Cancer Informatics

2015:14

HCsnip: An R Package for Semi-supervised Snipping of the Hierarchical Clustering Tree
Askar Obulkasim and Mark A. van de Wiel
Cancer Informatics 2015:14 1-19
Original research | Published on 22 Mar 2015

Case-Based Retrieval Framework for Gene Expression Data
Ali Anaissi, Madhu Goyal, Daniel R. Catchpoole, Ali Braytee and Paul J. Kennedy
Cancer Informatics 2015:14 21-31
Original research | Published on 19 Mar 2015

Computing Molecular Signatures as Optima of a Bi-Objective Function: Method and Application to Prediction in Oncogenomics
Vincent Gardeux, Rachid Chelouah, Maria F. Barbosa Wanderley, Patrick Siarry, Antônio P. Braga, Fabien Reyal, Roman Rouzier, Lajos Pusztai and René Natowicz
Cancer Informatics 2015:14 33-45
Original research | Published on 19 Apr 2015

Profiling Age-Related Epigenetic Markers of Stomach Adenocarcinoma in Young and Old Subjects
Byoung-Chul Kim, Hyoung Oh Jeong, Daeui Park, Chul-Hong Kim, Eun Kyeong Lee, Dae Hyun Kim, Eunok Im, Nam Deuk Kim, Sunghoon Lee, Byung Pal Yu, Jong Bhak and Hae Young Chung
Cancer Informatics 2015:14 47-54
Original research | Published on 20 Apr 2015

BioMiner: Paving the Way for Personalized Medicine
Chris Bauer, Karol Stec, Alexander Glintschert, Kristina Gruden, Christian Schichor, Michal Or-Guil, Joachim Selbig and Johannes Schuchhardt
Cancer Informatics 2015:14 55-63
Original research | Published on 20 Apr 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
Original research | Published on 17 May 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

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

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

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
Original research | Published on 13 Sep 2015

TIN: An R Package for Transcriptome Instability Analysis
Bjarne Johannessen, Anita Sveen, and Rolf I. Skotheim
Cancer Informatics 2015:14 109-112
Original research | Published on 20 Sep 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
Original research | Published on 12 Oct 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

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
Original research | Published on 02 Nov 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
Original research | Published on 10 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

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

2015:Suppl. 1 Sequencing Platform Modeling and Analysis

Mitochondrial Variations in Non-Small Cell Lung Cancer (NSCLC) Survival
Zhaoxi Wang, Sojung Choi, Jinseon Lee, Yen-Tsung Huang, Feng Chen, Yang Zhao, Xihong Lin, Donna Neuberg, Jhingook Kim and David C. Christiani
Cancer Informatics 2015:Suppl. 1 1-9
Original research | Published on 27 Jan 2015

Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data
Qian Wu, Kyoung-Jae Won and Hongzhe Li
Cancer Informatics 2015:Suppl. 1 11-22
Original research | Published on 27 Jan 2015

Prognostic Gene Signature Identification Using Causal Structure Learning: Applications in Kidney Cancer
Min Jin Ha, Veerabhadran Baladandayuthapani and Kim-Anh Do
Cancer Informatics 2015:Suppl. 1 23-35
Original research | Published on 27 Jan 2015

Toolbox for Mobile-Element Insertion Detection on Cancer Genomes
Wan-Ping Lee, Jiantao Wu, and Gabor T. Marth
Cancer Informatics 2015:Suppl. 1 37-44
Original research | Published on 12 Feb 2015

Mapping Splicing Quantitative Trait Loci in RNA-Seq
Cheng Jia, Yu Hu, Yichuan Liu and Mingyao Li
Cancer Informatics 2015:Suppl. 1 45-53
Original research | Published on 16 Feb 2015

Introductory Editorial: Sequencing Platform Modeling and Analysis
Li-Xuan Qin and Yen-Tsung Huang
Cancer Informatics 2015:Suppl. 1 55-56
Original research | Published on 02 Mar 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
Original research | Published on 13 Dec 2015

2015:Suppl. 2 Computer Simulation, Bioinformatics, and Statistical Analysis of Cancer Data and Processes

sfDM: Open-Source Software for Temporal Analysis and Visualization of Brain Tumor Diffusion MR Using Serial Functional Diffusion Mapping
Rafael Ceschin, Ashok Panigrahy, Vanathi Gopalakrishnan
Cancer Informatics 2015:Suppl. 2 1-9
Original research | Published on 01 Feb 2015

An Improved Version of Logistic Bayesian LASSO for Detecting Rare Haplotype-Environment Interactions with Application to Lung Cancer
Yuan Zhang and Swati Biswas
Cancer Informatics 2015:Suppl. 2 11-16
Original research | Published on 09 Feb 2015

Evaluating Methods for Modeling Epistasis Networks with Application to Head and Neck Cancer
Rajesh Talluri and Sanjay Shete
Cancer Informatics 2015:Suppl. 2 17-23
Original research | Published on 10 Feb 2015

What Tumor Dynamics Modeling Can Teach us About Exploiting the Stem-Cell View for Better Cancer Treatment
Roger S. Day
Cancer Informatics 2015:Suppl. 2 25-36
Original research | Published on 24 Feb 2015

Modeling Discrete Survival Time Using Genomic Feature Data
Kyle Ferber and Kellie J. Archer
Cancer Informatics 2015:Suppl. 2 37-43
Original research | Published on 02 Mar 2015

GeneMed: An Informatics Hub for the Coordination of Next-Generation Sequencing Studies that Support Precision Oncology Clinical Trials
Yingdong Zhao, Eric C. Polley, Ming-Chung Li, Chih-Jian Lih, Alida Palmisano, David J. Sims, Lawrence V. Rubinstein, Barbara A. Conley, Alice P. Chen, P. Mickey Williams, Shivaani Kummar, James H. Doroshow and Richard M. Simon
Cancer Informatics 2015:Suppl. 2 45-55
Original research | Published on 19 Mar 2015

Prioritization of Cancer-Related Genomic Variants by SNP Association Network
Changning Liu and Zhenyu Xuan
Cancer Informatics 2015:Suppl. 2 57-70
Original research | Published on 01 Apr 2015

Catchment Area Analysis Using Bayesian Regression Modeling
Aobo Wang and David C. Wheeler
Cancer Informatics 2015:Suppl. 2 71-79
Original research | Published on 19 Apr 2015

Selecting Spatial Scale of Covariates in Regression Models of Environmental Exposures
Lauren P. Grant, Chris Gennings and David C. Wheeler
Cancer Informatics 2015:Suppl. 2 81-96
Original research | Published on 27 Apr 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
Original research | 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
Original research | Published on 29 Apr 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

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

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
Original research | Published on 10 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
Original research | Published on 13 May 2015

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

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
Original research | Published on 25 May 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
Original research | Published on 27 May 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
Original research | Published on 04 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

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

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
Original research | Published on 01 Sep 2015

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

2015:Suppl. 3 In-vitro Tumor Regulation, Structural Analysis, and Carcinogenicity Modeling

Regulation of Epithelial-Mesenchymal Transition in Breast Cancer Cells by Cell Contact and Adhesion
Magdalena A. Cichon, Celeste M. Nelson, and Derek C. Radisky
Cancer Informatics 2015:Suppl. 3 1-13
Original research | Published on 09 Feb 2015 | Video Abstract Available

Expression of Polarity Genes in Human Cancer
Wan-Hsin Lin, Yan W. Asmann and Panos Z. Anastasiadis
Cancer Informatics 2015:Suppl. 3 15-28
Original research | Published on 30 Mar 2015

2015:Suppl. 4 Computer Simulation, Visualization, and Image Processing of Cancer Data and Processes

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
Original research | Published on 12 May 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

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

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
Original research | Published on 10 Aug 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

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
Original research | Published on 01 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

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

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
Original research | Published on 06 Dec 2015

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
Original research | Published on 12 Jan 2016

2015:Suppl. 5 Statistical Systems Theory in Cancer Modeling, Diagnosis, and Therapy

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
Original research | Published on 10 Sep 2015

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

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
Original research | Published on 13 Jan 2016

2014:13

stepwiseCM: An R Package for Stepwise Classification of Cancer Samples Using Multiple Heterogeneous Data Sets
Askar Obulkasim and Mark A van de Wiel
Cancer Informatics 2014:13 1-11
Original research | Published on 02 Jan 2014

OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data
Ying Hu, Chunhua Yan, Chih-Hao Hsu, Qing-Rong Chen, Kelvin Niu, George A. Komatsoulis and Daoud Meerzaman
Cancer Informatics 2014:13 13-20
Original research | Published on 16 Jan 2014

Prognostic features of signal transducer and activator of transcription 3 in an ER(+) breast cancer model system
Li-Yu D. Liu, Li-Yun Chang, Wen-Hung Kuo, Hsiao-Lin Hwa, Yi-Shing Lin, Meei-Huey Jeng, Don A. Roth, King-Jen Chang and Fon-Jou Hsieh
Cancer Informatics 2014:13 21-45
Original research | Published on 21 Jan 2014

A New Method for Predicting Patient Survivorship Using Efficient Bayesian Network Learning
Xia Jiang, Diyang Xue, Adam Brufsky, Seema Khan and Richard Neapolitan
Cancer Informatics 2014:13 47-57
Original research | Published on 13 Feb 2014

INsPeCT: INtegrative Platform for Cancer Transcriptomics
Piyush B. Madhamshettiwar, Stefan R. Maetschke, Melissa J. Davis, Antonio Reverter and Mark A. Ragan
Cancer Informatics 2014:13 59-66
Original research | Published on 12 Mar 2014

Nonlinear Optical Microscopy Signal Processing Strategies in Cancer
Javier Adur, Hernandes F. Carvalho, Carlos L. Cesar and Víctor H. Casco
Cancer Informatics 2014:13 67-76
Original research | Published on 02 Apr 2014

Modeling the Altered Expression Levels of Genes on Signaling Pathways in Tumors As Causal Bayesian Networks
Richard Neapolitan, Diyang Xue, and Xia Jiang
Cancer Informatics 2014:13 77-84
Original research | Published on 25 May 2014

On the Significance of Fuzzification of the N and M in Cancer Staging
Sara A. Yones, Ahmed S. Moussa, Hesham Hassan and Nelly H. Alieldin
Cancer Informatics 2014:13 85-91
Original research | Published on 24 Jul 2014

CSNK1A1 and Gli2 as Novel Targets Identified Through an Integrative Analysis of Gene Expression Data, Protein-Protein Interaction and Pathways Networks in Glioblastoma Tumors: Can These Two Be Antagonistic Proteins?
Seema Mishra
Cancer Informatics 2014:13 93-108
Original research | Published on 13 Oct 2014

A Comprehensive Comparison of Normalization Methods for Loading Control and Variance Stabilization of Reverse-Phase Protein Array Data
Wenbin Liu, Zhenlin Ju, Yiling Lu, Gordon B. Mills and Rehan Akbani
Cancer Informatics 2014:13 109-117
Original research | Published on 16 Oct 2014

Classification of Images Acquired with Colposcopy Using Artificial Neural Networks
Priscyla W. Simões, Narjara B. Izumi, Ramon S. Casagrande, Ramon Venson, Carlos D. Veronezi, Gustavo P. Moretti, Edroaldo L. da Rocha, Cristian Cechinel, Luciane B. Ceretta, Eros Comunello, Paulo J. Martins, Rogério A. Casagrande, Maria L. Snoeyer and Sandra A. Manenti
Cancer Informatics 2014:13 119-124
Original research | Published on 21 Oct 2014

Correction to: Prognostic Features of Signal Transducer and Activator of Transcription 3 in an ER(+) Breast Cancer Model System
Li-Yu D. Liu, Li-Yun Chang, Wen-Hung Kuo, Hsiao-Lin Hwa, Yi-Shing Lin, Meei-Huey Jeng, Don A. Roth, King-Jen Chang and Fon-Jou Hsieh
Cancer Informatics 2014:13 125-129
Original research | Published on 02 Nov 2014

Health Information Technology in Oncology Practice: A Literature Review
G. Fasola, M. Macerelli, A. Follador, K. Rihawi, G. Aprile and V. Della Mea
Cancer Informatics 2014:13 131-139
Original research | Published on 01 Dec 2014

Supervised Classification by Filter Methods and Recursive Feature Elimination Predicts Risk of Radiotherapy-Related Fatigue in Patients with Prostate Cancer
Leorey N. Saligan, Juan Luis Fernández-Martínez, Enrique J. deAndrés-Galiana and Stephen Sonis
Cancer Informatics 2014:13 141-152
Original research | Published on 01 Dec 2014

FocalCall: An R Package for the Annotation of Focal Copy Number Aberrations
Oscar Krijgsman, Christian Benner, Gerrit A. Meijer, Mark A. van de Wiel and Bauke Ylstra
Cancer Informatics 2014:13 153-156
Original research | Published on 01 Dec 2014

Trial Prospector: Matching Patients with Cancer Research Studies Using an Automated and Scalable Approach
Satya S. Sahoo, Shiqiang Tao, Andrew Parchman, Zhihui Luo, Licong Cui, Patrick Mergler, Robert Lanese, Jill S. Barnholtz-Sloan, Neal J. Meropol and Guo-Qiang Zhang
Cancer Informatics 2014:13 157-166
Original research | Published on 04 Dec 2014

