cran: WGCNA | Projects | Ecosyste.ms: Papers

10.3390/genes11080942

Advances in Genomics for Drug Development
Cited by: 18
Author(s): Roberto Spreafico, Leah Soriaga, Johannes Grosse, Herbert W. Virgin, Amalio Telenti
Software Mentions: 1
Published: about 6 years ago

Comparative Genomics of Spatholobus suberectus and Insight Into Flavonoid Biosynthesis
Cited by: 5
Author(s): Shuangshuang Qin, Kunhua Wei, Zhan-Hu Cui, Ying Liang, Mingjie Li, Li Gu, Chuyun Yang, Xiaolei Zhou, Linxuan Li, Wei Xü, Can Liu, Miao Jin, Zhongyi Zhang
Software Mentions: 1
Published: about 6 years ago

10.3390/genes12010087

K-Module Algorithm: An Additional Step to Improve the Clustering Results of WGCNA Co-Expression Networks
Cited by: 15
Author(s): Jie Hou, Xiufen Ye, Chuanlong Li, Yixing Wang
Software Mentions: 1
Published: over 5 years ago

10.3390/genes12030449

Identification of Chlorophyll Metabolism- and Photosynthesis-Related Genes Regulating Green Flower Color in Chrysanthemum by Integrative Transcriptome and Weighted Correlation Network Analyses
Cited by: 7
Author(s): Hansen Fu, Tuo Zeng, Yangyang Zhao, Tingting Luo, Huijie Deng, Chenwei Meng, Luo Jia, Caiyun Wang
Software Mentions: 1
Published: over 5 years ago

10.3389/fpls.2020.616338

Interspecific Variation in the Unsaturation Level of Seed Oils Were Associated With the Expression Pattern Shifts of Duplicated Desaturase Genes and the Potential Role of Other Regulatory Genes
Cited by: 3
Author(s): Mengli Wang, Lexuan Gao, Gengyun Li, Chengchuan Zhou, Jinjing Jian, Zhen Xing, Yuguo Wang, Wenju Zhang, Song Zhang, Yonghong Hu, Ji Hyun Yang
Software Mentions: 1
Published: over 5 years ago

10.3389/fpls.2021.624319

Grafting Delays Watermel on Fruit Ripening by Altering Gene Expression of ABA Centric Phytohormone Signaling
Cited by: 5
Author(s): Sheng Guo, Honghe Sun, Jiaxing Tian, Guoyu Zhang, Guoyi Gong, Yi Ren, Jie Zhang, Maoying Li, Haiying Zhang, Haizhen Li, Yong Xu
Software Mentions: 1
Published: over 5 years ago

10.3390/genes12081254

Pseudogene Transcripts in Head and Neck Cancer: Literature Review and In Silico Analysis
Cited by: 4
Author(s): Juliana Carron, Rafael Della Coletta, Gustavo Jacob Lourenço
Software Mentions: 1
Published: about 5 years ago

10.1186/s12263-019-0639-5

Weighted gene co-expression network analysis to explain the relationship between plasma total carotenoids and lipid profile
Cited by: 9
Author(s): Bénédicte L. Tremblay, Frédéric Guénard, Benoı̂t Lamarche, Louis Pérusse, Marie‐Claude Vohl
Software Mentions: 1
Published: over 7 years ago

10.1186/s12263-021-00697-1

Vegetarian diet duration’s influence on women’s gut environment
Cited by: 3
Author(s): Xinqi Deng, Jiangtao Si, Yonglong Qu, Jie Li, Yingkun He, Chun-Guo Wang, Yuping Zhang
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12711-016-0217-x

Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare
Cited by: 125
Author(s): Prashanth Suravajhala, Lisette J. A. Kogelman, Haja N. Kadarmideen
Software Mentions: 1
Published: over 10 years ago

10.1186/gb-2012-13-10-r97

Aging effects on DNA methylation modules in human brain and blood tissue
Cited by: 527
Author(s): Steve Horvath, Yafeng Zhang, Peter Langfelder, René S. Kahn, Marco P. Boks, Kristel R. van Eijk, Leonard H. van den Berg, Roel A. Ophoff
Software Mentions: 1
Published: over 14 years ago

10.3389/fpls.2014.00565

Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores
Cited by: 38
Author(s): Heidi M. Appel, Howard W. Fescemyer, Jürgen Ehlting, David J. Weston, Erin MacNeal Rehrig, Trupti Joshi, Dong Xu, Jöerg Bohlmann, Jack C. Schultz
Software Mentions: 1
Published: almost 12 years ago

