bioconductor: affy | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1000227

Analyzing ChIP-chip Data Using Bioconductor
Cited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Software Mentions: 39
Published: almost 16 years ago

ADAGE signature analysis: differential expression analysis with data-defined gene sets
Cited by: 15
Author(s): Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
Software Mentions: 25
Published: about 7 years ago

10.1371/journal.pcbi.1007792

eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research
Cited by: 38
Author(s): Augusto Anguita‐Ruiz, Alberto Segura‐Delgado, Rafael Alcalá, Concepción M. Aguilera, Jesús Alcalá‐Fdez
Software Mentions: 23
Published: over 4 years ago

10.1002/1878-0261.12960

KRAS mutant rectal cancer cells interact with surrounding fibroblasts to deplete the extracellular matrix
Cited by: 6
Author(s): Jin K. Kim, Michael R. Marco, Seo‐Hyun Choi, Xuan Qu, Chin-Tung Chen, Moshe Elkabets, Lauren Fairchild, Oliver Chow, Francisco M. Barriga, Lukas E. Dow, Kevin P. O’Rourke, Bryan Szeglin, Dmitry Yarilin, Sho Fujisawa, Katia Manova‐Todorova, Philip B. Paty, Jinru Shia, Christina Leslie, J. Joshua Smith, Scott W. Lowe, Raphael Pelossof, Francisco Sánchez-Vega, Julio García-Aguilar
Software Mentions: 18
Published: over 3 years ago

10.1186/s12859-018-2351-7

wTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool
Cited by: 36
Author(s): Deisy Morselli Gysi, André Voigt, Tiago de Miranda Fragoso, Eivind Almaas, Katja Nowick
Software Mentions: 17
Published: about 6 years ago

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

10.15252/msb.20188636

Unsupervised identification of disease states from high‐dimensional physiological and histopathological profiles
Cited by: 11
Author(s): Kenichi Shimada, Timothy J. Mitchison
Software Mentions: 17
Published: almost 6 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: over 3 years ago

10.3389/fonc.2021.690129

A Tumor Progression Related 7-Gene Signature Indicates Prognosis and Tumor Immune Characteristics of Gastric Cancer
Cited by: 6
Author(s): Fen Liu, Zongcheng Yang, Lixin Zheng, Wei Shao, Xiujie Cui, Yue Wang, Jihui Jia, Yue Fu
Software Mentions: 16
Published: over 3 years ago

10.1186/s13072-020-00342-y

ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation
Cited by: 39
Author(s): Jake J. Reske, Mike R. Wilson, Ronald L. Chandler
Software Mentions: 14
Published: over 4 years ago

10.1186/s12967-021-02952-w

Molecular subtype identification and prognosis stratification by a metabolism-related gene expression signature in colorectal cancer
Cited by: 20
Author(s): Daowei Lin, Wenhua Fan, Rongxin Zhang, Enen Zhao, Pansong Li, Wenhao Zhou, Jianhong Peng, Liren Li
Software Mentions: 14
Published: over 3 years ago

10.3389/fimmu.2019.02887

Meta-Analysis of in vitro-Differentiated Macrophages Identifies Transcriptomic Signatures That Classify Disease Macrophages in vivo
Cited by: 29
Author(s): Hung Jen Chen, Andrew Y. Li Yim, Guillermo R. Griffith, Wouter J. de Jonge, Marcel M.A.M. Mannens, Enrico Ferrero, Peter Henneman, Menno P.J. de Winther
Software Mentions: 13
Published: almost 5 years ago

10.1186/s12859-021-04268-4

A comprehensive database for integrated analysis of omics data in autoimmune diseases
Cited by: 10
Author(s): Jordi Martorell-Marugán, Raúl López-Domínguez, Adrián García-Moreno, Daniel Toro-Domínguez, Juan Antonio Villatoro-García, Guillermo Barturen, Adoración Martín-Gómez, Kevin Troulé, Gonzalo Gómez‐López, Fátima Al‐Shahrour, Víctor González‐Rumayor, María Peña‐Chilet, Joaquín Dopazo, Julio Sáez-Rodríguez, Marta E. Alarcón‐Riquelme, Pedro Carmona-Sáez
Software Mentions: 13
Published: over 3 years ago

10.1038/s42003-021-01842-7

Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer
Cited by: 35
Author(s): Ling Cai, Hongyu Liu, Fang Huang, Junya Fujimoto, Luc Girard, Jun Chen, Yongwen Li, Yu An Zhang, Dhruba Deb, Victor Stastny, Karine Pozo, Christin S. Kuo, Gaoxiang Jia, Chendong Yang, Wei Zou, Adeeb Alomar, Kenneth E. Huffman, Mahboubeh Papari-Zareei, Lin Yang, Benjamin J. Drapkin, Esra A. Akbay, David S. Shames, Ignacio I. Wistuba, Tao Wang, Jane E. Johnson, Guanghua Xiao, Ralph J. DeBerardinis, John D. Minna, Yang Xie, Adi F. Gazdar
Software Mentions: 13
Published: over 3 years ago

