Ecosyste.ms: Papers

10.3390/metabo9100200

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

10.1038/s41598-021-88698-3

In-depth transcriptomic analysis of human retina reveals molecular mechanisms underlying diabetic retinopathy
Cited by: 23
Author(s): Kolja Becker, H. Klein, Eric J. Simon, Coralie Viollet, Christian Haslinger, Germán Leparc, Christian Schultheis, Victor Chong, Markus H. Kuehn, Francesc Fernández-Albert, Remko A. Bakker
Software Mentions: 11
Published: over 3 years ago

10.1002/1878-0261.12850

High‐throughput proteomics of breast cancer interstitial fluid: identification of tumor subtype‐specific serologically relevant biomarkers
Cited by: 13
Author(s): Thilde Terkelsen, Maria Pernemalm, Pavel Gromov, Anna‐Lise Børresen‐Dale, Anders Krogh, Vilde Drageset Haakensen, Janne Lethiö, Elena Papaleo, Irina Gromova
Software Mentions: 10
Published: almost 4 years ago

10.1186/1471-2105-11-503

Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering
Cited by: 54
Author(s): Eva Freyhult, Mattias Landfors, Jenny Önskog, Torgeir R. Hvidsten, Patrik Rydén
Software Mentions: 9
Published: about 14 years ago

10.7717/peerj.7495

Metabolic alterations in pea leaves during arbuscular mycorrhiza development
Cited by: 21
Author(s): O. Y. Shtark, Roman Puzanskiy, G. S. Avdeeva, Andrey P. Yurkov, Galina Smolikova, Vladislav V. Yemelyanov, Marina S. Kliukova, А. Л. Шаварда, А. А. Кирпичникова, А. И. Жернаков, Alexey М. Afonin, И. А. Тихонович, В. А. Жуков, М. Ф. Шишова
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pntd.0006044

Exploratory metabolomics study of the experimental opisthorchiasis in a laboratory animal model (golden hamster, Mesocricetus auratus)
Cited by: 15
Author(s): Daria Kokova, Sarantos Kostidis, Judit Morello, Nataly Dementeva, Ekaterina A. Perina, V. V. Ivanov, Л. М. Огородова, А. Э. Сазонов, Irina V. Saltykova, Oleg A. Mayboroda
Software Mentions: 7
Published: about 7 years ago

10.1534/g3.118.200913

polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids
Cited by: 59
Author(s): Lindsay V. Clark, Alexander E. Lipka, Erik J. Sacks
Software Mentions: 7
Published: over 5 years ago

10.3390/ijms221910451

Differentiation of the High Night Temperature Response in Leaf Segments of Rice Cultivars with Contrasting Tolerance
Cited by: 1
Author(s): Stephanie Schaarschmidt, Ulrike Glaubitz, Alexander Erban, Joachim Kopka, Ellen Zuther
Software Mentions: 7
Published: about 3 years ago

10.3390/metabo9020024

Metabolic Alterations in Male-Sterile Potato as Compared to Male-Fertile
Cited by: 13
Author(s): М. Ф. Шишова, Roman Puzanskiy, О. А. Гаврилова, Shamuhommed Kurbanniazov, Kirill N. Demchenko, Vladislav V. Yemelyanov, Galina Pendinen, А. Л. Шаварда, Т. А. Гавриленко
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pntd.0008015

Plasma metabolomics of the time resolved response to Opisthorchis felineus infection in an animal model (golden hamster, Mesocricetus auratus)
Cited by: 9
Author(s): Daria Kokova, Aswin Verhoeven, Ekaterina A. Perina, В. В. Иванов, Elena M. Knyazeva, Irina V. Saltykova, Oleg A. Mayboroda
Software Mentions: 7
Published: almost 5 years ago

10.18632/aging.203208

miRNAs generated from Meg3-Mirg locus are downregulated during aging
Cited by: 1
Author(s): Ana-Mihaela Lupan, Evelyn Gabriela Rusu, Mihai Bogdan Preda, Catalina Iolanda Marinescu, Cristina Ivan, Alexandrina Burlacu
Software Mentions: 7
Published: over 3 years ago

10.3390/ijms21124236

Differential Urinary Proteome Analysis for Predicting Prognosis in Type 2 Diabetes Patients with and without Renal Dysfunction
Cited by: 25
Author(s): Hee‐Sung Ahn, Jong Ho Kim, Hee Jong Jeong, Jeesuk Yu, Jeonghun Yeom, Sang Heon Song, Sang Soo Kim, In Joo Kim, Kyunggon Kim
Software Mentions: 7
Published: over 4 years ago

