Scholars@Duke
Herbert Pang

Herbert Pang

Adjunct Assistant Professor in the Department of Biostatistics & Bioinformatics
Biostatistics & Bioinformatics, Division of Biostatistics
herbert.pang@duke.edu
Duke Box 2721, Durham, NC 27710
2424 Erwin Road Ste 1102, 11107 Hock Plaza, Durham, NC 27705

Scholarly Works - Journal articles

The impact of lowering the study design significance threshold to 0.005 on sample size in randomized cancer clinical trials.

Journal article J Clin Transl Sci · 2024 The proposal of improving reproducibility by lowering the significance threshold to 0.005 has been discussed, but the impact on conducting clinical trials has yet to be examined from a study design perspective. The impact on sample size and study duration ... Full text Open Access Link to item Cite

Trends and age, sex, and race disparities in time to second primary cancer from 1990 to 2019.

Journal article Cancer Med · December 2023 BACKGROUND: Despite the growth in primary cancer (PC) survivors, the trends and disparities in this population have yet to be comprehensively examined using competing risk analysis. The objective is to examine trends in time to second primary cancer (SPC) ... Full text Open Access Link to item Cite

Enrollment Success, Factors, and Prediction Models in Cancer Trials (2008-2019).

Journal article JCO Oncol Pract · November 2023 PURPOSE: To investigate the enrollment success rate of cancer clinical trials conducted in 2008-2019 and various factors lowering the enrollment success rate. METHODS: This is a cross-sectional study with clinical trial information from the largest registr ... Full text Link to item Cite

Global trends indicate increasing consumption of dietary sodium and fiber in middle-income countries: A study of 30-year global macrotrends.

Journal article Nutr Res · October 2023 According to the Global Burden of Disease Study, 3 million deaths were attributable to high sodium intake and low intake of whole grains. With the rapid evolution of the food industry, we hypothesize that dietary intake of sodium has increased and that die ... Full text Link to item Cite

CPAE: Contrastive predictive autoencoder for unsupervised pre-training in health status prediction.

Journal article Comput Methods Programs Biomed · June 2023 BACKGROUND AND OBJECTIVE: Fully-supervised learning approaches have shown promising results in some health status prediction tasks using Electronic Health Records (EHRs). These traditional approaches rely on sufficient labeled data to learn from. However, ... Full text Link to item Cite

New reporting items and recommendations for randomized trials impacted by COVID-19 and force majeure events: a targeted approach.

Journal article Ann Transl Med · January 15, 2023 BACKGROUND: Appropriate analyses and reporting are essential to the reproducibility and interpretation of clinical trials. However, the coronavirus disease 19 (COVID-19) pandemic and other force majeure events, like the war in Ukraine, have impacted the co ... Full text Link to item Cite

An Evaluation of Gene-Diet Interaction Statistical Methods and Discovery of rs7175421-Whole Grain Interaction in Lung Cancer.

Journal article Nutr Cancer · 2023 Dietary factors show different effects on genetically diverse populations. Scientific research uses gene-environment interaction models to study the effects of dietary factors on genetically diverse populations for lung cancer risk. However, previous study ... Full text Link to item Cite

Statistical Consideration for Fit-for-Use Real-World Data to Support Regulatory Decision Making in Drug Development

Journal article Statistics in Biopharmaceutical Research · January 1, 2023 A Real-World Evidence (RWE) scientific working group of the American Statistical Association Biopharmaceutical Section has been reviewing the statistical considerations for the generation of real-world evidence to support regulatory decision making. As par ... Full text Cite

Covariate handling approaches in combination with dynamic borrowing for hybrid control studies.

Journal article Pharm Stat · 2023 Borrowing data from external control has been an appealing strategy for evidence synthesis when conducting randomized controlled trials (RCTs). Often named hybrid control trials, they leverage existing control data from clinical trials or potentially real- ... Full text Link to item Cite

Associations between body mass index, weight loss and overall survival in patients with advanced lung cancer.

Journal article J Cachexia Sarcopenia Muscle · December 2022 BACKGROUND: Weight loss (WL) has been associated with shorter survival in patients with advanced cancer, while obesity has been associated with longer survival. Integrating body mass index (BMI) and WL provides a powerful prognostic tool but has not been w ... Full text Open Access Link to item Cite

Characteristics of toxicity occurrence patterns in concurrent chemoradiotherapy after induction chemotherapy for patients with locally advanced non-small cell lung cancer: a pooled analysis based on individual patient data of CALGB/Alliance trials.

Journal article Transl Cancer Res · October 2022 BACKGROUND: For patients with locally advanced non-small cell lung cancer (NSCLC), concurrent chemoradiotherapy is the foundational treatment strategy. Adding induction chemotherapy did not achieve a superior efficacy but increased the burden from toxicity ... Full text Open Access Link to item Cite

A multicenter retrospective cohort study on predicting the risk for amiodarone pulmonary toxicity.

