cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1186/s12885-018-4626-9

Fatty acid oxidation is associated with proliferation and prognosis in breast and other cancers
Cited by: 54
Author(s): Aziz Aiderus, Michael A. Black, Anita K. Dunbier
Software Mentions: 3
Published: about 8 years ago

10.1186/s12885-021-08331-4

Hsa_circ_0000301 facilitates the progression of cervical cancer by targeting miR-1228-3p/IRF4 Axis
Cited by: 9
Author(s): Zhanfeng Deng, Fangfang Dai, Quan Zhou, Yanxiang Cheng
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-017-4261-x

Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis
Cited by: 12
Author(s): Dejian Zhao, Mingyan Lin, Erika Pedrosa, Herbert M. Lachman, Deyou Zheng
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-016-2547-z

Bioinformatic analyses in early host response to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) reveals pathway differences between pigs with alternate genotypes for a major host response QTL
Cited by: 24
Author(s): Martine Schroyen, Christopher J. Eisley, James E. Koltes, Eric R. Fritz-Waters, Igseo Choi, Graham Plastow, Leluo Guan, Paul Stothard, Hua Bao, Arun Kommadath, James M. Reecy, Joan K. Lunney, R. Rowland, Jack C. M. Dekkers, Christopher K. Tuggle
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-021-07873-y

Third-generation sequencing and metabolome analysis reveal candidate genes and metabolites with altered levels in albino jackfruit seedlings
Cited by: 10
Author(s): Xiangxu Meng, Jiahong Xu, Maoning Zhang, Ruyue Du, Wenxiu Zhao, Qing Zeng, Zhihua Tu, Jinhui Chen, Beibei Chen
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-021-07649-4

Disentangling the aging gene expression network of termite queens
Cited by: 6
Author(s): José Manuel Monroy Kuhn, Karen Meusemann, Judith Korb
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-020-07040-9

Developmentally regulated activation of defense allows for rapid inhibition of infection in age-related resistance to Phytophthora capsici in cucumber fruit
Cited by: 8
Author(s): Ben N. Mansfeld, Marivi Colle, Chunqiu Zhang, Ying-Zu Lin, Rebecca Grumet
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-021-07953-z

Integrative lncRNA landscape reveals lncRNA-coding gene networks in the secondary cell wall biosynthesis pathway of moso bamboo (Phyllostachys edulis)
Cited by: 9
Author(s): Jiongliang Wang, Yinguang Hou, Yu Wang, Hansheng Zhao
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-019-5803-1

Expression dynamics of repetitive DNA in early human embryonic development
Cited by: 31
Author(s): Cihangir Yandım, Gökhan Karakülah
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-019-5923-7

Honey bee (Apis mellifera) larval pheromones may regulate gene expression related to foraging task specialization
Cited by: 15
Author(s): Rong Ma, Juliana Rangel, Christina M. Grozinger
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-018-5017-y

Genome wide transcriptome analysis provides bases on colonic mucosal immune system development affected by colostrum feeding strategies in neonatal calves
Cited by: 6
Author(s): Zhixiong He, Albert J. Fischer, Yang Song, M.A. Steele, Le Luo Guan
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-016-2935-4

Transcriptome profiling of the rumen epithelium of beef cattle differing in residual feed intake
Cited by: 84
Author(s): Rebecca S. G. Kong, Guanxiang Liang, Yanhong Chen, Paul Stothard, Le Luo Guan
Software Mentions: 3
Published: about 10 years ago

10.1186/s12864-021-07797-7

Transcriptome profiling of developing leaf and shoot apices to reveal the molecular mechanism and co-expression genes responsible for the wheat heading date
Cited by: 9
Author(s): Yuxin Yang, Xueying Zhang, Lifen Wu, Lichao Zhang, Guoxiang Liu, Chuan Xia, Lai Xu, Xiuying Kong
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-021-07423-6

Consensus module analysis of abdominal fat deposition across multiple broiler lines
Cited by: 7
Author(s): Hui Yuan, Jun Lü
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-12-264

Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)
Cited by: 104
Author(s): W. Walter Lorenz, Rob Alba, Yuan-Sheng Yu, John Michael Bordeaux, Marta Simões, Jeffrey F. D. Dean
Software Mentions: 3
Published: over 15 years ago

