cran: WGCNA | Projects | Ecosyste.ms: Papers

10.3389/pore.2021.604730

Identification of Key Genes Involved in Pancreatic Ductal Adenocarcinoma with Diabetes Mellitus Based on Gene Expression Profiling Analysis
Cited by: 4
Author(s): Wenbai Zhou, Yujing Wang, Hongmei Gao, Ying Jia, Yuanxin Xu, Xiaojing Wan, Zhiying Zhang, Haiqiao Yu, Shuang Yan
Software Mentions: 7
Published: over 4 years ago

10.1186/s13195-020-00733-z

Exploring the role of RALYL in Alzheimer’s disease reserve by network-based approaches
Cited by: 4
Author(s): Yixuan Zhang, Jiali Wang, Xiaoquan Liu, Haochen Liu
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 analysis
Cited by: 13
Author(s): Linlin Yang, Yunxia Cui, Xiao Sun, Yudong Wang
Software Mentions: 7
Published: over 4 years ago

10.1111/pbi.13205

Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass
Cited 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: almost 6 years ago

10.3389/fimmu.2019.02903

Co-expression Networks Identify DHX15 RNA Helicase as a B Cell Regulatory Factor
Cited by: 6
Author(s): Thiago Detanico, Richard Virgen-Slane, Seth Steen-Fuentes, Wai Wai Lin, Antje Rhode-Kurnow, Elizabeth Chappell, Ricardo G. Correa, Michael J Dicandido, Moustapha Mbow, Jun Li, Carl F. Ware
Software Mentions: 7
Published: over 5 years ago

10.1186/s13073-020-00806-6

Whole blood co-expression modules associate with metabolic traits and type 2 diabetes: an IMI-DIRECT study
Cited by: 8
Author(s): Valborg Guðmundsdóttir, Helle Pedersen, Gianluca Mazzoni, Kristine H. Allin, Anna Artati, Joline W.J. Beulens, Karina Banasik, Caroline Brorsson, Henna Cederberg, Elizaveta Chabanova, Federico De Masi, Petra Elders, Ian Forgie, G Giordano, Harald Grallert, Ramneek Gupta, Mark Haid, Torben Hansen, Tue H. Hansen, Andrew T. Hattersley, Alison Heggie, Mun‐Gwan Hong, Angus G. Jones, Robert W. Koivula, Tarja Kokkola, Markku Laakso, Peter Løngreen, Anubha Mahajan, Andrea Mari, Colin N.A. Palmer, Donna McEvoy, Petra B. Musholt, Imre Pávó, Cornelia Prehn, Hartmut Ruetten, Martin Ridderstråle, Femke Rutters, Sapna Sharma, Roderick C. Slieker, Ali Syed, Juan Fernández Tajes, Cecilia Engel Thomas, Henrik S. Thomsen, Jagadish Vangipurapu, Henrik Vestergaard, Ana Viñuela, Agata Wesolowska-Andersen, Mark Walker, Jerzy Adamski, Jochen M. Schwenk, Mark McCarthy, Ewan R. Pearson, Emmanouil T. Dermitzakis, Paul W. Franks, Oluf Pedersen, Søren Brunak
Software Mentions: 7
Published: over 4 years ago

10.3389/fonc.2020.553399

CD8+ T Cell Co-Expressed Genes Correlate With Clinical Phenotype and Microenvironments of Urothelial Cancer
Cited by: 20
Author(s): Yutao Wang, Kexin Yan, Jiaxing Lin, Yang Liu, Jianfeng Wang, Xuejie Li, Xinxin Li, Zhixiong Hua, Zhenhua Zheng, Jianxiu Shi, Siqing Sun, Jianbin Bi
Software Mentions: 7
Published: over 4 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: over 6 years ago

10.1128/mBio.03701-20

Inter- and Intra-Annual Bacterioplankton Community Patterns in a Deepwater Sub-Arctic Region: Persistent High Background Abundance of Putative Oil Degraders
Cited by: 8
Author(s): Angelina Angelova, Barbara Berx, Eileen Bresnan, Samantha B. Joye, Andrew Free, Tony Gutiérrez
Software Mentions: 7
Published: over 4 years ago

10.3389/fncel.2020.612560

Proteomic Characterization of Human Neural Stem Cells and Their Secretome During in vitro Differentiation
Cited 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: over 4 years ago

