cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0129610

Association of Protein Translation and Extracellular Matrix Gene Sets with Breast Cancer Metastasis: Findings Uncovered on Analysis of Multiple Publicly Available Datasets Using Individual Patient Data Approach
Cited by: 4
Author(s): Nilotpal Chowdhury, Shantanu Sapru
Software Mentions: 5
Published: about 11 years ago

10.3389/fmicb.2017.01120

The Arbuscular Mycorrhizal Fungus Funneliformis mosseae Alters Bacterial Communities in Subtropical Forest Soils during Litter Decomposition
Cited by: 31
Author(s): Heng Gui, Witoon Purahong, Kevin D. Hyde, Jianchu Xu, Peter E. Mortimer
Software Mentions: 5
Published: about 9 years ago

10.1186/s12935-021-01933-9

Low expression of CHRDL1 and SPARCL1 predicts poor prognosis of lung adenocarcinoma based on comprehensive analysis and immunohistochemical validation
Cited by: 13
Author(s): Huan Deng, Hang Qin, Deyan Shen, Yibi Zhang, Ming Chen
Software Mentions: 5
Published: over 5 years ago

10.3389/fmolb.2021.633299

Identification of Lymph Node Metastasis–Related Key Genes and Prognostic Risk Model in Bladder Cancer by Co-Expression Analysis
Cited by: 8
Author(s): Cheng Luo, Bin Huang, Yukun Wu, Yadong Xu, Wei Ou, Junxing Chen, Lingwu Chen
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0143128

RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in Maize
Cited by: 30
Author(s): Liu Ya, Miaoyi Zhou, Zhaoxu Gao, Wen Ren, Fan Yang, Hang He, Jiuran Zhao
Software Mentions: 5
Published: almost 11 years ago

10.3389/fgene.2016.00080

Recursive Indirect-Paths Modularity (RIP-M) for Detecting Community Structure in RNA-Seq Co-expression Networks
Cited by: 12
Author(s): Bahareh Rahmani, Michael T. Zimmermann, Diane E. Grill, Richard B. Kennedy, Ann L. Oberg, Bill C. White, Gregory A. Poland, Brett A. McKinney
Software Mentions: 5
Published: over 10 years ago

10.1186/s12967-020-02561-z

Gene correlation network analysis to identify regulatory factors in sepsis
Cited by: 25
Author(s): Zhongheng Zhang, Lin Chen, Ping Xu, Lifeng Xing, Yucai Hong, Pengpeng Chen
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12903-021-01587-z

A four-hypoxia-genes-based prognostic signature for oral squamous cell carcinoma
Cited by: 10
Author(s): Chenguang Zhao, Yingrui Zhou, Hongwei Ma, Jinhui Wang, Hongxu Guo, Hao Líu
Software Mentions: 5
Published: over 5 years ago

10.1186/s11689-020-09316-3

Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder
Cited by: 9
Author(s): Bonnie Alberry, Christina A Castellani, Shiva M. Singh
Software Mentions: 5
Published: over 6 years ago

10.3390/ijms22115744

BRAF Inhibitors Induce Feedback Activation of RAS Pathway in Thyroid Cancer Cells
Cited by: 8
Author(s): Elisa Bonaldi, Chiara Gargiuli, Loris De Cecco, Arianna Micali, Maria Grazia Rizzetti, Angela Greco, Maria Grazia Borrello, Emanuela Minna
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.649619

Long Non-coding RNAs: Mechanisms, Experimental, and Computational Approaches in Identification, Characterization, and Their Biomarker Potential in Cancer
Cited by: 21
Author(s): Anshika Chowdhary, Venkata Satagopam, Reinhard Schneider
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2020.00988

Identification of Candidate Biomarkers for Salt Sensitivity of Blood Pressure by Integrated Bioinformatics Analysis
Cited by: 3
Author(s): Chen Chen, Guanzhi Liu, Yue‐Yuan Liao, Chao Chu, Wenfang Zheng, Yang Wang, Jiawen Hu, Qiang Ma, Keke Wang, Yan Yu, Yue Yuan, Jianjun Mu
Software Mentions: 5
Published: about 6 years ago

10.3390/ijms22179146

Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses
Cited by: 5
Author(s): Mirosław Tyrka, Beata Bakera, Magdalena Szeliga, Magdalena Święcicka, Paweł Krajewski, Monika Mokrzycka, Monika Rakoczy-Trojanowska
Software Mentions: 5
Published: about 5 years ago

10.1186/s12974-017-0834-5

Myeloid C/EBPβ deficiency reshapes microglial gene expression and is protective in experimental autoimmune encephalomyelitis
Cited by: 17
Author(s): Marta Pulido-Salgado, José M. Vidal-Taboada, Gerardo Garcıa-Dıaz Barriga, Joan Serratosa, Tony Valente, Paola Castillo, Jonathan Matalonga, Marco Straccia, Josep M. Canals, Annabel F. Valledor, Carme Solà, Josep Saura
Software Mentions: 5
Published: over 9 years ago

