cran: WGCNA | Projects | Ecosyste.ms: Papers

10.7554/eLife.59201

A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin
Cited by: 32
Author(s): Morgan E. Levine, Ross A. McDevitt, Margarita Meer, Kathy A Perdue, Andrea Di Francesco, Theresa Meade, Colin Farrell, Kyra Thrush, Meng Wang, Christopher Dunn, Matteo Pellegrini, Rafael de Cabo, Luigi Ferrucci
Software Mentions: 2
Published: almost 6 years ago

10.3389/fgene.2020.565955

Integrative Analysis Extracts a Core ceRNA Network of the Fetal Hippocampus With Down Syndrome
Cited by: 2
Author(s): Shengran Wang, Xia Tang, Litao Qin, Weili Shi, Shasha Bian, Zhaokun Wang, Qingqing Wang, Xin Wang, Jianqin Gu, Bingtao Hao, Keyue Ding, Shixiu Liao
Software Mentions: 2
Published: almost 6 years ago

10.1002/mgg3.515

Gene coexpression network analysis identified potential biomarkers in gestational diabetes mellitus progression
Cited by: 11
Author(s): Xuefei Zhao, Wen Li
Software Mentions: 2
Published: almost 8 years ago

10.7554/eLife.20487

Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states
Cited by: 40
Author(s): Sumin Jang, Sandeep Choubey, Leon Furchtgott, Ling Nan Zou, Adele M. Doyle, Vilas Menon, Ethan Loew, Anne Rachel Krostag, Refugio A. Martinez, Linda Madisen, Boaz P. Levi, Sharad Ramanathan
Software Mentions: 2
Published: over 9 years ago

10.1186/s13024-018-0289-x

ABI3 and PLCG2 missense variants as risk factors for neurodegenerative diseases in Caucasians and African Americans
Cited by: 71
Author(s): Olivia J. Conway, Minerva M. Carrasquillo, Xue Wang, Jenny M. Bredenberg, Joseph S. Reddy, Samantha L. Strickland, Curtis S. Younkin, Jeremy D. Burgess, Mariet Allen, Sarah Lincoln, Thuy Nguyen, Kimberly G. Malphrus, Alexandra I. Soto, Ronald L. Walton, Bradley F. Boeve, Ronald C. Petersen, John A. Lucas, Tanis J. Ferman, William P. Cheshire, Jay A. van Gerpen, Ryan J. Uitti, Zbigniew K. Wszołek, Owen A. Ross, Dennis W. Dickson, Neill R. Graff‐Radford, Nilüfer Ertekin-Taner
Software Mentions: 2
Published: almost 8 years ago

10.3389/fgene.2020.563798

Integrated Analyses of Mouse Stem Cell Transcriptomes Provide Clues for Stem Cell Maintenance and Transdifferentiation
Cited by: 3
Author(s): Limin Wang, Xiaoxiao Li, Jie Hou, Xinhua Song, Wenhai Xie, Liang Shen
Software Mentions: 2
Published: about 6 years ago

10.3390/cancers12071876

Aspartic Aminopeptidase Is a Novel Biomarker of Aggressive Chronic Lymphocytic Leukemia
Cited by: 3
Author(s): Pramath Kakodkar, Sanket More, Kinga András, Nikos Papakonstantinou, Sharon M. Kelly, Mohammad A. Makrooni, Csaba Ortutay, Éva Szegezdi
Software Mentions: 2
Published: about 6 years ago

10.3389/fgene.2021.715526

Role of Sulfur Metabolism Gene and High-Sulfur Gene Expression in Wool Growth Regulation in the Cashmere Goat
Cited by: 1
Author(s): Yuan Chai, Yanyong Sun, Bin Liu, Lili Guo, Zaixia Liu, Le Zhou, Lingli Dai, Chunyan Jia, Wenguang Zhang, Li Chun
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2018.00698

Interactions Among Host–Parasite MicroRNAs During Nosema ceranae Proliferation in Apis mellifera
Cited by: 13
Author(s): Jay D. Evans, Qiang Huang
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2018.01568

Exploration of the Regulatory Mechanism of Secondary Metabolism by Comparative Transcriptomics in Aspergillus flavus
Cited by: 16
Author(s): Guangshan Yao, Yuewei Yue, Yishi Fu, Fang Zhou, Zhangling Xu, Genli Ma, Shihua Wang
Software Mentions: 2
Published: about 8 years ago

10.3389/fgene.2019.00166

SALMON: Survival Analysis Learning With Multi-Omics Neural Networks on Breast Cancer
Cited by: 128
Author(s): Zhi Huang, Xiaowei Zhan, Shunian Xiang, Travis Johnson, Bryan R. Helm, Christina Y. Yu, Jie Zhang, Paul Salama, Maher Rizkalla, Zhi Han, Kun Huang
Software Mentions: 2
Published: over 7 years ago

