Hongzhe Li

Hongzhe Li

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Hongzhe Li

Publications by authors named "Hongzhe Li"

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TET1-mediated DNA hydroxymethylation activates inhibitors of the Wnt/β-catenin signaling pathway to suppress EMT in pancreatic tumor cells.

J Exp Clin Cancer Res 2019 Aug 9;38(1):348. Epub 2019 Aug 9.

Department of General Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.

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http://dx.doi.org/10.1186/s13046-019-1334-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6688318PMC
August 2019

An Integrated Gaussian Graphical Model to evaluate the impact of exposures on metabolic networks.

Comput Biol Med 2019 Aug 31;114:103417. Epub 2019 Aug 31.

Department of Biomedical Data Science, Geisel School of Medicine, Lebanon, NH, USA. Electronic address:

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http://dx.doi.org/10.1016/j.compbiomed.2019.103417DOI Listing
August 2019

Inflammation up-regulates cochlear expression of TRPV1 to potentiate drug-induced hearing loss.

Sci Adv 2019 Jul 17;5(7):eaaw1836. Epub 2019 Jul 17.

Oregon Hearing Research Center, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.

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http://dx.doi.org/10.1126/sciadv.aaw1836DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6636990PMC
July 2019

Functional methylome analysis of human diabetic kidney disease.

JCI Insight 2019 06 6;4(11). Epub 2019 Jun 6.

Department of Medicine, Renal Electrolyte and Hypertension Division, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1172/jci.insight.128886DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6629092PMC
June 2019

Integrative analysis of genetical genomics data incorporating network structures.

Biometrics 2019 Apr 22. Epub 2019 Apr 22.

Department of Statistics and Probability, Michigan State University, East Lansing, Michigan.

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https://onlinelibrary.wiley.com/doi/abs/10.1111/biom.13072
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http://dx.doi.org/10.1111/biom.13072DOI Listing
April 2019

Generalized linear models with linear constraints for microbiome compositional data.

Biometrics 2019 03 10;75(1):235-244. Epub 2018 Aug 10.

Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A.

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http://doi.wiley.com/10.1111/biom.12956
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http://dx.doi.org/10.1111/biom.12956DOI Listing
March 2019

Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples.

Authors:
Yuan Gao Hongzhe Li

Nat Methods 2018 12 12;15(12):1041-1044. Epub 2018 Nov 12.

Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

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http://www.nature.com/articles/s41592-018-0182-0
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http://dx.doi.org/10.1038/s41592-018-0182-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6289653PMC
December 2018

Conditional Regression Based on a Multivariate Zero-Inflated Logistic-Normal Model for Microbiome Relative Abundance Data.

Stat Biosci 2018 Dec 10;10(3):587-608. Epub 2018 Jul 10.

Department of Biestatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1007/s12561-018-9219-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6432796PMC
December 2018

A Novel Neutralizing Antibody Specific to the DE Loop of VP1 Can Inhibit EV-D68 Infection in Mice.

J Immunol 2018 11 3;201(9):2557-2569. Epub 2018 Oct 3.

Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China; and Key Laboratory of Systemic Innovative Research on Virus Vaccine, Chinese Academy of Medical Sciences, Kunming 650118, China

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http://www.jimmunol.org/lookup/doi/10.4049/jimmunol.1800655
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http://dx.doi.org/10.4049/jimmunol.1800655DOI Listing
November 2018

miR-1303 regulates BBB permeability and promotes CNS lesions following CA16 infections by directly targeting MMP9.

Emerg Microbes Infect 2018 Sep 19;7(1):155. Epub 2018 Sep 19.

Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.

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http://dx.doi.org/10.1038/s41426-018-0157-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6143596PMC
September 2018

Melittin-induced long non-coding RNA NONHSAT105177 inhibits proliferation and migration of pancreatic ductal adenocarcinoma.

Cell Death Dis 2018 Sep 20;9(10):940. Epub 2018 Sep 20.

Research Institute of Pancreatic Disease, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.

