cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1038/s41398-019-0539-x

Differential transcriptional response following glucocorticoid activation in cultured blood immune cells: a novel approach to PTSD biomarker development
Cited by: 24
Author(s): Michael S. Breen, Linda M. Bierer, Nikolaos P. Daskalakis, Heather N. Bader, Iouri Makotkine, Matangini Chattopadhyay, Changxin Xu, Ariela Buxbaum Grice, Anna S. Tocheva, Janine D. Flory, Joseph D. Buxbaum, Michael J. Meaney, Kristen J. Brennand, Rachel Yehuda
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-015-2068-1

A novel approach identifies the first transcriptome networks in bats: a new genetic model for vocal communication
Cited by: 15
Author(s): Pedro Rodenas-Cuadrado, Xiaowei Sylvia Chen, Lutz Wiegrebe, Uwe Firzlaff, Sonja C. Vernes
Software Mentions: 3
Published: about 11 years ago

10.18632/oncotarget.19733

Overexpression of COL3A1 confers a poor prognosis in human bladder cancer identified by co-expression analysis
Cited by: 59
Author(s): Lushun Yuan, Bo Shu, Changhong Liang, Kaiyu Qian, Yongzhi Wang, Guofeng Qian, Yuan Zhu, Xinyue Cao, Conghua Xie, Yu Xiao, Xinghuan Wang
Software Mentions: 3
Published: over 9 years ago

10.3389/fonc.2020.00223

Oncogenic Network and Hub Genes for Natural Killer/T-Cell Lymphoma Utilizing WGCNA
Cited by: 15
Author(s): Huijiao Liu, Mei Liu, Hua You, Xiru Li, Xiangdong Li
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-020-07277-4

Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L
Cited by: 13
Author(s): Ning Li, Ziwei Meng, Tao Mei, Yueyuan Wang, Yulan Zhang, Shufen Li, Wu‐Jun Gao, Chuan‐Liang Deng
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-018-4807-6

Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress
Cited by: 56
Author(s): Liang Chen, Shilai Shi, Ninfei Jiang, Hira Khanzada, Ziming Wu, Zhu C, Xiaosong Peng, Jie Xu, Yujin Chen, Qi Yu, Xu He, Junru Fu, Xiaorong Chen, Lifang Hu, Liang Ouyang, Xiaotang Sun, Haohua He, Jianmin Bian
Software Mentions: 3
Published: over 8 years ago

10.3389/fonc.2021.644612

The Diagnostic and Immunotherapeutic Value of CD248 in Renal Cell Carcinoma
Cited by: 10
Author(s): Keying Zhang, Chao Xu, Shaojie Li, Yao Jiang, Xiaolong Zhao, Shanjin Ma, Yu Liu, Yang Fa, Yan Wang, Ping Meng, Changhong Shi, Donghui Han, Weihong Wen, Weijun Qin
Software Mentions: 3
Published: over 5 years ago

10.3389/fmed.2020.606461

Gene Co-expression Networks Identifies Common Hub Genes Between Cutaneous Sarcoidosis and Discoid Lupus Erythematosus
Cited by: 3
Author(s): Melissa A Nickles, Huang Kai, Yi-Shin Chang, Maria M. Tsoukas, Nadera J. Sweiss, David L. Perkins, Patricia W. Finn
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12916-015-0282-y

Multi-omic signature of body weight change: results from a population-based cohort study
Cited by: 58
Author(s): Simone Wahl, Susanne Vogt, Ferdinand Stückler, Jan Krumsiek, Jörg Bartel, Tim Kacprowski, Katharina Schramm, Maren Carstensen, Wolfgang Rathmann, Michael Roden, Carolin Jourdan, Antti J. Kangas, Pasi Soininen, Mika Ala‐Korpela, Ute Nöthlings, Heiner Boeing, Fabian J. Theis, Christa Meisinger, Mélanie Waldenberger, Karsten Suhre, Georg Homuth, Christian Gieger, Gabi Kastenmüller, Thomas Illig, Jakob Linseisen, Annette Peters, Holger Prokisch, Christian Herder, Barbara Thorand, Harald Grallert
Software Mentions: 3
Published: over 11 years ago

10.1186/s13195-019-0558-0

APOE2 orchestrated differences in transcriptomic and lipidomic profiles of postmortem AD brain
Cited by: 36
Author(s): Iliya Lefterov, Cody M. Wolfe, Nicholas F. Fitz, Kyong Nyon Nam, Florent Letronne, Richard J. Biedrzycki, Julia Kofler, Xianlin Han, Jianing Wang, Jonathan Schug, Radosveta Koldamova
Software Mentions: 3
Published: almost 7 years ago

