cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1155/2021/3947350

Identification of MEDAG as a Hub Candidate Gene in the Onset and Progression of Type 2 Diabetes Mellitus by Comprehensive Bioinformatics Analysis
Cited by: 3
Author(s): Jing Yang, Ping Yü
Software Mentions: 3
Published: over 5 years ago

10.1155/2020/1872962

Development of Autophagy Signature-Based Prognostic Nomogram for Refined Glioma Survival Prognostication
Cited by: 5
Author(s): Yuxiang Fan, Xinyu Peng, Baoqin Li, Gang Zhao
Software Mentions: 3
Published: about 6 years ago

10.1155/2021/5589101

Weighted Gene Coexpression Network Analysis to Construct Competitive Endogenous RNA Network in Chromogenic Renal Cell Carcinoma
Cited by: 1
Author(s): Yon-Bo Chen, Liang Gao, Jindong Zhang, Jiang Guo, Ping-Hong You, Liang-you Tang, Ying-Wen Liu
Software Mentions: 3
Published: over 5 years ago

10.1155/2020/6107865

Construction of a CXC Chemokine-Based Prediction Model for the Prognosis of Colon Cancer
Cited by: 14
Author(s): Kaisheng Liu, Minshan Lai, Shaoxiang Wang, Kai Zheng, Shouqi Xie, Wang Xiao
Software Mentions: 3
Published: over 6 years ago

10.1155/2020/7947208

Clinical Features and Prognostic Impact of Coexpression Modules Constructed by WGCNA for Diffuse Large B-Cell Lymphoma
Cited by: 4
Author(s): Jie Xiao, Xuemei Wang, Hao Bai
Software Mentions: 3
Published: over 6 years ago

10.1155/2019/1649423

A 6-Gene Risk Signature Predicts Survival of Glioblastoma Multiforme
Cited by: 14
Author(s): J. W. Zhao, Le Wang, Guozhang Hu, Bo Wei
Software Mentions: 3
Published: about 7 years ago

10.1155/2020/4927547

Integrated Transcriptomic Analysis Reveals the Molecular Mechanism of Meningiomas by Weighted Gene Coexpression Network Analysis
Cited by: 0
Author(s): Biao Yang, Shuxun Wei, Yupo Ma, Sheng‐Hua Chu
Software Mentions: 3
Published: over 6 years ago

10.1155/2017/8347085

Identification of Transcriptional Modules and Key Genes in Chickens Infected with Salmonella enterica Serovar Pullorum Using Integrated Coexpression Analyses
Cited by: 7
Author(s): Baohong Liu, Jianping Cai
Software Mentions: 3
Published: almost 10 years ago

10.1155/2020/1817094

Identification of Crucial lncRNAs, miRNAs, mRNAs, and Potential Therapeutic Compounds for Polycystic Ovary Syndrome by Bioinformatics Analysis
Cited by: 9
Author(s): Zhi Zeng, Xiao Lin, Tingting Xia, Wenxiu Liu, Xingui Tian, Manchao Li
Software Mentions: 3
Published: almost 6 years ago

10.1155/2021/5963868

Identification and Prognostic Value Exploration of Radiotherapy Sensitivity-Associated Genes in Non-Small-Cell Lung Cancer
Cited by: 6
Author(s): Qing Ma, Kai Geng, Ping Xiao, Lili Zeng
Software Mentions: 3
Published: about 5 years ago

10.1155/2020/4673250

Changes in Gut Microorganism in Patients with Positive Immune Antibody-Associated Recurrent Abortion
Cited by: 4
Author(s): Min Jin, Dong Li, Rui Ji, Wen Liu, Xiaofei Xu, Xin Feng
Software Mentions: 3
Published: about 6 years ago

10.3390/biomedicines9050546

Weighted Gene Co-Expression Network Analysis Reveals Key Genes and Potential Drugs in Abdominal Aortic Aneurysm
Cited by: 5
Author(s): Kejia Kan, Feng Guo, Lei Zhu, Prama Pallavi, Martin Sigl, Michael Keese
Software Mentions: 3
Published: over 5 years ago

10.1042/BSR20202921

Immune-associated biomarkers for early diagnosis of Parkinson’s disease based on hematological lncRNA–mRNA co-expression
Cited by: 8
Author(s): Kecheng Lei, Liwen Zhang, Yijing He, Hui Sun, Weifang Tong, Yawei Xu, Lingjing Jin
Software Mentions: 3
Published: almost 6 years ago

