cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0143128

RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in Maize
Cited by: 30
Author(s): Liu Ya, Miaoyi Zhou, Zhaoxu Gao, Wen Ren, Fan Yang, Hang He, Jiuran Zhao
Software Mentions: 5
Published: over 9 years ago

10.1186/s12864-020-06809-2

Gene expression predictions and networks in natural populations supports the omnigenic theory
Cited by: 22
Author(s): Aurélien Chateigner, Marie-Claude Lesage-Descauses, Odile Rogier, Véronique Jorge, Jean‐Charles Leplé, Véronique Brunaud, Christine Paysant‐Le Roux, Ludivine Soubigou‐Taconnat, Marie‐Laure Martin‐Magniette, Leopoldo Sánchez, Vincent Segura
Software Mentions: 5
Published: about 5 years ago

10.3389/fpls.2019.00156

Transcriptomics Identifies Modules of Differentially Expressed Genes and Novel Cyclotides in Viola pubescens
Cited by: 12
Author(s): Anne L. Sternberger, Megan J. Bowman, Colin Kruse, Kevin L. Childs, Harvey E. Ballard, Sarah E. Wyatt
Software Mentions: 5
Published: over 6 years ago

10.3389/fpls.2021.621561

Transcriptome Analysis Reveals Photoperiod-Associated Genes Expressed in Rice Anthers
Cited by: 14
Author(s): Shiyu Sun, Duoxiang Wang, Jingbin Li, Yaqi Lei, Gang Li, Wenguo Cai, Xiangxiang Zhao, Wanqi Liang, Dabing Zhang
Software Mentions: 5
Published: over 4 years ago

10.1186/s12935-019-0955-2

PD-1 and PD-L1 correlated gene expression profiles and their association with clinical outcomes of breast cancer
Cited by: 35
Author(s): Jiang Cui, Sunrun Cao, Na Li, Lei Jiang, Tao Sun
Software Mentions: 5
Published: almost 6 years ago

10.3389/fpls.2021.715683

Morphological, Physiological, and Molecular Responses of Sweetly Fragrant Luculia gratissima During the Floral Transition Stage Induced by Short-Day Photoperiod
Cited by: 0
Author(s): Xiongfang Liu, Yat-wah Wan, Jing An, Xiujiao Zhang, Yurong Cao, Zhenghong Li, Xiuxian Liu, Hong Ma
Software Mentions: 5
Published: almost 4 years ago

10.3389/fpls.2018.01309

A Dynamic Co-expression Map of Early Inflorescence Development in Setaria viridis Provides a Resource for Gene Discovery and Comparative Genomics
Cited by: 17
Author(s): Chuanmei Zhu, Jiani Yang, Mathew S. Box, Elizabeth A. Kellogg, Andrea L. Eveland
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0129610

Association of Protein Translation and Extracellular Matrix Gene Sets with Breast Cancer Metastasis: Findings Uncovered on Analysis of Multiple Publicly Available Datasets Using Individual Patient Data Approach
Cited by: 4
Author(s): Nilotpal Chowdhury, Shantanu Sapru
Software Mentions: 5
Published: about 10 years ago

10.1002/ece3.6899

Insights into the genetic basis of predator‐induced response inDaphnia galeata
Cited by: 9
Author(s): Verena Tams, Jana Nickel, Anne Ehring, Mathilde Cordellier
Software Mentions: 5
Published: almost 5 years ago

10.3390/diagnostics10050305

Characterization of Stem-like Circulating Tumor Cells in Pancreatic Cancer
Cited by: 7
Author(s): Lei Zhu, Bárbara Hissa, Balázs Győrffy, Johann-Christoph Jann, Cui Yang, Christoph Reißfelder, Sebastian Schölch
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pntd.0004992

Meta-transcriptome Profiling of the Human-Leishmania braziliensis Cutaneous Lesion
Cited by: 54
Author(s): Stephen M Christensen, Laura A. L. Dillon, Lucas P. Carvalho, Sara Passos, Fernanda O. Novais, V. K. Hughitt, Daniel P. Beiting, Edgar M. Carvalho, Phillip Scott, Najib M. El-Sayed, David M. Mosser
Software Mentions: 5
Published: almost 9 years ago