10.1186/1471-2164-10-405

Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients
Cited by: 151
Author(s): Christiaan G J Saris, Steve Horvath, Paul W.J. van Vught, Michael A. van Es, Hylke M. Blauw, Tova Fuller, Peter Langfelder, Joseph DeYoung, John H. J. Wokke, Jan H. Veldink, Leonard H van den Berg, Roel A. Ophoff
Software Mentions: 3
Published: about 17 years ago

10.1186/1471-2164-15-852

Transcriptional response to cardiac injury in the zebrafish: systematic identification of genes with highly concordant activity across in vivo models
Cited by: 10
Author(s): Sophie Rodius, Petr V. Nazarov, Isabel A. Nepomuceno-Chamorro, Céline Jeanty, Juan Manuel González‐Rosa, Mark Ibberson, Ricardo Costa, Ioannis Xénarios, Nadia Mercader, Francisco Azuaje
Software Mentions: 3
Published: about 12 years ago

10.1186/s12864-018-5345-y

Gene co-expression networks associated with carcass traits reveal new pathways for muscle and fat deposition in Nelore cattle
Cited by: 30
Author(s): Bárbara Silva-Vignato, Luiz Lehmann Coutinho, Mirele Daiana Poleti, A. S. M. César, Cristina Tschorny Moncau, Luciana Correia de Almeida Regitano, J. C. C. Balieiro
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-021-07584-4

Identification of co-expression network correlated with different periods of adipogenic and osteogenic differentiation of BMSCs by weighted gene co-expression network analysis (WGCNA)
Cited by: 13
Author(s): Yu Liu, Markus Tingart, Sophie Lecouturier, Jianzhang Li, Jörg Eschweiler
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-020-06805-6

Gene coexpression network analysis and tissue-specific profiling of gene expression in jute (Corchorus capsularis L.)
Cited by: 7
Author(s): Zemao Yang, Zhigang Dai, Xiaojun Chen, Dongwei Xie, Qing Tang, Chaohua Cheng, Ying Xu, Canhui Deng, Chan Lee, Jiquan Chen
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-021-07690-3

Functional prediction of de novo uni-genes from chicken transcriptomic data following infectious bursal disease virus at 3-days post-infection
Cited by: 0
Author(s): Bahiyah Azli, Sharanya Ravi, M. Hair-Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-021-08035-w

Construction of a ceRNA network in glioma and analysis of its clinical significance
Cited by: 4
Author(s): Guangdong Liu, Haihong Li, Wenyang Ji, Haidong Gong, Yan Jiang, Guomin Ji
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-021-07935-1

A validated generally applicable approach using the systematic assessment of disease modules by GWAS reveals a multi-omic module strongly associated with risk factors in multiple sclerosis
Cited by: 4
Author(s): Tejaswi V. S. Badam, Hendrik A de Weerd, David Martínez-Enguita, Tomas Olsson, Lars Alfredsson, Ingrid Kockum, Maja Jagodic, Zelmina Lubovac-Pilav, Mika Gustafsson
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-021-07977-5

Comparison of the transcriptome in circulating leukocytes in early lactation between primiparous and multiparous cows provides evidence for age-related changes
Cited by: 4
Author(s): Laura Buggiotti, Zhangrui Cheng, Mazdak Salavati, Claire Wathes
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-021-07366-y

PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response
Cited by: 18
Author(s): Xiaojie Liu, Xiaoshuang Li, Xiangying Wen, Yan Zhang, Yu Ding, Yiheng Zhang, Bei Gao, Daoyuan Zhang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-016-3198-9

Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems
Cited by: 81
Author(s): Le Shu, Yuqi Zhao, Zeyneb Kurt, Sean G. Byars, Taru Tukiainen, Johannes Kettunen, Luz D. Orozco, Matteo Pellegrini, Aldons J. Lusis, Samuli Ripatti, Bin Zhang, Michael Inouye, Ville Mäkinen, Xia Yang
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12864-020-06877-4

Pervasive duplication, biased molecular evolution and comprehensive functional analysis of the PP2C family in Glycine max
Cited by: 4
Author(s): Kai Fan, Yunrui Chen, Zhijun Mao, Fang Yao, Zhaowei Li, Weiwei Lin, Yongqiang Zhang, Jianping Liu, Jinwen Huang
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-15-905

