Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: cran: WGCNA
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/WGCNA
Weighted Correlation Network Analysis
52 versions
Latest release: almost 2 years ago
20 dependent packages
9,120 downloads last month
Papers Mentioning WGCNA 3,479
10.1186/s12864-021-07595-1
Dynamics of rumen gene expression, microbiome colonization, and their interplay in goatsCited by: 15
Author(s): Xiangyu Pan, Zongjun Li, Bibo Li, Chen Zhao, Yu Wang, Yulin Chen, Yu Jiang
Software Mentions: 7
Published: over 3 years ago
10.1111/eva.12935
The power and limitations of gene expression pathway analyses toward predicting population response to environmental stressorsCited by: 9
Author(s): Brenna Callista Moreau Stanford, Danielle Jessica Clake, Matthew R. J. Morris, Sean M. Rogers
Software Mentions: 7
Published: over 4 years ago
10.18632/aging.202417
Overexpression of TICRR and PPIF confer poor prognosis in endometrial cancer identified by gene co-expression network analysisCited by: 13
Author(s): Linlin Yang, Yunxia Cui, Xiao Sun, Yudong Wang
Software Mentions: 7
Published: almost 4 years ago
10.1186/s13195-020-00733-z
Exploring the role of RALYL in Alzheimer’s disease reserve by network-based approachesCited by: 4
Author(s): Yixuan Zhang, Jiali Wang, Xiaoquan Liu, Haochen Liu
Software Mentions: 7
Published: almost 4 years ago
10.3389/fncel.2020.612560
Proteomic Characterization of Human Neural Stem Cells and Their Secretome During in vitro DifferentiationCited by: 19
Author(s): Jakub Červenka, Jiřina Tylečková, Helena Kupcová Skalníková, Kateřina Vodičková Kepková, Ievgeniia Poliakh, Ivona Valeková, Lucie Pfeiferová, Michal Kolář, Michaela Vaškovičová, Tereza Pánková, Petr Vodička
Software Mentions: 7
Published: almost 4 years ago
10.1111/pbi.13205
Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrassCited by: 45
Author(s): Linkai Huang, Guangyan Feng, Haidong Yan, Zhongren Zhang, B. Shaun Bushman, Jianping Wang, Aureliano Bombarely, Mingzhou Li, Zhongfu Yang, Gang Nie, Wengang Xie, Lei Xu, Peilin Chen, Xinxin Zhao, Wenkai Jiang, Xinquan Zhang
Software Mentions: 7
Published: over 5 years ago
10.1002/ece3.4756
Symbiont type and environmental factors affect transcriptome‐wide gene expression in the coral <i>Montipora capitata</i>Cited by: 9
Author(s): Martin Helmkampf, M. Renee Bellinger, Monika Frazier, Misaki Takabayashi
Software Mentions: 7
Published: almost 6 years ago
10.3390/genes11101165
OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq DataCited by: 21
Author(s): Rui Li, Kai Hu, Haibo Liu, Michael R. Green, Lihua Julie Zhu
Software Mentions: 7
Published: about 4 years ago
10.15252/emmm.201910606
Novel Alzheimer risk genes determine the microglia response to amyloid‐β but not to TAU pathologyCited by: 149
Author(s): Annerieke Sierksma, Ashley Lu, Renzo Mancuso, Nicola Fattorelli, Nicola Thrupp, Evgenia Salta, Jesus Zoco, David Blum, Luc Buée, Bart De Strooper, Mark Fiers
Software Mentions: 7
Published: almost 5 years ago
10.7554/eLife.57843
Increased longevity due to sexual activity in mole-rats is associated with transcriptional changes in the HPA stress axisCited by: 17
Author(s): Arne Sahm, Matthias Platzer, Philipp Koch, Yoshiyuki Henning, Martin Bens, Marco Groth, Hynek Burda, Sabine Begall, Saskia Ting, Moritz Goetz, Paul Van Daele, Magdalena Staniszewska, Jasmin Klose, Pedro Fragoso Costa, Steve Hoffmann, Karol Szafranski, Philip Dammann
Software Mentions: 7
Published: over 3 years ago
10.3390/genes10070514
Transcriptional Analysis of the Early Ripening of ‘Kyoho’ Grape in Response to the Treatment of RiboflavinCited by: 9
Author(s): Zhenguang Wang, Lili Guo, Xiao-Ru Ji, Yi‐He Yu, Guohai Zhang, Da‐Long Guo
Software Mentions: 6
Published: over 5 years ago
10.3390/brainsci9120381
A Pathway-Based Genomic Approach to Identify Medications: Application to Alcohol Use DisorderCited by: 6
Author(s): Laura B. Ferguson, Shruti Patil, Bailey A. Moskowitz, Igor Ponomarev, R. Adron Harris, R. Dayne Mayfield, Robert O. Messing
Software Mentions: 6
Published: almost 5 years ago
10.1242/dmm.047225
Hearing impairment due to <i>Mir183/96/182</i> mutations suggests both loss-of-function and gain-of-function effectsCited by: 10
