Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: IPO

https://packages.ecosyste.ms/registries/bioconductor.org/packages/IPO

Automated Optimization of XCMS Data Processing parameters
1 version
Latest release: about 1 year ago
17,173 downloads total

Papers Mentioning IPO 20

10.3390/metabo6040037

Prediction, Detection, and Validation of Isotope Clusters in Mass Spectrometry Data
Cited by: 17
Author(s): Hendrik Treutler, Steffen Neumann
Software Mentions: 6
Published: about 8 years ago

A randomized 3-way crossover study indicates that high-protein feeding induces de novo lipogenesis in healthy humans
Cited by: 28
Author(s): Evelina Charidemou, Tom Ashmore, Xuefei Li, Ben D. McNally, James A. West, Sonia Liggi, Matthew Harvey, Elise Orford, Julian L. Griffin
Software Mentions: 4
Published: over 5 years ago

10.1002/jsp2.1099

Protocol for parallel proteomic and metabolomic analysis of mouse intervertebral disc tissues
Cited by: 4
Author(s): Matthew A Veras, Yong Jin Lim, Miljan Kuljanin, Gilles Lajoie, Bradley L. Urquhart, Cheryle A. Séguin
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0230813

Metabolic reprograming of LPS-stimulated human lung macrophages involves tryptophan metabolism and the aspartate-arginosuccinate shunt
Cited by: 14
Author(s): Fanta Fall, Elodie Lamy, Marion Brollo, Emmanuel Naline, Natacha Lenuzza, Etienne Thévenot, Philippe Devillier, Stanislas Grassin-Delyle
Software Mentions: 4
Published: over 4 years ago

10.3390/metabo9090171

WiPP: Workflow for Improved Peak Picking for Gas Chromatography-Mass Spectrometry (GC-MS) Data
Cited by: 18
Author(s): Nico Borgsmüller, Yoann Gloaguen, Tobias Opialla, Eric Blanc, Emilie Sicard, Anne-Lise Royer, Bruno Le Bizec, Stéphanie Durand, Carole Migné, Mélanie Petera, Estelle Pujos‐Guillot, Franck Giacomoni, Yann Guitton, Dieter Beule, Jennifer Kirwan
Software Mentions: 4
Published: over 5 years ago

10.3390/molecules26092715

Pure Ion Chromatograms Combined with Advanced Machine Learning Methods Improve Accuracy of Discriminant Models in LC–MS-Based Untargeted Metabolomics
Cited by: 0
Author(s): Miao Tian, Zhonglong Lin, Xu Wang, Jing Yang, Wentao Zhao, Hongmei Lü, Zhimin Zhang, Yi Chen
Software Mentions: 3
Published: over 3 years ago

10.1128/mSystems.00438-19

Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India
Cited by: 93
Author(s): Ankit Gupta, Darshan B. Dhakan, Abhijit Maji, Rituja Saxena, P K Vishnu Prasoodanan, Shruti Mahajan, Joby Pulikkan, Jacob Kurian, Andrés Gómez, Joy Scaria, Katherine R. Amato, Ashok Sharma, Vineet K. Sharma
Software Mentions: 3
Published: almost 5 years ago

10.7717/peerj.6547

Ultra-performance liquid chromatography-mass spectrometry for precise fatty acid profiling of oilseed crops
Cited by: 5
Author(s): Alina Chernova, Pavel Mazin, S. V. Goryunova, Denis Goryunov, Ya.N. Demurin, Л.А. Горлова, Anna Vanyushkina, Waltraud Mair, Nikolay Anikanov, Ekaterina Yushina, Anna Pavlova, Elena Martynova, Sergey Garkusha, Zhanna Mukhina, Elena Savenko, Philipp Khaitovich
Software Mentions: 3
Published: over 5 years ago

10.3390/metabo10050186

MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics
Cited by: 330
Author(s): Zhiqiang Pang, Jasmine Chong, Shuzhao Li, Jianguo Xia
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-42992-3

