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- 13:42, 4 March 2020 The impact of sample imbalance on identifying differentially expressed genes (hist) [1,518 bytes] Ckreutz (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Kun Yang, Jianzhong Li and Hong Gao, The impact of sample imbalance on identifying differentially expressed genes, 2006, BMC Bioinformati...")
- 16:49, 28 February 2020 Predicting Breast Cancer Survivability Using Data Mining Techniques (hist) [1,785 bytes] Ckreutz (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Sarvestani, A. S., Safavi, A. A., Parandeh, N. M., & Salehi, M., Predicting breast cancer survivability using data mining techniques, 20...")
- 16:41, 28 February 2020 Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data (hist) [2,147 bytes] Ckreutz (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Baolin Wu, Tom Abbott, David Fishman, Walter McMurray, Gil Mor, Kathryn Stone, David Ward, Kenneth Williams, Hongyu Zhao, Comparison of s...")
- 15:47, 27 February 2020 Bioinformatics and Statistics: LC‐MS (/MS) Data Preprocessing for Biomarker Discovery (hist) [1,604 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Horvatovich P, Suits F, Hoekman B, Bischoff R. Bioinformatics and Statistics: LC‐MS (/MS) Data Preprocessing for Biomarker Discovery. I...")
- 15:36, 27 February 2020 Preprocessing of tandem mass spectrometric data to support automatic protein identification (hist) [1,554 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Gentzel M, Köcher T, Ponnusamy S, Wilm M. Preprocessing of tandem mass spectrometric data to support automatic protein identification. P...")
- 15:32, 27 February 2020 Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ (hist) [1,600 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Cox J, Hein MY, Luber CA, Paron I, Nagaraj N, Mann M. Accurate proteome-wide label-free quantification by delayed normalization and maxim...")
- 07:53, 26 February 2020 Peak alignment using wavelet pattern matching and differential evolution (hist) [1,504 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Zhang ZM, Chen S, Liang YZ. Peak alignment using wavelet pattern matching and differential evolution. Talanta. 2011 Jan 30;83(4):1108-17....")
- 07:36, 26 February 2020 Identifying and quantifying metabolites by scoring peaks of GC-MS data (hist) [1,526 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Aggio RB, Mayor A, Reade S, Probert CS, Ruggiero K. Identifying and quantifying metabolites by scoring peaks of GC-MS data. BMC bioinform...")
- 07:26, 26 February 2020 Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes (hist) [1,638 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Lu J, Trnka MJ, Roh SH, Robinson PJ, Shiau C, Fujimori DG, Chiu W, Burlingame AL, Guan S. Improved peak detection and deconvolution of na...")
- 07:15, 26 February 2020 Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching (hist) [1,544 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Du P, Kibbe WA, Lin SM. Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. Bi...")
- 07:11, 26 February 2020 An improved algorithm for peak detection in mass spectra based on continuous wavelet transform (hist) [1,562 bytes] Bwday (talk | contribs) (Created page with "__ NUMBEREDHEADINGS__ === Citation === Zheng Y, Fan R, Qiu C, Liu Z, Tian D. An improved algorithm for peak detection in mass spectra based on continuous wavelet transform. In...")
- 16:29, 25 February 2020 Comparison of metaheuristic strategies for peakbin selection in proteomic mass spectrometry data (hist) [1,563 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === García-Torres M, Armañanzas R, Bielza C, Larrañaga P. Comparison of metaheuristic strategies for peakbin selection in proteomic mass s...")
- 16:24, 25 February 2020 Peakbin selection in mass spectrometry data using a consensus approach with estimation of distribution algorithms (hist) [1,650 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Armananzas R, Saeys Y, Inza I, Garcia-Torres M, Bielza C, Van de Peer Y, Larranaga P. Peakbin selection in mass spectrometry data using a...")
