cran: pamr | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0018850

Multiplexed Immunoassay Panel Identifies Novel CSF Biomarkers for Alzheimer's Disease Diagnosis and Prognosis
Cited by: 199
Author(s): Rebecca Craig‐Schapiro, Max Kühn, Chengjie Xiong, Eve H. Pickering, Jingxia Liu, Thomas P. Misko, Richard J. Perrin, Kelly R. Bales, Holly Soares, Anne M. Fagan, David M. Holtzman
Software Mentions: 15
Published: over 13 years ago

10.3389/fmicb.2015.00104

Long-term forest soil warming alters microbial communities in temperate forest soils
Cited by: 237
Author(s): Kristen M. DeAngelis, Grace Pold, Begüm D. Topçuoğlu, Linda T. A. van Diepen, Rebecca Varney, Jeffrey L. Blanchard, Jerry M. Melillo, Serita D. Frey
Software Mentions: 15
Published: over 9 years ago

10.1038/srep26451

Glycosyltransferase Gene Expression Profiles Classify Cancer Types and Propose Prognostic Subtypes
Cited by: 52
Author(s): Jahanshah Ashkani, Kevin J. Naidoo
Software Mentions: 12
Published: over 8 years ago

10.1186/1471-2105-10-74

RGG: A general GUI Framework for R scripts
Cited by: 7
Author(s): Ilhami Visne, Erkan Dilaveroǧlu, Klemens Vierlinger, Martin Lauss, Ahmet Yıldız, Andreas Weinhäusel, Christa Noehammer, Friedrich Leisch, Albert Kriegner
Software Mentions: 11
Published: over 15 years ago

10.3389/fgene.2020.569572

Aberrantly Methylated-Differentially Expressed Genes Identify Novel Atherosclerosis Risk Subtypes
Cited by: 6
Author(s): Yuzhou Xue, Yongzheng Guo, Suxin Luo, Wei Zhou, Jun Xiang, Yuansong Zhu, Zhenxian Xiang, Ju Shen
Software Mentions: 10
Published: almost 4 years ago

10.1371/journal.pone.0137132

Clustering of Expression Data in Chronic Lymphocytic Leukemia Reveals New Molecular Subdivisions
Cited by: 7
Author(s): Sally Yepes, María Mercedes Torres, Rafael Andrade
Software Mentions: 9
Published: about 9 years ago

10.18632/aging.101795

Predicting chromosome 1p/19q codeletion by RNA expression profile: a comparison of current prediction models
Cited by: 4
Author(s): Zhiliang Wang, Zheng Zhao, Zheng Wang, Chuanbao Zhang, Tao Jiang
Software Mentions: 9
Published: almost 6 years ago

10.1186/s13058-015-0550-y

Gene-expression molecular subtyping of triple-negative breast cancer tumours: importance of immune response
Cited by: 223
Author(s): Pascal Jézéquel, Delphine Loussouarn, Catherine Guérin‐Charbonnel, Loı̈c Campion, Antoine Vanier, Wilfried Gouraud, Hamza Lasla, Catherine Guette, Isabelle Valo, Véronique Verrièle, Mario Campone
Software Mentions: 8
Published: over 9 years ago

10.1371/journal.pone.0097678

Evaluation of Toxicogenomics Approaches for Assessing the Risk of Nongenotoxic Carcinogenicity in Rat Liver
Cited by: 16
Author(s): Johannes Eichner, Clemens Wrzodek, Michael Roemer, Heidrun Ellinger‐Ziegelbauer, Andreas Zell
Software Mentions: 7
Published: over 10 years ago

10.3389/fimmu.2021.656541

The Predictive Value of Monocytes in Immune Microenvironment and Prognosis of Glioma Patients Based on Machine Learning
Cited by: 32
Author(s): Nan Zhang, Ziyu Dai, Wantao Wu, Zeyu Wang, Hui Cao, Yakun Zhang, Zhanchao Wang, Hao Zhang, Quan Cheng
Software Mentions: 7
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

10.1371/journal.pone.0073938

A Toxicogenomic Approach for the Prediction of Murine Hepatocarcinogenesis Using Ensemble Feature Selection
Cited by: 16
Author(s): Johannes Eichner, Nadine Kossler, Clemens Wrzodek, Arno Kalkuhl, Dorthe Bach Toft, Nina Ostenfeldt, V. Espley Richard, Andreas Zell
Software Mentions: 6
Published: about 11 years ago