10.1186/1748-7188-4-7

Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity
Cited by: 71
Author(s): Koji Kadota, Yuji Nakai, Kentaro Shimizu
Software Mentions: 13
Published: over 15 years ago

10.1186/1471-2164-14-46

Systems infection biology: a compartmentalized immune network of pig spleen challenged with Haemophilus parasuis
Cited by: 9
Author(s): Ming Zhao, Xiangdong Liu, Xinyun Li, Hongbo Chen, Hui Jin, Rui Zhou, Mengjin Zhu, Shuhong Zhao
Software Mentions: 13
Published: almost 12 years ago

10.3389/fneur.2020.579683

Development and Validation of a Five-Gene Signature to Predict Relapse-Free Survival in Multiple Sclerosis
Cited by: 6
Author(s): Fei Ye, Jie Liang, Jiaoxing Li, Haiyan Li, Wenli Sheng
Software Mentions: 13
Published: almost 4 years ago

10.3390/cancers11010091

The Potential Mechanism of Bufadienolide-Like Chemicals on Breast Cancer via Bioinformatics Analysis
Cited by: 5
Author(s): Yingbo Zhang, Xiaomin Tang, Yuxin Pang, Luqi Huang, Dan Wang, Chao Yuan, Xuan Hu, Liping Qu
Software Mentions: 13
Published: almost 6 years ago

10.18632/aging.202317

Identification and validation of an immune-related gene signature predictive of overall survival in colon cancer
Cited by: 33
Author(s): Xuening Zhang, Hao Zhao, Xiaoguang Shi, Xiaocan Jia, Yongli Yang
Software Mentions: 12
Published: almost 4 years ago

10.1002/cam4.2786

FOLFOX treatment response prediction in metastatic or recurrent colorectal cancer patients via machine learning algorithms
Cited by: 24
Author(s): Wei Lu, Dongliang Fu, Xianglong Kong, Zhiheng Huang, Maxwell Hwang, Yaowu Zhu, Liubo Chen, Kai Jiang, Xinlin Li, Yihua Wu, Jun Li, Ying Yuan, Kefeng Ding
Software Mentions: 12
Published: almost 5 years ago

10.1007/s12032-017-0963-9

The identification of key genes and pathways in hepatocellular carcinoma by bioinformatics analysis of high-throughput data
Cited by: 107
Author(s): Chaoyang Zhang, Li Peng, Yaqin Zhang, Zhaoyang Liu, Wenling Li, Shilian Chen, Guancheng Li
Software Mentions: 12
Published: over 7 years ago

10.1186/1471-2105-11-194

Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data
Cited by: 32
Author(s): Benedikt Zacher, Pei Fen Kuan, Achim Tresch
Software Mentions: 12
Published: over 14 years ago

10.1371/journal.pone.0204123

Prediction of early breast cancer patient survival using ensembles of hypoxia signatures
Cited by: 8
Author(s): Inna Y. Gong, Natalie S. Fox, Vincent Huang, Paul C. Boutros
Software Mentions: 12
Published: about 6 years ago

10.1111/jcmm.16605

Leptin receptor is a key gene involved in the immunopathogenesis of thyroid‐associated ophthalmopathy
Cited by: 3
Author(s): Ziyi Chen, Zhe Chen, Jingya Wang, Meng Zhang, Xiaofei Wang, Deji Cuomu, Bingyin Shi, Yue Wang
Software Mentions: 12
Published: over 3 years ago

10.3389/fphar.2021.726529

CD3D, GZMK, and KLRB1 Are Potential Markers for Early Diagnosis of Rheumatoid Arthritis, Especially in Anti-Citrullinated Protein Antibody-Negative Patients
Cited by: 8
Author(s): Junqin Lu, Yihui Bi, Yapeng Zhu, Hanyu Shi, Wenxiu Duan, Jian Zhou
Software Mentions: 12
Published: about 3 years ago

10.3390/diagnostics10020066

Identification of Key Biomarkers in Bladder Cancer: Evidence from a Bioinformatics Analysis
Cited by: 22
Author(s): Chuan Zhang, Mandy Berndt‐Paetz, Jochen Neuhaus
Software Mentions: 12
Published: almost 5 years ago

