DIMI Lab Data science and Informatics for Multiomics Integration

Research

Highlighted

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
Theo A. Knijnenburg, Linghua Wang, Michael T. Zimmermann, Nyasha Chambwe, Galen F. Gao, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Reports   ·   03 Apr 2018   ·   doi:10.1016/j.celrep.2018.03.076
DNA damage repair, Genomic and Molecular Landscape, TCGA
Manuscript
Supplemental Data
Computational tumor stroma reaction evaluation led to novel prognosis-associated fibrosis and molecular signature discoveries in high-grade serous ovarian carcinoma
Computational tumor stroma reaction evaluation led to novel prognosis-associated fibrosis and molecular signature discoveries in high-grade serous ovarian carcinoma
Jun Jiang, Burak Tekin, Lin Yuan, Sebastian Armasu, Stacey J. Winham, Ellen L. Goode, Hongfang Liu, Yajue Huang, Ruifeng Guo, Chen Wang
Frontiers in Medicine   ·   07 Sep 2022   ·   doi:10.3389/fmed.2022.994467
Tumor stroma reaction
Manuscript
Source code

All

2024

Metabolome-wide association identifies altered metabolites and metabolic pathways in the serum of patients with cholangiocarcinoma
Metabolome-wide association identifies altered metabolites and metabolic pathways in the serum of patients with cholangiocarcinoma
Linsey E. Jackson, Jennifer L. Tomlinson, Roberto Alva-Ruiz, Lindsey A. Gregory, Seul Kee Byeon, ..., Sumera I. Ilyas, Gregory J. Gores, Akhilesh Pandey, Arjun P. Athreya, Rory L. Smoot
JHEP Reports   ·   01 Jun 2024   ·   doi:10.1016/j.jhepr.2024.101068
Real-world Trends, Rural-urban Differences, and Socioeconomic Disparities in Utilization of Narrow versus Broad Next-generation Sequencing Panels
Real-world Trends, Rural-urban Differences, and Socioeconomic Disparities in Utilization of Narrow versus Broad Next-generation Sequencing Panels
Yiqing Zhao, Anastasios Dimou, Zachary C. Fogarty, Jun Jiang, Hongfang Liu, William B. Wong, Chen Wang
Cancer Research Communications   ·   05 Feb 2024   ·   doi:10.1158/2767-9764.CRC-23-0190

2023

Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup
Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup
Nephi A Walton, Radha Nagarajan, Chen Wang, Murat Sincan, Robert R Freimuth, ..., Alper Uzun, Thomas Nate Person, Nadav Rappoport, Zhongming Zhao, Marc S Williams
Journal of the American Medical Informatics Association   ·   30 Nov 2023   ·   doi:10.1093/jamia/ocad211
Batch-effect correction with sample remeasurement in highly confounded case-control studies
Batch-effect correction with sample remeasurement in highly confounded case-control studies
Hanxuan Ye, Xianyang Zhang, Chen Wang, Ellen L. Goode, Jun Chen
Nature Computational Science   ·   23 Aug 2023   ·   doi:10.1038/s43588-023-00500-8
Multiplex Immunofluorescence Image Quality Checking Using DAPI Channel–referenced Evaluation
Multiplex Immunofluorescence Image Quality Checking Using DAPI Channel–referenced Evaluation
Jun Jiang, Raymond Moore, Clarissa E. Jordan, Ruifeng Guo, Rachel L. Maus, Hongfang Liu, Ellen Goode, Svetomir N. Markovic, Chen Wang
Journal of Histochemistry & Cytochemistry   ·   01 Mar 2023   ·   doi:10.1369/00221554231161693
Methylation Signature Implicated in Immuno-Suppressive Activities in Tubo-Ovarian High-Grade Serous Carcinoma
Methylation Signature Implicated in Immuno-Suppressive Activities in Tubo-Ovarian High-Grade Serous Carcinoma
Chen Wang, Matthew S. Block, Julie M. Cunningham, Mark E. Sherman, Bryan M. McCauley, ..., Tanja Pejovic, Jesus Gonzalez Bosquet, David D. Bowtell, Stacey J. Winham, Ellen L. Goode
Cancer Epidemiology, Biomarkers & Prevention   ·   15 Feb 2023   ·   doi:10.1158/1055-9965.EPI-22-0941

