cran: DA | Projects | Ecosyste.ms: Papers

10.3390/ijms22063251

Untargeted In Silico Compound Classification—A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes
Cited by: 11
Author(s): Kristian Peters, Gerd Ulrich Balcke, Niklas Kleinenkuhnen, Hendrik Treutler, Steffen Neumann
Software Mentions: 31
Published: about 3 years ago

10.1371/journal.pcbi.1005752

mixOmics: An R package for ‘omics feature selection and multiple data integration
Cited by: 1,902
Author(s): Florian Rohart, Benoît Gautier, Amrit Singh, Kim‐Anh Lê Cao
Software Mentions: 29
Published: over 6 years ago

10.3389/fchem.2021.734132

The “DOLPHINS” Project: A Low-Cost Real-Time Multivariate Process Control From Large Sensor Arrays Providing Sparse Binary Data
Cited by: 1
Author(s): Eugenio Alladio, Marcello Baricco, Vincenzo Leogrande, Renato Pagliari, Fabio Pozzi, Paolo Foglio, Marco Vincenti
Software Mentions: 15
Published: over 2 years ago

10.1186/s13072-020-00342-y

ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation
Cited by: 39
Author(s): Jake J. Reske, Mike R. Wilson, Ronald L. Chandler
Software Mentions: 14
Published: about 4 years ago

10.1038/s42003-019-0415-5

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering
Cited by: 137
Author(s): Lukas M. Weber, Małgorzata Nowicka, Charlotte Soneson, Mark D. Robinson
Software Mentions: 12
Published: almost 5 years ago

10.1107/S1600577518016570

Automated data collection and real-time data analysis suite for serial synchrotron crystallography
Cited by: 34
Author(s): Shibom Basu, Jakub Wojciech Kaminski, Ezequiel Panepucci, Chia‐Ying Huang, Rangana Warshamanage, Meitian Wang, Justyna Aleksandra Wojdyla
Software Mentions: 11
Published: over 5 years ago

10.1371/journal.pone.0223909

Effects of MCHM on yeast metabolism
Cited by: 6
Author(s): Amaury Pupo, Kang‐Mo Ku, Jennifer E. G. Gallagher
Software Mentions: 10
Published: over 4 years ago

10.3390/s21020436

A Methodology for Discriminant Time Series Analysis Applied to Microclimate Monitoring of Fresco Paintings
Cited by: 8
Author(s): Sandra Ramírez, Manuel Zarzo, Ángel Perles, Fernando-Juan García-Diego
Software Mentions: 10
Published: over 3 years ago

10.1093/gigascience/giz004

The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches
Cited by: 103
Author(s): Darshan B. Dhakan, Abhijit Maji, Ashok Sharma, Rituja Saxena, Joby Pulikkan, Tony Grace, Andrés Gómez, Joy Scaria, Katherine R. Amato, Vineet K. Sharma
Software Mentions: 8
Published: over 5 years ago

10.1101/2020.11.25.20235150

T cell and antibody functional correlates of severe COVID-19
Cited by: 8
Author(s): Krystle K. Q. Yu, Stephanie Fischinger, Malisa T. Smith, Caroline Atyeo, Deniz Cizmeci, Caitlin R Wolf, Erik D. Layton, Jennifer Logue, Melissa S. Aguilar, Kiel Shuey, Carolin Loos, Jingyou Yu, Nicholas Franko, Robert Y. Choi, Anna Wald, Dan H. Barouch, David M. Koelle, Douglas A. Lauffenburger, Helen Y. Chu, Galit Alter, Chetan Seshadri
Software Mentions: 8
Published: over 3 years ago

10.3389/fpls.2019.01581

Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch]
Cited by: 24
Author(s): Tomás Carrasco-Valenzuela, Claudia Muñoz-Espinoza, Aníbal Riveros, Romina Pedreschi, Pere Arús, Reinaldo Campos-Vargas, Claudio Meneses
Software Mentions: 7
Published: over 4 years ago

10.3390/microorganisms9091939

Human Milk Oligosaccharide-Stimulated Bifidobacterium Species Contribute to Prevent Later Respiratory Tract Infections
Cited by: 18
Author(s): Shaillay Kumar Dogra, François-Pierre Martin, Dominique Donnicola, Monique Julita, Bernard Berger, Norbert Sprenger
Software Mentions: 7
Published: over 2 years ago

10.1007/s12559-020-09773-x

Deep Learning in Mining Biological Data
Cited by: 197
Author(s): Mufti Mahmud, M. Shamim Kaiser, TM McGinnity, Amir Hussain
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-021-92927-0

A new CAM6 + DART reanalysis with surface forcing from CAM6 to other CESM models
Cited by: 5
Author(s): K. Raeder, T. J. Hoar, Mohamad El Gharamti, Benjamin K. Johnson, Nancy Collins, Jeffrey L. Anderson, Jeff Steward, Mick Coady
Software Mentions: 7
Published: over 2 years ago

10.1002/1873-3468.13278

The gut microbiome participates in transgenerational inheritance of low‐temperature responses in Drosophila melanogaster
Cited by: 23
Author(s): Aman Zare, Anna-Mia Johansson, Edvin Karlsson, Nicolas Delhomme, Per Stenberg
Software Mentions: 7
Published: over 5 years ago