Author(s): Morag A. Lewis, Francesca Di Domenico, Neil J. Ingham, Haydn M. Prosser, Karen P. Steel
Software Mentions: 6
Published: almost 4 years ago
10.15252/embj.2019101695
Phospho‐RNA‐seq: a modified small RNA‐seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasmaCited by: 61
Author(s): María D. Giraldez, Ryan M Spengler, Alton Etheridge, Annika Jane Goicochea, Missy Tuck, Sung Won Choi, David J. Galas, Muneesh Tewari
Software Mentions: 6
Published: over 5 years ago
10.1534/g3.117.041624
Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative CrossCited by: 35
Author(s): Richard Green, Courtney Wilkins, Sunil Thomas, Aimee Sekine, Duncan M. Hendrick, Kathleen Voss, Reneé C. Ireton, Michael A. Mooney, Jennifer T. Go, Gabrielle Choonoo, Sophia Jeng, Fernando P Pardo Manuel De Villena, Martin T. Ferris, Shannon K. McWeeney, Michael Gale
Software Mentions: 6
Published: over 7 years ago
10.1186/s12885-017-3832-1
Comparative gene co-expression network analysis of epithelial to mesenchymal transition reveals lung cancer progression stagesCited by: 9
Author(s): Daifeng Wang, John D. Haley, Patricia Thompson
Software Mentions: 6
Published: almost 7 years ago
10.1186/s12864-020-6767-x
Multipathway synergy promotes testicular transition from growth to spermatogenesis in early-puberty goatsCited by: 11
Author(s): Dongdong Bo, Xunping Jiang, Guiqiong Liu, Feng Xu, Ronggui Hu, Teketay Wassie, Yuqing Chong, S. Sohail Ahmed, Chenhui Liu, Shishay Girmay
Software Mentions: 6
Published: over 4 years ago
10.1186/s12885-018-4848-x
Genomic analysis of DNA repair genes and androgen signaling in prostate cancerCited by: 53
Author(s): Kasey Jividen, Katarzyna Kedzierska, Chunsong Yang, Karol Szlachta, Aakrosh Ratan, Bryce M. Paschal
Software Mentions: 6
Published: about 6 years ago
10.3389/fpsyt.2021.716722
Transcriptomics Analysis Reveals Shared Pathways in Peripheral Blood Mononuclear Cells and Brain Tissues of Patients With SchizophreniaCited by: 6
Author(s): Xuemian Song, Yiyun Liu, Juncai Pu, Siwen Gui, Xiaogang Zhong, Xiaopeng Chen, Weiyi Chen, Xiang Chen, Yue Chen, Haiyang Wang, Ke Cheng, Libo Zhao, Peng Xie
Software Mentions: 6
Published: about 3 years ago
10.1186/s12885-021-08052-8
Comprehensive analysis of immune-related prognostic genes in the tumour microenvironment of hepatocellular carcinomaCited by: 2
Author(s): Weike Gao, Luan Li, Xinyin Han, Siyao Liu, Chengzhen Li, Guanying Yu, Lei Zhang, Dongsheng Zhang, Caiyun Liu, Erhong Meng, Shuai Hong, Dongliang Wang, Peiming Guo, Guangjun Shi
Software Mentions: 6
Published: over 3 years ago
10.1093/conphys/coz018
Tracking transcriptomic responses to endogenous and exogenous variation in cetaceans in the Southern California BightCited by: 8
Author(s): Marisa L. Trego, Andrew Whitehead, Nicholas M. Kellar, Morgane Lauf, Rebecca L. Lewison
Software Mentions: 6
Published: almost 6 years ago
10.15252/embj.2019102808
HNF1A recruits KDM6A to activate differentiated acinar cell programs that suppress pancreatic cancerCited by: 36
Author(s): Jorge Ferrer, Edgar Bernardo, Anthony Beucher, Miguel A. Maestro, Natalia del Pozo, I.R. Hernández Millán, Lena Haeberle, Martin Schlensog, Sami-Alexander Safi, Wolfram Trudo Knoefel, Vanessa Grau, Matías De Vas, Karl B. Shpargel, Eva C. Vaquero, Terry Magnuson, Sagrario Ortega, Irene Espósito, Francisco X. Real, Jorge Ferrer
Software Mentions: 6
Published: over 4 years ago
10.18632/aging.103743
Identification of subtype-specific genes signature by WGCNA for prognostic prediction in diffuse type gastric cancerCited by: 6
Author(s): Qi Zhou, Liqun Zhou, Shihao Li, Yi‐Wu Yuan, Li Liu, Jinliang Wang, Deng-Zhong Wu, You Wu, Lin Xin
Software Mentions: 6
Published: about 4 years ago
10.18632/aging.203166
Identification and validation of inferior prognostic genes associated with immune signatures and chemotherapy outcome in acute myeloid leukemiaCited by: 7
Author(s): Jie Wang, Hao Jian-ping, Nazim Uddin, Yun Wu, Rong Chen, Dongfeng Li, Dai-qin Xiong, Nan Ding, Jianhua Yang, Xiaowen Ding
Software Mentions: 6
Published: over 3 years ago
10.18632/aging.202638
