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Jichun Xie

Jichun Xie

Associate Professor of Biostatistics & Bioinformatics
Biostatistics & Bioinformatics, Division of Integrative Genomics
jichun.xie@duke.edu
Duke Box 103854, Durham, NC 27710
Hock Plaza 10048, 2424 Erwin Rd, Durham, NC 27705, Durham, NC 27705

Selected Publications

SifiNet: a robust and accurate method to identify feature gene sets and annotate cells.

Journal Article Nucleic Acids Res · May 22, 2024 SifiNet is a robust and accurate computational pipeline for identifying distinct gene sets, extracting and annotating cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Uniquely, SifiNet bypasses the cell clusterin ... Full text Link to item Cite

SifiNet: A robust and accurate method to identify feature gene sets and annotate cells.

Journal Article bioRxiv · April 6, 2024 SifiNet is a robust and accurate computational pipeline for identifying distinct gene sets, extracting and annotating cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Uniquely, SifiNet bypasses the cell clusterin ... Full text Link to item Cite

DYNATE: Localizing rare-variant association regions via multiple testing embedded in an aggregation tree.

Journal Article Genet Epidemiol · February 2024 Rare-variants (RVs) genetic association studies enable researchers to uncover the variation in phenotypic traits left unexplained by common variation. Traditional single-variant analysis lacks power; thus, researchers have developed various methods to aggr ... Full text Link to item Cite

Immune Phenotype and Postoperative Complications After Elective Surgery.

Journal Article Ann Surg · December 1, 2023 OBJECTIVES: To characterize and quantify accumulating immunologic alterations, pre and postoperatively in patients undergoing elective surgical procedures. BACKGROUND: Elective surgery is an anticipatable, controlled human injury. Although the human respon ... Full text Link to item Cite

Single-cell landscape analysis unravels molecular programming of the human B cell compartment in chronic GVHD.

Journal Article JCI Insight · June 8, 2023 Alloreactivity can drive autoimmune syndromes. After allogeneic hematopoietic stem cell transplantation (allo-HCT), chronic graft-versus-host disease (cGVHD), a B cell-associated autoimmune-like syndrome, commonly occurs. Because donor-derived B cells cont ... Full text Open Access Link to item Cite

DART: Distance Assisted Recursive Testing

Journal Article Journal of Machine Learning Research · April 2023 In many applications, a large number of features are collected with the goal to identify a few important ones. Sometimes, these features lie in a metric space with a known distance matrix, which partially reflects their co-importance pattern. Proper use of ... Link to item Cite

TEAM: A MULTIPLE TESTING ALGORITHM ON THE AGGREGATION TREE FOR FLOW CYTOMETRY ANALYSIS.

Journal Article Ann Appl Stat · March 2023 In immunology studies, flow cytometry is a commonly used multivariate single-cell assay. One key goal in flow cytometry analysis is to detect the immune cells responsive to certain stimuli. Statistically, this problem can be translated into comparing two p ... Full text Link to item Cite

Neuroimaging and immunological features of neurocognitive function related to substance use in people with HIV.

Journal Article J Neurovirol · February 2023 This study sought to identify neuroimaging and immunological factors associated with substance use and that contribute to neurocognitive impairment (NCI) in people with HIV (PWH). We performed cross-sectional immunological phenotyping, neuroimaging, and ne ... Full text Link to item Cite

DART: Distance Assisted Recursive Testing.

Journal Article J Mach Learn Res · 2023 Multiple testing is a commonly used tool in modern data science. Sometimes, the hypotheses are embedded in a space; the distances between the hypotheses reflect their co-null/co-alternative patterns. Properly incorporating the distance information in testi ... Link to item Cite

Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering.

Journal Article Genome Biol · December 27, 2022 Most single-cell RNA sequencing (scRNA-seq) analyses begin with cell clustering; thus, the clustering accuracy considerably impacts the validity of downstream analyses. In contrast with the abundance of clustering methods, the tools to assess the clusterin ... Full text Link to item Cite

NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health.