10.1016/j.ccell.2017.08.017

Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma
Cited by: 662
Author(s): Alan Mackay, Anna Burford, Diana Carvalho, Elisa Izquierdo, Janat Fazal-Salom, Kathryn R. Taylor, Lynn Bjerke, Matthew Clarke, Maria Vinci, Meera Nandhabalan, Sara Temelso, Sergey Popov, Valeria Molinari, Pichai Raman, Angela J. Waanders, Harry Han, Saumya Gupta, Lynley V. Marshall, Stergios Zacharoulis, Sucheta Vaidya, Henry Mandeville, Leslie Bridges, Andrew Martin, Safa Al‐Sarraj, Christopher Chandler, Ho Keung Ng, Xingang Li, Kun Mu, Saoussen Trabelsi, Dorra H’mida-Ben Brahim, Alexei N. Kisljakov, Д. М. Коновалов, Andrew S. Moore, Ángel M. Carcaboso, Mariona Suñol, Carmen de Torres, Ofelia Cruz, Jaume Mora, Л. И. Шац, João N. Stávale, Lucas Tadeu Bidinotto, Rui Manuel Reis, Natacha Entz‐Werlé, Michael Farrell, Jane Cryan, Darach Crimmins, John Caird, Jane Pears, Michelle Monje, Marie‐Anne Debily, David Castel, Jacques Grill, Cynthia Hawkins, Hamid Nikbakht, Nada Jabado, Suzanne J. Baker, Stefan M. Pfister, David Jones, Maryam Fouladi, André O. von Bueren, Michael Baudis, Adam Resnick, Chris Jones
Software Mentions: 11
Published: about 7 years ago

10.1186/s12935-021-02041-4

Ten-gene signature reveals the significance of clinical prognosis and immuno-correlation of osteosarcoma and study on novel skeleton inhibitors regarding MMP9
Cited by: 17
Author(s): Weihang Li, Ziyi Ding, Dong Wang, Chengfei Li, Yikai Pan, Yingjing Zhao, Hongzhe Zhao, Tianxing Lu, Rui Xu, Shilei Zhang, Bin Yuan, Yunlong Zhao, Yanjiang Yin, Yuan Gao, Jing Li, Ming Yan
Software Mentions: 11
Published: over 3 years ago

10.1534/g3.120.401270

Application of Transcriptional Gene Modules to Analysis of <i>Caenorhabditis elegans</i>’ Gene Expression Data
Cited by: 7
Author(s): Michael Cary, Katie Podshivalova, Cynthia Kenyon
Software Mentions: 11
Published: about 4 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

10.1002/1878-0261.12117

Recurrence-associated gene signature optimizes recurrence-free survival prediction of colorectal cancer
Cited by: 37
Author(s): Xianglong Tian, Xiaoqiang Zhu, Tingting Yan, Chuangqi Yu, Chaoqin Shen, Ye Hu, Jie Hong, Haoyan Chen, Jing‐Yuan Fang
Software Mentions: 11
Published: about 7 years ago

10.3389/fonc.2020.00691

Immunoscore Predicts Survival in Early-Stage Lung Adenocarcinoma Patients
Cited by: 12
Author(s): Zihuan Zhao, Dan Zhao, Jianguo Xia, Yichuan Wang, Buhai Wang
Software Mentions: 11
Published: over 4 years ago

10.1111/jcmm.15939

Prognostic value and immune cell infiltration of hypoxic phenotype‐related gene signatures in glioblastoma microenvironment
Cited by: 10
Author(s): Kai Xiao, Jun Tan, Jian Yuan, Gang Peng, Wenyong Long, Jun Su, Yao Xiao, Qian Xiao, Changwu Wu, Chaoying Qin, Lili Hu, Kaili Liu, Shunlian Liu, Hao Zhou, Yichong Ning, Xiaojuan Ding, Qing Liu
Software Mentions: 11
Published: about 4 years ago

10.3390/diagnostics10030171

GRB10 and E2F3 as Diagnostic Markers of Osteoarthritis and Their Correlation with Immune Infiltration
Cited by: 56
Author(s): Yajun Deng, Enhui Ren, Wenhua Yuan, Guang-Zhi Zhang, Zhi-Xi Wu, Qiqi Xie
Software Mentions: 11
Published: over 4 years ago

10.1186/1756-0500-3-81

Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays
Cited by: 17
Author(s): Colin S. Gillespie, Guiyuan Lei, Richard J. Boys, Amanda Greenall, Darren J. Wilkinson
Software Mentions: 11
Published: over 14 years ago

10.1186/1471-2105-7-509

CoXpress: differential co-expression in gene expression data
Cited by: 149
Author(s): Michael Watson
Software Mentions: 11
Published: about 18 years ago

10.1016/j.cels.2018.09.003

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency
Cited by: 56
Author(s): Aleksandra Pękowska, Bernd Klaus, Wanqing Xiang, Jacqueline Severino, Nathalie Daigle, Felix A. Klein, Małgorzata Oleś, Rafael Casellas, Jan Ellenberg, Lars M. Steinmetz, Paul Bertone, Wolfgang Huber
Software Mentions: 11
Published: about 6 years ago

