bioconductor: CAMERA | Projects | 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

10.12688/f1000research.17824.2

Enhancing gene set enrichment using networks
Cited by: 2
Author(s): Michael Prummer
Software Mentions: 51
Published: over 5 years ago

10.3390/biology3010085

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms
Cited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Software Mentions: 28
Published: almost 11 years ago

10.1186/s13321-020-00477-w

patRoon: open source software platform for environmental mass spectrometry based non-target screening
Cited by: 76
Author(s): Rick Helmus, Thomas L. ter Laak, Annemarie P. van Wezel, P. de Voogt, Emma L. Schymanski
Software Mentions: 20
Published: almost 4 years ago

10.1038/sdata.2018.179

Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytes
Cited by: 13
Author(s): Kristian Peters, Karin Gorzolka, Helge Bruelheide, Steffen Neumann
Software Mentions: 17
Published: over 6 years ago

10.1002/ece3.4361

Seasonal variation of secondary metabolites in nine different bryophytes
Cited by: 28
Author(s): Kristian Peters, Karin Gorzolka, Helge Bruelheide, Steffen Neumann
Software Mentions: 16
Published: over 6 years ago

10.3390/metabo9100222

Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species
Cited by: 29
Author(s): Kristian Peters, Hendrik Treutler, Stefanie Döll, Alida Kindt, Thomas Hankemeier, Steffen Neumann
Software Mentions: 15
Published: about 5 years ago

10.1186/s12864-020-06856-9

mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling data
Cited by: 28
Author(s): Antony Kaspi, Mark Ziemann
Software Mentions: 15
Published: over 4 years ago

10.1093/bib/bbz158

Toward a gold standard for benchmarking gene set enrichment analysis
Cited by: 74
Author(s): Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity W. Law, Sean Davis, Vincent J. Carey, Martin Morgan, Ralf Zimmer, Levi Waldron
Software Mentions: 13
Published: almost 5 years ago

10.1093/gigascience/gix037

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

10.1371/journal.pone.0079217

A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity
Cited by: 154
Author(s): Adi L. Tarca, Gaurav Bhatti, Roberto Romero
Software Mentions: 12
Published: about 11 years ago

10.1371/journal.pcbi.1008979

netgsa: Fast computation and interactive visualization for topology-based pathway enrichment analysis
Cited by: 4
Author(s): Michael Hellstern, Jing Ma, Kun Yue, Ali Shojaie
Software Mentions: 12
Published: over 3 years ago

10.1007/s11306-016-1090-x

Discovery of A-type procyanidin dimers in yellow raspberries by untargeted metabolomics and correlation based data analysis
Cited by: 6
Author(s): Elisabete Carvalho, Pietro Franceschi, Antje Feller, Lorena Herrera, L. Palmieri, Panagiotis Arapitsas, Samantha Riccadonna, Stefan Martens
Software Mentions: 11
Published: over 8 years ago

10.1186/s12859-017-1579-y

metaX: a flexible and comprehensive software for processing metabolomics data
Cited by: 402
Author(s): Bo Wen, Zhanlong Mei, Chunwei Zeng, Siqi Liu
Software Mentions: 11
Published: almost 8 years ago

10.1186/s12859-020-03786-x

IP4M: an integrated platform for mass spectrometry-based metabolomics data mining
Cited by: 32
Author(s): Dandan Liang, Quan Liu, Kejun Zhou, Jia Wang, Guoxiang Xie, Tianlu Chen
Software Mentions: 11
Published: about 4 years ago

10.1186/1471-2105-15-S1-S11

The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again
Cited by: 19
Author(s): Alejandra N. González-Beltrán, Steffen Neumann, Eamonn Maguire, Susanna-Assunta Sansone, Philippe Rocca-Serra
Software Mentions: 11
Published: almost 11 years ago

10.1186/s12859-019-3146-1

A comparative study of topology-based pathway enrichment analysis methods
Cited by: 51
Author(s): Jing Ma, Ali Shojaie, George Michailidis
Software Mentions: 10
Published: about 5 years ago

10.1186/gb-2014-15-2-r29

voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Cited by: 4,221
Author(s): Charity W. Law, Yunshun Chen, Wei Shi, Gordon K. Smyth
Software Mentions: 10
Published: almost 11 years ago