Identification of key genes in coronary artery disease: an integrative approach based on weighted gene co-expression network analysis and their correlation with immune infiltrationCited by: 10
Author(s): Yang Yang, Xiangshan Xu
Software Mentions: 6
Published: over 3 years ago
10.1186/s12885-021-08711-w
Construction of a ceRNA network of hub genes affecting immune infiltration in ovarian cancer identified by WGCNACited by: 12
Author(s): Rongjia Su, Chengjuan Jin, Lina Zhou, Yannan Cao, Menghua Kuang, Linxia Li, Jianbin Xiang
Software Mentions: 6
Published: about 3 years ago
10.3389/fpls.2021.675208
Differential Regulation of Maize and Sorghum Orthologs in Response to the Fungal Pathogen Exserohilum turcicumCited by: 5
Author(s): Pragya Adhikari, Santiago X. Mideros, Tiffany M. Jamann
Software Mentions: 6
Published: over 3 years ago
10.1186/s12864-021-07720-0
Comparative neurotranscriptomics reveal widespread species differences associated with bondingCited by: 5
Author(s): Joel A. Tripp, Alejandro Berrío, Lisa A. McGraw, Mikhail V. Matz, Jamie K. Davis, Kiyoshi Inoue, James W. Thomas, Larry J. Young, Steve Phelps
Software Mentions: 6
Published: over 3 years ago
10.3390/biom9010012
Integrated Transcriptome Analysis Reveals Plant Hormones Jasmonic Acid and Salicylic Acid Coordinate Growth and Defense Responses upon Fungal Infection in PoplarCited by: 63
Author(s): Jie Luo, Wenxiu Xia, Pei Cao, Zheng’ang Xiao, Yan Zhang, Meifeng Liu, Chengjun Zhan, Nian Wang
Software Mentions: 6
Published: almost 6 years ago
10.3390/biomedicines9091120
Neural Precursor Cells Expanded Inside the 3D Micro-Scaffold Nichoid Present Different Non-Coding RNAs Profiles and Transcript Isoforms Expression: Possible Epigenetic Modulation by 3D GrowthCited by: 3
Author(s): Letizia Messa, Bianca Barzaghini, Federica Rey, Cecilia Pandini, Gian Vincenzo Zuccotti, Cristina Cereda, Stephana Carelli, Manuela Teresa Raimondi
Software Mentions: 6
Published: about 3 years ago
10.3389/fphys.2018.01778
Identification of Crucial Genes and Pathways in Human Arrhythmogenic Right Ventricular Cardiomyopathy by Coexpression AnalysisCited by: 11
Author(s): Peipei Chen, Bo Long, Yuanfu Xu, Wei Wu, Shuyang Zhang
Software Mentions: 6
Published: almost 6 years ago
10.1371/journal.pone.0205406
Examining the contribution of smoking and HPV towards the etiology of oral cavity squamous cell carcinoma using high-throughput sequencing: A prospective observational studyCited by: 10
Author(s): Andrew P Zammit, Rohit Anthony Sinha, Caroline Cooper, Christopher Perry, Ian H. Frazer, Zewen Kelvin Tuong
Software Mentions: 6
Published: about 6 years ago
10.3389/fphys.2019.01370
A Dynamic Transcriptional Analysis Reveals IL-6 Axis as a Prominent Mediator of Surgical Acute Response in Non-ischemic Mouse HeartCited by: 1
Author(s): Sally Badawi, Alexandre Paccalet, Zeina Harhous, Bruno Pillot, Lionel Augeul, Fabien Van Coppenolle, Joël Lachuer, Mazen Kurdi, Claire Crola Da Silva, Michel Ovize, Gabriel Bidaux
Software Mentions: 6
Published: about 5 years ago
10.1186/s12859-019-2840-3
m6Acomet: large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation networkCited by: 30
Author(s): Xiangyu Wu, Zhen Wei, Kunqi Chen, Qing Zhang, Jionglong Su, Hui Liu, Lin Zhang, Jia Meng
Software Mentions: 6
Published: over 5 years ago
10.1186/s12864-021-07443-2
Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencingCited by: 12
Author(s): Carolina P. Moraleda, Diego Robledo, Alejandro P. Gutiérrez, Jorge Del‐Pozo, José M. Yáñez, Ross D. Houston
Software Mentions: 6
Published: over 3 years ago
10.18632/aging.202474
Clinical and genomic characteristics of metabolic syndrome in colorectal cancerCited by: 2
Author(s): Yanyan Li, Jungang Zhao, Xiaoli Wu, Yini Zhang, Jia Yin, Weiyang Cai
Software Mentions: 6
Published: almost 4 years ago
10.3389/fonc.2021.587479
Identification of Mitochondrial-Related Prognostic Biomarkers Associated With Primary Bile Acid Biosynthesis and Tumor Microenvironment of Hepatocellular CarcinomaCited by: 21
Author(s): Tao Zhang, Yingli Nie, Jian Gu, Kailin Cai, Xiangdong Chen, Huili Li, Jiliang Wang
Software Mentions: 6
Published: over 3 years ago
10.3389/fonc.2020.01001