10.18632/aging.102373

Bioinformatic profiling of prognosis-related genes in the breast cancer immune microenvironment
Cited by: 29
Author(s): Fang Bai, Yu-Chun Jin, Peng Zhang, Hongliang Chen, Yi‐Peng Fu, Mingdi Zhang, Zhen Weng, Kangning Wu
Software Mentions: 5
Published: over 5 years ago

10.3389/fnagi.2021.686066

Significant Difference of Immune Cell Fractions and Their Correlations With Differential Expression Genes in Parkinson’s Disease
Cited by: 13
Author(s): Yilin Huang, Huisheng Liu, Jiaqi Hu, Chongyin Han, Zhenggang Zhong, Wei Luo, Yuhu Zhang, Fei Ling
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pgen.1008367

Integrating transcriptomic network reconstruction and eQTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development
Cited by: 15
Author(s): Robert L. Baker, Wen Fung Leong, Marcus T. Brock, Matthew J. Rubin, R. J. Cody Markelz, Stephen M. Welch, Julin Maloof, Cynthia Weinig
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0243857

Network preservation reveals shared and unique biological processes associated with chronic alcohol abuse in NAc and PFC
Cited by: 7
Author(s): Eric Vornholt, John W. Drake, Mohammed Mamdani, Gowon O. McMichael, Zachary N. Taylor, Silviu‐Alin Bacanu, Michael F. Miles, Vladimir I. Vladimirov
Software Mentions: 5
Published: over 4 years ago

10.18632/aging.103809

Landscape of transcription and expression regulated by DNA methylation related to age of donor and cell passage in adipose-derived mesenchymal stem cells
Cited by: 3
Author(s): Guan-Ming Lu, Yong-Xian Rong, Zheng Liang, Dong-Lin Hunag, Yuju Ma, Zhizhai Luo, Fengyao Wu, Xinheng Liu, Yu Liu, Steven Mo, Zhongquan Qi, Hong-Mian Li
Software Mentions: 5
Published: over 4 years ago

10.1155/2021/6633442

The Construction and Comprehensive Analysis of Inflammation-Related ceRNA Networks and Tissue-Infiltrating Immune Cells in Ulcerative Colitis Progression
Cited by: 8
Author(s): Jiawei Lu, Aimaier Rouzigu, Li-Hong Teng, Weili Liu
Software Mentions: 5
Published: about 4 years ago

10.1186/s12870-017-1043-1

The common transcriptional subnetworks of the grape berry skin in the late stages of ripening
Cited by: 38
Author(s): Ryan Ghan, Juli Petereit, Richard L. Tillett, Karen Schlauch, David Toubiana, Aaron Fait, Grant R. Cramer
Software Mentions: 5
Published: about 8 years ago

10.1186/s12859-021-04046-2

DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks
Cited by: 0
Author(s): Heeju Noh, Hua Ziyi, Panagiotis Chrysinas, Jason E. Shoemaker, Rudiyanto Gunawan
Software Mentions: 5
Published: over 4 years ago

10.1002/cam4.4109

A prognostic nomogram based on competing endogenous RNA network for clear‐cell renal cell carcinoma
Cited by: 2
Author(s): Yun Peng, Sanlan Wu, Zihan Xu, Dingkun Hou, Nan Li, Zheyu Zhang, Lili Wang, Haitao Wang
Software Mentions: 5
Published: about 4 years ago

10.3389/fonc.2021.738477

Identification of a Ferroptosis-Related Signature Model Including mRNAs and lncRNAs for Predicting Prognosis and Immune Activity in Hepatocellular Carcinoma
Cited by: 38
Author(s): Zian Chen, Hui Tian, Di Yao, Yuan Zhang, Feng Zhang, Chen Yang
Software Mentions: 5
Published: almost 4 years ago

10.3389/fphys.2019.00278

Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome
Cited by: 14
Author(s): Jianbin Zhang, Qiangqiang Nie, Chaozeng Si, Wang Cheng, Yang Chen, Weiliang Sun, Pei Lin, Jing Guo, Jie Kong, Yiyao Cui, Feng Wang, Xueqiang Fan, Zhidong Ye, Jianyan Wen, Peng Liu
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0118731

Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis
Cited by: 77
Author(s): Katherine C. H. Amrine, Bárbara Blanco-Ulate, Dario Cantu
Software Mentions: 5
Published: over 10 years ago

