bioinformatics tools for mass spectroscopy-based metabolomic data processing and analysis

Random Forests

Breiman, L. (2001) · Machine Learning · doi:10.1023/a:1010933404324 · Cited by 133,538 · see citing works

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works

An introduction to ROC analysis

Fawcett, T. (2006) · Pattern Recognition Letters · doi:10.1016/j.patrec.2005.10.010 · Cited by 21,879 · see citing works

Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications

Sørlie, T., Perou, C., Tibshirani, R., Aas, T., Geisler, S., Johnsen, H., Hastie, T., Eisen, M., van de Rijn, M., Jeffrey, S., et al. (2001) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.191367098 · Cited by 11,695 · see citing works

Proposed minimum reporting standards for chemical analysis: Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI)

Sumner, L. W., Amberg, A., Barrett, D., Beale, M. H., Beger, R., Daykin, C. A., Fan, T. W.-M., Fiehn, O., Goodacre, R., Griffin, J. L., et al. (2007) · Metabolomics · doi:10.1007/s11306-007-0082-2 · Cited by 5,368 · see citing works

XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification

Smith, C. A., Want, E. J., O’Maille, G., Abagyan, R. A., & Siuzdak, G. E. (2006) · Analytical Chemistry · doi:10.1021/ac051437y · Cited by 5,296 · see citing works

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

Pluskal, T., Castillo, S., Villar‐Briones, A., & Orešič, M. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-395 · Cited by 3,852 · see citing works

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395 · see citing works

Gene selection and classification of microarray data using random forest

Díaz‐Uriarte, R., & de Andrés, S. Á. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-3 · Cited by 2,924 · see citing works

MassBank: a public repository for sharing mass spectral data for life sciences

Horai, H., Arita, M., Kanaya, S., Nihei, Y., Ikeda, T., Suwa, K., Ojima, Y., Tanaka, K., Tanaka, S., Aoshima, K., et al. (2010) · Journal of Mass Spectrometry · doi:10.1002/jms.1777 · Cited by 2,529 · see citing works

Centering, scaling, and transformations: improving the biological information content of metabolomics data

van den Berg, R. A., Hoefsloot, H. C., Westerhuis, J. A., Smilde, A. K., & van der Werf, M. J. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-142 · Cited by 2,450 · see citing works

KEGG for representation and analysis of molecular networks involving diseases and drugs

Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., & Hirakawa, M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp896 · Cited by 2,322 · see citing works

MetaboAnalyst: a web server for metabolomic data analysis and interpretation

Xia, J., Psychogios, N., Young, N., & Wishart, D. S. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp356 · Cited by 2,238 · see citing works

Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression

Sreekumar, A., Poisson, L., Rajendiran, T. M., Khan, A. P., Cao, Q., Yu, J., Laxman, B., Mehra, R., Lonigro, R. J., Li, Y., et al. (2009) · Nature · doi:10.1038/nature07762 · Cited by 2,238 · see citing works

Metabolite profiling for plant functional genomics

Fiehn, O., Kopka, J., Dörmann, P., Altmann, T., Trethewey, R. N., & Willmitzer, L. (2000) · Nature Biotechnology · doi:10.1038/81137 · Cited by 2,129 · see citing works

The Human Serum Metabolome

Psychogios, N., Hau, D., Peng, J., Guo, A. C., Mandal, R., Bouatra, S., Sinelnikov, I. V., Krishnamurthy, R., Eisner, R., Gautam, B., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016957 · Cited by 1,718 · see citing works

Cytoscape: Software for Visualization and Analysis of Biological Networks

Kohl, M., Wiese, S., & Warscheid, B. (2010) · Methods in molecular biology · doi:10.1007/978-1-60761-987-1_18 · Cited by 1,539 · see citing works

Selection bias in gene extraction on the basis of microarray gene-expression data

Ambroise, C., & McLachlan, G. J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.102102699 · Cited by 1,487 · see citing works

