bioconductor: clusterProfiler | Projects

10.3389/fgene.2021.620705

Identification of Tumor Microenvironment-Related Prognostic Genes in Sarcoma
Cited by: 6
Author(s): Dongjun Dai, Lanyu Xie, Yongjie Shui, Jinfan Li, Qichun Wei
Software Mentions: 11
Published: almost 4 years ago

10.1371/journal.pgen.1009240

Analysis of cell-type-specific chromatin modifications and gene expression in Drosophila neurons that direct reproductive behavior
Cited by: 5
Author(s): Colleen M Palmateer, Shawn C. Moseley, Surjyendu Ray, Savannah G Brovero, Michelle N. Arbeitman
Software Mentions: 11
Published: over 3 years ago

10.1038/s41421-021-00314-w

Single-cell RNA-Seq reveals transcriptional heterogeneity and immune subtypes associated with disease activity in human myasthenia gravis
Cited by: 12
Author(s): Jin Wu, Qi Yang, Yuyao Peng, Chengkai Yan, Yi Li, Zhaohui Luo, Bo Xiao, Liqun Xu, Huan Yang
Software Mentions: 11
Published: about 3 years ago

10.3389/fonc.2021.709077

Pyroptosis-Related Gene Signatures Can Robustly Diagnose Skin Cutaneous Melanoma and Predict the Prognosis
Cited by: 57
Author(s): Anji Ju, Jintian Tang, Shuohua Chen, Yan Fu, Yongzhang Luo
Software Mentions: 11
Published: over 3 years ago

10.1186/s12859-020-03846-2

ARPIR: automatic RNA-Seq pipelines with interactive report
Cited by: 10
Author(s): Giulio Spinozzi, Valentina Tini, Alessia Adorni, Brunangelo Falini, Maria Paola Martelli
Software Mentions: 11
Published: almost 4 years ago

10.3389/fonc.2021.683582

Novel Prognostic Biomarkers in Gastric Cancer: CGB5, MKNK2, and PAPPA2
Cited by: 6
Author(s): Min Qin, Zhihai Liang, Hao Qin, Yifang Huo, Qing Yang Steve Wu, Huiying Yang, Guodu Tang
Software Mentions: 11
Published: over 3 years ago

10.3389/fonc.2020.570654

Prognostic Role of Tumor Mutation Burden Combined With Immune Infiltrates in Skin Cutaneous Melanoma Based on Multi-Omics Analysis
Cited by: 16
Author(s): Junya Yan, Xiaowen Wu, Jiayi Yu, Yanyan Zhu, Shundong Cang
Software Mentions: 11
Published: about 4 years ago

10.1155/2021/2291899

Crosstalk between Heart Failure and Cognitive Impairment via hsa-miR-933/RELB/CCL21 Pathway
Cited by: 8
Author(s): Wenxiao Feng, Jie Yang, Wen‐Chao Song, Yi-Tao Xue
Software Mentions: 11
Published: about 3 years ago

10.3389/fonc.2021.672928

Glioma-Associated Stromal Cells Stimulate Glioma Malignancy by Regulating the Tumor Immune Microenvironment
Cited by: 13
Author(s): Xiangming Cai, Feng Yuan, Junhao Zhu, Jin Yang, Chao Tang, Zixiang Cong, Chiyuan Ma
Software Mentions: 11
Published: over 3 years ago

10.3389/pore.2021.1609852

Identification of a Gene Prognostic Model of Gastric Cancer Based on Analysis of Tumor Mutation Burden
Cited by: 9
Author(s): Weijun Ma, Weidong Li, Xu Liu, Lu Liu, Xinbing Yu, Liping Yang, Mingxu Da
Software Mentions: 11
Published: about 3 years ago

10.1155/2021/6616908

Interpreting the Molecular Mechanisms of Yinchenhao Decoction on Hepatocellular Carcinoma through Absorbed Components Based on Network Pharmacology
Cited by: 5
Author(s): Jijia Sun, Tao Han, Tao Yang, Yunhui Chen, Jihan Huang
Software Mentions: 11
Published: over 3 years ago

10.3390/diagnostics10030171

GRB10 and E2F3 as Diagnostic Markers of Osteoarthritis and Their Correlation with Immune Infiltration
Cited by: 56
Author(s): Yajun Deng, Enhui Ren, Wenhua Yuan, Guang-Zhi Zhang, Zhi-Xi Wu, Qiqi Xie
Software Mentions: 11
Published: over 4 years ago

10.3389/fonc.2021.640150

Construction of Competitive Endogenous RNA Network and Verification of 3-Key LncRNA Signature Associated With Distant Metastasis and Poor Prognosis in Patients With Clear Cell Renal Cell Carcinoma
Cited by: 19
Author(s): Yang Su, Tianxiang Zhang, Jiapeng Tang, Li Zhang, Song Fan, Jun Zhou, Chaozhao Liang
Software Mentions: 11
Published: over 3 years ago