Journal article BMC Pulm Med · April 5, 2022 BACKGROUND: Amiodarone is one of the most commonly used anti-arrhythmic agents. Amiodarone pulmonary toxicity is a potentially fatal adverse effect associated with amiodarone use. Previous studies on the epidemiology and risk factors for amiodarone pulmona ... Full text Open Access Link to item Cite

Assessing surrogacy using restricted mean survival time ratio for overall survival in non-small cell lung cancer immunotherapy studies.

Journal article Chin Clin Oncol · February 2022 BACKGROUND: Proportional hazards (PH) assumption is often violated in cancer immunotherapy studies. Restricted mean survival time (RMST) ratio is a valid metric to quantify the size of treatment effect when non-proportional hazard (NPH) is present. This st ... Full text Link to item Cite

A meta-analysis with systematic review: Efficacy and safety of immune checkpoint inhibitors in patients with advanced gastric cancer.

Journal article Front Oncol · 2022 BACKGROUND: While the efficacy of immune checkpoint inhibitors (ICIs) is increasingly recognized in advanced gastric cancer (aGC), overall survival (OS) has not been consistently improved across the different randomized controlled trials (RCTs). This meta- ... Full text Open Access Link to item Cite

Role of dietary carbohydrates on risk of lung cancer.

Journal article Lung Cancer · May 2021 OBJECTIVES: Inconsistent findings have been reported on the link between dietary carbohydrates and lung cancer. This study aims to comprehensively evaluate the role of dietary carbohydrates on lung cancer risk. MATERIALS AND METHODS: The prospective study ... Full text Link to item Cite

Development and Validation of a Natural Language Processing Tool to Generate the CONSORT Reporting Checklist for Randomized Clinical Trials.

Journal article JAMA Netw Open · October 1, 2020 IMPORTANCE: Adherence to the Consolidated Standards of Reporting Trials (CONSORT) for randomized clinical trials is associated with improvingquality because inadequate reporting in randomized clinical trials may complicate the interpretation and the applic ... Full text Link to item Cite

Radiomics analysis using stability selection supervised component analysis for right-censored survival data.

Journal article Comput Biol Med · September 2020 Radiomics is a newly emerging field that involves the extraction of massive quantitative features from biomedical images by using data-characterization algorithms. Distinctive imaging features identified from biomedical images can be used for prognosis and ... Full text Open Access Link to item Cite

Endpoint surrogacy in oncology Phase 3 randomised controlled trials.

Journal article Br J Cancer · August 2020 Endpoint surrogacy is an important concept in oncology trials. Using a surrogate endpoint like progression-free survival as the primary endpoint-instead of overall survival-would lead to a potential faster drug approval and therefore more cancer patients w ... Full text Open Access Link to item Cite

Toxicity Related to Radiotherapy Dose and Targeting Strategy: A Pooled Analysis of Cooperative Group Trials of Combined Modality Therapy for Locally Advanced Non-Small Cell Lung Cancer.

Journal article J Thorac Oncol · February 2019 OBJECTIVE: Concurrent chemoradiotherapy (CRT) was the standard treatment for locally advanced NSCLC (LA-NSCLC). This study was performed to examine thoracic radiotherapy (TRT) parameters and their impact on adverse events (AEs). METHODS: We collected indiv ... Full text Link to item Cite

A pooled analysis of individual patient data from National Clinical Trials Network clinical trials of concurrent chemoradiotherapy for limited-stage small cell lung cancer in elderly patients versus younger patients.

Journal article Cancer · February 1, 2019 BACKGROUND: Platinum and etoposide with thoracic radiation followed by prophylactic cranial irradiation constitute the standard treatment for limited-stage small cell lung cancer (LS-SCLC). Many patients with LS-SCLC are elderly with comorbidities. METHODS ... Full text Link to item Cite

Exploring Radiotherapy Targeting Strategy and Dose: A Pooled Analysis of Cooperative Group Trials of Combined Modality Therapy for Stage III NSCLC.

Journal article J Thorac Oncol · August 2018 INTRODUCTION: Concurrent chemoradiotherapy (CRT) is standard therapy for locally advanced NSCLC (LA-NSCLC) patients. This study was performed to examine thoracic radiotherapy (TRT) parameters and their impact on patient survival. METHODS: We collected indi ... Full text Link to item Cite

A Phase I Trial of the IGF-1R Antibody Ganitumab (AMG 479) in Combination with Everolimus (RAD001) and Panitumumab in Patients with Advanced Cancer.

Journal article Oncologist · July 2018 PURPOSE: This study evaluated the maximum tolerated dose or recommended phase II dose (RPTD) and safety and tolerability of the ganitumab and everolimus doublet regimen followed by the ganitumab, everolimus, and panitumumab triplet regimen. MATERIALS AND M ... Full text Link to item Cite

Association of an Early Intervention Service for Psychosis With Suicide Rate Among Patients With First-Episode Schizophrenia-Spectrum Disorders.

