Peilin Jia

article

MicroRNA-124-3p suppresses mouse lip mesenchymal cell proliferation through the regulation of genes associated with cleft lip in the mouse

Akiko Suzuki, Hiroki Yoshioka, Dima Summakia, Neha G. Desai, more

BMC Genomics > 2019 > 20 > 1 > 1-17

Background Cleft lip (CL), one of the most common congenital birth defects, shows considerable geographic and ethnic variation, with contribution of both genetic and environmental factors. Mouse genetic studies have identified several CL-associated genes. However, it remains elusive how these CL-associated genes are regulated and involved in CL. Environmental factors may regulate these genes at the...

article

MicroRNA-655-3p and microRNA-497-5p inhibit cell proliferation in cultured human lip cells through the regulation of genes related to human cleft lip

Mona Gajera, Neha Desai, Akiko Suzuki, Aimin Li, more

BMC Medical Genomics > 2019 > 12 > 1 > 1-18

Background The etiology of cleft lip with or without cleft palate (CL/P), a common congenital birth defect, is complex and involves the contribution of genetic and environmental factors. Although many candidate genes have been identified, the regulation and interaction of these genes in CL/P remain unclear. In addition, the contribution of microRNAs (miRNAs), non-coding RNAs that regulate the expression...

article

Investigation of multi-trait associations using pathway-based analysis of GWAS summary statistics

Guangsheng Pei, Hua Sun, Yulin Dai, Xiaoming Liu, more

BMC Genomics > 2019 > 20 > 1 > 43-54

Background Genome-wide association studies (GWAS) have been successful in identifying disease-associated genetic variants. Recently, an increasing number of GWAS summary statistics have been made available to the research community, providing extensive repositories for studies of human complex diseases. In particular, cross-trait associations at the genetic level can be beneficial from large-scale...

article

Gene2vec: distributed representation of genes based on co-expression

Jingcheng Du, Peilin Jia, Yulin Dai, Cui Tao, more

BMC Genomics > 2019 > 20 > 1 > 7-15

Background Existing functional description of genes are categorical, discrete, and mostly through manual process. In this work, we explore the idea of gene embedding, distributed representation of genes, in the spirit of word embedding. Results From a pure data-driven fashion, we trained a 200-dimension vector representation of all human genes, using gene co-expression patterns in 984 data sets...

article

Network-based identification of critical regulators as putative drivers of human cleft lip

Aimin Li, Guimin Qin, Akiko Suzuki, Mona Gajera, more

BMC Medical Genomics > 2019 > 12 > 1 > 119-132

Background Cleft lip (CL) is one of the most common congenital birth defects with complex etiology. While genome-wide association studies (GWAS) have made significant advances in our understanding of mutations and their related genes with potential involvement in the etiology of CL, it remains unknown how these genes are functionally regulated and interact with each other in lip development. Currently,...

article

Multiple transcription factors contribute to inter-chromosomal interaction in yeast

Yulin Dai, Chao Li, Guangsheng Pei, Xiao Dong, more

BMC Systems Biology > 2018 > 12 > 8 > 67-76

Background Chromatin interactions medicated by genomic elements located throughout the genome play important roles in gene regulation and can be identified with the technologies such as high-throughput chromosome conformation capture (Hi-C), followed by next-generation sequencing. These techniques were wildly used to reveal the relative spatial disposition of chromatins in human, mouse and yeast....

article

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

Theo A. Knijnenburg, Linghua Wang, Michael T. Zimmermann, Nyasha Chambwe, more

Cell Reports > 2018 > 23 > 1 > 239-254.e6

DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heterozygosity were observed in over 1/3 of DDR genes, including TP53 and BRCA1/2. Other prevalent alterations included epigenetic silencing of the direct...

article

Weak sharing of genetic association signals in three lung cancer subtypes: evidence at the SNP, gene, regulation, and pathway levels

Timothy D. O’Brien, Peilin Jia, Neil E. Caporaso, Maria Teresa Landi, more

Genome Medicine > 2018 > 10 > 1 > 1-14

Background There are two main types of lung cancer: small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). NSCLC has many subtypes, but the two most common are lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). These subtypes are mainly classified by physiological and pathological characteristics, although there is increasing evidence of genetic and molecular differences...

article

An integrative functional genomics framework for effective identification of novel regulatory variants in genome–phenome studies

