bioconductor: CAMERA | Projects | Ecosyste.ms: Papers

10.3390/metabo11060364

Towards Standards for Human Fecal Sample Preparation in Targeted and Untargeted LC-HRMS Studies
Cited by: 8
Author(s): Farideh Hosseinkhani, Anne-Charlotte Dubbelman, Naama Karu, Amy C. Harms, Thomas Hankemeier
Software Mentions: 3
Published: over 3 years ago

10.3390/foods10061218

Extending the Lipidome Coverage by Combining Different Mass Spectrometric Platforms: An Innovative Strategy to Answer Chemical Food Safety Issues
Cited by: 4
Author(s): Justine Marchand, Yann Guitton, Estelle Martineau, Anne-Lise Royer, David Balgoma, Bruno Le Bizec, Patrick Giraudeau, Gaud Dervilly
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0251867

Dissecting contact tracing apps in the Android platform
Cited by: 15
Author(s): Vasileios Kouliaridis, Georgios Kambourakis, Efstratios Chatzoglou, Dimitris Geneiatakis, Hua Wang
Software Mentions: 3
Published: over 3 years ago

10.3389/fpls.2014.00209

An introduction to the analysis of shotgun metagenomic data
Cited by: 402
Author(s): Thomas J. Sharpton
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0132642

Spontaneous Deletion of an “ORFanage” Region Facilitates Host Adaptation in a “Photosynthetic” Cyanophage
Cited by: 12
Author(s): Richard John Puxty, Blanca Perez-Sepulveda, Branko Rihtman, David J. Evans, Andrew Millard, David J. Scanlan
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0007143

New Insights into the Diversity of Marine Picoeukaryotes
Cited by: 196
Author(s): Fabrice Not, Javier del Campo, Vanessa Balagué, Colomban de Vargas, Ramón Massana
Software Mentions: 3
Published: about 15 years ago

10.1093/gbe/evt189

The Complex Intron Landscape and Massive Intron Invasion in a Picoeukaryote Provides Insights into Intron Evolution
Cited by: 27
Author(s): Bram Verhelst, Yves Van de Peer, Pierre Rouzé
Software Mentions: 3
Published: about 11 years ago

10.1042/BSR20202915

Lipid profiling of mouse intestinal organoids for studying APC mutations
Cited by: 3
Author(s): Zoë H. Jukes, Anne Freier, Maria Glymenaki, Richard C. D. Brown, Lee Parry, Elizabeth J. Want, Panagiotis A. Vorkas, Jia V. Li
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1009085

Analyzing cancer gene expression data through the lens of normal tissue-specificity
Cited by: 8
Author(s): H. Robert Frost
Software Mentions: 3
Published: over 3 years ago

10.1186/s13568-021-01246-0

Identification of the molecular mechanisms underlying brisket disease in Holstein heifers via microbiota and metabolome analyses
Cited by: 1
Author(s): Kun Yao, Shuxiang Wang, Gaowa Naren, Shuai Huang, Shengli Li, Weijuan Shao
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2015.00265

Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions
Cited by: 46
Author(s): Cheryl-Emiliane T. Chow, Danielle M. Winget, Richard Allen White, Steven J. Hallam, Curtis A. Suttle
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pbio.3000830

Strigolactone signaling regulates specialized metabolism in tobacco stems and interactions with stem-feeding herbivores
Cited by: 16
Author(s): Suhua Li, Youngsung Joo, Dechang Cao, Ran Li, Gisuk Lee, Rayko Halitschke, Gundega Baldwin, Ian T. Baldwin, Ming Wang
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2019.00708

Immunological Molecular Responses of Human Retinal Pigment Epithelial Cells to Infection With Toxoplasma gondii
Cited by: 15
Author(s): Shervi Lie, E Rochet, Erik Segerdell, Yuefang Ma, Liam M. Ashander, Audra Shadforth, Timothy A. Blenkinsop, Michael Michael, Binoy Appukuttan, Beth Wilmot, Justine R. Smith
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2019.00598