Journal article JAMA Psychiatry · May 1, 2018 IMPORTANCE: Patients with schizophrenia have a substantially higher suicide rate than the general public. Early intervention (EI) services improve short-term outcomes. However, little is known about the association of EI with suicide reduction in the long ... Full text Link to item Cite

A comparison of graph- and kernel-based -omics data integration algorithms for classifying complex traits.

Journal article BMC Bioinformatics · December 6, 2017 BACKGROUND: High-throughput sequencing data are widely collected and analyzed in the study of complex diseases in quest of improving human health. Well-studied algorithms mostly deal with single data source, and cannot fully utilize the potential of these ... Full text Link to item Cite

Genetic predisposition to lung adenocarcinoma among never-smoking Chinese with different epidermal growth factor receptor mutation status.

Journal article Lung Cancer · December 2017 OBJECTIVES: The inconsistent findings from genetic association studies may be related to the heterogeneity in different molecular subtypes of lung cancer. This study evaluated the predisposing single-nucleotide polymorphisms (SNPs) in epidermal growth fact ... Full text Link to item Cite

Impact of patient education on influenza vaccine uptake among community-dwelling elderly: a randomized controlled trial.

Journal article Health Educ Res · October 1, 2017 This randomized controlled trial aimed to test the effectiveness of brief face-to-face patient education in increasing influenza vaccination rate among elderly in the community. Recruitment and intervention were conducted at two general outpatient clinics ... Full text Link to item Cite

Pooled Analysis of Individual Patient Data on Concurrent Chemoradiotherapy for Stage III Non-Small-Cell Lung Cancer in Elderly Patients Compared With Younger Patients Who Participated in US National Cancer Institute Cooperative Group Studies.

Journal article J Clin Oncol · September 1, 2017 Purpose Concurrent chemoradiotherapy is standard treatment for patients with stage III non-small-cell lung cancer. Elderly patients may experience increased rates of adverse events (AEs) or less benefit from concurrent chemoradiotherapy. Patients and Metho ... Full text Link to item Cite

Reporting and Guidelines in Propensity Score Analysis: A Systematic Review of Cancer and Cancer Surgical Studies.

Journal article J Natl Cancer Inst · August 1, 2017 BACKGROUND: : Propensity score (PS) analysis is increasingly being used in observational studies, especially in some cancer studies where random assignment is not feasible. This systematic review evaluates the use and reporting quality of PS analysis in on ... Full text Link to item Cite

Diabetes incidence and prevalence in Hong Kong, China during 2006-2014.

Journal article Diabet Med · July 2017 AIMS: To estimate recent secular changes in the incidence and prevalence of diabetes and pre-diabetes among Hong Kong Chinese adults, and thus show possible future trends for developing mainland China. METHODS: Based on a complete census of the public sect ... Full text Link to item Cite

Longitudinal Patterns and Predictors of Depression Trajectories Related to the 2014 Occupy Central/Umbrella Movement in Hong Kong.

Journal article Am J Public Health · April 2017 OBJECTIVES: To examine the longitudinal patterns and predictors of depression trajectories before, during, and after Hong Kong's 2014 Occupy Central/Umbrella Movement. METHODS: In a prospective study, between March 2009 and November 2015, we interviewed 11 ... Full text Link to item Cite

Cohort Profile: FAMILY Cohort.

Journal article Int J Epidemiol · April 1, 2017 The FAMILY Cohort is a longitudinal study of health, happiness and family harmony (the '3Hs') at individual, household and neighbourhood levels in Hong Kong. Using a family living in the same household as the sampling unit, the study (n = 20 279 households ... Full text Link to item Cite

Predictors of duloxetine response in patients with oxaliplatin-induced painful chemotherapy-induced peripheral neuropathy (CIPN): a secondary analysis of randomised controlled trial - CALGB/alliance 170601.

Journal article Eur J Cancer Care (Engl) · March 2017 Duloxetine is an effective treatment for oxaliplatin-induced painful chemotherapy-induced peripheral neuropathy (CIPN). However, predictors of duloxetine response have not been adequately explored. The objective of this secondary and exploratory analysis w ... Full text Link to item Cite

Validation of Progression-Free Survival as a Surrogate Endpoint for Overall Survival in Malignant Mesothelioma: Analysis of Cancer and Leukemia Group B and North Central Cancer Treatment Group (Alliance) Trials.

Journal article Oncologist · February 2017 PURPOSE: The aim of this study was to investigate whether progression-free survival (PFS) can be considered a surrogate endpoint for overall survival (OS) in malignant mesothelioma. MATERIALS AND METHODS: Individual data were collected from 15 Cancer and L ... Full text Link to item Cite

Bayesian Semiparametric Model for Pathway-Based Analysis with Zero-Inflated Clinical Outcomes

Journal article Journal of Agricultural Biological and Environmental Statistics · December 1, 2016 In this paper, we propose a semiparametric regression approach for identifying pathways related to zero-inflated clinical outcomes, where a pathway is a gene set derived from prior biological knowledge. Our approach is developed by using a Bayesian hierarc ... Full text Cite

Enrollment Trends and Disparity Among Patients With Lung Cancer in National Clinical Trials, 1990 to 2012.

