cran: PMA | Projects | Ecosyste.ms: Papers

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: about 7 years ago

10.1093/bib/bbv080

Public data and open source tools for multi-assay genomic investigation of disease
Cited by: 47
Author(s): Lavanya Kannan, Marcel Ramos, Angela Re, Nehmé El-Hachem, Zhaleh Safikhani, Deena M.A. Gendoo, Sean Davis, David Gomez-Cabrero, Robert Castelo, Kasper D. Hansen, Vincent J. Carey, Martin Morgan, Aedín C. Culhane, Benjamin Haibe‐Kains, Levi Waldron
Software Mentions: 15
Published: about 9 years ago

10.1186/s12859-016-1455-1

MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration
Cited by: 20
Author(s): Carles Hernández-Ferrer, Carlos Ruiz‐Arenas, Alba Beltran-Gomila, Juan R. González
Software Mentions: 14
Published: almost 8 years ago

10.1177/1177932219899051

Multi-omics Data Integration, Interpretation, and Its Application
Cited by: 527
Author(s): Indhupriya Subramanian, Srikant Verma, Sanjiv Kumar, Abhay Jere, Krishanpal Anamika
Software Mentions: 8
Published: almost 5 years ago

10.1186/s12859-020-03722-z

PAWER: protein array web exploreR
Cited by: 4
Author(s): Dmytro Fishman, Ivan Kuzmin, Priit Adler, Jaak Vilo, Hedi Peterson
Software Mentions: 7
Published: over 4 years ago

10.7717/peerj.9493

Microbial and chemical dynamics of a toxic dinoflagellate bloom
Cited by: 9
Author(s): Nastassia V. Patin, Emily R. Brown, Gabriella Chebli, Claire Garfield, Julia Kubanek, Frank J. Stewart
Software Mentions: 7
Published: over 4 years ago

10.1186/s12903-021-01832-5

The effects of removing dead bacteria by propidium monoazide on the profile of salivary microbiome
Cited by: 5
Author(s): Qidi Ren, Fangqiao Wei, Chao Yuan, Ce Zhu, Qian Zhang, Junkang Quan, Xiangyu Sun, Shuguo Zheng
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-019-1743-y

CONFINED: distinguishing biological from technical sources of variation by leveraging multiple methylation datasets
Cited by: 6
Author(s): Michael Thompson, Zeyuan Johnson Chen, Elior Rahmani, Eran Halperin
Software Mentions: 6
Published: over 5 years ago

10.18632/oncotarget.16417

Interaction of Epstein-Barr virus genes with human gastric carcinoma transcriptome
Cited by: 10
Author(s): Ruiyuan Zhang, Michael J. Strong, Melody Baddoo, Zhen Lin, Yuping Wang, Erik K. Flemington, Yaozhong Liu
Software Mentions: 5
Published: almost 8 years ago

10.1038/s41598-018-29433-3

Using Multi-Scale Genetic, Neuroimaging and Clinical Data for Predicting Alzheimer’s Disease and Reconstruction of Relevant Biological Mechanisms
Cited by: 46
Author(s): Shashank Khanna, Daniel Domingo‐Fernándéz, Anandhi Iyappan, Mohammad Asif Emon, Martin Hofmann-Apitius, Holger Fröhlich
Software Mentions: 4
Published: over 6 years ago

10.1002/cam4.3513

Efficacy of intravesical therapies on the prevention of recurrence and progression of non‐muscle‐invasive bladder cancer: A systematic review and network meta‐analysis
Cited by: 27
Author(s): Junlin Lu, Qi‐Dong Xia, Yilong Lu, Zheng Liu, Peng Zhou, Henglong Hu, Shaogang Wang
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-021-93869-3

Associations between lipids in selected brain regions, plasma miRNA, and behavioral and cognitive measures following 28Si ion irradiation
Cited by: 7
Author(s): Jessica Minnier, Mark R. Emmett, Ruby Perez, Liang Ding, Brooke L. Barnette, Rianna E. Larios, Changjin Hong, Tae Hyun Hwang, Yongjia Yu, Christina M. Fallgren, Michael D. Story, Michael M. Weil, Jacob Raber
Software Mentions: 3
Published: over 3 years ago

