bioconductor: TargetSearch | Projects

10.3390/metabo9100200

The metaRbolomics Toolbox in Bioconductor and beyond
Cited by: 61
Author(s): Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy A. Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Michael Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski, Michael A. Stravs, Etienne Thévenot, Hendrik Treutler, Ralf Weber, Egon Willighagen, Michael Witting, Steffen Neumann
Software Mentions: 92
Published: about 5 years ago

10.1093/gigascience/gix037

From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics
Cited by: 48
Author(s): Leonardo Perez de Souza, Thomas Naake, Takayuki Tohge, Alisdair R. Fernie
Software Mentions: 12
Published: over 7 years ago

10.3390/metabo11040211

gcProfileMakeR: An R Package for Automatic Classification of Constitutive and Non-Constitutive Metabolites
Cited by: 3
Author(s): Fernando Pérez-Sánz, Victoria Ruiz-Hernández, Marta I. Terry, Sara Arce-Gallego, Julia Weiß, Pedro J. Navarro, Marcos Egea‐Cortines
Software Mentions: 9
Published: over 3 years ago

10.1186/1471-2105-13-115

PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools
Cited by: 60
Author(s): Sean O’Callaghan, David P. De Souza, Andrew P. Isaac, Qiao Wang, Luke Hodkinson, Moshe Olshansky, Tim Erwin, Bill Appelbe, Dedreia Tull, Ute Roessner, Antony Bacic, Malcolm J. McConville, Vladimir A Likić
Software Mentions: 6
Published: over 12 years ago

10.1155/2010/896718

Feature Detection Techniques for Preprocessing Proteomic Data
Cited by: 4
Author(s): Kimberly F. Sellers, Jeffrey C. Miecznikowski
Software Mentions: 5
Published: almost 15 years ago

10.1186/1758-2946-5-12

Computational mass spectrometry for small molecules
Cited by: 124
Author(s): Kerstin Scheubert, Franziska Hufsky, Sebastian Böcker
Software Mentions: 5
Published: almost 12 years ago

10.1007/s11306-015-0927-z

GC–MS metabolic profiling of Cabernet Sauvignon and Merlot cultivars during grapevine berry development and network analysis reveals a stage- and cultivar-dependent connectivity of primary metabolites
Cited by: 51
Author(s): Álvaro Cuadros-Inostroza, Simón Ruíz-Lara, Enrique González, Änne Eckardt, Lothar Willmitzer, Hugo Peña‐Cortés
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pone.0090322

Poly(ADP-Ribose)Polymerase Activity Controls Plant Growth by Promoting Leaf Cell Number
Cited by: 29
Author(s): Philipp Schulz, Karel Jansseune, Thomas Degenkolbe, Michaël Méret, Hannes Claeys, Aleksandra Skirycz, Markus Teige, Lothar Willmitzer, Matthew A. Hannah
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pone.0047833

Metabolic Profiling Reveals Sphingosine-1-Phosphate Kinase 2 and Lyase as Key Targets of (Phyto-) Estrogen Action in the Breast Cancer Cell Line MCF-7 and Not in MCF-12A
Cited by: 22
Author(s): Nadja Engel, Jan Lisec, Birgit Piechulla, Barbara Nebe
Software Mentions: 3
Published: about 12 years ago

10.1186/s12859-015-0681-2

SIMAT: GC-SIM-MS data analysis tool
Cited by: 8
Author(s): Mohammad Ranjbar, Cristina Di Poto, Yue Joseph Wang, Habtom W. Ressom
Software Mentions: 3
Published: over 9 years ago

10.1016/j.mcpro.2021.100118

A Reductionist Approach Using Primary and Metastatic Cell–Derived Extracellular Vesicles Reveals Hub Proteins Associated with Oral Cancer Prognosis
Cited by: 10
Author(s): Ariane F. Busso-Lopes, Carolina Moretto Carnielli, Flávia Vischi Winck, Fábio Malta de Sá Patroni, Ana Karina de Oliveira, Daniela Campos Granato, Rute Alves Pereira e Costa, Romênia R. Domingues, Bianca Alves Pauletti, Diego Mauricio Riaño-Pachón, Juliana Aparecida Aricetti, Camila Caldana, Edgard Graner, Ricardo D. Coletta, Kelly A. Dryden, Jay W. Fox, Adriana Franco Paes Leme
Software Mentions: 3
Published: almost 4 years ago

10.3390/plants10020203

Bryo-Activities: A Review on How Bryophytes Are Contributing to the Arsenal of Natural Bioactive Compounds against Fungi
Cited by: 36
Author(s): Mauro Commisso, Francesco Guarino, Laura Marchi, Antonella Muto, Amalia Piro, Francesca Degola
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1006363