10.1155/2021/6664386

Hypoxia Molecular Characterization in Hepatocellular Carcinoma Identifies One Risk Signature and Two Nomograms for Clinical Management
Cited by: 23
Author(s): Xinwei Han, Long Liu, Taoyuan Lu, Libo Wang, Zhaonan Li, Dechao Jiao, Xinwei Han
Software Mentions: 11
Published: almost 4 years ago

10.1016/j.xpro.2021.100397

Protocol for comprehensive RNA sequencing analysis of murine long non-coding RNAs during aging
Cited by: 0
Author(s): Xinyue Lu, Qi Zhou, Jin Liu, Li Sun
Software Mentions: 11
Published: over 3 years ago

10.3390/cancers12030692

Hypoxia-Induced Adaptations of miRNomes and Proteomes in Melanoma Cells and Their Secreted Extracellular Vesicles
Cited by: 29
Author(s): Geoffroy Walbrecq, Odile Lecha, Anthoula Gaigneaux, Miriam Rebecca Fougeras, Demetra Philippidou, Christiane Margue, Miléne Tetsi Nomigni, François Bernardin, Gunnar Dittmar, Iris Behrmann, Stephanie Kreis
Software Mentions: 11
Published: over 4 years ago

10.1186/s12859-020-03866-y

Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline
Cited by: 7
Author(s): Yusuf Khan, Daniel Hammarström, Bent R. Rønnestad, Stian Ellefsen, Rafi Ahmad
Software Mentions: 10
Published: almost 4 years ago

10.1186/s12859-017-1487-1

A systematic comparative evaluation of biclustering techniques
Cited by: 94
Author(s): Victor Alexandre Padilha, Ricardo J. G. B. Campello
Software Mentions: 10
Published: almost 8 years ago

10.3390/ijms22157974

Transcriptomic and Metabolic Network Analysis of Metabolic Reprogramming and IGF-1 Modulation in SCA3 Transgenic Mice
Cited by: 4
Author(s): Yu Te Lin, Yong Shiou Lin, Wen Cheng, Jui-Chih Chang, Yi Chun Chao, Chin San Liu, An-Chi Wei
Software Mentions: 10
Published: over 3 years ago

10.1186/s12920-020-00754-5

Identification of potential crucial genes in atrial fibrillation: a bioinformatic analysis
Cited by: 15
Author(s): Junguo Zhang, Xin Huang, Xiaojie Wang, Yanhui Gao, Li Liu, Ziyi Li, Xuejiao Chen, Jie Zeng, Zebing Ye, Guowei Li
Software Mentions: 10
Published: over 4 years ago

10.18632/aging.202279

Exploration of the immune cell infiltration-related gene signature in the prognosis of melanoma
Cited by: 19
Author(s): Yongquan Zeng, Yue Zeng, Hang Yin, Fengxia Chen, Qingqing Wang, Xiaoyan Yu, Youwen Zhou
Software Mentions: 10
Published: almost 4 years ago

10.3389/fonc.2021.643465

Identification of the Roles of a Stemness Index Based on mRNA Expression in the Prognosis and Metabolic Reprograming of Pancreatic Ductal Adenocarcinoma
Cited by: 6
Author(s): Rong Tang, Xiaomeng Liu, Wei Wang, Jie Hua, Jin Xu, Chen Liang, Qingcai Meng, Jiang Liu, Bo Zhang, Xianjun Yu, Si Shi
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pone.0256016

Integration of chronological omics data reveals mitochondrial regulatory mechanisms during the development of hepatocellular carcinoma
Cited by: 2
Author(s): J. Noé García-Chávez, Verónica Rocío Vásquez-Garzón, Mercedes G. López, Saúl Villa‐Treviño, Rafaél Montiel
Software Mentions: 10
Published: over 3 years ago

10.1038/s41598-020-78228-y

Gastrointestinal adenocarcinoma analysis identifies promoter methylation-based cancer subtypes and signatures
Cited by: 7
Author(s): Renshen Xiang, Tao Fu
Software Mentions: 10
Published: almost 4 years ago

10.1155/2021/6365459

Identification of a Pyroptosis-Related Gene Signature for Prediction of Overall Survival in Lung Adenocarcinoma
Cited by: 14
Author(s): Donghai Zheng, Lv Bian, Minglang Wang, Luoqing Wang, Yilian Wang
Software Mentions: 10
Published: about 3 years ago

10.1371/journal.pone.0223909

Effects of MCHM on yeast metabolism
Cited by: 6
Author(s): Amaury Pupo, Kang‐Mo Ku, Jennifer E. G. Gallagher
Software Mentions: 10
Published: about 5 years ago

10.1186/s12935-021-01965-1

Elevated expression of LPCAT1 predicts a poor prognosis and is correlated with the tumour microenvironment in endometrial cancer
Cited by: 9
Author(s): Tianyi Zhao, Min Han, Xiaohong Ma, Lina Wei, Yixin Hou, Rui Sun, Jie Jiang
Software Mentions: 10
Published: over 3 years ago

10.1155/2020/1468980

Construction and Analysis of lncRNA-Mediated ceRNA Network in Nasopharyngeal Carcinoma Based on Weighted Correlation Network Analysis
Cited by: 7
Author(s): Zhenning Zou, Shuguang Liu, Yanping Ha, Bowan Huang
Software Mentions: 10
Published: about 4 years ago

