cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1002367

Integrating Genome-Wide Genetic Variations and Monocyte Expression Data Reveals Trans-Regulated Gene Modules in Humans
Cited by: 122
Author(s): Maxime Rotival, Tanja Zeller, Philipp S. Wild, Seraya Maouche, Silke Szymczak, Arne Schillert, Raphaële Castagné, Arne Deiseroth, Carole Proust, Jessy Brocheton, Tiphaine Godefroy, Claire Perret, Marine Germain, Medea Eleftheriadis, Christoph Sinning, Renate B. Schnabel, Edith Lubos, Karl J. Lackner, Heidi Rossmann, Thomas Münzel, Augusto Rendon, Cardiogenics Consortium, Jeanette Erdmann, Panos Deloukas, Christian Hengstenberg, Patrick Diemert, Gilles Montalescot, Willem H. Ouwehand, Nilesh J. Samani, Heribert Schunkert, David‐Alexandre Trégouët, Andreas Ziegler, Alison H. Goodall, François Cambien, Laurence Tiret, Stefan Blankenberg
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pgen.1001113

An Immune Response Network Associated with Blood Lipid Levels
Cited by: 122
Author(s): Michael Inouye, Kaisa Silander, Eija Hämäläinen, Veikko Salomaa, Kennet Harald, Pekka Jousilahti, Satu Männistö, Johan G. Eriksson, Janna Saarela, Samuli Ripatti, Markus Perola, Gert‐Jan B. van Ommen, Marja‐Riitta Taskinen, Aarno Palotie, Emmanouil T. Dermitzakis, Leena Peltonen
Software Mentions: 1
Published: about 16 years ago

10.1186/s12864-016-3176-2

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

10.1371/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: over 12 years ago

10.1186/s12967-015-0383-6

Berberine ameliorates nonalcoholic fatty liver disease by a global modulation of hepatic mRNA and lncRNA expression profiles
Cited by: 86
Author(s): Xinlu Yuan, Jie Wang, Xiaoyan Tang, Yixue Li, Pu Xia, Xin Gao
Software Mentions: 1
Published: over 11 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: over 7 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

10.1371/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

10.1371/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

10.1016/j.isci.2021.102265

Temporal metabolic and transcriptomic characteristics crossing islets and liver reveal dynamic pathophysiology in diet-induced diabetes
Cited by: 8
Author(s): Rui Gao, Qi Fu, Hemin Jiang, Min Shen, Ruipeng Zhao, Yu Q, Yunqiang He, Kuanfeng Xu, Xinyu Xu, Heng Chen, Quan Zhang, Tao Yang
Software Mentions: 1
Published: over 5 years ago

10.1111/acel.12788

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

10.3390/nu11061265

Network Analysis of the Potential Role of DNA Methylation in the Relationship between Plasma Carotenoids and Lipid Profile
Cited by: 18
Author(s): Bénédicte L. Tremblay, Frédéric Guénard, Benoı̂t Lamarche, Louis Pérusse, Marie‐Claude Vohl
Software Mentions: 1
Published: over 7 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/s13238-016-0247-8

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

10.1186/s13048-020-00710-y

Identification of WTAP-related genes by weighted gene co-expression network analysis in ovarian cancer
Cited by: 11
Author(s): Jing Wang, Jing Xu, Ke Li, Yunke Huang, Yilin Dai, Congjian Xu, Yu Kang
Software Mentions: 1
Published: almost 6 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: about 8 years ago

10.1371/journal.pgen.1006490

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation
Cited by: 97
Author(s): Sarah R. Smith, Jeroen Gillard, Adam B. Kustka, John P. McCrow, Jonathan H. Badger, Hong Zheng, Ashley M. New, Chris L. Dupont, Toshihiro Obata, Alisdair R. Fernie, Andrew E. Allen
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1006152

A High Temperature-Dependent Mitochondrial Lipase EXTRA GLUME1 Promotes Floral Phenotypic Robustness against Temperature Fluctuation in Rice (Oryza sativa L.)
Cited by: 27
Author(s): Biyao Zhang, Shifeng Wu, Yue Zhang, Ting Xu, Feifei Guo, Huashan Tang, Xiang Li, Pengfei Wang, Wenfeng Qian, Yongbiao Xue
Software Mentions: 1
Published: about 10 years ago

