bioconductor: frma | Projects | Ecosyste.ms: Papers

10.1186/s12920-015-0114-0

Integrated network analysis and logistic regression modeling identify stage-specific genes in Oral Squamous Cell Carcinoma
Cited by: 12
Author(s): Vinay Randhawa, Vishal Acharya
Software Mentions: 17
Published: over 9 years ago

10.1038/s41597-021-00998-5

A merged microarray meta-dataset for transcriptionally profiling colorectal neoplasm formation and progression
Cited by: 4
Author(s): Michael Rohr, Jordan M. Beardsley, Sai Preethi Nakkina, Xiang Zhu, Jihad Aljabban, Dexter Hadley, Deborah A. Altomare
Software Mentions: 17
Published: about 3 years ago

10.1002/1878-0261.12389

Using microarray‐based subtyping methods for breast cancer in the era of high‐throughput RNA sequencing
Cited by: 6
Author(s): Christina Bligaard Pedersen, Finn C. Nielsen, Maria Rossing, Lars Rønn Olsen
Software Mentions: 7
Published: about 6 years ago

10.1186/s12864-017-4167-7

SaVanT: a web-based tool for the sample-level visualization of molecular signatures in gene expression profiles
Cited by: 30
Author(s): David Lopez, Dennis Montoya, Michael Ambrose, Larry Lam, Leah Briscoe, Claire Adams, Robert L. Modlin, Matteo Pellegrini
Software Mentions: 7
Published: about 7 years ago

10.1186/1471-2164-14-14

Quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity
Cited by: 26
Author(s): Katie S Viljoen, Jonathan M. Blackburn
Software Mentions: 6
Published: almost 12 years ago

10.1371/journal.pone.0102579

Genomic Models of Short-Term Exposure Accurately Predict Long-Term Chemical Carcinogenicity and Identify Putative Mechanisms of Action
Cited by: 60
Author(s): Daniel Gusenleitner, Scott S. Auerbach, Tisha Melia, Harold F. Gómez, David H. Sherr, Stefano Monti
Software Mentions: 5
Published: over 10 years ago

10.18632/oncotarget.25218

Comprehensive identification of long noncoding RNAs in colorectal cancer
Cited by: 15
Author(s): Eric James de Bony, Martin Bizet, Olivier Van Grembergen, Bouchra Hassabi, Emilie Calonne, Pascale Putmans, Gianluca Bontempi, François Fuks
Software Mentions: 5
Published: over 6 years ago

10.1186/s13062-015-0051-z

Test on existence of histology subtype-specific prognostic signatures among early stage lung adenocarcinoma and squamous cell carcinoma patients using a Cox-model based filter
Cited by: 25
Author(s): Suyan Tian, Chi Wang, Ming-Wen An
Software Mentions: 5
Published: over 9 years ago

10.1136/annrheumdis-2020-217646

Unique expansion of IL-21+ Tfh and Tph cells under control of ICOS identifies Sjögren’s syndrome with ectopic germinal centres and MALT lymphoma
Cited by: 75
Author(s): Elena Pontarini, William Murray-Brown, Cristina Croia, Davide Lucchesi, James Conway, Felice Rivellese, Liliane Fossati-Jimack, Elisa Astorri, Edoardo Prediletto, Elisa Corsiero, Francesca Romana Delvecchio, Rachel Coleby, Eva Gelbhardt, Aurora Bono, Chiara Baldini, Ilaria Puxeddu, Piero Ruscitti, Roberto Giacomelli, Francesca Barone, Benjamin A Fisher, Simon Bowman, Serena Colafrancesco, Roberta Priori, Nurhan Sutcliffe, S. J. Challacombe, Gianluca Carlesso, Anwar R. Tappuni, Costantino Pitzalis, Michèle Bombardieri
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-017-1536-9

Network-based analysis of transcriptional profiles from chemical perturbations experiments
Cited by: 11
Author(s): Francesca Mulas, Amy Li, David H. Sherr, Stefano Monti
Software Mentions: 4
Published: over 7 years ago

10.3389/fonc.2020.610513

Tumor Immune Microenvironment Characterization in Hepatocellular Carcinoma Identifies Four Prognostic and Immunotherapeutically Relevant Subclasses
Cited by: 15
Author(s): Xingxing Gao, Hechen Huang, Yübo Wang, Caixu Pan, Shengyong Yin, Lin Zhou, Shusen Zheng
Software Mentions: 4
Published: over 3 years ago

10.1038/s41416-020-01252-2

Discovery of a biomarker candidate for surgical stratification in high-grade serous ovarian cancer
Cited by: 10
Author(s): Haonan Lu, Paula Cunnea, Katherine Nixon, Natasha Rinne, Eric O. Aboagye, Christina Fotopoulou
Software Mentions: 3
Published: almost 4 years ago

10.3389/fphys.2015.00410

Benchmarking Procedures for High-Throughput Context Specific Reconstruction Algorithms
Cited by: 22
Author(s): Maria Pires Pacheco, Thomas Pfau, Thomas Sauter
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-244X-13-213

