bioconductor: CAMERA | Projects | Ecosyste.ms: Papers

10.1186/s12870-019-2100-8

Transcriptomic analysis reveals flavonoid biosynthesis of Syringa oblata Lindl. in response to different light intensity
Cited by: 20
Author(s): Yanyan Liu, Xingru Chen, Jinpeng Wang, Weihong Cui, Xiao-Xu Xing, Xueying Chen, Wenya Ding, God’spower Bello-Onaghise, Nsabimana Eliphaz, Meng-Qing Sun, Yànhuá Lǐ
Software Mentions: 2
Published: about 5 years ago

10.1186/s12870-021-02841-w

Non-targeted and targeted metabolomics profiling of tea plants (Camellia sinensis) in response to its intercropping with Chinese chestnut
Cited by: 15
Author(s): Tian Wu, Rui Zou, Dian Pu, Lan Zeng-quan, Bingyu Zhao
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0074469

A New Approach for the Study of Lung Smooth Muscle Phenotypes and Its Application in a Murine Model of Allergic Airway Inflammation
Cited by: 22
Author(s): Jesus Paez-Cortez, Ramaswamy Krishnan, Anneliese Arno, Linh Aven, Sumati Ram-Mohan, Kruti Patel, Jining Lü, Oliver D. King, Xingbin Ai, Alan Fine
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.ppat.1007748

CD8+ T cells retain protective functions despite sustained inhibitory receptor expression during Epstein-Barr virus infection in vivo
Cited by: 42
Author(s): Bithi Chatterjee, Yun Deng, Angelika Holler, Nicolás Gonzalo Núñez, Tarik Azzi, Liliana Danusia Vanoaica, Anne Müller, Hana Zdimerova, Olga Antsiferova, Andrea Zbinden, Riccarda Capaul, Johannes H. Dreyer, David Nadal, Burkhard Becher, Mark D. Robinson, Hans J. Stauss, Christian Münz
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pbio.0050077

The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
Cited by: 1,787
Author(s): Douglas B. Rusch, Aaron L. Halpern, Granger Sutton, Karla B. Heidelberg, Shannon J. Williamson, Shibu Yooseph, Dongying Wu, Jonathan A. Eisen, Jeff Hoffman, Karin Remington, Karen Beeson, Benjamin Tran, Hamilton O. Smith, Holly Baden-Tillson, Clare Stewart, Joyce Thorpe, Jason Freeman, Cynthia Andrews-Pfannkoch, Joseph E. Venter, Kelvin Li, Saul Kravitz, John F. Heidelberg, Terry Utterback, Yu-Hui Rogers, Luisa I. Falcón, Valeria Souza, Germán Bonilla-Rosso, Luis E. Eguiarte, David M. Karl, Shubha Sathyendranath, Trevor Platt, Eldredge Bermingham, Víctor A. Gallardo, Giselle Tamayo‐Castillo, Michael R. Ferrari, Robert L. Strausberg, Kenneth H. Nealson, Robert M. Friedman, M.E. Frazier, J. Craig Venter
Software Mentions: 2
Published: over 17 years ago

10.3389/fmicb.2018.01590

Stoichio-Metagenomics of Ocean Waters: A Molecular Evolution Approach to Trace the Dynamics of Nitrogen Conservation in Natural Communities
Cited by: 7
Author(s): Hannes Dittberner, Niklas Ohlmann, Claudia Acquisti
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2013.00052

Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lō´ihi, Hawai´l
Cited by: 31
Author(s): Esther Singer, John F. Heidelberg, A. S. Dhillon, Katrina J. Edwards
Software Mentions: 2
Published: almost 12 years ago

10.1038/srep21016

Comparative genomics of mitochondria in chlorarachniophyte algae: endosymbiotic gene transfer and organellar genome dynamics
Cited by: 21
Author(s): Goro Tanifuji, John M. Archibald, Takeji Hashimoto
Software Mentions: 2
Published: almost 9 years ago

10.1038/srep22526

Untargeted plasma and tissue metabolomics in rats with chronic kidney disease given AST-120
Cited by: 58
Author(s): Thomas J. Velenosi, Anzel Hennop, David A. Feere, Alvin Tieu, Andrew S. Kucey, Panayiotis A. Kyriacou, Laura E. McCuaig, Stephanie E. Nevison, Michael A. Kerr, Bradley L. Urquhart
Software Mentions: 2
Published: over 8 years ago

