cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1186/s12864-021-07510-8

Gene co-expression network analysis reveals key pathways and hub genes in Chinese cabbage (Brassica rapa L.) during vernalization
Cited by: 18
Author(s): Yun Dai, Xiao Sun, Chenggang Wang, Fĕi Li, Shifan Zhang, Hui Zhang, Guoliang Li, Lingyun Yuan, Guohu Chen, Rifei Sun, Shujiang Zhang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-020-07122-8

Integrated analysis of co-expression, conserved genes and gene families reveal core regulatory network of heat stress response in Cleistogenes songorica, a xerophyte perennial desert plant
Cited by: 6
Author(s): Yan Qi, Xifang Zong, Fan Wu, Jie Li, Tiantian Ma, Yufeng Zhao, Qian Ma, Penglei Wang, Yanrong Wang, Jiyu Zhang
Software Mentions: 2
Published: about 6 years ago

10.1186/s12864-015-2292-8

Liver transcriptomic networks reveal main biological processes associated with feed efficiency in beef cattle
Cited by: 114
Author(s): Pâmela Almeida Alexandre, Lisette J. A. Kogelman, Miguel Henrique de Almeida Santana, Danielle Passarelli, Lidia Hildebrand Pulz, Paulo Fantinato Neto, Paulo L. Silva, Paulo Roberto Leme, Ricardo de Francisco Strefezzi, Luiz Lehmann Coutinho, José Bento Sterman Ferraz, Joanir Pereira Eler, Haja N. Kadarmideen, Heidge Fukumasu
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-017-4257-6

Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI
Cited by: 38
Author(s): Weijing Wang, Wenjie Jiang, Lin Hou, Haiping Duan, Yili Wu, Chunsheng Xu, Qihua Tan, Shuxia Li, Dongfeng Zhang
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-019-6329-2

ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks
Cited by: 22
Author(s): Nam D. Nguyen, Ian K. Blaby, Daifeng Wang
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-016-2492-x

A novel comparative pattern analysis approach identifies chronic alcohol mediated dysregulation of transcriptomic dynamics during liver regeneration
Cited by: 16
Author(s): Lakshmi Kuttippurathu, Egle Juskeviciute, Rachael P. Dippold, Jan B. Hoek, Rajanikanth Vadigepalli
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-11-638

Integrated genomics of susceptibility to alkylator-induced leukemia in mice
Cited by: 5
Author(s): Patrick Cahan, Timothy A. Graubert
Software Mentions: 2
Published: almost 16 years ago

10.1186/s12864-018-5072-4

Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize
Cited by: 23
Author(s): Yang Yu, Jianyang Shi, Xiyang Li, Jian Liu, Qi Geng, Shi Haichun, KE Yong-pei, Qun Sun
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-020-06853-y

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus
Cited by: 7
Author(s): Yue Zhang, Razgar Seyed Rahmani, Xingyu Yang, Jin‐Ming Chen, Tao Shi
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-15-644

Prediction of miRNA-mRNA associations in Alzheimer’s disease mice using network topology
Cited by: 24
Author(s): Hyun Ho Noh, Charny Park, Soojun Park, Young Seek Lee, Soo Young Cho, Hyemyung Seo
Software Mentions: 2
Published: about 12 years ago

10.1186/s12864-018-4871-y

Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits
Cited by: 33
Author(s): Aline Silva Mello Cesar, Luciana Correia de Almeida Regitano, James M. Reecy, Mirele Daiana Poleti, P. S. N. Oliveira, Guilherme Bueno de Oliveira, Gabriel Costa Monteiro Moreira, Maurício A. Mudadu, P. C. Tizioto, James E. Koltes, Eric R. Fritz-Waters, Luke M. Kramer, Dorian J. Garrick, Hamid Beiki, Ludwig Geistlinger, Gérson Barreto Mourão, Adhemar Zerlotini
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-019-6002-9

Comparative transcriptomics of early petal development across four diverse species of Aquilegia reveal few genes consistently associated with nectar spur development
Cited by: 18
Author(s): Evangeline S. Ballerini, Elena M. Kramer, Scott A. Hodges
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-019-5802-2

A single-cell transcriptomic atlas of the developing chicken limb
Cited by: 34
Author(s): Christian Feregrino, Fabio Sacher, Oren Parnas, Patrick Tschopp
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-11-585

Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse
Cited by: 56
Author(s): Ovidiu D. Iancu, Priscila Darakjian, Nicole A.R. Walter, Barry Malmanger, Denesa Oberbeck, John K. Belknap, Shannon K. McWeeney, Robert Hitzemann
Software Mentions: 2
Published: about 16 years ago

10.1186/s12864-016-3435-2

Meta-analysis reveals conserved cell cycle transcriptional network across multiple human cell types
Cited by: 29
Author(s): Bruno Giotti, Anagha Joshi, Tom C. Freeman
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-019-6180-5

The transcriptional events and their relationship to physiological changes during poplar seed germination and post-germination
Cited by: 2
Author(s): Chunpu Qu, Hongwei Zhao, Jinyuan Chen, Zhuang Zuo, Xue Sun, Jiahuan Huang, Chengjun Yang, Xiuli Zhang, Peng Zhang, Xiankui Quan, Xu Zhang, Guanjun Liu
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-019-6027-0

Investigation into the underlying regulatory mechanisms shaping inflorescence architecture in Chenopodium quinoa
Cited by: 15
Author(s): Qi Wu, Xue Bai, Wei Zhao, Xiaodong Shi, Dabing Xiang, Yan Wan, Xiaoyong Wu, Yanxia Sun, Jianglin Zhao, Lianxin Peng, Gang Zhao
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-018-4519-y

Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms
Cited by: 46
Author(s): Pierre De Wit, Evan Durland, Alexander Ventura, C. Langdon
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-016-2438-3

Molecular alterations induced by a high-fat high-fiber diet in porcine adipose tissues: variations according to the anatomical fat location
Cited by: 16
Author(s): Florence Gondret, Annie Vincent, Magalie Houée-Bigot, Anne Siegel, Sandrine Lagarrigue, Isabelle Louveau, David Causeur
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-14-689

Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa
Cited by: 155
Author(s): Chaobo Tong, Xiaowu Wang, Jingyin Yu, Jian Wu, Wanshun Li, Junyan Huang, Caihua Dong, Wei Hua, Liu S
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2164-15-596

An integrated genomic and metabolomic framework for cell wall biology in rice
Cited by: 24
Author(s): Kai Guo, Weihua Zou, Yue Feng, Mingliang Zhang, Jing Zhang, Fen Tu, Guosheng Xie, Lingqiang Wang, Yangting Wang, Sebastian Klie, Staffan Persson, Liangcai Peng
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-016-3385-8

Functional changes in mRNA expression and alternative pre-mRNA splicing associated with the effects of nutrition on apoptosis and spermatogenesis in the adult testis
Cited by: 20
Author(s): Yongjuan Guan, Guanxiang Liang, Graeme B. Martin, Le Luo Guan
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-020-6633-x

Genome-wide discovery and functional prediction of salt-responsive lncRNAs in duckweed
Cited by: 24
Author(s): Lili Fu, Zehong Ding, Tan D, Bingying Han, Xiaoyan Sun, Jiaming Zhang
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-015-2057-4

The WRKY transcription factor family and senescence in switchgrass
Cited by: 51
Author(s): Charles I Rinerson, Erin D. Scully, Nathan A. Palmer, Teresa Donze-Reiner, Roel C. Rabara, Prateek Tripathi, Qi Shen, Scott E. Sattler, Jai S. Rohila, Gautam Sarath, Paul J. Rushton
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-018-4979-0

Comparative transcriptomics reveals suppressed expression of genes related to auxin and the cell cycle contributes to the resistance of cucumber against Meloidogyne incognita
Cited by: 21
Author(s): Xing Wang, Chunyan Cheng, Kaijing Zhang, Zhen Tian, Jian Xu, Shuqiong Yang, Qunfeng Lou, Ji Li
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-015-1431-6

Pervasive and opposing effects of Unpredictable Chronic Mild Stress (UCMS) on hippocampal gene expression in BALB/cJ and C57BL/6J mouse strains
Cited by: 29
Author(s): Karim Malki, Yann S. Mineur, Maria Grazia Tosto, James Campbell, Priya Karia, Irfan Jumabhoy, Frans Sluyter, Wim E. Crusio, Leonard C. Schalkwyk
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-15-1001

