Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: GSVA
https://packages.ecosyste.ms/registries/pypi.org/packages/GSVA
Python CLI and module for running the GSVA R bioconductor package with Python Pandas inputs and outputs.
7 versions
Latest release: over 6 years ago
41 downloads last month
Papers Mentioning GSVA 893
10.3389/fonc.2020.617890
Comparative Proteome Identifies Complement Component 3-Mediated Immune Response as Key Difference of Colon Adenocarcinoma and Rectal AdenocarcinomaCited by: 9
Author(s): Jun-Ze Liang, Xiaoling Liang, Liye Zhong, Chutian Wu, Jing Zhang, Yang Wang
Software Mentions: 30
Published: over 3 years ago
10.3389/fimmu.2021.659444
Development and Validation of a CD8+ T Cell Infiltration-Related Signature for Melanoma PatientsCited by: 13
Author(s): Yuan Yuan, Zheng Zhu, Ying Lan, Saili Duan, Zijue Zhu, Xi Zhang, Guoyin Li, Hui Qü, Yao Feng, Hui Cai, Zewen Song
Software Mentions: 24
Published: over 3 years ago
10.18632/aging.103499
Multi-omics network analysis reveals distinct stages in the human aging progression in epidermal tissueCited by: 16
Author(s): Nicholas Holzscheck, Jörn Söhle, Boris Kristof, Elke Grönniger, Stefan Gallinat, Horst Wenck, Marc Winnefeld, Cassandra Falckenhayn, Lars Kaderali
Software Mentions: 18
Published: over 4 years ago
10.3389/fonc.2021.605810
A Novel Risk Factor Model Based on Glycolysis-Associated Genes for Predicting the Prognosis of Patients With Prostate CancerCited by: 6
Author(s): Kaixuan Guo, Cong Lai, Juan Shi, Zhuang Tang, Cheng Liu, Kuiqing Li, Kailin Xu
Software Mentions: 18
Published: about 3 years ago
10.1002/1878-0261.12960
KRAS mutant rectal cancer cells interact with surrounding fibroblasts to deplete the extracellular matrixCited by: 6
Author(s): Jin K. Kim, Michael R. Marco, Seo‐Hyun Choi, Xuan Qu, Chin-Tung Chen, Moshe Elkabets, Lauren Fairchild, Oliver Chow, Francisco M. Barriga, Lukas E. Dow, Kevin P. O’Rourke, Bryan Szeglin, Dmitry Yarilin, Sho Fujisawa, Katia Manova‐Todorova, Philip B. Paty, Jinru Shia, Christina Leslie, J. Joshua Smith, Scott W. Lowe, Raphael Pelossof, Francisco Sánchez-Vega, Julio García-Aguilar
Software Mentions: 18
Published: over 3 years ago
10.3389/fimmu.2020.01691
Leveraging Public Single-Cell and Bulk Transcriptomic Datasets to Delineate MAIT Cell Roles and Phenotypic Characteristics in Human MalignanciesCited by: 22
Author(s): Tony Yao, Parisa Shooshtari, S. M. Mansour Haeryfar
Software Mentions: 18
Published: over 4 years ago
10.1038/s41597-021-00998-5
A merged microarray meta-dataset for transcriptionally profiling colorectal neoplasm formation and progressionCited by: 4
Author(s): Michael Rohr, Jordan M. Beardsley, Sai Preethi Nakkina, Xiang Zhu, Jihad Aljabban, Dexter Hadley, Deborah A. Altomare
Software Mentions: 17
Published: about 3 years ago
10.1186/s40168-019-0725-3
Baseline microbiota composition modulates antibiotic-mediated effects on the gut microbiota and hostCited by: 43
Author(s): Aonghus Lavelle, Thomas Hoffmann, Hang-Phuong Pham, Philippe Langella, Éric Guédon, Harry Sokol
Software Mentions: 16
Published: over 5 years ago
10.3389/fonc.2021.644416
An Inflammatory Response-Related Gene Signature Can Impact the Immune Status and Predict the Prognosis of Hepatocellular CarcinomaCited by: 62
Author(s): Zhuo Lin, Xu Qian, Dan Miao, Fang Yu
Software Mentions: 16
Published: over 3 years ago
10.3389/fonc.2021.690129
A Tumor Progression Related 7-Gene Signature Indicates Prognosis and Tumor Immune Characteristics of Gastric CancerCited by: 6
Author(s): Fen Liu, Zongcheng Yang, Lixin Zheng, Wei Shao, Xiujie Cui, Yue Wang, Jihui Jia, Yue Fu
Software Mentions: 16
Published: over 3 years ago
10.1186/s12935-020-01571-7
RETRACTED ARTICLE: Aging-related tumor associated fibroblasts changes could worsen the prognosis of GBM patientsCited by: 7
Author(s): Hongwang Song, Xiaojun Fu, Chenxing Wu, Shouwei Li
Software Mentions: 16
Published: about 4 years ago
10.3389/fcell.2020.596679
Development and Validation of a Combined Ferroptosis and Immune Prognostic Classifier for Hepatocellular CarcinomaCited by: 77
Author(s): Yang Liu, Xi Zhang, Junjun Zhang, Juan Tan, Jie Li, Zewen Song
Software Mentions: 16
Published: almost 4 years ago
10.3389/fonc.2020.555632
Comprehensive Characterization of Alternative mRNA Splicing Events in Glioblastoma: Implications for Prognosis, Molecular Subtypes, and Immune Microenvironment RemodelingCited by: 8
