bioconductor: GEOquery | Projects

10.1002/pmic.201400392

Visualization of proteomics data using R and Bioconductor
Cited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
Cited by: 20
Author(s): Andrea Komljenović, Julien Roux, Julien Wollbrett, Marc Robinson‐Rechavi, Frederic Bastian
Software Mentions: 33
Published: over 6 years ago

10.3389/fimmu.2021.659444

Development and Validation of a CD8+ T Cell Infiltration-Related Signature for Melanoma Patients
Cited by: 13
Author(s): Yuan Yuan, Zheng Zhu, Ying Lan, Saili Duan, Zijue Zhu, Xi Zhang, Guoyin Li, Hui Qü, Yao Feng, Hui Cai, Zewen Song
Software Mentions: 24
Published: over 3 years ago

10.12688/f1000research.13577.2

Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies
Cited by: 2
Author(s): Enrico Ferrero
Software Mentions: 21
Published: over 6 years ago

10.1186/s12864-017-4353-7

DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism
Cited by: 72
Author(s): Ali Sharifi-Zarchi, Daniela Gerovska, Kenjiro Adachi, Mehdi Totonchi, Hamid Pezeshk, Ryan J. Taft, Hans R. Schöler, Hamidreza Chitsaz, Mehdi Sadeghi, Hossein Baharvand, Marcos J. Araúzo-Bravo
Software Mentions: 21
Published: almost 7 years ago

10.1155/2021/6613151

Genomic and Transcriptome Analysis to Identify the Role of the mTOR Pathway in Kidney Renal Clear Cell Carcinoma and Its Potential Therapeutic Significance
Cited by: 6
Author(s): Xiangyu Che, Xiaochen Qi, Yingkun Xu, Qifei Wang, Guangzhen Wu
Software Mentions: 19
Published: over 3 years ago

10.3389/fonc.2020.607727

Gene Panel of Persister Cells as a Prognostic Indicator for Tumor Repopulation After Radiation
Cited by: 3
Author(s): Yucui Zhao, Yanwei Song, Ruyi Zhao, Minghui Zhao, Qian Huang
Software Mentions: 18
Published: almost 4 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

10.1038/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

10.1186/s12864-021-07370-2

GCSscore: an R package for differential gene expression analysis in Affymetrix/Thermo-Fisher whole transcriptome microarrays
Cited by: 3
Author(s): Guy M. Harris, Shahroze Abbas, Michael F. Miles
Software Mentions: 17
Published: almost 4 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

10.3390/cells8111321

Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis: A Systematic Study Using Public Gene Expression and Transcription Factor Binding Datasets
Cited by: 16
Author(s): Mahmoud Ahmed, Trang Huyen Lai, Jin Seok Hwang, Sahib Zada, Trang Minh Pham, Deok Ryong Kim
Software Mentions: 15
Published: about 5 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

10.7717/peerj.11880

Integrated bioinformatics analysis of the NEDD4 family reveals a prognostic value of <i>NEDD4L</i> in clear-cell renal cell cancer
Cited by: 6
Author(s): Hui Zhao, Junjun Zhang, Xiaoliang Fu, Dongdong Mao, Xuesen Qi, Shuai Liang, Gang Ma, Zewen Song, Ru Yang, Zhenni Guo, Binghua Tong, Meiqing Sun, Baile Zuo, Guoyin Li
Software Mentions: 14
Published: about 3 years ago

10.1186/s40168-020-00914-w

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients
Cited by: 118
Author(s): Alfonsina D’Amato, Lorenzo Mannelli, Elena Lucarini, Angela L. Man, Gwénaëlle Le Gall, Jacopo Junio Valerio Branca, Carla Ghelardini, Amedeo Amedei, Eugenio Bertelli, Marì Regoli, Alessandra Pacini, Giulia Luciani, Pasquale Gallina, Annalisa Altera, Arjan Narbad, Massimo Gulisano, Lesley Hoyles, David Vauzour, Claudio Nicoletti
Software Mentions: 14
Published: about 4 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