Untargeted metabolomics reveals N, N, N-trimethyl-L-alanyl-L-proline betaine (TMAP) as a novel biomarker of kidney function
Cited by: 31
Author(s): Thomas J. Velenosi, Benjamin Thomson, Nicholas C. Tonial, Adrien A. E. RaoPeters, Megan A. Mio, Gilles Lajoie, Amit X. Garg, Andrew A. House, Bradley L. Urquhart
Software Mentions: 3
Published: over 5 years ago

10.3390/metabo10010028

A Case Report of Switching from Specific Vendor-Based to R-Based Pipelines for Untargeted LC-MS Metabolomics
Cited by: 14
Author(s): Álvaro Fernández-Ochoa, Rosa Quirantes-Piné, Isabel Borrás-Linares, María de la Luz Cádiz-Gurrea, Marta E. Alarcón‐Riquelme, Carl Brunius, Antonio Segura‐Carretero
Software Mentions: 3
Published: almost 5 years ago

10.6028/jres.113.022

Refining the In-Parameter-Order Strategy for Constructing Covering Arrays
Cited by: 133
Author(s): Michael A. Forbes, Jim Lawrence, Yu Lei, Raghu N. Kacker, D. Richard Kuhn
Software Mentions: 2
Published: about 16 years ago

10.1186/s12859-015-0562-8

IPO: a tool for automated optimization of XCMS parameters
Cited by: 225
Author(s): Gunnar Libiseller, Michaela Dvorzak, Ulrike Kleb, Edgar Gander, Tobias Eisenberg, Frank Madeo, Steffen Neumann, Gert Trausinger, Frank Sinner, Thomas R. Pieber, Christoph Magnes
Software Mentions: 2
Published: over 9 years ago

10.3390/foods8060212

Targeted and Untargeted Metabolomics as an Enhanced Tool for the Detection of Pomegranate Juice Adulteration
Cited by: 23
Author(s): Marilena E. Dasenaki, Sofia K. Drakopoulou, Reza Aalizadeh, Nikolaos S. Thomaidis
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2017.00551

Bioactivity in Rhododendron: A Systemic Analysis of Antimicrobial and Cytotoxic Activities and Their Phylogenetic and Phytochemical Origins
Cited by: 19
Author(s): Anne Grimbs, Abhinandan Shrestha, Ahmed Rezk, Sergio Grimbs, Inamullah Hakeem Said, Hartwig Schepker, Marc‐Thorsten Hütt, Dirk C. Albach, Klaudia Brix, Nikolai Kuhnert, Matthias S. Ullrich
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1007261

Stearoly-CoA desaturase 1 differentiates early and advanced dengue virus infections and determines virus particle infectivity
Cited by: 32
Author(s): Rebekah C. Gullberg, J. Jordan Steel, Venugopal Pujari, Joel Rovnak, Dean C. Crick, Rushika Perera
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-25428-2

Tissue storage affects lipidome profiling in comparison to in vivo microsampling approach
Cited by: 32
Author(s): Anna Roszkowska, Mengxiao Yu, Vincent Bessonneau, Leslie M. Bragg, Mark R. Servos, Janusz Pawliszyn
Software Mentions: 2
Published: over 6 years ago

10.1155/2014/698453

Interaction Prediction Optimization in Multidisciplinary Design Optimization Problems
Cited by: 11
Author(s): Debiao Meng, Xiaoling Zhang, Hong‐Zhong Huang, Zhonglai Wang, Huifu Xu
Software Mentions: 2
Published: almost 11 years ago

10.1007/s00216-020-03019-3

Adduct annotation in liquid chromatography/high-resolution mass spectrometry to enhance compound identification
Cited by: 14
Author(s): Thomas Stricker, Ron Bonner, Frédérique Lisacek, Gérard Hopfgartner
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-021-95531-4

From the 1990s climate change has decreased cool season catchment precipitation reducing river heights in Australia’s southern Murray-Darling Basin
Cited by: 10
Author(s): Milton S. Speer, Lance M. Leslie, Shev MacNamara, Joshua Hartigan
Software Mentions: 1
Published: over 3 years ago