10.1186/s12864-018-4870-z

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data
Cited by: 11
Author(s): Joseph C. Devlin, Thomas Battaglia, Martin J. Blaser, Kelly V. Ruggles
Software Mentions: 9
Published: over 6 years ago

10.1186/s13040-017-0125-9

Gene set analysis controlling for length bias in RNA-seq experiments
Cited by: 7
Author(s): Xing Ren, Qiang Hu, Song Liu, Jianmin Wang, Jeffrey C. Miecznikowski
Software Mentions: 9
Published: almost 8 years ago

10.7150/thno.53092

Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapy
Cited by: 7
Author(s): Xin Lai, Florian S. Dreyer, Martina Cantone, Martin Eberhardt, Kerstin F. Gerer, Tanushree Jaitly, Steffen Uebe, Christopher Lischer, Arif B. Ekici, Jürgen Wittmann, Hans‐Martin Jäck, Niels Schaft, Jan Dörrie, Julio Vera
Software Mentions: 9
Published: almost 4 years ago

10.1186/s13046-021-01955-1

What are the applications of single-cell RNA sequencing in cancer research: a systematic review
Cited by: 28
Author(s): Lvyuan Li, Fang Xiong, Yumin Wang, Shanshan Zhang, Zhaojian Gong, Xiayu Li, Yi He, Lei Shi, Fuyan Wang, Qianjin Liao, Bo Xiang, Ming Zhou, Xiaoling Li, Yong Li, Guiyuan Li, Zhaoyang Zeng, Wei Xiong, Can Guo
Software Mentions: 9
Published: over 3 years ago

10.1007/s11306-017-1242-7

Navigating freely-available software tools for metabolomics analysis
Cited by: 165
Author(s): Rachel Spicer, Reza M. Salek, Pablo Moreno-Ger, Daniel Cañueto, Christoph Steinbeck
Software Mentions: 8
Published: over 7 years ago

10.1186/s13073-021-00866-2

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium
Cited by: 21
Author(s): Silva Kasela, Victor E. Ortega, Molly Martorella, Suresh Garudadri, Jennifer Nguyen, Elizabeth J. Ampleford, Anu Pasanen, Srilaxmi Nerella, Kristina L. Buschur, Igor Barjaktarević, R. Graham Barr, Eugene R. Bleecker, Russell P. Bowler, Alejandro P. Comellas, Christopher B. Cooper, David Couper, Gerard J. Criner, Jeffrey L. Curtis, MeiLan K. Han, Nadia N. Hansel, Eric A. Hoffman, Robert J. Kaner, Jerry A. Krishnan, Fernando J. Martínez, Merry-Lynn McDonald, Deborah A. Meyers, Robert Paine, Stephen P. Peters, Mario Castro, Loren C. Denlinger, Serpil C. Erzurum, John V. Fahy, Elliot Israel, Nizar N. Jarjour, Bruce D. Levy, Xingnan Li, Wendy C. Moore, Sally E. Wenzel, Joe Zein, Charles Langelier, Prescott G. Woodruff, Tuuli Lappalainen, Stephanie A. Christenson
Software Mentions: 8
Published: over 3 years ago

10.7554/eLife.38519

Insulin mutations impair beta-cell development in a patient-derived iPSC model of neonatal diabetes
Cited by: 106
Author(s): Diego Balboa, Jonna Saarimäki-Vire, Daniel Borshagovski, Mantas Survila, Päivi Lindholm, Emilia Galli, Solja Eurola, Jarkko Ustinov, Heli Grym, Hanna Huopio, Juha Partanen, Kirmo Wartiovaara, Timo Otonkoski
Software Mentions: 8
Published: about 6 years ago

10.3389/fpls.2021.693739

Comparative Metabolomics of Fruits and Leaves in a Hyperdiverse Lineage Suggests Fruits Are a Key Incubator of Phytochemical Diversification
Cited by: 11
Author(s): Gerald Schneider, Diego Salazar, Sherry B. Hildreth, Richard Helm, Susan R. Whitehead
Software Mentions: 7
Published: over 3 years ago

10.1186/s13059-014-0465-4

DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging
Cited by: 84
Author(s): Belinda Phipson, Alicia Oshlack
Software Mentions: 7
Published: over 10 years ago

