Education/CredentialsFellowship : National Institute of Environmental Health Sciences ( Research Fellow)Doctoral Degree: Ohio State University (Biostatistics)Doctoral Degree: Ohio State University (Mathematics)Master's Degree: Peking University (Mathematics)Bachelor's Degree: Hubei University (Mathematics) Contact Information Medical Sciences Building 143 Office 513-558-7221 Email niulg@ucmail.uc.edu Research Interests1) Statistical bioinformatics (methodology): RNA-Seq, ChIA-PET, methylation array and PacBio sequencing; 2) Statistical bioinformatics (consulting): data analysis for RNA-Seq, ChIA-PET, methylation array, and mass spectrometry; 3) Biostatistical consulting: study planning and design, power calculations, and statistical modeling and analysis; 4) Data mining of public domain omics datasets (such as TCGA datasets). Peer Reviewed Publications Conrey, Shannon C; Burrell, Allison R; Brokamp, Cole; Burke, Rachel M; Couch, Sarah C; Niu, Liang; Mattison, Claire P; Piasecki, Alexandra; Payne, Daniel C; Staat, Mary A; Morrow, Ardythe L 2022. Neighbourhood socio-economic environment predicts adiposity and obesity risk in children under two. Pediatric obesity, 17 12, e12964Jiang, Lin; Liang, Jialiang; Huang, Wei; Ma, Jianyong; Park, Ki Ho; Wu, Zhichao; Chen, Peng; Zhu, Hua; Ma, Jian-Jie; Cai, Wenfeng; Paul, Christian; Niu, Liang; Fan, Guo-Chang; Wang, Hong-Sheng; Kanisicak, Onur; Xu, Meifeng; Wang, Yigang 2022. CRISPR activation of endogenous genes reprograms fibroblasts into cardiovascular progenitor cells for myocardial infarction therapy. Molecular therapy : the journal of the American Society of Gene Therapy, 30 1, 54-74Sprague, Alexander C; Niu, Liang; Jandarov, Roman; Zhang, Xiang; Zhang, Ge; Chen, Aimin; Šarac, Jelena; Čoklo, Miran; Missoni, Sasa; Rudan, Pavao; Langevin, Scott M; Deka, Ranjan 2022. Stable methylation loci are associated with systolic blood pressure in a Croatian island population. Epigenomics, 14 21, 1343-1354Morrow, Ardythe L; McClain, Janelle; Conrey, Shannon C; Niu, Liang; Kinzer, Alexandra; Cline, Allison R; Piasecki, Alexandra M; DeFranco, Emily; Ward, Laura; Ware, Julie; Payne, Daniel C; Staat, Mary A; Nommsen-Rivers, Laurie A 2021. Breastfeeding Disparities and Their Mediators in an Urban Birth Cohort of Black and White Mothers. Breastfeeding medicine : the official journal of the Academy of Breastfeeding Medicine, 16 6, 452-462Morrow, Ardythe L; Staat, Mary A; DeFranco, Emily A; McNeal, Monica M; Cline, Allison R; Conrey, Shannon C; Schlaudecker, Elizabeth P; Piasecki, Alexandra M; Burke, Rachel M; Niu, Liang; Hall, Aron J; Bowen, Michael D; Gerber, Susan I; Langley, Gayle E; Thornburg, Natalie J; Campbell, Angela P; Vinjé, Jan; Parashar, Umesh D; Payne, Daniel C 2021. Pediatric Respiratory and Enteric Virus Acquisition and Immunogenesis in US Mothers and Children Aged 0-2: PREVAIL Cohort Study. JMIR research protocols, 10 2, e22222Vilfranc, Chrystelle L; Che, Li-Xiao; Patra, Krushna C; Niu, Liang; Olowokure, Olugbenga; Wang, Jiang; Shah, Shimul A; Du, Chun-Ying 2021. BIR repeat-containing ubiquitin conjugating enzyme (BRUCE) regulation of ?