10.1038/s41598-020-70578-x

A proteogenomic profile of early lung adenocarcinomas by protein co-expression network and genomic alteration analysis
Cited by: 3
Author(s): Toshihide Nishimura, Hiroki Nakamura, Kien Thiam Tan, De-Wei Zhuo, Kiyonaga Fujii, Hirotaka Koizumi, Saeko Naruki, Masayuki Takagi, Naoki Furuya, Yasufumi Kato, Shu‐Jen Chen, Harubumi Kato, Hisashi Saji
Software Mentions: 1
Published: about 6 years ago

10.1007/s11306-017-1263-2

Estimation of metabolite networks with regard to a specific covariable: applications to plant and human data
Cited by: 9
Author(s): Georgios Bartzis, Joris Deelen, Júlio Maia, Wilco Ligterink, Henk W. M. Hilhorst, Jeanine J. Houwing-Duistermaat, Fred van Eeuwijk, Hae‐Won Uh
Software Mentions: 1
Published: about 9 years ago

10.1007/s11306-019-1511-8

Metabolite and transcript profiling of Guinea grass (Panicum maximum Jacq) response to elevated [CO2] and temperature
Cited by: 21
Author(s): Jessica M. Wedow, Craig R. Yendrek, Tathyana Rachel Palo Mello, Silvana Creste, Carlos A. Martínez, Elizabeth A. Ainsworth
Software Mentions: 1
Published: over 7 years ago

10.1007/s11306-020-01733-8

Evaluation of the use of untargeted metabolomics in the safety assessment of genetically modified crops
Cited by: 17
Author(s): Mohamed Bedair, Kevin C. Glenn
Software Mentions: 1
Published: about 6 years ago

10.3389/fgene.2019.01258

Candidate Regulators of Dyslipidemia in Chromosome 1 Substitution Lines Using Liver Co-Expression Profiling Analysis
Cited by: 1
Author(s): Fuyi Xu, Maochun Wang, Shixian Hu, Yuxun Zhou, John Collyer, Kai Li, Hongyan Xu, Junhua Xiao
Software Mentions: 1
Published: almost 7 years ago

10.3389/fgene.2019.01323

An Integrated Model Based on a Six-Gene Signature Predicts Overall Survival in Patients With Hepatocellular Carcinoma
Cited by: 40
Author(s): Wenli Li, Jianjun Lu, Zhu Ma, Jia-feng Zhao, Jun Li
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12885-021-08066-2

A novel tp53-associated nomogram to predict the overall survival in patients with pancreatic cancer
Cited by: 15
Author(s): Xun Liu, Bobo Chen, Jiahui Chen, Shung Shung Sun
Software Mentions: 1
Published: over 5 years ago

10.1002/jcla.23680

Constructing a 10‐core genes panel for diagnosis of pediatric sepsis
Cited by: 4
Author(s): Xiaojie Zhou, Yumin Wang, Jie Chen, Jingye Pan
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13072-019-0257-x

Retinal-input-induced epigenetic dynamics in the developing mouse dorsal lateral geniculate nucleus
Cited by: 4
Author(s): Jianlin He, Xiguang Xu, Aboozar Monavarfeshani, Sharmi Banerjee, Michael A. Fox, Hehuang Xie
Software Mentions: 1
Published: over 7 years ago

10.3389/fgene.2020.597888

Identifying Biomarkers to Predict the Progression and Prognosis of Breast Cancer by Weighted Gene Co-expression Network Analysis
Cited by: 6
Author(s): Gengsheng Shi, Zhenru Shen, Yi Liu, Wenqin Yin
Software Mentions: 1
Published: almost 6 years ago

10.3390/jcm8101719

Reformulating Pro-Oxidant Microglia in Neurodegeneration
Cited by: 45
Author(s): Juan García-Revilla, Isabel María Alonso-Bellido, Miguel Ángel Burguillos, Antonio J. Herrera, Ana M. Espinosa-Oliva, Rocío Ruiz, Luis Cruz-Hernández, Irene García-Domínguez, María Angustias Roca-Ceballos, Marti Santiago, José A. Rodríguez‐Gómez, Manuel Sarmiento Soto, Rocío M. de Pablos, José L. Venero
Software Mentions: 1
Published: about 7 years ago

10.3390/metabo10120511

The Metabolomics of Childhood Atopic Diseases: A Comprehensive Pathway-Specific Review
Cited by: 17
Author(s): M.S. Schjødt, Gözde Gürdeniz, Bo Chawes
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pgen.1004006

