cran: WGCNA | Projects | Ecosyste.ms: Papers

10.3389/fnmol.2019.00316

Single Cell and Single Nucleus RNA-Seq Reveal Cellular Heterogeneity and Homeostatic Regulatory Networks in Adult Mouse Stria Vascularis
Cited by: 62
Author(s): Soumya Korrapati, Ian Taukulis, Rafal T. Olszewski, Madeline Pyle, Shoujun Gu, Riya Singh, C. M. Griffiths, Daniel Martin, Erich T. Boger, Robert J. Morell, Michael Hoa
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0227258

Accelerated brain aging towards transcriptional inversion in a zebrafish model of the K115fs mutation of human PSEN2
Cited by: 29
Author(s): Nhi Hin, Morgan Newman, Jan Kaslin, Alon M. Douek, Amanda L. Lumsden, Seyyed Hani Moussavi Nik, Yang Dong, Xin Zhou, Noralyn B. Mañucat-Tan, Alastair J. Ludington, David L. Adelson, Stephen Pederson, Michael Lardelli
Software Mentions: 6
Published: over 6 years ago

10.18632/aging.202718

TMBIM6, a potential virus target protein identified by integrated multiomics data analysis in SARS-CoV-2-infected host cells
Cited by: 4
Author(s): Qizheng Han, Junhao Wang, Haihua Luo, Lei Li, Xinya Lu, Aihua Liu, Yongqiang Deng, Yong Jiang
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0183517

Integrated analysis of long non-coding RNAs in human gastric cancer: An in silico study
Cited by: 7
Author(s): Han Wang, Zhenyu Zhang, Bangshun He, Yu Xu, Jun Zhang, Weijun Cao
Software Mentions: 6
Published: about 9 years ago

10.1155/2020/2319194

Immune-Related lncRNA Correlated with Transcription Factors Provide Strong Prognostic Prediction in Gliomas
Cited by: 4
Author(s): Yantao Tian, Yiquan Ke, Yanxia Ma
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12920-018-0358-6

Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability
Cited by: 5
Author(s): Ute Scheller, Kathrin Pfisterer, Steffen Uebe, Arif B. Ekici, André Reis, Rami Abou Jamra, Fulvia Ferrazzi
Software Mentions: 6
Published: over 8 years ago

10.1186/s12866-020-01913-5

Deciphering the archaeal communities in tree rhizosphere of the Qinghai-Tibetan plateau
Cited by: 11
Author(s): Mengjun Zhang, Liwei Chai, Muke Huang, Weiqian Jia, Jiabao Guo, Yi Huang
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0254829

Tumor infiltrating lymphocytes associated competitive endogenous RNA networks as predictors of outcome in hepatic carcinoma based on WGCNA analysis
Cited by: 1
Author(s): Ying He, Xu Rui, Li Peng, Xiaoyu Hu
Software Mentions: 6
Published: about 5 years ago

10.1155/2018/4246703

Candidate Biomarkers and Molecular Mechanism Investigation for Glioblastoma Multiforme Utilizing WGCNA
Cited by: 64
Author(s): Qi Yang, Rui Wang, Bo Wei, Chuangang Peng, Le Wang, Guozhang Hu, Daliang Kong, Chao Du
Software Mentions: 6
Published: almost 8 years ago

10.1186/s42523-020-00042-8

Survey of rumen microbiota of domestic grazing yak during different growth stages revealed novel maturation patterns of four key microbial groups and their dynamic interactions
Cited by: 31
Author(s): Wei Guo, Mi Zhou, Tao Ma, Sisi Bi, Weiwei Wang, Ying Zhang, Xiaodan Huang, Le Luo Guan, Ruijun Long
Software Mentions: 6
Published: about 6 years ago

10.3389/fonc.2021.587479

Identification of Mitochondrial-Related Prognostic Biomarkers Associated With Primary Bile Acid Biosynthesis and Tumor Microenvironment of Hepatocellular Carcinoma
Cited by: 21
Author(s): Tao Zhang, Yingli Nie, Jian Gu, Kailin Cai, Xiangdong Chen, Huili Li, Jiliang Wang
Software Mentions: 6
Published: over 5 years ago

10.3389/fmolb.2021.636991

Identifying Dendritic Cell–Related Genes Through a Co-Expression Network to Construct a 12-Gene Risk-Scoring Model for Predicting Hepatocellular Carcinoma Prognosis
Cited by: 7
Author(s): Chao-Yuan Huang, Xiaotao Jiang, Yuancheng Huang, Lina Zhao, Peiwu Li, Fengbin Liu
Software Mentions: 6
Published: over 5 years ago

10.1186/s42523-020-00032-w

Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses
Cited by: 18
Author(s): Samuel Dupont, Ana Lokmer, Erwan Corre, Jean‐Christophe Auguet, Bruno Petton, Ève Toulza, Caroline Montagnani, Gwenn Tanguy, David Pecqueur, Christophe Salmeron, Laure Guillou, Christelle Desnues, Bernard La Scola, Jacques Bou Khalil, Julien de Lorgeril, Guillaume Mitta, Yannick Gueguen, Jean-Michel Escoubas
Software Mentions: 6
Published: over 6 years ago