10.3389/fimmu.2019.01002

Linking Cell Dynamics With Gene Coexpression Networks to Characterize Key Events in Chronic Virus Infections
Cited by: 6
Author(s): Mireia Pedragosa, Graciela Riera, Valentina Casella, Anna Esteve‐Codina, Yael Steuerman, Celina Marcella Seth, Gennady Bocharov, Simon Heath, Irit Gat‐Viks, Jordi Argilaguet, Andreas Meyerhans
Software Mentions: 3
Published: over 7 years ago

10.1186/s12920-020-0707-0

Transcriptome analysis reveals the link between lncRNA-mRNA co-expression network and tumor immune microenvironment and overall survival in head and neck squamous cell carcinoma
Cited by: 19
Author(s): Zhaoming Zhong, Min Hee Hong, Xiao Chen, Yan Xi, Yuanyuan Xu, Deyu Kong, Jun Deng, Yun Li, Rui Hu, Chuanzheng Sun, Jin Liang
Software Mentions: 3
Published: over 6 years ago

10.1186/s12920-020-00750-9

Weighted correlation network bioinformatics uncovers a key molecular biosignature driving the left-sided heart failure
Cited by: 8
Author(s): Jiamin Zhou, Wei Zhang, Chunying Wei, Zhiliang Zhang, Dasong Yi, Xiaoping Peng, Jianheng Peng, Rong Yin, Zeqi Zheng, Hongmei Qi, Yunfeng Wei, Tong-Chun Wen
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2020.571167

Identification of CHRNB4 as a Diagnostic/Prognostic Indicator and Therapeutic Target in Human Esophageal Squamous Cell Carcinoma
Cited by: 3
Author(s): Nan Li, Kaisheng Liu, Shaowei Dong, Ling Ou, Jieling Li, Minshan Lai, Yue Wang, Yifan Bao, Huidong Shi, Wang Xiao, Shaoxiang Wang
Software Mentions: 3
Published: almost 6 years ago

10.3389/fimmu.2021.717505

Follistatin-Like 3 Correlates With Lymph Node Metastasis and Serves as a Biomarker of Extracellular Matrix Remodeling in Colorectal Cancer
Cited by: 17
Author(s): Chao Yang, Fang Cao, Shuoyang Huang, Yongbin Zheng
Software Mentions: 3
Published: over 5 years ago

10.1155/2021/6692022

Identification of a Seven-lncRNA-mRNA Signature for Recurrence and Prognostic Prediction in Relapsed Acute Lymphoblastic Leukemia Based on WGCNA and LASSO Analyses
Cited by: 6
Author(s): Haiyan Qi, Long Chi, Xiaogang Wang, Xing Jin, Wensong Wang, Jianping Lan
Software Mentions: 3
Published: over 5 years ago

10.1038/s41398-019-0466-x

Antidepressants affect gut microbiota and Ruminococcus flavefaciens is able to abolish their effects on depressive-like behavior
Cited by: 137
Author(s): Iva Lukić, Dmitriy Getselter, Oren Ziv, Oded Oron, Eli Reuveni, Omry Koren, Evan Elliott
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2021.648917

Deciphering the Prognostic Implications of the Components and Signatures in the Immune Microenvironment of Pancreatic Ductal Adenocarcinoma
Cited by: 34
Author(s): Rong Tang, Xiaomeng Liu, Chen Liang, Jie Hua, Jin Xu, Wei Wang, Qingcai Meng, Jiang Liu, Bo Zhang, Xianjun Yu, Si Shi
Software Mentions: 3
Published: over 5 years ago

10.1155/2021/6697407

Identification of a 5-Gene-Based Scoring System by WGCNA and LASSO to Predict Prognosis for Rectal Cancer Patients
Cited by: 3
Author(s): He Huang, Shilei Xu, Aidong Chen, Fen Li, Jiezhong Wu, Xusheng Tu, Kunpeng Hu
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-021-07991-7

Morphological, physiological, and transcriptional responses to low nitrogen stress in Populus deltoides Marsh. clones with contrasting nitrogen use efficiency
Cited by: 2
Author(s): Cun Chen, Ying‐Hao Chu, Qinjun Huang, Weixi Zhang, Changjun Ding, Jing Zhang, Bo Li, Tengqian Zhang, Zhenghong Li, Xiaohua Su
Software Mentions: 3
Published: about 5 years ago

10.1186/s12920-020-00782-1

Improving lung cancer risk stratification leveraging whole transcriptome RNA sequencing and machine learning across multiple cohorts
Cited by: 11
Author(s): Yoonha Choi, Jianghan Qu, Esther Wu, Yangyang Hao, Jiarui Zhang, Jicai Ning, Xinwu Yang, Lori Lofaro, Daniel G. Pankratz, Joshua E. Babiarz, P. Sean Walsh, Ehab Billatos, Marc E. Lenburg, Giulia C. Kennedy, Jon McAuliffe, Jing Huang
Software Mentions: 3
Published: about 6 years ago