Author(s): Liang Zhao, Jiayue Zhang, Zhiyuan Liu, Yu Wang, Shurui Xuan, Peng Zhao
Software Mentions: 16
Published: almost 4 years ago
10.1186/s12864-020-06856-9
mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling dataCited by: 28
Author(s): Antony Kaspi, Mark Ziemann
Software Mentions: 15
Published: over 4 years ago
10.3389/fcell.2021.671736
Identification of a Novel Immune Landscape Signature for Predicting Prognosis and Response of Endometrial Carcinoma to Immunotherapy and ChemotherapyCited by: 6
Author(s): Jinhui Liu, Yichun Wang, Jie Mei, Song Nie, Yan Zhang
Software Mentions: 15
Published: over 3 years ago
10.1186/s12967-021-02773-x
Multi-omics characterization and validation of invasiveness-related molecular features across multiple cancer typesCited by: 5
Author(s): Guoshu Bi, Jiaqi Liang, Yuansheng Zheng, Runmei Li, Mengnan Zhao, Yiwei Huang, Cheng Zhan, Songtao Xu, Hong Fan
Software Mentions: 15
Published: over 3 years ago
10.3389/fcell.2021.642724
Identification of Stemness-Related Genes for Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma by Integrated Bioinformatics AnalysisCited by: 5
Author(s): Hongjun Guo, Siqiao Wang, Min Kyung Ju, Penghui Yan, Weiwei Sun, Zhenyu Li, Siyu Wu, Ruoyi Lin, Shuyuan Xian, Daoke Yang, Jun Wang, Zongqiang Huang
Software Mentions: 15
Published: over 3 years ago
10.3389/fonc.2021.650153
Identification and Validation of a Prognostic Immune-Related Alternative Splicing Events Signature for GliomaCited by: 5
Author(s): Minjie Wang, Zhongqiang Zhou, Jianglin Zheng, Wenjun Xiao, Jun Zhu, Chaocai Zhang, Xueshi Jiang
Software Mentions: 15
Published: over 3 years ago
10.3389/fcell.2020.00790
The Construction of Bone Metastasis-Specific Prognostic Model and Co-expressed Network of Alternative Splicing in Breast CancerCited by: 4
Author(s): Runzhi Huang, Jian Guo, Penghui Yan, Suna Zhai, Peng Hu, Xiaolong Zhu, Jiayao Zhang, Yannan Qiao, Yu Zhang, Hui Liu, Ling Huang, Jie Zhang, Daoke Yang, Zongqiang Huang
Software Mentions: 15
Published: about 4 years ago
10.1186/s12967-021-02894-3
Identification of immune subtypes of cervical squamous cell carcinoma predicting prognosis and immunotherapy responsesCited by: 8
Author(s): Yimin Li, Shun Lü, Shubin Wang, Xinhao Peng, Jinyi Lang
Software Mentions: 14
Published: over 3 years ago
10.1186/s12967-021-02952-w
Molecular subtype identification and prognosis stratification by a metabolism-related gene expression signature in colorectal cancerCited by: 20
Author(s): Daowei Lin, Wenhua Fan, Rongxin Zhang, Enen Zhao, Pansong Li, Wenhao Zhou, Jianhong Peng, Liren Li
Software Mentions: 14
Published: over 3 years ago
10.3389/fimmu.2021.646523
Systematic Pan-Cancer Analysis Identifies TREM2 as an Immunological and Prognostic BiomarkerCited by: 57
Author(s): Xin Cheng, Xiaowei Wang, Kechao Nie, Lin Cheng, Zheyu Zhang, Yang Hu, Weijun Peng
Software Mentions: 14
Published: over 3 years ago
10.1186/s40478-020-0880-6
Single-nucleus RNA-seq identifies Huntington disease astrocyte statesCited by: 147
Author(s): Osama Al‐Dalahmah, Alexander A. Sosunov, Ayesha Shaik, Kenneth Ofori, Yang Liu, Jean Paul Vonsattel, István Adorján, Vilas Menon, James E. Goldman
Software Mentions: 14
Published: over 4 years ago
10.1111/jcmm.15705
Collagen Type III Alpha 1 chain regulated by GATA‐Binding Protein 6 affects Type II IFN response and propanoate metabolism in the recurrence of lower grade gliomaCited by: 18
Author(s): Runzhi Huang, Zhenyu Li, Xiaolong Zhu, Penghui Yan, Dianwen Song, Huabin Yin, Peng Hu, Ruoyi Lin, Shengyu Wu, Tong Meng, Jie Zhang, Zongqiang Huang
Software Mentions: 14
Published: about 4 years ago
10.3389/fimmu.2021.557994
Investigation of Genetic Determinants of Glioma Immune Phenotype by Integrative Immunogenomic Scale AnalysisCited by: 10
Author(s): Binghao Zhao, Yuekun Wang, Yaning Wang, Congxin Dai
Software Mentions: 14
Published: over 3 years ago
10.18632/aging.203353
Development and validation of an intra-tumor heterogeneity-related signature to predict prognosis of bladder cancer: a study based on single-cell RNA-seqCited by: 7
Author(s): Ranran Zhou, Jingjing Liang, Qi Chen, Haijun Tian, Cheng Yang, Cundong Liu
Software Mentions: 14
Published: over 3 years ago
10.3389/fgene.2021.702072