10.7554/eLife.64846

NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1
Cited by: 36
Author(s): Carolina Marques, Thomas Unterkircher, Paula Kroon, Barbara Oldrini, Annalisa Izzo, Yuliia Dramaretska, Roberto Ferrarese, Eva Kling, Oliver Schnell, Sven Nelander, Erwin F. Wagner, Latifa Bakiri, Gaetano Gargiulo, Maria Stella Carro, Massimo Squatrito
Software Mentions: 11
Published: over 3 years ago

10.3389/fonc.2014.00147

An Integrative Analysis of Meningioma Tumors Reveals the Determinant Genes and Pathways of Malignant Transformation
Cited by: 7
Author(s): José Carlos Iglesias Gómez, Adrián Mosquera Orgueira
Software Mentions: 11
Published: over 10 years ago

10.1186/s40246-019-0226-2

Size matters: how sample size affects the reproducibility and specificity of gene set analysis
Cited by: 28
Author(s): Farhad Maleki, Katie Ovens, Ian McQuillan, Anthony Kusalik
Software Mentions: 10
Published: about 5 years ago

10.3389/fgene.2020.586602

Multi-Approach Bioinformatics Analysis of Curated Omics Data Provides a Gene Expression Panorama for Multiple Cancer Types
Cited by: 13
Author(s): Bruno César Feltes, Joice de Faria Poloni, Itamar José Guimarães Nunes, Sara Socorro Faria, Márcio Dorn
Software Mentions: 10
Published: about 4 years ago

10.1371/journal.pone.0224750

Gene expression microarray public dataset reanalysis in chronic obstructive pulmonary disease
Cited by: 3
Author(s): Lavida R. K. Rogers, Madison Verlinde, George I. Mias
Software Mentions: 10
Published: about 5 years ago

10.3389/fcell.2021.649265

Multi-Omics Analysis of Anlotinib in Pancreatic Cancer and Development of an Anlotinib-Related Prognostic Signature
Cited by: 4
Author(s): Xi Zhang, Yang Liu, Zhen Zhang, Juan Tan, Junjun Zhang, Hao Ou, Jie Li, Zewen Song
Software Mentions: 10
Published: over 3 years ago

10.1002/embj.201386825

Key regulators control distinct transcriptional programmes in blood progenitor and mast cells
Cited by: 48
Author(s): Fernando J. Calero-Nieto, Felicia Ng, Nicola K. Wilson, Rebecca Hannah, Victoria Moignard, Ana Leal-Cervantes, Isabel Jimenez-Madrid, Evangelia Diamanti, Lorenz Wernisch, Berthold Göttgens
Software Mentions: 10
Published: over 10 years ago

10.3389/fcell.2021.722841

Classification of Estrogen Receptor-Positive Breast Cancer Based on Immunogenomic Profiling and Validation at Single-Cell Resolution
Cited by: 0
Author(s): Xianxiong Ma, Hengyu Chen, Ming Yang, Zunxiang Ke, Mengyi Wang, Tao Huang, Lei Li
Software Mentions: 10
Published: about 3 years ago

10.1186/gb-2004-5-10-r80

Cited by: 10,848
Author(s): Robert Gentleman, Vincent J. Carey, Douglas M. Bates, Benjamin M. Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Maria Iacus, Rafael A. Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony Rossini, Günther Sawitzki, Colin A. Smith, Gordon K. Smyth, Luke Tierney, Jean Yee Hwa Yang, Jianhua Zhang
Software Mentions: 10
Published: almost 21 years ago

10.1155/2021/2191709

Establishment of an Immune-Related Gene Signature for Risk Stratification for Patients with Glioma
Cited by: 2
Author(s): Jiaxue He, Chun Zeng, Yong Long
Software Mentions: 10
Published: about 3 years ago

10.1186/1471-2105-8-457

GEDI: a user-friendly toolbox for analysis of large-scale gene expression data
Cited by: 11
Author(s): André Fujita, João Ricardo Sato, Carlos Eduardo Ferreira, Mari Cleide Sogayar
Software Mentions: 10
Published: about 17 years ago

10.3389/fgene.2021.692953

Identification of the Real Hub Gene and Construction of a Novel Prognostic Signature for Pancreatic Adenocarcinoma Based on the Weighted Gene Co-expression Network Analysis and Least Absolute Shrinkage and Selection Operator Algorithms
Cited by: 15
Author(s): Qihang Yuan, Jie Ren, Zhizhou Wang, Ji Li, Dawei Deng, Dong Shang
Software Mentions: 10
Published: over 3 years ago

