cran: WGCNA | Projects | Ecosyste.ms: Papers

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/s12864-019-6021-6

Transcriptomics analysis revealing candidate genes and networks for sex differentiation of yesso scallop (Patinopecten yessoensis)
Cited by: 17
Author(s): Liqing Zhou, Zhihong Liu, Yan Dong, Xiujun Sun, Biao Wu, Tao Yu, Yao Zheng, Aiguo Yang, Qing Zhao, Dan Zhao
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0214868

Reconstruction and inference of the Lactococcus lactis MG1363 gene co-expression network
Cited by: 5
Author(s): Jimmy Omony, Anne de Jong, Jan Kok, Sacha A. F. T. van Hijum
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms20092177

Polysome Profiling of a Human Glioblastoma Reveals Intratumoral Heterogeneity
Cited by: 9
Author(s): Fernanda C. S. Lupinacci, Hellen Kuasne, Martín Roffé, Julia Avian Vassalakis, Fernanda Ferreira da Silva, Tiago G. Santos, Victor Piana de Andrade, Paulo Sanematsu, Vilma R. Martins, Sílvia Regina Rogatto, Glaucia Noeli Maroso Hajj
Software Mentions: 4
Published: over 7 years ago

10.3389/fmolb.2021.708127

Glucotoxicity Activation of IL6 and IL11 and Subsequent Induction of Fibrosis May Be Involved in the Pathogenesis of Islet Dysfunction
Cited by: 6
Author(s): Laiwei Lu, Lili Zhuang, Xiaodong Shen, Liyong Yang
Software Mentions: 4
Published: about 5 years ago

10.3389/fmolb.2021.632950

Comprehensive Metabolomics Identified the Prominent Role of Glycerophospholipid Metabolism in Coronary Artery Disease Progression
Cited by: 10
Author(s): Hui Chen, Zixian Wang, Min Qin, Bin Zhang, Li Jen Lin, Qin Ma, Chen Liu, Xiaoping Chen, Hanping Li, Wen‐Ter Lai, Shilong Zhong
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.102190

Long non-coding RNA CASC19 is associated with the progression and prognosis of advanced gastric cancer
Cited by: 23
Author(s): Wenjie Wang, Changan Guo, Rui Li, Zipeng Xu, Jianping Yu, Ye Yan, Jun Zhao, Jing Wang, Wen-An Wang, An Zhang, Hongtao Li, Chen Wang, Hongbin Liu
Software Mentions: 4
Published: about 7 years ago

10.3389/fmolb.2021.622643

Immune-Inhibitory Gene Expression is Positively Correlated with Overall Immune Activity and Predicts Increased Survival Probability of Cervical and Head and Neck Cancer Patients
Cited by: 10
Author(s): Megha Budhwani, Gavin Turrell, Meihua Yu, Ian H. Frazer, Ahmed M. Mehdi, Janin Chandra
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.46981

Transcriptional landscape of myogenesis from human pluripotent stem cells reveals a key role of TWIST1 in maintenance of skeletal muscle progenitors
Cited by: 27
Author(s): In Young Choi, Hotae Lim, Hyeon Jin Cho, Yohan Oh, Bin Kuan Chou, Hao Bai, Linzhao Cheng, Yong Jun Kim, Sang‐Hwan Hyun, Hyesoo Kim, Joo Heon Shin, Gabsang Lee
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms19092500

Co-Expression Network Analysis Identifies miRNA–mRNA Networks Potentially Regulating Milk Traits and Blood Metabolites
Cited by: 12
Author(s): Adolf A. Ammah, Duy Ngoc, Nathalie Bissonnette, Nicolas Gévry, Eveline M. Ibeagha‐Awemu
Software Mentions: 4
Published: about 8 years ago

10.1186/1471-2164-14-728

Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivumL.)
Cited by: 80
Author(s): Karl G. Kugler, Gerald Siegwart, Thomas Nußbaumer, Christian Ametz, Manuel Spannagl, Barbara Steiner, Marc Lemmens, Klaus Mayer, Hermann Buerstmayr, Wolfgang Schweiger
Software Mentions: 4
Published: about 13 years ago