10.3390/ijms22062901

Age and Sex-Related Changes in Human First-Trimester Placenta Transcriptome and Insights into Adaptative Responses to Increased Oxygen
Cited by: 7
Author(s): Fulin Liu, Christelle Simasotchi, Françoise Vibert, Wencan Zhu, Sophie Gil, Séverine A. Degrelle, Thierry Fournier
Software Mentions: 5
Published: over 5 years ago

10.7717/peerj.11321

Identification of key genes and biological processes contributing to colitis associated dysplasia in ulcerative colitis
Cited by: 5
Author(s): Di Zhang, Pengguang Yan, Tian Han, Xiaoyun Cheng, Jingnan Li
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.616507

Molecular Subtypes Based on the Stemness Index Predict Prognosis in Glioma Patients
Cited by: 7
Author(s): Jun Tan, Hecheng Zhu, Guihua Tang, Hongwei Liu, Siyi Wanggou, Yudong Cao, Zhaoqi Xin, Quanwei Zhou, Chaohong Zhan, Zhaoping Wu, Youwei Guo, Zhipeng Jiang, Ming Zhao, Chao Ren, Xingjun Jiang, Yin Wu
Software Mentions: 5
Published: over 5 years ago

10.1128/mSystems.00550-20

A Comprehensive Coexpression Network Analysis in Vibrio cholerae
Cited by: 4
Author(s): Cory D. DuPai, Claus O. Wilke, Bryan William Davies
Software Mentions: 5
Published: about 6 years ago

10.1038/s41396-020-0606-6

Genetic variation and evolutionary history of a mycorrhizal fungus regulate the currency of exchange in symbiosis with the food security crop cassava
Cited by: 12
Author(s): Romain Savary, Cindy Dupuis, Frédéric G. Masclaux, Ivan D. Mateus, Edward C. Rojas, Ian R. Sanders
Software Mentions: 5
Published: over 6 years ago

10.1093/bib/bbaa072

Scoring functions for drug-effect similarity
Cited by: 13
Author(s): Stephan Struckmann, Markus Ernst, Sarah Fischer, Nancy Mah, Georg Fuellen, Steffen Möller
Software Mentions: 5
Published: over 6 years ago

10.1186/s12863-020-00852-4

Transcriptome analysis identifies genes and co-expression networks underlying heat tolerance in pigs
Cited by: 9
Author(s): Yuqing He, Christian Maltecca, Francesco Tiezzi, Emmanuel Lozada Soto, W. L. Flowers
Software Mentions: 5
Published: over 6 years ago

10.3389/fgene.2021.663787

Integrated Analysis of Microarray and RNA-Seq Data for the Identification of Hub Genes and Networks Involved in the Pancreatic Cancer
Cited by: 10
Author(s): Maryum Nisar, Rehan Zafar Paracha, Iqra Arshad, Sidra Adil, Sabaoon Zeb, Rumeza Hanif, Mehak Rafiq, Zamir Hussain
Software Mentions: 5
Published: about 5 years ago

10.1038/s41396-021-00923-z

Maize germplasm chronosequence shows crop breeding history impacts recruitment of the rhizosphere microbiome
Cited by: 38
Author(s): Alonso Favela, Martin Bohn, Angela D. Kent
Software Mentions: 5
Published: over 5 years ago

10.1038/s41398-021-01358-y

Zbtb16 regulates social cognitive behaviors and neocortical development
Cited by: 23
Author(s): Noriyoshi Usui, Stefano Berto, Ami Konishi, Makoto Kondo, Genevieve Konopka, Hideo Matsuzaki, Shoichi Shimada
Software Mentions: 5
Published: over 5 years ago

10.7717/peerj.1782

H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups
Cited by: 24
Author(s): Sarah Piché‐Choquette, Julien Tremblay, Susannah G. Tringe, Philippe Constant
Software Mentions: 5
Published: over 10 years ago

10.3389/fmolb.2020.576298

Identification of Immune-Related Genes MSR1 and TLR7 in Relation to Macrophage and Type-2 T-Helper Cells in Osteosarcoma Tumor Micro-Environments as Anti-metastasis Signatures
Cited by: 10
Author(s): Zhiyu Chen, Huanhuan Huang, Yang Wang, Fangbiao Zhan, Zhengxue Quan
Software Mentions: 5
Published: over 5 years ago

10.1186/s12935-021-01826-x

Systematic identification of key functional modules and genes in esophageal cancer
Cited by: 4
Author(s): Rui Wu, Hao Zhuang, Yukun Mei, Jin‐Yu Sun, Tao Dong, Lili Zhao, Zhining Fan, Li Liu
Software Mentions: 5
Published: over 5 years ago