10.18632/aging.102816

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

10.1136/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

10.1371/journal.pgen.1008734

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

10.3390/nu13072185

Association of Plasma Phospholipids with Age-Related Cognitive Impairment: Results from a Cross-Sectional Study
Cited by: 2
Author(s): Tingting Liu, Shaojie Pang, Shanshan Jia, Qingqing Man, Yuqian Li, Shuang Song, Jian Zhang
Software Mentions: 1
Published: about 5 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: about 5 years ago

10.18632/oncotarget.8496

Development of a prediction model for radiosensitivity using the expression values of genes and long non-coding RNAs
Cited by: 8
Author(s): Weian Wang, Liang‐Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1002556

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

10.1186/s12931-017-0558-1

Network-based analysis reveals novel gene signatures in peripheral blood of patients with chronic obstructive pulmonary disease
Cited by: 31
Author(s): Ma’en Obeidat, Yunlong Nie, Virginia Chen, Casey P. Shannon, Anand Kumar Andiappan, Bernett Lee, Olaf Rötzschke, Peter J. Castaldi, Craig P. Hersh, Nick Fishbane, Raymond T. Ng, Bruce M. McManus, Bruce E. Miller, Stephen I. Rennard, Peter D. Paré, Don D. Sin
Software Mentions: 1
Published: over 9 years ago

10.1186/s12931-018-0965-y

Do sputum or circulating blood samples reflect the pulmonary transcriptomic differences of COPD patients? A multi-tissue transcriptomic network META-analysis
Cited by: 8
Author(s): Rosa Faner, Jarrett Morrow, Sandra Casas-Recasens, Suzanne M. Cloonan, Guillaume Noell, Alejandra López-Giraldo, Ruth Tal‐Singer, Bruce E. Miller, Edwin K. Silverman, Àlvar Agustí, Craig P. Hersh
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1002038

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

10.1186/s12931-019-1105-z

Multi-level immune response network in mild-moderate Chronic Obstructive Pulmonary Disease (COPD)
Cited by: 33
Author(s): Tamara Cruz, Alejandra López-Giraldo, Guillaume Noell, Sandra Casas-Recasens, Tamara García, Laureano Molins, Manel Juan, Marco A. Fernández, Àlvar Agustí, Rosa Faner
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pcbi.1000117

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

10.18632/aging.103054

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

10.1186/s12284-020-00437-w

Long Non-coding RNAs Responsive to Blast Fungus Infection in Rice
Cited by: 16
Author(s): Lanlan Wang, Jingjing Jin, Lihua Li, Shaohong Qu
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12284-020-00439-8

Weighted Gene Co-Expression Network Coupled with a Critical-Time-Point Analysis during Pathogenesis for Predicting the Molecular Mechanism Underlying Blast Resistance in Rice
Cited by: 2
Author(s): Dagang Tian, Zaijie Chen, Yan Lin, Ziqiang Chen, Zonghua Wang, Wang Feng
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pcbi.1000707

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

10.18632/aging.202285

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

10.1371/journal.pcbi.1004332

Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks
Cited by: 42
Author(s): Xiaoke Ma, Long Gao, Georgios Karamanlidis, Peng Gao, Chi Fung Lee, Lorena Garcia-Menendez, Rong Tian, Kai Tan
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pcbi.1006436

Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network
Cited by: 17
Author(s): Yafei Lyu, Lingzhou Xue, Feipeng Zhang, Hillary Koch, Laura Saba, Katerina Kechris, Qunhua Li
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pcbi.1002773

Distinct Neurogenomic States in Basal Ganglia Subregions Relate Differently to Singing Behavior in Songbirds
Cited by: 25
Author(s): Austin T. Hilliard, Julie E. Miller, Steve Horvath, Stephanie A. White
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-12-S3-S3

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

10.1371/journal.pbio.3000986

Clustering of Tir during enteropathogenic E. coli infection triggers calcium influx–dependent pyroptosis in intestinal epithelial cells
Cited by: 13
Author(s): Qiyun Zhong, Theodoros I. Roumeliotis, Zuza Kozik, Massiel Cepeda-Molero, Luis A. Fernández, Avinash R. Shenoy, Chris Bakal, Gad Frankel, Jyoti S. Choudhary
Software Mentions: 1
Published: over 5 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