Characterization of Modification Patterns, Biological Function, Clinical Implication, and Immune Microenvironment Association of m6A Regulators in Pancreatic CancerCited by: 5
Author(s): Kun Fang, Hairong Qu, Jiapei Wang, Desheng Tang, Changsheng Yan, Jiamin Ma, Lei Gao
Software Mentions: 14
Published: about 3 years ago
10.3390/cancers13174311
Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex ImagingCited by: 15
Author(s): Daria Lazic, Florian Kromp, Fikret Rifatbegovic, Peter Repiščák, Michael Kirr, Filip Mívalt, Florian Halbritter, Marie Bernkopf, Andrea Bileck, Marek Ussowicz, Inge M. Ambros, Peter F. Ambros, Christopher Gerner, Ruth Ladenstein, Christian Ostalecki, Sabine Taschner‐Mandl
Software Mentions: 13
Published: about 3 years ago
10.1186/s12935-020-01362-0
Immune-related long non-coding RNA signature identified prognosis and immunotherapeutic efficiency in bladder cancer (BLCA)Cited by: 40
Author(s): Rui Cao, Lushun Yuan, Bo Ma, Gang Wang, Ye Tian
Software Mentions: 13
Published: over 4 years ago
10.3389/fonc.2021.678694
A Novel Ferroptosis-Related Pathway for Regulating Immune Checkpoints in Clear Cell Renal Cell CarcinomaCited by: 5
Author(s): Su Gao, Hailong Ruan, Jingchong Liu, Yuenan Liu, Di Liu, Junwei Tong, Jian Shi, Hongmei Yang, Tianbo Xu, Xiaoping Zhang
Software Mentions: 13
Published: over 3 years ago
10.1186/s13046-020-01684-x
KIAA1522 potentiates TNFα-NFκB signaling to antagonize platinum-based chemotherapy in lung adenocarcinomaCited by: 11
Author(s): Boshi Wang, Tiantian Jing, Wei‐Lin Jin, Biaohua Chen, Chengsi Wu, Ming-Rong Wang, Yizhen Liu
Software Mentions: 13
Published: about 4 years ago
10.1186/s12885-020-07695-3
Comprehensive analysis of prognostic gene signatures based on immune infiltration of ovarian cancerCited by: 18
Author(s): Shi-Bai Yan, Jinling Fang, Yongcai Chen, Yong Xie, Siyou Zhang, Xiaohui Zhu, Fang Fěng
Software Mentions: 13
Published: almost 4 years ago
10.1093/bib/bbz158
Toward a gold standard for benchmarking gene set enrichment analysisCited by: 74
Author(s): Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity W. Law, Sean Davis, Vincent J. Carey, Martin Morgan, Ralf Zimmer, Levi Waldron
Software Mentions: 13
Published: over 4 years ago
10.3390/cancers11010091
The Potential Mechanism of Bufadienolide-Like Chemicals on Breast Cancer via Bioinformatics AnalysisCited by: 5
Author(s): Yingbo Zhang, Xiaomin Tang, Yuxin Pang, Luqi Huang, Dan Wang, Chao Yuan, Xuan Hu, Liping Qu
Software Mentions: 13
Published: almost 6 years ago
10.1186/s12967-021-02889-0
Pan-cancer characterization of metabolism-related biomarkers identifies potential therapeutic targetsCited by: 6
Author(s): Guoshu Bi, Yunyi Bian, Jiaqi Liang, Jiacheng Yin, Runmei Li, Mengnan Zhao, Yiwei Huang, Tao Lu, Cheng Zhan, Hong Fan, Qun Wang
Software Mentions: 13
Published: over 3 years ago
10.18632/aging.202976
Development and validation of epithelial mesenchymal transition-related prognostic model for hepatocellular carcinomaCited by: 7
Author(s): Xuequan Wang, Ziming Xing, Huihui Xu, Haihua Yang, Tongjing Xing
Software Mentions: 13
Published: over 3 years ago
10.3389/fonc.2020.629909
Identification of an Immune Gene-Associated Prognostic Signature and Its Association With a Poor Prognosis in Gastric Cancer PatientsCited by: 15
Author(s): Xiaoqing Guan, Zhiyuan Xu, Runzhe Chen, Jiang‐Jiang Qin, Xiangdong Cheng
Software Mentions: 13
Published: over 3 years ago
10.12688/f1000research.19236.3
Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signaturesCited by: 11
Author(s): Dharmesh D. Bhuva, Momeneh Foroutan, Yi Xie, Ruqian Lyu, Joseph Cursons, Melissa J. Davis
Software Mentions: 13
Published: about 5 years ago
10.18632/aging.202831
Seven interferon gamma response genes serve as a prognostic risk signature that correlates with immune infiltration in lung adenocarcinomaCited by: 11
Author(s): Boyang Yao, Lixin Wang, Heyong Wang, Jinxia Bao, Qiwen Li, Fengzhi Yu, Wenjing Zhu, Li Zhang, Wang Li, Gu Zhan, Ke Fei, Peng Zhang, Fan Zhang, Xiaoying Huang
Software Mentions: 13
Published: over 3 years ago
10.18632/aging.103965
Establishing and validating a pathway prognostic signature in pancreatic cancer based on miRNA and mRNA sets using GSVACited by: 8
Author(s): Junfeng Zhang, Jianyou Gu, Shixiang Guo, Wenjie Huang, Yongqiang Zheng, Xianxing Wang, Tao Zhang, Weibo Zhao, Bing Ni, Yingfang Fan, Huaizhi Wang
