bioconductor: clusterProfiler | Projects

10.1038/s41438-021-00487-1

Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development
Cited by: 34
Author(s): Anzhen Fu, Qing Wang, Jianlou Mu, Lili Ma, Changlong Wen, Xiaoyan Zhao, Lipu Gao, Jian Li, Kai Shi, Yunxiang Wang, Xuechuan Zhang, Xuewen Zhang, Fengling Wang, Donald Grierson, Jinhua Zuo
Software Mentions: 5
Published: over 5 years ago

10.1038/s41438-021-00529-8

Chromatin accessibility and translational landscapes of tea plants under chilling stress
Cited by: 21
Author(s): Pengjie Wang, Shan Jin, Xuejin Chen, Lihua Wu, Yuanrun Zheng, Chuan Yue, Yan Guo, Xingtan Zhang, Jing Yang, Naixing Ye
Software Mentions: 5
Published: over 5 years ago

10.1186/s40168-020-00850-9

The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts
Cited by: 24
Author(s): Avihai Zolti, Stefan J. Green, Noa Sela, Yitzhak Hadar, Dror Minz
Software Mentions: 5
Published: about 6 years ago

10.1186/s13059-021-02417-9

Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells
Cited by: 10
Author(s): Haifeng Fu, Weiyu Zhang, Niannian Li, Jiao Yang, Xiaoying Ye, Chenglei Tian, Xinyi Lu, Lin Liu
Software Mentions: 5
Published: about 5 years ago

10.1186/s13068-018-1215-8

The primary transcriptome of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973
Cited by: 42
Author(s): Xiaoming Tan, Songjun Hou, Kuo Song, Jens Georg, Stephan Klähn, Xuefeng Lü, Wolfgang R. Hess
Software Mentions: 5
Published: about 8 years ago

10.1186/s41065-021-00181-1

Prognostic biomarkers and therapeutic targets in oral squamous cell carcinoma: a study based on cross-database analysis
Cited by: 10
Author(s): Wanli Yang, Wei Zhou, Xinhui Zhao, Xiaoqian Wang, Lili Duan, Yiding Li, Liaoran Niu, Junfeng Chen, Yujie Zhang, Yu Han, Daiming Fan, Liu Hong
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.62857

TAZ-CAMTA1 and YAP-TFE3 alter the TAZ/YAP transcriptome by recruiting the ATAC histone acetyltransferase complex
Cited by: 23
Author(s): Nicole Merritt, Keith Garcia, Dushyandi Rajendran, Zhen‐Yuan Lin, Xiaomeng Zhang, Katrina A. Mitchell, Nicholas Borcherding, Colleen Fullenkamp, Michael S. Chimenti, Anne‐Claude Gingras, Kieran F. Harvey, Munir R. Tanas
Software Mentions: 5
Published: over 5 years ago

10.17305/bjbms.2020.5096

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

10.1186/s12885-019-6249-1

Comprehensive transcriptomic analyses of tissue, serum, and serum exosomes from hepatocellular carcinoma patients
Cited by: 38
Author(s): Robin Mjelle, Simona Dima, Nicolae Bacalbaşa, Konika Chawla, Andrei Sorop, Dana Cucu, Vlad Herlea, Pål Sætrom, Irinel Popescu
Software Mentions: 5
Published: almost 7 years ago

10.3389/fimmu.2020.575488

Integrated Analysis of Transcriptome and Secretome From Umbilical Cord Mesenchymal Stromal Cells Reveal New Mechanisms for the Modulation of Inflammation and Immune Activation
Cited by: 18
Author(s): Mónica Cruz-Barrera, Nathalia Flórez-Zapata, Nicolás Lemus-Diaz, Carlos O. Medina, Cristian Camilo Galindo, Lorena-Xiomara González-Acero, Luz Correa, Bernardo Camacho, Jens Gruber, Gustavo Salguero
Software Mentions: 5
Published: almost 6 years ago