10.1038/srep23334

Metabolic phenotyping for monitoring ovarian cancer patients
Cited by: 41
Author(s): Chaofu Ke, Ang Li, Yan Hou, Meng Sun, Kai Yang, Jinlong Cheng, Jingtao Wang, Tingting Ge, Fan Zhang, Qiang Li, Junnan Li, Ying Wu, Ge Lou, Kang Li
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2017.00099

Metabolomic and Metagenomic Analysis of Two Crude Oil Production Pipelines Experiencing Differential Rates of Corrosion
Cited by: 34
Author(s): Vincent Bonifay, Boris Wawrik, Jan Sunner, Emily C. Snodgrass, Egemen Aydın, Kathleen E. Duncan, Amy V. Callaghan, Athenia L. Oldham, Turid Liengen, Iwona B. Beech
Software Mentions: 2
Published: almost 8 years ago

10.1038/srep32165

Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon
Cited by: 67
Author(s): Riccardo Rosselli, Ottavia Romoli, Nicola Vitulo, Alessandro Vezzi, Stefano Campanaro, Fabio De Pascale, Riccardo Schiavon, Maurizio Tiarca, Fabio Poletto, Giuseppe Concheri, Giorgio Valle, Andrea Squartini
Software Mentions: 2
Published: about 8 years ago

10.1038/srep35037

Comprehensive Plasma Metabolomic Analyses of Atherosclerotic Progression Reveal Alterations in Glycerophospholipid and Sphingolipid Metabolism in Apolipoprotein E-deficient Mice
Cited by: 50
Author(s): Vi Dang, Aric Huang, Lexy H Zhong, Yuanyuan Shi, Geoff H. Werstuck
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-017-01280-8

Metabolomic and Proteomic Analysis of Maize Embryonic Callus induced from immature embryo
Cited by: 32
Author(s): Fei Ge, Hongmei Hu, Xing Huang, Yanling Zhang, Yanli Wang, Zhaoling Li, Chaoying Zou, Huanwei Peng, Lujiang Li, Shibin Gao, Guangtang Pan, Yaou Shen
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-27440-y

Comprehensive metabolic and transcriptomic profiling of various tissues provide insights for saponin biosynthesis in the medicinally important Asparagus racemosus
Cited by: 15
Author(s): Prabhakar Lal Srivastava, Anurag Shukla, Raviraj M. Kalunke
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-29744-5

Gut microbiota modulation accounts for the neuroprotective properties of anthocyanins
Cited by: 68
Author(s): Cláudia Marques, Iva Fernandes, Manuela Meireles, Ana Faria, Jeremy P.E. Spencer, Nuno Mateus, Conceição Calhau
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-35807-4

Cross-Platform Comparison of Untargeted and Targeted Lipidomics Approaches on Aging Mouse Plasma
Cited by: 76
Author(s): Kévin Contrepois, Salah Mahmoudi, Baljit K. Ubhi, Katharina Papsdorf, Daniel Hornburg, Anne Brunet, M Snyder
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40679-017-0040-7

Trace: a high-throughput tomographic reconstruction engine for large-scale datasets
Cited by: 27
Author(s): Tekin Biçer, Doğa Gürsoy, Vincent De Andrade, Rajkumar Kettimuthu, William Scullin, Francesco De Carlo, Ian Foster
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pbio.1001088

The Genomic Standards Consortium
Cited by: 180
Author(s): Dawn Field, Linda Amaral‐Zettler, Guy Cochrane, James R. Cole, Peter Dawyndt, George M Garrity, Jack A. Gilbert, Frank Oliver Glöckner, Lynette Hirschman, Ilene Karsch-Mizrachi, Hans‐Peter Klenk, Rob Knight, Renzo Kottmann, Nikos C. Kyrpides, Patrick Meyer, Inigo San Gil, Susanna-Assunta Sansone, Lynn M. Schriml, Peter J. Sterk, Tatiana Tatusova, David W. Ussery, Owen White, John Wooley
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2105-13-264

Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource
Cited by: 23
Author(s): Thomas J. Sharpton, Guillaume Jospin, Dongying Wu, Morgan G. I. Langille, Katherine S. Pollard, Jonathan A. Eisen
Software Mentions: 2
Published: about 12 years ago