Software Mentions: 12
Published: almost 4 years ago
10.3389/fcimb.2021.687607
Early Leukocyte Responses in Ex-Vivo Models of Healing and Non-Healing Human Leishmania (Viannia) panamensis InfectionsCited by: 1
Author(s): María Adelaida Gómez, Ashton T. Belew, Adriana Navas, Mariana Rosales-Chilama, Julieth Murillo, Laura A. L. Dillon, Theresa A Alexander, Álvaro José Martínez-Valencia, Najib M. El-Sayed
Software Mentions: 12
Published: about 3 years ago
10.1371/journal.pcbi.1007753
Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signaturesCited by: 1
Author(s): Jacob Pfeil, Lauren Sanders, Ioannis N. Anastopoulos, A. Geoffrey Lyle, Alana S. Weinstein, Yuanqing Xue, Andrew Blair, Holly C. Beale, Alex Lee, Stanley G. Leung, Phuong Dinh, Avanthi Tayi Shah, Marcus R. Breese, W. Patrick Devine, Isabel Bjork, Sofie R. Salama, E. Alejandro Sweet-Cordero, David Haussler, Olena M. Vaske
Software Mentions: 12
Published: over 4 years ago
10.18632/aging.202871
A novel focal adhesion related gene signature for prognostic prediction in hepatocellular carcinomaCited by: 4
Author(s): Zhuo Lin, Dan Miao, Xu Qian, Xiaodong Wang, Fang Yu
Software Mentions: 12
Published: over 3 years ago
10.1186/s12967-021-02800-x
Identification of 4 immune cells and a 5-lncRNA risk signature with prognosis for early-stage lung adenocarcinomaCited by: 25
Author(s): Liancai Mu, Ke Ding, Ranran Tu, Wei Yang
Software Mentions: 12
Published: over 3 years ago
10.7717/peerj.10255
Comprehensive genomic analysis of microenvironment phenotypes in ovarian cancerCited by: 4
Author(s): Jingshu Wang, Tingting Zhang, Lina Yang, Gong Yang
Software Mentions: 12
Published: almost 4 years ago
10.3389/fimmu.2021.647832
Large-Scale Gene Expression Signatures Reveal a Microbicidal Pattern of Activation in Mycobacterium leprae-Infected Monocyte-Derived Macrophages With Low Multiplicity of InfectionCited by: 9
Author(s): Thyago Leal-Calvo, Bruna Letícia Martins, Daniele Ferreira de Faria Bertoluci, Patrícia Sammarco Rosa, Rodrigo Mendes de Camargo, G. Germano, Vânia Niéto Brito de Souza, Ana Carla Pereira Latini, Milton Ozório Moraes
Software Mentions: 12
Published: over 3 years ago
10.1111/jcmm.16605
Leptin receptor is a key gene involved in the immunopathogenesis of thyroid‐associated ophthalmopathyCited by: 3
Author(s): Ziyi Chen, Zhe Chen, Jingya Wang, Meng Zhang, Xiaofei Wang, Deji Cuomu, Bingyin Shi, Yue Wang
Software Mentions: 12
Published: over 3 years ago
10.3389/fmolb.2021.681526
Identification of Key Biomarkers and Immune Infiltration in Systemic Juvenile Idiopathic Arthritis by Integrated Bioinformatic AnalysisCited by: 2
Author(s): Min Zhang, Rongxin Dai, Qianqian Zhao, Lina Zhou, Yunfei An, Xuemei Tang, Xiaodong Zhao
Software Mentions: 12
Published: over 3 years ago
10.12688/f1000research.12544.1
Easy and efficient ensemble gene set testing with EGSEACited by: 45
Author(s): Monther Alhamdoosh, Charity W. Law, Tian Li, Julie Sheridan, Milica Ng, Matthew E. Ritchie
Software Mentions: 12
Published: almost 7 years ago
10.1371/journal.pone.0079217
A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and SpecificityCited by: 154
Author(s): Adi L. Tarca, Gaurav Bhatti, Roberto Romero
Software Mentions: 12
Published: almost 11 years ago
10.3389/fimmu.2021.698236
Comprehensive Analysis of Clinical Significance, Immune Infiltration and Biological Role of m6A Regulators in Early-Stage Lung AdenocarcinomaCited by: 3
Author(s): Bolun Zhou, Shugeng Gao
Software Mentions: 12
Published: about 3 years ago
10.3390/cancers11091248
Gastric Normal Adjacent Mucosa Versus Healthy and Cancer Tissues: Distinctive Transcriptomic Profiles and Biological FeaturesCited by: 28
Author(s): Sabino Russi, Giovanni Calice, Vitalba Ruggieri, Simona Laurino, Francesco La Rocca, Elena Amendola, Cinzia Lapadula, Debora Compare, Gerardo Nardone, Pellegrino Musto, Mario De Felice, Geppino Falco, Pietro Zoppoli
Software Mentions: 12
Published: about 5 years ago
10.3389/fgene.2021.609174
METTL14 Acts as a Potential Regulator of Tumor Immune and Progression in Clear Cell Renal Cell CarcinomaCited by: 11
Author(s): Tianbo Xu, Su Gao, Hailong Ruan, Jingchong Liu, Yuenan Liu, Di Liu, Junwei Tong, Jian Shi, Hongmei Yang, Ke Chen, Xiaoping Zhang
Software Mentions: 11
Published: over 3 years ago
10.1371/journal.pntd.0009321