Journal Article Nature aging · December 2022 Cells respond to many stressors by senescing, acquiring stable growth arrest, morphologic and metabolic changes, and a proinflammatory senescence-associated secretory phenotype. The heterogeneity of senescent cells (SnCs) and senescence-associated secretor ... Full text Cite

APOBEC Mutagenesis Inhibits Breast Cancer Growth through Induction of T cell-Mediated Antitumor Immune Responses.

Journal Article Cancer Immunol Res · January 2022 The APOBEC family of cytidine deaminases is one of the most common endogenous sources of mutations in human cancer. Genomic studies of tumors have found that APOBEC mutational signatures are enriched in the HER2 subtype of breast cancer and are associated ... Full text Link to item Cite

Evaluating immune response and metabolic related biomarkers pre-allogenic hematopoietic stem cell transplant in acute myeloid leukemia.

Journal Article PLoS One · 2022 Although hematopoietic stem cell transplantation (HCT) is the only curative treatment for acute myeloid leukemia (AML), it is associated with significant treatment related morbidity and mortality. There is great need for predictive biomarkers associated wi ... Full text Link to item Cite

Hypercapnia in Advanced Chronic Obstructive Pulmonary Disease: A Secondary Analysis of the National Emphysema Treatment Trial.

Journal Article Chronic Obstr Pulm Dis · October 2020 RATIONALE: Hypercapnia develops in one third of patients with advanced chronic obstructive pulmonary disease (COPD) and is associated with increased morbidity and mortality. Multiple factors in COPD are thought to contribute to the development of hypercapn ... Full text Link to item Cite

Microtransplantation in older patients with AML: A pilot study of safety, efficacy and immunologic effects.

Journal Article Am J Hematol · June 2020 Older AML patients have low remission rates and poor survival outcomes with standard chemotherapy. Microtransplantation (MST) refers to infusion of allogeneic hematopoietic stem cells without substantial engraftment. MST has been shown to improve clinical ... Full text Link to item Cite

Phase II Trial of Pasireotide to Prevent GI Toxicity and Acute Gvhd in Allogeneic HSCT

Conference BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION · March 1, 2020 Link to item Cite

Abstract P1-06-02: Characterization of gene- and sample-level APOBEC mutagenesis enrichment with respect to intrinsic subtypes, tumor mutational burden, and immune composition in breast cancer

Conference Cancer Research · February 15, 2020 AbstractIntroduction: APOlipoprotein B mRNA Editing enzyme Catalytic peptide-like, APOBEC, is a family of innate immune enzymes that catalyze cytosine to uracil deamination in single-stranded DNA, which lead ... Full text Cite

Prevalence and Cost Analysis of Chronic Pain After Hernia Repair: A Potential Alternative Approach With Neurostimulation.

Journal Article Neuromodulation · December 2019 OBJECTIVES: Chronic pain (CP) affects a significant number of patients following hernia repair, ranging from 11 to 54% in the literature. The aim of this study was to assess the prevalence, overall costs, and health care utilization associated with CP afte ... Full text Link to item Cite

Single-Cell RNA-Seq Identifies Potentially Pathogenic B Cell Populations That Uniquely Circulate in Patients with Chronic Gvhd

Conference Blood · November 13, 2019 While B cells are known to contribute to the pathogenesis of chronic graft-versus-host disease (cGVHD) in mice, it has been challenging to elucidate intrinsic mechanisms of tolerance loss in patients. To identify distinct and potentially targetable ... Full text Cite

Genetic variants in the calcium signaling pathway genes are associated with cutaneous melanoma-specific survival.