10.15252/emmm.202012595

Machine learning suggests polygenic risk for cognitive dysfunction in amyotrophic lateral sclerosis
Cited by: 11
Author(s): Katerina Placek, Michael Benatar, Joanne Wuu, Evadnie Rampersaud, Laura Hennessy, Vivianna M. Van Deerlin, Murray Grossman, David J. Irwin, Lauren Elman, Leo McCluskey, Colin Quinn, Volkan Granit, Jeffrey Statland, Ted M. Burns, John Ravits, Andrea Swenson, José Katz, Erik P. Pioro, Carlayne E. Jackson, James B. Caress, Yuen T. So, Samuel Maiser, David Walk, Edward B. Lee, John Q. Trojanowski, Philip A. Cook, James C. Gee, Sha Jiang, Adam C. Naj, Rosa Rademakers, Wenan Chen, Gang Wu, J. Paul Taylor, Corey T. McMillan
Software Mentions: 3
Published: about 4 years ago

10.1186/s12940-019-0462-x

Bootstrap approach to validate the performance of models for predicting mortality risk temperature in Portuguese Metropolitan Areas
Cited by: 11
Author(s): Mónica Rodrigues, Paula Santana, Alfredo Rocha
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12859-017-1740-7

Incorporating biological information in sparse principal component analysis with application to genomic data
Cited by: 15
Author(s): Ziyi Li, Sandra E. Safo, Qi Long
Software Mentions: 2
Published: over 7 years ago

10.3390/ma10111289

Effective Thermal Expansion Property of Consolidated Granular Materials
Cited by: 0
Author(s): Gülşad Küçük, Marcial Gonzalez, Alberto M. Cuitiño
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0059712

Derivation of Multivariate Syndromic Outcome Metrics for Consistent Testing across Multiple Models of Cervical Spinal Cord Injury in Rats
Cited by: 64
Author(s): Adam R. Ferguson, Karen Irvine, John C. Gensel, Jessica L. Nielson, Amity Lin, Johnathan Ly, Mark R. Segal, Rajiv R. Ratan, Jacqueline C. Bresnahan, Michael S. Beattie
Software Mentions: 2
Published: almost 12 years ago

10.1186/s40168-020-00874-1

Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants
Cited by: 58
Author(s): Marcus H. Y. Leung, Xinzhao Tong, Philippe Bastien, Florent Guinot, Arthur Tenenhaus, Brice Appenzeller, Richard J. Betts, Sakina Mezzache, Jing Li, Nasrine Bourokba, Lionel Breton, Cécile Clavaud, Patrick K. H. Lee
Software Mentions: 2
Published: over 4 years ago

10.1186/s13321-019-0402-3

Learning important features from multi-view data to predict drug side effects
Cited by: 7
Author(s): Xujun Liang, Peng Fei Zhang, Jun Li, Ying Fu, Lingzhi Qu, Yongheng Chen, Zhuchu Chen
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0150103

Iterative Reconstruction Improves Both Objective and Subjective Image Quality in Acute Stroke CTP
Cited by: 0
Author(s): Fabian Flottmann, Jan Paul Kabath, Till Illies, Tanja Schneider, Jan‐Hendrik Buhk, Jens Fiehler, André Kemmling
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12918-016-0312-1

Structured sparse CCA for brain imaging genetics via graph OSCAR
Cited by: 9
Author(s): Lei Du, Heng Huang, Jingwen Yan, Sungeun Kim, Shannon L. Risacher, Mark Inlow, Jason H. Moore, Andrew J. Saykin, Li Shen
Software Mentions: 2
Published: over 8 years ago

10.1186/s13104-018-3266-0

PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization
Cited by: 14
Author(s): Jessica Da Gama Duarte, Ryan Goosen, Peter J. Lawry, Jonathan M. Blackburn
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0107114

Phylogenetic Meta-Analysis of the Functional Traits of Clonal Plants Foraging in Changing Environments
Cited by: 21
Author(s): Xiufang Xie, Yue Song, Yalin Zhang, Xu Pan, Ming Dong
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0254775