Localized skin inflammation during cutaneous leishmaniasis drives a chronic, systemic IFN-γ signatureCited by: 15
Author(s): Camila Farias Amorim, Fernanda O. Novais, Ba Tiep Nguyen, Maurício T. Nascimento, Jamile Lago, Alexsandro S. Lago, Lucas P. Carvalho, Daniel P. Beiting, Phillip Scott
Software Mentions: 11
Published: over 3 years ago
10.3389/fgene.2021.733715
Development and Validation of a Novel Gene Signature for Predicting the Prognosis by Identifying m5C Modification Subtypes of Cervical CancerCited by: 2
Author(s): Jing Yu, Leilei Liang, Jing Liu, Tingting Liu, Jian Li, Lin Xiu, Jia Zeng, Tiantian Wang, Di Wang, Lijun Liang, Dawei Xie, Ding-Xiong Chen, Jusheng An, Lingying Wu
Software Mentions: 11
Published: about 3 years ago
10.1002/1878-0261.12117
Recurrence-associated gene signature optimizes recurrence-free survival prediction of colorectal cancerCited by: 37
Author(s): Xianglong Tian, Xiaoqiang Zhu, Tingting Yan, Chuangqi Yu, Chaoqin Shen, Ye Hu, Jie Hong, Haoyan Chen, Jing‐Yuan Fang
Software Mentions: 11
Published: about 7 years ago
10.1186/s12935-021-01795-1
Identification and development of a novel invasion-related gene signature for prognosis prediction in colon adenocarcinomaCited by: 15
Author(s): Jiahua Liu, Chunhui Jiang, Chunjie Xu, Dongyang Wang, Ya Shen, Ye Liu, Lei Gu
Software Mentions: 11
Published: over 3 years ago
10.1186/s12935-020-01393-7
Small nucleolar RNAs signature (SNORS) identified clinical outcome and prognosis of bladder cancer (BLCA)Cited by: 5
Author(s): Rui Cao, Bo Ma, Lushun Yuan, Gang Wang, Ye Tian
Software Mentions: 11
Published: over 4 years ago
10.1155/2021/6664386
Hypoxia Molecular Characterization in Hepatocellular Carcinoma Identifies One Risk Signature and Two Nomograms for Clinical ManagementCited 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
10.3390/ijms221910302
The Impact of m1A Methylation Modification Patterns on Tumor Immune Microenvironment and Prognosis in Oral Squamous Cell CarcinomaCited by: 17
Author(s): Li Gao, Ru Chen, Masahiro Sugimoto, Masanobu Mizuta, Yo Kishimoto, Koichi Omori
Software Mentions: 11
Published: about 3 years ago
10.1186/s12935-021-02041-4
Ten-gene signature reveals the significance of clinical prognosis and immuno-correlation of osteosarcoma and study on novel skeleton inhibitors regarding MMP9Cited by: 17
Author(s): Weihang Li, Ziyi Ding, Dong Wang, Chengfei Li, Yikai Pan, Yingjing Zhao, Hongzhe Zhao, Tianxing Lu, Rui Xu, Shilei Zhang, Bin Yuan, Yunlong Zhao, Yanjiang Yin, Yuan Gao, Jing Li, Ming Yan
Software Mentions: 11
Published: over 3 years ago
10.3389/fmolb.2021.684050
Characterization of Hypoxia-Related Molecular Subtypes in Clear Cell Renal Cell Carcinoma to Aid Immunotherapy and Targeted Therapy via Multi-Omics AnalysisCited by: 10
Author(s): Weimin Zhong, Hongbin Zhong, Fengling Zhang, Chaoqun Huang, Yao Lin, Jian Huang
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 gravisCited 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/fimmu.2021.599207
Molecular and Clinical Characterization of LAG3 in Breast Cancer Through 2994 SamplesCited by: 15
Author(s): Qiang Liu, Yihang Qi, Jie Zhai, Xiangyi Kong, Xiangyu Wang, Zhongzhao Wang, Yi Fang, Jing Wang
Software Mentions: 11
Published: over 3 years ago
10.3389/fcell.2021.707143
The Prognosis and Immune Checkpoint Blockade Efficacy Prediction of Tumor-Infiltrating Immune Cells in Lung CancerCited by: 11
Author(s): Xiangzheng Liu, Xueqian Shang, Jian Li, Shijie Zhang
Software Mentions: 11
Published: over 3 years ago
10.1016/j.cell.2016.08.041
A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer CompoundsCited by: 359
Author(s): Alejandra Bruna, Oscar M. Rueda, Wendy Greenwood, Ankita Batra, Maurizio Callari, R N Batra, Katherine Pogrebniak, José Luís Sandoval, John W. Cassidy, Ana Tufegdžić Vidaković, Stephen‐John Sammut, Linda Jones, Elena Provenzano, Richard D. Baird, Peter Eirew, James Hadfield, Matthew Eldridge, Anne McLaren-Douglas, Andrew Barthorpe, Howard Lightfoot, Mark J. O’Connor, Joe W. Gray, Javier Cortés, José Baselga, Elisabetta Marangoni, Alana L. Welm, Samuel Aparicio, Violeta Serra, Mathew J. Garnett, Carlos Caldas
Software Mentions: 11
Published: about 8 years ago
10.3389/fonc.2020.00691
Immunoscore Predicts Survival in Early-Stage Lung Adenocarcinoma PatientsCited by: 12
Author(s): Zihuan Zhao, Dan Zhao, Jianguo Xia, Yichuan Wang, Buhai Wang
Software Mentions: 11