10.7717/peerj.1845

A molecular classification of human mesenchymal stromal cells
Cited by: 42
Author(s): Florian Rohart, Elizabeth A. Mason, Nicholas Matigian, Rowland Mosbergen, Othmar Korn, Tyrone Chen, Suzanne Butcher, Jatin Patel, Kerry Atkinson, Kiarash Khosrotehrani, Nicholas M. Fisk, Kim‐Anh Lê Cao, Christine A. Wells
Software Mentions: 10
Published: over 8 years ago

10.1155/2008/147563

Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data: Tools for the First Steps
Cited by: 6
Author(s): Grier P. Page, Issa Coulibaly
Software Mentions: 10
Published: over 16 years ago

10.1111/jcmm.14918

An outcome model for human bladder cancer: A comprehensive study based on weighted gene co‐expression network analysis
Cited by: 24
Author(s): Yaoyi Xiong, Lushun Yuan, Jing Xiong, Huimin Xu, Yongwen Luo, Gang Wang, Lingao Ju, Yu Xiao, Xinghuan Wang
Software Mentions: 10
Published: almost 5 years ago

10.1038/s41416-020-0887-6

UGT2B17 modifies drug response in chronic lymphocytic leukaemia
Cited by: 12
Author(s): Éric P. Allain, Michèle Rouleau, Katrina Vanura, Sophie Tremblay, Joanie Vaillancourt, Vincent Bat, Patrick Caron, Lyne Villeneuve, Adrien Labriet, Véronique Turcotte, Trang Le, Medhat Shehata, Susanne Schnabl, Dita Demirtas, Rainer Hubmann, Charles Joly-Beauparlant, Arnaud Droit, Ulrich Jäger, Philipp B. Staber, Éric Lévesque, Chantal Guillemette
Software Mentions: 10
Published: over 4 years ago

10.3389/fmolb.2021.649363

Weighted Gene Co-expression Network Analysis Identifies CALD1 as a Biomarker Related to M2 Macrophages Infiltration in Stage III and IV Mismatch Repair-Proficient Colorectal Carcinoma
Cited by: 7
Author(s): Hongliang Zheng, Yuge Bai, Jingui Wang, Shanwen Chen, Junling Zhang, Jing Zhu, Yucun Liu, Xin Wang
Software Mentions: 10
Published: over 3 years ago

10.3390/cancers13081768

Systematic Analysis of the Transcriptome Profiles and Co-Expression Networks of Tumour Endothelial Cells Identifies Several Tumour-Associated Modules and Potential Therapeutic Targets in Hepatocellular Carcinoma
Cited by: 8
Author(s): Thomas Mohr, Sonja Katz, Verena Paulitschke, Nadim Aizarani, Alexander Tolios
Software Mentions: 9
Published: over 3 years ago

10.1186/1471-2105-8-221

Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts
Cited by: 156
Author(s): Joern Toedling, Oleg Sklyar, Wolfgang Huber
Software Mentions: 9
Published: over 17 years ago

10.3389/fimmu.2021.592303

Machine Learning Identifies Complicated Sepsis Course and Subsequent Mortality Based on 20 Genes in Peripheral Blood Immune Cells at 24 H Post-ICU Admission
Cited by: 35
Author(s): Shayantan Banerjee, Akram Mohammed, Hector R. Wong, Nades Palaniyar, Rishikesan Kamaleswaran
Software Mentions: 9
Published: almost 4 years ago

10.3389/fgene.2021.691465

ARG2, MAP4K5 and TSTA3 as Diagnostic Markers of Steroid-Induced Osteonecrosis of the Femoral Head and Their Correlation With Immune Infiltration
Cited by: 10
Author(s): Rongguo Yu, Jiayu Zhang, Youguang Zhuo, Hong Xu, Jie Ye, Susu Tang, Nannan Liu, Yiyuan Zhang
Software Mentions: 9
Published: over 3 years ago

10.1038/s41598-019-56829-6

Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues
Cited by: 18
Author(s): Mustafa Sibai, Cüneyd Parlayan, Pelin Tuğlu, Gürkan Öztürk, Turan Demircan
Software Mentions: 9
Published: almost 5 years ago

10.1371/journal.pone.0066902

Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data
Cited by: 16
Author(s): Darragh G. McArt, Philip D. Dunne, Jaine K. Blayney, Manuel Salto-Tellez, Sandra Van Schaeybroeck, Peter Hamilton, Shudong Zhang
Software Mentions: 9
Published: over 11 years ago

10.3389/fcell.2021.671359

Identification and Validation of a Novel Prognosis Prediction Model in Adrenocortical Carcinoma by Integrative Bioinformatics Analysis, Statistics, and Machine Learning
Cited by: 3
Author(s): Xin Yan, Zixin Guo, Donghu Yu, Chen Chen, Xiaoping Li, Zhiwei Yang, Tong-Zu Liu, Sheng Li
Software Mentions: 9
Published: over 3 years ago