10.3389/fpls.2018.00857

Metabolite Profiles of Sugarcane Culm Reveal the Relationship Among Metabolism and Axillary Bud Outgrowth in Genetically Related Sugarcane Commercial Cultivars
Cited by: 21
Author(s): Danilo Alves Ferreira, Marina C. M. Martins, Adriana Cheavegatti-Gianotto, Monalisa Sampaio Carneiro, Rodrigo R. Amadeu, Juliana Aparecida Aricetti, L. D. Wolf, Hermann Paulo Hoffmann, Luís Guilherme F. de Abreu, Camila Caldana
Software Mentions: 6
Published: over 6 years ago

10.1093/gigascience/giz050

Metabolic responses of rice cultivars with different tolerance to combined drought and heat stress under field conditions
Cited by: 48
Author(s): Lovely Mae F Lawas, Xia Li, Alexander Erban, Joachim Kopka, S. V. Krishna Jagadish, Ellen Zuther, Dirk K. Hincha
Software Mentions: 6
Published: over 5 years ago

10.1007/s11306-016-1030-9

Non-targeted UHPLC-MS metabolomic data processing methods: a comparative investigation of normalisation, missing value imputation, transformation and scaling
Cited by: 211
Author(s): Riccardo Di Guida, Jasper Engel, J. William Allwood, Ralf J. M. Weber, Steven J.M. Jones, Ulf Sommer, Mark R. Viant, Warwick B. Dunn
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0207051

A comparative venomic fingerprinting approach reveals that galling and non-galling fig wasp species have different venom profiles
Cited by: 4
Author(s): Leonardo Abdala Elias, Denise Brentan Silva, Ricardo Silva, Yan‐Qiong Peng, Da‐Rong Yang, Norberto P. Lopes, Rodrigo Augusto Santinelo Pereira
Software Mentions: 6
Published: about 6 years ago

10.1038/mt.2014.86

Characterizing Human Stem Cell–derived Sensory Neurons at the Single-cell Level Reveals Their Ion Channel Expression and Utility in Pain Research
Cited by: 105
Author(s): Gareth T. Young, Alex Gutteridge, Heather De Fox, Anna Wilbrey, Lishuang Cao, Lily T Cho, Adam R. Brown, Caroline Benn, Laura R Kammonen, Julia Friedman, Magda Bictash, Paul Whiting, James Bilsland, Edward B. Stevens
Software Mentions: 6
Published: over 10 years ago

10.1186/s12879-017-2351-7

1H-NMR analysis of feces: new possibilities in the helminthes infections research
Cited by: 19
Author(s): Sarantos Kostidis, Daria Kokova, Natalia Dementeva, Irina V. Saltykova, Hye Kyong Kim, Young Hae Choi, Oleg A. Mayboroda
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: over 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: over 3 years ago

10.3389/fncir.2019.00032

A Novel Type of Neuron Within the Dorsal Striatum
Cited by: 16
Author(s): Miaomiao Mao, Aditya Nair, George J Augustine
Software Mentions: 5
Published: over 5 years ago

10.3389/fmed.2017.00153

TruSeq-Based Gene Expression Analysis of Formalin-Fixed Paraffin-Embedded (FFPE) Cutaneous T-Cell Lymphoma Samples: Subgroup Analysis Results and Elucidation of Biases from FFPE Sample Processing on the TruSeq Platform
Cited by: 15
Author(s): Philippe Lefrançois, Michael T. Tetzlaff, Linda Moreau, Andrew Watters, Elena Netchiporouk, Nathalie Provost, Martin Gilbert, Xiao Ni, Denis Sasseville, Madeleine Duvic, Ivan V. Litvinov
Software Mentions: 5
Published: about 7 years ago

10.1007/s00394-016-1230-0

Cocoa polyphenols and fiber modify colonic gene expression in rats
Cited by: 14
Author(s): Malén Massot-Cladera, Àngels Franch, Margarida Castell, Francisco J. Pérez-Cano
Software Mentions: 5
Published: over 8 years ago

10.1186/s12859-016-1440-8

TTCA: an R package for the identification of differentially expressed genes in time course microarray data
Cited by: 15
Author(s): Marco Albrecht, Damian Stichel, Bettina Müller, Ruth Merkle, Carsten Sticht, Norbert Gretz, Ursula Klingmüller, Kai Breuhahn, Franziska Matthäus
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pone.0256918

Using climatic variables alone overestimate climate change impacts on predicting distribution of an endemic species
Cited by: 8
Author(s): Somayeh Zangiabadi, Hassan Zare‐Maivan, LIuis Brotons, Hossein Mostafavi, Hojjatollah Ranjbar
Software Mentions: 5
Published: about 3 years ago