10.3389/fgene.2021.672674

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

10.1155/2020/3909416

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

10.1186/s12864-016-3228-7

RNA-seq based transcriptomic map reveals new insights into mouse salivary gland development and maturation
Cited by: 30
Author(s): Christian Gluck, Sang‐Won Min, Akinsola Oyelakin, Kirsten Smalley, Satrajit Sinha, Rose‐Anne Romano
Software Mentions: 5
Published: over 9 years ago

10.18632/aging.203121

Identification of microenvironment related potential biomarkers of biochemical recurrence at 3 years after prostatectomy in prostate adenocarcinoma
Cited by: 9
Author(s): Xiaoru Sun, Lu Wang, Hongkai Li, Chuandi Jin, Yuanyuan Yu, Lei Hou, Xinhui Liu, Yifan Yu, Ran Yan, Fuzhong Xue
Software Mentions: 5
Published: about 5 years ago

10.1155/2021/8895723

Identification and Construction of a Long Noncoding RNA Prognostic Risk Model for Stomach Adenocarcinoma Patients
Cited by: 14
Author(s): Zhiqiang Zha, Peiling Zhang, Dailing Li, Guolong Liu, Lin Lü
Software Mentions: 5
Published: over 5 years ago

10.1111/jcmm.16714

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

10.3389/fonc.2021.738477

Identification of a Ferroptosis-Related Signature Model Including mRNAs and lncRNAs for Predicting Prognosis and Immune Activity in Hepatocellular Carcinoma
Cited by: 38
Author(s): Zian Chen, Hui Tian, Di Yao, Yuan Zhang, Feng Zhang, Chen Yang
Software Mentions: 5
Published: almost 5 years ago

10.1002/cam4.3526

Construction of a disease‐specific lncRNA‐miRNA‐mRNA regulatory network reveals potential regulatory axes and prognostic biomarkers for hepatocellular carcinoma
Cited by: 12
Author(s): Qi Zhang, Lin Sun, Qiuju Zhang, Wei Zhang, Wei Tian, Meina Liu, Yupeng Wang
Software Mentions: 5
Published: over 5 years ago

10.1155/2020/6034670

Bioinformatics Analysis to Screen the Key Prognostic Genes in Tumor Microenvironment of Bladder Cancer
Cited by: 6
Author(s): Zhao Zhang, Dongshan Chen, Zeyan Li, Zhao Liu, Lei Yan, Zhonghua Xu
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0257343

Analysis of potential genetic biomarkers and molecular mechanism of smoking-related postmenopausal osteoporosis using weighted gene co-expression network analysis and machine learning
Cited by: 7
Author(s): Shaoshuo Li, Baixing Chen, Hao Chen, Zhen Hua, Yang Shao, Heng Yin, Jianwei Wang
Software Mentions: 5
Published: almost 5 years ago

10.7150/jca.50868

Data mining analysis of the prognostic impact of N<sup>6</sup>-methyladenosine regulators in patients with endometrial adenocarcinoma
Cited by: 7
Author(s): Junyu Zhai, Shang Li, Yu Liu, Yanzhi Du
Software Mentions: 5
Published: over 5 years ago

10.1186/s40170-020-00216-7

Fine-tuning the metabolic rewiring and adaptation of translational machinery during an epithelial-mesenchymal transition in breast cancer cells
Cited by: 3
Author(s): Tamara Fernández-Calero, Marcos Davyt, Karen Perelmuter, Cora Chalar, Giovana Bavia Bampi, Helena Persson, Juan Pablo Tosar, Völundur Hafstað, Hugo Naya, Carlos Rovira, Mariela Bollati-Fogolín, Ricardo Ehrlich, Gilles Flouriot, Zoya Ignatova, Mónica Marı́n
Software Mentions: 5
Published: about 6 years ago

10.3389/fimmu.2021.711980

Characterization of Organ-Specific Regulatory B Cells Using Single-Cell RNA Sequencing
Cited by: 7
Author(s): Si Yu Yang, Jie Long, Meng Huang, Pan Luo, Zhen Bian, Ya Xu, Chengbo Wang, Shu Yang, Li Liang, Carlo Selmi, M. Eric Gershwin, Zhi Bin Zhao, Zhe Xiong Lian
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12863-020-00852-4