10.3389/fonc.2020.603717

Enhanced Angiogenesis in Salivary Duct Carcinoma Ex-Pleomorphic Adenoma
Cited by: 6
Author(s): Takayoshi Suzuki, Satoshi Kano, Masanobu Suzuki, Shinichiro Yasukawa, Takatsugu Mizumachi, Nobuko Tsushima, Kanako C. Hatanaka, Yutaka Hatanaka, Yoshihiro Matsuno, Akihiro Homma
Software Mentions: 7
Published: about 3 years ago

10.1038/sdata.2018.227

Global distribution data for cattle, buffaloes, horses, sheep, goats, pigs, chickens and ducks in 2010
Cited by: 298
Author(s): Marius Gilbert, G. Nicolas, Giuseppina Cinardi, Thomas Van Boeckel, Sophie Vanwambeke, William Wint, Timothy P. Robinson
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-017-08235-z

Discrimination of plant root zone water status in greenhouse production based on phenotyping and machine learning techniques
Cited by: 21
Author(s): Doudou Guo, J.A. de Juan, Liu Chang, Zhang Jing-jin, Dan Huang
Software Mentions: 6
Published: over 6 years ago

10.7150/thno.47627

Multi-omics study of silicosis reveals the potential therapeutic targets PGD2 and TXA2
Cited by: 25
Author(s): Junling Pang, Xianmei Qi, Yunbo Luo, Xiaona Li, Ting Shu, Baicun Li, Meiyue Song, Ying Liu, Wei Dong, Jingyu Chen, Jing Wang, Chen Wang
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-87886-5

Metabolomics and transcriptomics to decipher molecular mechanisms underlying ectomycorrhizal root colonization of an oak tree
Cited by: 14
Author(s): Mónica Sebastiana, Albert Gargallo‐Garriga, Jordi Sardans, Míriam Pérez‐Trujillo, Filipa Monteiro, Andreia Figueiredo, Marisa Maia, Rui Nascimento, Marta Sousa Silva, António E. N. Ferreira, Carlos Cordeiro, A. Marques, Lisete Sousa, Rui Malhó, Josep Peñuelas
Software Mentions: 6
Published: about 3 years ago

10.3389/fncom.2014.00139

Diffusion approximation-based simulation of stochastic ion channels: which method to use?
Cited by: 8
Author(s): Danilo Pezo, Daniel Soudry, Patricio Orio
Software Mentions: 6
Published: over 9 years ago

10.3390/metabo4020433

Influence of Missing Values Substitutes on Multivariate Analysis of Metabolomics Data
Cited by: 139
Author(s): Piotr S. Gromski, Yun Xu, Helen L. Kotze, Elon Correa, David I. Ellis, Emily G. Armitage, Michael L. Turner, Royston Goodacre
Software Mentions: 6
Published: almost 10 years ago

10.3390/ijms22136641

Transcriptomic and Metabolic Profiling of High-Temperature Treated Storage Roots Reveals the Mechanism of Saccharification in Sweetpotato (Ipomoea batatas (L.) Lam.)
Cited by: 5
Author(s): Chen Li, Meng Kou, Mohamed Hamed Arisha, Wei Tang, Meng Ma, Hui Yan, Xin Wang, Xiaoxiao Wang, Yungang Zhang, Yaju Liu, Runfei Gao, Qiang Li
Software Mentions: 6
Published: almost 3 years ago

10.1186/s40168-020-00806-z

RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs
Cited by: 178
Author(s): Leyuan Li, Zhibin Ning, Xu Zhang, Janice Mayne, Kai Cheng, Alain Stintzi, Daniel Figeys
Software Mentions: 6
Published: about 4 years ago

10.7717/peerj.2740

Harvest year effects on Apulian EVOOs evaluated by1H NMR based metabolomics
Cited by: 18
Author(s): Chiara Roberta Girelli, Laura Del Coco, Paride Papadia, Sandra Angelica De Pascali, Francesco Paolo Fanizzi
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0181033

Transcriptomic and metabolomic profiles of Chinese citrus fly, Bactrocera minax (Diptera: Tephritidae), along with pupal development provide insight into diapause program
Cited by: 14
Author(s): Jia Wang, Hong-Tao Fan, Ke-Cai Xiong, Ying‐Hong Liu
Software Mentions: 6
Published: almost 7 years ago

10.3390/plants10061033

Metabolic Alterations in Pisum sativum Roots during Plant Growth and Arbuscular Mycorrhiza Development
Cited by: 13
Author(s): O. Y. Shtark, Roman Puzanskiy, G. S. Avdeeva, Vladislav V. Yemelyanov, А. Л. Шаварда, Daria A. Romanyuk, Marina S. Kliukova, А. А. Кирпичникова, И. А. Тихонович, Vladimir A. Zhukov, М. Ф. Шишова
Software Mentions: 6
Published: almost 3 years ago

10.1186/s40168-020-00854-5

Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria
Cited by: 52
Author(s): Xingxing Jian, Yinghong Zhu, Jian Ouyang, Yihui Wang, Qian Lei, Jiliang Xia, Yongjun Guan, Jingyu Zhang, Jiaojiao Guo, Yanjuan He, Jinuo Wang, Jian Li, Jingchao Lin, Mingming Su, Guancheng Li, Minghua Wu, Lugui Qiu, Juanjuan Xiang, Lu Xie, Jia Wang, Wen Zhou
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12877-019-1156-5