SCIA: A Novel Gene Set Analysis Applicable to Data With Different Characteristics
Cited by: 2
Author(s): Yiqun Li, Ying Wu, Xiaohan Zhang, Yongping Bai, Luqman Muhammad Akthar, Xin Lü, Ming Shi, Jing Zhao, Qinghua Jiang, Li Yu
Software Mentions: 3
Published: over 5 years ago

10.1186/s12974-021-02191-2

Microglia RAGE exacerbates the progression of neurodegeneration within the SOD1G93A murine model of amyotrophic lateral sclerosis in a sex-dependent manner
Cited by: 13
Author(s): Michael MacLean, Judyta K. Juranek, Swetha Cuddapah, Raquel López‐Díez, Henry H. Ruiz, Jiyuan Hu, Laura Frye, Huilin Li, Paul F. Gugger, Ann Marie Schmidt
Software Mentions: 3
Published: over 3 years ago

10.3390/nu12041116

Urinary Metabolic Profiling via LC-MS/MS Reveals Impact of Bovine Lactoferrin on Bone Formation in Growing SD Rats
Cited by: 7
Author(s): Yan Xu, Tianyu Zhao, Hang Ren, Yindan Xie, Jie An, Jiaqi Shang, Dina Tabys, Ning Liu
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-019-2848-8

ROIMCR: a powerful analysis strategy for LC-MS metabolomic datasets
Cited by: 55
Author(s): Eva Gorrochategui, Joaquim Jaumot, Romà Tauler
Software Mentions: 3
Published: over 5 years ago

10.3389/fbioe.2015.00129

Joint Analysis of Dependent Features within Compound Spectra Can Improve Detection of Differential Features
Cited by: 2
Author(s): Diana Trutschel, Stephan Schmidt, Ivo Große, Steffen Neumann
Software Mentions: 3
Published: about 9 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

10.7554/eLife.57068

MondoA regulates gene expression in cholesterol biosynthesis-associated pathways required for zebrafish epiboly
Cited by: 7
Author(s): Meltem Weger, Benjamin D. Weger, Andrea Schink, Masanari Takamiya, Johannes Stegmaier, Cédric Gobet, Alice Parisi, Andrei Yu Kobitski, Jonas Mertes, Nils Krone, Uwe Strähle, G. Ulrich Nienhaus, Ralf Mikut, Frédéric Gachon, Philipp Gut, Thomas Dickmeis
Software Mentions: 3
Published: about 4 years ago

10.1242/dev.152413

Unraveling transcriptome dynamics in human spermatogenesis
Cited by: 107
Author(s): Sabrina Z. Jan, Tinke L. Vormer, Aldo Jongejan, Michael D. Röling, Sherman J. Silber, Dirk G. de Rooij, Geert Hamer, Sjoerd Repping, Ans M.M. van Pelt
Software Mentions: 3
Published: almost 8 years ago

10.3390/molecules26092769

Honey Phenolic Compound Profiling and Authenticity Assessment Using HRMS Targeted and Untargeted Metabolomics
Cited by: 28
Author(s): Georgios Koulis, Aristeidis S. Tsagkaris, Reza Aalizadeh, Marilena E. Dasenaki, Evridiki Panagopoulou, Spyros Drivelos, Michał Halagarda, Constantınos A. Georgiou, Charalampos Proestos, Nikolaos S. Thomaidis
Software Mentions: 3
Published: over 3 years ago

10.1128/mSystems.00610-21

Targeting Bacterial Gyrase with Cystobactamid, Fluoroquinolone, and Aminocoumarin Antibiotics Induces Distinct Molecular Signatures in Pseudomonas aeruginosa
Cited by: 2
Author(s): Raimo Franke, Heike Overwin, Susanne Häußler, Mark Brönstrup
Software Mentions: 3
Published: about 3 years ago

10.1186/s13046-020-01813-6

Let-7a regulates EV secretion and mitochondrial oxidative phosphorylation by targeting SNAP23 in colorectal cancer
Cited by: 15
Author(s): You Dong Liu, Xiao Peng Zhuang, Dong Cai, Can Cao, Qi Gu, Xue Ni Liu, Bin Zheng, Bing Guan, Liang Yu, Ji Kun Li, Hui Ding, Yan Dong
Software Mentions: 3
Published: almost 4 years ago