10.1371/journal.pcbi.1008769

COMSUC: A web server for the identification of consensus molecular subtypes of cancer based on multiple methods and multi-omics data
Cited by: 1
Author(s): Song He, Xinyu Song, Xisheng Yang, Jianyang Yu, Yao Wen, Lianlian Wu, Bowei Yan, Jiannan Feng, Xiaochen Bo
Software Mentions: 6
Published: over 3 years ago

10.1186/s12711-019-0453-y

Machine learning applied to transcriptomic data to identify genes associated with feed efficiency in pigs
Cited by: 24
Author(s): M. Piles, Carlos Fernández-Lozano, María Velasco-Galilea, Olga González‐Rodríguez, Juan Pablo Sánchez, D. Torrallardona, María Ballester, Raquel Quintanilla
Software Mentions: 6
Published: over 5 years ago

10.1002/1878-0261.12707

Classification of diffuse lower‐grade glioma based on immunological profiling
Cited by: 40
Author(s): Fan Wu, Zhiliang Wang, Kuan‐Yu Wang, Guanzhang Li, Rui‐Chao Chai, Yuqing Liu, Haiyan Jiang, You Zhai, Yuemei Feng, Zheng Zhao, Wei Zhang
Software Mentions: 6
Published: over 4 years ago

10.1038/srep31587

Hepatic and serum lipid signatures specific to nonalcoholic steatohepatitis in murine models
Cited by: 33
Author(s): Franck Chiappini, Christophe Desterke, Justine Bertrand‐Michel, Catherine Guettier, François Le Naour
Software Mentions: 5
Published: about 8 years ago

10.3389/fmed.2020.00475

Impact of Gut Microbiome on Hypertensive Patients With Low-Salt Intake: Shika Study Results
Cited by: 7
Author(s): Satoshi Nagase, Shigehiro Karashima, Hiromasa Tsujiguchi, Hirohito Tsuboi, Sakae Miyagi, Mitsuhiro Kometani, Daisuke Aono, Takuya Higashitani, Masashi Demura, Hiroyuki Sakakibara, Akihiro Yoshida, Akinori Hara, Hiroyuki Nakamura, Yoshiyu Takeda, Hidetaka Nambo, Takashi Yoneda, Shigefumi Okamoto
Software Mentions: 5
Published: about 4 years ago

10.3389/fmicb.2018.02721

Compounded Disturbance Chronology Modulates the Resilience of Soil Microbial Communities and N-Cycle Related Functions
Cited by: 14
Author(s): Kadiya Calderón, Laurent Philippot, Florian Bizouard, Marie-Christine Breuil, David Bru, Aymé Spor
Software Mentions: 5
Published: about 6 years ago

10.1186/1471-2105-14-75

virtualArray: a R/bioconductor package to merge raw data from different microarray platforms
Cited by: 51
Author(s): Andreas Heider, Rüdiger Alt
Software Mentions: 5
Published: over 11 years ago

10.1186/1471-2105-11-523

Class prediction for high-dimensional class-imbalanced data
Cited by: 169
Author(s): Rok Blagus, Lara Lusa
Software Mentions: 5
Published: about 14 years ago

10.1186/1756-0500-6-358

Identifying technical aliases in SELDI mass spectra of complex mixtures of proteins
Cited by: 1
Author(s): John C. Whitin, Srinivasa Rangan, Harvey J. Cohen
Software Mentions: 5
Published: about 11 years ago

10.1186/s13058-016-0714-4

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

10.7717/peerj.4584

Empirical evaluation of data normalization methods for molecular classification
Cited by: 12
Author(s): Hsin‐Chieh Huang, Li‐Xuan Qin
Software Mentions: 5
Published: over 6 years ago

10.18632/aging.102278

Association between promoter DNA methylation and gene expression in the pathogenesis of ischemic stroke
Cited by: 20
Author(s): Guo-Xiong Deng, Ning Xu, Qi Huang, Jin-Yue Tan, Zhao Zhang, Xianfeng Li, Jinru Wei
Software Mentions: 5
Published: about 5 years ago

10.1186/s40425-018-0328-8

Distinct predictive biomarker candidates for response to anti-CTLA-4 and anti-PD-1 immunotherapy in melanoma patients
Cited by: 140
Author(s): Priyanka B. Subrahmanyam, Zhiwan Dong, Daniel Gusenleitner, Anita Giobbie‐Hurder, Mariano Severgnini, Jun Zhou, Michael P. Manos, Lauren M. Eastman, Holden T. Maecker, F. Stephen Hodi
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0103514