10.3389/fonc.2020.577530

GPR115 Contributes to Lung Adenocarcinoma Metastasis Associated With LAMC2 and Predicts a Poor Prognosis
Cited by: 13
Author(s): Yingjing Wang, Muqi Shi, Nan Yang, Xiaoyu Zhou, Liqin Xu
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12920-017-0253-6

Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications
Cited by: 33
Author(s): Amir Foroushani, Rupesh Agrahari, T. Roderick Docking, Linda Chang, Gerben Duns, Monika Hudoba, Aly Karsan, Habil Zare
Software Mentions: 3
Published: over 9 years ago

10.1186/s12920-020-0693-2

Potential role of genomic imprinted genes and brain developmental related genes in autism
Cited by: 8
Author(s): Jian Li, Xue Lü, Mingya Wang, Yunyun Hu, Kaiyu Xue, Shuanglin Gu, Lili Lv, Saijun Huang, Wei Xie
Software Mentions: 3
Published: over 6 years ago

10.1186/s12920-019-0613-5

Improved cell composition deconvolution method of bulk gene expression profiles to quantify subsets of immune cells
Cited by: 19
Author(s): Yen Jung Chiu, Yi Hsuan Hsieh, Yen Hua Huang
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41438-020-0287-3

Transcriptome analysis and metabolic profiling reveal the key role of carotenoids in the petal coloration of Liriodendron tulipifera
Cited by: 39
Author(s): Zhaodong Hao, Siqin Liu, Lingfeng Hu, Jisen Shi, Jinhui Chen
Software Mentions: 3
Published: over 6 years ago

10.1038/s41398-018-0267-7

Global long non-coding RNA expression in the rostral anterior cingulate cortex of depressed suicides
Cited by: 43
Author(s): Yi Zhou, Pierre-Eric Lutz, Yu Chang Wang, Jiannis Ragoussis, Gustavo Turecki
Software Mentions: 3
Published: about 8 years ago

10.3389/fimmu.2021.657951

Multidimensional Analyses of Tumor Immune Microenvironment Reveal the Possible Rationality of Immunotherapy and Identify High Immunotherapy Response Subtypes for Renal Papillary Cell Carcinoma
Cited by: 1
Author(s): Bojun Wei, Meng Yu, Jihang Yao, Mengshi Jiang, Jing An, Jieping Yang, Jiaxing Lin, Yunan Zhao, Yuyan Zhu
Software Mentions: 3
Published: about 5 years ago

10.1186/s12920-021-01010-0

Identification of macrophage related gene in colorectal cancer patients and their functional roles
Cited by: 2
Author(s): Yingxiang Chen, Cui Zhang, Xiang Zou, Man Yu, Bo Yang, Chenfeng Ji, Shuangquan Gao, Jun Li, Bin Liu
Software Mentions: 3
Published: over 5 years ago

10.1038/s41398-017-0036-z

Psychiatric polygenic risk associates with cortical morphology and functional organization in aging
Cited by: 6
Author(s): Annie Lee, Mojun Shen, Anqi Qiu
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12920-021-00892-4

Identification of biomarkers and pathogenesis in severe asthma by coexpression network analysis
Cited by: 7
Author(s): Zeyi Zhang, Jingjing Wang, Ou Chen
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2021.687151

Integrative Transcriptomic Analysis Reveals the Immune Mechanism for a CyHV-3-Resistant Common Carp Strain
Cited by: 11
Author(s): Zhiying Jia, Nan Wu, Xiaona Jiang, Heng Li, Jing Sun, Minjun Shi, Chitao Li, Yuejing Ge, Xuesong Hu, Weidong Ye, Ying Tang, Junwei Shan, Yingyin Cheng, Xiao-Qin Xia, Shi Liu
Software Mentions: 3
Published: over 5 years ago

10.1038/tp.2016.229

Transcriptome sequencing of the choroid plexus in schizophrenia
Cited by: 42
Author(s): S Kim, Young Sun Hwang, Doheon Lee, Maree J. Webster
Software Mentions: 3
Published: almost 10 years ago

10.3389/fimmu.2017.01992

Gene Expression Analysis Reveals Novel Shared Gene Signatures and Candidate Molecular Mechanisms between Pemphigus and Systemic Lupus Erythematosus in CD4+ T Cells
Cited by: 39
Author(s): Tanya Sezin, Artem Vorobyev, Christian D. Sadik, Detlef Zillikens, Yask Gupta, Ralf J. Ludwig
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12920-018-0433-z

Identification of cancer subtypes from single-cell RNA-seq data using a consensus clustering method
Cited by: 31
Author(s): Yanglan Gan, Ning Li, Guobing Zou, Yongchang Xin, Jihong Guan
Software Mentions: 3
Published: almost 8 years ago