Multi-tissue Analysis of Co-expression Networks by Higher-Order Generalized Singular Value Decomposition Identifies Functionally Coherent Transcriptional Modules
Cited by: 53
Author(s): Xiaolin Xiao, Aida Moreno‐Moral, Maxime Rotival, Leonardo Bottolo, Enrico Petretto
Software Mentions: 1
Published: almost 13 years ago

10.1038/s41598-021-98381-2

Glycolysis-related gene expression profiling serves as a novel prognosis risk predictor for human hepatocellular carcinoma
Cited by: 11
Author(s): Lingyu Zhang, Li Yu, Yibei Dai, Danhua Wang, Xuchu Wang, Ying Cao, Weiwei Liu, Zhihua Tao
Software Mentions: 1
Published: about 5 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

10.3390/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

10.1038/s41398-018-0234-3

Identification and replication of RNA-Seq gene network modules associated with depression severity
Cited by: 33
Author(s): Trang T. Le, Jonathan Savitz, Hideo Suzuki, Masaya Misaki, T. Kent Teague, Bill C. White, Julie H. Marino, Graham B. Wiley, Patrick M. Gaffney, Wayne C. Drevets, Brett A. McKinney, Jerzy Bodurka
Software Mentions: 1
Published: about 8 years ago

10.3390/metabo9080157

Bronchoalveolar Lavage Fluid from COPD Patients Reveals More Compounds Associated with Disease than Matched Plasma
Cited by: 27
Author(s): Eitan Halper-Stromberg, Lucas A. Gillenwater, Charmion Cruickshank‐Quinn, Wanda K. O’Neal, Nichole Reisdorph, Irina Petrache, Yonghua Zhuang, Wassim W. Labaki, Jeffrey L. Curtis, James M. Wells, Stephen I. Rennard, Katherine Pratte, Prescott G. Woodruff, Kathleen A. Stringer, Katerina Kechris, Russell P. Bowler
Software Mentions: 1
Published: over 7 years ago

10.3389/fgene.2016.00218

A Systems Approach Implicates a Brain Mitochondrial Oxidative Homeostasis Co-expression Network in Genetic Vulnerability to Alcohol Withdrawal
Cited by: 5
Author(s): Nicole A.R. Walter, De Aunne L. Denmark, Laura B. Kozell, Kari J. Buck
Software Mentions: 1
Published: almost 10 years ago

10.3390/metabo11030161

Metabolomic Profiling Reveals Sex Specific Associations with Chronic Obstructive Pulmonary Disease and Emphysema
Cited by: 14
Author(s): Lucas A. Gillenwater, Katerina Kechris, Katherine Pratte, Nichole Reisdorph, Irina Petrache, Wassim W. Labaki, Wanda K. O’Neal, Jerry A. Krishnan, Victor E. Ortega, Dawn L. DeMeo, Russell P. Bowler
Software Mentions: 1
Published: over 5 years ago

10.4317/medoral.24385

Whole exome sequencing and system biology analysis support the "two-hit" mechanism in the onset of Ameloblastoma
Cited by: 4
Author(s): Yueqi Shi, Mengyu Li, Yinglan Yu, Yuqiong Zhou, Shaoyi Wang
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pgen.1007879

An interaction-based model for neuropsychiatric features of copy-number variants
Cited by: 38
Author(s): Matthew Jensen, Santhosh Girirajan
Software Mentions: 1
Published: almost 8 years ago

10.18632/oncotarget.19490

Using molecular functional networks to manifest connections between obesity and obesity-related diseases
Cited by: 6
Author(s): Jialiang Yang, Jing Qiu, Kejing Wang, Lijuan Zhu, Jingjing Fan, De-Yin Zheng, Xiaodi Meng, Jiasheng Yang, Lihong Peng, Yu Fu, Dahan Zhang, Shouneng Peng, Haiyun Huang, Yi Zhang
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-14-365

Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma
Cited by: 22
Author(s): Chao Wu, Jun Zhu, Xuegong Zhang
Software Mentions: 1
Published: almost 13 years ago

10.1038/s41598-020-75039-z

Crucial transcripts predict response to initial immunoglobulin treatment in acute Kawasaki disease
Cited by: 9
Author(s): Zhimin Geng, Jingjing Liu, Jian Hu, Ying Wang, Yijing Tao, Fei Zheng, Yujia Wang, Songling Fu, Wei Wang, Chunhong Xie, Yiying Zhang, Fangqi Gong
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-75511-w