Transcriptomics of the late gestation ovine fetal brain: modeling the co-expression of immune marker genes
Cited by: 11
Author(s): María Belén Rabaglino, Maureen Keller‐Wood, Charles E. Wood
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12864-016-2395-x

Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake
Cited by: 20
Author(s): Haibo Li, Yet Nguyen, Dan Nettleton, Jack C. M. Dekkers, Christopher K. Tuggle
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-019-5585-5

Strand-specific RNA-seq based identification and functional prediction of drought-responsive lncRNAs in cassava
Cited by: 41
Author(s): Zehong Ding, Weiwei Tie, Lili Fu, Yan Yan, Guanghua Liu, Wei Yan, Yanan Li, Chunlai Wu, Jiaming Zhang, Wei Hu
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-13-460

CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data
Cited by: 90
Author(s): Jason E. Shoemaker, Tiago J. S. Lopes, Samik Ghosh, Yoshikazu Matsuoka, Yoshihiro Kawaoka, Hiroaki Kitano
Software Mentions: 2
Published: almost 15 years ago

10.1186/s12864-021-07665-4

Structural variations in papaya genomes
Cited by: 9
Author(s): Zhenyang Liao, Xunxiao Zhang, Shengcheng Zhang, Zhicong Lin, Xingtan Zhang, Ray Ming
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-018-5422-2

Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos)
Cited by: 10
Author(s): Chao Lu, Yanling Xing, Han Cai, Yangguang Shi, Jinhua Liu, Yinhua Huang
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-015-1783-y

Cell cycle control, DNA damage repair, and apoptosis-related pathways control pre-ameloblasts differentiation during tooth development
Cited by: 28
Author(s): Chengcheng Liu, Yulong Niu, Xuedong Zhou, Xin Xu, Yi Yang, Yan Zhang, Liwei Zheng
Software Mentions: 2
Published: about 11 years ago

10.1186/s12864-017-4098-3

Biological networks in Parkinson’s disease: an insight into the epigenetic mechanisms associated with this disease
Cited by: 28
Author(s): Paulami Chatterjee, Dilip Roy, Malay Bhattacharyya, Sanghamitra Bandyopadhyay
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2164-14-533

Correlated mRNAs and miRNAs from co-expression and regulatory networks affect porcine muscle and finally meat properties
Cited by: 41
Author(s): Siriluck Ponsuksili, Yang Du, Frieder Hadlich, Puntita Siengdee, Eduard Muráni, Manfred Schwerin, Klaus Wimmers
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2164-12-607

Genetic architecture of gene expression in ovine skeletal muscle
Cited by: 17
Author(s): Lisette J. A. Kogelman, Keren Byrne, Tony Vuocolo, Nathan S. Watson-Haigh, Haja N. Kadarmideen, James W. Kijas, V. H. Oddy, G.E. Gardner, Cedric Gondro, Ross L. Tellam
Software Mentions: 2
Published: almost 15 years ago

10.1186/1471-2164-16-S7-S3

Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data
Cited by: 42
Author(s): Weirong Cui, Yulan Qian, Xiaoke Zhou, Yuxin Lin, Junfeng Jiang, Jiajia Chen, Zhongming Zhao, Bairong Shen
Software Mentions: 2
Published: over 11 years ago

10.1186/s12864-018-5301-x

The temporal expression patterns of brain transcriptome during chicken development and ageing
Cited by: 18
Author(s): Zhongxian Xu, Tiandong Che, Feng Li, Kai Tian, Qing Zhu, Suchismita Mishra, Yifei Dai, Mingzhou Li, Diyan Li
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-019-6228-6

Analyses of inter-individual variations of sperm DNA methylation and their potential implications in cattle
Cited by: 17
Author(s): Shuli Liu, Lingzhao Fang, Yang Zhou, D. R. dos Santos, Ruidong Xiang, Hans D. Daetwyler, Amanda J. Chamberlain, John B. Cole, Congjun Li, Ying Yu, Li Ma, Shengli Zhang, George E. Liu
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-019-6144-9

Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley
Cited by: 42
Author(s): Licao Cui, Guang Yang, Jiali Yan, Yan Pan, Xiaojun Nie
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-020-6725-7

The seasonal development dynamics of the yak hair cycle transcriptome
Cited by: 11
Author(s): Pengjia Bao, Jiayu Luo, Yanbin Liu, Min Chen, Qingmiao Ren, Xian Guo, Bolin Tang, Xuezhi Ding, Qiang Qiu, Heping Pan, Kun Wang, Ping Yan
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-015-2019-x

