bioconductor: GEOquery | Projects

10.1155/2021/6642939

Identification of a Potential PPAR-Related Multigene Signature Predicting Prognosis of Patients with Hepatocellular Carcinoma
Cited by: 7
Author(s): Wenfang Xu, Zhe Chen, Gang Liu, Yong Dai, Xuanfu Xu, Duan Ma, Lei Liu
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pone.0247669

Immune gene expression networks in sepsis: A network biology approach
Cited by: 13
Author(s): Kyung Soo Kim, Dong Wook Jekarl, Jaeeun Yoo, Seungok Lee, Myungshin Kim, Yonggoo Kim
Software Mentions: 5
Published: about 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: over 4 years ago

10.7717/peerj.10462

Development and clinical validation of a 3-miRNA signature to predict prognosis of gastric cancer
Cited by: 8
Author(s): Wenqian Qi, Qian Zhang
Software Mentions: 5
Published: over 3 years ago

10.1038/s42003-021-02520-4

CdGAP promotes prostate cancer metastasis by regulating epithelial-to-mesenchymal transition, cell cycle progression, and apoptosis
Cited by: 8
Author(s): Chahat Mehra, Jin‐Tae Chung, Yi He, Mónica Lara‐Márquez, Marie-Anne Goyette, Nadia Boufaied, Véronique Barrès, Véronique Ouellet, Karl-Philippe Guérard, Carine Delliaux, Fred Saad, Jacques Lapointe, Jean‐François Côté, David P. Labbé, Nathalie Lamarche-Vane
Software Mentions: 5
Published: over 2 years ago

10.3389/fmed.2021.637885

Acid pH Increases SARS-CoV-2 Infection and the Risk of Death by COVID-19
Cited by: 19
Author(s): Leandro Jimenez, Ana Campos Codo, Vanderson de Souza Sampaio, Antônio Edson Rocha Oliveira, Lucas Kaoru Kobo Ferreira, Gustavo Gastão Davanzo, Lauar de Brito Monteiro, João Victor Virgílio-da-Silva, Mayla Gabriela Silva Borba, Gabriela Fabiano de Souza, Nathalia Zini, F Gandolfi, Stéfanie Primon Muraro, José Luiz Proença-Módena, Fernando Almeida Val, Gisely Cardoso de Melo, Wuelton Marcelo Monteiro, Maurício Lacerda Nogueira, Marcus Vinícius Guimarães Lacerda, Pedro M. Moraes‐Vieira, Helder I. Nakaya
Software Mentions: 5
Published: almost 3 years ago

10.1002/cam4.3289

Predicting biomarkers from classifier for liver metastasis of colorectal adenocarcinomas using machine learning models
Cited by: 12
Author(s): Shuwen Han, Yang Xi, Qing Zhou, Zhuang Jing, Wei Wu
Software Mentions: 5
Published: almost 4 years ago

10.7150/jca.50443

Six Novel Biomarkers for Diagnosis and Prognosis of Esophageal squamous cell carcinoma: validated by scRNA-seq and qPCR
Cited by: 24
Author(s): Liuhai Zheng, Linzhi Li, Jun Xie, Hai Jin, Nianyong Zhu
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-020-06811-8

VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development
Cited by: 3
Author(s): Haley S. Toups, Noé Cochetel, D. J. Gray, Grant R. Cramer
Software Mentions: 5
Published: almost 4 years ago

10.3390/genes11070831

Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene Networks
Cited by: 5
Author(s): Fernando M. Delgado-Chaves, Francisco Gómez-Vela, Federico Divina, Miguel García-Torres, Domingo S. Rodríguez–Baena
Software Mentions: 5
Published: almost 4 years ago

10.1155/2020/7503605

Integrated Analyses Identify Immune-Related Signature Associated with Qingyihuaji Formula for Treatment of Pancreatic Ductal Adenocarcinoma Using Network Pharmacology and Weighted Gene Co-Expression Network
Cited by: 9
Author(s): Xiang Qian, Zhuo Chen, Sha Sha Chen, Lu Ming Liu, Ai Qin Zhang
Software Mentions: 5
Published: about 4 years ago

10.1186/s41065-021-00181-1

Prognostic biomarkers and therapeutic targets in oral squamous cell carcinoma: a study based on cross-database analysis
Cited by: 10
Author(s): Wanli Yang, Wei Zhou, Xinhui Zhao, Xiaoqian Wang, Lili Duan, Yiding Li, Liaoran Niu, Junfeng Chen, Yujie Zhang, Yu Han, Daiming Fan, Liu Hong
Software Mentions: 5
Published: about 3 years ago