10.3390/ijms20020263

Molecular Network-Based Drug Prediction in Thyroid Cancer
Cited by: 14
Author(s): Xingyu Xu, Hang Long, Baohang Xi, Binbin Ji, Zejun Li, Yunyue Dang, Cheng Jiang, Yao Yao, Jialiang Yang
Software Mentions: 6
Published: over 7 years ago

10.3390/ijms22063028

Characterization of Biological Pathways Regulating Acute Cold Resistance of Zebrafish
Cited by: 19
Author(s): Jing Ren, Yong Long, Ran Liu, Guangliang Song, Qing Li, Zongbin Cui
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0233372

Muscle transcriptome analysis identifies genes involved in ciliogenesis and the molecular cascade associated with intramuscular fat content in Large White heavy pigs
Cited by: 20
Author(s): Martina Zappaterra, Silvia Gioiosa, Giovanni Chillemi, Paolo Zambonelli, Roberta Davoli
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0241128

Kin recognition: Neurogenomic response to mate choice and sib mating avoidance in a parasitic wasp
Cited by: 0
Author(s): Aurore Gallot, Sandrine Sauzet, Emmanuel Desouhant
Software Mentions: 6
Published: almost 6 years ago

10.3390/ijms22126307

Transcriptional Profiling Identifies Upregulation of Neuroprotective Pathways in Retinitis Pigmentosa
Cited by: 4
Author(s): Christina B. Bielmeier, Saskia Roth, Sabrina I. Schmitt, Stefaniya Boneva, Anja Schlecht, Mario Vallon, Ernst R. Tamm, Süleyman Ergün, Andreas Neueder, Barbara M. Braunger
Software Mentions: 6
Published: about 5 years ago

10.3389/fmicb.2019.02491

Dynamic Changes in the Microbiome and Mucosal Immune Microenvironment of the Lower Respiratory Tract by Influenza Virus Infection
Cited by: 30
Author(s): Liming Gu, Huixiong Deng, Zhihui Ren, Ying Zhao, Shun Yu, Yingzhu Guo, Jianping Dai, Xiaoxuan Chen, Kangsheng Li, Rui Li, Gefei Wang
Software Mentions: 6
Published: almost 7 years ago

10.1155/2021/6693219

A Novel 8-Gene Prognostic Signature for Survival Prediction of Uveal Melanoma
Cited by: 3
Author(s): Zhongjun Tang, Kebo Cai
Software Mentions: 6
Published: about 5 years ago

10.1186/s12920-021-01036-4

Multi-factor regulatory network and different clusters in hypertrophic obstructive cardiomyopathy
Cited by: 3
Author(s): Xianyu Qin, Lei Huang, Sicheng Chen, Shaoxian Chen, Pengju Wen, Yueheng Wu, Jian Zhuang
Software Mentions: 6
Published: about 5 years ago

10.3389/fmicb.2020.01036

Niche Differentiation in the Composition, Predicted Function, and Co-occurrence Networks in Bacterial Communities Associated With Antarctic Vascular Plants
Cited by: 29
Author(s): Qian Zhang, Jacquelinne J. Acuña, Nitza G. Inostroza, Paola Durán, Marı́a de la Luz Mora, Michael J. Sadowsky, Milko A. Jorquera
Software Mentions: 6
Published: over 6 years ago

10.7717/peerj.10633

Gene signatures with predictive and prognostic survival values in human osteosarcoma
Cited by: 4
Author(s): Zhongpeng Qiu, Xuehui Du, Kai Chen, Yi Dai, Sibo Wang, Jun Xiao, Gang Li
Software Mentions: 6
Published: over 5 years ago

10.7717/peerj.8505

Identification and validation of key modules and hub genes associated with the pathological stage of oral squamous cell carcinoma by weighted gene co-expression network analysis
Cited by: 10
Author(s): Xuegang Hu, Genban Sun, Zhiqiang Shi, Hui Ni, Shan Jiang
Software Mentions: 6
Published: over 6 years ago

10.7554/eLife.35368

Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in Drosophila
Cited by: 92
Author(s): Zaijun Ma, Hui Wang, Yuping Cai, Han Wang, Kongyan Niu, Xiaofen Wu, Huanhuan Ma, Yun Yang, Wenhua Tong, Feng Liu, Zhandong Liu, Yaoyang Zhang, Rui Li, Zheng‐Jiang Zhu, Nan Liu
Software Mentions: 6
Published: over 8 years ago

10.3389/fgene.2019.01056

Meta-Analysis of HTLV-1-Infected Patients Identifies CD40LG and GBP2 as Markers of ATLL and HAM/TSP Clinical Status: Two Genes Beat as One
Cited by: 5
Author(s): Eduardo R. Fukutani, Pablo Ivan Pereira Ramos, José Irahe Kasprzykowski, Lucas Gentil Azevedo, Moreno Magalhães de Souza Rodrigues, João Victor Lima, Helton Fábio Santos de Araújo, Kiyoshi F. Fukutani, Artur T. L. Queiroz
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12864-019-5946-0

Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactions
Cited by: 19
Author(s): Jules Deforges, Rodrigo S. Reis, Philippe Jacquet, Dominique Jacques Vuarambon, Yves Poirier
Software Mentions: 6
Published: about 7 years ago

10.3389/fgene.2020.00311

Weighted Gene Coexpression Network Analysis of Features That Control Cancer Stem Cells Reveals Prognostic Biomarkers in Lung Adenocarcinoma
Cited by: 57
Author(s): Yi Liao, Yulei Wang, Mengqing Cheng, Chengliang Huang, Xiaoxuan Fan
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2020.00011

Novel Combined Tissue Transcriptome Analysis After Lentogenic Newcastle Disease Virus Challenge in Inbred Chicken Lines of Differential Resistance
Cited by: 6
Author(s): Melissa S. Deist, Rodrigo A. Gallardo, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont
Software Mentions: 6
Published: over 6 years ago

10.1186/s12920-021-00989-w

Identification of key genes in calcific aortic valve disease via weighted gene co-expression network analysis
Cited by: 7
Author(s): Jin-Yu Sun, Hua Yang, Hui Shen, Qiang Qu, Junyan Kan, Xiangqing Kong, Wei Sun, Yue-Yun Shen
Software Mentions: 6
Published: over 5 years ago

10.1186/s12866-020-01739-1

Alter between gut bacteria and blood metabolites and the anti-tumor effects of Faecalibacterium prausnitzii in breast cancer
Cited by: 57
Author(s): Ji Ma, Lingqi Sun, Ying Liu, Hui Ren, Yali Shen, Feng Bi, Tao Zhang, Xin Wang
Software Mentions: 6
Published: over 6 years ago

10.18632/aging.103433

SLC7A2 serves as a potential biomarker and therapeutic target for ovarian cancer
Cited by: 16
Author(s): Tianshui Sun, Fangfang Bi, Zhuonan Liu, Qing Yang
Software Mentions: 6
Published: about 6 years ago

10.1186/s13059-014-0483-2

Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia
Cited by: 140
Author(s): Ruth Pidsley, Joana Viana, Eilís Hannon, Helen Spiers, Claire Troakes, Safa Al-Saraj, Naguib Mechawar, Gustavo Turecki, Leonard C. Schalkwyk, Nicholas John Bray, Jonathan Mill
Software Mentions: 6
Published: almost 12 years ago

10.1038/s41380-020-0669-9

Transcriptome of iPSC-derived neuronal cells reveals a module of co-expressed genes consistently associated with autism spectrum disorder
Cited by: 37
Author(s): Karina Griesi-Oliveira, Mariana Soares Fogo, Bruna G G Pinto, Aline Yasuda Alves, Adriano K. Suzuki, Andressa Gois Morales, Suzana Ezquina, Omar Sosa, Gavin J. Sutton, Daniele Yumi Sunaga-Franze, Ana Paula Silva Bueno, Gabriela Seabra, Luis Roberto Sardinha, Silvia Souza da Costa, Carla Rosenberg, Elaine Cristina Zachi, Andréa L. Sertié, Daniel Martins‐de‐Souza, Eduardo M. Reis, Irina Voineagu, Maria Rita Passos‐Bueno
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pcbi.1008491

Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness
Cited by: 14
Author(s): Iván Cárcamo-Orive, Marc Henrion, Kuixi Zhu, Noam D. Beckmann, Paige Cundiff, Sara Moein, Zenan Zhang, Melissa Alamprese, Sunita L. D’Souza, Martin Wabitsch, Eric E. Schadt, Thomas Quertermous, Joshua W. Knowles, Rui Chang
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-91214-2

Chamber-enriched gene expression profiles in failing human hearts with reduced ejection fraction
Cited by: 12
Author(s): Xin Luo, Jun Yin, Denise Dwyer, Tracy M. Yamawaki, Hong Zhou, Hongfei Ge, Chun-Ya Han, Artem Shkumatov, K. F. Snyder, Brandon Ason, Chi-Ming Li, Oliver Homann, Marina Stolina
Software Mentions: 6
Published: about 5 years ago

10.1073/pnas.2008890118

OCT4 induces embryonic pluripotency via STAT3 signaling and metabolic mechanisms
Cited by: 23
Author(s): Giuliano Giuseppe Stirparo, Agata Kurowski, Akira Yanagida, Lawrence E. Bates, Stanley E. Strawbridge, Siarhei Hladkou, Hannah Stuart, Thorsten Boroviak, José C.R. Silva, Jennifer Nichols
Software Mentions: 6
Published: over 5 years ago

10.15252/embj.2019101695

Phospho‐RNA‐seq: a modified small RNA‐seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma
Cited by: 61
Author(s): María D. Giraldez, Ryan M Spengler, Alton Etheridge, Annika Jane Goicochea, Missy Tuck, Sung Won Choi, David J. Galas, Muneesh Tewari
Software Mentions: 6
Published: over 7 years ago