Assessment of PLSDA Cross Validation

Westerhuis, J. A., Hoefsloot, H. C. J., Smit, S., Vis, D. J., Smilde, A. K., van Velzen, E. J. J., van Duijnhoven, J. P. M., & van Dorsten, F. A. (2008) · Metabolomics · doi:10.1007/s11306-007-0099-6 · Cited by 1,471 · see citing works

Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst

Xia, J., & Wishart, D. S. (2011) · Nature Protocols · doi:10.1038/nprot.2011.319 · Cited by 1,332 · see citing works

Visualization of GC/TOF-MS-Based Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class Models

Wiklund, S., Johansson, E., Sjöström, L., Mellerowicz, E. J., Edlund, U. G., Shockcor, J. P., Gottfries, J., Möritz, T., & Trygg, J. (2007) · Analytical Chemistry · doi:10.1021/ac0713510 · Cited by 1,234 · see citing works

Highly sensitive feature detection for high resolution LC/MS

Tautenhahn, R., Böttcher, C., & Neumann, S. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-504 · Cited by 1,175 · see citing works

Understanding 'Global' Systems Biology: Metabonomics and the Continuum of Metabolism

Nicholson, J. K., & Wilson, I. D. (2003) · Nature Reviews Drug Discovery · doi:10.1038/nrd1157 · Cited by 1,121 · see citing works

Human metabolic phenotype diversity and its association with diet and blood pressure

Holmes, E., Loo, R. L., Stamler, J., Bictash, M., Yap, I. K. S., Chan, Q., Ebbels, T., De Iorio, M., Brown, I. J., Veselkov, K. A., et al. (2008) · Nature · doi:10.1038/nature06882 · Cited by 1,054 · see citing works

Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles

Sugimoto, M., Wong, D. T., Hirayama, A., Soga, T., & Tomita, M. (2009) · Metabolomics · doi:10.1007/s11306-009-0178-y · Cited by 999 · see citing works

Quantitative Metabolome Analysis Using Capillary Electrophoresis Mass Spectrometry

Soga, T., Ohashi, Y., Ueno, Y., Naraoka, H., Tomita, M., & Nishi­oka, T. (2003) · Journal of Proteome Research · doi:10.1021/pr034020m · Cited by 975 · see citing works

Quantitative Metabolome Profiling of Colon and Stomach Cancer Microenvironment by Capillary Electrophoresis Time-of-Flight Mass Spectrometry

Hirayama, A., Kami, K., Sugimoto, M., Sugawara, M., Toki, N., Onozuka, H., Kinoshitá, T., Saito, N., Ochiai, A., Tomita, M., et al. (2009) · Cancer Research · doi:10.1158/0008-5472.can-08-4806 · Cited by 959 · see citing works

Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy

Dunn, W. B., Broadhurst, D., Atherton, H. J., Goodacre, R., & Griffin, J. L. (2010) · Chemical Society Reviews · doi:10.1039/b906712b · Cited by 870 · see citing works

MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data

Katajamaa, M., Miettinen, J., & Orešič, M. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btk039 · Cited by 836 · see citing works

Statistical strategies for avoiding false discoveries in metabolomics and related experiments

Broadhurst, D., & Kell, D. B. (2006) · Metabolomics · doi:10.1007/s11306-006-0037-z · Cited by 819 · see citing works

A common open representation of mass spectrometry data and its application to proteomics research

Pedrioli, P. G. A., Eng, J. K., Hubley, R. M., Vogelzang, M., Deutsch, E. W., Raught, B., Pratt, B. S., Nilsson, E. J., Angeletti, R. H., Apweiler, R., et al. (2004) · Nature Biotechnology · doi:10.1038/nbt1031 · Cited by 782 · see citing works

MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data

Xia, J., & Wishart, D. S. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq329 · Cited by 777 · see citing works