10.1002/1878-0261.12595

Aberrant expression of RSK1 characterizes high‐grade gliomas with immune infiltration
Cited by: 14
Author(s): Glaucia Noeli Maroso Hajj, Fernanda F. da Silva, Bárbara de Bellis, Fernanda C. S. Lupinacci, Hermano Martins Bellato, Juvanier R. Cruz, Claudionor Nogueira Costa Segundo, Igor Vilela Faquini, Leuridan Cavalcante Torres, Paulo Sanematsu, María Dirlei Begnami, Vilma R. Martins, Martín Roffé
Software Mentions: 9
Published: almost 5 years ago

10.18632/aging.202956

Gene expression profiles for an immunoscore model in bone and soft tissue sarcoma
Cited by: 5
Author(s): Jingyuan Fan, Xinyi Qin, Rong‐Quan He, Jie Ma, Qingjun Wei
Software Mentions: 9
Published: over 3 years ago

10.1186/s13229-019-0262-8

Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer
Cited by: 25
Author(s): Jaume Forés-Martos, Ferrán Catalá-López, Jon Sánchez-Valle, Kristina Ibáñez, Héctor Tejero, Helena Palma-Gudiel, Joan Climent, Véra Pancaldi, Lourdes Fañanás, Celso Arango, Mara Parellada, Anaı̈s Baudot, Daniel Vogt, John L.R. Rubenstein, Alfonso Valencia, Rafael Tabarés‐Seisdedos
Software Mentions: 9
Published: over 5 years ago

10.1186/s12943-020-01170-0

m6A regulator-mediated methylation modification patterns and tumor microenvironment infiltration characterization in gastric cancer
Cited by: 600
Author(s): Bo Zhang, Qiong Wu, Ben Li, Defeng Wang, Lei Wang, You Zhou
Software Mentions: 9
Published: over 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

10.1186/gb-2014-15-3-r47

Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines
Cited by: 571
Author(s): Paul Geeleher, Nancy J. Cox, R. Stephanie Huang
Software Mentions: 9
Published: over 10 years ago

10.18632/aging.203040

Integrated bioinformatic analysis reveals the underlying molecular mechanism of and potential drugs for pulmonary arterial hypertension
Cited by: 16
Author(s): Haoru Dong, Xiuchun Li, Mengsi Cai, Chi Zhang, Mao Wei-qi, Ying Wang, Qinying Xu, Mayun Chen, Liangxing Wang, Xiaoying Huang
Software Mentions: 9
Published: over 3 years ago

10.1186/s13058-019-1148-6

Identification of three subtypes of triple-negative breast cancer with potential therapeutic implications
Cited by: 70
Author(s): Pascal Jézéquel, Olivier Kerdraon, Hubert Hondermarck, Catherine Guérin‐Charbonnel, Hamza Lasla, Wilfried Gouraud, Jean-Luc Canon, Andrea Gombos, Florence Dalenc, Suzette Delaloge, Jérôme Lemonnier, Delphine Loussouarn, Véronique Verrièle, Mario Campone
Software Mentions: 9
Published: over 5 years ago

10.1155/2021/8864436

Identification and Validation of a Tumor Microenvironment-Related Gene Signature for Prognostic Prediction in Advanced-Stage Non-Small-Cell Lung Cancer
Cited by: 10
Author(s): Xuening Zhang, Xiaoguang Shi, Hao Zhao, Xiaocan Jia, Yongli Yang
Software Mentions: 9
Published: over 3 years ago

10.1186/1471-2105-13-136

Down-weighting overlapping genes improves gene set analysis
Cited by: 120
Author(s): Adi L. Tarca, Sorin Drăghici, Gaurav Bhatti, Roberto Romero
Software Mentions: 9
Published: over 12 years ago

10.1186/s12885-017-3726-2

Guanylate-binding protein-1 is a potential new therapeutic target for triple-negative breast cancer
Cited by: 26
Author(s): Melissa Quintero, Douglas Adamóski, Larissa Menezes dos Reis, Carolline Fernanda Rodrigues Ascenção, Krishina Ratna Sousa de Oliveira, Kaliandra de Almeida Gonçalves, Milton Dias, Marcelo Falsarella Carazzolle, Sandra Martha Gomes Dias
Software Mentions: 9
Published: about 7 years ago

10.1186/1471-2105-10-211

puma: a Bioconductor package for propagating uncertainty in microarray analysis
Cited by: 67
Author(s): Richard D. Pearson, Xuejun Liu, Guido Sanguinetti, Marta Milo, Neil D. Lawrence, Magnus Rattray
Software Mentions: 9
Published: over 15 years ago