10.3389/fonc.2020.01710

Prognostic Implications of Metabolism Related Gene Signature in Cutaneous Melanoma
Cited by: 14
Author(s): Furong Zeng, Juan Su, Cong Peng, Mengting Liao, Shuang Zhao, Ying Guo, Xiang Chen, Guangtong Deng
Software Mentions: 10
Published: about 4 years ago

10.7717/peerj.9624

Genome‐wide identification of CpG island methylator phenotype related gene signature as a novel prognostic biomarker of gastric cancer
Cited by: 12
Author(s): Zhi Zeng, Daxing Xie, Jianping Gong
Software Mentions: 10
Published: over 4 years ago

10.18632/aging.203257

Characterization of ferroptosis signature to evaluate the predict prognosis and immunotherapy in glioblastoma
Cited by: 14
Author(s): Xiaopeng Zhu, Yuxiang Zhou, Yangqian Ou, Zebo Cheng, Deqing Han, Zhou Chu, Sian Pan
Software Mentions: 10
Published: over 3 years ago

10.1038/s41416-020-0887-6

UGT2B17 modifies drug response in chronic lymphocytic leukaemia
Cited by: 12
Author(s): Éric P. Allain, Michèle Rouleau, Katrina Vanura, Sophie Tremblay, Joanie Vaillancourt, Vincent Bat, Patrick Caron, Lyne Villeneuve, Adrien Labriet, Véronique Turcotte, Trang Le, Medhat Shehata, Susanne Schnabl, Dita Demirtas, Rainer Hubmann, Charles Joly-Beauparlant, Arnaud Droit, Ulrich Jäger, Philipp B. Staber, Éric Lévesque, Chantal Guillemette
Software Mentions: 10
Published: over 4 years ago

10.1038/s41598-017-06110-5

High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci
Cited by: 10
Author(s): Brian Gloss, Bethany Signal, Seth W. Cheetham, Franziska Gruhl, Dominik C. Kaczorowski, Andrew C. Perkins, Marcel E. Dinger
Software Mentions: 10
Published: over 7 years ago

10.3390/cells10050977

Identification of 15 lncRNAs Signature for Predicting Survival Benefit of Advanced Melanoma Patients Treated with Anti-PD-1 Monotherapy
Cited by: 22
Author(s): Jianguo Zhou, Bo Liang, Jianguo Liu, Sanli Jin, Sisi He, Benjamin Frey, Ning Gu, Rainer Fietkau, Markus Hecht, Hu Ma, Udo S. Gaipl
Software Mentions: 10
Published: over 3 years ago

10.1038/s41422-020-00451-z

Sequential fate-switches in stem-like cells drive the tumorigenic trajectory from human neural stem cells to malignant glioma
Cited by: 38
Author(s): Xiaofei Wang, Ran Zhou, Yanzhen Xiong, Lingling Zhou, Xiang Yan, Manli Wang, Li Fan, Chuanxing Xie, Yiming Zhang, Zongyao Huang, Chaoqiong Ding, Ke Shi, Weida Li, Liu Yu, Cao Zeyi, Zhenning Zhang, Shengtao Zhou, Chong Chen, Yan Zhang, Lu Chen, Yuan Wang
Software Mentions: 10
Published: almost 4 years ago

10.1242/dev.169474

An integrated transcriptional analysis of the developing human retina
Cited by: 67
Author(s): Carla Mellough, R. Bauer, Joseph Collin, Birthe Dorgau, Darin Zerti, David Dolan, Carl M. Jones, Osagie Izuogu, Min Yu, Dean Hallam, Jannetta S. Steyn, Kathryn White, David Steel, Mauro Santibanez‐Koref, David Elliott, Michael S. Jackson, Susan Lindsay, Sushma Nagaraja Grellscheid, Majlinda Lako
Software Mentions: 10
Published: almost 6 years ago

10.3389/fonc.2021.644956

A New Oxaliplatin Resistance-Related Gene Signature With Strong Predicting Ability in Colon Cancer Identified by Comprehensive Profiling
Cited by: 6
Author(s): Qiu Sheng Lin, Liang Luo, Hua Wang
Software Mentions: 10
Published: over 3 years ago

10.1038/s41422-021-00467-z

Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses
Cited by: 44
Author(s): Jian He, Yan Jing, Jianfang Wang, Liangyu Zhao, Xin Qian, Yang Zeng, Yuxi Sun, Han Zhang, Zhijie Bai, Zongcheng Li, Yanli Ni, Yandong Gong, Yunqiao Li, Han He, Zhilei Bian, Yu Lan, Chunyu Ma, Lihong Bian, Heng Zhu, Bing Liu, Rui Yue
Software Mentions: 10
Published: almost 4 years ago

