Yulan Li

Yulan Li
Breakthrough Prize Laureate
Tsinghua University | TH · Department of Engineering Physics

PhD

About

2,148
Publications
311,063
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107,351
Citations
Citations since 2016
680 Research Items
56750 Citations
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Publications

Publications (2,148)
Article
This study aimed to investigate the characteristics and prognosis of distant metastasis (DM) after primary treatment for early‐stage extranodal nasal‐type natural killer (NK)/T‐cell lymphoma (ENKTCL). A total of 1619 patients from the China Lymphoma Collaborative Group database were retrospectively reviewed. The cumulative incidence of DM was asses...
Article
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Tandem repeat expansions (TREs) are associated with over 60 monogenic disorders and have recently been implicated in complex disorders such as cancer and autism spectrum disorder. The role of TREs in schizophrenia is now emerging. In this study, we have performed a genome-wide investigation of TREs in schizophrenia. Using genome sequence data from...
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Purpose To investigate the prognostic value of gross tumor volume (GTV) in early-stage extranodal NK/T-cell lymphoma (ENKTCL) treated with intensity-modulated radiation therapy (IMRT) and explore the interactive effect of GTV and radiotherapy (RT) dose on locoregional recurrence (LRR). Methods The data of 319 early-stage ENKTCL patients who underw...
Preprint
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Background and purpose Multiple brain metastases (BMs) remain a therapeutic challenge. Helical tomotherapy (HT) is a novel equipment which has shown favorable dosimetric properties in previous studies. The aim of this single institutional phase II trial was to investigate the feasibility and toxicity of hypofractionated radiotherapy (HFRT) with or...
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Purpose This study aims to investigate the prognostic value of composition and spatial architecture of tumor-infiltrating lymphocytes (TILs) as well as PDL1 expression on TILs subpopulations in nasopharyngeal carcinoma (NPC). Methods A total of 121 patients with NPC were included and divided into two groups: favorable (n = 68) and unfavorable (n =...
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Integrative approaches that simultaneously model multi-omics data have gained increasing popularity because they provide holistic system biology views of multiple or all components in a biological system of interest. Canonical correlation analysis (CCA) is a correlation-based integrative method. It was initially designed to extract latent features...
Preprint
Mosaic mutations in blood are common with increasing age and are prognostic markers for cancer, cardiovascular dysfunction and other diseases. This group of acquired mutations include megabase-scale mosaic chromosomal alterations (mCAs). These large mutations have mainly been surveyed using SNP array data from individuals of European (EA) or Japane...
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Alzheimer's disease (AD) is the leading cause of death among individuals over 65. Despite many AD genetic variants detected by large genome-wide association studies (GWAS) a limited number of causal genes have been confirmed. Conventional machine learning techniques integrate functional annotation data and GWAS signals to assign variants functional...
Article
Purpose/Objective(s) To report acute toxicological outcomes of an ongoing prospective, multicenter, phase III, randomized controlled trial (NCT04320979) designed to evaluate the safety and efficacy of internal mammary node irradiation (IMNI) after mastectomy for high-risk node-positive breast cancer. Materials/Methods Eligible patients were random...
Article
Purpose/Objective(s) POTENTIAL is an ongoing prospective, multicenter, phase III, randomized trial investigating whether internal mammary nodal irradiation (IMNI) improves prognosis in high-risk breast cancer with positive axillary nodes after mastectomy. This study aimed to assess the incidence and risk factors of radiation-induced lymphopenia (RI...
Article
Purpose/Objective(s) Statistically, a disease is considered curable when the mortality rate of survivors returns to the same level as that of the general population. We aimed to assess the curability of extranodal nasal-type NK/T-cell lymphoma (ENKTCL) in the modern treatment era. Materials/Methods The data of 1995 patients treated between 2000 an...
Article
Purpose/Objective(s) This study investigated the failure pattern and prognosis of distant metastasis for early-stage extranodal nasal-type natural killer/T-cell lymphoma (ENKTCL). Materials/Methods 1619 patients with complete information on distant metastatic sites were identified. The distribution of distant metastatic sites was reported. The dis...
Article
Purpose/Objective(s) To assess the incidence and risk factors of radiation-induced hypothyroidism (RHT) after adjuvant hypofractionated radiotherapy (RT) in patients with breast cancer, and identify the dose constraint for the thyroid gland. The trends of RHT over time were also evaluated to determine the optimal timing of screening for RHT in brea...
Article
Purpose/Objective(s) Postmastectomy radiotherapy in Node-positive breast cancer with or without Internal mammary nodal irradiation (POTENTIAL) study is an ongoing study investigates the role of IMN irradiation in breast cancer patients. This study reported the result of the dosimetric quality assurance regarding individual case review of target cov...