10.3389/fgene.2020.00113

FBXW4 Acts as a Protector of FOLFOX-Based Chemotherapy in Metastatic Colorectal Cancer Identified by Co-Expression Network Analysis
Cited by: 6
Author(s): Yiyi Zhang, Lijun Sun, Xiaojie Wang, Yanwu Sun, Ying Chen, Meifang Xu, Pan Chi, Xingrong Lu, Zongbin Xu
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0201674

Network analysis of inflammatory responses to sepsis by neutrophils and peripheral blood mononuclear cells
Cited by: 17
Author(s): Rasoul Godini, Hossein Fallahi, Esmaeil Ebrahimie
Software Mentions: 2
Published: about 8 years ago

10.3389/fmicb.2020.01933

Metagenomic Insights Into the Effects of Rare-Earth Elements Supplementation on Rumen Digestibility and Meat Quality of Beef Cattle
Cited by: 4
Author(s): Long Xu, Wen LuHua, Ge Yu, Gen Wan, Mingren Qu, Fuguang Xue
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0231594

Computational analysis for identification of the extracellular matrix molecules involved in endometrial cancer progression
Cited by: 18
Author(s): Vijesh Kumar Yadav, Tzong-Yi Lee, Justin Bo Kai Hsu, Hsien Da Huang, Wei Yang, Tzu Hao Chang
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2021.659602

Interaction Between the Intestinal Microbial Community and Transcriptome Profile in Common Carp (Cyprinus carpio L.)
Cited by: 8
Author(s): Shengyan Su, Xiaojun Jing, Chengfeng Zhang, Yiran Hou, Zhixun Li, Xiao Yang, Xiaolin Zhou, Pao Xu, Yongkai Tang, Jian Zhu
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2020.00880

Integrative Analysis of Differential lncRNA/mRNA Expression Profiling in Helicobacter pylori Infection-Associated Gastric Carcinogenesis
Cited by: 14
Author(s): Nianshuang Li, Yaobin Ouyang, Sihai Chen, Chao Peng, Cong He, Junbo Hong, Xiaoyu Yang, Yin Zhu, Nonghua Lü
Software Mentions: 2
Published: over 6 years ago

10.3390/molecules24142564

Integration of Metabolite Profiling and Transcriptome Analysis Reveals Genes Related to Volatile Terpenoid Metabolism in Finger Citron (C. medica var. sarcodactylis)
Cited by: 37
Author(s): Yaying Xu, Changqing Zhu, Changjie Xu, Jun Sun, Donald Grierson, Bo Zhang, Kunsong Chen
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-55692-9

Characterization of cancer omics and drug perturbations in panels of lung cancer cells
Cited by: 13
Author(s): Ayako Suzuki, Keiichi Onodera, Kazuma Matsui, Masahide Seki, Hiroyasu Esumi, Tomoyoshi Soga, Sumio Sugano, Takashi Kohno, Yutaka Suzuki, Katsuya Tsuchihara
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2020.00687

Genome and Transcriptome Analyses Provide Insight Into the Omega-3 Long-Chain Polyunsaturated Fatty Acids Biosynthesis of Schizochytrium limacinum SR21
Cited by: 17
Author(s): Limin Liang, Xinqing Zheng, Wenfang Fan, Duo Chen, Zhen Huang, Jiangtao Peng, Jinmao Zhu, Weiqi Tang, Youqiang Chen, Ting Xue
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2020.01314

Network-Based Analysis of OMICs Data to Understand the HIV–Host Interaction
Cited by: 13
Author(s): Sergey Ivanov, Alexey Lagunin, Dmitry Filimonov, O. Tarasova
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2019.02845

Transcriptional Changes on Blight Fruiting Body of Flammulina velutipes Caused by Two New Bacterial Pathogens
Cited by: 8
Author(s): Qing Wang, Mengpei Guo, Ruiping Xu, Jingcheng Zhang, Yinbing Bian, Yang Xiao
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2021.712843

Metagenomic Survey Reveals More Diverse and Abundant Antibiotic Resistance Genes in Municipal Wastewater Than Hospital Wastewater
Cited by: 6
Author(s): Dengwei Zhang, Ye Peng, Chak-Lun Chan, Hilda On, Hogan Kok-Fung Wai, Sandeep Singh Shekhawat, Akhilendra Bhushan Gupta, Alok Varshney, Rungtip Chuanchuen, Xudong Zhou, Yankai Xia, Suisha Liang, Keiji Fukuda, Krishna Mohan Medicherla, Hein Min Tun
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2021.695445