No effect of 25-hydroxyvitamin D supplementation on the skeletal muscle transcriptome in vitamin D deficient frail older adults
Cited by: 11
Author(s): Roland W. J. Hangelbroek, Anouk M.M. Vaes, Mark V. Boekschoten, Lex B. Verdijk, Guido Hooiveld, Luc J. C. van Loon, Lisette C. P. G. M. de Groot, Sander Kersten
Software Mentions: 6
Published: almost 5 years ago

10.1002/ece3.5690

Genetic divergence and phenotypic plasticity contribute to variation in cuticular hydrocarbons in the seaweed fly Coelopa frigida
Cited by: 9
Author(s): Emma L. Berdan, Swantje Enge, Göran M. Nylund, Maren Wellenreuther, Gerrit A. Martens, Henrik Pavia
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-020-62911-1

Analyzing the impact of Mycobacterium tuberculosis infection on primary human macrophages by combined exploratory and targeted metabolomics
Cited by: 25
Author(s): Frank Vrieling, Sarantos Kostidis, Herman P. Spaink, Mariëlle C. Haks, Oleg A. Mayboroda, Tom H. M. Ottenhoff, Simone A. Joosten
Software Mentions: 6
Published: about 4 years ago

10.1186/s40104-021-00584-0

Weaning-associated feed deprivation stress causes microbiota disruptions in a novel mucin-containing in vitro model of the piglet colon (MPigut-IVM)
Cited by: 6
Author(s): Raphaële Gresse, Frédérique Chaucheyras‐Durand, Sylvain Denis, Martín Beaumont, Tom Van de Wiele, Evelyne Forano, Stéphanie Blanquet-Diot
Software Mentions: 6
Published: almost 3 years ago

10.1172/jci.insight.146242

Comorbid illnesses are associated with altered adaptive immune responses to SARS-CoV-2
Cited by: 36
Author(s): Krystle K. Q. Yu, Stephanie Fischinger, Malisa T. Smith, Caroline Atyeo, Deniz Cizmeci, Caitlin R Wolf, Erik D. Layton, Jennifer K. Logue, Melissa S. Aguilar, Kiel Shuey, Carolin Loos, Jingyou Yu, Nicholas Franko, Robert Y. Choi, Anna Wald, Dan H. Barouch, David M. Koelle, Douglas A. Lauffenburger, Helen Y. Chu, Galit Alter, Chetan Seshadri
Software Mentions: 6
Published: about 3 years ago

10.3390/s21051734

Convolutional Neural Network for Drowsiness Detection Using EEG Signals
Cited by: 45
Author(s): Siwar Chaabene, Bassem Bouaziz, Amal Boudaya, Anita Hökelmann, Achraf Ammar, Lotfi Chaâri
Software Mentions: 6
Published: about 3 years ago

10.1016/j.gpb.2019.02.003

Denoising Autoencoder, A Deep Learning Algorithm, Aids the Identification of A Novel Molecular Signature of Lung Adenocarcinoma
Cited by: 12
Author(s): Jun Wang, Xueying Xie, Junchao Shi, Wenjun He, Qi Chen, Liang Chen, Wanjun Gu, Tong Zhou
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12263-021-00688-2

An 8-week freeze-dried blueberry supplement impacts immune-related pathways: a randomized, double-blind placebo-controlled trial
Cited by: 7
Author(s): Michèle Rousseau, Justine Horne, Frédéric Guénard, Juan de Toro‐Martín, Véronique Garneau, Valérie Guay, Michèle Kearney, Geneviève Pilon, Denis Roy, Patrick Couture, Charles Couillard, André Marette
Software Mentions: 5
Published: almost 3 years ago

10.1007/s00442-021-04977-w

Bank vole alarm pheromone chemistry and effects in the field
Cited by: 1
Author(s): Thorbjörn Sievert, Hannu Ylönen, James D. Blande, Amélie Saunier, Dave van der Hulst, Olga Ylönen, Marko Haapakoski
Software Mentions: 5
Published: almost 3 years ago

10.1186/s40168-021-01052-7

Iron status influences non-alcoholic fatty liver disease in obesity through the gut microbiome
Cited by: 54
Author(s): Jordi Mayneris‐Perxachs, Marina Cardellini, Lesley Hoyles, Jéssica Latorre, Francesca Davato, José María Moreno-Navarrete, María Arnoriaga-Rodríguez, Matteo Sérino, James Abbott, Richard H. Barton, Josep Puig, Xavier Fernández-Real, Wifredo Ricart, Christopher Tomlinson, Mark Woodbridge, Paolo Gentileschi, Sarah Butcher, Elaine Holmes, Jeremy K. Nicholson, Vicente Pérez‐Brocal, Andrés Moya, Donald Mc Clain, Rémy Burcelin, Marc Dumas, Massimo Federici, José‐Manuel Fernández‐Real
Software Mentions: 5
Published: about 3 years ago

10.1007/s11306-020-01686-y

A comparison of high-throughput plasma NMR protocols for comparative untargeted metabolomics
Cited by: 15
Author(s): Nikolaos G. Bliziotis, Udo F. H. Engelke, Ruud L. E. G. Aspers, Jasper Engel, Jaap Deinum, Henri J L M Timmers, Ron A. Wevers, Leo A. J. Kluijtmans
Software Mentions: 5
Published: about 4 years ago