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http://dx.doi.org/10.1038/s41419-018-0965-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6148000PMC
September 2018

Medication class enrichment analysis: a novel algorithm to analyze multiple pharmacologic exposures simultaneously using electronic health record data.

J Am Med Inform Assoc 2018 07;25(7):780-789

Division of Gastroenterology, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1093/jamia/ocx162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6016702PMC
July 2018

Effects of JAK1/2 inhibition on bone marrow stromal cells of myeloproliferative neoplasm (MPN) patients and healthy individuals.

Eur J Haematol 2018 Jul 30;101(1):57-67. Epub 2018 Apr 30.

Division of Molecular Hematology & Lund Stem Cell Center, Lund University, Lund, Sweden.

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http://dx.doi.org/10.1111/ejh.13079DOI Listing
July 2018

A GLM-based latent variable ordination method for microbiome samples.

Biometrics 2018 06 9;74(2):448-457. Epub 2017 Oct 9.

Department of Biostatistics and Epidemiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania 19104, U.S.A.

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http://dx.doi.org/10.1111/biom.12775DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6173969PMC
June 2018

Joint testing and false discovery rate control in high-dimensional multivariate regression.

Biometrika 2018 Jun 16;105(2):249-269. Epub 2018 Feb 16.

Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, U.S.A.

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http://dx.doi.org/10.1093/biomet/asx085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6374004PMC
June 2018

Deficiency of Duffy Antigen Receptor for Chemokines Ameliorated Cochlear Damage From Noise Exposure.

Front Mol Neurosci 2018 30;11:173. Epub 2018 May 30.

Research Service, VA Loma Linda Healthcare System, Loma Linda, CA, United States.

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http://dx.doi.org/10.3389/fnmol.2018.00173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5988871PMC
May 2018

A model for paired-multinomial data and its application to analysis of data on a taxonomic tree.

Authors:
Pixu Shi Hongzhe Li

Biometrics 2017 12 30;73(4):1266-1278. Epub 2017 Mar 30.

Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, U.S.A.

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http://dx.doi.org/10.1111/biom.12681DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5623182PMC
December 2017

Different microRNA profiles reveal the diverse outcomes induced by EV71 and CA16 infection in human umbilical vein endothelial cells using high-throughput sequencing.

PLoS One 2017 22;12(5):e0177657. Epub 2017 May 22.

Yunnan Key Laboratory of Vaccine Research & Development on Severe Infections Disease, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177657PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5439704PMC
September 2017

Evaluation of the Hair Cell Regeneration in Zebrafish Larvae by Measuring and Quantifying the Startle Responses.

Neural Plast 2017 29;2017:8283075. Epub 2017 Jan 29.

Department of Biomedical Engineering, South University of Science and Technology of China, Guangdong, China.

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http://dx.doi.org/10.1155/2017/8283075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5303594PMC
August 2017

Integrated expression profiles analysis reveals novel predictive biomarker in pancreatic ductal adenocarcinoma.

Oncotarget 2017 Aug 31;8(32):52571-52583. Epub 2017 Mar 31.

Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China.

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http://dx.doi.org/10.18632/oncotarget.16732DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5581051PMC
August 2017

Optimal detection of weak positive latent dependence between two sequences of multiple tests.

J Multivar Anal 2017 Aug 14;160:169-184. Epub 2017 Jul 14.

Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.

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http://dx.doi.org/10.1016/j.jmva.2017.06.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5711487PMC
August 2017

Melittin inhibits tumor growth and decreases resistance to gemcitabine by downregulating cholesterol pathway gene CLU in pancreatic ductal adenocarcinoma.

Cancer Lett 2017 07 17;399:1-9. Epub 2017 Apr 17.

Research Institute of Pancreatic Disease, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Pancreatic Disease Centre, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Institute of Digestive Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S03043835173024
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http://dx.doi.org/10.1016/j.canlet.2017.04.012DOI Listing
July 2017

Behavioral methods for the functional assessment of hair cells in zebrafish.

Front Med 2017 Jun 27;11(2):178-190. Epub 2017 Mar 27.