Effects of Dietary Energy Levels on Rumen Fermentation, Gastrointestinal Tract Histology, and Bacterial Community Diversity in Fattening Male Hu Lambs
Cited by: 12
Author(s): Qiye Wang, Yutong Zeng, Xiangfang Zeng, Xin Wang, Yancan Wang, Chunpeng Dai, Jianzhong Li, Pengfei Huang, Jing Huang, Tarique Hussain, Mingzhi Zhu, Huansheng Yang
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2021.636550

Bovine Pre-adipocyte Adipogenesis Is Regulated by bta-miR-150 Through mTOR Signaling
Cited by: 6
Author(s): Xingyi Chen, Sayed Haidar Abbas Raza, Xinhao Ma, Jiangfang Wang, Xiaohui Wang, Chengcheng Liang, Xinran Yang, Chugang Mei, Syed Muhammad Suhail, Zan Liu
Software Mentions: 2
Published: over 5 years ago

10.1016/j.omtn.2019.04.004

Long Noncoding RNA SBF2-AS1 Is Critical for Tumorigenesis of Early-Stage Lung Adenocarcinoma
Cited by: 47
Author(s): Rui Chen, Wenjia Xia, Siwei Wang, Yongming Xu, Zhongliang Ma, Weizhang Xu, Erbao Zhang, Jie Wang, Fang Tian, Quan'an Zhang, Gaochao Dong, William Chi shing Cho, C. Patrick, Giovanni Brandi, Simona Tavolari, Peter Ujházy, Giulio Metro, Helmut Popper, Rong Yin, Mantang Qiu, Lin Xu
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0035901

Neurogenomic Evidence for a Shared Mechanism of the Antidepressant Effects of Exercise and Chronic Fluoxetine in Mice
Cited by: 42
Author(s): Guo-Jen Huang, Eyal Ben-David, Agnès Tort Piella, Andrew Edwards, Jonathan Flint, Sagiv Shifman
Software Mentions: 2
Published: over 14 years ago

10.3389/fmolb.2021.687760

m6A-Related lncRNAs Are Potential Biomarkers for the Prognosis of Metastatic Skin Cutaneous Melanoma
Cited by: 16
Author(s): Suyang Huang, Shanshan Lyu, Zhe Gao, Weifeng Zha, Ping Wang, Yuxi Shan, Jianzhong He, Yang Li
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-57182-4

Metabolomic networks and pathways associated with feed efficiency and related-traits in Duroc and Landrace pigs
Cited by: 23
Author(s): Victor Adriano Okstoft Carmelo, Priyanka Banerjee, Wellison J. S. Diniz, Haja N. Kadarmideen
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0026801

The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44
Cited by: 104
Author(s): Alicia N. Massa, Kevin L. Childs, Haining Lin, Glenn J. Bryan, Giovanni Giuliano, C. Robin Buell
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0199434

Coexpression network and phenotypic analysis identify metabolic pathways associated with the effect of warming on grain yield components in wheat
Cited by: 17
Author(s): Christine Girousse, Jane Roche, Claire Guérin, Jacques Le Gouis, Sandrine Balzegue, Saïd Mouzeyar, Mohamed Fouad Bouzidi
Software Mentions: 2
Published: about 8 years ago

10.7554/eLife.54822

Mouse brain transcriptome responses to inhaled nanoparticulate matter differed by sex and APOE in Nrf2-Nfkb interactions
Cited by: 18
Author(s): Amin Haghani, Mafalda Cacciottolo, Kevin R. Doty, Carla D’Agostino, Max Thorwald, Nikoo Safi, Morgan E. Levine, Constantinos Sioutas, Terrence Town, Henry Jay Forman, Todd E. Morgan, Caleb E. Finch
Software Mentions: 2
Published: about 6 years ago

10.1016/j.omtn.2018.05.003

Differential Co-expression and Regulatory Network Analysis Uncover the Relapse Factor and Mechanism of T Cell Acute Leukemia
Cited by: 18
Author(s): Mei Luo, Qiong Zhang, Mengxuan Xia, Feifei Hu, Zhaowu Ma, Zehua Chen, An‐Yuan Guo
Software Mentions: 2
Published: about 8 years ago

10.3389/fmolb.2020.563922

Characteristic Analysis of Featured Genes Associated With Stemness Indices in Colorectal Cancer
Cited by: 7
Author(s): Yongqu Lu, Xin Zhou, Zhenzhen Liu, Wendong Wang, Fēi Li, Wei Fu
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0118466

Ancestry Dependent DNA Methylation and Influence of Maternal Nutrition
Cited by: 40
Author(s): Khyobeni Mozhui, Alicia K. Smith, Frances A. Tylavsky
Software Mentions: 2
Published: over 11 years ago

10.3389/fmolb.2021.676138

Establishment of Novel Prostate Cancer Risk Subtypes and A Twelve-Gene Prognostic Model
Cited by: 1
Author(s): Enchong Zhang, Fujisawa Shiori, Mo Zhang, Peng Wang, Jieqian He, Yuntian Ge, Yi Song, Liping Shan
Software Mentions: 2
Published: over 5 years ago