10.1186/1751-0473-7-13

MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads
Cited by: 4
Author(s): Alexander Tyakht, Anna Popenko, Maxim S. Belenikin, Ilya Altukhov, Alexander V. Pavlenko, Elena S. Kostryukova, Oksana V. Selezneva, Andrei K. Larin, Irina Y. Karpova, Dmitry Alexeev
Software Mentions: 7
Published: about 12 years ago

10.1186/s13040-018-0166-8

Gene set analysis methods: a systematic comparison
Cited by: 57
Author(s): Ravi Mathur, Daniel M. Rotroff, Ma Jun, Ali Shojaie, Alison A. Motsinger‐Reif
Software Mentions: 7
Published: over 6 years ago

10.1038/srep29033

Natural variation of root exudates in Arabidopsis thaliana-linking metabolomic and genomic data
Cited by: 130
Author(s): Susann Mönchgesang, Nadine Strehmel, Stephan Schmidt, Lore Westphal, Franziska Taruttis, E. Müller, Siska Herklotz, Steffen Neumann, Dierk Scheel
Software Mentions: 7
Published: over 8 years ago

10.1186/s13059-020-02081-5

The Tug1 lncRNA locus is essential for male fertility
Cited by: 59
Author(s): Jordan P. Lewandowski, Gabrijela Dumbović, Audrey Watson, Tae-Young Hwang, Emily Jacobs-Palmer, Nydia P Chang, Christian Much, Kyle M. Turner, Christopher Kirby, Nimrod D. Rubinstein, Abigail F. Groff, Steve C. Liapis, Chiara Gerhardinger, Assaf C. Bester, Pier Paolo Pandolfi, John G. Clohessy, Hopi E. Hoekstra, Martin Sauvageau, John L. Rinn
Software Mentions: 6
Published: over 4 years ago

10.7554/eLife.35368

Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in Drosophila
Cited by: 92
Author(s): Zaijun Ma, Hui Wang, Yuping Cai, Han Wang, Kongyan Niu, Xiaofen Wu, Huanhuan Ma, Yun Yang, Wenhua Tong, Feng Liu, Zhandong Liu, Yaoyang Zhang, Rui Li, Zheng‐Jiang Zhu, Nan Liu
Software Mentions: 6
Published: over 6 years ago

10.3390/metabo11060361

Opposing Effects of Ceanothus velutinus Phytochemistry on Herbivore Communities at Multiple Scales
Cited by: 2
Author(s): Casey S. Philbin, M. J. Paulsen, Lora A. Richards
Software Mentions: 6
Published: over 3 years ago

10.3389/fmolb.2016.00026

biosigner: A New Method for the Discovery of Significant Molecular Signatures from Omics Data
Cited by: 46
Author(s): Philippe Rinaudo, Samia Boudah, Christophe Junot, Etienne Thévenot
Software Mentions: 6
Published: over 8 years ago

10.1186/s12859-015-0751-5

Comparative study on gene set and pathway topology-based enrichment methods
Cited by: 61
Author(s): Michaela Bayerlová, Klaus Jung, Frank Krämer, Florian Klemm, Annalen Bleckmann, Tim Beißbarth
Software Mentions: 6
Published: about 9 years ago

10.1186/1471-2105-14-38

FANTOM: Functional and taxonomic analysis of metagenomes
Cited by: 34
Author(s): Kemal Sanli, Fredrik Karlsson, Intawat Nookaew, Jens Nielsen
Software Mentions: 6
Published: almost 12 years ago

10.1128/AAC.00504-21

Expression Dysregulation as a Mediator of Fitness Costs in Antibiotic Resistance
Cited by: 4
Author(s): Andrej Trauner, Amir Banaei‐Esfahani, Sebastian M. Gygli, Philipp Warmer, Julia Feldmann, Mattia Zampieri, Sònia Borrell, Ben C. Collins, Christian Beisel, Ruedi Aebersold, Sébastien Gagneux
Software Mentions: 6
Published: over 3 years ago

10.1038/s41396-019-0549-y

Coordinated transformation of the gut microbiome and lipidome of bowhead whales provides novel insights into digestion
Cited by: 16
Author(s): Colin Miller, Henry C Holm, Lara Horstmann, J. C. George, Helen F. Fredricks, Benjamin A. S. Van Mooy, Amy Apprill
Software Mentions: 6
Published: about 5 years ago