10.1042/BSR20200514

Identification of co-expressed genes associated with MLL rearrangement in pediatric acute lymphoblastic leukemia
Cited by: 2
Author(s): Hao Zhang, Bei Liu, Juan Cheng, Haizhen Ma, Zijian Li, Yuandi Xi
Software Mentions: 3
Published: over 6 years ago

10.1042/BSR20181925

Co-expression of key gene modules and pathways of human breast cancer cell lines
Cited by: 13
Author(s): Yadong Wu, Lin Feng, Siyang Luo, Xinhai Yin, He Dan, Jianguo Liu, Zhao-hui Yue, Jukun Song
Software Mentions: 3
Published: over 7 years ago

10.1042/BSR20193938

Weighted gene correlation network analysis reveals novel regulatory modules associated with recurrent early pregnancy loss
Cited by: 5
Author(s): Xiaoxiao Li, Yuanqi He, Cuifang Hao, Xiaona Li, Xue Li
Software Mentions: 3
Published: over 6 years ago

10.1042/BSR20191247

HPO-Shuffle: an associated gene prioritization strategy and its application in drug repurposing for the treatment of canine epilepsy
Cited by: 5
Author(s): Shuguang Wang, Xiangyu Meng, Yuxing Wang, Ye-Mao Liu, Jingbo Xia
Software Mentions: 3
Published: about 7 years ago

10.1042/BSR20193377

Identification of hub genes related to prognosis in glioma
Cited by: 4
Author(s): De‐Long Zhang, Jinxin Zhao, Chengzheng Han, Xiaocen Liu, Jun Li, Hui Yang
Software Mentions: 3
Published: over 6 years ago

10.1042/BSR20210284

Expression level of long non-coding RNA colon adenocarcinoma hypermethylated serves as a novel prognostic biomarker in patients with thyroid carcinoma
Cited by: 5
Author(s): Yong Xiao, Youbing Tu, Yuantao Li
Software Mentions: 3
Published: over 5 years ago

10.1186/s13068-020-01810-z

Comparative transcriptome study of switchgrass (Panicum virgatum L.) homologous autopolyploid and its parental amphidiploid responding to consistent drought stress
Cited by: 17
Author(s): Peilin Chen, Jing Chen, Min Sun, Haidong Yan, Guangyan Feng, Bingchao Wu, Xinquan Zhang, Xiaoshan Wang, Linkai Huang
Software Mentions: 3
Published: about 6 years ago

10.1186/s13068-020-01728-6

Deciphering the transcriptional regulatory networks that control size, color, and oil content in Brassica rapa seeds
Cited by: 21
Author(s): Yue Niu, Limin Wu, Yànhuá Lǐ, Hualei Huang, Mingchao Qian, Wei Sun, Hong Zhu, Yingying Xu, Yonghai Fan, Umer Mahmood, Benbo Xu, Kai Zhang, Cunmin Qu, Jiana Li, Kun Lu
Software Mentions: 3
Published: over 6 years ago

10.1186/s13068-021-01946-6

Transcriptome analysis revealed the regulation of gibberellin and the establishment of photosynthetic system promote rapid seed germination and early growth of seedling in pearl millet
Cited by: 6
Author(s): Bingchao Wu, Min Sun, Huan Zhang, Dan Yang, Chuang Lin, İmran Khan, Xiaoshan Wang, Xinquan Zhang, Gang Nie, Guangyan Feng, Yanhong Yan, Li Zhou, Yan Peng, Linkai Huang
Software Mentions: 3
Published: over 5 years ago

10.1186/s13068-021-02032-7

Genome-wide association study and transcriptome analysis reveal key genes affecting root growth dynamics in rapeseed
Cited by: 17
Author(s): Keqi Li, Jie Wang, Lieqiong Kuang, Ze Tian, Xinfa Wang, Xiaoling Dun, Jinxing Tu, Hanzhong Wang
Software Mentions: 3
Published: about 5 years ago

10.1186/s13068-019-1630-5

Responses of Methanosarcina barkeri to acetate stress
Cited by: 21
Author(s): Pinjing He, Haowen Duan, Wenfeng Han, Yang Liu, Liming Shao
Software Mentions: 3
Published: almost 7 years ago

10.1590/1414-431X20198333

Screening potential prognostic biomarkers of long non-coding RNAs for predicting the risk of chronic kidney disease
Cited by: 11
Author(s): Na Li, Yan Cui, Min Yin, Feng Liu
Software Mentions: 3
Published: almost 8 years ago

10.1093/bib/bbw114

Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences
Cited by: 444
Author(s): Claudia Manzoni, Demis A. Kia, Jana Vandrovcová, John Hardy, Nicholas W. Wood, Patrick A. Lewis, Raffaele Ferrari
Software Mentions: 3
Published: almost 10 years ago