-catenin signaling in the progression of drug-induced hepatic fibrosis and carcinogenesis. World journal of hepatology, 13 3, 343-361von Allmen, Douglas; Tang, Alice; Takiar, Vinita; Zender, Chad; Romeo, Stephen; Masch, Jessica; Casper, Keith; Patil, Yash; Wilson, Keith; Khosla, Siddarth; Niu, Liang; Altaye, Mekibib; Tabangin, Meredith; Howell, Rebecca J 2021. Modified Head and Neck Swallow Scale: Using EORTC-QLQ-H&N35 to Predict Overall Survival. The Laryngoscope, , Xu, Zongli; Niu, Liang; Taylor, Jack A 2021. The ENmix DNA methylation analysis pipeline for Illumina BeadChip and comparisons with seven other preprocessing pipelines. Clinical epigenetics, 13 1, 216Xu, Zongli; Xie, Changchun; Taylor, Jack A; Niu, Liang 2021. ipDMR: identification of differentially methylated regions with interval P-values. Bioinformatics (Oxford, England), 37 5, 711-713de Gannes, Matthew; Ko, Chia-I; Zhang, Xiang; Biesiada, Jacek; Niu, Liang; Koch, Sheryl E; Medvedovic, Mario; Rubinstein, Jack; Puga, Alvaro 2020. Dioxin Disrupts Dynamic DNA Methylation Patterns in Genes That Govern Cardiomyocyte Maturation. Toxicological sciences : an official journal of the Society of Toxicology, 178 2, 325-337Sharma, Manju; Zhang, Shuangmin; Niu, Liang; Lewinsohn, David M; Zhang, Xiang; Huang, Shouxiong 2020. Mucosal-Associated Invariant T Cells Develop an Innate-Like Transcriptomic Program in Anti-mycobacterial Responses. Frontiers in immunology, 11 , 1136Ge, Chunmin; Vilfranc, Chrystelle L; Che, Lixiao; Pandita, Raj K; Hambarde, Shashank; Andreassen, Paul R; Niu, Liang; Olowokure, Olugbenga; Shah, Shimul; Waltz, Susan E; Zou, Lee; Wang, Jiang; Pandita, Tej K; Du, Chunying 2019. The BRUCE-ATR Signaling Axis Is Required for Accurate DNA Replication and Suppression of Liver Cancer Development. Hepatology (Baltimore, Md.), 69 6, 2608-2622Greene, Alexis D; Kendziorski, Jessica A; Buckholz, Jeanette M; Niu, Liang; Xie, Changchun; Pinney, Susan M; Burns, Katherine A 2019. Elevated serum chemokines are independently associated with both endometriosis and uranium exposure. Reproductive toxicology (Elmsford, N.Y.), 84 , 26-31Huang, Weichun; Medvedovic, Mario; Zhang, Jingwen; Niu, Liang 2019. ChIAPoP: a new tool for ChIA-PET data analysis. Nucleic acids research, 47 7, e37Langevin, Scott M; Kuhnell, Damaris; Niu, Liang; Biesiada, Jacek; Leung, Yuet-Kin; Deka, Ranjan; Chen, Aimin; Medvedovic, Mario; Kelsey, Karl T; Kasper, Susan; Zhang, Xiang 2019. Comprehensive mapping of the methylation landscape of 16 CpG-dense regions in oral and pharyngeal squamous cell carcinoma. Epigenomics, 11 9, 987-1002Xueheng Zhao, Liang Niu, Carlo Clerici, Roberta Russo, Melissa Byrd, and Kenneth DR Setchell 2019. Data analysis of MS-based clinical lipidomics studies with crossover design: A tutorial mini-review of statistical methods Clinical Mass Spectrometry, 13 , 5-17Haque, Sulsal-Ul; Niu, Liang; Kuhnell, Damaris; Hendershot, Jacob; Biesiada, Jacek; Niu, Wen; Hagan, Matthew C; Kelsey, Karl T; Casper, Keith A; Wise-Draper, Trisha M; Medvedovic, Mario; Langevin, Scott M 2018. Differential expression and prognostic value of long non-coding RNA in HPV-negative head and neck squamous cell carcinoma. Head & neck, 40 7, 1555-1564Leung, Yuet-Kin; Ouyang, Bin; Niu, Liang; Xie, Changchun; Ying, Jun; Medvedovic, Mario; Chen, Aimin; Weihe, Pal; Valvi, Damaskini; Grandjean, Philippe; Ho, Shuk-Mei 2018. Identification of sex-specific DNA methylation changes driven by specific chemicals in cord blood in a Faroese birth cohort. Epigenetics, 13 3, 290-300Liu, Hongqi; Feng, Xizhi; Ennis, Kelli N; Behrmann, Catherine