10.1186/s13059-014-0483-2

Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia
Cited by: 140
Author(s): Ruth Pidsley, Joana Viana, Eilís Hannon, Helen Spiers, Claire Troakes, Safa Al-Saraj, Naguib Mechawar, Gustavo Turecki, Leonard C. Schalkwyk, Nicholas John Bray, Jonathan Mill
Software Mentions: 6
Published: almost 11 years ago

10.15252/embj.2019102808

HNF1A recruits KDM6A to activate differentiated acinar cell programs that suppress pancreatic cancer
Cited 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 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 effects
Cited by: 10
Author(s): Morag A. Lewis, Francesca Di Domenico, Neil J. Ingham, Haydn M. Prosser, Karen P. Steel
Software Mentions: 6
Published: over 4 years ago

10.1111/mec.15743

The strength and form of natural selection on transcript abundance in the wild
Cited by: 9
Author(s): Freed Ahmad, Paul V. Debes, Ilkka Nousiainen, Siim Kahar, Lilian Pukk, Riho Gross, Mikhail Ozerov, Anti Vasemägi
Software Mentions: 6
Published: over 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 plasma
Cited 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: about 6 years ago

10.3390/genes12050665

Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods
Cited by: 6
Author(s): Hui Yu, Yan Guo, Jingchun Chen, Xiangning Chen, Peilin Jia, Zhongming Zhao
Software Mentions: 6
Published: about 4 years ago

10.3390/genes12091339

Integrated Bioinformatics Analysis Reveals Marker Genes and Potential Therapeutic Targets for Pulmonary Arterial Hypertension
Cited by: 8
Author(s): Aoqi Li, Jin He, Zhe Zhang, Shuhui Jiang, Yun Gao, Yuchun Pan, Huanan Wang, Lenan Zhuang
Software Mentions: 6
Published: almost 4 years ago

10.3390/genes12040491

Dissection of the Genetic Association between Anorexia Nervosa and Obsessive–Compulsive Disorder at the Network and Cellular Levels
Cited by: 4
Author(s): Weichen Song, Weidi Wang, Shunying Yu, Guan Ning Lin
Software Mentions: 6
Published: over 4 years ago

10.1186/s12864-021-07443-2

Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing
Cited 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 4 years ago

10.1186/s12885-017-3832-1

Comparative gene co-expression network analysis of epithelial to mesenchymal transition reveals lung cancer progression stages
Cited by: 9
Author(s): Daifeng Wang, John D. Haley, Patricia Thompson
Software Mentions: 6
Published: over 7 years ago

10.1186/s12885-018-4848-x

Genomic analysis of DNA repair genes and androgen signaling in prostate cancer
Cited by: 53
Author(s): Kasey Jividen, Katarzyna Kedzierska, Chunsong Yang, Karol Szlachta, Aakrosh Ratan, Bryce M. Paschal
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12885-021-08052-8

Comprehensive analysis of immune-related prognostic genes in the tumour microenvironment of hepatocellular carcinoma
Cited 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 4 years ago

10.3390/genes11101124

Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of qDTYs to Reproductive-Stage Drought Stress in Rice (Oryza sativa L.)
Cited by: 11
Author(s): Jeshurun Asher Tarun, Ramil Mauleon, Juan David Arbelaez, Sheryl Catausan, Shalabh Dixit, Arvind Kumar, Patrick J. Brown, Ajay Kohli, Tobias Kretzschmar
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pcbi.1008491

Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness
Cited 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: over 4 years ago

10.1093/conphys/coz018

Tracking transcriptomic responses to endogenous and exogenous variation in cetaceans in the Southern California Bight
Cited by: 8
Author(s): Marisa L. Trego, Andrew Whitehead, Nicholas M. Kellar, Morgane Lauf, Rebecca L. Lewison
Software Mentions: 6
Published: over 6 years ago

10.18632/aging.103743

Identification of subtype-specific genes signature by WGCNA for prognostic prediction in diffuse type gastric cancer
Cited 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: almost 5 years ago

10.18632/aging.203166

Identification and validation of inferior prognostic genes associated with immune signatures and chemotherapy outcome in acute myeloid leukemia
Cited 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: about 4 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 infiltration
Cited by: 10
Author(s): Yang Yang, Xiangshan Xu
Software Mentions: 6
Published: over 4 years ago