10.1186/s40168-018-0417-4

Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota
Cited by: 56
Author(s): Jane A. Mullaney, J. Stephens, Mary Ellen Costello, Cai Fong, Brooke E. Geeling, Patrick G. Gavin, Casey M. Wright, Timothy D. Spector, Matthew A. Brown, Emma E. Hamilton‐Williams
Software Mentions: 5
Published: about 6 years ago

10.3389/fcimb.2021.646348

Dysbiosis and Implication of the Gut Microbiota in Diabetic Retinopathy
Cited by: 62
Author(s): Yinhua Huang, Zhijie Wang, Hongjie Ma, Shangli Ji, Zhongping Chen, Zekai Cui, Jiansu Chen, Shibo Tang
Software Mentions: 5
Published: about 3 years ago

10.1107/S1600577517014503

DA+ data acquisition and analysis software at the Swiss Light Source macromolecular crystallography beamlines
Cited by: 54
Author(s): Justyna Aleksandra Wojdyla, Jakub Wojciech Kaminski, Ezequiel Panepucci, Simon Ebner, Xiaoqiang Wang, José Gabadinho, Meitian Wang
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0160169

MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities
Cited by: 125
Author(s): Kim‐Anh Lê Cao, Mary-Ellen Costello, Vanessa Lakis, François Bartolo, Xin-Yi Chua, Rémi Brazeilles, Pascale Rondeau
Software Mentions: 5
Published: over 7 years ago

10.1002/jssc.202000011

Recent applications of chemometrics in one‐ and two‐dimensional chromatography
Cited by: 37
Author(s): Tijmen S. Bos, Wouter C. Knol, Stef R.A. Molenaar, Leon E. Niezen, Peter J. Schoenmakers, Govert W. Somsen, Bob W.J. Pirok
Software Mentions: 5
Published: about 4 years ago

10.1186/s12859-018-2149-7

Ensemble outlier detection and gene selection in triple-negative breast cancer data
Cited by: 25
Author(s): Marta B. Lopes, André Veríssimo, Eunice Carrasquinha, Sandra Casimiro, Niko Beerenwinkel, Susana Vinga
Software Mentions: 5
Published: about 6 years ago

10.1128/mSphere.00005-17

Divergent Relationships between Fecal Microbiota and Metabolome following Distinct Antibiotic-Induced Disruptions
Cited by: 28
Author(s): Jocelyn M. Choo, Tokuwa Kanno, Nur Masirah M. Zain, Lex E. X. Leong, Guy C. J. Abell, Julie Keeble, Kenneth D. Bruce, A. James Mason, Geraint B. Rogers
Software Mentions: 5
Published: about 7 years ago

10.3390/metabo9060113

Cerebral Vitamin B5 (D-Pantothenic Acid) Deficiency as a Potential Cause of Metabolic Perturbation and Neurodegeneration in Huntington’s Disease
Cited by: 46
Author(s): Stefano Patassini, Paul Begley, Jiaolong Xu, Stephanie J. Church, Nina Kureishy, Suzanne J. Reid, Henry J. Waldvogel, Richard L.M. Faull, Russell G. Snell, Richard D. Unwin, Garth J. S. Cooper
Software Mentions: 5
Published: almost 5 years ago

10.1186/s40246-020-00291-3

Aldh1l2 knockout mouse metabolomics links the loss of the mitochondrial folate enzyme to deregulation of a lipid metabolism observed in rare human disorder
Cited by: 9
Author(s): Natalia I. Krupenko, Jaspreet Sharma, Peter Pediaditakis, Kristi L. Helke, Madeline S. Hall, Xiuxia Du, Susan Sumner, Sergey A. Krupenko
Software Mentions: 5
Published: over 3 years ago

10.1093/braincomms/fcab084

Integrative biochemical, proteomics and metabolomics cerebrospinal fluid biomarkers predict clinical conversion to multiple sclerosis
Cited by: 13
Author(s): Fay Probert, Tianrong Yeo, Yifan Zhou, Megan Sealey, Siddharth Arora, Jacqueline Palace, Timothy D. W. Claridge, Rainer Hillenbrand, Johanna Oechtering, David Leppert, Jens Kühle, D C Anthony
Software Mentions: 5
Published: about 3 years ago

10.1186/s13058-016-0714-4

Intermittent energy restriction induces changes in breast gene expression and systemic metabolism
Cited by: 33
Author(s): Michelle Harvie, Andrew H. Sims, Mary Pegington, Katherine Spence, Adam Mitchell, Andrew A. Vaughan, J. William Allwood, Yun Xu, Nicholas J. W. Rattray, Royston Goodacre, D. Gareth Evans, Ellen Sullivan Mitchell, Debbie McMullen, Robert B. Clarke, Anthony Howell
Software Mentions: 5
Published: almost 8 years ago

10.3389/fonc.2020.00981

Metabolomic Markers of Colorectal Tumor With Different Clinicopathological Features
Cited by: 15
Author(s): Zhiping Long, Jianqiu Zhou, Kun Xie, Zhiyong Wu, Huihui Yin, Volontovich Daria, Jingshen Tian, Nannan Zhang, Liangliang Li, Yong Zhao, Wei Fan, Maoqing Wang, Yunfu Cui
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-019-51432-1