10.1038/s41597-021-00828-8

Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera
Cited by: 22
Author(s): Hui Li, Xingyu Yang, Yue Zhang, Zhiyan Gao, Yuting Liang, Jin‐Ming Chen, Tao Shi
Software Mentions: 1
Published: over 5 years ago

10.1002/pld3.70

A sorghum <scp>NAC</scp> gene is associated with variation in biomass properties and yield potential
Cited by: 32
Author(s): Jingnu Xia, Yunjun Zhao, Payne S. Burks, Markus Pauly, Patrick J. Brown
Software Mentions: 1
Published: about 8 years ago

10.1186/s12864-018-5104-0

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

10.1038/srep12298

Network analysis of immunotherapy-induced regressing tumours identifies novel synergistic drug combinations
Cited by: 55
Author(s): W. Joost Lesterhuis, Catherine Rinaldi, Anya C. Jones, Esdy N. Rozali, Ian M. Dick, Andrea Khong, Louis Boon, Bruce Robinson, Anna K. Nowak, Anthony Bosco, Richard Lake
Software Mentions: 1
Published: about 11 years ago

10.1111/pbi.13325

DcMYB113, a root‐specific R2R3‐MYB, conditions anthocyanin biosynthesis and modification in carrot
Cited by: 74
Author(s): Zhihong Xu, Qingqing Yang, Kai Feng, Xin Yu, Ai‐Sheng Xiong
Software Mentions: 1
Published: over 6 years ago

10.1038/srep13248

Derivation of a fifteen gene prognostic panel for six cancers
Cited by: 22
Author(s): Mamata F. Khirade, Girdhari Lal, Sharmila A. Bapat
Software Mentions: 1
Published: about 11 years ago

10.1186/s12864-020-07250-1

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

10.1007/s00425-020-03544-6

Systematic identification and characterization of circular RNAs involved in flag leaf senescence of rice
Cited by: 15
Author(s): Xiaoping Huang, Hongyu Zhang, Rong Guo, Qiang Wang, Xuanzhi Liu, Weigang Kuang, Haiyan Song, Jiang-Lin Liao, Yongji Huang, Zhaohai Wang
Software Mentions: 1
Published: over 5 years ago

10.1038/srep17494

Honey bee microRNAs respond to infection by the microsporidian parasite Nosema ceranae
Cited by: 15
Author(s): Qiang Huang, Yanping Chen, Rui Wu Wang, Ryan S. Schwarz, Jay D. Evans
Software Mentions: 1
Published: almost 11 years ago

10.1038/srep18045

Proteome Analysis of Renoprotection Mediated by a Novel Cyclic Helix B Peptide in Acute Kidney Injury
Cited by: 18
Author(s): Cheng Yang, Junjun Liu, Li Long, Man Hu, Ya‐Qiu Long, Xiaohui Liu, Tongyu Zhu, Xiao Huang, Shouliang Zhao, Shangfeng Liu, Ruiming Rong
Software Mentions: 1
Published: almost 11 years ago

10.1038/srep19430

DNA co-methylation modules in postmortem prefrontal cortex tissues of European Australians with alcohol use disorders
Cited by: 66
Author(s): Fan Wang, Hao Xu, Hongyu Zhao, Joel Gelernter, Huiping Zhang
Software Mentions: 1
Published: over 10 years ago

10.14814/phy2.12208

Genetic modulation of diabetic nephropathy among mouse strains with Ins2Akitamutation
Cited by: 7
Author(s): Xinhui Wu, Richard C. Davis, Timothy S. McMillen, Valérie Schaeffer, Zhiqiang Zhou, Hongxiu Qi, Parisa N. Mazandarani, Roshanak Alialy, Kelly L. Hudkins, Aldons J. Lusis, Renée C. LeBoeuf
Software Mentions: 1
Published: almost 12 years ago

10.18632/oncotarget.10680

Aberrant transcriptional networks in step-wise neurogenesis of paroxysmal kinesigenic dyskinesia-induced pluripotent stem cells
Cited by: 4
Author(s): Chun Li, Yu Ma, Kunshan Zhang, Junjie Gu, Fan Tang, Shengdi Chen, Li Cao, Siguang Li, Ying Jin
Software Mentions: 1
Published: about 10 years ago