10.1038/s41598-019-49319-2

Metabolic modulations of Pseudomonas graminis in response to H2O2 in cloud water
Cited by: 7
Author(s): Nolwenn Wirgot, Marie Lagrée, Mounir Traı̈kia, Ludovic Besaury, Pierre Amato, Isabelle Canet, Martine Sancelme, Cyril Jousse, Binta Diémé, Bernard Lyan, Anne-Marie Delort
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-019-50413-8

Circulating Sphingosine-1-Phosphate as A Non-Invasive Biomarker of Heart Transplant Rejection
Cited by: 9
Author(s): Estefanía Tarazón, Carolina Gil-Cayuela, Maria García‐Manzanares, Marta Roca, Francisca Lago, José Ramón González-Juanatey, Elena Sánchez‐Lacuesta, Luis Martínez‐Dolz, Manuel Portolés, Esther Roselló‐Lletí
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pcbi.1007317

Executable pathway analysis using ensemble discrete-state modeling for large-scale data
Cited by: 10
Author(s): Rohith Palli, Mukta G Palshikar, Juilee Thakar
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0192486

UPLC-QTOF-MS metabolomics analysis revealed the contributions of metabolites to the pathogenesis of Rhizoctonia solani strain AG-1-IA
Cited by: 11
Author(s): Wenjin Hu, Xinli Pan, Fengfeng Li, Wubei Dong
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-020-60135-x

Microbiota and metabolome responses in the cecum and serum of broiler chickens fed with plant essential oils or virginiamycin
Cited by: 37
Author(s): Yan Chen, Jun Wang, Longfei Yu, Tianyue Xu, Ni Zhu
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-63122-4

Metabolomics Adaptation of Juvenile Pacific Abalone Haliotis discus hannai to Heat Stress
Cited by: 15
Author(s): Fei Xu, Tingting Gao, Xiao Liu
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-69845-8

The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients
Cited by: 58
Author(s): Qianqian Zeng, Jie Shen, Kangzhi Chen, Jinxia Zhou, Qiao Liao, Ke Lü, Jiao Yuan, Fangfang Bi
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-021-98729-8

The effect of air pollution on the transcriptomics of the immune response to respiratory infection
Cited by: 7
Author(s): Daniel Croft, David S. Burton, David J. Nagel, Soumyaroop Bhattacharya, Ann R. Falsey, Steve N. Georas, Philip K. Hopke, Carl J. Johnston, R. Matthew Kottmann, Augusto A. Litonjua, Thomas J. Mariani, David Q. Rich, Kelly Thevenet-Morrison, Sally W. Thurston, Mark J. Utell, Matthew N. McCall
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pcbi.1004468

Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities
Cited by: 21
Author(s): Andreas Henschel, Muhammad Zohaib Anwar, Vimitha Manohar
Software Mentions: 2
Published: about 9 years ago

10.1016/j.mex.2020.101179

Lessons Learned from a Two-Round Delphi-based Scenario Study
Cited by: 35
Author(s): Ulrike Schmalz, Stefan Spinler, Jürgen Ringbeck
Software Mentions: 2
Published: almost 4 years ago

10.4056/sigs.641096

Meeting Report: Metagenomics, Metadata and Meta-analysis; (M3) Special Interest Group at ISMB 2009
Cited by: 4
Author(s): Dawn Field, Iddo Friedberg, Peter J. Sterk, Renzo Kottmann, Frank Oliver Glöckner, Lynette Hirschman, George M Garrity, Guy Cochrane, John Wooley, Jack A. Gilbert
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pcbi.1000779

A Quick Guide to Large-Scale Genomic Data Mining
Cited by: 38
Author(s): Curtis Huttenhower, Oliver Hofmann
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pcbi.1004310

Time-Course Gene Set Analysis for Longitudinal Gene Expression Data
Cited by: 60
Author(s): Boris P. Hejblum, Jason A. Skinner, Rodolphe Thiébaut
Software Mentions: 2
Published: over 9 years ago

10.1186/s12859-015-0490-7

Spectral gene set enrichment (SGSE)
Cited by: 6
Author(s): H. Robert Frost, Zhigang Li, Jason H. Moore
Software Mentions: 2
Published: over 9 years ago

10.1007/s11306-016-1092-8

Metabolomics reveals dose effects of low-dose chronic exposure to uranium in rats: identification of candidate biomarkers in urine samples
Cited by: 20
Author(s): Stéphane Grison, Gaëlle Favé, Matthieu Maillot, Line Manens, Olivia Delissen, E. Blanchardon, Isabelle Dublineau, Jocelyne Aigueperse, Sandra Bohand, Jean‐Charles Martin, Maâmar Souidi
Software Mentions: 2
Published: about 8 years ago