Dynamic transcriptional response of Saccharomyces cerevisiae cells to copper
Cited by: 7
Author(s): Sebnem Oc, Serpil Eraslan, Betül Kırdar
Software Mentions: 1
Published: about 6 years ago

10.3390/plants10081699

Genome-Wide Identification and Functional Investigation of 1-Aminocyclopropane-1-carboxylic Acid Oxidase (ACO) Genes in Cotton
Cited by: 3
Author(s): Hengling Wei, Yujun Xue, Pengyun Chen, Pengbo Hao, Fei Wei, Lu Sun, Yonglin Yang
Software Mentions: 1
Published: about 5 years ago

10.3389/fgene.2021.685341

Identification of Regulatory Functions of LncRNAs Associated With T. circumcincta Infection in Adult Sheep
Cited by: 3
Author(s): P. K. Chitneedi, Rosemarie Weikard, Juan José Arranz, María Martínez‐Valladares, Christa Küehn, Beatriz Gutiérrez-Gil
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2021.650102

Identification of a MicroRNA Signature Associated With Lymph Node Metastasis in Endometrial Endometrioid Cancer
Cited by: 3
Author(s): Kaiyou Fu, Yanrui Li, Junxian Song, Weixiong Cai, Wei Wu, Xiaohang Ye, Jian Xu
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

10.1038/s41598-020-75945-2

Weighted miRNA co-expression networks analysis identifies circulating miRNA predicting overall survival in hepatocellular carcinoma patients
Cited by: 14
Author(s): Devis Pascut, Muhammad Yogi Pratama, F Gilardi, Mauro Giuffré, Lory Saveria Crocè, Claudio Tiribelli
Software Mentions: 1
Published: almost 6 years ago

10.1097/MD.0000000000009738

Identification of gene expression models for laryngeal squamous cell carcinoma using co-expression network analysis
Cited by: 9
Author(s): Chao Yang, Shufang Wang, Xiangli Yang, Lin Wang, Lin Niu, Jixiang Liu
Software Mentions: 1
Published: over 8 years ago

10.1038/s41398-018-0325-1

Dopamine perturbation of gene co-expression networks reveals differential response in schizophrenia for translational machinery
Cited by: 7
Author(s): Mark Z. Kos, Jubao Duan, Alan R. Sanders, Lucy Blondell, Eugene Drigalenko, Melanie A. Carless, Pablo V. Gejman, Harald H.H. Göring, Mgs
Software Mentions: 1
Published: almost 8 years ago

10.1186/1756-8935-6-28

Epigenetic coordination of signaling pathways during the epithelial-mesenchymal transition
Cited by: 42
Author(s): Marcin Cieślik, Stephen A. Hoang, Natalya Baranova, Sanjay V. Chodaparambil, Manish Kumar, David F. Allison, Xiaojiang Xu, J. Jacob Wamsley, Lisa G. Gray, David R. Jones, Marty W. Mayo, Stefan Bekiranov
Software Mentions: 1
Published: about 13 years ago

10.1038/s41598-020-76011-7

Singular manifolds of proteomic drivers to model the evolution of inflammatory bowel disease status
Cited by: 2
Author(s): Ian Morilla, Thibaut Léger, Assiya Marah, Isabelle Pic, Hatem Zaag, Éric Ogier–Denis
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-76117-y

Analysis of transcriptional modules during human fibroblast ageing
Cited by: 9
Author(s): Yaelim Lee, G. V. Shivashankar
Software Mentions: 1
Published: almost 6 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

10.1371/journal.pgen.1008155

Enhancing face validity of mouse models of Alzheimer’s disease with natural genetic variation
Cited by: 58
Author(s): Kristen D. Onos, Asli Uyar, Kelly J. Keezer, Harriet M. Jackson, Christoph Preuß, Casey Acklin, Rita O’Rourke, Rebecca A. Buchanan, Travis Cossette, Stacey J. Sukoff Rizzo, Ileana Soto, Gregory W. Carter, Gareth R. Howell
Software Mentions: 1
Published: over 7 years ago