Combined Use of Genome-Wide Association Data and Correlation Networks Unravels Key Regulators of Primary Metabolism in Arabidopsis thaliana
Cited by: 63
Author(s): Si Wu, Saleh Alseekh, Álvaro Cuadros-Inostroza, Corina M. Fusari, Marek Mutwil, Rik Kooke, Joost J. B. Keurentjes, Alisdair R. Fernie, Lothar Willmitzer, Yariv Brotman
Software Mentions: 3
Published: about 8 years ago

10.3389/fpls.2016.01954

Activation of Secondary Metabolism in Citrus Plants Is Associated to Sensitivity to Combined Drought and High Temperatures
Cited by: 113
Author(s): Sara I. Zandalinas, Carlos Sales, J. Beltrán, Aurelio Gómez-Cádenas
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2105-10-428

TargetSearch - a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data
Cited by: 185
Author(s): Álvaro Cuadros-Inostroza, Camila Caldana, Henning Redestig, Miyako Kusano, Jan Lisec, Hugo Peña‐Cortés, Lothar Willmitzer, Matthew A. Hannah
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0014101

Interaction with Diurnal and Circadian Regulation Results in Dynamic Metabolic and Transcriptional Changes during Cold Acclimation in Arabidopsis
Cited by: 153
Author(s): Carmen Espinoza, Thomas Degenkolbe, Camila Caldana, Ellen Zuther, Andrea Leisse, Lothar Willmitzer, Dirk K. Hincha, Matthew A. Hannah
Software Mentions: 2
Published: about 14 years ago

10.1038/s41598-017-15607-y

IGF-1-mediated PKM2/β-catenin/miR-152 regulatory circuit in breast cancer
Cited by: 30
Author(s): Yiyang Wen, Weitao Liu, Haoran Sun, Xin Ge, Zhumei Shi, Min Wang, Wei Li, Jianying Zhang, Lingzhi Liu, Bing-Hua Jiang
Software Mentions: 2
Published: about 7 years ago

10.3390/biom10040504

UV-B Radiation Largely Promoted the Transformation of Primary Metabolites to Phenols in Astragalus mongholicus Seedlings
Cited by: 21
Author(s): Yang Liu, Jia Liu, Ann Abozeid, Ke-Xin Wu, Xiao‐Na Guo, Liqiang Mu
Software Mentions: 2
Published: over 4 years ago

10.1186/s12870-015-0672-5

Metabolomics of dates (Phoenix dactylifera) reveals a highly dynamic ripening process accounting for major variation in fruit composition
Cited by: 40
Author(s): Ilhame Diboun, Sweety Mathew, Maryam Al-Rayyashi, Mohamed A. Elrayess, María Fernanda Torres, Anna Halama, Michaël Méret, Robert P. Mohney, Edward D. Karoly, Joel A. Malek, Karsten Suhre
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-019-53762-6

Differences in lipidome and metabolome organization of prefrontal cortex among human populations
Cited by: 2
Author(s): Anna Tkachev, Vita Stepanova, Lei Zhang, Ekaterina E. Khrameeva, Dmitry Zubkov, Patrick Giavalisco, Philipp Khaitovich
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-020-61081-4

Correlation-based network analysis combined with machine learning techniques highlight the role of the GABA shunt in Brachypodium sylvaticum freezing tolerance
Cited by: 12
Author(s): David Toubiana, Nir Sade, Lifeng Liu, María del Mar Rubio Wilhelmi, Yariv Brotman, Urszula Luzarowska, John P. Vogel, Eduardo Blumwald
Software Mentions: 2
Published: almost 5 years ago

10.3389/fpls.2019.01524

Network Analyses and Data Integration of Proteomics and Metabolomics From Leaves of Two Contrasting Varieties of Sugarcane in Response to Drought
Cited by: 22
Author(s): Ilara Gabriela Frasson Budzinski, Fabrício Edgar de Moraes, Thaís Regiani Cataldi, Lívia Maria Franceschini, Carlos Alberto Labate
Software Mentions: 1
Published: about 5 years ago

10.3389/fpls.2021.637508

Shedding Light on the Dynamic Role of the “Target of Rapamycin” Kinase in the Fast-Growing C4 Species Setaria viridis, a Suitable Model for Biomass Crops
Cited by: 6
Author(s): Viviane Cristina Heinzen da Silva, Marina C. M. Martins, Maria Juliana Calderan-Rodrigues, Anthony Artins, Carolina Cassano Monte Bello, Saurabh Gupta, Tiago J. P. Sobreira, Diego Mauricio Riaño‐Pachón, Valéria Mafra, Camila Caldana
Software Mentions: 1
Published: over 3 years ago