2022

Leveraging a pharmacogenomics knowledgebase to formulate a drug response phenotype terminology for genomic medicine
Leveraging a pharmacogenomics knowledgebase to formulate a drug response phenotype terminology for genomic medicine
Yiqing Zhao, Matthew Brush, Chen Wang, Alex H Wagner, Hongfang Liu, Robert R Freimuth
Bioinformatics   ·   12 Oct 2022   ·   doi:10.1093/bioinformatics/btac646
Computational tumor stroma reaction evaluation led to novel prognosis-associated fibrosis and molecular signature discoveries in high-grade serous ovarian carcinoma
Computational tumor stroma reaction evaluation led to novel prognosis-associated fibrosis and molecular signature discoveries in high-grade serous ovarian carcinoma
Jun Jiang, Burak Tekin, Lin Yuan, Sebastian Armasu, Stacey J. Winham, Ellen L. Goode, Hongfang Liu, Yajue Huang, Ruifeng Guo, Chen Wang
Frontiers in Medicine   ·   07 Sep 2022   ·   doi:10.3389/fmed.2022.994467
Tumor stroma reaction
Manuscript
Source code
SHP2 inhibition enhances Yes-associated protein–mediated liver regeneration in murine partial hepatectomy models
SHP2 inhibition enhances Yes-associated protein–mediated liver regeneration in murine partial hepatectomy models
Ryan D. Watkins, EeeLN H. Buckarma, Jennifer L. Tomlinson, Chantal E. McCabe, Jennifer A. Yonkus, ..., Patrick P. Starlinger, Keith D. Robertson, Chen Wang, Gregory J. Gores, Rory L. Smoot
JCI Insight   ·   08 Aug 2022   ·   doi:10.1172/jci.insight.159930
PO2RDF: representation of real-world data for precision oncology using resource description framework
PO2RDF: representation of real-world data for precision oncology using resource description framework
Yiqing Zhao, Anastasios Dimou, Feichen Shen, Nansu Zong, Jaime I. Davila, Hongfang Liu, Chen Wang
BMC Medical Genomics   ·   30 Jul 2022   ·   doi:10.1186/s12920-022-01314-9
Cross-lingual data transformation and combination for text classification
Cross-lingual data transformation and combination for text classification
[no author info]
arXiv   ·   07 Jun 2022   ·   eid:2-s2.0-85094353479
Adverse Drug Event-based Stratification of Tumor Mutations: A Case Study of Breast Cancer Patients Receiving Aromatase Inhibitors
Adverse Drug Event-based Stratification of Tumor Mutations: A Case Study of Breast Cancer Patients Receiving Aromatase Inhibitors
[no author info]
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium   ·   25 May 2022   ·   eid:2-s2.0-84964312834
Bioinformatics strategies for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing
Bioinformatics strategies for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing
[no author info]
BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015   ·   24 May 2022   ·   eid:2-s2.0-84938820322
Excerno: Filtering Mutations Caused by the Clinical Archival Process in Sequencing Data
Excerno: Filtering Mutations Caused by the Clinical Archival Process in Sequencing Data
Audrey Mitchell, Marco Ruiz, Soua Yang, Chen Wang, Jaime Davila
Computational Advances in Bio and Medical Sciences   ·   01 Jan 2022   ·   doi:10.1007/978-3-031-17531-2_3
DNA Methylation Profiles of Ovarian Clear Cell Carcinoma
DNA Methylation Profiles of Ovarian Clear Cell Carcinoma
Julie M. Cunningham, Stacey J. Winham, Chen Wang, Britta Weiglt, Zhuxuan Fu, ..., Kate Lawrenson, Elli Papaemmanuil, Kelly L. Bolton, Francesmary Modugno, Ellen L. Goode
Cancer Epidemiology, Biomarkers & Prevention   ·   01 Jan 2022   ·   doi:10.1158/1055-9965.EPI-21-0677

2021

Semi-Supervised Topological Analysis for Elucidating Hidden Structures in High-Dimensional Transcriptome Datasets
Semi-Supervised Topological Analysis for Elucidating Hidden Structures in High-Dimensional Transcriptome Datasets
Tianshu Feng, Jaime I. Davila, Yuanhang Liu, Sangdi Lin, Shuai Huang, Chen Wang
IEEE/ACM Transactions on Computational Biology and Bioinformatics   ·   01 Jul 2021   ·   doi:10.1109/TCBB.2019.2950657
Leveraging Genetic Reports and Electronic Health Records for the Prediction of Primary Cancers: Algorithm Development and Validation Study
Leveraging Genetic Reports and Electronic Health Records for the Prediction of Primary Cancers: Algorithm Development and Validation Study
Nansu Zong, Victoria Ngo, Daniel J Stone, Andrew Wen, Yiqing Zhao, Yue Yu, Sijia Liu, Ming Huang, Chen Wang, Guoqian Jiang
JMIR Medical Informatics   ·   25 May 2021   ·   doi:10.2196/23586
PO2RDF: Representation of Real-world Data for Precision Oncology Using Resource Description Framework
PO2RDF: Representation of Real-world Data for Precision Oncology Using Resource Description Framework
Yiqing ZHAO, Anastasios Dimou, Feichen Shen, Nansu Zong, Jaime I. Davila, Hongfang Liu, Chen Wang
Research Square Platform LLC   ·   11 Feb 2021   ·   doi:10.21203/rs.3.rs-219654/v1
Generating real-world evidence from unstructured clinical notes to examine clinical utility of genetic tests: use case in BRCAness
Generating real-world evidence from unstructured clinical notes to examine clinical utility of genetic tests: use case in BRCAness
Yiqing Zhao, Saravut J. Weroha, Ellen L. Goode, Hongfang Liu, Chen Wang
BMC Medical Informatics and Decision Making   ·   06 Jan 2021   ·   doi:10.1186/s12911-020-01364-y