10.1186/s12931-016-0459-8

Differential DNA methylation marks and gene comethylation of COPD in African-Americans with COPD exacerbations
Cited by: 47
Author(s): Robert S. Busch, Weiliang Qiu, Jessica Lasky‐Su, Jarrett Morrow, Gerard J. Criner, Dawn L. DeMeo
Software Mentions: 6
Published: almost 10 years ago

10.3389/fpls.2021.675208

Differential Regulation of Maize and Sorghum Orthologs in Response to the Fungal Pathogen Exserohilum turcicum
Cited by: 5
Author(s): Pragya Adhikari, Santiago X. Mideros, Tiffany M. Jamann
Software Mentions: 6
Published: over 5 years ago

10.1126/sciadv.abj1132

Plasma lipids and growth faltering: A longitudinal cohort study in rural Gambian children
Cited by: 2
Author(s): Gerard Bryan Gonzales, Daniëlla Brals, Bakary Sonko, Fatou Sosseh, Andrew M. Prentice, Sophie E. Moore, Albert Koulman
Software Mentions: 6
Published: almost 5 years ago

10.1080/22221751.2021.1942228

Single-cell immune checkpoint landscape of PBMCs stimulated with Candida albicans
Cited by: 8
Author(s): Wei‐Wei Deng, Zhen Su, Panpan Liang, Yubo Ma, Yufang Liu, Kai Zhang, Yi Zhang, Ting Liang, Jinyan Shao, X. Liu, Wenling Han, Ruoyu Li
Software Mentions: 6
Published: over 5 years ago

10.1038/sdata.2018.185

The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease
Cited by: 284
Author(s): Minghui Wang, Noam D. Beckmann, Panos Roussos, Erming Wang, Xianxiao Zhou, Qian Wang, Chi Ming, Ryan Neff, Wanli Ma, John F. Fullard, Mads E. Hauberg, Jaroslav Bendl, Mette A. Peters, Ben Logsdon, Pei Wang, Milind Mahajan, Lara M. Mangravite, Eric B. Dammer, Duc M. Duong, James J. Lah, Nicholas T. Seyfried, Aĺlan I. Levey, Joseph D. Buxbaum, Michelle E. Ehrlich, Sam Gandy, Pavel Katsel, Vahram Haroutunian, Eric E. Schadt, Bin Zhang
Software Mentions: 6
Published: almost 8 years ago

10.3389/fphys.2019.01370

A Dynamic Transcriptional Analysis Reveals IL-6 Axis as a Prominent Mediator of Surgical Acute Response in Non-ischemic Mouse Heart
Cited by: 1
Author(s): Sally Badawi, Alexandre Paccalet, Zeina Harhous, Bruno Pillot, Lionel Augeul, Fabien Van Coppenolle, Joël Lachuer, Mazen Kurdi, Claire Crola Da Silva, Michel Ovize, Gabriel Bidaux
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pgen.1009474

Dynamic neurogenomic responses to social interactions and dominance outcomes in female paper wasps
Cited by: 6
Author(s): Floria M. K. Uy, Christopher M. Jernigan, Natalie C. Zaba, Eshan Mehrotra, Sara Miller, Michael J. Sheehan
Software Mentions: 6
Published: about 5 years ago

10.3389/fphys.2018.01778

Identification of Crucial Genes and Pathways in Human Arrhythmogenic Right Ventricular Cardiomyopathy by Coexpression Analysis
Cited by: 11
Author(s): Peipei Chen, Bo Long, Yuanfu Xu, Wei Wu, Shuyang Zhang
Software Mentions: 6
Published: over 7 years ago

10.1002/ece3.7861

Effects of ecological environment and host genotype on the phyllosphere bacterial communities of cigar tobacco (Nicotiana tabacum L.)
Cited by: 9
Author(s): Lei Xing, Jianlei Yang, Yuping Jia, Xiaobing Hu, Yi Liu, Heng Xu, Huaqun Yin, Juan Li, Zhenxie Yi
Software Mentions: 6
Published: about 5 years ago

10.3389/fimmu.2021.645839

Multi-Omics Profiling Identifies Risk Hypoxia-Related Signatures for Ovarian Cancer Prognosis
Cited by: 11
Author(s): Xingyu Chen, Hua Lan, Dong He, Runshi Xu, Yao Zhang, Ying Cheng, Haotian Chen, Songshu Xiao, Ke Cao
Software Mentions: 6
Published: about 5 years ago

10.3389/fmicb.2021.666558

The Transcriptional Response of Soil Bacteria to Long-Term Warming and Short-Term Seasonal Fluctuations in a Terrestrial Forest
Cited by: 6
Author(s): Priyanka Chowdhury, Stefan Golas, Lauren Alteio, Joshua T. E. Stevens, Andrew F. Billings, Jeffrey L. Blanchard, Jerry M. Melillo, Kristen M. DeAngelis
Software Mentions: 6
Published: about 5 years ago