Article
Purpose To map supraclavicular fossa-involved lymph nodes (SCF-LNs) in nonmetastatic breast cancer patients, evaluate the coverage of widely adopted atlases and propose modified borders for individualized regional irradiation. Methods and materials M0 patients with biopsy-proven SCF-LNs who were SCF treatment-naïve were included. The SCF was spati...
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Genome editing tools such as CRISPR/Cas9 enable the rapid and precise manipulation of genomes. CRISPR-based genome editing has greatly simplified the study of gene function in cell lines, but its widespread use has also highlighted challenges of reproducibility. Phenotypic variability among different knockout clones of the same gene is a common pro...
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Background: Sinonasal squamous cell carcinoma (SNSCC) can arise as either inverted papilloma-associated SCC (IP-SCC) or as de novo SCC (DN-SCC). It is controversial as to whether survival differences between IP-SCC and DN-SCC exist. Methods: Between January 2000 and December 2016, 234 patients with SNSCC were analyzed retrospectively, including...
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Purpose The safety of an MRI simulation-guided boost after short-course preoperative radiotherapy (SCPRT) for unresectable rectal cancer is assessed with a planned interim analysis. Methods and materials Patients diagnosed with clinical stage T3-4 or regional lymph node-positive disease with positive mesorectal fascia (MRF) or T4b disease evaluate...
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Polygenic risk scores (PRS) have shown successes in clinics, but most PRS methods have focused only on individuals with one primary continental ancestry, thus poorly accommodating recently-admixed individuals. Here, we develop GAUDI, a novel penalized-regression-based method specifically designed for admixed individuals by explicitly modeling ances...
Article
The Circular Electron–Positron Collider (CEPC) has been proposed as a Higgs and high luminosity [Formula: see text] factory for the last few years in China. To achieve the high precision physical goals at CEPC, the high resolution ([Formula: see text]) tracker for the particle track reconstruction and particle identification are demanded. Time Proj...
Preprint
The renal medulla is a specialized region of the kidney with important homeostatic functions. It has also been implicated in genetic and developmental disorders and ischemic and drug-induced injuries. Despite its role in kidney function and disease, the medulla's baseline gene expression and epigenomic signatures have not been well described in the...
Article
Objective: Higher optimism is associated with reduced mortality and a lower risk of age-related chronic diseases. DNA methylation (DNAm) may provide insight into mechanisms underlying these relationships. We hypothesized DNAm would differ among older individuals who are more versus less optimistic. Methods: Using cross-sectional data from two po...
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Purpose To investigate the appropriate timing of radiotherapy (RT) after mastectomy and adjuvant chemotherapy for women with high-risk breast cancer. Patients and methods Post hoc analyses of 584 patients with stage II and III breast cancer from a randomised controlled clinical trial were performed. All patients underwent mastectomy followed by se...
Article
Individuals with cystic fibrosis (CF) develop complications of the gastrointestinal tract influenced by genetic variants outside of CFTR. Cystic fibrosis-related diabetes (CFRD) is a distinct form of diabetes with a variable age of onset that occurs frequently in individuals with CF, while meconium ileus (MI) is a severe neonatal intestinal obstruc...
Article
Purpose Our objective was to assess the incidence and risk factors of radiation-induced hypothyroidism (RHT) after adjuvant hypofractionated radiation therapy (RT) in patients with breast cancer. Methods and Materials Eligible patients with breast cancer who were treated with hypofractionated RT were prospectively evaluated. Thyroid function tests...
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Brain ventricular and subcortical structures are heritable both in size and shape. Genetic influences on brain region size have been studied using conventional volumetric measures, but little is known about the genetic basis of ventricular and subcortical shapes. Here we developed pipelines to extract seven complementary shape measures for lateral...
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Whole-genome sequencing (WGS) is the gold standard for fully characterizing genetic variation but is still prohibitively expensive for large samples. To reduce costs, many studies sequence only a subset of individuals or genomic regions, and genotype imputation is used to infer genotypes for the remaining individuals or regions without sequencing d...
Article
Background: Epigenetic age acceleration (EAA), a measure of accelerated biological aging, has been associated with increased risk of several age-related chronic conditions. This is the first study to prospectively examine the relationship between EAA and both multimorbidity count and a weighted multimorbidity score among long-lived postmenopausal...
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Objectives Identify genetic loci of enhanced susceptibility to Chlamydial trachomatis (Ct) upper genital tract infection in women. Methods We performed an integrated analysis of DNA genotypes and blood-derived mRNA profiles from 200 Ct- exposed women to identify expression quantitative trait loci (eQTL) and determine their association with endomet...
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Single cell Hi-C (scHi-C) has been used to map genome organization in complex tissues. However, computational tools to detect dynamic chromatin contacts from scHi-C datasets in development and through disease pathogenesis are still lacking. Here, we present SnapHiC-D, a computational pipeline to identify differential chromatin contacts (DCCs) betwe...