Journal article J Clin Oncol · November 20, 2016 Purpose Under-representation of elderly, women, and racial/ethnic minority patients with cancer in clinical trials is of national concern. The goal of this study was to characterize enrollment trends and disparities by age, sex, and race/ethnicity in lung ... Full text Link to item Cite

Composition of gut microbiota in infants in China and global comparison.

Journal article Sci Rep · November 9, 2016 Symbiotic gut microbiota is essential for human health, and its compositional changes have been associated with various complex disorders. However, systematic investigation of the acquisition and development of gut microbial communities during early infanc ... Full text Link to item Cite

Direct Participation in and Indirect Exposure to the Occupy Central Movement and Depressive Symptoms: A Longitudinal Study of Hong Kong Adults.

Journal article Am J Epidemiol · November 1, 2016 Despite the extensive history of social movements around the world, the evolution of population mental health before, during, and after a social movement remains sparsely documented. We sought to assess over time the prevalence of depressive symptoms durin ... Full text Link to item Cite

Blood-based markers of efficacy and resistance to cetuximab treatment in metastatic colorectal cancer: results from CALGB 80203 (Alliance).

Journal article Cancer Med · September 2016 Circulating protein markers were assessed in patients with colorectal cancer (CRC) treated with cetuximab in CALGB 80203 to identify prognostic and predictive biomarkers. Patients with locally advanced or metastatic CRC received FOLFOX or FOLFIRI chemother ... Full text Link to item Cite

Positive Interaction between Prophylactic Cranial Irradiation and Maintenance Sunitinib for Untreated Extensive-Stage Small Cell Lung Cancer Patients After Standard Chemotherapy: A Secondary Analysis of CALGB 30504 (ALLIANCE).

Journal article J Thorac Oncol · March 2016 BACKGROUND: Prophylactic cranial irradiation (PCI) has become a standard option for patients with extensive-stage small cell lung cancer (ES-SCLC). The Cancer and Leukemia Group B 30504 trial was a randomized phase II study of the effect of sunitinib versu ... Full text Link to item Cite

Statistical aspect of translational and correlative studies in clinical trials.

Journal article Chin Clin Oncol · February 2016 In this article, we describe statistical issues related to the conduct of translational and correlative studies in cancer clinical trials. In the era of personalized medicine, proper biomarker discovery and validation is crucial for producing groundbreakin ... Full text Link to item Cite

Shrinkage-based diagonal Hotelling's tests for high-dimensional small sample size data

Journal article Journal of Multivariate Analysis · January 1, 2016 High-throughput expression profiling techniques bring novel tools and also statistical challenges to genetic research. In addition to detecting differentially expressed genes, testing the significance of gene sets or pathway analysis has been recognized as ... Full text Cite

Seamless Phase IIa/IIb and enhanced dose-finding adaptive design.

Journal article J Biopharm Stat · 2016 In drug development, when the drug class has a relatively well-defined path to regulatory approval and the enrollment is slow with certain patient populations, one may want to consider combining studies of different phases. This article considers combining ... Full text Link to item Cite

Normative data and psychometric properties of the Connor-Davidson Resilience Scale (CD-RISC) and the abbreviated version (CD-RISC2) among the general population in Hong Kong.

Journal article Qual Life Res · January 2016 PURPOSE: To examine whether the two-item version (CD-RISC2) of the Connor-Davidson Resilience Scale (CD-RISC) has adequate internal consistency and construct validity, as well as significant correlation with the full scale, and to provide normative data fo ... Full text Link to item Cite

Validation of survival prognostic models for non-small-cell lung cancer in stage- and age-specific groups.

Journal article Lung Cancer · November 2015 PURPOSE: Prognostic models have been proposed to predict survival for non-small-cell lung cancer (NSCLC). It is important to evaluate whether these models perform better than performance status (PS) alone in stage- and age-specific subgroups. PATIENTS AND ... Full text Link to item Cite

Random Effects Model for Multiple Pathway Analysis with Applications to Type II Diabetes Microarray Data.

Journal article Stat Biosci · October 1, 2015 Close to three percent of the world's population suffer from diabetes. Despite the range of treatment options available for diabetes patients, not all patients benefit from them. Investigating how different pathways correlate with phenotype of interest may ... Full text Link to item Cite

Direct Evidence of Target Inhibition with Anti-VEGF, EGFR, and mTOR Therapies in a Clinical Model of Wound Healing.

Journal article Clin Cancer Res · August 1, 2015 PURPOSE: In early clinical testing, most novel targeted anticancer therapies have limited toxicities and limited efficacy, which complicates dose and schedule selection for these agents. Confirmation of target inhibition is critical for rational drug devel ... Full text Link to item Cite

Chemotherapy With or Without Maintenance Sunitinib for Untreated Extensive-Stage Small-Cell Lung Cancer: A Randomized, Double-Blind, Placebo-Controlled Phase II Study-CALGB 30504 (Alliance).

