10.1155/2021/5511507

The Identification of Childhood Asthma Progression-Related lncRNAs and mRNAs Suitable as Biomarkers Using Weighted Gene Coexpression Network Analysis
Cited by: 4
Author(s): Min Hao, Jinling Zan
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms21051707

Co-Expression Network Analysis of Spleen Transcriptome in Rock Bream (Oplegnathus fasciatus) Naturally Infected with Rock Bream Iridovirus (RBIV)
Cited by: 15
Author(s): Ahran Kim, Dahye Yoon, Yunjin Lim, Heyong Jin Roh, Suhkmann Kim, Chan-Il Park, Heui‐Soo Kim, Hee‐Jae Cha, You‐Jin Jeon, Do-Hyung Kim
Software Mentions: 2
Published: over 6 years ago

10.1097/MD.0000000000017100

Using weighted gene co-expression network analysis to identify key modules and hub genes in tongue squamous cell carcinoma
Cited by: 12
Author(s): Ke Yin, Ying Zhang, Suxin Zhang, Yong-Rui Bao, Jie Guo, Hang Zhang, Tianke Li
Software Mentions: 2
Published: about 7 years ago

10.3389/fimmu.2017.00918

Multitype Network-Guided Target Controllability in Phenotypically Characterized Osteosarcoma: Role of Tumor Microenvironment
Cited by: 17
Author(s): Ankush Sharma, Caterina Cinti, Enrico Capobianco
Software Mentions: 2
Published: over 9 years ago

10.1002/1878-0261.12670

Mast cell‐based molecular subtypes and signature associated with clinical outcome in early‐stage lung adenocarcinoma
Cited by: 26
Author(s): Xuanwen Bao, Run Shi, Tianyu Zhao, Yanfang Wang
Software Mentions: 2
Published: over 6 years ago

10.1111/eva.13054

Transcriptomic divergence between upland and lowland ecotypes contributes to rice adaptation to a drought‐prone agroecosystem
Cited by: 9
Author(s): Zhi Luo, Jie Xiong, Hui Xia, Xiaoyan Ma, Min Gao, Lei Wang, Guolan Liu, Yu Xing, Lijun Luo
Software Mentions: 2
Published: over 6 years ago

10.3389/fnmol.2021.623659

Targeted Quantification of Detergent-Insoluble RNA-Binding Proteins in Human Brain Reveals Stage and Disease Specific Co-aggregation in Alzheimer’s Disease
Cited by: 12
Author(s): Qi Guo, Eric B. Dammer, Maotian Zhou, Sean R. Kundinger, Marla Gearing, James J. Lah, Aĺlan I. Levey, Zhandong Liu, Nicholas T. Seyfried
Software Mentions: 2
Published: over 5 years ago

10.1038/s12276-020-00528-0

Single-cell network biology for resolving cellular heterogeneity in human diseases
Cited by: 66
Author(s): Junha Cha, Insuk Lee
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms21082908

Precision Medicine in Childhood Asthma: Omic Studies of Treatment Response
Cited by: 7
Author(s): Javier Pérez-García, Esther Herrera‐Luis, Fabián Lorenzo-Díaz, Mario González, Olaia Sardón, Jesús Villar, Maria Pino‐Yanes
Software Mentions: 2
Published: over 6 years ago

10.12688/f1000research.15271.1

Regulatory network characterization in development: challenges and opportunities
Cited by: 4
Author(s): Guangdun Peng, Jing‐Dong J. Han
Software Mentions: 2
Published: about 8 years ago

10.1186/s12920-016-0173-x

Efficient and biologically relevant consensus strategy for Parkinson’s disease gene prioritization
Cited by: 22
Author(s): Maykel Cruz-Monteagudo, Fernanda Borges, César Paz‐y‐Miño, M. Natália D. S. Cordeiro, Irene Rebelo, Yunierkis Pérez-Castillo, Aliuska Morales Helguera, Aminael Sánchez-Rodríguez, Eduardo Tejera
Software Mentions: 2
Published: over 10 years ago

10.1186/s13024-018-0289-x

ABI3 and PLCG2 missense variants as risk factors for neurodegenerative diseases in Caucasians and African Americans
Cited by: 71
Author(s): Olivia J. Conway, Minerva M. Carrasquillo, Xue Wang, Jenny M. Bredenberg, Joseph S. Reddy, Samantha L. Strickland, Curtis S. Younkin, Jeremy D. Burgess, Mariet Allen, Sarah Lincoln, Thuy Nguyen, Kimberly G. Malphrus, Alexandra I. Soto, Ronald L. Walton, Bradley F. Boeve, Ronald C. Petersen, John A. Lucas, Tanis J. Ferman, William P. Cheshire, Jay A. van Gerpen, Ryan J. Uitti, Zbigniew K. Wszołek, Owen A. Ross, Dennis W. Dickson, Neill R. Graff‐Radford, Nilüfer Ertekin-Taner
Software Mentions: 2
Published: about 8 years ago

10.3390/md19080404

Bacillus amyloliquefaciens-9 Reduces Somatic Cell Count and Modifies Fecal Microbiota in Lactating Goats
Cited by: 3
Author(s): Yongtao Li, Nannan Jiang, Wenying Zhang, Zhengbing Lv, Jianxin Liu, Hengbo Shi
Software Mentions: 2
Published: over 5 years ago