Network-Based Approach to Identify the Antiproliferative Mechanisms of Bruceine D in Breast Cancer From the Cancer Genome AtlasCited by: 3
Author(s): Sai Tian, Rui Jiang, Weidong Zhang
Software Mentions: 6
Published: over 4 years ago
10.3389/fmicb.2020.01036
Niche Differentiation in the Composition, Predicted Function, and Co-occurrence Networks in Bacterial Communities Associated With Antarctic Vascular PlantsCited by: 29
Author(s): Qian Zhang, Jacquelinne J. Acuña, Nitza G. Inostroza, Paola Durán, Marı́a de la Luz Mora, Michael J. Sadowsky, Milko A. Jorquera
Software Mentions: 6
Published: over 4 years ago
10.18632/aging.103832
Prognostic model of patients with liver cancer based on tumor stem cell content and immune processCited by: 7
Author(s): Jie Zhu, Miaomiao Gao, Yuchen Jin, Weiran Huang, Zhuo Huang, Zhengwei Xie
Software Mentions: 6
Published: about 4 years ago
10.1371/journal.pone.0233372
Muscle transcriptome analysis identifies genes involved in ciliogenesis and the molecular cascade associated with intramuscular fat content in Large White heavy pigsCited by: 20
Author(s): Martina Zappaterra, Silvia Gioiosa, Giovanni Chillemi, Paolo Zambonelli, Roberta Davoli
Software Mentions: 6
Published: over 4 years ago
10.1371/journal.pone.0208132
Identification of alterations in macrophage activation associated with disease activity in systemic lupus erythematosusCited by: 67
Author(s): Adam C. Labonte, Brian Kegerreis, Nicholas S. Geraci, Prathyusha Bachali, Sushma Madamanchi, Robert Robl, Michelle D. Catalina, Peter E. Lipsky, Amrie C. Grammer
Software Mentions: 6
Published: almost 6 years ago
10.18632/aging.103994
Molecular identification of protein kinase C beta in Alzheimer's diseaseCited by: 6
Author(s): Zhike Zhou, Fenqin Chen, Shanshan Zhong, Yi Zhou, Rongwei Zhang, Kexin Kang, Xiaoqian Zhang, Ying Xu, Mei Zhao, Chuansheng Zhao
Software Mentions: 6
Published: about 4 years ago
10.3389/fmicb.2019.02491
Dynamic Changes in the Microbiome and Mucosal Immune Microenvironment of the Lower Respiratory Tract by Influenza Virus InfectionCited by: 30
Author(s): Liming Gu, Huixiong Deng, Zhihui Ren, Ying Zhao, Shun Yu, Yingzhu Guo, Jianping Dai, Xiaoxuan Chen, Kangsheng Li, Rui Li, Gefei Wang
Software Mentions: 6
Published: about 5 years ago
10.1371/journal.pone.0227258
Accelerated brain aging towards transcriptional inversion in a zebrafish model of the K115fs mutation of human PSEN2Cited by: 29
Author(s): Nhi Hin, Morgan Newman, Jan Kaslin, Alon M. Douek, Amanda L. Lumsden, Seyyed Hani Moussavi Nik, Yang Dong, Xin Zhou, Noralyn B. Mañucat-Tan, Alastair J. Ludington, David L. Adelson, Stephen Pederson, Michael Lardelli
Software Mentions: 6
Published: almost 5 years ago
10.3389/fmolb.2021.628546
Identification of Molecular Subtypes and Key Genes of Atherosclerosis Through Gene Expression ProfilesCited by: 3
Author(s): Yujia Yang, Yuchen Cai, Yuan Zhang, Yuanfu Xu, Zhiqiang Xu
Software Mentions: 6
Published: over 3 years ago
10.18632/aging.202603
Functional analysis of brain derived neurotrophic factor (BDNF) in Huntington’s diseaseCited by: 6
Author(s): Zhike Zhou, Shanshan Zhong, Rongwei Zhang, Kexin Kang, Xiaoqian Zhang, Ying Xu, Chuansheng Zhao, Mei Zhao
Software Mentions: 6
Published: over 3 years ago
10.3389/fmolb.2021.636991
Identifying Dendritic Cell–Related Genes Through a Co-Expression Network to Construct a 12-Gene Risk-Scoring Model for Predicting Hepatocellular Carcinoma PrognosisCited by: 7
Author(s): Chao-Yuan Huang, Xiaotao Jiang, Yuancheng Huang, Lina Zhao, Peiwu Li, Fengbin Liu
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pone.0236186
Gene co-expression network analysis to identify critical modules and candidate genes of drought-resistance in wheatCited by: 16
Author(s): Liangjie Lv, Wenying Zhang, Lijing Sun, Aiju Zhao, Yingjun Zhang, Limei Wang, Yuping Liu, Ziqian Li, Xiyong Chen
Software Mentions: 6
Published: about 4 years ago
10.1155/2018/4246703
Candidate Biomarkers and Molecular Mechanism Investigation for Glioblastoma Multiforme Utilizing WGCNACited by: 64
Author(s): Qi Yang, Rui Wang, Bo Wei, Chuangang Peng, Le Wang, Guozhang Hu, Daliang Kong, Chao Du
Software Mentions: 6
Published: about 6 years ago
10.1371/journal.pone.0241128