A; Sarma, Pranjal; Jiang, Tony T; Kofuji, Satoshi; Niu, Liang; Stratton, Yiwen; Thomas, Hala Elnakat; Yoon, Sang-Oh; Sasaki, Atsuo T; Plas, David R 2017. Pharmacologic Targeting of S6K1 in PTEN-Deficient Neoplasia. Cell reports, 18 9, 2088-2095Sharma, Manju; Zhang, Xiang; Zhang, Shuangmin; Niu, Liang; Ho, Shuk-Mei; Chen, Aimin; Huang, Shouxiong 2017. Inhibition of endocytic lipid antigen presentation by common lipophilic environmental pollutants. Scientific reports, 7 1, 2085Xu, Zongli; Langie, Sabine A S; De Boever, Patrick; Taylor, Jack A; Niu, Liang 2017. RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip. BMC genomics, 18 1, 4Chen, Liang; Peng, Zhimin; Meng, Qinghang; Mongan, Maureen; Wang, Jingcai; Sartor, Maureen; Chen, Jing; Niu, Liang; Medvedovic, Mario; Kao, Winston; Xia, Ying 2016. Loss of I?B kinase ? promotes myofibroblast transformation and senescence through activation of the ROS-TGF? autocrine loop. Protein & cell, 7 5, 338-50Niu, Liang; Xu, Zongli; Taylor, Jack A 2016. RCP: a novel probe design bias correction method for Illumina Methylation BeadChip. Bioinformatics (Oxford, England), 32 17, 2659-63Xu, Zongli; Niu, Liang; Li, Leping; Taylor, Jack A 2016. ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip. Nucleic acids research, 44 3, e20Xu, Zongli; Taylor, Jack A; Leung, Yuet-Kin; Ho, Shuk-Mei; Niu, Liang 2016. oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA. Bioinformatics (Oxford, England), 32 23, 3667-3669Dong, Jing; Yang, Jingyun; Tranah, Greg; Franceschini, Nora; Parimi, Neeta; Alkorta-Aranburu, Gorka; Xu, Zongli; Alonso, Alvaro; Cummings, Steven R; Fornage, Myriam; Huang, Xuemei; Kritchevsky, Stephen; Liu, Yongmei; London, Stephanie; Niu, Liang; Wilson, Robert S; De Jager, Philip L; Yu, Lei; Singleton, Andrew B; Harris, Tamara; Mosley, Thomas H; Pinto, Jayant M; Bennett, David A; Chen, Honglei 2015. Genome-wide Meta-analysis on the Sense of Smell Among US Older Adults. Medicine, 94 47, e1892Niu, Liang; Lin, Shili 2015. A Bayesian mixture model for chromatin interaction data. Statistical applications in genetics and molecular biology, 14 1, 53-64Niu, Liang; Huang, Weichun; Umbach, David M; Li, Leping 2014. IUTA: a tool for effectively detecting differential isoform usage from RNA-Seq data. BMC genomics, 15 , 862Niu, Liang; Li, Guoliang; Lin, Shili 2014. Statistical models for detecting differential chromatin interactions mediated by a protein. PloS one, 9 5, e97560Li, Yuanyuan; Huang, Weichun; Niu, Liang; Umbach, David M; Covo, Shay; Li, Leping 2013. Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes. BMC genomics, 14 , 553Cai Heng Li, Liang Niu, Akos Seress, Ronald Solomon 2010. The vertex primitive and vertex bi-primitive s-arc regular graphs Journal of Combinatorial Theory, Series B, 100 4, 359-366
Research Interests1) Statistical bioinformatics (methodology): RNA-Seq, ChIA-PET, methylation array and PacBio sequencing; 2) Statistical bioinformatics (consulting): data analysis for RNA-Seq, ChIA-PET, methylation array, and mass spectrometry; 3) Biostatistical consulting: study planning and design, power calculations, and statistical modeling and analysis; 4) Data mining of public domain omics datasets (such as TCGA datasets).