10.1038/s41598-021-90654-0

Kernel weighted least square approach for imputing missing values of metabolomics data
Cited by: 7
Author(s): Nishith Kumar, Md. Rakibul Hoque, Masahiro Sugimoto
Software Mentions: 5
Published: over 3 years ago

10.1172/jci.insight.143058

Targeted DNA methylation profiling reveals epigenetic signatures in peanut allergy
Cited by: 26
Author(s): Xiaoying Zhou, Xiaorui Han, Shu‐Chen Lyu, Bryan Bunning, Laurie Kost, Iris Chang, Shu Cao, Vanitha Sampath, Kari Nadeau
Software Mentions: 5
Published: over 3 years ago

10.1007/s11306-015-0927-z

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

10.1186/s40168-020-00858-1

Using soil bacterial communities to predict physico-chemical variables and soil quality
Cited by: 113
Author(s): Syrie M. Hermans, Hannah Buckley, Bradley S. Case, Fiona Curran-Cournane, Mykel R. Taylor, Gavin Lear
Software Mentions: 5
Published: over 4 years ago

10.1186/s13229-020-00359-w

IGF-1 treatment causes unique transcriptional response in neurons from individuals with idiopathic autism
Cited by: 17
Author(s): Sara B. Linker, Ana Paula Mendes, Maria C. Marchetto
Software Mentions: 5
Published: over 4 years ago

10.3390/pharmaceutics13081105

Evaluation of an Intravitreal Rho-Associated Kinase Inhibitor Depot Formulation in a Rat Model of Diabetic Retinopathy
Cited by: 2
Author(s): Cécile Lebon, Heike Neubauer, Marianne Berdugo, Kimberley Delaunay, Elke Markert, Kolja Becker, Katja S. Baum-Kroker, J. Prestle, Holger Fuchs, Remko A. Bakker, Francine Behar‐Cohen
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pbio.3000799

5-Formylcytosine landscapes of human preimplantation embryos at single-cell resolution
Cited by: 5
Author(s): Yun Gao, Lin Li, Peng Yuan, Fan Zhai, Yixuan Ren, Liying Yan, Rong Li, Ying Lian, Xiaohui Zhu, Xinglong Wu, Kehkooi Kee, Lu Wen, Jie Qiao, Fuchou Tang
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pgen.1007406

Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen
Cited by: 101
Author(s): Darach Miller, Nathan Brandt, David Gresham
Software Mentions: 5
Published: over 6 years ago

10.3389/fpls.2018.00641

Detailed Phytochemical Analysis of High- and Low Artemisinin-Producing Chemotypes of Artemisia annua
Cited by: 22
Author(s): Tomasz Czechowski, Tony R. Larson, Theresa M. Catania, David Harvey, Cenxi Wei, Michel Essome, Geoffrey D. Brown, Ian A. Graham
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0032394

pcaGoPromoter - An R Package for Biological and Regulatory Interpretation of Principal Components in Genome-Wide Gene Expression Data
Cited by: 24
Author(s): Morten Hansen, Thomas Alexander Gerds, Ole Haagen Nielsen, Jakob Benedict Seidelin, Jesper T. Troelsen, Jørgen Olsen
Software Mentions: 4
Published: over 12 years ago

10.1186/1756-0500-5-85

Mathematical modeling and comparison of protein size distribution in different plant, animal, fungal and microbial species reveals a negative correlation between protein size and protein number, thus providing insight into the evolution of proteomes
Cited by: 84
Author(s): Axel Tiessen, Paulino Pérez‐Rodríguez, Luis Delaye
Software Mentions: 4
Published: almost 13 years ago

10.3389/fpls.2021.636915

Trait Diversity of Pulse Species Predicts Agroecosystem Properties Trade-Offs
Cited by: 0
Author(s): Julie Guiguitant, Denis Vile, Hélène Marrou
Software Mentions: 4
Published: over 3 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: over 7 years ago

10.1186/s12864-015-1266-1

Genetic diversity and trait genomic prediction in a pea diversity panel
Cited by: 80
Author(s): Judith Burstin, Pauline Salloignon, Marianne Chabert-Martinello, Jean Bernard Magnin-Robert, Mathieu Siol, Françoise Jacquin, Aurélie Chauveau, Caroline Pont, Grégoire Aubert, Catherine Delaitre, Caroline Truntzer, Gérard Duc
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2105-12-390