- 15:38, 25 February 2020 Toward a gold standard for benchmarking gene set enrichment analysis (hist) [2,449 bytes] Ckreutz (talk | contribs) (Created page with "__ NUMBEREDHEADINGS__ === Citation === Geistlinger, L., Csaba, G., Santarelli, M., Ramos, M., Schiffer, L., Law, C., ... & Zimmer, R., Toward a gold standard for benchmarking...")
- 15:36, 25 February 2020 A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data (hist) [1,601 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Wang T, Guan W, Lin J, Boutaoui N, Canino G, Luo J, Celedón JC, Chen W. A systematic study of normalization methods for Infinium 450K me...")
- 15:21, 25 February 2020 Data processing has major impact on the outcome of quantitative label-free LC-MS analysis (hist) [1,558 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Chawade A, Sandin M, Teleman J, Malmström J, Levander F. Data processing has major impact on the outcome of quantitative label-free LC-M...")
- 15:09, 25 February 2020 Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis (hist) [1,603 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Li B, Tang J, Yang Q, Cui X, Li S, Chen S, Cao Q, Xue W, Chen N, Zhu F. Performance evaluation and online realization of data-driven norm...")
- 15:03, 25 February 2020 OpenMS: a flexible open-source software platform for mass spectrometry data analysis (hist) [1,603 bytes] Bwday (talk | contribs) (Created page with "__ NUMBEREDHEADINGS__ === Citation === Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X. OpenMS: a...")
- 14:58, 25 February 2020 NOREVA: normalization and evaluation of MS-based metabolomics data (hist) [1,543 bytes] Bwday (talk | contribs) (Created page with "__ NUMBEREDHEADINGS__ === Citation === Li B, Tang J, Yang Q, Li S, Cui X, Li Y, Chen Y, Xue W, Li X, Zhu F. NOREVA: normalization and evaluation of MS-based metabolomics data....")
- 14:46, 25 February 2020 NormalyzerDE: Online Tool for Improved Normalization of Omics Expression Data and High-Sensitivity Differential Expression Analysis (hist) [1,590 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Willforss J, Chawade A, Levander F. Normalyzerde: Online tool for improved normalization of omics expression data and high-sensitivity di...")
- 14:46, 25 February 2020 Recursive partitioning for missing data imputation in the presence of interaction effects (hist) [217 bytes] Bwday (talk | contribs) (Created page with "--- Citation --- Doove, L., Buuren, S. V., and Dusseldorp, E. (2014). Recursive partitioning for missing data imputation in the presence of interaction effects. Computational...")
- 14:44, 25 February 2020 Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics (hist) [1,804 bytes] Bwday (talk | contribs) (Created page with " === Citation === Webb-Robertson, B.-J. M.; Wiberg, H. K.; Matzke, M. M.; Brown, J. N.; Wang, J.; McDermott, J. E.; Smith, R. D.; Rodland, K. D.; Metz, T. O.; Pounds, J. G.; W...")
- 14:32, 25 February 2020 Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data (hist) [1,547 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Tsuji J, Weng Z. Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data....")
- 14:31, 25 February 2020 Missing value estimation methods for DNA microarrays (hist) [1,173 bytes] Bwday (talk | contribs) (Created page with " === Citation === Troyanskaya, O., Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., Botstein, D., and Altman, R. B. (2001). Missing value estimation methods fo...")
- 14:12, 25 February 2020 MetaboAnalyst: a web server for metabolomic data analysis and interpretation (hist) [1,531 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Xia J, Psychogios N, Young N, Wishart DS. MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Nucleic acids res...")
- 14:04, 25 February 2020 MeltDB: a software platform for the analysis and integration of metabolomics experiment data (hist) [1,589 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A. MeltDB: a software platform for the analysis and in...")
- 14:00, 25 February 2020 A general modular framework for gene set enrichment analysis (hist) [6,266 bytes] Ckreutz (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === M Ackermann and K Strimmer, A general modular framework for gene set enrichment analysis, 2009, BMC Bioinformatics, 10:47, pages etc in a...")