10.1038/s41398-019-0384-y

Analysis of whole genome-transcriptomic organization in brain to identify genes associated with alcoholism
Cited by: 63
Author(s): Manav Kapoor, Jen Chyong Wang, Sean P. Farris, Yunlong Liu, Jeanette N. McClintick, Ishaan Gupta, Jacquelyn L. Meyers, Sarah Bertelsen, Michael J. Chao, John I. Nürnberger, Jay A. Tischfield, Oscar Harari, Zeran Li, Victor Hesselbrock, Lance O. Bauer, Towfique Raj, Bernice Porjesz, Arpana Agrawal, Tatiana Foroud, Howard J. Edenberg, R. Dayne Mayfield, Alison Goate
Software Mentions: 5
Published: over 7 years ago

10.3390/ijms22041989

Transcriptome Analysis of Subcutaneous Adipose Tissue from Severely Obese Patients Highlights Deregulation Profiles in Coding and Non-Coding Oncogenes
Cited by: 5
Author(s): Federica Rey, Letizia Messa, Cecilia Pandini, Rossella Launi, Bianca Barzaghini, Giancarlo Micheletto, Manuela Teresa Raimondi, Simona Bertoli, Cristina Cereda, Gian Vincenzo Zuccotti, Raffaella Cancello, Stephana Carelli
Software Mentions: 5
Published: over 5 years ago

10.1186/s12974-021-02154-7

Identification of aberrant innate and adaptive immunity based on changes in global gene expression in the blood of adults with autism spectrum disorder
Cited by: 11
Author(s): Fumie Horiuchi, Yuta Yoshino, Hiroshi Kumon, Rie Hosokawa, Kiwamu Nakachi, Kentaro Kawabe, Jun‐ichi Iga, Shu‐ichi Ueno
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2020.00650

Genome Regulation and Gene Interaction Networks Inferred From Muscle Transcriptome Underlying Feed Efficiency in Pigs
Cited by: 9
Author(s): Victor Adriano Okstoft Carmelo, Haja N. Kadarmideen
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-021-91534-3

A defective interleukin-17 receptor A1 causes weight loss and intestinal metabolism-related gene downregulation in Japanese medaka, Oryzias latipes
Cited by: 4
Author(s): Yo Okamura, Hiroshi Miyanishi, Masato Kinoshita, Tomoya Kono, Masahiro Sakai, Jun-ichi Hikima
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2021.661296

Combined Analysis of Volatile Terpenoid Metabolism and Transcriptome Reveals Transcription Factors Related to Terpene Synthase in Two Cultivars of Dendrobium officinale Flowers
Cited by: 20
Author(s): Ninghong Li, Yan Dong, Min Lv, Qian Li, Xinwei Sun, Liu Lin, Yongping Cai, Honghong Fan
Software Mentions: 4
Published: over 5 years ago

10.1186/s12862-021-01762-4

Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume
Cited by: 10
Author(s): Man Zhang, Ping Li, Xiao-lan Yan, Jia Wang, Tangren Cheng, Qixiang Zhang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-87720-y

Macrophages with reduced expressions of classical M1 and M2 surface markers in human bronchoalveolar lavage fluid exhibit pro-inflammatory gene signatures
Cited by: 19
Author(s): Hiroto Takiguchi, Chen Yang, Yang Cheng, Başak Şahin, Beth A. Whalen, Stephen Milne, Kentaro Akata, Kei Yamasaki, Julia Yang, Chung Yan Cheung, Ryan Vander Werff, Kelly M. McNagny, Fernando Sergio Leitão Filho, Tawimas Shaipanich, Stephan F. van Eeden, Ma’en Obeidat, Janice M. Leung, Don D. Sin
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2021.668448

Integrated Analysis of lncRNAs, mRNAs, and TFs to Identify Regulatory Networks Underlying MAP Infection in Cattle
Cited by: 6
Author(s): Maryam Heidari, A. Pakdel, Mohammad Reza Bakhtiarizadeh, Fariba Dehghanian
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-021-86207-0

Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease
Cited by: 17
Author(s): Peng-Fei Zheng, Lu-Zhu Chen, Yao-Zong Guan, Peng Liu
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.8061

Identification of genes and functional coexpression modules closely related to ulcerative colitis by gene datasets analysis
Cited by: 7
Author(s): Jie Zhu, Zheng Wang, Fengzhe Chen, Changhong Liu
Software Mentions: 4
Published: almost 7 years ago

10.3389/fgene.2019.01214

Weighted Gene Co-Expression Network Analysis Identifies Critical Genes in the Development of Heart Failure After Acute Myocardial Infarction
Cited by: 59
Author(s): Xiaowei Niu, Jingjing Zhang, Lanlan Zhang, Yufei Hou, Shuangshuang Pu, Ai-Ai Chu, Ming Bai, Zheng Zhang
Software Mentions: 4
Published: almost 7 years ago