10.7554/eLife.68130

Cellular, circuit and transcriptional framework for modulation of itch in the central amygdala
Cited by: 19
Author(s): Vijay K. Samineni, Gary E. Grajales‐Reyes, Eric Tycksen, Bryan A. Copits, Christian Pedersen, Edem S Ankudey, Julian N Sackey, Sienna B Sewell, Michael R. Bruchas, Robert W. Gereau
Software Mentions: 4
Published: over 5 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

10.1186/s12864-015-1522-4

Transcriptomic profiles of aging in purified human immune cells
Cited by: 57
Author(s): Lindsay M. Reynolds, Jingzhong Ding, Jeanette Taylor, Kurt Lohman, Nicola Soranzo, Alberto de la Fuente, Tie Fu Liu, Craig W. Johnson, R. Graham Barr, Thomas C. Register, Kathleen Donohue, Monica V. Talor, Daniela Čiháková, C. Charles Gu, Jasmin Divers, David S. Siscovick, Gregory L. Burke, Wendy S. Post, Steven Shea, David R. Jacobs, Ina Hoeschele, Charles E. McCall, Stephen B. Kritchevsky, David M. Herrington, Russell P. Tracy, Yongmei Liu
Software Mentions: 4
Published: over 11 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

10.18632/aging.202228

Identification of SCARA3 with potential roles in metabolic disorders
Cited by: 7
Author(s): Hui Peng, Qi Guo, Tian Su, Ye Xiao, Changjun Li, Yan Huang, Xiang‐Hang Luo
Software Mentions: 4
Published: almost 6 years ago

10.3390/ijms21249560

Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses
Cited by: 2
Author(s): Francesco Monticolo, Emanuela Palomba, Maria Luisa Chiusano
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-020-07118-4

Transcriptome-IPMS analysis reveals a tissue-dependent miR156/SPL13 regulatory mechanism in alfalfa drought tolerance
Cited by: 6
Author(s): Biruk A. Feyissa, Justin B. Renaud, Vida Nasrollahi, Susanne E. Kohalmi, Abdelali Hannoufa
Software Mentions: 4
Published: about 6 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

10.7554/eLife.46149

Identification of potential biomarkers of vaccine inflammation in mice
Cited by: 23
Author(s): Paul F. McKay, Deniz Cizmeci, Yoann Aldon, Jeroen Maertzdorf, January Weiner, Stefan H. E. Kaufmann, David Lewis, Robert A. van den Berg, Giuseppe Del Giudice, Robin J. Shattock
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-018-2053-1

CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses
Cited by: 176
Author(s): Pedro Russo, Gustavo Rodrigues Ferreira, Lucas Esteves Cardozo, Matheus Carvalho Bürger, Raúl Arias‐Carrasco, Sandra Regina Maruyama, Thiago Dominguez Crespo Hirata, Diógenes Saulo de Lima, Fernando M. Passos, Kiyoshi F. Fukutani, Melissa Lever, João Silva, Vinicius Maracaja‐Coutinho, Hidehiko Nakaya
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.34613

Transcriptional profiling reveals extraordinary diversity among skeletal muscle tissues
Cited by: 93
Author(s): Erin E. Terry, Xiping Zhang, Christy Hoffmann, Laura D. Hughes, Scott A. Lewis, Jiajia Li, Marianne Wallace, Lance A. Riley, Collin M Douglas, Miguel A. Gutiérrez-Monreal, Nicholas F. Lahens, Ming Gong, Francisco H. Andrade, Karyn A. Esser, Michael Hughes
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-021-07731-x

Exposure to hypoxia causes stress erythropoiesis and downregulates immune response genes in spleen of mice
Cited by: 16
Author(s): Haijing Wang, Daoxin Liu, Pengfei Song, Feng Jiang, Xiaowei Chi, Tongzuo Zhang
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.579290

Spatiotemporal Patterns in Diversity and Assembly Process of Marine Protist Communities of the Changjiang (Yangtze River) Plume and Its Adjacent Waters
Cited by: 8
Author(s): Xin Guo, Lianghuan Wu, Lingfeng Huang
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2016.01688

