cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1186/s12870-021-02952-4

Explore the gene network regulating the composition of fatty acids in cottonseed
Cited by: 7
Author(s): Lihong Ma, Xinqi Cheng, Chuan Wang, Xinyu Zhang, Fei Xue, Yanjun Li, Qian Zhu, Jie Sun, Feng Liu
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-017-10127-1

Analysis of temporal expression profiles after sciatic nerve injury by bioinformatic method
Cited by: 4
Author(s): Yichong Zhang, Yuanbo Zhan, Ning Han, Yuhui Kou, Xiaofeng Yin, Peixun Zhang
Software Mentions: 1
Published: about 9 years ago

10.3390/ijms20184358

Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation
Cited by: 5
Author(s): Xiaoxiang Zhang, Niansheng Huang, Lanjing Mo, Minjia Lv, Yujiao Gao, Junpeng Wang, Chang Liu, Yin Su, Juan Zhou, Ning Xiao, Cunhong Pan, Yabin Xu, Guichun Dong, Zefeng Yang, Aihong Li, Jianye Huang, Yulong Wang, Youli Yao
Software Mentions: 1
Published: about 7 years ago

10.1186/s12870-021-02961-3

Analysis of miRNA-mediated regulation of flowering induction in Lilium × formolongi
Cited by: 4
Author(s): Qian Zhang, Yuqian Zhao, Xue Gao, Guanqing Jia
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0094868

Rat Hepatocytes Weighted Gene Co-Expression Network Analysis Identifies Specific Modules and Hub Genes Related to Liver Regeneration after Partial Hepatectomy
Cited by: 20
Author(s): Yun Zhou, Jiucheng Xu, Yunqing Liu, Juntao Li, Cuifang Chang, Chi Xu
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0219837

A comprehensive expression analysis of the expansin gene family in potato (Solanum tuberosum) discloses stress-responsive expansin-like B genes for drought and heat tolerances
Cited by: 29
Author(s): Yongkun Chen, Bo Zhang, Canhui Li, Chunxia Lei, Chunyan Kong, Yang Yu, Ming Gong
Software Mentions: 1
Published: over 7 years ago

10.1186/s12870-019-2125-z

PI signal transduction and ubiquitination respond to dehydration stress in the red seaweed Gloiopeltis furcata under successive tidal cycles
Cited by: 10
Author(s): Shun Liu, Zi‐Min Hu, Quansheng Zhang, Xiaoqi Yang, Alan T. Critchley, Delin Duan
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0163812

Alcohol-Induced Molecular Dysregulation in Human Embryonic Stem Cell-Derived Neural Precursor Cells
Cited by: 12
Author(s): Yi Young Kim, Ivan Roubal, Youn Soo Lee, Jin Seok Kim, Michael Hoang, Nathan Mathiyakom, Yong Kim
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-017-14120-6

Early-onset and classical forms of type 2 diabetes show impaired expression of genes involved in muscle branched-chain amino acids metabolism
Cited by: 45
Author(s): María Isabel Hernández‐Álvarez, Ángels Díaz-Ramos, María Berdasco, Jeff E. Cobb, Evarist Planet, Diane Cooper, Agnieszka Pazderska, Krzystof Wanic, Declan O’Hanlon, Antonio Gómez, Laura Rodríguez de la Ballina, Manel Esteller, Manuel Palacı́n, Donal J. O'Gorman, John J. Nolan, António Zorzano
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0061505

When Is Hub Gene Selection Better than Standard Meta-Analysis?
Cited by: 229
Author(s): Peter Langfelder, Paul S. Mischel, Steve Horvath
Software Mentions: 1
Published: over 13 years ago

10.1111/acel.12788

Synergistic effects of TGFβ2, WNT9a, and FGFR4 signals attenuate satellite cell differentiation during skeletal muscle development
Cited by: 19
Author(s): Weiya Zhang, Yongming Xu, Lu Zhang, Sheng Wang, Binxu Yin, Zhao Song, Xinyun Li
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms21051675

Genetic Identification and Transcriptome Analysis of Lintless and Fuzzless Traits in Gossypium arboreum L.
Cited by: 18
Author(s): Xueying Liu, Philippe Moncuquet, Qian Zhu, Warwick N. Stiller, Zhengsheng Zhang, Iain W. Wilson
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.23219

Co-expression analysis revealed PTCH1-3'UTR promoted cell migration and invasion by activating miR-101-3p/SLC39A6 axis in non-small cell lung cancer: implicating the novel function of PTCH1
Cited by: 21
Author(s): Xuechao Wan, Zhe Kong, Kaili Chu, Chuanyou Yi, Jian Hu, Rui Qin, Chunxia Zhao, Fangqiu Fu, Hai Wu, Yao Li, Yan Huang
Software Mentions: 1
Published: almost 9 years ago