10.7717/peerj.1066

Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree
Cited by: 33
Author(s): Nagesh A. Kuravadi, Vijay A. Yenagi, Kannan Rangiah, H. B. Mahesh, Anantharamanan Rajamani, Meghana Deepak Shirke, Heikham Russiachand, Ramya Malarini Loganathan, Chandana Shankara Lingu, S Shilpa, Aishwarya Ramamurthy, B. N. Sathyanarayana, Malali Gowda
Software Mentions: 4
Published: about 11 years ago

10.1038/s41598-021-82866-1

The protective role of daidzein in intestinal health of turbot (Scophthalmus maximus L.) fed soybean meal-based diets
Cited by: 14
Author(s): Guijuan Yu, Yang Liu, Weihao Ou, Jihong Dai, Qinghui Ai, Wenbing Zhang, Kangsen Mai, Yan-Jiao Zhang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-86536-0

Modular genome-wide gene expression architecture shared by early traits of osteoporosis and atherosclerosis in the Young Finns Study
Cited by: 6
Author(s): Binisha H. Mishra, Pashupati P. Mishra, Emma Raitoharju, Saara Marttila, Nina Mononen, Harri Sievänen, Jorma Viikari, Markus Juonala, Marika Laaksonen, Nina Hutri‐Kähönen, Mika Kähönen, Olli T. Raitakari, Terho Lehtimäki
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2021.634171

Weighted Gene Co-expression Network Analysis Reveals Different Immunity but Shared Renal Pathology Between IgA Nephropathy and Lupus Nephritis
Cited by: 6
Author(s): Niya Jia, Xing-Zi Liu, Zhao Zhang, Hong Zhang
Software Mentions: 4
Published: over 5 years ago

10.1186/1755-8794-6-51

Co-expression network analysis and genetic algorithms for gene prioritization in preeclampsia
Cited by: 26
Author(s): Eduardo Tejera, João Bernardes, Irene Rebelo
Software Mentions: 4
Published: almost 13 years ago

10.1038/s41598-020-79740-x

Combinatorial analyses reveal cellular composition changes have different impacts on transcriptomic changes of cell type specific genes in Alzheimer’s Disease
Cited by: 12
Author(s): Travis Johnson, Shunian Xiang, Tianhan Dong, Zhi Huang, Michael Cheng, Tianfu Wang, Kai Yang, Dong Ni, Kun Huang, Jie Zhang
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2021.695699

Integrated Analysis of mRNA- and miRNA-Seq in the Ovary of Rare Minnow Gobiocypris rarus in Response to 17α-Methyltestosterone
Cited by: 3
Author(s): Shaozhen Liu, Qiong Yang, Yue Chen, Qing Liu, Weiwei Wang, Jing Song, Yao Zheng, Wenzhong Liu
Software Mentions: 4
Published: about 5 years ago

10.1186/s12872-020-01838-x

Bioinformatics analysis of common key genes and pathways of intracranial, abdominal, and thoracic aneurysms
Cited by: 4
Author(s): Siwei Bi, Ruiqi Liu, Linfeng He, Jingyi Li, Jun Gu
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2021.680413

Identification of a Prognostic Signature for Ovarian Cancer Based on the Microenvironment Genes
Cited by: 9
Author(s): Xiao Huo, Hengzi Sun, Shuangwu Liu, Bing Liang, Huimin Bai, Shuzhen Wang, Shuhong Li
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-81689-4

Polycomb represses a gene network controlling puberty via modulation of histone demethylase Kdm6b expression
Cited by: 19
Author(s): Hollis Wright, Carlos F. Aylwin, Carlos A. Toro, Sergio R. Ojeda, Alejandro Lomniczi
Software Mentions: 4
Published: over 5 years ago

10.1186/s12920-015-0133-x

Meta-analysis derived atopic dermatitis (MADAD) transcriptome defines a robust AD signature highlighting the involvement of atherosclerosis and lipid metabolism pathways
Cited by: 115
Author(s): David Adrian Ewald, Dana Malajian, James G. Krueger, Christopher T. Workman, Tianjiao Wang, Suyan Tian, Thomas Litman, Emma Guttman‐Yassky, Mayte Suárez‐Fariñas
Software Mentions: 4
Published: almost 11 years ago

10.1038/s41598-020-78997-6

Genes associated with cognitive performance in the Morris water maze: an RNA-seq study
Cited by: 18
Author(s): Vasiliy V. Reshetnikov, Polina E. Kisaretova, Nikita I. Ershov, Anastasia S. Shulyupova, Dmitry Oshchepkov, Н. В. Климова, Anna V. Ivanchihina, T. I. Merkulova, Natalia P. Bondar
Software Mentions: 4
Published: over 5 years ago

10.1186/s12920-019-0518-3

Integrative genomic and transcriptomic analysis of genetic markers in Dupuytren’s disease
Cited by: 9
Author(s): Junghyun Jung, Go Woon Kim, Byungjo Lee, Jong Wha J. Joo, Wonhee Jang
Software Mentions: 4
Published: about 7 years ago