A Pan-Cancer Analysis of Alternative Splicing Events Reveals Novel Tumor-Associated Splice Variants of Matriptase
Daryanaz Dargahi, Richard D. Swayze, Leanna Yee, Peter J. Bergqvist, Bradley J. Hedberg, Alireza Heravi-Moussavi, Edie M. Dullaghan, Ryan Dercho, Jianghong An, John S. Babcook, and Steven J.M. Jones
Cancer Informatics 2014:13 167-177
Original research | Published on 04 Dec 2014

Computational Construction of Antibody–Drug Conjugates Using Surface Lysines as the Antibody Conjugation Site and a Non-cleavable Linker
Arianna Filntisi, Dimitrios Vlachakis, George K. Matsopoulos and Sophia Kossida
Cancer Informatics 2014:13 179-186
Original research | Published on 08 Dec 2014

ordinalgmifs: An R Package for Ordinal Regression in High-dimensional Data Settings
Kellie J. Archer, Jiayi Hou, Qing Zhou, Kyle Ferber, John G. Layne and Amanda E. Gentry
Cancer Informatics 2014:13 187-195
Original research | Published on 10 Dec 2014

Web Tool for Estimating the Cancer Hazard Rates in Aging
Tengiz Mdzinarishvili, Alexander Sherman, Oleg Shats, and Simon Sherman
Cancer Informatics 2014:13 197-205
Original research | Published on 17 Dec 2014

2014:Suppl. 4 Array Platform Modeling and Analysis (A)

Integrative Pathway Analysis Using Graph-Based Learning with Applications to TCGA Colon and Ovarian Data
Andrew E. Dellinger, Andrew B. Nixon and Herbert Pang
Cancer Informatics 2014:13 Suppl. 4 1-9
Original research | Published on 28 Jul 2014

CORM: An R Package Implementing the Clustering of Regression Models Method for Gene Clustering
Jiejun Shi and Li-Xuan Qin
Cancer Informatics 2014:Suppl. 4 11-13
Original research | Published on 15 Oct 2014

TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile
Yen-Tsung Huang, Thomas Hsu and David C. Christiani
Cancer Informatics 2014:Suppl. 4 15-23
Original research | Published on 15 Oct 2014

Unsupervised Outlier Profile Analysis
Debashis Ghosh and Song Li
Cancer Informatics 2014:Suppl. 4 25-33
Original research | Published on 15 Oct 2014

Mapping Splicing Quantitative Trait Loci in RNA-Seq
Cheng Jia, Yu Hu, Yichuan Liu and Mingyao Li
Cancer Informatics 2014:Suppl. 4 35-43
Original research | Published on 15 Oct 2014

Toolbox for Mobile-Element Insertion Detection on Cancer Genomes
Wan-Ping Lee, Jiantao Wu and Gabor T. Marth
Cancer Informatics 2014:Suppl. 4 45-52
Original research | Published on 15 Oct 2014

Normal Cell-Type Epigenetics and Breast Cancer Classification: A Case Study of Cell Mixture–Adjusted Analysis of DNA Methylation Data from Tumors
Eugene Andrés Houseman and Tan A. Ince
Cancer Informatics 2014:Suppl. 4 53-64
Original research | Published on 09 Dec 2014

Growth Rate Analysis and Efficient Experimental Design for Tumor Xenograft Studies
Gregory Hather, Ray Liu, Syamala Bandi, Jerome Mettetal, Mark Manfredi, Wen-Chyi Shyu, Jill Donelan and Arijit Chakravarty
Cancer Informatics 2014:Suppl. 4 65-72
Original research | Published on 09 Dec 2014

Stratified Pathway Analysis to Identify Gene Sets Associated with Oral Contraceptive Use and Breast Cancer
Herbert Pang and Hongyu Zhao
Cancer Informatics 2014:Suppl. 4 73-78
Original research | Published on 09 Dec 2014

Bayesian Hierarchical Models for Protein Networks in Single-Cell Mass Cytometry
Riten Mitra, Peter Müller, Peng Qiu and Yuan Ji
Cancer Informatics 2014:Suppl. 4 79-89
Original research | Published on 10 Dec 2014

Introductory Editorial: Array Platform Modeling and Analysis (A)
Li-Xuan Qin, Shuangge Ma, Yen-Tsung Huang, Hui Zhang, Hongyuan Cao
Cancer Informatics 2014:Suppl. 4 91-93
Original research | Published on 17 Feb 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
Original research | Published on 16 Jul 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

2014:Suppl. 2 Classification, Predictive Modelling, and Statistical Analysis of Cancer Data (A)

Introductory Editorial: Classification, Predictive Modelling, and Statistical Analysis of Cancer Data (A)
Hongmei Jiang, Lingling An, Veerabhadran Baladandayuthapani, Paul Livermore Auer
Cancer Informatics 2014:Suppl. 2 1-3
Original research | Published on 21 Sep 2014

Functional Annotation of Putative Regulatory Elements at Cancer Susceptibility Loci
Stephanie A. Rosse, Paul L. Auer, and Christopher S. Carlson
Cancer Informatics 2014:Suppl. 2 5-17
Original research | Published on 21 Sep 2014

A Review of Cancer Risk Prediction Models with Genetic Variants
Xuexia Wang, Michael J. Oldani, Xingwang Zhao, Xiaohui Huang and Dajun Qian
Cancer Informatics 2014:Suppl. 2 19-28
Original research | Published on 21 Sep 2014

A Bayesian Integrative Model for Genetical Genomics with Spatially Informed Variable Selection
Alberto Cassese, Michele Guindani and Marina Vannucci
Cancer Informatics 2014:Suppl. 2 29-37
Original research | Published on 21 Sep 2014

Integrative Bayesian Network Analysis of Genomic Data
Yang Ni, Francesco C. Stingo and Veerabhadran Baladandayuthapani
Cancer Informatics 2014:Suppl. 2 39-48
Original research | Published on 21 Sep 2014

Integrated Analysis of Whole-Genome Paired-End and Mate-Pair Sequencing Data for Identifying Genomic Structural Variations in Multiple Myeloma
Rendong Yang, Li Chen, Scott Newman, Khanjan Gandhi, Gregory Doho, Carlos S. Moreno, Paula M. Vertino, Leon Bernal-Mizarchi, Sagar Lonial, Lawrence H. Boise, Michael Rossi, Jeanne Kowalski, and Zhaohui S. Qin
Cancer Informatics 2014:Suppl. 2 49-53
Original research | Published on 21 Sep 2014

Comparative Study of Computational Methods for Reconstructing Genetic Networks of Cancer-Related Pathways
Nafiseh Sedaghat, Takumi Saegusa, Timothy Randolph and Ali Shojaie
Cancer Informatics 2014:Suppl. 2 55-66
Original research | Published on 21 Sep 2014

Review of Current Methods, Applications, and Data Management for the Bioinformatics Analysis of Whole Exome Sequencing
Riyue Bao, Lei Huang, Jorge Andrade, Wei Tan, Warren A. Kibbe, Hongmei Jiang and Gang Feng
Cancer Informatics 2014:Suppl. 2 67-82
Original research | Published on 21 Sep 2014

Bayesian Disease Classification Using Copy Number Data
Subharup Guha, Yuan Ji, and Veerabhadran Baladandayuthapani
Cancer Informatics 2014:Suppl. 2 83-91
Original research | Published on 01 Oct 2014

Combined Benefit of Prediction and Treatment: A Criterion for Evaluating Clinical Prediction Models
Dean Billheimer, Eugene W. Gerner, Christine E. McLaren and Bonnie LaFleur
Cancer Informatics 2014:Suppl. 2 93-103
Original research | Published on 05 Oct 2014

eMBI: Boosting Gene Expression-based Clustering for Cancer Subtypes
Zheng Chang, Zhenjia Wang, Cody Ashby, Chuan Zhou, Guojun Li, Shuzhong Zhang and Xiuzhen Huang
Cancer Informatics 2014:Suppl. 2 105-112
Original research | Published on 21 Oct 2014

Bayesian Joint Selection of Genes and Pathways: Applications in Multiple Myeloma Genomics
Lin Zhang, Jeffrey S. Morris, Jiexin Zhang, Robert Z. Orlowski and Veerabhadran Baladandayuthapani
Cancer Informatics 2014:Suppl. 2 113-123
Original research | Published on 07 Dec 2014

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
Original research | Published on 23 Nov 2015

2014:Suppl. 5 Network and Pathway Analysis of Cancer Susceptibility (A)

Inferring the Effects of Honokiol on the Notch Signaling Pathway in SW480 Colon Cancer Cells
Michelle L. Wynn, Nikita Consul, Sofia D. Merajver and Santiago Schnell
Cancer Informatics 2014:Suppl. 5 1-12
Original research | Published on 13 Oct 2014

Integrated DNA Copy Number and Gene Expression Regulatory Network Analysis of Non-small Cell Lung Cancer Metastasis
Seyed M. Iranmanesh and Nancy L. Guo
Cancer Informatics 2014:Suppl. 5 13-23
Original research | Published on 14 Oct 2014

Profiling the microRNA Expression in Human iPS and iPS-derived Retinal Pigment Epithelium
Heuy-Ching Wang, Whitney A. Greene, Ramesh R. Kaini, Jane Shen-Gunther, Hung-I H Chen, Hong Cai and Yufeng Wang
Cancer Informatics 2014:Suppl. 5 25-35
Original research | Published on 15 Oct 2014

Network-Based Identification of Biomarkers Coexpressed with Multiple Pathways
Nancy Lan Guo and Ying-Wooi Wan
Cancer Informatics 2014:Suppl. 5 37-47
Original research | Published on 16 Oct 2014

Co-expression Network Analysis of Human lncRNAs and Cancer Genes
Steven B. Cogill and Liangjiang Wang
Cancer Informatics 2014:Suppl. 5 49-59
Original research | Published on 19 Oct 2014

Learning Dysregulated Pathways in Cancers from Differential Variability Analysis
Bahman Afsari, Donald Geman and Elana J. Fertig
Cancer Informatics 2014:Suppl. 5 61-67
Original research | Published on 23 Oct 2014

A Pan-Cancer Modular Regulatory Network Analysis to Identify Common and Cancer-Specific Network Components
Sara A. Knaack, Alireza Fotuhi Siahpirani, and Sushmita Roy
Cancer Informatics 2014:Suppl. 5 69-84
Original research | Published on 28 Oct 2014

Predicting Cancer Prognosis Using Functional Genomics Data Sets
Jishnu Das, Kaitlyn M. Gayvert and Haiyuan Yu
Cancer Informatics 2014:Suppl. 5 85-88
Original research | Published on 02 Nov 2014

A Novel Subset of Human Tumors That Simultaneously Overexpress Multiple E2F-responsive Genes Found in Breast, Ovarian, and Prostate Cancers
Stanley E. Shackney, Salim Akhter Chowdhury and Russell Schwartz
Cancer Informatics 2014:Suppl. 5 89-100
Original research | Published on 03 Nov 2014

Pathway-based Biomarkers for Breast Cancer in Proteomics
Fan Zhang, Youping Deng, Mu Wang, Li Cui and Renee Drabier
Cancer Informatics 2014:Suppl. 5 101-108
Original research | Published on 09 Feb 2015

Network Analysis of Circular Permutations in Multidomain Proteins Reveals Functional Linkages for Uncharacterized Proteins
Donald Adjeroh, Yue Jiang, Bing-Hua Jiang and Jie Lin
Cancer Informatics 2014:Suppl. 5 109-124
Original research | Published on 19 Feb 2015

Introductory Editorial: Network and Pathway Analysis of Cancer Susceptibility (A)
Nancy Guo, Russell S. Schwartz, Jiang Qian, Peilin Jia, Youping Deng
Cancer Informatics 2014:Suppl. 5 125-127
Original research | Published on 12 Mar 2015

RNA-Seq and Network Analysis Revealed Interacting Pathways in TGF-β-Treated Lung Cancer Cell Lines
Yan Li, Omid Rouhi, Hankui Chen, Rolando Ramirez, Jeffrey A. Borgia and Youping Deng
Cancer Informatics 2014:Suppl. 5 129-140
Original research | Published on 01 Apr 2015

2014:Suppl. 6 Network and Pathway Analysis of Cancer Susceptibility (B)

RNAseqPS: A Web Tool for Estimating Sample Size and Power for RNAseq Experiment
Yan Guo, Shilin Zhao, Chung-I Li, Quanhu Sheng and Yu Shyr
Cancer Informatics 2014:Suppl. 6 1-5
Original research | Published on 13 Oct 2014

The Axis of Progression of Disease
Alan M. Tartakoff and Di Wu
Cancer Informatics 2014:Suppl. 6 7-13
Original research | Published on 19 Oct 2014

Assessment of Subnetwork Detection Methods for Breast Cancer
Biaobin Jiang and Michael Gribskov
Cancer Informatics 2014:Suppl. 6 15-23
Original research | Published on 02 Dec 2014

Network-Constrained Group Lasso for High-Dimensional Multinomial Classification with Application to Cancer Subtype Prediction
Xinyu Tian, Xuefeng Wang, and Jun Chen
Cancer Informatics 2014:Suppl. 6 25-33
Original research | Published on 12 Jan 2015