Peer Reviewed Publications Conrey, Shannon C; Burrell, Allison R; Brokamp, Cole; Burke, Rachel M; Couch, Sarah C; Niu, Liang; Mattison, Claire P; Piasecki, Alexandra; Payne, Daniel C; Staat, Mary A; Morrow, Ardythe L 2022. Neighbourhood socio-economic environment predicts adiposity and obesity risk in children under two. Pediatric obesity, 17 12, e12964Jiang, Lin; Liang, Jialiang; Huang, Wei; Ma, Jianyong; Park, Ki Ho; Wu, Zhichao; Chen, Peng; Zhu, Hua; Ma, Jian-Jie; Cai, Wenfeng; Paul, Christian; Niu, Liang; Fan, Guo-Chang; Wang, Hong-Sheng; Kanisicak, Onur; Xu, Meifeng; Wang, Yigang 2022. CRISPR activation of endogenous genes reprograms fibroblasts into cardiovascular progenitor cells for myocardial infarction therapy. Molecular therapy : the journal of the American Society of Gene Therapy, 30 1, 54-74Sprague, Alexander C; Niu, Liang; Jandarov, Roman; Zhang, Xiang; Zhang, Ge; Chen, Aimin; Šarac, Jelena; Čoklo, Miran; Missoni, Sasa; Rudan, Pavao; Langevin, Scott M; Deka, Ranjan 2022. Stable methylation loci are associated with systolic blood pressure in a Croatian island population. Epigenomics, 14 21, 1343-1354Morrow, Ardythe L; McClain, Janelle; Conrey, Shannon C; Niu, Liang; Kinzer, Alexandra; Cline, Allison R; Piasecki, Alexandra M; DeFranco, Emily; Ward, Laura; Ware, Julie; Payne, Daniel C; Staat, Mary A; Nommsen-Rivers, Laurie A 2021. Breastfeeding Disparities and Their Mediators in an Urban Birth Cohort of Black and White Mothers. Breastfeeding medicine : the official journal of the Academy of Breastfeeding Medicine, 16 6, 452-462Morrow, Ardythe L; Staat, Mary A; DeFranco, Emily A; McNeal, Monica M; Cline, Allison R; Conrey, Shannon C; Schlaudecker, Elizabeth P; Piasecki, Alexandra M; Burke, Rachel M; Niu, Liang; Hall, Aron J; Bowen, Michael D; Gerber, Susan I; Langley, Gayle E; Thornburg, Natalie J; Campbell, Angela P; Vinjé, Jan; Parashar, Umesh D; Payne, Daniel C 2021. Pediatric Respiratory and Enteric Virus Acquisition and Immunogenesis in US Mothers and Children Aged 0-2: PREVAIL Cohort Study. JMIR research protocols, 10 2, e22222Vilfranc, Chrystelle L; Che, Li-Xiao; Patra, Krushna C; Niu, Liang; Olowokure, Olugbenga; Wang, Jiang; Shah, Shimul A; Du, Chun-Ying 2021. BIR repeat-containing ubiquitin conjugating enzyme (BRUCE) regulation of ?-catenin signaling in the progression of drug-induced hepatic fibrosis and carcinogenesis. World journal of hepatology, 13 3, 343-361von Allmen, Douglas; Tang, Alice; Takiar, Vinita; Zender, Chad; Romeo, Stephen; Masch, Jessica; Casper, Keith; Patil, Yash; Wilson, Keith; Khosla, Siddarth; Niu, Liang; Altaye, Mekibib; Tabangin, Meredith; Howell, Rebecca J 2021. Modified Head and Neck Swallow Scale: Using EORTC-QLQ-H&N35 to Predict Overall Survival. The Laryngoscope, , Xu, Zongli; Niu, Liang; Taylor, Jack A 2021. The ENmix DNA methylation analysis pipeline for Illumina BeadChip and comparisons with seven other preprocessing pipelines. Clinical epigenetics, 13 1, 216Xu, Zongli; Xie, Changchun; Taylor, Jack A; Niu, Liang 2021. ipDMR: identification of differentially methylated regions with interval P-values. Bioinformatics (Oxford, England), 37 5, 711-713de Gannes, Matthew; Ko, Chia-I; Zhang, Xiang; Biesiada, Jacek; Niu, Liang; Koch, Sheryl E; Medvedovic, Mario; Rubinstein, Jack; Puga, Alvaro 2020. Dioxin Disrupts Dynamic DNA Methylation Patterns in Genes That Govern Cardiomyocyte Maturation. Toxicological sciences : an official journal of the Society of Toxicology, 178 2, 