10.3389/fpls.2016.00043

Analysis of Sensitive CO2 Pathways and Genes Related to Carbon Uptake and Accumulation in Chlamydomonas reinhardtii through Genomic Scale Modeling and Experimental Validation
Cited by: 11
Author(s): Flávia Vischi Winck, David Orlando Páez Melo, Diego Mauricio Riaño-Pachón, Marina C. M. Martins, Camila Caldana, Andrés Fernando González Barrios
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12870-019-1665-6

Transcriptome and metabolome analyses of two contrasting sesame genotypes reveal the crucial biological pathways involved in rapid adaptive response to salt stress
Cited by: 79
Author(s): Yujuan Zhang, Donghua Li, Rong Zhou, Xiao Wang, Komivi Dossa, Linhai Wang, Yanxin Zhang, Jingyin Yu, Huihui Gong, Jun You
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12870-019-1880-1

Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress
Cited by: 132
Author(s): Jun You, Yujuan Zhang, Aili Liu, Donghua Li, Xiao Wang, Komivi Dossa, Rong Zhou, Jingyin Yu, Yanxin Zhang, Linhai Wang
Software Mentions: 1
Published: over 5 years ago

10.1007/s11306-018-1369-1

Group-wise ANOVA simultaneous component analysis for designed omics experiments
Cited by: 17
Author(s): Edoardo Saccenti, Age K. Smilde, José Camacho
Software Mentions: 1
Published: over 6 years ago

10.1186/s13007-016-0146-2

Protocol: a fast, comprehensive and reproducible one-step extraction method for the rapid preparation of polar and semi-polar metabolites, lipids, proteins, starch and cell wall polymers from a single sample
Cited by: 140
Author(s): Mohamed A. Salem, Jessica Jüppner, Krzysztof Bajdzienko, Patrick Giavalisco
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0098783

Undesired Small RNAs Originate from an Artificial microRNA Precursor in Transgenic Petunia (Petunia hybrida)
Cited by: 12
Author(s): Yang-Dong Guo, Yuepeng Han, Jing Ma, Huiping Wang, Xianchun Sang, Mingyang Li
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2229-14-121

VMP1-deficient Chlamydomonas exhibits severely aberrant cell morphology and disrupted cytokinesis
Cited by: 20
Author(s): Hezi Tenenboim, Julia Smirnova, Lothar Willmitzer, Martin Steup, Yariv Brotman
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0130744

Transcriptome Response Signatures Associated with the Overexpression of a Mitochondrial Uncoupling Protein (AtUCP1) in Tobacco
Cited by: 10
Author(s): Alessandra Vasconcellos Nunes Laitz, Márcio Luís Acencio, Ilara Gabriela Frasson Budzinski, Mônica Teresa Veneziano Labate, Ney Lemke, Paulo Eduardo Martins Ribolla, Ivan de Godoy Maia
Software Mentions: 1
Published: over 9 years ago

10.3389/fpls.2014.00770

Optimizing experimental procedures for quantitative evaluation of crop plant performance in high throughput phenotyping systems
Cited by: 119
Author(s): Astrid Junker, Moses M. Muraya, Kathleen Weigelt‐Fischer, Fernando Alberto Arana-Ceballos, Christian Klukas, Albrecht E. Melchinger, Rhonda C. Meyer, David Riewe, Thomas Altmann
Software Mentions: 1
Published: almost 10 years ago

10.3389/fpls.2016.01108

Analysis of Drought-Induced Proteomic and Metabolomic Changes in Barley (Hordeum vulgare L.) Leaves and Roots Unravels Some Aspects of Biochemical Mechanisms Involved in Drought Tolerance
Cited by: 89
Author(s): Klaudia Chmielewska, Paweł Rodziewicz, Barbara Sgorbini, Aneta Sawikowska, Paweł Krajewski, Łukasz Marczak, Danuta Ciesiołka, Anetta Kuczyńska, Krzysztof Mikołajczak, Piotr Ogrodowicz, Karolina Krystkowiak, M. Surma, T. Adamski, Paweł Bednarek, Maciej Stobiecki
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms21072513

Early pH Changes in Musculoskeletal Tissues upon Injury—Aerobic Catabolic Pathway Activity Linked to Inter-Individual Differences in Local pH
Cited by: 21
Author(s): Julia C. Berkmann, Aaron X. Herrera Martin, Agnes Ellinghaus, Claudia Schlundt, Hanna Schell, Evi Lippens, Georg N. Duda, Serafeim Tsitsilonis, Katharina Schmidt‐Bleek
Software Mentions: 1
Published: over 4 years ago

Ecosyste.ms: Papers

Projects: bioconductor: TargetSearch

Papers Mentioning TargetSearch 34