Published: over 4 years ago
10.1074/mcp.TIR120.002155
ReactomeGSA - Efficient Multi-Omics Comparative Pathway AnalysisCited by: 129
Author(s): Johannes Griss, Guilherme Viteri, Konstantinos Sidiropoulos, Vy Kim Nguyen, Antonio Fabregat, Henning Hermjakob
Software Mentions: 11
Published: almost 4 years ago
10.3389/fgene.2021.692426
A Ferroptosis-Related Gene Signature Identified as a Novel Prognostic Biomarker for Colon CancerCited by: 15
Author(s): Xin Qi, Rui Wang, Yuxin Lin, Donghui Yan, Jiachen Zuo, Jiajia Chen, Bairong Shen
Software Mentions: 11
Published: over 3 years ago
10.1042/BSR20210527
Construction of a prognostic model for non-small-cell lung cancer based on ferroptosis-related genesCited by: 10
Author(s): Ke Han, Jukun Wang, Kun Qian, Teng Zhao, Xingsheng Liu, Yi Zhang
Software Mentions: 11
Published: over 3 years ago
10.3389/fonc.2021.672928
Glioma-Associated Stromal Cells Stimulate Glioma Malignancy by Regulating the Tumor Immune MicroenvironmentCited 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/fbioe.2020.00101
The Integrated Transcriptome Bioinformatics Analysis Identifies Key Genes and Cellular Components for Spinal Cord Injury-Related Neuropathic PainCited by: 8
Author(s): Runzhi Huang, Tong Meng, Rui Zhu, Lijuan Zhao, Dianwen Song, Huabin Yin, Zongqiang Huang, Liming Cheng, Jie Zhang
Software Mentions: 11
Published: over 4 years ago
10.3389/fgene.2019.01380
Germ Cell-Specific Gene 1-Like Protein Regulated by Splicing Factor CUGBP Elav-Like Family Member 5 and Primary Bile Acid Biosynthesis are Prognostic in Glioblastoma MultiformeCited by: 6
Author(s): Runzhi Huang, Zhenyu Li, Chen Li, Guanghua Wang, Penghui Yan, Li P, Jiaqi Wang, Xiaolong Zhu, Peng Hu, Junfang Zhang, Zhengyan Chang, Zongqiang Huang, Liming Cheng, Jie Zhang
Software Mentions: 11
Published: over 4 years ago
10.3390/ijms20225621
APOBEC3-Mediated RNA Editing in Breast Cancer is Associated with Heightened Immune Activity and Improved SurvivalCited by: 45
Author(s): Mariko Asaoka, Takashi Ishikawa, Kazuaki Takabe, Santosh K. Patnaik
Software Mentions: 11
Published: almost 5 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 AdenocarcinomaCited 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
10.3389/fonc.2021.704038
Fatty Acid Metabolism-Related lncRNAs Are Potential Biomarkers for Predicting the Overall Survival of Patients With Colorectal CancerCited by: 13
Author(s): Yue Peng, Chang Xu, Jun Wen, Yuanchuan Zhang, Meng Wang, Xiaoxiao Liu, Kang Zhao, Zheng Wang, Yanjun Liu, Tongtong Zhang
Software Mentions: 10
Published: about 3 years ago
10.1155/2021/1031906
Development of a Ferroptosis-Related lncRNA Signature to Predict the Prognosis and Immune Landscape of Bladder CancerCited by: 14
Author(s): Ranran Zhou, Jingjing Liang, Haijun Tian, Qi Chen, Cheng Yang, Cundong Liu
Software Mentions: 10
Published: over 3 years ago
10.1002/1878-0261.12747
Identification and validation of a combined hypoxia and immune index for triple‐negative breast cancerCited by: 57
Author(s): Shaoquan Zheng, Yutian Zou, Jie Liang, Weikai Xiao, Anli Yang, Tiebao Meng, Shilin Lu, Zhong-Bing Luo, Xiaoming Xie
Software Mentions: 10
Published: over 4 years ago
10.18632/aging.103517
Identifying CpG methylation signature as a promising biomarker for recurrence and immunotherapy in non–small-cell lung carcinomaCited by: 13
Author(s): Ruihan Luo, Song Jing, Xiao Xiao, Zhengbo Xie, Zhuochen Zhao, Wanfeng Zhang, Shiqi Miao, Yongyao Tang, Longke Ran
Software Mentions: 10
Published: over 4 years ago
10.3389/fcell.2021.722841
Classification of Estrogen Receptor-Positive Breast Cancer Based on Immunogenomic Profiling and Validation at Single-Cell ResolutionCited by: 0
Author(s): Xianxiong Ma, Hengyu Chen, Ming Yang, Zunxiang Ke, Mengyi Wang, Tao Huang, Lei Li
Software Mentions: 10
Published: about 3 years ago
10.3389/fcell.2021.676485
The Pyroptosis-Related Signature Predicts Prognosis and Indicates Immune Microenvironment Infiltration in Gastric CancerCited by: 116
Author(s): Wei Shao, Zongcheng Yang, Yue Fu, Lixin Zheng, Fen Liu, Li Chai, Jihui Jia
Software Mentions: 10
Published: over 3 years ago
10.3389/fgene.2021.584164
Four Novel Prognostic Genes Related to Prostate Cancer Identified Using Co-expression Structure Network AnalysisCited by: 14
Author(s): Tao Feng, Dechao Wei, Qiankun Li, Xiaobing Yang, Yili Han, Yunping Luo, Yongguang Jiang