10.1534/g3.117.041624

Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross
Cited by: 35
Author(s): Richard Green, Courtney Wilkins, Sunil Thomas, Aimee Sekine, Duncan M. Hendrick, Kathleen Voss, Reneé C. Ireton, Michael A. Mooney, Jennifer T. Go, Gabrielle Choonoo, Sophia Jeng, Fernando P Pardo Manuel De Villena, Martin T. Ferris, Shannon K. McWeeney, Michael Gale
Software Mentions: 6
Published: over 9 years ago

10.3389/fimmu.2021.632798

Comprehensive Transcriptomic Analysis Identifies Novel Antiviral Factors Against Influenza A Virus Infection
Cited by: 11
Author(s): Ao Zhou, Dong Xia, Mengyun Liu, Bin Tang
Software Mentions: 6
Published: about 5 years ago

10.1242/dmm.047225

Hearing impairment due to Mir183/96/182 mutations suggests both loss-of-function and gain-of-function effects
Cited by: 10
Author(s): Morag A. Lewis, Francesca Di Domenico, Neil J. Ingham, Haydn M. Prosser, Karen P. Steel
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-86048-x

A ceRNA-associated risk model predicts the poor prognosis for head and neck squamous cell carcinoma patients
Cited by: 9
Author(s): Yuzi Xu, Fengqin Xu, Yiming Lv, Siyuan Wang, Jia Li, Chuan Zhou, Jimin Jiang, Binbin Xie, Fuming He
Software Mentions: 6
Published: over 5 years ago

10.3389/fgene.2020.634634

A Novel Prognostic Model of Early-Stage Lung Adenocarcinoma Integrating Methylation and Immune Biomarkers
Cited by: 17
Author(s): Jin Ren, Yun Yang, Chuanyin Li, Lu Xie, Ronggui Hu, Qin Xiong, Menghuan Zhang
Software Mentions: 6
Published: over 5 years ago

10.15252/embj.2019102808

HNF1A recruits KDM6A to activate differentiated acinar cell programs that suppress pancreatic cancer
Cited by: 36
Author(s): Jorge Ferrer, Edgar Bernardo, Anthony Beucher, Miguel A. Maestro, Natalia del Pozo, I.R. Hernández Millán, Lena Haeberle, Martin Schlensog, Sami-Alexander Safi, Wolfram Trudo Knoefel, Vanessa Grau, Matías De Vas, Karl B. Shpargel, Eva C. Vaquero, Terry Magnuson, Sagrario Ortega, Irene Espósito, Francisco X. Real, Jorge Ferrer
Software Mentions: 6
Published: over 6 years ago

10.3389/fimmu.2018.00056

The Immune and Non-Immune Pathways That Drive Chronic Gastrointestinal Helminth Burdens in the Wild
Cited by: 20
Author(s): Simon A. Babayan, Wei Liu, Graham Hamilton, Elizabeth Kilbride, Evelyn C. Rynkiewicz, Melanie Clerc, Amy B. Pedersen
Software Mentions: 6
Published: over 8 years ago

10.1038/ismej.2017.165

Recurrent patterns of microdiversity in a temperate coastal marine environment
Cited by: 110
Author(s): Meghan Chafee, Antonio Fernández-Guerra, Pier Luigi Buttigieg, Gunnar Gerdts, A. Murat Eren, Hanno Teeling, Rudolf Amann
Software Mentions: 6
Published: almost 9 years ago

10.1038/s41598-021-98059-9

Sex-dependent gene co-expression in the human body
Cited by: 9
Author(s): Robin Hartman, Michal Mokrý, Gérard Pasterkamp, Hester M. den Ruijter
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41398-021-01531-3

Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study
Cited by: 22
Author(s): Xiuxia Yuan, Yunpeng Wang, Xue Li, Jiajun Jiang, Yulin Kang, Lijuan Pang, Peifen Zhang, Ang Li, Luxian Lv, Ole A. Andreassen, Xiaoduo Fan, Shaohua Hu, Xueqin Song
Software Mentions: 6
Published: about 5 years ago

10.1038/s41598-021-85848-5

Abnormal upregulation of cardiovascular disease biomarker PLA2G7 induced by proinflammatory macrophages in COVID-19 patients
Cited by: 18
Author(s): Yang Li, Yongzhong Jiang, Yi Zhang, Naizhe Li, Qiangling Yin, Linlin Liu, Xin Lv, Yan Liu, Aqian Li, Bin Fang, Jiajia Li, Hengping Ye, Gang Ye, Xiaoxian Cui, Yang Liu, Yuanyuan Qu, Chuan Li, Jiandong Li, Dexin Li, Zhongtao Gai, Shiwen Wang, Faxian Zhan, Mifang Liang
Software Mentions: 6
Published: over 5 years ago

10.1038/s41398-021-01447-y

Essential genes from genome-wide screenings as a resource for neuropsychiatric disorders gene discovery
Cited by: 2
Author(s): Wei Zhang, Joao L De Quevedo, Gabriel R. Fries
Software Mentions: 6
Published: over 5 years ago