10.1186/s13024-018-0296-y

Genome-wide RNAseq study of the molecular mechanisms underlying microglia activation in response to pathological tau perturbation in the rTg4510 tau transgenic animal model
Cited by: 46
Author(s): Hong Wang, Yupeng Li, John Ryder, Justin T. Hole, Philip J. Ebert, David Airey, Hui-Rong Qian, Benjamin A. Logsdon, Alice Fisher, Zeshan Ahmed, Tracey K. Murray, Annalisa Cavallini, Suchira Bose, Brian J. Eastwood, David A. Collier, Jeffrey L. Dage, Bradley B. Miller, Kalpana Merchant, Michael O’Neill, Ronald B. DeMattos
Software Mentions: 2
Published: almost 8 years ago

10.7150/thno.54476

Pectin supplement significantly enhanced the anti-PD-1 efficacy in tumor-bearing mice humanized with gut microbiota from patients with colorectal cancer
Cited by: 66
Author(s): Shilong Zhang, Yuqin Mao, Zhengyan Zhang, Zhanming Li, Chao‐Yue Kong, Huiling Chen, Pei-Ran Cai, Bing Han, Tao Ye, Li‐Shun Wang
Software Mentions: 2
Published: almost 6 years ago

10.7150/thno.56202

Identification and validation of hypoxia-derived gene signatures to predict clinical outcomes and therapeutic responses in stage I lung adenocarcinoma patients
Cited by: 38
Author(s): Run Shi, Xuanwen Bao, Kristian Unger, Jing Sun, Shun Lü, Farkhad Manapov, Xuanbin Wang, Claus Belka, Minglun Li
Software Mentions: 2
Published: almost 6 years ago

10.3389/fnmol.2018.00091

Profiling of Long Non-coding RNAs and mRNAs by RNA-Sequencing in the Hippocampi of Adult Mice Following Propofol Sedation
Cited by: 9
Author(s): Jun Fan, Quan Zhou, Yan Li, Xiuling Song, Jijie Hu, Zaisheng Qin, Jing Tang, Tao Tao
Software Mentions: 2
Published: over 8 years ago

10.1186/s12859-017-1889-0

Repositioning drugs by targeting network modules: a Parkinson’s disease case study
Cited by: 24
Author(s): Zongliang Yue, Itika Arora, Eric Y. Zhang, Vincent A. Laufer, S. Louis Bridges, Jake Y. Chen
Software Mentions: 2
Published: almost 9 years ago

10.1128/mSystems.00293-21

High Transcriptional Activity and Diverse Functional Repertoires of Hundreds of Giant Viruses in a Coastal Marine System
Cited by: 22
Author(s): Anh D. Ha, Mohammad Moniruzzaman, Frank O. Aylward
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2021.709164

Defining a Methylation Signature Associated With Operational Tolerance in Kidney Transplant Recipients
Cited by: 5
Author(s): Ramón María Alvargonzález Rodríguez, María P. Hernández-Fuentes, Viviana Corte-Iglesias, María Laura Sáiz, Juan José Lozano, Ana R. Cortázar, Isabel Mendizabal, María Luisa Suárez-Fernández, Eliécer Coto, Antonio López-Vázquez, Carmen Díaz‐Corte, Ana M. Aransay, Carlos López‐Larrea, Beatriz Suárez-Álvarez
Software Mentions: 2
Published: about 5 years ago

10.1186/s40246-021-00303-w

Screening of disease-related biomarkers related to neuropathic pain (NP) after spinal cord injury (SCI)
Cited by: 11
Author(s): Jia Zhao, Yang Li, Li-Min Huang, Zinan Li
Software Mentions: 2
Published: almost 6 years ago

10.1002/2211-5463.12964

LMTK3 promotes tumorigenesis in bladder cancer via the ERK/MAPK pathway
Cited by: 15
Author(s): Tao Jiang, Xia Lu, Feiya Yang, Mingshuai Wang, Hua Yang, Nianzeng Xing
Software Mentions: 2
Published: about 6 years ago

10.1111/1759-7714.13836

Identification of small proline‐rich protein <scp>1B</scp> ( <scp>SPRR1B</scp> ) as a prognostically predictive biomarker for lung adenocarcinoma by integrative bioinformatic analysis
Cited by: 11
Author(s): Zihe Zhang, Ruifeng Shi, Songlin Xu, Yongwen Li, Hongbing Zhang, Minghui Liu, Guangsheng Zhu, Chen Chen, Zhengxia Pan, Hongyu Liu, Jun Chen
Software Mentions: 2
Published: almost 6 years ago

10.1002/fsn3.2283

Chain length‐dependent inulin alleviates diet‐induced obesity and metabolic disorders in mice
Cited by: 9
Author(s): Liangkui Li, Lu Zhang, Linkang Zhou, Meijun Jin, Li Xu
Software Mentions: 2
Published: over 5 years ago

10.3389/fendo.2020.00510

Identification of a Prognostic 3-Gene Risk Prediction Model for Thyroid Cancer
Cited by: 8
Author(s): Haiping Zhao, Shiwei Zhang, Shijie Shao, Haixing Fang
Software Mentions: 2
Published: about 6 years ago

