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Efficient algorithms for covariate analysis with dynamic data using nonlinear mixed-effects model.
Published in:
Statistical Methods in Medical Research, 2021, v. 30, n. 1, p. 233, doi. 10.1177/0962280220949898
By:
- Yuan, Min;
- Zhu, Zhi;
- Yang, Yaning;
- Zhao, Minghua;
- Sasser, Kate;
- Hamadeh, Hisham;
- Pinheiro, Jose;
- Xu, Xu Steven
Publication type:
Article
Discovery in toxicology: Mediation by gene expression array technology.
Published in:
Journal of Biochemical & Molecular Toxicology, 2001, v. 15, n. 5, p. 231, doi. 10.1002/jbt.10006
By:
- Hamadeh, Hisham K.;
- Bushel, Pierre;
- Paules, Richard;
- Afshari, Cynthia A.
Publication type:
Article
Common Handling Procedures Conducted in Preclinical Safety Studies Result in Minimal Hepatic Gene Expression Changes in Sprague-Dawley Rats.
Published in:
PLoS ONE, 2014, v. 9, n. 2, p. 1, doi. 10.1371/journal.pone.0088750
By:
- He, Yudong D.;
- Karbowski, Christine M.;
- Werner, Jon;
- Everds, Nancy;
- Di Palma, Chris;
- Chen, Yuan;
- Higgins-Garn, Marnie;
- Tran, Sandra;
- Afshari, Cynthia A.;
- Hamadeh, Hisham K.
Publication type:
Article
Perturbation of microRNAs in Rat Heart during Chronic Doxorubicin Treatment.
Published in:
PLoS ONE, 2012, v. 7, n. 7, p. 1, doi. 10.1371/journal.pone.0040395
By:
- Vacchi-Suzzi, Caterina;
- Bauer, Yasmina;
- Berridge, Brian R.;
- Bongiovanni, Sandrine;
- Gerrish, Kevin;
- Hamadeh, Hisham K.;
- Letzkus, Martin;
- Lyon, Jonathan;
- Moggs, Jonathan;
- Paules, Richard S.;
- Pognan, François;
- Staedtler, Frank;
- Vidgeon-Hart, Martin P.;
- Grenet, Olivier;
- Couttet, Philippe
Publication type:
Article
A Novel Statistical Algorithm for Gene Expression Analysis Helps Differentiate Pregnane X Receptor-Dependent and Independent Mechanisms of Toxicity.
Published in:
PLoS ONE, 2010, v. 5, n. 12, p. 1, doi. 10.1371/journal.pone.0015595
By:
- Mongan, M. Ann;
- Dunn, II, Robert T.;
- Vonderfecht, Steven;
- Everds, Nancy;
- Guang Chen;
- Cheng Su;
- Higgins-Garn, Marnie;
- Yuan Chen;
- Afshari, Cynthia A.;
- Williamson, Toni L.;
- Carlock, Linda;
- DiPalma, Christopher;
- Moss, Suzanne;
- Bussiere, Jeanine;
- Qualls, Jr., Charles;
- He, Yudong D.;
- Hamadeh, Hisham K.
Publication type:
Article
Identification of Putative Gene-Based Markers of Renal Toxicity.
Published in:
Environmental Health Perspectives, 2004, v. 112, n. 4, p. 465, doi. 10.1289/ehp.6683
By:
- Amin, Rupesh P.;
- Vickers, Alison E.;
- Sistare, Frank;
- Thompson, Karol L.;
- Roman, Richard J.;
- Lawton, Michael;
- Kramer, Jeffrey;
- Hamadeh, Hisham K.;
- Collins, Jennifer;
- Grissom, Sherry;
- Bennett, Lee;
- Tucker, C. Jeffrey;
- Wild, Stacie;
- Kind, Clive;
- Oreffo, Victor;
- Davis II, John W.;
- Curtiss, Sandra;
- Naciff, Jorge M.;
- Cunningham, Michael
Publication type:
Article
Progress in the Application of DNA Microarrays.