10.1186/s12885-021-08711-w

Construction of a ceRNA network of hub genes affecting immune infiltration in ovarian cancer identified by WGCNA
Cited by: 12
Author(s): Rongjia Su, Chengjuan Jin, Lina Zhou, Yannan Cao, Menghua Kuang, Linxia Li, Jianbin Xiang
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12864-021-07720-0

Comparative neurotranscriptomics reveal widespread species differences associated with bonding
Cited 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: about 4 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 Poplar
Cited 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: over 6 years ago

10.3390/genes10070514

Transcriptional Analysis of the Early Ripening of ‘Kyoho’ Grape in Response to the Treatment of Riboflavin
Cited by: 9
Author(s): Zhenguang Wang, Lili Guo, Xiao-Ru Ji, Yi‐He Yu, Guohai Zhang, Da‐Long Guo
Software Mentions: 6
Published: about 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 Growth
Cited 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: almost 4 years ago

10.1534/g3.117.041624

Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross
Cited 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: about 8 years ago

10.3389/fpsyt.2021.716722

Transcriptomics Analysis Reveals Shared Pathways in Peripheral Blood Mononuclear Cells and Brain Tissues of Patients With Schizophrenia
Cited 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: almost 4 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 study
Cited by: 10
Author(s): Andrew P Zammit, Rohit Anthony Sinha, Caroline Cooper, Christopher Perry, Ian H. Frazer, Zewen Kelvin Tuong
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12859-019-2840-3

m6Acomet: large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation network
Cited by: 30
Author(s): Xiangyu Wu, Zhen Wei, Kunqi Chen, Qing Zhang, Jionglong Su, Hui Liu, Lin Zhang, Jia Meng
Software Mentions: 6
Published: about 6 years ago

10.18632/aging.202474

Clinical and genomic characteristics of metabolic syndrome in colorectal cancer
Cited by: 2
Author(s): Yanyan Li, Jungang Zhao, Xiaoli Wu, Yini Zhang, Jia Yin, Weiyang Cai
Software Mentions: 6
Published: over 4 years ago

10.3389/fpls.2021.675208

Differential Regulation of Maize and Sorghum Orthologs in Response to the Fungal Pathogen Exserohilum turcicum
Cited by: 5
Author(s): Pragya Adhikari, Santiago X. Mideros, Tiffany M. Jamann
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 Infection
Cited 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: over 5 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 Heart
Cited 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: over 5 years ago

10.3389/fphys.2018.01778

Identification of Crucial Genes and Pathways in Human Arrhythmogenic Right Ventricular Cardiomyopathy by Coexpression Analysis
Cited by: 11
Author(s): Peipei Chen, Bo Long, Yuanfu Xu, Wei Wu, Shuyang Zhang
Software Mentions: 6
Published: over 6 years ago

10.18632/aging.103994

Molecular identification of protein kinase C beta in Alzheimer's disease
Cited 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: over 4 years ago

10.3389/fimmu.2021.645839

Multi-Omics Profiling Identifies Risk Hypoxia-Related Signatures for Ovarian Cancer Prognosis
Cited 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: about 4 years ago

10.1371/journal.pone.0227258

Accelerated brain aging towards transcriptional inversion in a zebrafish model of the K115fs mutation of human PSEN2
Cited 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: over 5 years ago

10.3389/fmolb.2021.628546

Identification of Molecular Subtypes and Key Genes of Atherosclerosis Through Gene Expression Profiles
Cited by: 3
Author(s): Yujia Yang, Yuchen Cai, Yuan Zhang, Yuanfu Xu, Zhiqiang Xu
Software Mentions: 6
Published: about 4 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 Vascularis
Cited 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: over 5 years ago

10.18632/aging.202603

Functional analysis of brain derived neurotrophic factor (BDNF) in Huntington’s disease
Cited 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 4 years ago

10.1371/journal.pone.0241128

Kin recognition: Neurogenomic response to mate choice and sib mating avoidance in a parasitic wasp
Cited by: 0
Author(s): Aurore Gallot, Sandrine Sauzet, Emmanuel Desouhant
Software Mentions: 6
Published: almost 5 years ago