Journal Article Carcinogenesis · April 29, 2019 Remodeling or deregulation of the calcium signaling pathway is a relevant hallmark of cancer including cutaneous melanoma (CM). In this study, using data from a published genome-wide association study (GWAS) from The University of Texas M.D. Anderson Cance ... Full text Open Access Link to item Cite

Independent Associations With 30- and 90-Day Unplanned Readmissions After Elective Lumbar Spine Surgery: A National Trend Analysis of 144 123 Patients.

Journal Article Neurosurgery · March 1, 2019 BACKGROUND: Unplanned hospital readmissions contribute significantly to soaring national healthcare expenditures. To alleviate this burden, Centers for Medicare and Medicaid Services implemented initiatives to penalize hospitals for unplanned 30-d hospital ... Full text Link to item Cite

Genetic variant of IRAK2 in the toll-like receptor signaling pathway and survival of non-small cell lung cancer.

Journal Article Int J Cancer · November 15, 2018 The toll-like receptor (TLR) signaling pathway plays an important role in the innate immune responses and antigen-specific acquired immunity. Aberrant activation of the TLR pathway has a significant impact on carcinogenesis or tumor progression. Therefore, ... Full text Open Access Link to item Cite

False discovery rate control for high dimensional networks of quantile associations conditioning on covariates.

Journal Article J R Stat Soc Series B Stat Methodol · November 2018 Motivated by gene coexpression pattern analysis, we propose a novel sample quantile contingency (SQUAC) statistic to infer quantile associations conditioning on covariates. It features enhanced flexibility in handling variables with both arbitrary distribu ... Full text Open Access Link to item Cite

bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens.

Journal Article Bioinformatics · October 15, 2018 SUMMARY: CRISPR-Cas9 and shRNA high-throughput sequencing screens have abundant applications for basic and translational research. Methods and tools for the analysis of these screens must properly account for sequencing error, resolve ambiguous mappings am ... Full text Link to item Cite

Sex Differences in Genetic Associations With Longevity.

Journal Article JAMA network open · August 2018 ImportanceSex differences in genetic associations with human longevity remain largely unknown; investigations on this topic are important for individualized health care.ObjectiveTo explore sex differences in genetic associations with long ... Full text Cite

Prevalence and Cost Analysis of Complex Regional Pain Syndrome (CRPS): A Role for Neuromodulation.

Journal Article Neuromodulation · July 2018 OBJECTIVE: The diagnosis and treatment of complex regional pain syndrome (CRPS) is challenging and there is a paucity of data describing its overall cost burden and quantifying its impact on the US healthcare system. The aim of this study was to assess the ... Full text Link to item Cite

Genetic variants in the platelet-derived growth factor subunit B gene associated with pancreatic cancer risk.

Journal Article Int J Cancer · April 1, 2018 The platelet-derived growth factor (PDGF) signaling pathway plays important roles in development and progression of human cancers. In our study, we aimed to identify genetic variants of the PDGF pathway genes associated with pancreatic cancer (PC) risk in ... Full text Open Access Link to item Cite

Novel genetic variants in the P38MAPK pathway gene ZAK and susceptibility to lung cancer.

Journal Article Mol Carcinog · February 2018 The P38MAPK pathway participates in regulating cell cycle, inflammation, development, cell death, cell differentiation, and tumorigenesis. Genetic variants of some genes in the P38MAPK pathway are reportedly associated with lung cancer risk. To substantiat ... Full text Open Access Link to item Cite

Prevalence, healthcare resource utilization and overall burden of fungal meningitis in the United States.

Journal Article J Med Microbiol · February 2018 PURPOSE: Previous epidemiological and cost studies of fungal meningitis have largely focused on single pathogens, leading to a poor understanding of the disease in general. We studied the largest and most diverse group of fungal meningitis patients to date ... Full text Link to item Cite

Drivers and Risk Factors of Unplanned 30-Day Readmission Following Spinal Cord Stimulator Implantation.