Department of Biology, South University of Science and Technology of China, Shenzhen, 518000, China.

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http://dx.doi.org/10.1007/s11684-017-0507-xDOI Listing
June 2017

Genetic-Variation-Driven Gene-Expression Changes Highlight Genes with Important Functions for Kidney Disease.

Am J Hum Genet 2017 Jun;100(6):940-953

Renal-Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2017.05.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473735PMC
June 2017

A Model-Based Approach For Species Abundance Quantification Based On Shotgun Metagenomic Data.

Stat Biosci 2017 Jun 16;9(1):13-27. Epub 2016 May 16.

Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://link.springer.com/10.1007/s12561-016-9148-x
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http://dx.doi.org/10.1007/s12561-016-9148-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5612490PMC
June 2017

A general framework for association analysis of microbial communities on a taxonomic tree.

Bioinformatics 2017 05;33(9):1278-1285

Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408811PMC
May 2017

HLA Amino Acid Polymorphisms and Kidney Allograft Survival.

Transplantation 2017 05;101(5):e170-e177

1 Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA. 2 Arbor Research Collaborative for Health, Ann Arbor, MI. 3 National Marrow Donor Program, Minneapolis, MN. 4 Department of Pathology, Stanford University, Palo Alto, CA. 5 Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA.

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http://dx.doi.org/10.1097/TP.0000000000001670DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5642346PMC
May 2017

Sparse simultaneous signal detection for identifying genetically controlled disease genes.

J Am Stat Assoc 2017 5;112(519):1032-1046. Epub 2017 Jan 5.

Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania.

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http://dx.doi.org/10.1080/01621459.2016.1270825DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5784841PMC
January 2017

Activation of basolateral amygdala in juvenile C57BL/6J mice during social approach behavior.

Neuroscience 2016 Oct 9;335:184-94. Epub 2016 Aug 9.

Center for Neurobiology and Behavior, Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Translational Research Laboratory, 125 South 31st Street, Room 2220, Philadelphia, PA 19104-3403, USA. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5056014PMC
http://dx.doi.org/10.1016/j.neuroscience.2016.08.006DOI Listing
October 2016

A two-part mixed-effects model for analyzing longitudinal microbiome compositional data.

Bioinformatics 2016 09 14;32(17):2611-7. Epub 2016 May 14.

Genomics and Computational Biology Graduate Group Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860434PMC
September 2016

A Statistical Method for Identifying Trait-Associated Copy Number Variants.

Hum Hered 2015 28;79(3-4):147-56. Epub 2015 Jul 28.

Department of Statistics, North Carolina State University, Raleigh, N.C., USA.

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http://dx.doi.org/10.1159/000381585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862672PMC
April 2016

Isolation and characterization of primary bone marrow mesenchymal stromal cells.

Ann N Y Acad Sci 2016 04;1370(1):109-18

Lund Stem Cell Center and Division of Molecular Hematology, Lund University, Lund, Sweden.

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http://dx.doi.org/10.1111/nyas.13102DOI Listing
April 2016

Joint Estimation of Multiple High-dimensional Precision Matrices.

Stat Sin 2016 Apr;26(2):445-464

Assistant Professor, Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27707.

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http://dx.doi.org/10.5705/ss.2014.256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5351783PMC
April 2016

Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants.

JAMA Pediatr 2016 Mar;170(3):212-9

Children's Environmental Health and Disease Prevention Research Center at Dartmouth, Hanover, New Hampshire3Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire9Center for Molecular Epidemiology, The Geisel School.

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http://dx.doi.org/10.1001/jamapediatrics.2015.3732DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4783194PMC
March 2016

Uptake of fluorescent gentamicin by peripheral vestibular cells after systemic administration.

PLoS One 2015 20;10(3):e0120612. Epub 2015 Mar 20.

Oregon Hearing Research Center, Oregon Health & Science University, Portland, Oregon, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0120612PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4368668PMC
February 2016

Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production.

Gut 2016 Jan 26;65(1):63-72. Epub 2014 Nov 26.