10.1155/2018/4246703

Candidate Biomarkers and Molecular Mechanism Investigation for Glioblastoma Multiforme Utilizing WGCNA
Cited by: 64
Author(s): Qi Yang, Rui Wang, Bo Wei, Chuangang Peng, Le Wang, Guozhang Hu, Daliang Kong, Chao Du
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12864-019-6375-9

Genetic regulatory networks for salt-alkali stress in Gossypium hirsutum with differing morphological characteristics
Cited 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: over 5 years ago

10.18632/aging.103832

Prognostic model of patients with liver cancer based on tumor stem cell content and immune process
Cited by: 7
Author(s): Jie Zhu, Miaomiao Gao, Yuchen Jin, Weiran Huang, Zhuo Huang, Zhengwei Xie
Software Mentions: 6
Published: almost 5 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 pigs
Cited by: 20
Author(s): Martina Zappaterra, Silvia Gioiosa, Giovanni Chillemi, Paolo Zambonelli, Roberta Davoli
Software Mentions: 6
Published: about 5 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 Prognosis
Cited by: 7
Author(s): Chao-Yuan Huang, Xiaotao Jiang, Yuancheng Huang, Lina Zhao, Peiwu Li, Fengbin Liu
Software Mentions: 6
Published: about 4 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 Atlas
Cited by: 3
Author(s): Sai Tian, Rui Jiang, Weidong Zhang
Software Mentions: 6
Published: about 5 years ago

10.3389/fonc.2021.587479

Identification of Mitochondrial-Related Prognostic Biomarkers Associated With Primary Bile Acid Biosynthesis and Tumor Microenvironment of Hepatocellular Carcinoma
Cited by: 21
Author(s): Tao Zhang, Yingli Nie, Jian Gu, Kailin Cai, Xiangdong Chen, Huili Li, Jiliang Wang
Software Mentions: 6
Published: over 4 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 organoids
Cited 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: almost 4 years ago

10.18632/oncotarget.16544

The integrative metabolomic-transcriptomic landscape of glioblastome multiforme
Cited 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 8 years ago

10.1186/s12967-021-03078-9

Low CCL19 expression is associated with adverse clinical outcomes for follicular lymphoma patients treated with chemoimmunotherapy
Cited 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: almost 4 years ago

10.1371/journal.pgen.1009474

Dynamic neurogenomic responses to social interactions and dominance outcomes in female paper wasps
Cited 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: almost 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 Plants
Cited 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: about 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 Forest
Cited 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: almost 4 years ago

10.1155/2020/2319194

Immune-Related lncRNA Correlated with Transcription Factors Provide Strong Prognostic Prediction in Gliomas
Cited by: 4
Author(s): Yantao Tian, Yiquan Ke, Yanxia Ma
Software Mentions: 6
Published: over 4 years ago

10.3389/fimmu.2021.632798

Comprehensive Transcriptomic Analysis Identifies Novel Antiviral Factors Against Influenza A Virus Infection
Cited by: 11
Author(s): Ao Zhou, Dong Xia, Mengyun Liu, Bin Tang
Software Mentions: 6
Published: about 4 years ago

10.1186/s12864-016-3020-8

RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphins
Cited 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: almost 9 years ago

10.1186/s12864-020-6767-x

Multipathway synergy promotes testicular transition from growth to spermatogenesis in early-puberty goats
Cited 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: about 5 years ago

10.3389/fimmu.2018.00056

The Immune and Non-Immune Pathways That Drive Chronic Gastrointestinal Helminth Burdens in the Wild
Cited 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: over 7 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 networks
Cited by: 12
Author(s): Jim A. Mossman, Leann M. Biancani, David M. Rand
Software Mentions: 6
Published: almost 6 years ago

10.1038/ismej.2017.165

Recurrent patterns of microdiversity in a temperate coastal marine environment
Cited by: 110
Author(s): Meghan Chafee, Antonio Fernández-Guerra, Pier Luigi Buttigieg, Gunnar Gerdts, A. Murat Eren, Hanno Teeling, Rudolf Amann
Software Mentions: 6
Published: almost 8 years ago

10.3390/ijms22063028

Characterization of Biological Pathways Regulating Acute Cold Resistance of Zebrafish
Cited by: 19
Author(s): Jing Ren, Yong Long, Ran Liu, Guangliang Song, Qing Li, Zongbin Cui
Software Mentions: 6
Published: over 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 caspofungin
Cited 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: almost 7 years ago