10.3390/ijms21051824

The Role of Gibberellins in Regulation of Nitrogen Uptake and Physiological Traits in Maize Responding to Nitrogen Availability
Cited by: 20
Author(s): Yubin Wang, Qizheng Yao, Yushi Zhang, Yuexia Zhang, Jiapeng Xing, Benzhou Yang, Guohua Mi, Zhaohu Li, Mingcai Zhang
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0167543

The rs3957357C>T SNP in GSTA1 Is Associated with a Higher Risk of Occurrence of Hepatocellular Carcinoma in European Individuals
Cited by: 19
Author(s): Hanane Akhdar, Said El Shamieh, Orlando Musso, Romain Désert, Wissam H. Joumaa, Dominique Guyader, Caroline Aninat, Anne Corlu, Franck Morel
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pgen.1008734

Leveraging gene co-expression patterns to infer trait-relevant tissues in genome-wide association studies
Cited by: 23
Author(s): Lulu Shang, Jennifer A. Smith, Xiang Zhou
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-017-18287-w

Integrated transcriptional analysis unveils the dynamics of cellular differentiation in the developing mouse hippocampus
Cited by: 6
Author(s): Giovanni Iacono, Marco Benevento, Aline Dubos, Yann Hérault, Hans van Bokhoven, Nael Nadif Kasri, Hendrik G. Stunnenberg
Software Mentions: 1
Published: almost 9 years ago

10.1186/s40478-015-0203-5

Induction of a common microglia gene expression signature by aging and neurodegenerative conditions: a co-expression meta-analysis
Cited by: 436
Author(s): Inge R. Holtman, Divya Raj, Jeremy A. Miller, W. Schaafsma, Zhuoran Yin, Nieske Brouwer, Paul D. Wes, Thomas Møller, Marie Orre, Willem Kamphuis, Elly M. Hol, Erik Boddeke, Bart J. L. Eggen
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0218528

Distinct leaf transcriptomic response of water deficient Eucalyptus grandis submitted to potassium and sodium fertilization
Cited by: 13
Author(s): Bénédicte Favreau, Marie Denis, Raphaël Ployet, Fabien Mounet, Hana Peireira da Silva, Lívia Maria Franceschini, Jean‐Paul Laclau, Carlos Alberto Labate, Helaine Carrer
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-18084-5

A Global View of Transcriptome Dynamics During Male Floral Bud Development in Populus tomentosa
Cited by: 25
Author(s): Zhong Chen, Pian Rao, Xiaoyu Yang, Xiaoxing Su, Tianyun Zhao, Kai Gao, Xiong Yang, Xinmin An
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0116644

Glioma-Associated Microglia/Macrophages Display an Expression Profile Different from M1 and M2 Polarization and Highly Express Gpnmb and Spp1
Cited by: 295
Author(s): Frank Szulzewsky, Andreas Pelz, Xi Feng, Michael Synowitz, Darko Marković, Thomas Langmann, Inge R. Holtman, Xi Wang, Bart J. L. Eggen, Hendrikus Boddeke, Dolores Hambardzumyan, Susanne Wolf, Helmut Kettenmann
Software Mentions: 1
Published: over 11 years ago

10.1186/s12870-021-03133-z

Comparative transcriptome analysis reveals regulatory network and regulators associated with proanthocyanidin accumulation in persimmon
Cited by: 10
Author(s): Qingyou Zheng, Wenxing Chen, Man Luo, Lingfei Xu, Qinglin Zhang, Zhitian Luo
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-019-2192-1

Full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of Medicago falcata roots
Cited by: 40
Author(s): Guowen Cui, Hua Chai, Hang Yin, Mei Yang, Guofu Hu, Mingying Guo, Rugeletu Yi, Pan Zhang
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0150850

Immune-Mediated Inflammation May Contribute to the Pathogenesis of Cardiovascular Disease in Mucopolysaccharidosis Type I
Cited by: 16
Author(s): Omar Khalid, Moin Vera, Philip L.S.M. Gordts, N. Matthew Ellinwood, Philip H. Schwartz, Patricia Dickson, Jeffrey D. Esko, Raymond Wang
Software Mentions: 1
Published: over 10 years ago

10.1186/s12935-021-02052-1

GNRH1 and LTB4R might be novel immune-related prognostic biomarkers in clear cell renal cell carcinoma (ccRCC)
Cited by: 10
Author(s): Hua-Hui Wu, Xin Yan, Chen Zhao, Guo-Wei Du, Xiaojie Bai, Kurerban Tuoheti, Tong-Zu Liu
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-21524-5

Consequences of VHL Loss on Global DNA Methylome
Cited by: 14
Author(s): Claire M. Robinson, François Lefebvre, Betty Poon, Aurélie Bousard, Xiaojun Fan, Mark Lathrop, Jörg Tost, William Y. Kim, Yasser Riazalhosseini, Michael Ohh
Software Mentions: 1
Published: over 8 years ago

10.18632/aging.102816

Cancer stem cell-specific expression profiles reveal emerging bladder cancer biomarkers and identify circRNA_103809 as an important regulator in bladder cancer
Cited by: 19
Author(s): Tao Tao, Simin Yuan, Jinjian Liu, Da Shi, Mian Peng, Chong Li, Song Wu
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-21779-y

