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Transformation based on likelihood ratio.
Published in:
Statistical Methods in Medical Research, 2021, v. 30, n. 2, p. 354, doi. 10.1177/0962280220925509
By:
- Yang, Jianping;
- Kuan, Pei-Fen;
- Li, Jialiang
Publication type:
Article
Non-monotone transformation of biomarkers to improve diagnostic and screening accuracy in a DNA methylation study with trichotomous phenotypes.
Published in:
2020
By:
- Yang, Jianping;
- Kuan, Pei-Fen;
- Li, Jialiang
Publication type:
journal article
Proteomic analysis of cognitive impairment in responders traumatized by the World Trade Center disaster: Biomarkers (non‐neuroimaging) / plasma/serum/urine biomarkers.
Published in:
Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 2020, v. 16, n. 11, p. 1, doi. 10.1002/alz.040497
By:
- Luft, Benjamin;
- Clouston, Sean;
- Kotov, Roman;
- Bromet, Evelyn;
- Kuan, Pei‐Fen
Publication type:
Article
Polygenic association of glomerular filtration rate decline in world trade center responders.
Published in:
2022
By:
- Koraishy, Farrukh M.;
- Mann, Frank D.;
- Waszczuk, Monika A.;
- Kuan, Pei-Fen;
- Jonas, Katherine;
- Yang, Xiaohua;
- Docherty, Anna;
- Shabalin, Andrey;
- Clouston, Sean;
- Kotov, Roman;
- Luft, Benjamin
Publication type:
journal article
A systematic evaluation of nucleotide properties for CRISPR sgRNA design.
Published in:
BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1697-6
By:
- Pei Fen Kuan;
- Powers, Scott;
- Shuyao He;
- Kaiqiao Li;
- Xiaoyu Zhao;
- Bo Huang
Publication type:
Article
HIF1α and HIF2α independently activate SRC to promote melanoma metastases.
Published in:
Journal of Clinical Investigation, 2013, v. 123, n. 5, p. 2078, doi. 10.1172/JCI66715
By:
- Hanna, Sara C.;
- Krishnan, Bhavani;
- Bailey, Sean T.;
- Moschos, Stergios J.;
- Pei-Fen Kuan;
- Takeshi Shimamura;
- Osborne, Lukas D.;
- Siegel, Marni B.;
- Duncan, Lyn M.;
- O¿Brien III, E. Tim;
- Superfine, Richard;
- Miller, C. Ryan;
- Simon, M. Celeste;
- Kwok-Kin Wong;
- Kim, William Y.
Publication type:
Article
MERTK receptor tyrosine kinase is a therapeutic target in melanoma.
Published in:
Journal of Clinical Investigation, 2013, v. 123, n. 5, p. 2257, doi. 10.1172/JCI67816
By:
- Schlegel, Jennifer;
- Sambade, Maria J.;
- Sather, Susan;
- Moschos, Stergios J.;
- Aik-Choon Tan;
- Winges, Amanda;
- DeRyckere, Deborah;
- Carson, Craig C.;
- Trembath, Dimitri G.;
- Tentler, John J.;
- Eckhardt, S. Gail;
- Pei-Fen Kuan;
- Hamilton, Ronald L.;
- Duncan, Lyn M.;
- Miller, C. Ryan;
- Nikolaishvili-Feinberg, Nana;
- Midkiff, Bentley R.;
- Jing Liu;
- Weihe Zhang;
- Chao Yang
Publication type:
Article
Mapping the transcriptomics landscape of post-traumatic stress disorder symptom dimensions in World Trade Center responders.
Published in:
Translational Psychiatry, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41398-021-01431-6
By:
- Kuan, Pei-Fen;
- Yang, Xiaohua;
- Ren, Xu;
- Che, Chang;
- Waszczuk, Monika;
- Kotov, Roman;
- Clouston, Sean;
- Singh, Prashant K.;
- Glenn, Sean T.;
- Gomez, Eduardo Cortes;
- Wang, Jianmin;
- Bromet, Evelyn;
- Luft, Benjamin J.
Publication type:
Article
PTSD is associated with accelerated transcriptional aging in World Trade Center responders.
Published in:
Translational Psychiatry, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41398-021-01437-0
By:
- Kuan, Pei-Fen;
- Ren, Xu;
- Clouston, Sean;
- Yang, Xiaohua;
- Jonas, Katherine;
- Kotov, Roman;
- Bromet, Evelyn;
- Luft, Benjamin J.