Classification of microarrays; synergistic effects between normalization, gene selection and machine learning
Cited by: 28
Author(s): Jenny Önskog, Eva Freyhult, Mattias Landfors, Patrik Rydén, Torgeir R. Hvidsten
Software Mentions: 4
Published: about 13 years ago

10.1371/journal.pone.0251396

Fullerenol changes metabolite responses differently depending on the iron status of cucumber plants
Cited by: 5
Author(s): Nikolai P. Bityutskii, Kirill L. Yakkonen, Roman Puzanskiy, Kseniia A. Lukina, А. Л. Шаварда, Konstantin N. Semenov
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-95268-0

Potential of rice landraces with strong culms as genetic resources for improving lodging resistance against super typhoons
Cited by: 4
Author(s): Taishin Nomura, Yosuke Seki, Makoto Matsuoka, Kenji Yano, Koki Chigira, Shunsuke Adachi, Francisco J Piñera-Chávez, Matthew Reynolds, Shuichi Ohkubo, Taiichiro Ookawa
Software Mentions: 4
Published: over 3 years ago

10.1186/s12859-017-1501-7

Mixture model normalization for non-targeted gas chromatography/mass spectrometry metabolomics data
Cited by: 31
Author(s): Anna C. Reisetter, Michael J. Muehlbauer, James R. Bain, Michael Nodzenski, Robert Stevens, Olga Ilkayeva, Boyd E. Metzger, Christopher B. Newgard, William L. Lowe
Software Mentions: 4
Published: almost 8 years ago

10.3390/plants9091149

Response of Downy Oak (Quercus pubescens Willd.) to Climate Change: Transcriptome Assembly, Differential Gene Analysis and Targeted Metabolomics
Cited by: 7
Author(s): Jean-Philippe Mévy, Béatrice Loriod, Xi Liu, Erwan Corre, Magali Torres, Michael Büttner, Anne Haguenauer, Ilja M. Reiter, Catherine Fernandez, Thierry Gauquelin
Software Mentions: 4
Published: about 4 years ago

10.1038/cr.2017.82

Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cells
Cited by: 262
Author(s): Fan Guo, Lin Li, Jingyun Li, Xinglong Wu, Boqiang Hu, Ping Zhu, Lu Wen, Fuchou Tang
Software Mentions: 4
Published: over 7 years ago

10.1186/1752-0509-5-1

Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach
Cited by: 118
Author(s): Atsushi Fukushima, Miyako Kusano, Henning Redestig, Masanori Arita, Kazuki Saito
Software Mentions: 4
Published: almost 14 years ago

10.3390/metabo10060220

Non-Targeted Metabolite Profiles and Sensory Properties Elucidate Commonalities and Differences of Wines Made with the Same Variety but Different Cultivar Clones
Cited by: 6
Author(s): Álvaro Cuadros-Inostroza, Claudio Verdugo-Alegría, Lothar Willmitzer, Yerko Moreno-Simunovic, José G. Vallarino
Software Mentions: 4
Published: over 4 years ago

10.1128/mBio.02500-18

Determination of the Global Pattern of Gene Expression in Yeast Cells by Intracellular Levels of Guanine Nucleotides
Cited by: 8
Author(s): Andrew Hesketh, Marta Vergnano, Stephen G. Oliver
Software Mentions: 4
Published: over 5 years ago

10.1093/gigascience/giz102

Metabolic responses of rice source and sink organs during recovery from combined drought and heat stress in the field
Cited by: 13
Author(s): Lovely Mae F Lawas, Alexander Erban, Joachim Kopka, S. V. Krishna Jagadish, Ellen Zuther, Dirk K. Hincha
Software Mentions: 4
Published: over 5 years ago

10.3390/microarrays1020084

Quality Visualization of Microarray Datasets Using Circos
Cited by: 2
Author(s): Martin Koch, Michael Wiese
Software Mentions: 4
Published: over 12 years ago

10.1186/gm551

Early aberrant DNA methylation events in a mouse model of acute myeloid leukemia
Cited by: 28
Author(s): Miriam Sonnet, Rainer Claus, Natália Becker, Manuela Zucknick, Jana Petersen, Daniel B. Lipka, Christopher C. Oakes, Mindaugas Andrulis, Amelie Lier, Michael D. Milsom, Tania Witte, Lei Gu, Soo Zin Kim-Wanner, Peter Schirmacher, Michael Wulfert, Norbert Gattermann, Michael Lübbert, Frank Rosenbauer, Michael Rehli, Lars Bullinger, Dieter Weichenhan, Christoph Plass
Software Mentions: 4
Published: almost 11 years ago