Increasing oxygen deficiency changes rare and moderately abundant bacterial communities in coastal soft sediments
Cited by: 9
Author(s): Hanna Sinkko, Iina Hepolehto, Christina Lyra, Johanna M. Rinta-Kanto, Anna Villnäs, Joanna Norkko, Alf Norkko, Sari Timonen
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2015.00024

Resuscitation of the rare biosphere contributes to pulses of ecosystem activity
Cited by: 150
Author(s): Zachary T. Aanderud, Stuart Jones, Noah Fierer, Jay T. Lennon
Software Mentions: 5
Published: over 9 years ago

10.3389/fphys.2017.00535

The Effects of Weaning Methods on Gut Microbiota Composition and Horse Physiology
Cited by: 52
Author(s): Núria Mach, Aline Foury, Sandra Kittelmann, Fabrice Reigner, Marco Moroldo, María Ballester, Diane Esquerré, Julie Rivière, Guillaume Sallé, Philippe Gérard, Marie‐Pierre Moisan, Léa Lansade
Software Mentions: 5
Published: almost 7 years ago

10.3389/fmicb.2018.03203

Bark and Grape Microbiome of Vitis vinifera: Influence of Geographic Patterns and Agronomic Management on Bacterial Diversity
Cited by: 61
Author(s): Nicola Vitulo, Wilson José Fernandes Lemos, Matteo Calgaro, Marco Confalone, Giovanna E. Felis, Giacomo Zapparoli, Tiziana Nardi
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-29971-w

Addition of dairy lipids and probiotic Lactobacillus fermentum in infant formula programs gut microbiota and entero-insular axis in adult minipigs
Cited by: 28
Author(s): Marion Lemaire, Samir Dou, Armelle Cahu, Michèle Formal, Laurence Le Normand, Véronique Rome, Isabelle Nogret, Stéphanie Ferret‐Bernard, Moez Rhimi, Isabelle Cuinet, Cécile Canlet, Marie Tremblay-Franco, Pascale Le Ruyet, Charlotte Baudry, Philippe Gérard, Isabelle Le Huërou‐Luron, Sophie Blat
Software Mentions: 4
Published: almost 6 years ago

10.3390/ani11041024

Effects of Dietary Protein Level on the Gut Microbiome and Nutrient Metabolism in Tilapia (Oreochromis niloticus)
Cited by: 20
Author(s): Changgeng Yang, Ming Jiang, Xin Lü, Wen Huang
Software Mentions: 4
Published: about 3 years ago

10.1111/gcb.13357

Biodiversity in marine invertebrate responses to acute warming revealed by a comparative multi‐omics approach
Cited by: 75
Author(s): Melody S. Clark, Ulf Sommer, Jaspreet K Sihra, Michael A. S. Thorne, Simon A. Morley, Michelle King, Mark R. Viant
Software Mentions: 4
Published: almost 8 years ago

10.3390/life11060578

Comparative Analysis of Flavonoid Metabolites in Foxtail Millet (Setaria italica) with Different Eating Quality
Cited by: 8
Author(s): Yakun Zhang, Jianhua Gao, Qianru Qie, Yulu Yang, Siyu Hou, Xingchun Wang, Xukai Li, Yuanhuai Han
Software Mentions: 4
Published: almost 3 years ago

10.3390/molecules24142562

Assessing Geographical Origin of Gentiana Rigescens Using Untargeted Chromatographic Fingerprint, Data Fusion and Chemometrics
Cited by: 13
Author(s): Tao Shen, Hong Yu, Yuanzhong Wang
Software Mentions: 4
Published: almost 5 years ago

10.3389/fpls.2021.626301

Seed Priming With Protein Hydrolysates Improves Arabidopsis Growth and Stress Tolerance to Abiotic Stresses
Cited by: 25
Author(s): Mirella Sorrentino, Nuria De Diego, Lydia Ugena, Lukáš Spíchal, Luigi Lucini, Begoña Miras-Moreno, Leilei Zhang, Youssef Rouphael, G. Colla, Klára Panzarová
Software Mentions: 4
Published: almost 3 years ago

10.1172/jci.insight.124819

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: almost 5 years ago

10.18632/aging.203046

Aging-related markers in rat urine revealed by dynamic metabolic profiling using machine learning
Cited by: 4
Author(s): Dan Shi, Qilong Tan, Jingqi Ruan, Zhen Tian, Xinyue Wang, Jinxiao Liu, Xin Liu, Zhipeng Liu, Yuntao Zhang, Chongde Sun, Yucun Niu
Software Mentions: 4
Published: almost 3 years ago

10.1002/ece3.7523

A deep dive into fat: Investigating blubber lipidomic fingerprint of killer whales and humpback whales in northern Norway
Cited by: 9
Author(s): Pierre Bories, Audun H. Rikardsen, P.E.G. Leonards, Aaron T. Fisk, Sabrina Tartu, Emma F. Vogel, Jenny Bytingsvik, Pierre Blévin
Software Mentions: 4
Published: about 3 years ago

10.1038/s42003-019-0521-4

Multi-omic analysis in transgenic mice implicates omega-6/omega-3 fatty acid imbalance as a risk factor for chronic disease
Cited by: 49
Author(s): Kanakaraju Kaliannan, Xiangyong Li, Bin Wang, Qian Pan, Chih-Yu Chen, Lei Hao, Shanfu Xie, Jing Kang
Software Mentions: 4
Published: almost 5 years ago