2020

Generating Real-world Evidence from Unstructured Clinical Notes to Examine Clinical Utility of Genetic Tests: Use Case in BRCAness
Generating Real-world Evidence from Unstructured Clinical Notes to Examine Clinical Utility of Genetic Tests: Use Case in BRCAness
Yiqing ZHAO, Saravut J Weroha, Ellen Goode, Hongfang Liu, Chen Wang
Research Square Platform LLC   ·   17 Dec 2020   ·   doi:10.21203/rs.3.rs-41553/v3
Image-to-image translation for automatic ink removal in whole slide images
Image-to-image translation for automatic ink removal in whole slide images
Jun Jiang, Naresh Prodduturi, David Chen, Qiangqiang Gu, Thomas Flotte, Qianjin Feng, Steven Hart
Journal of Medical Imaging   ·   16 Oct 2020   ·   doi:10.1117/1.JMI.7.5.057502
Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE)
Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE)
Aline Talhouk, Joshy George, Chen Wang, Timothy Budden, Tuan Zea Tan, ..., Ellen L. Goode, Susan J. Ramus, Jennifer A. Doherty, David D. Bowtell, Michael S. Anglesio
Clinical Cancer Research   ·   15 Oct 2020   ·   doi:10.1158/1078-0432.CCR-20-0103
Generating Real-world Evidence from Unstructured Clinical Notes to Examine Clinical Utility of Genetic Tests: Use Case in BRCAness
Generating Real-world Evidence from Unstructured Clinical Notes to Examine Clinical Utility of Genetic Tests: Use Case in BRCAness
Yiqing ZHAO, Saravut J Weroha, Ellen Goode, Hongfang Liu, Chen Wang
Research Square Platform LLC   ·   18 Sep 2020   ·   doi:10.21203/rs.3.rs-41553/v2
Targeting tumor-associated macrophages and granulocytic myeloid-derived suppressor cells augments PD-1 blockade in cholangiocarcinoma
Targeting tumor-associated macrophages and granulocytic myeloid-derived suppressor cells augments PD-1 blockade in cholangiocarcinoma
Emilien Loeuillard, Jingchun Yang, EeeLN Buckarma, Juan Wang, Yuanhang Liu, ..., Chen Wang, Rondell P. Graham, Rory L. Smoot, Haidong Dong, Sumera Ilyas
Journal of Clinical Investigation   ·   14 Sep 2020   ·   doi:10.1172/JCI137110
Leveraging Genetic Reports and Electronic Health Records for the Prediction of Primary Cancers: Algorithm Development and Validation Study (Preprint)
Leveraging Genetic Reports and Electronic Health Records for the Prediction of Primary Cancers: Algorithm Development and Validation Study (Preprint)
Nansu Zong, Victoria Ngo, Daniel J Stone, Andrew Wen, Yiqing Zhao, Yue Yu, Sijia Liu, Ming Huang, Chen Wang, Guoqian Jiang
JMIR Publications Inc.   ·   17 Aug 2020   ·   doi:10.2196/preprints.23586
Generating Real-World Evidence from Unstructured Clinical Notes to Examine Clinical Utility of Genetic Tests: Use Case in BRCAness
Generating Real-World Evidence from Unstructured Clinical Notes to Examine Clinical Utility of Genetic Tests: Use Case in BRCAness
Yiqing ZHAO, Saravut J Weroha, Ellen Goode, Hongfang Liu, Chen Wang
Research Square Platform LLC   ·   21 Jul 2020   ·   doi:10.21203/rs.3.rs-41553/v1
The YAP-Interacting Phosphatase SHP2 Can Regulate Transcriptional Coactivity and Modulate Sensitivity to Chemotherapy in Cholangiocarcinoma
The YAP-Interacting Phosphatase SHP2 Can Regulate Transcriptional Coactivity and Modulate Sensitivity to Chemotherapy in Cholangiocarcinoma
EeeLN H. Buckarma, Nathan W. Werneburg, Caitlin B. Conboy, Ayano Kabashima, Daniel R. O'Brien, Chen Wang, Sumera I. Ilyas, Rory L. Smoot
Molecular Cancer Research   ·   09 Jul 2020   ·   doi:10.1158/1541-7786.MCR-20-0165
Combining copy number, methylation markers, and mutations as a panel for endometrial cancer detection via intravaginal tampon collection
Combining copy number, methylation markers, and mutations as a panel for endometrial cancer detection via intravaginal tampon collection
Ajleeta Sangtani, Chen Wang, Amy Weaver, Nicole L. Hoppman, Sarah E. Kerr, ..., Karl C. Podratz, Nicolas Wentzensen, John B. Kisiel, Mark E. Sherman, Jamie N. Bakkum-Gamez
Gynecologic Oncology   ·   01 Feb 2020   ·   doi:10.1016/j.ygyno.2019.11.028
Dilution of Molecular–Pathologic Gene Signatures by Medically Associated Factors Might Prevent Prediction of Resection Status After Debulking Surgery in Patients With Advanced Ovarian Cancer
Dilution of Molecular–Pathologic Gene Signatures by Medically Associated Factors Might Prevent Prediction of Resection Status After Debulking Surgery in Patients With Advanced Ovarian Cancer
Florian Heitz, Stefan Kommoss, Roshan Tourani, Anthony Grandelis, Locke Uppendahl, ..., Philipp Harter, Sean C. Dowdy, Boris J. Winterhoff, Jacobus Pfisterer, Andreas du Bois
Clinical Cancer Research   ·   01 Jan 2020   ·   doi:10.1158/1078-0432.CCR-19-1741