An Epidemiological Human Disease Network Derived from Disease Co-occurrence in Taiwan
Cited by: 19
Author(s): Yefei Jiang, Shuangge Ma, Ben‐Chang Shia, Tian Shyug Lee
Software Mentions: 1
Published: over 8 years ago

10.7717/peerj.4107

Constructing a comprehensive gene co-expression based interactome in <i>Bos taurus</i>
Cited by: 9
Author(s): Yan Chen, Yining Liu, Min Du, Wengang Zhang, Lei Xu, Xue Gao, Lupei Zhang, Huijiang Gao, Lingyang Xu, Junya Li, Min Zhao
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-018-23647-1

Identification of The Aberrantly Expressed LncRNAs in Hepatocellular Carcinoma: A Bioinformatics Analysis Based on RNA-sequencing
Cited by: 25
Author(s): Haotian Liao, Jiwei Huang, Tian Lan, Jinju Wang, Bo Zhu, Kefei Yuan, Yong Zeng
Software Mentions: 1
Published: over 8 years ago

10.7717/peerj.9773

Significance of hub genes and immune cell infiltration identified by bioinformatics analysis in pelvic organ prolapse
Cited by: 8
Author(s): Ying Zhao, Zhijun Xia, Te Yu Lin, Yitong Yin
Software Mentions: 1
Published: about 6 years ago

10.3390/metabo9070145

Metabolomics Analytics Workflow for Epidemiological Research: Perspectives from the Consortium of Metabolomics Studies (COMETS)
Cited by: 27
Author(s): Mary C. Playdon, Amit D. Joshi, Fred K. Tabung, Susan Cheng, Mir Henglin, Andy Kim, Tengda Lin, Eline H. van Roekel, Jiaqi Huang, Jan Krumsiek, Ying Wang, Ewy A. Mathé, Marinella Temprosa, Steven C. Moore, Bo Chawes, A. Heather Eliassen, Andrea Gsur, Marc J. Gunter, Sei Harada, Claudia Langenberg, Matej Orešič, Wei Perng, Wei Jie Seow, Oana A. Zeleznik
Software Mentions: 1
Published: over 7 years ago

10.18632/aging.103054

A novel immune-related genes prognosis biomarker for melanoma: associated with tumor microenvironment
Cited by: 73
Author(s): Rongzhi Huang, Min Mao, Yong Lu, Qingliang Yu, Liang Liao
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-020-02442-z

Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton
Cited by: 23
Author(s): Kashif Shahzad, Xuexian Zhang, Liping Guo, Ting Qi, Lisheng Bao, Meng Zhang, Bingbing Zhang, Hailin Wang, Huini Tang, Xin Qiao, Juanjuan Feng, Jianyong Wu, Chaozhu Xing
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0178006

Disease-related gene module detection based on a multi-label propagation clustering algorithm
Cited by: 7
Author(s): Xue Jiang, Han Zhang, Xiongwen Quan, Zhandong Liu, Yanbin Yin
Software Mentions: 1
Published: over 9 years ago

10.1093/molbev/msab004

Functional Diversification, Redundancy, and Epistasis among Paralogs of the <i>Drosophila melanogaster Obp50a–d</i> Gene Cluster
Cited by: 10
Author(s): Joel A. Johnstun, Vijay Shankar, Sneha S Mokashi, Lakshmi T. Sunkara, Ugonna E Ihearahu, Roberta Lyman, Trudy F. C. Mackay, Robert R. H. Anholt
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-26310-x

Sorting Five Human Tumor Types Reveals Specific Biomarkers and Background Classification Genes
Cited by: 9
Author(s): Kimberly Roche, Marvin Weinstein, Leland J. Dunwoodie, William L. Poehlman, F. Alex Feltus
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-26495-1

Convergent Pathways in Idiopathic Autism Revealed by Time Course Transcriptomic Analysis of Patient-Derived Neurons
Cited by: 63
Author(s): Brooke A. DeRosa, Jimmy El Hokayem, Elena Artimovich, Catherine Garcia‐Serje, Andrè W. Phillips, Derek Van Booven, Jonathan E. Nestor, Lily Wang, Michael L. Cuccaro, Jeffery M. Vance, Margaret A. Pericak‐Vance, Holly N. Cukier, Michael W. Nestor, Derek M. Dykxhoorn
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1002556

Networks of Neuronal Genes Affected by Common and Rare Variants in Autism Spectrum Disorders
Cited by: 137
Author(s): Eyal Ben-David, Sagiv Shifman
Software Mentions: 1
Published: over 14 years ago

10.1186/s12864-021-07714-y

Transcriptomic insights into the effects of CytCo, a novel nematotoxic protein, on the pine wood nematode Bursaphelenchus xylophilus
Cited by: 4
Author(s): Ye Chen, Xiang Zhou, Kai Guo, Sha-Ni Chen, Xiu Su
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1002038