Identification of a Novel Luminal Molecular Subtype of Breast Cancer
Cited by: 14
Author(s): Anna Dvorkin‐Gheva, John A. Hassell
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0017493

Combining Clinical, Pathological, and Demographic Factors Refines Prognosis of Lung Cancer: A Population-Based Study
Cited by: 22
Author(s): Joseph Putila, Scot C. Remick, Nancy Lan Guo
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pone.0101239

Visualizing Molecular Profiles of Glioblastoma with GBM-BioDP
Cited by: 49
Author(s): Orieta Celiku, Seth Johnson, Shuping Zhao, Kevin Camphausen, Uma Shankavaram
Software Mentions: 4
Published: over 10 years ago

10.1007/s00109-014-1212-8

Transcriptomic profiling facilitates classification of response to influenza challenge
Cited by: 34
Author(s): Emma E Davenport, Richard Antrobus, Patrick Lillie, Sarah C. Gilbert, Julian C. Knight
Software Mentions: 4
Published: about 10 years ago

10.1186/1479-5876-10-185

Whole genome methylation profiles as independent markers of survival in stage IIIC melanoma patients
Cited by: 49
Author(s): Luca Sigalotti, Alessia Covre, Elisabetta Fratta, Giulia Parisi, Paolo Sonego, Francesca Colizzi, Sandra Coral, Samuele Massarut, John M. Kirkwood, Michele Maio
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pone.0109291

Systematic Analysis of Blood Cell Transcriptome in End-Stage Chronic Respiratory Diseases
Cited by: 28
Author(s): Julie Chesné, Richard Danger, K. Botturi, Martine Reynaud‐Gaubert, Sacha Mussot, M. Stern, Isabelle Danner-Boucher, Jean‐François Mornex, Christophe Pison, C. Dromer, Romain Kessler, Marcel Dahan, Olivier Brugière, Jérôme Le Pavec, Frédèric Perros, Marc Humbert, Carine Gomez, Sophie Brouard, A. Magnan
Software Mentions: 4
Published: about 10 years ago

10.7448/IAS.18.5.20479

8th IAS Conference on HIV Pathogenesis, Treatment & Prevention 19-22 July 2015, Vancouver, Canada
Cited by: 9
Author(s):
Software Mentions: 4
Published: over 9 years ago

10.1093/biostatistics/kxv027

Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses
Cited by: 235
Author(s): Vegard Nygaard, Einar Andreas Rødland, Eivind Hovig
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0045178

An Accurate Prostate Cancer Prognosticator Using a Seven-Gene Signature Plus Gleason Score and Taking Cell Type Heterogeneity into Account
Cited by: 30
Author(s): Xin Chen, Shizhong Xu, Michael McClelland, Farah Rahmatpanah, Anne Sawyers, Zhenyu Jia, Dan Mercola
Software Mentions: 3
Published: about 12 years ago

10.1186/s12916-016-0617-3

Human newborn bacille Calmette–Guérin vaccination and risk of tuberculosis disease: a case-control study
Cited by: 47
Author(s): Helen A. Fletcher, Ali Filali‐Mouhim, Elisa Nemes, Anthony Hawkridge, Alana Keyser, Samuel Njikan, Mark Hatherill, Thomas J. Scriba, Brian Abel, Benjamin M. Kagina, Ashley Veldsman, Nancy Marín Agudelo, Gilla Kaplan, Gregory Hussey, Rafick‐Pierre Sékaly, Willem A. Hanekom
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0034247

Cell Cycle Gene Networks Are Associated with Melanoma Prognosis
Cited by: 32
Author(s): Li Wang, Daniel Hurley, Wendy Watkins, Hiromitsu Araki, Yoshinori Tamada, Anita Muthukaruppan, Louis Ranjard, Eliane Derkac, Seiya Imoto, Satoru Miyano, Edmund J. Crampin, Cristin G. Print
Software Mentions: 3
Published: over 12 years ago

10.1186/1755-8794-1-42

The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets – improving meta-analysis and prediction of prognosis
Cited by: 127
Author(s): Andrew H. Sims, Graeme J. Smethurst, Yvonne Hey, Michał Okoniewski, Stuart D Pepper, Anthony Howell, Crispin Miller, Robert B. Clarke
Software Mentions: 3
Published: about 16 years ago