10.3389/fonc.2019.01497

Identification of Distinct Immune Subtypes in Colorectal Cancer Based on the Stromal Compartment
Cited by: 27
Author(s): Rongfang Shen, Ping Li, Bing Li, Botao Zhang, Feng Li, Shujun Cheng
Software Mentions: 5
Published: over 4 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: almost 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: over 5 years ago

10.7717/peerj.8128

Identification of prognostic gene signature associated with microenvironment of lung adenocarcinoma
Cited by: 57
Author(s): Yufeng Cheng, Hongwen Ma, Yuting Zhou
Software Mentions: 5
Published: over 4 years ago

10.3389/fnins.2019.00002

A Microglial Signature Directing Human Aging and Neurodegeneration-Related Gene Networks
Cited by: 51
Author(s): Shradha Mukherjee, Christine Klaus, Mihaela Pricop-Jeckstadt, Jeremy A. Miller, Felix L Struebing
Software Mentions: 5
Published: over 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: almost 9 years ago

10.1371/journal.pone.0129610

Association of Protein Translation and Extracellular Matrix Gene Sets with Breast Cancer Metastasis: Findings Uncovered on Analysis of Multiple Publicly Available Datasets Using Individual Patient Data Approach
Cited by: 4
Author(s): Nilotpal Chowdhury, Shantanu Sapru
Software Mentions: 5
Published: almost 9 years ago

10.3389/fphys.2019.01226

Integrative Analysis of miRNA and mRNA Expression Profiles Associated With Human Atrial Aging
Cited by: 12
Author(s): Yan Yao, Chen‐Xi Jiang, Fan Wang, Han Yan, Deyong Long, Jinghua Zhao, Jiangang Wang, Chunxiao Zhang, Yang Li, Xiao-Li Tian, Qing Kenneth Wang, Gang Wu, Zhihui Zhang
Software Mentions: 4
Published: over 4 years ago

10.1093/database/bau092

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease
Cited by: 18
Author(s): Qingzhou Zhang, Bo Yang, Xujiao Chen, Jing Xu, Changlin Mei, Zhiguo Mao
Software Mentions: 4
Published: over 9 years ago

10.3390/cancers12061431

Characterization of a Myeloid Activation Signature That Correlates with Survival in Melanoma Patients
Cited by: 1
Author(s): Mirela Kremenovic, Nives Rombini, Alfred A. Chan, Thomas Gruber, Lukas Bäriswyl, Delphine J. Lee, Mirjam Schenk
Software Mentions: 4
Published: about 4 years ago

10.18632/aging.101847

Integrated DNA methylation and gene expression analysis in the pathogenesis of coronary artery disease
Cited by: 30
Author(s): Miao Liu, Rong Yin, Qinghui Zhang, Xi‐Jiang Hu, Feng Huang, Wu-Xian Chen, Xiaoli Cao, Jin‐Zhen Wu
Software Mentions: 4
Published: about 5 years ago

10.1002/2211-5463.13130

<i>CCR7</i> and its related molecules may be potential biomarkers of pulmonary arterial hypertension
Cited by: 5
Author(s): Mengsi Cai, Xiuchun Li, Haoru Dong, Ying Wang, Xiaoying Huang
Software Mentions: 4
Published: about 3 years ago

10.12688/f1000research.9893.2

exprso: an R-package for the rapid implementation of machine learning algorithms
Cited by: 12
Author(s): Thomas P. Quinn, Daniel S. Tylee, Stephen J. Glatt
Software Mentions: 4
Published: over 6 years ago

10.3390/cancers13174250

Transcriptional Reprogramming and Constitutive PD-L1 Expression in Melanoma Are Associated with Dedifferentiation and Activation of Interferon and Tumour Necrosis Factor Signalling Pathways
Cited by: 10
Author(s): Antonio Ahn, Euan J. Rodger, Jyoti Motwani, Grégory Gimenez, Peter A. Stockwell, Matthew Parry, Peter Hersey, Aniruddha Chatterjee, Michael R. Eccles
Software Mentions: 4
Published: almost 3 years ago