10.3390/molecules24061064

Metabolome and Transcriptome Sequencing Analysis Reveals Anthocyanin Metabolism in Pink Flowers of Anthocyanin-Rich Tea (Camellia sinensis)
Cited by: 49
Author(s): Dylan O’Neill Rothenberg, Haijun Yang, Meiban Chen, Wenting Zhang, Lingyun Zhang
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms21093288

Comparative Transcriptome Analysis Combining SMRT- and Illumina-Based RNA-Seq Identifies Potential Candidate Genes Involved in Betalain Biosynthesis in Pitaya Fruit
Cited by: 22
Author(s): Yanyan Wu, Juan Xu, Xuelei Han, Guo Qiao, Kun Yang, Wen Zhuang, Xiaopeng Wen
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2019.00454

Multi-Omic Analysis of the Microbiome and Metabolome in Healthy Subjects Reveals Microbiome-Dependent Relationships Between Diet and Metabolites
Cited by: 93
Author(s): Zheng-Zheng Tang, Guanhua Chen, Qilin Hong, Shi Huang, Holly Smith, Rachana Shah, Matthew Scholz, Jane F. Ferguson
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms21124316

Comparative Transcriptome Analysis of Two Contrasting Soybean Varieties in Response to Aluminum Toxicity
Cited by: 16
Author(s): Lijuan Zhao, Jingjing Cui, Yuanyuan Cai, Songnan Yang, Juge Liu, Wei Wang, Junyi Gai, Zhubing Hu, Yan Li
Software Mentions: 2
Published: about 6 years ago

10.3389/fmolb.2020.568954

Identifying Pathways and Networks Associated With the SARS-CoV-2 Cell Receptor ACE2 Based on Gene Expression Profiles in Normal and SARS-CoV-2-Infected Human Tissues
Cited by: 17
Author(s): Qiushi Feng, Lin Li, Xiaosheng Wang
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0248104

Repetitive in vivo manual loading of the spine elicits cellular responses in porcine annuli fibrosi
Cited by: 1
Author(s): John R. Matyas, Claudia Klein, Dragana Ponjevic, Neil A. Duncan, Gregory N. Kawchuk
Software Mentions: 2
Published: over 5 years ago

10.15252/msb.20209443

Proteomic patterns associated with response to breast cancer neoadjuvant treatment
Cited by: 31
Author(s): Anjana Shenoy, Nishanth Belugali Nataraj, Gili Perry, Fabricio Loayza‐Puch, Remco Nagel, I Marin, Nora Balint, Noa Bossel, A J Pavlovsky, Iris Barshack, Bella Kaufman, Reuven Agami, Maya Dadiani, Tamar Geiger
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-61016-z

Gene regulatory network analysis with drug sensitivity reveals synergistic effects of combinatory chemotherapy in gastric cancer
Cited by: 6
Author(s): Jeong Hoon Lee, Yu Rang Park, Min-A Jung, Sun Gyo Lim
Software Mentions: 2
Published: over 6 years ago

10.3389/fnmol.2021.623659

Targeted Quantification of Detergent-Insoluble RNA-Binding Proteins in Human Brain Reveals Stage and Disease Specific Co-aggregation in Alzheimer’s Disease
Cited by: 12
Author(s): Qi Guo, Eric B. Dammer, Maotian Zhou, Sean R. Kundinger, Marla Gearing, James J. Lah, Aĺlan I. Levey, Zhandong Liu, Nicholas T. Seyfried
Software Mentions: 2
Published: over 5 years ago

10.3389/fnmol.2018.00091

Profiling of Long Non-coding RNAs and mRNAs by RNA-Sequencing in the Hippocampi of Adult Mice Following Propofol Sedation
Cited by: 9
Author(s): Jun Fan, Quan Zhou, Yan Li, Xiuling Song, Jijie Hu, Zaisheng Qin, Jing Tang, Tao Tao
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-020-60231-y

Shared transcriptional responses to con- and heterospecific behavioral antagonists in a wild songbird
Cited by: 10
Author(s): Matthew I. M. Louder, Michael Lafayette, Amber A. Louder, Floria M. K. Uy, Christopher N. Balakrishnan, Ken Yasukawa, Márk E. Hauber
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-61162-4

Identification of the key genes and pathways involved in the tumorigenesis and prognosis of kidney renal clear cell carcinoma
Cited by: 36
Author(s): Hao Cui, Hong‐Wei Shan, Michael Z. Miao, Zhiguo Jiang, Yuanyuan Meng, Ran Chen, Longzhen Zhang, Yong Liu
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0243507