10.1371/journal.pone.0236186

Gene co-expression network analysis to identify critical modules and candidate genes of drought-resistance in wheat
Cited 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: almost 5 years ago

10.1080/21623945.2019.1595269

Transcriptome profiling reveals association of peripheral adipose tissue pathology with type-2 diabetes in Asian Indians
Cited 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: over 6 years ago

10.3390/ijms22126307

Transcriptional Profiling Identifies Upregulation of Neuroprotective Pathways in Retinitis Pigmentosa
Cited 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: about 4 years ago

10.1038/s41598-021-91214-2

Chamber-enriched gene expression profiles in failing human hearts with reduced ejection fraction
Cited by: 12
Author(s): Xin Luo, Jun Yin, Denise Dwyer, Tracy M. Yamawaki, Hong Zhou, Hongfei Ge, Chun-Ya Han, Artem Shkumatov, K. F. Snyder, Brandon Ason, Chi-Ming Li, Oliver Homann, Marina Stolina
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-021-98059-9

Sex-dependent gene co-expression in the human body
Cited by: 9
Author(s): Robin Hartman, Michal Mokrý, Gérard Pasterkamp, Hester M. den Ruijter
Software Mentions: 6
Published: almost 4 years ago

10.3389/fgene.2020.634634

A Novel Prognostic Model of Early-Stage Lung Adenocarcinoma Integrating Methylation and Immune Biomarkers
Cited by: 17
Author(s): Jin Ren, Yun Yang, Chuanyin Li, Lu Xie, Ronggui Hu, Qin Xiong, Menghuan Zhang
Software Mentions: 6
Published: over 4 years ago

10.3389/fgene.2020.00099

A FITM1-Related Methylation Signature Predicts the Prognosis of Patients With Non-Viral Hepatocellular Carcinoma
Cited by: 4
Author(s): J Chen, X Wang, Wei Li, Chao Shang, T Chen, Y Chen
Software Mentions: 6
Published: over 5 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 Patients
Cited by: 2
Author(s): Cangang Zhang, Zhe Zhao, Haibo Li, Shukun Yao, Dongyan Zhao
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-021-86048-x

A ceRNA-associated risk model predicts the poor prognosis for head and neck squamous cell carcinoma patients
Cited by: 9
Author(s): Yuzi Xu, Fengqin Xu, Yiming Lv, Siyuan Wang, Jia Li, Chuan Zhou, Jimin Jiang, Binbin Xie, Fuming He
Software Mentions: 6
Published: over 4 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 Analysis
Cited by: 6
Author(s): Yaozhong Liu, Na Liu, Fan Bai, Qiming Liu
Software Mentions: 6
Published: about 4 years ago

10.3389/fgene.2021.701065

Identification of Tumor Antigens and Immune Landscape in Glioblastoma for mRNA Vaccine Development
Cited by: 12
Author(s): Liguo Ye, Long Wang, Jian Yang, Ping Hu, Chunyu Zhang, Shiao Tong, Zhennan Liu, Daofeng Tian
Software Mentions: 6
Published: almost 4 years ago

10.1038/s41598-021-85848-5

Abnormal upregulation of cardiovascular disease biomarker PLA2G7 induced by proinflammatory macrophages in COVID-19 patients
Cited by: 18
Author(s): Yang Li, Yongzhong Jiang, Yi Zhang, Naizhe Li, Qiangling Yin, Linlin Liu, Xin Lv, Yan Liu, Aqian Li, Bin Fang, Jiajia Li, Hengping Ye, Gang Ye, Xiaoxian Cui, Yang Liu, Yuanyuan Qu, Chuan Li, Jiandong Li, Dexin Li, Zhongtao Gai, Shiwen Wang, Faxian Zhan, Mifang Liang
Software Mentions: 6
Published: over 4 years ago

10.1038/s41398-021-01447-y

Essential genes from genome-wide screenings as a resource for neuropsychiatric disorders gene discovery
Cited by: 2
Author(s): Wei Zhang, Joao L De Quevedo, Gabriel R. Fries
Software Mentions: 6
Published: about 4 years ago