10.7554/eLife.65435

T cell self-reactivity during thymic development dictates the timing of positive selection
Cited by: 16
Author(s): Lydia K. Lutes, Zoë Steier, Laura L. McIntyre, Shraddha Pandey, James J. Kaminski, Ashley R. Hoover, Silvia Ariotti, Aaron Streets, Nir Yosef, Ellen A. Robey
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-018-29506-3

Analysis of public RNA-sequencing data reveals biological consequences of genetic heterogeneity in cell line populations
Cited by: 18
Author(s): Erik Fasterius, Cristina Al‐Khalili Szigyarto
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-017-01765-6

Detecting the Molecular System Signatures of Idiopathic Pulmonary Fibrosis through Integrated Genomic Analysis
Cited by: 20
Author(s): Indu Gangwar, Nitesh Kumar Sharma, Ganesh Panzade, Supriya Awasthi, Anurag Agrawal, Ravi Shankar
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-018-29329-2

Determination of system level alterations in host transcriptome due to Zika virus (ZIKV) Infection in retinal pigment epithelium
Cited by: 33
Author(s): Pawan Kumar Singh, Indu Khatri, Alokkumar Jha, Carla D. Pretto, Katherine R. Spindler, Vaithilingaraja Arumugaswami, Shailendra Giri, Ashok Kumar, Manoj Bhasin
Software Mentions: 4
Published: almost 6 years ago

10.1038/srep33752

Transcriptome meta-analysis reveals a dysregulation in extra cellular matrix and cell junction associated gene signatures during Dengue virus infection
Cited by: 27
Author(s): Sumbul Afroz, Jeevan Giddaluru, Mohd. Manzar Abbas, Nooruddin Khan
Software Mentions: 4
Published: over 7 years ago

10.3390/microarrays1020084

Quality Visualization of Microarray Datasets Using Circos
Cited by: 2
Author(s): Martin Koch, Michael Wiese
Software Mentions: 4
Published: almost 12 years ago

10.15252/msb.20177998

The relative resistance of children to sepsis mortality: from pathways to drug candidates
Cited by: 10
Author(s): Rose Bernadette Joachim, Gabriel Altschuler, John N. Hutchinson, Hector R. Wong, Winston Hide, Lester Kobzik
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-019-47046-2

SMAC, a computational system to link literature, biomedical and expression data
Cited by: 2
Author(s): S. Pirro, Emanuela Gadaleta, Andrea Galgani, Vittorio Colizzi, Claude Chelala
Software Mentions: 4
Published: almost 5 years ago

10.1155/2020/1932948

The SLC Family Are Candidate Diagnostic and Prognostic Biomarkers in Clear Cell Renal Cell Carcinoma
Cited by: 20
Author(s): Weiting Kang, Meng Zhang, Qiang Wang, Dawei Gu, Zhilong Huang, Hanbo Wang, Yuzhu Xiang, Qinghua Xia, Zilian Cui, Xunbo Jin
Software Mentions: 4
Published: about 4 years ago

10.3389/pore.2021.588532

Bioinformatics Analysis of Candidate Genes and Pathways Related to Hepatocellular Carcinoma in China: A Study Based on Public Databases
Cited by: 15
Author(s): Peng Zhang, Jing Feng, Xue Wu, Weike Chu, Yilian Zhang, Ping Li
Software Mentions: 4
Published: about 3 years ago

10.7717/peerj.8873

Bioinformatics analyses of retinoblastoma reveal the retinoblastoma progression subtypes
Cited by: 6
Author(s): Manjing Cao, Sha Wang, Jing Zou, Wanpeng Wang
Software Mentions: 4
Published: about 4 years ago

10.1111/jcmm.15393

DNA methylation profiling to predict recurrence risk in stage Ι lung adenocarcinoma: Development and validation of a nomogram to clinical management
Cited by: 12
Author(s): Xianxiong Ma, Jiancheng Cheng, Peng Zhao, Lei Li, Kaixiong Tao, Hengyu Chen
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-020-70368-5

Transcriptomic analysis delineates potential signature genes and miRNAs associated with the pathogenesis of asthma
Cited by: 16
Author(s): Prithvi Singh, Archana Sharma, Jha R, Shweta Arora, Rafiq Ahmad, Arshad Husain Rahmani, Saleh A. Almatroodi, Ravins Dohare, Mansoor Ali Syed
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-020-70540-x

Identification of C3 as a therapeutic target for diabetic nephropathy by bioinformatics analysis
Cited by: 16
Author(s): Shumei Tang, Xiufen Wang, Tianci Deng, Huipeng Ge, Xiangcheng Xiao
Software Mentions: 4
Published: almost 4 years ago

