cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1038/srep43446

Characterization of gene expression profiles in HBV-related liver fibrosis patients and identification of ITGBL1 as a key regulator of fibrogenesis
Cited by: 61
Author(s): Mingjie Wang, Qiming Gong, Jiming Zhang, Liang Chen, Zhanqing Zhang, Lungen Lu, Demin Yu, Yue Han, Donghua Zhang, Peizhan Chen, Xiaonan Zhang, Zhenghong Yuan, Huang Jy, Xinxin Zhang
Software Mentions: 5
Published: over 9 years ago

10.1186/s12890-016-0303-4

The bronchial epithelial cell bacterial microbiome and host response in patients infected with human immunodeficiency virus
Cited by: 6
Author(s): Marc A. Sze, Stella Xu, Janice M. Leung, Emily A. Vucic, Tawimas Shaipanich, Aida Moghadam, Marianne Harris, Silvia Guillemi, Sunita Sinha, Corey Nislow, Darra Murphy, Cameron Hague, Jonathon Leipsic, Stephen Lam, Wan L. Lam, Julio S. G. Montaner, Don D. Sin, S. F. Paul Man
Software Mentions: 5
Published: almost 10 years ago

10.1186/s12935-020-01243-6

Identification of a competing endogenous RNA network associated with prognosis of pancreatic adenocarcinoma
Cited by: 24
Author(s): Wanqing Weng, Zhongjing Zhang, Weiguo Huang, Xiangxiang Xu, Boda Wu, Tingbo Ye, Yunfeng Shan, Ke–Qing Shi, Zhuo Lin
Software Mentions: 5
Published: over 6 years ago

10.3390/life11020172

Integrative Analysis Identified Key Schizophrenia Risk Factors from an Abnormal Behavior Mouse Gene Set
Cited by: 1
Author(s): Chen Miao, Weidi Wang, Weichen Song, Wei Qian, Guan Ning Lin
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.672674

Four Prognosis-Associated lncRNAs Serve as Biomarkers in Ovarian Cancer
Cited by: 10
Author(s): Jianfeng Zheng, Jialu Guo, Huizhi Zhang, Benben Cao, XU Guomin, Zhifen Zhang, Jinyi Tong
Software Mentions: 5
Published: over 5 years ago

10.1002/cam4.4206

Key sunitinib‐related biomarkers for renal cell carcinoma
Cited by: 9
Author(s): Yun Peng, Shiqiang Dong, Yuxuan Song, Dingkun Hou, Lili Wang, Bowen Li, Haitao Wang
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2020.01009

RNA-Seq Analysis Reveals Hub Genes Involved in Chicken Intramuscular Fat and Abdominal Fat Deposition During Development
Cited by: 22
Author(s): Siyuan Xing, Ranran Liu, Guiping Zhao, Lu Liu, M.A.M. Groenen, Ole Madsen, Maiqing Zheng, Xinting Yang, R.P.M.A. Crooijmans, Jie Wen
Software Mentions: 5
Published: about 6 years ago

10.3389/fgene.2020.00680

Identification of a Six-Immune-Related Long Non-coding RNA Signature for Predicting Survival and Immune Infiltrating Status in Breast Cancer
Cited by: 24
Author(s): Zheng Li, Yaming Li, Xiaolong Wang
Software Mentions: 5
Published: over 6 years ago

10.3389/fimmu.2020.607314

Genetic Dissection of the Regulatory Mechanisms of Ace2 in the Infected Mouse Lung
Cited by: 11
Author(s): Fuyi Xu, Jun Gao, Silke Bergmann, Amy C. Sims, David G. Ashbrook, Ralph S. Baric, Yan Cui, Colleen B. Jonsson, Kui Li, Robert W. Williams, Klaus Schughart, Lu Lu
Software Mentions: 5
Published: almost 6 years ago

10.3390/genes11050543

Weighted Gene Correlation Network Meta-Analysis Reveals Functional Candidate Genes Associated with High- and Sub-Fertile Reproductive Performance in Beef Cattle
Cited by: 13
Author(s): Pablo Augusto de Souza Fonseca, Aroa Suárez-Vega, Ángela Cánovas
Software Mentions: 5
Published: over 6 years ago

10.1264/jsme2.ME20153

Inoculation of Mimosa Pudica with Paraburkholderia phymatum Results in Changes to the Rhizoplane Microbial Community Structure
Cited by: 5
Author(s): Shashini U. Welmillage, Qian Zhang, Virinchipuram S. Sreevidya, Michael J. Sadowsky, Prasad Gyaneshwar
Software Mentions: 5
Published: almost 6 years ago

10.3390/genes11070831

Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene Networks
Cited by: 5
Author(s): Fernando M. Delgado-Chaves, Francisco Gómez-Vela, Federico Divina, Miguel García-Torres, Domingo S. Rodríguez–Baena
Software Mentions: 5
Published: over 6 years ago

10.18632/oncotarget.25330

Global isoform-specific transcript alterations and deregulated networks in clear cell renal cell carcinoma
Cited by: 14
Author(s): Michael Hamilton, Thomas Girke, Ernest Martinez
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-021-85061-4

Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility
Cited by: 12
Author(s): Jerry C. Wang, Gokul Ramaswami, Daniel H. Geschwind
Software Mentions: 5
Published: over 5 years ago

10.1093/gigascience/giab067

Association of female reproductive tract microbiota with egg production in layer chickens
Cited by: 5
Author(s): Yuan Su, Shilin Tian, Diyan Li, Wei Zhu, Tao Wang, Suchismita Mishra, Ranlei Wei, Zhongxian Xu, Mengnan He, Xiaoling Zhao, Huadong Yin, Xiaolan Fan, Bo Zeng, Mingyao Yang, Deying Yang, Qingyong Ni, Yan Li, Mingwang Zhang, Qing Zhu, Mingzhou Li
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2021.617133

Weighted Correlation Gene Network Analysis Reveals New Potential Mechanisms and Biomarkers in Non-obstructive Azoospermia
Cited by: 10
Author(s): Meng Dong, Hao Li, Xue Zhang, Jichun Tan
Software Mentions: 5
Published: over 5 years ago

10.1186/s12967-020-02561-z

Gene correlation network analysis to identify regulatory factors in sepsis
Cited by: 25
Author(s): Zhongheng Zhang, Lin Chen, Ping Xu, Lifeng Xing, Yucai Hong, Pengpeng Chen
Software Mentions: 5
Published: about 6 years ago

10.1186/s12935-021-01826-x

Systematic identification of key functional modules and genes in esophageal cancer
Cited by: 4
Author(s): Rui Wu, Hao Zhuang, Yukun Mei, Jin‐Yu Sun, Tao Dong, Lili Zhao, Zhining Fan, Li Liu
Software Mentions: 5
Published: over 5 years ago

10.1038/s41396-020-0606-6

Genetic variation and evolutionary history of a mycorrhizal fungus regulate the currency of exchange in symbiosis with the food security crop cassava
Cited by: 12
Author(s): Romain Savary, Cindy Dupuis, Frédéric G. Masclaux, Ivan D. Mateus, Edward C. Rojas, Ian R. Sanders
Software Mentions: 5
Published: over 6 years ago

10.1038/s41396-021-00923-z

Maize germplasm chronosequence shows crop breeding history impacts recruitment of the rhizosphere microbiome
Cited by: 38
Author(s): Alonso Favela, Martin Bohn, Angela D. Kent
Software Mentions: 5
Published: over 5 years ago

10.1186/s12974-021-02154-7

Identification of aberrant innate and adaptive immunity based on changes in global gene expression in the blood of adults with autism spectrum disorder
Cited by: 11
Author(s): Fumie Horiuchi, Yuta Yoshino, Hiroshi Kumon, Rie Hosokawa, Kiwamu Nakachi, Kentaro Kawabe, Jun‐ichi Iga, Shu‐ichi Ueno
Software Mentions: 5
Published: over 5 years ago

10.1093/bib/bbaa072

Scoring functions for drug-effect similarity
Cited by: 13
Author(s): Stephan Struckmann, Markus Ernst, Sarah Fischer, Nancy Mah, Georg Fuellen, Steffen Möller
Software Mentions: 5
Published: over 6 years ago

10.1111/cpr.12968

Systemic transcriptome comparison between early‐ And late‐onset pre‐eclampsia shows distinct pathology and novel biomarkers
Cited by: 15
Author(s): Fang Guo, Zhenan Bao, Hao Yang, Yixi Fu, Yaning Wang, Jianming Huang, Min Cheng, Xiaobo Li, Zhuo Shen, Li Li, Ping He, Andy Peng Xiang, Shuaiyu Wang, Hongbo Zhang
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-020-69494-x

Immune network dysregulation precedes clinical diagnosis of asthma
Cited by: 3
Author(s): Yi-Shin Chang, Benjamin A. Turturice, Cody Schott, Patricia W. Finn, David L. Perkins
Software Mentions: 5
Published: about 6 years ago

10.1186/s12974-017-0834-5

Myeloid C/EBPβ deficiency reshapes microglial gene expression and is protective in experimental autoimmune encephalomyelitis
Cited by: 17
Author(s): Marta Pulido-Salgado, José M. Vidal-Taboada, Gerardo Garcıa-Dıaz Barriga, Joan Serratosa, Tony Valente, Paola Castillo, Jonathan Matalonga, Marco Straccia, Josep M. Canals, Annabel F. Valledor, Carme Solà, Josep Saura
Software Mentions: 5
Published: over 9 years ago

10.1038/s41598-020-70581-2

Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach
Cited by: 12
Author(s): José Arturo Molina-Mora, Diana Chinchilla-Montero, Maribel Chavarría-Azofeifa, Alejandro Ulloa-Morales, Rebeca Campos-Sánchez, Rodrigo Mora-Rodríguez, Leming Shi, Fernando García
Software Mentions: 5
Published: about 6 years ago