10.3390/cells10010185

Beneficial Effects of Akkermansia muciniphila Are Not Associated with Major Changes in the Circulating Endocannabinoidome but Linked to Higher Mono-Palmitoyl-Glycerol Levels as New PPARα Agonists
Cited by: 39
Author(s): Clara Depommier, Rosa Maria Vitale, Fabio Arturo Iannotti, Cristoforo Silvestri, Nicolas Flamand, Céline Druart, Amandine Everard, Rudy Pelicaen, Dominique Maiter, Jean‐Paul Thissen, Audrey Loumaye, Michel P. Hermans, Nathalie M. Delzenne, Willem M. de Vos, Vincenzo Di Marzo, Patrice D. Cani
Software Mentions: 4
Published: over 3 years ago

10.1155/2021/5579736

Glycine-Serine-Threonine Metabolic Axis Delays Intervertebral Disc Degeneration through Antioxidant Effects: An Imaging and Metabonomics Study
Cited by: 9
Author(s): Xiaolin Wu, Chang Liu, Shuai Yang, Nana Shen, Yan Wang, Yi Zhu, Zhaoyang Guo, Sihyung Yang, Dongming Xing, Houxi Li, Bohua Chen, Hongfei Xiang
Software Mentions: 4
Published: over 2 years ago

10.18632/oncotarget.26022

Metabolite quantification of faecal extracts from colorectal cancer patients and healthy controls
Cited by: 25
Author(s): Gwénaëlle Le Gall, Kiran Guttula, Lee Kellingray, Adrian Tett, Rogier ten Hoopen, E. Kate Kemsley, George M. Savva, Ashraf E.K. Ibrahim, Arjan Narbad
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0160001

Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae)
Cited by: 31
Author(s): Ljiljana Šašić, Jelena Ačanski, Ante Vujić, Gunilla Ståhls, Snežana Radenković, Dubravka Milić, Dragana Obreht Vidaković, Dan Mo
Software Mentions: 4
Published: over 7 years ago

10.1002/1878-0261.12369

Metabolomic profiling of human lung tumor tissues – nucleotide metabolism as a candidate for therapeutic interventions and biomarkers
Cited by: 37
Author(s): Paula Moreno, Carla Jiménez‐Jiménez, Martín Garrido‐Rodriguez, M. Calderón-Santiago, Susana Molina, Maribel Lara‐Chica, Feliciano Priego‐Capote, A. Salvatierra, Eduardo Muñóz, Marco A. Calzado
Software Mentions: 4
Published: over 5 years ago

10.1038/hortres.2017.17

A community resource for exploring and utilizing genetic diversity in the USDA pea single plant plus collection
Cited by: 34
Author(s): William L. Holdsworth, Élodie Gazave, Cheng Peng, James R. Myers, Michael A. Gore, Clarice J. Coyne, Rebecca J. McGee, Michael Mazourek
Software Mentions: 4
Published: about 7 years ago

10.1002/advs.201902862

Gut Microbial Signatures Can Discriminate Unipolar from Bipolar Depression
Cited by: 75
Author(s): Peng Zheng, Jian Yang, Yifan Li, Jing Wu, Weiwei Liang, Bangmin Yin, Xunmin Tan, Yu Huang, Tingjia Chai, Hanping Zhang, Jiajia Duan, Jingjing Zhou, Zuoli Sun, Chen Xu, Subhi Marwari, Jianbo Lai, Tingting Huang, Yanli Du, Peifen Zhang, Seth W. Perry, Ma‐Li Wong, Júlio Licinio, Shaohua Hu, Peng Xie, Gang Wang
Software Mentions: 4
Published: over 4 years ago

10.3390/nu12123858

Effects of Daily Raspberry Consumption on Immune-Metabolic Health in Subjects at Risk of Metabolic Syndrome: A Randomized Controlled Trial
Cited by: 18
Author(s): Maximilien Franck, Juan de Toro‐Martín, Véronique Garneau, Valérie Guay, Michèle Kearney, Geneviève Pilon, Denis Roy, Patrick Couture, Charles Couillard, André Marette, Marie‐Claude Vohl
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0124467

A Four-Compartment Metabolomics Analysis of the Liver, Muscle, Serum, and Urine Response to Polytrauma with Hemorrhagic Shock following Carbohydrate Prefeed
Cited by: 15
Author(s): Nancy E. Witowski, Elizabeth R. Lusczek, Charles Determan, Daniel R. Lexcen, Kristine E. Mulier, Beverly Gaul Ostrowski, Greg J. Beilman
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0223031

Lipidomics analysis of juveniles’ blue mussels (Mytilus edulis L. 1758), a key economic and ecological species
Cited by: 13
Author(s): Vincenzo Alessandro Laudicella, Christine Beveridge, Stefano Carboni, Sofia C. Franco, Mary K. Doherty, Nina Long, Elaine Mitchell, Michele S. Stanley, Phillip D. Whitfield, Adam D. Hughes
Software Mentions: 4
Published: about 4 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: almost 4 years ago