10.3389/pore.2021.594649

Bcl-2 Associated Athanogene 2 (BAG2) is Associated With Progression and Prognosis of Hepatocellular Carcinoma: A Bioinformatics-Based Analysis
Cited by: 7
Author(s): Xi Zhang, Junjun Zhang, Yang Liu, Jie Li, Juan Tan, Zewen Song
Software Mentions: 10
Published: over 3 years ago

10.1186/s41065-021-00202-z

RNA-Seq based transcriptome analysis in oral lichen planus
Cited by: 5
Author(s): Haoyu Wang, Yiwen Deng, Siqi Peng, Yán Li, Hui Xu, Qingzhong Wang, Zhenhua Shen
Software Mentions: 10
Published: about 3 years ago

10.1172/jci.insight.147535

The relationship between cytokine and neutrophil gene network distinguishes SARS-CoV-2–infected patients by sex and age
Cited by: 12
Author(s): Paula Paccielli Freire, Amélia Pasqual Marques, G. Baiocchi, Lena F. Schimke, Dennyson Leandro M. Fonseca, Ranieri Coelho Salgado, Igor Salerno Filgueiras, Sarah M.S. Napoleao, Desirée Rodrigues Plaça, Karen Tiemi Akashi, Thiago Dominguez Crespo Hirata, Nadia El Khawanky, Lasse Melvær Giil, Gustavo Cabral-Miranda, Robson Francisco Carvalho, Luís Carlos S. Ferreira, Antônio Condino‐Neto, Helder I. Nakaya, Igor Jurišica, Hans D. Ochs, Niels Olsen Saraiva Câmara, Vera Lúcia Garcia Calich, Otávio Cabral-Marques
Software Mentions: 10
Published: over 3 years ago

10.3389/fgene.2021.692953

Identification of the Real Hub Gene and Construction of a Novel Prognostic Signature for Pancreatic Adenocarcinoma Based on the Weighted Gene Co-expression Network Analysis and Least Absolute Shrinkage and Selection Operator Algorithms
Cited by: 15
Author(s): Qihang Yuan, Jie Ren, Zhizhou Wang, Ji Li, Dawei Deng, Dong Shang
Software Mentions: 10
Published: over 3 years ago

10.1172/jci.insight.138970

Hypoxia acts as an environmental cue for the human tissue-resident memory T cell differentiation program
Cited by: 21
Author(s): Farah Hasan, Yulun Chiu, Rebecca Shaw, Junmei Wang, Cassian Yee
Software Mentions: 10
Published: over 3 years ago

10.1111/jcmm.15848

m6A RNA methylation regulators could contribute to the occurrence of chronic obstructive pulmonary disease
Cited by: 43
Author(s): Xinwei Huang, Dongjin Lv, Yao Xiao, Min Li, Hong Zhang
Software Mentions: 10
Published: about 4 years ago

10.3389/fmicb.2018.01095

CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software
Cited by: 99
Author(s): Toby Wilkinson, Sharon Huws, Joan E. Edwards, Alison H. Kingston‐Smith, Karen Siu-Ting, Martin Hughes, Francesco Rubino, Maximillian Friedersdorff, Christopher J. Creevey
Software Mentions: 10
Published: over 6 years ago

10.1001/jamanetworkopen.2021.14162

Association of Copy Number Variation Signature and Survival in Patients With Serous Ovarian Cancer
Cited by: 14
Author(s): Ryon P. Graf, Ramez N. Eskander, Leo Brueggeman, Dwayne G. Stupack
Software Mentions: 10
Published: over 3 years ago

10.1186/s13059-021-02360-9

Role of epigenetics in unicellular to multicellular transition in Dictyostelium
Cited by: 8
Author(s): Simon Yuan Wang, Elizabeth A. Pollina, I‐Hao Wang, Lindsay K. Pino, Henry L. Bushnell, Ken Takashima, Colette Fritsche, George Sabin, Benjamin A. Garcia, Paul L. Greer, Eric Lieberman Greer
Software Mentions: 10
Published: over 3 years ago

10.3389/fmolb.2021.649363

Weighted Gene Co-expression Network Analysis Identifies CALD1 as a Biomarker Related to M2 Macrophages Infiltration in Stage III and IV Mismatch Repair-Proficient Colorectal Carcinoma
Cited by: 7
Author(s): Hongliang Zheng, Yuge Bai, Jingui Wang, Shanwen Chen, Junling Zhang, Jing Zhu, Yucun Liu, Xin Wang
Software Mentions: 10
Published: over 3 years ago

10.3389/fmolb.2021.692530

Ferroptosis-Related Gene Signature and Patterns of Immune Infiltration Predict the Overall Survival in Patients With Lung Adenocarcinoma
Cited by: 5
Author(s): Yuxuan Wang, Weikang Chen, Minqi Zhu, Lei Xian
Software Mentions: 10
Published: over 3 years ago

10.3389/fcell.2021.708066

Integrated Chromatin Accessibility and Transcriptome Landscapes of Doxorubicin-Resistant Breast Cancer Cells
Cited by: 15
Author(s): Xuelong Wang, Jizhou Yan, Baiyong Shen, Gang Wei
Software Mentions: 9
Published: over 3 years ago

