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1. Full Text A regression framework for assessing covariate effects on the reproducibility of high-throughput experiments
: Assess Covariate Effects on Reproducibility
by Li, Qunhua and Zhang, Feipeng
Biometrics, ISSN 0006-341X, 09/2018, Volume 74, Issue 3, pp. 803 - 813
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2. Full Text MEASURING REPRODUCIBILITY OF HIGH-THROUGHPUT EXPERIMENTS
by Qunhua Li and James B. Brown and Haiyan Huang and Peter J. Bickel
The Annals of Applied Statistics, ISSN 1932-6157, 9/2011, Volume 5, Issue 3, pp. 1752 - 1779
Reproducibility is essential to reliable scientific discovery in high-throughput experiments. In this work we propose a unified approach to measure the... 
Datasets | Simulations | Gaussian distributions | Heuristics | Signal noise | P values | Fall lines | Geometric lines | Parametric models | Estimation methods | Association | Copula | Reproducibility | Genomics | Mixture model | Irreproducible discovery rate | Iterative algorithm | High-throughput experiment | TESTS | copula | association | STATISTICS & PROBABILITY | RANK CORRELATION | mixture model | iterative algorithm | irreproducible discovery rate | DEPENDENCE | FALSE DISCOVERY RATE | CHIP-SEQ DATA | high-throughput experiment | genomics | PLOTS | BINDING-SITES | Statistics - Applications
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3. Full Text A regression framework for assessing covariate effects on the reproducibility of high‐throughput experiments
by Li, Qunhua and Zhang, Feipeng
Biometrics, ISSN 0006-341X, 09/2018, Volume 74, Issue 3, pp. 803 - 813
The outcome of high-throughput biological experiments is affected by many operational factors in the experimental and data-analytical procedures. Understanding... 
Correspondence curve regression | Copula | Cumulative link model | Reproducibility | Genomics | High‐throughput experiment | High-throughput experiment | COPULAS | BIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | STATISTICS & PROBABILITY | OF-FIT TESTS | Reproducibility of Results | Humans | CCCTC-Binding Factor - chemistry | Calibration | Models, Statistical | High-Throughput Screening Assays - statistics & numerical data | Microarray Analysis - statistics & numerical data | Regression Analysis | Algorithms | Confounding Factors (Epidemiology) | Gene Expression Profiling - statistics & numerical data | Computer Simulation | High-Throughput Screening Assays - standards | Binding Sites
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4. Full Text Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
by Bailey, Timothy and Krajewski, Pawel and Ladunga, Istvan and Lefebvre, Celine and Li, Qunhua and Liu, Tao and Madrigal, Pedro and Taslim, Cenny and Zhang, Jie
PLoS Computational Biology, ISSN 1553-734X, 11/2013, Volume 9, Issue 11, p. e1003326
Mapping the chromosomal locations of transcription factors, nucleosomes, histone modifications, chromatin remodeling enzymes, chaperones, and polymerases is... 
PLATFORM | DNA BINDING-SITES | BIOCONDUCTOR PACKAGE | ALIGNMENT | ALGORITHM | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | R-PACKAGE | NORMALIZATION | GENOME-WIDE IDENTIFICATION | DIFFERENTIAL EXPRESSION ANALYSIS | SOFTWARE | Computational Biology - methods | Reproducibility of Results | High-Throughput Nucleotide Sequencing | Chromatin Immunoprecipitation | Sequence Analysis, DNA - methods | Humans | Proteins | Enzymes | Chromatin | Deoxyribonucleic acid | DNA | Software | Genomes | Gene expression | Experiments | Binding sites
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5. Full Text HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient
by Yang, Tao and Zhang, Feipeng and Yardımci, Galip Gürkan and Song, Fan and Hardison, Ross C and Noble, William Stafford and Yue, Feng and Li, Qunhua
Genome Research, ISSN 1088-9051, 11/2017, Volume 27, Issue 11, pp. 1939 - 1949
Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce... 