Systematic review of genome-wide gene expression studies of bipolar disorder
Cited by: 66
Author(s): Fayaz Seifuddin, Mehdi Pirooznia, Jennifer Judy, Fernando S. Goes, James B. Potash, Peter P. Zandi
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2105-12-369

Thawing Frozen Robust Multi-array Analysis (fRMA)
Cited by: 38
Author(s): Matthew N. McCall, Rafael A. Irizarry
Software Mentions: 3
Published: about 13 years ago

10.3390/cancers12051090

Integrative Transcriptome Analyses of the Human Fallopian Tube: Fimbria and Ampulla—Site of Origin of Serous Carcinoma of the Ovary
Cited by: 12
Author(s): Ramlogan Sowamber, Omar L. Nelson, Leah V. Dodds, Victoria Decastro, Iru Paudel, Anca Milea, Michael Considine, Leslie Cope, André Pinto, Matthew Schlumbrecht, Brian M. Slomovitz, Patricia Shaw, Sophia George
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0161967

CYR61 and TAZ Upregulation and Focal Epithelial to Mesenchymal Transition May Be Early Predictors of Barrett’s Esophagus Malignant Progression
Cited by: 6
Author(s): Joana Cardoso, Marta Mesquita, António Dias Pereira, Mónica Bettencourt-Dias, Paula Chaves, José B. Pereira-Leal
Software Mentions: 3
Published: about 8 years ago

10.1186/gb-2012-13-11-r104

InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor
Cited by: 41
Author(s): Alain Coletta, Colin Molter, Robin Duqué, David Steenhoff, Jonatan Taminau, Virginie de Schaetzen, Stijn Meganck, Cosmin Lazar, David Venet, Vincent Detours, Ann Nowé, Hugues Bersini, David Solis
Software Mentions: 3
Published: almost 13 years ago

10.1186/1471-2105-13-272

Gene expression anti-profiles as a basis for accurate universal cancer signatures
Cited by: 43
Author(s): Héctor Corrada Bravo, Vasyl Pihur, Matthew N. McCall, Rafael A. Irizarry, Jeffrey T. Leek
Software Mentions: 2
Published: about 12 years ago

10.1038/cddis.2016.224

Exosome-mediated delivery of miR-9 induces cancer-associated fibroblast-like properties in human breast fibroblasts
Cited by: 221
Author(s): Sara Baroni, Sandra Romero-Córdoba, Ilaria Plantamura, Matteo Dugo, Elvira D’Ippolito, Alessandra Cataldo, Giulia Cosentino, Valentina Angeloni, Anna Rossini, Maria Grazia Daidone, Marilena V. Iorio
Software Mentions: 2
Published: over 8 years ago

10.1038/srep40508

Inference of immune cell composition on the expression profiles of mouse tissue
Cited by: 110
Author(s): Ziyi Chen, Anfei Huang, Jiya Sun, Taijiao Jiang, F. Xiao-Feng Qin, Aiping Wu
Software Mentions: 2
Published: almost 8 years ago

10.3389/fncel.2015.00075

The neural stem cell fate determinant TRIM32 regulates complex behavioral traits
Cited by: 18
Author(s): Anna-Lena Hillje, Elisabeth Beckmann, Maria Angeliki S. Pavlou, Christian Jaeger, Maria Pires Pacheco, Thomas Sauter, Jens Christian Schwamborn, Lars Lewejohann
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0157368

Refinement of Triple-Negative Breast Cancer Molecular Subtypes: Implications for Neoadjuvant Chemotherapy Selection
Cited by: 847
Author(s): Brian D. Lehmann, Bojana Jovanović, Xi Chen, Mónica V. Estrada, Kimberly N. Johnson, Yu Shyr, Harold L. Moses, Melinda E. Sanders, Jennifer A. Pietenpol
Software Mentions: 1
Published: over 8 years ago

10.1186/s13058-017-0871-0

The footprint of the ageing stroma in older patients with breast cancer
Cited by: 20
Author(s): Barbara Brouwers, Debora Fumagalli, Sylvain Brohée, Sigrid Hatse, Olivier Govaere, Giuseppe Floris, Kathleen Van den Eynde, Yacine Barèche, Patrick Schöffski, Ann Smeets, Patrick Neven, Diether Lambrechts, Christos Sotiriou, Hans Wildiers
Software Mentions: 1
Published: over 7 years ago

10.3389/fphar.2021.715721

Global Pattern of CD8+ T-Cell Infiltration and Exhaustion in Colorectal Cancer Predicts Cancer Immunotherapy Response
Cited by: 8
Author(s): Sun Tian, Fulong Wang, Rongxin Zhang, Gong Chen
Software Mentions: 1
Published: about 3 years ago

Ecosyste.ms: Papers

Projects: bioconductor: frma

Papers Mentioning frma 26