10.5966/sctm.2016-0088

Directing Differentiation of Pluripotent Stem Cells Toward Retinal Pigment Epithelium Lineage
Cited by: 40
Author(s): Parul Choudhary, Heather Booth, Alex Gutteridge, Beata Surmacz, Irene Louca, Juliette Steer, Julie Kerby, Paul J. Whiting
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-021-95116-1

Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance
Cited by: 19
Author(s): Ricardo José Gonzaga Pimenta, Alexandre Hild Aono, Roberto Carlos Villavicencio Burbano, Alisson Esdras Coutinho, Carla Cristina da Silva, Ivan Antônio dos Anjos, Dilermando Pérecin, Marcos Guimarães de Andrade Landell, Marcos César Gonçalves, Luciana Rossini Pinto, Anete Pereira de Souza
Software Mentions: 3
Published: over 3 years ago

10.3390/antiox10091484

Aryl Hydrocarbon Receptor and Cysteine Redox Dynamics Underlie (Mal)adaptive Mechanisms to Chronic Intermittent Hypoxia in Kidney Cortex
Cited by: 6
Author(s): Maria João Correia, António B. Pimpão, Filipa Lopes‐Coelho, Catarina O. Sequeira, Nuno R. Coelho, Clara Gonçalves-Dias, Robert Barouki, Xavier Coumoul, Jacinta Serpa, Judit Morelló, Emília C. Monteiro, Sofia A. Pereira
Software Mentions: 3
Published: about 3 years ago

10.1186/s12859-015-0494-3

Impact of missing data imputation methods on gene expression clustering and classification
Cited by: 66
Author(s): Michael Vandesteen Silva Souto, Pablo Andretta Jaskowiak, Ivan G. Costa
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2407-10-628

Merging transcriptomics and metabolomics - advances in breast cancer profiling
Cited by: 100
Author(s): Eldrid Borgan, Beathe Sitter, Ole Christian Lingjærde, Hilde Johnsen, Steinar Lundgren, Tone Frost Bathen, Thérese Sørlie, Anne‐Lise Børresen‐Dale, Ingrid S. Gribbestad
Software Mentions: 3
Published: almost 14 years ago

10.1186/s12862-017-1005-0

Paternal personality and social status influence offspring activity in zebrafish
Cited by: 16
Author(s): Susanne Zajitschek, James E. Herbert‐Read, Nasir M. Abbasi, Felix Zajitschek, Simone Immler
Software Mentions: 3
Published: over 7 years ago

10.1590/0074-02760190364

Human acute Chagas disease: changes in factor VII, activated protein C and hepatic enzymes from patients of oral outbreaks in Pará State (Brazilian Amazon)
Cited by: 6
Author(s): Valéria Regina Cavalcante dos Santos, Dina Antunes, Dilma do Socorro Moraes de Souza, Otacílio C. Moreira, Igor Campos de Almeida Lima, Désio Aurélio Farias-de-Oliveira, João Pedro Lobo, Ernesto de Meis, José Rodrigues Coura, Wilson Savino, Ângela Cristina Veríssimo Junqueira, Juliana de Meis
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0047833

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

10.1371/journal.pone.0130128

Oviductal Transcriptome Is Modified after Insemination during Spontaneous Ovulation in the Sow
Cited by: 37
Author(s): Rebeca López‐Úbeda, Francisco Alberto García–Vázquez, Raquel Romar, J. Gadea, Marta Muñoz, Richard Hunter, Pilar Coy
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0025186

Cranial Growth and Variation in Edmontosaurs (Dinosauria: Hadrosauridae): Implications for Latest Cretaceous Megaherbivore Diversity in North America
Cited by: 115
Author(s): Nicolás E. Campione, David C. Evans
Software Mentions: 3
Published: about 13 years ago

10.3390/cells9092092

An Evolutionary Cancer Epigenetic Approach Revealed DNA Hypermethylation of Ultra-Conserved Non-Coding Elements in Squamous Cell Carcinoma of Different Mammalian Species
Cited by: 2
Author(s): Luca Morandi, Silvia Sabattini, Andrea Renzi, Antonella Rigillo, Giuliano Bettini, Eva Dervas, A Schauer, M. Morandi, Davide Bartolomeo Gissi, Achille Tarsitano, Stefania Evangelisti, Caterina Tonon
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-018-34191-3

Transcriptome analysis of extended-spectrum β-lactamase-producing Escherichia coli and methicillin-resistant Staphylococcus aureus exposed to cefotaxime
Cited by: 12
Author(s): P. R. Brochmann, Andrew Hesketh, Bimal Jana, G. H. Brodersen, Luca Guardabassi
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-021-81279-4