10.1128/AEM.01851-20

Ecophysiological Study of Paraburkholderia sp. Strain 1N under Soil Solution Conditions: Dynamic Substrate Preferences and Characterization of Carbon Use Efficiency
Cited by: 6
Author(s): K. Taylor Cyle, Annaleise R. Klein, Ludmilla Aristilde, Carmen Enid Martı́nez
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0238694

A detection method for android application security based on TF-IDF and machine learning
Cited by: 21
Author(s): Hongli Yuan, Yongchuan Tang, Wenping Sun, Li Liu
Software Mentions: 3
Published: about 4 years ago

10.1007/s00248-015-0568-9

Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences
Cited by: 37
Author(s): Sandra Pucciarelli, Raghul Rajan Devaraj, Alessio Mancini, Patrizia Ballarini, Michele Castelli, Martina Schrallhammer, Giulio Petroni, Cristina Miceli
Software Mentions: 3
Published: over 9 years ago

10.1186/1475-2859-11-72

Isolation identification and biochemical characterization of a novel halo-tolerant lipase from the metagenome of the marine sponge Haliclona simulans
Cited by: 73
Author(s): Joseph Selvin, Jonathan Kennedy, David Lejon, George Seghal Kiran, Alan D. W. Dobson
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0059831

Construction of Customized Sub-Databases from NCBI-nr Database for Rapid Annotation of Huge Metagenomic Datasets Using a Combined BLAST and MEGAN Approach
Cited by: 48
Author(s): Ke Yu, Tong Zhang
Software Mentions: 3
Published: over 11 years ago

10.1007/s00401-020-02252-5

Mitochondrial bioenergetic deficits in C9orf72 amyotrophic lateral sclerosis motor neurons cause dysfunctional axonal homeostasis
Cited by: 66
Author(s): Arpan R. Mehta, Jenna M Gregory, Owen Dando, Roderick N. Carter, Karen Burr, Jyoti Nanda, David Story, Karina McDade, Colin Smith, Nicholas M. Morton, Don J. Mahad, Giles E. Hardingham, Siddharthan Chandran, Bhuvaneish T. Selvaraj
Software Mentions: 3
Published: almost 4 years ago

10.4056/sigs.1694706

TheViral MetaGenome Annotation Pipeline (VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data
Cited by: 45
Author(s): Hernán Lorenzi, Jeff Hoover, Jason M. Inman, Todd Safford, Sean D. Murphy, Leonid Kagan, Shannon J. Williamson
Software Mentions: 3
Published: over 13 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

10.1007/s11306-017-1202-2

Untargeted metabolomics reveals a mild impact of remote ischemic conditioning on the plasma metabolome and α-hydroxybutyrate as a possible cardioprotective factor and biomarker of tissue ischemia
Cited by: 11
Author(s): Mia Roest Laursen, Jakob Hansen, Casper Carlsen Elkjær, Ninna Stavnager, Camilla Bak Nielsen, Kasper Pryds, Jacob Johnsen, Jesper Nielsen, Hans Erik Bøtker, Mogens Johannsen
Software Mentions: 2
Published: over 7 years ago

10.1007/s11306-013-0544-7

Metabolomics identifies a biological response to chronic low-dose natural uranium contamination in urine samples
Cited by: 27
Author(s): Stéphane Grison, Gaëlle Favé, Matthieu Maillot, Line Manens, Olivia Delissen, E. Blanchardon, Nathalie Banzet, Catherine Defoort, Raoul Bott, Isabelle Dublineau, Jocelyne Aigueperse, P. Gourmelon, Jean-Charles Martin, Maâmar Souidi
Software Mentions: 2
Published: over 11 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