Systems Biomedicine of Rabies Delineates the Affected Signaling Pathways
Cited by: 19
Author(s): Sadegh Azimzadeh Jamalkandi, Sayed‐Hamidreza Mozhgani, Hamid Gholami Pourbadie, Mehdi Mirzaie, Farshid Noorbakhsh, Behrouz Vaziri, Alireza Gholami, Naser Ansari-Pour, Mohieddin Jafari
Software Mentions: 4
Published: almost 10 years ago

10.7554/eLife.65582

Neural correlates of ingroup bias for prosociality in rats
Cited by: 25
Author(s): Inbal Ben-Ami Bartal, Jocelyn Breton, Huanjie Sheng, Kimberly L.P. Long, Stella Chen, Aline Halliday, Justin W. Kenney, Anne L. Wheeler, Paul W. Frankland, Carrie Shilyansky, Karl Deisseroth, Dacher Keltner, Daniela Kaufer
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.573829

Evolution and Plasticity of the Transcriptome Under Temperature Fluctuations in the Fungal Plant Pathogen Zymoseptoria tritici
Cited by: 2
Author(s): Arthur J. Jallet, Arnaud Le Rouzic, Anne Génissel
Software Mentions: 4
Published: about 6 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/s12864-019-5850-7

Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks
Cited by: 6
Author(s): Kevin B. Walters, Radmir Sarsenov, Wen Siong Too, Roseanna K. Hare, Ian C. Paterson, D Lambert, Stephen Brown, James R. Bradford
Software Mentions: 4
Published: over 7 years ago

10.3389/fmolb.2021.719982

Identification of Mast Cell-Based Molecular Subtypes and a Predictive Signature in Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Hanxiang Liu, Yi Yang
Software Mentions: 4
Published: about 5 years ago

10.3389/fnins.2020.00774

Lasting and Sex-Dependent Impact of Maternal Immune Activation on Molecular Pathways of the Amygdala
Cited by: 19
Author(s): Marissa R Keever, Pan Zhang, Courtni R. Bolt, Adrienne M. Antonson, Haley E Rymut, Megan P. Caputo, Alexandra K Houser, Álvaro Gonzalez Hernández, Bruce R. Southey, Laurie A. Rund, Rodney W. Johnson, Sandra L. Rodriguez-Zas
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0148818

Meta-Analysis of Tumor Stem-Like Breast Cancer Cells Using Gene Set and Network Analysis
Cited by: 14
Author(s): Wonjun Lee, Sang Cheol Kim, Jong Ho Yoon, Sang Jun Yoon, Jong-Tae Lim, You Sun Kim, Sung Won Kwon, Jeong Hill Park
Software Mentions: 4
Published: over 10 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

10.7554/eLife.55851

Genetic mapping of etiologic brain cell types for obesity
Cited by: 62
Author(s): Pascal Timshel, Jonatan J Thompson, Tune H. Pers
Software Mentions: 4
Published: about 6 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

10.1084/jem.20202446

GSAP regulates lipid homeostasis and mitochondrial function associated with Alzheimer’s disease
Cited by: 14
Author(s): Peng Xu, Jerry C. Chang, Xiaopu Zhou, Wei Wang, Michael Bamkole, Eitan Wong, Karima Bettayeb, LuLin Jiang, Timothy Huang, Wenjie Luo, Huaxi Xu, Angus C. Nairn, Marc Flajolet, Nancy Y. Ip, Yueming Li, Paul Greengard
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2017.01561

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing
Cited by: 211
Author(s): Luisa W. Hugerth, Anders F. Andersson
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0185682

Meta-analysis of peripheral blood gene expression modules for COPD phenotypes
Cited by: 15
Author(s): Dominik Reinhold, Jarrett Morrow, Sean Jacobson, Junxiao Hu, Benjamin Ringel, Max A. Seibold, Craig P. Hersh, Katerina Kechris, Russell P. Bowler
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0210672

Identification of new regulators through transcriptome analysis that regulate anthocyanin biosynthesis in apple leaves at low temperatures
Cited by: 28
Author(s): Tingting Song, Keting Li, Ting Wu, Yi Wang, Xinzhong Zhang, Xuefeng Xu, Yuncong Yao, Zhenhai Han
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-020-06909-z

Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle
Cited by: 23
Author(s): Ze Yan, Hanyu Huang, Ellen Freebern, D. R. dos Santos, Dongmei Dai, Jingfang Si, Chengbin Ma, Jie Cao, Gang Guo, George E. Liu, Li Ma, Lingzhao Fang, Yi Zhang
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0252647

Co-expression analysis identifies neuro-inflammation as a driver of sensory neuron aging in Aplysia californica
Cited by: 2
Author(s): Nicholas S. Kron, Lynne A. Fieber
Software Mentions: 4
Published: over 5 years ago

10.1186/s13046-020-01752-2

MiRNA-340-5p mediates the functional and infiltrative promotion of tumor-infiltrating CD8+ T lymphocytes in human diffuse large B cell lymphoma
Cited by: 9
Author(s): Yangyang Xu, Zhenchuan Liu, Lixin Lv, Ping Li, Bing Xu, Wenbin Qian, Aibin Liang
Software Mentions: 4
Published: almost 6 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

10.1084/jem.20170412

A multidimensional blood stimulation assay reveals immune alterations underlying systemic juvenile idiopathic arthritis
Cited by: 43
Author(s): Alma-Martina Cepika, Romain Banchereau, Élodie Segura, Marina Ohouo, Brandi L. Cantarel, Kristina Goller, V. Ashley Cantrell, Emily Ruchaud, Elizabeth Gatewood, Phuong Nguyen, Jin Gu, Esperanza Anguiano, Sandra Zurawski, Jeanine Baisch, Marilynn Punaro, Nicole Baldwin, Gerlinde Obermoser, Karolina Palucka, Jacques Banchereau, Sebastián Amigorena, Virginia Pascual
Software Mentions: 4
Published: about 9 years ago

10.18632/aging.102275

Co-expression network analysis identified hub genes critical to triglyceride and free fatty acid metabolism as key regulators of age-related vascular dysfunction in mice
Cited by: 52
Author(s): Huimin Li, Xinhui Wang, Xinyue Lu, Hongxin Zhu, Sheng Li, Shiwei Duan, Xinzhi Zhao, Fuquan Zhang, Gil Alterovitz, Fudi Wang, Qiang Li, Xiao-Li Tian, Mingqing Xu
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0056228

canEvolve: A Web Portal for Integrative Oncogenomics
Cited by: 39
Author(s): Mehmet K. Samur, Zhenyu Yan, Xujun Wang, Qingyi Cao, Nikhil C. Munshi, Li Cheng, Parantu K. Shah
Software Mentions: 4
Published: over 13 years ago

10.1186/s12864-018-5115-x

Genome-wide identification and differentially expression analysis of lncRNAs in tilapia
Cited by: 19
Author(s): Bi Jun Li, Dan Jiang, Zhijun Meng, Yong Zhang, Zong Xian Zhu, Haoran Lin, Jun Xia
Software Mentions: 4
Published: about 8 years ago

10.1084/jem.20190430

An anti-CRF antibody suppresses the HPA axis and reverses stress-induced phenotypes
Cited by: 7
Author(s): Hunter S. Futch, Karen N. McFarland, Brenda D. Moore, M. Zino Kuhn, Benoit I. Giasson, Thomas B. Ladd, Karen A. Scott, Melanie R. Shapiro, Rachel L. Nosacka, Marshall S. Goodwin, Yong Ran, Pedro Cruz, Doojin Ryu, Cara L. Croft, Yona Levites, Christopher Janus, Paramita Chakrabarty, Andrew R. Judge, Todd M. Brusko, Annette D. de Kloet, Eric G. Krause, Todd E. Golde
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-020-57467-z

Transcriptome analysis of fibroblasts from schizophrenia patients reveals differential expression of schizophrenia-related genes
Cited by: 17
Author(s): Mitra Etemadikhah, Adnan Niazi, Lennart Wetterberg, Lars Feuk
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-020-59934-z