10.3389/fgene.2019.00294

Network Medicine in the Age of Biomedical Big Data
Cited by: 119
Author(s): Abhijeet R. Sonawane, Scott T. Weiss, Kimberly Glass, Amitabh Sharma
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-021-03987-y

ComHub: Community predictions of hubs in gene regulatory networks
Cited by: 9
Author(s): Julia Åkesson, Zelmina Lubovac-Pilav, Rasmus Magnusson, Mika Gustafsson
Software Mentions: 2
Published: over 5 years ago

10.1186/1755-8794-5-61

Adipose Co-expression networks across Finns and Mexicans identify novel triglyceride-associated genes
Cited by: 30
Author(s): Blake E. Haas, Steve Horvath, Kirsi H. Pietiläinen, Rita M. Cantor, Elina Nikkola, Daphna Weissglas‐Volkov, Aila Rissanen, Mete Civelek, Ivette Cruz-Bautista, Laura Riba, Johanna Kuusisto, Jaakko Kaprio, Teresa Tusié-Luna, Markku Laakso, Carlos A. Aguilar-Salinas, Päivi Pajukanta
Software Mentions: 2
Published: almost 14 years ago

10.3389/fnagi.2018.00153

Integrative Analysis of Hippocampus Gene Expression Profiles Identifies Network Alterations in Aging and Alzheimer’s Disease
Cited by: 53
Author(s): Vinay Lanke, S.T.R. Moolamalla, Dipanjan Roy, P. Vinod
Software Mentions: 2
Published: over 8 years ago

10.3389/fnagi.2020.605961

Co-expression Network Analysis Reveals Novel Genes Underlying Alzheimer’s Disease Pathogenesis
Cited by: 16
Author(s): Ruiting Hu, Qian Yu, Shao-Dan Zhou, Yuqing Yin, Rui-guang Hu, Hai-peng Lu, Bang-li Hu
Software Mentions: 2
Published: almost 6 years ago

10.3390/toxins13060401

Transcriptional Profiling of Aflatoxin B1-Induced Oxidative Stress and Inflammatory Response in Macrophages
Cited by: 27
Author(s): Jun Ma, Yanrong Liu, Yongpeng Guo, Qiugang Ma, Cheng Ji, Lihong Zhao
Software Mentions: 2
Published: over 5 years ago

10.1186/s12920-020-0689-y

Differential co-expression analysis reveals early stage transcriptomic decoupling in alzheimer’s disease
Cited by: 2
Author(s): Y. M. Upadhyaya, Linhui Xie, Paul Salama, Sha Cao, Kwangsik Nho, Andrew J. Saykin, Jingwen Yan
Software Mentions: 2
Published: over 6 years ago

10.1186/s12920-018-0431-1

Condition-specific gene co-expression network mining identifies key pathways and regulators in the brain tissue of Alzheimer’s disease patients
Cited by: 21
Author(s): Shunian Xiang, Zhi Huang, Tianfu Wang, Zhi Han, Christina Y. Yu, Dong Ni, Kun Huang, Jie Zhang
Software Mentions: 2
Published: almost 8 years ago

10.1002/mgg3.515

Gene coexpression network analysis identified potential biomarkers in gestational diabetes mellitus progression
Cited by: 11
Author(s): Xuefei Zhao, Wen Li
Software Mentions: 2
Published: almost 8 years ago

10.3389/frai.2021.674370

Similarities and Differences in Gene Expression Networks Between the Breast Cancer Cell Line Michigan Cancer Foundation-7 and Invasive Human Breast Cancer Tissues
Cited by: 6
Author(s): Vy Tran, Robert Kim, Mikhail Maertens, Thomas Hartung, Alexandra Maertens
Software Mentions: 2
Published: over 5 years ago

10.18632/aging.203360

A combined hypoxia and immune gene signature for predicting survival and risk stratification in triple-negative breast cancer
Cited by: 28
Author(s): Yang Xia, Xin Weng, Yong Yang, Meng Zhang, Yingjie Xiu, Wenfeng Peng, Xuhui Liao, Meiquan Xu, Yan Sun, Xia Liu
Software Mentions: 2
Published: about 5 years ago

10.1093/brain/awaa217

Dystonia genes functionally converge in specific neurons and share neurobiology with psychiatric disorders
Cited by: 45
Author(s): Niccolò E. Mencacci, Regina H Reynolds, Sonia García-Ruiz, Jana Vandrovcová, Paola Forabosco, Álvaro Sánchez‐Ferrer, Viola Volpato, Juan A. Botía, Karishma D’Sa, Paola Forabosco, Sebastian Guelfi, John Hardy, Jana Vandrovcová, Chris-Ann Mackenzie, Adaikalavan Ramasamy, Mina Ryten, Colin Smith, Daniah Trabzuni, Michael E. Weale, Alastair Noyce, Rauan Kaiyrzhanov, Ben Middlehurst, Demis A. Kia, Manuela Tan, Henry Houlden, Huw R. Morris, Hélène Plun‐Favreau, Peter Holmans, John Hardy, Daniah Trabzuni, José Brás, John P. Quinn, Kin Y. Mok, Kerri J. Kinghorn, Kimberley Billingsley, Nicholas W. Wood, Patrick A. Lewis, Rita Guerreiro, Ruth C. Lovering, Lea R’Bibo, Claudia Manzoni, Mie Rizig, Mina Ryten, Sebastian Guelfi, Valentina Escott‐Price, Viorica Chelban, Thomas Foltynie, Nigel Williams, Chingiz Shashakin, Nazira Zharkinbekova, Elena Zholdybayeva, Akbota Aitkulova, Kirsten Harvey, Michael E. Weale, Kailash P. Bhatia, Caleb Webber, John Hardy, Juan A. Botía, Mina Ryten
Software Mentions: 2
Published: about 6 years ago