10.3389/fcell.2021.671359

Identification and Validation of a Novel Prognosis Prediction Model in Adrenocortical Carcinoma by Integrative Bioinformatics Analysis, Statistics, and Machine Learning
Cited by: 3
Author(s): Xin Yan, Zixin Guo, Donghu Yu, Chen Chen, Xiaoping Li, Zhiwei Yang, Tong-Zu Liu, Sheng Li
Software Mentions: 9
Published: over 3 years ago

10.3389/fimmu.2021.592303

Machine Learning Identifies Complicated Sepsis Course and Subsequent Mortality Based on 20 Genes in Peripheral Blood Immune Cells at 24 H Post-ICU Admission
Cited by: 35
Author(s): Shayantan Banerjee, Akram Mohammed, Hector R. Wong, Nades Palaniyar, Rishikesan Kamaleswaran
Software Mentions: 9
Published: over 3 years ago

10.3389/fimmu.2021.719628

Comprehensive Characterization of RNA Processing Factors in Gastric Cancer Identifies a Prognostic Signature for Predicting Clinical Outcomes and Therapeutic Responses
Cited by: 17
Author(s): Shenghan Lou, Fanzheng Meng, Xin Yin, Yao Zhang, Bangling Han, Yingwei Xue
Software Mentions: 9
Published: over 3 years ago

10.3389/fcell.2021.654504

Role of CXCR4 as a Prognostic Biomarker Associated With the Tumor Immune Microenvironment in Gastric Cancer
Cited by: 5
Author(s): Yuyang Gu, Wenyue Gu, Rongrong Xie, Zhi Chen, Tongpeng Xu, Zhenghua Fei
Software Mentions: 9
Published: about 3 years ago

10.3389/fmolb.2020.604252

Prognostic Model of Colorectal Cancer Constructed by Eight Immune-Related Genes
Cited by: 14
Author(s): Shuting Wen, Lina He, Zhuotai Zhong, Hong Mi, Fengbin Liu
Software Mentions: 9
Published: almost 4 years ago

10.1172/jci.insight.138729

CD28 costimulation drives tumor-infiltrating T cell glycolysis to promote inflammation
Cited by: 45
Author(s): Kathryn E. Beckermann, Rachel Hongo, Xiang Ye, Kirsten Young, Katie Carbonell, Diana C Contreras Healey, Peter J. Siska, Sierra Barone, Caroline E. Roe, Christof C. Smith, Benjamin G. Vincent, Frank M. Mason, Jonathan M. Irish, W. Kimryn Rathmell, Jeffrey C. Rathmell
Software Mentions: 9
Published: over 4 years ago

10.3389/fendo.2021.538364

Prognostic Alternative mRNA Splicing in Adrenocortical Carcinoma
Cited by: 4
Author(s): Weiwei Liang, Fangfang Sun
Software Mentions: 9
Published: over 3 years ago

10.3389/fcell.2020.00268

Comparative Transcriptome Landscape of Mouse and Human Hearts
Cited by: 14
Author(s): Tatsuya Anzai, Takanori Yamagata, Hideki Uosaki
Software Mentions: 9
Published: over 4 years ago

10.1128/mSystems.00897-19

Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters
Cited by: 26
Author(s): Zachary Liechty, Christian Santos‐Medellín, Joseph Edwards, Bao‐Anh Thi Nguyen, David Mikhail, Shane Eason, Gregory C. Phillips, Venkatesan Sundaresan
Software Mentions: 9
Published: almost 5 years ago

10.3390/jof6030182

ATAC-Seq Identifies Chromatin Landscapes Linked to the Regulation of Oxidative Stress in the Human Fungal Pathogen Candida albicans
Cited by: 14
Author(s): Sabrina Jenull, Michael Tscherner, Theresia Mair, Karl Kuchler
Software Mentions: 9
Published: about 4 years ago

10.3389/fendo.2020.554922

Chenodeoxycholic Acid Modulates Bile Acid Synthesis Independent of Fibroblast Growth Factor 19 in Primary Human Hepatocytes
Cited by: 6
Author(s): H Johansson, Jonas Nørskov Søndergaard, Carl Jorns, Claudia Kutter, Ewa Ellis
Software Mentions: 9
Published: over 3 years ago

10.3389/fgene.2021.623424

Correlations Between Tumor Mutation Burden and Immunocyte Infiltration and Their Prognostic Value in Colon Cancer
Cited by: 17
Author(s): Zhangjian Zhou, Xin Xie, Xuan Wang, Xin Zhang, Wenxin Li, Tuanhe Sun, Yifan Cai, Jianhua Wu, Chengxue Dang, Hao Zhang
Software Mentions: 9
Published: almost 4 years ago

10.1155/2020/5069204

Dysregulated Expression and Methylation Analysis Identified TLX1NB as a Novel Recurrence Marker in Low-Grade Gliomas
Cited by: 1
Author(s): Hongzhou Duan, Zuozhen Yang, Chen Li, Jiayong Zhang, Shengli Shen, Changwei Yuan, Yingjin Wang
Software Mentions: 9
Published: about 4 years ago