Kin recognition: Neurogenomic response to mate choice and sib mating avoidance in a parasitic waspCited by: 0
Author(s): Aurore Gallot, Sandrine Sauzet, Emmanuel Desouhant
Software Mentions: 6
Published: about 4 years ago
10.1186/s12864-019-6375-9
Genetic regulatory networks for salt-alkali stress in Gossypium hirsutum with differing morphological characteristicsCited by: 27
Author(s): Yanchao Xu, Richard Odongo Magwanga, Xiaomin Yang, Dingsha Jin, Xiaoyan Cai, Yuqing Hou, Yangyang Wei, Kunbo Wang, Fang Liu
Software Mentions: 6
Published: almost 5 years ago
10.1186/s12967-021-03078-9
Low CCL19 expression is associated with adverse clinical outcomes for follicular lymphoma patients treated with chemoimmunotherapyCited by: 1
Author(s): Yu Zhou, Shasha Wang, Yunxia Tao, Haizhu Chen, Yan Qin, Xiaohong He, Shengyu Zhou, Peng Liu, Jianliang Yang, Sheng Yang, Lin Gui, Ning Lou, Zhishang Zhang, Jiarui Yao, Xiaohong Han, Yuankai Shi
Software Mentions: 6
Published: about 3 years ago
10.3389/fnmol.2019.00316
Single Cell and Single Nucleus RNA-Seq Reveal Cellular Heterogeneity and Homeostatic Regulatory Networks in Adult Mouse Stria VascularisCited by: 62
Author(s): Soumya Korrapati, Ian Taukulis, Rafal T. Olszewski, Madeline Pyle, Shoujun Gu, Riya Singh, C. M. Griffiths, Daniel Martin, Erich T. Boger, Robert J. Morell, Michael Hoa
Software Mentions: 6
Published: almost 5 years ago
10.3389/fmicb.2021.666558
The Transcriptional Response of Soil Bacteria to Long-Term Warming and Short-Term Seasonal Fluctuations in a Terrestrial ForestCited by: 6
Author(s): Priyanka Chowdhury, Stefan Golas, Lauren Alteio, Joshua T. E. Stevens, Andrew F. Billings, Jeffrey L. Blanchard, Jerry M. Melillo, Kristen M. DeAngelis
Software Mentions: 6
Published: about 3 years ago
10.1371/journal.pgen.1009474
Dynamic neurogenomic responses to social interactions and dominance outcomes in female paper waspsCited by: 6
Author(s): Floria M. K. Uy, Christopher M. Jernigan, Natalie C. Zaba, Eshan Mehrotra, Sara Miller, Michael J. Sheehan
Software Mentions: 6
Published: about 3 years ago
10.3389/fimmu.2018.00056
The Immune and Non-Immune Pathways That Drive Chronic Gastrointestinal Helminth Burdens in the WildCited by: 20
Author(s): Simon A. Babayan, Wei Liu, Graham Hamilton, Elizabeth Kilbride, Evelyn C. Rynkiewicz, Melanie Clerc, Amy B. Pedersen
Software Mentions: 6
Published: almost 7 years ago
10.1155/2020/2319194
Immune-Related lncRNA Correlated with Transcription Factors Provide Strong Prognostic Prediction in GliomasCited by: 4
Author(s): Yantao Tian, Yiquan Ke, Yanxia Ma
Software Mentions: 6
Published: about 4 years ago
10.3389/fimmu.2021.632798
Comprehensive Transcriptomic Analysis Identifies Novel Antiviral Factors Against Influenza A Virus InfectionCited by: 11
Author(s): Ao Zhou, Dong Xia, Mengyun Liu, Bin Tang
Software Mentions: 6
Published: over 3 years ago
10.1186/s12864-016-3020-8
RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphinsCited by: 27
Author(s): Jeanine S. Morey, Marion G. Neely, Denise Lunardi, Paul E. Anderson, Lori H. Schwacke, Michelle R. Campbell, Frances M. Van Dolah
Software Mentions: 6
Published: about 8 years ago
10.18632/oncotarget.16544
The integrative metabolomic-transcriptomic landscape of glioblastome multiformeCited by: 20
Author(s): Dieter Henrik Heiland, Jakob Wörner, Jan Gerrit Haaker, Daniel Delev, Nils Pompe, Bianca Mercas, Pamela Franco, Annette Gäbelein, Sabrina Heynckes, Dietmar Pfeifer, Stefan Weber, Irina Mader, Oliver Schnell
Software Mentions: 6
Published: over 7 years ago
10.3390/ijms20020263
Molecular Network-Based Drug Prediction in Thyroid CancerCited by: 14
Author(s): Xingyu Xu, Hang Long, Baohang Xi, Binbin Ji, Zejun Li, Yunyue Dang, Cheng Jiang, Yao Yao, Jialiang Yang
Software Mentions: 6
Published: almost 6 years ago
10.3389/fimmu.2021.645839
Multi-Omics Profiling Identifies Risk Hypoxia-Related Signatures for Ovarian Cancer PrognosisCited by: 11
Author(s): Xingyu Chen, Hua Lan, Dong He, Runshi Xu, Yao Zhang, Ying Cheng, Haotian Chen, Songshu Xiao, Ke Cao
Software Mentions: 6
Published: over 3 years ago
10.1186/s12864-019-6061-y
Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networksCited by: 12