10.1371/journal.pone.0198874

Whole blood transcriptome analysis in amyotrophic lateral sclerosis: A biomarker study
Cited by: 35
Author(s): Wouter van Rheenen, Frank P. Diekstra, Oliver Harschnitz, Henk Jan Westeneng, Kristel R. van Eijk, Christiaan G J Saris, Ewout J N Groen, Michael A. van Es, Hylke M. Blauw, Paul W.J. van Vught, Jan H. Veldink, Leonard H van den Berg
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2105-6-265

Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes
Cited by: 206
Author(s): Patrick Warnat, Roland Eils, Benedikt Brors
Software Mentions: 3
Published: about 19 years ago

10.1371/journal.pone.0039932

Using Rule-Based Machine Learning for Candidate Disease Gene Prioritization and Sample Classification of Cancer Gene Expression Data
Cited by: 99
Author(s): Enrico Glaab, Jaume Bacardit, Jonathan M. Garibaldi, Natalio Krasnogor
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2105-9-337

Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands
Cited by: 15
Author(s): Wei Dai, Jens M. Teodoridis, Janet Graham, Constanze Zeller, Tim Hui-Ming Huang, Pearlly S. Yan, J. Keith Vass, Robert E. Brown, Jim Paul
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2164-14-102

Biclustering reveals breast cancer tumour subgroups with common clinical features and improves prediction of disease recurrence
Cited by: 26
Author(s): Yi Kan Wang, Cristin G. Print, Edmund J. Crampin
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12864-019-5997-2

HetEnc: a deep learning predictive model for multi-type biological dataset
Cited by: 5
Author(s): Leihong Wu, Xiangwen Liu, Joshua Xu
Software Mentions: 2
Published: over 5 years ago

10.1186/1755-8794-4-30

Identification of SERPINA1 as single marker for papillary thyroid carcinoma through microarray meta analysis and quantification of its discriminatory power in independent validation
Cited by: 41
Author(s): Klemens Vierlinger, Markus Mansfeld, Oskar Koperek, Christa Nöhammer, Klaus Kaserer, Friedrich Leisch
Software Mentions: 2
Published: over 13 years ago

10.7717/peerj.9440

Exploring the classification of cancer cell lines from multiple omic views
Cited by: 6
Author(s): Xisheng Yang, Yao Wen, Xinyu Song, Song He, Xiaochen Bo
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pgen.1000142

Efficient Genetic Method for Establishing Drosophila Cell Lines Unlocks the Potential to Create Lines of Specific Genotypes
Cited by: 55
Author(s): Amanda Simcox, Srabani Mitra, Sharon L. Truesdell, Litty Paul, Ting Chen, Jonathan P. Butchar, Steven E. Justiniano
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0243935

Development and validation of a NanoString BASE47 bladder cancer gene classifier
Cited by: 7
Author(s): Jordan Kardos, Tracy L. Rose, Ujjawal Manocha, Sara E. Wobker, Jeffrey S. Damrauer, Trinity J. Bivalaqua, Max Kates, Kristin J. Moore, Joel S. Parker, William Y. Kim
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0064543

A New Algorithm for Integrated Analysis of miRNA-mRNA Interactions Based on Individual Classification Reveals Insights into Bladder Cancer
Cited by: 32
Author(s): Nikolai Hecker, Carsten Stephan, Hans-Joachim Mollenkopf, Klaus Jung, Robert Preißner, Hellmuth-A. Meyer
Software Mentions: 2
Published: over 11 years ago

10.3389/fmicb.2016.00775

Ecotoxicological Impact of the Bioherbicide Leptospermone on the Microbial Community of Two Arable Soils
Cited by: 26
Author(s): Sana Romdhane, Marion Devers‐Lamrani, Lise Barthelmebs, Christophe Calvayrac, Cédric Bertrand, Jean‐François Cooper, Franck E. Dayan, Fabrice Martin-Laurent
Software Mentions: 2
Published: over 8 years ago

10.3389/fonc.2019.01281

A Diagnostic Panel of DNA Methylation Biomarkers for Lung Adenocarcinoma
Cited by: 30
Author(s): Nan Shen, Jie Du, Hui Zhou, Nan Chen, Yi Pan, Jörg D. Hoheisel, Zonghui Jiang, Ling Xiao, Yue Tao, Xi Mo
Software Mentions: 2
Published: almost 5 years ago

10.1186/gb-2006-7-12-r121

Cited by: 19
Author(s): Hojin Moon, Hongshik Ahn, Ralph L. Kodell, Chiao‐Wen Lin, Songjoon Baek, James J. Chen
Software Mentions: 2
Published: almost 19 years ago