Mouse Genome-Wide Association and Systems Genetics Identify Asxl2 As a Regulator of Bone Mineral Density and Osteoclastogenesis
Cited by: 107
Author(s): Charles R. Farber, Brian J. Bennett, Luz D. Orozco, Wei Zou, Ana Lira, Emrah Kostem, Hyun Min Kang, Nicholas A. Furlotte, Ani Berberyan, Anatole Ghazalpour, Jaijam Suwanwela, Thomas A. Drake, Eleazar Eskin, Q. Tian Wang, Steven L. Teitelbaum, Aldons J. Lusis
Software Mentions: 1
Published: over 15 years ago

10.3390/ijms20163846

Gene Modules Co-regulated with Biosynthetic Gene Clusters for Allelopathy between Rice and Barnyardgrass
Cited by: 7
Author(s): Most. Humaira Sultana, FangJie Liu, Md. Alamin, Limin Mao, Jia Lu, Hongyu Chen, Dongya Wu, Yingying Wang, Fei Fu, Sanling Wu, Weidi Wang, Chu-Yu Ye, Qian Zhu, Jie Qiu, Longjiang Fan
Software Mentions: 1
Published: about 7 years ago

10.1186/2040-2392-5-22

DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics
Cited by: 111
Author(s): Li Liu, Jing Lei, Stephan Sanders, A. Jeremy Willsey, Yan Kou, A. Ercüment Çiçek, Lambertus Klei, Cong Lu, Xin He, Mingfeng Li, Rebecca Muhle, Avi Ma’ayan, James P. Noonan, Nenad Šestan, Kathryn McFadden, Matthew W. State, Joseph D. Buxbaum, Bernie Devlin, Kathryn Roeder
Software Mentions: 1
Published: over 12 years ago

10.3390/ijms18040828

Delineating the Common Biological Pathways Perturbed by ASD’s Genetic Etiology: Lessons from Network-Based Studies
Cited by: 25
Author(s): Oded Oron, Evan Elliott
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-30302-2

The age-regulated zinc finger factor ZNF367 is a new modulator of neuroblast proliferation during embryonic neurogenesis
Cited by: 12
Author(s): Valentina Naef, Sara Monticelli, Debora Corsinovi, Maria Teresa Mazzetto, Alessandro Cellerino, Michela Ori
Software Mentions: 1
Published: about 8 years ago

10.1007/s00335-016-9656-5

Uncovering the liver’s role in immunity through RNA co-expression networks
Cited by: 11
Author(s): Kylie K. Harrall, Katerina Kechris, Boris Tabakoff, Paula L. Hoffman, Lisa M. Hines, Hidekazu Tsukamoto, Michal Pravenec, Morton P. Printz, Laura Saba
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-018-30779-x

Transcriptional network analysis of human astrocytic endfoot genes reveals region-specific associations with dementia status and tau pathology
Cited by: 41
Author(s): Matthew Simon, Marie X. Wang, Charles Murchison, Natalie Roese, Erin L. Boespflug, Randall L. Woltjer, Jeffrey J. Iliff
Software Mentions: 1
Published: about 8 years ago

10.18632/aging.202285

Identification of key modules and genes associated with breast cancer prognosis using WGCNA and ceRNA network analysis
Cited by: 44
Author(s): Xin Yin, Pei Wang, Tianshu Yang, Gen Li, Xu Teng, Wei Huang, Hefen Yu
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13229-015-0029-9

Atypical miRNA expression in temporal cortex associated with dysregulation of immune, cell cycle, and other pathways in autism spectrum disorders
Cited by: 59
Author(s): Bradley P. Ander, Nicole Barger, Boryana Stamova, Frank R. Sharp, Cynthia M. Schumann
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-018-4999-9

Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis)
Cited by: 57
Author(s): Yuling Tai, Liu Chun, Shijie Yu, Hua Yang, Jun Sun, Chunxiao Guo, Bei Huang, Zhaoye Liu, Yuan Yang, Enhua Xia, Chaoling Wei, Xiaochun Wan
Software Mentions: 1
Published: about 8 years ago

10.1186/s40478-020-01109-y

Type 2 diabetes mellitus-associated transcriptome alterations in cortical neurones and associated neurovascular unit cells in the ageing brain
Cited by: 16
Author(s): Joanna J. Bury, Annabelle Chambers, Paul R. Heath, Paul G. Ince, Pamela J. Shaw, Fiona E. Matthews, Carol Brayne, Julie E. Simpson, Stephen B. Wharton
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12870-020-02569-z

Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice
Cited by: 31
Author(s): Yinghua Pan, He Liang, Lijun Gao, Gaoxing Dai, Weiwei Chen, Yang Xiao-ling, Dongjin Qing, Ju Gao, Hao Wu, Juan Huang, Weiyong Zhou, Chengcui Huang, Yuntao Liang, Gaofeng Deng
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-018-34149-5