10.3390/nu12061792

Untargeted Metabolomics Identifies Key Metabolic Pathways Altered by Thymoquinone in Leukemic Cancer Cells
Cited by: 17
Author(s): Asma Ahmed AlGhamdi, Mohammed Razeeth Shait Mohammed, Mazin A. Zamzami, Abdulrahman L. Al-Malki, Mohamad Qari, Mohammad Imran Khan, Hani Choudhry
Software Mentions: 1
Published: over 4 years ago

10.1002/advs.202000681

EGF Relays Signals to COP1 and Facilitates FOXO4 Degradation to Promote Tumorigenesis
Cited by: 22
Author(s): Hyun Ho Choi, Shaomin Zou, Jian‐Lin Wu, Huashe Wang, Liem Phan, Kai Li, Peng Zhang, Daici Chen, Qingxin Liu, Baifu Qin, Thu Anh Nguyen, Sai‐Ching Jim Yeung, Lishan Fang, Mong Hong Lee
Software Mentions: 1
Published: about 4 years ago

10.1007/s00726-017-2391-8

β-N-Methylamino-l-alanine (BMAA) perturbs alanine, aspartate and glutamate metabolism pathways in human neuroblastoma cells as determined by metabolic profiling
Cited by: 31
Author(s): Mikael K.R. Engskog, Lisa Ersson, Jakob Haglöf, Torbjörn Arvidsson, Curt Pettersson, Eva B. Brittebo
Software Mentions: 1
Published: almost 8 years ago

10.1007/s00216-014-7797-5

Comprehensive and simultaneous coverage of lipid and polar metabolites for endogenous cellular metabolomics using HILIC-TOF-MS
Cited by: 61
Author(s): Fei Fan, Dawn M. E. Bowdish, Brian E. McCarry
Software Mentions: 1
Published: over 10 years ago

10.1093/aobpla/plt002

Honing in on phenotypes: comprehensive two-dimensional gas chromatography of herbivory-induced volatile emissions and novel opportunities for system-level analyses
Cited by: 6
Author(s): Emmanuel Gaquerel, Ian Thomas Baldwin
Software Mentions: 1
Published: almost 12 years ago

10.1007/s00204-021-03135-8

Altered metabolic pathways elucidated via untargeted in vivo toxicometabolomics in rat urine and plasma samples collected after controlled application of a human equivalent amphetamine dose
Cited by: 3
Author(s): Selina Hemmer, Lea Wagmann, Markus R. Meyer
Software Mentions: 1
Published: over 3 years ago

10.1007/s00204-020-02742-1

Toxicometabolomics of the new psychoactive substances α-PBP and α-PEP studied in HepaRG cell incubates by means of untargeted metabolomics revealed unexpected amino acid adducts
Cited by: 17
Author(s): Sascha K. Manier, Lea Wagmann, Veit Flockerzi, Markus R. Meyer
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2105-9-182

Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering
Cited by: 44
Author(s): Shibu Yooseph, Weizhong Li, Granger Sutton
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-13-183

Short-read reading-frame predictors are not created equal: sequence error causes loss of signal
Cited by: 42
Author(s): W. Trimble, Kevin P. Keegan, Mark D’Souza, Andreas Wilke, Jared Wilkening, Jack A. Gilbert, Patrick Meyer
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-11-S1-S12

Short clones or long clones? A simulation study on the use of paired reads in metagenomics
Cited by: 13
Author(s): Suparna Mitra, Max Schubach, Daniel H. Huson
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12859-016-1299-8

Unsupervised gene set testing based on random matrix theory
Cited by: 1
Author(s): H. Robert Frost, Christopher I. Amos
Software Mentions: 1
Published: about 8 years ago

10.1186/s12859-015-0707-9

Quantitative gene set analysis generalized for repeated measures, confounder adjustment, and continuous covariates
Cited by: 12
Author(s): Jacob Turner, Christopher R. Bolen, Derek Blankenship
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2105-10-S1-S12

Methods for comparative metagenomics
Cited by: 114
Author(s): Daniel H. Huson, Daniel C. Richter, Suparna Mitra, Alexander F. Auch, Stephan C. Schuster
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2105-15-239

Structure-revealing data fusion
Cited by: 93
Author(s): Evrim Acar, Evangelos E. Papalexakis, Gözde Gürdeniz, Morten Arendt Rasmussen, Anders J. Lawaetz, Mathias Nilsson, Rasmus Bro
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2105-10-359

