Cancer Informatics

Correlation between Gene Variants, Signaling Pathways, and Efficacy of Chemotherapy Drugs against Colon Cancers
Swarnendu Tripathi, Louiza Belkacemi, Margaret S. Cheung and Rathindra N. Bose
Cancer Informatics 2016:15 1-13
Original Research | Published on 20 Jan 2016

Integrating Multiscale Modeling with Drug Effects for Cancer Treatment
Xiangfang L. Li, Wasiu O. Oduola, Lijun Qian and Edward R. Dougherty
Cancer Informatics 2015:Suppl. 5 21-31
Review | Published on 13 Jan 2016

Introductory Editorial: Computer Simulation, Visualization, and Image Processing of Cancer Data and Processes
David Johnson, James Osborne, Zhihui Wang, Kostas Marias
Cancer Informatics 2015:Suppl. 4 105-108
Editorial | Published on 12 Jan 2016

Simulation of the Protein-Shedding Kinetics of a Fully Vascularized Tumor
Hermann B. Frieboes, Louis T. Curtis, Min Wu, Kian Kani and Parag Mallick
Cancer Informatics 2015:14 163-175
Original Research | Published on 20 Dec 2015

Improving Cancer Gene Expression Data Quality through a TCGA Data-Driven Evaluation of Identifier Filtering
Kevin K. McDade, Uma Chandran and Roger S. Day
Cancer Informatics 2015:14 149-161
Original Research | Published on 16 Dec 2015

Differential Expression Analysis for RNA-Seq: An Overview of Statistical Methods and Computational Software
Huei-Chung Huang, Yi Niu, and Li-Xuan Qin
Cancer Informatics 2015:Suppl. 1 57-67
Review | Published on 13 Dec 2015

The Impact of Age and Sex in DLBCL: Systems Biology Analyses Identify Distinct Molecular Changes and Signaling Networks
Afshin Beheshti, Donna Neuberg, J. Tyson McDonald, Charles R. Vanderburg and Andrew M. Evens
Cancer Informatics 2015:14 141-148
Rapid Communication | Published on 10 Dec 2015

Predictive Modeling of Drug Treatment in the Area of Personalized Medicine
Lesley A. Ogilvie, Christoph Wierling, Thomas Kessler, Hans Lehrach, and Bodo M. H. Lange
Cancer Informatics 2015:Suppl. 4 95-103
Commentary | Published on 06 Dec 2015

Characterizing Cancer-Specific Networks by Integrating TCGA Data
Yanxun Xu, Yitan Zhu, Peter Müller, Riten Mitra and Yuan Ji
Cancer Informatics 2014:Suppl. 2 125-131
Methodology | Published on 23 Nov 2015

Multigroup Equivalence Analysis for High-Dimensional Expression Data
Celeste Yang, Alfred A. Bartolucci and Xiangqin Cui
Cancer Informatics 2015:Suppl. 2 253-263
Methodology | Published on 23 Nov 2015

Multivariate Boosting for Integrative Analysis of High-Dimensional Cancer Genomic Data
Lie Xiong, Pei-Fen Kuan, Jianan Tian, Sunduz Keles, and Sijian Wang
Cancer Informatics 2014:Suppl. 7 123-131
Methodology | Published on 15 Nov 2015

Cancer Bioinformatic Methods to Infer Meaningful Data From Small-Size Cohorts
Nabila Bennani-Baiti and Idriss M. Bennani-Baiti
Cancer Informatics 2015:14 131-139
Review | Published on 02 Nov 2015

Effectiveness and Usability of Bioinformatics Tools to Analyze Pathways Associated with miRNA Expression
Lila E. Mullany, Roger K. Wolff and Martha L. Slattery
Cancer Informatics 2015:14 121-130
Original Research | Published on 29 Oct 2015