Transcriptome Dynamics During Turbot Spermatogenesis Predicting the Potential Key Genes Regulating Male Germ Cell Proliferation and Maturation
Cited by: 15
Author(s): Xueying Wang, Qinghua Liu, Shihong Xu, Yongshuang Xiao, Yanfeng Wang, Chengcheng Feng, Rui Xue, Huihui Zhao, Zongcheng Song, Jun Li
Software Mentions: 1
Published: about 8 years ago

10.18632/aging.102309

Hypermethylated long noncoding RNA MEG3 promotes the progression of gastric cancer
Cited by: 15
Author(s): Lei Ding, Yuan Tian, Ling Wang, Miaomiao Bi, Dengke Teng, Sen Hong
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-018-34839-0

Lung fibroblasts express a miR-19a-19b-20a sub-cluster to suppress TGF-β-associated fibroblast activation in murine pulmonary fibrosis
Cited by: 18
Author(s): Kunihiko Souma, Shigeyuki Shichino, Shinichi Hashimoto, Satoshi Ueha, Tohru Tsukui, T. Nakajima, Hiroshi Suzuki, Francis H.W. Shand, Yutaka Inagaki, Takahide Nagase, Kouji Matsushima
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-35315-5

An integrative transcriptome analysis indicates regulatory mRNA-miRNA networks for residual feed intake in Nelore cattle
Cited by: 30
Author(s): P. S. N. Oliveira, Luiz Lehmann Coutinho, P. C. Tizioto, Guilherme Bueno de Oliveira, Wellison J. S. Diniz, A. O. de Lima, James M. Reecy, Gérson Barreto Mourão, Adhemar Zerlotini, Luciana Correia de Almeida Regitano
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12870-020-02606-x

Transcriptome analysis provides new insights into the transcriptional regulation of methyl jasmonate-induced flavonoid biosynthesis in pear calli
Cited by: 34
Author(s): Apekshika T Premathilake, Junbei Ni, Jiemin Shen, Songling Bai, Yuanwen Teng
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-018-35968-2

Extracellular vesicles produced in B cells deliver tumor suppressor miR-335 to breast cancer cells disrupting oncogenic programming in vitro and in vivo
Cited by: 14
Author(s): Gonzalo Almanza, Jeffrey J. Rodvold, Brian Tsui, Kristen Jepsen, Hannah Carter, Maurizio Zanetti
Software Mentions: 1
Published: almost 8 years ago

10.1002/cam4.3240

Development and validation of an immune‐related prognostic signature in lung adenocarcinoma
Cited by: 69
Author(s): Sijin Sun, Wei Guo, Zhen Wang, Xin Wang, Guochao Zhang, Hao Zhang, Renda Li, Yibo Gao, Bin Qiu, Fengwei Tan, Yushun Gao, Qi Xue, Shugeng Gao, Jie He
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-36703-7

Induction of Human T-cell and Cytokine Responses Following Vaccination with a Novel Influenza Vaccine
Cited by: 32
Author(s): David Skibinski, Leigh Ann Jones, Yuan Zhu, Lin Wu Xue, Bijin Au, Bernett Lee, Ahmad Nazri Mohamed Naim, Audrey Lee, Nivashini Kaliaperumal, Jenny G. Low, Lawrence S. Lee, Michael Poidinger, Philippe Saudan, Martin F. Bachmann, Eng Eong Ooi, Brendon J. Hanson, Veronica Novotny‐Diermayr, Alex Matter, Anna‐Marie Fairhurst, Martin L. Hibberd, John E. Connolly
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13229-020-00382-x

Functional relationships between recessive inherited genes and genes with de novo variants in autism spectrum disorder
Cited by: 4
Author(s): Lin Wang, Yi Zhang, Kuokuo Li, Zheng Wang, Xiaomeng Wang, Bin Li, Guizhe Zhao, Zhenghuan Fang, Zhengbao Ling, Tengfei Luo, Xia Lu, Yanping Li, Hui Guo, Zhengmao Hu, Jinchen Li, Zhen Sun, Kun Xia
Software Mentions: 1
Published: about 6 years ago

10.3390/microorganisms8040518

iTRAQ-based Quantitative Proteomics Analysis Identifies Host Pathways Modulated during Toxoplasma gondii Infection in Swine
Cited by: 7
Author(s): Jun-Jun He, Jun Ma, Jin‐Lei Wang, Fu-Kai Zhang, Jiexi Li, Bintao Zhai, Hany M. Elsheikha, Xing‐Quan Zhu
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.19828

Identification of long non-coding RNA signature for paclitaxel-resistant patients with advanced ovarian cancer
Cited by: 15
Author(s): Luqing Wang, Yan-Jun Hu, Xiaohong Xiang, Kai Qu, Yue Teng
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2164-11-161

Functional annotation of novel lineage-specific genes using co-expression and promoter analysis
Cited by: 8
Author(s): Charu G. Kumar, Robin E. Everts, Juan J. Loor, Harris A. Lewin
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pcbi.1000117