2019

Hippocampus Segmentation Based on Iterative Local Linear Mapping With Representative and Local Structure-Preserved Feature Embedding
Hippocampus Segmentation Based on Iterative Local Linear Mapping With Representative and Local Structure-Preserved Feature Embedding
Shumao Pang, Qianjin Feng, Zhentai Lu, Jun Jiang, Lei Zhao, Liyan Lin, Xueli Li, Tao Lian, Meiyan Huang, Wei Yang
IEEE Transactions on Medical Imaging   ·   01 Oct 2019   ·   doi:10.1109/TMI.2019.2906727
Genes associated with bowel metastases in ovarian cancer
Genes associated with bowel metastases in ovarian cancer
Andrea Mariani, Chen Wang, Ann L. Oberg, Shaun M. Riska, Michelle Torres, ..., Kimberly R. Kalli, Lynn C. Hartmann, Scott H. Kaufmann, Ellen L. Goode, Viji Shridhar
Gynecologic Oncology   ·   01 Sep 2019   ·   doi:10.1016/j.ygyno.2019.06.010
Robust hierarchical density estimation and regression for re-stained histological whole slide image co-registration
Robust hierarchical density estimation and regression for re-stained histological whole slide image co-registration
Jun Jiang, Nicholas B. Larson, Naresh Prodduturi, Thomas J. Flotte, Steven N. Hart
PLOS ONE   ·   24 Jul 2019   ·   doi:10.1371/journal.pone.0220074
Use of FFPE-derived DNA in next generation sequencing: DNA extraction methods
Use of FFPE-derived DNA in next generation sequencing: DNA extraction methods
Samantha J. McDonough, Aditya Bhagwate, Zhifu Sun, Chen Wang, Michael Zschunke, Joshua A. Gorman, Karla J. Kopp, Julie M. Cunningham
PLOS ONE   ·   11 Apr 2019   ·   doi:10.1371/journal.pone.0211400
Robust Hierarchical Density Estimation and Regression for Re-stained Histological Whole Slide Image Co-registration
Robust Hierarchical Density Estimation and Regression for Re-stained Histological Whole Slide Image Co-registration
Jun Jiang, Nicholas B. Larson, Naresh Prodduturi, Thomas J. Flotte, Steven N. Hart
Cold Spring Harbor Laboratory   ·   06 Mar 2019   ·   doi:10.1101/565564
Automatic Nasopharyngeal Carcinoma Segmentation Using Fully Convolutional Networks with Auxiliary Paths on Dual-Modality PET-CT Images
Automatic Nasopharyngeal Carcinoma Segmentation Using Fully Convolutional Networks with Auxiliary Paths on Dual-Modality PET-CT Images
Lijun Zhao, Zixiao Lu, Jun Jiang, Yujia Zhou, Yi Wu, Qianjin Feng
Journal of Digital Imaging   ·   04 Feb 2019   ·   doi:10.1007/s10278-018-00173-0
Mesenchymal molecular subtype is an independent predictor of severe postoperative complications after primary debulking surgery for advanced ovarian cancer
Mesenchymal molecular subtype is an independent predictor of severe postoperative complications after primary debulking surgery for advanced ovarian cancer
Diogo Torres, Amanika Kumar, Jamie N. Bakkum-Gamez, Amy L. Weaver, Michaela E. McGree, Chen Wang, Carrie L. Langstraat, William A. Cliby
Gynecologic Oncology   ·   01 Feb 2019   ·   doi:10.1016/j.ygyno.2018.11.019
Cancer-associated stroma significantly contributes to the mesenchymal subtype signature of serous ovarian cancer
Cancer-associated stroma significantly contributes to the mesenchymal subtype signature of serous ovarian cancer
Qing Zhang, Chen Wang, William A. Cliby
Gynecologic Oncology   ·   01 Feb 2019   ·   doi:10.1016/j.ygyno.2018.11.014
Use of FFPE-Derived DNA in Next Generation Sequencing: DNA extraction methods
Use of FFPE-Derived DNA in Next Generation Sequencing: DNA extraction methods
Samantha J. McDonough, Aditya Bhagwate, Zhifu Sun, Chen Wang, Michael Zschunke, Joshua A. Gorman, Karla J. Kopp, Julie M. Cunningham
Cold Spring Harbor Laboratory   ·   15 Jan 2019   ·   doi:10.1101/521534

2018

Factors that influence survival in high-grade serous ovarian cancer: A complex relationship between molecular subtype, disease dissemination, and operability
Factors that influence survival in high-grade serous ovarian cancer: A complex relationship between molecular subtype, disease dissemination, and operability
Diogo Torres, Chen Wang, Amanika Kumar, Jamie N. Bakkum-Gamez, Amy L. Weaver, Michaela E. McGree, Gottfried E. Konecny, Ellen L. Goode, William A. Cliby
Gynecologic Oncology   ·   01 Aug 2018   ·   doi:10.1016/j.ygyno.2018.06.002
Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
Theo A. Knijnenburg, Linghua Wang, Michael T. Zimmermann, Nyasha Chambwe, Galen F. Gao, ..., Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze
Cell Reports   ·   03 Apr 2018   ·   doi:10.1016/j.celrep.2018.03.076
DNA damage repair, Genomic and Molecular Landscape, TCGA
Manuscript
Supplemental Data
Robustness versus disease differentiation when varying parameter settings in radiomics features: application to nasopharyngeal PET/CT
Robustness versus disease differentiation when varying parameter settings in radiomics features: application to nasopharyngeal PET/CT
Wenbing Lv, Qingyu Yuan, Quanshi Wang, Jianhua Ma, Jun Jiang, Wei Yang, Qianjin Feng, Wufan Chen, Arman Rahmim, Lijun Lu
European Radiology   ·   08 Mar 2018   ·   doi:10.1007/s00330-018-5343-0

2017

Intraperitoneal disease dissemination patterns are associated with residual disease, extent of surgery, and molecular subtypes in advanced ovarian cancer
Intraperitoneal disease dissemination patterns are associated with residual disease, extent of surgery, and molecular subtypes in advanced ovarian cancer
Diogo Torres, Amanika Kumar, Sumer K. Wallace, Jamie N. Bakkum-Gamez, Gottfried E. Konecny, Amy L. Weaver, Michaela E. McGree, Ellen L. Goode, William A. Cliby, Chen Wang
Gynecologic Oncology   ·   01 Dec 2017   ·   doi:10.1016/j.ygyno.2017.09.021
Doublecortin domain containing protein 2 (DCDC2) genetic variants in primary sclerosing cholangitis
Doublecortin domain containing protein 2 (DCDC2) genetic variants in primary sclerosing cholangitis
Angela C. Cheung, Brian D. Juran, Raymond M. Moore, Nicholas F. LaRusso, Konstantinos N. Lazaridis
Journal of Hepatology   ·   01 Sep 2017   ·   doi:10.1016/j.jhep.2017.02.036
Hippocampus Segmentation Based on Local Linear Mapping
Hippocampus Segmentation Based on Local Linear Mapping
Shumao Pang, Jun Jiang, Zhentai Lu, Xueli Li, Wei Yang, Meiyan Huang, Yu Zhang, Yanqiu Feng, Wenhua Huang, Qianjin Feng
Scientific Reports   ·   03 Apr 2017   ·   doi:10.1038/srep45501