CHROMATIN | HUMAN-CELLS | BIOCHEMISTRY & MOLECULAR BIOLOGY | PRINCIPLES | ORGANIZATION | HUMAN GENOME | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | HIGH-RESOLUTION | GENETICS & HEREDITY | ARCHITECTURE | CHROMOSOME CONFORMATION | DIFFERENTIATION | DOMAINS | Cell Line | Cell Lineage | Computational Biology - methods | Reproducibility of Results | Sequence Analysis, RNA | Humans | Chromatin Immunoprecipitation - methods | High-Throughput Nucleotide Sequencing | Software | Chromatin | Usage | Genomes | Research | Cell lines | Method
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6. Advances in study on gastrointestinal mucosal low-grade inflammation in functional dyspepsia
by Li, Qunhua and He, Guobin
Chinese Journal of Gastroenterology, ISSN 1008-7125, 11/2015, Volume 20, Issue 11, pp. 698 - 700
Helicobacter pylori | Dyspepsia | Psychological Factor | Inflammation | Intestinal Mucosal Barrier
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7. Full Text Systematic evaluation of factors influencing ChIP-seq fidelity
by Chen, Yiwen and Negre, Nicolas and Li, Qunhua and Mieczkowska, Joanna O and Slattery, Matthew and Liu, Tao and Zhang, Yong and Kim, Tae-Kyung and He, Housheng Hansen and Zieba, Jennifer and Ruan, Yijun and Bickel, Peter J and Myers, Richard M and Wold, Barbara J and White, Kevin P and Lieb, Jason D and Liu, X Shirley
Nature Methods, ISSN 1548-7091, 06/2012, Volume 9, Issue 6, pp. 609 - 614
We evaluated how variations in sequencing depth and other parameters influence interpretation of chromatin immunoprecipitation-sequencing (ChIP-seq)... 
MODEL-BASED ANALYSIS | FACTOR-BINDING SITES | RNA-SEQ | GENOME | BIOCHEMICAL RESEARCH METHODS | Histone-Lysine N-Methyltransferase - genetics | Gene Library | Oligonucleotide Array Sequence Analysis | Repressor Proteins - genetics | False Positive Reactions | Algorithms | Animals | Sensitivity and Specificity | Chromatin Immunoprecipitation - methods | Chromatin Immunoprecipitation - standards | High-Throughput Nucleotide Sequencing | Drosophila Proteins - genetics | Drosophila melanogaster | Chromatin - chemistry | Chromatin | Usage | Transcription factors | Physiological aspects | Research | Nucleotide sequencing | DNA sequencing | Genomes | Insects | Genomics
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8. Full Text Multiple Luminescence Responses towards Mechanical Stimulus and Photo‐Induction: The Key Role of the Stuck Packing Mode and Tunable Intermolecular Interactions
by Dang, Qianxi and Hu, Lanzhen and Wang, Jiaqiang and Zhang, Qunhua and Han, Mengmeng and Luo, Simeng and Gong, Yanbin and Wang, Can and Li, Qianqian and Li, Zhen
Chemistry – A European Journal, ISSN 0947-6539, 05/2019, Volume 25, Issue 28, pp. 7031 - 7037
Organic luminescence with different forms continues to be one of the most active research fields in science and technology. Herein, an ultra‐simple organic... 
intermolecular interactions | molecular packing | mechanoluminescence | photo-induced room-temperature phosphorescence | ROOM-TEMPERATURE PHOSPHORESCENCE | AGGREGATION-INDUCED EMISSION | BEHAVIOR | DERIVATIVES | CHEMISTRY, MULTIDISCIPLINARY | Structure | Crystals | TPA | Optical properties | Luminescence | Mechanoluminescence | Phosphorescence | Light effects | Crystal structure | Functional materials
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9. Full Text powerTCR: A model-based approach to comparative analysis of the clone size distribution of the T cell receptor repertoire
by Koch, Hillary and Starenki, Dmytro and Cooper, Sara J and Myers, Richard M and Li, Qunhua
PLoS Computational Biology, ISSN 1553-734X, 11/2018, Volume 14, Issue 11, p. e1006571
Sequencing of the T cell receptor repertoire is a powerful tool for deeper study of immune response, but the unique structure of this type of data makes its... 
THRESHOLD | DIVERSITY | DIVERGENCE | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Receptors, Antigen, T-Cell - chemistry | Alternative Splicing | CD4-Positive T-Lymphocytes - cytology | Humans | Brain Neoplasms - metabolism | Likelihood Functions | Animals | Immune System | Computer Simulation | Programming Languages | Glioblastoma - metabolism | Clone Cells | Lung - metabolism | Mice | Receptors, Antigen, T-Cell - genetics | Software | High-Throughput Nucleotide Sequencing - methods | Sarcoidosis - metabolism | Cluster Analysis | Physiological aspects | Usage | Cell receptors | Mathematical models | Models | T cells | Antigens | Biotechnology | Size distribution | Sequences | Immune response | Funding | Cloning | T cell receptors | Lymphocytes T | Stability analysis | Gene expression | T-cell receptor | Lymphocytes | Stem cells | Diabetes | Cancer | Immune system
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10. Full Text Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network
by Lyu, Yafei and Xue, Lingzhou and Zhang, Feipeng and Koch, Hillary and Saba, Laura and Kechris, Katerina and Li, Qunhua
PLoS Computational Biology, ISSN 1553-734X, 09/2018, Volume 14, Issue 9, p. e1006436
Co-expression network analysis provides useful information for studying gene regulation in biological processes. Examining condition-specific patterns of... 