10.7717/peerj.7313

Bioinformatics analysis of microarray data to identify the candidate biomarkers of lung adenocarcinoma
Cited by: 37
Author(s): Tingting Guo, Hongwen Ma, Yuting Zhou
Software Mentions: 4
Published: almost 5 years ago

10.1155/2019/1742341

Based on Integrated Bioinformatics Analysis Identification of Biomarkers in Hepatocellular Carcinoma Patients from Different Regions
Cited by: 9
Author(s): Linxin Teng, Kaiyuan Wang, Yu Liu, Yanxia Ma, Weiping Chen, Lei Bi
Software Mentions: 4
Published: over 4 years ago

10.1155/2014/145243

Integration of High-Volume Molecular and Imaging Data for Composite Biomarker Discovery in the Study of Melanoma
Cited by: 7
Author(s): Κωνσταντίνος Μούτσελος, Ilias Maglogiannis, Aristotelis Chatziioannou
Software Mentions: 4
Published: over 10 years ago

10.1186/1756-0381-6-17

Using random walks to identify cancer-associated modules in expression data
Cited by: 32
Author(s): Deanna Petrochilos, Ali Shojaie, John H. Gennari, Neil F. Abernethy
Software Mentions: 4
Published: over 10 years ago

10.3390/ijerph17031035

A Network-Based Bioinformatics Approach to Identify Molecular Biomarkers for Type 2 Diabetes that Are Linked to the Progression of Neurological Diseases
Cited by: 48
Author(s): Habibur Rahman, Shou-Li Peng, Xiyuan Hu, Chen Chen, Rezanur Rahman, Shahadat Uddin, Julian M.W. Quinn, Mohammad Ali Moni
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pgen.1006589

Robust stratification of breast cancer subtypes using differential patterns of transcript isoform expression
Cited by: 52
Author(s): Thomas Stricker, Christopher D. Brown, Chaitanya Bandlamudi, Megan E. McNerney, Ralf Kittler, Vanessa Montoya, April Peterson, Robert L. Grossman, Kevin P. White
Software Mentions: 4
Published: about 7 years ago

10.3390/cells9092047

Rebuilding Tendons: A Concise Review on the Potential of Dermal Fibroblasts
Cited by: 10
Author(s): Jin Chu, Ming Lu, Christian Pfeifer, Volker Alt, Denitsa Docheva
Software Mentions: 4
Published: over 3 years ago

10.1186/1755-8794-6-51

Co-expression network analysis and genetic algorithms for gene prioritization in preeclampsia
Cited by: 26
Author(s): Eduardo Tejera, João Bernardes, Irene Rebelo
Software Mentions: 4
Published: over 10 years ago

10.1186/s13195-018-0394-7

Alzheimer’s disease master regulators analysis: search for potential molecular targets and drug repositioning candidates
Cited by: 62
Author(s): Daiani Machado de Vargas, Marco Antônio De Bastiani, Eduardo R. Zimmer, Fábio Klamt
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0140885

Increased Transcript Complexity in Genes Associated with Chronic Obstructive Pulmonary Disease
Cited by: 18
Author(s): Lela Lackey, Evonne McArthur, Alain Laederach
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-016-2650-1

Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.)
Cited by: 101
Author(s): Yuanda Lv, Zhikai Liang, Min Ge, Weicong Qi, Tifu Zhang, Feng Lin, Zhaohua Peng, Han Zhao
Software Mentions: 4
Published: about 8 years ago

10.3389/fmolb.2021.703307

A Potential circRNA-miRNA-mRNA Regulatory Network in Asthmatic Airway Epithelial Cells Identified by Integrated Analysis of Microarray Datasets
Cited by: 7
Author(s): Dian Chen, Wenliang Wu, Lingling Yi, Yuchen Feng, Chenli Chang, Shengchong Chen, Jiali Gao, Gongqi Chen, Guohua Zhen
Software Mentions: 4
Published: almost 3 years ago

10.1080/21623945.2020.1829852

Curated gene expression dataset of differentiating 3T3-L1 adipocytes under pharmacological and genetic perturbations
Cited by: 7
Author(s): Mahmoud Ahmed, Do Sik Min, Deok Ryong Kim
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-016-3065-8

Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex
Cited by: 35
Author(s): Jason R. Gerstner, John N. Koberstein, Adam Watson, Nikolai Zapero, Davide Risso, Terence P. Speed, Marcos G. Frank, Lucı́a Peixoto
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0250660

System biology and bioinformatics pipeline to identify comorbidities risk association: Neurodegenerative disorder case study
Cited by: 3
Author(s): Utpala Nanda Chowdhury, Shamim Ahmad, M. Babul Islam, Salem A. Alyami, Julian M.W. Quinn, Valsamma Eapen, Mohammad Ali Moni
Software Mentions: 4
Published: about 3 years ago

10.1093/database/baaa115

HeartBioPortal2.0: new developments and updates for genetic ancestry and cardiometabolic quantitative traits in diverse human populations
Cited by: 4
Author(s): Bohdan B. Khomtchouk, Christopher S. Nelson, Kasra A. Vand, Salvator Palmisano, Robert L. Grossman
Software Mentions: 4
Published: over 4 years ago

10.1186/1471-2105-15-S1-S6

CorrelaGenes: a new tool for the interpretation of the human transcriptome
Cited by: 1
Author(s): Paolo Cremaschi, Sergio Rovida, Lucia Sacchi, Antonella Lisa, Francesca Calvi, Alessandra Montecucco, Giuseppe Biamonti, Silvia Bione, Gianni Sacchi
Software Mentions: 4
Published: over 10 years ago

10.18632/aging.103127

Identification of HMG-box family establishes the significance of SOX6 in the malignant progression of glioblastoma
Cited by: 7
Author(s): Lan Jiang, Hui Yang, Tianbing Chen, Xiaolong Zhu, Jingjing Ye, Kun Lv
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-015-0485-4

NMF-mGPU: non-negative matrix factorization on multi-GPU systems
Cited by: 44
Author(s): Edgardo Mejía-Roa, Daniel Tabas-Madrid, Javier Setoaín, Carlos Garcı́a, Francisco Tirado, Alberto Pascual-Montano
Software Mentions: 4
Published: over 9 years ago

10.3390/genes11060634

metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming
Cited by: 7
Author(s): Daria D. Novikova, Pavel Cherenkov, Yana Sizentsova, В. В. Миронова
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12872-020-01838-x

Bioinformatics analysis of common key genes and pathways of intracranial, abdominal, and thoracic aneurysms
Cited by: 4
Author(s): Siwei Bi, Ruiqi Liu, Linfeng He, Jingyi Li, Jun Gu
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0234062

Exploration of the effects of the CYCLOPS gene RBM17 in hepatocellular carcinoma
Cited by: 6
Author(s): Can Li, Shanghua Ge, Jie Zhou, Jie Peng, Jiayu Chen, Shu-Hui Dong, Xiaoran Feng, Ning Su, Lunli Zhang, Zhong Ye, Libin Deng, Xiaoli Tang
Software Mentions: 3
Published: almost 4 years ago

10.31557/APJCP.2019.20.11.3399

Repurposing Drugs by In Silico Methods to Target BCR Kinase Domain in Chronic Myeloid Leukemia
Cited by: 1
Author(s): Aparna Natarajan, Thangarajan Rajkumar, K.S. Sabitha
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-016-1226-z

Improving sensitivity of linear regression-based cell type-specific differential expression deconvolution with per-gene vs. global significance threshold
Cited by: 10
Author(s): Edmund Glass, Mikhail G. Dozmorov
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-020-03564-9

Clustering analysis of tumor metabolic networks
Cited by: 10
Author(s): Ichcha Manipur, Ilaria Granata, Lucia Maddalena, Mario Rosario Guarracino
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12885-021-08203-x

A genomic-clinicopathologic Nomogram for the preoperative prediction of lymph node metastasis in gastric cancer
Cited by: 5
Author(s): Xin Zhong, Feichao Xuan, Yun Qian, Junhai Pan, Suihan Wang, Wenchao Chen, Tianyu Lin, Hepan Zhu, Xianfa Wang, Guanyu Wang
Software Mentions: 3
Published: about 3 years ago

10.1186/1471-2407-11-450

Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa
Cited by: 30
Author(s): Stefan Enroth, Alvaro Rada-Iglesisas, Robin Andersson, Ola Wallerman, Alkwin Wanders, Lars Påhlman, Jan Komorowski, Claes Wadelius
Software Mentions: 3
Published: over 12 years ago