10.1534/g3.118.200852

Tissue-Specific Transcriptome Analysis Reveals Candidate Genes for Terpenoid and Phenylpropanoid Metabolism in the Medicinal Plant Ferula assafoetida
Cited by: 21
Author(s): Hajar Amini, Mohammad Reza Naghavi, Tong Shen, Yanhong Wang, Jaber Nasiri, Ikhlas A. Khan, Oliver Fiehn, Philipp Zerbe, Julin Maloof
Software Mentions: 5
Published: over 6 years ago

10.3389/fimmu.2018.01661

Integrated Systems Biology Approach Identifies Novel Maternal and Placental Pathways of Preeclampsia
Cited by: 128
Author(s): Nándor Gábor Than, Roberto Romero, Adi L. Tarca, Katalin A. Kékesi, Yi Xu, Zhonghui Xu, Kata Juhász, Gaurav Bhatti, Ron Leavitt, Zsolt Gelencser, János Pálhalmi, Tzu Hung Chung, Balázs Győrffy, László Orosz, Attila Demeter, Anett Szecsi, Éva Hunyadi‐Gulyás, Zsuzsanna Darula, Attila Simor, Katalin Éder, S. Szabó, Vanessa Topping, Haidy Elazzamy, Christopher LaJeunesse, Andrea Balogh, Gábor Szalai, Susan Land, Olga Török, Zhong Dong, Ilona Kovalszky, András Falus, Hamutal Meiri, Sorin Drăghici, Sonia S. Hassan, Tinnakorn Chaiworapongsa, M Krispin, Martin Knöfler, Offer Erez, Graham J. Burton, Chong Jai Kim, Gábor Juhász, Zoltán Papp
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pcbi.1004847

Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes
Cited by: 40
Author(s): Jeffrey J. Sutherland, Robert A. Jolly, Keith M. Goldstein, James Stevens
Software Mentions: 5
Published: over 9 years ago

10.1155/2021/9998697

Comprehensive Analysis of the Systemic Transcriptomic Alternations and Inflammatory Response during the Occurrence and Progress of COVID-19
Cited by: 12
Author(s): Shaocong Mo, Leijie Dai, Yulin Wang, Biao Song, Zongcheng Yang, Wenchao Gu
Software Mentions: 5
Published: almost 4 years ago

10.1155/2021/5553811

Identification of Potential Biomarkers Associated with Acute Myocardial Infarction by Weighted Gene Coexpression Network Analysis
Cited by: 12
Author(s): Yan Wang, Xiangyang Zhang, Min Duan, Chenguang Zhang, Ke Wang, Lili Feng, Linlin Song, Sheng Xi Wu, Xuyan Chen
Software Mentions: 5
Published: almost 4 years ago

10.1155/2020/8853348

Systematic Identification of Key Functional Modules and Genes in Gastric Cancer
Cited by: 2
Author(s): Rui Wu, Jin‐Yu Sun, Lili Zhao, Zhining Fan, Cheng Yang
Software Mentions: 5
Published: over 4 years ago

10.18632/aging.104001

Three-gene risk model in papillary renal cell carcinoma: a robust likelihood-based survival analysis
Cited by: 12
Author(s): Yutao Wang, Kexin Yan, Jiaxing Lin, Jianfeng Wang, Zhenhua Zheng, Xinxin Li, Zhixiong Hua, Yue-Peng Bu, Jianxiu Shi, Siqing Sun, Xuejie Li, Yang Liu, Jianbin Bi
Software Mentions: 5
Published: over 4 years ago

10.3389/fonc.2019.00898

Genome-Wide Identification of a Novel Eight-lncRNA Signature to Improve Prognostic Prediction in Head and Neck Squamous Cell Carcinoma
Cited by: 26
Author(s): Bowen Yang, Jiming Shen, Xu Lu, Ying Chen, Xiaofang Che, Xiujuan Qu, Yunpeng Liu, Yuee Teng, Zhi Li
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12864-020-6545-9

Trait differentiation and modular toxin expression in palm-pitvipers
Cited by: 16
Author(s): Andrew J. Mason, Mark J. Margres, Jason L. Strickland, Darin R. Rokyta, Mahmood Sasa, Christopher L. Parkinson
Software Mentions: 5
Published: over 5 years ago