10.1093/bib/bbw139

Gene co-expression analysis for functional classification and gene–disease predictions
Cited by: 511
Author(s): Sipko van Dam, Urmo Võsa, Adriaan van der Graaf, Lude Franke, João Pedro de Magalhães
Software Mentions: 3
Published: almost 10 years ago

10.1093/bfgp/elx046

Mapping gene regulatory networks from single-cell omics data
Cited by: 165
Author(s): Mark Fiers, Liesbeth Minnoye, Sara Aibar, Carmen Bravo González-Blas, Zeynep Kalender Atak, Stein Aerts
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12935-021-02008-5

Prognostic signature composed of transcription factors accurately predicts the prognosis of gastric cancer patients
Cited by: 4
Author(s): Liqun Zhou, Zhiqing Chen, You Wu, Hao Lü, Lin Xin
Software Mentions: 3
Published: over 5 years ago

10.1186/s12935-020-01587-z

Identified IGSF9 association with prognosis and hypoxia in nasopharyngeal carcinoma by bioinformatics analysis
Cited by: 6
Author(s): Danxia Huang, Qianqian Liu, Weijun Zhang, Chunyue Huang, Ronghui Zheng, Gaoqiang Xie, Hongmei Wang, Baochang Jia, Jianjun Shi, Yawei Yuan, Min Deng
Software Mentions: 3
Published: about 6 years ago

10.1186/s12935-021-01929-5

ESR1 as a recurrence-related gene in intrahepatic cholangiocarcinoma: a weighted gene coexpression network analysis
Cited by: 3
Author(s): Fengwei Li, Qinjunjie Chen, Yang Yang, Meihui Li, Lei Zhang, Zhenlin Yan, Junjie Zhang, Kui Wang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12935-021-02033-4

Immune signature-based hepatocellular carcinoma subtypes may provide novel insights into therapy and prognosis predictions
Cited by: 13
Author(s): Qiuxian Zheng, Qin Yang, Jiaming Zhou, Xinyu Gu, Haibo Zhou, Xuejun Dong, Haihong Zhu, Zhi Chen
Software Mentions: 3
Published: over 5 years ago

10.1186/s12935-021-01871-6

Identifying SLC27A5 as a potential prognostic marker of hepatocellular carcinoma by weighted gene co-expression network analysis and in vitro assays
Cited by: 9
Author(s): Fan Zhang, Mengzhou Xue, Xin Jiang, Huiyuan Yu, Yixuan Qiu, J. Yu, Fan Yang, Zhijun Bao
Software Mentions: 3
Published: over 5 years ago

10.1186/s12935-021-01982-0

Identification of collagen genes related to immune infiltration and epithelial-mesenchymal transition in glioma
Cited by: 25
Author(s): Yin Wu, Hecheng Zhu, Jun Tan, Zhaoqi Xin, Quanwei Zhou, Yudong Cao, Zhaoping Wu, Lei Wang, Ming Zhao, Xingjun Jiang, Chao Ren, Guihua Tang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12935-018-0513-3

Integrated TCGA analysis implicates lncRNA CTB-193M12.5 as a prognostic factor in lung adenocarcinoma
Cited by: 26
Author(s): Wang Xue-hai, Gang Li, Qingsong Luo, Jianyong Xie, Chongzhi Gan
Software Mentions: 3
Published: over 8 years ago

10.1186/s12935-019-0859-1

Eleven genes associated with progression and prognosis of endometrial cancer (EC) identified by comprehensive bioinformatics analysis
Cited by: 54
Author(s): Jinhui Liu, Shulin Zhou, Siyue Li, Yi Jiang, Yicong Wan, Xiaoling Ma, Wenjun Cheng
Software Mentions: 3
Published: over 7 years ago

10.1186/s12935-020-01672-3

Assessing immune infiltration and the tumor microenvironment for the diagnosis and prognosis of sarcoma
Cited by: 28
Author(s): Naiqiang Zhu, Jingyi Hou
Software Mentions: 3
Published: almost 6 years ago

10.1002/cam4.3946

WGCNA identification of TLR7 as a novel diagnostic biomarker, progression and prognostic indicator, and immunotherapeutic target for stomach adenocarcinoma
Cited by: 16
Author(s): Qihang Yuan, Qi Zhou, Jie Ren, Guan Wang, Chunlai Yin, Dong Shang, Shilin Xia
Software Mentions: 3
Published: over 5 years ago