10.1186/s13059-020-02001-7

Leveraging biological and statistical covariates improves the detection power in epigenome-wide association testing
Cited by: 7
Author(s): Jinyan Huang, Lijun Bai, Bowen Cui, Liang Wu, Liwen Wang, Zhiyin An, Shulin Ruan, Yue Yu, Xianyang Zhang, Jun Chen
Software Mentions: 13
Published: over 4 years ago

10.3390/cancers13163922

Transcriptomic Profiling Reveals Novel Candidate Genes and Signalling Programs in Breast Cancer Quiescence and Dormancy
Cited by: 4
Author(s): Lewis A. Quayle, Amy Spicer, Penelope D. Ottewell, Ingunn Holen
Software Mentions: 13
Published: over 3 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

10.1186/s13046-020-01684-x

KIAA1522 potentiates TNFα-NFκB signaling to antagonize platinum-based chemotherapy in lung adenocarcinoma
Cited by: 11
Author(s): Boshi Wang, Tiantian Jing, Wei‐Lin Jin, Biaohua Chen, Chengsi Wu, Ming-Rong Wang, Yizhen Liu
Software Mentions: 13
Published: about 4 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

10.1371/journal.pone.0075146

NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations
Cited by: 29
Author(s): Ivan Merelli, Píetro Lió, Luciano Milanesi
Software Mentions: 12
Published: about 11 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

10.1186/1756-0500-5-282

Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results
Cited by: 9
Author(s): Yilin Dai, Ling Guo, Meng Li, Yibu Chen
Software Mentions: 11
Published: over 12 years ago

10.3389/fgene.2015.00040

Integrating multi-omic features exploiting Chromosome Conformation Capture data
Cited by: 9
Author(s): Ivan Merelli, Fabio Tordini, Maurizio Drocco, Marco Aldinucci, Píetro Lió, Luciano Milanesi
Software Mentions: 11
Published: over 9 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

10.1371/journal.pcbi.1002276

BeadArray Expression Analysis Using Bioconductor
Cited by: 50
Author(s): Matthew E. Ritchie, Mark J. Dunning, Mike L. Smith, Wei Shi, Andy G. Lynch
Software Mentions: 11
Published: almost 13 years ago

10.1080/21623945.2019.1697563

Modelling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes
Cited by: 6
Author(s): Mahmoud Ahmed, Deok Ryong Kim
Software Mentions: 11
Published: almost 6 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

10.3390/cancers13133371

Meta-Analysis of Microdissected Breast Tumors Reveals Genes Regulated in the Stroma but Hidden in Bulk Analysis
Cited by: 7
Author(s): Aurora Savino, Niccolò De Marzo, Paolo Provero, Valeria Poli
Software Mentions: 10
Published: over 3 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: almost 4 years ago

10.12688/f1000research.13925.3

BED: a Biological Entity Dictionary based on a graph data model
Cited by: 1
Author(s): Patrice Godard, Jonathan van Eyll
Software Mentions: 10
Published: over 6 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

10.3389/pore.2021.594649

Bcl-2 Associated Athanogene 2 (BAG2) is Associated With Progression and Prognosis of Hepatocellular Carcinoma: A Bioinformatics-Based Analysis
Cited by: 7
Author(s): Xi Zhang, Junjun Zhang, Yang Liu, Jie Li, Juan Tan, Zewen Song
Software Mentions: 10
Published: over 3 years ago

10.1186/s12859-016-1321-1

GEN3VA: aggregation and analysis of gene expression signatures from related studies
Cited by: 17
Author(s): Gregory W. Gundersen, Kathleen M. Jagodnik, Holly Woodland, Nicholas F. Fernandez, Kevin Sani, Anders B. Dohlman, Peter M.U. Ung, Caroline D. Monteiro, Avner Schlessinger, Avi Ma’ayan
Software Mentions: 9
Published: almost 8 years ago