10.3389/fonc.2021.679262

RNA Sequence Profiling Reveals Unique Immune and Metabolic Features of Breast Cancer Brain Metastases
Cited by: 4
Author(s): Liuling Xiao, Jie Zhou, Hongyi Liu, Yuanyuan Zhou, Weibin Chen, Wugeng Cui, Yilin Zhao
Software Mentions: 3
Published: about 5 years ago

10.3390/ani11030628

Dissecting the Gene Expression Networks Associated with Variations in the Major Components of the Fatty Acid Semimembranosus Muscle Profile in Large White Heavy Pigs
Cited by: 8
Author(s): Martina Zappaterra, Silvia Gioiosa, Giovanni Chillemi, Paolo Zambonelli, Roberta Davoli
Software Mentions: 3
Published: over 5 years ago

10.3390/ani11071863

Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep
Cited by: 8
Author(s): Aiju Liu, Xiaoyong Chen, Menghe Liu, Limeng Zhang, Xiaofei Ma, Shujun Tian
Software Mentions: 3
Published: over 5 years ago

10.1186/s40035-021-00249-y

Several miRNAs derived from serum extracellular vesicles are potential biomarkers for early diagnosis and progression of Parkinson’s disease
Cited by: 31
Author(s): Shulei He, Lu Huang, Ci Shao, Tiejian Nie, Xia Li, Bozhou Cui, Fangfang Lu, Lin Zhu, Bolin Chen, Qian Yang
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2019.00180

Sex Differences in Older Adults' Immune Responses to Seasonal Influenza Vaccination
Cited by: 53
Author(s): Emily A. Voigt, Inna G. Ovsyannikova, Richard B. Kennedy, Diane E. Grill, Krista M. Goergen, Daniel J. Schaid, Gregory A. Poland
Software Mentions: 3
Published: over 7 years ago

10.1186/s12891-021-03958-7

HEMGN and SLC2A1 might be potential diagnostic biomarkers of steroid-induced osteonecrosis of femoral head: study based on WGCNA and DEGs screening
Cited by: 10
Author(s): Zhixin Wu, Yinxian Wen, Guanlan Fan, Hangyuan He, Siqi Zhou, Liaobin Chen
Software Mentions: 3
Published: almost 6 years ago

10.1186/s40035-020-00215-0

Integrated lipidomics and proteomics network analysis highlights lipid and immunity pathways associated with Alzheimer’s disease
Cited by: 30
Author(s): Jin Xu, Giulia Bankov, Min Kim, Asger Wretlind, Jodie Lord, Rebecca Green, Angela Hodges, Abdul Hye, Dag Aarsland, Latha Velayudhan, Richard Dobson, Petroula Proitsi, Cristina Legido‐Quigley
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2202-15-11

Genes showing altered expression in the medial preoptic area in the highly social maternal phenotype are related to autism and other disorders with social deficits
Cited by: 33
Author(s): Terri M. Driessen, Brian E. Eisinger, Changjiu Zhao, Sharon A. Stevenson, Michael C. Saul, Stephen C. Gammie
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41438-020-0249-9

Application of an antibody chip for screening differentially expressed proteins during peach ripening and identification of a metabolon in the SAM cycle to generate a peach ethylene biosynthesis model
Cited by: 10
Author(s): Wenfang Zeng, Liang Niu, Zhaohui Wang, Xiaobei Wang, Yan Wang, Lei Pan, Zhenhua Lü, Guochao Cui, Weining Weng, Mingqiao Wang, Xianghong Meng, Zhiqiang Wang
Software Mentions: 3
Published: over 6 years ago

10.1186/s12870-014-0348-6

chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes
Cited by: 7
Author(s): Thomas Nußbaumer, Karl G. Kugler, Wolfgang Schweiger, Kai Christian Bader, Heidrun Gundlach, Manuel Spannagl, Naser Poursarebani, Matthias Pfeifer, Klaus Mayer
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12870-021-03051-0

Study on the differences of gene expression between pear and apple wild cultivation materials based on RNA-seq technique
Cited by: 3
Author(s): Huangwei Zhang, Meng Li, Min Jung Kong, Jim M. Dunwell, Yuyan Zhang, Chao Yue, Juyou Wu, Shaoling Zhang
Software Mentions: 3
Published: over 5 years ago

10.7150/thno.47525

Transcriptomic analysis identifies a tumor subtype mRNA classifier for invasive non-functioning pituitary neuroendocrine tumor diagnostics
Cited by: 9
Author(s): Xinjie Bao, Gengchao Wang, Shan Yu, Jian Sun, Li He, Hua-Lu Zhao, Yupo Ma, Fang Wang, Xiaoshuang Wang, Renzhi Wang, Jia Yu
Software Mentions: 3
Published: almost 6 years ago