10.3389/fimmu.2021.699633

IRF7-Associated Immunophenotypes Have Dichotomous Responses to Virus/Allergen Coexposure and OM-85-Induced Reprogramming
Cited by: 3
Author(s): Emma de Jong, Jean-François Lauzon-Joset, Jonatan Leffler, Michael Serralha, Alexander N. Larcombe, Claus T. Christophersen, Patrick G. Holt, Deborah H. Strickland, Anthony Bosco
Software Mentions: 2
Published: over 5 years ago

10.1038/s41416-019-0477-7

Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRASG13D mutation
Cited by: 32
Author(s): Theodosia Charitou, Sriganesh Srihari, Miriam A. Lynn, Mohamed Ali Jarboui, Erik Fasterius, Max Moldovan, Senji Shirasawa, Toshiyuki Tsunoda, Marius Ueffing, Jianling Xie, Xin Jin, Xuemin Wang, Christopher G. Proud, Karsten Boldt, Cristina Al‐Khalili Szigyarto, Walter Kölch, David J. Lynn
Software Mentions: 2
Published: over 7 years ago

10.3389/fbioe.2014.00048

Protein Network Signatures Associated with Exogenous Biofuels Treatments in Cyanobacterium Synechocystis sp. PCC 6803
Cited by: 11
Author(s): Guangsheng Pei, Lei Chen, Jiangxin Wang, Jianjun Qiao, Weiwen Zhang
Software Mentions: 2
Published: almost 12 years ago

10.3389/fbioe.2020.00729

OASL as a Diagnostic Marker for Influenza Infection Revealed by Integrative Bioinformatics Analysis With XGBoost
Cited by: 7
Author(s): Yang Li, Hongjie Liu, Quan Xu, Rui Wu, Yi Zhang, Naizhe Li, Xiaozhou He, Mengjie Yang, Mifang Liang, Xuejun Ma
Software Mentions: 2
Published: over 6 years ago

10.3389/fbioe.2020.00031

Transcriptomic Analyses for Identification and Prioritization of Genes Associated With Alzheimer’s Disease in Humans
Cited by: 17
Author(s): Yuchen Shi, Hui Liu, Changbo Yang, Kang Xu, Yangyang Cai, Zhao Wang, Zheng Zhao, Tingting Shao, Yixue Li
Software Mentions: 2
Published: over 6 years ago

10.3390/molecules24142564

Integration of Metabolite Profiling and Transcriptome Analysis Reveals Genes Related to Volatile Terpenoid Metabolism in Finger Citron (C. medica var. sarcodactylis)
Cited by: 37
Author(s): Yaying Xu, Changqing Zhu, Changjie Xu, Jun Sun, Donald Grierson, Bo Zhang, Kunsong Chen
Software Mentions: 2
Published: over 7 years ago

10.3389/fbioe.2018.00151

Gene Co-expression Network Reveals Potential New Genes Related to Sugarcane Bagasse Degradation in Trichoderma reesei RUT-30
Cited by: 19
Author(s): Gustavo Pagotto Borin, Marcelo Falsarella Carazzolle, Renato Augusto Corrêa dos Santos, Diego Mauricio Riaño‐Pachón, Juliana Velasco de Castro Oliveira
Software Mentions: 2
Published: about 8 years ago

10.1186/s13059-017-1279-y

An interaction map of circulating metabolites, immune gene networks, and their genetic regulation
Cited by: 38
Author(s): Artika P. Nath, Scott C. Ritchie, Sean G. Byars, Liam G. Fearnley, Aki S. Havulinna, Anni Joensuu, Antti J. Kangas, Pasi Soininen, Annika Wennerström, Lili Milani, Andres Metspalu, Satu Männistö, Peter Würtz, Johannes Kettunen, Emma Raitoharju, Mika Kähönen, Markus Juonala, Aarno Palotie, Mika Ala‐Korpela, Samuli Ripatti, Terho Lehtimäki, Gad Abraham, Olli T. Raitakari, Veikko Salomaa, Markus Perola, Michael Inouye
Software Mentions: 2
Published: about 9 years ago

10.1186/s13293-019-0259-1

The developmental origins of sex-biased expression in cardiac development
Cited by: 30
Author(s): Daniel F. Deegan, Reza Karbalaei, Jozef Madžo, Rob J. Kulathinal, Nora Engel
Software Mentions: 2
Published: about 7 years ago

10.1186/1471-2105-14-42

A new unsupervised gene clustering algorithm based on the integration of biological knowledge into expression data
Cited by: 21
Author(s): Marie Verbanck, Sébastien Lê, Jacques Pagès
Software Mentions: 2
Published: over 13 years ago