Geometric Interpretation of Gene Coexpression Network Analysis
Cited by: 663
Author(s): Steve Horvath, Jun Dong
Software Mentions: 1
Published: about 18 years ago

10.1186/s40170-016-0143-y

Integration of omics: more than the sum of its parts
Cited by: 84
Author(s): Joerg M. Buescher, Edward M. Driggers
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-019-39236-9

WRINKLED1 transcription factor orchestrates the regulation of carbon partitioning for C18:1 (oleic acid) accumulation in Siberian apricot kernel
Cited by: 18
Author(s): Shuya Deng, Yiting Mai, Lanya Shui, Jun Niu
Software Mentions: 1
Published: over 7 years ago

10.3389/fimmu.2021.730300

Integration of Molecular Inflammatory Interactome Analyses Reveals Dynamics of Circulating Cytokines and Extracellular Vesicle Long Non-Coding RNAs and mRNAs in Heroin Addicts During Acute and Protracted Withdrawal
Cited by: 7
Author(s): Zunyue Zhang, Hongjin Wu, Qingyan Peng, Zhenrong Xie, Fengrong Chen, Yuru Ma, Yizhi Zhang, Yong Zhou, Jun Yang, Cheng Chen, Shaoyou Li, Yongjin Zhang, Wen Tian, Yuan Wang, Yu Xu, Huayou Luo, Mei Zhu, Yi‐Qun Kuang, Juehua Yu, Kunhua Wang
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-019-39463-0

Transcriptome analysis reveals the impact of arbuscular mycorrhizal symbiosis on Sesbania cannabina expose to high salinity
Cited by: 17
Author(s): Changliang Ren, Kong Chen, Yan Ke, Zhihong Xie
Software Mentions: 1
Published: over 7 years ago

10.1515/med-2021-0286

A nomogram for predicting metabolic steatohepatitis: The combination of NAMPT, RALGDS, GADD45B, FOSL2, RTP3, and RASD1
Cited by: 4
Author(s): Shenling Liao, He He, Yuping Zeng, Yang Lin-de, Zhi Liu, Zhenmei An, Mei Zhang
Software Mentions: 1
Published: almost 6 years ago

10.3389/fimmu.2020.00616

A Signaling Pathway to Mediate the Combined Immunomodulation of Acetylcholine and Enkephalin in Oyster Crassostrea gigas
Cited by: 3
Author(s): Zhaoqun Liu, Zhi Zhou, Lingling Wang, Yukun Zhang, Yanan Zong, Yan Zheng, Meijia Li, Weilin Wang, Linsheng Song
Software Mentions: 1
Published: over 6 years ago

10.3389/fimmu.2020.01281

Identification of Immune-Related Genes Contributing to the Development of Glioblastoma Using Weighted Gene Co-expression Network Analysis
Cited by: 30
Author(s): Yahui Kong, Zichao Feng, Yulin Zhang, Xiaofei Liu, Yuan Ma, Zhimin Zhao, Bin Huang, An-Jing Chen, Di Zhang, Frits Thorsen, Jian Wang, Ning Yang, Xingang Li
Software Mentions: 1
Published: over 6 years ago

10.3389/fimmu.2020.603337

Identifying Potential Candidate Hub Genes and Functionally Enriched Pathways in the Immune Responses to Quadrivalent Inactivated Influenza Vaccines in the Elderly Through Co-Expression Network Analysis
Cited by: 1
Author(s): Jing Yang, Jiayou Zhang, Renfeng Fan, Wei Zhao, Han Tian, Kai Duan, Xinguo Li, Peiyu Zeng, Jinglong Deng, Jikai Zhang, Xiaoming Yang
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12870-018-1544-6

Canopy attachment position influences metabolism and peel constituency of European pear fruit
Cited by: 20
Author(s): Sara Serra, Nathanael Sullivan, James P. Mattheis, Stefano Musacchi, David R. Rudell
Software Mentions: 1
Published: almost 8 years ago

10.3389/fimmu.2020.01070

Human Monocyte Subset Distinctions and Function: Insights From Gene Expression Analysis
Cited by: 48
Author(s): Sarah Cormican, Matthew D. Griffin
Software Mentions: 1
Published: over 6 years ago

10.3389/fimmu.2020.01194

Expression of S100A Alarmins in Cord Blood Monocytes Is Highly Associated With Chorioamnionitis and Fetal Inflammation in Preterm Infants
Cited by: 12
Author(s): Veronika Golubinskaya, Henri Puttonen, Ing‐Marie Fyhr, Halfdan Rydbeck, Ann Hellström, Bo Jacobsson, Holger Nilsson, Carina Mallard, Karin Sävman
Software Mentions: 1
Published: over 6 years ago

10.3389/fimmu.2021.739514

Circulating Metabolomic Signature in Generalized Pustular Psoriasis Blunts Monocyte Hyperinflammation by Triggering Amino Acid Response
Cited by: 7
Author(s): Na Yu, Peng Chen, Wenjuan Chen, Zengqi Sun, Jianfeng Zheng, Shujie Zhang, Yangfeng Ding, Yujun Shi
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-016-3176-2