10.1186/1471-2164-11-574

Heading Down the Wrong Pathway: on the Influence of Correlation within Gene Sets
Cited by: 74
Author(s): Daniel M. Gatti, William T. Barry, Andrew B. Nobel, Ivan Rusyn, Fred A. Wright
Software Mentions: 3
Published: over 13 years ago

10.1186/s12920-017-0252-7

Computational analysis of the mesenchymal signature landscape in gliomas
Cited by: 3
Author(s): Orieta Celiku, Anita Tandle, Joon‐Yong Chung, Stephen M. Hewitt, Kevin Camphausen, Uma Shankavaram
Software Mentions: 3
Published: about 7 years ago

10.1186/s12920-021-00971-6

Bioinformatic identification of hub genes and related transcription factors in low shear stress treated endothelial cells
Cited by: 2
Author(s): Yang Yang, Xiangshan Xu
Software Mentions: 3
Published: about 3 years ago

10.1186/s12893-021-01298-w

Identification of potential hub genes associated with skin wound healing based on time course bioinformatic analyses
Cited by: 2
Author(s): Hongtu Zhu, Meng Fan, Gao Wei
Software Mentions: 3
Published: almost 3 years ago

10.1016/j.bbrep.2015.08.012

Xanthophylls lutein and zeaxanthin modify gene expression and induce synthesis of hyaluronan in keratinocyte model of human skin
Cited by: 9
Author(s): Rasia Li, Stephen D. Turner, David L. Brautigan
Software Mentions: 3
Published: over 8 years ago

10.1155/2020/9780981

Integrated Analysis Identifies an Immune-Based Prognostic Signature for the Mesenchymal Identity in Gastric Cancer
Cited by: 3
Author(s): Dongzhu Peng, Bin Gu, Li-Ming Ruan, Xingguo Zhang, Ping Shu
Software Mentions: 3
Published: about 4 years ago

10.1038/s41416-020-01145-4

A balance score between immune stimulatory and suppressive microenvironments identifies mediators of tumour immunity and predicts pan-cancer survival
Cited by: 12
Author(s): Tolga Turan, Sarah Kongpachith, Kyle Halliwill, Jessica Roelands, Wouter Hendrickx, Francesco M. Marincola, Thomas J. Hudson, Howard J. Jacob, Davide Bedognetti, Josue Samayoa, Michele Ceccarelli
Software Mentions: 3
Published: over 3 years ago

10.1002/cam4.2833

Identification of three m6A‐related mRNAs signature and risk score for the prognostication of hepatocellular carcinoma
Cited by: 50
Author(s): Zedong Li, Fazhan Li, Pei Yu, Jianyu Fang, Jun Zhou
Software Mentions: 3
Published: over 4 years ago

10.7717/peerj.10884

Predicting lung adenocarcinoma disease progression using methylation-correlated blocks and ensemble machine learning classifiers
Cited by: 5
Author(s): Xin Yu, Qian Yang, Dong Wang, Zhaoyang Li, Nianhang Chen, De-Xin Kong
Software Mentions: 3
Published: over 3 years ago

10.7717/peerj.5743

Effects of rheumatoid arthritis associated transcriptional changes on osteoclast differentiation network in the synovium
Cited by: 6
Author(s): Shilpa Harshan, Poulami Dey, Srivatsan Ragunathan
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0229276

Unveiling prognostics biomarkers of tyrosine metabolism reprogramming in liver cancer by cross-platform gene expression analyses
Cited by: 25
Author(s): Tran Nguyen, Ha Nguyen, Duc-Hau Le
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0031333

Cancer Gene Prioritization for Targeted Resequencing Using FitSNP Scores
Cited by: 3
Author(s): Annelies Fieuw, Bram De Wilde, Franki Speleman, Jo Vandesompele, Katleen De Preter
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0189223

Systematic integrative analysis of gene expression identifies HNF4A as the central gene in pathogenesis of non-alcoholic steatohepatitis
Cited by: 47
Author(s): Cristina Baciu, Elisa Pasini, Marc Angeli, Katherine J. P. Schwenger, Jenifar Afrin, Atul Humar, Sandra E. Fischer, Keyur Patel, Johane P. Allard, Mamatha Bhat
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0035322

Nuclear Reprogramming: Kinetics of Cell Cycle and Metabolic Progression as Determinants of Success
Cited by: 23
Author(s): Sebastian T. Balbach, Telma C. Esteves, Franchesca D. Houghton, Marcin Siatkowski, Martin J. Pfeiffer, Chizuko Tsurumi, Benoı̂t Kanzler, Georg Fuellen, Michele Boiani
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0203824