Limited sex-biased neural gene expression patterns across strains in Zebrafish (Danio rerio)
Cited by: 54
Author(s): Ryan Y. Wong, Melissa M McLeod, John Godwin
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12864-021-07683-2

A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
Cited by: 11
Author(s): Aliki Xanthopoulou, Javier Montero‐Pau, Belén Picó, Panagiotis Boumpas, Eleni Tsaliki, Harry S. Paris, Athanasios Tsaftaris, Apostolos Kalivas, Ιfigeneia Mellidou, Ioannis Ganopoulos
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-020-07310-6

Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia)
Cited by: 23
Author(s): Shan Feng, Hongcheng Fang, Xia Liu, Yixin Dong, Qingpeng Wang, Ke Qiang Yang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-020-07191-9

Immune challenge reduces gut microbial diversity and triggers fertility-dependent gene expression changes in a social insect
Cited by: 5
Author(s): Matteo Negroni, Francisca H. I. D. Segers, Fanny Vogelweith, Susanne Foitzik
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-018-5021-2

Long non-coding RNAs potentially function synergistically in the cellular reprogramming of SCNT embryos
Cited by: 20
Author(s): Fengrui Wu, Yong Liu, Qingqing Wu, Dengkun Li, Ling Zhang, Xiaoqing Wu, Rong Wang, Di Zhang, Shaorong Gao, Wenyong Li
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-020-07151-3

Methylome and transcriptome profiles in three yak tissues revealed that DNA methylation and the transcription factor ZGPAT co-regulate milk production
Cited by: 3
Author(s): Jinwei Xin, Zhixin Chai, Chengfu Zhang, Qiang Zhang, Yong Zhu, Hanwen Cao, Yangji Cidan, Xiaoying Chen, Hui Jiang, Jincheng Zhong, Qiumei Ji
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-016-3384-9

Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation
Cited by: 25
Author(s): Sam Buckberry, Tina Bianco‐Miotto, Stephen J. Bent, Vicki L. Clifton, Cheryl Shoubridge, Kartik Shankar, Claire T. Roberts
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12864-016-2720-4

Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus
Cited by: 27
Author(s): Jamie M. Wilkinson, Hua Bao, Andrea Ladinig, Linjun Hong, Paul Stothard, Joan K. Lunney, Graham Plastow, John C. S. Harding
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2164-16-S8-S5

Bioinformatics analysis of thousands of TCGA tumors to determine the involvement of epigenetic regulators in human cancer
Cited by: 30
Author(s): Florian Gnad, Sophia Doll, Gerard Manning, David Arnott, Zemin Zhang
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-018-5176-x

funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data
Cited by: 5
Author(s): Liis Kolberg, Ivan Kuzmin, Priit Adler, Jaak Vilo, Hedi Peterson
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2164-11-20

Gene expression profiling in C57BL/6J and A/J mouse inbred strains reveals gene networks specific for brain regions independent of genetic background
Cited by: 17
Author(s): Simone de Jong, Tova Fuller, Esther Janson, Eric Strengman, Steve Horvath, Martien Kas, Roel A. Ophoff
Software Mentions: 3
Published: almost 17 years ago

10.1186/1471-2164-14-450

Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution
Cited by: 49
Author(s): Gang Fang, Karla D. Passalacqua, Jason Hocking, Paula Montero Llopis, Mark Gerstein, Nicholas H. Bergman, Christine Jacobs‐Wagner
Software Mentions: 3
Published: over 13 years ago

10.1186/s12864-020-06918-y

Multi-omics sequencing provides insight into floral transition in Catalpa bungei. C.A. Mey
Cited by: 1
Author(s): Zhi Wang, Wenjun Ma, Tianqing Zhu, Nan Lu, Fangqun Ouyang, Nan Wang, Guijuan Yang, Lisheng Kong, Guanzheng Qu, Shougong Zhang, Junhui Wang
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-019-6245-5

Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response
Cited by: 44
Author(s): Yuanda Lv, Fengqin Hu, Yongfeng Zhou, Feilong Wu, Brandon S. Gaut
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-018-5091-1