Publication Bias in Methodological Computational Research
Anne-Laure Boulesteix, Veronika Stierle and Alexander Hapfelmeier
Cancer Informatics 2015:Suppl. 5 11-19
Methodology | Published on 15 Oct 2015

FXYD5 is a Marker for Poor Prognosis and a Potential Driver for Metastasis in Ovarian Carcinomas
Pichai Raman, Timothy Purwin, Richard Pestell and Aydin Tozeren
Cancer Informatics 2015:14 113-119
Short Report | Published on 12 Oct 2015

Multiscale Model of Colorectal Cancer Using the Cellular Potts Framework
James M. Osborne
Cancer Informatics 2015:Suppl. 4 83-93
Original Research | Published on 04 Oct 2015

TIN: An R Package for Transcriptome Instability Analysis
Bjarne Johannessen, Anita Sveen, and Rolf I. Skotheim
Cancer Informatics 2015:14 109-112
Software or database review | Published on 20 Sep 2015

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files
Richard P. Finney, Qing-Rong Chen, Cu V. Nguyen, Chih Hao Hsu, Chunhua Yan, Ying Hu, Massih Abawi, Xiaopeng Bian and Daoud M. Meerzaman
Cancer Informatics 2015:14 105-107
Software or database review | Published on 13 Sep 2015

An Application of Sequential Meta-Analysis to Gene Expression Studies
Putri W. Novianti, Ingeborg van der Tweel, Victor L. Jong, Kit C. B. Roes and Marinus J. C. Eijkemans
Cancer Informatics 2015:Suppl. 5 1-10
Methodology | Published on 10 Sep 2015

The Importance of Neighborhood Scheme Selection in Agent-based Tumor Growth Modeling
Georgios Tzedakis, Eleftheria Tzamali, Kostas Marias and Vangelis Sakkalis
Cancer Informatics 2015:Suppl. 4 67-81
Original Research | Published on 07 Sep 2015

Preprocessing Steps for Agilent MicroRNA Arrays: Does the Order Matter?
Li-Xuan Qin, Huei-Chung Huang and Qin Zhou
Cancer Informatics 2014:Suppl. 4 105-109
Original Research | Published on 03 Sep 2015

Introductory Editorial: Computer Simulation, Bioinformatics, and Statistical Analysis of Cancer Data and Processes
Kellie J. Archer, Kevin Dobbin, Swati Biswas, Roger S. Day, David C. Wheeler, Hao Wu
Cancer Informatics 2015:Suppl. 2 247-251
Editorial | Published on 01 Sep 2015

CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and Cancer
Simone Rubinacci, Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri, James Osborne, Joe Pitt-Francis and Marco Antoniotti
Cancer Informatics 2015:Suppl. 4 53-65
Technical Advance | Published on 01 Sep 2015

Assessing Treatment Response Through Generalized Pharmacokinetic Modeling of DCE-MRI Data
Eleftherios Kontopodis, Georgia Kanli, Georgios C. Manikis, Sofie Van Cauter and Kostas Marias
Cancer Informatics 2015:Suppl. 4 41-51
Original Research | Published on 12 Aug 2015

In Silico Neuro-Oncology: Brownian Motion-Based Mathematical Treatment as a Potential Platform for Modeling the Infiltration of Glioma Cells into Normal Brain Tissue
Markos Antonopoulos and Georgios Stamatakos
Cancer Informatics 2015:Suppl. 4 33-40
Review | Published on 10 Aug 2015

HMPL: A Pipeline for Identifying Hemimethylation Patterns by Comparing Two Samples
Shuying Sun and Peng Li
Cancer Informatics 2015:Suppl. 2 235-245
Original Research | Published on 09 Aug 2015

Secondary Data Analytics of Aquaporin Expression Levels in Glioblastoma Stem-Like Cells
Raphael D. Isokpehi, Katharina C. Wollenberg Valero, Barbara E. Graham, Maricica Pacurari, Jennifer N. Sims, Udensi K. Udensi and Kenneth Ndebele
Cancer Informatics 2015:14 95-103
Original Research | Published on 30 Jul 2015