- 13:58, 25 February 2020 Software platform for high-throughput glycomics (hist) [1,496 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Vakhrushev SY, Dadimov D, Peter-Katalinic J. Software platform for high-throughput glycomics. Analytical chemistry. 2009 May 1;81(9):3252...")
- 13:56, 25 February 2020 The effects of nonignorable missing data on label-free mass spectrometry proteomics experiments (hist) [1,845 bytes] Bwday (talk | contribs) (Created page with "=== Citation === O'Brien JJ, Gunawardena HP, Paulo JA, Chen X, Ibrahim JG, Gygi SP, Qaqish BF (2018). The effects of nonignorable missing data on label-free mass spectrometry...")
- 13:46, 25 February 2020 Machine learning methods for predictive proteomics (hist) [1,529 bytes] Bwday (talk | contribs) (Created page with "__ NUMBEREDHEADINGS__ === Citation === Barla A, Jurman G, Riccadonna S, Merler S, Chierici M, Furlanello C. Machine learning methods for predictive proteomics. Briefings in bi...")
- 13:29, 25 February 2020 Data-driven normalization strategies for high-throughput quantitative RT-PCR (hist) [1,570 bytes] Bwday (talk | contribs) (Created page with "__ NUMBEREDHEADINGS__ === Citation === Mar JC, Kimura Y, Schroder K, Irvine KM, Hayashizaki Y, Suzuki H, Hume D, Quackenbush J. Data-driven normalization strategies for high-t...")
- 13:06, 25 February 2020 Comprehensive evaluation of untargeted metabolomics data processing software in feature detection, quantification and discriminating marker selection (hist) [1,602 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Li Z, Lu Y, Guo Y, Cao H, Wang Q, Shui W. Comprehensive evaluation of untargeted metabolomics data processing software in feature detecti...")
- 13:02, 25 February 2020 Comparison of peak‐picking workflows for untargeted liquid chromatography/high‐resolution mass spectrometry metabolomics data analysis (hist) [1,581 bytes] Bwday (talk | contribs) (Created page with "__ NUMBEREDHEADINGS__ === Citation === Rafiei A, Sleno L. Comparison of peak‐picking workflows for untargeted liquid chromatography/high‐resolution mass spectrometry metab...")
- 12:56, 25 February 2020 Comparative evaluation of preprocessing freeware on chromatography/mass spectrometry data for signature discovery (hist) [1,553 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ === Citation === Coble JB, Fraga CG. Comparative evaluation of preprocessing freeware on chromatography/mass spectrometry data for signature discovery. Jo...")
- 12:24, 25 February 2020 An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics (hist) [1,611 bytes] Bwday (talk | contribs) (Created page with "__ NUMBEREDHEADINGS__ === Citation === Weisser H, Nahnsen S, Grossmann J, Nilse L, Quandt A, Brauer H, Sturm M, Kenar E, Kohlbacher O, Aebersold R, Malmström L. An automated...")
- 12:07, 25 February 2020 MS‐Analyzer: preprocessing and data mining services for proteomics applications on the Grid (hist) [1,549 bytes] Bwday (talk | contribs) (Created page with "__ NUMBEREDHEADINGS__ === Citation === Cannataro M, Veltri P. MS‐Analyzer: preprocessing and data mining services for proteomics applications on the Grid. Concurrency and Co...")
- 11:45, 25 February 2020 Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (hist) [4,351 bytes] Ckreutz (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ == Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 == Tintle, N. L., Borchers, B., Brown, M.,...")
- 11:37, 25 February 2020 Missing values in mass spectrometry based metabolomics: an undervalued step in the data processing pipeline (hist) [1,508 bytes] Bwday (talk | contribs) (Created page with " === Citation === Hrydziuszko O., Viant M.R. Missing values in mass spectrometry based metabolomics: an undervalued step in the data processing pipeline (2012). Metabolomics....")