Publication type:
Article
Molecular linkage between post-traumatic stress disorder and cognitive impairment: a targeted proteomics study of World Trade Center responders.
Published in:
Translational Psychiatry, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41398-020-00958-4
By:
- Kuan, Pei-Fen;
- Clouston, Sean;
- Yang, Xiaohua;
- Kotov, Roman;
- Bromet, Evelyn;
- Luft, Benjamin J.
Publication type:
Article
DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.
Published in:
Nucleic Acids Research, 2013, v. 41, n. 2, p. e39, doi. 10.1093/nar/gks1026
By:
- Hu, Yin;
- Huang, Yan;
- Du, Ying;
- Orellana, Christian F.;
- Singh, Darshan;
- Johnson, Amy R.;
- Monroy, Anaïs;
- Kuan, Pei-Fen;
- Hammond, Scott M.;
- Makowski, Liza;
- Randell, Scott H.;
- Chiang, Derek Y.;
- Hayes, D. Neil;
- Jones, Corbin;
- Liu, Yufeng;
- Prins, Jan F.;
- Liu, Jinze
Publication type:
Article
Hit selection with false discovery rate control in genome-scale RNAi screens.
Published in:
Nucleic Acids Research, 2008, v. 36, n. 14, p. 4667, doi. 10.1093/nar/gkn435
By:
- Zhang, Xiaohua Douglas;
- Kuan, Pei Fen;
- Ferrer, Marc;
- Shu, Xiaohua;
- Liu, Yingxue C.;
- Gates, Adam T.;
- Kunapuli, Priya;
- Stec, Erica M.;
- Xu, Min;
- Marine, Shane D.;
- Holder, Daniel J.;
- Strulovici, Berta;
- Heyse, Joseph F.;
- Espeseth, Amy S.
Publication type:
Article
A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets.
Published in:
Nucleic Acids Research, 2008, v. 36, n. 9, p. 2926, doi. 10.1093/nar/gkn133
By:
- Wei, Hairong;
- Kuan, Pei Fen;
- Tian, Shulan;
- Yang, Chuhu;
- Nie, Jeff;
- Sengupta, Srikumar;
- Ruotti, Victor;
- Jonsdottir, Gudrun A.;
- Keles, Sunduz;
- Thomson, James A.;
- Stewart, Ron
Publication type:
Article
Epigenome-wide association of PTSD from heterogeneous cohorts with a common multi-site analysis pipeline.
Published in:
American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 2017, v. 174, n. 6, p. 619, doi. 10.1002/ajmg.b.32568
By:
- Ratanatharathorn, Andrew;
- Boks, Marco P.;
- Maihofer, Adam X.;
- Aiello, Allison E.;
- Amstadter, Ananda B.;
- Ashley‐Koch, Allison E.;
- Baker, Dewleen G.;
- Beckham, Jean C.;
- Bromet, Evelyn;
- Dennis, Michelle;
- Garrett, Melanie E.;
- Geuze, Elbert;
- Guffanti, Guia;
- Hauser, Michael A.;
- Kilaru, Varun;
- Kimbrel, Nathan A.;
- Koenen, Karestan C.;
- Kuan, Pei‐Fen;
- Logue, Mark W.;
- Luft, Benjamin J.
Publication type:
Article
Covariate adjusted differential variability analysis of DNA methylation with propensity score method.
Published in:
Statistical Applications in Genetics & Molecular Biology, 2014, v. 13, n. 6, p. 645, doi. 10.1515/sagmb-2013-0072
By:
- Kuan, Pei Fen
Publication type:
Article
A Non-Homogeneous Hidden-State Model on First Order Differences for Automatic Detection of Nucleosome Positions.
Published in:
Statistical Applications in Genetics & Molecular Biology, 2009, v. 8, n. 1, p. 1, doi. 10.2202/1544-6115.1454
By:
- Pei Fen Kuan;
- Huebert, Dana;
- Gasch, Audrey;
- Keles, Sunduz
Publication type:
Article
Efficient gradient boosting for prognostic biomarker discovery.
Published in:
Bioinformatics, 2022, v. 38, n. 6, p. 1631, doi. 10.1093/bioinformatics/btab869
By:
- Li, Kaiqiao;
- Yao, Sijie;
- Zhang, Zhenyu;
- Cao, Biwei;
- Wilson, Christopher M;
- Kalos, Denise;
- Kuan, Pei Fen;
- Zhu, Ruoqing;
- Wang, Xuefeng
Publication type:
Article
Discovery and replication of blood-based proteomic signature of PTSD in 9/11 responders.