2016

Robustness of Radiomic Features in [11C]Choline and [18F]FDG PET/CT Imaging of Nasopharyngeal Carcinoma: Impact of Segmentation and Discretization
Robustness of Radiomic Features in [11C]Choline and [18F]FDG PET/CT Imaging of Nasopharyngeal Carcinoma: Impact of Segmentation and Discretization
Lijun Lu, Wenbing Lv, Jun Jiang, Jianhua Ma, Qianjin Feng, Arman Rahmim, Wufan Chen
Molecular Imaging and Biology   ·   20 Jun 2016   ·   doi:10.1007/s11307-016-0973-6
Accurate clinical detection of hemoglobin variants via combined top-down and bottom-up proteomics
Accurate clinical detection of hemoglobin variants via combined top-down and bottom-up proteomics
[no author info]
ASMS 63th Conference Proceedings   ·   09 Jun 2016   ·   :
Retrieval of Brain Tumors by Adaptive Spatial Pooling and Fisher Vector Representation
Retrieval of Brain Tumors by Adaptive Spatial Pooling and Fisher Vector Representation
Jun Cheng, Wei Yang, Meiyan Huang, Wei Huang, Jun Jiang, ..., Ru Yang, Jie Zhao, Yanqiu Feng, Qianjin Feng, Wufan Chen
PLOS ONE   ·   06 Jun 2016   ·   doi:10.1371/journal.pone.0157112
Gene-expression signatures in ovarian cancer: Promise and challenges for patient stratification
Gene-expression signatures in ovarian cancer: Promise and challenges for patient stratification
Gottfried E. Konecny, Boris Winterhoff, Chen Wang
Gynecologic Oncology   ·   01 May 2016   ·   doi:10.1016/j.ygyno.2016.01.026
Gene expression, methylation and neuropathology correlations at progressive supranuclear palsy risk loci
Gene expression, methylation and neuropathology correlations at progressive supranuclear palsy risk loci
Mariet Allen, Jeremy D. Burgess, Travis Ballard, Daniel Serie, Xue Wang, ..., Yan Asmann, Tamas Ordog, Julia Crook, Dennis Dickson, Nilüfer Ertekin-Taner
Acta Neuropathologica   ·   26 Apr 2016   ·   doi:10.1007/s00401-016-1576-7
Genes associated with histopathologic features of triple negative breast tumors predict molecular subtypes
Genes associated with histopathologic features of triple negative breast tumors predict molecular subtypes
Kristen S. Purrington, Daniel W. Visscher, Chen Wang, Drakoulis Yannoukakos, Ute Hamann, ..., Wei Zheng, Arto Mannermaa, Diana M. Eccles, Celine M. Vachon, Fergus J. Couch
Breast Cancer Research and Treatment   ·   15 Apr 2016   ·   doi:10.1007/s10549-016-3775-2
Molecular classification of high grade endometrioid and clear cell ovarian cancer using TCGA gene expression signatures
Molecular classification of high grade endometrioid and clear cell ovarian cancer using TCGA gene expression signatures
Boris Winterhoff, Habib Hamidi, Chen Wang, Kimberly R. Kalli, Brooke L. Fridley, ..., Sean Dowdy, Bobbie S. Gostout, Gary L. Keeney, Ellen L. Goode, Gottfried E. Konecny
Gynecologic Oncology   ·   01 Apr 2016   ·   doi:10.1016/j.ygyno.2016.02.023
Label-Free Proteomic Analysis of Protein Changes in the Striatum during Chronic Ethanol Use and Early Withdrawal
Label-Free Proteomic Analysis of Protein Changes in the Striatum during Chronic Ethanol Use and Early Withdrawal
Jennifer R. Ayers-Ringler, Alfredo Oliveros, Yanyan Qiu, Daniel M. Lindberg, David J. Hinton, Raymond M. Moore, Surendra Dasari, Doo-Sup Choi
Frontiers in Behavioral Neuroscience   ·   11 Mar 2016   ·   doi:10.3389/fnbeh.2016.00046
Germline polymorphisms in an enhancer of <i>PSIP1</i> are associated with progression-free survival in epithelial ovarian cancer
Germline polymorphisms in an enhancer of PSIP1 are associated with progression-free survival in epithelial ovarian cancer
Juliet D. French, Sharon E. Johnatty, Yi Lu, Jonathan Beesley, Bo Gao, ..., Kerstin B. Meyer, Georgia Chenevix-Trench, Anna deFazio, Stacey L. Edwards, Stuart MacGregor
Oncotarget   ·   31 Jan 2016   ·   doi:10.18632/oncotarget.7047
Prevalence of Pathogenic Mutations in Cancer Predisposition Genes among Pancreatic Cancer Patients
Prevalence of Pathogenic Mutations in Cancer Predisposition Genes among Pancreatic Cancer Patients
Chunling Hu, Steven N. Hart, William R. Bamlet, Raymond M. Moore, Kannabiran Nandakumar, Bruce W. Eckloff, Yean K. Lee, Gloria M. Petersen, Robert R. McWilliams, Fergus J. Couch
Cancer Epidemiology, Biomarkers & Prevention   ·   01 Jan 2016   ·   doi:10.1158/1055-9965.EPI-15-0455

