cran: WGCNA | Projects | Ecosyste.ms: Papers

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 6 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 10 years ago

10.3390/ijms21041512

Dynamics of the Transcriptome Response to Heat in the Moss, Physcomitrella patens
Cited by: 11
Author(s): Osama Elzanati, Saïd Mouzeyar, Jane Roche
Software Mentions: 5
Published: over 6 years ago

10.3390/ijms19113421

Composition and Genetic Diversity of the Nicotiana tabacum Microbiome in Different Topographic Areas and Growth Periods
Cited by: 14
Author(s): Xiaolong Yuan, Min Cao, Xinmin Liu, Yongmei Du, Guoming Shen, Zhongfeng Zhang, Jinhai Li, Peng Zhang
Software Mentions: 5
Published: almost 8 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: over 14 years ago

10.3390/ijms19010071

Transcriptome-Wide Identification and Characterization of Potato Circular RNAs in Response to Pectobacterium carotovorum Subspecies brasiliense Infection
Cited by: 42
Author(s): Ran Zhou, Yong‐Guan Zhu, Jiao Zhao, Zhengwu Fang, Shuping Wang, Jia Yin, Chu Zhang, Dongfang Ma
Software Mentions: 5
Published: over 8 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 5 years ago

10.3390/ijms20092202

Dynamic Transcriptome Changes Related to Oil Accumulation in Developing Soybean Seeds
Cited by: 22
Author(s): Songnan Yang, Long Miao, Jianbo He, Kai Zhang, Yan Li, Junyi Gai
Software Mentions: 5
Published: over 7 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 5 years ago

10.7554/eLife.39188

Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury
Cited by: 27
Author(s): Jordan W. Squair, Seth Tigchelaar, Kyung‐Mee Moon, Jie Liu, Wolfram Tetzlaff, Brian K. Kwon, Andrei V. Krassioukov, Christopher R. West, Leonard J. Foster, Michael A. Skinnider
Software Mentions: 5
Published: almost 8 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: about 6 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 6 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 10 years ago

10.7554/eLife.23253

Analogous mechanism regulating formation of neocortical basal radial glia and cerebellar Bergmann glia
Cited by: 32
Author(s): Xin Heng, Qiu Guo, Alan W. Leung, Kairong Li
Software Mentions: 5
Published: over 9 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 5 years ago

10.7554/eLife.14997

Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons
Cited by: 326
Author(s): Mark S. Cembrowski, Lihua Wang, Ken Sugino, Brenda C. Shields, Nelson Spruston
Software Mentions: 5
Published: over 10 years ago

10.7554/eLife.60100

Sequential perturbations to mouse corticogenesis following in utero maternal immune activation
Cited by: 15
Author(s): Cesar P Canales, Myka L. Estes, Karol Cichewicz, Kartik Angara, John Paul Aboubechara, Scott A. Cameron, Kathryn Prendergast, Linda Su-Feher, Iva Zdilar, Ellie J Kreun, Emma C Connolly, Jin Myeong Seo, Jack B Goon, Kathleen Farrelly, Tyler W. Stradleigh, Deborah van der List, Lori Haapanen, Judy Van de Water, Daniel Vogt, A. Kimberley McAllister, A. Nord
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.64932

Castration delays epigenetic aging and feminizes DNA methylation at androgen-regulated loci
Cited by: 41
Author(s): Victoria J Sugrue, Joseph A. Zoller, Pritika Narayan, Ake T. Lu, Oscar Ortega‐Recalde, Megan Grant, C. Simon Bawden, Skye R. Rudiger, Amin Haghani, Donna M. Bond, Reuben R Hore, Michael Garratt, Karen E. Sears, Nan Wang, Xiangdong Yang, Russell G. Snell, Timothy A Hore, Steve Horvath
Software Mentions: 5
Published: about 5 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 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 8 years ago

