005022, R15ES023148, R15ES023148 Front Environ Sci (2016 Mar) 27642585 Exiting the NIEHS site 2016 
Supporting read-across using biological data.   Zhu, Hao; Bouhifd, Mounir; Donley, Elizabeth; Egnash, Laura; Kleinstreuer, Nicole; Kroese, E D ... P30ES005022, R15ES023148, R15ES023148, T32ES007141 ALTEX (2016) 26863516 Exiting the NIEHS site 2016 
Toward Good Read-Across Practice (GRAP) guidance.   Ball, Nicholas; Cronin, Mark T D; Shen, Jie; Blackburn, Karen; Booth, Ewan D; Bouhifd, Mounir; ... P30ES005022, R15ES023148, R15ES023148, T32ES007141 ALTEX (2016) 26863606 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 
Developing Enhanced Blood-Brain Barrier Permeability Models: Integrating External Bio-Assay Data in ...   Wang, Wenyi; Kim, Marlene T; Sedykh, Alexander; Zhu, Hao R15ES023148, R15ES023148 Pharm Res (2015 Sep) 25862462 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 
Experimental modulation and computational model of nano-hydrophobicity.   Li, Shuhuan; Zhai, Shumei; Liu, Yin; Zhou, Hongyu; Wu, Jinmei; Jiao, Qing; Zhang, Bin; Zhu, ... R15ES023148, R15ES023148 Biomaterials (2015 Jun) 25818437 Exiting the NIEHS site 2015 
Improving both aqueous solubility and anti-cancer activity by assessing progressive lead optimizatio ...   Liu, Yin; Li, Fei; Wu, Ling; Wang, Wenyi; Zhu, Hao; Zhang, Qiu; Zhou, Hongyu; Yan, Bing R15ES023148, R15ES023148 Bioorg Med Chem Lett (2015 May 01) 25827524 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 
Big data in chemical toxicity research: the use of high-throughput screening assays to identify pote ...   Zhu, Hao; Zhang, Jun; Kim, Marlene T; Boison, Abena; Sedykh, Alexander; Moran, Kimberlee R15ES023148, R15ES023148 Chem Res Toxicol (2014 Oct 20) 25195622 Exiting the NIEHS site 2014 
Critical evaluation of human oral bioavailability for pharmaceutical drugs by using various cheminfo ...   Kim, Marlene T; Sedykh, Alexander; Chakravarti, Suman K; Saiakhov, Roustem D; Zhu, Hao R15ES023148, R15ES023148 Pharm Res (2014 Apr) 24306326 Exiting the NIEHS site 2014 
Design, synthesis and experimental validation of novel potential chemopreventive agents using random ...   Sprague, Brienne; Shi, Qian; Kim, Marlene T; Zhang, Liying; Sedykh, Alexander; Ichiishi, Eiich ... R15ES023148, R15ES023148 J Comput Aided Mol Des (2014 Jun) 24840854 Exiting the NIEHS site 2014 
Profiling animal toxicants by automatically mining public bioassay data: a big data approach for com ...   Zhang, Jun; Hsieh, Jui-Hua; Zhu, Hao R15ES023148, R15ES023148 PLoS One (2014) 24950175 Exiting the NIEHS site 2014 
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 
Tuning cell autophagy by diversifying carbon nanotube surface chemistry.   Wu, Ling; Zhang, Yi; Zhang, Chengke; Cui, Xuehui; Zhai, Shumei; Liu, Yin; Li, Changlong; Zhu, ... R15ES023148, R15ES023148 ACS Nano (2014 Mar 25) 24552177 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 
Discovery of novel antimalarial compounds enabled by QSAR-based virtual screening.   Zhang, Liying; Fourches, Denis; Sedykh, Alexander; Zhu, Hao; Golbraikh, Alexander; Ekins, Sean ... R15ES023148, R15ES023148 J Chem Inf Model (2013 Feb 25) 23252936 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 
From QSAR to QSIIR: searching for enhanced computational toxicology models.   Zhu, Hao R15ES023148, R15ES023148 Methods Mol Biol (2013) 23086837 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 
Human intestinal transporter database: QSAR modeling and virtual profiling of drug uptake, efflux an ...   Sedykh, Alexander; Fourches, Denis; Duan, Jianmin; Hucke, Oliver; Garneau, Michel; Zhu, Hao; B ... R15ES023148, R15ES023148 Pharm Res (2013 Apr) 23269503 Exiting the NIEHS site 2013 
Identification of putative estrogen receptor-mediated endocrine disrupting chemicals using QSAR- and ...   Zhang, Liying; Sedykh, Alexander; Tripathi, Ashutosh; Zhu, Hao; Afantitis, Antreas; Mouchlis, ... R15ES023148, R15ES023148 Toxicol Appl Pharmacol (2013 Oct 01) 23707773 Exiting the NIEHS site 2013 
The use of pseudo-equilibrium constant affords improved QSAR models of human plasma protein binding.   Zhu, Xiang-Wei; Sedykh, Alexander; Zhu, Hao; Liu, Shu-Shen; Tropsha, Alexander R15ES023148, R15ES023148 Pharm Res (2013 Jul) 23568522 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 
Predicting chemical ocular toxicity using a combinatorial QSAR approach.   Solimeo, Renee; Zhang, Jun; Kim, Marlene; Sedykh, Alexander; Zhu, Hao R15ES023148, R15ES023148 Chem Res Toxicol (2012 Dec 17) 23148656 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, R01ES019566 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 
Back
to Top