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Genome-wide association studies have discovered hundreds of associations between common genotypes and kidney function but cannot comprehensively investigate rare coding variants. Here, we applied a genotype imputation approach to whole exome sequencing data from the UK Biobank to increase sample size from 166,891 to 408,511. We detected 158 rare va...
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Purpose To assess the influence of age as a continuous variable on the prognosis of pT1-2N1 breast cancer and examine its decision-making value for postmastectomy radiotherapy (PMRT). Methods We retrospectively evaluated 5438 patients with pT1-2N1 breast cancer after mastectomy in 11 hospitals. A multivariable Cox proportional hazards regression m...
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Genome-wide association studies (GWAS) have identified a vast number of variants associated with various complex human diseases and traits. However, most of these GWAS variants reside in non-coding regions producing no proteins, making the interpretation of these variants a daunting challenge. Prior evidence indicates that a subset of non-coding va...
Article
Importance: Accelerated biological aging is associated with decreased physical capability and cognitive functioning, which are associated with increased risk of morbidity and mortality. Objective: We investigated associations between epigenetic age acceleration (EAA), a biomarker associated with aging, and healthy longevity among older women. D...
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Objective This study aimed to determine the long-term survival of patients with cT4 esophageal cancer (EC) and whether neoadjuvant chemoradiotherapy/radiotherapy plus surgery (nCRT/RT + S) is superior to definitive CRT(dCRT)/RT in terms of survival in cT4 EC downstaged after nCRT/RT. Summary background data Treatment options for cT4 EC include dCR...
Article
Background: MG53, a member of the tripartite motif (TRIM) protein family, plays an essential role in cell membrane repair and promotes cell survival. Recent studies show that systemic delivery of recombinant human MG53 (rhMG53) protein markedly attenuates tissue injury/inflammation, and facilitates healing. This study was performed to test whether...
Preprint
Background: The effect of age on long-term mortality and net survival benefit of radiotherapy (RT) for early-stage follicular lymphoma (FL) was not evaluated. Methods: 8,803 patients with early-stage FL in the Surveillance, Epidemiology, and End Results (SEER) database (2000-2015) were identified for this study. Primary therapy included RT (27.0%),...
Article
Purpose To estimate the variations in clinical target volumes (CTVs) and organs at risk delineation within the quality assurance (QA) program of the POTENTIAL trial, which is a multicenter, randomized phase 3 trial evaluating postmastectomy radiation therapy (RT), with or without internal mammary nodal irradiation, for patients with high-risk breas...
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Spatial transcriptomics (ST) technologies allow researchers to examine transcriptional profiles along with maintained positional information. Such spatially resolved transcriptional characterization of intact tissue samples provides an integrated view of gene expression in its natural spatial and functional context. However, high-throughput sequenc...
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Reduced glomerular filtration rate (GFR) can progress to kidney failure. Risk factors include genetics and diabetes mellitus (DM), but little is known about their interaction. We conducted genome-wide association meta-analyses for estimated GFR based on serum creatinine (eGFR), separately for individuals with or without DM (nDM = 178,691, nnoDM = 1...
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Clinical and biomarker phenotypic associations for carriers of protein function-altering variants may help to elucidate gene function and health effects in populations. We genotyped 1127 Strong Heart Family Study participants for protein function-altering single nucleotide variants (SNV) and indels selected from a low coverage whole exome sequencin...
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Single cell Hi-C (scHi-C) technologies enable the study of chromatin spatial organization directly from complex tissues at single cell resolution. However, the identification of chromatin loops from single cells is challenging, largely due to the extremely sparse data. Our recently developed SnapHiC pipeline provides the first tool to map chromatin...
Article
BACKGROUND Given the lower incidence of lymphoma-related death but higher background mortality in patients with early-stage mucosa-associated lymphoid tissue (MALT) lymphoma, it is critically important to examine how age affects a treatment’s survival benefit. METHODS 9,467 patients with early-stage MALT lymphoma in the Surveillance, Epidemiology,...
Article
Estimated glomerular filtration rate (eGFR) reflects kidney function. Progressive eGFR-decline can lead to kidney failure, necessitating dialysis or transplantation. Hundreds of loci from genome-wide association studies (GWAS) for eGFR help explain population cross section variability. Since the contribution of these or other loci to eGFR-decline r...
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Background: Magnetic resonance imaging (MRI) performs well in the locoregional assessment of extranodal nasal-type NK/T-cell lymphoma (ENKTCL). It’s important to assess the value of multi-modal MRI-based radiomics for estimating overall survival (OS) in patients with ENKTCL. Methods: Patients with ENKTCL in a prospectively cohort were systemically...