10.1007/s11306-016-1147-x

Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy
Cited by: 64
Author(s): Ralf Weber, Thomas N. Lawson, Reza M. Salek, Timothy M. D. Ebbels, Robert C. Glen, Royston Goodacre, Julian L. Griffin, Kenneth Haug, Albert Koulman, Pablo Moreno-Ger, Markus Ralser, Christoph Steinbeck, Warwick B. Dunn, Mark R. Viant
Software Mentions: 2
Published: almost 8 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

10.1007/s11306-020-01745-4

Comprehensive metabolomic profiling of osteosarcoma based on UHPLC-HRMS
Cited by: 9
Author(s): Dongming Lv, Yutong Zou, Ziliang Zeng, Hao Yao, S. Ding, Yiying Bian, Li-Li Wen, Xianbiao Xie
Software Mentions: 2
Published: about 4 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/s41598-019-49319-2

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

10.3390/metabo10030105

Intracellular Metabolites in Marine Microorganisms during an Experiment Evaluating Microbial Mortality
Cited by: 5
Author(s): Krista Longnecker, Elizabeth B. Kujawinski
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-020-06830-5

A comprehensive survey of integron-associated genes present in metagenomes
Cited by: 18
Author(s): Mariana Buongermino Pereira, Tobias Österlund, Karl‐Erik Eriksson, Thomas Backhaus, Marina Axelson-Fisk, Erik Kristiansson
Software Mentions: 2
Published: over 4 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

10.3390/metabo3030517

The Critical Assessment of Small Molecule Identification (CASMI): Challenges and Solutions
Cited by: 32
Author(s): Emma L. Schymanski, Steffen Neumann
Software Mentions: 2
Published: over 11 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/s41598-019-50413-8

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

10.1038/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

10.3390/metabo11020063

Metabotypes of Pseudomonas aeruginosa Correlate with Antibiotic Resistance, Virulence and Clinical Outcome in Cystic Fibrosis Chronic Infections
Cited by: 17
Author(s): Oriane Moyne, Florence Castelli, Dominique Bicout, Julien Bernard, B. Camara, Benoît Cournoyer, Eric Faudry, Samuel Terrier, Dalil Hannani, Sarah Huot-Marchand, Claire Léger, Max Maurin, Tuan-Dung Ngo, Caroline Plazy, Robert A. Quinn, Ina Attrée, François Fenaille, Bertrand Toussaint, Audrey Le Gouëllec
Software Mentions: 2
Published: almost 4 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

10.1007/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

10.1371/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

10.1186/1471-2105-11-538

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
Cited by: 821
Author(s): F. A. Matsen, Robin Kodner, E. Virginia Armbrust
Software Mentions: 2
Published: about 14 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

10.1007/s10886-018-0979-4

Gastropods and Insects Prefer Different Solanum dulcamara Chemotypes
Cited by: 8
Author(s): Onno W Calf, Heidrun Huber, Janny L. Peters, Alexander Weinhold, Yvonne Poeschl, Nicole M. van Dam
Software Mentions: 2
Published: over 6 years ago

10.1111/acel.13021

Age attenuates the transcriptional changes that occur with sleep in the medial prefrontal cortex
Cited by: 17
Author(s): Xiaofeng Guo, Brendan T. Keenan, Dimitra Sarantopoulou, Diane C. Lim, Jie Liu, Gregory R. Grant, Allan I. Pack
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0174609

MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool
Cited by: 7
Author(s): Bin Zou, JieFu Li, Quan Zhou, Zhe‐Xue Quan
Software Mentions: 2
Published: over 7 years ago

10.1002/hep.29877

Impact of Interferon Lambda 4 Genotype on Interferon‐Stimulated Gene Expression During Direct‐Acting Antiviral Therapy for Hepatitis C
Cited by: 17
Author(s): Narayan Ramamurthy, Emanuele Marchi, Azim Ansari, Vincent Pedergnana, Angela R. McLean, Emma Hudson, Rory Bowden, Chris C. A. Spencer, Eleanor Barnes, Paul Klenerman
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0040695