10.1371/journal.pone.0095224

Two-Stage, In Silico Deconvolution of the Lymphocyte Compartment of the Peripheral Whole Blood Transcriptome in the Context of Acute Kidney Allograft Rejection
Cited by: 18
Author(s): Casey P. Shannon, Robert Balshaw, Raymond T. Ng, J. Wilson-McManus, Paul Keown, Robert McMaster, Bruce M. McManus, David Landsberg, Nicole M. Isbel, Greg Knoll, Scott J. Tebbutt
Software Mentions: 9
Published: over 10 years ago

10.1371/journal.pgen.1009094

Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression
Cited by: 2
Author(s): Aziz Aiderus, Justin Y. Newberg, Liliana Guzmán-Rojas, Ana M. Contreras-Sandoval, Amanda L. Meshey, Devin J. Jones, Felipe Amaya-Manzanares, Roberto Rangel, Jerrold M. Ward, Song Choon Lee, Kenneth Ban, Keith Rogers, Susan Rogers, Luxmanan Selvanesan, Leslie A. McNoe, Neal G. Copeland, Nancy A. Jenkins, Kenneth Y. Tsai, Michael A. Black, Karen Mann, Michael B. Mann
Software Mentions: 8
Published: over 3 years ago

10.1038/s41598-021-93034-w

Altered expression of genes controlling metabolism characterizes the tissue response to immune injury in lupus
Cited by: 20
Author(s): Kathryn M. Kingsmore, Prathyusha Bachali, Michelle D. Catalina, Andrea R. Daamen, Sarah Heuer, Robert Robl, Amrie C. Grammer, Peter E. Lipsky
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pmed.1002223

Master Regulators of Oncogenic KRAS Response in Pancreatic Cancer: An Integrative Network Biology Analysis
Cited by: 38
Author(s): Shivan Sivakumar, Inês de Santiago, L Chlon, Florian Markowetz
Software Mentions: 8
Published: almost 8 years ago

10.1038/s41598-020-70596-9

Identification of potential diagnostic gene biomarkers in patients with osteoarthritis
Cited by: 13
Author(s): Xinling Wang, Yu Yang, Yong Huang, Zhu Ming-shuang, Rigao Chen, Zhanghui Liao, Shipeng Yang
Software Mentions: 8
Published: over 4 years ago

10.1186/s12864-015-2319-1

Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes
Cited by: 3
Author(s): Youko Horiuchi, Yoshiaki Harushima, Hironori Fujisawa, Takako Mochizuki, Masahiro Fujita, Hajime Ohyanagi, Nori Kurata
Software Mentions: 8
Published: almost 9 years ago

10.3389/fimmu.2021.649551

TSPAN1, TMPRSS4, SDR16C5, and CTSE as Novel Panel for Pancreatic Cancer: A Bioinformatics Analysis and Experiments Validation
Cited by: 11
Author(s): Yi-Jun Hua, Tiandong Li, Hua Wang, Jinyu Wu, Chuncheng Yi, Jianxiang Shi, Peng Wang, Chunhua Song, Liping Dai, Guozhong Jiang, Yuguang Huang, Yu Ye, Jitian Li
Software Mentions: 8
Published: over 3 years ago

10.1186/s12964-019-0397-4

Subtyping of microsatellite instability-high colorectal cancer
Cited by: 28
Author(s): Wangxiong Hu, Yanmei Yang, Ling Qi, Jiani Chen, Weiting Ge, Shu Zheng
Software Mentions: 8
Published: over 5 years ago

10.7717/peerj.7816

CELSR3 mRNA expression is increased in hepatocellular carcinoma and indicates poor prognosis
Cited by: 11
Author(s): Xuefeng Gu, Hongbo Li, Ling Sha, Man Yuan, Chao Shi, Wei Zhao
Software Mentions: 8
Published: about 5 years ago

10.7717/peerj.11233

Identification of a ferroptosis-related gene signature (FRGS) for predicting clinical outcome in lung adenocarcinoma
Cited by: 11
Author(s): Sheng Wang, Chunlei Wu, Dehua Mao, Quanteng Hu
Software Mentions: 8
Published: over 3 years ago

10.18632/aging.103475

Constructing a global transcriptional regulatory landscape for early non-small cell lung cancer to identify hub genes and key pathways
Cited by: 6
Author(s): Jianlong Bu, Pinyi Zhang, Kaibin Zhu, Yubo Yan, Bowen Shi, Junfeng Wang, Shidong Xu
Software Mentions: 8
Published: about 4 years ago

10.1038/s41598-020-60998-0

Temporal changes in the gene expression heterogeneity during brain development and aging
Cited by: 28
Author(s): Ulas Işıldak, Mehmet Somel, Janet M. Thornton, Handan Melike Dönertaş
Software Mentions: 8
Published: over 4 years ago