Large-scale gene co-expression network as a source of functional annotation for cattle genes
Cited by: 16
Author(s): Hamid Beiki, A. Nejati‐Javaremi, A. Pakdel, Ali Masoudi‐Nejad, Zhi-Liang Hu, James M. Reecy
Software Mentions: 1
Published: almost 10 years ago

10.3389/fimmu.2020.592084

Therapeutic Potential of Triptolide as an Anti-Inflammatory Agent in Dextran Sulfate Sodium-Induced Murine Experimental Colitis
Cited by: 31
Author(s): Bufu Tang, Jinyu Zhu, Baohui Zhang, Fazong Wu, Yajie Wang, Qiaoyou Weng, Shiji Fang, Zheng Lu, Yang Yang, Rongfang Qiu, Minjiang Chen, Min Xu, Zhongwei Zhao, Jiansong Ji
Software Mentions: 1
Published: almost 6 years ago

10.3389/fimmu.2019.00402

Transcriptional Analysis of the Human IgE-Expressing Plasma Cell Differentiation Pathway
Cited by: 10
Author(s): Faruk Ramadani, H. J. M. Bowen, Hannah Gould, David Fear
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pcbi.1000707

Modeling Co-Expression across Species for Complex Traits: Insights to the Difference of Human and Mouse Embryonic Stem Cells
Cited by: 26
Author(s): Jun Cai, Dan Xie, Z. Fan, Hiram Chipperfield, John I. Marden, Wing Hung Wong, Sheng Zhong
Software Mentions: 1
Published: over 16 years ago

10.3389/fmed.2020.584747

Integrating Tumor Stroma Biomarkers With Clinical Indicators for Colon Cancer Survival Stratification
Cited by: 4
Author(s): Yong Chen, Wenlong Wang, Bo Jiang, Lei Yao, Fada Xia, Xinying Li
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms21041445

Cross-Species Root Transcriptional Network Analysis Highlights Conserved Modules in Response to Nitrate between Maize and Sorghum
Cited by: 5
Author(s): Hongyang Du, Lei Ning, Bing He, Yuancong Wang, Min Ge, Jing Xu, Han Zhao
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2015.00487

Identification of a transporter Slr0982 involved in ethanol tolerance in cyanobacterium Synechocystis sp. PCC 6803
Cited by: 25
Author(s): Yanan Zhang, Xiangfeng Niu, Mengliang Shi, Guangsheng Pei, Xiaoqing Zhang, Lei Chen, Weiwen Zhang
Software Mentions: 1
Published: over 11 years ago

10.3389/fmicb.2019.00352

Alterations of the Mice Gut Microbiome via Schistosoma japonicum Ova-Induced Granuloma
Cited by: 29
Author(s): Yanqing Zhao, Shuxu Yang, Bei Li, Wei Li, Jue Wang, Zongyun Chen, Jing Yang, Huabing Tan, Jian Li
Software Mentions: 1
Published: over 7 years ago

10.3389/fimmu.2019.01459

A Combined Transcriptomic and Genomic Analysis Identifies a Gene Signature Associated With the Response to Anti-TNF Therapy in Rheumatoid Arthritis
Cited by: 22
Author(s): Adrià Aterido, Juan D. Cañete, Jesús Tornero, Francisco J. Blanco, Benjamín Fernández‐Gutiérrez, Carolina Pérez, Mercedes Alperi-López, A Olivé, Hèctor Corominas, Víctor M. Martínez‐Taboada, Inmaculada Fernández González, Antonio Fernández‐Nebro, Alba Erra, María López-Lasanta, Mireia López-Corbeto, Núria Palau, Sara Marsal, Antonio Julià
Software Mentions: 1
Published: over 7 years ago

10.1093/jnci/djx121

Targeting the Myofibroblastic Cancer-Associated Fibroblast Phenotype Through Inhibition of NOX4
Cited by: 125
Author(s): Christopher J. Hanley, Massimiliano Mellone, Kirsty Ford, Steve Thirdborough, Toby Mellows, Steven J. Frampton, David M. Smith, Elena L. Harden, Cédric Szyndralewiez, Marc D. Bullock, Fergus Noble, Karwan A. Moutasim, Emma V. King, Pandurangan Vijayanand, Alex H. Mirnezami, Tim Underwood, Christian Ottensmeier, Gareth J. Thomas
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-020-07193-7

Temporal transcriptomic differences between tolerant and susceptible genotypes contribute to rice drought tolerance
Cited by: 8
Author(s): Hui Xia, Xiaoyan Ma, Kai Xu, Lei Wang, Hongyan Liu, Liang Chen, Lijun Luo
Software Mentions: 1
Published: almost 6 years ago