10.3389/fpsyt.2021.716722

Transcriptomics Analysis Reveals Shared Pathways in Peripheral Blood Mononuclear Cells and Brain Tissues of Patients With Schizophrenia
Cited by: 6
Author(s): Xuemian Song, Yiyun Liu, Juncai Pu, Siwen Gui, Xiaogang Zhong, Xiaopeng Chen, Weiyi Chen, Xiang Chen, Yue Chen, Haiyang Wang, Ke Cheng, Libo Zhao, Peng Xie
Software Mentions: 6
Published: almost 5 years ago

10.1093/conphys/coz018

Tracking transcriptomic responses to endogenous and exogenous variation in cetaceans in the Southern California Bight
Cited by: 8
Author(s): Marisa L. Trego, Andrew Whitehead, Nicholas M. Kellar, Morgane Lauf, Rebecca L. Lewison
Software Mentions: 6
Published: over 7 years ago

10.7717/peerj.4327

Evidence for widespread dysregulation of circadian clock progression in human cancer
Cited by: 66
Author(s): Jarrod Shilts, Guanhua Chen, Jacob J. Hughey
Software Mentions: 5
Published: over 8 years ago

10.1111/pbi.13236

Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton ( Gossypium hirsutum )
Cited by: 42
Author(s): Syed Shan-e-Ali Zaidi, Rubab Zahra Naqvi, Muhammad Asif, Susan R. Strickler, Sara Shakir, Muhammad Shafiq, Ayesha Khan, Imran Amin, Bharat Mishra, M. Shahid Mukhtar, Brian E. Scheffler, Jodi A. Scheffler, Lukas A. Mueller, Shahid Mansoor
Software Mentions: 5
Published: almost 7 years ago

10.1111/pbi.13483

The genome of Cleistogenes songorica provides a blueprint for functional dissection of dimorphic flower differentiation and drought adaptability
Cited by: 18
Author(s): Jiyu Zhang, Fan Wu, Yan Qi, Ulrik P. John, Mingshu Cao, Pao Xu, Zhengshe Zhang, Tiantian Ma, Xifang Zong, Jie Li, Ruijuan Liu, Yufei Zhang, Yufeng Zhao, Gisele Kanzana, Yunyun Lv, Nan Zhang, Germán Spangenberg, Yanrong Wang
Software Mentions: 5
Published: almost 6 years ago

10.1111/tpj.14202

Gene networks orchestrated by Me<scp>GI</scp>: a single‐factor mechanism underlying sex determination in persimmon
Cited by: 43
Author(s): Ho Wen Yang, Takashi Akagi, Taiji Kawakatsu, Ryutaro Tao
Software Mentions: 5
Published: over 7 years ago

10.1007/s11103-020-01041-8

Integrative transcriptomics reveals genotypic impact on sugar beet storability
Cited by: 7
Author(s): Silvia Madritsch, Svenja Bomers, Alexandra Posekany, Agnes Burg, Rebekka Birke, Florian Emerstorfer, Reinhard Turetschek, Sandra Otte, Herbert Eigner, Eva Maria Sehr
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pcbi.1009021

MiMeNet: Exploring microbiome-metabolome relationships using neural networks
Cited by: 33
Author(s): Derek Reiman, Brian T. Layden, Yang Dai
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pcbi.1008976

MetaGSCA: A tool for meta-analysis of gene set differential coexpression
Cited by: 2
Author(s): Yan Guo, Hui Yu, Haocan Song, Jia-Peng He, Olufunmilola Oyebamiji, Huining Kang, Jie Ping, Scott A. Ness, Yu Shyr, Fei Ye
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pcbi.1004847

Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes
Cited by: 40
Author(s): Jeffrey J. Sutherland, Robert A. Jolly, Keith M. Goldstein, James Stevens
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pgen.1008367

Integrating transcriptomic network reconstruction and eQTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development
Cited by: 15
Author(s): Robert L. Baker, Wen Fung Leong, Marcus T. Brock, Matthew J. Rubin, R. J. Cody Markelz, Stephen M. Welch, Julin Maloof, Cynthia Weinig
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pntd.0004992

Meta-transcriptome Profiling of the Human-Leishmania braziliensis Cutaneous Lesion
Cited by: 54
Author(s): Stephen M Christensen, Laura A. L. Dillon, Lucas P. Carvalho, Sara Passos, Fernanda O. Novais, V. K. Hughitt, Daniel P. Beiting, Edgar M. Carvalho, Phillip Scott, Najib M. El-Sayed, David M. Mosser
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pone.0243857

Network preservation reveals shared and unique biological processes associated with chronic alcohol abuse in NAc and PFC
Cited by: 7
Author(s): Eric Vornholt, John W. Drake, Mohammed Mamdani, Gowon O. McMichael, Zachary N. Taylor, Silviu‐Alin Bacanu, Michael F. Miles, Vladimir I. Vladimirov
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0118731

Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis
Cited by: 77
Author(s): Katherine C. H. Amrine, Bárbara Blanco-Ulate, Dario Cantu
Software Mentions: 5
Published: over 11 years ago

10.1038/s42003-021-01892-x

Transcriptomic analyses of the termite, Cryptotermes secundus, reveal a gene network underlying a long lifespan and high fecundity
Cited by: 15
Author(s): Silu Lin, Jana Werle, Judith Korb
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-021-01659-4