Journal article J Clin Oncol · May 20, 2015 PURPOSE: To evaluate the efficacy of maintenance sunitinib after chemotherapy for small-cell lung cancer (SCLC). PATIENTS AND METHODS: The Cancer and Leukemia Group B 30504 trial was a randomized, placebo-controlled, phase II study that enrolled patients b ... Full text Link to item Cite

Biomarker signatures correlate with clinical outcome in refractory metastatic colorectal cancer patients receiving bevacizumab and everolimus.

Journal article Mol Cancer Ther · April 2015 A novel combination of bevacizumab and everolimus was evaluated in refractory colorectal cancer patients in a phase II trial. In this retrospective analysis, plasma samples from 49 patients were tested for over 40 biomarkers at baseline and after one or tw ... Full text Link to item Cite

VATS lobectomy has better perioperative outcomes than open lobectomy: CALGB 31001, an ancillary analysis of CALGB 140202 (Alliance).

Journal article Ann Thorac Surg · February 2015 BACKGROUND: The short-term superiority of video-assisted thoracoscopic surgery lobectomy compared with open lobectomy for early-stage lung cancer has been suggested by single-institution studies. Lack of equipoise limits the feasibility of a randomized stu ... Full text Link to item Cite

A Phase I/biomarker study of bevacizumab in combination with CNTO 95 in patients with advanced solid tumors.

Journal article Cancer Chemother Pharmacol · February 2015 PURPOSE: Inhibition of tumor angiogenesis is an effective mechanism to limit tumor growth; dual inhibition may result in additional benefit. Bevacizumab is a monoclonal antibody directed against vascular endothelial growth factor (VEGF), and intetumumab is ... Full text Link to item Cite

A leave-one-out cross-validation SAS macro for the identification of markers associated with survival.

Journal article Comput Biol Med · February 2015 A proper internal validation is necessary for the development of a reliable and reproducible prognostic model for external validation. Variable selection is an important step for building prognostic models. However, not many existing approaches couple the ... Full text Link to item Cite

Transmissibility of the Ice Bucket Challenge among globally influential celebrities: retrospective cohort study.

Journal article BMJ · December 16, 2014 OBJECTIVES: To estimate the transmissibility of the Ice Bucket Challenge among globally influential celebrities and to identify associated risk factors. DESIGN: Retrospective cohort study. SETTING: Social media (YouTube, Facebook, Twitter, Instagram). PART ... Full text Link to item Cite

Repair-related activation of hedgehog signaling in stromal cells promotes intrahepatic hypothyroidism.

Journal article Endocrinology · November 2014 Thyroid hormone (TH) is important for tissue repair because it regulates cellular differentiation. Intrahepatic TH activity is controlled by both serum TH levels and hepatic deiodinases. TH substrate (T4) is converted into active hormone (T3) by deiodinase ... Full text Link to item Cite

Reply: To PMID 23913408.

Journal article Hepatology · October 2014 Full text Link to item Cite

Phase I study of capecitabine, oxaliplatin, bevacizumab, and everolimus in advanced solid tumors.

Journal article Invest New Drugs · August 2014 PURPOSE: To define maximum tolerated dose (MTD), toxicities, and pharmacodynamics of capecitabine, oxaliplatin, bevacizumab, and everolimus in advanced solid tumor patients. DESIGN: This was a standard "3 + 3" dose-escalation trial. All subjects received b ... Full text Link to item Cite

Integrative pathway analysis using Graph-Based learning with applications to TCGA colon and ovarian data

Journal article Cancer Informatics · July 28, 2014 Recent method development has included multi-dimensional genomic data algorithms because such methods have more accurately pre-dicted clinical phenotypes related to disease. This study is the first to conduct an integrative genomic pathway-based analysis w ... Full text Cite

Modulation of circulating protein biomarkers following TRC105 (anti-endoglin antibody) treatment in patients with advanced cancer.

Journal article Cancer Med · June 2014 TRC105 is an endoglin-targeting drug that possesses anti-angiogenic and antitumor potential. Analysis of the initial phase I trial of TRC105 demonstrated good tolerability and efficacy in cancer patients. In this report, we analyzed multiple circulating bi ... Full text Link to item Cite

Phase I study of dasatinib in combination with capecitabine, oxaliplatin and bevacizumab followed by an expanded cohort in previously untreated metastatic colorectal cancer.

Journal article Invest New Drugs · April 2014 PURPOSE: Dasatinib inhibits src family kinases and has anti-angiogenic properties. We conducted a phase I study of dasatinib, capecitabine, oxaliplatin, and bevacizumab (CapeOx/bevacizumab), with an expansion cohort in metastatic colorectal cancer (CRC). M ... Full text Link to item Cite

Methodological considerations in the design and implementation of clinical trials.