10.1111/tpj.14202

Gene networks orchestrated by Me<scp>GI</scp>: a single‐factor mechanism underlying sex determination in persimmon
Cited by: 43
Author(s): Ho Wen Yang, Takashi Akagi, Taiji Kawakatsu, Ryutaro Tao
Software Mentions: 5
Published: over 7 years ago

10.1002/cam4.4180

Identification of a novel 10 immune‐related genes signature as a prognostic biomarker panel for gastric cancer
Cited by: 9
Author(s): Tingna Chen, Chaogang Yang, Rongzhang Dou, Bin Xiong
Software Mentions: 5
Published: about 5 years ago

10.3389/fcimb.2021.654074

Intestinal Microbiota Mediates High-Fructose and High-Fat Diets to Induce Chronic Intestinal Inflammation
Cited by: 30
Author(s): Rong Tan, Huiwei Dong, Zhengshan Chen, Min Jin, Jing Yin, Haibei Li, Danyang Shi, Yi-fan Shao, Huaran Wang, Tianjiao Chen, Dong Yang, Jùnwén Lǐ
Software Mentions: 5
Published: over 5 years ago

10.1007/s13238-020-00720-y

Integrative analysis of in vivo recording with single-cell RNA-seq data reveals molecular properties of light-sensitive neurons in mouse V1
Cited by: 9
Author(s): Jianwei Liu, Mengdi Wang, Le Sun, Na Pan, Changjiang Zhang, Junjing Zhang, Zhentao Zuo, Sheng He, Qian Wu, Xiaoqun Wang
Software Mentions: 5
Published: over 6 years ago

10.1038/tp.2016.67

Candidate gene networks and blood biomarkers of methamphetamine-associated psychosis: an integrative RNA-sequencing report
Cited by: 26
Author(s): Michael S. Breen, Anne Uhlmann, Christiane M. Nday, Stephen J. Glatt, Mario Mitt, A. Metsalpu, Dan J. Stein, Nicola Illing
Software Mentions: 4
Published: over 10 years ago

10.3389/fmicb.2020.618287

Niche Differentiation of Comammox Nitrospira in the Mudflat and Reclaimed Agricultural Soils Along the North Branch of Yangtze River Estuary
Cited by: 22
Author(s): Xinxin Wang, Lu Lu, Xue Zhou, Xiufeng Tang, Lu Kuang, Junhui Chen, Jun Shan, Huijie Lü, Hua Qin, Jonathan M. Adams, Baozhan Wang
Software Mentions: 4
Published: almost 6 years ago

10.1002/cam4.3372

Identification of prognostic biomarkers associated with stromal cell infiltration in muscle‐invasive bladder cancer by bioinformatics analyses
Cited by: 10
Author(s): Pan Li, Jinlong Cao, Jianpeng Li, Zhiqiang Yao, Dali Han, Lijun Ying, Zhiping Wang, Junqiang Tian
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2017.00138

Feeding a High Concentration Diet Induces Unhealthy Alterations in the Composition and Metabolism of Ruminal Microbiota and Host Response in a Goat Model
Cited by: 71
Author(s): Chenlei Hua, Jing Tian, Ping Tian, Rihua Cong, Yanwen Luo, Geng Yang, Shiyu Tao, Yingdong Ni, Ruqian Zhao
Software Mentions: 4
Published: over 9 years ago

10.1002/cam4.4022

A pharmacophore‐based classification better predicts the outcomes of HER2‐negative breast cancer patients receiving the anthracycline‐ and/or taxane‐based neoadjuvant chemotherapy
Cited by: 1
Author(s): Xuan Li, Hefen Sun, Qiqi Liu, Yang Liu, Yifeng Hou, Wei Jin
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.01707

Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803
Cited by: 16
Author(s): Ulysse Guyet, Ngoc-An Nguyen, Hugo Doré, Julie Haguait, Justine Pittera, Maël Conan, Morgane Ratin, Erwan Corre, Gildas Le Corguillé, Loraine Brillet-Guéguen, Mark Hoebeke, Christophe Six, Claudia Steglich, Anne Siegel, Damien Eveillard, Frédéric Partensky, Laurence Garczarek
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2019.01359

Host Gender and Androgen Levels Regulate Gut Bacterial Taxa in Pigs Leading to Sex-Biased Serum Metabolite Profiles
Cited by: 26
Author(s): Maozhang He, Jun Gao, Jinyuan Wu, Yunyan Zhou, Hao Fu, Shanlin Ke, Hui Yang, Congying Chen, Lusheng Huang
Software Mentions: 4
Published: over 7 years ago

10.1186/s12931-020-01368-2

IRF4 and STAT3 activities are associated with the imbalanced differentiation of T-cells in responses to inhalable particulate matters
Cited by: 2
Author(s): Jinzhun Wu, Dongyu Ge, Taoling Zhong, Zuojia Chen, Ying Zhou, Lingyun Hou, Xinhua Lin, Jiaxu Hong, Kuai Liu, Hui Qi, Chaoying Wang, Yulin Zhou, Cheng Li, Chuan Wu, Shi Wu, Zuguo Liu, Qiyuan Li
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2021.647921