Service delivery point and individual characteristics associated with the adoption of modern contraceptive: A multi-country longitudinal analysis
Cited by: 2
Author(s): Philip Anglewicz, Carolina Cardona, Titilope Akinlose, Peter Gichangi, Funmilola OlaOlorun, Elizabeth Omoluabi, Mary Thiongo, Pierre Akilimali, Amy O. Tsui, Patrick Kayembé
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0028772

Intraspecific Variation in Pinus Pinaster PSII Photochemical Efficiency in Response to Winter Stress and Freezing Temperatures
Cited by: 24
Author(s): Leyre Corcuera, Eustaquio Gil‐Pelegrín, Eduardo Notivol
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0256295

Assessing quality of family planning counseling and its determinants in Kenya: Analysis of health facility exit interviews
Cited by: 7
Author(s): Susan Ontiri, Mark Kabue, Regien Biesma, Jelle Stekelenburg, Peter Gichangi
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0087950

Metabolic Evolution of a Deep-Branching Hyperthermophilic Chemoautotrophic Bacterium
Cited by: 30
Author(s): Rogier Braakman, Eric Smith
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0069085

Comparison of Arterial Spin Labeling and Dynamic Susceptibility Contrast Perfusion MRI in Patients with Acute Stroke
Cited by: 35
Author(s): Yen Chu Huang, Ho-Ling Anthony Liu, Jiann Der Lee, Jing‐Tang Yang, Hsu–Huei Weng, Meng Lee, Mei‐Yu Yeh, Yuan-Hsiung Tsai
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0199744

Robust and automatic motion-capture data recovery using soft skeleton constraints and model averaging
Cited by: 21
Author(s): Mickaël Tits, Joëlle Tilmanne, Thierry Dutoit
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms22189869

Tumor Necrosis Factor-Alpha Exacerbates Viral Entry in SARS-CoV2-Infected iPSC-Derived Cardiomyocytes
Cited by: 8
Author(s): Chiu Yang Lee, Chih Heng Huang, Elham Rastegari, Vimalan Rengganaten, Ping Cheng Liu, Ping-Hsing Tsai, Yuan‐Fan Chin, Jing Wu, Shih Hwa Chiou, Yuan Teng, Chih Wei Lee, Yanwen Liang, An Yu Chen, Shu Chen Hsu, Yi Jen Hung, Jun‐Ren Sun, Chian‐Shiu Chien, Yueh Chien
Software Mentions: 1
Published: over 3 years ago

10.2463/mrms.mp.2015-0167

Tmax Determined Using a Bayesian Estimation Deconvolution Algorithm Applied to Bolus Tracking Perfusion Imaging: A Digital Phantom Validation Study
Cited by: 1
Author(s): Ikuko Uwano, Makoto Sasaki, Kohsuke Kudo, T. Boutelier, Hiroyuki Kameda, Futoshi Mori, Fumio Yamashita
Software Mentions: 1
Published: almost 8 years ago

10.3389/fimmu.2021.663303

Neutrophil Extracellular Traps Induce the Epithelial-Mesenchymal Transition: Implications in Post-COVID-19 Fibrosis
Cited by: 40
Author(s): Laura Pandolfi, Sara Beigrezaei, Vanessa Frangipane, Elena Percivalle, Ada De Luigi, Martina Bruna Violatto, Gianluca Lopez, Elisa Gabanti, Luca Carsana, Maura D’Amato, Monica Morosini, Mara De Amici, Manuela Nebuloni, Tommaso Fossali, Riccardo Colombo, Laura Saracino, Veronica Codullo, Massimiliano Gnecchi, Paolo Bigini, Fausto Baldanti, Daniele Lilleri, Federica Meloni
Software Mentions: 1
Published: over 3 years ago

10.3389/fneur.2019.01211

Blood–Brain Barrier Disruption as a Potential Target for Therapy in Posterior Reversible Encephalopathy Syndrome: Evidence From Multimodal MRI in Rats
Cited by: 5
Author(s): Wang Quan-lai, Bin Huang, Guiquan Shen, Yu Zeng, Zheng Chen, Chun-Qiang Lu, Alexander Lerner, Bo Gao
Software Mentions: 1
Published: about 5 years ago

10.3389/fpls.2016.00603

Biomass Allocation of Stoloniferous and Rhizomatous Plant in Response to Resource Availability: A Phylogenetic Meta-Analysis
Cited by: 23
Author(s): Xiufang Xie, Yukun Hu, Xu Pan, Fenghong Liu, Yue Song, Ming Dong
Software Mentions: 1
Published: over 8 years ago