10.1186/1756-9966-28-149

Comparison of linear discriminant analysis methods for the classification of cancer based on gene expression data
Cited by: 33
Author(s): Desheng Huang, Quan Yu, Miao He, Baosen Zhou
Software Mentions: 2
Published: almost 15 years ago

10.3390/ijms20194867

iPSC-Derived Embryoid Bodies as Models of c-Met-Mutated Hereditary Papillary Renal Cell Carcinoma
Cited by: 19
Author(s): Jin Wook Hwang, Christophe Desterke, Olivier Féraud, Stéphane Richard, Sophie Ferlicot, Virginie Verkarre, Jean Jacques Patard, Julien Loisel‐Duwattez, Adlen Foudi, Frank Griscelli, Annelise Bennaceur-Griscelli, Ali G. Turhan
Software Mentions: 1
Published: about 5 years ago

10.1186/s13148-017-0331-9

DNA methylation signatures for 2016 WHO classification subtypes of diffuse gliomas
Cited by: 22
Author(s): Yashna Paul, Baisakhi Mondal, Vikas Patil, Kumaravel Somasundaram
Software Mentions: 1
Published: over 7 years ago

10.1186/s40478-020-01066-6

Clinical and mutational profiles of adult medulloblastoma groups
Cited by: 27
Author(s): Gabriel Chun-Hei Wong, Kay Ka‐Wai Li, Weiwei Wang, Anthony Pak-Yin Liu, Queenie Jun-Qi Huang, Aden Ka-Yin Chan, Manix Fung‐Man Poon, Nellie Yuk‐Fei Chung, Queenie Hoi‐Wing Wong, Hong Chen, Danny Tat Ming Chan, Xianzhi Liu, Ying Mao, Zhenyu Zhang, Zhifeng Shi, Ho‐Keung Ng
Software Mentions: 1
Published: almost 4 years ago

10.7150/thno.40944

Dissecting the heterogeneity of the alternative polyadenylation profiles in triple-negative breast cancers
Cited by: 25
Author(s): Lei Wang, Guan-Tian Lang, Mengzhu Xue, Yang Liu, Li Chen, Ling Yao, Xiaoguang Li, Peng Wang, Xin Hu, Zhi‐Ming Shao
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2105-5-180

Cited by: 42
Author(s): Neal Jeffries
Software Mentions: 1
Published: almost 21 years ago

10.1371/journal.pone.0014758

Effect of Xpcl1 Activation and p27Kip1 Loss on Gene Expression in Murine Lymphoma
Cited by: 7
Author(s): Daniel A. Kuppers, Harry C. Hwang, Aimee L. Jackson, Peter S. Linsley, Bruce E. Clurman, Matthew L. Fero
Software Mentions: 1
Published: over 13 years ago

10.1186/1755-8794-4-66

mRNA expression profiles of primary high-grade central osteosarcoma are preserved in cell lines and xenografts
Cited by: 31
Author(s): Marieke L. Kuijjer, Heidi M. Namløs, Esther Hauben, Isidro Machado, Stine H. Kresse, Massimo Serra, Antonio Llombart‐Bosch, Pancras C.W. Hogendoorn, Leonardo A. Meza‐Zepeda, Ola Myklebost, Anne Marie Cleton-Jansen
Software Mentions: 1
Published: about 13 years ago

10.1155/2017/7687851

Metabolic Footprints and Molecular Subtypes in Breast Cancer
Cited by: 48
Author(s): Vera Cappelletti, Egidio Iorio, Patrizia Miodini, M. Silvestri, Matteo Dugo, Maria Grazia Daidone
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-5945-10-1

Personalized medicine in psoriasis: developing a genomic classifier to predict histological response to Alefacept
Cited by: 40
Author(s): Mayte Suárez‐Fariñas, Kejal R. Shah, Asifa Haider, James G. Krueger, Michelle A. Lowes
Software Mentions: 1
Published: over 14 years ago

10.1016/j.dib.2015.08.013

A predictive toxicogenomics signature to classify genotoxic versus non-genotoxic chemicals in human TK6 cells
Cited by: 19
Author(s): Andrew Williams, Julie K. Buick, Ivy D. Moffat, Carol D. Swartz, Leslie Recio, Daniel R. Hyduke, Heng‐Hong Li, Albert J. Fornace, Jiri Aubrecht, Carole L. Yauk
Software Mentions: 1
Published: almost 9 years ago

Projects: cran: pamr

Papers Mentioning pamr 63