A comparative study of evaluating missing value imputation methods in label-free proteomics
Cited by: 43
Author(s): Lina Jin, Yingtao Bi, Chenqi Hu, Jun Qu, Shichen Shen, Xue Wang, Yu Tian
Software Mentions: 3
Published: almost 4 years ago

10.1002/stem.2095

Molecular Mechanisms Mediating Retinal Reactive Gliosis Following Bone Marrow Mesenchymal Stem Cell Transplantation
Cited by: 62
Author(s): Alessia Tassoni, Alex Gutteridge, Amanda C. Barber, Andrew Osborne, Keith R Martin
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.57468

Plasticity and evolutionary convergence in the locomotor skeleton of Greater Antillean Anolis lizards
Cited by: 9
Author(s): Nathalie Feiner, Illiam S. C. Jackson, Kirke L. Munch, Reinder Radersma, Tobias Uller
Software Mentions: 3
Published: about 4 years ago

10.3390/ijms22158172

Characterization of the Heat-Stable Proteome during Seed Germination in Arabidopsis with Special Focus on LEA Proteins
Cited by: 9
Author(s): Orarat Ginsawaeng, Michał Górka, Alexander Erban, Carolin Heise, Franziska Brueckner, Rainer Hoefgen, Joachim Kopka, Aleksandra Skirycz, Dirk K. Hincha, Ellen Zuther
Software Mentions: 3
Published: over 3 years ago

10.1186/s13048-016-0252-9

The oviductal transcriptome is influenced by a local ovarian effect in the sow
Cited by: 3
Author(s): Rebeca López‐Úbeda, Marta Muñoz, Luis Alberto Vieira, Richard Hunter, Pilar Coy, Sebastián Cánovas
Software Mentions: 3
Published: over 8 years ago

10.18632/oncotarget.7579

A nuclear-directed human pancreatic ribonuclease (PE5) targets the metabolic phenotype of cancer cells
Cited by: 15
Author(s): Anna Vert, Jessica Castro, Marc Ribó, Antoni Benito, María Vilanova
Software Mentions: 3
Published: over 8 years ago

10.18632/oncotarget.14302

Activating transcription factor 3 is crucial for antitumor activity and to strengthen the antiviral properties of Onconase
Cited by: 20
Author(s): Anna Vert, Jessica Castro, Marc Ribó, Antoni Benito, María Vilanova
Software Mentions: 3
Published: almost 8 years ago

10.3390/nu6051913

Urinary Metabolite Profiles in Premature Infants Show Early Postnatal Metabolic Adaptation and Maturation
Cited by: 36
Author(s): Sissel J. Moltu, Daniel Sachse, Elin Wahl Blakstad, Kenneth Strømmen, Britt Nakstad, Astrid Nylander Almaas, Ane C. Westerberg, Arild Rønnestad, Kristin Brække, Marit B. Veierød, Per Ole Iversen, Frode Rise, Jens Petter Berg, Christian A. Drevon
Software Mentions: 3
Published: over 10 years ago

10.1186/s13059-019-1859-0

Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize
Cited by: 61
Author(s): Jing Xu, Chao-Yu Guo, Peter J. Hermanson, Qiang Xu, Changshuo Sun, Wenqing Chen, Qiuxin Kan, Minqi Li, Peter A. Crisp, Jianbing Yan, Li Lin, Nathan M. Springer, Qing Li
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12859-021-04336-9

Reproducibility of mass spectrometry based metabolomics data
Cited by: 11
Author(s): Tusharkanti Ghosh, Daisy Philtron, Weimin Zhang, Katerina Kechris, Debashis Ghosh
Software Mentions: 2
Published: about 3 years ago

10.1186/2049-2618-1-20

Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants
Cited by: 131
Author(s): Erika C. Claud, Kevin P. Keegan, Jennifer M. Brulc, Lei Lü, Daniela Bartels, Elizabeth M. Glass, Eugene B. Chang, Patrick Meyer, Dionysios A. Antonopoulos
Software Mentions: 2
Published: over 11 years ago

10.1038/s41598-020-60166-4

Evaluation of pulse crops’ functional diversity supporting food production
Cited by: 4
Author(s): Julie Guiguitant, Denis Vile, Michel Edmond Ghanem, Jacques Wéry, Hélène Marrou
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-61081-4

Correlation-based network analysis combined with machine learning techniques highlight the role of the GABA shunt in Brachypodium sylvaticum freezing tolerance
Cited by: 12
Author(s): David Toubiana, Nir Sade, Lifeng Liu, María del Mar Rubio Wilhelmi, Yariv Brotman, Urszula Luzarowska, John P. Vogel, Eduardo Blumwald
Software Mentions: 2
Published: over 4 years ago