MetPA: a web-based metabolomics tool for pathway analysis and visualization

Xia, J., & Wishart, D. S. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq418 · Cited by 767 · see citing works

Metabolomics for Functional Genomics, Systems Biology, and Biotechnology

Saito, K., & Matsuda, F. (2009) · Annual Review of Plant Biology · doi:10.1146/annurev.arplant.043008.092035 · Cited by 749 · see citing works

Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum

Gieger, C., Geistlinger, L., Altmaier, E., Hrabé de Angelis, M., Kronenberg, F., Meitinger, T., Mewes, H.-W., Wichmann, H.-E., Weinberger, K. M., Adamski, J., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000282 · Cited by 737 · see citing works

MetAlign: Interface-Driven, Versatile Metabolomics Tool for Hyphenated Full-Scan Mass Spectrometry Data Preprocessing

Lommen, A. (2009) · Analytical Chemistry · doi:10.1021/ac900036d · Cited by 735 · see citing works

Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications

Matese, J. C., Sorlie, T., Tibshirani, R., et al. (2020) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/qpxp-y103 · Cited by 699 · see citing works

In silico fragmentation for computer assisted identification of metabolite mass spectra

Wolf, S., Schmidt, S., Müller-Hannemann, M., & Neumann, S. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-148 · Cited by 698 · see citing works

Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations

Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., et al. (2007) · Science · doi:10.1126/science.1132067 · Cited by 668 · see citing works

Quantification of Proteins and Metabolites by Mass Spectrometry without Isotopic Labeling or Spiked Standards

Wang, W., Zhou, H., Lin, H., Roy, S., Shaler, T. A., Hill, L. R., Norton, S. M., Kumar, P., Anderle, M., & Becker, C. H. (2003) · Analytical Chemistry · doi:10.1021/ac026468x · Cited by 654 · see citing works

OpenMS – An open-source software framework for mass spectrometry

Sturm, M., Bertsch, A., Gröpl, C., Hildebrandt, A., Hussong, R., Lange, E., Pfeifer, N., Schulz-Trieglaff, O. B., Zerck, A., Reinert, K., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-163 · Cited by 646 · see citing works

Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm

Kind, T., & Fiehn, O. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-234 · Cited by 639 · see citing works

Parametric Time Warping

Eilers, P. H. C. (2003) · Analytical Chemistry · doi:10.1021/ac034800e · Cited by 637 · see citing works

Data processing for mass spectrometry-based metabolomics

Katajamaa, M., & Orešič, M. (2007) · Journal of Chromatography A · doi:10.1016/j.chroma.2007.04.021 · Cited by 616 · see citing works

Metabolomic Analysis and Visualization Engine for LC−MS Data

Melamud, E., Vastag, L., & Rabinowitz, J. D. (2010) · Analytical Chemistry · doi:10.1021/ac1021166 · Cited by 603 · see citing works

Organization of GC/MS and LC/MS metabolomics data into chemical libraries

DeHaven, C. D., Evans, A. M., Dai, H., & Lawton, K. A. (2010) · Journal of Cheminformatics · doi:10.1186/1758-2946-2-9 · Cited by 601 · see citing works

Identification of Uncommon Plant Metabolites Based on Calculation of Elemental Compositions Using Gas Chromatography and Quadrupole Mass Spectrometry

Fiehn, O., Kopka, J., Trethewey, R. N., et al. (2000) · Analytical Chemistry · doi:10.1021/ac991142i · Cited by 592 · see citing works

The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

Caspi, R. R., Foerster, H., Fulcher, C., Kaipa, P., Krummenacker, M., Latendresse, M., Paley, S., Rhee, S. Y., Shearer, A. G., Tissier, C. P., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm900 · Cited by 580 · see citing works

Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research

Scalbert, A., Brennan, L., Fiehn, O., Hankemeier, T., Kristal, B. S., van Ommen, B., Pujos-Guillot, E., Verheij, E., Wishart, D., & Wopereis, S. (2009) · Metabolomics · doi:10.1007/s11306-009-0168-0 · Cited by 565 · see citing works