10.3389/fnins.2020.00209

A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer’s Disease
Cited by: 6
Author(s): Sze Chung Yuen, Hongmei Zhu, Siu-wai Leung
Software Mentions: 9
Published: over 4 years ago

10.1186/s12943-020-01170-0

m6A regulator-mediated methylation modification patterns and tumor microenvironment infiltration characterization in gastric cancer
Cited by: 600
Author(s): Bo Zhang, Qiong Wu, Ben Li, Defeng Wang, Lei Wang, You Zhou
Software Mentions: 9
Published: over 4 years ago

10.3389/fgene.2021.610291

RNA-Binding Proteins Play an Important Role in the Prognosis of Patients With Testicular Germ Cell Tumor
Cited by: 7
Author(s): Liangyu Yao, Rong Cong, Chengjian Ji, Xiang Zhou, Jiaochen Luan, Xuhui Meng, Ninghong Song
Software Mentions: 9
Published: over 3 years ago

10.3390/microorganisms8010038

Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota
Cited by: 13
Author(s): Matteo Chialva, Stefano Ghignone, Mara Novero, Wael N. Hozzein, Luisa Lanfranco, Paola Bonfante
Software Mentions: 9
Published: almost 5 years ago

10.1038/s41598-021-81773-9

Verifying explainability of a deep learning tissue classifier trained on RNA-seq data
Cited by: 26
Author(s): Melvyn Yap, Rebecca L. Johnston, Helena Foley, Samual MacDonald, Olga Kondrashova, Khoa Tran, Kátia Nones, Lambros T. Koufariotis, Cameron Bean, John V. Pearson, Maciej Trzaskowski, Nicola Waddell
Software Mentions: 9
Published: almost 4 years ago

10.1038/s41598-020-71315-0

Characterisation of the novel spontaneously immortalized and invasively growing human skin keratinocyte line HaSKpw
Cited by: 8
Author(s): Elizabeth Pavez Loriè, Nicola Stricker, Beata Patrycja Plitta-Michalak, I-Peng Chen, Beate Volkmer, Rüdiger Greinert, Anna Jauch, Petra Boukamp, Alexander Rapp
Software Mentions: 9
Published: about 4 years ago

10.1042/BSR20202898

Comprehensive analysis reveals a prognostic and therapeutic biomarker CD3D in the breast carcinoma microenvironment
Cited by: 13
Author(s): Zhipeng Zhu, Weipeng Ye, Xiaofang Wu, Sihao Lin, Jiuhua Xu, Lulu Li, Jiayi Li, Haibin Wang, Zhengjie Huang
Software Mentions: 9
Published: almost 4 years ago

10.1242/bio.052993

Site-1 protease ablation in the osterix-lineage in mice results in bone marrow neutrophilia and hematopoietic stem cell alterations
Cited by: 2
Author(s): Debabrata Patra, Joongho Kim, Qiang Zhang, Eric Tycksen, Linda J. Sandell
Software Mentions: 9
Published: over 4 years ago

10.3389/fgene.2020.00785

Systematic Evaluation of the Diagnostic and Prognostic Significance of Competitive Endogenous RNA Networks in Prostate Cancer
Cited by: 3
Author(s): Zihu Guo, Han Liang, Yingxue Fu, Ziyin Wu, Yaohua Ma, Yueping Liu, Haiqing Wang, Li Jiang, Shengnan Liang, Zhenzhong Wang, Furong Li, Wei Xiao, Jingbo Wang, Yonghua Wang
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-020-77201-z

An improved de novo assembling and polishing of Solea senegalensis transcriptome shed light on retinoic acid signalling in larvae
Cited by: 3
Author(s): José Córdoba-Caballero, Pedro Seoane, Fernando M. Jabato, James R. Perkins, Manuel Manchado, M. Gonzalo Claros
Software Mentions: 9
Published: almost 4 years ago

10.3389/fgene.2021.691465

ARG2, MAP4K5 and TSTA3 as Diagnostic Markers of Steroid-Induced Osteonecrosis of the Femoral Head and Their Correlation With Immune Infiltration
Cited by: 10
Author(s): Rongguo Yu, Jiayu Zhang, Youguang Zhuo, Hong Xu, Jie Ye, Susu Tang, Nannan Liu, Yiyuan Zhang
Software Mentions: 9
Published: over 3 years ago

10.18632/aging.102847

Risk score based on expression of five novel genes predicts survival in soft tissue sarcoma
Cited by: 21
Author(s): Hao Gu, Zhang Chao, Jia Guo, Min Yang, Hongshan Zhong, Wei Jin, Yang Liu, Liping Gao, Renxiong Wei
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-019-56829-6

Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues
Cited by: 18
Author(s): Mustafa Sibai, Cüneyd Parlayan, Pelin Tuğlu, Gürkan Öztürk, Turan Demircan
Software Mentions: 9
Published: almost 5 years ago

10.1080/21655979.2020.1822715

A novel prognostic models for identifying the risk of hepatocellular carcinoma based on epithelial-mesenchymal transition-associated genes
Cited by: 15
Author(s): Chen Xiong, Guifu Wang, Dou‐Sheng Bai
Software Mentions: 9
Published: almost 5 years ago