Amynthas corticis genome reveals molecular mechanisms behind global distribution
Cited by: 4
Author(s): Xing Wang, Yi Zhang, Yufeng Zhang, Mingming Kang, Yuanbo Li, Samuel W. James, Yang Yang, Yang Bi, Hao Jiang, Yi Zhao, Zhenjun Sun
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-021-01859-y

A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology
Cited by: 16
Author(s): Sara Calhoun, Tisza Ann Szeremy Bell, Lukas R. Dahlin, Yuliya A. Kunde, Kurt LaButti, Katherine Louie, Andrea Kuftin, Daniel Treen, David Dilworth, Sirma Mihaltcheva, Christopher Daum, Benjamin P. Bowen, Trent Northen, Michael T. Guarnieri, Shawn R. Starkenburg, Igor V. Grigoriev
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-021-02520-4

CdGAP promotes prostate cancer metastasis by regulating epithelial-to-mesenchymal transition, cell cycle progression, and apoptosis
Cited by: 8
Author(s): Chahat Mehra, Jin‐Tae Chung, Yi He, Mónica Lara‐Márquez, Marie-Anne Goyette, Nadia Boufaied, Véronique Barrès, Véronique Ouellet, Karl-Philippe Guérard, Carine Delliaux, Fred Saad, Jacques Lapointe, Jean‐François Côté, David P. Labbé, Nathalie Lamarche-Vane
Software Mentions: 5
Published: almost 5 years ago

10.1155/2021/7922594

Identification of the Molecular Subgroups in Idiopathic Pulmonary Fibrosis by Gene Expression Profiles
Cited by: 4
Author(s): Ning Zhang, Yubiao Guo, Cong Wu, Bohan Jiang, Yuguang Wang
Software Mentions: 5
Published: almost 5 years ago

10.1093/database/bax079

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species
Cited by: 9
Author(s): Leandro Costa do Nascimento, Marcela Salazar, Jorge Lepikson-Neto, Eduardo Leal Oliveira Camargo, Lucas S. Parreiras, Gonçalo Amarante Guimarães Pereira, Marcelo Falsarella Carazzolle
Software Mentions: 5
Published: over 9 years ago

10.3390/diagnostics10050305

Characterization of Stem-like Circulating Tumor Cells in Pancreatic Cancer
Cited by: 7
Author(s): Lei Zhu, Bárbara Hissa, Balázs Győrffy, Johann-Christoph Jann, Cui Yang, Christoph Reißfelder, Sebastian Schölch
Software Mentions: 5
Published: over 6 years ago

10.1016/j.ebiom.2021.103538

Airway microbial communities, smoking and asthma in a general population sample
Cited by: 21
Author(s): Elena Turek, Michael J. Cox, Michael Hunter, Jennie Hui, Phillip James, Saffron A.G. Willis‐Owen, Leah Cuthbertson, Alan James, A.W. Musk, Miriam F. Moffatt, William Cookson
Software Mentions: 5
Published: about 5 years ago

10.15252/emmm.202013328

Peripheral blood transcriptome profiling enables monitoring disease progression in dystrophic mice and patients
Cited by: 11
Author(s): Mirko Signorelli, Mitra Ebrahimpoor, Olga Veth, Kristina Hettne, Nisha Verwey, R. García-Rodríguez, Christa L Tanganyika-deWinter, Luz Berenice López-Hernández, Rosa Escobar Cedillo, Benjamín Gómez-D́iaz, Ólafur Þ. Magnússon, Hailiang Mei, Roula Tsonaka, Annemieke Aartsma‐Rus, Pietro Spitali
Software Mentions: 5
Published: over 5 years ago

10.1002/ece3.6930

Immunogenetic and tolerance strategies against a novel parasitoid of wild field crickets
Cited by: 0
Author(s): Kristin L. Sikkink, Nathan W. Bailey, Marlene Zuk, Susan L. Balenger
Software Mentions: 5
Published: almost 6 years ago

10.1002/ece3.2685

Transcriptome predictors of coral survival and growth in a highly variable environment
Cited by: 53
Author(s): Rachael A. Bay, Stephen R. Palumbi
Software Mentions: 5
Published: over 9 years ago

10.1002/ece3.6899

Insights into the genetic basis of predator‐induced response inDaphnia galeata
Cited by: 9
Author(s): Verena Tams, Jana Nickel, Anne Ehring, Mathilde Cordellier
Software Mentions: 5
Published: almost 6 years ago

10.1080/22221751.2020.1738277

Competing endogenous RNA network profiling reveals novel host dependency factors required for MERS-CoV propagation
Cited by: 50
Author(s): Xi Zhang, Hin Chu, Lei Wen, Huiping Shuai, Dong Yang, Yixin Wang, Yuxin Hou, Zheng Zhu, Shuofeng Yuan, Feifei Yin, Jasper Fuk‐Woo Chan, Kwok‐Yung Yuen
Software Mentions: 5
Published: over 6 years ago