Higher Abundance of Sediment Methanogens and Methanotrophs Do Not Predict the Atmospheric Methane and Carbon Dioxide Flows in Eutrophic Tropical Freshwater Reservoirs
Cited by: 11
Author(s): Gabrielle Maria Fonseca Pierangeli, Mércia Regina Domingues, Tatiane Araújo de Jesus, Lúcia Helena Gomes Coelho, Werner Siegfried Hanisch, Marcelo Luiz Martins Pompêo, Flávia Talarico Saia, Gustavo Bueno Gregoracci, Roseli Frederigi Benassi
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2021.674897

Analysis of Immune-Related Signatures Related to CD4+ T Cell Infiltration With Gene Co-Expression Network in Pancreatic Adenocarcinoma
Cited by: 3
Author(s): Zhen Tan, Yubin Lei, Bo Zhang, Si Shi, Jiang Liu, Xianjun Yu, Jin Xu, Chen Liang
Software Mentions: 4
Published: over 5 years ago

10.1002/cam4.4104

Improving the overall survival prognosis prediction accuracy: A 9‐gene signature in CRC patients
Cited by: 6
Author(s): Wenbo Zheng, Yijia Lu, Xiaochuang Feng, Chuanxin Yang, Ling Qiu, Haijun Deng, Qi Xue, Kai Sun
Software Mentions: 4
Published: about 5 years ago

10.18632/oncotarget.23065

Transcriptome evolution from breast epithelial cells to basal-like tumors
Cited by: 11
Author(s): Gabriel Santpere, Ana Alcaráz-Sanabria, Verónica Corrales-Sánchez, Atanasio Pandiella, Balázs Győrffy, Alberto Ocaña
Software Mentions: 4
Published: almost 9 years ago

10.3389/fonc.2020.01374

Immunogenomic Profiling and Classification of Prostate Cancer Based on HIF-1 Signaling Pathway
Cited by: 8
Author(s): Jukun Song, Wei-Ming Chen, Guohua Zhu, Wei Wang, Fa Sun, Jianguo Zhu
Software Mentions: 4
Published: about 6 years ago

10.3389/fonc.2019.01030

Novel Biomarkers Associated With Progression and Prognosis of Bladder Cancer Identified by Co-expression Analysis
Cited by: 42
Author(s): Yejinpeng Wang, Changhong Liang, Lingao Ju, Kaiyu Qian, Xuefeng Li, Xinghuan Wang, Yu Xiao
Software Mentions: 4
Published: about 7 years ago

10.1002/cam4.4108

Expression of 5‐methylcytosine regulators is highly associated with the clinical phenotypes of prostate cancer and DNMTs expression predicts biochemical recurrence
Cited by: 3
Author(s): Lin Wang, Guoping Ren, Biaoyang Lin
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.624752

Down-Regulation of Long Non-Coding RNA TINCR Induces Cell Dedifferentiation and Predicts Progression in Oral Squamous Cell Carcinoma
Cited by: 6
Author(s): Zerui Zhuang, Jing Huang, Weiwang Wang, Cheng Wang, Pei Yu, Jing Hu, Haichao Liu, Hanqi Yin, Jinsong Hou, Xiqiang Liu
Software Mentions: 4
Published: over 5 years ago

10.1186/s12870-020-02637-4

Revealing the full-length transcriptome of caucasian clover rhizome development
Cited by: 13
Author(s): Xiujie Yin, Kun Yi, Yihang Zhao, Yue Hu, Li Xu, Taotao He, Jiaxue Liu, Guowen Cui
Software Mentions: 4
Published: about 6 years ago

10.3389/fonc.2020.613333

Construction of Bone Metastasis-Specific Regulation Network Based on Prognostic Stemness-Related Signatures in Breast Invasive Carcinoma
Cited by: 2
Author(s): Runzhi Huang, Zhenyu Li, Jiayao Zhang, Zhiwei Zeng, Jiaqi Zhang, Mingxiao Li, Siqao Wang, Shuyuan Xian, Yuna Xue, Xi Chen, Jie Li, Wing Yan Elizabeth Cheng, Bin Wang, Penghui Yan, Daoke Yang, Zongqiang Huang
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms22147266

Key Regulators of Sucrose Metabolism Identified through Comprehensive Comparative Transcriptome Analysis in Peanuts
Cited by: 12
Author(s): Weitao Li, Li Huang, Nian Liu, Manish K. Pandey, Yuning Chen, Cheng Ling, Jianbin Guo, Bin Yu, Huaiyong Luo, Xiaojing Zhou, Dongxin Huai, Weigang Chen, Liying Yan, Xin Wang, Yong Lei, Rajeev K. Varshney, Boshou Liao, Huifang Jiang
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms22094864