Identifying Driver Genes in Cancer by Triangulating Gene Expression, Gene Location, and Survival Data
Sigrid Rouam, Lance D. Miller and R. Krishna Murthy Karuturi
Cancer Informatics 2014:Suppl. 6 35-48
Original research | Published on 03 Feb 2015

2014:Suppl. 3 Computational Advances in Cancer Informatics (B)

Automated Recommendation for Cervical Cancer Screening and Surveillance
Kavishwar B. Wagholikar, Kathy L. MacLaughlin, Petra M. Casey, Thomas M. Kastner, Michael R. Henry, Ronald A. Hankey, Steve G. Peters, Robert A. Greenes, Christopher G. Chute, Hongfang Liu and Rajeev Chaudhry
Cancer Informatics 2014:Suppl. 3 1-6
Original research | Published on 15 Oct 2014 | Video Abstract Available

Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline
Karl W. Kroll, Nima E. Mokaram, Alexander R. Pelletier, David E. Frankhouser, Maximillian S. Westphal, Paige A. Stump, Cameron L. Stump, Ralf Bundschuh, James S. Blachly and Pearlly Yan
Cancer Informatics 2014:Suppl. 3 7-14
Original research | Published on 15 Oct 2014

Network-based Prediction of Cancer under Genetic Storm
Ahmet Ay, Dihong Gong, Tamer Kahveci
Cancer Informatics 2014:Suppl. 3 15-31
Original research | Published on 15 Oct 2014

Master Regulators, Regulatory Networks, and Pathways of Glioblastoma Subtypes
Serdar Bozdag, Aiguo Li, Mehmet Baysan, and Howard A. Fine
Cancer Informatics 2014:Suppl. 3 33-44
Original research | Published on 15 Oct 2014

Network Analysis of Cancer-focused Association Network Reveals Distinct Network Association Patterns
Yuji Zhang and Cui Tao
Cancer Informatics 2014:Suppl. 3 45-51
Original research | Published on 16 Oct 2014

Developing a Comprehensive Database Management System for Organization and Evaluation of Mammography Datasets
Yirong Wu, Daniel L. Rubin, Ryan W. Woods, Mai Elezaby and Elizabeth S. Burnside
Cancer Informatics 2014:Suppl. 3 53-62
Original research | Published on 16 Oct 2014

StickWRLD as an Interactive Visual Pre-Filter for Canceromics-Centric Expression Quantitative Trait Locus Data
Robert Wolfgang Rumpf, Samuel L. Wolock and William C. Ray
Cancer Informatics 2014:Suppl. 3 63-69
Original research | Published on 16 Oct 2014

In Silico Prediction of Synthetic Lethality by Meta-Analysis of Genetic Interactions, Functions, and Pathways in Yeast and Human Cancer
Min Wu, Xuejuan Li, Fan Zhang, Xiaoli Li, Chee-Keong Kwoh and Jie Zheng
Cancer Informatics 2014:Suppl. 3 71-80
Original research | Published on 05 Nov 2014

Conducting Retrospective Ontological Clinical Trials in ICD-9-CM in the Age of ICD-10-CM
Neeta K. Venepalli, Ardaman Shergill, Parvaneh Dorestani and Andrew D. Boyd
Cancer Informatics 2014:Suppl. 3 81-88
Original research | Published on 09 Nov 2014

Correction to "Network Analysis of Cancer-focused Association Network Reveals Distinct Network Association Patterns"
Yuji Zhang and Cui Tao
Cancer Informatics 2014:Suppl. 3 89-89
Original research | Published on 20 Nov 2014

Correction to “Master Regulators, Regulatory Networks, and Pathways of Glioblastoma Subtypes”
Serdar Bozdag, Aiguo Li, Mehmet Baysan, and Howard A. Fine
Cancer Informatics 2014:Suppl. 3 91-91
Original research | Published on 30 Nov 2014

Comprehensive Evaluation of Composite Gene Features in Cancer Outcome Prediction
Dezhi Hou and Mehmet Koyutürk
Cancer Informatics 2014:Suppl. 3 93-104
Original research | Published on 24 Feb 2015

Identification of Medium-Sized Copy Number Alterations in Whole-Genome Sequencing
Hatice Gulcin Ozer, Aisulu Usubalieva, Adrienne Dorrance, Ayse Selen Yilmaz, Michael Caligiuri, Guido Marcucci and Kun Huang
Cancer Informatics 2014:Suppl. 3 105-111
Original research | Published on 05 Mar 2015

Design and Implementation of a Comprehensive Web-based Survey for Ovarian Cancer Survivorship with an Analysis of Prediagnosis Symptoms via Text Mining
Jiayang Sun, Kath M. Bogie, Joe Teagno, Yu-Hsiang (Sam) Sun, Rebecca R. Carter, Licong Cui and Guo-Qiang Zhang
Cancer Informatics 2014:Suppl. 3 113-123
Original research | Published on 23 Mar 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

2014:Suppl. 7 Array Platform Modeling and Analysis (B)

Propensity Score Method for Partially Matched Omics Studies
Pei-Fen Kuan
Cancer Informatics 2014:Suppl. 7 1-10
Original research | Published on 29 Oct 2014

Type I Error Control for Tree Classification
Sin-Ho Jung, Yong Chen and Hongshik Ahn
Cancer Informatics 2014:Suppl. 7 11-18
Original research | Published on 16 Nov 2014

A Bayesian Framework to Improve MicroRNA Target Prediction by Incorporating External Information
Zixing Wang, Wenlong Xu, Haifeng Zhu and Yin Liu
Cancer Informatics 2014:Suppl. 7 19-25
Original research | Published on 18 Nov 2014

CARAT-GxG: CUDA-Accelerated Regression Analysis Toolkit for Large-Scale Gene–Gene Interaction with GPU Computing System
Sungyoung Lee, Min-Seok Kwon and Taesung Park
Cancer Informatics 2014:Suppl. 7 27-33
Original research | Published on 09 Dec 2014

Statistical Issues in the Design and Analysis of nCounter Projects
Sin-Ho Jung and Insuk Sohn
Cancer Informatics 2014:Suppl. 7 35-43
Original research | Published on 14 Dec 2014

Detection of Pancreatic Cancer Biomarkers Using Mass Spectrometry
Kiyoun Kim, Soohyun Ahn, Johan Lim, Byong Chul Yoo, Jin-Hyeok Hwang and Woncheol Jang
Cancer Informatics 2014:Suppl. 7 45-53
Original research | Published on 06 Jan 2015

Practical Issues in Screening and Variable Selection in Genome-Wide Association Analysis
Sungyeon Hong, Yongkang Kim and Taesung Park
Cancer Informatics 2014:Suppl. 7 55-65
Original research | Published on 14 Jan 2015

Inferring Active and Prognostic Ligand-Receptor Pairs with Interactions in Survival Regression Models
Christina Ruggeri and Kevin H. Eng
Cancer Informatics 2014:Suppl. 7 67-75
Original research | Published on 26 Jan 2015

Hidden Markov Model-Based CNV Detection Algorithms for Illumina Genotyping Microarrays
Eric L. Seiser and Federico Innocenti
Cancer Informatics 2014:Suppl. 7 77-83
Original research | Published on 27 Jan 2015

Extending Information Retrieval Methods to Personalized Genomic-Based Studies of Disease
Shuyun Ye, John A. Dawson and Christina Kendziorski
Cancer Informatics 2014:Suppl. 7 85-95
Original research | Published on 10 Feb 2015

Next Generation Distributed Computing for Cancer Research
Pankaj Agarwal and Kouros Owzar
Cancer Informatics 2014:Suppl. 7 97-109
Original research | Published on 27 Apr 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
Original research | Published on 10 Jun 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
Original research | Published on 15 Nov 2015

2014:Suppl. 1 Computational Advances in Cancer Informatics (A)

Evaluating Gene Set Enrichment Analysis Via a Hybrid Data Model
Jianping Hua, Michael L. Bittner and Edward R. Dougherty
Cancer Informatics 2014:13(S1)1-16
Original research | Published on 12 Feb 2014

Optimization of Network Topology in Computer-Aided Detection Schemes Using Phased Searching with NEAT in a Time-Scaled Framework
Maxine Tan, Jiantao Pu and Bin Zheng
Cancer Informatics 2014:Suppl. 1 17-27
Original research | Published on 13 Oct 2014

Inferring Aberrant Signal Transduction Pathways in Ovarian Cancer from TCGA Data
Richard Neapolitan and Xia Jiang
Cancer Informatics 2014:Suppl. 1 29-36
Original research | Published on 13 Oct 2014

Mining Cancer-Specific Disease Comorbidities from a Large Observational Health Database
Yang Chen and Rong Xu
Cancer Informatics 2014:Suppl. 1 37-44
Original research | Published on 13 Oct 2014

Introductory Editorial: Computational Advances in Cancer Informatics (A)
Xiaoqian Jiang, Rui Chen, Samuel Cheng, Xia Jiang, Bairong Shen, Rong Xu, Song Yi
Cancer Informatics 2014:Suppl. 1 45-48
Original research | Published on 13 Oct 2014

Feasibility and Implementation of a Literature Information Management System for Human Papillomavirus in Head and Neck Cancers with Imaging
Dee H. Wu, Chance L. Matthiesen, Anthony M. Alleman, Aaron L. Fournier and Tyler C. Gunter
Cancer Informatics 2014:Suppl. 1 49-57
Original research | Published on 13 Oct 2014

Modeling Signal Transduction from Protein Phosphorylation to Gene Expression
Chunhui Cai, Lujia Chen, Xia Jiang and Xinghua Lu
Cancer Informatics 2014:Suppl. 1 59-67
Original research | Published on 13 Oct 2014

Text Mining in Cancer Gene and Pathway Prioritization
Yuan Luo, Gregory Riedlinger and Peter Szolovits
Cancer Informatics 2014:Suppl. 1 69-79
Original research | Published on 13 Oct 2014

Disease Biomarker Query from RNA-Seq Data
Henry Han and Xiaoqian Jiang
Cancer Informatics 2014:Suppl. 1 81-94
Original research | Published on 14 Oct 2014

Prediction of MicroRNA Precursors Using Parsimonious Feature Sets
Petra Stepanowsky, Eric Levy, Jihoon Kim, Xiaoqian Jiang and Lucila Ohno-Machado
Cancer Informatics 2014:Suppl. 1 95-102
Original research | Published on 14 Oct 2014

Exploiting Literature-derived Knowledge and Semantics to Identify Potential Prostate Cancer Drugs
Rui Zhang, Michael J. Cairelli, Marcelo Fiszman, Halil Kilicoglu, Thomas C. Rindflesch, Serguei V. Pakhomov and Genevieve B. Melton
Cancer Informatics 2014:Suppl. 1 103-111
Original research | Published on 14 Oct 2014

Revealing Biological Pathways Implicated in Lung Cancer from TCGA Gene Expression Data Using Gene Set Enrichment Analysis
Binghuang Cai and Xia Jiang
Cancer Informatics 2014:Suppl. 1 113-121
Original research | Published on 01 Dec 2014

Streamlined Genome Sequence Compression using Distributed Source Coding
Shuang Wang, Xiaoqian Jiang, Feng Chen, Lijuan Cui and Samuel Cheng
Cancer Informatics 2014:Suppl. 1 123-131
Original research | Published on 02 Dec 2014

Semantically Linking In Silico Cancer Models
David Johnson, Anthony J. Connor, Steve McKeever, Zhihui Wang, Thomas S. Deisboeck, Tom Quaiser and Eliezer Shochat
Cancer Informatics 2014:Suppl. 1 133-143
Original research | Published on 08 Dec 2014

Overcome Support Vector Machine Diagnosis Overfitting
Henry Han and Xiaoqian Jiang
Cancer Informatics 2014:Suppl. 1 145-158
Original research | Published on 09 Dec 2014

Empirical Transition Probability Indexing Sparse-Coding Belief Propagation (ETPI-SCoBeP) Genome Sequence Alignment
Aminmohammad Roozgard, Nafise Barzigar, Shuang Wang, Xiaoqian Jiang and Samuel Cheng
Cancer Informatics 2014:Suppl. 1 159-165
Original research | Published on 01 Feb 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
Original research | Published on 12 May 2015

2013:12

An Integrative Genomics Approach for Associating GWAS Information with Triple-Negative Breast Cancer
Chindo Hicks, Ranjit Kumar, Antonio Pannuti, Kandis Backus, Alexandra Brown, Jesus Monico and Lucio Miele
Cancer Informatics 2013:12 1-20
Original research | Published on 29 Jan 2013

Design of an Expert System for Mitigating Trace Element Toxicity in Cancer Risk Management
P.T. Krishna Kumar, P.T. Vinod, Vir V. Phoha, S.S. Iyengar and Puneeth Iyengar
Cancer Informatics 2013:12 21-29
Original research | Published on 04 Feb 2013

In Silico Discovery of Mitosis Regulation Networks Associated with Early Distant Metastases in Estrogen Receptor Positive Breast Cancers
Yuriy Gusev, Rebecca B. Riggins, Krithika Bhuvaneshwar, Robinder Gauba, Laura Sheahan, Robert Clarke and Subha Madhavan
Cancer Informatics 2013:12 31-51
Original research | Published on 13 Feb 2013