10.1007/s10616-020-00384-w

Genome-wide expression profiling reveals increased stability and mitochondrial energy metabolism of the human liver cell line HepaRG-CAR
Cited by: 1
Author(s): Aziza A. A. Adam, Aldo Jongejan, Perry D. Moerland, Vincent A. van der Mark, Ronald P.J. Oude Elferink, R. A. F. M. Chamuleau, Ruurdtje Hoekstra
Software Mentions: 6
Published: almost 5 years ago

10.3389/fpls.2021.613059

Identification of ABA-Mediated Genetic and Metabolic Responses to Soil Flooding in Tomato (Solanum lycopersicum L. Mill)
Cited by: 24
Author(s): Vicent Arbona, Miguel González-Guzmán, Zara Pitarch, José Tomás Matus, Héctor Candela, José L. Rambla, Antonio Granell, Aurelio Gómez‐Cadenas
Software Mentions: 6
Published: almost 4 years ago

10.3390/biom10071041

Untargeted LC-MS Metabolomics Differentiates Between Virulent and Avirulent Clinical Strains of Pseudomonas aeruginosa
Cited by: 18
Author(s): Tobias Depke, Janne G. Thöming, Adrian Kordes, Susanne Häußler, Mark Brönstrup
Software Mentions: 6
Published: over 4 years ago

10.3390/metabo6040037

Prediction, Detection, and Validation of Isotope Clusters in Mass Spectrometry Data
Cited by: 17
Author(s): Hendrik Treutler, Steffen Neumann
Software Mentions: 6
Published: about 8 years ago

10.1371/journal.pone.0219507

Discovery of potential urine-accessible metabolite biomarkers associated with muscle disease and corticosteroid response in the mdx mouse model for Duchenne
Cited by: 5
Author(s): Mathula Thangarajh, Aiping Zhang, Kirandeep Gill, Habtom W. Ressom, Zhenzhi Li, Rency S. Varghese, Eric P. Hoffman, Kanneboyina Nagaraju, Yetrib Hathout, Simina M. Boca
Software Mentions: 6
Published: over 5 years ago

10.18632/oncotarget.23206

Coagulation cascade and complement system in systemic lupus erythematosus
Cited by: 19
Author(s): Yan Liang, Shangbo Xie, Changhao Wu, Yuan Hu, Qin Zhang, Si Li, Yin‐Guang Fan, Rui‐Xue Leng, Hai‐Feng Pan, Huabao Xiong, Dong‐Qing Ye
Software Mentions: 5
Published: about 7 years ago

10.1186/1471-2164-15-749

Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities
Cited by: 22
Author(s): Johan Bengtsson‐Palme, Magnus Alm Rosenblad, Mikael Molin, Anders Blomberg
Software Mentions: 5
Published: almost 11 years ago

10.3389/fnins.2018.00136

Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids
Cited by: 4
Author(s): Sofie Derycke, Loïc Kéver, Koen Herten, Koen Van Den Berge, Maarten Van Steenberge, Jeroen Van Houdt, Lieven Clement, Pascal Poncin, Éric Parmentier, Erik Verheyen
Software Mentions: 5
Published: almost 7 years ago

10.3389/fgene.2013.00168

Meta4: a web application for sharing and annotating metagenomic gene predictions using web services
Cited by: 7
Author(s): Emily J. Richardson, Franck Escalettes, Ian Fotheringham, Robert John Wallace, Michael Watson
Software Mentions: 5
Published: almost 12 years ago

10.1093/gigascience/giy149

PhenoMeNal: processing and analysis of metabolomics data in the cloud
Cited by: 58
Author(s): Kristian Peters, J. H. Bradbury, Sven Bergmann, Marco Capuccini, Marta Cascante, Pedro de Atauri, Timothy M. D. Ebbels, Carles Foguet, Robert C. Glen, Alejandra González-Beltrán, Ulrich L. Günther, Evangelos Handakas, Thomas Hankemeier, Kenneth Haug, Stephanie Herman, Petr Holub, Massimiliano Izzo, Daniel Jacob, David Johnson, Fabien Jourdan, Namrata Kale, Íbrahím Karaman, Bita Khalili, Payam Emami Khonsari, Kim Kultima, Samuel Lampa, Anders Larsson, Christian Ludwig, Pablo Moreno-Ger, Steffen Neumann, Jon Ander Novella, Claire O’Donovan, Jake T M Pearce, Alina Peluso, Marco Piras, Luca Pireddu, Michelle A.C. Reed, Philippe Rocca-Serra, Pierrick Roger, Antonio Rosato, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M. Salek, Susanna-Assunta Sansone, Vitaly A. Selivanov, Ola Spjuth, Daniel Schober, Etienne Thévenot, Mattia Tomasoni, Merlijn van Rijswijk, Michael Van Vliet, Mark R. Viant, Ralf Weber, Gianluigi Zanetti, Christoph Steinbeck
Software Mentions: 5
Published: about 6 years ago