Immunosuppressive effect and global dysregulation of blood transcriptome in response to psychosocial stress in vervet monkeys (Chlorocebus sabaeus)
Cited by: 2
Author(s): Anna J. Jasinska, Ivona Pandrea, Tianyu He, Cassandra Benjamin, Maurice Newton, Jen‐Chieh Lee, Nelson B. Freimer, Giovanni Coppola, J. David Jentsch
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-54051-y

Widespread Sexual Dimorphism in the Transcriptome of Human Airway Epithelium in Response to Smoking
Cited by: 12
Author(s): Cheng Wei Tony Yang, Henry Shi, Irving Ding, Stephen Milne, Ana I Hernández Cordero, Edward Kyoo Hoon Kim, Tillie L. Hackett, Janice M. Leung, Don D. Sin, Ma’en Obeidat
Software Mentions: 4
Published: almost 7 years ago

10.3389/fgene.2021.645443

Global Transcriptome and Weighted Gene Co-expression Network Analyses of Growth-Stage-Specific Drought Stress Responses in Maize
Cited by: 21
Author(s): Songtao Liu, Tinashe Zenda, Anyi Dong, Yatong Yang, Nan Wang, Huijun Duan
Software Mentions: 4
Published: almost 6 years ago

10.3389/fgene.2020.549213

Stemness Related Genes Revealed by Network Analysis Associated With Tumor Immune Microenvironment and the Clinical Outcome in Lung Adenocarcinoma
Cited by: 41
Author(s): Hao Zeng, Jianrui Ji, Xindi Song, Yeqian Huang, Hui Li, Juan Huang, Xuelei Ma
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0165059

Drug Repositioning through Systematic Mining of Gene Coexpression Networks in Cancer
Cited by: 19
Author(s): Alexander E. Ivliev, Peter A.C. ’t Hoen, Dmitrii Borisevich, Yuri Nikolsky, Marina G. Sergeeva
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12864-019-6161-8

Weighted gene co-expression network analysis unveils gene networks associated with the Fusarium head blight resistance in tetraploid wheat
Cited by: 17
Author(s): Ehsan Sari, Adrian L. Cabral, Brittany Polley, Yifang Tan, Emma Hsueh, David Konkin, Ron Knox, Yuefeng Ruan, Pierre R. Fobert
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0253037

A meta-analysis of transcriptomic profiles of Huntington’s disease patients
Cited by: 14
Author(s): Manuel Seefelder, Stefan Kochanek
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-44266-4

Transcriptomics Analysis Reveals New Insights into the Roles of Notch1 Signaling on Macrophage Polarization
Cited by: 21
Author(s): Chetan P. Hans, Neekun Sharma, Sidharth Sen, Shuai Zeng, Rishabh Dev, Yuyong Jiang, Advitiya Mahajan, Trupti Joshi
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0206665

Identification of highly connected and differentially expressed gene subnetworks in metastasizing endometrial cancer
Cited by: 11
Author(s): Kanthida Kusonmano, Mari K. Halle, Elisabeth Wik, Erling A. Høivik, Camilla Krakstad, Karen Klepsland Mauland, Ingvild L. Tangen, Ansgar Berg, Henrica M.J. Werner, Jone Trovik, Anne Margrete Øyan, Karl‐Henning Kalland, Inge Jonassen, Helga B. Salvesen, Kjell Petersen
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-019-45236-6

In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data
Cited by: 55
Author(s): Remzi Çelebi, Oliver Bear Don't Walk, Rajiv Movva, Semih Alpsoy, Michel Dumontier
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-019-47454-4

Glial gene networks associated with alcohol dependence
Cited by: 38
Author(s): Emma K. Erickson, Yuri A. Blednov, R. Adron Harris
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-020-61633-8

MicroRNA hsa-mir-3923 serves as a diagnostic and prognostic biomarker for gastric carcinoma
Cited by: 11
Author(s): Xiaohui Yang, Ze Zhang, Lichao Zhang, Li Zhou
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0177750

Inflammatory and apoptotic remodeling in autonomic nervous system following myocardial infarction
Cited by: 23
Author(s): Chen Gao, Kimberly Howard‐Quijano, Christoph Rau, Tatsuo Takamiya, Yang Song, Kalyanam Shivkumar, Yibin Wang, Aman Mahajan
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-018-37284-1