10.1186/s12920-020-0672-7

Pathway mapping of leukocyte transcriptome in influenza patients reveals distinct pathogenic mechanisms associated with progression to severe infection
Cited by: 12
Author(s): Yoann Zerbib, Emily Jenkins, Maryam Shojaei, Adrienne F. A. Meyers, John Ho, T. Blake Ball, Yoav Keynan, Amarnath Pisipati, Aseem Kumar, Anand Kumar, Marek Nalos, Benjamin Tang, Klaus Schughart, Anthony S. McLean
Software Mentions: 2
Published: over 6 years ago

10.3389/fcvm.2021.647953

The Integrative Analysis of Competitive Endogenous RNA Regulatory Networks in Coronary Artery Disease
Cited by: 3
Author(s): Yuyao Ji, Tao Yan, Shijie Zhu, Runda Wu, Miao Zhu, Yangyang Zhang, Changfa Guo, Kang Yao
Software Mentions: 2
Published: about 5 years ago

10.3389/fcvm.2020.631775

Integrative Identification of Hub Genes Associated With Immune Cells in Atrial Fibrillation Using Weighted Gene Correlation Network Analysis
Cited by: 9
Author(s): Tao Yan, Shijie Zhu, Miao Zhu, Chunsheng Wang, Changfa Guo
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12920-014-0060-2

A common gene expression signature in Huntington’s disease patient brain regions
Cited by: 46
Author(s): Andreas Neueder, Gillian P. Bates
Software Mentions: 2
Published: about 12 years ago

10.1186/s13059-019-1700-9

Addressing confounding artifacts in reconstruction of gene co-expression networks
Cited by: 68
Author(s): Princy Parsana, Claire Ruberman, Andrew E. Jaffe, Michael C. Schatz, Alexis Battle, Jeffrey T. Leek
Software Mentions: 2
Published: over 7 years ago

10.1186/s13059-019-1786-0

Regulation of rumen development in neonatal ruminants through microbial metagenomes and host transcriptomes
Cited by: 81
Author(s): Nilusha Malmuthuge, Guanxiang Liang, Le Luo Guan
Software Mentions: 2
Published: about 7 years ago

10.3390/molecules24061064

Metabolome and Transcriptome Sequencing Analysis Reveals Anthocyanin Metabolism in Pink Flowers of Anthocyanin-Rich Tea (Camellia sinensis)
Cited by: 49
Author(s): Dylan O’Neill Rothenberg, Haijun Yang, Meiban Chen, Wenting Zhang, Lingyun Zhang
Software Mentions: 2
Published: over 7 years ago

10.3390/molecules22122228

Multi-Objective Optimization Algorithm to Discover Condition-Specific Modules in Multiple Networks
Cited by: 5
Author(s): Xiaoke Ma, Penggang Sun, Jun Zhao
Software Mentions: 2
Published: almost 9 years ago

10.3389/fcvm.2021.712061

Association of Circulating, Inflammatory-Response Exosomal mRNAs With Acute Myocardial Infarction
Cited by: 7
Author(s): Guangbin He, Yu-Qing Huang, Lin Liu, Jiayi Huang, Kenneth Lo, Yu-Ling Yu, Chaolei Chen, Bin Zhang, Yingqing Feng
Software Mentions: 2
Published: about 5 years ago

10.1186/s12920-014-0072-y

Identifying a gene expression signature of frequent COPD exacerbations in peripheral blood using network methods
Cited by: 49
Author(s): Jarrett Morrow, Weiliang Qiu, Divya Chhabra, Stephen I. Rennard, Paula Belloni, Anton Belousov, Sreekumar Pillai, Craig P. Hersh
Software Mentions: 2
Published: almost 12 years ago

10.3389/fcell.2021.742421

An Advanced Systems Pharmacology Strategy Reveals AKR1B1, MMP2, PTGER3 as Key Genes in the Competing Endogenous RNA Network of Compound Kushen Injection Treating Gastric Carcinoma by Integrated Bioinformatics and Experimental Verification
Cited by: 3
Author(s): Wei Zhou, Chao Wu, Chao Zhao, Zhihong Huang, Shan Lu, Xiaotian Fan, Yingying Tan, Antony Stalin, Rongli You, Xinkui Liu, Jingyuan Zhang, Zhishan Wu, Jiarui Wu
Software Mentions: 2
Published: about 5 years ago

10.1186/s12881-019-0791-1

Weighted correlation network and differential expression analyses identify candidate genes associated with BRAF gene in melanoma
Cited by: 9
Author(s): Bin Zhao, Yanqiu You, Weiping Zheng, Yunhan Ma, Yani Huo, Hongyi Liu, Yuanyuan Zhou, Wei Quan, Weibin Chen, Xiaohong Zhang, Fujun Li, Yilin Zhao
Software Mentions: 2
Published: over 7 years ago

10.1186/s12881-020-01145-4

Development of an immunogenomic landscape for the competing endogenous RNAs network of peri-implantitis
Cited by: 7
Author(s): Li Yang, Jie Zheng, Chan Juan Gong, Keng Fu Lan, Yu Qing Shen, Xiao Jun Ding
Software Mentions: 2
Published: about 6 years ago

