MBD3 localizes at promoters, gene bodies and enhancers of active genes
Shimbo, Takashi, Du, Ying, Grimm, Sara A, Dhasarathy, Archana, Mav, Deepak, Shah, Ruchir R, Shi, Huidong, Wade, Paul A
Published in PLoS genetics (01.12.2013)
Published in PLoS genetics (01.12.2013)
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A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics
Mav, Deepak, Shah, Ruchir R, Howard, Brian E, Auerbach, Scott S, Bushel, Pierre R, Collins, Jennifer B, Gerhold, David L, Judson, Richard S, Karmaus, Agnes L, Maull, Elizabeth A, Mendrick, Donna L, Merrick, B Alex, Sipes, Nisha S, Svoboda, Daniel, Paules, Richard S
Published in PloS one (20.02.2018)
Published in PloS one (20.02.2018)
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SWIFT-Active Screener: Accelerated document screening through active learning and integrated recall estimation
Howard, Brian E., Phillips, Jason, Tandon, Arpit, Maharana, Adyasha, Elmore, Rebecca, Mav, Deepak, Sedykh, Alex, Thayer, Kristina, Merrick, B. Alex, Walker, Vickie, Rooney, Andrew, Shah, Ruchir R.
Published in Environment international (01.05.2020)
Published in Environment international (01.05.2020)
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Journal Article
An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers
Roberts, Steven A, Lawrence, Michael S, Klimczak, Leszek J, Grimm, Sara A, Fargo, David, Stojanov, Petar, Kiezun, Adam, Kryukov, Gregory V, Carter, Scott L, Saksena, Gordon, Harris, Shawn, Shah, Ruchir R, Resnick, Michael A, Getz, Gad, Gordenin, Dmitry A
Published in Nature genetics (01.09.2013)
Published in Nature genetics (01.09.2013)
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BMDExpress 2: enhanced transcriptomic dose-response analysis workflow
Phillips, Jason R, Svoboda, Daniel L, Tandon, Arpit, Patel, Shyam, Sedykh, Alex, Mav, Deepak, Kuo, Byron, Yauk, Carole L, Yang, Longlong, Thomas, Russell S, Gift, Jeff S, Davis, J Allen, Olszyk, Louis, Merrick, B Alex, Paules, Richard S, Parham, Fred, Saddler, Trey, Shah, Ruchir R, Auerbach, Scott S
Published in Bioinformatics (15.05.2019)
Published in Bioinformatics (15.05.2019)
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Low-calorie sweeteners and health outcomes: A demonstration of rapid evidence mapping (rEM)
Lam, Juleen, Howard, Brian E., Thayer, Kristina, Shah, Ruchir R.
Published in Environment international (01.02.2019)
Published in Environment international (01.02.2019)
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Journal Article
Runx2 transcriptome of prostate cancer cells: insights into invasiveness and bone metastasis
Baniwal, Sanjeev K, Khalid, Omar, Gabet, Yankel, Shah, Ruchir R, Purcell, Daniel J, Mav, Deepak, Kohn-Gabet, Alice E, Shi, Yunfan, Coetzee, Gerhard A, Frenkel, Baruch
Published in Molecular cancer (23.09.2010)
Published in Molecular cancer (23.09.2010)
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Transcriptional pathways linked to fetal and maternal hepatic dysfunction caused by gestational exposure to perfluorooctanoic acid (PFOA) or hexafluoropropylene oxide-dimer acid (HFPO-DA or GenX) in CD-1 mice
Blake, Bevin E., Miller, Colette N., Nguyen, Helen, Chappell, Vesna A., Phan, Trina P., Phadke, Dhiral P., Balik-Meisner, Michele R., Mav, Deepak, Shah, Ruchir R., Fenton, Suzanne E.