10.7717/peerj.9848

Identification of key modules and hub genes associated with lung function in idiopathic pulmonary fibrosis
Cited by: 5
Author(s): Yuechong Xia, Lei Cheng, Danhui Yang, Hong Luo
Software Mentions: 4
Published: almost 6 years ago

10.18632/aging.202173

A novel immune-related genes prognosis biomarker for hepatocellular carcinoma
Cited by: 7
Author(s): Kunpeng Wang, Xinyi Chen, Chong Jin, Jinggang Mo, Hao Jiang, Bin Yi, Xiang Chen
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.3509

GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis
Cited by: 9
Author(s): Raquel L. Costa, Luiz M. R. Gadelha, Marcelo Ribeiro-Alves, Fábio Porto
Software Mentions: 4
Published: about 9 years ago

10.3389/fgene.2020.00427

Bioinformatics Analysis Reveals Biomarkers With Cancer Stem Cell Characteristics in Lung Squamous Cell Carcinoma
Cited by: 38
Author(s): Yi Liao, Hua Xiao, Mengqing Cheng, Xiaoxuan Fan
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-021-82976-w

Integrated analysis identifies oxidative stress genes associated with progression and prognosis in gastric cancer
Cited by: 29
Author(s): Zhengyuan Wu, Lin Wang, Zhenpei Wen, Jun Yao
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-15-300

Visual gene-network analysis reveals the cancer gene co-expression in human endometrial cancer
Cited by: 81
Author(s): Wei-Chun Chou, An‐Lin Cheng, Marco Brotto, Chun‐Yu Chuang
Software Mentions: 4
Published: over 12 years ago

10.1038/s41598-020-74391-4

Analysis of gene expression from systemic lupus erythematosus synovium reveals myeloid cell-driven pathogenesis of lupus arthritis
Cited by: 9
Author(s): Erika L. Hubbard, Michelle D. Catalina, Sarah Heuer, Prathyusha Bachali, Robert Robl, Nicholas S. Geraci, Amrie C. Grammer, Peter E. Lipsky
Software Mentions: 4
Published: almost 6 years ago

10.3389/fgene.2020.581789

Integrated Analysis of Key Genes and Pathways Involved in Fetal Growth Restriction and Their Associations With the Dysregulation of the Maternal Immune System
Cited by: 2
Author(s): Xue Wang, Hong Zhu, Lei Lei, Yang Zhang, Chao Tang, Jingyi Wu, Jing Zhou, Xirong Xiao
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-70540-x

Identification of C3 as a therapeutic target for diabetic nephropathy by bioinformatics analysis
Cited by: 16
Author(s): Shumei Tang, Xiufen Wang, Tianci Deng, Huipeng Ge, Xiangcheng Xiao
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-71905-y

Whole transcriptome approach to evaluate the effect of aluminium hydroxide in ovine encephalon
Cited by: 9
Author(s): Endika Varela-Martínez, Martin Bilbao‐Arribas, Naiara Abendaño, Javier Asín, Marta Pérez, Damián F. de Andrés, Lluís Luján, Begoña M. Jugo
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-76657-3

Distinct regional ontogeny and activation of tumor associated macrophages in human glioblastoma
Cited by: 64
Author(s): Alexander Landry, Michael Balas, Saira Alli, Julian Spears, Zsolt Zádor
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-65916-y

Alterations of transcriptome signatures in head trauma-related neurodegenerative disorders
Cited by: 13
Author(s): Hyesun Cho, Seung Jae Hyeon, Jong-Yeon Shin, Victor E. Alvarez, Thor D. Stein, Jung‐Hee Lee, Neil W. Kowall, Ann C. McKee, Hoon Ryu, Jeong-Sun Seo
Software Mentions: 4
Published: over 6 years ago

10.1186/s13071-021-04597-6

Gene co-expression network analysis of Trypanosoma brucei in tsetse fly vector
Cited by: 5
Author(s): Kennedy W. Mwangi, Rosaline W. Macharia, Joel L. Bargul
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-65638-1

Genomic analyses of early responses to radiation in glioblastoma reveal new alterations at transcription, splicing, and translation levels
Cited by: 11
Author(s): Saket Choudhary, Suzanne Perea Burns, Hoda Mirsafian, Wenzheng Li, Dat T. Vo, Mu Qiao, Xiufen Lei, Andrew D. Smith, Luiz O. F. Penalva
Software Mentions: 4
Published: over 6 years ago

10.3389/pore.2021.1609789

Comprehensive Analysis of Metabolic Genes in Breast Cancer Based on Multi-Omics Data
Cited by: 2
Author(s): Yu Hua, Lihong Gao, Xiaobo Li
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-020-6467-6