10.1007/s10456-021-09788-4

The endosomal RIN2/Rab5C machinery prevents VEGFR2 degradation to control gene expression and tip cell identity during angiogenesis
Cited by: 20
Author(s): Lanette Kempers, Yuki Wakayama, Ivo van der Bijl, Charita Furumaya, Iris M. De Cuyper, Aldo Jongejan, Marije Kat, Anne-Marieke D. van Stalborch, Antonius L. van Boxtel, Marvin Hubert, Dirk Geerts, Jaap D. van Buul, Dirk de Korte, Wiebke Herzog, Coert Margadant
Software Mentions: 5
Published: over 3 years ago

10.1177/0748730418813785

LimoRhyde: A Flexible Approach for Differential Analysis of Rhythmic Transcriptome Data
Cited by: 47
Author(s): Jordan M. Singer, Jacob J. Hughey
Software Mentions: 5
Published: about 6 years ago

10.1186/s13059-015-0844-5

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
Cited by: 1,843
Author(s): Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian H. Gersuk, Alex K. Shalek, Chloe K. Slichter, Hannah W. Miller, M. Juliana McElrath, Martin Prlic, Peter S. Linsley, Raphaël Gottardo
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pbio.3000481

Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias
Cited by: 45
Author(s): Shir Mandelboum, Zohar Manber, Orna Elroy‐Stein, Ran Elkon
Software Mentions: 5
Published: about 5 years ago

10.1186/1758-2946-5-12

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

10.1186/s40478-019-0805-4

Profiling the unique protective properties of intracranial arterial endothelial cells
Cited by: 7
Author(s): Dorien Hermkens, Olga C.G. Stam, Nienke M. de Wit, Ruud D. Fontijn, Aldo Jongejan, Perry D. Moerland, Claire Mackaaij, Ingeborg S. E. Waas, M. J. A. P. Daemen, Helga E. de Vries
Software Mentions: 5
Published: about 5 years ago

10.1186/s12859-017-1674-0

Ranking metrics in gene set enrichment analysis: do they matter?
Cited by: 47
Author(s): Joanna Żyła, Michał Marczyk, January Weiner, Joanna Polańska
Software Mentions: 5
Published: over 7 years ago

10.3389/fphar.2020.599760

Modulation of the Gut Microbiota and Liver Transcriptome by Red Yeast Rice and Monascus Pigment Fermented by Purple Monascus SHM1105 in Rats Fed with a High-Fat Diet
Cited by: 10
Author(s): Hua Yang, Ronghua Pan, Jing Wang, Lizhong Zheng, Zhenjing Li, Qingbin Guo, Changlu Wang
Software Mentions: 5
Published: almost 4 years ago

10.1186/1471-2105-10-391

JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes
Cited by: 6
Author(s): Chunguang Liang, Alexander Schmid, María José López‐Sánchez, Andrés Moya, Roy Gross, Jörg Bernhardt, Thomas Dandekar
Software Mentions: 5
Published: about 15 years ago

10.7554/eLife.47214

In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation
Cited by: 15
Author(s): Daniel Andergassen, Zachary D. Smith, Jordan P. Lewandowski, Chiara Gerhardinger, Alexander Meissner, John L. Rinn
Software Mentions: 5
Published: about 5 years ago

10.4056/sigs.1353455

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9
Cited by: 4
Author(s): Tanja Davidsen, Ramana Madupu, Peter J. Sterk, Dawn Field, George M Garrity, Jack A. Gilbert, Frank Oliver Glöckner, Lynette Hirschman, Eugene Kolker, Renzo Kottmann, Nikos C. Kyrpides, Patrick Meyer, Norman Morrison, Lynn M. Schriml, Tatiana Tatusova, John Wooley
Software Mentions: 5
Published: almost 15 years ago