Medical Image Retrieval: A Multimodal Approach
Yu Cao, Shawn Steffey, Jianbiao He, Degui Xiao, Cui Tao, Ping Chen and Henning Müller
Cancer Informatics 2014:Suppl. 3 125-136
Original Research | Published on 22 Jul 2015

A Single-Array-Based Method for Detecting Copy Number Variants Using Affymetrix High Density SNP Arrays and its Application to Breast Cancer
Ming Li, Yalu Wen and Wenjiang Fu
Cancer Informatics 2014:Suppl. 4 95-103
Technical Advance | Published on 16 Jul 2015

The Impact of Microenvironmental Heterogeneity on the Evolution of Drug Resistance in Cancer Cells
Shannon M. Mumenthaler, Jasmine Foo, Nathan C. Choi, Nicholas Heise, Kevin Leder, David B. Agus, William Pao, Franziska Michor, and Parag Mallick
Cancer Informatics 2015:Suppl. 4 19-31
Original Research | Published on 15 Jul 2015

Identification of Genetic Mutations in Human Lung Cancer by Targeted Sequencing
Hongxiang Feng, Xiaowei Wang, Zhenrong Zhang, Chuanning Tang, Hua Ye, Lindsey Jones, Feng Lou, Dandan Zhang, Shouwen Jiang, Hong Sun, Haichao Dong, Guangchun Zhang, Zhiyuan Liu, Zhishou Dong, Baishuai Guo, He Yan, Chaowei Yan, Lu Wang, Ziyi Su, Yangyang Li, Vijayalakshmi Nandakumar, Xue F. Huang, Si-Yi Chen and Deruo Liu
Cancer Informatics 2015:14 83-93
Original Research | Published on 29 Jun 2015

Time-Frequency Analysis of Peptide Microarray Data: Application to Brain Cancer Immunosignatures
Brian O'Donnell, Alexander Maurer, Antonia Papandreou-Suppappola and Phillip Stafford
Cancer Informatics 2015:Suppl. 2 219-233
Original Research | Published on 18 Jun 2015

Managing Multi-center Flow Cytometry Data for Immune Monitoring
Scott White, Karoline Laske, Marij J.P. Welters, Nicole Bidmon, Sjoerd H. van der Burg, Cedrik M. Britten, Jennifer Enzor, Janet Staats, Kent J. Weinhold, Cécile Gouttefangeas and Cliburn Chan
Cancer Informatics 2014:Suppl. 7 111-122
Review | Published on 10 Jun 2015

A Proposed Paradigm Shift in Initializing Cancer Predictive Models with DCE-MRI Based PK Parameters: A Feasibility Study
Alexandros Roniotis, Mariam-Eleni Oraiopoulou, Eleftheria Tzamali, Eleftherios Kontopodis, Sofie Van Cauter, Vangelis Sakkalis, Kostas Marias
Cancer Informatics 2015:Suppl. 4 7-18
Original Research | Published on 10 Jun 2015

Gene Expression Signatures Based on Variability can Robustly Predict Tumor Progression and Prognosis
Wikum Dinalankara and Héctor Corrada Bravo
Cancer Informatics 2015:14 71-81
Original Research | Published on 07 Jun 2015

Powerful Tukey’s One Degree-of-Freedom Test for Detecting Gene–Gene and Gene–Environment Interactions
Yaping Wang, Donghui Li and Peng Wei
Cancer Informatics 2015:Suppl. 2 209-218
Review | Published on 04 Jun 2015

Penalized Ordinal Regression Methods for Predicting Stage of Cancer in High-Dimensional Covariate Spaces
Amanda Elswick Gentry, Colleen K. Jackson-Cook, Debra E. Lyon and Kellie J. Archer
Cancer Informatics 2015:Suppl. 2 201-208
Review | Published on 27 May 2015