10.1002/cam4.2468

Comprehensive analysis of five long noncoding RNAs expression as competing endogenous RNAs in regulating hepatoma carcinoma
Cited by: 13
Author(s): Xin Lou, Jun Li, Yu Dong, Yaqing Wei, Feng Shan, Jinjin Sun
Software Mentions: 3
Published: about 7 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: almost 7 years ago

10.1186/s12944-020-01299-3

Ubiquitin-specific protease as the underlying gene biomarker for aortic stenosis
Cited by: 3
Author(s): Yin Yuan, Lianqun Wang, Bo-Chen Yao, Zhigang Guo
Software Mentions: 3
Published: over 6 years ago

10.1155/2020/1937387

Protein Level and Infantile Diarrhea in a Postweaning Piglet Model
Cited by: 10
Author(s): Jing Gao, Jie Yin, Kang Xu, Hui Han, Zemin Liu, Chenyu Wang, Tiejun Li, Yulong Yin
Software Mentions: 3
Published: over 6 years ago

10.1186/s12934-019-1265-z

Improved utilization of soybean meal through fermentation with commensal Shewanella sp. MR-7 in turbot (Scophthalmus maximus L.)
Cited by: 31
Author(s): Chaoqun Li, Beili Zhang, Xin Wang, Xionge Pi, X Wang, Huihui Zhou, Kangsen Mai, Gang He
Software Mentions: 3
Published: almost 7 years ago

10.1186/s40168-017-0264-8

Chemical and pathogen-induced inflammation disrupt the murine intestinal microbiome
Cited by: 93
Author(s): Mikayla A. Borton, Anice Sabag-Daigle, Jikang Wu, Lindsey Solden, Bridget S. O’Banion, Rebecca A. Daly, Richard A. Wolfe, Juan F. González, Vicki H. Wysocki, Brian M. M. Ahmer, Kelly Wrighton
Software Mentions: 3
Published: over 9 years ago

10.1186/s40168-021-01061-6

Gut microbiome variation modulates the effects of dietary fiber on host metabolism
Cited by: 54
Author(s): Sofia M Murga-Garrido, Qilin Hong, Tzu Wen L. Cross, Evan Hutchison, Jessica Han, Sydney P. Thomas, Eugenio I. Vivas, John M. Denu, Danilo Guillermo Ceschin, Zheng-Zheng Tang, Federico E. Rey
Software Mentions: 3
Published: over 5 years ago

10.3390/microorganisms9030465

Unraveling the Gut Microbiome of the Invasive Small Indian Mongoose (Urva auropunctata) in the Caribbean
Cited by: 6
Author(s): Anne A.M.J. Becker, KC Hill, Patrick Butaye
Software Mentions: 3
Published: over 5 years ago

10.3390/microorganisms9020385

Transcriptome Analysis Reveals the Genes Involved in Bifidobacterium Longum FGSZY16M3 Biofilm Formation
Cited by: 12
Author(s): Zongmin Liu, Lingzhi Li, Qianwen Wang, Faizan Ahmed Sadiq, Yuan‐Kun Lee, Jianxin Zhao, Hao Zhang, Haitao Li, Wenwei Liu
Software Mentions: 3
Published: over 5 years ago

10.1186/s13229-020-00355-0

Transcriptional signatures of participant-derived neural progenitor cells and neurons implicate altered Wnt signaling in Phelan-McDermid syndrome and autism
Cited by: 23
Author(s): Michael S. Breen, Andrew Browne, Gabriel E. Hoffman, Sofia Stathopoulos, Kristen J. Brennand, Joseph D. Buxbaum, Elodie Drapeau
Software Mentions: 3
Published: over 6 years ago

10.1186/s13229-020-00354-1

Transcriptional consequences of MBD5 disruption in mouse brain and CRISPR-derived neurons
Cited by: 11
Author(s): Catarina M. Seabra, Tatsiana Aneichyk, Serkan Erdin, Derek J.C. Tai, Celine de Esch, Parisa Razaz, Yu An, Poornima Manavalan, Ashok Ragavendran, Alexei Stortchevoi, Clemer Abad, Juan I. Young, Patrı́cia Maciel, Michael E. Talkowski, James F. Gusella
Software Mentions: 3
Published: over 6 years ago

10.1093/molbev/msaa002

Disrupted Gene Networks in Subfertile Hybrid House Mice
Cited by: 20
Author(s): Katy Morgan, Bettina Harr, Michael A. White, Bret A. Payseur, Leslie M. Turner
Software Mentions: 3
Published: almost 7 years ago