10.3389/fgene.2019.00964

Transcriptomic and Functional Analyses of Phenotypic Plasticity in a Higher Termite, Macrotermes barneyi Light
Cited by: 10
Author(s): Pengdong Sun, Ganghua Li, Jianbo Jian, Long Liu, Junhui Chen, Shuxin Yu, Huan Xu, Chaoliang Lei, Xuguo Zhou, Qiuying Huang
Software Mentions: 1
Published: about 7 years ago

10.26508/lsa.202101091

Serum proteomics reveals disorder of lipoprotein metabolism in sepsis
Cited by: 2
Author(s): Xi Liang, Tianzhou Wu, Qi Chen, Jing Jiang, Yongpo Jiang, Yiwen Ruan, Huaping Zhang, Sheng Zhang, Zhang Chao, Peng Chen, Yuhang Lv, Jiaojiao Xin, Dongyan Shi, Xin Chen, Li Jun, Yinghe Xu
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-76750-7

Transcriptome profiling and weighted gene co-expression network analysis of early floral development in Aquilegia coerulea
Cited by: 11
Author(s): Ya Min, Elena M. Kramer
Software Mentions: 1
Published: almost 6 years ago

10.1155/2021/6651009

Candidate Genes Identified in Systemic Sclerosis-Related Pulmonary Arterial Hypertension Were Associated with Immunity, Inflammation, and Cytokines
Cited by: 5
Author(s): Zhixiao Xu, Jiaxing Ruan, Lingyun Pan, Chengshui Chen
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1002596

The Transcription Factor Ultraspiracle Influences Honey Bee Social Behavior and Behavior-Related Gene Expression
Cited by: 74
Author(s): Seth A. Ament, Ying Wang, Chieh Chun Chen, Charles Blatti, Feng Hong, Zhengzheng S. Liang, Nicolas Nègre, Kevin P. White, Sandra L. Rodriguez-Zas, Craig A. Mizzen, Saurabh Sinha, Sheng Zhong, Gene E. Robinson
Software Mentions: 1
Published: over 14 years ago

10.3389/fgene.2015.00301

Moving from capstones toward cornerstones: successes and challenges in applying systems biology to identify mechanisms of autism spectrum disorders
Cited by: 14
Author(s): Nathan Kopp, Sharlee Climer, Joseph D. Dougherty
Software Mentions: 1
Published: about 11 years ago

10.3389/fgene.2015.00255

Potential role of lncRNA cyp2c91–protein interactions on diseases of the immune system
Cited by: 17
Author(s): Prashanth Suravajhala, Lisette J. A. Kogelman, Gianluca Mazzoni, Haja N. Kadarmideen
Software Mentions: 1
Published: over 11 years ago

10.1155/2020/3946913

Metabolic Modulation and Potential Biomarkers of the Prognosis Identification for Severe Aortic Stenosis after TAVR by a Metabolomics Study
Cited by: 6
Author(s): Yanbiao Liao, Chang Liu, Tingting Xiong, Mingyue Zhao, Wen Zheng, Yuan Feng, Yijian Li, Yuanweixiang Ou, Zhengang Zhang, Yong Peng, Jiafu Wei, Qiao Li, Wei Meng, Xiaojing Liu, Mao Chen
Software Mentions: 1
Published: about 6 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

10.1093/jxb/eraa206

Low temperature modulates natural peel degreening in lemon fruit independently of endogenous ethylene
Cited by: 24
Author(s): Oscar W. Mitalo, Takumi Otsuki, Rui Okada, Saeka Obitsu, Kanae Masuda, Yuko Hojo, Takakazu Matsuura, Izumi C. Mori, Daigo Abe, William Olubero Asiche, Takashi Akagi, Yasutaka Kubo, Koichiro Ushijima
Software Mentions: 1
Published: over 6 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

10.3390/ani11061745

Gene Expression Profile and Co-Expression Network of Pearl Gentian Grouper under Cold Stress by Integrating Illumina and PacBio Sequences
Cited by: 10
Author(s): Ben‐Ben Miao, Su‐Fang Niu, Renxie Wu, Zhen‐Bang Liang, Tang Baogui, Yun Zhai, Xue-Qi Xu
Software Mentions: 1
Published: over 5 years ago

10.3390/ani11020314

Lactation Associated Genes Revealed in Holstein Dairy Cows by Weighted Gene Co-Expression Network Analysis (WGCNA)
Cited by: 8
Author(s): Yongliang Fan, Abdelaziz Adam Idriss Arbab, Huimin Zhang, Yi Yang, Mudasir Nazar, Ziyin Han, Zhangping Yang
Software Mentions: 1
Published: almost 6 years ago