2015

Gene signature model for breast cancer risk prediction for women with sclerosing adenosis
Gene signature model for breast cancer risk prediction for women with sclerosing adenosis
Amy C. Degnim, Aziza Nassar, Melody Stallings-Mann, S. Keith Anderson, Ann L. Oberg, ..., Stacey J. Winham, Marlene H. Frost, Lynn C. Hartmann, Daniel W. Visscher, Derek C. Radisky
Breast Cancer Research and Treatment   ·   23 Jul 2015   ·   doi:10.1007/s10549-015-3513-1
Variability of Gross Tumor Volume in Nasopharyngeal Carcinoma Using 11C-Choline and 18F-FDG PET/CT
Variability of Gross Tumor Volume in Nasopharyngeal Carcinoma Using 11C-Choline and 18F-FDG PET/CT
Jun Jiang, Hubing Wu, Meiyan Huang, Yao Wu, Quanshi Wang, Jianqi Zhao, Wei Yang, Wufan Chen, Qianjin Feng
PLOS ONE   ·   10 Jul 2015   ·   doi:10.1371/journal.pone.0131801
PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data
PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data
Steven N. Hart, Raymond M. Moore, Michael T. Zimmermann, Gavin R. Oliver, Jan B. Egan, Alan H. Bryce, Jean-Pierre A. Kocher
PeerJ   ·   19 May 2015   ·   doi:10.7717/peerj.970

2014

Genetic diversity of newly diagnosed follicular lymphoma
Genetic diversity of newly diagnosed follicular lymphoma
Y W Asmann, M J Maurer, C Wang, V Sarangi, S M Ansell, ..., Z-Z Yang, S L Slager, T M Habermann, J R Cerhan, A J Novak
Blood Cancer Journal   ·   31 Oct 2014   ·   doi:10.1038/bcj.2014.80
Brain Tumor Segmentation Based on Local Independent Projection-Based Classification
Brain Tumor Segmentation Based on Local Independent Projection-Based Classification
Meiyan Huang, Wei Yang, Yao Wu, Jun Jiang, Wufan Chen, Qianjin Feng
IEEE Transactions on Biomedical Engineering   ·   01 Oct 2014   ·   doi:10.1109/TBME.2014.2325410
Prognostic and Therapeutic Relevance of Molecular Subtypes in High-Grade Serous Ovarian Cancer
Prognostic and Therapeutic Relevance of Molecular Subtypes in High-Grade Serous Ovarian Cancer
Gottfried E. Konecny, Chen Wang, Habib Hamidi, Boris Winterhoff, Kimberly R. Kalli, ..., Gary Keeney, He-Jing Wang, Lynn C. Hartmann, Dennis J. Slamon, Ellen L. Goode
JNCI: Journal of the National Cancer Institute   ·   30 Sep 2014   ·   doi:10.1093/jnci/dju249
MACE: model based analysis of ChIP-exo
MACE: model based analysis of ChIP-exo
Liguo Wang, Junsheng Chen, Chen Wang, Liis Uusküla-Reimand, Kaifu Chen, ..., Stephen T. Wu, Haojie Huang, Michael D. Wilson, Jean-Pierre A. Kocher, Wei Li
Nucleic Acids Research   ·   23 Sep 2014   ·   doi:10.1093/nar/gku846
RVboost: RNA-seq variants prioritization using a boosting method
RVboost: RNA-seq variants prioritization using a boosting method
Chen Wang, Jaime I. Davila, Saurabh Baheti, Aditya V. Bhagwate, Xue Wang, ..., Andrew L. Feldman, Anne J. Novak, James R. Cerhan, E. Aubrey Thompson, Yan W. Asmann
Bioinformatics   ·   27 Aug 2014   ·   doi:10.1093/bioinformatics/btu577
Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer
Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer
Debarshi Roy, Susmita Mondal, Chen Wang, Xiaoping He, Ashwani Khurana, ..., Ann L Oberg, Edward D Karoly, Lauren N Bell, Jeremy Chien, Viji Shridhar
Cancer & Metabolism   ·   18 Aug 2014   ·   doi:10.1186/2049-3002-2-13
HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data
HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data
Huihuang Yan, Jared Evans, Mike Kalmbach, Raymond Moore, Sumit Middha, ..., Aditya Bhagwate, Ying Li, Zhifu Sun, Xianfeng Chen, Jean-Pierre A Kocher
BMC Bioinformatics   ·   15 Aug 2014   ·   doi:10.1186/1471-2105-15-280
Content-Based Image Retrieval Using Spatial Layout Information in Brain Tumor T1-Weighted Contrast-Enhanced MR Images
Content-Based Image Retrieval Using Spatial Layout Information in Brain Tumor T1-Weighted Contrast-Enhanced MR Images
Meiyan Huang, Wei Yang, Yao Wu, Jun Jiang, Yang Gao, Yang Chen, Qianjin Feng, Wufan Chen, Zhentai Lu
PLoS ONE   ·   16 Jul 2014   ·   doi:10.1371/journal.pone.0102754
Prostate Segmentation Based on Variant Scale Patch and Local Independent Projection
Prostate Segmentation Based on Variant Scale Patch and Local Independent Projection
Yao Wu, Guoqing Liu, Meiyan Huang, Jiacheng Guo, Jun Jiang, Wei Yang, Wufan Chen, Qianjin Feng
IEEE Transactions on Medical Imaging   ·   01 Jun 2014   ·   doi:10.1109/TMI.2014.2308901
Tumor Hypomethylation at 6p21.3 Associates with Longer Time to Recurrence of High-Grade Serous Epithelial Ovarian Cancer
Tumor Hypomethylation at 6p21.3 Associates with Longer Time to Recurrence of High-Grade Serous Epithelial Ovarian Cancer
Chen Wang, Mine S. Cicek, Bridget Charbonneau, Kimberly R. Kalli, Sebastian M. Armasu, ..., Daniel W. Visscher, Julie M. Cunningham, Keith L. Knutson, Brooke L. Fridley, Ellen L. Goode
Cancer Research   ·   29 May 2014   ·   doi:10.1158/0008-5472.CAN-13-3198
PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data
PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data
Chen Wang, Jared M. Evans, Aditya V. Bhagwate, Naresh Prodduturi, Vivekananda Sarangi, ..., Matthew J. Maurer, Anne J. Novak, Susan L. Slager, James R. Cerhan, Yan W. Asmann
Bioinformatics   ·   29 May 2014   ·   doi:10.1093/bioinformatics/btu363
Brain extraction based on locally linear representation-based classification
Brain extraction based on locally linear representation-based classification
Meiyan Huang, Wei Yang, Jun Jiang, Yao Wu, Yu Zhang, Wufan Chen, Qianjin Feng
NeuroImage   ·   01 May 2014   ·   doi:10.1016/j.neuroimage.2014.01.059
Methylation of leukocyte DNA and ovarian cancer: relationships with disease status and outcome
Methylation of leukocyte DNA and ovarian cancer: relationships with disease status and outcome
Brooke L Fridley, Sebastian M Armasu, Mine S Cicek, Melissa C Larson, Chen Wang, ..., David N Rider, Viji Shridhar, Janet E Olson, Julie M Cunningham, Ellen L Goode
BMC Medical Genomics   ·   28 Apr 2014   ·   doi:10.1186/1755-8794-7-21
Large-Scale Evaluation of Common Variation in Regulatory T Cell–Related Genes and Ovarian Cancer Outcome
Large-Scale Evaluation of Common Variation in Regulatory T Cell–Related Genes and Ovarian Cancer Outcome
Bridget Charbonneau, Kirsten B. Moysich, Kimberly R. Kalli, Ann L. Oberg, Robert A. Vierkant, ..., Roberta B. Ness, Kunle Odunsi, Lara E. Sucheston, Keith L. Knutson, Ellen L. Goode
Cancer Immunology Research   ·   01 Apr 2014   ·   doi:10.1158/2326-6066.CIR-13-0136
The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation
The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation
Jean-Pierre A. Kocher, Daniel J. Quest, Patrick Duffy, Michael A. Meiners, Raymond M. Moore, David Rider, Asif Hossain, Steven N. Hart, Valentin Dinu
Bioinformatics   ·   10 Mar 2014   ·   doi:10.1093/bioinformatics/btu137
Clinical Characteristics of Ovarian Cancer Classified by BRCA1, BRCA2 and RAD51C Status
Clinical Characteristics of Ovarian Cancer Classified by BRCA1, BRCA2 and RAD51C Status
J. M. Cunningham, M. S. Cicek, N. B. Larson, J. Davila, C. Wang, ..., K. R. Kalli, N. M. Lindor, B. L. Fridley, P. P. D. Pharoah, E. L. Goode
Scientific Reports   ·   07 Feb 2014   ·   doi:10.1038/srep04026
Multimodal Brain-Tumor Segmentation Based on Dirichlet Process Mixture Model with Anisotropic Diffusion and Markov Random Field Prior
Multimodal Brain-Tumor Segmentation Based on Dirichlet Process Mixture Model with Anisotropic Diffusion and Markov Random Field Prior
Yisu Lu, Jun Jiang, Wei Yang, Qianjin Feng, Wufan Chen
Computational and Mathematical Methods in Medicine   ·   01 Jan 2014   ·   doi:10.1155/2014/717206