10.7150/thno.44456

Cartilage Oligomeric Matrix Protein promotes epithelial-mesenchymal transition by interacting with Transgelin in Colorectal Cancer
Cited by: 57
Author(s): Weilong Zhong, Huiqin Hou, Tianyu Li, Shuai Su, Xiaonan Xi, Yusheng Liao, Runxiang Xie, Ge Jin, Xiang Liu, Lanping Zhu, Hongxia Zhang, Xueli Song, Cheng Yang, Tao Sun, Hailong Cao, Bangmao Wang
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13287-021-02498-0

EGR1 dysregulation defines an inflammatory and leukemic program in cell trajectory of human-aged hematopoietic stem cells (HSC)
Cited by: 14
Author(s): Christophe Desterke, Annelise Bennaceur‐Griscelli, Ali G. Turhan
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2019.00100

The Long Non-coding RNA NRIR Drives IFN-Response in Monocytes: Implication for Systemic Sclerosis
Cited by: 52
Author(s): Barbara Mariotti, Nila Hendrika Servaas, Marzia Rossato, Nicola Tamassia, Marco A. Cassatella, Marta Cossu, Lorenzo Beretta, Maarten van der Kroef, Timothy R D J Radstake, Flavia Bazzoni
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12870-021-02893-y

Composition and diversity of bacterial communities in the rhizosphere of the Chinese medicinal herb Dendrobium
Cited by: 32
Author(s): Jiajia Zuo, Mengting Zu, Lei Liu, Xiaomei Song, Yingdan Yuan
Software Mentions: 3
Published: over 5 years ago

10.1186/s40478-021-01186-7

VISTA regulates microglia homeostasis and myelin phagocytosis, and is associated with MS lesion pathology
Cited by: 3
Author(s): Malte Borggrewe, Susanne M. Kooistra, Evelyn Wesseling, Fenja L. Gierschek, Maaike L. Brummer, Elizabeth C. Nowak, Tiago Medeiros-Furquim, Tegan Otto, Sam W. Lee, Randolph J. Noelle, Bart J. L. Eggen, Jon D. Laman
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.13104

Identification of KLK10 as a therapeutic target to reverse trastuzumab resistance in breast cancer
Cited by: 15
Author(s): Zhuo Wang, Beihong Ruan, Y. Jin, Yulong Zhang, Jiaqiu Li, Liyuan Zhu, Wenxia Xu, Lifeng Feng, Hongchuan Jin, Xian Wang
Software Mentions: 3
Published: almost 10 years ago

10.18632/oncotarget.13569

Proteomic profiling of NCI-60 extracellular vesicles uncovers common protein cargo and cancer type-specific biomarkers
Cited by: 187
Author(s): Stephanie N. Hurwitz, Mark A. Rider, Joseph L. Bundy, Xia Liu, Rakesh Kumar Singh, David G. Meckes
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13287-020-01613-x

Transcriptome differences in adipose stromal cells derived from pre- and postmenopausal women
Cited by: 2
Author(s): Yun Xie, Bin Fang, Wenhui Liu, Guangshuai Li, Ru‐Lin Huang, Lu Zhang, Jiahao He, Shuang-Bai Zhou, Kai Li, Qingfeng Li
Software Mentions: 3
Published: over 6 years ago

10.1186/s40478-020-01037-x

Network analysis of the progranulin-deficient mouse brain proteome reveals pathogenic mechanisms shared in human frontotemporal dementia caused by GRN mutations
Cited by: 38
Author(s): Meixiang Huang, Erica Modeste, Eric B. Dammer, Paola Merino, Georgia Taylor, Duc M. Duong, Qiudong Deng, Christopher J. Holler, Marla Gearing, Dennis W. Dickson, Nicholas T. Seyfried, Thomas Kukar
Software Mentions: 3
Published: about 6 years ago

10.18632/aging.202351

Four hub genes regulate tumor infiltration by immune cells, antitumor immunity in the tumor microenvironment, and survival outcomes in lung squamous cell carcinoma patients
Cited by: 6
Author(s): Tuo Zhang, Haitang Yang, Beibei Sun, Feng Yao
Software Mentions: 3
Published: almost 6 years ago

10.1161/ATVBAHA.119.312399

Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mice Defined by Single-Cell RNA Sequencing
Cited by: 73
Author(s): Wenduo Gu, Zhichao Ni, Yuan Qing Tan, Jiacheng Deng, Si Jin Zhang, Zi Lv, Xiao Jian Wang, Ting Chen, Zhongyi Zhang, Yanhua Hu, Zhi‐Cheng Jing, Qingbo Xu
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-014-0307-2

RNA-sequencing reveals early, dynamic transcriptome changes in the corollas of pollinated petunias
Cited by: 39
Author(s): Shaun R. Broderick, Saranga Wijeratne, Asela J Wijeratn, Laura J. Chapin, Tea Meulia, Michelle L. Jones
Software Mentions: 3
Published: almost 12 years ago