Integrated Metabolo-Proteomic Approach to Decipher the Mechanisms by Which Wheat QTL (Fhb1) Contributes to Resistance against Fusarium graminearum
Cited by: 212
Author(s): Raghavendra Gunnaiah, Ajjamada C. Kushalappa, Raj Duggavathi, S. L. Fox, Daryl J. Somers
Software Mentions: 2
Published: over 12 years ago

10.3390/metabo10060257

Tumor Tissue-Specific Biomarkers of Colorectal Cancer by Anatomic Location and Stage
Cited by: 14
Author(s): Yuping Cai, Nicholas A. Rattray, Qian Zhang, Varvara Mironova, Álvaro José Santos-Neto, Engjel Muca, Ana K Rosen Vollmar, Kuo-Shun Hsu, Zahra Rattray, Justin R. Cross, Yawei Zhang, Philip B. Paty, Sajid Khan, Caroline H. Johnson
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0071952

Microbial Life in a Fjord: Metagenomic Analysis of a Microbial Mat in Chilean Patagonia
Cited by: 14
Author(s): Juan A. Ugalde, María José Gallardo, Camila Belmar, Práxedes Muñoz, Nathaly Ruiz‐Tagle, Sandra Ferrada-Fuentes, Claudia Espinoza, Eric E. Allen, Víctor A. Gallardo
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0002945

Comparative Metagenomics Reveals Host Specific Metavirulomes and Horizontal Gene Transfer Elements in the Chicken Cecum Microbiome
Cited by: 242
Author(s): Ani Qu, Jennifer M. Brulc, Melissa K. Wilson, Bibiana Law, James R. Theoret, Lynn A. Joens, Michael E. Konkel, Florent E. Angly, Elizabeth A. Dinsdale, Robert A. Edwards, Karen E. Nelson, Bryan A. White
Software Mentions: 2
Published: over 16 years ago

10.1186/s12864-021-07410-x

Multi-omics analysis reveals the glycolipid metabolism response mechanism in the liver of genetically improved farmed Tilapia (GIFT, Oreochromis niloticus) under hypoxia stress
Cited by: 24
Author(s): Jun-Lei Ma, Jun Qiang, Yifan Tao, Jing‐Wen Bao, Haojun Zhu, Lian-Ge Li, Pao Xu
Software Mentions: 2
Published: almost 4 years ago

10.1093/jas/skab101

The effects of birth weight and estimated breeding value for protein deposition on nitrogen efficiency in growing pigs
Cited by: 2
Author(s): C.M.C. van der Peet–Schwering, L.M.G. Verschuren, R. Bergsma, Mette Skou Hedemann, G.P. Binnendijk, A.J.M. Jansman
Software Mentions: 2
Published: over 3 years ago

10.3390/metabo7020027

Furanoterpene Diversity and Variability in the Marine Sponge Spongia officinalis, from Untargeted LC–MS/MS Metabolomic Profiling to Furanolactam Derivatives
Cited by: 9
Author(s): Cléa Bauvais, Natacha Bonneau, Alain Blond, Thierry Pérez, Marie‐Lise Bourguet‐Kondracki, Séverine Zirah
Software Mentions: 2
Published: over 7 years ago

10.1186/s12862-015-0378-1

Insights into the evolution of enzyme substrate promiscuity after the discovery of (βα)8 isomerase evolutionary intermediates from a diverse metagenome
Cited by: 16
Author(s): Lianet Noda‐Garcia, Ana Lilia Juárez-Vázquez, María C. Ávila-Arcos, E.A. Verduzco-Castro, Gabriela M. Montero-Morán, Paul Gaytán, Mauricio Carrillo‐Tripp, Francisco Barona‐Gómez
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-015-0834-7

Metagenome-assembled genomes uncover a global brackish microbiome
Cited by: 165
Author(s): Luisa W. Hugerth, Jenny Larsson, Johannes Alneberg, Markus V. Lindh, Catherine Legrand, Jarone Pinhassi, Anders F. Andersson
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12885-018-4894-4