Analysis and comparison of very large metagenomes with fast clustering and functional annotation
Cited by: 110
Author(s): Weizhong Li
Software Mentions: 1
Published: about 15 years ago

10.1186/s12915-015-0207-4

A novel group of diverse Polinton-like viruses discovered by metagenome analysis
Cited by: 77
Author(s): Natalya Yutin, Sofiya Shevchenko, Vladimir V. Kapitonov, Mart Krupovìč, Eugene V. Koonin
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2164-13-695

A novel method to discover fluoroquinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequences
Cited by: 26
Author(s): Fredrik Boulund, Anna Johnning, Mariana Buongermino Pereira, D. G. Joakim Larsson, Erik Kristiansson
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-15-202

Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs
Cited by: 24
Author(s): Anna Gogleva, Mikhail S. Gelfand, Irena I. Artamonova
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-15-888

De novo assembly and characterization of the transcriptome of the toxic dinoflagellate Karenia brevis
Cited by: 33
Author(s): Darcie E Ryan, Alan E. Pepper, Lisa Campbell
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2164-15-374

Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae
Cited by: 33
Author(s): Goro Tanifuji, Naoko T. Onodera, Matthew W. Brown, Bruce A. Curtis, Andrew J. Roger, Gane Ka‐Shu Wong, Michael Melkonian, John M. Archibald
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-10-268

Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'
Cited by: 60
Author(s): Michelle M. Meyer, Tyler D. Ames, Daniel P. Smith, Zasha Weinberg, Michael S. Schwalbach, Stephen J. Giovannoni, Ronald R. Breaker
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-12-444

WebMGA: a customizable web server for fast metagenomic sequence analysis
Cited by: 542
Author(s): Sitao Wu, Zhengwei Zhu, Liming Fu, Beifang Niu, Weizhong Li
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2180-12-66

Coverage evaluation of universal bacterial primers using the metagenomic datasets
Cited by: 156
Author(s): Dan-Ping Mao, Quan Zhou, Chong-Yu Chen, Zhe‐Xue Quan
Software Mentions: 1
Published: over 12 years ago

10.1186/s12891-016-0878-1

DAS steered therapy in clinical practice; cross-sectional results from the METEOR database
Cited by: 2
Author(s): E. Gvozdenovic, Ron Wolterbeek, Désirée van der Heijde, Tom W J Huizinga, Cornelia F Allaart, Robert Landewé
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2229-14-116

Transcriptomic and metabolomic analysis of copper stress acclimation in Ectocarpus siliculosus highlights signaling and tolerance mechanisms in brown algae
Cited by: 89
Author(s): Andrés Ritter, Simon M. Dittami, Sophie Goulitquer, Juan A. Correa, Catherine Boyen, Philippe Potin, Thierry Tonon
Software Mentions: 1
Published: over 10 years ago

10.1186/s12870-018-1412-4

Comparative metabolomics reveals the metabolic variations between two endangered Taxus species (T. fuana and T. yunnanensis) in the Himalayas
Cited by: 62
Author(s): Chunna Yu, Xiujun Luo, Xiaowei Zhan, Juan Hao, Lei Zhang, Yue Song, Chenjia Shen, Ming Dong
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2229-13-73

NaMYC2 transcription factor regulates a subset of plant defense responses in Nicotiana attenuata
Cited by: 41
Author(s): Melkamu Woldemariam, Son Truong Dinh, Younjae Oh, Emmanuel Gaquerel, Ian Thomas Baldwin, Ivan Gàlis
Software Mentions: 1
Published: over 11 years ago

10.1186/1752-0509-6-S1-S16

Parallel-META: efficient metagenomic data analysis based on high-performance computation
Cited by: 30
Author(s): Xiaoquan Su, Jian Xu, Kang Ning
Software Mentions: 1
Published: over 12 years ago

10.1136/bmjopen-2018-025943

Remediating doctors’ performance to restore patient safety: a realist review protocol
Cited by: 8
Author(s): Tristan Price, Nicola Brennan, Jennifer Cleland, Linda Prescott‐Clements, Amanda Wanner, Lyndsey Withers, Geoff Wong, Julian Archer
Software Mentions: 1
Published: about 6 years ago

10.1093/bioinformatics/btu813

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics
Cited by: 307
Author(s): Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Péricard, Mélanie Petera, Christophe Dupérier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne Thévenot, Christophe Caron
Software Mentions: 1
Published: almost 10 years ago