10.1038/s41598-020-71315-0

Characterisation of the novel spontaneously immortalized and invasively growing human skin keratinocyte line HaSKpw
Cited by: 8
Author(s): Elizabeth Pavez Loriè, Nicola Stricker, Beata Patrycja Plitta-Michalak, I-Peng Chen, Beate Volkmer, Rüdiger Greinert, Anna Jauch, Petra Boukamp, Alexander Rapp
Software Mentions: 9
Published: about 4 years ago

10.3389/fimmu.2021.709173

The Role of Hemoglobin Subunit Delta in the Immunopathy of Multiple Sclerosis: Mitochondria Matters
Cited by: 6
Author(s): Afshin Derakhshani, Hossein Safarpour, Behzad Baradaran, Nima Hemmat, Patrizia Leone, Zahra Asadzadeh, Mehrdad Pashazadeh, Behzad Baradaran, Vito Racanelli
Software Mentions: 9
Published: about 3 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

10.1155/2021/9920234

Bioinformatic Analysis Reveals Central Role for Tumor-Infiltrating Immune Cells in Uveal Melanoma Progression
Cited by: 6
Author(s): Mieszko Lachota, Anton Lennikov, Karl‐Johan Malmberg, Radosław Zagożdżon
Software Mentions: 8
Published: over 3 years ago

10.18632/aging.202405

Construction and analysis of a joint diagnosis model of random forest and artificial neural network for heart failure
Cited by: 25
Author(s): Yuqing Tian, Jiefu Yang, Ming Lan, Tong Zou
Software Mentions: 8
Published: almost 4 years ago

10.1038/s41598-021-95068-6

CENPL, ISG20L2, LSM4, MRPL3 are four novel hub genes and may serve as diagnostic and prognostic markers in breast cancer
Cited by: 17
Author(s): Jun Yin, Chen Lin, Meng Jiang, Xuhai Tang, Danlin Xie, Jingwen Chen, Rongqin Ke
Software Mentions: 8
Published: over 3 years ago

10.1038/s41389-019-0157-8

DeepCC: a novel deep learning-based framework for cancer molecular subtype classification
Cited by: 119
Author(s): Feng Gao, Wei Wang, Miaomiao Tan, Lina Zhu, Yuchen Zhang, Evelyn Fessler, Louis Vermeulen, Xin Wang
Software Mentions: 8
Published: about 5 years ago

10.3390/ijerph18115564

Identification of Hub Genes in Different Stages of Colorectal Cancer through an Integrated Bioinformatics Approach
Cited by: 2
Author(s): Abhijeet R. Patil, Ming-Ying Leung, Sourav Roy
Software Mentions: 8
Published: over 3 years ago

10.1186/s13059-020-02223-9

Equivalent DNA methylation variation between monozygotic co-twins and unrelated individuals reveals universal epigenetic inter-individual dissimilarity
Cited by: 17
Author(s): Benjamin Planterose Jiménez, Fan Liu, Amke Caliebe, Diego Montiel González, Jordana T. Bell, Manfred Kayser, Athina Vidaki
Software Mentions: 8
Published: almost 4 years ago

10.3389/fcell.2021.651575

An N6-Methyladenosine-Related Gene Set Variation Score as a Prognostic Tool for Lung Adenocarcinoma
Cited by: 8
Author(s): Huijuan Zhang, Jing Hu, Aina Liu, Huajun Qu, Fenge Jiang, Congcong Wang, Steven Mo, Ping Sun
Software Mentions: 8
Published: over 3 years ago

10.1016/j.ebiom.2021.103444

A diagnostic miRNA signature for pulmonary arterial hypertension using a consensus machine learning approach
Cited by: 24
Author(s): Niamh Errington, James Iremonger, Josephine Pickworth, Sokratis Kariotis, Christopher J. Rhodes, Alexander Rothman, Robin Condliffe, Charles Elliot, David G. Kiely, Luke Howard, John Wharton, A. A. Roger Thompson, Nicholas W. Morrell, Martin R. Wilkins, Dennis Wang, Allan Lawrie
Software Mentions: 8
Published: over 3 years ago