10.3389/fonc.2020.566183

Comprehensive Analysis of CDCAs Methylation and Immune Infiltrates in Hepatocellular Carcinoma
Cited by: 8
Author(s): Yongkang Wang, Yinfeng Yang, Honglei Gao, Ting Ouyang, Luyao Zhang, Jili Hu, Hu Sheng, Hongxing Kan
Software Mentions: 5
Published: over 4 years ago

10.1186/s12967-018-1707-0

Evaluation of the prognostic value of paraoxonase 1 in the recurrence and metastasis of hepatocellular carcinoma and establishment of a liver-specific predictive model of survival
Cited by: 18
Author(s): Zhenzhen Yu, Qifeng Ou, Chongxi Fan, Jiong Bi, Wen Li, Jiachi Ma, Rongchang Wang, Xiaohui Huang
Software Mentions: 5
Published: over 6 years ago

10.3389/fonc.2020.00444

Multi-Omics Integration Reveals a Competitive Endogenous RNAs Network for the Identification of Progression Biomarkers and the Stratification of Patients Diagnosed With Nephroblastoma
Cited by: 2
Author(s): Jingbo Wang, Yuan Wang, Han Liang, Mohamed Shahen, Chaofeng Hu, Furong Li
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pcbi.1008976

MetaGSCA: A tool for meta-analysis of gene set differential coexpression
Cited by: 2
Author(s): Yan Guo, Hui Yu, Haocan Song, Jia-Peng He, Olufunmilola Oyebamiji, Huining Kang, Jie Ping, Scott A. Ness, Yu Shyr, Fei Ye
Software Mentions: 5
Published: about 4 years ago

10.1002/advs.202004973

In Vivo Induction of Regulatory T Cells Via CTLA‐4 Signaling Peptide to Control Autoimmune Encephalomyelitis and Prevent Disease Relapse
Cited by: 13
Author(s): Gil Ran Kim, Won-Ju Kim, Su-Ho Lim, Hong-Gyun Lee, Ja Hyun Koo, Kyung Ho Nam, Sung Min Kim, Sung Dong Park, Je-Min Choi
Software Mentions: 5
Published: about 4 years ago

10.1186/s12864-018-4987-0

PdumBase: a transcriptome database and research tool for Platynereis dumerilii and early development of other metazoans
Cited by: 16
Author(s): Hsien-Chao Chou, Natalia Acevedo-Luna, Julie A. Kuhlman, Stephan Schneider
Software Mentions: 5
Published: almost 7 years ago

10.1186/1471-2105-13-30

ICGE: an R package for detecting relevant clusters and atypical units in gene expression
Cited by: 7
Author(s): Itziar Irigoien, Basilio Sierra, C. Arenas
Software Mentions: 5
Published: over 13 years ago

10.1371/journal.pcbi.1009021

MiMeNet: Exploring microbiome-metabolome relationships using neural networks
Cited by: 33
Author(s): Derek Reiman, Brian T. Layden, Yang Dai
Software Mentions: 5
Published: about 4 years ago

10.1155/2021/6648093

Integrated Analysis to Identify a Redox-Related Prognostic Signature for Clear Cell Renal Cell Carcinoma
Cited by: 16
Author(s): Yue Wu, Wa Xian, Huan Feng, Bintao Hu, Bo Liu, Yang Luan, Yajun Ruan, Xiaohui Liu, Zhuo Liu, Jihong Liu, Tao Wang
Software Mentions: 5
Published: over 4 years ago

10.1186/s12967-021-02716-6

The potential role of chemotaxis and the complement system in the formation and progression of thoracic aortic aneurysms inferred from the weighted gene coexpression network analysis
Cited by: 5
Author(s): Chuxiang Lei, Dan Yang, Wenlin Chen, Haoxuan Kan, Feifei Xu, Hui Zhang, Wei Wang, Lei Ji, Yuehong Zheng
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-021-07849-y

Genome-wide identification and characterization of caffeoyl-coenzyme A O-methyltransferase genes related to the Fusarium head blight response in wheat
Cited by: 7
Author(s): Guang Yang, Wenqiu Pan, Ruoyu Zhang, Yan Pan, Qifan Guo, Weining Song, Wenbin Zheng, Xiaojun Nie
Software Mentions: 5
Published: about 4 years ago