Untargeted lipidomic features associated with colorectal cancer in a prospective cohort
Cited by: 20
Author(s): Kelsi Perttula, Courtney Schiffman, William M. B. Edmands, Lauren Petrick, Hasmik Grigoryan, Xiaoming Cai, Marc J. Gunter, Alessio Naccarati, Silvia Polidoro, Sandrine Dudoit, Paolo Víneis, Stephen M. Rappaport
Software Mentions: 2
Published: about 6 years ago

10.3390/metabo10110456

Obesity-Related Metabolome and Gut Microbiota Profiles of Juvenile Göttingen Minipigs—Long-Term Intake of Fructose and Resistant Starch
Cited by: 14
Author(s): Mihai Victor Curtasu, Valeria Tafintseva, Zachary A. Bendiks, Maria L. Marco, Achim Köhler, Yetong Xu, Natalja P. Nørskov, Helle Nygaard Lærke, Knud Erik Bach Knudsen, Mette Skou Hedemann
Software Mentions: 2
Published: about 4 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

10.1371/journal.pone.0101605

The Metagenomic Telescope
Cited by: 7
Author(s): Balázs Szalkai, Ildikó Scheer, Krisztina Nagy, Beáta G. Vértessy, Vince Grolmusz
Software Mentions: 2
Published: over 10 years ago

10.1186/gb-2013-14-11-r123

Metabolic reprogramming by viruses in the sunlit and dark ocean
Cited by: 188
Author(s): Bonnie Hurwitz, Steven J. Hallam, Matthew B. Sullivan
Software Mentions: 2
Published: almost 12 years ago

10.3389/fnsys.2021.655695

Effect of Anesthesia/Surgery on Gut Microbiota and Fecal Metabolites and Their Relationship With Cognitive Dysfunction
Cited by: 20
Author(s): Xinrong Lian, Qianmei Zhu, Sun Li, Yaozhong Cheng
Software Mentions: 2
Published: over 3 years ago

10.1152/ajpgi.00046.2020

Ridinilazole, a narrow spectrum antibiotic for treatment of Clostridioides difficile infection, enhances preservation of microbiota-dependent bile acids
Cited by: 24
Author(s): Xi Qian, Karin Yanagi, Anne Kane, Nicholas Alden, Ming Lei, David R. Snydman, Richard Vickers, Kyongbum Lee, Cheleste M. Thorpe
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2019.01790

Associated Bacteria Affect Sexual Reproduction by Altering Gene Expression and Metabolic Processes in a Biofilm Inhabiting Diatom
Cited by: 18
Author(s): Emilio Cirri, Sam De Decker, Gust Bilcke, Markus Werner, Cristina Maria Osuna-Cruz, Lieven De Veylder, Klaas Vandepoele, Oliver Werz, Wim Vyverman, Georg Pohnert
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2020.01841

Comparative Genomic and Metabolomic Analyses of Two Pseudomonas aeruginosa Strains With Different Antifungal Activities
Cited by: 13
Author(s): Shumin Wang, Zhun Huang, Qianbing Wan, Shuo Feng, Xiaochen Xie, Ruiling Zhang, Zhong Zhang
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2016.01790

Distribution and Classification of Serine β-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases
Cited by: 10
Author(s): Adriana M. Fróes, Fábio Faria da Mota, Rafael R. C. Cuadrat, Alberto M. R. Dávila
Software Mentions: 2
Published: about 8 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

10.1186/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

10.3389/fmicb.2019.00356

Saponin-Induced Shifts in the Rumen Microbiome and Metabolome of Young Cattle
Cited by: 68
Author(s): Bing Wang, Man Peng, Qi Yu Diao, Tiebin Yan
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2015.00364

Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: molecular evidence for metabolic interchange
Cited by: 104
Author(s): Cara L. Fiore, Micheline S. Labrie, Jessica K. Jarett, Michael P. Lesser
Software Mentions: 2
Published: over 9 years ago

10.3390/metabo10030109

Metabolic Phenotypes of Hypoxic-Ischemic Encephalopathy with Normal vs. Pathologic Magnetic Resonance Imaging Outcomes
Cited by: 15
Author(s): José David Piñeiro-Ramos, Antonio Núñez-Ramiro, Roberto Llorens-Salvador, Anna Parra-Llorca, Ángel Sánchez-Illana, Guillermo Quintás, Nuria Boronat-González, Juan Martínez-Rodilla, Julia Kuligowski, Máximo Vento
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0053253