Division of Gastroenterology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA Departments of Biostatistics & Epidemiology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1136/gutjnl-2014-308209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4583329PMC
January 2016

Sodium-glucose transporter-2 (SGLT2; SLC5A2) enhances cellular uptake of aminoglycosides.

PLoS One 2014 30;9(9):e108941. Epub 2014 Sep 30.

Oregon Hearing Research Center, Oregon Health & Science University, Portland, Oregon, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0108941PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4182564PMC
December 2015

glmgraph: an R package for variable selection and predictive modeling of structured genomic data.

Bioinformatics 2015 Dec 26;31(24):3991-3. Epub 2015 Aug 26.

Division of Biomedical Statistics and Informatics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905,USA.

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http://dx.doi.org/10.1093/bioinformatics/btv497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4692967PMC
December 2015

Genome wide nucleosome mapping for HSV-1 shows nucleosomes are deposited at preferred positions during lytic infection.

PLoS One 2015 24;10(2):e0117471. Epub 2015 Feb 24.

Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117471PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4339549PMC
November 2015

Morphological correlates of hearing loss after cochlear implantation and electro-acoustic stimulation in a hearing-impaired Guinea pig model.

Hear Res 2015 Sep 16;327:163-74. Epub 2015 Jun 16.

Oregon Hearing Research Center, Department of Otolaryngology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S03785955150012
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http://dx.doi.org/10.1016/j.heares.2015.06.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905574PMC
September 2015

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA.

Bioinformatics 2015 Aug 29;31(15):2461-8. Epub 2015 Mar 29.

Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btv183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4514928PMC
August 2015

Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn's Disease.

Inflamm Bowel Dis 2015 Aug;21(8):1786-93

*Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; †Department of Pediatric, Division of Gastroenterology and Nutrition Seattle Children's Hospital, Seattle, Washington; and University of Washington; ‡Department of Pediatrics, IWK Health Centre, Halifax, NS, Canada; §Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada; ||School of Nursing, University of Pennsylvania, Philadelphia, Pennsylvania; ¶Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; **Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; and ††Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.

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http://pdfs.journals.lww.com/ibdjournal/2015/08000/Comparati
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http://dx.doi.org/10.1097/MIB.0000000000000426DOI Listing
August 2015

Endotoxemia-mediated inflammation potentiates aminoglycoside-induced ototoxicity.

Sci Transl Med 2015 Jul;7(298):298ra118

Oregon Hearing Research Center, Department of Otolaryngology, Oregon Health & Science University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239, USA.

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http://dx.doi.org/10.1126/scitranslmed.aac5546DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4534720PMC
July 2015

The Ovarian Cancer Chemokine Landscape Is Conducive to Homing of Vaccine-Primed and CD3/CD28-Costimulated T Cells Prepared for Adoptive Therapy.

Clin Cancer Res 2015 Jun 23;21(12):2840-50. Epub 2015 Feb 23.

Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, Pennsylvania. Ludwig Cancer Research Center, University of Lausanne, Lausanne, Switzerland. Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1158/1078-0432.CCR-14-2777DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987088PMC
June 2015

Testing in Microbiome-Profiling Studies with MiRKAT, the Microbiome Regression-Based Kernel Association Test.

Am J Hum Genet 2015 May;96(5):797-807

Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2015.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570290PMC
May 2015

Local mechanisms for loud sound-enhanced aminoglycoside entry into outer hair cells.

Front Cell Neurosci 2015 14;9:130. Epub 2015 Apr 14.

Oregon Hearing Research Center, Oregon Health & Science University Portland, OR, USA.

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http://dx.doi.org/10.3389/fncel.2015.00130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4396448PMC
April 2015

Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data.

Cancer Inform 2015 27;14(Suppl 1):11-22. Epub 2015 Jan 27.

Department of Biostatistics and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.

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http://dx.doi.org/10.4137/CIN.S13972DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4310510PMC
February 2015

Regularization Methods for High-Dimensional Instrumental Variables Regression With an Application to Genetical Genomics.

J Am Stat Assoc 2015;110(509):270-288

Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.