10.3389/fpls.2017.01292

Stress-Related Mitogen-Activated Protein Kinases Stimulate the Accumulation of Small Molecules and Proteins in Arabidopsis thaliana Root Exudates
Cited by: 13
Author(s): Nadine Strehmel, Wolfgang Hoehenwarter, Susann Mönchgesang, Petra Majovsky, Sylvia Krüger, Dierk Scheel, Justin Lee
Software Mentions: 2
Published: over 7 years ago

10.1186/1755-8794-7-58

Protein and microRNA biomarkers from lavage, urine, and serum in military personnel evaluated for dyspnea
Cited by: 13
Author(s): Joseph N. Brown, Heather M. Brewer, Carrie Nicora, Karl K. Weitz, Michael J. Morris, Andrew Skabelund, Joshua N. Adkins, Richard Smith, Ji Hoon Cho, Richard Gelinas
Software Mentions: 2
Published: about 10 years ago

10.1186/bcr3597

Interplay of choline metabolites and genes in patient-derived breast cancer xenografts
Cited by: 45
Author(s): Maria Tunset Grinde, Nirma Skrbo, Siver Andreas Moestue, Einar Andreas Rødland, Eldrid Borgan, Alexander Kristian, Beathe Sitter, Tone Frost Bathen, Anne Lise Børresen-Dale, Gunhild Mari Mælandsmo, Olav Engebraaten, Thérese Sørlie, Elisabetta Marangoni, Ingrid S. Gribbestad
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-14-908

A genome-wide scan for signatures of differential artificial selection in ten cattle breeds
Cited by: 86
Author(s): Sophie Rothammer, Doris Seichter, M. Förster, Ivica Međugorac
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0062680

Proteomic Characterization of Inbreeding-Related Cold Sensitivity in Drosophila melanogaster
Cited by: 6
Author(s): Cornelis J Vermeulen, Kamilla Pedersen, Hans Christian Beck, Jørn Henrik Petersen, Kristina K. Gagalova, Volker Loeschcke
Software Mentions: 2
Published: over 11 years ago

10.3389/fpls.2016.00525

Population Genomic Analysis Reveals Differential Evolutionary Histories and Patterns of Diversity across Subgenomes and Subpopulations of Brassica napus L.
Cited by: 24
Author(s): Élodie Gazave, Erica E. Tassone, Daniel C. Ilut, Megan Wingerson, Erwin Datema, H. Witsenboer, James B. Davis, David Grant, John M. Dyer, Matthew A. Jenks, J. Brown, Michael A. Gore
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2015.01521

Global Regulation of Gene Expression by the MafR Protein of Enterococcus faecalis
Cited by: 16
Author(s): Sofía Ruiz‐Cruz, Manuel Espinosa, Oliver Goldmann, Alicia Bravo
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2105-16-S18-S7

Principal component analysis for designed experiments
Cited by: 48
Author(s): Tomokazu Konishi
Software Mentions: 2
Published: almost 9 years ago

10.3390/ijerph14050549

An Ensemble Spatiotemporal Model for Predicting PM2.5 Concentrations
Cited by: 26
Author(s): Lianfa Li, Jiehao Zhang, Wenyang Qiu, Jinfeng Wang, Fang Ying
Software Mentions: 2
Published: over 7 years ago

10.3389/fmolb.2021.595712

Quantitative Proteomic Analysis in Alveolar Type II Cells Reveals the Different Capacities of RAS and TGF-β to Induce Epithelial–Mesenchymal Transition
Cited by: 3
Author(s): Yilu Zhou, Catherine M. Hill, Liudi Yao, Juanjuan Li, David C. Hancock, Julian Downward, Mark G. Jones, Donna E. Davies, Rob M. Ewing, Paul Skipp, Yihua Wang
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0240849

Metabolomics of primary cutaneous melanoma and matched adjacent extratumoral microenvironment
Cited by: 10
Author(s): Nicholas Taylor, Irina Gaynanova, Steven A. Eschrich, Eric A. Welsh, Timothy J. Garrett, Chris Beecher, Ritin Sharma, John M. Koomen, Keiran S.M. Smalley, Jane L. Messina, Peter A. Kanetsky
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0222171

Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method
Cited by: 13
Author(s): Sukithar Rajan, Carl Mårten Lindqvist, Robert Jan Brummer, Ida Schoultz, Dirk Repsilber
Software Mentions: 2
Published: about 5 years ago