10.1186/s12967-021-02705-9

Eight-lncRNA signature of cervical cancer were identified by integrating DNA methylation, copy number variation and transcriptome data
Cited by: 23
Author(s): Qihang Zhong, Minzhen Lu, Wei Yuan, Yueyi Cui, Hanqiang Ouyang, Yong Fan, Zhaohui Wang, Congying Wu, Jie Qiao, Jing Hang
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-019-3017-9

Guide for library design and bias correction for large-scale transcriptome studies using highly multiplexed RNAseq methods
Cited by: 8
Author(s): Shintaro Katayama, Tiina Skoog, Cilla Söderhäll, Elisabet Einarsdottir, Kaarel Krjutškov, Juha Kere
Software Mentions: 5
Published: almost 6 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: almost 5 years ago

10.3389/fonc.2021.615234

Combined Analysis of RNA Sequence and Microarray Data Reveals a Competing Endogenous RNA Network as Novel Prognostic Markers in Malignant Pleural Mesothelioma
Cited by: 5
Author(s): Weicheng Duan, Kang Wang, Yijie Duan, Xiuyi Chen, Xufeng Chu, Ping Hu, Bo Xiong
Software Mentions: 5
Published: over 4 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: about 7 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 6 years ago

10.1186/1471-2105-13-113

Molecular ecological network analyses
Cited by: 1,612
Author(s): Ye Deng, Yi-Huei Jiang, Yunfeng Yang, Zhili He, Feng Luo, Jizhong Zhou
Software Mentions: 5
Published: about 13 years ago

10.18632/aging.203294

An interactive nomogram based on clinical and molecular signatures to predict prognosis in multiple myeloma patients
Cited by: 3
Author(s): Linxin Liu, Jian Qu, Yuxin Dai, Tingting Qi, Xin-Qi Teng, Guohua Li, Qiang Qu
Software Mentions: 5
Published: about 4 years ago

10.1111/pbi.13236

Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton ( Gossypium hirsutum )
Cited by: 42
Author(s): Syed Shan-e-Ali Zaidi, Rubab Zahra Naqvi, Muhammad Asif, Susan R. Strickler, Sara Shakir, Muhammad Shafiq, Ayesha Khan, Imran Amin, Bharat Mishra, M. Shahid Mukhtar, Brian E. Scheffler, Jodi A. Scheffler, Lukas A. Mueller, Shahid Mansoor
Software Mentions: 5
Published: almost 6 years ago

10.1111/pbi.13483

The genome of Cleistogenes songorica provides a blueprint for functional dissection of dimorphic flower differentiation and drought adaptability
Cited by: 18
Author(s): Jiyu Zhang, Fan Wu, Yan Qi, Ulrik P. John, Mingshu Cao, Pao Xu, Zhengshe Zhang, Tiantian Ma, Xifang Zong, Jie Li, Ruijuan Liu, Yufei Zhang, Yufeng Zhao, Gisele Kanzana, Yunyun Lv, Nan Zhang, Germán Spangenberg, Yanrong Wang
Software Mentions: 5
Published: almost 5 years ago

10.1007/s11103-020-01041-8

Integrative transcriptomics reveals genotypic impact on sugar beet storability
Cited by: 7
Author(s): Silvia Madritsch, Svenja Bomers, Alexandra Posekany, Agnes Burg, Rebekka Birke, Florian Emerstorfer, Reinhard Turetschek, Sandra Otte, Herbert Eigner, Eva Maria Sehr
Software Mentions: 5
Published: almost 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: about 4 years ago

10.3389/fonc.2021.621430

Identification of Hub Genes Associated With Melanoma Development by Comprehensive Bioinformatics Analysis
Cited by: 8
Author(s): Jie Jiang, Chong Liu, Guoyong Xu, Tuo Liang, Chaojie Yu, Shijie Liao, Zide Zhang, Zhaojun Lu, Zequn Wang, Jiarui Chen, Tianyou Chen, Hao Li, Xinli Zhan
Software Mentions: 5
Published: over 4 years ago

10.3390/ijms22179146

Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses
Cited by: 5
Author(s): Mirosław Tyrka, Beata Bakera, Magdalena Szeliga, Magdalena Święcicka, Paweł Krajewski, Monika Mokrzycka, Monika Rakoczy-Trojanowska
Software Mentions: 5
Published: almost 4 years ago