10.1155/2021/5588429

Crosstalk between RNA-Binding Proteins and Immune Microenvironment Revealed Two RBP Regulatory Patterns with Distinct Immunophenotypes in Periodontitis
Cited by: 0
Author(s): Xing Lü, Guanqun Meng, Tian Chen, Xiaoqi Zhang, Ding Bai, Hui Xu
Software Mentions: 5
Published: about 5 years ago

10.1155/2018/7691794

Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse
Cited by: 6
Author(s): Minjung Kim, Yi Yin Yu, Ji-Hoi Moon, Insong Koh, Jae Hyung Lee
Software Mentions: 5
Published: over 8 years ago

10.1111/tpj.14202

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

10.1038/s41396-020-0606-6

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

10.1186/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: about 7 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: about 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 5 years ago

10.1038/s41396-021-00923-z

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

10.17305/bjbms.2020.5096

Bionformatics analysis reveals TSPAN1 as a candidate biomarker of progression and prognosis in pancreatic cancer
Cited by: 5
Author(s): Chenhui Ma, Zelong Cui, YiChao Wang, Lei Zhang, Jiaxin Wen, Huaibin Guo, Na Li, Wanxing Zhang
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 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 5 years ago

10.1186/s12918-016-0298-8

petal: Co-expression network modelling in R
Cited by: 30
Author(s): Juli Petereit, Sebastian Smith, Frederick C. Harris, Karen Schlauch
Software Mentions: 5
Published: about 10 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 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 7 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 5 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 7 years ago

10.1093/brain/awaa242

Functional gene networks reveal distinct mechanisms segregating in migraine families
Cited by: 14
Author(s): Anne Marie Rasmussen, Lisette J. A. Kogelman, David M. Kristensen, Mona Ameri Chalmer, Jes Olesen, Thomas Folkmann Hansen
Software Mentions: 5
Published: almost 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: about 8 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: over 5 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: about 6 years ago

10.3389/fgene.2021.617133

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

10.3389/fgene.2020.00680

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

10.3389/fgene.2020.01009

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

10.1042/BSR20191547

Transcriptome profiling of digital flexor tendons after injury in a chicken model
Cited by: 1
Author(s): Wenfei Mao, Yancun Yu, Chen Chen, Ya Fang Wu
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-021-85061-4

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

10.1038/s41598-020-77284-8

Lung squamous cell carcinoma and lung adenocarcinoma differential gene expression regulation through pathways of Notch, Hedgehog, Wnt, and ErbB signalling
Cited by: 34
Author(s): Dorota Anusewicz, Magdalena Orzechowska, Andrzej K. Bednarek
Software Mentions: 5
Published: almost 6 years ago

10.7717/peerj.11321

Identification of key genes and biological processes contributing to colitis associated dysplasia in ulcerative colitis
Cited by: 5
Author(s): Di Zhang, Pengguang Yan, Tian Han, Xiaoyun Cheng, Jingnan Li
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.672674

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

10.1186/s12919-018-0130-0

Network analysis of drug effect on triglyceride-associated DNA methylation
Cited by: 5
Author(s): Elise Lim, Hanfei Xu, Peitao Wu, Daniel Posner, Jiayi Wu, Gina M. Peloso, Achilleas Pitsillides, Anita L. DeStefano, L. Adrienne Cupples, Ching‐Ti Liu
Software Mentions: 5
Published: about 8 years ago

10.1038/s41598-020-77318-1

Improving existing analysis pipeline to identify and analyze cancer driver genes using multi-omics data
Cited by: 9
Author(s): Quang-Huy Nguyen, Duc-Hau Le
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-020-69494-x

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

10.1038/s41598-020-70581-2

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

10.3389/fcimb.2021.654074

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

10.1038/s41598-017-06355-0

Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity
Cited by: 5
Author(s): Prashanna Balaji Venkatasubramanian, Gamze Toydemir, Nicole de Wit, Edoardo Saccenti, Vítor A. P. Martins dos Santos, Peter van Baarlen, Jerry M. Wells, María Suárez-Diez, Jurriaan J. Mes
Software Mentions: 5
Published: about 9 years ago