Published in:
Translational Psychiatry, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41398-022-02302-4
By:
- Waszczuk, Monika A.;
- Kuan, Pei-Fen;
- Yang, Xiaohua;
- Miao, Jiaju;
- Kotov, Roman;
- Luft, Benjamin J.
Publication type:
Article
Application of Multiplexed Kinase Inhibitor Beads to Study Kinome Adaptations in Drug-Resistant Leukemia.
Published in:
PLoS ONE, 2013, v. 8, n. 6, p. 1, doi. 10.1371/journal.pone.0066755
By:
- Cooper, Matthew J.;
- Cox, Nathan J.;
- Zimmerman, Eric I.;
- Dewar, Brian J.;
- Duncan, James S.;
- Whittle, Martin C.;
- Nguyen, Thien A.;
- Jones, Lauren S.;
- Ghose Roy, Sreerupa;
- Smalley, David M.;
- Kuan, Pei Fen;
- Richards, Kristy L.;
- Christopherson, Richard I.;
- Jin, Jian;
- Frye, Stephen V.;
- Johnson, Gary L.;
- Baldwin, Albert S.;
- Graves, Lee M.
Publication type:
Article
Metabolomic Profiling Reveals Mitochondrial-Derived Lipid Biomarkers That Drive Obesity-Associated Inflammation.
Published in:
PLoS ONE, 2012, v. 7, n. 6, p. 1, doi. 10.1371/journal.pone.0038812
By:
- Sampey, Brante P.;
- Freemerman, Alex J.;
- Zhang, Jimmy;
- Kuan, Pei-Fen;
- Galanko, Joseph A.;
- O'Connell, Thomas M.;
- Ilkayeva, Olga R.;
- Muehlbauer, Michael J.;
- Stevens, Robert D.;
- Newgard, Christopher B.;
- Brauer, Heather A.;
- Troester, Melissa A.;
- Makowski, Liza
Publication type:
Article
Integrating Prior Knowledge in Multiple Testing under Dependence with Applications to Detecting Differential DNA Methylation.
Published in:
Biometrics, 2012, v. 68, n. 3, p. 774, doi. 10.1111/j.1541-0420.2011.01730.x
By:
- Kuan, Pei Fen;
- Chiang, Derek Y.
Publication type:
Article
Metabolomics analysis of post-traumatic stress disorder symptoms in World Trade Center responders.
Published in:
Translational Psychiatry, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41398-022-01940-y
By:
- Kuan, Pei-Fen;
- Yang, Xiaohua;
- Kotov, Roman;
- Clouston, Sean;
- Bromet, Evelyn;
- Luft, Benjamin J.
Publication type:
Article
Reduced cerebellar cortical thickness in World Trade Center responders with cognitive impairment.
Published in:
Translational Psychiatry, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41398-022-01873-6
By:
- Clouston, Sean A. P.;
- Kritikos, Minos;
- Huang, Chuan;
- Kuan, Pei-Fen;
- Vaska, Paul;
- Pellecchia, Alison C.;
- Santiago-Michels, Stephanie;
- Carr, Melissa A.;
- Gandy, Sam;
- Sano, Mary;
- Bromet, Evelyn J.;
- Lucchini, Roberto G.;
- Luft, Benjamin J.
Publication type:
Article
Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data.
Published in:
BMC Bioinformatics, 2010, v. 11, p. 194, doi. 10.1186/1471-2105-11-194
By:
- Zacher, Benedikt;
- Pei Fen Kuan;
- Tresch, Achim
Publication type:
Article
Cell type-specific gene expression patterns associated with posttraumatic stress disorder in World Trade Center responders.
Published in:
Translational Psychiatry, 2019, v. 9, n. 1, p. 1, doi. 10.1038/s41398-018-0355-8
By:
- Kuan, Pei-Fen;
- Yang, Xiaohua;
- Clouston, Sean;
- Ren, Xu;
- Kotov, Roman;
- Waszczuk, Monika;
- Singh, Prashant K.;
- Glenn, Sean T.;
- Gomez, Eduardo Cortes;
- Wang, Jianmin;
- Bromet, Evelyn;
- Luft, Benjamin J.
Publication type:
Article
DNA methylation profiling in the Carolina Breast Cancer Study defines cancer subclasses differing in clinicopathologic characteristics and survival.