Using WGCNA (weighted gene co-expression network analysis) to identify the hub genes of skin hair follicle development in fetus stage of Inner Mongolia cashmere goat
Cited by: 10
Author(s): Zhihong Wu, Erhan Hai, Zhengyang Di, Rong Ma, Fangzheng Shang, Yu Wang, Min Wang, Lili Liang, Youjun Rong, Jianfeng Pan, Wenbin Wu, Rui Su, Zhiying Wang, Ruijun Wang, Yanjun Zhang, Jinquan Li
Software Mentions: 2
Published: over 5 years ago

10.3390/molecules22122228

Multi-Objective Optimization Algorithm to Discover Condition-Specific Modules in Multiple Networks
Cited by: 5
Author(s): Xiaoke Ma, Penggang Sun, Jun Zhao
Software Mentions: 2
Published: over 8 years ago

10.3390/ijms21145095

Transcriptomic Profiling of Young Cotyledons Response to Chilling Stress in Two Contrasting Cotton (Gossypium hirsutum L.) Genotypes at the Seedling Stage
Cited by: 21
Author(s): Gongmin Cheng, Longyan Zhang, Hantao Wang, Jianhua Lü, Hengling Wei, Shuxun Yu
Software Mentions: 2
Published: about 6 years ago

10.3389/fnins.2016.00396

Comparative Gene Expression Analysis of Two Mouse Models of Autism: Transcriptome Profiling of the BTBR and En2−/− Hippocampus
Cited by: 27
Author(s): Giovanni Provenzano, Zelia Corradi, Katia Monsorno, Tarcisio Fedrizzi, Laura Ricceri, María Luisa Scattoni, Yuri Bozzi
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0170458

Transcriptome-wide co-expression analysis identifies LRRC2 as a novel mediator of mitochondrial and cardiac function
Cited by: 10
Author(s): Chris McDermott-Roe, Marion Leleu, Glenn C. Rowe, Oleg Palygin, John D. Bukowy, Judy Kuo, Monika Rech, Steffie Hermans-Beijnsberger, S. Schaefer, Eleonora Adami, Esther E. Creemers, Matthias Heinig, Blanche Schroen, Zoltàn Arany, Enrico Petretto, Aron M. Geurts
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-020-61942-y

Co-abundance analysis reveals hidden players associated with high methane yield phenotype in sheep rumen microbiome
Cited by: 13
Author(s): Leila Ghanbari Maman, Fahimeh Palizban, Fereshteh Fallah Atanaki, Naser Elmi, Shohreh Ariaeenejad, Mohammad Reza Ghaffari, Kaveh Kavousi
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0253012

Investigation of lncRNA-mRNA co-expression network in ETV6-RUNX1-positive pediatric B-cell acute lymphoblastic leukemia
Cited by: 1
Author(s): Wei-Juan Yu, Weihua Wang, Xiumei Yu
Software Mentions: 2
Published: over 5 years ago

10.3389/fnins.2019.01357

Temporal Changes of Spinal Transcriptomic Profiles in Mice With Spinal Nerve Ligation
Cited by: 7
Author(s): Hong Yu, Haining Zhang, Yeru Chen, Yongjie Wang, Xiao Lin, Xiang-Yao Li, Gang Chen
Software Mentions: 2
Published: over 6 years ago

10.3389/fnins.2021.678548

Gene Expression Analysis in Three Posttraumatic Stress Disorder Cohorts Implicates Inflammation and Innate Immunity Pathways and Uncovers Shared Genetic Risk With Major Depressive Disorder
Cited by: 10
Author(s): Melanie E. Garrett, Xue Qin, Divya Mehta, Michelle F. Dennis, Christine E. Marx, Gerald A. Grant, VA Mid-Atlantic Mirecc Workgroup, Ptsd Initiative, Injury, Murray B. Stein, Nathan A. Kimbrel, Jean C. Beckham, Michael A. Hauser, Allison Ashley‐Koch
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-020-62853-8

Network-based metabolic characterization of renal cell carcinoma
Cited by: 48
Author(s): Nishtha Pandey, Vinay Lanke, P. K. Vinod
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-63326-8

Species specific gene expression dynamics during harmful algal blooms
Cited by: 8
Author(s): Gabriel Metegnier, Sauvann Paulino, Pierre Ramond, Raffaele Siano, Marc Sourisseau, Christophe Destombe, Mickaël Le Gac
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-63214-1

Microbial modulation of host body composition and plasma metabolic profile
Cited by: 13
Author(s): Md. Nazmul Huda, Jason H. Winnike, Jocelyn M. Crowell, Annalouise O’Connor, Brian J. Bennett
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-63440-7

Rhythms of Transcription in Field-Grown Sugarcane Are Highly Organ Specific
Cited by: 14
Author(s): Luíza Lane de Barros Dantas, Felipe Marcelo Almeida-Jesus, Natalia Oliveira de Lima, Cícero Alves-Lima, Milton Yutaka Nishiyama-Jr, Monalisa Sampaio Carneiro, Gláucia Mendes Souza, Carlos Takeshi Hotta
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2021.636934