10.1038/s41598-020-59516-z

Variability in estimated gene expression among commonly used RNA-seq pipelines
Cited by: 37
Author(s): Sonali Arora, Siobhan S. Pattwell, Eric C. Holland, Hamid Bolouri
Software Mentions: 9
Published: almost 5 years ago

10.1186/s12885-021-07807-7

Molecular subtypes based on DNA methylation predict prognosis in lung squamous cell carcinoma
Cited by: 10
Author(s): Xiushen Li, Kechao Nie, Zhihua Zheng, Ruisheng Zhou, Yu‐Sheng Huang, Zeng Jie Ye, Fan He, Ying Tang
Software Mentions: 9
Published: almost 4 years ago

10.1186/s12935-020-01230-x

A Gleason score-related outcome model for human prostate cancer: a comprehensive study based on weighted gene co-expression network analysis
Cited by: 19
Author(s): Yongzhi Wang, Zhonghua Yang
Software Mentions: 9
Published: over 4 years ago

10.18632/aging.203390

Comprehensive analysis of new prognostic signature based on ferroptosis-related genes in clear cell renal cell carcinoma
Cited by: 8
Author(s): Bin Zheng, Zhihong Niu, Shubin Si, Guiting Zhao, Jianwei Wang, Zhongshun Yao, Fajuan Cheng
Software Mentions: 9
Published: over 3 years ago

10.1186/s12935-021-02215-0

Identification of the prognostic value of a 2-gene signature of the WNT gene family in UCEC using bioinformatics and real-world data
Cited by: 9
Author(s): Yuexin Hu, Mingjun Zheng, Dandan Zhang, Rui Gou, Ouxuan Liu, Shuang Wang, Bei Lin
Software Mentions: 9
Published: about 3 years ago

10.3389/fonc.2020.573141

Significance of Tumor Mutation Burden in Immune Infiltration and Prognosis in Cutaneous Melanoma
Cited by: 57
Author(s): Kai Kang, Fucun Xie, Jianshan Mao, Yi Bai, Xiang Wang
Software Mentions: 9
Published: about 4 years ago

10.1186/s12885-021-08328-z

The tumor immune microenvironment and immune-related signature predict the chemotherapy response in patients with osteosarcoma
Cited by: 16
Author(s): Lijiang He, Hainan Yang, Jingshan Huang
Software Mentions: 9
Published: over 3 years ago

10.3389/fgene.2021.663617

Multi-Omics Data Analyses Construct a Six Immune-Related Genes Prognostic Model for Cervical Cancer in Tumor Microenvironment
Cited by: 10
Author(s): Fangfang Xu, Jiacheng Shen, Shaohua Xu
Software Mentions: 9
Published: over 3 years ago

10.3389/fgene.2021.661988

Identification of Aging-Related Genes Associated With Clinical and Prognostic Features of Hepatocellular Carcinoma
Cited by: 12
Author(s): Xingte Chen, Lei Wang, Liang Hong, Zhiying Su, Xiaohong Zhong, Han Zhou, Xueqing Zhang, Junxin Wang, Lingdong Shao
Software Mentions: 9
Published: over 3 years ago

10.3389/fonc.2020.602498

Metabolism-Associated Molecular Classification of Colorectal Cancer
Cited by: 13
Author(s): Meng Zhang, Haizhou Wang, Ruyi Peng, Fei Xu, Fan Wang, Qiu Zhao
Software Mentions: 9
Published: almost 4 years ago

10.3389/fonc.2021.709210

Single-Cell Transcriptomics Reveals the Complexity of the Tumor Microenvironment of Treatment-Naive Osteosarcoma
Cited by: 45
Author(s): Yun Liu, Wei Feng, Yan Dai, Mengying Bao, Zhenchao Yuan, Mingwei He, Zhaojie Qin, Shijie Liao, Jun He, Qian Huang, Zhenyuan Yu, Yanyu Zeng, Binqian Guo, Rong Huang, Rongliang Yang, Yonghua Jiang, Jinling Liao, Zengming Xiao, Xinli Zhan, Chengsen Lin, Jiake Xu, Yu Ye, Jie Ma, Qingjun Wei, Zengnan Mo
Software Mentions: 9
Published: over 3 years ago

10.3389/fonc.2020.593760

Medication for Acromegaly Reduces Expression of MUC16, MACC1 and GRHL2 in Pituitary Neuroendocrine Tumour Tissue
Cited by: 4
Author(s): Rihards Saksis, Ivars Silamiķelis, Pola Laksa, Kaspars Megnis, Raitis Pečulis, Ilona Mandrika, Olesja Rogoza, Ramona Petrovska, Inga Balcere, Ilze Konrāde, Liva Steina, Jānis Stukēns, Austra Breikša, Jurijs Nazarovs, Jeļizaveta Sokolovska, Valdis Pīrāgs, Jānis Kloviņš, Vita Rovīte
Software Mentions: 9
Published: almost 4 years ago