325-337Sharma, Manju; Zhang, Shuangmin; Niu, Liang; Lewinsohn, David M; Zhang, Xiang; Huang, Shouxiong 2020. Mucosal-Associated Invariant T Cells Develop an Innate-Like Transcriptomic Program in Anti-mycobacterial Responses. Frontiers in immunology, 11 , 1136Ge, Chunmin; Vilfranc, Chrystelle L; Che, Lixiao; Pandita, Raj K; Hambarde, Shashank; Andreassen, Paul R; Niu, Liang; Olowokure, Olugbenga; Shah, Shimul; Waltz, Susan E; Zou, Lee; Wang, Jiang; Pandita, Tej K; Du, Chunying 2019. The BRUCE-ATR Signaling Axis Is Required for Accurate DNA Replication and Suppression of Liver Cancer Development. Hepatology (Baltimore, Md.), 69 6, 2608-2622Greene, Alexis D; Kendziorski, Jessica A; Buckholz, Jeanette M; Niu, Liang; Xie, Changchun; Pinney, Susan M; Burns, Katherine A 2019. Elevated serum chemokines are independently associated with both endometriosis and uranium exposure. Reproductive toxicology (Elmsford, N.Y.), 84 , 26-31Huang, Weichun; Medvedovic, Mario; Zhang, Jingwen; Niu, Liang 2019. ChIAPoP: a new tool for ChIA-PET data analysis. Nucleic acids research, 47 7, e37Langevin, Scott M; Kuhnell, Damaris; Niu, Liang; Biesiada, Jacek; Leung, Yuet-Kin; Deka, Ranjan; Chen, Aimin; Medvedovic, Mario; Kelsey, Karl T; Kasper, Susan; Zhang, Xiang 2019. Comprehensive mapping of the methylation landscape of 16 CpG-dense regions in oral and pharyngeal squamous cell carcinoma. Epigenomics, 11 9, 987-1002Xueheng Zhao, Liang Niu, Carlo Clerici, Roberta Russo, Melissa Byrd, and Kenneth DR Setchell 2019. Data analysis of MS-based clinical lipidomics studies with crossover design: A tutorial mini-review of statistical methods Clinical Mass Spectrometry, 13 , 5-17Haque, Sulsal-Ul; Niu, Liang; Kuhnell, Damaris; Hendershot, Jacob; Biesiada, Jacek; Niu, Wen; Hagan, Matthew C; Kelsey, Karl T; Casper, Keith A; Wise-Draper, Trisha M; Medvedovic, Mario; Langevin, Scott M 2018. Differential expression and prognostic value of long non-coding RNA in HPV-negative head and neck squamous cell carcinoma. Head & neck, 40 7, 1555-1564Leung, Yuet-Kin; Ouyang, Bin; Niu, Liang; Xie, Changchun; Ying, Jun; Medvedovic, Mario; Chen, Aimin; Weihe, Pal; Valvi, Damaskini; Grandjean, Philippe; Ho, Shuk-Mei 2018. Identification of sex-specific DNA methylation changes driven by specific chemicals in cord blood in a Faroese birth cohort. Epigenetics, 13 3, 290-300Liu, Hongqi; Feng, Xizhi; Ennis, Kelli N; Behrmann, Catherine A; Sarma, Pranjal; Jiang, Tony T; Kofuji, Satoshi; Niu, Liang; Stratton, Yiwen; Thomas, Hala Elnakat; Yoon, Sang-Oh; Sasaki, Atsuo T; Plas, David R 2017. Pharmacologic Targeting of S6K1 in PTEN-Deficient Neoplasia. Cell reports, 18 9, 2088-2095Sharma, Manju; Zhang, Xiang; Zhang, Shuangmin; Niu, Liang; Ho, Shuk-Mei; Chen, Aimin; Huang, Shouxiong 2017. Inhibition of endocytic lipid antigen presentation by common lipophilic environmental pollutants. Scientific reports, 7 1, 2085Xu, Zongli; Langie, Sabine A S; De Boever, Patrick; Taylor, Jack A; Niu, Liang 2017. RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip. BMC genomics, 18 1, 4Chen, Liang; Peng, Zhimin; Meng, Qinghang; Mongan, Maureen; Wang, Jingcai; Sartor, Maureen; Chen, Jing; Niu, Liang; Medvedovic, Mario; Kao, Winston; Xia, Ying 2016. Loss of I?B kinase ? promotes myofibroblast transformation and senescence through activation of the ROS-TGF? autocrine loop. Protein & cell, 7 5, 338-50Niu, Liang; Xu, Zongli; Taylor, Jack A 2016. RCP: a novel probe design bias correction method for Illumina Methylation BeadChip. Bioinformatics (Oxford, England), 32 17, 2659-63Xu, Zongli; Niu, Liang; Li, Leping; Taylor, Jack A 2016. ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip. Nucleic acids research, 44 3, e20Xu, Zongli; Taylor, Jack A; Leung, Yuet-Kin; Ho, Shuk-Mei; Niu, Liang 2016. oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA. Bioinformatics (Oxford, England), 32 23, 3667-3669Dong, Jing; Yang, Jingyun; Tranah, Greg; Franceschini, Nora; Parimi, Neeta; Alkorta-Aranburu, Gorka; Xu, Zongli; Alonso, Alvaro; Cummings, Steven R; Fornage, Myriam; Huang, Xuemei; Kritchevsky, Stephen; Liu, Yongmei; London, Stephanie; Niu, Liang; Wilson, Robert S; De Jager, Philip L; Yu, Lei; Singleton, Andrew B; Harris, Tamara; Mosley, Thomas H; Pinto, Jayant M; Bennett, David A; Chen, Honglei 2015. Genome-wide Meta-analysis on the Sense of Smell Among US Older Adults. Medicine, 94 47, e1892Niu, Liang; Lin, Shili 2015. A Bayesian mixture model for chromatin interaction data. Statistical applications in genetics and molecular biology, 14 1, 53-64Niu, Liang; Huang, Weichun; Umbach, David M; Li, Leping 2014. IUTA: a tool for effectively detecting differential isoform usage from RNA-Seq data. BMC genomics, 15 , 862Niu, Liang; Li, Guoliang; Lin, Shili 2014. Statistical models for detecting differential chromatin interactions mediated by a protein. PloS one, 9 5, e97560Li, Yuanyuan; Huang, Weichun; Niu, Liang; Umbach, David M; Covo, Shay; Li, Leping 2013. Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes. BMC genomics, 14 , 553Cai Heng Li, Liang Niu, Akos Seress, Ronald Solomon 2010. The vertex primitive and vertex bi-primitive s-arc regular graphs Journal of Combinatorial Theory, Series B, 100 4, 359-366
Conrey, Shannon C; Burrell, Allison R; Brokamp, Cole; Burke, Rachel M; Couch, Sarah C; Niu, Liang; Mattison, Claire P; Piasecki, Alexandra; Payne, Daniel C; Staat, Mary A; Morrow, Ardythe L 2022. Neighbourhood socio-economic environment predicts adiposity and obesity risk in children under two. Pediatric obesity, 17 12, e12964Jiang, Lin; Liang, Jialiang; Huang, Wei; Ma, Jianyong; Park, Ki Ho; Wu, Zhichao; Chen, Peng; Zhu, Hua; Ma, Jian-Jie; Cai, Wenfeng; Paul, Christian; Niu, Liang; Fan, Guo-Chang; Wang, Hong-Sheng; Kanisicak, Onur; Xu, Meifeng; Wang, Yigang 2022. CRISPR activation of endogenous genes reprograms fibroblasts into cardiovascular progenitor cells for myocardial infarction therapy. Molecular therapy : the journal of the American Society of Gene Therapy, 30 1, 54-74Sprague, Alexander C; Niu, Liang; Jandarov, Roman; Zhang, Xiang; Zhang, Ge; Chen, Aimin; Šarac, Jelena; Čoklo, Miran; Missoni, Sasa; Rudan, Pavao; Langevin, Scott M; Deka, Ranjan 2022. Stable methylation loci are associated with systolic blood pressure in a Croatian island population. Epigenomics, 14 21, 1343-1354Morrow, Ardythe L; McClain, Janelle; Conrey, Shannon C; Niu, Liang; Kinzer, Alexandra; Cline, Allison R; Piasecki, Alexandra M; DeFranco, Emily; Ward, Laura; Ware, Julie; Payne, Daniel C; Staat, Mary A; Nommsen-Rivers, Laurie A 2021. Breastfeeding Disparities and Their Mediators in an Urban Birth Cohort of Black and White Mothers. Breastfeeding medicine : the official journal of the Academy of Breastfeeding Medicine, 16 6, 