De novo transcriptome analysis of Medicago falcata reveals novel insights about the mechanisms underlying abiotic stress-responsive pathway
Cited by: 40
Author(s): Zhenyan Miao, Wei Xu, Daofeng Li, Xiaona Hu, Jiaxing Liu, Rongxue Zhang, Zongyong Tong, Jiangli Dong, Zhen Su, Liwei Zhang, Min Sun, Wenjie Li, Zhenglin Du, Songnian Hu, Tao Wang
Software Mentions: 2
Published: about 11 years ago

10.1186/s12864-021-07537-x

Comparative transcriptomic analysis of the different developmental stages of ovary in red swamp crayfish Procambarus clarkii
Cited by: 5
Author(s): Yang Zhong, Wei Zhao, Tang ZhangSheng, Liming Huang, Xiao-feng Zhu, Xiang Liang, Aifen Yan, Lu ZhiFa, Yanling Yu, Dongsheng Tang, Dapeng Wang, Zhuan-Ling Lu
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-021-07709-9

Dual species dynamic transcripts reveal the interaction mechanisms between Chrysanthemum morifolium and Alternaria alternata
Cited by: 5
Author(s): Lina Liu, Fadi Chen, Sumei Chen, Weimin Fang, Ye Liu, Zhiyong Guan
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-15-756

Transcriptional profiles of bovine in vivo pre-implantation development
Cited by: 134
Author(s): Zongliang Jiang, Jianfang Sun, Hong Dai, Oscar Junhong Luo, Xinbao Zheng, Craig Obergfell, Yong Tang, Jinbo Bi, Rachel J. O’Neill, Yijun Ruan, Jingbo Chen, X. Cindy Tian
Software Mentions: 2
Published: about 12 years ago

10.1186/s12864-020-06854-x

Maternal dietary resistant starch does not improve piglet’s gut and liver metabolism when challenged with a high fat diet
Cited by: 2
Author(s): Martine Schroyen, Julie Leblois, Julie Uerlings, Bing Li, Ester Arévalo Sureda, Sébastien Massart, José Wavreille, Jérôme Bindelle, Nadia Everaert
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-016-3188-y

Network analysis of psoriasis reveals biological pathways and roles for coding and long non-coding RNAs
Cited by: 63
Author(s): Richard Ahn, Rashmi Gupta, Kevin Lai, Nitin Chopra, Sarah T. Arron, Wilson Liao
Software Mentions: 2
Published: about 10 years ago

10.1186/s12864-019-5433-7

Cluster analysis of replicated alternative polyadenylation data using canonical correlation analysis
Cited by: 0
Author(s): Michael Fraser, Yuqi Long, Guoli Ji, Yangfeng Su, Pengchao Ye, Hongjuan Fu, Xiaohui Wu
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-019-6261-5

Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis
Cited by: 25
Author(s): Lina Zhang, Qiuyun Zhang, Wenhui Li, Shikui Zhang, Wanpeng Xi
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-019-6036-z

Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii
Cited by: 16
Author(s): Na Liu, Fangyun Cheng, Yuan Zhong, Xin Guo
Software Mentions: 2
Published: about 7 years ago

10.1186/1471-2164-16-S3-S4

Mining the bladder cancer-associated genes by an integrated strategy for the construction and analysis of differential co-expression networks
Cited by: 99
Author(s): Su-Ping Deng, Lin Zhu, De-Shuang Huang
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12864-018-5117-8

Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus
Cited by: 37
Author(s): Enhui Shen, Xintian Zhu, Shuijin Hua, Hongyu Chen, Chu-Yu Ye, Longhua Zhou, Qing Liu, Qian‐Hao Zhu, Longjiang Fan, Xi Chen
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-017-4005-y

Differentiated transcriptional signatures in the maize landraces of Chiapas, Mexico
Cited by: 12
Author(s): Matthew A. Kost, Hugo Perales, Saranga Wijeratne, Asela J. Wijeratne, Eric J. Stockinger, Kristin L. Mercer
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-021-07557-7

Post-diapause transcriptomic restarts: insight from a high-latitude copepod
Cited by: 5
Author(s): Vittoria Roncalli, Matthew Cieslak, Ann M. Castelfranco, Russell R. Hopcroft, Daniel K. Hartline, Petra H. Lenz
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-021-07763-3