10.7150/ijms.48244

Identification of Key Genes and Pathways in Myeloma side population cells by Bioinformatics Analysis
Cited by: 21
Author(s): Yang Qin, Kaihu Li, Xin Li, Jing Liu
Software Mentions: 8
Published: almost 5 years ago

10.18632/aging.202486

Constructing a ceRNA-immunoregulatory network associated with the development and prognosis of human atherosclerosis through weighted gene co-expression network analysis
Cited by: 11
Author(s): Yaozhong Liu, Na Liu, Qiming Liu
Software Mentions: 8
Published: almost 4 years ago

10.1186/1471-2105-13-222

Wavelet-based detection of transcriptional activity on a novel Staphylococcus aureus tiling microarray
Cited by: 3
Author(s): Víctor Segura, Alejandro Toledo‐Arana, Maite Uzqueda, Íñigo Lasa, Arrate Muñoz-Barrutia
Software Mentions: 8
Published: about 12 years ago

10.1371/journal.pone.0240824

A novel computational approach for predicting complex phenotypes in Drosophila (starvation-sensitive and sterile) by deriving their gene expression signatures from public data
Cited by: 0
Author(s): Dobril Ivanov, Gerrit Bostelmann, Benoît Lan-Leung, Julie Williams, Linda Partridge, Valentina Escott‐Price, Janet M. Thornton
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0183264

The transcriptional profiling of human in vivo-generated plasma cells identifies selective imbalances in monoclonal gammopathies
Cited by: 12
Author(s): Luis M. Valor, Beatriz Rodrı́guez-Bayona, Ana Ramos-Amaya, José A. Brieva, Antonio Campos‐Caro
Software Mentions: 8
Published: over 7 years ago

10.1038/s41597-020-00696-8

Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients
Cited by: 10
Author(s): Antonio Federico, Veera Hautanen, Nils Christian, Andreas Kremer, Angela Serra, Dario Greco
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0203346

Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays
Cited by: 3
Author(s): Vinu José, Debora Fumagalli, Françoise Rothé, Samira Majjaj, Sherene Loi, Stefan Michiels, Christos Sotiriou
Software Mentions: 8
Published: about 6 years ago

10.1186/gm385

Exploiting the noise: improving biomarkers with ensembles of data analysis methodologies
Cited by: 14
Author(s): Maud H.W. Starmans, Melania Pintilie, Thomas John, Sandy D. Der, Frances A. Shepherd, Igor Jurišica, Philippe Lambin, Ming‐Sound Tsao, Paul C. Boutros
Software Mentions: 8
Published: almost 13 years ago

10.18632/aging.103707

A 12-immune cell signature to predict relapse and guide chemotherapy for stage II colorectal cancer
Cited by: 4
Author(s): Xianglong Tian, Xiaoqiang Zhu, Meng Wu, Shiguang Bai, Min Shi, Shihao Xiang, Zhao Chun-hua, Yugang Wang
Software Mentions: 8
Published: about 4 years ago

10.1016/j.csbj.2020.06.023

Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities
Cited by: 10
Author(s): Susan Idicula‐Thomas, Ulka Gawde, Sameeksha Bhaye, Khushal Pokar, Gary D. Bader
Software Mentions: 8
Published: almost 5 years ago

10.1186/1471-2105-12-464

From hybridization theory to microarray data analysis: performance evaluation
Cited by: 4
Author(s): Fabrice Berger, Enrico Carlon
Software Mentions: 8
Published: almost 13 years ago

10.7717/peerj.10682

Identification of the hub genes in gastric cancer through weighted gene co-expression network analysis
Cited by: 7
Author(s): Chunyang Li, Haopeng Yu, Yajing Sun, Xiaoxi Zeng, Wei Zhang
Software Mentions: 8
Published: over 3 years ago

10.1186/s12957-018-1519-y

Identification of hub genes with diagnostic values in pancreatic cancer by bioinformatics analyses and supervised learning methods
Cited by: 23
Author(s): Chunyang Li, Xiaoxi Zeng, Haopeng Yu, Yuanxia Gu, Wei Zhang
Software Mentions: 8
Published: about 6 years ago

10.1186/1471-2105-12-467

Empirical comparison of cross-platform normalization methods for gene expression data
Cited by: 88
Author(s): Jason R. Rudy, Faramarz Valafar
Software Mentions: 8
Published: almost 13 years ago

10.1371/journal.pone.0240523

Whole transcriptomic network analysis using Co-expression Differential Network Analysis (CoDiNA)
Cited by: 12
Author(s): Deisy Morselli Gysi, Tiago de Miranda Fragoso, Fatemeh Zebardast, Wesley Bertoli, Volker Busskamp, Eivind Almaas, Katja Nowick
Software Mentions: 8
Published: about 4 years ago

Projects: bioconductor: affy

Papers Mentioning affy 989