452-462Morrow, Ardythe L; Staat, Mary A; DeFranco, Emily A; McNeal, Monica M; Cline, Allison R; Conrey, Shannon C; Schlaudecker, Elizabeth P; Piasecki, Alexandra M; Burke, Rachel M; Niu, Liang; Hall, Aron J; Bowen, Michael D; Gerber, Susan I; Langley, Gayle E; Thornburg, Natalie J; Campbell, Angela P; Vinjé, Jan; Parashar, Umesh D; Payne, Daniel C 2021. Pediatric Respiratory and Enteric Virus Acquisition and Immunogenesis in US Mothers and Children Aged 0-2: PREVAIL Cohort Study. JMIR research protocols, 10 2, e22222Vilfranc, Chrystelle L; Che, Li-Xiao; Patra, Krushna C; Niu, Liang; Olowokure, Olugbenga; Wang, Jiang; Shah, Shimul A; Du, Chun-Ying 2021. BIR repeat-containing ubiquitin conjugating enzyme (BRUCE) regulation of ?-catenin signaling in the progression of drug-induced hepatic fibrosis and carcinogenesis. World journal of hepatology, 13 3, 343-361von Allmen, Douglas; Tang, Alice; Takiar, Vinita; Zender, Chad; Romeo, Stephen; Masch, Jessica; Casper, Keith; Patil, Yash; Wilson, Keith; Khosla, Siddarth; Niu, Liang; Altaye, Mekibib; Tabangin, Meredith; Howell, Rebecca J 2021. Modified Head and Neck Swallow Scale: Using EORTC-QLQ-H&N35 to Predict Overall Survival. The Laryngoscope, , Xu, Zongli; Niu, Liang; Taylor, Jack A 2021. The ENmix DNA methylation analysis pipeline for Illumina BeadChip and comparisons with seven other preprocessing pipelines. Clinical epigenetics, 13 1, 216Xu, Zongli; Xie, Changchun; Taylor, Jack A; Niu, Liang 2021. ipDMR: identification of differentially methylated regions with interval P-values. Bioinformatics (Oxford, England), 37 5, 711-713de Gannes, Matthew; Ko, Chia-I; Zhang, Xiang; Biesiada, Jacek; Niu, Liang; Koch, Sheryl E; Medvedovic, Mario; Rubinstein, Jack; Puga, Alvaro 2020. Dioxin Disrupts Dynamic DNA Methylation Patterns in Genes That Govern Cardiomyocyte Maturation. Toxicological sciences : an official journal of the Society of Toxicology, 178 2, 325-337Sharma, Manju; Zhang, Shuangmin; Niu, Liang; Lewinsohn, David M; Zhang, Xiang; Huang, Shouxiong 2020. Mucosal-Associated Invariant T Cells Develop an Innate-Like Transcriptomic Program in Anti-mycobacterial Responses. Frontiers in immunology, 11 , 1136Ge, Chunmin; Vilfranc, Chrystelle L; Che, Lixiao; Pandita, Raj K; Hambarde, Shashank; Andreassen, Paul R; Niu, Liang; Olowokure, Olugbenga; Shah, Shimul; Waltz, Susan E; Zou, Lee; Wang, Jiang; Pandita, Tej K; Du, Chunying 2019. The BRUCE-ATR Signaling Axis Is Required for Accurate DNA Replication and Suppression of Liver Cancer Development. Hepatology (Baltimore, Md.), 69 6, 2608-2622Greene, Alexis D; Kendziorski, Jessica A; Buckholz, Jeanette M; Niu, Liang; Xie, Changchun; Pinney, Susan M; Burns, Katherine A 2019. Elevated serum chemokines are independently associated with both endometriosis and uranium exposure. Reproductive toxicology (Elmsford, N.Y.), 84 , 26-31Huang, Weichun; Medvedovic, Mario; Zhang, Jingwen; Niu, Liang 2019. ChIAPoP: a new tool for ChIA-PET data analysis. Nucleic acids research, 47 7, e37Langevin, Scott M; Kuhnell, Damaris; Niu, Liang; Biesiada, Jacek; Leung, Yuet-Kin; Deka, Ranjan; Chen, Aimin; Medvedovic, Mario; Kelsey, Karl T; Kasper, Susan; Zhang, Xiang 2019. Comprehensive mapping of the methylation landscape of 16 CpG-dense regions in oral and pharyngeal squamous cell carcinoma. Epigenomics, 11 9, 987-1002Xueheng Zhao, Liang Niu, Carlo