Classification of Tumor Samples from Expression Data Using Decision Trunks
Benjamin Ulfenborg, Karin Klinga-Levan and Björn Olsson
Cancer Informatics 2013:12 53-66
Original research | Published on 13 Feb 2013

Basic Equations and Computing Procedures for Frailty Modeling of Carcinogenesis: Application to Pancreatic Cancer Data
Tengiz Mdzinarishvili and Simon Sherman
Cancer Informatics 2013:12 67-81
Original research | Published on 18 Feb 2013

An Empirical Evaluation of Normalization Methods for MicroRNA Arrays in a Liposarcoma Study
Li-Xuan Qin, Tom Tuschl and Samuel Singer
Cancer Informatics 2013:12 83-101
Original research | Published on 18 Mar 2013

Prognostic Estimator of Survival for Patients with Localized and Extended Pancreatic Ductal Adenocarcinoma
Michael X. Gleason, Tengiz Mdzinarishvili, Chandrakanth Are, Aaron Sasson, Alexander Sherman, Oleg Shats, and Simon Sherman,
Cancer Informatics 2013:12 103-114
Original research | Published on 18 Mar 2013

Dealing with Diversity in Computational Cancer Modeling
David Johnson, Steve McKeever, Georgios Stamatakos, Dimitra Dionysiou, Norbert Graf, Vangelis Sakkalis, Konstantinos Marias, Zhihui Wang and Thomas S. Deisboeck
Cancer Informatics 2013:12 115-124
Original research | Published on 07 May 2013

Novel Integrative Genomics Approach for Associating GWAS Information with Intrinsic Subtypes of Breast Cancer
Chindo Hicks, Tejaswi Koganti, Alexandra S. Brown, Jesus Monico, Kandis Backus and Lucio Miele
Cancer Informatics 2013:12 125-142
Original research | Published on 15 May 2013

Improved Sparse Multi-Class SVM and Its Application for Gene Selection in Cancer Classification
Lingkang Huang, Hao Helen Zhang, Zhao-Bang Zeng and Pierre R. Bushel
Cancer Informatics 2013:12 143-153
Original research | Published on 04 Aug 2013

Analysis of Patterns of Gene Expression Variation within and between Ethnic Populations in Pediatric B-ALL
Chindo Hicks, Lucio Miele, Tejaswi Koganti, LaFarra Young-Gaylor, Deidre Rogers, Vani Vijayakumar and Gail Megason
Cancer Informatics 2013:12 155-173
Original research | Published on 27 Aug 2013

Comprehensive Assessment and Network Analysis of the Emerging Genetic Susceptibility Landscape of Prostate Cancer
Chindo Hicks, Lucio Miele, Tejaswi Koganti and Srinivasan Vijayakumar
Cancer Informatics 2013:12 175-191
Original research | Published on 28 Aug 2013

Monitoring of Technical Variation in Quantitative High-Throughput Datasets
Martin Lauss, Ilhami Visne, Albert Kriegner, Markus Ringnér, Göran Jönsson and Mattias Höglund
Cancer Informatics 2013:12 193-201
Original research | Published on 23 Sep 2013

Gene Expression Meta-Analysis Identifies Cytokine Pathways and 5q Aberrations Involved in Metastasis of ERBB2 Amplified and Basal Breast Cancer
Mads Thomassen, Qihua Tan, Mark Burton and Torben A. Kruse
Cancer Informatics 2013:12 203-219
Original research | Published on 25 Nov 2013

Are the Somatic Mutation and Tissue Organization Field Theories of Carcinogenesis Incompatible?
Simon Rosenfeld
Cancer Informatics 2013:12 221-229
Original research | Published on 01 Dec 2013

2012:11

Linear Discriminant Functions in Connection with the micro-RNA Diagnosis of Colon Cancer
Jason B. Nikas and Walter C. Low
Cancer Informatics 2012:11 1-14
Original research | Published on 20 Dec 2011

Evaluating Translocation Gene Fusions by SNP Array Data
Hong Liu, Asher Zilberstein, Pascal Pannier, Frederic Fleche, Christopher Arendt, Christoph Lengauer and Chang S. Hahn
Cancer Informatics 2012:11 15-27
Original research | Published on 21 Dec 2011

Gene Selection using a High-Dimensional Regression Model with Microarrays in Cancer Prognostic Studies
Shuhei Kaneko, Akihiro Hirakawa and Chikuma Hamada
Cancer Informatics 2012:11 29-39
Original research | Published on 27 Feb 2012

A Systems Biology Approach in Therapeutic Response Study for Different Dosing Regimens—a Modeling Study of Drug Effects on Tumor Growth using Hybrid Systems
Xiangfang Li, Lijun Qian, Michale L. Bittner and Edward R. Dougherty
Cancer Informatics 2012:11 41-60
Original research | Published on 27 Feb 2012

Integrated Analysis Reveals hsa-miR-142 as a Representative of a Lymphocyte-Specific Gene Expression and Methylation Signature
Bill Andreopoulos and Dimitris Anastassiou
Cancer Informatics 2012:11 61-75
Original research | Published on 12 Mar 2012

Surface Adjustment of Reverse Phase Protein Arrays using Positive Control Spots
E. Shannon Neeley, Keith A. Baggerly and Steven M. Kornblau
Cancer Informatics 2012:11 77-86
Original research | Published on 11 Apr 2012

Major Functional Transcriptome of an Inferred Center Regulator of an ER(-) Breast Cancer Model System
Li-Yu Daisy Liu, Li-Yun Chang, Wen-Hung Kuo, Hsiao-Lin Hwa, Yi-Shing Lin, Shiu-Feng Huang, Chiung-Nien Chen, King-Jen Chang, Fon-Jou Hsieh
Cancer Informatics 2012:11 87-111
Original research | Published on 19 Apr 2012

In Silico Prediction for Regulation of Transcription Factors onTheir Shared Target Genes Indicates Relevant Clinical Implications in a Breast Cancer Population
Li-Yu D Liu, Li-Yun Chang, Wen-Hung Kuo, Hsiao-Lin Hwa, Ming-Kwang Shyu, King-Jen Chang and Fon-Jou Hsieh
Cancer Informatics 2012:11 113-137
Original research | Published on 19 Apr 2012

Identification of a Gene Expression Signature Common to Distinct Cancer Pathways
Niklaus Fankhauser, Igor Cima, Peter Wild, and Wilhelm Krek
Cancer Informatics 2012:11 139-146
Original research | Published on 08 May 2012

TNBCtype: A Subtyping Tool for Triple-Negative Breast Cancer
Xi Chen, Jiang Li, William H. Gray, Brian D. Lehmann, Joshua A. Bauer, Yu Shyr, and Jennifer A. Pietenpol
Cancer Informatics 2012:11 147-156
Original research | Published on 24 Jul 2012

Haploinsufficiency of Tumor Suppressor Genes is Driven by the Cumulative Effect of microRNAs, microRNA Binding Site Polymorphisms and microRNA Polymorphisms: An In silico Approach
Mayakannan Manikandan, Ganesh Raksha and Arasambattu Kannan Munirajan
Cancer Informatics 2012:11 157-171
Original research | Published on 29 Aug 2012

Significance Analysis of Microarrays (SAM) Offers Clues to Differences Between the Genomes of Adult Philadelphia Positive ALL and the Lymphoid Blast Transformation of CML
Colin Grace and Elisabeth P. Nacheva
Cancer Informatics 2012:11 173-183
Original research | Published on 12 Sep 2012

Newton, Laplace, and The Epistemology of Systems Biology
Michael L. Bittner and Edward R. Dougherty
Cancer Informatics 2012:11 185-190
Original research | Published on 30 Oct 2012

Mapping the Future—Merging the Old with the New Across Disciplines
J.T. Efird
Cancer Informatics 2012:11 191-192
Original research | Published on 26 Nov 2012

Prediction of Breast Cancer Metastasis by Gene Expression Profiles: A Comparison of Metagenes and Single Genes
Mark Burton, Mads Thomassen, Qihua Tan and Torben A. Kruse
Cancer Informatics 2012:11 193-217
Original research | Published on 10 Dec 2012

2011:10

Skin Cancer Recognition by Using a Neuro-Fuzzy System
Bareqa Salah, Mohammad Alshraideh, Rasha Beidas and Ferial Hayajneh
Cancer Informatics 2011:10 1-11
Original research | Published on 02 Feb 2011

In silico Analysis of Combinatorial microRNA Activity Reveals Target Genes and Pathways Associated with Breast Cancer Metastasis
Alan A. Dombkowski, Zakia Sultana, Douglas B. Craig and Hasan Jamil
Cancer Informatics 2011:10 13-29
Original research | Published on 17 Feb 2011

Extension of Cox Proportional Hazard Model for Estimation of Interrelated Age-Period-Cohort Effects on Cancer Survival
Tengiz Mdzinarishvili, Michael X. Gleason, Leo Kinarsky and Simon Sherman
Cancer Informatics 2011:10 31-44
Original research | Published on 23 Feb 2011

Reproducibility of SELDI Spectra Across Time and Laboratories
Lixia Diao, Charlotte H. Clarke, Kevin R. Coombes, Stanley R. Hamilton, Jack Roth, Li Mao, Bogdan Czerniak, Keith A. Baggerly, Jeffrey S. Morris, Eric T. Fung and Robert C. Bast Jr
Cancer Informatics 2011:10 45-64
Original research | Published on 14 Mar 2011

Self-Calibrated Warping for Mass Spectra Alignment
Q. Peter He, Jin Wang, James A. Mobley, Joshua Richman and William E. Grizzle
Cancer Informatics 2011:10 65-82
Original research | Published on 22 Mar 2011

PCCR: Pancreatic Cancer Collaborative Registry
Simon Sherman, Oleg Shats, Marsha A. Ketcham, Michelle A. Anderson, David C. Whitcomb, Henry T. Lynch, Paola Ghiorzo, Wendy S. Rubinstein, Aaron R. Sasson, William E. Grizzle, Gleb Haynatzki, Jianmin Feng, Alexander Sherman, Leo Kinarsky and Randall E. Brand
Cancer Informatics 2011:10 83-91
Original research | Published on 23 Mar 2011

Associating GWAS Information with the Notch Signaling Pathway Using Transcription Profiling
Chindo Hicks, Antonio Pannuti and Lucio Miele
Cancer Informatics 2011:10 93-108
Original research | Published on 06 Apr 2011

A Comparison of Methods for Data-Driven Cancer Outlier Discovery, and An Application Scheme to Semisupervised Predictive Biomarker Discovery
Seppo Karrila, Julian Hock Ean Lee and Greg Tucker-Kellogg
Cancer Informatics 2011:10 109-120
Original research | Published on 18 Apr 2011

Bioinformatic Prediction of Ultraviolet Light Mutagenesis Sensitivity of Human Genes and a Method for Genetically Engineering UVB Resistance
Kevin A. Lease and Chris Papageorgio
Cancer Informatics 2011:10 121-131
Original research | Published on 18 Apr 2011

A Jackknife and Voting Classifier Approach to Feature Selection and Classification
Sandra L. Taylor and Kyoungmi Kim
Cancer Informatics 2011:10 133-147
Original research | Published on 27 Apr 2011

GENT: Gene Expression Database of Normal and Tumor Tissues
Gwangsik Shin, Tae-Wook Kang, Sungjin Yang, Su-Jin Baek, Yong-Su Jeong and Seon-Young Kim
Cancer Informatics 2011:10 149-157
Original research | Published on 09 May 2011

Model-Integrated Estimation of Normal Tissue Contamination for Cancer SNP Allelic Copy Number Data
Susann Stjernqvist, Tobias Rydén and Chris D. Greenman
Cancer Informatics 2011:10 159-173
Original research | Published on 25 May 2011

Metagenes Associated with Survival in Non-Small Cell Lung Cancer
Egon Urgard, Tõnu Vooder, Urmo Võsa, Kristjan Välk, Mingming Liu, Cheng Luo, Fabian Hoti, Retlav Roosipuu, Tarmo Annilo, Jukka Laine, Christopher M. Frenz, Liqing Zhang and Andres Metspalu
Cancer Informatics 2011:10 175-183
Original research | Published on 02 Jun 2011

An Integrative Genomics Approach to Biomarker Discovery in Breast Cancer
Chindo Hicks, Rozana Asfour, Antonio Pannuti and Lucio Miele
Cancer Informatics 2011:10 185-204
Original research | Published on 25 Jul 2011

On Differential Gene Expression Using RNA-Seq Data
Juhee Lee, Yuan Ji, Shoudan Liang, Guoshuai Cai and Peter Müller
Cancer Informatics 2011:10 205-215
Original research | Published on 01 Aug 2011

Multicenter Breast Cancer Collaborative Registry
Simon Sherman, Oleg Shats, Elizabeth Fleissner, George Bascom, Kevin Yiee, Mehmet Copur, Kate Crow, James Rooney, Zubeena Mateen, Marsha A. Ketcham, Jianmin Feng, Alexander Sherman, Michael Gleason, Leo Kinarsky, Edibaldo Silva-Lopez, James Edney, Elizabeth Reed, Ann Berger and Kenneth Cowan
Cancer Informatics 2011:10 217-226
Original research | Published on 31 Aug 2011 | Highly accessed (previous month)

