Works matching AU Shah, Ruchir R.

Results: 28

Genome-wide promoter DNA methylation profiling of hepatocellular carcinomas arising either spontaneously or due to chronic exposure to Ginkgo biloba extract (GBE) in B6C3F1/N mice.

Published in:

Archives of Toxicology, 2019, v. 93, n. 8, p. 2219, doi. 10.1007/s00204-019-02505-7

By:

Kovi, Ramesh C.;
Bhusari, Sachin;
Mav, Deepak;
Shah, Ruchir R.;
Ton, Thai Vu;
Hoenerhoff, Mark J.;
Sills, Robert C.;
Pandiri, Arun R.

Publication type:

Article

RNA-Seq-based toxicogenomic assessment of fresh frozen and formalin-fixed tissues yields similar mechanistic insights.

Published in:

Journal of Applied Toxicology, 2015, v. 35, n. 7, p. 766, doi. 10.1002/jat.3068

By:

Auerbach, Scott S.;
Phadke, Dhiral P.;
Mav, Deepak;
Holmgren, Stephanie;
Gao, Yuan;
Xie, Bin;
Shin, Joo Heon;
Shah, Ruchir R.;
Merrick, B. Alex;
Tice, Raymond R.

Publication type:

Article

MBD3 Localizes at Promoters, Gene Bodies and Enhancers of Active Genes.

Published in:

PLoS Genetics, 2013, v. 9, n. 12, p. 1, doi. 10.1371/journal.pgen.1004028

By:

Shimbo, Takashi;
Du, Ying;
Grimm, Sara A.;
Dhasarathy, Archana;
Mav, Deepak;
Shah, Ruchir R.;
Shi, Huidong;
Wade, Paul A.

Publication type:

Article

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers.

Published in:

Nature Genetics, 2013, v. 45, n. 9, p. 970, doi. 10.1038/ng.2702

By:

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

Publication type:

Article

Characterizing PFAS hazards and risks: a human population-based in vitro cardiotoxicity assessment strategy.

Published in:

Human Genomics, 2024, v. 18, n. 1, p. 1, doi. 10.1186/s40246-024-00665-x

By:

Ford, Lucie C.;
Lin, Hsing-Chieh;
Zhou, Yi-Hui;
Wright, Fred A.;
Gombar, Vijay K.;
Sedykh, Alexander;
Shah, Ruchir R.;
Chiu, Weihsueh A.;
Rusyn, Ivan

Publication type:

Article

Impact of Aligner, Normalization Method, and Sequencing Depth on TempO-seq Accuracy.

Published in:

Bioinformatics & Biology Insights, 2022, p. 1, doi. 10.1177/11779322221095216

By:

Everett, Logan J;
Mav, Deepak;
Phadke, Dhiral P;
Balik-Meisner, Michele R;
Shah, Ruchir R

Publication type:

Article

Impact of Aligner, Normalization Method, and Sequencing Depth on TempO-seq Accuracy.

Published in:

Bioinformatics & Biology Insights, 2022, v. 16, p. 1, doi. 10.1177/11779322221095216

By:

Everett, Logan J.;
Mav, Deepak;
Phadke, Dhiral P.;
Balik-Meisner, Michele R.;
Shah, Ruchir R.

Publication type:

Article

Utility of Extrapolating Human S1500+ Genes to the Whole Transcriptome: Tunicamycin Case Study.

Published in:

Bioinformatics & Biology Insights, 2020, p. 1, doi. 10.1177/1177932220952742

By:

Mav, Deepak;
Phadke, Dhiral P;
Balik-Meisner, Michele R;
Merrick, B Alex;
Auerbach, Scott;
Niemeijer, Marije;
Huppelschoten, Suzanna;
Baze, Audrey;
Parmentier, Celine;
Richert, Lysiane;
van de Water, Bob;
Shah, Ruchir R;
Paules, Richard S

Publication type:

Article

Utility of Extrapolating Human S1500+ Genes to the Whole Transcriptome: Tunicamycin Case Study.

Published in:

Bioinformatics & Biology Insights, 2020, p. 1, doi. 10.1177/1177932220952742

By:

Mav, Deepak;
Phadke, Dhiral P;
Balik-Meisner, Michele R;
Merrick, B Alex;
Auerbach, Scott;
Niemeijer, Marije;
Huppelschoten, Suzanna;
Baze, Audrey;
Parmentier, Celine;
Richert, Lysiane;
van de Water, Bob;
Shah, Ruchir R;
Paules, Richard S

Publication type:

Article

A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics.