10.3390/ijms21124470

Differences between Well-Differentiated Neuroendocrine Tumors and Ductal Adenocarcinomas of the Pancreas Assessed by Multi-Omics Profiling
Cited by: 8
Author(s): Teresa Starzyńska, Jakub Karczmarski, Agnieszka Paziewska, Maria Kulecka, Katarzyna Kuśnierz, Natalia Żeber‐Lubecka, Filip Ambrożkiewicz, Michał Mikula, Beata Kos‐Kudła, Jerzy Ostrowski
Software Mentions: 4
Published: almost 4 years ago

10.3390/biology10070658

Targeted Lipidomic Analysis of Aqueous Humor Reveals Signaling Lipid-Mediated Pathways in Primary Open-Angle Glaucoma
Cited by: 7
Author(s): Nadezhda V. Azbukina, Dmitry V. Chistyakov, Sergei V. Goriainov, В. И. Котелин, Е. В. Федосеева, S. Yu. Petrov, Marina G. Sergeeva, Elena N. Iomdina, Evgeni Yu Zernii
Software Mentions: 4
Published: almost 3 years ago

10.1038/s41598-021-95455-z

Evaluation of two highly effective lipid-lowering therapies in subjects with acute myocardial infarction
Cited by: 6
Author(s): Aline Klassen, Andréa Tedesco Faccio, Carolina R. C. Picossi, Priscilla Bento Matos Cruz Derogis, Carlos Eduardo dos Santos Ferreira, Aline Soriano Lopes, Alessandra Sussulini, Elisa Castañeda Santa Cruz, Rafaela Tudela Bastos, Stefanie Caroline Fontoura, Antônio Martins Figueiredo Neto, Marina Franco Maggi Tavares, Maria Cristina Izar, Francisco Antônio Helfenstein Fonseca
Software Mentions: 4
Published: almost 3 years ago

10.3390/ph14070662

Insulin-Mimic Components in Acer truncatum Leaves: Bio-Guided Isolation, Annual Variance Profiling and Regulating Pathway Investigated by Omics
Cited by: 11
Author(s): Xiaoyue Zhang, Yihan Liu, Dazhi Liu, Jianing Xu, Qiang Zhang
Software Mentions: 4
Published: almost 3 years ago

10.18632/aging.101170

Metabolomic signature associated with reproduction-regulated aging in Caenorhabditis elegans
Cited by: 39
Author(s): Qin-Li Wan, Xiaohuo Shi, Jiangxin Liu, Aijun Ding, Yuan-Zhu Pu, Zhigang Li, Gui-Sheng Wu, Huai‐Rong Luo
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-65137-3

Morphological, genotypic and metabolomic signatures confirm interfamilial hybridization between the ubiquitous kelps Macrocystis (Arthrothamnaceae) and Lessonia (Lessoniaceae)
Cited by: 9
Author(s): Pedro Murúa, Ru Angelie Edrada-Ebel, Liliana Muñoz, Sylvia Soldatou, Nathalie Legrave, Dieter G. Müller, David J. Patiño, Pieter van West, Frithjof C. Küpper, R. Westermeier, Rainer Ebel, Akira F. Peters
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12915-019-0693-x

Cold-induced lipid dynamics and transcriptional programs in white adipose tissue
Cited by: 70
Author(s): Zhonglin Xu, Wenjing You, Yanbing Zhou, Wentao Chen, Yizhen Wang, Tizhong Shan
Software Mentions: 3
Published: over 4 years ago

10.3390/molecules24142582

Comprehensive Chemical Profiling and Multidirectional Biological Investigation of Two Wild Anthemis Species (Anthemis tinctoria var. Pallida and A. cretica subsp. tenuiloba): Focus on Neuroprotective Effects
Cited by: 22
Author(s): Giustino Orlando, Gökhan Zengin, Claudio Ferrante, Maurizio Ronci, Lucia Recinella, İsmail Şenkardeş, Reneta Gevrenova, Dimitrina Zheleva‐Dimitrova, Annalisa Chiavaroli, Sheila Leone, Simonetta Cristina Di Simone, Luigi Brunetti, Marie Carene Nancy Picot-Allain, Mohamad Fawzi Mahomoodally, Kouadio Ibrahime Sinan, Luigi Menghini
Software Mentions: 3
Published: almost 5 years ago

10.1002/hbm.24803

Accurate and robust segmentation of neuroanatomy in T1‐weighted MRI by combining spatial priors with deep convolutional neural networks
Cited by: 20
Author(s): Philip Novosad, Vladimir Fonov, D. Louis Collins, Alzheimer’s Disease Neuroimaging Initiative
Software Mentions: 3
Published: over 4 years ago

10.1093/gigascience/giy073

Arabidopsis phenotyping through geometric morphometrics
Cited by: 19
Author(s): Carlos Augusto Manacorda, Sebastián Asurmendi
Software Mentions: 3
Published: almost 6 years ago

10.1002/1878-0261.12642

Deciphering tissue‐based proteome signatures revealed novel subtyping and prognostic markers for thymic epithelial tumors
Cited by: 7
Author(s): Xin Ku, Qiangling Sun, Lei Zhu, Zhenyu Gu, Yuchen Han, Ning Xu, Chen Meng, Xiaohua Yang, Wei Yan, Wentao Fang
Software Mentions: 3
Published: over 4 years ago