Identification of Hub Genes and MicroRNAs Associated With Idiopathic Pulmonary Arterial Hypertension by Integrated Bioinformatics Analyses
Cited by: 8
Author(s): Xue Qiu, Junyu Lin, Bixiao Liang, Yanbing Chen, Guoqun Liu, Jing Zheng
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2019.01275

Comparative Transcriptome Analysis Reveals Key Pathways and Hub Genes in Rapeseed During the Early Stage of Plasmodiophora brassicae Infection
Cited by: 27
Author(s): Lixia Li, Ying Long, Hao Li, Xiaoming Wu
Software Mentions: 2
Published: over 6 years ago

10.3389/fonc.2021.624145

Human Cerebrospinal Fluid Modulates Pathways Promoting Glioblastoma Malignancy
Cited by: 9
Author(s): Anna Carrano, Natanael Zarco, Jordan Phillipps, Montserrat Lara-Velazquez, Paola Suárez‐Meade, Emily S. Norton, Kaisorn L. Chaichana, Alfredo Quiñones‐Hinojosa, Yan W. Asmann, Hugo Guerrero-Cázares
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms21228730

Network Analysis of Gut Microbiome and Metabolome to Discover Microbiota-Linked Biomarkers in Patients Affected by Non-Small Cell Lung Cancer
Cited by: 60
Author(s): Pamela Vernocchi, Tommaso Gili, Federica Conte, Federica Del Chierico, Giorgia Conta, Alfredo Miccheli, Andrea Botticelli, Paola Paci, Guido Caldarelli, Marianna Nuti, Paolo Marchetti, Lorenza Putignani
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13046-019-1318-5

A positive feedback between IDO1 metabolite and COL12A1 via MAPK pathway to promote gastric cancer metastasis
Cited by: 75
Author(s): Zhen Xiang, Jun Li, Shuzheng Song, Jiexuan Wang, Wei Cai, Wenjun Hu, Jun Ji, Zhenggang Zhu, Lu Zang, Ranlin Yan, Yingyan Yu
Software Mentions: 2
Published: about 7 years ago

10.3389/fonc.2020.564733

MYCT1 Inhibits the Adhesion and Migration of Laryngeal Cancer Cells Potentially Through Repressing Collagen VI
Cited by: 10
Author(s): Pengpeng Wang, Siyu Ding, Yuanyuan Sun, Yunhui Li, Wei‐Neng Fu
Software Mentions: 2
Published: over 5 years ago

10.3389/fonc.2020.01092

Identification of DGUOK-AS1 as a Prognostic Factor in Breast Cancer by Bioinformatics Analysis
Cited by: 11
Author(s): Yalun Li, Yiran Liang, Tingting Ma, Qifeng Yang
Software Mentions: 2
Published: about 6 years ago

10.7717/peerj.9000

Identification of key miRNAs in the progression of hepatocellular carcinoma using an integrated bioinformatics approach
Cited by: 3
Author(s): Qi Zheng, Xiaoyong Wei, Jun Rao, Cuncai Zhou
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.9633

Identification of 10 Hub genes related to the progression of colorectal cancer by co-expression analysis
Cited by: 7
Author(s): Jie Meng, Rui Su, Yun Liao, Yanyan Li, Ling Li
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.30649

FoxP2 isoforms delineate spatiotemporal transcriptional networks for vocal learning in the zebra finch
Cited by: 18
Author(s): Zachary Daniel Burkett, Nancy F. Day, Todd Kimball, Caitlin M. Aamodt, Jonathan B. Heston, Austin T. Hilliard, Xinshu Xiao, Stephanie A. White
Software Mentions: 2
Published: over 8 years ago

10.3390/genes7120109

Divergent Expression Patterns in Two Vernicia Species Revealed the Potential Role of the Hub Gene VmAP2/ERF036 in Resistance to Fusarium oxysporum in Vernicia montana
Cited by: 7
Author(s): Qiyan Zhang, Ming Gao, Liwen Wu, Yangdong Wang, Yicun Chen
Software Mentions: 2
Published: almost 10 years ago

10.1155/2019/7859121

Gene Expression Pattern and Regulatory Network of α-Toxin Treatment in Bombyx mori
Cited by: 0
Author(s): Tieshan Feng, Ping Lin, Jiao Gong, Chen Dong, Xi Yang, Quan Zhang, Tingcai Cheng
Software Mentions: 2
Published: over 7 years ago

10.3390/genes8120359

Transcriptional and Hormonal Regulation of Weeping Trait in Salix matsudana
Cited by: 12
Author(s): Juanjuan Liu, Yan‐Fei Zeng, Peiyao Yan, Caiyun He, Jianguo Zhang
Software Mentions: 2
Published: almost 9 years ago

