Research

Increased Interaction between B Cells and CD3+ T Cells in Nonprogressors with Human Papillomavirus–Associated Oropharyngeal Squamous Cell Carcinoma

Kathleen R. Bartemes, Raymond M. Moore, Brenna C. Novotny, Kevin D. Pavelko, Will A. Sherman, ..., Linda X. Yin, Daniel J. Ma, Eric J. Moore, Kathryn M. Van Abel, David M. Routman

Clinical Cancer Research · 18 Mar 2025 · doi:10.1158/1078-0432.CCR-24-2425

Towards H&E Referenced Multiplex Immunofluorescence Interpretation: Spatial Co-localization, Cell Feature Validation, and Virtual H&E Generation

Chen Wang, Jun Jiang, Raymond Moore, Brenna Novotny, Ruifeng Guo, Zachary Fogarty, Yuanhang Liu, Ellen Goode, Stacey Winham, Svetomir Markovic

Springer Science and Business Media LLC · 06 Jan 2025 · doi:10.21203/rs.3.rs-5619126/v1

SpaFlow: a Nextflow pipeline for QC and clustering of MxIF datasets

Brenna C Novotny, Raymond Moore, Lynn Langit, David Haley, Rachel L Maus, ..., Caitlin Ward, Ray Guo, Ellen L Goode, Svetomir N Markovic, Chen Wang

Bioinformatics Advances · 26 Dec 2024 · doi:10.1093/bioadv/vbaf032

Melanoma-Derived Extracellular Vesicles Induce CD36-Mediated Pre-Metastatic Niche

Shankar Suman, Wendy K. Nevala, Alexey A. Leontovich, Caitlin Ward, James W. Jakub, ..., Raymond M. Moore, Jill M. Schimke, Fabrice Lucien-Matteoni, Sarah A. McLaughlin, Svetomir N. Markovic

Biomolecules · 11 Jul 2024 · doi:10.3390/biom14070837

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

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

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

Hanxuan Ye, Xianyang Zhang, Chen Wang, Ellen L. Goode, Jun Chen

Nature Computational Science · 23 Aug 2023 · doi:10.1038/s43588-023-00500-8

Single-nucleus RNA-sequencing of autosomal dominant Alzheimer disease and risk variant carriers

Logan Brase, Shih-Feng You, Ricardo D’Oliveira Albanus, Jorge L. Del-Aguila, Yaoyi Dai, ..., Greg T. Sutherland, Jonathan Kipnis, Celeste M. Karch, Bruno A. Benitez, Oscar Harari

Nature Communications · 21 Apr 2023 · doi:10.1038/s41467-023-37437-5

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

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

Brain cross-omics integration in Alzheimer’s disease

Abdallah M. Eteleeb, Brenna C. Novotny, Carolina Soriano Tarraga, Christopher Sohn, Eliza Dhungel, ..., John C. Morris, Celeste M. Karch, Richard J. Perrin, Bruno A. Benitez, Oscar Harari

Cold Spring Harbor Laboratory · 13 Dec 2022 · doi:10.1101/2022.12.10.22283295

Metabolomic and lipidomic signatures in autosomal dominant and late‐onset Alzheimer's disease brains

Brenna C. Novotny, Maria Victoria Fernandez, Ciyang Wang, John P. Budde, Kristy Bergmann, ..., Helena Chui, Celeste M. Karch, Carlos Cruchaga, Bruno A. Benitez, Oscar Harari

Alzheimer's & Dementia · 17 Oct 2022 · doi:10.1002/alz.12800

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

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

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

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

[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

[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

[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

Audrey Mitchell, Marco Ruiz, Soua Yang, Chen Wang, Jaime Davila

Lecture Notes in Computer Science · 01 Jan 2022 · doi:10.1007/978-3-031-17531-2_3

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

A landscape of the genetic and cellular heterogeneity in Alzheimer disease

Logan Brase, Shih-Feng You, Ricardo D’Oliveira Albanus, Jorge L. Del-Aguila, Yaoyi Dai, ..., Jonathan Kipnis, Celeste M Karch, Bruno A Benitez, Carlos Cruchaga, Oscar Harari

Cold Spring Harbor Laboratory · 02 Dec 2021 · doi:10.1101/2021.11.30.21267072

Metabolomic and lipidomic signatures in autosomal dominant and late-onset Alzheimer disease brains

Brenna C Novotny, Maria Victoria Fernandez, Ciyang Wang, John P Budde, Kristy Bergmann, ..., Helena Chui, Celeste M Karch, Bruno A Benitez, Carlos Cruchaga, Oscar Harari

Cold Spring Harbor Laboratory · 05 Nov 2021 · doi:10.1101/2021.11.04.21265941

Multi-tissue proteomics identifies molecular signatures for sporadic and genetically defined Alzheimer disease cases

Carlos Cruchaga, Yun Ju Sung, Chengran Yang, Fengxian Wang, Adam Suhy, ..., Helena Chui, Herve Rhinn, Celeste Karch, Suzanne Schindler, Oscar Harari

Research Square Platform LLC · 21 Oct 2021 · doi:10.21203/rs.3.rs-923492/v1

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

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

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

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

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

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)

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

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

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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[no author info]

ASMS 63th Conference Proceedings · 09 Jun 2016 · :

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Yisu Lu, Jun Jiang, Wei Yang, Qianjin Feng, Wufan Chen

Computational and Mathematical Methods in Medicine · 01 Jan 2014 · doi:10.1155/2014/717206

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

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

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

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

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

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

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

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

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

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

Xi Chen, Chen Wang, Ayesha N. Shajahan, Rebecca B. Riggins, Robert Clarke, Jianhua Xuan

Lecture Notes in Computer Science · 01 Jan 2012 · doi:10.1007/978-3-642-30191-9_4

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

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

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

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

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

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

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

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

Chen Wang, Jianhua Xuan, Li Chen, Po Zhao, Yue Wang, Robert Clarke, Eric P. Hoffman

Lecture Notes in Computer Science · [no date info] · doi:10.1007/978-3-540-79450-9_19

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