Published in:
Environmental Health Perspectives, 2001, v. 109, n. 9, p. 881, doi. 10.1289/ehp.01109881
By:
- Lobenhofer, Edward K.;
- Bushel, Pierre R.;
- Afshari, Cynthia A.;
- Hamadeh, Hisham K.
Publication type:
Article
Genome-scale metabolic model of the rat liver predicts effects of diet restriction.
Published in:
Scientific Reports, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1038/s41598-019-46245-1
By:
- Baloni, Priyanka;
- Sangar, Vineet;
- Yurkovich, James T.;
- Robinson, Max;
- Taylor, Scott;
- Karbowski, Christine M.;
- Hamadeh, Hisham K.;
- He, Yudong D.;
- Price, Nathan D.
Publication type:
Article
Use of a mixed tissue RNA design for performance assessments on multiple microarray formats.
Published in:
Nucleic Acids Research, 2005, v. 33, n. 22, p. e187, doi. 10.1093/nar/gni186
By:
- Thompson, Karol L.;
- Rosenzweig, Barry A.;
- Pine, P. Scott;
- Retief, Jacques;
- Turpaz, Yaron;
- Afshari, Cynthia A.;
- Hamadeh, Hisham K.;
- Damore, Michael A.;
- Boedigheimer, Michael;
- Blomme, Eric;
- Ciurlionis, Rita;
- Waring, Jeffrey F.;
- Fuscoe, James C.;
- Paules, Richard;
- Tucker, Charles J.;
- Fare, Thomas;
- Coffey, Ernest M.;
- He, Yudong;
- Collins, Patrick J.;
- Jarnagin, Kurt
Publication type:
Article
Coordination of Altered DNA Repair and Damage Pathways in Arsenite-Exposed Keratinocytes.
Published in:
Toxicological Sciences, 2002, v. 69, n. 2, p. 306, doi. 10.1093/toxsci/69.2.306
By:
- Hamadeh, Hisham K.;
- Trouba, Kevin J.;
- Amin, Rupesh P.;
- Afshari, Cynthia A.;
- Germolec, Dori
Publication type:
Article
Gene Expression Analysis Reveals Chemical-Specific Profiles.
Published in:
Toxicological Sciences, 2002, v. 67, n. 2, p. 219, doi. 10.1093/toxsci/67.2.219
By:
- Hamadeh, Hisham K.;
- Bushel, Pierre R.;
- Jayadev, Supriya;
- Martin, Karla;
- DiSorbo, Olimpia;
- Sieber, Stella;
- Bennett, Lee;
- Tennant, Raymond;
- Stoll, Raymond;
- Barrett, J. Carl;
- Blanchard, Kerry;
- Paules, Richard S.;
- Afshari, Cynthia A.
Publication type:
Article
Prediction of Compound Signature Using High Density Gene Expression Profiling.
Published in:
Toxicological Sciences, 2002, v. 67, n. 2, p. 232, doi. 10.1093/toxsci/67.2.232
By:
- Hamadeh, Hisham K.;
- Bushel, Pierre R.;
- Jayadev, Supriya;
- DiSorbo, Olimpia;
- Bennett, Lee;
- Leping Li;
- Tennant, Raymond;
- Stoll, Raymond;
- Barrett, J. Carl;
- Paules, Richard S.;
- Blanchard, Kerry;
- Afshari, Cynthia A.
Publication type:
Article
MAPS: a microarray project system for gene expression experiment information and data validation.
Published in:
Bioinformatics, 2001, v. 17, n. 6, p. 564, doi. 10.1093/bioinformatics/17.6.564
By:
- Bushel, Pierre R.;
- Hamadeh, Hisham;
- Bennett, Lee;
- Sieber, Stella;
- Martin, Karla;
- Nuwaysir, Emile F.;
- Johnson, Kate;
- Reynolds, Kelli;
- Paules, Richard S.;
- Afshari, Cynthia A.