10.1186/s11689-020-09316-3

Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder
Cited by: 9
Author(s): Bonnie Alberry, Christina A Castellani, Shiva M. Singh
Software Mentions: 5
Published: about 5 years ago

10.3390/ijms22115744

BRAF Inhibitors Induce Feedback Activation of RAS Pathway in Thyroid Cancer Cells
Cited by: 8
Author(s): Elisa Bonaldi, Chiara Gargiuli, Loris De Cecco, Arianna Micali, Maria Grazia Rizzetti, Angela Greco, Maria Grazia Borrello, Emanuela Minna
Software Mentions: 5
Published: about 4 years ago

10.1186/s12864-019-6003-8

RNAi based transcriptome suggests genes potentially regulated by HSF1 in the Pacific oyster Crassostrea gigas under thermal stress
Cited by: 14
Author(s): Youli Liu, Li Li, Baoyu Huang, Wei Wang, Guofan Zhang
Software Mentions: 5
Published: almost 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 8 years ago

10.3389/fonc.2021.613668

Development and Validation of a Radiomic Nomogram for Predicting the Prognosis of Kidney Renal Clear Cell Carcinoma
Cited by: 6
Author(s): Ruizhi Gao, Hui Qin, Peng Lin, Chenjun Ma, Chengyang Li, Rong Wen, Jing Huang, Da Wan, Dong‐Yue Wen, Yi-Qiong Liang, Jian Huang, Xin Li, Xinrong Wang, Gang Chen, Yun He, Hong Yang
Software Mentions: 5
Published: about 4 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 4 years ago

10.7717/peerj.4327

Evidence for widespread dysregulation of circadian clock progression in human cancer
Cited by: 66
Author(s): Jarrod Shilts, Guanhua Chen, Jacob J. Hughey
Software Mentions: 5
Published: over 7 years ago

10.1093/molbev/msab122

Role of Sex-Concordant Gene Expression in the Coevolution of Exaggerated Male and Female Genitalia in a Beetle Group
Cited by: 4
Author(s): Shota Nomura, Tomochika Fujisawa, Teiji Sota
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2016.01335

Visual Comparative Omics of Fungi for Plant Biomass Deconstruction
Cited by: 31
Author(s): Shingo Miyauchi, David Navarro, Igor V. Grigoriev, Anna Lipzen, Robert Riley, Didier Chevret, Sacha Grisel, Jean‐Guy Berrin, Bernard Henrissat, Marie‐Noëlle Rosso
Software Mentions: 5
Published: almost 9 years ago

10.3390/ijms22041989

Transcriptome Analysis of Subcutaneous Adipose Tissue from Severely Obese Patients Highlights Deregulation Profiles in Coding and Non-Coding Oncogenes
Cited by: 5
Author(s): Federica Rey, Letizia Messa, Cecilia Pandini, Rossella Launi, Bianca Barzaghini, Giancarlo Micheletto, Manuela Teresa Raimondi, Simona Bertoli, Cristina Cereda, Gian Vincenzo Zuccotti, Raffaella Cancello, Stephana Carelli
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2016.01637

Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats
Cited by: 60
Author(s): Mathilde Jeanbille, Jérôme Gury, Robert Duran, Jacek Tronczyński, Hélène Agogué, Olfa Ben Saïd, Jean-François Ghiglione, Jean‐Christophe Auguet
Software Mentions: 5
Published: almost 9 years ago

10.3389/fmicb.2020.00571

Composition, Predicted Functions and Co-occurrence Networks of Rhizobacterial Communities Impacting Flowering Desert Events in the Atacama Desert, Chile
Cited by: 17
Author(s): Marcia Astorga-Eló, Qian Zhang, Giovanni Larama, Alexandra Stoll, Michael J. Sadowsky, Milko A. Jorquera
Software Mentions: 5
Published: over 5 years ago

10.1155/2020/7575862

Coexpression Network Analysis of Genes Related to the Characteristics of Tumor Stemness in Triple-Negative Breast Cancer
Cited by: 11
Author(s): Huandan Suo, Tao Zuo, Lei Zhang, Zining Jin, Xiaoying Li, Wei Ma, Zhen Wang, Yue Qiu, Feng Jin, Bin Chen, Yu Cao
Software Mentions: 5
Published: about 5 years ago