Class Prediction and Feature Selection with Linear Optimization for Metagenomic Count Data
Cited by: 5
Author(s): Zhenqiu Liu, Dechang Chen, Li Sheng, Amy Liu
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pntd.0006452

Metabolite profiling for biomarkers in Schistosoma haematobium infection and associated bladder pathologies
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Author(s): Adewale Adebayo, Swapnil Mundhe, Henrietta Oluwatoyin Awobode, Olugbenga Samson Onile, Atinuke M Agunloye, Raphael D. Isokpehi, Yogesh S. Shouche, Santhakumari Bayatigeri, Chiaka I. Anumudu
Software Mentions: 2
Published: over 6 years ago

10.3390/metabo10090378

Comparison of Three Untargeted Data Processing Workflows for Evaluating LC-HRMS Metabolomics Data
Cited by: 18
Author(s): Selina Hemmer, Sascha K. Manier, Svenja Fischmann, Folker Westphal, Lea Wagmann, Markus R. Meyer
Software Mentions: 2
Published: about 4 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/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

10.3389/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

10.1371/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.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

10.1371/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.pbio.1001088

The Genomic Standards Consortium
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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

10.3389/fmicb.2020.526266

Enzymatic Browning in Wheat Kernels Produces Symptom of Black Point Caused by Bipolaris sorokiniana
Cited by: 5
Author(s): Qiaoyun Li, Kaige Xu, Siyu Wang, Mengyu Li, Yumei Jiang, Xiaolong Liang, Jishan Niu, Chenyang Wang
Software Mentions: 2
Published: almost 4 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

10.1371/journal.pbio.0050077

The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
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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

10.7717/peerj.9786

Chemotype classification and biomarker screening of male Eucommia ulmoides Oliv. flower core collections using UPLC-QTOF/MS-based non-targeted metabolomics
Cited by: 8
Author(s): Panfeng Liu, Lu Wang, Qingxin Du, Hongyan Du
Software Mentions: 2
Published: over 4 years ago

10.3389/fcimb.2019.00410

Serum Lipidomics Analysis of Classical Swine Fever Virus Infection in Piglets and Emerging Role of Free Fatty Acids in Virus Replication in vitro
Cited by: 19
Author(s): Shuaipeng Ma, Qian Mao, Wenxian Chen, Mengpo Zhao, Keke Wu, Dehai Song, Xin Li, Erpeng Zhu, Songqing Fan, Lin Yi, Hongxing Ding, Mingqiu Zhao, Jinding Chen
Software Mentions: 2
Published: almost 5 years ago

10.3389/fendo.2020.00215

Assessing Urinary Metabolomics in Giant Pandas Using Chromatography/Mass Spectrometry: Pregnancy-Related Changes in the Metabolome
Cited by: 11
Author(s): Maosheng Cao, Li ChunJin, Yuliang Liu, Kailai Cai, Lu Chen, Chenfeng Yuan, Zijiao Zhao, Boqi Zhang, Rong Hou, Xu Zhou
Software Mentions: 2
Published: over 4 years ago

10.3389/fimmu.2021.684430

CD22 Blockage Restores Age-Related Impairments of Microglia Surveillance Capacity
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Author(s): Vanessa Aires, Claire Coulon-Bainier, Anto Pavlovic, Martin Ebeling, Roland Schmucki, Christophe Schweitzer, Erich Kueng, Simon Gutbier, Eva Harde
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2021.628685

Integrated Microbiome and Metabolome Analysis Reveals a Positive Change in the Intestinal Environment of Myostatin Edited Large White Pigs
Cited by: 13
Author(s): Yangli Pei, Chujie Chen, Yulian Mu, Yalan Yang, Feng Zheng, Bugao Li, Hua Li, Kui Li
Software Mentions: 2
Published: almost 4 years ago

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