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Caspi, R., Altman, T., Dale, J. M., Dreher, K. A., Fulcher, C. A., Gilham, F., Kaipa, P., Karthikeyan, A. S., Kothari, A., Krummenacker, M., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp875 · Cited by 483 · see citing works

MetaboliteDetector: Comprehensive Analysis Tool for Targeted and Nontargeted GC/MS Based Metabolome Analysis

Hiller, K., Hangebrauk, J., Jäger, C., Spura, J., Schreiber, K., & Schomburg, D. (2009) · Analytical Chemistry · doi:10.1021/ac802689c · Cited by 440 · see citing works

Nontargeted Metabolome Analysis by Use of Fourier Transform Ion Cyclotron Mass Spectrometry

Aharoni, A., Vos, C. H. R. D., Verhoeven, H. A., Maliepaard, C. A., Kruppa, G. H., Bino, R. J., & Goodenowe, D. B. (2002) · OMICS A Journal of Integrative Biology · doi:10.1089/15362310260256882 · Cited by 428 · see citing works

The role of metabolites and metabolomics in clinically applicable biomarkers of disease

Mamas, M. A., Dunn, W. B., Neyses, L., & Goodacre, R. (2010) · Archives of Toxicology · doi:10.1007/s00204-010-0609-6 · Cited by 379 · see citing works

Normalization method for metabolomics data using optimal selection of multiple internal standards

Sysi‐Aho, M., Katajamaa, M., Yetukuri, L., & Orešič, M. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-93 · Cited by 358 · see citing works

Normalization strategies for metabonomic analysis of urine samples

Warrack, B. M., Hnatyshyn, S. Y., Ott, K., Reily, M. D., Sanders, M., Zhang, H., & Drexler, D. M. (2009) · Journal of Chromatography B · doi:10.1016/j.jchromb.2009.01.007 · Cited by 332 · see citing works

Metabolome analysis by capillary electrophoresis–mass spectrometry

Monton, M. R. N., & Soga, T. (2007) · Journal of Chromatography A · doi:10.1016/j.chroma.2007.02.065 · Cited by 319 · see citing works

Decision tree supported substructure prediction of metabolites from GC-MS profiles

Hummel, J., Strehmel, N., Selbig, J., Walther, D., & Kopka, J. (2010) · Metabolomics · doi:10.1007/s11306-010-0198-7 · Cited by 313 · see citing works

Mass defect filter technique and its applications to drug metabolite identification by high‐resolution mass spectrometry

Zhang, H., Zhang, D., Ray, K. L., et al. (2009) · Journal of Mass Spectrometry · doi:10.1002/jms.1610 · Cited by 294 · see citing works

NMR-BASED METABOLOMICS

Reo, N. V. (2002) · Drug and Chemical Toxicology · doi:10.1081/dct-120014789 · Cited by 288 · see citing works

A proposed framework for the description of plant metabolomics experiments and their results

JENKINS, H. A., Hardy, N. W., Beckmann, M., Draper, J., SMITH, A. R., Taylor, J., Fiehn, O., Goodacre, R., Bino, R. J., Hall, R. D., et al. (2004) · Nature Biotechnology · doi:10.1038/nbt1041 · Cited by 285 · see citing works

CE‐MS in metabolomics

Ramautar, R., Somsen, G. W., & de Jong, G. J. (2008) · Electrophoresis · doi:10.1002/elps.200800512 · Cited by 282 · see citing works

Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes

Dunn, W. B. (2008) · Physical Biology · doi:10.1088/1478-3975/5/1/011001 · Cited by 279 · see citing works

Metabolite fingerprinting: detecting biological features by independent component analysis

Scholz, M., Gatzek, S., Sterling, A., Fiehn, O., & Selbig, J. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth270 · Cited by 278 · see citing works