Transcriptome analysis identifies genes and co-expression networks underlying heat tolerance in pigs
Cited by: 9
Author(s): Yuqing He, Christian Maltecca, Francesco Tiezzi, Emmanuel Lozada Soto, W. L. Flowers
Software Mentions: 5
Published: over 6 years ago

10.18632/aging.102399

DNA methylation profile is a quantitative measure of biological aging in children
Cited by: 23
Author(s): Xiaohui Wu, Weidan Chen, Fangqin Lin, Qingsheng Huang, Jiayong Zhong, Huan Gao, Yanyan Song, Huiying Liang
Software Mentions: 5
Published: over 6 years ago

10.3389/fncel.2020.00131

Loss of Arid1a Promotes Neuronal Survival Following Optic Nerve Injury
Cited by: 3
Author(s): Xue-Qi Peng, Shang-Kun Dai, Changping Li, Peipei Li, Zhimeng Wang, Heng Du, Zhao‐Qian Teng, Shuguang Yang, Chang‐Mei Liu
Software Mentions: 5
Published: about 6 years ago

10.1186/s12935-021-02117-1

Plastin-3 is a diagnostic and prognostic marker for pancreatic adenocarcinoma and distinguishes from diffuse large B-cell lymphoma
Cited by: 6
Author(s): Fei Xiong, Guanhua Wu, Bing Wang, Yongjun Chen
Software Mentions: 5
Published: about 5 years ago

10.1186/s12935-021-01826-x

Systematic identification of key functional modules and genes in esophageal cancer
Cited by: 4
Author(s): Rui Wu, Hao Zhuang, Yukun Mei, Jin‐Yu Sun, Tao Dong, Lili Zhao, Zhining Fan, Li Liu
Software Mentions: 5
Published: over 5 years ago

10.7150/jca.55719

MRPS17 promotes invasion and metastasis through PI3K/AKT signal pathway and could be potential prognostic marker for gastric cancer
Cited by: 5
Author(s): Wenjie Zhou, Jun Ouyang, Junqing Li, Fangjie Liu, Tailai An, Lv-Jia Cheng, Zi Chong Kuo, Changhua Zhang, Yulong He
Software Mentions: 5
Published: over 5 years ago

10.1186/s12866-020-01938-w

A comprehensive analysis of the microbiota composition and gene expression in colorectal cancer
Cited by: 15
Author(s): Qian Zhang, Huan Zhao, Dedong Wu, D Y Cao, Wei Ma
Software Mentions: 5
Published: almost 6 years ago

10.7150/thno.63416

Mapping the landscape of synthetic lethal interactions in liver cancer
Cited by: 7
Author(s): Chen Yang, Yuchen Guo, Ruolan Qian, Yi‐Wen Huang, Linmeng Zhang, Jun Wang, Xiaowen Huang, Zhicheng Liu, Wenxin Qin, Cun Wang, Huimin Chen, Xuhui Ma, Dayong Zhang
Software Mentions: 5
Published: over 5 years ago

10.1186/s12935-019-0866-2

LncRNA H19 regulates PI3K–Akt signal pathway by functioning as a ceRNA and predicts poor prognosis in colorectal cancer: integrative analysis of dysregulated ncRNA-associated ceRNA network
Cited by: 45
Author(s): Min-Er Zhong, Yanyu Chen, Guannan Zhang, Lai Xu, Wei Ge, Bin Wu
Software Mentions: 5
Published: about 7 years ago

10.1002/cam4.4206

Key sunitinib‐related biomarkers for renal cell carcinoma
Cited by: 9
Author(s): Yun Peng, Shiqiang Dong, Yuxuan Song, Dingkun Hou, Lili Wang, Bowen Li, Haitao Wang
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12935-021-02038-z

Identification of methylation-driven genes prognosis signature and immune microenvironment in uterus corpus endometrial cancer
Cited by: 10
Author(s): Jinhui Liu, Chengjian Ji, Yichun Wang, Cheng Zhang, Hongjun Zhu
Software Mentions: 5
Published: about 5 years ago