10.1038/srep43446

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

10.1186/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: over 11 years ago

10.1038/srep46156

Integrated host and viral transcriptome analyses reveal pathology and inflammatory response mechanisms to ALV-J injection in SPF chickens
Cited by: 18
Author(s): Xi Lan, Yan Wang, Kai Tian, Fei Ye, Huadong Yin, Xiaoling Zhao, Hengyong Xu, Yong Huang, Haibo Li, John Hsieh, Susan J. Lamont, Qing Zhu
Software Mentions: 5
Published: over 9 years ago

10.1186/s12870-021-03042-1

Transcriptome and proteome analysis of walnut (Juglans regia L.) fruit in response to infection by Colletotrichum gloeosporioides
Cited by: 12
Author(s): Hongcheng Fang, Xia Liu, Yixin Dong, Shan Feng, Rui Zhou, Changxi Wang, Xinmei Ma, Jianning Liu, Ke Yang
Software Mentions: 5
Published: over 5 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 6 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 8 years ago

10.1038/s41598-017-04016-w

Deciphering biodiversity and interactions between bacteria and microeukaryotes within epilithic biofilms from the Loue River, France
Cited by: 30
Author(s): Anouk Zancarini, Isidora Echenique‐Subiabre, Didier Debroas, Najwa Taïb, Catherine Quiblier, Jean‐François Humbert
Software Mentions: 5
Published: about 9 years ago

10.3389/fcell.2020.593653

PECAM1 Combines With CXCR4 to Trigger Inflammatory Cell Infiltration and Pulpitis Progression Through Activating the NF-κB Signaling Pathway
Cited by: 10
Author(s): Liu Yong-hong, Zhiyong Zhang, Wenjing Li, Shaomin Tian
Software Mentions: 5
Published: over 5 years ago

10.1098/rsos.200792

Tissue-specific developmental regulation and isoform usage underlie the role ofdoublesexin sex differentiation and mimicry inPapilioswallowtails
Cited by: 13
Author(s): Riddhi Deshmukh, Dhanashree Lakhe, Krushnamegh Kunte
Software Mentions: 5
Published: about 6 years ago

10.3389/fcell.2021.652408

Integrating Spatial Transcriptomics and Single-Cell RNA-seq Reveals the Gene Expression Profling of the Human Embryonic Liver
Cited by: 21
Author(s): Xianliang Hou, Yane Yang, Ping Li, Zhipeng Zeng, Wenlong Hu, Ruilian Zhe, Xinqiong Liu, Donge Tang, Minglin Ou, Yong Dai
Software Mentions: 5
Published: over 5 years ago

10.1093/jxb/eraa108

Crosstalk between heterotrimeric G protein-coupled signaling pathways and WRKY transcription factors modulating plant responses to suboptimal micronutrient conditions
Cited by: 16
Author(s): Tai‐Hsi Wu, Shalini Krishnamoorthi, Honzhen Goh, Richalynn Leong, Amy Catherine Sanson, Daisuke Urano
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.ppat.1004856

An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation
Cited by: 27
Author(s): Jason E. Shoemaker, Satoru Fukuyama, Amie J. Eisfeld, Dongming Zhao, Eiryo Kawakami, Saori Sakabe, Tadashi Maemura, Takeo Gorai, Hiroaki Katsura, Yukiko Muramoto, Shinji Watanabe, Tokiko Watanabe, Ken Fuji, Yoshikazu Matsuoka, Hiroaki Kitano, Yoshihiro Kawaoka
Software Mentions: 5
Published: over 11 years ago

10.1111/jcmm.16714

Single‐cell RNA sequencing identify SDCBP in ACE2‐positive bronchial epithelial cells negatively correlates with COVID‐19 severity
Cited by: 16
Author(s): Ding Ma, Shuwen Liu, Lili Hu, Qinyu He, Weiwei Shi, Dongming Yan, Chunyue Yin, Guang Zhang, Zhong‐Xia Wang, Junhua Wu, Chunping Jiang
Software Mentions: 5
Published: about 5 years ago