Transcriptional defects and reprogramming barriers in somatic cell nuclear reprogramming as revealed by single-embryo RNA sequencing
Cited by: 23
Author(s): Yong Liu, Fengrui Wu, Ling Zhang, Xiaoqing Wu, Dengkun Li, Xin Jing, Juan Xie, Feng Kong, Wenying Wang, Qiaoqin Wu, Di Zhang, Rong Wang, Shaorong Gao, Wenyong Li
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-021-07991-7

Morphological, physiological, and transcriptional responses to low nitrogen stress in Populus deltoides Marsh. clones with contrasting nitrogen use efficiency
Cited by: 2
Author(s): Cun Chen, Ying‐Hao Chu, Qinjun Huang, Weixi Zhang, Changjun Ding, Jing Zhang, Bo Li, Tengqian Zhang, Zhenghong Li, Xiaohua Su
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-020-6482-7

Dynamic accumulation of fatty acids in duck (Anas platyrhynchos) breast muscle and its correlations with gene expression
Cited by: 15
Author(s): Wenlei Fan, Wenjing Liu, Hehe Liu, Qingshi Meng, Yaxi Xu, Yuming Guo, Baowei Wang, Zhengkui Zhou, Shuisheng Hou
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-021-07969-5

Integrated analysis of lncRNA and mRNA in liver of Megalobrama amblycephala post Aeromonas hydrophila infection
Cited by: 7
Author(s): Qianhui Sun, Jixiu Wang, Guowen Wang, Huanling Wang, Hong Liu
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-015-1741-8

Whole blood microarray analysis of pigs showing extreme phenotypes after a porcine reproductive and respiratory syndrome virus infection
Cited by: 13
Author(s): Martine Schroyen, Juan P. Steibel, James E. Koltes, Igseo Choi, Nancy E. Raney, Christopher J. Eisley, Eric R. Fritz-Waters, James M. Reecy, Jack C. M. Dekkers, R. Rowland, Joan K. Lunney, Catherine W. Ernst, Christopher K. Tuggle
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-018-4967-4

Comparative transcriptome analysis of the interaction between Actinidia chinensis var. chinensis and Pseudomonas syringae pv. actinidiae in absence and presence of acibenzolar-S-methyl
Cited by: 30
Author(s): V. Michelotti, Antonella Lamontanara, Giampaolo Buriani, Luigi Orrù, Antonio Cellini, Irene Donati, J. L. Vanneste, Luigi Cattivelli, G. Tacconi, Francesco Spinelli
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-015-1390-y

Transcript profiling of Populus tomentosa genes in normal, tension, and opposite wood by RNA-seq
Cited by: 41
Author(s): Jinhui Chen, Beibei Chen, Deqiang Zhang
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-016-3259-0

Pan-cancer analysis of frequent DNA co-methylation patterns reveals consistent epigenetic landscape changes in multiple cancers
Cited by: 46
Author(s): Jie Zhang, Kun Huang
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12864-018-4514-3

Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle
Cited by: 31
Author(s): Guilherme Bueno de Oliveira, Luciana Correia de Almeida Regitano, Aline Silva Mello Cesar, James M. Reecy, Karina Y. Degaki, Mirele Daiana Poleti, Andrezza Maria Felício, James E. Koltes
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-020-07037-4

Gene expression within the periaqueductal gray is linked to vocal behavior and early-onset parkinsonism in Pink1 knockout rats
Cited by: 12
Author(s): Cynthia A. Kelm‐Nelson, Stephen C. Gammie
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-015-1626-x

Characterizing the neurotranscriptomic states in alternative stress coping styles
Cited by: 37
Author(s): Ryan Y. Wong, Melissa S. Lamm, John Godwin
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-019-6055-9

Dynamics of transcriptome changes during subcutaneous preadipocyte differentiation in ducks
Cited by: 9
Author(s): Zheng Wang, Zhong-Tao Yin, Fan Zhang, Xiao-qin Li, Si-Rui Chen, Ning Yang, Tom E. Porter, Zhuocheng Hou
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-018-5406-2

Identification of a metabolomic signature associated with feed efficiency in beef cattle
Cited by: 48
Author(s): Francisco José de Novais, Pedro Ratto Lisboa Pires, Pâmela Almeida Alexandre, Robert A. Dromms, Amadeu Hoshi Iglesias, José Bento Sterman Ferraz, Mark P. Styczynski, Heidge Fukumasu
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-015-2142-8