10.1186/s12935-021-01933-9

Low expression of CHRDL1 and SPARCL1 predicts poor prognosis of lung adenocarcinoma based on comprehensive analysis and immunohistochemical validation
Cited by: 13
Author(s): Huan Deng, Hang Qin, Deyan Shen, Yibi Zhang, Ming Chen
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0237006

RNAAgeCalc: A multi-tissue transcriptional age calculator
Cited by: 31
Author(s): Ruwei Xu, Pei Fen Kuan
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0237066

Lack of TLR4 modifies the miRNAs profile and attenuates inflammatory signaling pathways
Cited by: 12
Author(s): Juan R. Ureña‐Peralta, Raúl Pérez-Moraga, Francisco García‐García, Consuelo Guerri
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-021-96966-5

Molecular characterization and cell type composition deconvolution of fibrosis in NAFLD
Cited by: 26
Author(s): Lorena Pantano, George Agyapong, Yang Shen, Zhuo Zhu, Francesc Fernández-Albert, Werner Rust, Dagmar Knebel, Jon Hill, Carine M. Boustany-Kari, Julia F. Doerner, Jörg F. Rippmann, Raymond T. Chung, Shannan Ho Sui, Eric J. Simon, Kathleen E. Corey
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12859-019-2656-1

Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information
Cited by: 13
Author(s): Zaixiang Tang, Shu‐Feng Lei, Xinyan Zhang, Zixuan Yi, Boyi Guo, Jake Y. Chen, Yueping Shen, Nengjun Yi
Software Mentions: 4
Published: over 7 years ago

10.3389/fcell.2020.588368

A Novel Signature Constructed by RNA-Binding Protein Coding Genes to Improve Overall Survival Prediction of Glioma Patients
Cited by: 11
Author(s): Zewei Tu, Lei Shu, Jingying Li, Lei Wu, Chuming Tao, Minhua Ye, Xingen Zhu, Kai Huang
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers13051109

Bacterial, Archaea, and Viral Transcripts (BAVT) Expression in Gynecological Cancers and Correlation with Regulatory Regions of the Genome
Cited by: 6
Author(s): Jesús González Bosquet, Silvana Pedra-Nobre, Eric J. Devor, Kristina W. Thiel, Michael J. Goodheart, David Bender, Kimberly K. Leslie
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers12051325

Tumor Cell Associated Hyaluronan-CD44 Signaling Promotes Pro-Tumor Inflammation in Breast Cancer
Cited by: 18
Author(s): Patrice M Witschen, Thomas S. Chaffee, Nicholas J. Brady, Danielle N. Huggins, Todd P. Knutson, Rebecca S. LaRue, Sarah A. Munro, Lyubov Tiegs, James B. McCarthy, Andrew C. Nelson, Kathryn L. Schwertfeger
Software Mentions: 4
Published: about 6 years ago

10.1186/s12885-021-08536-7

SERPINE1 associated with remodeling of the tumor microenvironment in colon cancer progression: a novel therapeutic target
Cited by: 26
Author(s): Shaokun Wang, Li Pang, Zuolong Liu, Xiangchuan Meng
Software Mentions: 4
Published: about 5 years ago

10.3390/cancers13163954

Prognostication of Primary Tumor Location in Early-Stage Nodal Diffuse Large B-Cell Lymphoma: An Analysis of the SEER Database
Cited by: 2
Author(s): Yi Xia, Silan Huang, Yu Wang, Dexin Lei, Yanlou Wang, Hang Yang, Yan Gao, Panpan Li
Software Mentions: 4
Published: about 5 years ago

10.1155/2021/7331821

Identification of Neuropeptides as Potential Crosstalks Linking Down Syndrome and Periodontitis Revealed by Transcriptomic Analyses
Cited by: 6
Author(s): Yue Chen, Xiaofei Yu, Jia Kong
Software Mentions: 4
Published: almost 5 years ago

10.1016/j.csbj.2020.07.010

MU-PseUDeep: A deep learning method for prediction of pseudouridine sites
Cited by: 8
Author(s): Saad Khan, Fei He, Duolin Wang, Yongbing Chen, Dong Xu
Software Mentions: 4
Published: over 6 years ago