10.1186/s13287-019-1191-3

In vitro expansion affects the response of human bone marrow stromal cells to irradiation
Cited by: 8
Author(s): Yang Xiang, Chun Wu, Jiang Wu, Weili Quan, Chao Cheng, Jian Zhou, Li Chen, Lan Xiang, Fengjie Li, Kebin Zhang, Qian Ran, Yi Zhang, Zhongjun Li
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-019-2169-0

Differential gene expression among three sex types reveals a MALE STERILITY 1 (CpMS1) for sex differentiation in papaya
Cited by: 11
Author(s): Dessireé Zerpa‐Catanho, Jennifer Wai, Ming Li Wang, Liang Yu, Julie Nguyen, Ray Ming
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-021-97319-y

An integrated analysis of mRNAs, lncRNAs, and miRNAs based on weighted gene co-expression network analysis involved in bovine endometritis
Cited by: 11
Author(s): Negin Sheybani, Mohammad Reza Bakhtiarizadeh, Abdolreza Salehi
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-96952-x

RNA-seq profiling reveals PBMC RNA as a potential biomarker for hepatocellular carcinoma
Cited by: 14
Author(s): Zhiyi Han, Wenxing Feng, Rui Hu, Qinyu Ge, Wenfeng Ma, Wei Zhang, Shaomin Xu, Bolin Zhan, Lai Zhang, Xinfeng Sun, Xiaozhou Zhou
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-96278-8

Murine neuronatin deficiency is associated with a hypervariable food intake and bimodal obesity
Cited by: 5
Author(s): Irène Cimino, Debra Rimmington, Y.C. Loraine Tung, Katherine Lawler, Pierre Larraufie, Richard G. Kay, Samuel Virtue, Brian Lam, Luca Fagnocchi, Kenneth L. Marcella, Vladimı́r Saudek, Ilona Zvetkova, António Vidal-Puig, Giles S.H. Yeo, I. Sadaf Farooqi, J. Andrew Pospisilik, Fiona M. Gribble, Frank Reimann, Stephen O’Rahilly, Anthony P. Coll
Software Mentions: 3
Published: about 5 years ago

10.1186/s12967-021-03014-x

Identification of tumor antigens and immune subtypes in lower grade gliomas for mRNA vaccine development
Cited by: 14
Author(s): Liguo Ye, Long Wang, Jian Yang, Ping Hu, Chunyu Zhang, Shiao Tong, Zhennan Liu, Daofeng Tian
Software Mentions: 3
Published: about 5 years ago

10.18632/oncotarget.10249

Gene network analysis reveals a novel 22-gene signature of carbon metabolism in hepatocellular carcinoma
Cited by: 16
Author(s): Jinqiang Zhang, Melody Baddoo, Chang Han, Michael J. Strong, Jennifer Cvitanovic, Krzysztof Moroz, Srikanta Dash, Erik K. Flemington, Tong Wu
Software Mentions: 3
Published: over 10 years ago

10.1186/s12859-020-03921-8

MiBiOmics: an interactive web application for multi-omics data exploration and integration
Cited by: 39
Author(s): Johanna Zoppi, Jean-François Guillaume, Michel Neunlist, Samuel Chaffron
Software Mentions: 3
Published: almost 6 years ago

10.3389/fimmu.2019.00869

Immunomodulatory Effects and Induction of Apoptosis by Different Molecular Weight Chitosan Oligosaccharides in Head Kidney Macrophages From Blunt Snout Bream (Megalobrama amblycephala)
Cited by: 17
Author(s): Changcai Wu, Yishan Dai, Gailing Yuan, Jian Su, Xiaoling Liu
Software Mentions: 3
Published: over 7 years ago

10.3389/fphar.2019.00574

LncRNA Profile Study Reveals a Three-LncRNA Signature Associated With the Pathological Complete Response Following Neoadjuvant Chemotherapy in Breast Cancer
Cited by: 20
Author(s): Ying Zeng, Wei Guo, Chengfang Zhou, Hai Bo Zhang, Hong Sun, Wei Zhang, Hong‐Hao Zhou, Rong Liu, Yuan‐Shan Zhu
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-11-497

DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules
Cited by: 190
Author(s): Bruno Tesson, Rainer Breitling, Ritsert C. Jansen
Software Mentions: 3
Published: about 16 years ago

10.1186/s12864-018-5091-1

Transcriptional defects and reprogramming barriers in somatic cell nuclear reprogramming as revealed by single-embryo RNA sequencing
Cited by: 23
Author(s): Yong Liu, Fengrui Wu, Ling Zhang, Xiaoqing Wu, Dengkun Li, Xin Jing, Juan Xie, Feng Kong, Wenying Wang, Qiaoqin Wu, Di Zhang, Rong Wang, Shaorong Gao, Wenyong Li
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-021-92091-5

Bioinformatic profiling identifies prognosis-related genes in the immune microenvironment of endometrial carcinoma
Cited by: 5
Author(s): Pu Cheng, Jiong Ma, Xia Zheng, Chunxia Zhou, Xuejun Chen
Software Mentions: 3
Published: over 5 years ago