10.1186/s13395-017-0144-8

Comparison of multiple transcriptomes exposes unified and divergent features of quiescent and activated skeletal muscle stem cells
Cited by: 29
Author(s): Natalia Pietrosemoli, Sébastien Mella, Siham Yennek, Meryem B. Baghdadi, Hiroshi Sakai, Ramkumar Sambasivan, Francesca Pala, Daniela Di Girolamo, Shahragim Tajbakhsh
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pone.0089323

Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization
Cited by: 60
Author(s): Xiaoquan Su, Weihua Pan, Baoxing Song, Jian Xu, Kang Ning
Software Mentions: 5
Published: almost 11 years ago

10.1093/gigascience/giz083

iMicrobe: Tools and data-driven discovery platform for the microbiome sciences
Cited by: 24
Author(s): Ken Youens‐Clark, Matt Bomhoff, Alise J. Ponsero, Elisha M. Wood‐Charlson, Joshua Lynch, Illyoung Choi, John H. Hartman, Bonnie Hurwitz
Software Mentions: 5
Published: over 5 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

10.1172/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: over 5 years ago

10.1186/s12859-017-1571-6

Avoiding the pitfalls of gene set enrichment analysis with SetRank
Cited by: 87
Author(s): Cédric Simillion, Robin Liechti, Heidi E. L. Lischer, Vassilios Ioannidis, Rémy Bruggmann
Software Mentions: 4
Published: almost 8 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: almost 8 years ago

10.1186/1471-2164-15-989

Evaluation of viral genome assembly and diversity estimation in deep metagenomes
Cited by: 31
Author(s): Daniel Aguirre de Cárcer, Florent E. Angly, Antonio Alcamı́
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12859-016-1403-0

Robust multi-group gene set analysis with few replicates
Cited by: 4
Author(s): Pashupati P. Mishra, Alan Medlar, Liisa Holm, Petri Törönen
Software Mentions: 4
Published: about 8 years ago

10.3390/metabo9090171

WiPP: Workflow for Improved Peak Picking for Gas Chromatography-Mass Spectrometry (GC-MS) Data
Cited by: 18
Author(s): Nico Borgsmüller, Yoann Gloaguen, Tobias Opialla, Eric Blanc, Emilie Sicard, Anne-Lise Royer, Bruno Le Bizec, Stéphanie Durand, Carole Migné, Mélanie Petera, Estelle Pujos‐Guillot, Franck Giacomoni, Yann Guitton, Dieter Beule, Jennifer Kirwan
Software Mentions: 4
Published: over 5 years ago

10.3390/metabo10040143

Metabolomics Benefits from Orbitrap GC–MS—Comparison of Low- and High-Resolution GC–MS
Cited by: 29
Author(s): Daniel Stettin, Remington X. Poulin, Georg Pohnert
Software Mentions: 4
Published: over 4 years ago

10.3390/ijms19051385

Current Challenges in Plant Eco-Metabolomics
Cited by: 90
Author(s): Kristian Peters, Anja Worrich, Alexander Weinhold, Oliver Alka, Gerd Ulrich Balcke, Claudia Birkemeyer, Helge Bruelheide, Onno W Calf, Sophie Dietz, Kai Dührkop, Emmanuel Gaquerel, Uwe Heinig, Marlen Kücklich, Mirka Máčel, Caroline Müller, Yvonne Poeschl, Georg Pohnert, Christian Ristok, Víctor M. Rodríguez, Christoph Ruttkies, Meredith C. Schuman, Rabea Schweiger, Nir Shahaf, Christoph Steinbeck, María Tortosa, Hendrik Treutler, Nico Ueberschaar, Pablo Velasco, B. Weiß, Anja Widdig, Steffen Neumann, Nicole M. van Dam
Software Mentions: 4
Published: over 6 years ago

10.3389/fimmu.2021.638571

Different Disease Endotypes in Phenotypically Similar Vasculitides Affecting Small-to-Medium Sized Blood Vessels
Cited by: 7
Author(s): Erin E. Gill, Maren L. Smith, Kristen M Gibson, Kimberly Morishita, Ahwon Lee, Reza Falsafi, Jinko Graham, Dirk Foell, Susanne M. Benseler, Colin J. Ross, Raashid Luqmani, David A. Cabral, Robert E. W. Hancock, Kelly L. Brown, PedVas Initiative Investigators
Software Mentions: 4
Published: almost 4 years ago

