Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: cran: PMA
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/PMA
Penalized Multivariate Analysis
16 versions
Latest release: over 1 year ago
10 dependent packages
927 downloads last month
Papers Mentioning PMA 55
10.1371/journal.pcbi.1005752
mixOmics: An R package for ‘omics feature selection and multiple data integrationCited 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 diseaseCited 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 integrationCited 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 ApplicationCited 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 exploreRCited by: 4
Author(s): Dmytro Fishman, Ivan Kuzmin, Priit Adler, Jaak Vilo, Hedi Peterson
Software Mentions: 7
Published: about 4 years ago
10.7717/peerj.9493
Microbial and chemical dynamics of a toxic dinoflagellate bloomCited 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 microbiomeCited by: 5
Author(s): Qidi Ren, Fangqiao Wei, Chao Yuan, Ce Zhu, Qian Zhang, Junkang Quan, Xiangyu Sun, Shuguo Zheng
Software Mentions: 6
Published: about 3 years ago
10.1186/s13059-019-1743-y
CONFINED: distinguishing biological from technical sources of variation by leveraging multiple methylation datasetsCited 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 transcriptomeCited by: 10
Author(s): Ruiyuan Zhang, Michael J. Strong, Melody Baddoo, Zhen Lin, Yuping Wang, Erik K. Flemington, Yaozhong Liu
Software Mentions: 5
Published: over 7 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 MechanismsCited 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‐analysisCited 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 irradiationCited 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 sclerosisCited 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: almost 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 AreasCited by: 11
Author(s): Mónica Rodrigues, Paula Santana, Alfredo Rocha
Software Mentions: 3
Published: over 5 years ago
10.1186/s12859-017-1740-7
Incorporating biological information in sparse principal component analysis with application to genomic dataCited 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 MaterialsCited 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 RatsCited 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: over 11 years ago
10.1186/s40168-020-00874-1
Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutantsCited 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 effectsCited by: 7
Author(s): Xujun Liang, Peng Fei Zhang, Jun Li, Ying Fu, Lingzhi Qu, Yongheng Chen, Zhuchu Chen
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.pone.0150103
Iterative Reconstruction Improves Both Objective and Subjective Image Quality in Acute Stroke CTPCited by: 0
Author(s): Fabian Flottmann, Jan Paul Kabath, Till Illies, Tanja Schneider, Jan‐Hendrik Buhk, Jens Fiehler, André Kemmling
Software Mentions: 2
Published: over 8 years ago
10.1186/s12918-016-0312-1
Structured sparse CCA for brain imaging genetics via graph OSCARCited 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 normalizationCited by: 14
Author(s): Jessica Da Gama Duarte, Ryan Goosen, Peter J. Lawry, Jonathan M. Blackburn
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0107114
Phylogenetic Meta-Analysis of the Functional Traits of Clonal Plants Foraging in Changing EnvironmentsCited by: 21
Author(s): Xiufang Xie, Yue Song, Yalin Zhang, Xu Pan, Ming Dong
Software Mentions: 1
Published: about 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 analysisCited 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 TemperaturesCited by: 24
Author(s): Leyre Corcuera, Eustaquio Gil‐Pelegrín, Eduardo Notivol
Software Mentions: 1
Published: almost 13 years ago
10.1371/journal.pone.0256295
Assessing quality of family planning counseling and its determinants in Kenya: Analysis of health facility exit interviewsCited by: 7
Author(s): Susan Ontiri, Mark Kabue, Regien Biesma, Jelle Stekelenburg, Peter Gichangi
Software Mentions: 1
Published: about 3 years ago
10.1371/journal.pone.0087950
Metabolic Evolution of a Deep-Branching Hyperthermophilic Chemoautotrophic BacteriumCited 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 StrokeCited 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 averagingCited 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 CardiomyocytesCited 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: about 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 StudyCited 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 FibrosisCited 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 RatsCited 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: almost 5 years ago
10.3389/fpls.2016.00603
Biomass Allocation of Stoloniferous and Rhizomatous Plant in Response to Resource Availability: A Phylogenetic Meta-AnalysisCited 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 SolvingCited by: 4
Author(s): Isabel Ramírez-Uclés, Rafael Ramírez Uclés
Software Mentions: 1
Published: over 4 years ago
10.12688/gatesopenres.13119.2
Performance monitoring and accountability: The Agile Project’s protocol, record and experienceCited 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 healthCited 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: about 4 years ago
10.1186/1471-2342-12-16
Automated vs manual delineations of regions of interest- a comparison in commercially available perfusion MRI softwareCited 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 AfricaCited 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 dataCited by: 11
Author(s): Tianwei Yu
Software Mentions: 1
Published: about 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 pathwaysCited 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 lociCited 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 SearchCited by: 0
Author(s): Yang Li, Huahu Xu, Junsheng Xiao
Software Mentions: 1
Published: about 4 years ago
10.1186/1745-6215-12-104
The methodology for developing a prospective meta-analysis in the family planning communityCited 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 OrganoidsCited 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 AssessmentCited 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 derivativesCited 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 analysisCited 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 speciesCited 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 MappingCited 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 studyCited 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: almost 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 CancerCited 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 regimensCited by: 1
Author(s): Simon Daniels, Jacob Hepworth, Meriel Moore-Colyer
Software Mentions: 1
Published: about 4 years ago