Dissecting cancer heterogeneity based on dimension reduction of transcriptomic profiles using extreme learning machines
Cited by: 11
Author(s): Kejun Wang, Xin Duan, Feng Gao, Wei Wang, Liangliang Liu, Xin Wang
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0215495

CiiiDER: A tool for predicting and analysing transcription factor binding sites
Cited by: 120
Author(s): Linden J. Gearing, Helen E. Cumming, R. A. Chapman, Alexander M. Finkel, Isaac Woodhouse, Kevin Luu, Jodee Gould, Samuel C. Forster, Paul J. Hertzog
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0173664

The miR-200 family is increased in dysplastic lesions in ulcerative colitis patients
Cited by: 14
Author(s): Amy Lewis, Carla Felice, Tomoko Kumagai, Claudia K. Y. Lai, Kriti Singh, Rosemary Jeffery, Roger Feakins, Eleni Giannoulatou, Alessandro Armuzzi, Noor Jawad, James O. Lindsay, Andrew Silver
Software Mentions: 3
Published: about 7 years ago

10.3390/cancers13153716

Primary Aldosteronism: Metabolic Reprogramming and the Pathogenesis of Aldosterone-Producing Adenomas
Cited by: 6
Author(s): Siyuan Gong, Martina Tetti, Martín Reincke, Tracy Ann Williams
Software Mentions: 3
Published: almost 3 years ago

10.1186/s13148-020-00858-w

Histone deacetylase 9 promoter hypomethylation associated with adipocyte dysfunction is a statin-related metabolic effect
Cited by: 10
Author(s): Amna Khamis, Raphaël Boutry, Mickaël Canouil, Sunil Mathew, Stéphane Lobbens, Hutokshi Crouch, Toby Andrew, Amar Abderrahmani, Filippo Tamanini, Philippe Froguel
Software Mentions: 3
Published: about 4 years ago

10.1186/s13148-017-0409-4

Identification of a key role of widespread epigenetic drift in Barrett’s esophagus and esophageal adenocarcinoma
Cited by: 17
Author(s): E. Georg Luebeck, Kit Curtius, William D. Hazelton, Sean K. Maden, Ming Yu, Prashanthi N. Thota, Deepa T. Patil, Amitabh Chak, Joseph E. Willis, William M. Grady
Software Mentions: 3
Published: over 6 years ago

10.1155/2012/650842

ArraySearch: A Web-Based Genomic Search Engine
Cited by: 1
Author(s): Tyler J. Wilson, Xijin Ge
Software Mentions: 3
Published: over 12 years ago

10.3389/fcimb.2021.672472

P2x7 Receptor Signaling Blockade Reduces Lung Inflammation and Necrosis During Severe Experimental Tuberculosis
Cited by: 11
Author(s): Igor Santiago-Carvalho, Gislane Almeida-Santos, Caio César Barbosa Bomfim, Paula Carolina de Souza, Juan Carlo Santos e Silva, Bruno Marcel Silva de Melo, Eduardo Pinheiro Amaral, Marcos Vinícios Pinheiro Cione, Elena B. Lasunskaia, Mário Hiroyuki Hirata, José C. Alves‐Filho, Helder I. Nakaya, José María Álvarez, Maria Regina D’Império Lima
Software Mentions: 3
Published: about 3 years ago

10.3389/fimmu.2015.00536

Precision Subtypes of T Cell-Mediated Rejection Identified by Molecular Profiles
Cited by: 4
Author(s): Paul Ostrom Kadota, Zahraa Hajjiri, Patricia W. Finn, David L. Perkins
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2018.01757

PARP1 Is Up-Regulated in Non-small Cell Lung Cancer Tissues in the Presence of the Cyanobacterial Toxin Microcystin
Cited by: 63
Author(s): Patrick L. Apopa, Lisa Alley, Rosalind B. Penney, Konstantinos Arnaoutakis, Matthew A. Steliga, Susan Jeffus, Emine Bircan, Banu Gopalan, Jing Jin, Preecha Patumcharoenpol, Piroon Jenjaroenpun, Thidathip Wongsurawat, Nishi Shah, Gunnar Boysen, David W. Ussery, Intawat Nookaew, Pebbles Fagan, Gürkan Bebek, Mohammed S. Orloff
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmolb.2020.598221