10.1111/j.1365-294X.2010.04986.x

Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates
Cited by: 83
Author(s): Pauline Charruau, Carlos Fernandes, Pablo Orozco‐terWengel, Joris Peters, Luke Hunter, Hooshang Ziaie, Alireza Jourabchian, Houman Jowkar, George B. Schaller, Stéphane Ostrowski, Paul Vercammen, Thierry Grange, Christian Schlötterer, Antoinette Kotzé, Eva-María Geigl, Chris Walzer, Pamela A. Burger
Software Mentions: 3
Published: over 13 years ago

10.1002/jbm4.10478

Metabolic Alterations in Older Women With Low Bone Mineral Density Supplemented With Lactobacillus reuteri
Cited by: 14
Author(s): Peishun Li, Daniel Sundh, Boyang Ji, Dimitra Lappa, Lingqun Ye, Jens Nielsen, Mattias Lorentzon
Software Mentions: 3
Published: about 3 years ago

10.1186/1471-2105-8-90

Importance of data structure in comparing two dimension reduction methods for classification of microarray gene expression data
Cited by: 10
Author(s): Caroline Truntzer, Catherine Mercier, Jacques Estève, Christian Gautier, Pascal Roy
Software Mentions: 3
Published: about 17 years ago

10.3389/fpls.2019.00339

Flooding Responses on Grapevine: A Physiological, Transcriptional, and Metabolic Perspective
Cited by: 36
Author(s): Benedetto Ruperti, Alessandro Botton, Francesca Populin, Giulia Eccher, Matteo Brilli, Silvia Quaggiotti, Sara Trevisan, Nadia Cainelli, Paola Guarracino, Elisabetta Schievano, Franco Meggio
Software Mentions: 3
Published: about 5 years ago

10.1186/s40168-019-0738-y

Batch effect exerts a bigger influence on the rat urinary metabolome and gut microbiota than uraemia: a cautionary tale
Cited by: 16
Author(s): David Randall, Julius Kieswich, Jonathan R. Swann, Kieran McCafferty, Christoph Thiemermann, Michael A. Curtis, Lesley Hoyles, M. Yaqoob
Software Mentions: 3
Published: over 4 years ago

10.3389/fcell.2021.648209

Melatonin Modulates Lipid Metabolism in Porcine Cumulus–Oocyte Complex via Its Receptors
Cited by: 4
Author(s): Tianqi Zhu, Shengyu Guan, Dongying Lv, Mengmeng Zhao, Laiqing Yan, Li Shi, Pengyun Ji, Lu Zhang, Guoshi Liu
Software Mentions: 3
Published: about 3 years ago

10.1186/s40168-017-0246-x

Microbiome and metabolome modifying effects of several cardiovascular disease interventions in apo-E−/− mice
Cited by: 73
Author(s): Paul M. Ryan, Lis E. E. London, Trent C. Bjorndahl, Rupasri Mandal, Kiera Murphy, Gerald F. Fitzgerald, Fergus Shanahan, R. Paul Ross, David S. Wishart, Noel M. Caplice, Catherine Stanton
Software Mentions: 3
Published: about 7 years ago

10.1186/s40168-021-01085-y

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics
Cited by: 14
Author(s): Patrick T. West, Samantha L. Peters, Matthew R. Olm, Feiqiao Brian Yu, Haley Gause, Yue Clare Lou, Brian Firek, Robyn Baker, Alexander D. Johnson, Michael J. Morowitz, Robert L. Hettich, Jillian F. Banfield
Software Mentions: 3
Published: almost 3 years ago

10.3390/foods8120641

Temporal Check-All-That-Apply (TCATA) Reveals Matrix Interaction Effects on Flavor Perception in a Model Wine Matrix
Cited by: 10
Author(s): Andrew R. Poveromo, Helene Hopfer
Software Mentions: 3
Published: over 4 years ago

10.3389/fchem.2021.662659

The Effects of Sampling and Storage Conditions on the Metabolite Profile of the Marine Sponge Geodia barretti
Cited by: 4
Author(s): Ida Erngren, E.F. Smit, Curt Pettersson, Paco Cárdenas, Mikael Hedeland
Software Mentions: 3
Published: almost 3 years ago

10.3389/fpls.2021.697889

Identification of a New Giant Emrbryo Allele, and Integrated Transcriptomics and Metabolomics Analysis of Giant Embryo Development in Rice
Cited by: 7
Author(s): Zejun Hu, Qiangqiang Xiong, Kai Wang, Lixia Zhang, Ying Yan, Liming Cao, Fuan Niu, Zhu Jun, Jinlong Hu, Shujun Wu
Software Mentions: 3
Published: over 2 years ago

10.1002/ece3.4859

Physical, but not chemical, antiherbivore defense expression is related to the clustered spatial distribution of tropical trees in an Amazonian forest
Cited by: 7
Author(s): Johanna Cobo-Quinche, María‐José Endara, Renato Valencia, Dolly Muñoz-Upegui, Rafael E. Cárdenas
Software Mentions: 3
Published: over 5 years ago

10.1007/s11306-020-01717-8

MetaboShiny: interactive analysis and metabolite annotation of mass spectrometry-based metabolomics data
Cited by: 14
Author(s): Joanna C. Wolthuis, Stefanía Magnúsdóttir, Mia L. Pras‐Raves, Maryam Moshiri, Judith Jans, Boudewijn M.T. Burgering, Saskia W.C. van Mil, Jeroen de Ridder
Software Mentions: 3
Published: over 3 years ago

Projects: cran: DA

Papers Mentioning DA 1,541