Diverse biological processes coordinate the transcriptional response to nutritional changes in a Drosophila melanogaster multiparent population
Cited by: 8
Author(s): Enoch Ng’oma, Patricka A. Williams-Simon, Aniqa Rahman, King Eg
Software Mentions: 4
Published: over 6 years ago

10.3389/fnagi.2019.00083

Identification of Temporal Characteristic Networks of Peripheral Blood Changes in Alzheimer’s Disease Based on Weighted Gene Co-expression Network Analysis
Cited by: 18
Author(s): Run-Hong Tang, Huayan Liu
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-017-05724-z

Comprehensive transcriptomics and proteomics analyses of pollinated and parthenocarpic litchi (Litchi chinensis Sonn.) fruits during early development
Cited by: 14
Author(s): Wei Liu, Maoshan Chen, Lijun Bai, Zhenhua Zhuang, Chao Fan, Jiang Nong-hui, Junsheng Zhao, Shuaipeng Ma, Xiang Xu
Software Mentions: 4
Published: about 9 years ago

10.1186/s12957-021-02201-w

Gene coexpression network approach to develop an immune prognostic model for pancreatic adenocarcinoma
Cited by: 5
Author(s): Xing Gu, Qiqi Zhang, Xueying Wu, Yue Fan, Ji Qian
Software Mentions: 4
Published: over 5 years ago

10.3389/pore.2021.601693

Identification of Biomarkers Related to Immune Cell Infiltration in Hepatocellular Carcinoma Using Gene Co-Expression Network
Cited by: 2
Author(s): Wanbang Zhou, Yiyang Chen, Ruixing Luo, Zifan Li, Guanwei Jiang, Xi Ou
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.11045

Analysis of differences in the transcriptomic profiles of eutopic and ectopic endometriums in women with ovarian endometriosis
Cited by: 5
Author(s): Xiao Feng, Lingbin Qi, Xiaoyu Xu, Yun Feng, Xiaoming Gong, Aixingzi Aili, Yu Chen, Zhigang Xue, Jinfeng Xue, Xiaowen Tong
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-2650-1

Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.)
Cited by: 101
Author(s): Yuanda Lv, Zhikai Liang, Min Ge, Weicong Qi, Tifu Zhang, Feng Lin, Zhaohua Peng, Han Zhao
Software Mentions: 4
Published: over 10 years ago

10.1186/s12864-019-5428-4

New insights in the control of antioxidants accumulation in tomato by transcriptomic analyses of genotypes exhibiting contrasting levels of fruit metabolites
Cited by: 20
Author(s): Adriana Sacco, Assunta Raiola, Roberta Calafiore, Amalia Barone, Maria Manuela Rigano
Software Mentions: 4
Published: over 7 years ago

10.1186/s12957-021-02248-9

Potential role of chimeric genes in pathway-related gene co-expression modules
Cited by: 7
Author(s): Piaopiao Li, Yingxia Li, Lei Ma
Software Mentions: 4
Published: over 5 years ago

10.1126/sciadv.abf9808

Mechanisms underlying divergent responses of genetically distinct macrophages to IL-4
Cited by: 23
Author(s): Marten A. Hoeksema, Zeyang Shen, Inge R. Holtman, An Zheng, Nathan Spann, Isidoro Cobo, Melissa Gymrek, Christopher K. Glass
Software Mentions: 4
Published: about 5 years ago

10.1186/s12931-020-01368-2

IRF4 and STAT3 activities are associated with the imbalanced differentiation of T-cells in responses to inhalable particulate matters
Cited by: 2
Author(s): Jinzhun Wu, Dongyu Ge, Taoling Zhong, Zuojia Chen, Ying Zhou, Lingyun Hou, Xinhua Lin, Jiaxu Hong, Kuai Liu, Hui Qi, Chaoying Wang, Yulin Zhou, Cheng Li, Chuan Wu, Shi Wu, Zuguo Liu, Qiyuan Li
Software Mentions: 4
Published: over 6 years ago

10.1038/srep12615

Decrease of mRNA Editing after Spinal Cord Injury is Caused by Down-regulation of ADAR2 that is Triggered by Inflammatory Response
Cited by: 27
Author(s): Antonio Fabio Di Narzo, Alexey Kozlenkov, Yongchao Ge, Bin Zhang, Leo Sanelli, Zacnicte May, Yanqing Li, Karim Fouad, Christopher P. Cardozo, Eugene V. Koonin, David J. Bennett, Stella Dracheva
Software Mentions: 4
Published: about 11 years ago

10.1186/s12915-020-00793-5

Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns
Cited by: 28
Author(s): Yang Zhou, Shuli Liu, Yan Hu, Lingzhao Fang, Yahui Gao, Han Xia, Steven G. Schroeder, Benjamin D. Rosen, Erin E. Connor, Congjun Li, R.L. Baldwin, John B. Cole, Curtis P. Van Tassell, Liguo Yang, Li Ma, George E. Liu
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-020-06793-7

Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress
Cited by: 8
Author(s): Caitlin M. A. Simopoulos, Mitchell MacLeod, Solmaz Irani, Wilson W L Sung, Marc J. Champigny, Peter S. Summers, G. Brian Golding, Elizabeth A. Weretilnyk
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.ppat.1004959

Fungal Morphology, Iron Homeostasis, and Lipid Metabolism Regulated by a GATA Transcription Factor in Blastomyces dermatitidis
Cited by: 16
Author(s): Amber J. Marty, Aimee Teo Broman, Robert Żarnowski, Teigan G. Dwyer, Laura M. Bond, Anissa Lounès-Hadj Sahraoui, Joël Fontaine, James M. Ntambi, Sündüz Keleş, Christina Kendziorski, Gregory M. Gauthier
Software Mentions: 4
Published: about 11 years ago

10.1186/s12915-020-00862-9

Genome-enabled insights into the biology of thrips as crop pests
Cited by: 44
Author(s): Dorith Rotenberg, Aaron A. Baumann, Sulley Ben-Mahmoud, Olivier Christiaens, Wannes Dermauw, Panagiotis Ioannidis, Chris G.C. Jacobs, Iris M. Vargas Jentzsch, Jonathan E. Oliver, Monica Poelchau, Swapna Priya Rajarapu, Derek J. Schneweis, Simon Snoeck, Clauvis Nji Tizi Taning, Dong Wei, Shirani M. K. Widana Gamage, Daniel Hughes, Shwetha C. Murali, Samuel T. Bailey, Nicolás Bejerman, Christopher J. Holmes, Emily C. Jennings, Andrew J. Rosendale, Andrew E. Rosselot, Kaylee Hervey, Brandi A. Schneweis, Sammy Cheng, Christopher P. Childers, Felipe A. Simão, Ralf G. Dietzgen, Hsu Chao, Huyen Dinh, Harshavardhan Doddapaneni, Shannon Dugan, Yi Han, Sandra L. Lee, Donna M. Muzny, Jiaxin Qu, Kim C. Worley, Joshua B. Benoit, Markus Friedrich, Jeffery W. Jones, Kristen A. Panfilio, Yoonseong Park, Hugh M. Robertson, Guy Smagghe, Diane E. Ullman, Maurijn van der Zee, Thomas Van Leeuwen, Jan A. Veenstra, Robert M. Waterhouse, Matthew T. Weirauch, John H. Werren, Anna E. Whitfield, Evgeny M. Zdobnov, Richard A. Gibbs, Stephen Richards
Software Mentions: 4
Published: almost 6 years ago

10.1002/ece3.6203

Caterpillars on a phytochemical landscape: The case of alfalfa and the Melissa blue butterfly
Cited by: 6
Author(s): Matthew L. Forister, Su’ad A. Yoon, Casey S. Philbin, Craig D. Dodson, Bret Hart, Joshua G. Harrison, Oren Shelef, James A. Fordyce, Zachary H. Marion, Chris C. Nice, Lora A. Richards, C. Alex Buerkle, Zachariah Gompert
Software Mentions: 4
Published: over 6 years ago

10.1002/ece3.4029

Changes in intestinal microbiota across an altitudinal gradient in the lizard Phrynocephalus vlangalii
Cited by: 44
Author(s): Wenya Zhang, Na Li, Xiaolong Tang, Naifa Liu, Zhao Wang
Software Mentions: 4
Published: over 8 years ago

10.1002/2211-5463.12983

Identification of modules and novel prognostic biomarkers in liver cancer through integrated bioinformatics analysis
Cited by: 5
Author(s): Bo Shen, Kun Li, Yuting Zhang
Software Mentions: 4
Published: almost 6 years ago

10.1093/jxb/erw006

Evidence for maternal control of seed size in maize from phenotypic and transcriptional analysis
Cited by: 32
Author(s): Xia Zhang, Candice N. Hirsch, Rajandeep S. Sekhon, Natalia de León, Shawn M. Kaeppler
Software Mentions: 4
Published: over 10 years ago

10.1186/s12864-016-3390-y

LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells
Cited by: 11
Author(s): Alicja Pacholewska, Eliane Marti, Tosso Leeb, Vidhya Jagannathan, Vinzenz Gerber
Software Mentions: 4
Published: over 9 years ago

10.18632/aging.202634

Long non-coding RNAs ENST00000429730.1 and MSTRG.93125.4 are associated with metabolic activity in tuberculosis lesions of sputum-negative tuberculosis patients
Cited by: 5
Author(s): Lin Wang, Wen Zhu, Hui Ma, Liwei Wu, Hui Chen, Yijun Zhu, Liangfei Niu, Qihang Wu, Hongwei Li, Lei Shi, Leilei Li, Leiyi Wan, Jun Wang, Ka-Wing Wong, Yanzheng Song
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-13-S10-S7