10.1093/bioinformatics/btaa856

LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications
Cited by: 7
Author(s): Jorge Álvarez-Jarreta, Patrícia Rodrigues, Eoin Fahy, Anne E O’Connor, Anna Price, Caroline Gaud, Simon Andrews, Paul Benton, Gary Siuzdak, Jade Hawksworth, Maria Valdivia-Garcia, Stuart M. Allen, Valerie Bridget O'Donnell
Software Mentions: 1
Published: almost 4 years ago

10.1093/bioinformatics/bty699

Container-based bioinformatics with Pachyderm
Cited by: 38
Author(s): Jon Ander Novella, Payam Emami Khoonsari, Stephanie Herman, Daniel Whitenack, Marco Capuccini, Joachim Burman, Kim Kultima, Ola Spjuth
Software Mentions: 1
Published: over 6 years ago

10.1093/bioinformatics/btu370

MetAssign: probabilistic annotation of metabolites from LC–MS data using a Bayesian clustering approach
Cited by: 58
Author(s): Rónán Daly, Simon Rogers, Joe Wandy, Andris Jankevics, Karl Burgess, Rainer Breitling
Software Mentions: 1
Published: over 10 years ago

10.1186/1745-6150-7-13

A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses
Cited by: 145
Author(s): Geoffrey S. Diemer, Kenneth M. Stedman
Software Mentions: 1
Published: almost 13 years ago

10.3390/biom11030343

Optimizing Calcium Detection Methods in Animal Systems: A Sandbox for Synthetic Biology
Cited by: 12
Author(s): Elizabeth S Li, Margaret S. Saha
Software Mentions: 1
Published: over 3 years ago

10.1155/2015/121735

Metagenomics: Retrospect and Prospects in High Throughput Age
Cited by: 36
Author(s): Satish Kumar, Kishore Kumar Krishnani, Bharat Bhushan, M. P. Brahmane
Software Mentions: 1
Published: about 9 years ago

10.1186/s12944-018-0948-5

Untargeted Mass Spectrometry Lipidomics identifies correlation between serum sphingomyelins and plasma cholesterol
Cited by: 21
Author(s): Pierre Zalloua, Hanane Kadar, Essa Hariri, Layal Abi Farraj, François Brial, Lyamine Hedjazi, Aurélie Le Lay, Alexandre Colleu, Justine Dubus, David Touboul, Fumihiko Matsuda, Mark Lathrop, Jeremy K. Nicholson, Marc Dumas, Dominique Guyader
Software Mentions: 1
Published: almost 6 years ago

10.3390/md8041011

Biosynthesis and Molecular Genetics of Polyketides in Marine Dinoflagellates
Cited by: 108
Author(s): Ralf Kellmann, Anke Stüken, Russell J. S. Orr, Helene M. Svendsen, Kjetill S. Jakobsen
Software Mentions: 1
Published: over 14 years ago

10.3390/md14040080

Discovery Strategies of Bioactive Compounds Synthesized by Nonribosomal Peptide Synthetases and Type-I Polyketide Synthases Derived from Marine Microbiomes
Cited by: 56
Author(s): Grigoris D. Amoutzias, Anargyros Chaliotis, Dimitris Mossialos
Software Mentions: 1
Published: over 8 years ago

10.3390/metabo10050183

Pathway-Activity Likelihood Analysis and Metabolite Annotation for Untargeted Metabolomics Using Probabilistic Modeling
Cited by: 10
Author(s): Ramtin Hosseini, Neda Hassanpour, Liping Liu, Soha Hassoun
Software Mentions: 1
Published: over 4 years ago

10.3390/metabo10010037

Metabolomics in the Context of Plant Natural Products Research: From Sample Preparation to Metabolite Analysis
Cited by: 120
Author(s): Mohamed A. Salem, Leonardo Perez de Souza, Ahmed Serag, Alisdair R. Fernie, Mohamed A. Farag, Shahira M. Ezzat, Saleh Alseekh
Software Mentions: 1
Published: almost 5 years ago

10.3390/metabo9110251

Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics
Cited by: 30
Author(s): Isao Tada, Hiroshi Tsugawa, Isabel Meister, Pei Zhang, Rie Shu, Riho Katsumi, Craig E. Wheelock, Masanori Arita, Romanas Chaleckis
Software Mentions: 1
Published: about 5 years ago