10.7717/peerj.8456

Key genes and co-expression modules involved in asthma pathogenesis
Cited by: 12
Author(s): Yuyi Huang, Hui Liu, Li Zuo, Ailin Tao
Software Mentions: 3
Published: over 6 years ago

10.7717/peerj.10977

Comparative transcriptomic analysis reveals the cold acclimation during chilling stress in sensitive and resistant passion fruit (Passiflora edulis) cultivars
Cited by: 7
Author(s): Yanyan Wu, Weihua Huang, Qian Tian, Jieyun Liu, Xiuzhong Xia, Yang Xiao-ling, Haifei Mou
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.9622

Gut microbiota of obese and diabetic Thai subjects and interplay with dietary habits and blood profiles
Cited by: 7
Author(s): Lucsame Gruneck, Niwed Kullawong, Kongkiat Kespechara, Siam Popluechai
Software Mentions: 3
Published: over 6 years ago

10.3390/ph12040156

C3orf70 Is Involved in Neural and Neurobehavioral Development
Cited by: 8
Author(s): Yoshifumi Ashikawa, Takashi Shiromizu, Koki Miura, Yoshiyuki Adachi, Takaaki Matsui, Yasumasa Bessho, Toshio Tanaka, Yuhei Nishimura
Software Mentions: 3
Published: about 7 years ago

10.1111/pbi.13132

Genome sequencing and <scp>CRISPR</scp>/Cas9 gene editing of an early flowering Mini‐Citrus (Fortunella hindsii)
Cited by: 76
Author(s): Chenqiao Zhu, Xiongjie Zheng, Yue Huang, Junli Ye, Peng Chen, Chenglei Zhang, Fei Zhao, Zongzhou Xie, Siqi Zhang, Nan Wang, Hang Li, Lun Wang, Xiaomei Tang, Lijun Chai, Qiang Xu, Xiuxin Deng
Software Mentions: 3
Published: over 7 years ago

10.1002/pld3.154

Network‐based feature selection reveals substructures of gene modules responding to salt stress in rice
Cited by: 13
Author(s): Qian Du, Malachy T. Campbell, Huihui Yu, Kan Liu, Harkamal Walia, Chi Zhang, Chi Zhang
Software Mentions: 3
Published: over 7 years ago

10.3390/plants10040646

New Cross-Talks between Pathways Involved in Grapevine Infection with ‘Candidatus Phytoplasma solani’ Revealed by Temporal Network Modelling
Cited by: 3
Author(s): Blaž Škrlj, Maruša Pompe-Novak, Günter Brader, Barbara Anžič, Živa Ramšak, Kristina Gruden, Jan Kralj, Aleš Kladnik, Nada Lavrač, Thomas Roitsch, Marina Dermastia
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pbio.3000830

Strigolactone signaling regulates specialized metabolism in tobacco stems and interactions with stem-feeding herbivores
Cited by: 16
Author(s): Suhua Li, Youngsung Joo, Dechang Cao, Ran Li, Gisuk Lee, Rayko Halitschke, Gundega Baldwin, Ian T. Baldwin, Ming Wang
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pcbi.1005244

Utility and Limitations of Using Gene Expression Data to Identify Functional Associations
Cited by: 47
Author(s): Sahra Uygun, Cheng Peng, Melissa D. Lehti-Shiu
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pcbi.1005680

Interactions between the tumor and the blood systemic response of breast cancer patients
Cited by: 21
Author(s): Vanessa Dumeaux, Bjørn Fjukstad, Hans E. Fjøsne, Jan Ole Frantzen, Marit Muri Holmen, Enno Rodegerdts, Ellen Schlichting, Anne Lise Børresen-Dale, Lars Ailo Bongo, Eiliv Lund, Michael Hallett
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pgen.1009270

Physiological and genetic convergence supports hypoxia resistance in high-altitude songbirds
Cited by: 10
Author(s): Ying Xiong, Liqing Fan, Yan Hao, Yalin Cheng, Ying Chang, Jing Wang, Haiyan Lin, Gang Song, Yanhua Qu, Fumin Lei
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1005963

De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects
Cited by: 87
Author(s): James R. Priest, Kazutoyo Osoegawa, Nebil Mohammed, Vivek Nanda, Ramendra K. Kundu, Kathleen Schultz, Edward J. Lammer, Santhosh Girirajan, Todd E. Scheetz, Daryl Waggott, François Haddad, Sushma Reddy, Daniel Bernstein, Trudy L. Burns, Jeffrey D. Steimle, Xinan Yang, Ivan P. Moskowitz, Matthew E. Hurles, Richard P. Lifton, Debbie Nickerson, Michael J. Bamshad, Evan E. Eichler, Seema Mital, Val C. Sheffield, Thomas Quertermous, Bruce D. Gelb, Michael A. Portman, Euan A. Ashley
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1008768