A systematic comparison of genome-scale clustering algorithms
Cited by: 45
Author(s): Jeremy J. Jay, John D. Eblen, Yun Zhang, Mikael Benson, Andy D. Perkins, Arnold M. Saxton, Brynn H. Voy, Elissa J. Chesler, Michael A. Langston
Software Mentions: 4
Published: over 14 years ago

10.1093/jxb/erx224

Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype
Cited by: 38
Author(s): Noé Cochetel, Frédéric Escudié, Sarah Jane Cookson, Zhanwu Dai, Philippe Vivin, Pierre‐François Bert, Mindy Muñoz, Serge Delrot, Christophe Klopp, Nathalie Ollat, Virginie Lauvergeat
Software Mentions: 4
Published: about 9 years ago

10.1038/srep33956

A systems biology approach to defining regulatory mechanisms for cartilage and tendon cell phenotypes
Cited by: 19
Author(s): Alan Mueller, Simon R. Tew, Olga Vasieva, Peter Clegg, Elizabeth G. Canty‐Laird
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12864-019-6021-6

Transcriptomics analysis revealing candidate genes and networks for sex differentiation of yesso scallop (Patinopecten yessoensis)
Cited by: 17
Author(s): Liqing Zhou, Zhihong Liu, Yan Dong, Xiujun Sun, Biao Wu, Tao Yu, Yao Zheng, Aiguo Yang, Qing Zhao, Dan Zhao
Software Mentions: 4
Published: about 7 years ago

10.15252/emmm.201708202

A proteomic network approach across the <scp>ALS</scp> ‐ <scp>FTD</scp> disease spectrum resolves clinical phenotypes and genetic vulnerability in human brain
Cited by: 115
Author(s): Mfon Umoh, Eric B. Dammer, Jingting Dai, Duc M. Duong, James J. Lah, Aĺlan I. Levey, Marla Gearing, Jonathan D. Glass, Nicholas T. Seyfried
Software Mentions: 4
Published: almost 9 years ago

10.1155/2021/7331821

Identification of Neuropeptides as Potential Crosstalks Linking Down Syndrome and Periodontitis Revealed by Transcriptomic Analyses
Cited by: 6
Author(s): Yue Chen, Xiaofei Yu, Jia Kong
Software Mentions: 4
Published: almost 5 years ago

10.18632/aging.102190

Long non-coding RNA CASC19 is associated with the progression and prognosis of advanced gastric cancer
Cited by: 23
Author(s): Wenjie Wang, Changan Guo, Rui Li, Zipeng Xu, Jianping Yu, Ye Yan, Jun Zhao, Jing Wang, Wen-An Wang, An Zhang, Hongtao Li, Chen Wang, Hongbin Liu
Software Mentions: 4
Published: about 7 years ago

10.1186/1471-2164-14-728

Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivumL.)
Cited by: 80
Author(s): Karl G. Kugler, Gerald Siegwart, Thomas Nußbaumer, Christian Ametz, Manuel Spannagl, Barbara Steiner, Marc Lemmens, Klaus Mayer, Hermann Buerstmayr, Wolfgang Schweiger
Software Mentions: 4
Published: almost 13 years ago

10.1186/s12864-015-1522-4

Transcriptomic profiles of aging in purified human immune cells
Cited by: 57
Author(s): Lindsay M. Reynolds, Jingzhong Ding, Jeanette Taylor, Kurt Lohman, Nicola Soranzo, Alberto de la Fuente, Tie Fu Liu, Craig W. Johnson, R. Graham Barr, Thomas C. Register, Kathleen Donohue, Monica V. Talor, Daniela Čiháková, C. Charles Gu, Jasmin Divers, David S. Siscovick, Gregory L. Burke, Wendy S. Post, Steven Shea, David R. Jacobs, Ina Hoeschele, Charles E. McCall, Stephen B. Kritchevsky, David M. Herrington, Russell P. Tracy, Yongmei Liu
Software Mentions: 4
Published: over 11 years ago

10.18632/aging.202228

Identification of SCARA3 with potential roles in metabolic disorders
Cited by: 7
Author(s): Hui Peng, Qi Guo, Tian Su, Ye Xiao, Changjun Li, Yan Huang, Xiang‐Hang Luo
Software Mentions: 4
Published: over 5 years ago

10.15252/msb.20156108

Cell cycle networks link gene expression dysregulation, mutation, and brain maldevelopment in autistic toddlers
Cited by: 72
Author(s): Tiziano Pramparo, Michael Lombardo, Kathleen Campbell, Cynthia Carter Barnes, Steven Marinero, Stephanie Solso, Julia Young, Maisi Mayo, Anders M. Dale, Clelia Ahrens‐Barbeau, Sarah Murray, Linda Lopez, Nathan E. Lewis, Karen Pierce, Eric Courchesne
Software Mentions: 4
Published: almost 11 years ago

Projects: cran: WGCNA

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning WGCNA 3,479