2013

SoftSearch: Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations
SoftSearch: Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations
Steven N. Hart, Vivekananda Sarangi, Raymond Moore, Saurabh Baheti, Jaysheel D. Bhavsar, Fergus J. Couch, Jean-Pierre A. Kocher
PLoS ONE   ·   16 Dec 2013   ·   doi:10.1371/journal.pone.0083356
3D brain tumor segmentation in multimodal MR images based on learning population- and patient-specific feature sets
3D brain tumor segmentation in multimodal MR images based on learning population- and patient-specific feature sets
Jun Jiang, Yao Wu, Meiyan Huang, Wei Yang, Wufan Chen, Qianjin Feng
Computerized Medical Imaging and Graphics   ·   01 Oct 2013   ·   doi:10.1016/j.compmedimag.2013.05.007
Integrated genomic characterization of endometrial carcinoma
Integrated genomic characterization of endometrial carcinoma
Douglas A. Levine
Nature   ·   01 May 2013   ·   doi:10.1038/nature12113
Epigenome-wide ovarian cancer analysis identifies a methylation profile differentiating clear-cell histology with epigenetic silencing of the HERG K+ channel
Epigenome-wide ovarian cancer analysis identifies a methylation profile differentiating clear-cell histology with epigenetic silencing of the HERG K+ channel
Mine S. Cicek, Devin C. Koestler, Brooke L. Fridley, Kimberly R. Kalli, Sebastian M. Armasu, ..., Lynn C. Hartmann, Marina Bibikova, Jeremy Chien, Julie M. Cunningham, Ellen L. Goode
Human Molecular Genetics   ·   09 Apr 2013   ·   doi:10.1093/hmg/ddt160
Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk
Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk
Fergus J. Couch, Xianshu Wang, Lesley McGuffog, Andrew Lee, Curtis Olswold, ..., Vernon S. Pankratz, Kenneth Offit, Douglas F. Easton, Georgia Chenevix-Trench, Antonis C. Antoniou
PLoS Genetics   ·   27 Mar 2013   ·   doi:10.1371/journal.pgen.1003212
Inherited Variants in Regulatory T Cell Genes and Outcome of Ovarian Cancer
Inherited Variants in Regulatory T Cell Genes and Outcome of Ovarian Cancer
Ellen L. Goode, Melissa DeRycke, Kimberly R. Kalli, Ann L. Oberg, Julie M. Cunningham, ..., Lara E. Sucheston, Kunle Odunsi, Lynn C. Hartmann, Kirsten B. Moysich, Keith L. Knutson
PLoS ONE   ·   30 Jan 2013   ·   doi:10.1371/journal.pone.0053903
Semi-automatic Segmentation of Brain Tumors Using Population and Individual Information
Semi-automatic Segmentation of Brain Tumors Using Population and Individual Information
Yao Wu, Wei Yang, Jun Jiang, Shuanqian Li, Qianjin Feng, Wufan Chen
Journal of Digital Imaging   ·   15 Jan 2013   ·   doi:10.1007/s10278-012-9568-1