Additive and mostly adaptive plastic responses of gene expression to multiple stress in Tribolium castaneum
Cited by: 30
Author(s): Eva L. Koch, Frédéric Guillaume
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1008513

Drosophila RpS12 controls translation, growth, and cell competition through Xrp1
Cited by: 34
Author(s): Zhejun Ji, Marianthi Kiparaki, Virginia Folgado, Amit Kumar, Jorge Polo Blanco, Gerard Rimesso, Jacky Chuen, Yang Liu, Deyou Zheng, Nicholas E. Baker
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pgen.1006745

GRHL3 binding and enhancers rearrange as epidermal keratinocytes transition between functional states
Cited by: 39
Author(s): Rachel Herndon Klein, Ziguang Lin, Amelia Soto Hopkin, William Gordon, Lam C. Tsoi, Yun Liang, Jóhann E. Guðjónsson, Bogi Andersen
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pgen.1003053

Network Analysis of a Pkd1-Mouse Model of Autosomal Dominant Polycystic Kidney Disease Identifies HNF4α as a Disease Modifier
Cited by: 72
Author(s): Luís F. Menezes, Fang Zhou, Andrew D. Patterson, Klaus Piontek, Kristopher W. Krausz, Frank J. Gonzalez, Gregory G. Germino
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.pgen.1009461

The long noncoding RNA FRILAIR regulates strawberry fruit ripening by functioning as a noncanonical target mimic
Cited by: 28
Author(s): Yajun Tang, Zhibo Qu, Jiajun Li, Reqing He, David L. Adelson, Youlin Zhu, Zhenbiao Yang, Dong Wang
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pntd.0007764

Identification of a systemic interferon-γ inducible antimicrobial gene signature in leprosy patients undergoing reversal reaction
Cited by: 20
Author(s): Rosane M. B. Teles, Jing Lü, Maria Tió-Coma, Isabela M. B. Goulart, Sayera Banu, Deanna A. Hagge, Kidist Bobosha, Tom H. M. Ottenhoff, Matteo Pellegrini, Annemieke Geluk, Robert L. Modlin
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pntd.0007589

The cell fate regulator NUPR1 is induced by Mycobacterium leprae via type I interferon in human leprosy
Cited by: 5
Author(s): Priscila Ribeiro Andrade, Manali Mehta, Jing Lü, Rosane M. B. Teles, Dennis Montoya, Phillip Scumpia, Euzenir Nunes Sarno, Marîa Teresa Ochoa, Feiyang Ma, Matteo Pellegrini, Robert L. Modlin
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0087499

Analysis of Global Gene Expression in Brachypodium distachyon Reveals Extensive Network Plasticity in Response to Abiotic Stress
Cited by: 80
Author(s): Henry D. Priest, Samuel E. Fox, Erik R. Rowley, Jessica R. Murray, Todd P. Michael, Todd C. Mockler
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0156723

Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.)
Cited by: 76
Author(s): Xuke Lu, Xiugui Chen, Mingchun Mu, Junjuan Wang, Xiaoge Wang, Delong Wang, Zujun Yin, Weili Fan, Shuai Wang, Lixue Guo, Wuwei Ye
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0192606

Maternal high-fat diet associated with altered gene expression, DNA methylation, and obesity risk in mouse offspring
Cited by: 86
Author(s): Madeline Rose Keleher, Syeda Nuzhat Fatima Zaidi, Shyam Shah, MaryAnn Oakley, Cassondra Pavlatos, Samir El Idrissi, Xiaoyun Xing, Daofeng Li, Ting Wang, James M. Cheverud
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0172389

Analysis of long noncoding RNA and mRNA using RNA sequencing during the differentiation of intramuscular preadipocytes in chicken
Cited by: 34
Author(s): Tao Zhang, Xiangqian Zhang, Kai Han, Genxi Zhang, Jinyu Wang, Kaizhou Xie, Qingwu Xue, Xiaolong Fan
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0239061

In silico transcriptional analysis of mRNA and miRNA reveals unique biosignatures that characterizes different types of diabetes
Cited by: 4
Author(s): J Carlos Angulo, Caian L. Vinhaes, Eduardo R. Fukutani, Victor V. S. Albuquerque, Artur T. L. Queiroz, Bruno B. Andrade, Kiyoshi F. Fukutani
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0147147