10.18632/oncotarget.11304

Identification and functional analysis of long non-coding RNAs in human and mouse early embryos based on single-cell transcriptome data
Cited by: 27
Author(s): Jiajun Qiu, Zhaorui Ren, Jingbin Yan
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-019-5424-8

Transcriptional regulatory networks controlling taste and aroma quality of apricot (Prunus armeniaca L.) fruit during ripening
Cited by: 36
Author(s): Qiuyun Zhang, Chao Feng, Wenhui Li, Zehui Qu, Ming Zeng, Wanpeng Xi
Software Mentions: 1
Published: over 7 years ago

10.1038/srep25261

Elucidation of molecular and functional heterogeneity through differential expression network analyses of discrete tumor subsets
Cited by: 6
Author(s): Rutika R. Naik, Nilesh Gardi, Sharmila A. Bapat
Software Mentions: 1
Published: over 10 years ago

10.1038/srep26396

The simple neuroendocrine-immune regulatory network in oyster Crassostrea gigas mediates complex functions
Cited by: 38
Author(s): Zhaoqun Liu, Lingling Wang, Zhi Zhou, Ying Sun, Mengqiang Wang, Hao Wang, Zujun Hou, Dahai Gao, Qiang Gao, Linsheng Song
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-019-5773-3

A deficiency in SUMOylation activity disrupts multiple pathways leading to neural tube and heart defects in Xenopus embryos
Cited by: 11
Author(s): Michelle M. Bertke, Kyle M. Dubiak, Laura Cronin, Erliang Zeng, Paul W. Huber
Software Mentions: 1
Published: over 7 years ago

10.1038/srep28422

Construction and application of a co-expression network in Mycobacterium tuberculosis
Cited by: 31
Author(s): Jun Jiang, Xian Sun, Wei Wu, Li Li, Hai Wu, Lu Zhang, Guohua Yu, Yao Li
Software Mentions: 1
Published: about 10 years ago

10.18632/aging.102309

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

10.1038/srep29052

Integrative Network-based Analysis of Magnetic Resonance Spectroscopy and Genome Wide Expression in Glioblastoma multiforme
Cited by: 19
Author(s): Dieter Henrik Heiland, Irina Mader, Pascal Schlosser, Dietmar Pfeifer, Maria Stella Carro, Thomas Lange, Ralf Schwarzwald, Ioannis Vasilikos, Horst Urbach, Astrid Weyerbrock
Software Mentions: 1
Published: about 10 years ago

10.1038/srep28663

Indexing Effects of Copy Number Variation on Genes Involved in Developmental Delay
Cited by: 35
Author(s): Mohammed Uddin, Giovanna Pellecchia, Bhooma Thiruvahindrapuram, Lia D’Abate, Daniele Merico, Ada J.S. Chan, Mehdi Zarrei, Kristiina Tammimies, Susan Walker, Matthew J. Gazzellone, Thomas Nalpathamkalam, Ryan K. C. Yuen, Koenraad Devriendt, Géraldine Mathonnet, Emmanuelle Lemyre, Sonia Nizard, Mary Shago, Ann M. Joseph-George, Abdul Noor, Melissa T. Carter, Grace Yoon, Peter Kannu, Frédérique Tihy, Erik C. Thorland, Christian R. Marshall, Janet A. Buchanan, Marsha Speevak, Dimitri J. Stavropoulos, Stephen W. Scherer
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-016-3201-5

Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass
Cited by: 14
Author(s): Taylor P. Frazier, Nathan A. Palmer, Fuliang Xie, Christian M. Tobias, Teresa Donze-Reiner, Aureliano Bombarely, Kevin L. Childs, Shengqiang Shu, Jerry Jenkins, Jeremy Schmutz, Baohong Zhang, Gautam Sarath, Bingyu Zhao
Software Mentions: 1
Published: almost 10 years ago