Journal Article Neuromodulation · January 2018 OBJECTIVES: Unplanned 30-day readmission rates contribute significantly to growing national healthcare expenditures. Drivers of unplanned 30-day readmission after spinal cord stimulator (SCS) implantation are relatively unknown. The aim of this study was t ... Full text Link to item Cite

Increasing Rates of Imaging in Failed Back Surgery Syndrome Patients: Implications for Spinal Cord Stimulation.

Journal Article Pain Physician · September 2017 BACKGROUND: Failed back surgery syndrome (FBSS) has a high incidence following spinal surgery, is notoriously refractory to treatment, and results in high health care utilization. Spinal cord stimulation (SCS) is a well-accepted modality for pain relief in ... Link to item Cite

Long-term Cost Utility of Spinal Cord Stimulation in Patients with Failed Back Surgery Syndrome.

Journal Article Pain physician · September 2017 BackgroundFailed back surgery syndrome (FBSS) is a cause of significant morbidity for up to 40% of patients following spine surgery, and is estimated to cost almost $20 billion. Treatment options for these patients currently include conventional m ... Cite

Explantation Rates and Healthcare Resource Utilization in Spinal Cord Stimulation.

Journal Article Neuromodulation · June 2017 OBJECTIVES: Certain patients ultimately undergo explantation of their spinal cord stimulation (SCS) devices. Understanding the predictors and rates of SCS explantation has important implications for healthcare resource utilization (HCRU) and pain managemen ... Full text Link to item Cite

Impact of Insurance Provider on Overall Costs in Failed Back Surgery Syndrome: A Cost Study of 122,827 Patients.

Journal Article Neuromodulation · June 2017 OBJECTIVES: Failed back surgery syndrome (FBSS) affects 40% of patients following spine surgery with estimated costs of $20 billion to the US health care system. The aim of this study was to assess the cost differences across the different insurance provid ... Full text Link to item Cite

Specialty-Based Variations in Spinal Cord Stimulation Success Rates for Treatment of Chronic Pain.

Journal Article Neuromodulation · June 2017 OBJECTIVES: Spinal cord stimulation (SCS) has emerged as an appropriate modality of treatment for intractable chronic pain. The present study examines variations in SCS trial-to-permanent conversion rates based on provider types performing the procedure. M ... Full text Link to item Cite

The Volume-Outcome Effect: Impact on Trial-to-Permanent Conversion Rates in Spinal Cord Stimulation.

Journal Article Neuromodulation · April 2017 OBJECTIVES: Conversion rates from trial leads to permanent spinal cord stimulation (SCS) systems have important implications for healthcare resource utilization (HCRU) and pain management. We hypothesized that there is a volume-outcome effect, with chronic ... Full text Link to item Cite

High-dimensional tests for functional networks of brain anatomic regions.

Journal Article J Multivar Anal · April 2017 Exploring resting-state brain functional connectivity of autism spectrum disorders (ASD) using functional magnetic resonance imaging (fMRI) data has become a popular topic over the past few years. The data in a standard brain template consist of over 170,0 ... Full text Link to item Cite

Comparing outcomes of early, late, and non-surgical management of intraspinal abscess.

Journal Article J Clin Neurosci · February 2017 Intraspinal abscesses (ISAs) are rare lesions that are often neurologically devastating. Current treatment paradigms vary widely including early surgical decompression, drainage, and systemic antibiotics, delayed surgery, and sole medical management. The N ... Full text Link to item Cite

Prevalence of Specific Types of Pain Diagnoses in a Sample of United States Adults.

Journal Article Pain Physician · February 2017 BACKGROUND: Patients with pain conditions place significant demands on health care services globally. Health economists have reported the annual economic cost of pain in the United States as high as $635 billion. A common challenge in treating patients suf ... Link to item Cite

Racial, Socioeconomic, and Gender Disparities in the Presentation, Treatment, and Outcomes of Adult Chiari I Malformations.