Systematic Identification and Characterization of Long Non-Coding RNAs in the Silkworm, Bombyx mori
Cited by: 94
Author(s): Yuqian Wu, Tingcai Cheng, Chun Li, Duolian Liu, Quan Zhang, Rodney Long, Ping Zhao, Qingyou Xia
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0212513

Lenvatinib plus anti-PD-1 antibody combination treatment activates CD8+ T cells through reduction of tumor-associated macrophage and activation of the interferon pathway
Cited by: 262
Author(s): Yu Kato, Kimiyo Tabata, Takayuki Kimura, Ayako Yachie‐Kinoshita, Yoichi Ozawa, Kazuhiko Yamada, Junichi Ito, Sho Tachino, Yusaku Hori, Masahiro Matsuki, Yoshikazu Matsuoka, Samik Ghosh, Hiroaki Kitano, Ken’ichi Nomoto, Junji Matsui, Yasuhiro Funahashi
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0105685

Analysis of Papaya Cell Wall-Related Genes during Fruit Ripening Indicates a Central Role of Polygalacturonases during Pulp Softening
Cited by: 56
Author(s): João Paulo Fabi, Sabrina Garcia Broetto, Sarah Lígia Garcia Leme da Silva, Silin Zhong, Franco Maria Lajolo, João Roberto Oliveira do Nascimento
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0068878

Whole Brain and Brain Regional Coexpression Network Interactions Associated with Predisposition to Alcohol Consumption
Cited by: 29
Author(s): Lauren A. Vanderlinden, Laura Saba, Katerina Kechris, Michael F. Miles, Paula L. Hoffman, Boris Tabakoff
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0179065

Proteome profiling in IL-1β and VEGF-activated human umbilical vein endothelial cells delineates the interlink between inflammation and angiogenesis
Cited by: 64
Author(s): Thomas Mohr, Verena Haudek-Prinz, Astrid Slany, Johannes Grillari, M. Micksche, Christopher Gerner
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0138236

Long Noncoding RNA Expression during Human B-Cell Development
Cited by: 73
Author(s): Andreas Petri, Karen Dybkær, Martin Bøgsted, Charlotte Albæk Thrue, Peter Hagedorn, Alexander Schmitz, Julie Støve Bødker, Hans Erik Johnsen, Sakari Kauppinen
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0157426

An Integrative Transcriptomic Analysis for Identifying Novel Target Genes Corresponding to Severity Spectrum in Spinal Muscular Atrophy
Cited by: 6
Author(s): Chunrong Yang, Chien‐Lin Chen, Wei-Chun Chou, Ho-Chen Lin, Yuh Jyh Jong, Li-Kai Tsai, Chun‐Yu Chuang
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0163832

The Role of Vitamin D in the Transcriptional Program of Human Pregnancy
Cited by: 30
Author(s): Amal Al-Garawi, Vincent J. Carey, Divya Chhabra, Hooman Mirzakhani, Jarrett Morrow, Jessica Lasky‐Su, Weiliang Qiu, Nancy Laranjo, Augusto A. Litonjua, Scott T. Weiss
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0160520

RNAseq Analyses Identify Tumor Necrosis Factor-Mediated Inflammation as a Major Abnormality in ALS Spinal Cord
Cited by: 55
Author(s): David G. Brohawn, Laura C. O’Brien, James P. Bennett
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0111681

Taxonomic and Functional Diversity Provides Insight into Microbial Pathways and Stress Responses in the Saline Qinghai Lake, China
Cited by: 12
Author(s): Qiuyuan Huang, Brandon R. Briggs, Hailiang Dong, Hongchen Jiang, Geng Wu, Christian F. Edwardson, Iwijn De Vlaminck, Stephen R. Quake
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0183928

Triple DMARD treatment in early rheumatoid arthritis modulates synovial T cell activation and plasmablast/plasma cell differentiation pathways
Cited by: 27
Author(s): Alice M. Walsh, Mihir D. Wechalekar, Yanxia Guo, Xiaoli Yin, Helen Weedon, Susanna Proudman, Malcolm D. Smith, Sunil Nagpal
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0211913

Comparative transcriptome analysis of resistant and susceptible kiwifruits in response to Pseudomonas syringae pv. Actinidiae during early infection
Cited by: 17
Author(s): Yun‐Chun Song, Lei Sun, Miaomiao Lin, Jinyong Chen, Xiujuan Qi, Chun-Gen Hu, Jinbao Fang
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0152648