Cellular Imaging Using Equivalent Cross-Relaxation Rate Technique in Rabbit VX-2 Tumor Model
Hideyuki Nishiofuku, Shigeru Matsushima, Osamu Taguchi, Yoshitaka Inaba, Hidekazu Yamaura, Yozo Sato, Toshihiro Tanaka and Kimihiko Kichikawa
Cancer Informatics 2011:10 227-232
Original research | Published on 31 Aug 2011

Mathematical Prognostic Biomarker Models for Treatment Response and Survival in Epithelial Ovarian Cancer
Jason B. Nikas, Kristin L.M. Boylan, Amy P.N. Skubitz, and Walter C. Low
Cancer Informatics 2011:10 233-247
Original research | Published on 03 Oct 2011

Improved Statistical Analysis for Array CGH-Based DNA Copy Number Aberrations
Hongmei Jiang, Zhong-Zheng Zhu, Yue Yu, Simon Lin and Lifang Hou
Cancer Informatics 2011:10 249-258
Original research | Published on 19 Oct 2011

New Short Term Prediction Method for Chemical Carcinogenicity by Hepatic Transcript Profiling Following 28-Day Toxicity Tests in Rats
Hiroshi Matsumoto, Yoshikuni Yakabe, Fumiyo Saito, Koichi Saito, Kayo Sumida, Masaru Sekijima, Koji Nakayama, Hideki Miyaura, Masanori Otsuka and Tomoyuki Shirai
Cancer Informatics 2011:10 259-271
Original research | Published on 27 Oct 2011

Aberrant Signaling Pathways in Squamous Cell Lung Carcinoma
Ivy Shi, Nooshin Hashemi Sadraei, Zhong-Hui Duan, and Ting Shi
Cancer Informatics 2011:10 273-285
Original research | Published on 21 Nov 2011

Mouse 11β-Hydroxysteroid Dehydrogenase Type 2 for Human Application: Homology Modeling, Structural Analysis and Ligand-Receptor Interaction
Hideaki Yamaguchi, Tatsuo Akitaya, Yumi Kidachi, Katsuyoshi Kamiie, Toshiro Noshita, Hironori Umetsu and Kazuo Ryoyama
Cancer Informatics 2011:10 287-295
Original research | Published on 01 Dec 2011

2010:9

Dual KS: Defining Gene Sets with Tissue Set Enrichment Analysis
Yarong Yang, Eric J. Kort, Nader Ebrahimi, Zhongfa Zhang and Bin T. Teh
Cancer Informatics 2010:9 1-9
Original research | Published on 21 Jan 2010

Bimodal Gene Expression and Biomarker Discovery
Adam Ertel
Cancer Informatics 2010:9 11-14
Original research | Published on 04 Feb 2010

A Robust Gene Selection Method for Microarray-based Cancer Classification
Xiaosheng Wang and Osamu Gotoh
Cancer Informatics 2010:9 15-30
Original research | Published on 04 Feb 2010

The Power of the Web in Cancer Drug Discovery and Clinical Trial Design: Research without a Laboratory?
Christine Galustian and Angus G. Dalgleish
Cancer Informatics 2010:9 31-35
Original research | Published on 18 Feb 2010

Expression a La Bimode
James C. Willey
Cancer Informatics 2010:9 37-38
Original research | Published on 03 Mar 2010

Comparison of Two Output-Coding Strategies for Multi-Class Tumor Classification Using Gene Expression Data and Latent Variable Model as Binary Classifier
Sandeep J. Joseph, Kelly R. Robbins, Wensheng Zhang and Romdhane Rekaya
Cancer Informatics 2010:9 39-48
Original research | Published on 10 Mar 2010

Characterization of the Effectiveness of Reporting Lists of Small Feature Sets Relative to the Accuracy of the Prior Biological Knowledge
Chen Zhao, Michael L. Bittner, Robert S. Chapkin and Edward R. Dougherty
Cancer Informatics 2010:9 49-60
Original research | Published on 18 Mar 2010

Protein-protein Interaction Reveals Synergistic Discrimination of Cancer Phenotype
Jianghui Xiong, Juan Liu, Simon Rayner, Yinghui Li and Shanguang Chen
Cancer Informatics 2010:9 61-66
Original research | Published on 26 Mar 2010

Estimation of Hazard Functions in the Log-Linear Age-Period-Cohort Model: Application to Lung Cancer Risk Associated with Geographical Area
Tengiz Mdzinarishvili, Michael X. Gleason and Simon Sherman
Cancer Informatics 2010:9 67-78
Original research | Published on 14 Apr 2010

Genes with Relevance for Early to Late Progression of Colon Carcinoma Based on Combined Genomic and Transcriptomic Information from the Same Patients
Kristina K. Lagerstedt, Erik Kristiansson, Christina Lönnroth, Marianne Andersson, Britt-Marie Iresjö, Annika Gustafsson, Elisabeth Hansson, Ulf Kressner, Svante Nordgren, Fredrik Enlund and Kent Lundholm
Cancer Informatics 2010:9 79-91
Original research | Published on 23 Apr 2010

A Penalized Mixture Model Approach in Genotype/Phenotype Association Analysis for Quantitative Phenotypes
Lang Li, Silvana Borges, Robarge D. Jason, Changyu Shen, Zeruesenay Desta and David Flockhart
Cancer Informatics 2010:9 93-103
Original research | Published on 27 Apr 2010

Development and Validation of Predictive Indices for a Continuous Outcome Using Gene Expression Profiles
Yingdong Zhao and Richard Simon
Cancer Informatics 2010:9 105-114
Original research | Published on 07 May 2010

An Efficient Gatekeeper Algorithm for Detecting GxE
Jimmy T. Efird
Cancer Informatics 2010:9 115-120
Original research | Published on 12 May 2010

Optimal Network Alignment with Graphlet Degree Vectors
Tijana Milenković, Weng Leong Ng, Wayne Hayes and Nataša Pržulj
Cancer Informatics 2010:9 121-137
Original research | Published on 30 Jun 2010

Rough Set Soft Computing Cancer Classification and Network: One Stone, Two Birds
Yue Zhang
Cancer Informatics 2010:9 139-145
Original research | Published on 15 Jul 2010

Clinical Omics Analysis of Colorectal Cancer Incorporating Copy Number Aberrations and Gene Expression Data
Tsuyoshi Yoshida, Takumi Kobayashi, Masaya Itoda, Taika Muto, Ken Miyaguchi, Kaoru Mogushi, Satoshi Shoji, Kazuro Shimokawa, Satoru Iida, Hiroyuki Uetake, Toshiaki Ishikawa, Kenichi Sugihara, Hiroshi Mizushima and Hiroshi Tanaka
Cancer Informatics 2010:9 147-161
Original research | Published on 29 Jul 2010

Relationship between Selected Socio-Demographic Factors and Cancer of Oral Cavity - A Case Control Study
Abdoul Hossain Madani, Madhurima Dikshit, Debanshu Bhaduri, Abdolreza Sotoodeh Jahromi and Teamur Aghamolaei
Cancer Informatics 2010:9 163-168
Original research | Published on 11 Aug 2010

Inhibition of Antiapoptotic BCL-XL, BCL-2, and MCL-1 Proteins by Small Molecule Mimetics
D.S. Dalafave and G. Prisco
Cancer Informatics 2010:9 169-177
Original research | Published on 12 Aug 2010

Weibull-like Model of Cancer Development in Aging
Tengiz Mdzinarishvili and Simon Sherman
Cancer Informatics 2010:9 179-188
Original research | Published on 24 Aug 2010

Professional Networks in the Life Sciences: Linking the Linked
Thomas S. Deisboeck and Jonathan Sagotsky
Cancer Informatics 2010:9 189-195
Original research | Published on 25 Aug 2010

LTR: Linear Cross-Platform Integration of Microarray Data
Paul C. Boutros
Cancer Informatics 2010:9 197-208
Original research | Published on 27 Aug 2010

Heterogeneity Between Ducts of the Same Nuclear Grade Involved by Duct Carcinoma In Situ (DCIS) of the Breast
Naomi A. Miller, Judith-Anne W. Chapman, Jin Qian, William A. Christens-Barry, Yuejiao Fu, Yan Yuan, H. Lavina A. Lickley and David E. Axelrod
Cancer Informatics 2010:9 209-216
Original research | Published on 07 Sep 2010

BeadDataPackR: A Tool to Facilitate the Sharing of Raw Data from Illumina BeadArray Studies
Mike L. Smith and Andy G. Lynch
Cancer Informatics 2010:9 217-227
Original research | Published on 29 Sep 2010

Estimating Shared Copy Number Aberrations for Array CGH Data: The Linear-Median Method
Y.-X. Lin, V. Baladandayuthapani, V. Bonato and K.-A. Do
Cancer Informatics 2010:9 229-249
Original research | Published on 12 Oct 2010

Blasted Cell Line Names
Jing Wang, Lauren A. Byers, John S. Yordy, Wenbin Liu, Li Shen, Keith A. Baggerly, Uma Giri, Jeffrey N. Myers, K. Kian Ang, Michael D. Story, Luc Girard, John D. Minna, John V. Heymach and Kevin R. Coombes
Cancer Informatics 2010:9 251-255
Original research | Published on 14 Oct 2010

Cross-platform Comparison of Two Pancreatic Cancer Phenotypes
Robert B. Scharpf, Christine A. Iacobuzio-Donahue, Leslie Cope, Ingo Ruczinski, Elizabeth Garrett-Mayer, Sindhu Lakkur, Domenico Campagna and Giovanni Parmigiani
Cancer Informatics 2010:9 257-264
Original research | Published on 01 Nov 2010

Sinusoidal Cox Regression—A Rare Cancer Example
Jimmy Thomas Efird
Cancer Informatics 2010:9 265-279
Original research | Published on 28 Nov 2010

Identification of Predictive Pathways for Non-Hodgkin Lymphoma Prognosis
Xuesong Han, Yang Li, Jian Huang, Yawei Zhang, Theodore Holford, Qing Lan, Nathaniel Rothman, Tongzhang Zheng, Michael R. Kosorok and Shuangge Ma
Cancer Informatics 2010:9 281-292
Original research | Published on 07 Dec 2010

2009:7

Simulation of Different Truncated p16INK4a Forms and In Silico Study of Interaction with Cdk4
Najmeh Fahham, Mohammad Hossein Ghahremani, Soroush Sardari, Behrouz Vaziri and Seyed Nasser Ostad
Cancer Informatics 2009:7 1-11
Original research | Published on 03 Dec 2008

Applications of Microarray Technology to Acute Myelogenous Leukemia
Rashmi S. Goswami, Mahadeo A. Sukhai, Mariam Thomas, Patricia P. Reis and Suzanne Kamel-Reid
Cancer Informatics 2009:7 13-28
Original research | Published on 22 Dec 2008

Quantitative Assessment of Tissue Biomarkers and Construction of a Model to Predict Outcome in Breast Cancer Using Multiple Imputation
John W. Emerson, Marisa Dolled-Filhart, Lyndsay Harris, David L. Rimm and David P. Tuck
Cancer Informatics 2009:7 29-40
Original research | Published on 23 Dec 2008

Use of Gene Expression Profiles of Peripheral Blood Lymphocytes to Distinguish BRCA1 Mutation Carriers in High Risk Breast Cancer Families
Marie-Laure Vuillaume, Nancy Uhrhammer, Véronique Vidal, Valérie Sylvain Vidal, Valérie Chabaud, Beline Jesson, Fabrice Kwiatkowski and Yves-Jean Bignon
Cancer Informatics 2009:7 41-56
Original research | Published on 02 Mar 2009

Staging of Prostate Cancer Using Automatic Feature Selection, Sampling and Dempster-Shafer Fusion
Sandeep Chandana, Henry Leung and Kiril Trpkov
Cancer Informatics 2009:7 57-73
Original research | Published on 03 Feb 2009

An Algorithm for Identifying Novel Targets of Transcription Factor Families: Application to Hypoxia-inducible Factor 1 Targets
Yue Jiang, Bojan Cukic, Donald A. Adjeroh, Heath D. Skinner, Jie Lin, Qingxi J. Shen and Bing-Hua Jiang
Cancer Informatics 2009:7 75-89
Original research | Published on 04 Mar 2009

Combining Chromosomal Arm Status and Significantly Aberrant Genomic Locations Reveals New Cancer Subtypes
Tal Shay, Wanyu L. Lambiv, Anat Reiner-Benaim, Monika E. Hegi and Eytan Domany
Cancer Informatics 2009:7 91-104
Original research | Published on 12 Mar 2009

Dedication: Joan Elaine Althouse Weiler
James Lyons-Weiler
Cancer Informatics 2009:7 105-107
Original research | Published on 30 Apr 2009

Estrogen Exposure, Metabolism, and Enzyme Variants in a Model for Breast Cancer Risk Prediction
Fritz F. Parl, Kathleen M. Egan, Chun Li and Philip S. Crooke
Cancer Informatics 2009:7 109-121
Original research | Published on 05 May 2009