10.3389/fpsyg.2020.00191

Gender Differences in Visuospatial Abilities and Complex Mathematical Problem Solving
Cited by: 4
Author(s): Isabel Ramírez-Uclés, Rafael Ramírez Uclés
Software Mentions: 1
Published: almost 5 years ago

10.12688/gatesopenres.13119.2

Performance monitoring and accountability: The Agile Project’s protocol, record and experience
Cited by: 3
Author(s): Amy O. Tsui, Philip Anglewicz, Titilope Akinlose, Varsha Srivatsan, Pierre Akilimali, Souleymane Alzouma, Fiacre Bazié, Peter Gichangi, Georges Guiella, Patrick Kayembé, Anupam Mehrotra, Funmilola OlaOlorun, Elizabeth Omoluabi, Sani Oumarou, P. R. Sodani, Mary Thiongo, Meagan E. Byrne, Kurt Dreger, Michele R. Decker, Carolina Cardona, Pierre Muhoza, Carolyn Combs, Alain K. Koffi, Scott Radloff
Software Mentions: 1
Published: over 4 years ago

10.12688/gatesopenres.13161.1

Protocol for PMA-Ethiopia: A new data source for cross-sectional and longitudinal data of reproductive, maternal, and newborn health
Cited by: 36
Author(s): Linnea Zimmerman, Selam Desta, Mahari Yihdego, Ann M. Rogers, Ayanaw Amogne, Celia Karp, Shannon N. Wood, Andreea A. Creanga, Saifuddin Ahmed, Assefa Seme, Solomon Shiferaw
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2342-12-16

Automated vs manual delineations of regions of interest- a comparison in commercially available perfusion MRI software
Cited by: 11
Author(s): Ivana Galinović, Ann-Christin Ostwaldt, Carina Soemmer, Helena Bros, Benjamin Hotter, Peter Brunecker, Jochen B. Fiebach
Software Mentions: 1
Published: over 12 years ago

10.9745/GHSP-D-20-00468

Remote Interviewer Training for COVID-19 Data Collection: Challenges and Lessons Learned From 3 Countries in Sub-Saharan Africa
Cited by: 3
Author(s): Shani Turke, Sarah Nehrling, Samuel Olanipekun Adebayo, Pierre Akilimali, Ivan Idiodi, Anthony Mwangi, Elizabeth Larson, Caroline Moreau, Philip Anglewicz
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2105-11-440

An exploratory data analysis method to reveal modular latent structures in high-throughput data
Cited by: 11
Author(s): Tianwei Yu
Software Mentions: 1
Published: over 14 years ago

10.1038/s41598-019-48372-1

A network-based pathway-extending approach using DNA methylation and gene expression data to identify altered pathways
Cited by: 5
Author(s): Jie Li, Qiaosheng Zhang, Zhuo Chen, Dechen Xu, Yadong Wang
Software Mentions: 1
Published: over 5 years ago

10.1002/ajmg.b.32635

A data-driven investigation of relationships between bipolar psychotic symptoms and schizophrenia genome-wide significant genetic loci
Cited by: 10
Author(s): Ganna Leonenko, Arianna Di Florio, Judith Allardyce, Liz Forty, Sarah Knott, Lisa Jones, Katherine Gordon‐Smith, Michael John Owen, Ian Jones, James Walters, Nick Craddock, Valentina Escott‐Price
Software Mentions: 1
Published: over 6 years ago

10.3390/s20185279

Hybrid Attention Network for Language-Based Person Search
Cited by: 0
Author(s): Yang Li, Huahu Xu, Junsheng Xiao
Software Mentions: 1
Published: over 4 years ago

10.1186/1745-6215-12-104

The methodology for developing a prospective meta-analysis in the family planning community
Cited by: 11
Author(s): David K. Turok, Eve Espey, Alison Edelman, Pamela S. Lotke, Eva Lathrop, Stephanie Teal, Janet C. Jacobson, Sara Simonsen, Kenneth F. Schulz
Software Mentions: 1
Published: over 13 years ago