10.1097/MD.0000000000026194

Integrated analysis of ceRNA network in hepatocellular carcinoma using bioinformatics analysis
Cited by: 5
Author(s): Yu Luo, Hongjuan Li, Hongli Huang, Ling Xue, Haiwen Li, Li Liu, Haiyan Fu
Software Mentions: 8
Published: over 3 years ago

10.1002/cam4.3655

Immune landscape and a promising immune prognostic model associated with TP53 in early‐stage lung adenocarcinoma
Cited by: 17
Author(s): Chia-Chien Wu, Rong Xiang, Lin Wei
Software Mentions: 8
Published: almost 4 years ago

10.1136/jitc-2020-000588

Monocyte-derived APCs are central to the response of PD1 checkpoint blockade and provide a therapeutic target for combination therapy
Cited by: 30
Author(s): Sjoerd Schetters, Elizabeth Rodríguez, Laura Kruijssen, Matheus H.W. Crommentuijn, Louis Boon, Jan Van den Bossche, Joke M. M. den Haan, Yvette van Kooyk
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0244122

Easyreporting simplifies the implementation of Reproducible Research layers in R software
Cited by: 0
Author(s): Dario Righelli, Claudia Angelini
Software Mentions: 8
Published: over 3 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

10.3389/fcell.2021.653357

Combination of Immune-Related Genomic Alterations Reveals Immune Characterization and Prediction of Different Prognostic Risks in Ovarian Cancer
Cited by: 2
Author(s): Xibo Zhao, Shanshan Cong, Qiuyan Guo, Yan Cheng, Tian Liang, Jing Wang, Guangmei Zhang
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

10.1038/s41598-018-34129-9

SAC3D1: a novel prognostic marker in hepatocellular carcinoma
Cited by: 37
Author(s): Myoung‐Eun Han, Jiyoung Kim, Ga Hyun Kim, Si Young Park, Yun Hak Kim, Sae‐Ock Oh
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pone.0196836

Multiclass classification for skin cancer profiling based on the integration of heterogeneous gene expression series
Cited by: 17
Author(s): Juan Manuel Gálvez, Daniel Castillo, José Benavente Herrera, Belén San Román, Olga Valenzuela, Francisco M. Ortuño Guzman, Ignacio Rojas
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-020-69082-z

Immune expression signatures as candidate prognostic biomarkers of age and gender survival differences in cutaneous melanoma
Cited by: 6
Author(s): Yi Jun Kim, Kyubo Kim, Kye Hwa Lee, Jiyoung Kim, Wonguen Jung
Software Mentions: 7
Published: over 4 years ago

10.1186/s12864-016-3260-7

DeSigN: connecting gene expression with therapeutics for drug repurposing and development
Cited by: 52
Author(s): Bernard Kok Bang Lee, Kai Hung Tiong, Jit Kang Chang, Chee Sun Liew, Zainal Ariff Abdul Rahman, Aik Choon Tan, Tsung Fei Khang, Sok Ching Cheong
Software Mentions: 7
Published: almost 8 years ago

10.1093/gigascience/giy167

SMAGEXP: a galaxy tool suite for transcriptomics data meta-analysis
Cited by: 2
Author(s): Samuel Blanck, Guillemette Marot
Software Mentions: 7
Published: almost 6 years ago

10.1186/1471-2105-15-69

MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data
Cited by: 15
Author(s): Gan Zhang, Jianwu Wang, Nathan Salomonis, Jennifer Stowe, Gabriel G. Haddad, Andrew D. McCulloch, Ilkay Altıntaş, Alexander C. Zambon
Software Mentions: 7
Published: over 10 years ago

10.1371/journal.pcbi.1006826

Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas
Cited by: 65
Author(s): David G.P. van IJzendoorn, Károly Szuhai, Inge H. Briaire-de Bruijn, Marie Kostine, Marieke L. Kuijjer, Judith V.M.G. Bovée
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pgen.1002704

Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue
Cited by: 45
Author(s): Leopold Parts, Åsa K. Hedman, Sarah Keildson, Andrew Knights, Cei Abreu‐Goodger, Martijn van de Bunt, José Afonso Guerra-Assunção, Nenad Bartoniček, Stijn van Dongen, Reedik Mägi, James Nisbet, Amy Barrett, Mattias Rantalainen, Alexandra C. Nica, Michael A. Quail, Kerrin S. Small, Daniel Glass, Anton J. Enright, John Winn, Panos Deloukas, Emmanouil T. Dermitzakis, Mark I. McCarthy, Timothy D. Spector, Richard Durbin, Cecilia M. Lindgren
Software Mentions: 7
Published: over 12 years ago

10.1371/journal.pone.0201751

Pancreatic cancer survival analysis defines a signature that predicts outcome
Cited by: 52
Author(s): Pichai Raman, Ravikanth Maddipati, Kian Huat Lim, Aydın Tözeren
Software Mentions: 7
Published: over 6 years ago

10.7150/thno.54134

Single-cell melanoma transcriptomes depicting functional versatility and clinical implications of STIM1 in the tumor microenvironment
Cited by: 2
Author(s): Henry Sung Ching Wong, Wei Chiao Chang
Software Mentions: 7
Published: almost 4 years ago

10.3389/fonc.2021.671892

A Liquid-Liquid Phase Separation-Related Gene Signature as Prognostic Biomarker for Epithelial Ovarian Cancer
Cited by: 9
Author(s): Yan Qiu, Min Pan, Xuemei Chen
Software Mentions: 7
Published: over 3 years ago

10.1016/j.diabres.2019.01.008

Differential methylation of the type 2 diabetes susceptibility locus KCNQ1 is associated with insulin sensitivity and is predicted by CpG site specific genetic variation
Cited by: 14
Author(s): Ushma Jaykamal Shah, Wenting Xie, Allan Flyvbjerg, John J. Nolan, Kurt Højlund, Mark Walker, Caroline L Relton, Hannah R Elliott
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41598-021-92036-y

Capitalizing on transcriptome profiling to optimize and identify targets for promoting early murine folliculogenesis in vitro
Cited by: 6
Author(s): Andrea Jones, Beatriz Peñalver Bernabé, Vasantha Padmanabhan, Jun Li, Ariella Shikanov
Software Mentions: 7
Published: over 3 years ago

10.1186/s12885-021-08462-8

Construction and comprehensive analysis of a ceRNA network to reveal potential prognostic biomarkers for lung adenocarcinoma
Cited by: 12
Author(s): Lei Gao, Ling Zhang
Software Mentions: 7
Published: over 3 years ago

10.7717/peerj.11018

Integrated analysis of immune-related long noncoding RNAs as diagnostic biomarkers in psoriasis
Cited by: 13
Author(s): Feixiang Fan, Zhen Huang, Yongfeng Chen
Software Mentions: 7
Published: over 3 years ago

10.3389/fendo.2021.712513

Construction of a Prognostic Risk Prediction Model for Obesity Combined With Breast Cancer
Cited by: 1
Author(s): Na Sun, Dandan Ma, Peng Gao, Yanling Li, Zexuan Yan, Zaihui Peng, Fei Han, Yi Zhang, Xiaowei Qi
Software Mentions: 7
Published: about 3 years ago

10.1186/s12885-021-08052-8

Comprehensive analysis of immune-related prognostic genes in the tumour microenvironment of hepatocellular carcinoma
Cited by: 2
Author(s): Weike Gao, Luan Li, Xinyin Han, Siyao Liu, Chengzhen Li, Guanying Yu, Lei Zhang, Dongsheng Zhang, Caiyun Liu, Erhong Meng, Shuai Hong, Dongliang Wang, Peiming Guo, Guangjun Shi
Software Mentions: 6
Published: over 3 years ago