10.3389/fcell.2021.700607

Comprehensive Analysis of a Nine-Gene Signature Related to Tumor Microenvironment in Lung Adenocarcinoma
Cited by: 23
Author(s): Haihui Zhong, Jie Wang, Yaru Zhu, Yefeng Shen
Software Mentions: 5
Published: about 5 years ago

10.1111/jcmm.16615

Transcriptome and DNA methylation analysis reveals molecular mechanisms underlying intrahepatic cholangiocarcinoma progression
Cited by: 4
Author(s): Yunyan Peng, Guohao Meng, Xinyi Sheng, Hongqiang Gao
Software Mentions: 5
Published: over 5 years ago

10.3390/jcm10163520

An Integrative Systems Biology Approach Identifies Molecular Signatures Associated with Gallbladder Cancer Pathogenesis
Cited by: 3
Author(s): Nabanita Roy, Mrinmoy Kshattry, Subhrangsu S. Mandal, Mohit Kumar Jolly, Dhruba K. Bhattacharyya, Pankaj Barah
Software Mentions: 5
Published: about 5 years ago

10.3389/fcell.2021.691161

Identification of Novel Metabolism-Associated Subtypes for Pancreatic Cancer to Establish an Eighteen-Gene Risk Prediction Model
Cited by: 6
Author(s): Yang Gao, Enchong Zhang, Xiang Fei, Lingming Kong, Peng Liu, Xiaodong Tan
Software Mentions: 5
Published: about 5 years ago

10.3389/fcell.2020.560766

Transcriptome Reveals Multi Pigmentation Genes Affecting Dorsoventral Pattern in Avian Body
Cited by: 6
Author(s): Xi Yang, Hehe Liu, Li Liang, Qian Xu, Yisi Liu, Lei Wang, Shengchao Ma, Jianmei Wang, Lili Bai, Rongping Zhang, Chunchun Han
Software Mentions: 5
Published: almost 6 years ago

10.1111/jcmm.16469

m6A regulator‐mediated RNA methylation modification patterns are involved in immune microenvironment regulation of periodontitis
Cited by: 57
Author(s): Xiaoqi Zhang, Shizhen Zhang, Xinyu Yan, Yue Shan, Ling Lü, Jing Zhou, Qianyun Kuang, Minqi Li, Hu Long, Wenli Lai
Software Mentions: 5
Published: over 5 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: over 9 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 6 years ago

10.3389/fcell.2020.616972

A Novel m6A Gene Signature Associated With Regulatory Immune Function for Prognosis Prediction in Clear-Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Siteng Chen, Ning Zhang, Encheng Zhang, Tao Wang, Lingge Jiang, Xiang Wang, Junhua Zheng
Software Mentions: 5
Published: over 5 years ago

10.3389/fcell.2021.719192

PARP1 Inhibitor Combined With Oxaliplatin Efficiently Suppresses Oxaliplatin Resistance in Gastric Cancer-Derived Organoids via Homologous Recombination and the Base Excision Repair Pathway
Cited by: 1
Author(s): Huafu Li, Chunming Wang, Linxiang Lan, Wenhui Wu, Ian M. Evans, E Josue Ruiz, Le-Ping Yan, Zhijun Zhou, Joaquím M. Oliveira, Rui L. Reis, Zhenran Hu, Wei Chen, Axel Behrens, Yulong He, Changhua Zhang
Software Mentions: 5
Published: about 5 years ago

10.3389/fcvm.2021.694238

AKR1C3 and Its Transcription Factor HOXB4 Are Promising Diagnostic Biomarkers for Acute Myocardial Infarction
Cited by: 7
Author(s): Jingjing Liang, Yue Cao, Minqiang He, Weiwen Li, Guan‐Jiang Huang, Tianyi Ma, Meijun Li, Yuli Huang, Xiaohui Huang, Yunzhao Hu
Software Mentions: 5
Published: almost 5 years ago