10.7717/peerj.10633

Gene signatures with predictive and prognostic survival values in human osteosarcoma
Cited by: 4
Author(s): Zhongpeng Qiu, Xuehui Du, Kai Chen, Yi Dai, Sibo Wang, Jun Xiao, Gang Li
Software Mentions: 6
Published: over 4 years ago

10.18632/aging.102714

ISG20 serves as a potential biomarker and drives tumor progression in clear cell renal cell carcinoma
Cited 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: over 5 years ago

10.7717/peerj.8505

Identification and validation of key modules and hub genes associated with the pathological stage of oral squamous cell carcinoma by weighted gene co-expression network analysis
Cited by: 10
Author(s): Xuegang Hu, Genban Sun, Zhiqiang Shi, Hui Ni, Shan Jiang
Software Mentions: 6
Published: over 5 years ago

10.18632/aging.202718

TMBIM6, a potential virus target protein identified by integrated multiomics data analysis in SARS-CoV-2-infected host cells
Cited 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 4 years ago

10.1038/s41598-020-65320-6

IRE1α and IGF signaling predict resistance to an endoplasmic reticulum stress-inducing drug in glioblastoma cells
Cited by: 10
Author(s): Jeffrey J. Rodvold, Xian Su, Julia K. Nussbacher, Brian Tsui, Thomas Waller, Stephen Searles, Alyssa Lew, Pengfei Jiang, Ivan Babić, Natsuko Nomura, Jonathan H. Lin, Santosh Kesari, Hannah Carter, Maurizio Zanetti
Software Mentions: 6
Published: about 5 years ago

10.3389/fcell.2021.724837

Integrative Analysis of m6A Regulator-Mediated RNA Methylation Modification Patterns and Immune Characteristics in Lupus Nephritis
Cited by: 14
Author(s): Huanhuan Zhao, Shaokang Pan, Jiayu Duan, Fengxun Liu, Guangpu Li, Dongwei Li, Zhangsuo Liu
Software Mentions: 6
Published: almost 4 years ago

10.3389/fcell.2021.641629

Dysregulation of miR-138-5p/RPS6KA1-AP2M1 Is Associated With Poor Prognosis in AML
Cited by: 10
Author(s): Donghu Yu, Chen Chen, Xiaoping Li, Jie Yao, Sheng Li, Xiaolan Ruan
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 disease
Cited 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: almost 7 years ago

10.3389/fcell.2021.646774

CRISPR-cas9 Screening Identified Lethal Genes Enriched in Cell Cycle Pathway and of Prognosis Significance in Breast Cancer
Cited by: 6
Author(s): Xi Sun, Zheng Wang, Xiaosong Chen, Kunwei Shen
Software Mentions: 6
Published: over 4 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 interactions
Cited 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: about 5 years ago

10.1126/sciadv.abj1132

Plasma lipids and growth faltering: A longitudinal cohort study in rural Gambian children
Cited 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: almost 4 years ago

10.1038/s41598-020-67842-5

Molecular dissection of CRC primary tumors and their matched liver metastases reveals critical role of immune microenvironment, EMT and angiogenesis in cancer metastasis
Cited by: 18
Author(s): Jiangang Liu, Yong Beom Cho, Hye Kyung Hong, Song Wu, Philip J. Ebert, Steven M. Bray, Suei Nee Wong, Jason C. Ting, John N. Calley, Catherine F. Whittington, Shripad V. Bhagwat, Christoph Reinhard, Robert A. Wild, Do‐Hyun Nam, Amit Aggarwal, Woo Yong Lee, Sheng-Bin Peng
Software Mentions: 6
Published: about 5 years ago

10.1038/s41398-021-01531-3

Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study
Cited by: 22
Author(s): Xiuxia Yuan, Yunpeng Wang, Xue Li, Jiajun Jiang, Yulin Kang, Lijuan Pang, Peifen Zhang, Ang Li, Luxian Lv, Ole A. Andreassen, Xiaoduo Fan, Shaohua Hu, Xueqin Song
Software Mentions: 6
Published: almost 4 years ago

10.1186/s42523-020-00032-w

Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses
Cited 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: about 5 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 cancer
Cited 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 5 years ago

10.1186/s12920-018-0358-6

Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability
Cited 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 7 years ago

Projects: cran: WGCNA

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning WGCNA 3,479