Author(s): Jim A. Mossman, Leann M. Biancani, David M. Rand
Software Mentions: 6
Published: about 5 years ago
10.7554/eLife.35368
Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in DrosophilaCited by: 92
Author(s): Zaijun Ma, Hui Wang, Yuping Cai, Han Wang, Kongyan Niu, Xiaofen Wu, Huanhuan Ma, Yun Yang, Wenhua Tong, Feng Liu, Zhandong Liu, Yaoyang Zhang, Rui Li, Zheng‐Jiang Zhu, Nan Liu
Software Mentions: 6
Published: over 6 years ago
10.3390/ijms22063028
Characterization of Biological Pathways Regulating Acute Cold Resistance of ZebrafishCited by: 19
Author(s): Jing Ren, Yong Long, Ran Liu, Guangliang Song, Qing Li, Zongbin Cui
Software Mentions: 6
Published: over 3 years ago
10.3389/fgene.2020.634634
A Novel Prognostic Model of Early-Stage Lung Adenocarcinoma Integrating Methylation and Immune BiomarkersCited by: 17
Author(s): Jin Ren, Yun Yang, Chuanyin Li, Lu Xie, Ronggui Hu, Qin Xiong, Menghuan Zhang
Software Mentions: 6
Published: almost 4 years ago
10.1186/s12918-018-0620-8
Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofunginCited by: 11
Author(s): Theresia Conrad, Olaf Kniemeyer, Sebastian Henkel, Thomas Krüger, Derek J. Mattern, Vito Valiante, Reinhard Guthke, Ilse D. Jacobsen, Axel A. Brakhage, Sebastian Vlaic, Jörg Linde
Software Mentions: 6
Published: about 6 years ago
10.1371/journal.pcbi.1008491
Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsivenessCited by: 14
Author(s): Iván Cárcamo-Orive, Marc Henrion, Kuixi Zhu, Noam D. Beckmann, Paige Cundiff, Sara Moein, Zenan Zhang, Melissa Alamprese, Sunita L. D’Souza, Martin Wabitsch, Eric E. Schadt, Thomas Quertermous, Joshua W. Knowles, Rui Chang
Software Mentions: 6
Published: almost 4 years ago
10.3389/fgene.2021.701065
Identification of Tumor Antigens and Immune Landscape in Glioblastoma for mRNA Vaccine DevelopmentCited by: 12
Author(s): Liguo Ye, Long Wang, Jian Yang, Ping Hu, Chunyu Zhang, Shiao Tong, Zhennan Liu, Daofeng Tian
Software Mentions: 6
Published: about 3 years ago
10.1080/21623945.2019.1595269
Transcriptome profiling reveals association of peripheral adipose tissue pathology with type-2 diabetes in Asian IndiansCited by: 17
Author(s): Aditya Saxena, Prabhat Tiwari, Nitin Wahi, Arpana Soni, Ram Chandra Bansiwal, Anshul Kumar, Balram Sharma, Prakash P Punjabi, Nidhi Gupta, Babita Malik, Krishna Mohan Medicherla, Prashanth Suravajhala, Sandeep Kumar Mathur
Software Mentions: 6
Published: almost 6 years ago
10.3389/fgene.2020.00099
A FITM1-Related Methylation Signature Predicts the Prognosis of Patients With Non-Viral Hepatocellular CarcinomaCited by: 4
Author(s): J Chen, X Wang, Wei Li, Chao Shang, T Chen, Y Chen
Software Mentions: 6
Published: over 4 years ago
10.3390/ijms22126307
Transcriptional Profiling Identifies Upregulation of Neuroprotective Pathways in Retinitis PigmentosaCited by: 4
Author(s): Christina B. Bielmeier, Saskia Roth, Sabrina I. Schmitt, Stefaniya Boneva, Anja Schlecht, Mario Vallon, Ernst R. Tamm, Süleyman Ergün, Andreas Neueder, Barbara M. Braunger
Software Mentions: 6
Published: over 3 years ago
10.18632/oncotarget.28058
Novel insights into the molecular mechanisms underlying risk of colorectal cancer from smoking and red/processed meat carcinogens by modeling exposure in normal colon organoidsCited by: 4
Author(s): Matthew Devall, Christopher H. Dampier, Stephen Eaton, Mourad W. Ali, Virginia Díez-Obrero, Ferrán Moratalla-Navarro, Jennifer Bryant, Lucas T. Jennelle, Vı́ctor Moreno, Steven M. Powell, Ulrike Peters, Graham Casey
Software Mentions: 6
Published: about 3 years ago
10.3389/fgene.2021.653474
Identifying ceRNA Networks Associated With the Susceptibility and Persistence of Atrial Fibrillation Through Weighted Gene Co-Expression Network AnalysisCited by: 6
Author(s): Yaozhong Liu, Na Liu, Fan Bai, Qiming Liu
Software Mentions: 6
Published: over 3 years ago
10.3389/fcell.2021.641629
Dysregulation of miR-138-5p/RPS6KA1-AP2M1 Is Associated With Poor Prognosis in AMLCited by: 10
Author(s): Donghu Yu, Chen Chen, Xiaoping Li, Jie Yao, Sheng Li, Xiaolan Ruan
Software Mentions: 6
Published: over 3 years ago
10.3389/fcell.2021.724860
Integrative Analysis of Biomarkers Through Machine Learning Identifies Stemness Features in Colorectal CancerCited by: 7