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http://www.tandfonline.com/doi/full/10.1080/01621459.2014.90
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http://dx.doi.org/10.1080/01621459.2014.908125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573639PMC
January 2015

More powerful genetic association testing via a new statistical framework for integrative genomics.

Biometrics 2014 Dec 26;70(4):881-90. Epub 2014 Jun 26.

Department of Statistics, University of Illinois at Urbana-Champaign, Champaign, Illinois 61820, U.S.A.

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http://doi.wiley.com/10.1111/biom.12206
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http://dx.doi.org/10.1111/biom.12206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4425276PMC
December 2014

Low/negative expression of PDGFR-α identifies the candidate primary mesenchymal stromal cells in adult human bone marrow.

Stem Cell Reports 2014 Dec 30;3(6):965-74. Epub 2014 Oct 30.

Lund Stem Cell Center, Lund University, 22184 Lund, Sweden; Department of Hematology, Skåne University Hospital Lund, 22184 Lund, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2014.09.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4264066PMC
December 2014

Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota.

Gastroenterology 2014 Nov 18;147(5):1055-63.e8. Epub 2014 Jul 18.

Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2014.07.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4252572PMC
November 2014

Systems biology approaches to epidemiological studies of complex diseases.

Authors:
Hongzhe Li

Wiley Interdiscip Rev Syst Biol Med 2013 Nov-Dec;5(6):677-86. Epub 2013 Sep 9.

Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1002/wsbm.1242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3947451PMC
October 2014

A functional genomic approach identifies FAL1 as an oncogenic long noncoding RNA that associates with BMI1 and represses p21 expression in cancer.

Cancer Cell 2014 Sep;26(3):344-357

Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccr.2014.07.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159613PMC
September 2014

A change-point model for identifying 3'UTR switching by next-generation RNA sequencing.

Bioinformatics 2014 Aug 11;30(15):2162-70. Epub 2014 Apr 11.

Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102 and Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103598PMC
August 2014

Parametric modeling of whole-genome sequencing data for CNV identification.

Biostatistics 2014 Jul 28;15(3):427-41. Epub 2014 Jan 28.

Division of Biostatistics, University of Pennsylvania, Philadelphia, PA 19104, USA

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http://dx.doi.org/10.1093/biostatistics/kxt060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4059462PMC
July 2014

Direct estimation of differential networks.

Biometrika 2014 Jun;101(2):253-268

Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA.

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http://www-stat.wharton.upenn.edu/~tcai/paper/Estimating-Dif
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http://biomet.oxfordjournals.org/cgi/doi/10.1093/biomet/asu0
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http://dx.doi.org/10.1093/biomet/asu009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443936PMC
June 2014

PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution.

Nucleic Acids Res 2014 Feb 20;42(3):e20. Epub 2013 Dec 20.

Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA and Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1093/nar/gkt1304DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919567PMC
February 2014

A logistic normal multinomial regression model for microbiome compositional data analysis.

Biometrics 2013 Dec 15;69(4):1053-63. Epub 2013 Oct 15.

Department of Statistics and Actuarial Science, The University of Hong Kong, Pokfulam, Hong Kong.

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http://dx.doi.org/10.1111/biom.12079DOI Listing
December 2013

MATCHCLIP: locate precise breakpoints for copy number variation using CIGAR string by matching soft clipped reads.

Front Genet 2013 16;4:157. Epub 2013 Aug 16.

Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine Philadelphia, PA, USA.

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http://dx.doi.org/10.3389/fgene.2013.00157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744852PMC
August 2013

Network-based analysis of multivariate gene expression data.

Methods Mol Biol 2013 ;972:121-39

Department of Biostatistics and Epidemiology, New Jersey Institute of Technology, Newark, NJ, USA.

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http://dx.doi.org/10.1007/978-1-60327-337-4_8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692268PMC
July 2013

Association of CETP Taq1B and -629C > A polymorphisms with coronary artery disease and lipid levels in the multi-ethnic Singaporean population.

Lipids Health Dis 2013 Jun 8;12:85. Epub 2013 Jun 8.

Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.