10.3390/ijms21093288

Comparative Transcriptome Analysis Combining SMRT- and Illumina-Based RNA-Seq Identifies Potential Candidate Genes Involved in Betalain Biosynthesis in Pitaya Fruit
Cited by: 22
Author(s): Yanyan Wu, Juan Xu, Xuelei Han, Guo Qiao, Kun Yang, Wen Zhuang, Xiaopeng Wen
Software Mentions: 2
Published: over 6 years ago

10.1186/s13059-020-02213-x

An integrated multi-omics approach to identify regulatory mechanisms in cancer metastatic processes
Cited by: 10
Author(s): Saba Ghaffari, Casey Hanson, Remington E. Schmidt, Kelly J. Bouchonville, Steven M. Offer, Saurabh Sinha
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12881-019-0832-9

A novel risk score system for assessment of ovarian cancer based on co-expression network analysis and expression level of five lncRNAs
Cited by: 30
Author(s): Qian Zhao, Conghong Fan
Software Mentions: 2
Published: over 7 years ago

10.1186/s12575-019-0108-y

Comprehensive Transcriptomic Analysis of Mouse Gonadal Development Involving Sexual Differentiation, Meiosis and Gametogenesis
Cited by: 10
Author(s): Jian Wang, Geng Tian, Zhan‐Jiang Zheng, Bo Li, Qinghe Xing, Ji Wu
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-021-07763-3

Transcriptome analysis reveals Vernalization is independent of cold acclimation in Arabidopsis
Cited by: 12
Author(s): Fēi Li, Qian Hu, Fadi Chen, Jingle Jiang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12943-020-01259-6

Circular HER2 RNA positive triple negative breast cancer is sensitive to Pertuzumab
Cited by: 83
Author(s): Jie Li, Maoguang Ma, Xuesong Yang, Maolei Zhang, Jixian Luo, Huangkai Zhou, Nunu Huang, Feizhe Xiao, Bingquan Lai, Weiming Lv, Nu Zhang
Software Mentions: 2
Published: about 6 years ago

10.3389/fcell.2020.604627

Identification of a Gene Signature for Renal Cell Carcinoma–Associated Fibroblasts Mediating Cancer Progression and Affecting Prognosis
Cited by: 24
Author(s): Bitian Liu, Xiaonan Chen, Yunhong Zhan, Bin Wu, Pan Shen
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-021-02366-3

Cellular and transcriptomic analyses reveal two-staged chloroplast biogenesis underpinning photosynthesis build-up in the wheat leaf
Cited by: 22
Author(s): Naresh Loudya, Pravas Mishra, Kotaro Takahagi, Yukiko Uehara‐Yamaguchi, Komaki Inoue, László Bögre, Keiichi Mochida, Enrique López‐Juez
Software Mentions: 2
Published: over 5 years ago

10.1186/s12943-021-01342-6

Identification of tumor antigens and immune subtypes of cholangiocarcinoma for mRNA vaccine development
Cited by: 66
Author(s): Xing Huang, Tianyu Tang, Gang Zhang, Tingbo Liang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12935-018-0703-z

Identification of biomarkers of chromophobe renal cell carcinoma by weighted gene co-expression network analysis
Cited by: 17
Author(s): Xiaomao Yin, Jianfeng Wang, Jin Zhang
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-021-07557-7

Post-diapause transcriptomic restarts: insight from a high-latitude copepod
Cited by: 5
Author(s): Vittoria Roncalli, Matthew Cieslak, Ann M. Castelfranco, Russell R. Hopcroft, Daniel K. Hartline, Petra H. Lenz
Software Mentions: 2
Published: over 5 years ago

10.1186/s13041-021-00829-z

RNA-seq co-expression network analysis reveals anxiolytic behavior of mice with Efnb2 knockout in parvalbumin+ neurons
Cited by: 1
Author(s): Ying Sun, Le Ma, Jianhua Chen, Weidi Wang, Shi-Yu Peng, Ying Cheng, Yu Zhang, Jinghong Chen, Peijun Ju
Software Mentions: 2
Published: over 5 years ago

10.1186/s13568-019-0763-z

Altered diversity and composition of the gut microbiome in patients with cervical cancer
Cited by: 45
Author(s): Zhongqiu Wang, Qingxin Wang, Jing Zhao, Lei Gong, Yan Zhang, Xia Wang, Zhiyong Yuan
Software Mentions: 2
Published: over 7 years ago

10.3389/fcell.2020.577032

The Landscape of Coronavirus Disease 2019 (COVID-19) and Integrated Analysis SARS-CoV-2 Receptors and Potential Inhibitors in Lung Adenocarcinoma Patients
Cited by: 6
Author(s): Bufu Tang, Jinyu Zhu, Ying Cong, Wenting Yang, Chunli Kong, Weiyue Chen, Yajie Wang, Yong Zeng, Jiansong Ji
Software Mentions: 2
Published: about 6 years ago

10.1242/bio.016402

Co-expression networks in generation of induced pluripotent stem cells
Cited by: 3
Author(s): Sharan Paul, Lance Pflieger, Warunee Dansithong, Karla P. Figueroa, Fuying Gao, Giovanni Coppola, Stefan M. Pulst
Software Mentions: 2
Published: over 10 years ago