10.3389/fimmu.2018.01829

Human Bone Marrow-Resident Natural Killer Cells Have a Unique Transcriptional Profile and Resemble Resident Memory CD8+ T Cells
Cited by: 28
Author(s): Janine Melsen, Gertjan Lugthart, Carly Vervat, Szymon M. Kiełbasa, Sander A.J. van der Zeeuw, Henk P.J. Buermans, Monique M. van Ostaijen-ten Dam, Arjan C. Lankester, Marco W. Schilham
Software Mentions: 4
Published: over 6 years ago

10.1186/s40168-018-0460-1

Flexible metagenome analysis using the MGX framework
Cited by: 18
Author(s): Sebastian Jaenicke, Stefan P. Albaum, Patrick Blumenkamp, Burkhard Linke, Jens Stoye, Alexander Goesmann
Software Mentions: 4
Published: over 6 years ago

10.1186/s13045-014-0089-x

Splicing factor 3b subunit 1 (Sf3b1) haploinsufficient mice display features of low risk Myelodysplastic syndromes with ring sideroblasts
Cited by: 20
Author(s): Valeria Visconte, Ali Tabarroki, Li Zhang, Yvonne Parker, Edy Hasrouni, R. Mahfouz, Kyoichi Isono, Haruhiko Koseki, Mikkael A. Sekeres, Yogen Saunthararajah, John Barnard, Daniel J. Lindner, Heesun J. Rogers, Ramon V. Tiu
Software Mentions: 4
Published: about 10 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: over 4 years ago

10.1186/2042-5783-2-3

Metagenomics - a guide from sampling to data analysis
Cited by: 673
Author(s): Torsten Thomas, Jack Gilbert, Patrick Meyer
Software Mentions: 4
Published: almost 13 years ago

10.1128/mSystems.00607-19

Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer
Cited by: 16
Author(s): Lauren M. Seyler, William J. Brazelton, Craig McLean, Lindsay I. Putman, Alex Hyer, M. D. Kubo, Tori M. Hoehler, D. Cardace, M. O. Schrenk
Software Mentions: 4
Published: over 4 years ago

10.3390/cancers13174250

Transcriptional Reprogramming and Constitutive PD-L1 Expression in Melanoma Are Associated with Dedifferentiation and Activation of Interferon and Tumour Necrosis Factor Signalling Pathways
Cited by: 10
Author(s): Antonio Ahn, Euan J. Rodger, Jyoti Motwani, Grégory Gimenez, Peter A. Stockwell, Matthew Parry, Peter Hersey, Aniruddha Chatterjee, Michael R. Eccles
Software Mentions: 4
Published: over 3 years ago

10.4056/sigs.1423520

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10
Cited by: 8
Author(s): Elizabeth M. Glass, Patrick Meyer, Jack A. Gilbert, Dawn Field, Sarah Hunter, Renzo Kottmann, Nikos C. Kyrpides, Susanna Assunta Sansone, Lynn M. Schriml, Peter J. Sterk, Owen White, John Wooley
Software Mentions: 4
Published: almost 15 years ago

10.1093/bioinformatics/btz160

Interoperable and scalable data analysis with microservices: applications in metabolomics
Cited by: 24
Author(s): Payam Emami Khoonsari, Pablo Moreno-Ger, Sven Bergmann, Joachim Burman, Marco Capuccini, Matteo Carone, Marta Cascante, Pedro de Atauri, Carles Foguet, Alejandra N. González-Beltrán, Thomas Hankemeier, Kenneth Haug, Sijin He, Stephanie Herman, David Johnson, Namrata Kale, Anders Larsson, Steffen Neumann, Kristian Peters, Luca Pireddu, Philippe Rocca-Serra, Pierrick Roger, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M. Salek, Susanna-Assunta Sansone, Daniel Schober, Vitaly A. Selivanov, Etienne Thévenot, Michael Van Vliet, Gianluigi Zanetti, Christoph Steinbeck, Kim Kultima, Ola Spjuth
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13040-015-0059-z

Principal component gene set enrichment (PCGSE)
Cited by: 20
Author(s): H. Robert Frost, Zhigang Li, Jason H. Moore
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0230813