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http://dx.doi.org/10.1186/1476-511X-12-85DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3699414PMC
June 2013

Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts.

PLoS One 2012 6;7(9):e42786. Epub 2012 Sep 6.

Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3435383PMC
May 2013

A Hierarchical Bayesian Model for Estimating and Inferring Differential Isoform Expression for Multi-Sample RNA-Seq Data.

Stat Biosci 2013 May;5(1):119-137

Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA, Tel.: 215-573-5038.

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http://dx.doi.org/10.1007/s12561-011-9052-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669631PMC
May 2013

Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis.

Biostatistics 2013 Apr 15;14(2):244-58. Epub 2012 Oct 15.

Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA19104, USA.

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http://dx.doi.org/10.1093/biostatistics/kxs038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3590923PMC
April 2013

Adjusting for High-dimensional Covariates in Sparse Precision Matrix Estimation by ℓ-Penalization.

J Multivar Anal 2013 Apr;116:365-381

Center for Applied Statistics and School of Statistics, Renmin University of China, No. 59 Zhongguancun Street, Haidian District, Beijing 100872, China and Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6021, USA.

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http://dx.doi.org/10.1016/j.jmva.2013.01.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3653344PMC
April 2013

The role of NF-кB in SAA-induced peroxisome proliferator-activated receptor γ activation.

Atherosclerosis 2013 Mar 4;227(1):72-8. Epub 2013 Jan 4.

Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, NUHS Tower Block, Level 12, 1E Kent Ridge Road, Singapore 119228, Singapore.

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http://dx.doi.org/10.1016/j.atherosclerosis.2012.12.007DOI Listing
March 2013

Covariate-Adjusted Precision Matrix Estimation with an Application in Genetical Genomics.

Biometrika 2013 Mar 30;100(1):139-156. Epub 2012 Nov 30.

Department of Statistics, Fox School of Business, Temple University, Philadelphia, Pennsylvania 19122, USA.

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http://dx.doi.org/10.1093/biomet/ass058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5351557PMC
March 2013

VARIABLE SELECTION FOR SPARSE DIRICHLET-MULTINOMIAL REGRESSION WITH AN APPLICATION TO MICROBIOME DATA ANALYSIS.

Authors:
Jun Chen Hongzhe Li

Ann Appl Stat 2013 Mar;7(1)

Department of Biostatistics and Epidemiology, University of Pennsylvania

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http://dx.doi.org/10.1214/12-AOAS592DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3846354PMC
March 2013

Simultaneous Discovery of Rare and Common Segment Variants.

Biometrika 2013;100(1):157-172

Department of Statistics, North Carolina State University, Raleigh, North Carolina, 27695, USA.

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http://dx.doi.org/10.1093/biomet/ass059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696347PMC
January 2013

LEARNING LOCAL DIRECTED ACYCLIC GRAPHS BASED ON MULTIVARIATE TIME SERIES DATA.

Ann Appl Stat 2013 ;7(3):1249-1835

Department of Statistics and Probability, Peking University, Beijing 100871, PR China. Department of Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3898602PMC
January 2013

Robust Gaussian graphical modeling via l1 penalization.

Biometrics 2012 Dec 28;68(4):1197-206. Epub 2012 Sep 28.

Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1111/j.1541-0420.2012.01785.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535542PMC
December 2012

Robust Detection and Identification of Sparse Segments in Ultra-High Dimensional Data Analysis.

J R Stat Soc Series B Stat Methodol 2012 Nov;74(5):773-797

Department of Statistics, University of Pennsylvania, Philadelphia, USA.

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http://dx.doi.org/10.1111/j.1467-9868.2012.01028.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3563068PMC
November 2012

A SPARSE CONDITIONAL GAUSSIAN GRAPHICAL MODEL FOR ANALYSIS OF GENETICAL GENOMICS DATA.

Ann Appl Stat 2011 Dec;5(4):2630-2650

University of Pennsylvania School of Medicine.

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http://projecteuclid.org/euclid.aoas/1324399609
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http://dx.doi.org/10.1214/11-AOAS494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419502PMC
December 2011