Microarray-Based Cancer Prediction Using Soft Computing Approach
Xiaosheng Wang and Osamu Gotoh
Cancer Informatics 2009:7 123-139
Original research | Published on 26 May 2009

Robust Model Selection for Classification of Microarrays
Ikumi Suzuki, Takashi Takenouchi, Miki Ohira, Shigeyuki Oba and Shin Ishii
Cancer Informatics 2009:7 141-157
Original research | Published on 25 Jun 2009

Linguistic Processing and Classification of Semi Structured Bibliographic Data on Complementary Medicine
Thomas Ostermann, Christa K. Raak, Peter F. Matthiessen, Arndt Büssing and Hartmut Zillmann
Cancer Informatics 2009:7 159-169

Original research | Published on 06 Jul 2009

In silico Analysis of Human Telomerase Reverse Transcriptase (hTERT ) Gene: Identification of a Distant Homolog of Melanoma Antigen Family Gene (MAGE)
Ruhul Amin, Jesmin, Hasan Jamil and M. Anwar Hossain
Cancer Informatics 2009:7 171-181
Original research | Published on 24 Nov 2009

A Generalized Beta Model for the Age Distribution of Cancers: Application to Pancreatic and Kidney Cancer
Tengiz Mdzinarishvili, Michael X. Gleason, Leo Kinarsky and Simon Sherman
Cancer Informatics 2009:7 183-197
Original research | Published on 04 Aug 2009

The Bimodality Index: A Criterion for Discovering  and Ranking Bimodal Signatures from Cancer Gene Expression Profiling Data
Jing Wang, Sijin Wen, W. Fraser Symmans, Lajos Pusztai and Kevin R. Coombes
Cancer Informatics 2009:7 199-216
Original research | Published on 05 Aug 2009

New Advanced Technologies to Provide Decentralised  and Secure Access to Medical Records: Case Studies  in Oncology
Catherine Quantin, Gouenou Coatrieux, François André Allaert, Maniane Fassa, Karima Bourquard, Jean-Yves Boire, Paul de Vlieger, Lydia Maigne and Vincent Breton
Cancer Informatics 2009:7 217-229
Original research | Published on 07 Aug 2009

Unblocking Blockbusters: Using Boolean Text-Mining to Optimise Clinical Trial Design and Timeline for Novel Anticancer Drugs
Richard J. Epstein
Cancer Informatics 2009:7 231-238

Original research | Published on 17 Aug 2009

Introduction of Hypermatrix and Operator Notation into a Discrete Mathematics Simulation Model of Malignant Tumour Response to Therapeutic Schemes In Vivo. Some Operator Properties
Georgios S. Stamatakos and Dimitra D. Dionysiou
Cancer Informatics 2009:7 239-251
Original research | Published on 21 Oct 2009

Discrimination of Carcinogens by Hepatic Transcript Profiling in Rats Following 28-day Administration
Hiroshi Matsumoto, Yoshikuni Yakabe, Koichi Saito, Kayo Sumida, Masaru Sekijima, Koji Nakayama, Hideki Miyaura, Fumiyo Saito, Masanori Otsuka and Tomoyuki Shirai
Cancer Informatics 2009:7 253-269
Original research | Published on 13 Nov 2009

A Novel Approach for Analysis of the Log-Linear Age-Period-Cohort Model: Application to Lung Cancer Incidence
Tengiz Mdzinarishvili, Michael X. Gleason and Simon Sherman
Cancer Informatics 2009:7 271-280
Original research | Published on 14 Dec 2009

Modeling Prognostic Factors in Resectable Pancreatic Adenocarcinomas
Taxiarchis Botsis, Valsamo K. Anagnostou, Gunnar Hartvigsen, George Hripcsak and Chunhua Weng
Cancer Informatics 2009:7 281-291
Original research | Published on 20 Jan 2010

2009:Semantic Technologies Special Issue (2009)

A Novel Information Retrieval Model for High-Throughput Molecular Medicine Modalities
Firas H. Wehbe, Steven H. Brown, Pierre P. Massion, Cynthia S. Gadd, Daniel R. Masys and Constantin F. Aliferis
Cancer Informatics 2009:8 1-17
Original research | Published on 09 Feb 2009

Semantic Web-Based Integration of Cancer Pathways and Allele Frequency Data
Matthew E. Holford, Haseena Rajeevan, Hongyu Zhao, Kenneth K. Kidd and Kei-Hoi Cheung
Cancer Informatics 2009:8 19-30
Original research | Published on 15 Jan 2009

Semantic Integration of Cervical Cancer Data Repositories to Facilitate Multicenter Association Studies: The ASSIST Approach
Theodoros Agorastos, Vassilis Koutkias, Manolis Falelakis, Irini Lekka, Themistoklis Mikos, Anastasios Delopoulos, Pericles A. Mitkas, Antonios Tantsis, Steven Weyers, Pascal Coorevits, Andreas M. Kaufmann, Roberto Kurzeja and Nicos Maglaveras
Cancer Informatics 2009:8 31-44
Original research | Published on 03 Feb 2009

Development of the Lymphoma Enterprise Architecture Database: A caBIG(TM) Silver Level Compliant System
Taoying Huang, Pareen J. Shenoy, Rajni Sinha, Michael Graiser, Kevin W. Bumpers and Christopher R. Flowers
Cancer Informatics 2009:8 45-64
Original research | Published on 03 Apr 2009

Using Semantic Web Technologies to Annotate and Align Microarray Designs
Sebastian Szpakowski, James McCusker and Michael Krauthammer
Cancer Informatics 2009:8 65-73
Original research | Published on 13 May 2009

Integration of Neuroimaging and Microarray Datasets  through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes
Spiro P. Pantazatos, Jianrong Li, Paul Pavlidis and Yves A. Lussier
Cancer Informatics 2009:8 75-94
Original research | Published on 08 Jun 2009

2008:1

Bayesian Estimation of Performance Measures of Cervical Cancer Screening Tests in the Presence of Covariates and Absence of a Gold Standard
Edson Zangiacomi Martinez, Francisco Louzada-Neto, Sophie Françoise Mauricette Derchain, Jorge Alberto Achcar, Renata Clementino Gontijo, Luis Otávio Zanatta Sarian and Kari Juhani Syrjänen
Cancer Informatics 2008:6 33-46
Original research | Published on 14 Feb 2008

Global Associations between Copy Number and Transcript mRNA Microarray Data: An Empirical Study
Wenjuan Gu, Hyungwon Choi and Debashis Ghosh
Cancer Informatics 2008:6 17-23
Original research | Published on 09 Feb 2008

Estimating the Proportion of True Null Hypotheses for Multiple Comparisons
Hongmei Jiang and R.W. Doerge
Cancer Informatics 2008:6 25-32
Original research | Published on 14 Feb 2008

Evaluating Microarray-based Classifiers: An Overview
A.-L. Boulesteix, C. Strobl, T. Augustin and M. Daumer
Cancer Informatics 2008:6 77-97
Original research | Published on 29 Feb 2008

Effect of Quantitative Nuclear Image Features on Recurrence of Ductal Carcinoma In Situ (DCIS) of the Breast
David E. Axelrod, Naomi A. Miller, H. Lavina Lickley, Jin Qian, William A. Christens-Barry, Yan Yuan, Yuejiao Fu and Judith-Anne W. Chapman
Cancer Informatics 2008:6 99-109
Original research | Published on 01 Mar 2008

A Computational Model of Quantitative Chromatin Immunoprecipitation (ChIP) Analysis
Jingping Xie, Philip S. Crooke, Brett A. McKinney, Joel Soltman and Stephen J. Brandt
Cancer Informatics 2008:6 138-146
Original research | Published on 12 Mar 2008

Chromosome 20q Amplification Regulates in Vitro Response to Kinesin-5 Inhibitor
Aimee L. Jackson, Mao Mao, Sumire Kobayashi, Teresa Ward, Matthew Biery, Hongyue Dai, Steven R. Bartz and Peter S. Linsley
Cancer Informatics 2008:6 147-164
Original research | Published on 26 Mar 2008

DNA Copy Number Analysis in Gastrointestinal Stromal Tumors Using Gene Expression Microarrays
Cristina R. Antonescu, Kai Wu, Guoliang Leon Xing, Manqiu Cao, Yaron Turpaz, Margaret A. Leversha, Earl Hubbell, Robert G. Maki, C. Garrett Miyada, and Raji Pillai
Cancer Informatics 2008:6 59-75
Original research | Published on 27 Mar 2008

Comparisons of Robustness and Sensitivity between Cancer and Normal Cells by Microarray Data
Liang-Hui Chu and Bor-Sen Chen
Cancer Informatics 2008:6 165-181
Original research | Published on 28 Mar 2008

MCAM: A Database to Accelerate the Identification of Functional Cell Adhesion Molecules
Anguraj Sadanandam, Sudipendra Nath Pal, Joe Ziskovsky, Prathibha Hegde and Rakesh K. Singh
Cancer Informatics 2008:6 47-50
Original research | Published on 31 Mar 2008

A Standards based Ontological Approach to Information Handling for use by Organizations Providing Human Tissue for Research
Mary E. Edgerton, Carl Morrison, Virginia A. LiVolsi, Christopher A. Moskaluk, Stephen J. Qualman, M. Kay Washington and William E. Grizzle
Cancer Informatics 2008:6 127-137
Original research | Published on 10 Apr 2008

Sample Preparation for in vitro Analysis of Iodine in Thyroid Tissue using X-ray Fluorescence
Marie Hansson, Mats Isaksson and Gertrud Berg
Cancer Informatics 2008:6 51-57
Original research | Published on 10 Apr 2008

An Application of a Service-oriented System to Support ArrayAnnotation in Custom Chip Design for Epigenomic Analysis
Junghee Han, Dustin Potter, Tahsin Kurc, Greg Singer, Pearlly S. Yan, Sun Hao, Shannon Hastings, Stephen Langella, Scott Oster, Ramana V. Davuluri,Tim H.-M. Huang and Joel H. Saltz
Cancer Informatics 2008:6 111-125
Original research | Published on 10 Apr 2008

Bayesian Mass Spectra Peak Alignment from Mass Charge Ratios
Junfeng Liu, Weichuan Yu, Baolin Wu and Hongyu Zhao
Cancer Informatics 2008:6 217-241
Original research | Published on 11 Apr 2008

Uncovering Biological Network Function via Graphlet Degree Signatures
Tijana Milenković and Nataša Pržulj
Cancer Informatics 2008:6 257-273

Original research | Published on 14 Apr 2008

Comparison of a Label-Free Quantitative Proteomic Method Based on Peptide Ion Current Area to the Isotope Coded Affinity Tag Method
Soyoung Ryu, Byron Gallis, Young Ah Goo, Scott A. Shaffer, Dragan Radulovic, David R. Goodlett
Cancer Informatics 2008:6 243-255
Original research | Published on 17 Apr 2008

Classifying Variants of Undetermined Significance in BRCA2 with Protein Likelihood Ratios
Rachel Karchin, Mukesh Agarwal, Andrej Sali, Fergus Couch and Mary S. Beattie
Cancer Informatics 2008:6 203-216
Original research | Published on 18 Apr 2008

Connections Between ETV6-Modulated Genes: Identification of Shared Features
Gino Boily, Patrick Beaulieu, Jasmine Healy and Daniel Sinnett
Cancer Informatics 2008:6 183-201
Original research | Published on 21 Apr 2008

BRB-ArrayTools Data Archive for Human Cancer Gene Expression: A Unique and Efficient Data Sharing Resource
Yingdong Zhao and Richard Simon
Cancer Informatics 2008:6 9-15
Original research | Published on 21 Apr 2008

Constructing Tumor Progression Pathways and Biomarker Discovery with Fuzzy Kernel Kmeans and DNA Methylation Data
Zhenqiu Liu, Zhongmin Guo and Ming Tan
Cancer Informatics 2008:6 1-7
Original research | Published on 25 Jan 2008

An Analysis of Risk Factors for Developing Hepatocellular Carcinoma in a Group of Hepatitis C Patients with Stage 3 Fibrosis following Interferon Therapy
Sabina Mahmood , Kazumi Togawa, Miwa Kawanaka, Gouichi Niiyama, Gotaro Yamada
Cancer Informatics 2008:6 381-387
Original research | Published on 23 Apr 2008

Non-Negative Matrix Factorization for the Analysis of Complex Gene Expression Data: Identification of Clinically Relevant Tumor Subtypes
Attila Frigyesi and Mattias Höglund
Cancer Informatics 2008:6 275-292
Original research | Published on 29 May 2008

Detecting Role Errors in the Gene Hierarchy of the NCI Thesaurus
Hua Min, Barry Cohen, Michael Halper, Marc Oren and Yehoshua Perl
Cancer Informatics 2008:6 293-313
Original research | Published on 27 May 2008

The Anti-tumour Agent, Cisplatin, and its Clinically Ineffective Isomer, Transplatin, Produce Unique Gene Expression Profiles in Human Cells
Anne M. Galea and Vincent Murray
Cancer Informatics 2008:6 315-355

Original research | Published on 10 Jun 2008

An Integrative Analysis of microRNA and mRNA Expression - A Case Study
Li-Xuan Qin
Cancer Informatics 2008:6 369-379
Original research | Published on 17 Jun 2008