10.1186/s13059-014-0457-4

The small RNA diversity from Medicago truncatularoots under biotic interactions evidences the environmental plasticity of the miRNAome
Cited by: 69
Author(s): Damien Formey, Erika Sallet, Christine Lelandais‐Brière, Cécile Ben, Pilar Bustos-Sanmamed, Andréas Niebel, Florian Frugier, Jean Combier, Frederic Debellé, Caroline Hartmann, Julie Poulain, Fréderick Gavory, Patrick Wincker, Christophe Roux, Laurent Gentzbittel, Jérôme Gouzy, Martín Crespi
Software Mentions: 1
Published: about 12 years ago

10.1186/s13059-014-0525-9

Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis
Cited by: 58
Author(s): Assieh Saadatpour, Guoji Guo, Stuart H. Orkin, Guo Cheng Yuan
Software Mentions: 1
Published: almost 12 years ago

10.1186/s13059-014-0475-2

Big effects of small RNAs on legume root biotic interactions
Cited by: 2
Author(s): Huan Wang, Nam‐Hai Chua
Software Mentions: 1
Published: about 12 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

10.3389/fpls.2018.00137

A Systems Biology Study in Tomato Fruit Reveals Correlations between the Ascorbate Pool and Genes Involved in Ribosome Biogenesis, Translation, and the Heat-Shock Response
Cited by: 9
Author(s): Rebecca Stevens, Piérre Baldet, Jean‐Paul Bouchet, Mathilde Causse, Catherine Deborde, Claire Deschodt, Mireille Faurobert, Cécile Garchery, Virginie Garcia, Hélène Gautier, Barbara Gouble, Mickaël Maucourt, Annick Moing, David L. Page, J. Petit, Jean‐Luc Poëssel, Vincent Truffault, Christophe Rothan
Software Mentions: 1
Published: over 8 years ago

10.3389/fphys.2019.00662

Analysis of Genes Involved in Ulcerative Colitis Activity and Tumorigenesis Through Systematic Mining of Gene Co-expression Networks
Cited by: 28
Author(s): Wu Shi, Rongjun Zou, Minglei Yang, Lei Mai, Jiangnan Ren, Ji Wen, Zhaoshi Liu, Renxu Lai
Software Mentions: 1
Published: over 7 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/gm452

Genes and pathways underlying regional and cell type changes in Alzheimer's disease
Cited by: 209
Author(s): Jeremy A. Miller, Randall L. Woltjer, Jeff M Goodenbour, Steve Horvath, Daniel H. Geschwind
Software Mentions: 1
Published: over 13 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

10.18632/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

10.1186/s13073-017-0444-y

brain-coX: investigating and visualising gene co-expression in seven human brain transcriptomic datasets
Cited by: 11
Author(s): Saskia Freytag, Rosemary Burgess, Karen Oliver, Melanie Bahlo
Software Mentions: 1
Published: over 9 years ago

10.1186/s13073-017-0466-5

Parkinson’s disease is associated with DNA methylation levels in human blood and saliva
Cited by: 111
Author(s): Yen Chuang, Kimberly C. Paul, Jeff M. Bronstein, Yvette Bordelon, Steve Horvath, Beate Ritz
Software Mentions: 1
Published: about 9 years ago

10.1186/s13073-021-00845-7

Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer
Cited by: 36
Author(s): Hryhorii Chereda, Annalen Bleckmann, Kerstin Menck, Júlia Perera-Bel, Philip Stegmaier, Florian Auer, Frank Krämer, Andreas Leha, Tim Beißbarth
Software Mentions: 1
Published: over 5 years ago

10.1093/gigascience/gix059

The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization
Cited by: 145
Author(s): Xiaodong Du, Guangyi Fan, Yu Jiao, He Zhang, Ximing Guo, Ronglian Huang, Zhe Zheng, Chao Bian, Yuewen Deng, Qingheng Wang, Zhongduo Wang, Xinming Liang, Haiying Liang, Chengcheng Shi, Xiyang Zhao, Fengming Sun, Ruijuan Hao, Jie Bai, Liu Jialiang, Wenbin Chen, Jinlian Liang, Weiqing Liu, Zhe Xu, Qiong Shi, Xun Xu, Guofan Zhang, Xin Liu
Software Mentions: 1
Published: about 9 years ago

10.1186/s41065-019-0089-5

Identification of the defense-related gene VdWRKY53 from the wild grapevine Vitis davidii using RNA sequencing and ectopic expression analysis in Arabidopsis
Cited by: 10
Author(s): Ying Zhang, Jia‐Long Yao, Hui Feng, Jianfu Jiang, Xiucai Fan, Yunfei Jia, Ran Wang, Chonghuai Liu
Software Mentions: 1
Published: over 7 years ago