Published in:

PLoS ONE, 2018, v. 13, n. 2, p. 1, doi. 10.1371/journal.pone.0191105

By:

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.

Publication type:

Article

HAfTs are novel lncRNA transcripts from aflatoxin exposure.

Published in:

PLoS ONE, 2018, v. 13, n. 1, p. 1, doi. 10.1371/journal.pone.0190992

By:

Merrick, B. Alex;
Chang, Justin S.;
Phadke, Dhiral P.;
Bostrom, Meredith A.;
Shah, Ruchir R.;
Wang, Xinguo;
Gordon, Oksana;
Wright, Garron M.

Publication type:

Article

Runx2 transcriptome of prostate cancer cells: insights into invasiveness and bone metastasis.

Published in:

Molecular Cancer, 2010, v. 9, p. 258, doi. 10.1186/1476-4598-9-258

By:

Baniwal, Sanjeev K.;
Khalid, Omar;
Gabet, Yankel;
Shah, Ruchir R.;
Purcell, Daniel J.;
Mav, Deepak;
Kohn-Gabet, Alice E.;
Yunfan Shi;
Coetzee, Gerhard A.;
Frenkel, Baruch

Publication type:

Article

BMDExpress 2: enhanced transcriptomic dose-response analysis workflow.

Published in:

Bioinformatics, 2019, v. 35, n. 10, p. 1780, doi. 10.1093/bioinformatics/bty878

By:

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

Publication type:

Article

Autoimmunity is triggered by cPR-3(105-201), a protein complementary to human autoantigen proteinase-3.

Published in:

Nature Medicine, 2004, v. 10, n. 1, p. 72, doi. 10.1038/nm968

By:

Pendergraft III, William F.;
Preston, Gloria A.;
Shah, Ruchir R.;
Tropsha, Alexander;
Carter Jr., Charles W.;
Jennette, J. Charles;
Falk, Ronald J.

Publication type:

Article

Analysis of Chromatin Dynamics during Glucocorticoid Receptor Activation.

Published in:

Molecular & Cellular Biology, 2012, v. 32, n. 10, p. 1805, doi. 10.1128/MCB.06206-11

By:

Burd, Craig J.;
Ward, James M.;
Crusselle-Davis, Valerie J.;
Kissling, Grace E.;
Phadke, Dhiral;
Shah, Ruchir R.;
Archer, Trevor K.

Publication type:

Article

Evaluation of 5-day In Vivo Rat Liver and Kidney With High-throughput Transcriptomics for Estimating Benchmark Doses of Apical Outcomes.

Published in:

Toxicological Sciences, 2020, v. 176, n. 2, p. 343, doi. 10.1093/toxsci/kfaa081

By:

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

Publication type:

Article

Power of Resolution: Contextualized Understanding of Biological Responses to Liver Injury Chemicals Using High-throughput Transcriptomics and Benchmark Concentration Modeling.

Published in:

Toxicological Sciences, 2019, v. 169, n. 2, p. 553, doi. 10.1093/toxsci/kfz065

By:

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

Publication type:

Article

Arsenite malignantly transforms human prostate epithelial cells in vitro by gene amplification of mutated KRAS.

Published in:

PLoS ONE, 2019, v. 14, n. 4, p. 1, doi. 10.1371/journal.pone.0215504

By:

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.

Publication type:

Article

Whole exome sequencing in the rat.

Published in:

BMC Genomics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12864-018-4858-8

By:

Foley, Julie F.;
Phadke, Dhiral P.;
Hardy, Owen;
Hardy, Sara;
Miller, Victor;
Madan, Anup;
Howard, Kellie;
Kruse, Kimberly;
Lord, Cara;
Ramaiahgari, Sreenivasa;
Solomon, Gregory G.;
Shah, Ruchir R.;
Pandiri, Arun R.;
Herbert, Ronald A.;
Sills, Robert C.;
Alex Merrick, B.

Publication type:

Article

Human Variation and Risk Assessment: Microarray and Other Studies Utilizing Human Hepatocytes and Human Liver Subcellular Preparations.