10.18632/oncotarget.22181

Identification of differentially expressed genes, lncRNAs and miRNAs which are associated with tumor malignant phenotypes in hepatoblastoma patients
Cited by: 16
Author(s): Sida Liu, Fujing Xie, Xiaohong Xiang, Sinan Liu, Shunbin Dong, Kai Qu, Ting Lin
Software Mentions: 1
Published: almost 9 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

10.1002/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

10.1371/journal.ppat.1003196

Modeling Host Genetic Regulation of Influenza Pathogenesis in the Collaborative Cross
Cited by: 179
Author(s): Martin T. Ferris, David L. Aylor, Daniel Bottomly, Alan C. Whitmore, Lauri Aicher, Timothy A. Bell, Birgit Bradel-Tretheway, Janine T. Bryan, Ryan J. Buus, Lisa E. Gralinski, Bart L. Haagmans, Leonard McMillan, Darla R. Miller, Elizabeth Rosenzweig, William Valdar, Jeremy Wang, Gary A. Churchill, David W. Threadgill, Shannon K. McWeeney, Michael G. Katze, Fernando Pardo-Manuel de Villena, Ralph S. Baric, Mark T. Heise
Software Mentions: 1
Published: over 13 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

10.1038/s41598-020-75217-z

Quantitative comparison of the biomass-degrading enzyme repertoires of five filamentous fungi
Cited by: 46
Author(s): Magnus Ø. Arntzen, Oskar Bengtsson, Anikó Várnai, Francesco Delogu, Geir Mathiesen, Vincent G. H. Eijsink
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-019-6035-0

MiR-190a potentially ameliorates postoperative cognitive dysfunction by regulating Tiam1
Cited by: 18
Author(s): Qiang Liu, Aisheng Hou, Yongyi Zhang, Ying Guo, Jingjing Li, Yinghao Yao, Kaimeng Niu, Hao Li, Yunlong Ma, Jiangbei Cao
Software Mentions: 1
Published: about 7 years ago

10.1186/s12859-017-1590-3

Preservation affinity in consensus modules among stages of HIV-1 progression
Cited by: 14
Author(s): Sk Md Mosaddek Hossain, Sumanta Ray, Anirban Mukhopadhyay
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-019-5978-5

Long non-coding RNAs and their potential functions in Ligon-lintless-1 mutant cotton during fiber development
Cited by: 16
Author(s): Haron Salih, Wenfang Gong, Shoupu He, Xia Wang, Magwanga Richard Odongo, Xinying Du
Software Mentions: 1
Published: about 7 years ago

10.1186/s12859-016-1319-8

SABRE: a method for assessing the stability of gene modules in complex tissues and subject populations
Cited by: 14
Author(s): Casey P. Shannon, Virginia Chen, Mandeep Takhar, Zsuzsanna Hollander, Robert Balshaw, Bruce M. McManus, Scott J. Tebbutt, Don D. Sin, Raymond T. Ng
Software Mentions: 1
Published: almost 10 years ago

10.2217/epi-2016-0017

How to make DNA methylome wide association studies more powerful
Cited by: 27
Author(s): Xinyi Lin, Sheila J. Barton, Joanna D. Holbrook
Software Mentions: 1
Published: about 10 years ago

10.3389/fgene.2020.555540

Theoretical and in silico Analyses Reveal MYC as a Dynamic Network Biomarker in Colon and Rectal Cancer
Cited by: 3
Author(s): Yanqiu Tong, Yang Song, Cathy H. Xia, Shixiong Deng
Software Mentions: 1
Published: about 6 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

10.3389/fgene.2018.00349

Prioritized High-Confidence Risk Genes for Intellectual Disability Reveal Molecular Convergence During Brain Development
Cited by: 10
Author(s): Zhenwei Liu, Na Zhang, Yu Zhang, Yaoqiang Du, Tao Zhang, Zhongshan Li, Jinyu Wu, Xiaobing Wang
Software Mentions: 1
Published: about 8 years ago

10.3389/fgene.2021.656637

Recovering Spatially-Varying Cell-Specific Gene Co-expression Networks for Single-Cell Spatial Expression Data
Cited by: 0
Author(s): Jianping Yu, Xiangyu Luo
Software Mentions: 1
Published: over 5 years ago