A gene expression signature in developing Purkinje cells predicts autism and intellectual disability co-morbidity status
Cited by: 12
Author(s): Harry Clifford, Anna Dulneva, Chris P. Ponting, Wilfried Haerty, Esther B. E. Becker
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-019-39274-3

Genome analysis of the rice coral Montipora capitata
Cited by: 49
Author(s): Alexander Shumaker, Hollie M. Putnam, Huan Qiu, Dana C. Price, Ehud Zelzion, Amnon Harel, Nicole Wagner, Ruth D. Gates, Hwan Su Yoon, Debashish Bhattacharya
Software Mentions: 4
Published: over 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

10.1038/s41598-018-35578-y

Gene mutation associated with esl mediates shifts on fungal community composition in rhizosphere soil of rice at grain-filling stage
Cited by: 1
Author(s): Puleng Letuma, Yasir Arafat, Muhammad Mohsin Waqas, Feifan Lin, Wenxiong Lin, Yiyang Zhang, Mamello Masita, Kai Fan, Zhaowei Li
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-019-38965-1

Initial findings of striatum tripartite model in OCD brain samples based on transcriptome analysis
Cited by: 14
Author(s): Bianca Cristina Garcia Lisbôa, Kátia C. Oliveira, Ana Carolina Tahira, André Rocha Barbosa, Arthur Sant’Anna Feltrin, Gisele Rodrigues Gouveia, Luzia Carreira Lima, Ana Cecília Feio dos Santos, David Martins, Renato Puga, Ariane Cristine Moretto, Carlos Alberto de Bragança Pereira, Beny Lafer, Renata Elaine Paraízo Leite, Renata Eloah de Lucena Ferretti‐Rebustini, José Marcelo Farfel, Lea T. Grinberg, Wilson Jacob‐Filho, Eurípedes Constantino Miguel, Marcelo Q. Hoexter, Helena Brentani
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2021.650874

Investigating Transcriptional Dynamics Changes and Time-Dependent Marker Gene Expression in the Early Period After Skeletal Muscle Injury in Rats
Cited by: 6
Author(s): Kangning Ren, Liangliang Wang, Liang Wang, Qiu-xiang Du, Jie Cao, Qianqian Jin, Guo-shuai An, Na Li, Li-hong Dang, Yingjie Tian, Ying-Yuan Wang, Jun-hong Sun
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-020-07091-y

Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning
Cited by: 10
Author(s): Fernando Henrique Correr, Guilherme Kenichi Hosaka, Fernando Barreto, Isabella Barros Valadão, Thiago Willian Almeida Balsalobre, Agnelo Furtado, Robert J. Henry, Monalisa Sampaio Carneiro, Gabriel Rodrigues Alves Margarido
Software Mentions: 4
Published: about 6 years ago

10.3389/fgene.2020.00176

Integrative Analysis of MicroRNA and Gene Interactions for Revealing Candidate Signatures in Prostate Cancer
Cited by: 34
Author(s): Jingchao Wei, Yinghao Yin, Qiancheng Deng, Jun Zhou, Yong Wang, Guangming Yin, Jianfu Yang, Yuxin Tang
Software Mentions: 4
Published: over 6 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

10.1038/s41598-019-41298-8

Regeneration associated transcriptional signature of retinal microglia and macrophages
Cited by: 54
Author(s): Diana Mitchell, Chi Sun, Samuel S. Hunter, Daniel D. New, Deborah L. Stenkamp
Software Mentions: 4
Published: over 7 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/fgene.2018.00228

Network Rewiring in Cancer: Applications to Melanoma Cell Lines and the Cancer Genome Atlas Patients
Cited by: 6
Author(s): Kuan Fu Ding, Darren Finlay, Hongwei Yin, William P.D. Hendricks, Chris Sereduk, Jeffrey Kiefer, Aleksandar Sekulić, Patricia LoRusso, Kristiina Vuori, Jeffrey M. Trent, Nicholas J. Schork
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-018-26438-w