10.7717/peerj.4107

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

10.7717/peerj.9773

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

10.1186/1471-2164-11-589

Is human blood a good surrogate for brain tissue in transcriptional studies?
Cited by: 101
Author(s): Chaochao Cai, Peter Langfelder, Tova Fuller, Michael C. Oldham, Rui Luo, Leonard H van den Berg, Roel A. Ophoff, Steve Horvath
Software Mentions: 1
Published: almost 16 years ago

10.1038/srep31851

Single-cell RNA-seq reveals distinct injury responses in different types of DRG sensory neurons
Cited by: 109
Author(s): Ganlu Hu, Kevin Huang, Youjin Hu, Guizhen Du, Zhigang Xue, Xianmin Zhu, Guoping Fan
Software Mentions: 1
Published: about 10 years ago

10.1038/srep32005

Integrative effect of drought and low temperature on litchi (Litchi chinensis Sonn.) floral initiation revealed by dynamic genome-wide transcriptome analysis
Cited by: 24
Author(s): Jiyuan Shen, Qiusheng Xiao, Haiji Qiu, Chengjie Chen, Houbin Chen
Software Mentions: 1
Published: about 10 years ago

10.1038/srep33227

Network Analysis of Fine Particulate Matter (PM2.5) Emissions in China
Cited by: 12
Author(s): Shaomin Yan, Guang Wu
Software Mentions: 1
Published: about 10 years ago

10.1038/srep33655

Drought response transcriptomes are altered in poplar with reduced tonoplast sucrose transporter expression
Cited by: 24
Author(s): Liang‐Jiao Xue, Christopher J. Frost, Chung‐Jui Tsai, Chung‐Jui Tsai
Software Mentions: 1
Published: almost 10 years ago

10.1093/molbev/msab004

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

10.1186/2040-2392-5-22

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

10.1186/1471-2164-10-327

Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells
Cited by: 189
Author(s): Mike J. Mason, Guoping Fan, Kathrin Plath, Qing Zhou, Steve Horvath
Software Mentions: 1
Published: about 17 years ago

10.1038/srep38575

Expression profiling and functional annotation of noncoding genes across 11 distinct organs in rat development
Cited by: 4
Author(s): Zhiping Wen, Geng Chen, Sibo Zhu, Jiaquan Zhu, Bin Li, Yunjie Song, Suqing Li, Leming Shi, Yuanting Zheng, Menglong Li
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep38956

Pan- and core- network analysis of co-expression genes in a model plant
Cited by: 20
Author(s): Fei He, Sergei Maslov
Software Mentions: 1
Published: over 9 years ago

10.18632/aging.202713

LncRNA-mRNA co-expression analysis discovered the diagnostic and prognostic biomarkers and potential therapeutic agents for myocardial infarction
Cited by: 6
Author(s): Xiaocong Zhang, Ziqi Chen, Jiabin Zang, Chun Yao, Jian Shi, Ruqiong Nie, Guifu Wu
Software Mentions: 1
Published: over 5 years ago

10.18632/oncotarget.14739

A methodological study of genome-wide DNA methylation analyses using matched archival formalin-fixed paraffin embedded and fresh frozen breast tumors
Cited by: 8
Author(s): Allyson C. Espinal, Dan Wang, Li Yan, Song Liu, Li Tang, Qiang Hu, Carl Morrison, Christine B. Ambrosone, Michael J. Higgins, Lara E. Sucheston‐Campbell
Software Mentions: 1
Published: over 9 years ago

10.1038/srep39614

Genetically regulated hepatic transcripts and pathways orchestrate haematological, biochemical and body composition traits
Cited by: 7
Author(s): Siriluck Ponsuksili, Nares Trakooljul, Frieder Hadlich, Fiete Haack, Eduard Muráni, Klaus Wimmers
Software Mentions: 1
Published: over 9 years ago

10.1186/s13229-015-0029-9

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

10.1186/s12863-015-0311-z

Gene expression in large pedigrees: analytic approaches
Cited by: 5
Author(s): Rita M. Cantor, Heather J. Cordell
Software Mentions: 1
Published: over 10 years ago

10.1186/s13229-020-00382-x

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

10.1038/srep43523

Integrative Diffusion-Weighted Imaging and Radiogenomic Network Analysis of Glioblastoma multiforme
Cited by: 18
Author(s): Dieter Henrik Heiland, Carl Philipp Simon-Gabriel, Theo Demerath, Gerrit Haaker, Dietmar Pfeifer, Elias Kellner, Valerij G. Kiselev, Ori Staszewski, Horst Urbach, Astrid Weyerbrock, Irina Mader
Software Mentions: 1
Published: over 9 years ago