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Current publicly available tools that allow rapid exploration of linkage disequilibrium (LD) between markers (e.g., HaploReg and LDlink) are based on whole-genome sequence (WGS) data from 2,504 individuals in the 1000 Genomes Project. Here, we present TOP-LD, an online tool to explore LD inferred with high-coverage (∼30×) WGS data from 15,578 indiv...
Chapter
In this chapter, we will provide a review on imputation in the context of DNA methylation, specifically focusing on a penalized functional regression (PFR) method we have previously developed. We will start with a brief review of DNA methylation, genomic and epigenomic contexts where imputation has proven beneficial in practice, and statistical or...
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Background This study aimed to evaluate the feasibility and safety of online adapt-to-shape (ATS) workflow for prostate cancer patients on 1.5-T MR linac in China. Methods This prospective phase II study enrolled patients with localized or oligometastatic prostate cancer. Ultra-hypofractionated radiotherapy (UHF-RT) with dose of 36.25-40 Gy in five...
Preprint
Background This study aimed to evaluate the feasibility and safety of online adapt-to-shape (ATS) workflow for prostate cancer patients on 1.5-T MR linac in China. Methods This prospective phase II study enrolled patients with localized or oligometastatic prostate cancer. Ultra-hypofractionated radiotherapy (UHF-RT) with dose of 36.25-40 Gy in five...
Article
The three-dimensional organization of chromatin plays a critical role in gene regulation. Recently developed technologies, such as HiChIP and proximity ligation-assisted ChIP-Seq (PLAC-seq) (hereafter referred to as HP for brevity), can measure chromosome spatial organization by interrogating chromatin interactions mediated by a protein of interest...
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UMOD is a major risk gene for monogenic and complex forms of kidney disease. The encoded kidney-specific protein uromodulin is highly abundant in urine and related to chronic kidney disease, hypertension, and pathogen defense. To gain insights into potential systemic roles, we performed genome-wide screens of circulating uromodulin using complement...
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Background Expression quantitative trait methylation (eQTM) analysis identifies DNA CpG sites at which methylation is associated with gene expression and may reveal molecular mechanisms of disease. The present study describes an eQTM resource of CpG-transcript pairs. Methods DNA methylation was measured in blood samples from 1,045 Framingham Heart...
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Osteopontin (OPN), encoded by SPP1, is a phosphorylated glycoprotein predominantly synthesized in kidney tissue. Increased OPN mRNA and protein expression correlates with proteinuria, reduced creatinine clearance, and kidney fibrosis in animal models of kidney disease. But its genetic underpinnings are incompletely understood. We therefore conducte...
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The human brain forms functional networks of correlated activity, which have been linked with both cognitive and clinical outcomes. However, the genetic variants affecting brain function are largely unknown. Here, we used resting-state functional magnetic resonance images from 47,276 individuals to discover and validate common genetic variants infl...
Article
Recent advances in high-throughput chromatin conformation capture (Hi-C) technologies at the single-cell level enable the identification of cell type-specific chromatin loops directly from complex tissues. This may help to interpret noncoding variants identified by genome-wide association studies (GWAS) in disease-relevant cell types. We briefly re...
Article
Purpose We investigated the safety and efficacy profile of intensity-modulated radiation therapy (IMRT) followed by gemcitabine, dexamethasone, cisplatin (GDP), plus chidamide in the first-line setting for intermediate- and high-risk early-stage extranodal natural killer/T-cell lymphoma, nasal type (ENKTCL). Methods This was an open-label, randomi...
Article
Epigenetic mechanisms may underlie air pollution-health outcome associations. We estimated gaseous air pollutant-DNA methylation (DNAm) associations using twelve subpopulations within Women's Health Initiative (WHI) and Atherosclerosis Risk in Communities (ARIC) cohorts (n = 8397; mean age 61.3 years; 83% female; 46% African-American, 46% European-...
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Objective We evaluated and compared the efficacy and safety of neoadjuvant chemoradiotherapy (NACRT) versus neoadjuvant chemotherapy (NACT) for locally advanced gastric cancer (LAGC) in a single-center randomized phase II trial. Methods Patients with LAGC were enrolled and received either NACT or NACRT, followed by gastrectomy and adjuvant chemoth...
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Background The low incidence of primary mediastinal seminomas has precluded the development of clinical trials on mediastinal seminomas. We investigated the clinicopathologic characteristics, prognosis of patients with primary mediastinal seminomas as well as the efficiency of nonsurgical treatments compared with treatments containing surgery. Met...
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The human genome has a complex and dynamic three-dimensional (3D) organization, which plays a critical role for gene regulation and genome function. The importance of 3D genome organization in brain development and function has been well characterized in a region- and cell-type-specific fashion. Recent technological advances in chromosome conformat...