Metabolic reprograming of LPS-stimulated human lung macrophages involves tryptophan metabolism and the aspartate-arginosuccinate shunt
Cited by: 14
Author(s): Fanta Fall, Elodie Lamy, Marion Brollo, Emmanuel Naline, Natacha Lenuzza, Etienne Thévenot, Philippe Devillier, Stanislas Grassin-Delyle
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-020-61851-0

Sex Differences in Colon Cancer Metabolism Reveal A Novel Subphenotype
Cited by: 39
Author(s): Yuping Cai, Nicholas A. Rattray, Qian Zhang, Varvara Mironova, Álvaro José Santos-Neto, Kuo-Shun Hsu, Zahra Rattray, Justin R. Cross, Yawei Zhang, Philip B. Paty, Sajid Khan, Caroline H. Johnson
Software Mentions: 4
Published: almost 5 years ago

10.1126/scisignal.abf8483

Kynurenic acid may underlie sex-specific immune responses to COVID-19
Cited by: 55
Author(s): Yuping Cai, Daniel Kim, Takehiro Takahashi, David Broadhurst, Yan Hong, Shuanagge Ma, Nicholas J. W. Rattray, Arnau Casanovas‐Massana, Benjamin Israelow, Jonathan Klein, Carolina Lucas, Tianyang Mao, Adam J. Moore, M. Catherine Muenker, Ji Eun Oh, Julio Silva, Patrick Wong, Albert Icksang Ko, Sajid Khan, Akiko Iwasaki, Caroline H. Johnson
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.ppat.1007290

Longitudinal transcriptomic characterization of the immune response to acute hepatitis C virus infection in patients with spontaneous viral clearance
Cited by: 33
Author(s): Brad R. Rosenberg, Marion Depla, Catherine A. Freije, Denis Gaucher, Sabrina Mazouz, Maude Boisvert, Nathalie Bédard, Julie Bruneau, Charles M. Rice, Naglaa H. Shoukry
Software Mentions: 4
Published: over 6 years ago

10.3390/s19245387

Design and Construction of an ROV for Underwater Exploration
Cited by: 32
Author(s): O.A. Aguirre-Castro, Everardo Inzunza-González, E. E. García-Guerrero, Esteban Tlelo‐Cuautle, Oscar Roberto López-Bonilla, Jesús Everardo Olguín Tiznado, José Ricardo Cárdenas-Valdez
Software Mentions: 4
Published: about 5 years ago

10.1128/mSystems.00187-19

Systems Analyses Reveal the Resilience of Escherichia coli Physiology during Accumulation and Export of the Nonnative Organic Acid Citramalate
Cited by: 10
Author(s): Joseph P. Webb, V S Springthorpe, Luca Rossoni, David-Paul Minde, Swen Langer, Heather Walker, Amias Alstrom-Moore, Tony R. Larson, Kathryn S. Lilley, Graham R. Eastham, Gill Stephens, Gavin H. Thomas, David J. Kelly, Jeffrey Green
Software Mentions: 4
Published: over 5 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

10.1186/1471-2180-12-122

Metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system
Cited by: 82
Author(s): Vicente Gomez-Alvarez, Randy P. Revetta, Jorge W. Santo Domingo
Software Mentions: 3
Published: over 12 years ago

10.1186/s12864-019-5574-8

YPR2 is a regulator of light modulated carbon and secondary metabolism in Trichoderma reesei
Cited by: 28
Author(s): Eva Hitzenhammer, Christoph Büschl, Michael Sulyok, Rainer Schuhmacher, Bernhard Kluger, Elisabeth Wischnitzki, Monika Schmoll
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2105-14-202

MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information
Cited by: 94
Author(s): Kishori M. Konwar, Niels W. Hanson, Antoine Pagé, Steven J. Hallam
Software Mentions: 3
Published: over 11 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

10.1186/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

10.1371/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

10.1093/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

10.3389/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

10.3389/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

10.1186/s40168-021-01029-6

Xylitol enhances synthesis of propionate in the colon via cross-feeding of gut microbiota
Cited by: 45
Author(s): Shasha Xiang, Kun Ye, Mian Li, Jian Ying, Huanhuan Wang, Jianzhong Han, Lihua Shi, Jie Xiao, Yubiao Shen, Xiao Feng, Xuan Bao, Yiqing Zheng, Guofu Yin, Yalin Zhang, Chang Liu, Jie Chen, Yuewen Chen, Shiping Tian, Xuan Zhu
Software Mentions: 3
Published: almost 4 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

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