10.1111/1462-2920.14498

Gut microbiota in patients after surgical treatment for colorectal cancer
Cited by: 21
Author(s): Ye Jin, Yang Liu, Lei Zhao, Fuya Zhao, Jing Feng, Shengda Li, Huinan Chen, Jiayu Sun, Bihai Zhu, Rui Geng, Yunwei Wei
Software Mentions: 5
Published: over 7 years ago

10.1111/eva.12278

Patterns of differential gene expression in adult rotation‐resistant and wild‐type western corn rootworm digestive tracts
Cited by: 10
Author(s): Chia‐Ching Chu, Jorge A. Zavala, Joseph L. Spencer, M. Curzi, Christopher J. Fields, Jenny Drnevich, Blair D. Siegfried, Manfredo J. Seufferheld
Software Mentions: 5
Published: about 11 years ago

10.12688/f1000research.18705.2

Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models
Cited by: 1
Author(s): Katharina Baum, Jagath C. Rajapakse, Francisco Azuaje
Software Mentions: 5
Published: about 7 years ago

10.1002/2211-5463.13134

Identification of hub lncRNAs in head and neck cancer based on weighted gene co‐expression network analysis and experiments
Cited by: 13
Author(s): Longquan Shao
Software Mentions: 5
Published: over 5 years ago

10.3389/fnagi.2021.686066

Significant Difference of Immune Cell Fractions and Their Correlations With Differential Expression Genes in Parkinson’s Disease
Cited by: 13
Author(s): Yilin Huang, Huisheng Liu, Jiaqi Hu, Chongyin Han, Zhenggang Zhong, Wei Luo, Yuhu Zhang, Fei Ling
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2021.648898

A Novel Method to Identify the Differences Between Two Single Cell Groups at Single Gene, Gene Pair, and Gene Module Levels
Cited by: 1
Author(s): Lingyu Cui, Bo Wang, Caixia Ren, Ailan Wang, Hong An, Wei Liang
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2018.01661

Integrated Systems Biology Approach Identifies Novel Maternal and Placental Pathways of Preeclampsia
Cited by: 128
Author(s): Nándor Gábor Than, Roberto Romero, Adi L. Tarca, Katalin A. Kékesi, Yi Xu, Zhonghui Xu, Kata Juhász, Gaurav Bhatti, Ron Leavitt, Zsolt Gelencser, János Pálhalmi, Tzu Hung Chung, Balázs Győrffy, László Orosz, Attila Demeter, Anett Szecsi, Éva Hunyadi‐Gulyás, Zsuzsanna Darula, Attila Simor, Katalin Éder, S. Szabó, Vanessa Topping, Haidy Elazzamy, Christopher LaJeunesse, Andrea Balogh, Gábor Szalai, Susan Land, Olga Török, Zhong Dong, Ilona Kovalszky, András Falus, Hamutal Meiri, Sorin Drăghici, Sonia S. Hassan, Tinnakorn Chaiworapongsa, M Krispin, Martin Knöfler, Offer Erez, Graham J. Burton, Chong Jai Kim, Gábor Juhász, Zoltán Papp
Software Mentions: 5
Published: about 8 years ago

10.3389/fimmu.2017.01071

Gene Expression Contributes to the Recent Evolution of Host Resistance in a Model Host Parasite System
Cited by: 33
Author(s): Brian K. Lohman, Natalie C. Steinel, Jesse N. Weber, Daniel I. Bolnick
Software Mentions: 5
Published: almost 9 years ago

10.3389/fimmu.2020.607314

Genetic Dissection of the Regulatory Mechanisms of Ace2 in the Infected Mouse Lung
Cited by: 11
Author(s): Fuyi Xu, Jun Gao, Silke Bergmann, Amy C. Sims, David G. Ashbrook, Ralph S. Baric, Yan Cui, Colleen B. Jonsson, Kui Li, Robert W. Williams, Klaus Schughart, Lu Lu
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2021.666137

Construction and Validation of an Immune Infiltration-Related Gene Signature for the Prediction of Prognosis and Therapeutic Response in Breast Cancer
Cited by: 9
Author(s): Yang Peng, Haochen Yu, Yudi Jin, Fanli Qu, Haoyu Ren, Zhenrong Tang, Yingzi Zhang, Chi Qu, Beige Zong, Shengchun Liu
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2020.00571

Composition, Predicted Functions and Co-occurrence Networks of Rhizobacterial Communities Impacting Flowering Desert Events in the Atacama Desert, Chile
Cited by: 17
Author(s): Marcia Astorga-Eló, Qian Zhang, Giovanni Larama, Alexandra Stoll, Michael J. Sadowsky, Milko A. Jorquera
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2016.01335

Visual Comparative Omics of Fungi for Plant Biomass Deconstruction
Cited by: 31
Author(s): Shingo Miyauchi, David Navarro, Igor V. Grigoriev, Anna Lipzen, Robert Riley, Didier Chevret, Sacha Grisel, Jean‐Guy Berrin, Bernard Henrissat, Marie‐Noëlle Rosso
Software Mentions: 5
Published: about 10 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479