Journal article Semin Oncol Nurs · February 2014 OBJECTIVES: To review study design issues related to clinical trials led by oncology nurses, with special attention to those conducted within the cooperative group setting; to emphasize the importance of the statistician's role in the process of clinical t ... Full text Link to item Cite

Hepatic gene expression profiles differentiate presymptomatic patients with mild versus severe nonalcoholic fatty liver disease.

Journal article Hepatology · February 2014 UNLABELLED: Clinicians rely upon the severity of liver fibrosis to segregate patients with well-compensated nonalcoholic fatty liver disease (NAFLD) into subpopulations at high- versus low-risk for eventual liver-related morbidity and mortality. We compare ... Full text Link to item Cite

Integrative Pathway Analysis Using Graph-Based Learning with Applications to TCGA Colon and Ovarian Data.

Journal article Cancer Inform · 2014 Recent method development has included multi-dimensional genomic data algorithms because such methods have more accurately predicted clinical phenotypes related to disease. This study is the first to conduct an integrative genomic pathway-based analysis wi ... Full text Link to item Cite

Stratified pathway analysis to identify gene sets associated with oral contraceptive use and breast cancer.

Journal article Cancer Inform · 2014 Cancer biomarker discovery can facilitate drug development, improve staging of patients, and predict patient prognosis. Because cancer is the result of many interacting genes, analysis based on a set of genes with related biological functions or pathways m ... Full text Link to item Cite

Prognostic and predictive blood-based biomarkers in patients with advanced pancreatic cancer: results from CALGB80303 (Alliance).

Journal article Clin Cancer Res · December 15, 2013 PURPOSE: CALGB80303 was a phase III trial of 602 patients with locally advanced or metastatic pancreatic cancer comparing gemcitabine/bevacizumab versus gemcitabine/placebo. The study found no benefit in any outcome from the addition of bevacizumab to gemc ... Full text Link to item Cite

Predictors of pulmonary toxicity in limited stage small cell lung cancer patients treated with induction chemotherapy followed by concurrent platinum-based chemotherapy and 70 Gy daily radiotherapy: CALGB 30904.

Journal article Lung Cancer · December 2013 INTRODUCTION: Standard therapy for limited stage small cell lung cancer (L-SCLC) is concurrent chemotherapy and radiotherapy followed by prophylactic cranial radiotherapy. Predictors of post chemoradiotherapy pulmonary toxicity in limited stage (LS) small ... Full text Link to item Cite

Relationship between methylome and transcriptome in patients with nonalcoholic fatty liver disease.

Journal article Gastroenterology · November 2013 BACKGROUND & AIMS: Cirrhosis and liver cancer are potential outcomes of advanced nonalcoholic fatty liver disease (NAFLD). It is not clear what factors determine whether patients will develop advanced or mild NAFLD, limiting noninvasive diagnosis and treat ... Full text Link to item Cite

A pooled analysis of limited-stage small-cell lung cancer patients treated with induction chemotherapy followed by concurrent platinum-based chemotherapy and 70 Gy daily radiotherapy: CALGB 30904.

Journal article J Thorac Oncol · August 2013 INTRODUCTION: Standard therapy for limited-stage small-cell lung cancer (L-SCLC) is concurrent chemotherapy and radiotherapy (RT) followed by prophylactic cranial radiotherapy. Although many consider the standard RT regimen to be 45 Gy in 1.5 Gy twice-dail ... Full text Link to item Cite

Surrogate endpoints for overall survival in chemotherapy and radiotherapy trials in operable and locally advanced lung cancer: a re-analysis of meta-analyses of individual patients' data.

Journal article Lancet Oncol · June 2013 BACKGROUND: The gold standard endpoint in clinical trials of chemotherapy and radiotherapy for lung cancer is overall survival. Although reliable and simple to measure, this endpoint takes years to observe. Surrogate endpoints that would enable earlier ass ... Full text Link to item Cite

A phase I study of ABT-510 plus bevacizumab in advanced solid tumors.

Journal article Cancer Med · June 2013 Targeting multiple regulators of tumor angiogenesis have the potential to improve treatment efficacy. Bevacizumab is a monoclonal antibody directed against vascular endothelial growth factor and ABT-510 is a synthetic analog of thrombospondin, an endogenou ... Full text Open Access Link to item Cite

Block-diagonal discriminant analysis and its bias-corrected rules.

Journal article Stat Appl Genet Mol Biol · June 2013 High-throughput expression profiling allows simultaneous measure of tens of thousands of genes at once. These data have motivated the development of reliable biomarkers for disease subtypes identification and diagnosis. Many methods have been developed in ... Full text Link to item Cite

Effect of duloxetine on pain, function, and quality of life among patients with chemotherapy-induced painful peripheral neuropathy: a randomized clinical trial.

Journal article JAMA · April 3, 2013 IMPORTANCE: There are no known effective treatments for painful chemotherapy-induced peripheral neuropathy. OBJECTIVE: To determine the effect of duloxetine, 60 mg daily, on average pain severity. DESIGN, SETTING, AND PATIENTS: Randomized, double-blind, pl ... Full text Link to item Cite

Statistical properties on semiparametric regression for evaluating pathway effects.