10.3390/metabo10100417

The Peptide Chain Release Factor Methyltransferase PrmC Influences the Pseudomonas aeruginosa PA14 Endo- and Exometabolome
Cited by: 0
Author(s): Tobias Depke, Susanne Häußler, Mark Brönstrup
Software Mentions: 1
Published: about 4 years ago

10.3390/metabo10070269

Multifactorial Analysis of Environmental Metabolomic Data in Ecotoxicology: Wild Marine Mussel Exposed to WWTP Effluent as a Case Study
Cited by: 18
Author(s): Thibaut Dumas, Julien Bernard, Elena Góméz, Hélène Fenet, Frédérique Courant
Software Mentions: 1
Published: over 4 years ago

10.3390/metabo9110254

Quantification of Urinary Phenyl-γ-Valerolactones and Related Valeric Acids in Human Urine on Consumption of Apples
Cited by: 26
Author(s): Andrea Anesi, Pedro Mena, Achim Bub, Marynka Ulaszewska, Daniele Del Rio, Sabine E. Kulling, Fulvio Mattivi
Software Mentions: 1
Published: about 5 years ago

10.3390/metabo11010003

Liquid Chromatography-High-Resolution Mass Spectrometry-Based In Vitro Toxicometabolomics of the Synthetic Cathinones 4-MPD and 4-MEAP in Pooled Human Liver Microsomes
Cited by: 10
Author(s): Sascha K. Manier, Florian Schwermer, Lea Wagmann, Niels Eckstein, Markus R. Meyer
Software Mentions: 1
Published: almost 4 years ago

10.3390/metabo11010055

Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations
Cited by: 47
Author(s): Santosh Lamichhane, Partho Sen, Marina Amaral Alves, Henrique Caracho Ribeiro, Peppi Raunioniemi, Tuulia Hyötyläinen, Matej Orešič
Software Mentions: 1
Published: almost 4 years ago

10.3390/metabo9110255

Metabolomic Dynamics Reveals Oxidative Stress in Spongy Tissue Disorder During Ripening of Mangifera indica L. Fruit
Cited by: 16
Author(s): Pranjali S. Oak, Ashish Deshpande, Ashok P. Giri, Vidya S. Gupta
Software Mentions: 1
Published: about 5 years ago

10.3390/metabo10050199

Using Metabolomics to Identify Cell Line-Independent Indicators of Growth Inhibition for Chinese Hamster Ovary Cell-Based Bioprocesses
Cited by: 13
Author(s): Nicholas Alden, Ravali Raju, Kyle McElearney, James Lambropoulos, Rashmi Kshirsagar, A. Gilbert, Kyongbum Lee
Software Mentions: 1
Published: over 4 years ago

10.3390/metabo11080492

MStractor: R Workflow Package for Enhancing Metabolomics Data Pre-Processing and Visualization
Cited by: 2
Author(s): Luca Nicolotti, Jeremy Hack, Markus Herderich, Natoiya D. R. Lloyd
Software Mentions: 1
Published: over 3 years ago

10.3390/metabo2040775

A Guideline to Univariate Statistical Analysis for LC/MS-Based Untargeted Metabolomics-Derived Data
Cited by: 209
Author(s): María Vinaixa, Sara Samino, Isabel Sáez, Jordi Durán, Joan J. Guinovart, Óscar Yanes
Software Mentions: 1
Published: about 12 years ago

10.1007/s11306-013-0523-z

Comparative analysis of volatile metabolomics signals from melanoma and benign skin: a pilot study
Cited by: 71
Author(s): Tatjana Abaffy, Mecker G. Möller, D. D. Riemer, Clara Milikowski, R. Anthony DeFazio
Software Mentions: 1
Published: over 11 years ago

10.1007/s11306-014-0711-5

Metabolic profiling of a transgenic Caenorhabditis elegans Alzheimer model
Cited by: 30
Author(s): Roel Van Assche, Liesbet Temmerman, Daniel A. Dias, Berin A. Boughton, Kurt Boonen, Bart P. Braeckman, Liliane Schoofs, Ute Roessner
Software Mentions: 1
Published: over 10 years ago

10.1007/s11306-019-1595-1

An LCMS-based untargeted metabolomics protocol for cochlear perilymph: highlighting metabolic effects of hydrogen gas on the inner ear of noise exposed Guinea pigs
Cited by: 14
Author(s): Kristian Pirttilä, Pernilla Videhult Pierre, Jakob Haglöf, Mikael K.R. Engskog, Mikael Hedeland, Göran Laurell, Torbjörn Arvidsson, Curt Pettersson
Software Mentions: 1
Published: about 5 years ago