10.3389/fgene.2019.01056

Meta-Analysis of HTLV-1-Infected Patients Identifies CD40LG and GBP2 as Markers of ATLL and HAM/TSP Clinical Status: Two Genes Beat as One
Cited by: 5
Author(s): Eduardo R. Fukutani, Pablo Ivan Pereira Ramos, José Irahe Kasprzykowski, Lucas Gentil Azevedo, Moreno Magalhães de Souza Rodrigues, João Victor Lima, Helton Fábio Santos de Araújo, Kiyoshi F. Fukutani, Artur T. L. Queiroz
Software Mentions: 6
Published: about 5 years ago

10.3390/cancers13133330

Differential Regulation of Lacto-/Neolacto- Glycosphingolipid Biosynthesis Pathway Reveals Transcription Factors as Potential Candidates in Triple-Negative Breast Cancer
Cited by: 1
Author(s): Rui-chao Zeng, Ahmed Mohamed, Kum Kum Khanna, Michelle M. Hill
Software Mentions: 6
Published: over 3 years ago

10.3389/fgene.2018.00052

Gene Expression Meta-Analysis of Seven Candidate Gene Sets for Diabetes Traits Following a GWAS Pathway Study
Cited by: 2
Author(s): Hao Mei, Lianna Li, Michael Griswold, Thomas H. Mosley
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2021.678747

Identification of CXCL10-Relevant Tumor Microenvironment Characterization and Clinical Outcome in Ovarian Cancer
Cited by: 5
Author(s): Jing Jin, Yang Li, Tobias Achu Muluh, Liangke Zhi, Qijie Zhao
Software Mentions: 6
Published: over 3 years ago

10.1038/srep26136

SOX7 co-regulates Wnt/β-catenin signaling with Axin-2: both expressed at low levels in breast cancer
Cited by: 25
Author(s): Huidi Liu, Emilio Mastriani, Zi-Qiao Yan, Shuai Yin, Zheng Zeng, Hong Wang, Qinghai Li, Hongyu Liu, Xiaoyu Wang, Hongchu Bao, Yujie Zhou, Junjie Kou, Dongsheng Li, Ting Li, Jianrui Liu, Yongfang Liu, Lin Yin, Li Qiu, Liling Gong, Shulin Liu
Software Mentions: 6
Published: over 8 years ago

10.3390/nu12041042

Green Tea Polyphenol EGCG Attenuates MDSCs-mediated Immunosuppression through Canonical and Non-Canonical Pathways in a 4T1 Murine Breast Cancer Model
Cited by: 33
Author(s): Ping Xu, Feng Yan, Yuhai Zhao, Xiangbo Chen, Shili Sun, Yuefei Wang, Le Ying
Software Mentions: 6
Published: over 4 years ago

10.3390/ijms21218160

Proteomic Profiling of Archived Tissue of Primary Melanoma Identifies Proteins Associated with Metastasis
Cited by: 3
Author(s): Andrew Shapanis, Chester Lai, Mathew Sommerlad, Erika Parkinson, Eugene Healy, Paul Skipp
Software Mentions: 6
Published: about 4 years ago

10.3389/fgene.2019.01111

Translated Long Non-Coding Ribonucleic Acid ZFAS1 Promotes Cancer Cell Migration by Elevating Reactive Oxygen Species Production in Hepatocellular Carcinoma
Cited by: 17
Author(s): Zhi-Wei Guo, Yijun Meng, Xiang-Ming Zhai, Chen Xie, Na Zhao, Min Li, Chen Zhou, Kun Li, Tiancai Liu, Xu Yang, Yangyang Wu
Software Mentions: 6
Published: almost 5 years ago

10.18632/oncotarget.15749

Gene regulatory pattern analysis reveals essential role of core transcriptional factors’ activation in triple-negative breast cancer
Cited by: 15
Author(s): Li Min, Cheng Zhang, Like Qu, Jialiang Huang, Lan Jiang, Jiafei Liu, Luca Pinello, Guo‐Cheng Yuan, Chengchao Shou
Software Mentions: 6
Published: over 7 years ago