Unravelling miRNA regulation in yield of rice (Oryza sativa) based on differential network model
Cited by: 21
Author(s): Jihong Hu, Tao Zeng, Xia QiongMei, Qian Qian, Chunrong Yang, Yi Ding, Luonan Chen, Wen Wang
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0178532

Integrative genomic analyses for identification and prioritization of long non-coding RNAs associated with autism
Cited by: 21
Author(s): Brian Gudenas, Anand Srivastava, Liangjiang Wang
Software Mentions: 4
Published: over 9 years ago

10.1002/cam4.2969

Identification of hub methylated‐CpG sites and associated genes in oral squamous cell carcinoma
Cited by: 14
Author(s): Yuxin Dai, Qiao‐Li Lv, Tingting Qi, Jian Qu, Hongli Ni, Yongkang Liao, Peng Liu, Qiang Qu
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-19072-5

Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency in pigs
Cited by: 45
Author(s): Yuliaxis Ramayo-Caldas, María Ballester, Juan Pablo Sánchez, Olga González‐Rodríguez, Manuel Revilla, Henry Reyer, Klaus Wimmers, D. Torrallardona, Raquel Quintanilla
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-018-27172-z

Heterogeneity of interactions of microbial communities in regions of Taihu Lake with different nutrient loadings: A network analysis
Cited by: 32
Author(s): Xinyi Cao, Dayong Zhao, Huimin Xu, Rui Huang, Jin Zeng, Zhigang Yu
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-019-43881-5

Comprehensive and Systematic Analysis of Gene Expression Patterns Associated with Body Mass Index
Cited by: 13
Author(s): Paule V. Joseph, Rosario B. Jaime-Lara, Yupeng Wang, Lichen Xiang, Wendy A. Henderson
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-019-6043-0

Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird
Cited by: 12
Author(s): Veronika N. Laine, Irene Verhagen, A. Christa Mateman, Agata Pijl, Tony Williams, Phillip Gienapp, Kees van Oers, Marcel E. Visser
Software Mentions: 4
Published: about 7 years ago

10.1186/s12935-020-01352-2

Co-expression network analysis identifies a gene signature as a predictive biomarker for energy metabolism in osteosarcoma
Cited by: 19
Author(s): Naiqiang Zhu, Jingyi Hou, Guiyun Ma, Shuai Guo, Chengliang Zhao, Bin Chen
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2019.00697

Cross-Species Gene Expression Analysis Reveals Gene Modules Implicated in Human Osteosarcoma
Cited by: 12
Author(s): Zheng Jin, Shanshan Liu, Pei‐Wen Zhu, Mengyan Tang, Yuanxin Wang, Yuan Tian, Li Dong, X. D. Zhu, Dongmei Yan, Zhifeng Zhu
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-019-5625-1

Integrated analysis of lncRNA and mRNA repertoires in Marek’s disease infected spleens identifies genes relevant to resistance
Cited by: 21
Author(s): Zhen You, Qinghe Zhang, Changjun Liu, Jiuzhou Song, Ning Yang, Ling Lian
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-017-05724-z

Comprehensive transcriptomics and proteomics analyses of pollinated and parthenocarpic litchi (Litchi chinensis Sonn.) fruits during early development
Cited by: 14
Author(s): Wei Liu, Maoshan Chen, Lijun Bai, Zhenhua Zhuang, Chao Fan, Jiang Nong-hui, Junsheng Zhao, Shuaipeng Ma, Xiang Xu
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-017-11327-5

Genome-wide identification and co-expression network analysis provide insights into the roles of auxin response factor gene family in chickpea
Cited by: 26
Author(s): Vikash Singh, Mohan Singh Rajkumar, Rohini Garg, Mukesh Jain
Software Mentions: 4
Published: about 9 years ago

10.1038/srep33956

A systems biology approach to defining regulatory mechanisms for cartilage and tendon cell phenotypes
Cited by: 19
Author(s): Alan Mueller, Simon R. Tew, Olga Vasieva, Peter Clegg, Elizabeth G. Canty‐Laird
Software Mentions: 4
Published: about 10 years ago