10.7717/peerj.11687

Construction and validation of a 15-gene ferroptosis signature in lung adenocarcinoma
Cited by: 5
Author(s): Guangxu Tu, Weilin Peng, Qidong Cai, Zhenyu Zhao, Ping Xiong, Boxue He, Pengfei Zhang, Shuai Shi, Yongguang Tao, Xiang Wang
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pbio.3001158

Disparate temperature-dependent virus–host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium
Cited by: 66
Author(s): Philip V’kovski, Mitra Gultom, Jenna N. Kelly, Silvio Steiner, Julie Russeil, Bastien Mangeat, Elisa Cora, Joern Pezoldt, Melle Holwerda, Annika Kratzel, Laura Laloli, Manon Wider, Jasmine Portmann, Thao Thi Phuong Tran, Nadine Ebert, Hanspeter Stalder, Rune Hartmann, Vincent Gardeux, Daniel Alpern, Bart Deplancke, Volker Thiel, Ronald Dijkman
Software Mentions: 9
Published: over 3 years ago

10.1186/s12885-021-08470-8

Alternative splicing associated with cancer stemness in kidney renal clear cell carcinoma
Cited by: 12
Author(s): Lixing Xiao, Guoying Zou, Rui Cheng, Pingping Wang, Kexin Ma, Huimin Cao, Wenyang Zhou, Xiyun Jin, Zhaochun Xu, Yan Huang, Xiaoyu Lin, Huan Nie, Qinghua Jiang
Software Mentions: 9
Published: over 3 years ago

10.1155/2020/8816070

Progressive and Prognostic Performance of an Extracellular Matrix-Receptor Interaction Signature in Gastric Cancer
Cited by: 20
Author(s): Xiangchou Yang, Liping Chen, Yuting Mao, Zijing Hu, Min He
Software Mentions: 9
Published: about 4 years ago

10.3389/fonc.2021.575425

Systematic Chromatin Accessibility Analysis Based on Different Immunological Subtypes of Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Shiqiang Zhang, Wenzhong Zheng, Donggen Jiang, Haiyun Xiong, Guolong Liao, Xiangwei Yang, He Ma, Jun Li, Miaojuan Qiu, Binbin Li, Chunhui Sun, Jing Zhao, Liling Wang, Jun Pang
Software Mentions: 9
Published: over 3 years ago

10.7717/peerj.10008

A model of twenty-three metabolic-related genes predicting overall survival for lung adenocarcinoma
Cited by: 3
Author(s): Zhenyu Zhao, Boxue He, Qidong Cai, Pengfei Zhang, Ping Xiong, Yuqian Zhang, Hui Xie, Xiang Wang
Software Mentions: 9
Published: about 4 years ago

10.1155/2021/9911184

Identification of Disease-Specific Hub Biomarkers and Immune Infiltration in Osteoarthritis and Rheumatoid Arthritis Synovial Tissues by Bioinformatics Analysis
Cited by: 7
Author(s): Fei Sun, Jian Zhou, Peiyu Pu, Chen Qiu, Jia rui Cao, Hao Peng
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pbio.2004045

A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates
Cited by: 41
Author(s): Jean-Louis Plouhinec, Sofía Medina-Ruíz, Caroline Borday, Elsa Bernard, Jean-Philippe Vert, Michael B. Eisen, Richard M. Harland, Anne H. Monsoro-Burq
Software Mentions: 9
Published: about 7 years ago

10.1002/cam4.2774

Identification of prognostic genes in adrenocortical carcinoma microenvironment based on bioinformatic methods
Cited by: 39
Author(s): Xiao Li, Yang Gao, Zicheng Xu, Zheng Zhang, Yuxiao Zheng, Feng Qi
Software Mentions: 9
Published: almost 5 years ago

10.3389/fonc.2020.626912

Molecular Subtypes and CD4+ Memory T Cell-Based Signature Associated With Clinical Outcomes in Gastric Cancer
Cited by: 15
Author(s): Zhikun Ning, Cegui Hu, Chao Huang, Jiang Liu, Taicheng Zhou, Zhen Zong
Software Mentions: 9
Published: over 3 years ago

10.1038/s41421-021-00274-1

Integrating longitudinal clinical laboratory tests with targeted proteomic and transcriptomic analyses reveal the landscape of host responses in COVID-19
Cited by: 21
Author(s): Yun Tan, Wei Zhang, Zhaoqin Zhu, Na Qiao, Yun Ling, Mingquan Guo, Tong Yin, Hai Fang, Xiaoguang Xu, Gang Lu, Peipei Zhang, Shuangshuang Yang, Ziyu Fu, Dongguo Liang, Yinyin Xie, Ruihong Zhang, Lu Jiang, Shuting Yu, Jing Lu, Fang-Ying Jiang, Jian Chen, Chenlu Xiao, Shengyue Wang, Shuo Chen, Xiu‐Wu Bian, Hongzhou Lu, Feng Liu, Sai‐Juan Chen
Software Mentions: 9
Published: over 3 years ago

Projects: bioconductor: clusterProfiler

Papers Mentioning clusterProfiler 2,223