Junfei Zhao, Feixiong Cheng, Peilin Jia, Nancy Cox, more

Genome Medicine > 2018 > 10 > 1 > 1-15

Background Genome–phenome studies have identified thousands of variants that are statistically associated with disease or traits; however, their functional roles are largely unclear. A comprehensive investigation of regulatory mechanisms and the gene regulatory networks between phenome-wide association study (PheWAS) and genome-wide association study (GWAS) is needed to identify novel regulatory variants...

article

Unique protein expression signatures of survival time in kidney renal clear cell carcinoma through a pan-cancer screening

Guangchun Han, Wei Zhao, Xiaofeng Song, Patrick Kwok-Shing Ng, more

BMC Genomics > 2017 > 18 > 6 > 79-93

Background In 2016, it is estimated that there will be 62,700 new cases of kidney cancer in the United States, and 14,240 patients will die from the disease. Because the incidence of kidney renal clear cell carcinoma (KIRC), the most common type of kidney cancer, is expected to continue to increase in the US, there is an urgent need to find effective diagnostic biomarkers for KIRC that could help...

article

Cerebrospinal fluid (CSF) biomarkers of iron status are associated with CSF viral load, antiretroviral therapy, and demographic factors in HIV-infected adults

Stephanie M. Patton, Quan Wang, Todd Hulgan, James R. Connor, more

Fluids and Barriers of the CNS > 2017 > 14 > 1 > 1-16

Background HIV-associated neurocognitive disorder (HAND) remains common, despite antiretroviral therapy (ART). HIV dysregulates iron metabolism, but cerebrospinal fluid (CSF) levels of iron and iron-transport proteins in HIV-infected (HIV+) persons are largely unknown. The objectives of this study were to characterize CSF iron-related biomarkers in HIV+ adults and explore their relationships to known...

article

Targeted activation of CREB in reactive astrocytes is neuroprotective in focal acute cortical injury

Luis Pardo, Agatha Schlüter, Luis M. Valor, Angel Barco, more

Glia > 64 > 5 > 853 - 874

The clinical challenge in acute injury as in traumatic brain injury (TBI) is to halt the delayed neuronal loss that occurs hours and days after the insult. Here we report that the activation of CREB‐dependent transcription in reactive astrocytes prevents secondary injury in cerebral cortex after experimental TBI. The study was performed in a novel bitransgenic mouse in which a constitutively active...

article

Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer

Timothy D. O’Brien, Peilin Jia, Junfeng Xia, Uma Saxena, more

Methods > 2015 > 83 > Complete > 118-127

Whole exome sequencing (WES) and RNA sequencing (RNA-Seq) are two main platforms used for next-generation sequencing (NGS). While WES is primarily for DNA variant discovery and RNA-Seq is mainly for measurement of gene expression, both can be used for detection of genetic variants, especially single nucleotide variants (SNVs). How consistently variants can be detected from WES and RNA-Seq has not...

article

VERSE: a novel approach to detect virus integration in host genomes through reference genome customization

Qingguo Wang, Peilin Jia, Zhongming Zhao

Genome Medicine > 2015 > 7 > 1 > 1-9

Fueled by widespread applications of high-throughput next generation sequencing (NGS) technologies and urgent need to counter threats of pathogenic viruses, large-scale studies were conducted recently to investigate virus integration in host genomes (for example, human tumor genomes) that may cause carcinogenesis or other diseases. A limiting factor in these studies, however, is rapid virus evolution...

article

Heterogeneous DNA methylation contributes to tumorigenesis through inducing the loss of coexpression connectivity in colorectal cancer

Quan Wang, Peilin Jia, Feixiong Cheng, Zhongming Zhao

Genes, Chromosomes and Cancer > 54 > 2 > 110 - 121

Increasing evidence indicates the high heterogeneity of cancer cells. Recent studies have revealed distinct subtypes of DNA methylation in colorectal cancer (CRC); however, the mechanism of heterogeneous methylation remains poorly understood. Gene expression is a natural, intermediate quantitative trait that bridges genotypic and phenotypic features. In this work, we studied the role of heterogeneous...

article

Acquired Resistance of EGFR-Mutant Lung Adenocarcinomas to Afatinib plus Cetuximab Is Associated with Activation of mTORC1

Valentina Pirazzoli, Caroline Nebhan, Xiaoling Song, Anna Wurtz, more

Cell Reports > 2014 > 7 > 4 > 999-1008

Patients with EGFR-mutant lung adenocarcinomas (LUADs) who initially respond to first-generation tyrosine kinase inhibitors (TKIs) develop resistance to these drugs. A combination of the irreversible TKI afatinib and the EGFR antibody cetuximab can be used to overcome resistance to first-generation TKIs; however, resistance to this drug combination eventually emerges. We identified activation of the...