10.1155/2020/3451610

A Pipeline to Call Multilevel Expression Changes between Cancer and Normal Tissues and Its Applications in Repurposing Drugs Effective for Gastric Cancer
Cited by: 3
Author(s): Wei Gao, Jun Yang, Changhua Zhuo, Sha Huang, Lin Jia, Guangfeng Wu, Min Zhou
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12935-020-01283-y

Identification and validation of m6A RNA methylation regulators with clinical prognostic value in Papillary thyroid cancer
Cited by: 34
Author(s): Xinyi Wang, Xiaorui Fu, Junjia Zhang, Xiong Cai, Shuyong Zhang, Yali Lv
Software Mentions: 5
Published: about 5 years ago

10.3390/ijms22062901

Age and Sex-Related Changes in Human First-Trimester Placenta Transcriptome and Insights into Adaptative Responses to Increased Oxygen
Cited by: 7
Author(s): Fulin Liu, Christelle Simasotchi, Françoise Vibert, Wencan Zhu, Sophie Gil, Séverine A. Degrelle, Thierry Fournier
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-020-07180-y

Transcriptome analysis reveals mechanism of early ripening in Kyoho grape with hydrogen peroxide treatment
Cited by: 22
Author(s): Da‐Long Guo, Zhenguang Wang, Mao-Song Pei, Lili Guo, Yi‐He Yu
Software Mentions: 5
Published: over 4 years ago

10.3389/fimmu.2021.666137

Construction and Validation of an Immune Infiltration-Related Gene Signature for the Prediction of Prognosis and Therapeutic Response in Breast Cancer
Cited by: 9
Author(s): Yang Peng, Haochen Yu, Yudi Jin, Fanli Qu, Haoyu Ren, Zhenrong Tang, Yingzi Zhang, Chi Qu, Beige Zong, Shengchun Liu
Software Mentions: 5
Published: over 4 years ago

10.1128/mSystems.00550-20

A Comprehensive Coexpression Network Analysis in Vibrio cholerae
Cited by: 4
Author(s): Cory D. DuPai, Claus O. Wilke, Bryan William Davies
Software Mentions: 5
Published: almost 5 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: over 4 years ago

10.1186/s12864-015-1540-2

Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus
Cited by: 185
Author(s): Rachel M. Wright, Galina V. Aglyamova, Eli Meyer, Mikhail V. Matz
Software Mentions: 5
Published: about 10 years ago

10.1186/s12864-020-06811-8

VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development
Cited by: 3
Author(s): Haley S. Toups, Noé Cochetel, D. J. Gray, Grant R. Cramer
Software Mentions: 5
Published: about 5 years ago

10.1186/s13293-018-0205-7

Tissue-specific pathways and networks underlying sexual dimorphism in non-alcoholic fatty liver disease
Cited by: 55
Author(s): Zeyneb Kurt, Rio Barrere‐Cain, Jonnby LaGuardia, Margarete Mehrabian, Calvin Pan, Simon T. Hui, Frode Norheim, Zhiqiang Zhou, Yehudit Hasin, Aldons J. Lusis, Xia Yang
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41398-019-0384-y

Analysis of whole genome-transcriptomic organization in brain to identify genes associated with alcoholism
Cited by: 63
Author(s): Manav Kapoor, Jen Chyong Wang, Sean P. Farris, Yunlong Liu, Jeanette N. McClintick, Ishaan Gupta, Jacquelyn L. Meyers, Sarah Bertelsen, Michael J. Chao, John I. Nürnberger, Jay A. Tischfield, Oscar Harari, Zeran Li, Victor Hesselbrock, Lance O. Bauer, Towfique Raj, Bernice Porjesz, Arpana Agrawal, Tatiana Foroud, Howard J. Edenberg, R. Dayne Mayfield, Alison Goate
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: over 4 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 4 years ago

10.1038/s41598-021-97258-8

Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology
Cited by: 3
Author(s): Cristina Cheroni, Lara Manganaro, Lorena Donnici, Valeria Bevilacqua, Raoul J. P. Bonnal, Riccardo Rossi, Raffaele De Francesco
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41398-021-01358-y

Zbtb16 regulates social cognitive behaviors and neocortical development
Cited by: 23
Author(s): Noriyoshi Usui, Stefano Berto, Ami Konishi, Makoto Kondo, Genevieve Konopka, Hideo Matsuzaki, Shoichi Shimada
Software Mentions: 5
Published: over 4 years ago