Author(s): Ran Wei, Jichuan Quan, Shuofeng Li, Hengchang Liu, Xu Guan, Zheng Jiang, Xishan Wang
Software Mentions: 6
Published: about 3 years ago
10.1038/s41598-018-31192-0
Disruption of mesoderm formation during cardiac differentiation due to developmental exposure to 13-cis-retinoic acidCited by: 18
Author(s): Qing Liu, Kevin Van Bortle, Yue Zhang, Ming Zhao, Joe Z. Zhang, Benjamin Geller, Joshua J. Gruber, Chao Jiang, Joseph C. Wu, M Snyder
Software Mentions: 6
Published: about 6 years ago
10.3389/fgene.2021.657658
Weighted Gene Co-expression Network Analysis Identified a Novel Thirteen-Gene Signature Associated With Progression, Prognosis, and Immune Microenvironment of Colon Adenocarcinoma PatientsCited by: 2
Author(s): Cangang Zhang, Zhe Zhao, Haibo Li, Shukun Yao, Dongyan Zhao
Software Mentions: 6
Published: over 3 years ago
10.1186/s13229-019-0287-z
A meta-analysis of two high-risk prospective cohort studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord bloodCited by: 12
Author(s): Charles E. Mordaunt, Bo Y. Park, Kelly M. Bakulski, Jason I. Feinberg, Lisa Croen, Christine Ladd‐Acosta, Craig J. Newschaffer, Heather E. Volk, Sally J Ozonoff, Irva Hertz‐Picciotto, Janine M. LaSalle, Rebecca Jean Schmidt, M. Daniele Fallin
Software Mentions: 6
Published: about 5 years ago
10.1038/s41598-018-21161-y
Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome responseCited by: 16
Author(s): Yukie Kashima, Ayako Suzuki, Ying Liu, Masahito Hosokawa, Hiroko Matsunaga, Masamitsu Shirai, Kohji Arikawa, Sumio Sugano, Takashi Kohno, Haruko Takeyama, Katsuya Tsuchihara, Yutaka Suzuki
Software Mentions: 6
Published: over 6 years ago
10.1038/s41598-018-33498-5
Distinct co-expression networks using multi-omic data reveal novel interventional targets in HPV-positive and negative head-and-neck squamous cell cancerCited by: 28
Author(s): Raquel L. Costa, Mariana Boroni, Marcelo A. Soares
Software Mentions: 6
Published: about 6 years ago
10.3389/fcell.2021.646774
CRISPR-cas9 Screening Identified Lethal Genes Enriched in Cell Cycle Pathway and of Prognosis Significance in Breast CancerCited by: 6
Author(s): Xi Sun, Zheng Wang, Xiaosong Chen, Kunwei Shen
Software Mentions: 6
Published: over 3 years ago
10.18632/aging.102714
ISG20 serves as a potential biomarker and drives tumor progression in clear cell renal cell carcinomaCited by: 22
Author(s): Tianbo Xu, Hailong Ruan, Su Gao, Jingchong Liu, Yuenan Liu, Zhengshuai Song, Qi Cao, Keshan Wang, Lin Bao, Di Liu, Junwei Tong, Jian Shi, Huageng Liang, Hongmei Yang, Ke Chen, Xiaoping Zhang
Software Mentions: 6
Published: almost 5 years ago
10.1186/s13100-019-0180-5
Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elementsCited by: 20
Author(s): Nicky Chung, G. M. Jonaid, Sophia Quinton, Austin Ross, Corinne E. Sexton, Adrian Alberto, Cody Clymer, Daphnie Churchill, Omar Navarro Leija, Mira V. Han
Software Mentions: 6
Published: about 5 years ago
10.1186/s40168-021-01150-6
Gammaproteobacteria, a core taxon in the guts of soil fauna, are potential responders to environmental concentrations of soil pollutantsCited by: 40
Author(s): Qi Zhang, Zhenyan Zhang, Tao Lu, Yitian Yu, Josep Peñuelas, Yan Zhu, Haifeng Qian
Software Mentions: 6
Published: about 3 years ago
10.18632/aging.202718
TMBIM6, a potential virus target protein identified by integrated multiomics data analysis in SARS-CoV-2-infected host cellsCited by: 4
Author(s): Qizheng Han, Junhao Wang, Haihua Luo, Lei Li, Xinya Lu, Aihua Liu, Yongqiang Deng, Yong Jiang
Software Mentions: 6
Published: over 3 years ago
10.1038/s41598-017-09094-4
Discovering Condition-Specific Gene Co-Expression Patterns Using Gaussian Mixture Models: A Cancer Case StudyCited by: 33
Author(s): Stephen P. Ficklin, Leland J. Dunwoodie, William L. Poehlman, Christopher Watson, Kimberly Roche, F. Alex Feltus
Software Mentions: 6
Published: over 7 years ago
10.3390/metabo11060361
Opposing Effects of Ceanothus velutinus Phytochemistry on Herbivore Communities at Multiple ScalesCited by: 2
Author(s): Casey S. Philbin, M. J. Paulsen, Lora A. Richards
Software Mentions: 6
Published: over 3 years ago