10.3389/fcell.2021.607782

Hypermethylation and Downregulation of UTP6 Are Associated With Stemness Properties, Chemoradiotherapy Resistance, and Prognosis in Rectal Cancer: A Co-expression Network Analysis
Cited by: 1
Author(s): Yiyi Zhang, Qun Gao, Yong Wu, Yong Peng, Jinfu Zhuang, Yuanfeng Yang, Weizhong Jiang, Xing Liu, Guoxian Guan
Software Mentions: 2
Published: about 5 years ago

10.1186/s13073-014-0075-5

Alteration in basal and depolarization induced transcriptional network in iPSC derived neurons from Timothy syndrome
Cited by: 72
Author(s): Yuan Tian, Irina Voineagu, Sergiu P. Pașca, Hyejung Won, Vijayendran Chandran, Steve Horvath, Ricardo E. Dolmetsch, Daniel H. Geschwind
Software Mentions: 2
Published: about 12 years ago

10.1186/s13073-015-0162-2

Transcriptomic landscape of lncRNAs in inflammatory bowel disease
Cited by: 134
Author(s): Aashiq H. Mirza, Claus Hb Berthelsen, Stefan E. Seemann, Xiaoyong Pan, Klaus Stensgaard Frederiksen, M. Vilien, Jan Gorodkin, Flemming Pociot
Software Mentions: 2
Published: over 11 years ago

10.1186/s13073-015-0229-0

An integrative systems genetics approach reveals potential causal genes and pathways related to obesity
Cited by: 31
Author(s): Lisette J. A. Kogelman, Daria V. Zhernakova, Harm-Jan Westra, Susanna Cirera, Merete Fredholm, Lude Franke, Haja N. Kadarmideen
Software Mentions: 2
Published: about 11 years ago

10.1186/s12864-017-4005-y

Differentiated transcriptional signatures in the maize landraces of Chiapas, Mexico
Cited by: 12
Author(s): Matthew A. Kost, Hugo Perales, Saranga Wijeratne, Asela J. Wijeratne, Eric J. Stockinger, Kristin L. Mercer
Software Mentions: 2
Published: about 9 years ago

10.1186/s13229-019-0278-0

CYFIP1 overexpression increases fear response in mice but does not affect social or repetitive behavioral phenotypes
Cited by: 16
Author(s): Catherine J. Fricano-Kugler, Aaron Gordon, Grace S. Shin, Kun Gao, Jade Nguyen, Jamee M Berg, Mary e. Starks, Daniel H. Geschwind
Software Mentions: 2
Published: over 7 years ago

10.1186/s13062-018-0229-2

Integrative analysis based on survival associated co-expression gene modules for predicting Neuroblastoma patients’ survival time
Cited by: 21
Author(s): Han Ying, Xiufen Ye, Jun Cheng, Siyuan Zhang, Weixing Feng, Zhi Han, Jie Zhang, Kun Huang
Software Mentions: 2
Published: over 7 years ago

10.3389/fnins.2016.00396

Comparative Gene Expression Analysis of Two Mouse Models of Autism: Transcriptome Profiling of the BTBR and En2−/− Hippocampus
Cited by: 27
Author(s): Giovanni Provenzano, Zelia Corradi, Katia Monsorno, Tarcisio Fedrizzi, Laura Ricceri, María Luisa Scattoni, Yuri Bozzi
Software Mentions: 2
Published: about 10 years ago

10.1186/s13073-017-0417-1

A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis
Cited by: 83
Author(s): Jaclyn N. Taroni, Casey S. Greene, Viktor Martyanov, Tammara A. Wood, Romy B. Christmann, Harrison W. Farber, Robert Lafyatis, Christopher P. Denton, Monique Hinchcliff, Patricia A. Pioli, James Mahoney, Michael L. Whitfield
Software Mentions: 2
Published: over 9 years ago

10.1186/s13229-017-0147-7

Hierarchical cortical transcriptome disorganization in autism
Cited by: 23
Author(s): Michael Lombardo, Eric Courchesne, Nathan E. Lewis, Tiziano Pramparo
Software Mentions: 2
Published: over 9 years ago

10.1186/s13062-019-0244-y

Integration of molecular features with clinical information for predicting outcomes for neuroblastoma patients
Cited by: 22
Author(s): Han Ying, Xiufen Ye, Chao Wang, Yusong Liu, Siyuan Zhang, Weixing Feng, Kun Huang, Jie Zhang
Software Mentions: 2
Published: about 7 years ago

10.3389/fimmu.2021.738435

Recognition of Tumor-Associated Antigens and Immune Subtypes in Glioma for mRNA Vaccine Development
Cited by: 10
Author(s): Shuai Ma, Yixu Ba, Hang Ji, Fang Wang, Jianyang Du, Shaoshan Hu
Software Mentions: 2
Published: about 5 years ago

10.1186/s13073-018-0519-4

Characterization of cross-tissue genetic-epigenetic effects and their patterns in schizophrenia
Cited by: 45
Author(s): Dongdong Lin, Jiayu Chen, Nora I. Perrone‐Bizzozero, Juan Bustillo, Yuhui Du, Vince D. Calhoun, Jingyu Liu
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-018-5117-8

Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus
Cited by: 37
Author(s): Enhui Shen, Xintian Zhu, Shuijin Hua, Hongyu Chen, Chu-Yu Ye, Longhua Zhou, Qing Liu, Qian‐Hao Zhu, Longjiang Fan, Xi Chen
Software Mentions: 2
Published: about 8 years ago

10.3389/fcell.2021.691540

Multi-Omics Integrative Bioinformatics Analyses Reveal Long Non-coding RNA Modulates Genomic Integrity via Competing Endogenous RNA Mechanism and Serves as Novel Biomarkers for Overall Survival in Lung Adenocarcinoma
Cited by: 4
Author(s): Zhong Lin Wang, Ziyuan Ren, Rui Li, Junpeng Ge, Guoming Zhang, Yaodong Xin, Yi-Qing Qu
Software Mentions: 2
Published: over 5 years ago

10.1186/1745-6150-9-12

Selecting biologically informative genes in co-expression networks with a centrality score
Cited by: 51
Author(s): Francisco Azuaje
Software Mentions: 2
Published: almost 13 years ago

10.3389/fimmu.2021.658341

Exploration of the Shared Gene Signatures and Molecular Mechanisms Between Systemic Lupus Erythematosus and Pulmonary Arterial Hypertension: Evidence From Transcriptome Data
Cited by: 31
Author(s): Meng Yao, Chunyi Zhang, Congcong Gao, Qianqian Wang, Mengmeng Dai, Runzhi Yue, Wenbo Sun, Wenfang Liang, Zhaohui Zheng
Software Mentions: 2
Published: over 5 years ago

10.3390/microorganisms7070195

Dynamic Gene Network Analysis of Caco-2 Cell Response to Shiga Toxin-Producing Escherichia coli-Associated Hemolytic–Uremic Syndrome
Cited by: 6
Author(s): Sílvia Yumi Bando, Priscila Iamashita, Filipi Nascimento Silva, Luciano da Fontoura Costa, Cecília M. Abe, Fernanda Bernardi Bertonha, Beatriz Ernestina Cabílio Guth, André Fujita, Carlos Alberto Moreira-Filho
Software Mentions: 2
Published: over 7 years ago

10.1186/s12935-019-0928-5

A nomogram based on 9-lncRNAs signature for improving prognostic prediction of clear cell renal cell carcinoma
Cited by: 24
Author(s): Wen Jiang, Qing Guo, Chenghe Wang, Yu Zhu
Software Mentions: 2
Published: about 7 years ago

10.1186/s40168-018-0441-4

Gut-dependent microbial translocation induces inflammation and cardiovascular events after ST-elevation myocardial infarction
Cited by: 167
Author(s): Xin Zhou, Jing Li, Junli Guo, Bin Geng, Wenjie Ji, Qian Zhao, Jinxin Li, Xinlin Liu, Junxiang Liu, Zhao-Zeng Guo, Wei Cai, Yun Ma, Dong Ren, Jun Miao, Shaobo Chen, Zhuoli Zhang, Junru Chen, Jiuchang Zhong, Wenbin Liu, Ming‐Hui Zou, Yuming Li, Jun Cai
Software Mentions: 2
Published: over 8 years ago

10.3389/fcell.2021.606106

Identification of Biomarkers Related to CD8+ T Cell Infiltration With Gene Co-expression Network in Lung Squamous Cell Carcinoma
Cited by: 10
Author(s): Min Tang, Yukun Li, Xianyu Luo, Jianru Xiao, Juan Wang, Xiaofeng Zeng, Qi-hao Hu, Xiaoyan Chen, Sijie Tan, Jun Hu
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-16-S3-S4

Mining the bladder cancer-associated genes by an integrated strategy for the construction and analysis of differential co-expression networks
Cited by: 99
Author(s): Su-Ping Deng, Lin Zhu, De-Shuang Huang
Software Mentions: 2
Published: almost 12 years ago

10.6026/97320630015480

Identification of putative drought-responsive genes in rice using gene co-expression analysis
Cited by: 22
Author(s): Yan-Mei Lv, Lei Xu, Komivi Dossa, Kun Zhou, Mei-Ling Zhu, Hongjun Xie, Tang Shan-jun, Yaying Yu, Ximing Guo, Bin Zhou
Software Mentions: 2
Published: over 7 years ago

10.1186/s12934-014-0151-y

Metabolomic basis of laboratory evolution of butanol tolerance in photosynthetic Synechocystis sp. PCC 6803
Cited by: 54
Author(s): Yaxing Wang, Mengliang Shi, Xiangfeng Niu, Xiaoqing Zhang, Linfeng Gao, Lei Chen, Jiangxin Wang, Weiwen Zhang
Software Mentions: 2
Published: almost 12 years ago

10.1038/tp.2016.249

Methylomic profiling of cortex samples from completed suicide cases implicates a role for PSORS1C3 in major depression and suicide
Cited by: 61
Author(s): Therese M. Murphy, Bethany Crawford, Emma Dempster, Eilís Hannon, Joe Burrage, Gustavo Turecki, Zachary Kaminsky, Jonathan Mill
Software Mentions: 2
Published: almost 10 years ago