Inferring Stable Acquisition Durations for Applications of Perfusion Imaging in Oncology
Brian P. Hobbs and Chaan S. Ng
Cancer Informatics 2015:Suppl. 2 193-199
Review | Published on 25 May 2015

Identifying CDKN3 Gene Expression as a Prognostic Biomarker in Lung Adenocarcinoma via Meta-analysis
Xiao Zang, Min Chen, Yunyun Zhou, Guanghua Xiao, Yang Xie, and Xinlei Wang
Cancer Informatics 2015:Suppl. 2 183-191
Original Research | Published on 24 May 2015

A Hypothesis-Directed Approach to the Targeted Development of a Multiplexed Proteomic Biomarker Assay for Cancer
Emily M. Mackay, Jennifer Koppel, Pooja Das, Joanna Woo, David C. Schriemer and Oliver F. Bathe
Cancer Informatics 2015:14 65-70
Technical Advance | Published on 17 May 2015

Integrative Analyses of Cancer Data: A Review from a Statistical Perspective
Yingying Wei
Cancer Informatics 2015:Suppl. 2 173-181
Review | Published on 14 May 2015

Assessment of Weighted Quantile Sum Regression for Modeling Chemical Mixtures and Cancer Risk
Jenna Czarnota, Chris Gennings and David C. Wheeler
Cancer Informatics 2015:Suppl. 2 159-171
Review | Published on 13 May 2015

PathoQC: Computationally Efficient Read Preprocessing and Quality Control for High-Throughput Sequencing Data Sets
Changjin Hong, Solaiappan Manimaran and William Evan Johnson
Cancer Informatics 2014:Suppl. 1 167-176
Review | Published on 12 May 2015

The Standardized Histogram Shift of T2 Magnetic Resonance Image (MRI) Signal Intensities of Nephroblastoma Does Not Predict Histopathological Diagnostic Information
Sabine Müller, Ruslan David, Kostas Marias and Norbert Graf
Cancer Informatics 2015:Suppl. 4 1-5
Review | Published on 12 May 2015

Recent Enhancements to the Genetic Risk Prediction Model BRCAPRO
Emanuele Mazzola, Amanda Blackford, Giovanni Parmigiani and Swati Biswas
Cancer Informatics 2015:Suppl. 2 147-157
Review | Published on 10 May 2015

Identifying Molecular Features Associated with Psychoneurological Symptoms in Women with Breast Cancer Using Multivariate Mixed Models
Qing Zhou, Colleen Jackson-Cook, Debra Lyon, Robert Perera and Kellie J. Archer
Cancer Informatics 2015:Suppl. 2 139-145
Original Research | Published on 07 May 2015

Evaluating Geographically Weighted Regression Models for Environmental Chemical Risk Analysis
Jenna Czarnota, David C. Wheeler and Chris Gennings
Cancer Informatics 2015:Suppl. 2 117-127
Original Research | Published on 05 May 2015

Prediction of Early Breast Cancer Metastasis from DNA Microarray Data Using High-Dimensional Cox Regression Models
Christophe Zemmour, François Bertucci, Pascal Finetti, Bernard Chetrit, Daniel Birnbaum, Thomas Filleron and Jean-Marie Boher
Cancer Informatics 2015:Suppl. 2 129-138
Original Research | Published on 05 May 2015

Generalized Monotone Incremental Forward Stagewise Method for Modeling Count Data: Application Predicting Micronuclei Frequency
Mateusz Makowski and Kellie J. Archer
Cancer Informatics 2015:Suppl. 2 97-105
Review | Published on 29 Apr 2015

Evaluation of the Performance of Smoothing Functions in Generalized Additive Models for Spatial Variation in Disease
Umaporn Siangphoe and David C. Wheeler
Cancer Informatics 2015:Suppl. 2 107-116
Review | Published on 29 Apr 2015