10.3389/fimmu.2020.01795

Multiple Processes May Involve in the IgG4-RD Pathogenesis: An Integrative Study via Proteomic and Transcriptomic Analysis
Cited by: 8
Author(s): Shaozhe Cai, Yu Chen, Shaochong Lin, Cong Ye, Fang Zheng, Lingli Dong
Software Mentions: 1
Published: about 6 years ago

10.18632/oncotarget.18646

Identification of two novel biomarkers of rectal carcinoma progression and prognosis via co-expression network analysis
Cited by: 19
Author(s): Min Sun, Taojiao Sun, Zhong He, Bin Xiong
Software Mentions: 1
Published: over 9 years ago

10.1186/s12974-016-0603-x

Pathways and gene networks mediating the regulatory effects of cannabidiol, a nonpsychoactive cannabinoid, in autoimmune T cells
Cited by: 51
Author(s): Ewa Kozela, Ana Juknat, Fuying Gao, Nathali Kaushansky, Giovanni Coppola, Zvi Vogel
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-12-S3-S3

Liverome: a curated database of liver cancer-related gene signatures with self-contained context information
Cited by: 40
Author(s): Langho Lee, Kai Wang, Gang Li, Zhi Xie, Yuli Wang, Jiangchun Xu, Shaoxian Sun, David Pocalyko, Jong Bhak, Chulhong Kim, Kee-Ho Lee, Ye Jin Jang, Young Il Yeom, Hyang Sook Yoo, Seungwoo Hwang
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2229-12-245

OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize
Cited by: 46
Author(s): Christian Colmsee, Martin Mascher, Tobias Czauderna, Anja Hartmann, Urte Schlüter, Nina Zellerhoff, J. E. Schmitz, Andrea Bräutigam, Thea R. Pick, Philipp Alter, Manfred Gahrtz, Sandra A. Witt, Alisdair R. Fernie, Frederik Börnke, Holger Fahnenstich, Marcel Bucher, Thomas Dresselhaus, Andreas P.M. Weber, Falk Schreiber, Uwe Scholz, Uwe Sonnewald
Software Mentions: 1
Published: almost 14 years ago

10.3389/fimmu.2021.702733

Transcriptome Analysis of CCR9+ T Helper Cells From Primary Sjögren’s Syndrome Patients Identifies CCL5 as a Novel Effector Molecule
Cited by: 8
Author(s): Anneline C. Hinrichs, Sofie L M Blokland, Ana P Lopes, Catharina G K Wichers, Aike A. Kruize, Aridaman Pandit, Timothy R D J Radstake, Joël A G van Roon
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-018-5104-0

Integration of small RNAs and transcriptome sequencing uncovers a complex regulatory network during vernalization and heading stages of orchardgrass (Dactylis glomerata L.)
Cited by: 13
Author(s): Guangyan Feng, Lei Xu, Jianping Wang, Gang Nie, B. Shaun Bushman, Wengang Xie, Haidong Yan, Zhongfu Yang, Hao Guan, Linkai Huang, Xinquan Zhang
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-019-41813-x

Liver proteomics unravel the metabolic pathways related to Feed Efficiency in beef cattle
Cited by: 37
Author(s): Leydiana Duarte Fonseca, Joanir Pereira Eler, Mikaele Alexandre Pereira, Alessandra Fernandes Rosa, Pâmela Almeida Alexandre, Cristina Tschorny Moncau, Fernanda Salvato, Lívia Rosa-Fernandes, Giuseppe Palmisano, José Bento Sterman Ferraz, Heidge Fukumasu
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-020-07250-1

Deficiencies in the formation and regulation of anther cuticle and tryphine contribute to male sterility in cotton PGMS line
Cited by: 5
Author(s): Meng Zhang, Ji Liu, Qiang Ma, Yuan Qin, Hantao Wang, Pengyun Chen, Liang Ma, Xiaokang Fu, Longfu Zhu, Hengling Wei, Shuang Yu
Software Mentions: 1
Published: almost 6 years ago

10.3389/fimmu.2021.624614

Predicted Disease-Specific Immune Infiltration Patterns Decode the Potential Mechanisms of Long Non-Coding RNAs in Primary Sjogren’s Syndrome
Cited by: 6
Author(s): Caiqi Cheng, Jun Zhou, Ruiying Chen, Yo Shibata, Ryouichi Tanaka, Jun Wang, Jiaming Zhang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0213501

Distinct transcriptional modules in the peripheral blood mononuclear cells response to human respiratory syncytial virus or to human rhinovirus in hospitalized infants with bronchiolitis
Cited by: 9
Author(s): Sandra Elisabete Vieira, Sílvia Yumi Bando, Milena de Paulis, Danielle Bruna Leal Oliveira, Luciano Matsumiya Thomazelli, Edison Luiz Durigon, Marina Baquerizo Martinez, Carlos Alberto Moreira-Filho
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0082656

Neurobiological Signatures of Alcohol Dependence Revealed by Protein Profiling
Cited by: 29
Author(s): Giorgio Gorini, Amanda J. Roberts, R. Dayne Mayfield
Software Mentions: 1
Published: almost 13 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479