10.1186/s12866-020-01739-1
Alter between gut bacteria and blood metabolites and the anti-tumor effects of Faecalibacterium prausnitzii in breast cancerCited by: 57
Author(s): Ji Ma, Lingqi Sun, Ying Liu, Hui Ren, Yali Shen, Feng Bi, Tao Zhang, Xin Wang
Software Mentions: 6
Published: over 4 years ago
10.1038/sdata.2018.185
The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's diseaseCited by: 284
Author(s): Minghui Wang, Noam D. Beckmann, Panos Roussos, Erming Wang, Xianxiao Zhou, Qian Wang, Chi Ming, Ryan Neff, Wanli Ma, John F. Fullard, Mads E. Hauberg, Jaroslav Bendl, Mette A. Peters, Ben Logsdon, Pei Wang, Milind Mahajan, Lara M. Mangravite, Eric B. Dammer, Duc M. Duong, James J. Lah, Nicholas T. Seyfried, Aĺlan I. Levey, Joseph D. Buxbaum, Michelle E. Ehrlich, Sam Gandy, Pavel Katsel, Vahram Haroutunian, Eric E. Schadt, Bin Zhang
Software Mentions: 6
Published: about 6 years ago
10.1186/s42523-020-00042-8
Survey of rumen microbiota of domestic grazing yak during different growth stages revealed novel maturation patterns of four key microbial groups and their dynamic interactionsCited by: 31
Author(s): Wei Guo, Mi Zhou, Tao Ma, Sisi Bi, Weiwei Wang, Ying Zhang, Xiaodan Huang, Le Luo Guan, Ruijun Long
Software Mentions: 6
Published: over 4 years ago
10.1126/sciadv.abj1132
Plasma lipids and growth faltering: A longitudinal cohort study in rural Gambian childrenCited by: 2
Author(s): Gerard Bryan Gonzales, Daniëlla Brals, Bakary Sonko, Fatou Sosseh, Andrew M. Prentice, Sophie E. Moore, Albert Koulman
Software Mentions: 6
Published: about 3 years ago
10.1038/s41598-017-10930-w
Human hepatic gene expression signature of non-alcoholic fatty liver disease progression, a meta-analysisCited by: 69
Author(s): Maria Ryaboshapkina, Mårten Hammar
Software Mentions: 6
Published: about 7 years ago
10.3389/fcvm.2020.580573
Comprehensive Identification of Key Genes Involved in Development of Diabetes Mellitus-Related Atherogenesis Using Weighted Gene Correlation Network AnalysisCited by: 14
Author(s): Qi Huang, Guo-Xiong Deng, Rongguo Wei, Qiaoye Wang, Donghua Zou, Jinru Wei
Software Mentions: 6
Published: about 4 years ago
10.1186/s42523-020-00032-w
Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and virusesCited by: 18
Author(s): Samuel Dupont, Ana Lokmer, Erwan Corre, Jean‐Christophe Auguet, Bruno Petton, Ève Toulza, Caroline Montagnani, Gwenn Tanguy, David Pecqueur, Christophe Salmeron, Laure Guillou, Christelle Desnues, Bernard La Scola, Jacques Bou Khalil, Julien de Lorgeril, Guillaume Mitta, Yannick Gueguen, Jean-Michel Escoubas
Software Mentions: 6
Published: over 4 years ago
10.1186/s12920-018-0358-6
Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disabilityCited by: 5
Author(s): Ute Scheller, Kathrin Pfisterer, Steffen Uebe, Arif B. Ekici, André Reis, Rami Abou Jamra, Fulvia Ferrazzi
Software Mentions: 6
Published: over 6 years ago
10.1002/cam4.3576
Establishment and validation of a prognostic nomogram based on a novel five‐DNA methylation signature for survival in endometrial cancer patientsCited by: 6
Author(s): Xingchen Li, Fufen Yin, Fan Yuan, Yuan Cheng, Yangyang Dong, Jingyi Zhou, Zhiqi Wang, Jianliu Wang
Software Mentions: 6
Published: almost 4 years ago
10.1073/pnas.2008890118
OCT4 induces embryonic pluripotency via STAT3 signaling and metabolic mechanismsCited by: 23
Author(s): Giuliano Giuseppe Stirparo, Agata Kurowski, Akira Yanagida, Lawrence E. Bates, Stanley E. Strawbridge, Siarhei Hladkou, Hannah Stuart, Thorsten Boroviak, José C.R. Silva, Jennifer Nichols
Software Mentions: 6
Published: almost 4 years ago
10.1186/s13073-021-00939-2
Identification of TBX15 as an adipose master trans regulator of abdominal obesity genesCited by: 17
Author(s): David Z. Pan, Min‐Hua Zong, Caroline Comenho, Sandhya Rajkumar, Amogha Koka, Seung Hyuk Lee, Marcus Alvarez, Dorota Kaminska, Arthur Ko, Janet S. Sinsheimer, Karen L. Mohlke, Nicholas Mancuso, Linda Liliana Muñóz-Hernández, Miguel Francisco Herrera-Hernández, Marı́a Teresa Tusié-Luna, Carlos A. Aguilar-Salinas, Kirsi H. Pietiläinen, Jussi Pihlajamäki, Markku Laakso, Kristina M. Garske, Päivi Pajukanta
Software Mentions: 6
Published: over 3 years ago