10.1038/s41396-020-00874-x

Specificity of assemblage, not fungal partner species, explains mycorrhizal partnerships of mycoheterotrophic Burmannia plants
Cited by: 8
Author(s): Zhongtao Zhao, Xiaojuan Li, Ming Fai Liu, Vincent Merckx, Richard M. Saunders, Dianxiang Zhang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-019-6245-5

Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response
Cited by: 44
Author(s): Yuanda Lv, Fengqin Hu, Yongfeng Zhou, Feilong Wu, Brandon S. Gaut
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12870-019-2196-x

Comparative transcriptome analysis indicates that a core transcriptional network mediates isonuclear alloplasmic male sterility in wheat (Triticum aestivum L.)
Cited by: 20
Author(s): Zihan Liu, Sha Li, Wei Li, Qi Liu, Lingli Zhang, Xiyue Song
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-021-88948-4

Genetic network and gene set enrichment analyses identify MND1 as potential diagnostic and therapeutic target gene for lung adenocarcinoma
Cited by: 4
Author(s): Jinying Wei, Guangping Meng, Jing Wu, Qiang Zhang, Jie Zhang
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-88029-6

Transcriptomic analysis to infer key molecular players involved during host response to NDV challenge in Gallus gallus (Leghorn & Fayoumi)
Cited by: 4
Author(s): Venkata Krishna Vanamamalai, Priyanka Garg, Gautham Kolluri, Ravi Kumar Gandham, Itishree Jali, Shailesh Sharma
Software Mentions: 3
Published: over 5 years ago

10.1186/s12870-017-1143-y

Co-expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium-responsive genes
Cited by: 80
Author(s): Tan Ming, Dan Cheng, Yunhai Yang, Guoqiang Zhang, Mengjie Qin, Jun Chen, Yahua Chen, Mingyi Jiang
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-021-86742-w

Transcriptional circuitry atlas of genetic diverse unstimulated murine and human macrophages define disparity in population-wide innate immunity
Cited by: 5
Author(s): Bharat Mishra, Mohammad Athar, M. Shahid Mukhtar
Software Mentions: 3
Published: over 5 years ago

10.18632/aging.202165

Autophagy-mediated regulation patterns contribute to the alterations of the immune microenvironment in periodontitis
Cited by: 6
Author(s): Xiaoqi Zhang, Yu Jin, Qingxuan Wang, Jian Fan, Minqi Li, Hu Long, Wenli Lai
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-020-06918-y

Multi-omics sequencing provides insight into floral transition in Catalpa bungei. C.A. Mey
Cited by: 1
Author(s): Zhi Wang, Wenjun Ma, Tianqing Zhu, Nan Lu, Fangqun Ouyang, Nan Wang, Guijuan Yang, Lisheng Kong, Guanzheng Qu, Shougong Zhang, Junhui Wang
Software Mentions: 3
Published: over 6 years ago

10.18632/aging.102196

Comprehensive transcriptomic analysis indicates brain regional specific alterations in type 2 diabetes
Cited by: 3
Author(s): Zhe Zhou, Yizhang Zhu, Yang Liu, Yuxin Yin
Software Mentions: 3
Published: about 7 years ago

10.1186/s12870-019-1952-2

Genome-wide transcriptional adaptation to salt stress in Populus
Cited by: 28
Author(s): Jin-Gui Liu, Xiao Han, Tianbo Yang, Wenhui Cui, Aimin Wu, Chunxiang Fu, Baichen Wang, Lijun Liu
Software Mentions: 3
Published: about 7 years ago

10.1186/s12870-020-02419-y

Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency
Cited by: 16
Author(s): Yang Xiao-ling, Xiuzhong Xia, Zhen Yu, Baoxuan Nong, Zongqiong Zhang, Yanyan Wu, Qian Tian, Weiying Zeng, Ju Gao, Weiyong Zhou, He Liang, Danting Li, Gaofeng Deng
Software Mentions: 3
Published: over 6 years ago

10.1186/s12870-015-0568-4

Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease
Cited by: 43
Author(s): Nidhi Rawat, Sandhya.P. Kiran, Dongliang Du, Fred G. Gmitter, Zhanao Deng
Software Mentions: 3
Published: over 11 years ago

10.1002/2211-5463.12433

An integrated analysis of genome‐wide <scp>DNA</scp> methylation and gene expression data in hepatocellular carcinoma
Cited by: 32
Author(s): Xiaojiang Sun, Mingchun Wang, Fenghua Zhang, Xiao Kong
Software Mentions: 3
Published: over 8 years ago

10.3389/fgene.2021.687813

Mechanism-Centric Approaches for Biomarker Detection and Precision Therapeutics in Cancer
Cited by: 7
Author(s): Christina Y. Yu, Antonina Mitrofanova
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2020.00810