A Biological Evaluation of Six Gene Set Analysis Methods for Identification of Differentially Expressed Pathways in Microarray Data
Irina Dinu, Qi Liu, John D. Potter, Adeniyi J. Adewale, Gian S. Jhangri, Thomas Mueller, Gunilla Einecke, Konrad Famulsky, Philip Halloran and Yutaka Yasui
Cancer Informatics 2008:6 357-368
Original research | Published on 20 Jun 2008

Efficiency Analysis of Competing Tests for Finding Differentially Expressed Genes in Lung Adenocarcinoma
Rick Jordan, Satish Patel, Hai Hu, and James Lyons-Weiler
Cancer Informatics 2008:6 389-421

Original research | Published on 14 Jul 2008

What Does PLIER Really Do?
Terry M.Therneau and Karla V.Ballman
Cancer Informatics 2008:6 423-431
Original research | Published on 27 Aug 2008

Grammatical Immune System Evolution for Reverse Engineering Nonlinear Dynamic Bayesian Models
B.A. McKinney and D. Tian
Cancer Informatics 2008:6 433-447
Original research | Published on 28 Aug 2008

Algorithmic Discovery of Methylation “Hot Spots” in DNA from Lymphoma Patients
Chris Papageorgio, Robert Harrison, Farahnaz B. Rahmatpanah, Kristen Taylor, Wade Davis and Charles W. Caldwell
Cancer Informatics 2008:6 449-453
Original research | Published on 04 Sep 2008

An Analysis Pipeline for Genome-wide Association Studies
Stefan Stefanov, James Lautenberger and Bert Gold
Cancer Informatics 2008:6 455-461
Original research | Published on 24 Sep 2008

Modeling and Analyzing Gene Co-Expression in Hepatocellular Carcinoma Using Actor-Semiotic Networks and Centrality Signatures
David C.Y. Fung
Cancer Informatics 2008:6 463-474
Original research | Published on 05 Nov 2008

2007:1

Asterias: A Parallelized Web-based Suite for the Analysis of Expression and aCGH Data
Andreu Alibés, Edward R. Morrissey, Andrés Cañada, Oscar M. Rueda, David Casado, Patricio Yankilevich and Ramón Díaz-Uriarte
Cancer Informatics 2007:3 1-9
Original research | Published on 03 Feb 2007

Analysis of Gene Expression Data Using BRB-Array Tools
Richard Simon, Amy Lam, Ming-Chung Li, Michael Ngan, Supriya Menenzes and Yingdong Zhao
Cancer Informatics 2007:3 11-17
Original research | Published on 04 Feb 2007

Identifying Biomarkers from Mass Spectrometry Data with Ordinal Outcome
Deukwoo Kwon, Mahlet G. Tadesse, Naijun Sha, Ruth M. Pfeiffer and Marina Vannucci
Cancer Informatics 2007:3 19-28
Original research | Published on 05 Feb 2007

Statistical Redundancy Testing for Improved Gene Selection in Cancer Classification Using Microarray Data
Simin Hu and J. Sunil Rao
Cancer Informatics 2007:3 29-41
Original research | Published on 06 Feb 2007

Gamma-Normal-Gamma Mixture Model for Detecting Differentially Methylated Loci in Three Breast Cancer Cell Lines
Abbas Khalili, Dustin Potter, Pearlly Yan, Lang Li, Joe Gray, Tim Huang and Shili Lin
Cancer Informatics 2007:3 43-54
Original research | Published on 07 Feb 2007

CGHregions: Dimension Reduction for Array CGH Data with Minimal Information Loss
Mark A. van de Wiel and Wessel N. van Wieringen
Cancer informatics 2007:3 55-63
Original research | Published on 08 Feb 2007

Identification and Characterization of Renal Cell Carcinoma Gene Markers
Gul S. Dalgin, Dustin T. Holloway, Louis S. Liou and Charles DeLisi
Cancer Informatics 2007:3 65-92
Original research | Published on 09 Feb 2007

Data Mining for Gene Networks Relevant to Poor Prognosis in Lung Cancer via Backward-Chaining Rule Induction
Mary E. Edgerton, Douglas H. Fisher, Lianhong Tang, Lewis J. Frey and Zhihua Chen

Cancer Informatics 2007:3 93-114

Original research | Published on 10 Feb 2007

Dedication: Chiara Silvestrini
Mary E. Edgerton
Cancer Informatics 2007:3 123
Original research | Published on 12 Feb 2007

Comparison of Predicted Probabilities of Proportional Hazards Regression and Linear Discriminant Analysis Methods Using a Colorectal Cancer Molecular Biomarker Database
Sreelatha Meleth, Chakrapani Chatla, Venkat R. Katkoori, Billie Anderson, James M. Hardin, Nirag C. Jhala, Al Bartolucci, William E. Grizzle, Upender Manne
Cancer Informatics 2007:3 115-122
Original research | Published on 02 Mar 2007

Feature Selection for Predicting Tumor Metastases in Microarray Experiments using Paired Design
Qihua Tan, Mads Thomassen and Torben A. Kruse
Cancer Informatics 2007:3 213-218
Original research | Published on 20 Mar 2007

Global Tumor RNA Expression in Early Establishment of Experimental Tumor Growth and Related Angiogenesis following Cox-Inhibition Evaluated by Microarray Analysis
Hans Axelsson, Christina Lönnroth, Marianne Andersson, Wenhua Wang and Kent Lundholm
Cancer Informatics 2007:3 125-139
Original research | Published on 01 May 2007

Cross-platform Analysis of Cancer Biomarkers: A Bayesian Network Approach to Incorporating Mass Spectrometry and Microarray Data
Xutao Deng, Huimin Geng and Hesham H. Ali
Cancer Informatics 2007:3 183-202
Original research | Published on 29 Apr 2007

Development of Query Strategies to Identify a Histologic Lymphoma Subtype in a Large Linked Database System
Michael Graiser, Susan G. Moore, Rochelle Victor, Ashley Hilliard, Leroy Hill, Michael S. Keehan and Christopher R. Flowers
Cancer Informatics 2007:3 149-158
Original research | Published on 04 May 2007

Statistical Issues and Analyses of in vivo and in vitro Genomic Data in order to Identify Clinically Relevant Profiles
Laila M. Poisson and Debashis Ghosh
Cancer Informatics 2007:3 231-243
Original research | Published on 10 May 2007

Investigation of miRNA Biology by Bioinformatic Tools and Impact of miRNAs in Colorectal Cancer: Regulatory Relationship of c-Myc and p53 with miRNAs
Yaguang Xi, John R. Edwards and Jingfang Ju
Cancer Informatics 2007:3 245-253
Original research | Published on 31 May 2007

A Novel Cross-Disciplinary Multi-Institute Approach to Translational Cancer Research: Lessons Learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC)
Ashokkumar A. Patel, John R. Gilbertson, Louise C. Showe, Jack W. London, Eric Ross, Michael F. Ochs, Joseph Carver, Andrea Lazarus, Anil V. Parwani, Rajiv Dhir, J. Robert Beck, Michael Liebman, Fernando U. Garcia, Jeff Prichard, Myra Wilkerson, Ronald B. Herberman, Michael J. Becich, and the PCABC.
Cancer Informatics 2007:3 255-274
Original research | Published on 08 Jun 2007

Simultaneous EGFR and VEGF Alterations in Non-Small Cell Lung Carcinoma Based on Tissue Microarrays
Evangelos Tsiambas, Athanasios Stamatelopoulos, Andreas Karameris, Ioannis Panagiotou, Dimitrios Rigopoulos, Antonios Chatzimichalis, Demosthenes Bouros and Efstratios Patsouris
Cancer Informatics 2007:3 275-284
Original research | Published on 12 Jun 2007

Comparison of Supervised Classification Methods for Protein Profiling in Cancer Diagnosis
Nadège Dossat, Alain Mangé, Jérôme Solassol, William Jacot, Ludovic Lhermitte, Thierry Maudelonde, Jean-Pierre Daurès and Nicolas Molinari
Cancer Informatics 2007:3 295-305
Original research | Published on 19 Jul 2007

Overlay Tool© for aCGHViewer©: An Analysis Module Built for aCGHViewer© used to Perform Comparisons of Data Derived from Different Microarray Platforms
Ken C. Lo, Ganesh Shankar, Yaron Turpaz, Dione Bailey, Michael R. Rossi, Tania Burkhardt, Ping Liang and John K. Cowell
Cancer Informatics 2007:3 307-319
Original research | Published on 08 Aug 2007

Parametric Power Spectral Density Analysis of Noise from Instrumentation in MALDI TOF Mass Spectrometry
Hyunjin Shin, Miray Mutlu, John M. Koomen and Mia K. Markey
Cancer Informatics 2007:3 219-230
Original research | Published on 17 Sep 2007

Tumor Genome Wide DNA Alterations Assessed by Array CGH in Patients with Poor and Excellent Survival Following Operation for Colorectal Cancer
Kristina K. Lagerstedt, Johan Staaf, Göran Jönsson, Elisabeth Hansson, Christina Lönnroth, Ulf Kressner, Lars Lindström, Svante Nordgren, Åke Borg and Kent Lundholm
Cancer Informatics 2007:3 341-355
Original research | Published on 12 Oct 2007

Combining Clinical and Genomic Covariates via Cov-TGDR
Shuangge Ma and Jian Huang
Cancer Informatics 2007:3 371-378
Original research | Published on 15 Oct 2007

Systems Level Modeling of the Cell Cycle Using Budding Yeast
B.P. Ingalls, B.P. Duncker, D.R. Kim and B.J. McConkey
Cancer Informatics 2007:3 357-370
Original research | Published on 11 Dec 2007

Comparison of Computational Algorithms for the Classification of Liver Cancer using SELDI Mass Spectrometry: A Case Study
Changyu Shen, Timothy E Breen, Lacey E Dobrolecki, C. Max Schmidt, George W. Sledge , Kathy D. Miller and Robert J Hickey
Cancer Informatics 2007:3 329-339
Original research | Published on 11 Dec 2007

Germinal Center B Cell-Like (GCB) and Activated B Cell-Like (ABC) Type of Diffuse Large B Cell Lymphoma (DLBCL): Analysis of Molecular Predictors, Signatures, Cell Cycle State and Patient Survival
S. Blenk, J. Engelmann, M. Weniger, J. Schultz, M. Dittrich, A. Rosenwald, H.K. Müller-Hermelink, T. Müller and T. Dandekar
Cancer Informatics 2007:3 399-420
Original research | Published on 12 Dec 2007

Public Databases and Software for the Pathway Analysis of Cancer Genomes
Ivy F.L. Tsui, Raj Chari, Timon P.H. Buys and Wan L. Lam
Cancer Informatics 2007:3 379-397
Original research | Published on 12 Dec 2007

Common Peak Approach Using Mass Spectrometry Data Sets for Predicting the Effects of Anticancer Drugs on Breast Cancer
Masaru Ushijima, Satoshi Miyata, Shinto Eguchi, Masanori Kawakita, Masataka Yoshimoto, Takuji Iwase, Futoshi Akiyama, Goi Sakamoto, Koichi Nagasaki, Yoshio Miki, Tetsuo Noda, Yutaka Hoshikawa and Masaaki Matsuura
Cancer Informatics 2007:3 285-293
Original research | Published on 14 Dec 2007

A Practical Multifaceted Approach to Selecting Differentially Expressed Genes
Yingye Zheng and Margaret Pepe
Cancer Informatics 2007:3 203-212
Original research | Published on 15 Jan 2008

Estimating the False Discovery Rate Using Mixed Normal Distribution for Identifying Differentially Expressed Genes in Microarray Data Analysis
Akihiro Hirakawa, Yasunori Sato, Takashi Sozu, Chikuma Hamada, Isao Yoshimura
Cancer Informatics 2007:3 140-148
Original research | Published on 22 Jan 2008

The Roles of β²-Tubulin Mutations and Isotype Expression in Acquired Drug Resistance
J. Torin Huzil, Ke Chen, Lukasz Kurgan and Jack A. Tuszynski
Cancer Informatics 2007:3 159-181
Original research | Published on 27 Apr 2007

Normalized, Segmented or Called aCGH Data?
Wessel N. van Wieringen, Mark A. van de Wiel and Bauke Ylstra
Cancer Informatics 2007:3 321-327
Original research | Published on 17 Sep 2007

2007:Systems Biology Special Issue (2007)

Advancing Cancer Systems Biology: Introducing the Center for the Development of a Virtual Tumor, CViT
Thomas S. Deisboeck, Le Zhang and Sean Martin
Cancer Informatics 2007:5 1-8
Original research | Published on 30 Mar 2007

Cancer as a System Failure
Dennis Wigle and Igor Jurisica
Cancer Informatics 2007:5 10-18
Original research | Published on 03 Apr 2007

Exploratory Visual Analysis of Statistical Results from Microarray Experiments Comparing High and Low Grade Glioma
David M. Reif, Mark A. Israel and Jason H. Moore
Cancer Informatics 2007:5 19-24
Original research | Published on 01 Apr 2007