Nonlinear Data Alignment for UPLC−MS and HPLC−MS Based Metabolomics: Quantitative Analysis of Endogenous and Exogenous Metabolites in Human Serum

Nordström, A., O’Maille, G., Qin, C., & Siuzdak, G. E. (2006) · Analytical Chemistry · doi:10.1021/ac060245f · Cited by 273 · see citing works

Metabonomics in pharmaceutical R & D

Lindon, J., Holmes, E., & Nicholson, J. K. (2007) · The FEBS Journal · doi:10.1111/j.1742-4658.2007.05673.x · Cited by 267 · see citing works

XCMS2: Processing Tandem Mass Spectrometry Data for Metabolite Identification and Structural Characterization

Benton, H. P., Wong, D. M., Trauger, S. A., & Siuzdak, G. E. (2008) · Analytical Chemistry · doi:10.1021/ac800795f · Cited by 266 · see citing works

A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS

Bellew, M., Coram, M., Fitzgibbon, M., Igra, M., Randolph, T. R., Wang, P., May, D., Eng, J. K., Fang, R., Lin, C., et al. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl276 · Cited by 265 · see citing works

Serum metabolomics reveals γ-glutamyl dipeptides as biomarkers for discrimination among different forms of liver disease

Soga, T., Sugimoto, M., Honma, M., Mori, M., Igarashi, K., Kashikura, K., Ikeda, S., Hirayama, A., Yamamoto, T., Yoshida, H., et al. (2011) · Journal of Hepatology · doi:10.1016/j.jhep.2011.01.031 · Cited by 234 · see citing works

Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks

Gao, J., Tarcea, V. G., Karnovsky, A., Mirel, B. R., Weymouth, T. E., Beecher, C., Cavalcoli, J. D., Athey, B. D., Omenn, G. S., Burant, C., et al. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq048 · Cited by 231 · see citing works

Software Tools for Analysis of Mass Spectrometric Lipidome Data

Haimi, P., Uphoff, A., Hermansson, M., & Somerharju, P. J. (2006) · Analytical Chemistry · doi:10.1021/ac061390w · Cited by 230 · see citing works

Metabolic Signatures of Lung Cancer in Biofluids: NMR-Based Metabonomics of Urine

Carrola, J., Rocha, C., Barros, A. S., Gil, A. M., Goodfellow, B. J., Carreira, I. M., Bernardo, J., Gomes, A., de Sousa, V. M. L., Carvalho, L., et al. (2010) · Journal of Proteome Research · doi:10.1021/pr100899x · Cited by 225 · see citing works

Informatics and computational strategies for the study of lipids

Yetukuri, L., Ekroos, K., Vidal‐Puig, A., & Orešič, M. (2007) · Molecular BioSystems · doi:10.1039/b715468b · Cited by 220 · see citing works

An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry

Castrillo, J. I., Hayes, A., Mohammed, S., Gaskell, S. J., & Oliver, S. G. (2003) · Phytochemistry · doi:10.1016/s0031-9422(02)00713-6 · Cited by 220 · see citing works

Mass spectrometry‐based holistic analytical approaches for metabolite profiling in systems biology studies

Theodoridis, G. A., Gika, H., & Wilson, I. D. (2011) · Mass Spectrometry Reviews · doi:10.1002/mas.20306 · Cited by 218 · see citing works

Peer Reviewed: So What’s the Deal with Metabonomics?