Characterization of Extracellular Vesicle Cargo in Sjögren’s Syndrome through a SWATH-MS Proteomics Approach
Cited by: 11
Author(s): Francesco Finamore, Antonella Cecchettini, Elisa Ceccherini, Giovanni Signore, Francesco Ferro, Silvia Rocchiccioli, Chiara Baldini
Software Mentions: 4
Published: over 5 years ago

10.3390/life11050367

Activation of Blood Vessel Development in Endometrial Stromal Cells In Vitro Cocultured with Human Peri-Implantation Embryos Revealed by Single-Cell RNA-Seq
Cited by: 4
Author(s): Bo Lv, Xiaoyu Xu, Xunyi Zhang, Lingbin Qi, He We, Lu Wang, Xian Chen, Luying Peng, Jinfeng Xue, Yao Ji, Zhigang Xue
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2021.633899

High BLM Expression Predicts Poor Clinical Outcome and Contributes to Malignant Progression in Human Cholangiocarcinoma
Cited by: 7
Author(s): Xiaoqiang Du, Chen Zhang, Chuanzheng Yin, Wenjie Wang, Xueke Yan, Dawei Xie, Xichuan Zheng, Qi Zheng, Min Li, Zifang Song
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.ppat.1004959

Fungal Morphology, Iron Homeostasis, and Lipid Metabolism Regulated by a GATA Transcription Factor in Blastomyces dermatitidis
Cited by: 16
Author(s): Amber J. Marty, Aimee Teo Broman, Robert Żarnowski, Teigan G. Dwyer, Laura M. Bond, Anissa Lounès-Hadj Sahraoui, Joël Fontaine, James M. Ntambi, Sündüz Keleş, Christina Kendziorski, Gregory M. Gauthier
Software Mentions: 4
Published: over 11 years ago

10.18632/oncotarget.22475

Organotypic three-dimensional cancer cell cultures mirror drug responsesin vivo: lessons learned from the inhibition of EGFR signaling
Cited by: 35
Author(s): Nico Jacobi, Rita Seeboeck, Elisabeth Hofmann, Helmut Schweiger, Veronika Smolinská, Thomas Mohr, Alexandra Boyer, Wolfgang Sommergruber, P. Lechner, Corina Pichler-Huebschmann, Kamil Önder, Harald Hundsberger, Christoph Wiesner, Andreas Eger
Software Mentions: 4
Published: almost 9 years ago

10.1093/jxb/erx224

Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype
Cited by: 38
Author(s): Noé Cochetel, Frédéric Escudié, Sarah Jane Cookson, Zhanwu Dai, Philippe Vivin, Pierre‐François Bert, Mindy Muñoz, Serge Delrot, Christophe Klopp, Nathalie Ollat, Virginie Lauvergeat
Software Mentions: 4
Published: over 9 years ago

10.3389/fonc.2020.541401

Prognosis Analysis and Validation of m6A Signature and Tumor Immune Microenvironment in Glioma
Cited by: 46
Author(s): Sheng Lin, Houshi Xu, Anke Zhang, Yunjia Ni, Yuanzhi Xu, Tong Meng, Mingjie Wang, Meiqing Lou
Software Mentions: 4
Published: about 6 years ago

10.3389/fonc.2020.00681

Identification of Hub Genes Associated With Development of Head and Neck Squamous Cell Carcinoma by Integrated Bioinformatics Analysis
Cited by: 50
Author(s): Chia‐Ying Li, Jia-Hua Cai, Jeffrey J. P. Tsai, Charles C.N. Wang
Software Mentions: 4
Published: over 6 years ago

10.3389/fonc.2021.636451

Integrative Analysis of Histopathological Images and Genomic Data in Colon Adenocarcinoma
Cited by: 7
Author(s): Hui Li, Linyan Chen, Hao Zeng, Qimeng Liao, Jianrui Ji, Xuelei Ma
Software Mentions: 4
Published: about 5 years ago

10.3389/fonc.2021.685515

Regulatory Network Analysis of Mutated Genes Based on Multi-Omics Data Reveals the Exclusive Features in Tumor Immune Microenvironment Between Left-Sided and Right-Sided Colon Cancer
Cited by: 10
Author(s): Tianfei Yi, Yuwei Zhang, Derry Minyao Ng, Yang Xi, Meng Ye, Lvjun Cen, Jianjiong Li, Xiaoxiang Fan, Yanguo Li, Shiyun Hu, Hao Rong, Yangyang Xie, Guofang Zhao, Leyi Chen, Chen Chen, Shujing Ni, Jiaying Mi, Xiaoyu Dai, Qi Liao
Software Mentions: 4
Published: over 5 years ago

10.1093/jxb/erw006

Evidence for maternal control of seed size in maize from phenotypic and transcriptional analysis
Cited by: 32
Author(s): Xia Zhang, Candice N. Hirsch, Rajandeep S. Sekhon, Natalia de León, Shawn M. Kaeppler
Software Mentions: 4
Published: over 10 years ago

10.1155/2020/4581954

Comprehensive Analysis of Differentially Expressed miRNAs and mRNAs Reveals That miR-181a-5p Plays a Key Role in Diabetic Dermal Fibroblasts
Cited by: 4
Author(s): Peng Liu, Yi Zhu, Qin Li, Biao Cheng
Software Mentions: 4
Published: about 6 years ago