Application of Gene Shaving and Mixture Models to Cluster Microarray Gene Expression Data
K-A. Do, G.J. McLachlan, R. Bean and S. Wen
Cancer Informatics 2007:5 25-43
Original research | Published on 02 Apr 2007

Perturbation of Interaction Networks for Application to Cancer Therapy
Adrian P. Quayle, Asim S. Siddiqui and Steven J. M. Jones
Cancer Informatics 2007:5 45-65
Original research | Published on 01 Apr 2007

2007:Imaging Special Issue (2007)

An Architecture for Computer-Aided Detection and Radiologic Measurement of Lung Nodules in Clinical Trials
Matthew S. Brown, Richard Pais, Peiyuan Qing, Sumit Shah, Michael F. McNitt-Gray, Jonathan G. Goldin, Iva Petkovska, Lien Tran and Denise R. Aberle
Cancer Informatics 2007:4 25-31
Original research | Published on 12 May 2007

Change Detection & Characterization: a New Tool for Imaging Informatics and Cancer Research
Julia W. Patriarche and Bradley J. Erickson
Cancer Informatics 2007:4 1-11
Original research | Published on 12 May 2007

Imaging in Clinical Trials
Bradley J Erickson and Jan C Buckner
Cancer Informatics 2007:4 13-18
Original research | Published on 12 May 2007

Image Registration Improves Confidence and Accuracy of Image Interpretation
Bradley J. Erickson, Julia Patriarche, Christopher Wood, Norbert Campeau, E. Paul Lindell, Vladimir Savcenko, Norman Arslanlar and Liqin Wang
Cancer Informatics 2007:4 19-24
Original research | Published on 12 May 2007

DICOM Structured Reporting and Cancer Clinical Trials Results
David A. Clunie
Cancer Informatics 2007:4 33-56
Original research | Published on 12 May 2007

2006:1

Plasma Protein Profiles Differ Between Women Diagnosed with Cervical Intraepithelial Neoplasia (CIN) 1 and 3
Chandrika J. Piyathilake, Denise K. Oelschlager, Sreelatha Meleth, Edward E. Partridge and William E. Grizzle
Cancer Informatics 2006:2 345-349
Original research | Published on 27 Feb 2007

Cancer Informatics in the U.K.: The NCRI Informatics Initiative
Fiona Reddington, J. Max Wilkinson, Robin Clark, Helen Parkinson, Peter Kerr and Richard Begent
Cancer Informatics 2006:2 389-394
Original research | Published on 26 Feb 2007

Application of a New Probabilistic Model for Mining Implicit Associated Cancer Genes from OMIM and Medline
Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto and Hiroshi Mamitsuka
Cancer Informatics 2006:2 361-371
Original research | Published on 25 Feb 2007

Detecting Outlier Microarray Arrays by Correlation and Percentage of Outliers Spots
Song Yang, Xiang Guo, Yaw-Ching Yang, Denise Papcunik, Caroline Heckman, Jeffrey Hooke, Craig D. Shriver, Michael N. Liebman and Hai Hu
Cancer Informatics 2006:2 351-360
Original research | Published on 24 Feb 2007

An Empirical Study of Univariate and Genetic Algorithm-Based Feature Selection in Binary Classification with Microarray Data
Michael Lecocke and Kenneth Hess
Cancer Informatics 2006:2 313-327
Original research | Published on 23 Feb 2007

A Hybrid Approach for Biomarker Discovery from Microarray Gene Expression Data for Cancer Classification
Yanxiong Peng, Wenyuan Li and Ying Liu
Cancer Informatics 2006:2 301-311
Original research | Published on 22 Feb 2007

Integrative Analysis of Gene Expression Data Including an Assessment of Pathway Enrichment for Predicting Prostate Cancer
Pingzhao Hu, Celia M.T. Greenwood and Joseph Beyene
Cancer Informatics 2006:2 289-300
Original research | Published on 21 Feb 2007

Heterogeneous Biomedical Database Integration Using a Hybrid Strategy: A p53 Cancer Research Database
Vadim Y. Bichutskiy, Richard Colman, Rainer K. Brachmann and Richard H. Lathrop
Cancer Informatics 2006:2 277-287
Original research | Published on 20 Feb 2007

Data Perturbation Independent Diagnosis and Validation of Breast Cancer Subtypes Using Clustering and Patterns
G. Alexe, G.S. Dalgin, R. Ramaswamy, C. DeLisi and G. Bhanot
Cancer Informatics 2006:2 243-274
Original research | Published on 19 Feb 2007

Construction and Clarification of Dynamic Gene Regulatory Network of Cancer Cell Cycle via Microarray Data
Cheng-Wei Li, Yung-Hsiang Chu and Bor-Sen Chen
Cancer Informatics 2006:2 223-241
Original research | Published on 18 Feb 2007

Tumor Growth Rate Approximation-Assisted Estimation
Lihua An, S. Ejaz Ahmed and Adnan Ali
Cancer Informatics 2006:2 214-221
Original research | Published on 17 Feb 2007

On the Number of Close-to-Optimal Feature Sets
Edward R. Dougherty and Marcel Brun
Cancer Informatics 2006:2 189-196
Original research | Published on 16 Feb 2007

A mathematical model for the onset of avascular tumor growth in response to the loss of p53 function
Howard A. Levine, Michael W. Smiley, Anna L. Tucker and Marit Nilsen-Hamilton
Cancer Informatics 2006:2 163-188
Original research | Published on 17 Feb 2007

Challenges in the Analysis of Mass-Throughput Data: A Technical Commentary from the Statistical Machine Learning Perspective
Constantin F. Aliferis, Alexander Statnikov and Ioannis Tsamardinos
Cancer Informatics 2006:2 133-162
Original research | Published on 16 Feb 2007

Ovarian Cancer Classification based on Mass Spectrometry Analysis of Sera
Baolin Wu, Tom Abbott, David Fishman, Walter McMurray, Gil Mor, Kathryn Stone, David Ward, Kenneth Williams, Hongyu Zhao
Cancer Informatics 2006:2 123-132
Original research | Published on 17 Feb 2007

Applying a 4D multiscale in vivo tumor growth model to the exploration of radiotherapy scheduling: The effects of weekend treatment gaps and p53 gene status on the response of fast growing solid tumors
Dimitra D. Dionysiou and Georgios S. Stamatakos
Cancer Informatics 2006:2 113-121
Original research | Published on 16 Feb 2007

Databases and QSAR for Cancer Research
Adeel Malik, Hemajit Singh, Munazah Andrabi, Syed Akhtar Husain and Shandar Ahmad
Cancer Informatics 2006:2 99-111
Original research | Published on 15 Feb 2007

Merging microarray data, robust feature selection, and predicting prognosis in prostate cancer
Jing Wang, Kim Anh Do, Sijin Wen, Spyros Tsavachidis, Timothy J. McDonnell, Christopher J. Logothetis and Kevin R. Coombes
Cancer Informatics 2006:2 87-97
Original research | Published on 14 Feb 2007

PubMed QUEST: The PubMed Query Search Tool. An informatics tool to aid cancer centers and cancer investigators in searching the PubMed databases
David A. Hanauer and Arul M. Chinnaiyan
Cancer Informatics 2006:2 79-82
Original research | Published on 12 Feb 2007

Computational Methods for the Analysis of Array Comparative Genomic Hybridization
Raj Chari, William W. Lockwood and Wan L. Lam
Cancer Informatics 2006:2 48-58
Original research | Published on 10 Feb 2007

Multi-marker testing for cancer: what can we learn from modern prenatal testing for Trisomy-21
Erasmus Schneider and Gerald Mizejewski
Cancer Informatics 2006:2 44-47
Original research | Published on 09 Feb 2007

aCGHViewer: A Generic Visualization Tool For aCGH data
Ganesh Shankar, Michael R. Rossi, Devin E. McQuaid, Jeffrey M. Conroy, Daniel G. Gaile, John K. Cowell, Norma J. Nowak, Ping Liang
Cancer Informatics 2006:2 36-43
Original research | Published on 08 Feb 2007

Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools
Daisuke Kihara, Yifeng David Yang & Troy Hawkins
Cancer Informatics 2006:2 25-35
Original research | Published on 07 Feb 2007

Cancer Informatics Vision: caBIG
Andrew C. von Eschenbach, M.D. and Kenneth Buetow, Ph.D.
Cancer Informatics 2006:2 22-24
Original research | Published on 06 Feb 2007

Magellan: A Web Based System for the Integrated Analysis of Heterogeneous Biological Data and Annotations; Application to DNA Copy Number and Expression Data in Ovarian Cancer
Chris B. Kingsley, Wen-Lin Kuo, Daniel Polikoff, Andy Berchuck, Joe W. Gray, and Ajay N. Jain
Cancer Informatics 2006:2 10-21
Original research | Published on 05 Feb 2007

Spotlight on Cancer Informatics: Constantin Alifieris, M.D., Ph.D.
Constantin Alifieris
Cancer Informatics 2006:2 3-9
Original research | Published on 04 Feb 2007

Biomarker Development Study Publication Standards are Dead - Long Live Biomarker Development Study Publication Standards!
Dr James Lyons-Weiler
Cancer Informatics 2006:2 1-2
Original research | Published on 03 Feb 2007

Spotlight on Cancer Informatics: Georgios S Stamatakos, PhD
Georgios S Stamatakos
Cancer Informatics 2006:2 83-86
Original research | Published on 13 Feb 2007

Decentralized Data Sharing of Tissue Microarrays for Investigative Research in Oncology
Wenjin Chen, Cristina Schmidt, Manish Parashar, Michael Reiss,and David J. Foran
Cancer Informatics 2006:2 373-388
Original research | Published on 06 Jun 2007

Spatial Turing-type Pattern Formation in a Model of Signal Transduction Involving Membrane-based Receptors Coupled by G Proteins
Chontita Rattanakul, Yongwimon Lenbury, Jonathan Bell, Varanuj Chatsudthipong, Wannapong Triampo and Philip S.Crooke
Cancer Informatics 2006:2 329-343
Original research | Published on 06 Jun 2007

Applications of Machine Learning in Cancer Prediction and Prognosis
Joseph A. Cruz and David S. Wishart
Cancer Informatics 2006:2 59-77
Original research | Published on 11 Feb 2007

2005:1

Standards of Excellence and Open Questions in Cancer Biomarker Research: An Informatics Perspective
Dr James Lyons-Weiler
Cancer Informatics 2005:1 1-7
Original research | Published on 28 Feb 2007

Design of Early Validation Trials of Biomarkers
Daniel Normolle, Mack T. Ruffin IV and Dean Brenner
Cancer Informatics 2005:1 25-31
Original research | Published on 25 Feb 2007

Proteomics: Analysis of Spectral Data
Harry B Burke
Cancer Informatics 2005:1 15-24
Original research | Published on 24 Feb 2007

Characterising phase variations in MALDI-TOF data and correcting them by peak alignment
Simon M Lin, Richard P Haney, Michael J Campa, Michael C Fitzgerald and Edward F Patz, Jr.
Cancer Informatics 2005:1 32-40
Original research | Published on 23 Feb 2007

Impact of Freeze-thaw Cycles and Storage Time on Plasma Samples Used in Mass Spectrometry Based Biomarker Discovery Projects
Breeana L Mitchell, Yutaka Yasui, Christopher I Li, Annette L. Fitzpatrick, Paul D Lampe
Cancer Informatics 2005:1 98-104
Original research | Published on 22 Feb 2007

Assessing the Statistical Significance of the Achieved Classification Error of Classifiers Constructed using Serum Peptide Profiles, and a Prescription for Random Sampling Repeated Studies for Massive High-Throughput Genomic and Proteomic Studies
James Lyons-Weiler, Richard Pelikan, Herbert J Zeh III, David C Whitcomb, David E Malehorne, William L Bigbeee, Milos Hauskrecht
Cancer Informatics 2005:1 53-77
Original research | Published on 21 Feb 2007

Novel approaches to smoothing and comparing SELDI TOF spectra
Sreelatha Meleth, Isam-Eldin Eltoum, Liu Zhu, Denise Oelschlager, Chandrika Piyathilake, David Chhieng and William E. Grizzle
Cancer Informatics 2005:1 78-85
Original research | Published on 20 Feb 2007

The Need for Review and Understanding of SELDI/MALDI Mass Spectroscopy Data Prior to Analysis
William E. Grizzle, O. John Semmes, William Bigbee, Liu Zhu, Gunjan Malik, Denise K Oelschlager, Barkha Manne, Upender Manne
Cancer Informatics 2005:1 86-97
Original research | Published on 19 Feb 2007

Understanding the characteristics of mass spectrometry data through the use of simulation
Kevin R. Coombes, John M. Koomen, Keith A. Baggerly, Jeffrey S. Morris, and Ryuji Kobayashi
Cancer Informatics 2005:1 41-52
Original research | Published on 18 Feb 2007

Dedication: Sarah Amy Hill
Cancer Informatics 2005:1 8
Original research | Published on 27 Feb 2007

Bias, Randomization, and Ovarian Proteomic Data: A Reply to "Producers and Consumers"
Keith A. Baggerly, Kevin R. Coombes, and Jeffrey S. Morris
Cancer Informatics 2005:1 9-14
Original research | Published on 26 Feb 2007