Difference between revisions of "Literature Studies"

(Papers added)
Line 3: Line 3:
  
 
== Results from Literature ==
 
== Results from Literature ==
 +
 +
 +
=== Classification ===
 +
===== 2003 =====
 +
Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data
 +
===== 2005 =====
 +
* [[A review and comparison of classification algorithms for medical decision making]]
 +
===== 2016 =====
 +
* [[Predicting Breast Cancer Survivability Using Data Mining Techniques]]
 +
 +
 +
 +
=== Feature Selection ===
 +
==== Identifying differences ====
 +
===== 2017 =====
 +
* [[Identification of differentially expressed peptides in high-throughput proteomics data]]
 +
* [[In-depth method assessments of differentially expressed protein detection for shotgun proteomics data with missing values]]
 +
==== Dimension reduction ====
 +
===== 2008 =====
 +
* [[On the Relationship Between Feature Selection and Classification Accuracy]]
 +
===== 2015 =====
 +
* [[Comparing feature selection methods for highdimensional imbalanced data: identifying rheumatoid arthritis cohorts from routine data]]
 +
 +
 +
=== Imputation methods for missing values ===
 +
===== 2001 =====
 +
* [[Missing value estimation methods for DNA microarrays]]
 +
===== 2015 =====
 +
* [[Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies]]
 +
* [[Multiple imputation and analysis for high-dimensional incomplete proteomics data]]
 +
===== 2018 =====
 +
* [[Missing Value Imputation Approach for Mass Spectrometry-based Metabolomics Data]]
 +
 +
  
 
=== ODE-based Modelling ===
 
=== ODE-based Modelling ===
 +
===== 2001 =====
 +
* [[Ways to Fit a PK Model with Some Data Below the Quantification Limit]]
 +
===== 2008 =====
 
* [[Hybrid optimization method with general switching strategy for parameter estimation]]
 
* [[Hybrid optimization method with general switching strategy for parameter estimation]]
 +
===== 2013 =====
 
* [[Lessons Learned from Quantitative Dynamical Modeling in Systems Biology]]
 
* [[Lessons Learned from Quantitative Dynamical Modeling in Systems Biology]]
* [[Ways to Fit a PK Model with Some Data Below the Quantification Limit]]
 
 
* [[ODE parameter inference using adaptive gradient matching with Gaussian processes]]
 
* [[ODE parameter inference using adaptive gradient matching with Gaussian processes]]
 +
===== 2018 =====
 +
* [[Benchmarking optimization methods for parameter estimation in large kinetic models]]
 +
  
=== High-throughput data preprocessing ===
+
 
 +
=== Omics Workflows ===
 +
===== 2017 =====
 +
* [[A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation]]
 +
 
 +
 
 +
 
 +
=== Preprocessing high-throughput data===
 
===== 2009 =====
 
===== 2009 =====
 
* [[Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations]]
 
* [[Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations]]
Line 20: Line 67:
 
* [[Normalyzer: A Tool for Rapid Evaluation of Normalization Methods
 
* [[Normalyzer: A Tool for Rapid Evaluation of Normalization Methods
 
for Omics Data Sets]]
 
for Omics Data Sets]]
 
=== Feature Selection and Dimension Reduction ===
 
===== 2015 =====
 
* [[Comparing feature selection methods for highdimensional imbalanced data: identifying rheumatoid arthritis cohorts from routine data]]
 
 
=== Classification ===
 
* [[Predicting Breast Cancer Survivability Using Data Mining Techniques]]
 

Revision as of 12:05, 9 August 2018

Here outcomes of benchmarking studies from the literature are collected. 
Please extend this list by creating a new page and adding a link below. Use the guidelines described here. The goal is achieving a consensus within the scientific community. 

Results from Literature

Classification

2003

Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data

2005
2016


Feature Selection

Identifying differences

2017

Dimension reduction

2008
2015


Imputation methods for missing values

2001
2015
2018


ODE-based Modelling

2001
2008
2013
2018


Omics Workflows

2017


Preprocessing high-throughput data

2009
2010
2012
2014
  • [[Normalyzer: A Tool for Rapid Evaluation of Normalization Methods

for Omics Data Sets]]