10.3389/fphar.2021.618773

Combination of Ginsenosides Rb2 and Rg3 Promotes Angiogenic Phenotype of Human Endothelial Cells via PI3K/Akt and MAPK/ERK Pathways
Cited by: 12
Author(s): Ran Joo Choi, Siti Zuraidah Mohamad Zobir, Benjamin Alexander-Dann, Naomi L. Sharma, Kenneth L. Marcella, Brian Lam, Giles S.H. Yeo, Guoqing Zhang, Tai-Ping Fan, Andreas Bender
Software Mentions: 4
Published: over 5 years ago

10.3389/fphar.2021.678256

Dysregulated lncRNAs are Involved in the Progress of Sepsis by Constructing Regulatory Networks in Whole Blood Cells
Cited by: 5
Author(s): Yanwei Cheng, Xue Cao, Jiange Zhang, Dong Chen, Juan Zhu, Lijun Xu, Lijie Qin
Software Mentions: 4
Published: about 5 years ago

10.3390/metabo9060117

Integration of Metabolomic and Other Omics Data in Population-Based Study Designs: An Epidemiological Perspective
Cited by: 42
Author(s): Su H. Chu, Mengna Huang, Rachel S. Kelly, Elisa Benedetti, Jalal K. Siddiqui, Oana A. Zeleznik, Alexandre Pereira, David M. Herrington, Craig E. Wheelock, Jan Krumsiek, Michael J. McGeachie, Steven C. Moore, Peter Kraft, Ewy A. Mathé, Jessica Lasky‐Su
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms22020574

The Resistance of Narrow-Leafed Lupin to Diaporthe toxica Is Based on the Rapid Activation of Defense Response Genes
Cited by: 7
Author(s): Michał Książkiewicz, Sandra Rychel-Bielska, Piotr Plewiński, Maria Nuc, Witold Irzykowski, M. Jędryczka, Paweł Krajewski
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41438-020-00432-8

Transcriptional regulation of bark freezing tolerance in apple (Malus domestica Borkh.)
Cited by: 9
Author(s): Yin Liang, Shanshan Wang, Chang Zhao, Xinwei Ma, Yiyong Zhao, Jing Shao, Yuebo Li, Honglian Li, Song Hong‐wei, Hong Mā, Hao Li, Bingbing Zhang, Liangsheng Zhang
Software Mentions: 4
Published: almost 6 years ago

10.18632/oncotarget.15842

Identifying biomarkers of papillary renal cell carcinoma associated with pathological stage by weighted gene co-expression network analysis
Cited by: 29
Author(s): Zhong He, Min Sun, Ke Yuan, Rongjie Lin, Youde Xiao, Shaosheng Zhou, Hong Zhao, Yan Wang, Fuxiang Zhou, Youwen Zhou
Software Mentions: 4
Published: over 9 years ago

10.1186/s12870-020-02336-0

Morpho-physiological integrators, transcriptome and coexpression network analyses signify the novel molecular signatures associated with axillary bud in chrysanthemum
Cited by: 10
Author(s): Sagheer Ahmad, Cunquan Yuan, Qingqing Yang, Yujie Yang, Tangren Cheng, Jia Wang, Huitang Pan, Qixiang Zhang
Software Mentions: 4
Published: over 6 years ago

10.3390/genes9010044

Molecular Network-Based Identification of Competing Endogenous RNAs in Thyroid Carcinoma
Cited by: 23
Author(s): Minjia Lu, Xingyu Xu, Baohang Xi, Qi Dai, Chenli Li, Li Su, Xiaobin Zhou, Min Tang, Yanwen Yao, Jialiang Yang
Software Mentions: 4
Published: almost 9 years ago

10.1186/s41065-021-00193-x

Identification of glioblastoma immune subtypes and immune landscape based on a large cohort
Cited by: 5
Author(s): Huiyuan Zhang, Ying Chen
Software Mentions: 4
Published: about 5 years ago

10.3390/genes10090719

WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice
Cited by: 50
Author(s): Mei-Ling Zhu, Hongjun Xie, Xiangjin Wei, Komivi Dossa, Yaying Yu, Suozhen Hui, Guohua Tang, Xiaoshan Zeng, Ye Yu, Jianlong Wang
Software Mentions: 4
Published: about 7 years ago

10.1186/s41065-019-0100-1

A co-expression network for differentially expressed genes in bladder cancer and a risk score model for predicting survival
Cited by: 16
Author(s): Zihao Chen, Guojun Liu, Aslam Hossain, И. Г. Данилова, Mikhail A. Bolkov, Guoqing Liu, Irina A. Tuzankina, Wanlong Tan
Software Mentions: 4
Published: over 7 years ago