Clerici, Roberta Russo, Melissa Byrd, and Kenneth DR Setchell 2019. Data analysis of MS-based clinical lipidomics studies with crossover design: A tutorial mini-review of statistical methods Clinical Mass Spectrometry, 13 , 5-17Haque, Sulsal-Ul; Niu, Liang; Kuhnell, Damaris; Hendershot, Jacob; Biesiada, Jacek; Niu, Wen; Hagan, Matthew C; Kelsey, Karl T; Casper, Keith A; Wise-Draper, Trisha M; Medvedovic, Mario; Langevin, Scott M 2018. Differential expression and prognostic value of long non-coding RNA in HPV-negative head and neck squamous cell carcinoma. Head & neck, 40 7, 1555-1564Leung, Yuet-Kin; Ouyang, Bin; Niu, Liang; Xie, Changchun; Ying, Jun; Medvedovic, Mario; Chen, Aimin; Weihe, Pal; Valvi, Damaskini; Grandjean, Philippe; Ho, Shuk-Mei 2018. Identification of sex-specific DNA methylation changes driven by specific chemicals in cord blood in a Faroese birth cohort. Epigenetics, 13 3, 290-300Liu, Hongqi; Feng, Xizhi; Ennis, Kelli N; Behrmann, Catherine A; Sarma, Pranjal; Jiang, Tony T; Kofuji, Satoshi; Niu, Liang; Stratton, Yiwen; Thomas, Hala Elnakat; Yoon, Sang-Oh; Sasaki, Atsuo T; Plas, David R 2017. Pharmacologic Targeting of S6K1 in PTEN-Deficient Neoplasia. Cell reports, 18 9, 2088-2095Sharma, Manju; Zhang, Xiang; Zhang, Shuangmin; Niu, Liang; Ho, Shuk-Mei; Chen, Aimin; Huang, Shouxiong 2017. Inhibition of endocytic lipid antigen presentation by common lipophilic environmental pollutants. Scientific reports, 7 1, 2085Xu, Zongli; Langie, Sabine A S; De Boever, Patrick; Taylor, Jack A; Niu, Liang 2017. RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip. BMC genomics, 18 1, 4Chen, Liang; Peng, Zhimin; Meng, Qinghang; Mongan, Maureen; Wang, Jingcai; Sartor, Maureen; Chen, Jing; Niu, Liang; Medvedovic, Mario; Kao, Winston; Xia, Ying 2016. Loss of I?B kinase ? promotes myofibroblast transformation and senescence through activation of the ROS-TGF? autocrine loop. Protein & cell, 7 5, 338-50Niu, Liang; Xu, Zongli; Taylor, Jack A 2016. RCP: a novel probe design bias correction method for Illumina Methylation BeadChip. Bioinformatics (Oxford, England), 32 17, 2659-63Xu, Zongli; Niu, Liang; Li, Leping; Taylor, Jack A 2016. ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip. Nucleic acids research, 44 3, e20Xu, Zongli; Taylor, Jack A; Leung, Yuet-Kin; Ho, Shuk-Mei; Niu, Liang 2016. oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA. Bioinformatics (Oxford, England), 32 23, 3667-3669Dong, Jing; Yang, Jingyun; Tranah, Greg; Franceschini, Nora; Parimi, Neeta; Alkorta-Aranburu, Gorka; Xu, Zongli; Alonso, Alvaro; Cummings, Steven R; Fornage, Myriam; Huang, Xuemei; Kritchevsky, Stephen; Liu, Yongmei; London, Stephanie; Niu, Liang; Wilson, Robert S; De Jager, Philip L; Yu, Lei; Singleton, Andrew B; Harris, Tamara; Mosley, Thomas H; Pinto, Jayant M; Bennett, David A; Chen, Honglei 2015. Genome-wide Meta-analysis on the Sense of Smell Among US Older Adults. Medicine, 94 47, e1892Niu, Liang; Lin, Shili 2015. A Bayesian mixture model for chromatin interaction data. Statistical applications in genetics and molecular biology, 14 1, 53-64Niu, Liang; Huang, Weichun; Umbach, David M; Li, Leping 2014. IUTA: a tool for effectively detecting differential isoform usage from RNA-Seq data. BMC genomics, 15 , 862Niu, Liang; Li, Guoliang; Lin, Shili 2014. 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