Journal article J Stat Plan Inference · April 2013 Most statistical methods for microarray data analysis consider one gene at a time, and they may miss subtle changes at the single gene level. This limitation may be overcome by considering a set of genes simultaneously where the gene sets are derived from ... Full text Link to item Cite

Sample size considerations of prediction-validation methods in high-dimensional data for survival outcomes.

Journal article Genet Epidemiol · April 2013 Featured Publication A variety of prediction methods are used to relate high-dimensional genome data with a clinical outcome using a prediction model. Once a prediction model is developed from a data set, it should be validated using a resampling method or an independent data ... Full text Link to item Cite

Correlation of angiogenic biomarker signatures with clinical outcomes in metastatic colorectal cancer patients receiving capecitabine, oxaliplatin, and bevacizumab.

Journal article Cancer Med · April 2013 A novel combination of capecitabine, oxaliplatin, and bevacizumab was evaluated in colorectal cancer patients enrolled in a phase II clinical trial. In this retrospective analysis, plasma samples from patients receiving capecitabine, oxaliplatin, and bevac ... Full text Link to item Cite

Determinants of a subject's decision to participate in clinical anesthesia research.

Journal article Anesth Analg · February 2013 Featured Publication BACKGROUND: A top priority for research studies is to ensure that potential participants receive adequate information to make a truly informed decision. Understanding patient experiences with the recruitment process may identify areas for improvement in th ... Full text Link to item Cite

Phase II study of induction cisplatin and irinotecan followed by concurrent carboplatin, etoposide, and thoracic radiotherapy for limited-stage small-cell lung cancer, CALGB 30206.

Journal article J Thorac Oncol · January 2013 Featured Publication INTRODUCTION: We sought to determine the efficacy of using both irinotecan- and etoposide-containing regimens sequentially for patients with untreated limited-stage small-cell lung cancer. METHODS: Patients with untreated, measurable, limited-stage small-c ... Full text Link to item Cite

A phase II study of capecitabine, oxaliplatin, and bevacizumab in the treatment of metastatic esophagogastric adenocarcinomas.

Journal article Oncologist · 2013 BACKGROUND: Esophageal and gastric cancers often present at an advanced stage. Systemic chemotherapy is the mainstay of treatment, but survival with current regimens remains poor. We evaluated the safety, tolerability, and efficacy of the combination capec ... Full text Link to item Cite

NKT-associated hedgehog and osteopontin drive fibrogenesis in non-alcoholic fatty liver disease.

Journal article Gut · September 2012 Featured Publication OBJECTIVE: Immune responses are important in dictating non-alcoholic steatohepatitis (NASH) outcome. We previously reported that upregulation of hedgehog (Hh) and osteopontin (OPN) occurs in NASH, that Hh-regulated accumulation of natural killer T (NKT) ce ... Full text Link to item Cite

Bayesian semiparametric regression models for evaluating pathway effects on continuous and binary clinical outcomes.

Journal article Stat Med · July 10, 2012 Featured Publication Many statistical methods for microarray data analysis consider one gene at a time, and they may miss subtle changes at the single gene level. This limitation may be overcome by considering a set of genes simultaneously where the gene sets are derived from ... Full text Link to item Cite

Phase II study of dasatinib in patients with previously treated malignant mesothelioma (cancer and leukemia group B 30601): a brief report.

Journal article J Thorac Oncol · April 2012 Featured Publication INTRODUCTION: We conducted a phase II trial of dasatinib in malignant mesothelioma (MM) patients to evaluate its toxicity and efficacy as a second-line treatment. METHODS: Patients with unresectable MM and no symptomatic effusions were given dasatinib 70 m ... Full text Link to item Cite

Gene selection using iterative feature elimination random forests for survival outcomes.

Journal article IEEE/ACM Trans Comput Biol Bioinform · 2012 Featured Publication Although many feature selection methods for classification have been developed, there is a need to identify genes in high-dimensional data with censored survival outcomes. Traditional methods for gene selection in classification problems have several drawb ... Full text Open Access Link to item Cite

Relationship type, condom use and HIV/AIDS risks among men who have sex with men in six Chinese cities.

Journal article AIDS Care · 2012 Featured Publication This study is the first to examine the role of partner type in sexual practices of men who have sex with men (MSM) in China. Using cross-sectional self-administered questionnaires (N=692) with MSM in six Chinese cities (Shanghai, Guangzhou, Shenzhen, Xi'an ... Full text Link to item Cite

Cisplatin, irinotecan, and bevacizumab for untreated extensive-stage small-cell lung cancer: CALGB 30306, a phase II study.