Lindon, J. C., Holmes, E. C., & Nicholson, J. K. (2003) · Analytical Chemistry · doi:10.1021/ac031386+ · Cited by 217 · see citing works

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks

Cottret, L., Wildridge, D., Vinson, F., Barrett, M. P., Charles, H., Sagot, M., & Jourdan, F. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq312 · Cited by 199 · see citing works

Dealing with the unknown: Metabolomics and Metabolite Atlases

Bowen, B. P., & Northen, T. R. (2010) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2010.04.003 · Cited by 198 · see citing works

Spectral relative standard deviation: a practical benchmark in metabolomics

Parsons, H. M., Ekman, D. R., Collette, T. W., et al. (2008) · The Analyst · doi:10.1039/b808986h · Cited by 193 · see citing works

Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets

Brown, M., Wedge, D. C., Goodacre, R., Kell, D. B., Baker, P. N., Kenny, L. C., Mamas, M. A., Neyses, L., & Dunn, W. B. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr079 · Cited by 192 · see citing works

Knowledge discovery in metabolomics: An overview of MS data handling

Boccard, J., Veuthey, J., & Rudaz, S. L. (2010) · Journal of Separation Science · doi:10.1002/jssc.200900609 · Cited by 189 · see citing works

Understanding the human salivary metabolome

Takeda, I., Stretch, C., Barnaby, P., Bhatnager, K., Rankin, K. N., Fu, H., Weljie, A. M., Jha, N., & Slupsky, C. M. (2009) · NMR in Biomedicine · doi:10.1002/nbm.1369 · Cited by 188 · see citing works

Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements

Lange, E., Tautenhahn, R., Neumann, S., & Gröpl, C. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-375 · Cited by 188 · see citing works

Probabilistic principal component analysis for metabolomic data

Nyamundanda, G., Brennan, L., & Gormley, I. C. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-571 · Cited by 176 · see citing works

A comparison of three algorithms for chromatograms alignment

van Nederkassel, A. M., Daszykowski, M., Eilers, P. H. C., & Heyden, Y. V. (2006) · Journal of Chromatography A · doi:10.1016/j.chroma.2006.03.114 · Cited by 170 · see citing works

Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour ’rules’

Draper, J., Enot, D. P., Parker, D., Beckmann, M., Snowdon, S., Lin, W., & Zubair, H. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-227 · Cited by 169 · see citing works

MathDAMP: a package for differential analysis of metabolite profiles

Baran, R., Kochi, H., Saito, N., Suematsu, M., Soga, T., Nishi­oka, T., Robert, M., & Tomita, M. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-530 · Cited by 162 · see citing works

Inference from Clustering with Application to Gene-Expression Microarrays

Dougherty, E. R., Barrera, J., Marcel Brun, A., Kim, S., Junior, R. M. C., Chen, Y., Bittner, M. L., & Trent, J. M. (2002) · Journal of Computational Biology · doi:10.1089/10665270252833217 · Cited by 158 · see citing works

An introduction to biological nuclear magnetic resonance spectroscopy

Bothwell, J. H. F., & Griffin, J. L. (2010) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/j.1469-185x.2010.00157.x · Cited by 156 · see citing works

1H-[13C] NMR measurements of [4-13C]glutamate turnover in human brain.

Rothman, D. L., Novotny, E. J., Shulman, G. I., Howseman, A., Petroff, O. A. C., Mason, G. F., Nixon, T. W., Hanstock, C. C., Prichard, J. W., & Shulman, R. G. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.20.9603 · Cited by 155 · see citing works

Combining tissue transcriptomics and urine metabolomics for breast cancer biomarker identification

Nam, H., Chung, B. C., Kim, Y.-H., Lee, K., & Lee, D. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp558 · Cited by 154 · see citing works

Web-based resources for mass-spectrometry-based metabolomics: a user’s guide

Tohge, T., & Fernie, A. R. (2009) · Phytochemistry · doi:10.1016/j.phytochem.2009.02.004 · Cited by 152 · see citing works

'Omics Data Sharing

Field, D., Sansone, S., Collis, A., Booth, T., Dukes, P., Gregurick, S. K., Kennedy, K., Kolar, P., Kolker, E., Maxon, M. E., et al. (2009) · Science · doi:10.1126/science.1180598 · Cited by 152 · see citing works

CE‐MS for metabolomics: Developments and applications in the period 2008–2010

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