10.3390/microorganisms8040518

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

10.3390/microorganisms8060951

Functional Associations and Resilience in Microbial Communities
Cited by: 11
Author(s): María Luisa Ávila-Jiménez, Gavin Burns, Zhili He, Jizhong Zhou, Andy Hodson, Jose-Luis Avila-Jimenez, David A. Pearce
Software Mentions: 1
Published: about 6 years ago

10.1186/2049-2618-1-17

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships
Cited by: 230
Author(s): Ian Howard Mchardy, Maryam Goudarzi, Man‐Li Tong, Paul Ruegger, Emma Schwager, John R. Weger, Thomas G. Graeber, Justin L. Sonnenburg, Steve Horvath, Curtis Huttenhower, Dermot P. McGovern, Albert J. Fornace, James Borneman, Jonathan Braun
Software Mentions: 1
Published: over 13 years ago

10.18632/oncotarget.17023

Prognosis of stage III colorectal carcinomas with FOLFOX adjuvant chemotherapy can be predicted by molecular subtype
Cited by: 33
Author(s): Yu-Jin Kwon, Min Hee Park, Mi Jang, SeongJu Yun, Won Kyu Kim, Sora Kim, Soonmyung Paik, Hyun Jung Lee, Suck Joon Hong, Tae Il Kim, Byung-Soh Min, Hoguen Kim
Software Mentions: 1
Published: over 9 years ago

10.1186/s12934-020-01349-6

Repeated fed-batch strategy and metabolomic analysis to achieve high docosahexaenoic acid productivity in Crypthecodinium cohnii
Cited by: 9
Author(s): Liangsen Liu, Fangzhong Wang, Guangsheng Pei, Jinyu Cui, Jinjin Diao, Mingming Lv, Lei Chen, Weiwen Zhang
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-017-00952-9

Global gene expression profiling of healthy human brain and its application in studying neurological disorders
Cited by: 49
Author(s): Simarjeet Negi, Chittibabu Guda
Software Mentions: 1
Published: over 9 years ago

10.18632/oncotarget.15031

Comprehensive analysis of PD-L1 expression in glioblastoma multiforme
Cited by: 73
Author(s): Dieter Henrik Heiland, Gerrit Haaker, Daniel Delev, Bianca Mercas, Waseem Masalha, Sabrina Heynckes, Annette Gäbelein, Dietmar Pfeifer, Maria Stella Carro, Astrid Weyerbrock, Marco Prinz, Oliver Schnell
Software Mentions: 1
Published: over 9 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: almost 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

10.1038/s41598-017-00808-2

Organ-specific transcriptome profiling of metabolic and pigment biosynthesis pathways in the floral ornamental progenitor species Anthurium amnicola Dressler
Cited by: 13
Author(s): Jon Y. Suzuki, T.D. Amore, Bernarda Calla, Nathan A. Palmer, Erin D. Scully, Scott E. Sattler, Gautam Sarath, J.S. Lichty, Roxana Y. Myers, Lisa M. Keith, Tracie K. Matsumoto, Scott M. Geib
Software Mentions: 1
Published: over 9 years ago

10.18632/oncotarget.17785

Gene co-expression network reveals shared modules predictive of stage and grade in serous ovarian cancers
Cited by: 43
Author(s): Qian Sun, Hongbo Zhao, Cong Zhang, Ting Hu, Jiankang Wu, Xingguang Lin, Danfeng Luo, Changyu Wang, Meng Li, Xi Liu, Kezhen Li, Junbo Hu, Ding Ma, Tao Zhu
Software Mentions: 1
Published: over 9 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: almost 6 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: over 5 years ago

10.18632/aging.104083

Identification of novel prognosis-related genes in the endometrial cancer immune microenvironment
Cited by: 14
Author(s): Jian Ma, Jingkai Zhang, Di Yang, Xiaoxin Ma
Software Mentions: 1
Published: almost 6 years ago

10.3390/metabo9070145

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

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479