Publication type:
Article
The integration of pharmacophore-based 3D QSAR modeling and virtual screening in safety profiling: A case study to identify antagonistic activities against adenosine receptor, A2A, using 1,897 known drugs.
Published in:
PLoS ONE, 2019, v. 14, n. 01, p. 1, doi. 10.1371/journal.pone.0204378
By:
- Fan, Fan;
- Toledo Warshaviak, Dora;
- Hamadeh, Hisham K.;
- IIDunn, Robert T.
Publication type:
Article
Transcriptional Profiling of Laser Capture Microdissected Subpopulations of the Osteoblast Lineage Provides Insight Into the Early Response to Sclerostin Antibody in Rats.
Published in:
Journal of Bone & Mineral Research, 2015, v. 30, n. 8, p. 1457, doi. 10.1002/jbmr.2482
By:
- Nioi, Paul;
- Taylor, Scott;
- Hu, Rong;
- Pacheco, Efrain;
- He, Yudong D;
- Hamadeh, Hisham;
- Paszty, Chris;
- Pyrah, Ian;
- Ominsky, Michael S;
- Boyce, Rogely Waite
Publication type:
Article
Dose-related Differences in the Pharmacodynamic and Toxicologic Response to a Novel Hyperglycosylated Analog of Recombinant Human Erythropoietin in Sprague-Dawley Rats with Similarly High Hematocrit.
Published in:
Toxicologic Pathology, 2014, v. 42, n. 3, p. 524, doi. 10.1177/0192623313486319
By:
- Andrews, Dina A.;
- Boren, Babette M.;
- Turk, James R.;
- Boyce, Rogely W.;
- He, Yudong D.;
- Hamadeh, Hisham K.;
- Mytych, Daniel T.;
- Barger, Troy E.;
- Salimi-Moosavi, Hossein;
- Sloey, Bethlyn;
- Elliott, Steve;
- McElroy, Patricia;
- Sinclair, Angus M.;
- Shimamoto, Grant;
- Pyrah, Ian T. G.;
- Lightfoot-Dunn, Ruth M.
Publication type:
Article
Cytokines Associated with Increased Erythropoiesis in Sprague-Dawley Rats Administered a Novel Hyperglycosylated Analog of Recombinant Human Erythropoietin.
Published in:
Toxicologic Pathology, 2014, v. 42, n. 3, p. 540, doi. 10.1177/0192623313486318
By:
- Andrews, Dina A.;
- Hamadeh, Hisham K.;
- He, Yudong D.;
- Boren, Babette M.;
- Turk, James R.;
- Boyce, Rogely W.;
- Mytych, Daniel T.;
- Barger, Troy E.;
- Salimi-Moosavi, Hossein;
- Sloey, Bethlyn;
- Elliott, Steve;
- McElroy, Patricia;
- Sinclair, Angus M.;
- Shimamoto, Grant;
- Pyrah, Ian T. G.;
- Lightfoot-Dunn, Ruth M.
Publication type:
Article
Methapyrilene Toxicity: Anchorage of Pathologic Observations to Gene Expression Alterations.
Published in:
Toxicologic Pathology, 2002, v. 30, n. 4, p. 470, doi. 10.1080/01926230290105712
By:
- Hamadeh, Hisham K.;
- Knight, Brian L.;
- Haugen, Astrid C.;
- Sieber, Stella;
- Amin, Rupesh P.;
- Bushel, Pierre R.;
- Stoll, Raymond;
- Blanchard, Kerry;
- Jayadev, Supriya;
- Tennant, Raymond W.;
- Cunningham, Michael L.;
- Afshari, Cynthia A.;
- Paules, Richard S.
Publication type:
Article
Utilization of Human Nuclear Receptors as an Early Counter Screen for Off-Target Activity: A Case Study with a Compendium of 615 Known Drugs.