Journal Article World Neurosurg · January 2017 OBJECTIVE: To examine the influence of race, gender, and socioeconomic factors on presentations and outcomes of adult Chiari I malformations. METHODS: The charts of 638 adult patients with Chiari I malformations were reviewed, and 287 patients were include ... Full text Link to item Cite

Joint Estimation of Multiple High-dimensional Precision Matrices.

Journal Article Stat Sin · April 2016 Motivated by analysis of gene expression data measured in different tissues or disease states, we consider joint estimation of multiple precision matrices to effectively utilize the partially shared graphical structures of the corresponding graphs. The pro ... Full text Open Access Link to item Cite

Implantable Neurostimulation for Headache Disorders: Effect on Healthcare Utilization and Expenditures.

Journal Article Neuromodulation · April 2016 OBJECTIVES: Chronic daily headache is a considerable source of morbidity for patients and also carries an enormous economic burden. Patients who fail standard medication regimens lack well-defined therapies, and neurostimulation is an emerging option for t ... Full text Link to item Cite

PenPC: A two-step approach to estimate the skeletons of high-dimensional directed acyclic graphs.

Journal Article Biometrics · March 2016 Estimation of the skeleton of a directed acyclic graph (DAG) is of great importance for understanding the underlying DAG and causal effects can be assessed from the skeleton when the DAG is not identifiable. We propose a novel method named PenPC to estimat ... Full text Open Access Link to item Cite

Correction to the paper “Optimal False Discovery Rate Control for Dependent Data”

Journal Article Statistics and its Interface · January 1, 2016 We have found a mistake in the proof Theorem 6 in our published paper “Optimal False Discovery Rate Control for Dependent Data” [4].We apologize to the readers and thank Professor Jens Ledet Jensen at Aarhus University for his question which led to identif ... Full text Cite

Understanding the temporal evolution of neuronal connectivity in cultured networks using statistical analysis.

Journal Article BMC Neurosci · January 21, 2014 BACKGROUND: Micro-Electrode Array (MEA) technology allows researchers to perform long-term non-invasive neuronal recordings in-vitro while actively interacting with the cultured neurons. Despite numerous studies carried out using MEAs, many functional, che ... Full text Link to item Cite

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

Journal Article Biometrika · March 2013 Motivated by analysis of genetical genomics data, we introduce a sparse high dimensional multivariate regression model for studying conditional independence relationships among a set of genes adjusting for possible genetic effects. The precision matrix in ... Full text Link to item Cite

A sparse structured shrinkage estimator for nonparametric varying-coefficient model with an application in genomics

Journal Article Journal of Computational and Graphical Statistics · April 23, 2012 Many problems in genomics are related to variable selection where high-dimensional genomic data are treated as covariates. Such genomic covariates often have certain structures and can be represented as vertices of an undirected graph. Biological processes ... Full text Cite

Sample size and power analysis for sparse signal recovery in genome-wide association studies.

Journal Article Biometrika · June 2011 Genome-wide association studies have successfully identified hundreds of novel genetic variants associated with many complex human diseases. However, there is a lack of rigorous work on evaluating the statistical power for identifying these variants. In th ... Full text Link to item Cite

A penalized likelihood approach for bivariate conditional normal models for dynamic co-expression analysis.

Journal Article Biometrics · March 2011 Gene co-expressions have been widely used in the analysis of microarray gene expression data. However, the co-expression patterns between two genes can be mediated by cellular states, as reflected by expression of other genes, single nucleotide polymorphis ... Full text Link to item Cite

Optimal False Discovery Rate Control for Dependent Data.

Journal Article Stat Interface · 2011 This paper considers the problem of optimal false discovery rate control when the test statistics are dependent. An optimal joint oracle procedure, which minimizes the false non-discovery rate subject to a constraint on the false discovery rate is develope ... Full text Link to item Cite

Quasi-least squares with mixed linear correlation structures

Journal Article Statistics and Its Interface · 2010 Full text Cite