10.3390/ijms19123881

Tissue-Specific Down-Regulation of the Long Non-Coding RNAs PCAT18 and LINC01133 in Gastric Cancer Development
Cited by: 34
Author(s): Kobra Foroughi, Mohammad Amini, Amir Atashi, Habibollah Mahmoodzadeh, Ute Hamann, Mehdi Manoochehri
Software Mentions: 2
Published: almost 8 years ago

10.3390/genes9020092

Identification of Key Pathways and Genes in the Dynamic Progression of HCC Based on WGCNA
Cited by: 115
Author(s): Yin Li, Zhihui Cai, Baoan Zhu, Chi Xu
Software Mentions: 2
Published: over 8 years ago

10.3390/genes9100478

An Improved Method for Prediction of Cancer Prognosis by Network Learning
Cited by: 32
Author(s): Min‐Seon Kim, Ilhwan Oh, Jaegyoon Ahn
Software Mentions: 2
Published: almost 8 years ago

10.3390/genes10020119

Co-Expression Network Analysis and Hub Gene Selection for High-Quality Fiber in Upland Cotton (Gossypium hirsutum) Using RNA Sequencing Analysis
Cited by: 27
Author(s): Xianyan Zou, Àiyīng Liú, Zhen Zhang, Qún Gě, Senmiao Fan, Wànkuí Gǒng, Jùnwén Lǐ, Jǔwǔ Gōng, Yùzhēn Shí, Bin Tian, Yanling Wang, Ruixian Liu, Kang Lei, Qi Zhang, Xiao Jiang, Yulong Feng, Shuya Zhang, Tingting Jia, Lipeng Zhang, Yǒulù Yuán, Hǎihóng Shāng
Software Mentions: 2
Published: over 7 years ago

10.3390/genes10030225

Gene Expression Networks Across Multiple Tissues Are Associated with Rates of Molecular Evolution in Wild House Mice
Cited by: 13
Author(s): Katya L. Mack, Megan Phifer‐Rixey, Bettina Harr, Michael W. Nachman
Software Mentions: 2
Published: over 7 years ago

10.3390/genes10060408

Analysis of miRNAs Targeted Storage Regulatory Genes during Soybean Seed Development Based on Transcriptome Sequencing
Cited by: 13
Author(s): Jingquan Yu, Zhanguo Zhang, Shi-Yu Huang, Xue Han, Xinyu Wang, Wenjing Pan, Hui Qin, Hongbo Qi, Zhan Yin, Kun Qu, Zexin Zhang, Shanshan Liu, Hongwei Jiang, Chunyan Liu, Zhenbang Hu, Xiaoxia Wu, Qingshan Chen, Dawei Xin, Zhaoming Qi
Software Mentions: 2
Published: over 7 years ago

10.3389/fgene.2020.00574

Long Non-coding RNA and mRNA Profile of Liver Tissue During Four Developmental Stages in the Chicken
Cited by: 10
Author(s): Chunyou Ning, Tianyuan Ma, Silu Hu, Zhongxian Xu, Pu Zhang, Xiaoling Zhao, Yan Wang, Huadong Yin, Yaodong Hu, Xiaolan Fan, Bo Zeng, Mingyao Yang, Dapeng Yang, Qingyong Ni, Yan Li, Mingwang Zhang, Huailiang Xu, Yongfang Yao, Qing Zhu, Diyan Li
Software Mentions: 2
Published: about 6 years ago

10.1038/s41419-021-03499-w

Establishment of a novel mesenchymal stem cell-based regimen for chronic myeloid leukemia differentiation therapy
Cited by: 5
Author(s): Shiman Zuo, Lijuan Sun, Yuxin Wang, Bing Chen, Jingyue Wang, Xin Ge, Yan Lu, Nanfei Yang, Pingping Shen
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2020.00641

Neutrophils, Crucial, or Harmful Immune Cells Involved in Coronavirus Infection: A Bioinformatics Study
Cited by: 68
Author(s): Nima Hemmat, Afshin Derakhshani, Hossein Bannazadeh Baghi, Nicola Silvestris, Behzad Baradaran, Simona De Summa
Software Mentions: 2
Published: over 6 years ago

10.1186/s13041-021-00829-z

RNA-seq co-expression network analysis reveals anxiolytic behavior of mice with Efnb2 knockout in parvalbumin+ neurons
Cited by: 1
Author(s): Ying Sun, Le Ma, Jianhua Chen, Weidi Wang, Shi-Yu Peng, Ying Cheng, Yu Zhang, Jinghong Chen, Peijun Ju
Software Mentions: 2
Published: about 5 years ago