Published in:
Breast Cancer Research, 2014, v. 16, n. 5, p. 1, doi. 10.1186/s13058-014-0450-6
By:
- Conway, Kathleen;
- Edmiston, Sharon N.;
- May, Ryan;
- Pei Fen Kuan;
- Haitao Chu;
- Bryant, Christopher;
- Chiu-Kit Tse;
- Swift-Scanlan, Theresa;
- Geradts, Joseph;
- Troester, Melissa A.
Publication type:
Article
DNA methylation profiling in the Carolina Breast Cancer Study defines cancer subclasses differing in clinicopathologic characteristics and survival.
Published in:
2014
By:
- Conway, Kathleen;
- Edmiston, Sharon N;
- May, Ryan;
- Kuan, Pei Fen;
- Chu, Haitao;
- Bryant, Christopher;
- Tse, Chiu-Kit;
- Swift-Scanlan, Theresa;
- Geradts, Joseph;
- Troester, Melissa A;
- Millikan, Robert C
Publication type:
journal article
RNAAgeCalc: A multi-tissue transcriptional age calculator.
Published in:
PLoS ONE, 2020, v. 15, n. 8, p. 1, doi. 10.1371/journal.pone.0237006
By:
- Ren, Xu;
- Kuan, Pei Fen
Publication type:
Article
Comparison of the restricted mean survival time with the hazard ratio in superiority trials with a time-to-event end point.
Published in:
Pharmaceutical Statistics, 2018, v. 17, n. 3, p. 202, doi. 10.1002/pst.1846
By:
- Huang, Bo;
- Kuan, Pei‐Fen
Publication type:
Article
Negative binomial additive model for RNA-Seq data analysis.
Published in:
BMC Bioinformatics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12859-020-3506-x
By:
- Ren, Xu;
- Kuan, Pei-Fen
Publication type:
Article
Multiple-kernel learning for genomic data mining and prediction.
Published in:
BMC Bioinformatics, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s12859-019-2992-1
By:
- Wilson, Christopher M.;
- Li, Kaiqiao;
- Yu, Xiaoqing;
- Kuan, Pei-Fen;
- Wang, Xuefeng
Publication type:
Article
Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data.
Published in:
PLoS Computational Biology, 2011, v. 7, n. 7, p. 1, doi. 10.1371/journal.pcbi.1002111
By:
- Chung, Dongjun;
- Kuan, Pei Fen;
- Li, Bo;
- Sanalkumar, Rajendran;
- Liang, Kun;
- Bresnick, Emery H.;
- Dewey, Colin;
- Keles, Sündüz
Publication type:
Article
Time-to-event continual reassessment method incorporating treatment cycle information with application to an oncology phase I trial.
Published in:
Biometrical Journal, 2014, v. 56, n. 6, p. 933, doi. 10.1002/bimj.201300261
By:
- Huang, Bo;
- Kuan, Pei Fen
Publication type:
Article
A deep learning approach for monitoring parietal-dominant Alzheimer's disease in World Trade Center responders at midlife.
Published in:
Brain Communications, 2021, v. 3, n. 3, p. 1, doi. 10.1093/braincomms/fcab145
By:
- Chen, Allen P. F.;
- Clouston, Sean A. P.;
- Kritikos, Minos;
- Richmond, Lauren;
- Meliker, Jaymie;
- Mann, Frank;
- Santiago-Michels, Stephanie;
- Pellecchia, Alison C.;
- Carr, Melissa A.;
- Pei-Fen Kuan;
- Bromet, Evelyn J.;
- Luft, Benjamin J.
Publication type:
Article
Incidence of Dementia Before Age 65 Years Among World Trade Center Attack Responders.
Published in:
JAMA Network Open, 2024, v. 7, n. 6, p. e2416504, doi. 10.1001/jamanetworkopen.2024.16504
By:
- Clouston, Sean A. P.;
- Mann, Frank D.;
- Meliker, Jaymie;
- Kuan, Pei-Fen;
- Kotov, Roman;
- Richmond, Lauren L.;
- Babalola, Tesleem;
- Kritikos, Minos;
- Yang, Yuan;
- Carr, Melissa A.;
- Luft, Benjamin J.
Publication type:
Article
Plasma amyloid beta 40/42, phosphorylated tau 181, and neurofilament light are associated with cognitive impairment and neuropathological changes among World Trade Center responders: A prospective cohort study of exposures and cognitive aging at midlife.