10.7150/thno.48064

ROS production and mitochondrial dysfunction driven by PU.1-regulated NOX4-p22^phox activation in Aβ-induced retinal pigment epithelial cell injury
Cited by: 18
Author(s): Junran Sun, Jieqiong Chen, Tong Li, Peng Huang, Jie Li, Mengxi Shen, Min Gao, Yang Sun, Jian Liang, Xiaomeng Li, Yimin Wang, Yushu Xiao, Xiang Shi, Yifan Hu, Jing Feng, Huixun Jia, Te Liu, Xiaodong Sun
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-015-1238-5

Gene coexpression networks reveal key drivers of phenotypic divergence in porcine muscle
Cited by: 10
Author(s): Xiao Ling Zhao, Zhaoyang Liu, Qingxin Liu
Software Mentions: 1
Published: over 11 years ago

10.1186/s12859-018-2433-6

A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids
Cited by: 41
Author(s): Gualter Silva Pereira, Antônio Augusto Franco Garcia, Gabriel Rodrigues Alves Margarido
Software Mentions: 1
Published: almost 8 years ago

10.1002/cam4.3369

Microarray profiling of differentially expressed lncRNAs and mRNAs in lung adenocarcinomas and bioinformatics analysis
Cited by: 12
Author(s): Fei He, Liping Huang, Qiuping Xu, Weimin Xiong, Shuang Liu, Huimin Yang, Wenzhou Lu, Rendong Xiao, Zhijian Hu, Lin Cai
Software Mentions: 1
Published: about 6 years ago

10.1038/s41398-019-0492-8

Postmortem transcriptional profiling reveals widespread increase in inflammation in schizophrenia: a comparison of prefrontal cortex, striatum, and hippocampus among matched tetrads of controls with subjects diagnosed with schizophrenia, bipolar or major depressive disorder
Cited by: 107
Author(s): Thomas A. Lanz, Veronica Reinhart, Mark J. Sheehan, Stacey J. Sukoff Rizzo, Susan E. Bove, Larry C. James, Dmitri Volfson, David A. Lewis, Robin J. Kleiman
Software Mentions: 1
Published: over 7 years ago

10.1186/s12935-021-01880-5

Silencing SHMT2 inhibits the progression of tongue squamous cell carcinoma through cell cycle regulation
Cited by: 12
Author(s): Yan Liao, Fang Wang, Yadong Zhang, Hao Cai, Song Fan, Jinsong Hou
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1004402

Mosaic Epigenetic Dysregulation of Ectodermal Cells in Autism Spectrum Disorder
Cited by: 90
Author(s): Esther R. Berko, Masako Suzuki, Faygel Beren, Christophe Lemetre, Christine M. Alaimo, R. Brent Calder, Karen Ballaban‐Gil, Batya Gounder, Kaylee Kampf, Jill Kirschen, Shahina Maqbool, Zeineen Momin, David M. Reynolds, Natalie Russo, Lisa H. Shulman, Edyta Stasiek, Jessica N. Tozour, Maria Valicenti-McDermott, Shenglong Wang, Brett S. Abrahams, Joseph Hargitai, Dov Inbar, Zhengdong Zhang, Joseph D. Buxbaum, Sophie Molholm, John J. Foxe, Robert W. Marion, Adam Auton, John M. Greally
Software Mentions: 1
Published: over 12 years ago

10.3389/fgene.2021.610087

Stratification of Estrogen Receptor-Negative Breast Cancer Patients by Integrating the Somatic Mutations and Transcriptomic Data
Cited by: 2
Author(s): Jie Hou, Xiufen Ye, Yixing Wang, Chuanlong Li
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-81509-9

Protein co-expression networks identified from HOT lesions of ER+HER2–Ki-67high luminal breast carcinomas
Cited by: 3
Author(s): Kimito Yamada, Toshihide Nishimura, Midori Wakiya, Eiichi Satoh, Tetsuya Fukuda, Keigo Amaya, Yoshio Bando, Hiroshi Honda, Takashi Ishikawa
Software Mentions: 1
Published: almost 6 years ago

10.3389/fgene.2021.698598

Integrative Identification of Crucial Genes Associated With Plant Hormone-Mediated Bud Dormancy in Prunus mume
Cited by: 6
Author(s): Ping Li, Tangchun Zheng, Zhiyong Zhang, Weichao Liu, Like Qiu, Jia Wang, Tangren Cheng, Qixiang Zhang
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2020.596174