10.3390/genes11050472

Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii
Cited by: 7
Author(s): Mushtaque Ali, Hongyan Cheng, Mahtab Soomro, Shuyan Li, Muhammad Tufail, Mian Faisal Nazir, Feng Xu, Youping Zhang, Dongyun Zuo, Limin Lv, Qiaolian Wang, Guoli Song
Software Mentions: 4
Published: over 6 years ago

10.1186/s40168-021-01145-3

Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling
Cited by: 19
Author(s): Hwee Sze Tee, David W. Waite, Gavin Lear, Kim M. Handley
Software Mentions: 4
Published: about 5 years ago

10.18632/oncotarget.14303

Pan-organ transcriptome variation across 21 cancer types
Cited by: 6
Author(s): Wangxiong Hu, Yanmei Yang, Xiaofen Li, Shu Zheng
Software Mentions: 4
Published: almost 10 years ago

10.3390/genes12071101

Unveiling the Pathogenesis of Psychiatric Disorders Using Network Models
Cited by: 7
Author(s): Yanning Zuo, Wei Don, Carissa Zhu, Ormina Naveed, Weizhe Hong, Xia Yang
Software Mentions: 4
Published: over 5 years ago

10.3390/genes12091337

The Tomato ddm1b Mutant Shows Decreased Sensitivity to Heat Stress Accompanied by Transcriptional Alterations
Cited by: 4
Author(s): Prashant Kumar Singh, Golan Miller, Adi Faigenboim, Michal Lieberman‐Lazarovich
Software Mentions: 4
Published: about 5 years ago

10.1016/j.gpb.2019.01.006

Global Analysis of Gene Expression Profiles Provides Novel Insights into the Development and Evolution of the Large Crustacean Eriocheir sinensis
Cited by: 3
Author(s): Jun Wang, Xiaowen Chen, Funan He, Xian‐Rong Song, Shu Huang, Wucheng Yue, Yipei Chen, Zhixi Su
Software Mentions: 4
Published: about 6 years ago

10.5808/GI.2020.18.3.e26

A semi-automatic cell type annotation method for single-cell RNA sequencing dataset
Cited by: 0
Author(s): Wan Kim, Sung Min Yoon, Sang Soo Kim
Software Mentions: 4
Published: about 6 years ago

10.1186/s12711-021-00656-9

Large-scale transcriptome sequencing in broiler chickens to identify candidate genes for breast muscle weight and intramuscular fat content
Cited by: 7
Author(s): Hao Kang, Di Zhao, Hai Xiang, Jing Li, Guiping Zhao, Hua Li
Software Mentions: 4
Published: about 5 years ago

10.1016/j.gdata.2016.10.006

Identifying protective host gene expression signatures within the spleen during West Nile virus infection in the collaborative cross model
Cited by: 15
Author(s): Richard Green, Courtney Wilkins, Sunil Thomas, Aimee Sekine, Reneé C. Ireton, Martin T. Ferris, Duncan M. Hendrick, Kathleen Voss, Fernando Pardo-Manuel de Villena, Ralph S. Baric, Mark T. Heise, Michael Gale
Software Mentions: 4
Published: almost 10 years ago

10.1186/s13059-016-1062-5

CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types
Cited by: 17
Author(s): Brad Nelms, Levi Waldron, Luis Barrera, Andrew W. Weflen, Jeremy A. Goettel, Guoji Guo, Robert K. Montgomery, Marian R. Neutra, David T. Breault, Scott B. Snapper, Stuart H. Orkin, Martha L. Bulyk, Curtis Huttenhower, Wayne I. Lencer
Software Mentions: 4
Published: about 10 years ago

10.1186/s13059-016-1140-8

Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome
Cited by: 54
Author(s): Agata Wesolowska-Andersen, Jamie L. Everman, Rebecca M. Davidson, Cydney Rios, Rachelle Herrin, Celeste Eng, William J. Janssen, Andrew H. Liu, Sam S. Oh, Rajesh Kumar, Tasha E. Fingerlin, José Rodríguez‐Santana, Esteban G. Burchard, Max A. Seibold
Software Mentions: 4
Published: almost 10 years ago

10.1186/s40168-018-0404-9

Commensal microbiota modulate gene expression in the skin
Cited by: 126
Author(s): Jacquelyn S. Meisel, Georgia Sfyroera, Casey Bartow‐McKenney, Ciara Gimblet, Julia Bugayev, Joseph Horwinski, Brian Kim, Jonathan R. Brestoff, Amanda S. Tyldsley, Qi Zheng, Brendan P. Hodkinson, David Artis, Elizabeth A. Grice
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-017-1328-6

Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS
Cited by: 49
Author(s): Hung‐Ying Lin, Qiang Liu, Li Xiao, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable
Software Mentions: 4
Published: about 9 years ago

10.1186/s13059-019-1866-1

547 transcriptomes from 44 brain areas reveal features of the aging brain in non-human primates
Cited by: 25
Author(s): Mingli Li, Shihao Wu, Jinjin Zhang, Hang-Yu Tian, Yong Shao, Zhengbo Wang, David M. Irwin, Jiali Li, Xintian Hu, Dongdong Wu
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13059-020-02257-z

