Difference between revisions of "Literature Studies"

(Years in bold face instead of headings)
Line 8: Line 8:
  
 
=== Classification ===
 
=== Classification ===
===== 2003 =====
+
''' 2003 '''
 
Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data
 
Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data
===== 2005 =====
+
''' 2005 '''</br>
 
* [[A review and comparison of classification algorithms for medical decision making]]
 
* [[A review and comparison of classification algorithms for medical decision making]]
===== 2016 =====
+
''' 2016 '''</br>
 
* [[Predicting Breast Cancer Survivability Using Data Mining Techniques]]
 
* [[Predicting Breast Cancer Survivability Using Data Mining Techniques]]
  
Line 19: Line 19:
 
=== Feature Selection ===
 
=== Feature Selection ===
 
==== Identifying differences ====
 
==== Identifying differences ====
===== 2017 =====
+
''' 2017 '''</br>
 
* [[Identification of differentially expressed peptides in high-throughput proteomics data]]
 
* [[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]]
+
* [[In-depth method assessments of di?erentially expressed protein detection for shotgun proteomics data with missing values]]
 
==== Dimension reduction ====
 
==== Dimension reduction ====
===== 2008 =====
+
''' 2008 '''</br>
 
* [[On the Relationship Between Feature Selection and Classification Accuracy]]
 
* [[On the Relationship Between Feature Selection and Classification Accuracy]]
===== 2015 =====
+
''' 2015 '''</br>
 
* [[Comparing feature selection methods for highdimensional imbalanced data: identifying rheumatoid arthritis cohorts from routine data]]
 
* [[Comparing feature selection methods for highdimensional imbalanced data: identifying rheumatoid arthritis cohorts from routine data]]
  
  
 
=== Imputation methods for missing values ===
 
=== Imputation methods for missing values ===
===== 2001 =====
+
''' 2001 '''</br>
 
* [[Missing value estimation methods for DNA microarrays]]
 
* [[Missing value estimation methods for DNA microarrays]]
===== 2015 =====
+
''' 2015 '''</br>
 
* [[Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies]]
 
* [[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]]
 
* [[Multiple imputation and analysis for high-dimensional incomplete proteomics data]]
===== 2018 =====
+
''' 2018 '''</br>
 
* [[Missing Value Imputation Approach for Mass Spectrometry-based Metabolomics Data]]
 
* [[Missing Value Imputation Approach for Mass Spectrometry-based Metabolomics Data]]
  
Line 41: Line 41:
  
 
=== ODE-based Modelling ===
 
=== ODE-based Modelling ===
===== 2001 =====
+
''' 2001 '''</br>
 
* [[Ways to Fit a PK Model with Some Data Below the Quantification Limit]]
 
* [[Ways to Fit a PK Model with Some Data Below the Quantification Limit]]
===== 2008 =====
+
''' 2008 '''</br>
 
* [[Hybrid optimization method with general switching strategy for parameter estimation]]
 
* [[Hybrid optimization method with general switching strategy for parameter estimation]]
===== 2013 =====
+
''' 2013 '''</br>
 
* [[Lessons Learned from Quantitative Dynamical Modeling in Systems Biology]]
 
* [[Lessons Learned from Quantitative Dynamical Modeling in Systems Biology]]
 
* [[ODE parameter inference using adaptive gradient matching with Gaussian processes]]
 
* [[ODE parameter inference using adaptive gradient matching with Gaussian processes]]
===== 2018 =====
+
''' 2018 '''</br>
 
* [[Benchmarking optimization methods for parameter estimation in large kinetic models]]
 
* [[Benchmarking optimization methods for parameter estimation in large kinetic models]]
  
Line 54: Line 54:
  
 
=== Omics Workflows ===
 
=== Omics Workflows ===
===== 2017 =====
+
''' 2017 '''</br>
 
* [[A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation]]
 
* [[A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation]]
  
Line 60: Line 60:
  
 
=== Preprocessing high-throughput data===
 
=== Preprocessing high-throughput data===
===== 2009 =====
+
''' 2009 '''</br>
 
* [[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]]
===== 2010 =====
+
''' 2010 '''</br>
 
* [[Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments]]
 
* [[Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments]]
===== 2012 =====
+
''' 2012 '''</br>
 
* [[A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis]]
 
* [[A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis]]
===== 2014 =====
+
''' 2014 '''</br>
 
* [[Normalyzer: A Tool for Rapid Evaluation of Normalization Methods for Omics Data Sets]]
 
* [[Normalyzer: A Tool for Rapid Evaluation of Normalization Methods for Omics Data Sets]]

Revision as of 13:27, 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. 

1 Results from Literature

1.1 Classification

2003 Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data 2005

2016


1.2 Feature Selection

1.2.1 Identifying differences

2017

1.2.2 Dimension reduction

2008

2015


1.3 Imputation methods for missing values

2001

2015

2018


1.4 ODE-based Modelling

2001

2008

2013

2018


1.5 Omics Workflows

2017


1.6 Preprocessing high-throughput data

2009

2010

2012

2014