Software Mentions: 10
Published: over 3 years ago
10.1155/2021/6365459
Identification of a Pyroptosis-Related Gene Signature for Prediction of Overall Survival in Lung AdenocarcinomaCited by: 14
Author(s): Donghai Zheng, Lv Bian, Minglang Wang, Luoqing Wang, Yilian Wang
Software Mentions: 10
Published: about 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 CarcinomaCited 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
10.1186/s40246-019-0226-2
Size matters: how sample size affects the reproducibility and specificity of gene set analysisCited by: 28
Author(s): Farhad Maleki, Katie Ovens, Ian McQuillan, Anthony Kusalik
Software Mentions: 10
Published: about 5 years ago
10.1016/j.cell.2019.10.007
Integrated Proteogenomic Characterization of Clear Cell Renal Cell CarcinomaCited by: 375
Author(s): David Clark, Saravana M. Dhanasekaran, Francesca Petralia, Jianbo Pan, Xiaoyu Song, Yingwei Hu, Felipe da Veiga Leprevost, Boris Reva, Tung-Shing Mamie Lih, Hui-Yin Chang, Wanli Ma, Chen Huang, Christopher J. Ricketts, Lijun Chen, Azra Krek, Yize Li, Dmitry Rykunov, Qing Kay Li, Lin S. Chen, Umut Özbek, Suhas Vasaikar, Yige Wu, Seungyeul Yoo, Shrabanti Chowdhury, Matthew A. Wyczalkowski, Jiayi Ji, Michael Schnaubelt, Andy T. Kong, Sunantha Sethuraman, Dmitry M. Avtonomov, Minghui Ao, Antonio Colaprico, Song Cao, Kyung-Cho Cho, Selim Kalayci, Shiyong Ma, Wenke Liu, Kelly V. Ruggles, Anna Calinawan, Zeynep H. Gümüş, Daniel Geiszler, Emily Kawaler, Guo Ci Teo, Bo Wen, Yuping Zhang, Sarah Keegan, Kai Li, Feng Chen, Nathan Edwards, Phillip M. Pierorazio, Xi Steven Chen, Christian P. Pavlovich, A. Ari Hakimi, Gabriel Bromiński, James J. Hsieh, Andrzej Antczak, Tatiana Omelchenko, Jan Lubiński, Maciej Wiznerowicz, W. Marston Linehan, Christopher R. Kinsinger, Mathangi Thiagarajan, Emily S. Boja, Mehdi Mesri, Tara Hiltke, Ana I. Robles, Henry Rodriguez, Jiang Qian, David Fenyö, Bing Zhang, Ding Li, Eric E. Schadt, Arul M. Chinnaiyan, Zhen Zhang, Gilbert S. Omenn, Marcin Cieślik, Daniel W. Chan, Alexey I. Nesvizhskii, Pei Wang, Hui Zhang, A. Samad Hashimi, Alexander Pico, Alla Karpova, Alyssa Charamut, Amanda G. Paulovich, Amy M. Perou, Anna Malovannaya, Annette Marrero-Oliveras, Anupriya Agarwal, Barbara Hindenach, Barbara L. Pruetz, Beom-Jun Kim, Brian J. Druker, Chelsea J. Newton, Chet Birger, Corbin D. Jones, Cristina E. Tognon, D. R. Mani, Dana R. Valley, Daniel C. Rohrer, Daniel Cui Zhou, Darlene Tansil, David Chesla, David I. Heiman, David A. Wheeler, Donghui Tan, Doug W. Chan, Emek Demir, Ewa Malc, Francesmary Modugno, Gaddy Getz, Galen Hostetter, George Wilson, Gerald W. Hart, Heng Zhu, Hongwei Liu, Houston Culpepper, Hua Sun, Hua Zhou, Jacob Day, James Suh, Jasmine Huang, Jason McDermott, Jeffrey R. Whiteaker, Jeffrey W. Tyner, Jennifer Eschbacher, Jin Chen, John P. McGee, Jun Zhu, Karen A. Ketchum, Karin D. Rodland, Karl R. Clauser, Karna Robinson, Karsten Krug, Katherine A. Hoadley, Ki Sung Um, Kim Elburn, Kimberly Holloway, Liang-Bo Wang, Lili M. Blumenberg, Linda Hannick, Liqun Qi, Lori J. Sokoll, MacIntosh Cornwell, Marc Loriaux, Marcin J. Domagalski, Marina Gritsenko, Matthew L. Anderson, Matthew E. Monroe, Matthew J. Ellis, Maureen A. Dyer, Meenakshi Anurag, Meghan C. Burke, Melissa Borucki, Michael A. Gillette, Michael J. Birrer, Michael R. Lewis, Michael Ittmann, Michael J. Smith, Michael Vernon, Michelle Chaikin, Milan G. Chheda, Munziba Khan, Nancy Roche, Nathan Edwards, Negin Vatanian, Nicole Tignor, Noam D. Beckmann, Pamela Grady, Patricia Castro, Paul Piehowski, Peter B. McGarvey, Piotr A. Mieczkowski, Pushpa Hariharan, Qingsong Gao, Rajiv Dhir, Ramani B. Kothadia, Ratna R. Thangudu, Rebecca Montgomery, Reyka G. Jayasinghe, Richard Smith, Robert A. Edwards, Robert Zelt, Ross M. Bremner, Ruiyang Liu, Runyu Hong, Sailaja Mareedu, Samuel H. Payne, Sandra Cottingham, Sanford P. Markey, Scott D. Jewell, Shalin Patel, Shankha Satpathy, Shannon Richey, Sherri R. Davies, Shuang Cai, Simina M. Boca, Snehal Patil, Sohini Sengupta, Sonya Carter, Stacey Gabriel, Stefani N. Thomas, Stephanie Young, Stephen E. Stein, Steven A. Carr, Steven M. Foltz, S. G. Hilsenbeck, Tanya Krubit, Tao Liu, Tara Skelly, Thomas F. Westbrook, Uma Borate, Uma Velvulou, Vladislav Petyuk, William Bocik, Xi Chen, Yan Shi, Yifat Geffen, Yihao Lu, Ying Wang, Yosef E. Maruvka, Zhi Li, Zhiao Shi, Zhidong Tu