Identification of a Novel Immune-Related Prognostic Biomarker and Small-Molecule Drugs in Clear Cell Renal Cell Carcinoma (ccRCC) by a Merged Microarray-Acquired Dataset and TCGA Database
Cited by: 12
Author(s): Guan-Fa Xiao, Xin Yan, Zhao Chun-hua, Ren‐Jie Zhang, Tong-Zu Liu, Wanli Hu
Software Mentions: 3
Published: about 6 years ago

10.1038/s41438-019-0120-z

Differential gene regulatory pathways and co-expression networks associated with fire blight infection in apple (Malus × domestica)
Cited by: 17
Author(s): Katchen Julliany Pereira Silva, Jugpreet Singh, Ryland Bednarek, Zhangjun Fei, Awais Khan
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-020-3446-5

Efficient identification of multiple pathways: RNA-Seq analysis of livers from 56Fe ion irradiated mice
Cited by: 8
Author(s): Anna M. Nia, Tianlong Chen, Brooke L. Barnette, Kamil Khanipov, Robert L. Ullrich, Suresh K. Bhavnani
Software Mentions: 3
Published: over 6 years ago

10.3389/fphys.2020.00542

Critical Roles of ELVOL4 and IL-33 in the Progression of Obesity-Related Cardiomyopathy via Integrated Bioinformatics Analysis
Cited by: 6
Author(s): Jun Tao, Yajing Wang, Ling Li, Junmeng Zheng, Shi Liang
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-14-450

Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution
Cited by: 49
Author(s): Gang Fang, Karla D. Passalacqua, Jason Hocking, Paula Montero Llopis, Mark Gerstein, Nicholas H. Bergman, Christine Jacobs‐Wagner
Software Mentions: 3
Published: over 13 years ago

10.3390/genes8120357

Non-Additive Transcriptomic Responses to Inoculation with Rhizobia in a Young Allopolyploid Compared with Its Diploid Progenitors
Cited by: 6
Author(s): Adrian F. Powell, Jeff J. Doyle
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12870-020-02612-z

Insights into the resistance of a synthetically-derived wheat to Septoria tritici blotch disease: less is more
Cited by: 6
Author(s): Harriet R. Benbow, Ciarán J. Brennan, Binbin Zhou, Thalia Christodoulou, Simon Berry, Cristóbal Uauy, Ewen Mullins, Fiona M. Doohan
Software Mentions: 3
Published: about 6 years ago

10.1038/s41419-020-02973-1

Immune signature driven by ADT-induced immune microenvironment remodeling in prostate cancer is correlated with recurrence-free survival and immune infiltration
Cited by: 32
Author(s): Xingbo Long, Huimin Hou, Xuan Wang, Shengjie Liu, Tongxiang Diao, Shicong Lai, Mao‐Lin Hu, Shengqi Zhang, Ming Liu, Hong Zhang
Software Mentions: 3
Published: about 6 years ago

10.1186/s12870-020-02735-3

Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum)
Cited by: 5
Author(s): Wenqing Zhang, Shengkui Zhang, Xianqin Lu, Can Li, Xingwang Liu, Geyu Dong, Tao Xia
Software Mentions: 3
Published: almost 6 years ago

10.1155/2021/6697848

Identification of Molecular Regulatory Features and Markers for Acute Type A Aortic Dissection
Cited by: 5
Author(s): Rui Li, Guochao Zhang, Shaomin Yan, Lichao Sun, Guoqiang Zhang
Software Mentions: 3
Published: over 5 years ago

10.1093/gigascience/giaa009

De novo genome assembly and Hi-C analysis reveal an association between chromatin architecture alterations and sex differentiation in the woody plant Jatropha curcas
Cited by: 15
Author(s): Maosheng Chen, Longjian Niu, Miaomiao Zhao, Chuan-Jia Xu, Bang-Zhen Pan, Qi Fu, Yongfu Tao, Hua He, Chaoqi Hou, Zeng-Fu Xu
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-020-64170-6

Whole transcriptome analysis and validation of metabolic pathways in subcutaneous adipose tissues during FGF21-induced weight loss in non-human primates
Cited by: 7
Author(s): Scott O. Murray, Louise S. Dalbøge, Karalee Baquero, Christina A. Sanford, Ayesha Misquith, Aaron J. Mercer, Thomas H. Meek, Mette Guldbrandt, Birgitte Andersen, Paul Kievit, Kevin L. Grove, Burak Kutlu
Software Mentions: 3
Published: over 6 years ago

10.18632/aging.101496

Signatures of photo-aging and intrinsic aging in skin were revealed by transcriptome network analysis
Cited by: 25
Author(s): Byuri Angela Cho, Seong-Keun Yoo, Jong-Soo Seo
Software Mentions: 3
Published: over 8 years ago

Projects: cran: WGCNA

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning WGCNA 3,479