10.1264/jsme2.ME11274

Genetic Evidence for Bacterial Chemolithoautotrophy Based on the Reductive Tricarboxylic Acid Cycle in Groundwater Systems
Cited by: 12
Author(s): Albin Alfreider, Carsten Vogt
Software Mentions: 1
Published: almost 13 years ago

10.1264/jsme2.ME17203

Taxon Richness of “Megaviridae” Exceeds those of Bacteria and Archaea in the Ocean
Cited by: 79
Author(s): Tomoko Mihara, Hitoshi Koyano, Pascal Hingamp, Nigel Grimsley, Susumu Goto, Hiroyuki Ogata
Software Mentions: 1
Published: almost 7 years ago

10.1186/2049-2618-2-17

The Amazon continuum dataset: quantitative metagenomic and metatranscriptomic inventories of the Amazon River plume, June 2010
Cited by: 52
Author(s): Brandon M. Satinsky, Brian L. Zielinski, Mary K. Doherty, Christa B. Smith, Shalabh Sharma, John H. Paul, Byron C. Crump, Mary Ann Moran
Software Mentions: 1
Published: over 10 years ago

10.3390/microorganisms8040556

Applications of Prodigiosin Extracted from Marine Red Pigmented Bacteria Zooshikella sp. and Actinomycete Streptomyces sp.
Cited by: 27
Author(s): Chatragadda Ramesh, Nambali Valsalan Vinithkumar, Ramalingam Kirubagaran, Chidambaram Kulandaisamy Venil, Laurent Dufossé
Software Mentions: 1
Published: over 4 years ago

10.1074/mcp.M114.046508

Optimized Analytical Procedures for the Untargeted Metabolomic Profiling of Human Urine and Plasma by Combining Hydrophilic Interaction (HILIC) and Reverse-Phase Liquid Chromatography (RPLC)–Mass Spectrometry*
Cited by: 169
Author(s): Kévin Contrepois, Lihua Jiang, M Snyder
Software Mentions: 1
Published: over 9 years ago

10.3390/molecules26144124

Lipidomic Profiling of Ipsilateral Brain and Plasma after Celastrol Post-Treatment in Transient Middle Cerebral Artery Occlusion Mice Model
Cited by: 7
Author(s): Maozhu Liu, Mengyuan Chen, Ying Luo, Hong Wang, Haifeng Huang, Zhe Peng, Miaomiao Li, Huizhi Fei, Wen Luo, Junqing Yang
Software Mentions: 1
Published: over 3 years ago

10.3390/molecules24203780

Quality Formation Mechanism of Stiff Silkworm, Bombyx batryticatus Using UPLC-Q-TOF-MS-Based Metabolomics
Cited by: 4
Author(s): Dongxu Xing, Guanghui Shen, Qingrong Li, Yang Xiao, Qiong Yang, Qingyou Xia
Software Mentions: 1
Published: about 5 years ago

10.1186/1743-422X-5-12

Marine mimivirus relatives are probably large algal viruses
Cited by: 103
Author(s): Adam Monier, Jens Borggaard Larsen, Ruth‐Anne Sandaa, Gunnar Bratbak, Jean‐Michel Claverie, Hiroyuki Ogata
Software Mentions: 1
Published: almost 17 years ago

10.1186/1743-422X-8-427

Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids
Cited by: 13
Author(s): Takashi Yoshida, Jean‐Michel Claverie, Hiroyuki Ogata
Software Mentions: 1
Published: about 13 years ago

10.3390/v11010073

Characterization of the Lipidomic Profile of Human Coronavirus-Infected Cells: Implications for Lipid Metabolism Remodeling upon Coronavirus Replication
Cited by: 210
Author(s): Bingpeng Yan, Hin Chu, Dong Yang, Kong Hung Sze, Pok-Man Lai, Shuofeng Yuan, Huiping Shuai, Yixin Wang, Richard Yi Tsun Kao, Jasper Fuk‐Woo Chan, Kwok‐Yung Yuen
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj.2870

Sponge exhalent seawater contains a unique chemical profile of dissolved organic matter
Cited by: 31
Author(s): Cara L. Fiore, Christopher Freeman, Elizabeth B. Kujawinski
Software Mentions: 1
Published: almost 8 years ago

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