10.1186/1471-2105-10-201

A-MADMAN: Annotation-based microarray data meta-analysis tool
Cited by: 35
Author(s): Andrea Bisognin, Alessandro Coppe, Francesco Ferrari, Davide Risso, Chiara Romualdi, Silvio Bicciato, Stefania Bortoluzzi
Software Mentions: 6
Published: over 15 years ago

10.1371/journal.pone.0106397

RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data
Cited by: 138
Author(s): Mehmet K. Samur
Software Mentions: 6
Published: about 10 years ago

10.1186/s12859-019-2643-6

First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_
Cited by: 8
Author(s): Marco Moretto, Paolo Sonego, Ana B. Villasenõr-Altamirano, Kristof Engelen
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pgen.1004994

Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling
Cited by: 147
Author(s): Kristofer Davie, Jelle Jacobs, Mardelle Atkins, Delphine Potier, Valerie Christiaens, Georg Halder, Stein Aerts
Software Mentions: 6
Published: over 9 years ago

10.1128/mBio.01037-19

Reprogramming of Small Noncoding RNA Populations in Peripheral Blood Reveals Host Biomarkers for Latent and Active Mycobacterium tuberculosis Infection
Cited by: 24
Author(s): Leonardo Silva de Araujo, Marcelo Ribeiro-Alves, Thyago Leal-Calvo, Janaina Aparecida Medeiros Leung, Verónica Durán, Mohamed Samir, Steven R. Talbot, Aravind Tallam, Fernanda Carvalho de Queiroz Mello, Robert Geffers, Maria Helena Féres Saad, Frank Peßler
Software Mentions: 6
Published: almost 5 years ago

10.3389/fonc.2021.718644

N6-Methyladenosine Writer Gene ZC3H13 Predicts Immune Phenotype and Therapeutic Opportunities in Kidney Renal Clear Cell Carcinoma
Cited by: 10
Author(s): Tao Guo, Duan Huang, Jinbo Chen, Jinhui Liu, Belaydi Othmane, Jiao Hu, Huihuang Li, Xiongbing Zu
Software Mentions: 6
Published: about 3 years ago

10.7717/peerj.9975

Identification of NUF2 and FAM83D as potential biomarkers in triple-negative breast cancer
Cited by: 11
Author(s): Xiuming Zhai, Zhaowei Yang, Xiji Liu, Z P Dong, Dandan Zhou
Software Mentions: 6
Published: about 4 years ago

10.1111/jcmm.14999

A stroma‐related lncRNA panel for predicting recurrence and adjuvant chemotherapy benefit in patients with early‐stage colon cancer
Cited by: 13
Author(s): Rui Zhou, Huiying Sun, Songbai Zheng, Jingwen Zhang, Dongqiang Zeng, Jianhua Wu, Zhenhua Huang, Xiaoxiang Rong, Jianping Bin, Yulin Liao, Min Shi, Wangjun Liao
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-021-89531-7

Reconstruction of the miR-506-Quaking axis in Idiopathic Pulmonary Fibrosis using integrative multi-source bioinformatics
Cited by: 2
Author(s): Stevan D. Stojanović, Maximilian Fuchs, Chunguang Liang, Kevin Schmidt, Xiaoyan Ke, Annette Just, Angelika Pfanne, Andreas Pich, G. Warnecke, Peter Braubach, Christina Petzold, Danny Jonigk, Jörg H W Distler, Jan Fiedler, Thomas Thum, Meik Kunz
Software Mentions: 6
Published: over 3 years ago

10.3389/fonc.2021.639600

Identification of VWF as a Novel Biomarker in Lung Adenocarcinoma by Comprehensive Analysis
Cited by: 8
Author(s): Yi He, Ruijie Liu, Minghui Yang, Wu Bi, Liuyin Zhou, Sai Zhang, Jin Jin, Xujun Liang, Pengfei Zhang
Software Mentions: 6
Published: over 3 years ago