Transcriptome analysis reveals Vernalization is independent of cold acclimation in Arabidopsis
Cited by: 12
Author(s): Fēi Li, Qian Hu, Fadi Chen, Jingle Jiang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12881-019-0832-9

A novel risk score system for assessment of ovarian cancer based on co-expression network analysis and expression level of five lncRNAs
Cited by: 30
Author(s): Qian Zhao, Conghong Fan
Software Mentions: 2
Published: over 7 years ago

10.1186/s12881-020-01145-4

Development of an immunogenomic landscape for the competing endogenous RNAs network of peri-implantitis
Cited by: 7
Author(s): Li Yang, Jie Zheng, Chan Juan Gong, Keng Fu Lan, Yu Qing Shen, Xiao Jun Ding
Software Mentions: 2
Published: about 6 years ago

10.1186/s12881-019-0791-1

Weighted correlation network and differential expression analyses identify candidate genes associated with BRAF gene in melanoma
Cited by: 9
Author(s): Bin Zhao, Yanqiu You, Weiping Zheng, Yunhan Ma, Yani Huo, Hongyi Liu, Yuanyuan Zhou, Wei Quan, Weibin Chen, Xiaohong Zhang, Fujun Li, Yilin Zhao
Software Mentions: 2
Published: over 7 years ago

10.1186/s12920-014-0072-y

Identifying a gene expression signature of frequent COPD exacerbations in peripheral blood using network methods
Cited by: 49
Author(s): Jarrett Morrow, Weiliang Qiu, Divya Chhabra, Stephen I. Rennard, Paula Belloni, Anton Belousov, Sreekumar Pillai, Craig P. Hersh
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12920-014-0060-2

A common gene expression signature in Huntington’s disease patient brain regions
Cited by: 46
Author(s): Andreas Neueder, Gillian P. Bates
Software Mentions: 2
Published: about 12 years ago

10.1186/s12920-020-0672-7

Pathway mapping of leukocyte transcriptome in influenza patients reveals distinct pathogenic mechanisms associated with progression to severe infection
Cited by: 12
Author(s): Yoann Zerbib, Emily Jenkins, Maryam Shojaei, Adrienne F. A. Meyers, John Ho, T. Blake Ball, Yoav Keynan, Amarnath Pisipati, Aseem Kumar, Anand Kumar, Marek Nalos, Benjamin Tang, Klaus Schughart, Anthony S. McLean
Software Mentions: 2
Published: over 6 years ago

10.1186/s12920-018-0431-1

Condition-specific gene co-expression network mining identifies key pathways and regulators in the brain tissue of Alzheimer’s disease patients
Cited by: 21
Author(s): Shunian Xiang, Zhi Huang, Tianfu Wang, Zhi Han, Christina Y. Yu, Dong Ni, Kun Huang, Jie Zhang
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12920-020-0689-y

Differential co-expression analysis reveals early stage transcriptomic decoupling in alzheimer’s disease
Cited by: 2
Author(s): Y. M. Upadhyaya, Linhui Xie, Paul Salama, Sha Cao, Kwangsik Nho, Andrew J. Saykin, Jingwen Yan
Software Mentions: 2
Published: over 6 years ago

10.1186/1755-8794-5-61

Adipose Co-expression networks across Finns and Mexicans identify novel triglyceride-associated genes
Cited by: 30
Author(s): Blake E. Haas, Steve Horvath, Kirsi H. Pietiläinen, Rita M. Cantor, Elina Nikkola, Daphna Weissglas‐Volkov, Aila Rissanen, Mete Civelek, Ivette Cruz-Bautista, Laura Riba, Johanna Kuusisto, Jaakko Kaprio, Teresa Tusié-Luna, Markku Laakso, Carlos A. Aguilar-Salinas, Päivi Pajukanta
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12920-016-0173-x

Efficient and biologically relevant consensus strategy for Parkinson’s disease gene prioritization
Cited by: 22
Author(s): Maykel Cruz-Monteagudo, Fernanda Borges, César Paz‐y‐Miño, M. Natália D. S. Cordeiro, Irene Rebelo, Yunierkis Pérez-Castillo, Aliuska Morales Helguera, Aminael Sánchez-Rodríguez, Eduardo Tejera
Software Mentions: 2
Published: over 10 years ago