10.7717/peerj.8312

Identification and validation of a three-gene signature as a candidate prognostic biomarker for lower grade glioma
Cited by: 26
Author(s): Kai Xiao, Qing Liu, Gang Peng, Jun Su, Chaoying Qin, Xiangyu Wang
Software Mentions: 5
Published: over 6 years ago

10.7150/jca.50868

Data mining analysis of the prognostic impact of N6-methyladenosine regulators in patients with endometrial adenocarcinoma
Cited by: 7
Author(s): Junyu Zhai, Shang Li, Yu Liu, Yanzhi Du
Software Mentions: 5
Published: over 5 years ago

10.1007/s13353-020-00569-1

Differential expression of lung adenocarcinoma transcriptome with signature of tobacco exposure
Cited by: 11
Author(s): Raneem Y Hammouz, Joanna Kostanek, Aleksandra Dudzisz, Piotr J Witas, Magdalena Orzechowska, Andrzej K. Bednarek
Software Mentions: 5
Published: about 6 years ago

10.1172/jci.insight.142680

Exhausted-like CD8+ T cell phenotypes linked to C-peptide preservation in alefacept-treated T1D subjects
Cited by: 33
Author(s): Kirsten E. Diggins, Elisavet Serti, Virginia S. Muir, Mario G. Rosasco, Tingting Lü, Elisa Balmas, Gerald T. Nepom, S. Alice Long, Peter S. Linsley
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: about 5 years ago

10.12688/f1000research.18705.2

Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models
Cited by: 1
Author(s): Katharina Baum, Jagath C. Rajapakse, Francisco Azuaje
Software Mentions: 5
Published: about 7 years ago

10.1186/s13024-018-0282-4

Deep proteomic network analysis of Alzheimer’s disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease
Cited by: 147
Author(s): Erik C. B. Johnson, Eric B. Dammer, Duc M. Duong, Luming Yin, Madhav Thambisetty, Juan C. Troncoso, James J. Lah, Aĺlan I. Levey, Nicholas T. Seyfried
Software Mentions: 5
Published: almost 8 years ago

10.1155/2020/3909416

Recognition of Immune Microenvironment Landscape and Immune-Related Prognostic Genes in Breast Cancer
Cited by: 7
Author(s): Huiling Wang, Sylvaine You, Meng Fang, Qian Fang
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41438-021-00606-y

Integrative genomics reveals paths to sex dimorphism in Salix purpurea L
Cited by: 8
Author(s): Brennan Hyden, Craig H. Carlson, Fred E. Gouker, Jeremy Schmutz, Kerrie Barry, Anna Lipzen, Aarti Sharma, Laura Sandor, Gerald A. Tuskan, Guanying Feng, Matthew S. Olson, Stephen P. DiFazio, Lawrence B. Smart
Software Mentions: 5
Published: about 5 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: over 5 years ago

10.1111/jcmm.15205

Characterization of the relationship between FLI1 and immune infiltrate level in tumour immune microenvironment for breast cancer
Cited by: 14
Author(s): Shiyuan Wang, Yakun Wang, Changhong Yu, Yiyin Cao, Yao Yu, Yi Pan, Dongqing Su, Qianzi Lu, Weihao Yang, Yongchun Zuo, Lei Yang
Software Mentions: 5
Published: over 6 years ago

10.1186/s13024-020-00415-2

Diabetic phenotype in mouse and humans reduces the number of microglia around β-amyloid plaques
Cited by: 16
Author(s): Teemu Natunen, Henna Martiskainen, Mikael Marttinen, Sami Gabbouj, Hennariikka Koivisto, Susanna Kemppainen, Satu Kaipainen, Mari Takalo, Hélèna Svobodova, Luukas Leppänen, Benjam Kemiläinen, Simo Ryhänen, Teemu Kuulasmaa, Eija Rahunen, Sisko Juutinen, Petra Mäkinen, Pasi Miettinen, Tuomas Rauramaa, Jussi Pihlajamäki, Annakaisa Haapasalo, Ville Leinonen, Heikki Tanila, Mikko Hiltunen
Software Mentions: 5
Published: almost 6 years ago