Published in:

Journal of Biochemical & Molecular Toxicology, 2014, v. 28, n. 1, p. 1, doi. 10.1002/jbt.21534

By:

Hodgson, Ernest;
Wallace, Andrew D.;
Shah, Ruchir R.;
Choi, Kyoungju;
Joo, Hyun

Publication type:

Article

Quantifying liver-toxic responses from dose-dependent chemical exposures using a rat genome-scale metabolic model.

Published in:

Toxicological Sciences, 2025, v. 204, n. 2, p. 154, doi. 10.1093/toxsci/kfaf005

By:

Pannala, Venkat R;
Hari, Archana;
AbdulHameed, Mohamed Diwan M;
Balik-Meisner, Michele R;
Mav, Deepak;
Phadke, Dhiral P;
Scholl, Elizabeth H;
Shah, Ruchir R;
Auerbach, Scott S;
Wallqvist, Anders

Publication type:

Article

Low-calorie sweeteners and health outcomes: an evaluation of rapid versus traditional evidence mapping.

Published in:

BMC Research Notes, 2022, v. 15, n. 1, p. 1, doi. 10.1186/s13104-022-05926-3

By:

Lam, Juleen;
Elmore, Rebecca;
Howard, Brian;
Shah, Ruchir R.

Publication type:

Article

Exposure to PFAS chemicals induces sex-dependent alterations in key rate-limiting steps of lipid metabolism in liver steatosis.

Published in:

Frontiers in Toxicology, 2024, p. 1, doi. 10.3389/ftox.2024.1390196

By:

Hari, Archana;
AbdulHameed, Mohamed Diwan M.;
Balik-Meisner, Michele R.;
Mav, Deepak;
Phadke, Dhiral P.;
Scholl, Elizabeth H.;
Shah, Ruchir R.;
Casey, Warren;
Auerbach, Scott S.;
Wallqvist, Anders;
Pannala, Venkat R.

Publication type:

Article

SWIFT-Review: a text-mining workbench for systematic review.

Published in:

Systematic Reviews, 2016, v. 2, p. 1, doi. 10.1186/s13643-016-0263-z

By:

Howard, Brian E.;
Phillips, Jason;
Miller, Kyle;
Tandon, Arpit;
Mav, Deepak;
Shah, Mihir R.;
Holmgren, Stephanie;
Pelch, Katherine E.;
Walker, Vickie;
Rooney, Andrew A.;
Macleod, Malcolm;
Shah, Ruchir R.;
Thayer, Kristina

Publication type:

Article

Deep Sequencing Identification of Novel Glucocorticoid-Responsive miRNAs in Apoptotic Primary Lymphocytes.

Published in:

PLoS ONE, 2013, v. 8, n. 10, p. 1, doi. 10.1371/journal.pone.0078316

By:

Smith, Lindsay K.;
Tandon, Arpit;
Shah, Ruchir R.;
Mav, Deepak;
Scoltock, Alyson B.;
Cidlowski, John A.

Publication type:

Article

RNA-Seq Profiling Reveals Novel Hepatic Gene Expression Pattern in Aflatoxin B1 Treated Rats.

Published in:

PLoS ONE, 2013, v. 8, n. 4, p. 1, doi. 10.1371/journal.pone.0061768

By:

Merrick, B. Alex;
Phadke, Dhiral P.;
Auerbach, Scott S.;
Mav, Deepak;
Stiegelmeyer, Suzy M.;
Shah, Ruchir R.;
Tice, Raymond R.

Publication type:

Article

The Transcription Factors Snail and Slug Activate the Transforming Growth Factor-Beta Signaling Pathway in Breast Cancer.

Published in:

PLoS ONE, 2011, v. 6, n. 10, p. 1, doi. 10.1371/journal.pone.0026514

By:

Dhasarathy, Archana;
Phadke, Dhiral;
Mav, Deepak;
Shah, Ruchir R.;
Wade, Paul A.

Publication type:

Article

Whole genome sequencing of low input circulating cell‐free DNA obtained from normal human subjects.

Published in:

Physiological Reports, 2021, v. 9, n. 15, p. 1, doi. 10.14814/phy2.14993

By:

Foley, Julie F.;
Elgart, Brian;
Alex Merrick, B.;
Phadke, Dhiral P.;
Cook, Molly E.;
Malphurs, Jason A.;
Solomon, Gregory G.;
Shah, Ruchir R.;
Fessler, Michael B.;
Miller, Frederick W.;
Gerrish, Kevin E.

Publication type:

Article