Gene expression analysis at the onset of sex differentiation in turbot (Scophthalmus maximus)
Cited by: 35
Author(s): Diego Robledo, Laia Ribas, Rosa Cal, Laura Sánchez, Francesc Piferrer, Paulino Martı́nez, Ana Viñas
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12864-020-07195-5

Characterizing glycosyltransferases by a combination of sequencing platforms applied to the leaf tissues of Stevia rebaudiana
Cited by: 12
Author(s): Shaoshan Zhang, Qiong Liu, Chengcheng Lyu, Jinsong Chen, Ruofu Xiao, Jingtian Chen, Yunshu Yang, Huihui Zhang, Kai Hou, Wei Wu
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-015-2068-1

A novel approach identifies the first transcriptome networks in bats: a new genetic model for vocal communication
Cited by: 15
Author(s): Pedro Rodenas-Cuadrado, Xiaowei Sylvia Chen, Lutz Wiegrebe, Uwe Firzlaff, Sonja C. Vernes
Software Mentions: 3
Published: about 11 years ago

10.1186/s12864-020-07277-4

Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L
Cited by: 13
Author(s): Ning Li, Ziwei Meng, Tao Mei, Yueyuan Wang, Yulan Zhang, Shufen Li, Wu‐Jun Gao, Chuan‐Liang Deng
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-018-4807-6

Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress
Cited by: 56
Author(s): Liang Chen, Shilai Shi, Ninfei Jiang, Hira Khanzada, Ziming Wu, Zhu C, Xiaosong Peng, Jie Xu, Yujin Chen, Qi Yu, Xu He, Junru Fu, Xiaorong Chen, Lifang Hu, Liang Ouyang, Xiaotang Sun, Haohua He, Jianmin Bian
Software Mentions: 3
Published: over 8 years ago

10.1186/s12916-015-0282-y

Multi-omic signature of body weight change: results from a population-based cohort study
Cited by: 58
Author(s): Simone Wahl, Susanne Vogt, Ferdinand Stückler, Jan Krumsiek, Jörg Bartel, Tim Kacprowski, Katharina Schramm, Maren Carstensen, Wolfgang Rathmann, Michael Roden, Carolin Jourdan, Antti J. Kangas, Pasi Soininen, Mika Ala‐Korpela, Ute Nöthlings, Heiner Boeing, Fabian J. Theis, Christa Meisinger, Mélanie Waldenberger, Karsten Suhre, Georg Homuth, Christian Gieger, Gabi Kastenmüller, Thomas Illig, Jakob Linseisen, Annette Peters, Holger Prokisch, Christian Herder, Barbara Thorand, Harald Grallert
Software Mentions: 3
Published: over 11 years ago

10.1186/s12920-020-0707-0

Transcriptome analysis reveals the link between lncRNA-mRNA co-expression network and tumor immune microenvironment and overall survival in head and neck squamous cell carcinoma
Cited by: 19
Author(s): Zhaoming Zhong, Min Hee Hong, Xiao Chen, Yan Xi, Yuanyuan Xu, Deyu Kong, Jun Deng, Yun Li, Rui Hu, Chuanzheng Sun, Jin Liang
Software Mentions: 3
Published: over 6 years ago

10.1186/s12920-020-00750-9

Weighted correlation network bioinformatics uncovers a key molecular biosignature driving the left-sided heart failure
Cited by: 8
Author(s): Jiamin Zhou, Wei Zhang, Chunying Wei, Zhiliang Zhang, Dasong Yi, Xiaoping Peng, Jianheng Peng, Rong Yin, Zeqi Zheng, Hongmei Qi, Yunfeng Wei, Tong-Chun Wen
Software Mentions: 3
Published: over 6 years ago

10.1186/s12920-020-00782-1

Improving lung cancer risk stratification leveraging whole transcriptome RNA sequencing and machine learning across multiple cohorts
Cited by: 11
Author(s): Yoonha Choi, Jianghan Qu, Esther Wu, Yangyang Hao, Jiarui Zhang, Jicai Ning, Xinwu Yang, Lori Lofaro, Daniel G. Pankratz, Joshua E. Babiarz, P. Sean Walsh, Ehab Billatos, Marc E. Lenburg, Giulia C. Kennedy, Jon McAuliffe, Jing Huang
Software Mentions: 3
Published: about 6 years ago