10.3389/fimmu.2021.671201

Identification and Validation of the Signatures of Infiltrating Immune Cells in the Eutopic Endometrium Endometria of Women With Endometriosis
Cited by: 22
Author(s): Xinglong Wu, Jin-Jiao Chen, Huiling Zhou, Yu Wu, Fei Lin, Jing Shi, Hong-Zhen Wu, Hai-Qun Xiao, Wei Wang
Software Mentions: 6
Published: about 3 years ago

10.7717/peerj.791

A reproducible approach to high-throughput biological data acquisition and integration
Cited by: 12
Author(s): Daniela Börnigen, Yo Sup Moon, Ali Rahnavard, Levi Waldron, Lauren J. McIver, Afrah Shafquat, Eric A. Franzosa, Larissa Miropolsky, Christopher J. Sweeney, Xochitl C. Morgan, Wendy S. Garrett, Curtis Huttenhower
Software Mentions: 6
Published: over 9 years ago

10.1186/s12885-015-1993-3

TGFβ isoforms and receptors mRNA expression in breast tumours: prognostic value and clinical implications
Cited by: 23
Author(s): Chenfeng Chen, Kong‐Nan Zhao, Paul P. Masci, Sunil R. Lakhani, Annika Antonsson, Peter T. Simpson, Luis Vitetta
Software Mentions: 6
Published: almost 9 years ago

10.1371/journal.pone.0208132

Identification of alterations in macrophage activation associated with disease activity in systemic lupus erythematosus
Cited by: 67
Author(s): Adam C. Labonte, Brian Kegerreis, Nicholas S. Geraci, Prathyusha Bachali, Sushma Madamanchi, Robert Robl, Michelle D. Catalina, Peter E. Lipsky, Amrie C. Grammer
Software Mentions: 6
Published: almost 6 years ago

10.1038/srep29251

Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data
Cited by: 21
Author(s): Tin Nguyen, Diana Diaz, Rebecca Tagett, Sorin Drăghici
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-018-33234-z

Low dose dimethyl sulfoxide driven gross molecular changes have the potential to interfere with various cellular processes
Cited by: 65
Author(s): Sinem Tunçer, Rafig Gurbanov, Ilir Sheraj, Ege Solel, Okan Esentürk, Sreeparna Banerjee
Software Mentions: 5
Published: about 6 years ago

10.1186/s12885-020-6533-0

PDAC-ANN: an artificial neural network to predict pancreatic ductal adenocarcinoma based on gene expression
Cited by: 30
Author(s): Palloma Porto Almeida, Cristina Padre Cardoso, Leandro Martins de Freitas
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0154531

Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq
Cited by: 63
Author(s): Shiva Marthandan, Mario Baumgart, Stefan Priebe, Marco Groth, Jonas Schaer, Christoph Kaether, Reinhard Guthke, Alessandro Cellerino, Matthias Platzer, Stephan Diekmann, Peter Hemmerich
Software Mentions: 5
Published: over 8 years ago

10.3389/fgene.2021.622683

Bioinformatics Analysis Identifies Molecular Markers Regulating Development and Progression of Endometriosis and Potential Therapeutic Drugs
Cited by: 7
Author(s): Ying Peng, Cheng Peng, Fang Zheng, Gang Chen
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-019-57108-0

Transcriptional analysis identifies potential biomarkers and molecular regulators in pneumonia and COPD exacerbation
Cited by: 15
Author(s): Wilhelm Bertrams, Kathrin Griss, Maria Han, Kerstin Seidel, Andreas Klemmer, Alexandra Sittka-Stark, Stefan Hippenstiel, Norbert Suttorp, Florian Finkernagel, Jochen Wilhelm, Timm Greulich, Claus Vogelmeier, Julio Vera, Bernd Schmeck
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12859-015-0708-8

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment
Cited by: 13
Author(s): Anwesha Bohler, Lars Eijssen, Martijn P. van Iersel, C. René Leemans, Egon Willighagen, Martina Kutmon, Magali Jaillard, Chris T. Evelo
Software Mentions: 5
Published: about 9 years ago

Projects: bioconductor: GEOquery

Papers Mentioning GEOquery 328