10.3390/genes10100747

Common Nevus and Skin Cutaneous Melanoma: Prognostic Genes Identified by Gene Co-Expression Network Analysis
Cited by: 16
Author(s): Lingge Yang, Yu Xu, Yan Yan, Peng Luo, Shiqi Chen, Biqiang Zheng, Wangjun Yan, Yong Chen, Chunmeng Wang
Software Mentions: 2
Published: almost 7 years ago

10.3389/fgene.2020.00153

Identification of 13 Key Genes Correlated With Progression and Prognosis in Hepatocellular Carcinoma by Weighted Gene Co-expression Network Analysis
Cited by: 33
Author(s): Yang Gu, Jun Li, Deliang Guo, Baiyang Chen, Pengpeng Liu, Yusha Xiao, Kuo‐Chung Yang, Zhisu Liu, Quanyan Liu
Software Mentions: 2
Published: over 6 years ago

10.3390/genes11010106

Hormonal and Molecular Regulation of Phallus Differentiation in a Marsupial Tammar Wallaby
Cited by: 0
Author(s): Yu Chen, Marilyn B. Renfree
Software Mentions: 2
Published: over 6 years ago

10.15252/msb.20188202

Identification of an oncogenic network with prognostic and therapeutic value in prostate cancer
Cited by: 23
Author(s): Fiorella Magani, Eric R. Bray, María Julia Martínez, Ning Zhao, Valeria A. Copello, Laine M. Heidman, Stephanie Peacock, David J. Wiley, Gennaro D’Urso, Kerry L. Burnstein
Software Mentions: 2
Published: about 8 years ago

10.7717/peerj.12143

Construction of competing endogenous RNA interaction network as prognostic markers in metastatic melanoma
Cited by: 1
Author(s): Zan He, Zijuan Xin, Yongfei Peng, Hua Zhao, Xiangdong Fang
Software Mentions: 2
Published: almost 5 years ago

10.3390/jof6030108

Modeling Approaches Reveal New Regulatory Networks in Aspergillus fumigatus Metabolism
Cited by: 2
Author(s): Enzo Acerbi, Marcela Hortová-Kohoutková, Tsokyi Choera, Nancy P. Keller, Jan Frič, Fabio Stella, Luigina Romani, Teresa Zelante
Software Mentions: 1
Published: about 6 years ago

10.3389/fonc.2020.01201

Editorial: Using Cancer ‘Omics’ to Understand Cancer
Cited by: 4
Author(s): Barbara K. Dunn, Daoud Meerzaman
Software Mentions: 1
Published: about 6 years ago

10.3390/jof7040270

Identifying Conserved Generic Aspergillus spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics
Cited by: 4
Author(s): Tim J. H. Baltussen, Jordy P. M. Coolen, Paul E. Verweij, Jan Dijksterhuis, Willem J. G. Melchers
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2019.00037

Co-expression Network Analysis Identifies Four Hub Genes Associated With Prognosis in Soft Tissue Sarcoma
Cited by: 29
Author(s): Zhifeng Zhu, Zheng Jin, Yuyou Deng, Lai Wei, Xiaowei Yuan, Mei Zhang, Dahui Sun
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.10385

The m6A reader protein YTHDC2 is a potential biomarker and associated with immune infiltration in head and neck squamous cell carcinoma
Cited by: 27
Author(s): Yang Li, Ji-Na Zheng, En-Hao Wang, Chan-Juan Gong, Keng-Fu Lan, Xiaobo Ding
Software Mentions: 1
Published: almost 6 years ago

10.1155/2020/9827349

The Effect of Inflammation on the Formation of Thyroid Nodules
Cited by: 4
Author(s): Zexin Li, Yiteng Huang, Xiang Cheng, Chiju Wei, Peixuan Yang, Weilai Xu
Software Mentions: 1
Published: about 6 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

10.1053/j.gastro.2021.01.221

Mucosal Genomics Implicate Lymphocyte Activation and Lipid Metabolism in Refractory Environmental Enteric Dysfunction
Cited by: 34
Author(s): Yael Haberman, Najeeha Talat Iqbal, Sudhir Ghandikota, Indika Mallawaarachchi, Tzipi Braun, Phillip Dexheimer, Najeeb Rahman, Rotem Hadar, Kamran Sadiq, Zubair Ahmad, Romana Idress, Junaid Iqbal, Sheraz Ahmed, Aneeta Hotwani, Fayyaz Umrani, Lubaina Ehsan, Greg Medlock, Sana Syed, Chris Moskaluk, Z. Jennie, Anil G. Jegga, Sean R. Moore, Syed Asad Ali, Lee A. Denson
Software Mentions: 1
Published: over 5 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/s13046-018-1002-1

Classification of triple-negative breast cancers based on Immunogenomic profiling
Cited by: 274
Author(s): Hanlin Yin, Zhongshan Jiang, Chen Cai, Xiaosheng Wang
Software Mentions: 1
Published: almost 8 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

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479