10.1186/s12920-017-0253-6

Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications
Cited by: 33
Author(s): Amir Foroushani, Rupesh Agrahari, T. Roderick Docking, Linda Chang, Gerben Duns, Monika Hudoba, Aly Karsan, Habil Zare
Software Mentions: 3
Published: over 9 years ago

10.1186/s12920-020-0693-2

Potential role of genomic imprinted genes and brain developmental related genes in autism
Cited by: 8
Author(s): Jian Li, Xue Lü, Mingya Wang, Yunyun Hu, Kaiyu Xue, Shuanglin Gu, Lili Lv, Saijun Huang, Wei Xie
Software Mentions: 3
Published: over 6 years ago

10.1186/s12920-019-0613-5

Improved cell composition deconvolution method of bulk gene expression profiles to quantify subsets of immune cells
Cited by: 19
Author(s): Yen Jung Chiu, Yi Hsuan Hsieh, Yen Hua Huang
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12920-021-01010-0

Identification of macrophage related gene in colorectal cancer patients and their functional roles
Cited by: 2
Author(s): Yingxiang Chen, Cui Zhang, Xiang Zou, Man Yu, Bo Yang, Chenfeng Ji, Shuangquan Gao, Jun Li, Bin Liu
Software Mentions: 3
Published: over 5 years ago

10.1186/s12920-021-00892-4

Identification of biomarkers and pathogenesis in severe asthma by coexpression network analysis
Cited by: 7
Author(s): Zeyi Zhang, Jingjing Wang, Ou Chen
Software Mentions: 3
Published: over 5 years ago

10.1186/s12920-018-0433-z

Identification of cancer subtypes from single-cell RNA-seq data using a consensus clustering method
Cited by: 31
Author(s): Yanglan Gan, Ning Li, Guobing Zou, Yongchang Xin, Jihong Guan
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12891-021-03958-7

HEMGN and SLC2A1 might be potential diagnostic biomarkers of steroid-induced osteonecrosis of femoral head: study based on WGCNA and DEGs screening
Cited by: 10
Author(s): Zhixin Wu, Yinxian Wen, Guanlan Fan, Hangyuan He, Siqi Zhou, Liaobin Chen
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2202-15-11

Genes showing altered expression in the medial preoptic area in the highly social maternal phenotype are related to autism and other disorders with social deficits
Cited by: 33
Author(s): Terri M. Driessen, Brian E. Eisinger, Changjiu Zhao, Sharon A. Stevenson, Michael C. Saul, Stephen C. Gammie
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12870-014-0348-6

chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes
Cited by: 7
Author(s): Thomas Nußbaumer, Karl G. Kugler, Wolfgang Schweiger, Kai Christian Bader, Heidrun Gundlach, Manuel Spannagl, Naser Poursarebani, Matthias Pfeifer, Klaus Mayer
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12870-021-03051-0

Study on the differences of gene expression between pear and apple wild cultivation materials based on RNA-seq technique
Cited by: 3
Author(s): Huangwei Zhang, Meng Li, Min Jung Kong, Jim M. Dunwell, Yuyan Zhang, Chao Yue, Juyou Wu, Shaoling Zhang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12870-021-02893-y

Composition and diversity of bacterial communities in the rhizosphere of the Chinese medicinal herb Dendrobium
Cited by: 32
Author(s): Jiajia Zuo, Mengting Zu, Lei Liu, Xiaomei Song, Yingdan Yuan
Software Mentions: 3
Published: over 5 years ago

10.1186/s12870-014-0307-2

RNA-sequencing reveals early, dynamic transcriptome changes in the corollas of pollinated petunias
Cited by: 39
Author(s): Shaun R. Broderick, Saranga Wijeratne, Asela J Wijeratn, Laura J. Chapin, Tea Meulia, Michelle L. Jones
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12870-019-2169-0

Differential gene expression among three sex types reveals a MALE STERILITY 1 (CpMS1) for sex differentiation in papaya
Cited by: 11
Author(s): Dessireé Zerpa‐Catanho, Jennifer Wai, Ming Li Wang, Liang Yu, Julie Nguyen, Ray Ming
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12870-019-2196-x