article

Network-assisted analysis to prioritize GWAS results: principles, methods and perspectives

Peilin Jia, Zhongming Zhao

Human Genetics > 2014 > 133 > 2 > 125-138

Genome-wide association studies (GWAS) have rapidly become a powerful tool in genetic studies of complex diseases and traits. Traditionally, single marker-based tests have been used prevalently in GWAS and have uncovered tens of thousands of disease-associated SNPs. Network-assisted analysis (NAA) of GWAS data is an emerging area in which network-related approaches are developed and utilized to perform...

chapter

Network-based mutation analysis of putative cancer genes from next-generation sequencing data

Peilin Jia, Zhongming Zhao

2013 IEEE International Conference on Bioinformatics and Biomedicine > 41

2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Next-generation sequencing (NGS) has enabled fast detection of somatic mutations in cancer genomes. A major challenge in interpreting the large volume of mutation data is to distinguish driver mutations from neutral passenger mutations. Current approaches are primarily single-gene based prioritization according to mutation frequencies, which harbors both high false positive and false negative discoveries...

article

Gastric adenocarcinoma has a unique microRNA signature not present in esophageal adenocarcinoma

Zheng Chen, Rama Saad, Peilin Jia, DunFa Peng, more

Cancer > 119 > 11 > 1985 - 1993

BACKGROUNDMicroRNAs (miRNAs) play critical roles in tumor development and progression. The finding that a single miRNA can regulate hundreds of genes places miRNAs at critical hubs of signaling pathways. For the current study, the authors investigated the miRNA expression profile of gastric adenocarcinomas and compared it with esophageal adenocarcinomas to better identify a unique miRNA signature...

article

NGS catalog: A database of next generation sequencing studies in humans

Junfeng Xia, Qingguo Wang, Peilin Jia, Bing Wang, more

Human Mutation > 33 > 6 > E2341 - E2355

Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research since its advent only a few years ago, and they are expected to advance at an unprecedented pace in the following years. To provide the research community with a comprehensive NGS resource, we have developed the database Next Generation Sequencing Catalog (NGS Catalog, http://bioinfo.mc.vanderbilt...

INFONA - science communication portal

Search results for: Peilin Jia

MicroRNA-124-3p suppresses mouse lip mesenchymal cell proliferation through the regulation of genes associated with cleft lip in the mouse

MicroRNA-655-3p and microRNA-497-5p inhibit cell proliferation in cultured human lip cells through the regulation of genes related to human cleft lip

Investigation of multi-trait associations using pathway-based analysis of GWAS summary statistics

Gene2vec: distributed representation of genes based on co-expression

Network-based identification of critical regulators as putative drivers of human cleft lip

Multiple transcription factors contribute to inter-chromosomal interaction in yeast

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

Weak sharing of genetic association signals in three lung cancer subtypes: evidence at the SNP, gene, regulation, and pathway levels

An integrative functional genomics framework for effective identification of novel regulatory variants in genome–phenome studies

Unique protein expression signatures of survival time in kidney renal clear cell carcinoma through a pan-cancer screening

Cerebrospinal fluid (CSF) biomarkers of iron status are associated with CSF viral load, antiretroviral therapy, and demographic factors in HIV-infected adults

Targeted activation of CREB in reactive astrocytes is neuroprotective in focal acute cortical injury

Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer

VERSE: a novel approach to detect virus integration in host genomes through reference genome customization

Heterogeneous DNA methylation contributes to tumorigenesis through inducing the loss of coexpression connectivity in colorectal cancer

Acquired Resistance of EGFR-Mutant Lung Adenocarcinomas to Afatinib plus Cetuximab Is Associated with Activation of mTORC1

Network-assisted analysis to prioritize GWAS results: principles, methods and perspectives

Network-based mutation analysis of putative cancer genes from next-generation sequencing data

Gastric adenocarcinoma has a unique microRNA signature not present in esophageal adenocarcinoma

NGS catalog: A database of next generation sequencing studies in humans

Filter options

Publication date

Publication type

Keywords

Data set

Journal

INFONA - science communication portal

Search results for: Peilin Jia

Add recipient

Sending message cancelled

Are you sure you want to cancel sending this message?

Send message

Filter options

Publication date

Date range setting

Set the date range to filter the displayed results. You can set a starting date, ending date or both. You can enter the dates manually or choose them from the calendar.

Publication type

Keywords

Data set

Journal

Reporting an error / abuse

Sending the report failed

Accessibility options