BREAST-CANCER | INVASION | METASTASIS | INVERSE COVARIANCE ESTIMATION | MICROARRAY | CEACAM6 | LACTOFERRIN | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | VARIABLE SELECTION | EXPRESSION | CARCINOMA | Heart | Neoplasms - metabolism | Area Under Curve | Humans | Gene Expression Regulation, Neoplastic | Rats | Male | Gene Expression Profiling | Normal Distribution | Breast Neoplasms - metabolism | Brain - metabolism | Computer Graphics | Algorithms | Animals | Breast Neoplasms - genetics | Computer Simulation | Myocardium - metabolism | Female | Software | Databases, Factual | Usage | Models | Gene expression | Graphic methods | Genes | Gene regulation | Modules | Genomics | Genomes | Statistical methods | Metastasis | Variables | Heterogeneity | Network hubs | Network analysis | Trends | Pharmaceutical sciences | Breast cancer | Clustering | College campuses | Biological activity | Sparsity | Data sets | Regulatory mechanisms (biology) | Statistical inference | Methods | Cancer | Tumors
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11. Full Text Measuring the reproducibility and quality of Hi-C data
by Yardımcı, Galip Gürkan and Ozadam, Hakan and Sauria, Michael E. G and Ursu, Oana and Yan, Koon-Kiu and Yang, Tao and Chakraborty, Abhijit and Kaul, Arya and Lajoie, Bryan R and Song, Fan and Zhan, Ye and Ay, Ferhat and Gerstein, Mark and Kundaje, Anshul and Li, Qunhua and Taylor, James and Yue, Feng and Dekker, Job and Noble, William S
Genome Biology, ISSN 1474-7596, 03/2019, Volume 20, Issue 1, pp. 57 - 19
BackgroundHi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA... 
ORGANIZATION | SINGLE | CHIP | 3D GENOME | CHROMATIN | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | HIGH-RESOLUTION | GENETICS & HEREDITY | INACTIVE X-CHROMOSOME | PRINCIPLES | Gene regulation | Genomics | Cell division | Genomes | Experiments | Datasets | DNA biosynthesis | Correlation analysis | Quality control | Cell lines | Gene loci | Bioinformatics | Chromosomes
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12. Full Text Metabolomic analysis reveals the composition differences in 13 Chinese tea cultivars of different manufacturing suitabilities
by Li, Pengliang and Dai, Weidong and Lu, Meiling and Xie, Dongchao and Tan, Junfeng and Yang, Chen and Zhu, Yin and Lv, Haipeng and Peng, Qunhua and Zhang, Yue and Guo, Li and Ni, Dejiang and Lin, Zhi
Journal of the Science of Food and Agriculture, ISSN 0022-5142, 02/2018, Volume 98, Issue 3, pp. 1153 - 1161
BACKGROUNDGreen tea and black tea are manufactured using appropriate tea cultivars in China. However, the metabolite differences relating to the manufacturing... 
tea cultivar | manufacturing suitability | metabolomics | LC–MS | METABOLITES | QUALITY | FOOD SCIENCE & TECHNOLOGY | COMPONENTS | TASTE | CATECHINS | MASS-SPECTROMETRY | GREEN TEA | LC-MS | POLYPHENOLS | BIOSYNTHESIS | AGRICULTURE, MULTIDISCIPLINARY | CAMELLIA-SINENSIS L | CHEMISTRY, APPLIED | Chemical industry | Herbicides | Pesticides industry | Flavonoids | Metabolites | Flavones | Bioflavonoids | Amino acids | Mass spectrometry | Green tea | High performance liquid chromatography | Cultivars | Cluster analysis | Statistical analysis | Breeding | Mass spectroscopy | Liquid chromatography | Black tea | High-performance liquid chromatography | Quadrupoles | Phenolic acids | Studies | Alkaloids | Catechins | Tea | Synthesis | Acids | Multivariate statistical analysis | Phenols | Glycosides | Manufacturing
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13. Full Text A semi-parametric statistical model for integrating gene expression profiles across different platforms
by Lyu, Yafei and Li, Qunhua
BMC Bioinformatics, ISSN 1471-2105, 01/2016, Volume 17, Issue 1, p. 5
Background: Determining differentially expressed genes (DEGs) between biological samples is the key to understand how genotype gives rise to phenotype. RNA-seq... 