- 11:02, 25 February 2020 Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes (hist) [1,568 bytes] Bwday (talk | contribs) (Created page with " === Citation === G. N., Shaffer, J. R., Blakesley, R. E., Lotz, M. J., and Tseng, G. C. (2008). Which missing value imputation method to use in expression profiles: a compara...")
- 10:56, 25 February 2020 Recursive partitioning for missing data imputation in the presence of interaction effects. (hist) [1,544 bytes] Bwday (talk | contribs) (Created page with " === Citation === Doove, L., Buuren, S. V., and Dusseldorp, E. (2014). Recursive partitioning for missing data imputation in the presence of interaction effects. Computational...")
- 10:52, 25 February 2020 Normalization regarding non-random missing values in high-throughput mass spectrometry data (hist) [1,564 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ == General information == Wang P, Tang H, Zhang H, Whiteaker J, Paulovich AG, Mcintosh M. Normalization regarding non-random missing values in high-throug...")
- 10:51, 25 February 2020 Performance of objective functions and optimization procedures for parameter estimation in system biology models (hist) [2,825 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ == Performance of objective functions and optimisation procedures for parameter estimation in system biology models == Andrea Degasperi, Dirk Fey & Boris...")
- 10:48, 25 February 2020 Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis (hist) [3,552 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ == Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis == Paul Stapor, Fabian Fro¨ hlich1, and Jan Hasenau...")
- 10:43, 25 February 2020 Efficient computation of steady states in large-scale ODE models of biochemical reaction networks (hist) [280 bytes] Bwday (talk | contribs) (Created page with "== Paper name == Lines, Glenn Terje, et al. "Efficient computation of steady states in large-scale ODE models of biochemical reaction networks." IFAC-PapersOnLine 52.26 (2019)...")
- 10:42, 25 February 2020 Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics. (hist) [1,849 bytes] Bwday (talk | contribs) (Created page with " == General information == (13) Webb-Robertson, B.-J. M.; Wiberg, H. K.; Matzke, M. M.; Brown, J. N.; Wang, J.; McDermott, J. E.; Smith, R. D.; Rodland, K. D.; Metz, T. O.; Po...")
- 10:41, 25 February 2020 Tracking for parameter and state estimation in possibly misspecified partially observed linear Ordinary Differential Equations (hist) [352 bytes] Bwday (talk | contribs) (Created page with "== Paper name == Authors, title, year, journal, volume, pages etc in any possible citation style. [https://doi.org/10.1371/journal.pone.0074335: Permanent link to the paper]")
- 10:41, 25 February 2020 Parameter Estimation and Variable Selection for Big Systems of Linear Ordinary Differential Equations: A Matrix-Based Approach (hist) [335 bytes] Bwday (talk | contribs) (Created page with "== Paper name == Authors, title, year, journal, volume, pages etc in any possible citation style. [https://doi.org/10.1371/journal.pone.0074335: Permanent link to the paper]")
- 10:40, 25 February 2020 Benchmark problems for dynamic modeling of intracellular processes (hist) [2,407 bytes] Bwday (talk | contribs) (Created page with "== Paper name == Hass, Helge, et al. "Benchmark problems for dynamic modeling of intracellular processes." Bioinformatics 35.17 (2019): 3073-3082. [https://doi.org/10.1093/bi...")
- 10:39, 25 February 2020 Prevention, diagnosis and treatment of high-throughput sequencing data pathologies (hist) [1,509 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ == General information == Zhou X, Rokas A. Prevention, diagnosis and treatment of high‐throughput sequencing data pathologies. Molecular ecology. 2014 A...")
- 10:37, 25 February 2020 Fast derivatives of likelihood functionals for ODE based models using adjoint-state method (hist) [6,211 bytes] Bwday (talk | contribs) (Created page with "__NUMBEREDHEADINGS__ == Paper name == Melicher, V., Haber, T. & Vanroose, W. [https://doi.org/10.1007/s00180-017-0765-8 Fast derivatives of likelihood functionals for ODE base...")