Comparative transcriptome analysis indicates that a core transcriptional network mediates isonuclear alloplasmic male sterility in wheat (Triticum aestivum L.)
Cited by: 20
Author(s): Zihan Liu, Sha Li, Wei Li, Qi Liu, Lingli Zhang, Xiyue Song
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12870-017-1143-y

Co-expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium-responsive genes
Cited by: 80
Author(s): Tan Ming, Dan Cheng, Yunhai Yang, Guoqiang Zhang, Mengjie Qin, Jun Chen, Yahua Chen, Mingyi Jiang
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12870-019-1952-2

Genome-wide transcriptional adaptation to salt stress in Populus
Cited by: 28
Author(s): Jin-Gui Liu, Xiao Han, Tianbo Yang, Wenhui Cui, Aimin Wu, Chunxiang Fu, Baichen Wang, Lijun Liu
Software Mentions: 3
Published: about 7 years ago

10.1186/s12870-020-02419-y

Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency
Cited by: 16
Author(s): Yang Xiao-ling, Xiuzhong Xia, Zhen Yu, Baoxuan Nong, Zongqiong Zhang, Yanyan Wu, Qian Tian, Weiying Zeng, Ju Gao, Weiyong Zhou, He Liang, Danting Li, Gaofeng Deng
Software Mentions: 3
Published: over 6 years ago

10.1186/s12870-015-0568-4

Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease
Cited by: 43
Author(s): Nidhi Rawat, Sandhya.P. Kiran, Dongliang Du, Fred G. Gmitter, Zhanao Deng
Software Mentions: 3
Published: over 11 years ago

10.1186/s12870-020-02612-z

Insights into the resistance of a synthetically-derived wheat to Septoria tritici blotch disease: less is more
Cited by: 6
Author(s): Harriet R. Benbow, Ciarán J. Brennan, Binbin Zhou, Thalia Christodoulou, Simon Berry, Cristóbal Uauy, Ewen Mullins, Fiona M. Doohan
Software Mentions: 3
Published: about 6 years ago

10.1186/s12870-020-02735-3

Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum)
Cited by: 5
Author(s): Wenqing Zhang, Shengkui Zhang, Xianqin Lu, Can Li, Xingwang Liu, Geyu Dong, Tao Xia
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13104-015-1141-9

Dysregulated mechanisms underlying Duchenne muscular dystrophy from co-expression network preservation analysis
Cited by: 15
Author(s): Kavitha Mukund, Shankar Subramaniam
Software Mentions: 3
Published: over 11 years ago

10.1186/s12918-017-0420-6

An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks
Cited by: 196
Author(s): Juan A. Botía, Jana Vandrovcová, Paola Forabosco, Sebastian Guelfi, Karishma D’Sa, John Hardy, Cathryn M. Lewis, Mina Ryten, Michael E. Weale
Software Mentions: 3
Published: over 9 years ago

10.1186/s12918-016-0366-0

Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion
Cited by: 87
Author(s): Mingyan Lin, Erika Pedrosa, Anastasia Hrabovsky, Jian Chen, Benjamin R. Puliafito, Stephanie R. Gilbert, Deyou Zheng, Herbert M. Lachman
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12918-016-0336-6

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus
Cited by: 51
Author(s): Jason McDermott, Hugh D. Mitchell, Lisa E. Gralinski, Amie J. Eisfeld, Laurence Josset, Armand Bankhead, Gabriele Neumann, Susan C. Tilton, Alexandra Schäfer, Chengjun Liu, Shufang Fan, Shannon K. McWeeney, Ralph S. Baric, Michael G. Katze, Katrina M. Waters
Software Mentions: 3
Published: about 10 years ago

10.1186/1752-0509-2-95

Integrated Weighted Gene Co-expression Network Analysis with an Application to Chronic Fatigue Syndrome
Cited by: 152
Author(s): Angela P. Presson, Eric M. Sobel, Jeanette C. Papp, Charlyn Suarez, Toni Whistler, Mangalathu S. Rajeevan, Suzanne D. Vernon, Steve Horvath
Software Mentions: 3
Published: almost 18 years ago