DTW-MIC Coexpression Networks from Time-Course Data
Cited by: 9
Author(s): Samantha Riccadonna, Giuseppe Jurman, Roberto Visintainer, Michele Filosi, Cesare Furlanello
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0219486

Caenorhabditis elegans hub genes that respond to amyloid beta are homologs of genes involved in human Alzheimer’s disease
Cited by: 14
Author(s): Rasoul Godini, Roger Pocock, Hossein Fallahi
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0143436

Analysis of Stage-Specific Gene Expression Profiles in the Uterine Endometrium during Pregnancy in Pigs
Cited by: 17
Author(s): Mingoo Kim, Heewon Seo, Yohan Choi, Inkyu Yoo, Minseok Seo, Chang Kyu Lee, Heebal Kim, Hakhyun Ka
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0200049

Variation and diversification of the microbiome of Schlechtendalia chinensis on two alternate host plants
Cited by: 8
Author(s): Haixia Wu, Xiaoming Chen, Hang Chen, Qin Lu, Zixiang Yang, Weibin Ren, Juan Liu, Shihe Shao, Chao Wang, Kirst King-Jones, Ming‐Shun Chen
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0156006

Gene Co-Expression Network Analysis for Identifying Modules and Functionally Enriched Pathways in Type 1 Diabetes
Cited by: 48
Author(s): Ignacio Riquelme Medina, Zelmina Lubovac-Pilav
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0202309

Comparison of gene co-networks analysis provide a systems view of rice (Oryza sativa L.) response to Tilletia horrida infection
Cited by: 6
Author(s): aijun wang, Xinyue Shu, Xianyu Niu, Wenjuan Zhao, Peng Ai, Ping Li, Aiping Zheng
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0248796

Evidence that synergism between potassium and nitrate enhances the alleviation of ammonium toxicity in rice seedling roots
Cited by: 12
Author(s): Gen Fang, Jing Yang, Tong Sun, Xiaoxin Wang, Yangsheng Li
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0231771

Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California current system
Cited by: 3
Author(s): Irina N. Shilova, Jonathan D. Magasin, Matthew M. Mills, Julie Robidart, Kendra A. Turk‐Kubo, Jonathan P. Zehr
Software Mentions: 3
Published: over 6 years ago

10.1038/s42003-021-01946-0

Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod
Cited by: 14
Author(s): Petra H. Lenz, Vittoria Roncalli, Matthew Cieslak, Ann M. Tarrant, Ann M. Castelfranco, Daniel K. Hartline
Software Mentions: 3
Published: over 5 years ago

10.1038/s42003-019-0574-4

Hibernation induces widespread transcriptional remodeling in metabolic tissues of the grizzly bear
Cited by: 57
Author(s): Heiko T. Jansen, Shawn Trojahn, Michael W. Saxton, Corey R. Quackenbush, Brandon D. Evans Hutzenbiler, O. Lynne Nelson, Omar E. Cornejo, Charles T. Robbins, Joanna L. Kelley
Software Mentions: 3
Published: about 7 years ago

10.1038/s42003-020-01172-0

Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression
Cited by: 23
Author(s): Ryoichi Yano, Tohru Ariizumi, Satoko Nonaka, Yoichi Kawazu, Silin Zhong, Lukas A. Mueller, James Giovannoni, Jocelyn K. C. Rose, Hiroshi Ezura
Software Mentions: 3
Published: about 6 years ago

10.1038/s42003-020-01235-2

Floral transcriptomes reveal gene networks in pineapple floral growth and fruit development
Cited by: 30
Author(s): Lulu Wang, Yang Li, Xingyue Jin, Liping Liu, Xiaozhuan Dai, Qing Liu, Lihua Zhao, Ping Zheng, Xiaomei Wang, Yeqiang Liu, Deshu Lin, Yuan Qin
Software Mentions: 3
Published: about 6 years ago

10.1155/2020/8183420

Weighed Gene Coexpression Network Analysis Screens the Potential Long Noncoding RNAs and Genes Associated with Progression of Coronary Artery Disease
Cited by: 6
Author(s): Lang Wang, Jun Hu, Jiali Zhou, Fan Guo, Yong Tan, Liang Zhang
Software Mentions: 3
Published: over 6 years ago

10.1155/2020/4574792

Functional Modular Network Identifies the Key Genes of Preoperative Inhalation Anesthesia and Intravenous Anesthesia in Off-Pump Coronary Artery Bypass Grafting
Cited by: 3
Author(s): Hongfei Zhao, Weitian Wang, Liping Liu, Junlong Wang, Quanzhang Yan
Software Mentions: 3
Published: about 6 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479