10.1186/s12920-017-0288-8

Integrative model of leukocyte genomics and organ dysfunction in heart failure patients requiring mechanical circulatory support: a prospective observational study
Cited by: 5
Author(s): N. Wisniewski, G. Bondar, Christoph Rau, J. Chittoor, En‐Ting Chang, Azadeh Esmaeili, Martín Cadeiras, Mario C. Deng
Software Mentions: 2
Published: about 9 years ago

10.1186/s12920-021-00888-0

Novel prognostic genes and subclasses of acute myeloid leukemia revealed by survival analysis of gene expression data
Cited by: 4
Author(s): Yanli Lai, Guifang Ouyang, Lixia Sheng, Yanli Zhang, Binbin Lai, Miao Zhou
Software Mentions: 2
Published: over 5 years ago

10.1186/s12920-015-0078-0

Integrative network analysis reveals different pathophysiological mechanisms of insulin resistance among Caucasians and African Americans
Cited by: 15
Author(s): Swapan K. Das, Neeraj Kumar Sharma, Bin Zhang
Software Mentions: 2
Published: over 11 years ago

10.1186/s12920-021-00908-z

Identification of major depressive disorder disease-related genes and functional pathways based on system dynamic changes of network connectivity
Cited by: 6
Author(s): Ruijie Geng, Xiao Huang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12866-020-01853-0

Comparative transcriptome analysis of two Cercospora sojina strains reveals differences in virulence under nitrogen starvation stress
Cited by: 2
Author(s): Xiaorong Gu, Shuai Yang, Xiaoxue Yang, Liangliang Yao, Xuedong Gao, Maoming Zhang, Wei Liu, Haiming Zhao, Qingsheng Wang, Zengjie Li, Zhimin Li, Junjie Ding
Software Mentions: 2
Published: over 6 years ago

10.1186/s12866-020-1701-6

Marine bacterial communities in the upper gulf of Thailand assessed by Illumina next-generation sequencing platform
Cited by: 26
Author(s): Pongrawee Nimnoi, Neelawan Pongsilp
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12882-021-02447-2

Comprehensive analysis of diabetic nephropathy expression profile based on weighted gene co-expression network analysis algorithm
Cited by: 17
Author(s): Alieh Gholaminejad, Mohammad Fathalipour, Amir Roointan
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-019-1908-6

Time-series transcriptome provides insights into the gene regulation network involved in the volatile terpenoid metabolism during the flower development of lavender
Cited by: 32
Author(s): Hui Li, Jingrui Li, Yanmei Dong, Haiping Hao, Zhengyi Ling, Hongtong Bai, Huafang Wang, Hongxia Cui, Lei Shi
Software Mentions: 2
Published: over 7 years ago

10.1186/s12870-020-02522-0

Characterization and transcriptome analysis of a dominant genic male sterile cotton mutant
Cited by: 10
Author(s): Xinqi Cheng, Xinyu Zhang, Fei Xue, Shanfeng Zhu, Yanjun Li, Qian-Hao Zhu, Feng Liu, Jie Sun
Software Mentions: 2
Published: over 6 years ago

10.1186/s12870-019-1862-3

Comprehensive dissection of transcript and metabolite shifts during seed germination and post-germination stages in poplar
Cited by: 14
Author(s): Chunpu Qu, Zhuang Zuo, Lina Cao, Jiahuan Huang, Xue Sun, Peng Zhang, Chengjun Yang, Lixin Li, Xu Zhang, Guanjun Liu
Software Mentions: 2
Published: over 7 years ago

10.1186/s12870-017-1138-8

Gene coexpression network analysis of fruit transcriptomes uncovers a possible mechanistically distinct class of sugar/acid ratio-associated genes in sweet orange
Cited by: 20
Author(s): Liang Qiao, Minghao Cao, Jian Zheng, Yihong Zhao, Zhi‐Liang Zheng
Software Mentions: 2
Published: about 9 years ago

10.1186/s12870-017-1086-3

Genome-wide transcriptome profiling provides overwintering mechanism of Agropyron mongolicum
Cited by: 4
Author(s): J. Du, Xiaoquan Li, Tingting Li, Dongyang Yu, Bing Han
Software Mentions: 2
Published: about 9 years ago