10.3390/ijerph17082633

National Monitoring for Menstrual Health and Hygiene: Is the Type of Menstrual Material Used Indicative of Needs Across 10 Countries?
Cited by: 13
Author(s): Annie D. Smith, A. Muli, Kellogg J. Schwab, Julie Hennegan
Software Mentions: 1
Published: over 4 years ago

10.3390/ijms22031320

Expression of Endogenous Angiotensin-Converting Enzyme 2 in Human Induced Pluripotent Stem Cell-Derived Retinal Organoids
Cited by: 27
Author(s): Henkie Isahwan Ahmad Mulyadi Lai, Shih Jie Chou, Yueh Chien, Ping-Hsing Tsai, Chian‐Shiu Chien, Chih Chien Hsu, Ying Chun Jheng, Mong‐Lien Wang, Shih Hwa Chiou, Yu Bai Chou, De‐Kuang Hwang, Tzu‐Chin Lin, Shih‐Jen Chen, Yi Yang
Software Mentions: 1
Published: almost 4 years ago

10.1007/s10643-017-0854-x

Developing a Multi-Dimensional Early Elementary Mathematics Screener and Diagnostic Tool: The Primary Mathematics Assessment
Cited by: 6
Author(s): Jonathan L. Brendefur, Evelyn S. Johnson, Keith W. Thiede, Sam Strother, Herbert H. Severson
Software Mentions: 1
Published: over 7 years ago

10.1186/1475-2859-13-31

Bacterial degradation of chlorophenols and their derivatives
Cited by: 171
Author(s): Pankaj Arora, Hyeun‐Jong Bae
Software Mentions: 1
Published: almost 11 years ago

10.1186/1753-6561-8-S1-S95

Testing for associations between systolic blood pressure and single-nucleotide polymorphism profiles obtained from sparse principal component analysis
Cited by: 2
Author(s): Alice D. Bonner, Binod Neupane, Joseph Beyene
Software Mentions: 1
Published: over 10 years ago

10.3897/phytokeys.134.37979

A taxonomic synopsis of Virola (Myristicaceae) in Mesoamerica, including six new species
Cited by: 7
Author(s): Daniel Santamaría-Aguilar, Reinaldo Aguilar, Laura P. Lagomarsino
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pcbi.1002707

Discovering Relations Between Mind, Brain, and Mental Disorders Using Topic Mapping
Cited by: 131
Author(s): Russell A. Poldrack, Jeanette A. Mumford, Tom Schönberg, Donald J. Kalar, Bishal Barman, Tal Yarkoni
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2377-9-60

Prospective study on the mismatch concept in acute stroke patients within the first 24 h after symptom onset - 1000Plus study
Cited by: 82
Author(s): Benjamin Hotter, Sandra Pittl, Martin Ebinger, Gabriele Oepen, Kati Jegzentis, Kohsuke Kudo, Michał Różański, W. U. Schmidt, Peter Brunecker, Chao Xu, Peter Martus, Matthias Endres, Gerhard Jan Jungehülsing, Arno Villringer, Jochen B. Fiebach
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pmed.1000068

DEAR1 Is a Dominant Regulator of Acinar Morphogenesis and an Independent Predictor of Local Recurrence-Free Survival in Early-Onset Breast Cancer
Cited by: 38
Author(s): Steven T. Lott, Nanyue Chen, Dawn S. Chandler, Qifeng Yang, Wei Luo, Marivonne Rodriguez, Hongyan Xie, Seetharaman Balasenthil, Thomas A. Buchholz, Ayşegül Şahin, Katrina Chaung, Baili Zhang, Shodimu Emmanu Olufemi, Jinyun Chen, H. R. Adams, Vimla Band, Adel K. El‐Naggar, Marsha L. Frazier, Khandan Keyomarsi, Kelly K. Hunt, Subrata Sen, Bruce G. Haffty, Stephen M. Hewitt, Ralf Krahe, Ann M. Killary
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0242373

The haybiome: Characterising the viable bacterial community profile of four different hays for horses following different pre-feeding regimens
Cited by: 1
Author(s): Simon Daniels, Jacob Hepworth, Meriel Moore-Colyer
Software Mentions: 1
Published: about 4 years ago

Projects: cran: PMA

Papers Mentioning PMA 55