Published in:
Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring, 2023, v. 15, n. 1, p. 1, doi. 10.1002/dad2.12409
By:
- Kritikos, Minos;
- Diminich, Erica D.;
- Meliker, Jaymie;
- Mielke, Michelle;
- Bennett, David A.;
- Finch, Caleb E.;
- Gandy, Sam E.;
- Carr, Melissa A.;
- Yang, Xiaohua;
- Kotov, Roman;
- Kuan, Pei‐Fen;
- Bromet, Evelyn J.;
- Clouston, Sean A. P.;
- Luft, Benjamin J.
Publication type:
Article
Single-cell transcriptomics analysis of mild cognitive impairment in World Trade Center disaster responders.
Published in:
Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring, 2021, v. 13, n. 1, p. 1, doi. 10.1002/dad2.12154
By:
- Pei-Fen Kuan;
- Clouston, Sean;
- Xiaohua Yang;
- Chang Che;
- Gandy, Samuel;
- Kotov, Roman;
- Bromet, Evelyn;
- Luft, Benjamin J.
Publication type:
Article
Propensity Score Method for Partially Matched Omics Studies.
Published in:
Cancer Informatics, 2014, n. 13, p. 1, doi. 10.4137/CIN.S16352
By:
- Pei-Fen Kuan
Publication type:
Article
DNA methylation profiles in primary cutaneous melanomas are associated with clinically significant pathologic features.
Published in:
Pigment Cell & Melanoma Research, 2014, v. 27, n. 6, p. 1097, doi. 10.1111/pcmr.12289
By:
- Thomas, Nancy E.;
- Slater, Nathaniel A.;
- Edmiston, Sharon N.;
- Zhou, Xin;
- Kuan, Pei ‐ Fen;
- Groben, Pamela A.;
- Carson, Craig C.;
- Hao, Honglin;
- Parrish, Eloise;
- Moschos, Stergios J.;
- Berwick, Marianne;
- Ollila, David W.;
- Conway, Kathleen
Publication type:
Article
DNA-methylation profiling distinguishes malignant melanomas from benign nevi.
Published in:
Pigment Cell & Melanoma Research, 2011, v. 24, n. 2, p. 352, doi. 10.1111/j.1755-148X.2011.00828.x
By:
- Conway, Kathleen;
- Edmiston, Sharon N.;
- Khondker, Zakaria S.;
- Groben, Pamela A.;
- Xin Zhou;
- Haitao Chu;
- Pei Fen Kuan;
- Honglin Hao;
- Carson, Craig;
- Berwick, Marianne;
- Olilla, David W.;
- Thomas, Nancy E.
Publication type:
Article
A network approach to compute hypervolume under receiver operating characteristic manifold for multi‐class biomarkers.
Published in:
Statistics in Medicine, 2023, v. 42, n. 6, p. 834, doi. 10.1002/sim.9646
By:
- Feng, Qunqiang;
- Liu, Pan;
- Kuan, Pei‐Fen;
- Zou, Fei;
- Chen, Jianan;
- Li, Jialiang
Publication type:
Article
A simple and robust method for partially matched samples using the p-values pooling approach.
Published in:
Statistics in Medicine, 2013, v. 32, n. 19, p. 3247, doi. 10.1002/sim.5758
By:
- Kuan, Pei Fen;
- Huang, Bo
Publication type:
Article
methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing.
Published in:
Bioinformatics, 2019, v. 35, n. 11, p. 1958, doi. 10.1093/bioinformatics/bty892
By:
- Ren, Xu;
- Kuan, Pei Fen
Publication type:
Article
A statistical framework for Illumina DNA methylation arrays.
Published in:
Bioinformatics, 2010, v. 26, n. 22, p. 2849, doi. 10.1093/bioinformatics/btq553
By:
- Pei Fen Kuan;
- Sijian Wang;
- Xin Zhou;
- Haitao Chu
Publication type:
Article
Epstein-barr virus infected gastric adenocarcinoma expresses latent and lytic viral transcripts and has a distinct human gene expression profile.
Published in:
Infectious Agents & Cancer, 2012, v. 7, n. 1, p. 21, doi. 10.1186/1750-9378-7-21
By:
- Weihua Tang;
- Morgan, Douglas R.;
- Meyers, Michael O.;
- Dominguez, Ricardo L.;
- Martinez, Enrique;
- Kakudo, Kennichi;
- Kuan, Pei Fen;
- Banet, Natalie;
- Muallem, Hind;
- Woodward, Kimberly;
- Speck, Olga;
- Gulley, Margaret L.
Publication type:
Article

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