Software Mentions: 10
Published: about 5 years ago
10.1111/jcmm.16619
Systematic profiling of invasion‐related gene signature predicts prognostic features of lung adenocarcinomaCited by: 17
Author(s): Ping Yu, L. Tong, Yujia Song, Hui Qü, Ying Chen
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 analysesCited 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
10.1155/2020/5858092
Profiles of Immune Infiltration and Prognostic Immunoscore in Lung AdenocarcinomaCited by: 9
Author(s): Yanyan Li, Liping Tao, Weiyang Cai
Software Mentions: 10
Published: over 4 years ago
10.18632/aging.102087
Identification of hub genes in prostate cancer using robust rank aggregation and weighted gene co-expression network analysisCited by: 71
Author(s): Zhenyu Song, Chongxi Fan, Zhiyuan Zhuo, Zhe Ma, Wenzhi Li, Gang Chen
Software Mentions: 10
Published: over 5 years ago
10.1111/jcmm.14918
An outcome model for human bladder cancer: A comprehensive study based on weighted gene co‐expression network analysisCited by: 24
Author(s): Yaoyi Xiong, Lushun Yuan, Jing Xiong, Huimin Xu, Yongwen Luo, Gang Wang, Lingao Ju, Yu Xiao, Xinghuan Wang
Software Mentions: 10
Published: almost 5 years ago
10.7554/eLife.62210
Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cellsCited by: 18
Author(s): Balyn W. Zaro, Joseph J. Noh, Victoria L. Mascetti, János Demeter, Benson M. George, Monika Żukowska, Gunsagar S. Gulati, Rahul Sinha, Ryan A. Flynn, Allison Banuelos, Allison Zhang, Adam C. Wilkinson, Peter K. Jackson, Irving L. Weissman
Software Mentions: 10
Published: almost 4 years ago
10.3389/fonc.2021.747300
High Throughput Transcriptome Data Analysis and Computational Verification Reveal Immunotherapy Biomarkers of Compound Kushen Injection for Treating Triple-Negative Breast CancerCited by: 2
Author(s): Xinkui Liu, Yang Wu, Yingying Zhang, Dechao Bu, Chao Wu, Shan Lu, Zhihong Huang, Yurong Song, Yi Zhao, Fengying Guo, Peizhi Ye, Changgeng Fu, Liangliang Shen, Jingyuan Zhang, Haojia Wang, Xianchun Duan, Jiarui Wu
Software Mentions: 10
Published: about 3 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 cancerCited 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
10.3389/fimmu.2021.622563
9-Gene Signature Correlated With CD8+ T Cell Infiltration Activated by IFN-γ: A Biomarker of Immune Checkpoint Therapy Response in MelanomaCited by: 17
Author(s): Kexin Yan, Yuxiu Lu, Zhangyong Yan, Yutao Wang
Software Mentions: 10
Published: over 3 years ago
10.3389/fbioe.2019.00270
Identification of Prognostic and Metastatic Alternative Splicing Signatures in Kidney Renal Clear Cell CarcinomaCited by: 46
Author(s): Tong Meng, Runzhi Huang, Zhiwei Zeng, Zongqiang Huang, Huabin Yin, Chenchen Jiao, Penghui Yan, Peng Hu, Xiaolong Zhu, Zhenyu Li, Dianwen Song, Jie Zhang, Liming Cheng
Software Mentions: 10
Published: about 5 years ago
10.3390/cancers13133371
Meta-Analysis of Microdissected Breast Tumors Reveals Genes Regulated in the Stroma but Hidden in Bulk AnalysisCited by: 7
Author(s): Aurora Savino, Niccolò De Marzo, Paolo Provero, Valeria Poli
Software Mentions: 10
Published: over 3 years ago
10.3390/cancers13020230
A Set of Cell Lines Derived from a Genetic Murine Glioblastoma Model Recapitulates Molecular and Morphological Characteristics of Human TumorsCited by: 10
Author(s): Bárbara Costa, Michael Fletcher, Pavle Boskovic, Ekaterina Ivanova, Tanja Eisemann, Sabrina Lohr, Lukas Bunse, Martin Löwer, Stefanie Burchard, Andrey Korshunov, Nadia Coltella, Melania Cusimano, Luigi Naldini, Hai-Kun Liu, Michael Platten, Bernhard Radlwimmer, Peter Angel, Heike Peterziel
Software Mentions: 10
Published: almost 4 years ago
10.3389/fonc.2021.709210
Single-Cell Transcriptomics Reveals the Complexity of the Tumor Microenvironment of Treatment-Naive OsteosarcomaCited 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
10.1002/1878-0261.12595
Aberrant expression of RSK1 characterizes high‐grade gliomas with immune infiltrationCited by: 14
Author(s): Glaucia Noeli Maroso Hajj, Fernanda F. da Silva, Bárbara de Bellis, Fernanda C. S. Lupinacci, Hermano Martins Bellato, Juvanier R. Cruz, Claudionor Nogueira Costa Segundo, Igor Vilela Faquini, Leuridan Cavalcante Torres, Paulo Sanematsu, María Dirlei Begnami, Vilma R. Martins, Martín Roffé
Software Mentions: 9
Published: almost 5 years ago