Evolutionary conservation and divergence of the human brain transcriptome
Cited by: 22
Author(s): William G Pembroke, Christopher Hartl, Daniel H. Geschwind
Software Mentions: 4
Published: over 5 years ago

10.1186/s13073-016-0355-3

Integrative network analysis of nineteen brain regions identifies molecular signatures and networks underlying selective regional vulnerability to Alzheimer’s disease
Cited by: 191
Author(s): Minghui Wang, Panos Roussos, Andrew McKenzie, Xianxiao Zhou, Yuji Kajiwara, Kristen J. Brennand, Gabriele C. DeLuca, John F. Crary, Patrizia Casaccia, Joseph D. Buxbaum, Michelle E. Ehrlich, Sam Gandy, Alison M. Goate, Pavel Katsel, Eric E. Schadt, Vahram Haroutunian, Bin Zhang
Software Mentions: 4
Published: almost 10 years ago

10.1186/s13073-016-0262-7

Signatures of early frailty in the gut microbiota
Cited by: 267
Author(s): Matthew A. Jackson, Ian B. Jeffery, Michelle Beaumont, Jordana T. Bell, Andrew G. Clark, Ruth E. Ley, Paul W. O’Toole, Tim D. Spector, Claire J. Steves
Software Mentions: 4
Published: over 10 years ago

10.1186/s12920-021-00960-9

Gene network analyses unveil possible molecular basis underlying drug-induced glaucoma
Cited by: 3
Author(s): Ruofan Ding, Qian Yu, Ke Liu, Juan Du, Huajun Yin, Zhi-Liang Ji
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.9627

Mining of prognosis-related genes in cervical squamous cell carcinoma immune microenvironment
Cited by: 5
Author(s): Jiong Ma, Pu Cheng, Xuejun Chen, Chunxia Zhou, Zheng Wei
Software Mentions: 4
Published: about 6 years ago

10.1128/mSystems.00596-19

Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics
Cited by: 7
Author(s): Matthew Chung, Laura Teigen, Silvia Libro, Robin E. Bromley, Dustin Olley, Nikhil Kumar, Lisa Sadzewicz, Luke J. Tallon, Anup Mahurkar, Jeremy M. Foster, Michelle L. Michalski, Julie C. Dunning Hotopp
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12870-021-03149-5

Pathogen and drought stress affect cell wall and phytohormone signaling to shape host responses in a sorghum COMT bmr12 mutant
Cited by: 6
Author(s): Maya Khasin, Lois F. Bernhardson, Patrick M. O’Neill, Nathan A. Palmer, Erin D. Scully, Scott E. Sattler, Deanna L. Funnell‐Harris
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.10594

Identification of hub genes and biological pathways in hepatocellular carcinoma by integrated bioinformatics analysis
Cited by: 6
Author(s): Qian Zhao, Yan Zhang, Shichun Shao, Yeqing Sun, Zhengkui Lin
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.6694

Integrated analysis reveals five potential ceRNA biomarkers in human lung adenocarcinoma
Cited by: 14
Author(s): Yu Liu, Deyao Xie, Zuhua He, Liangcheng Zheng
Software Mentions: 4
Published: over 7 years ago

10.1128/mSphere.01044-20

Gut Bacteria Shared by Children and Their Mothers Associate with Developmental Level and Social Deficits in Autism Spectrum Disorder
Cited by: 5
Author(s): Yu Chen, Hui Fang, Chunyan Li, Guojun Wu, Ting Xu, Xin Yang, Liping Zhao, Xiaoyan Ke, Chenhong Zhang
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12870-020-2268-y

Modulation of volatile compound metabolome and transcriptome in grape berries exposed to sunlight under dry-hot climate
Cited by: 24
Author(s): Lei He, Xiaoqing Xu, Yu Wang, Wei-Kai Chen, Ruonan Sun, Guodong Cheng, Bin Liu, Changyong Wu, Chang‐Qing Duan, Jun Wang, Qiu-Hong Pan
Software Mentions: 4
Published: over 6 years ago

10.1111/pbi.13516

Genome‐wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness
Cited by: 23
Author(s): Gopal Misra, Saurabh Badoni, Sabiha Parween, Rakesh Kumar Singh, Hei Leung, Olufunmilayo Ladejobi, Richard Mott, Nese Sreenivasulu
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12967-020-02491-w

Analyzing and validating the prognostic value and mechanism of colon cancer immune microenvironment
Cited by: 46
Author(s): Xinyi Wang, Jinzhong Duanmu, Xiaorui Fu, Taiyuan Li, Qunguang Jiang
Software Mentions: 4
Published: about 6 years ago

10.1186/s13007-021-00797-4

AprGPD: the apricot genomic and phenotypic database
Cited by: 2
Author(s): Chen Chen, Huimin Liu, Ningning Gou, Mengzhen Huang, Wei Xu, Xuchun Zhu, Mingyu Yin, Haikun Bai, Lin Wang, Tana Wuyun
Software Mentions: 4
Published: about 5 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479