10.1186/s12870-020-02726-4

Comparative transcriptome analysis reveals evolutionary divergence and shared network of cold and salt stress response in diploid D-genome cotton
Cited by: 5
Author(s): Yanchao Xu, Richard Odongo Magwanga, Dingsha Jin, Xiaoyan Cai, Yuqing Hou, Jie Zheng, Stephen Gaya Agong, Kunbo Wang, Fang Liu, Zhongli Zhou
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12870-018-1529-5

Comparative functional genomics analysis of bHLH gene family in rice, maize and wheat
Cited by: 56
Author(s): Kaifa Wei, Huiqin Chen
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12870-017-0998-2

Transcriptional analysis of defense mechanisms in upland tetraploid switchgrass to greenbugs
Cited by: 32
Author(s): Teresa Donze-Reiner, Nathan A. Palmer, Erin D. Scully, T. J. Prochaska, Kyle G. Koch, Tiffany Heng-Moss, Jeffrey D. Bradshaw, Paul Twigg, Keenan Amundsen, Scott E. Sattler, Gautam Sarath
Software Mentions: 2
Published: over 9 years ago

10.1186/s12870-021-02939-1

Comprehensive transcriptional analysis reveals salt stress-regulated key pathways, hub genes and time-specific responsive gene categories in common bermudagrass (Cynodon dactylon (L.) Pers.) roots
Cited by: 13
Author(s): An Shao, Wei Wang, Shugao Fan, Xiao Xu, Yanling Yin, Erick Amombo, Xiaoning Li, Guangyang Wang, Hongli Wang, Jinmin Fu
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-021-02889-8

Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour
Cited by: 9
Author(s): Elise Bizouerne, Julia Buitink, Benoît Ly Vu, Joseph Ly Vu, Eddi Esteban, Asher Pasha, Nicholas J. Provart, Jérôme Verdier, Olivier Leprince
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-021-02983-x

Comparative transcriptome profiling and co-expression network analysis uncover the key genes associated withearly-stage resistance to Aspergillus flavus in maize
Cited by: 13
Author(s): Huanhuan Liu, Haofeng Wu, Yan Wang, Huan Wang, Saihua Chen, Zhitong Yin
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-020-02705-9

Weighted gene coexpression network analysis-based identification of key modules and hub genes associated with drought sensitivity in rice
Cited by: 15
Author(s): Baiyang Yu, Jianbin Liu, Di Wu, Ying Liu, Weijian Cen, Shaokui Wang, Rongbai Li, Jijing Luo
Software Mentions: 2
Published: about 6 years ago

10.1186/s12870-020-2322-9

Identification of the regulatory networks and hub genes controlling alfalfa floral pigmentation variation using RNA-sequencing analysis
Cited by: 21
Author(s): Huirong Duan, Lirong Wang, Guangxin Cui, Xingyue Zhou, Xiaorong Duan, Hongshan Yang
Software Mentions: 2
Published: over 6 years ago

10.1186/s12870-021-02965-z

Transcriptome regulation of carotenoids in five flesh-colored watermelons (Citrullus lanatus)
Cited by: 13
Author(s): Pingli Yuan, Muhammad Umer, Nan He, Shanjiang Zhao, Xingrong Lu, Huiling Zhu, Chengsheng Gong, Weinan Diao, Haileslassie Gebremeskel, Hanhui Kuang, Wenge Liu
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-020-2245-5

Comparative transcriptome analysis reveals the response mechanism of Cf-16-mediated resistance to Cladosporium fulvum infection in tomato
Cited by: 16
Author(s): Dongye Zhang, Yufang Bao, Yaoguang Sun, Huanhuan Yang, Tingting Zhao, Hui-Jia Li, Chong Du, Jingbin Jiang, Jin-Fu Li, Libo Xie, Xiangyang Xu
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12870-019-2021-6

Exploring gene networks in two sunflower lines with contrasting leaf senescence phenotype using a system biology approach
Cited by: 9
Author(s): Sebastián Moschen, Johanna Marino, Salvador Nicosia, Janet Higgins, Saleh Alseekh, Francisco Horacio Astigueta, Sofía A. Bengoa Luoni, Máximo Rivarola, Alisdair R. Fernie, Nicolas Blanchet, Nicolas B. Langlade, Norma Paniego, Paula Fernández, Ruth Amelia Heinz
Software Mentions: 2
Published: about 7 years ago