10.1080/22221751.2020.1738277

Competing endogenous RNA network profiling reveals novel host dependency factors required for MERS-CoV propagation
Cited by: 50
Author(s): Xi Zhang, Hin Chu, Lei Wen, Huiping Shuai, Dong Yang, Yixin Wang, Yuxin Hou, Zheng Zhu, Shuofeng Yuan, Feifei Yin, Jasper Fuk‐Woo Chan, Kwok‐Yung Yuen
Software Mentions: 5
Published: over 6 years ago

10.1007/s11357-021-00329-x

Are the 50’s, the transition decade, in choroid plexus aging?
Cited by: 5
Author(s): Ana Carolina Tahira, Fernanda Marques, Bianca Cristina Garcia Lisbôa, Arthur Sant’Anna Feltrin, André Rocha Barbosa, Kátia C. Oliveira, Carlos Alberto de Bragança Pereira, Renata Leite, Lea T. Grinberg, Cláudia Kimie Suemoto, Renata Eloah de Lucena Ferretti‐Rebustini, Carlos Augusto Pasqualucci, Wilson Jacob‐Filho, Helena Brentani, Joana Almeida Palha
Software Mentions: 5
Published: over 5 years ago

10.1111/1462-2920.14498

Gut microbiota in patients after surgical treatment for colorectal cancer
Cited by: 21
Author(s): Ye Jin, Yang Liu, Lei Zhao, Fuya Zhao, Jing Feng, Shengda Li, Huinan Chen, Jiayu Sun, Bihai Zhu, Rui Geng, Yunwei Wei
Software Mentions: 5
Published: over 7 years ago

10.1016/j.gpb.2018.04.008

Agricultural Risk Factors Influence Microbial Ecology in Honghu Lake
Cited by: 25
Author(s): Maozhen Han, Melissa Dsouza, Chunyu Zhou, Hongjun Li, Junqian Zhang, Chaoyun Chen, Qi Yao, Chunrong Zhong, Hao Zhou, Jack A. Gilbert, Zhi Wen, Kang Ning
Software Mentions: 5
Published: over 7 years ago

10.1093/gigascience/giab067

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

10.1155/2019/4250613

A Six-Gene Signature Predicts Survival of Adenocarcinoma Type of Non-Small-Cell Lung Cancer Patients: A Comprehensive Study Based on Integrated Analysis and Weighted Gene Coexpression Network
Cited by: 23
Author(s): Hui Xie, Conghua Xie
Software Mentions: 5
Published: almost 7 years ago

10.1186/s13073-021-00924-9

The host transcriptional response to Candidemia is dominated by neutrophil activation and heme biosynthesis and supports novel diagnostic approaches
Cited by: 8
Author(s): Julie M. Steinbrink, Rachel A. Myers, Kaiyuan Hua, Melissa D. Johnson, Jessica Seidelman, Ephraim L. Tsalik, Ricardo Henao, Geoffrey S. Ginsburg, Christopher W. Woods, Barbara D. Alexander, Micah T. McClain
Software Mentions: 5
Published: about 5 years ago

10.1186/s13073-016-0319-7

Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer
Cited by: 20
Author(s): Safiye Çelik, Benjamin A. Logsdon, Stephanie L. Battle, Charles W. Drescher, Mara H. Rendi, R. David Hawkins, Su-In Lee
Software Mentions: 5
Published: about 10 years ago

10.1002/ece3.2685

Transcriptome predictors of coral survival and growth in a highly variable environment
Cited by: 53
Author(s): Rachael A. Bay, Stephen R. Palumbi
Software Mentions: 5
Published: over 9 years ago

10.1093/gbe/evz108

Divergent Allometric Trajectories in Gene Expression and Coexpression Produce Species Differences in Sympatrically Speciating Midas Cichlid Fish
Cited by: 8
Author(s): Carmelo Fruciano, Axel Meyer, Paolo Franchini
Software Mentions: 5
Published: over 7 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479