Identification of Key Modules and Hub Genes of Annulus Fibrosus in Intervertebral Disc Degeneration
Cited by: 2
Author(s): Hantao Wang, Liu Wen-hui, Bo Yu, Xiaosheng Yu, Bin Chen
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-021-81303-7

Weighted gene co-expression network analysis identifies molecular pathways and hub genes involved in broiler White Striping and Wooden Breast myopathies
Cited by: 19
Author(s): Martina Bordini, Martina Zappaterra, Francesca Soglia, Massimiliano Petracci, Roberta Davoli
Software Mentions: 1
Published: almost 6 years ago

10.1007/s13238-016-0247-8

Coupled electrophysiological recording and single cell transcriptome analyses revealed molecular mechanisms underlying neuronal maturation
Cited by: 34
Author(s): Xiaoying Chen, Kunshan Zhang, Libing Zhou, Xinpei Gao, Junbang Wang, Yinan Yao, Fei He, Yuan Luo, Yongchun Yu, Siguang Li, Liming Cheng, Yi Sun
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1004550

Dysfunction of the CNS-Heart Axis in Mouse Models of Huntington's Disease
Cited by: 75
Author(s): Michał Mielcarek, Linda Inuabasi, Marie K. Bondulich, Thomas Müller, Georgina F Osborne, Sophie A. Franklin, Donna Smith, Andreas Neueder, Jim Rosinski, Ivan Rattray, Andrea Protti, Gillian P. Bates
Software Mentions: 1
Published: about 12 years ago

10.1007/s13238-018-0559-y

Unbiased transcriptomic analyses reveal distinct effects of immune deficiency in CNS function with and without injury
Cited by: 9
Author(s): Dandan Luo, Weihong Ge, Xiao Hu, Chen Li, Chia Ming Lee, Libing Zhou, Zhourui Wu, Juehua Yu, Shaochong Lin, Jing Yu, Wei Xu, Lei Chen, Chong Zhang, Kun Jiang, Xuding Zhu, Haotian Li, Xinpei Gao, Yanan Geng, Bo Jing, Zhen Wang, Changhong Zheng, Rongrong Zhu, Yan Qiao, Qing Lin, Keqiang Ye, Yi Sun, Liming Cheng
Software Mentions: 1
Published: over 8 years ago

10.3389/fgene.2020.614195

Integrated WGCNA and PPI Network to Screen Hub Genes Signatures for Infantile Hemangioma
Cited by: 14
Author(s): Miao Xu, Tao Ouyang, Kaiyang Lv, Xiaohua Ma
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41398-019-0486-6

Dysregulation of a specific immune-related network of genes biologically defines a subset of schizophrenia
Cited by: 21
Author(s): Svenja V. Trossbach, Laura Hecher, David Schafflick, René Deenen, Ovidiu Popa, Tobias Lautwein, Sarah K. Tschirner, Karl Köhrer, Karin Fehsel, Irina Papazova, Berend Malchow, Alkomiet Hasan, Georg Winterer, Aurore Schmitt, Gerd Meyer zu Hörste, Peter Falkai, Carsten Korth
Software Mentions: 1
Published: over 7 years ago

10.1002/2211-5463.12872

SPC25 may promote proliferation and metastasis of hepatocellular carcinoma via p53
Cited by: 12
Author(s): Fengjuan Chen, Ka Zhang, Yilin Huang, Fang Luo, Kunpeng Hu, Qing-Qing Cai
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2019.00005

Long Non-coding RNA LINC00941 as a Potential Biomarker Promotes the Proliferation and Metastasis of Gastric Cancer
Cited by: 42
Author(s): Haiming Liu, Nan Wu, Zhe Zhang, Xiaodan Zhong, Hao Zhang, Hao Guo, Yongzhan Nie, Yuanning Liu
Software Mentions: 1
Published: almost 8 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

10.3389/fgene.2019.01136

Integrating the Ribonucleic Acid Sequencing Data From Various Studies for Exploring the Multiple Sclerosis-Related Long Noncoding Ribonucleic Acids and Their Functions
Cited by: 7
Author(s): Zhijie Han, Jing Hua, Weiwei Xue, Feng Zhu
Software Mentions: 1
Published: almost 7 years ago