2012

Computational analysis of muscular dystrophy sub-types using a novel integrative scheme
Computational analysis of muscular dystrophy sub-types using a novel integrative scheme
Chen Wang, Sook Ha, Jianhua Xuan, Yue Wang, Eric Hoffman
Neurocomputing   ·   01 Sep 2012   ·   doi:10.1016/j.neucom.2011.08.037
Regulatory component analysis: A semi-blind extraction approach to infer gene regulatory networks with imperfect biological knowledge
Regulatory component analysis: A semi-blind extraction approach to infer gene regulatory networks with imperfect biological knowledge
Chen Wang, Jianhua Xuan, Ie-Ming Shih, Robert Clarke, Yue Wang
Signal Processing   ·   01 Aug 2012   ·   doi:10.1016/j.sigpro.2011.11.028
Detecting aberrant signal transduction pathways from high-throughput data using GIST algorithm
Detecting aberrant signal transduction pathways from high-throughput data using GIST algorithm
Jinghua Gu, Jianhua Xuan, Chen Wang, Li Chen, Tian-Li Wang, Ie-Ming Shih
2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)   ·   01 May 2012   ·   doi:10.1109/CIBCB.2012.6217240
Reconstruction of Transcription Regulatory Networks by Stability-Based Network Component Analysis
Reconstruction of Transcription Regulatory Networks by Stability-Based Network Component Analysis
Xi Chen, Chen Wang, Ayesha N. Shajahan, Rebecca B. Riggins, Robert Clarke, Jianhua Xuan
Bioinformatics Research and Applications   ·   01 Jan 2012   ·   doi:10.1007/978-3-642-30191-9_4

2011

GIST: A Gibbs sampler to identify intracellular signal transduction pathways
GIST: A Gibbs sampler to identify intracellular signal transduction pathways
Jinghua Gu, Chen Wang, Le-Ming Shih, Tian-Li Wang, Yue Wang, R. Clarke, Jianhua Xuan
2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society   ·   01 Aug 2011   ·   doi:10.1109/IEMBS.2011.6090677

2010

Distinct DNA methylation profiles in ovarian serous neoplasms and their implications in ovarian carcinogenesis
Distinct DNA methylation profiles in ovarian serous neoplasms and their implications in ovarian carcinogenesis
Ie-Ming Shih, Li Chen, Chen C. Wang, Jinghua Gu, Ben Davidson, Leslie Cope, Robert J. Kurman, Jianhua Xuan, Tian-Li Wang
American Journal of Obstetrics and Gynecology   ·   01 Dec 2010   ·   doi:10.1016/j.ajog.2010.08.003
Computational Analysis of Muscular Dystrophy Sub-types Using a Novel Integrative Scheme
Computational Analysis of Muscular Dystrophy Sub-types Using a Novel Integrative Scheme
Chen Wang, Sook Ha, Yue Wang, Jianhua Xuan, Eric Hoffman
2010 Ninth International Conference on Machine Learning and Applications   ·   01 Dec 2010   ·   doi:10.1109/ICMLA.2010.49
Knowledge-guided gene ranking by coordinative component analysis
Knowledge-guided gene ranking by coordinative component analysis
Chen Wang, Jianhua Xuan, Huai Li, Yue Wang, Ming Zhan, Eric P Hoffman, Robert Clarke
BMC Bioinformatics   ·   30 Mar 2010   ·   doi:10.1186/1471-2105-11-162

2009

Biomarker identification by knowledge-driven multilevel ICA and motif analysis
Biomarker identification by knowledge-driven multilevel ICA and motif analysis
Li Chen, Jianhua Xuan, Chen Wang, Yue Wang, Ie Ming Shih, Tian Li Wang, Zhen Zhang, Robert Clarke, Eric P. Hoffman
International Journal of Data Mining and Bioinformatics   ·   01 Jan 2009   ·   doi:10.1504/IJDMB.2009.029201

2008

Knowledge-guided multi-scale independent component analysis for biomarker identification
Knowledge-guided multi-scale independent component analysis for biomarker identification
Li Chen, Jianhua Xuan, Chen Wang, Ie-Ming Shih, Yue Wang, Zhen Zhang, Eric Hoffman, Robert Clarke
BMC Bioinformatics   ·   06 Oct 2008   ·   doi:10.1186/1471-2105-9-416
Motif-directed network component analysis for regulatory network inference
Motif-directed network component analysis for regulatory network inference
Chen Wang, Jianhua Xuan, Li Chen, Po Zhao, Yue Wang, Robert Clarke, Eric Hoffman
BMC Bioinformatics   ·   01 Feb 2008   ·   doi:10.1186/1471-2105-9-S1-S21

2007

Web-based parallel corpora for statistical machine translation
Web-based parallel corpora for statistical machine translation
Bo Li, Juan Liu, Wenjuan Shi
Sixth International Conference on Machine Learning and Applications (ICMLA 2007)   ·   01 Dec 2007   ·   doi:10.1109/ICMLA.2007.24

Integrative Network Component Analysis for Regulatory Network Reconstruction
Integrative Network Component Analysis for Regulatory Network Reconstruction
Chen Wang, Jianhua Xuan, Li Chen, Po Zhao, Yue Wang, Robert Clarke, Eric P. Hoffman
Bioinformatics Research and Applications   ·   [no date info]   ·   doi:10.1007/978-3-540-79450-9_19