Journal article J Clin Oncol · November 20, 2011 Featured Publication PURPOSE: The efficacy of cisplatin, irinotecan, and bevacizumab was evaluated in patients with extensive-stage small-cell lung cancer (ES-SCLC). PATIENTS AND METHODS: Patients with ES-SCLC received cisplatin 30 mg/m(2) and irinotecan 65 mg/m(2) on days 1 a ... Full text Link to item Cite

A phase II study of oxaliplatin, dose-intense capecitabine, and high-dose bevacizumab in the treatment of metastatic colorectal cancer.

Journal article Clin Colorectal Cancer · September 2011 Featured Publication BACKGROUND: This study was designed to determine the efficacy and tolerability of a novel 2-week regimen of capecitabine, oxaliplatin (OHP), and bevacizumab in patients with chemo-naive advanced colorectal cancer. PATIENTS AND METHODS: Nineteen patients wi ... Full text Link to item Cite

Pathway-based identification of SNPs predictive of survival.

Journal article Eur J Hum Genet · June 2011 Featured Publication In recent years, several association analysis methods for case-control studies have been developed. However, as we turn towards the identification of single nucleotide polymorphisms (SNPs) for prognosis, there is a need to develop methods for the identific ... Full text Link to item Cite

A phase II trial of bevacizumab plus everolimus for patients with refractory metastatic colorectal cancer.

Journal article Oncologist · 2011 Featured Publication PURPOSE: For patients with metastatic colorectal cancer (mCRC), no standard therapy exists after progression on 5-fluorouracil, oxaliplatin, irinotecan, bevacizumab, and cetuximab or panitumumab. Preclinical data demonstrated that combined vascular endothe ... Full text Link to item Cite

A phase II study of capecitabine, oxaliplatin, bevacizumab and cetuximab in the treatment of metastatic colorectal cancer.

Journal article Anticancer Res · January 2011 Featured Publication AIM: This study was designed to determine the efficacy and tolerability of capecitabine, oxaliplatin and bevacizumab in combination with cetuximab as first-line therapy for advanced colorectal cancer. PATIENTS AND METHODS: Patients with previously untreate ... Link to item Cite

A phase II study of sorafenib in malignant mesothelioma: results of Cancer and Leukemia Group B 30307.

Journal article J Thorac Oncol · October 2010 Featured Publication HYPOTHESIS: Malignant mesotheliomas (MMs) express vascular endothelial growth factor receptor (VEGFR), platelet-derived growth factor receptor, and cKIT. Sorafenib is a potent inhibitor of the ras/raf/MEK pathway and also targets VEGFR and cKIT. We evaluat ... Full text Link to item Cite

Phase II study of the histone deacetylase inhibitor Romidepsin in relapsed small cell lung cancer (Cancer and Leukemia Group B 30304).

Journal article J Thorac Oncol · October 2010 Featured Publication INTRODUCTION: Treatment of small cell lung cancer (SCLC) is initially gratifying with most patients responding to platinum-based chemotherapy. Treatment of relapsed disease gives much lower response rates of short duration. We undertook this study of the p ... Full text Link to item Cite

Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysis.

Journal article Hum Genomics · October 2010 Featured Publication Breast cancer tumours among African Americans are usually more aggressive than those found in Caucasian populations. African-American patients with breast cancer also have higher mortality rates than Caucasian women. A better understanding of the disease a ... Full text Link to item Cite

A phase II study of dasatinib in patients with chemosensitive relapsed small cell lung cancer (Cancer and Leukemia Group B 30602).

Journal article J Thorac Oncol · March 2010 Featured Publication INTRODUCTION: SRC is an oncogene with an essential role in the invasiveness and metastasis of solid tumors including small cell lung cancer. Dasatinib is a potent inhibitor of SRC as well as other tyrosine kinases. The primary objective of this study was t ... Full text Link to item Cite

Pathway analysis using random forests with bivariate node-split for survival outcomes.

Journal article Bioinformatics · January 15, 2010 Featured Publication MOTIVATION: There is great interest in pathway-based methods for genomics data analysis in the research community. Although machine learning methods, such as random forests, have been developed to correlate survival outcomes with a set of genes, no study h ... Full text Link to item Cite

Shrinkage-based diagonal discriminant analysis and its applications in high-dimensional data.

Journal article Biometrics · December 2009 Featured Publication High-dimensional data such as microarrays have brought us new statistical challenges. For example, using a large number of genes to classify samples based on a small number of microarrays remains a difficult problem. Diagonal discriminant analysis, support ... Full text Link to item Cite

Building pathway clusters from Random Forests classification using class votes.

Journal article BMC Bioinformatics · February 6, 2008 Featured Publication BACKGROUND: Recent years have seen the development of various pathway-based methods for the analysis of microarray gene expression data. These approaches have the potential to bring biological insights into microarray studies. A variety of methods have bee ... Full text Link to item Cite

Pathway analysis using random forests classification and regression.

Journal article Bioinformatics · August 15, 2006 Featured Publication MOTIVATION: Although numerous methods have been developed to better capture biological information from microarray data, commonly used single gene-based methods neglect interactions among genes and leave room for other novel approaches. For example, most c ... Full text Link to item Cite