10.1093/jxb/ert349

Deciphering genetic diversity and inheritance of tomato fruit weight and composition through a systems biology approach
Cited by: 19
Author(s): Laura Pascual, Jiaxin Xu, Benoît Biais, Mickaël Maucourt, Patricia Ballias, Stéphane Bernillon, Catherine Deborde, Daniel Jacob, Aurore Desgroux, Mireille Faurobert, Jean‐Paul Bouchet, Yves Gibon, Annick Moing, Mathilde Causse
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0007359

Multivariate Statistical Analyses Demonstrate Unique Host Immune Responses to Single and Dual Lentiviral Infection
Cited by: 14
Author(s): Sunando Roy, Jennie S. Lavine, Francesca Chiaromonte, Julie A. TerWee, Sue VandeWoude, Ottar N. Bjørnstad, Mary Poss
Software Mentions: 2
Published: about 15 years ago

10.1093/jxb/eru027

The essential role of sugar metabolism in the acclimation response of Arabidopsis thaliana to high light intensities
Cited by: 57
Author(s): J. E. Schmitz, Luisa Heinrichs, Federico Scossa, Alisdair R. Fernie, Marie-Luise Oelze, Karl‐Josef Dietz, Maxi Rothbart, Bernhard Grimm, Ulf‐Ingo Flügge, Rainer E. Häusler
Software Mentions: 2
Published: over 10 years ago

10.3389/fmolb.2016.00077

Non-targeted Plasma Metabolome of Early and Late Lactation Gilts
Cited by: 3
Author(s): Lea A. Rempel, Jeremy R. Miles, W. T. Oliver, Corey D. Broeckling
Software Mentions: 2
Published: almost 8 years ago

10.1098/rspb.2021.0226

A highly conserved ontogenetic limb allometry and its evolutionary significance in the adaptive radiation of <i>Anolis</i> lizards
Cited by: 10
Author(s): Nathalie Feiner, Illiam S. C. Jackson, Eliane Van der Cruyssen, Tobias Uller
Software Mentions: 2
Published: over 3 years ago

10.1093/molbev/msaa295

Properties of Markov Chain Monte Carlo Performance across Many Empirical Alignments
Cited by: 10
Author(s): Sean Harrington, Van Wishingrad, Robert C. Thomson
Software Mentions: 2
Published: almost 4 years ago

10.1016/j.dib.2020.106148

An automated data extraction and classification pipeline to identify a novel type of neuron within the dorsal striatum based on single-cell patch clamp and confocal imaging data
Cited by: 0
Author(s): Miaomiao Mao, Aditya Nair, George J Augustine
Software Mentions: 2
Published: about 4 years ago

10.1002/ece3.6716

Association of genetic and climatic variability in giant sequoia, <i>Sequoiadendron giganteum</i> , reveals signatures of local adaptation along moisture‐related gradients
Cited by: 6
Author(s): Rainbow DeSilva, Richard S. Dodd
Software Mentions: 2
Published: about 4 years ago

10.1111/acel.12632

Analysis of individual cells identifies cell-to-cell variability following induction of cellular senescence
Cited by: 167
Author(s): Christopher D. Wiley, James M. Flynn, Christapher S. Morrissey, Ronald Lebofsky, Joe Shuga, Xiao Dong, Marc Unger, Jan Vijg, Simon Melov, Judith Campisi
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2105-14-151

Analysis of multiple phenotypes in genome-wide genetic mapping studies
Cited by: 26
Author(s): Chen Suo, Timothea Toulopoulou, Elvira Bramon, Muriel Walshe, Marco Picchioni, Robin M. Murray, Jürg Ott
Software Mentions: 1
Published: over 11 years ago

10.3390/nu13030726

A Comparison of the In Vitro Effects of 2’Fucosyllactose and Lactose on the Composition and Activity of Gut Microbiota from Infants and Toddlers
Cited by: 27
Author(s): Pieter Van den Abbeele, Norbert Sprenger, Jonas Ghyselinck, Benoît Marsaux, Massimo Marzorati, Florence Rochat
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0195189

Interaction of childhood urbanicity and variation in dopamine genes alters adult prefrontal function as measured by functional magnetic resonance imaging (fMRI)
Cited by: 9
Author(s): Jessica Reed, Enrico D’Ambrosio, Stefano Marenco, Gianluca Ursini, Amanda B Zheutlin, Giuseppe Blasi, Barbara E. Spencer, Raffaella Romano, Jesse Hochheiser, Ann Reifman, Justin Sturm, Karen F. Berman, Alessandro Bertolino, Daniel R. Weinberger, Joseph H. Callicott
Software Mentions: 1
Published: over 6 years ago