10.1186/s12870-015-0496-3

Seedling development traits in Brassica napus examined by gene expression analysis and association mapping
Cited by: 24
Author(s): Niklas Körber, Anja Bus, Jinquan Li, Janet Higgins, Ian Bancroft, Erin E. Higgins, Isobel A. P. Parkin, Bertha M. Salazar-Colqui, Rod J. Snowdon, Benjamin Stich
Software Mentions: 2
Published: over 11 years ago

10.1186/s12870-018-1526-8

Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress
Cited by: 31
Author(s): Lingling Wang, Zhaoen Yang, Bin Zhang, Daoqian Yu, Ji Liu, Qian Gong, Ghulam Qanmber, Yi Li, Lili Lu, Yongjun Lin, Zuoren Yang, Fuguang Li
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12870-019-1695-0

Transcriptomic analysis reveals the regulatory module of apple (Malus × domestica) floral transition in response to 6-BA
Cited by: 19
Author(s): Youmei Li, Dong Zhang, Na An, Shiliang Fan, Xia Zuo, Xin Zhang, Lizhi Zhang, Giampiero Cai, Mingyu Han, Libo Xing
Software Mentions: 2
Published: over 7 years ago

10.1186/s12870-020-2288-7

Comparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize
Cited by: 45
Author(s): Yixuan Li, Kaifa Wei
Software Mentions: 2
Published: over 6 years ago

10.1186/s12870-021-02927-5

The mechanism of sesame resistance against Macrophomina phaseolina was revealed via a comparison of transcriptomes of resistant and susceptible sesame genotypes
Cited by: 11
Author(s): Wenqing Yan, Yunxia Ni, Xintao Liu, Hui Zhao, Yanhua Chen, Min Jiang, Mingming Liu, Hongyan Liu, Bin Tian
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-020-02697-6

BrrICE1.1 is associated with putrescine synthesis through regulation of the arginine decarboxylase gene in freezing tolerance of turnip (Brassica rapa var. rapa)
Cited by: 12
Author(s): Xin Yin, Yunqiang Yang, Yanqiu Lv, Yan Li, Danni Yang, Yanling Yue, Yongping Yang
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12870-020-02582-2

Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)
Cited by: 4
Author(s): Xiaofei Xu, Guangyan Feng, Yueyang Liang, Shuai Yang, Qiuxu Liu, Gang Nie, Zhongfu Yang, Linkai Hang, Xinquan Zhang
Software Mentions: 2
Published: about 6 years ago

10.1186/s12870-017-1220-2

Identification of AUXIN RESPONSE FACTOR gene family from Prunus sibirica and its expression analysis during mesocarp and kernel development
Cited by: 14
Author(s): Jun Niu, Quanxin Bi, Shuya Deng, Huiping Chen, Haiyan Yu, Libing Wang, Senjie Lin
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12870-018-1430-2

The key genes and pathways related to male sterility of eggplant revealed by comparative transcriptome analysis
Cited by: 28
Author(s): Yan Yang, Shengyou Bao, Xiaohui Zhou, Jun Li, Yun Zhuang
Software Mentions: 2
Published: about 8 years ago

10.1186/s12870-021-02921-x

Dynamic transcriptome analysis identifies genes related to fatty acid biosynthesis in the seeds of Prunus pedunculata Pall
Cited by: 1
Author(s): Wenquan Bao, Dun Ao, Lin Wang, Zhihao Ling, Maoshan Chen, Yue Bai, Tana Wuyun, Junxing Chen, Shuning Zhang, Fengming Li
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-019-1976-7

Gene co-expression network analysis reveals pathways associated with graft healing by asymmetric profiling in tomato
Cited by: 35
Author(s): Lulu Xie, C.Y. Dong, Qingmao Shang
Software Mentions: 2
Published: about 7 years ago

10.1186/s12870-020-02694-9

Integration analysis of PacBio SMRT- and Illumina RNA-seq reveals candidate genes and pathway involved in selenium metabolism in hyperaccumulator Cardamine violifolia
Cited by: 23
Author(s): Shen Rao, Yu Tian, Xin Cong, Feng Xu, Xiaozhuo Lai, Weiwei Zhang, Yongling Liao, Shuiyuan Cheng
Software Mentions: 2
Published: about 6 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479