10.18632/aging.202996

Circular RNA circitga7 accelerates glioma progression via miR-34a-5p/VEGFA axis
Cited by: 10
Author(s): Ling Qi, Weiyao Wang, Guifang Zhao, Hong Jiang, Yu Zhang, Donghai Zhao, Hong Jin, Haojun Yu, Haidong Xu
Software Mentions: 1
Published: over 5 years ago

10.1155/2021/6522191

Application of Multigroup Technology in Non-Small-Cell Lung Cancer with Qi Stagnation and Blood Stasis Syndrome
Cited by: 0
Author(s): Guan-Jun Ma, Qian Xiang, Zhuo Chen, Shasha Chen, Aiqin Zhang
Software Mentions: 1
Published: over 5 years ago

10.1136/rmdopen-2015-000183

Leucocyte subset-specific type 1 interferon signatures in SLE and other immune-mediated diseases
Cited by: 25
Author(s): Shaun Flint, Vojislav Jovanović, Boon Wee Teo, Anselm Mak, Julian Thumboo, Eoín McKinney, James C. Lee, Paul A. MacAry, David M. Kemeny, David Jayne, Kok Yong Fong, Paul Lyons, Kenneth G. C. Smith
Software Mentions: 1
Published: over 10 years ago

10.1098/rsos.172062

Transcriptional analyses provide new insight into the late-stage immune response of a diseased Caribbean coral
Cited by: 28
Author(s): Lauren E. Fuess, Whitney T. Mann, Lea R. Jinks, Vanessa Brinkhuis, Laura D. Mydlarz
Software Mentions: 1
Published: over 8 years ago

10.1186/s12935-021-02047-y

LRRK2 is a candidate prognostic biomarker for clear cell renal cell carcinoma
Cited by: 3
Author(s): Chunxiu Yang, Jingjing Pang, Jian Xu, He Pan, Yueying Li, Huainian Zhang, Huan Liu, Shu‐Yuan Xiao
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-020-07106-8

Transcriptional landscape of the embryonic chicken Müllerian duct
Cited by: 8
Author(s): Zahida Yesmin Roly, Rasoul Godini, Martín Estermann, Andrew T. Major, Roger Pocock, Craig A. Smith
Software Mentions: 1
Published: about 6 years ago

10.1186/s12859-016-0952-6

A NMF based approach for integrating multiple data sources to predict HIV-1–human PPIs
Cited by: 17
Author(s): Sumanta Ray, Sanghamitra Bandyopadhyay
Software Mentions: 1
Published: over 10 years ago

10.1016/j.redox.2021.101933

Network analysis of nitrate-sensitive oral microbiome reveals interactions with cognitive function and cardiovascular health across dietary interventions
Cited by: 20
Author(s): Anni Vanhatalo, Joanna E. L’Heureux, James Kelly, Jamie R. Blackwell, Lee J. Wylie, Jonathan Fulford, Paul G. Winyard, David Wynne Williams, Mark van der Giezen, Andrew M. Jones
Software Mentions: 1
Published: over 5 years ago

10.1186/s12958-021-00785-2

Abnormally increased DNA methylation in chorionic tissue might play an important role in development of ectopic pregnancy
Cited by: 1
Author(s): Chen Wen, Yang Liu, Ruiqing Zhang, Yang Yao, Shuangdi Li, Jiarong Zhang
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2021.720888

Construction of a Novel Gene-Based Model for Survival Prediction of Hepatitis B Virus Carriers With HCC Development
Cited by: 1
Author(s): Yuan Huang, Wenling Tu, Yan-Qiu Yao, Ye-Ling Cai, Liping Ma
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2105-15-S15-S3

Gene differential coexpression analysis based on biweight correlation and maximum clique
Cited by: 35
Author(s): Chun-Hou Zheng, Yandan Lin, Shengjun Wen, Zhan-Li Sun
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12864-018-4756-0

Transcriptome display during tilapia sex determination and differentiation as revealed by RNA-Seq analysis
Cited by: 49
Author(s): Wenjing Tao, Jinlin Chen, Dejie Tan, Jing Yang, Lina Sun, Jing Wei, Matthew A. Conte, Thomas D. Kocher, Deshou Wang
Software Mentions: 1
Published: over 8 years ago

10.1186/s12935-017-0458-y

Integrated genomic characterization of cancer genes in glioma
Cited by: 22
Author(s): Aijun Liang, Bin Zhou, Wei Sun
Software Mentions: 1
Published: about 9 years ago