Mixture model | Rank | Copula | Gene expression | Data integration | Meta-analysis | PROJECT | METAANALYSIS | MICROARRAY | BIOCHEMICAL RESEARCH METHODS | REPRODUCIBILITY | ARRAYS | ENCYCLOPEDIA | DATABASE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ANNOTATION | MATHEMATICAL & COMPUTATIONAL BIOLOGY | DNA ELEMENTS | RNA-SEQ DATA | Sequence Analysis, RNA - methods | Reproducibility of Results | Oligonucleotide Array Sequence Analysis - methods | Humans | Transcriptome | Gene Expression Profiling - methods | Models, Statistical | High-Throughput Nucleotide Sequencing - methods | RNA - genetics
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14. Full Text Analysis of the Genome and Chromium Metabolism-Related Genes of Serratia sp. S2
by Dong, Lanlan and Zhou, Simin and He, Yuan and Jia, Yan and Bai, Qunhua and Deng, Peng and Gao, Jieying and Li, Yingli and Xiao, Hong
Applied Biochemistry and Biotechnology, ISSN 0273-2289, 05/2018, Volume 185, Issue 1, pp. 140 - 152
This study is to investigate the genome sequence of Serratia sp. S2. The genomic DNA of Serratia sp. S2 was extracted and the sequencing library was... 
Genome sequencing | Bioinformatics | Chromium metabolism genes | Serratia sp. S2 | Serratia sp S2 | RNA GENES | PROTEIN | CHROMATE REDUCTASE-ACTIVITY | PSEUDOMONAS-PUTIDA | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | DECOLORIZATION | HEXAVALENT CHROMIUM | REMOVAL | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | RESISTANCE | REDUCES CHROMATE | Genes, Bacterial | Serratia - genetics | Chromium - metabolism | Databases, Nucleic Acid | Molecular Sequence Annotation | Serratia - metabolism | Biotechnology | Yuan (China) | Anopheles | Analysis | Genes | Genomics | DNA | Genomes | Health aspects | Nucleotide sequence | Metabolism | Serratia | Data bases | Gene sequencing | Databases | Annotations | Chromium | Deoxyribonucleic acid--DNA | DNA sequencing
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15. Full Text Adherence to Healthy Lifestyle and Cardiovascular Diseases in the Chinese Population
by Lv, Jun, PhD and Yu, Canqing, PhD and Guo, Yu, MSc and Bian, Zheng, MSc and Yang, Ling, PhD and Chen, Yiping, DPhil and Tang, Xuefeng, MPH and Zhang, Weiyuan, MPH and Qian, Yijian, MD and Huang, Yuelong, MD and Wang, Xiaoping, MD and Chen, Junshi, MD and Chen, Zhengming, DPhil and Qi, Lu, PhD and Li, Liming, MPH and China Kadoorie Biobank and China Kadoorie Biobank Collaborative Group
JACC (Journal of the American College of Cardiology), ISSN 0735-1097, 2017, Volume 69, Issue 9, pp. 1116 - 1125
Abstract Background Adherence to a combination of healthy lifestyle factors has been related to a considerable reduction of cardiovascular risk in white... 
Cardiovascular | Internal Medicine | cohort studies | health behavior | cardiovascular diseases | lifestyle | GLOBAL BURDEN | MORTALITY | CARDIAC & CARDIOVASCULAR SYSTEMS | METAANALYSIS | MYOCARDIAL-INFARCTION | MEDITERRANEAN DIET | RISK | ALCOHOL-CONSUMPTION | BODY-MASS INDEX | ASSOCIATION | PRIMARY PREVENTION | Cardiovascular Diseases - ethnology | Cardiovascular Diseases - prevention & control | Humans | Middle Aged | Male | Health Behavior | Asian Continental Ancestry Group - psychology | China | Healthy Lifestyle | Adult | Female | Aged | Patient Compliance | Cohort Studies | Cardiovascular diseases | Analysis | Hypertension | Heart | Stroke | Cardiovascular disease | Alcohol | Family medical history | Metabolism | Studies | Body mass index | Tobacco | Illnesses | Marital status | Womens health | Health behavior | Questionnaires | Population | Blood pressure | Lifestyles | Health risk assessment | Age | Smoking
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