Published in:
Toxicological Sciences, 2015, v. 145, n. 2, p. 283, doi. 10.1093/toxsci/kfv052
By:
- Fan Fan;
- Rong Hu;
- Munzli, Anke;
- Yuan Chen;
- Dunn II, Robert T.;
- Weikl, Kerstin;
- Strauch, Simone;
- Schwandner, Ralf;
- Afshari, Cynthia A.;
- Hamadeh, Hisham;
- Nioi, Paul
Publication type:
Article
A Systematic Assessment of Mitochondrial Function Identified Novel Signatures for Drug-Induced Mitochondrial Disruption in Cells.
Published in:
Toxicological Sciences, 2014, v. 142, n. 1, p. 261, doi. 10.1093/toxsci/kfu176
By:
- Nianyu Li;
- Oquendo, Elisa;
- Capaldi, Roderick A.;
- Robinson, J. Paul;
- He, Yudong D.;
- Hamadeh, Hisham K.;
- Afshari, Cynthia A.;
- Lightfoot-Dunn, Ruth;
- Narayanan, Padma Kumar
Publication type:
Article
A Multifactorial Approach to Hepatobiliary Transporter Assessment Enables Improved Therapeutic Compound Development.
Published in:
Toxicological Sciences, 2013, v. 136, n. 1, p. 216, doi. 10.1093/toxsci/kft176
By:
- Morgan, Ryan E.;
- van Staden, Carlo J.;
- Chen, Yuan;
- Kalyanaraman, Natarajan;
- Kalanzi, Jackson;
- Dunn, Robert T.;
- Afshari, Cynthia A.;
- Hamadeh, Hisham K.
Publication type:
Article
The Evolution of Bioinformatics in Toxicology: Advancing Toxicogenomics.
Published in:
Toxicological Sciences, 2011, v. 120, n. suppl_1, p. S225, doi. 10.1093/toxsci/kfq373
By:
- Afshari, Cynthia A.;
- Hamadeh, Hisham K.;
- Bushel, Pierre R.
Publication type:
Article
Interference with Bile Salt Export Pump Function Is a Susceptibility Factor for Human Liver Injury in Drug Development.
Published in:
Toxicological Sciences, 2010, v. 118, n. 2, p. 485, doi. 10.1093/toxsci/kfq269
By:
- Morgan, Ryan E.;
- Trauner, Michael;
- van Staden, Carlo J.;
- Lee, Paul H.;
- Ramachandran, Bharath;
- Eschenberg, Michael;
- Afshari, Cynthia A.;
- Qualls, Charles W.;
- Lightfoot-Dunn, Ruth;
- Hamadeh, Hisham K.
Publication type:
Article
High-throughput and efficient multilocus genome-wide association study on longitudinal outcomes.
Published in:
Bioinformatics, 2020, v. 36, n. 10, p. 3004, doi. 10.1093/bioinformatics/btaa120
By:
- Xu, Huang;
- Li, Xiang;
- Yang, Yaning;
- Li, Yi;
- Pinheiro, Jose;
- Sasser, Kate;
- Hamadeh, Hisham;
- Steven, Xu;
- Yuan, Min;
- Initiative, and for the Alzheimer's Disease Neuroimaging
Publication type:
Article
Improving accuracy of GPT-3/4 results on biomedical data using a retrieval-augmented language model.
Published in:
PLoS Digital Health, 2024, v. 3, n. 8, p. 1, doi. 10.1371/journal.pdig.0000568
By:
- Soong, David;
- Sridhar, Sriram;
- Si, Han;
- Wagner, Jan-Samuel;
- Sá, Ana Caroline Costa;
- Yu, Christina Y.;
- Karagoz, Kubra;
- Guan, Meijian;
- Kumar, Sanyam;
- Hamadeh, Hisham;
- Higgs, Brandon W.
Publication type:
Article

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