10.3389/fphys.2019.00275

Identification of the Biomarkers and Pathological Process of Osteoarthritis: Weighted Gene Co-expression Network Analysis
Cited by: 36
Author(s): Hao Gu, Min Yang, Jia Guo, Zhang Chao, Lu-Lu Lin, Yang Liu, Renxiong Wei
Software Mentions: 1
Published: over 7 years ago

10.1186/s41065-019-0083-y

Bladder cancer stage-associated hub genes revealed by WGCNA co-expression network analysis
Cited by: 63
Author(s): Yu Di, Dongshan Chen, Wenxia Yu, Lei Yan
Software Mentions: 1
Published: over 7 years ago

10.3389/fphys.2018.01841

Biological Pathways Leading From ANGPTL8 to Diabetes Mellitus–A Co-expression Network Based Analysis
Cited by: 7
Author(s): Amnah Siddiqa, Elisa Cirillo, Samar Tareen, Amjad Ali, Martina Kutmon, Lars Eijssen, Jamil Ahmad, Chris T. Evelo, Susan L. Coort
Software Mentions: 1
Published: over 7 years ago

10.1111/jcmm.16703

Transcriptome wide analysis of long non‐coding RNA‐associated ceRNA regulatory circuits in psoriasis
Cited by: 12
Author(s): Jingxia Lin, Xuefei Li, Fangfei Zhang, Lei Zhu, Yongfeng Chen
Software Mentions: 1
Published: over 5 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

10.1002/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

10.3390/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: almost 7 years ago

10.18632/oncotarget.19828

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

10.1093/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

10.1371/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

10.18632/oncotarget.18646

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

10.3389/fonc.2020.598801

Identification of Metabolism-Associated Prostate Cancer Subtypes and Construction of a Prognostic Risk Model
Cited by: 14
Author(s): Yanlong Zhang, Ruiqiao Zhang, Fangzhi Liang, Liyun Zhang, Xingwei Liang
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

10.1007/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

10.1136/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

10.3389/fonc.2020.01787

Transcriptome-Based Network Analysis Unveils Eight Immune-Related Genes as Molecular Signatures in the Immunomodulatory Subtype of Triple-Negative Breast Cancer
Cited by: 24
Author(s): Jinguo Zhang, Li Wang, Xiaolin Xu, Xin Li, Wencai Guan, Ting Meng, Guoxiong Xu
Software Mentions: 1
Published: almost 6 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

10.1186/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

10.1186/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

10.1186/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

10.1038/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

10.3389/fnins.2021.647974

ABCA7 Regulates Brain Fatty Acid Metabolism During LPS-Induced Acute Inflammation
Cited by: 11
Author(s): Tomonori Aikawa, Yingxue Ren, Magnus Holm, Yan W. Asmann, Amer Alam, Michael L. Fitzgerald, Guojun Bu, Takahisa Kanekiyo
Software Mentions: 1
Published: over 5 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

10.1038/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

10.1038/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

10.1038/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

10.1038/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

10.1038/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

10.1038/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

10.18632/oncotarget.21262

Vemurafenib-resistance via de novo RBM genes mutations and chromosome 5 aberrations is overcome by combined therapy with palbociclib in thyroid carcinoma with BRAFV600E
Cited by: 38
Author(s): Zeus A. Antonello, Nancy Hsu, Manoj Bhasin, Giovanni Roti, Mukta Joshi, Paul Van Hummelen, Emily Ye, Agnes S. Lo, S. Ananth Karumanchi, Christine R. Bryke, Carmelo Nucera
Software Mentions: 1
Published: almost 9 years ago

10.3389/fnins.2019.00926

Pilot Study of Metabolomic Clusters as State Markers of Major Depression and Outcomes to CBT Treatment
Cited by: 13
Author(s): Sudeepa Bhattacharyya, Boadie W. Dunlop, Siamak MahmoudianDehkordi, Ahmed T. Ahmed, Gregory Louie, Mark A. Frye, Richard M. Weinshilboum, Ranga Krishnan, A. John Rush, Helen S. Mayberg, W. Edward Craighead, Rima Kaddurah‐Daouk
Software Mentions: 1
Published: almost 7 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

10.1038/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

10.1038/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

10.1038/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

10.1038/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

10.3389/fnins.2020.00571

Gene Deregulation and Underlying Mechanisms in Spinocerebellar Ataxias With Polyglutamine Expansion
Cited by: 15
Author(s): Anna Niewiadomska-Cimicka, Antoine Hache, Yvon Trottier
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-017-05280-6

The integrated pathway of TGFβ/Snail with TNFα/NFκB may facilitate the tumor-stroma interaction in the EMT process and colorectal cancer prognosis
Cited by: 44
Author(s): Hui Li, Anjing Zhong, Si Li, Xianwen Meng, Xue Wang, Fangying Xu, Maode Lai
Software Mentions: 1
Published: about 9 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: about 9 years ago