10.1002/cam4.2927

Identification of key lncRNAs in the tumorigenesis of intraductal pancreatic mucinous neoplasm by coexpression network analysis
Cited by: 11
Author(s): Jun Ding, Yang Li, Yong Zhang, Bin Fan, Qinghe Li, Jian Zhang
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-60564-8

16S rRNA gene sequencing reveals an altered composition of the gut microbiota in chickens infected with a nephropathogenic infectious bronchitis virus
Cited by: 10
Author(s): Puzhi Xu, Yan Shi, Ping Liu, Yulin Yang, Changming Zhou, Guyue Li, Junrong Luo, Caiying Zhang, Cao H, Guoliang Hu, Xiaomin Guo
Software Mentions: 5
Published: over 5 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 4 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: almost 4 years ago

10.18632/aging.102697

Identification of a nomogram based on long non-coding RNA to improve prognosis prediction of esophageal squamous cell carcinoma
Cited by: 45
Author(s): Wenli Li, Jun Li, Hetong Zhao
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-019-57108-0

Transcriptional analysis identifies potential biomarkers and molecular regulators in pneumonia and COPD exacerbation
Cited by: 15
Author(s): Wilhelm Bertrams, Kathrin Griss, Maria Han, Kerstin Seidel, Andreas Klemmer, Alexandra Sittka-Stark, Stefan Hippenstiel, Norbert Suttorp, Florian Finkernagel, Jochen Wilhelm, Timm Greulich, Claus Vogelmeier, Julio Vera, Bernd Schmeck
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-38209-8

Differentially expressed gene networks, biomarkers, long noncoding RNAs, and shared responses with cocaine identified in the midbrains of human opioid abusers
Cited by: 30
Author(s): Manal H. Saad, Matthew Rumschlag, Michael H. Guerra, Candace Savonen, Alaina M Jaster, Philip D. Olson, Adnan Alazizi, Francesca Luca, Roger Piqué-Regi, Carl J. Schmidt, Michael J. Bannon
Software Mentions: 5
Published: over 6 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: almost 4 years ago

10.1038/s41598-018-34412-9

RNA-Seq transcriptomic profiling of primary murine microglia treated with LPS or LPS + IFNγ
Cited by: 29
Author(s): Marta Pulido-Salgado, José M. Vidal-Taboada, Gerardo Garcıa-Dıaz Barriga, Carme Solà, Josep Saura
Software Mentions: 5
Published: over 6 years ago

10.3389/fgene.2021.648898

A Novel Method to Identify the Differences Between Two Single Cell Groups at Single Gene, Gene Pair, and Gene Module Levels
Cited by: 1
Author(s): Lingyu Cui, Bo Wang, Caixia Ren, Ailan Wang, Hong An, Wei Liang
Software Mentions: 5
Published: over 4 years ago

10.1186/s13229-020-00359-w

IGF-1 treatment causes unique transcriptional response in neurons from individuals with idiopathic autism
Cited by: 17
Author(s): Sara B. Linker, Ana Paula Mendes, Maria C. Marchetto
Software Mentions: 5
Published: about 5 years ago

10.3389/fimmu.2017.01071

Gene Expression Contributes to the Recent Evolution of Host Resistance in a Model Host Parasite System
Cited by: 33
Author(s): Brian K. Lohman, Natalie C. Steinel, Jesse N. Weber, Daniel I. Bolnick
Software Mentions: 5
Published: almost 8 years ago

10.1002/2211-5463.13134

Identification of hub lncRNAs in head and neck cancer based on weighted gene co‐expression network analysis and experiments
Cited by: 13
Author(s): Longquan Shao
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-018-25760-7

Different rearing conditions alter gut microbiota composition and host physiology in Shaoxing ducks
Cited by: 36
Author(s): Shumei Wang, Li Chen, Maozhang He, Junda Shen, Guoqin Li, Tao Zhang, Ru‐Rong Wu, Lizhi Liu
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-017-17460-5

Integrated DNA methylome and transcriptome analysis reveals the ethylene-induced flowering pathway genes in pineapple
Cited by: 22
Author(s): Jiabin Wang, Zhiying Li, Ming Lei, Yuhua Fu, Jiaju Zhao, Meng-Fei Ao, Li Xu
Software Mentions: 5
Published: over 7 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479