Published in Ecotoxicology and environmental safety (15.12.2022)
Published in Ecotoxicology and environmental safety (15.12.2022)
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Evaluation of 5-day In Vivo Rat Liver and Kidney With High-throughput Transcriptomics for Estimating Benchmark Doses of Apical Outcomes
Gwinn, William M, Auerbach, Scott S, Parham, Fred, Stout, Matthew D, Waidyanatha, Suramya, Mutlu, Esra, Collins, Brad, Paules, Richard S, Merrick, Bruce Alex, Ferguson, Stephen, Ramaiahgari, Sreenivasa, Bucher, John R, Sparrow, Barney, Toy, Heather, Gorospe, Jenni, Machesky, Nick, Shah, Ruchir R, Balik-Meisner, Michele R, Mav, Deepak, Phadke, Dhiral P, Roberts, Georgia, DeVito, Michael J
Published in Toxicological sciences (01.08.2020)
Published in Toxicological sciences (01.08.2020)
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Clustered Mutations in Yeast and in Human Cancers Can Arise from Damaged Long Single-Strand DNA Regions
Roberts, Steven A., Sterling, Joan, Thompson, Cole, Harris, Shawn, Mav, Deepak, Shah, Ruchir, Klimczak, Leszek J., Kryukov, Gregory V., Malc, Ewa, Mieczkowski, Piotr A., Resnick, Michael A., Gordenin, Dmitry A.
Published in Molecular cell (25.05.2012)
Published in Molecular cell (25.05.2012)
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Correction: Pannala et al. High-Throughput Transcriptomics Differentiates Toxic versus Non-Toxic Chemical Exposures Using a Rat Liver Model. Int. J. Mol. Sci. 2023, 24 , 17425
Pannala, Venkat R, Balik-Meisner, Michele R, Mav, Deepak, Phadke, Dhiral P, Scholl, Elizabeth H, Shah, Ruchir R, Auerbach, Scott S, Wallqvist, Anders
Published in International journal of molecular sciences (28.06.2024)
Published in International journal of molecular sciences (28.06.2024)
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Arsenite malignantly transforms human prostate epithelial cells in vitro by gene amplification of mutated KRAS
Merrick, B Alex, Phadke, Dhiral P, Bostrom, Meredith A, Shah, Ruchir R, Wright, Garron M, Wang, Xinguo, Gordon, Oksana, Pelch, Katherine E, Auerbach, Scott S, Paules, Richard S, DeVito, Michael J, Waalkes, Michael P, Tokar, Erik J
Published in PloS one (22.04.2019)
Published in PloS one (22.04.2019)
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Journal Article
Glucocorticoids Modulate MicroRNA Expression and Processing during Lymphocyte Apoptosis
Smith, Lindsay K., Shah, Ruchir R., Cidlowski, John A.
Published in The Journal of biological chemistry (19.11.2010)
Published in The Journal of biological chemistry (19.11.2010)
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RNA polymerase is poised for activation across the genome
Adelman, Karen, Muse, Ginger W, Gilchrist, Daniel A, Nechaev, Sergei, Shah, Ruchir, Parker, Joel S, Grissom, Sherry F, Zeitlinger, Julia
Published in Nature genetics (01.12.2007)
Published in Nature genetics (01.12.2007)
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The Power of Resolution: Contextualized Understanding of Biological Responses to Liver Injury Chemicals Using High-throughput Transcriptomics and Benchmark Concentration Modeling
Ramaiahgari, Sreenivasa C, Auerbach, Scott S, Saddler, Trey O, Rice, Julie R, Dunlap, Paul E, Sipes, Nisha S, DeVito, Michael J, Shah, Ruchir R, Bushel, Pierre R, Merrick, Bruce A, Paules, Richard S, Ferguson, Stephen S
Published in Toxicological sciences (01.06.2019)
Published in Toxicological sciences (01.06.2019)
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RNA-Seq profiling reveals novel hepatic gene expression pattern in aflatoxin B1 treated rats
Merrick, B Alex, Phadke, Dhiral P, Auerbach, Scott S, Mav, Deepak, Stiegelmeyer, Suzy M, Shah, Ruchir R, Tice, Raymond R
Published in PloS one (22.04.2013)
Published in PloS one (22.04.2013)
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Low-calorie sweeteners and health outcomes: an evaluation of rapid versus traditional evidence mapping
Lam, Juleen, Elmore, Rebecca, Howard, Brian, Shah, Ruchir R
Published in BMC research notes (19.02.2022)
Published in BMC research notes (19.02.2022)
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Hazard and risk characterization of 56 structurally diverse PFAS using a targeted battery of broad coverage assays using six human cell types
Ford, Lucie C., Lin, Hsing-Chieh, Tsai, Han-Hsuan D., Zhou, Yi-Hui, Wright, Fred A., Sedykh, Alexander, Shah, Ruchir R., Chiu, Weihsueh A., Rusyn, Ivan
Published in Toxicology (Amsterdam) (01.03.2024)
Published in Toxicology (Amsterdam) (01.03.2024)
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