10.1038/s41598-017-06701-2

Characterization and expression analysis of the WRKY gene family in moso bamboo
Cited by: 34
Author(s): Long Li, Shaohua Mu, Zhanchao Cheng, Yuanwen Cheng, Ying Zhang, Ying Miao, Cheng‐Lin Hou, Xueping Li, Jian Gao
Software Mentions: 1
Published: about 9 years ago

10.3389/fnins.2020.00228

Erosion of Gene Co-expression Networks Reveal Deregulation of Immune System Processes in Late-Onset Alzheimer’s Disease
Cited by: 5
Author(s): John Malamon, Andres Kriete
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-017-10127-1

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

10.18632/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

10.3389/fnins.2021.629156

Characterizing the Expression Patterns of Parkinson’s Disease Associated Genes
Cited by: 5
Author(s): Bin Li, Guizhe Zhao, Kuokuo Li, Zheng Wang, Zhenghuan Fang, Xiaomeng Wang, Tengfei Luo, Yi Zhang, Yijing Wang, Qian Chen, Yuanfeng Huang, Lijie Dong, Jifeng Guo, Beisha Tang, Jinchen Li
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-017-14120-6

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

10.3389/fnins.2014.00331

Neuroinformatic analyses of common and distinct genetic components associated with major neuropsychiatric disorders
Cited by: 70
Author(s): Amit Lotan, Michaela Fencková, Janita Bralten, Aet Alttoa, Luanna Dixson, Robert W. Williams, Monique van der Voet
Software Mentions: 1
Published: almost 12 years ago

10.1038/s41598-017-18287-w

Integrated transcriptional analysis unveils the dynamics of cellular differentiation in the developing mouse hippocampus
Cited by: 6
Author(s): Giovanni Iacono, Marco Benevento, Aline Dubos, Yann Hérault, Hans van Bokhoven, Nael Nadif Kasri, Hendrik G. Stunnenberg
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-017-18084-5

A Global View of Transcriptome Dynamics During Male Floral Bud Development in Populus tomentosa
Cited by: 25
Author(s): Zhong Chen, Pian Rao, Xiaoyu Yang, Xiaoxing Su, Tianyun Zhao, Kai Gao, Xiong Yang, Xinmin An
Software Mentions: 1
Published: over 8 years ago

10.3389/fnins.2015.00176

Epigenetic modulation of brain gene networks for cocaine and alcohol abuse
Cited by: 47
Author(s): Sean P. Farris, R. Adron Harris, Igor Ponomarev
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-018-21524-5

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

10.3389/fneur.2020.00233

The Predicted Key Molecules, Functions, and Pathways That Bridge Mild Cognitive Impairment (MCI) and Alzheimer's Disease (AD)
Cited by: 42
Author(s): Tao Ye, Yoo Min Han, Lujiao Yu, Qi Wang, Sean X. Leng, Haiyan Zhang
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-21779-y

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

10.1038/s41598-018-23647-1

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

10.3389/fneur.2020.578972

Phenotypic Subtyping and Re-analyses of Existing Transcriptomic Data from Autistic Probands in Simplex Families Reveal Differentially Expressed and ASD Trait-Associated Genes
Cited by: 4
Author(s): Valerie W. Hu, Chongfeng Bi
Software Mentions: 1
Published: almost 6 years ago

10.3389/fnmol.2019.00197

Cross-Species Co-analysis of Prefrontal Cortex Chronic Ethanol Transcriptome Responses in Mice and Monkeys
Cited by: 21
Author(s): James W. Bogenpohl, Maren L. Smith, Sean P. Farris, Catherine I. Dumur, Marcelo F. López, Howard C. Becker, Kathleen A. Grant, Michael F. Miles
Software Mentions: 1
Published: about 7 years ago

10.3389/fnmol.2015.00042

Dynamical properties of gene regulatory networks involved in long-term potentiation
Cited by: 4
Author(s): Gonzalo S. Nido, Margaret M. Ryan, Ľubica Beňušková, Joanna M. Williams
Software Mentions: 1
Published: about 11 years ago

10.1038/s41598-018-26310-x

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

10.1038/s41598-018-26495-1

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

10.3389/fnmol.2017.00399

Co-expression Patterns between ATN1 and ATXN2 Coincide with Brain Regions Affected in Huntington’s Disease
Cited by: 10
Author(s): Arlin Keo, N. Ahmad Aziz, Oleh Dzyubachyk, Jeroen van der Grond, Willeke M. C. van Roon‐Mom, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Mahfouz
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-018-30302-2

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

10.1038/s41598-018-30779-x

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

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479