10.1136/bmjdrc-2019-000751

Peritoneal macrophages have an impaired immune response in obesity which can be reversed by subsequent weight loss
Cited by: 10
Author(s): Lisa Willemsen, Annette E. Neele, Saskia van der Velden, K.H.M. Prange, Myrthe den Toom, Cindy P. A. A. van Roomen, Myrthe E. Reiche, Guillermo R. Griffith, Marion J.J. Gijbels, Esther Lutgens, Menno P.J. de Winther
Software Mentions: 3
Published: about 7 years ago

10.1155/2019/6469420

Integrated Analysis of Oncogenic Networks in Colorectal Cancer Identifies GUCA2A as a Molecular Marker
Cited by: 24
Author(s): Hui Zhang, Yuanyuan Du, Zhuo Wang, Rui Lou, Jianzhong Wu, Jifeng Feng
Software Mentions: 3
Published: over 7 years ago

10.1590/1414-431X20198333

Screening potential prognostic biomarkers of long non-coding RNAs for predicting the risk of chronic kidney disease
Cited by: 11
Author(s): Na Li, Yan Cui, Min Yin, Feng Liu
Software Mentions: 3
Published: almost 8 years ago

10.1093/bib/bbw114

Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences
Cited by: 444
Author(s): Claudia Manzoni, Demis A. Kia, Jana Vandrovcová, John Hardy, Nicholas W. Wood, Patrick A. Lewis, Raffaele Ferrari
Software Mentions: 3
Published: almost 10 years ago

10.1093/bib/bbw139

Gene co-expression analysis for functional classification and gene–disease predictions
Cited by: 511
Author(s): Sipko van Dam, Urmo Võsa, Adriaan van der Graaf, Lude Franke, João Pedro de Magalhães
Software Mentions: 3
Published: almost 10 years ago

10.1093/bfgp/elx046

Mapping gene regulatory networks from single-cell omics data
Cited by: 165
Author(s): Mark Fiers, Liesbeth Minnoye, Sara Aibar, Carmen Bravo González-Blas, Zeynep Kalender Atak, Stein Aerts
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12935-021-02008-5

Prognostic signature composed of transcription factors accurately predicts the prognosis of gastric cancer patients
Cited by: 4
Author(s): Liqun Zhou, Zhiqing Chen, You Wu, Hao Lü, Lin Xin
Software Mentions: 3
Published: over 5 years ago

10.1186/s12935-020-01587-z

Identified IGSF9 association with prognosis and hypoxia in nasopharyngeal carcinoma by bioinformatics analysis
Cited by: 6
Author(s): Danxia Huang, Qianqian Liu, Weijun Zhang, Chunyue Huang, Ronghui Zheng, Gaoqiang Xie, Hongmei Wang, Baochang Jia, Jianjun Shi, Yawei Yuan, Min Deng
Software Mentions: 3
Published: about 6 years ago

10.1186/s12935-021-01929-5

ESR1 as a recurrence-related gene in intrahepatic cholangiocarcinoma: a weighted gene coexpression network analysis
Cited by: 3
Author(s): Fengwei Li, Qinjunjie Chen, Yang Yang, Meihui Li, Lei Zhang, Zhenlin Yan, Junjie Zhang, Kui Wang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12935-021-02033-4

Immune signature-based hepatocellular carcinoma subtypes may provide novel insights into therapy and prognosis predictions
Cited by: 13
Author(s): Qiuxian Zheng, Qin Yang, Jiaming Zhou, Xinyu Gu, Haibo Zhou, Xuejun Dong, Haihong Zhu, Zhi Chen
Software Mentions: 3
Published: over 5 years ago

10.1186/s12935-021-01871-6

Identifying SLC27A5 as a potential prognostic marker of hepatocellular carcinoma by weighted gene co-expression network analysis and in vitro assays
Cited by: 9
Author(s): Fan Zhang, Mengzhou Xue, Xin Jiang, Huiyuan Yu, Yixuan Qiu, J. Yu, Fan Yang, Zhijun Bao
Software Mentions: 3
Published: over 5 years ago

10.1186/s12935-021-01982-0

Identification of collagen genes related to immune infiltration and epithelial-mesenchymal transition in glioma
Cited by: 25
Author(s): Yin Wu, Hecheng Zhu, Jun Tan, Zhaoqi Xin, Quanwei Zhou, Yudong Cao, Zhaoping Wu, Lei Wang, Ming Zhao, Xingjun Jiang, Chao Ren, Guihua Tang
Software Mentions: 3
Published: over 5 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479