10.3389/fgene.2021.735103

Editorial: Computational Tools in Inferring Cancer Tissue-of-Origin and Molecular Classification Towards Personalized Cancer Therapy, Volume II
Cited by: 0
Author(s): Ling Kui, Wenzhe Mao, Aasim Majeed, Jian Chen
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-017-4392-0

Molecular characterization of larval development from fertilization to metamorphosis in a reef-building coral
Cited by: 36
Author(s): Marie E. Strader, Galina V. Aglyamova, Mikhail V. Matz
Software Mentions: 4
Published: almost 9 years ago

10.1038/srep12615

Decrease of mRNA Editing after Spinal Cord Injury is Caused by Down-regulation of ADAR2 that is Triggered by Inflammatory Response
Cited by: 27
Author(s): Antonio Fabio Di Narzo, Alexey Kozlenkov, Yongchao Ge, Bin Zhang, Leo Sanelli, Zacnicte May, Yanqing Li, Karim Fouad, Christopher P. Cardozo, Eugene V. Koonin, David J. Bennett, Stella Dracheva
Software Mentions: 4
Published: about 11 years ago

10.3389/fgene.2019.01214

Weighted Gene Co-Expression Network Analysis Identifies Critical Genes in the Development of Heart Failure After Acute Myocardial Infarction
Cited by: 59
Author(s): Xiaowei Niu, Jingjing Zhang, Lanlan Zhang, Yufei Hou, Shuangshuang Pu, Ai-Ai Chu, Ming Bai, Zheng Zhang
Software Mentions: 4
Published: almost 7 years ago

10.3389/fgene.2020.00427

Bioinformatics Analysis Reveals Biomarkers With Cancer Stem Cell Characteristics in Lung Squamous Cell Carcinoma
Cited by: 38
Author(s): Yi Liao, Hua Xiao, Mengqing Cheng, Xiaoxuan Fan
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2020.00650

Genome Regulation and Gene Interaction Networks Inferred From Muscle Transcriptome Underlying Feed Efficiency in Pigs
Cited by: 9
Author(s): Victor Adriano Okstoft Carmelo, Haja N. Kadarmideen
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.202781

One potential biomarker for teratozoospermia identified by in-depth integrative analysis of multiple microarray data
Cited by: 3
Author(s): Baoquan Han, Lu Wang, Shuai Yu, Wei Ge, Yaqi Li, Hui Jiang, Wei Shen, Zhongyi Sun
Software Mentions: 4
Published: over 5 years ago

10.1155/2020/4348371

DHX36, BAX, and ARPC1B May Be Critical for the Diagnosis and Treatment of Tuberculosis
Cited by: 3
Author(s): Yunli Zhang, Yanming Liu, Hongling Li, Qingxia Liu, Wei Wang, Zijuan Jian, Wenen Liu
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2020.00253

Integrated Analysis to Evaluate the Prognostic Value of Signature mRNAs in Glioblastoma Multiforme
Cited by: 11
Author(s): Jian Yang, Long Wang, Zhou Xu, Liquan Wu, Baohui Liu, Junmin Wang, Daofeng Tian, Xiaoxing Xiong, Qianxue Chen
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2021.668448

Integrated Analysis of lncRNAs, mRNAs, and TFs to Identify Regulatory Networks Underlying MAP Infection in Cattle
Cited by: 6
Author(s): Maryam Heidari, A. Pakdel, Mohammad Reza Bakhtiarizadeh, Fariba Dehghanian
Software Mentions: 4
Published: over 5 years ago

10.1126/sciadv.abf9808

Mechanisms underlying divergent responses of genetically distinct macrophages to IL-4
Cited by: 23
Author(s): Marten A. Hoeksema, Zeyang Shen, Inge R. Holtman, An Zheng, Nathan Spann, Isidoro Cobo, Melissa Gymrek, Christopher K. Glass
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2020.597459

Pearl Sac Gene Expression Profiles Associated With Pearl Attributes in the Silver-Lip Pearl Oyster, Pinctada maxima
Cited by: 9
Author(s): Carmel McDougall, Felipe Aguilera, Ali Shokoohmand, Patrick Moase, Bernard M. Degnan
Software Mentions: 4
Published: almost 6 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

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479