ANTXR1 Is a Prognostic Biomarker and Correlates With Stromal and Immune Cell Infiltration in Gastric Cancer
Cited by: 9
Author(s): Xiaodong Huang, Jie Zhang, Yongbin Zheng
Software Mentions: 3
Published: over 3 years ago

10.3389/fneur.2020.00184

Identification of Co-expressed Genes Between Atrial Fibrillation and Stroke
Cited by: 13
Author(s): Yanfei Zhang, Ling‐Bing Meng, Meng-lei Hao, Jiao Yang, Tong Zou
Software Mentions: 3
Published: about 4 years ago

10.3389/fphar.2018.00583

DeCoST: A New Approach in Drug Repurposing From Control System Theory
Cited by: 15
Author(s): Thanh Nguyen, Syed Aun Muhammad, Sara Ibrahim, Lin Ma, Jinchao Guo, Baogang Bai, Bixin Zeng
Software Mentions: 3
Published: almost 6 years ago

10.3389/fphar.2020.549804

Riproximin Exhibits Diversity in Sugar Binding, and Modulates some Metastasis-Related Proteins with Lectin like Properties in Pancreatic Ductal Adenocarcinoma
Cited by: 5
Author(s): Micah N. Sagini, Karel D. Klika, Andrew Orry, Michael Zepp, Joshua M. Mutiso, Martin R. Berger
Software Mentions: 3
Published: over 3 years ago

10.3390/genes10090665

Gene Co-Expression Networks Restructured Gene Fusion in Rhabdomyosarcoma Cancers
Cited by: 5
Author(s): Bryan R. Helm, Xiaowei Zhan, Pankita H. Pandya, Mary Ellen Murray, Karen E. Pollok, Jamie L. Renbarger, Michael J. Ferguson, Zhi Han, Dong Ni, Jie Zhang, Kun Huang
Software Mentions: 3
Published: almost 5 years ago

10.21203/rs.3.rs-100914/v1

Sex differences in viral entry protein expression, host responses to SARS-CoV-2, and in vitro responses to sex steroid hormone treatment in COVID-19
Cited by: 5
Author(s): Mengying Sun, Rama Shankar, Meehyun Ko, Christopher Daniel Chang, Shan-Ju Yeh, Shilong Li, Ke Liu, Guoli Zhou, Jing Xing, Austin VanVelsen, Tyler VanVelsen, Shreya Paithankar, Benjamin Y. Feng, Krista Young, Michael Strug, Lauren Turco, Zichen Wang, Eric E. Schadt, Rong Chen, Xiaohong Li, Tomiko Oskotsky, Marina Sirota, Benjamin S. Glicksberg, Girish N. Nadkarni, Adam J. Moeser, Li Li, Seungtaek Kim, Jiayu Zhou, Bin Chen
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-017-03133-w

PCDH18 is frequently inactivated by promoter methylation in colorectal cancer
Cited by: 15
Author(s): Dan Zhou, Weiwei Tang, Guoqiang Su, Mingquan Cai, Han‐Xiang An, Yun Zhang
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-017-12084-1

DNA Methylomes Reveal Biological Networks Involved in Human Eye Development, Functions and Associated Disorders
Cited by: 36
Author(s): María Berdasco, Antonio Gómez, Marc Rubio, Jaume Català‐Mora, Vicente Zanón‐Moreno, Miguel López, Cristina Hernández, Shigeo Yoshida, Takahito Nakama, Keijiro Ishikawa, Tatsuro Ishibashi, Amina Boubekeur, Lotfi Louhibi, Miguel Ángel Pujana, Sergi Sayols, Fernando Setién, Dolores Corella, Carmen de Torres, Andreu Parareda, Ling Zhao, Kang Zhang, Matilde E. Lleonart, Javier Alonso, Rafael Simó, Josep M. Caminal, Manel Esteller
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-33238-9

Genome-wide methylation analysis identifies ELOVL5 as an epigenetic biomarker for the risk of type 2 diabetes mellitus
Cited by: 23
Author(s): Joo-Yeon Hwang, Hyo‐Jung Lee, Min Jin Go, Han Byul Jang, Nak-Hyun Choi, Jae Bum Bae, Juan Castillo-Fernandez, Jordana T. Bell, Tim D. Spector, Hye-Ja Lee, Bong-Jo Kim
Software Mentions: 3
Published: over 5 years ago

Projects: bioconductor: GEOquery

Papers Mentioning GEOquery 328