10.3390/cancers12123847

The YAP/TEAD Axis as a New Therapeutic Target in Osteosarcoma: Effect of Verteporfin and CA3 on Primary Tumor Growth
Cited by: 25
Author(s): Sarah Morice, Mathilde Mullard, Régis Brion, Maryne Dupuy, Sarah Renault, Robel Tesfaye, Bénédicte Brounais-Le Royer, Benjamin Ory, Françoise Rédini, Franck Verrecchia
Software Mentions: 4
Published: over 5 years ago

10.3389/fcell.2021.714718

Opposite Roles of Tumor Cell Proliferation and Immune Cell Infiltration in Postoperative Liver Metastasis of PDAC
Cited by: 0
Author(s): Guangfu Wang, Shangnan Dai, Hao Gao, Yong Gao, Lingdi Yin, Kai Zhang, Xumin Huang, Zipeng Lu, Yi Miao
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmed.2021.675842

Exosomal Circular RNA RNA-seq Profiling and the Carcinogenic Role of Exosomal circ-CYP24A1 in Cutaneous Squamous Cell Carcinoma
Cited by: 9
Author(s): Zheng Zhang, Hao Guo, Wen‐Jia Yang, Jiu‐Hong Li
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2018.00265

Identification of Potential Key Genes Associated With the Pathogenesis and Prognosis of Gastric Cancer Based on Integrated Bioinformatics Analysis
Cited by: 119
Author(s): Xinkui Liu, Jiarui Wu, Dan Zhang, Zhitong Bing, Jinhui Tian, Mengwei Ni, Xiaomeng Zhang, Ziqi Meng, Shuyu Liu
Software Mentions: 4
Published: about 8 years ago

10.1186/s12885-020-6513-4

Immunogenomic pathways associated with cytotoxic lymphocyte infiltration and survival in colorectal cancer
Cited by: 8
Author(s): Yuanyuan Shen, Yue Guan, Justin Hummel, Chi‐Ren Shyu, Jonathan B. Mitchem
Software Mentions: 4
Published: over 6 years ago

10.1002/cbf.3491

Identification and functional analysis of long non‐coding RNAs in the synovial membrane of osteoarthritis patients
Cited by: 7
Author(s): Xiaolong Shui, Qipeng Xie, Shaomin Chen, Chengwei Zhou, Jianzhong Kong, Yi Wang
Software Mentions: 4
Published: over 6 years ago

10.3389/fimmu.2021.670777

Decidual NR2F2-Expressing CD4+ T Cells Promote TH2 Transcriptional Program During Early Pregnancy
Cited by: 2
Author(s): Yan Lin, Di Zhang, Yangyang Li, Yunyun Li, Bin Li, Meirong Du
Software Mentions: 4
Published: about 5 years ago

10.3389/fcell.2020.558961

Identification of Prognostic Model and Biomarkers for Cancer Stem Cell Characteristics in Glioblastoma by Network Analysis of Multi-Omics Data and Stemness Indices
Cited by: 27
Author(s): Jianyang Du, Xiuwei Yan, Shan Mi, Yuan Li, Hang Ji, Kezuo Hou, Shuai Ma, Yixu Ba, Peng Zhou, Lei Chen, Rui Xie, Shaoshan Hu
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41388-019-1005-1

Identifying functions and prognostic biomarkers of network motifs marked by diverse chromatin states in human cell lines
Cited by: 12
Author(s): Li Wang, Hongying Zhao, Jing Li, Yingqi Xu, Yujia Lan, Wenkang Yin, Xiaoqin Liu, Lei Yu, Shan Lin, Michael Yifei Du, Xia Li, Yun Xiao, Yunpeng Zhang
Software Mentions: 4
Published: almost 7 years ago

10.3389/fonc.2019.01269

An Integrated Three-Long Non-coding RNA Signature Predicts Prognosis in Colorectal Cancer Patients
Cited by: 27
Author(s): Yuhang Liu, Bingxin Liu, Guoying Jin, Jia Zhang, Xue Wang, Yuyang Feng, Zehua Bian, Bojian Fei, Yuan Yin, Zhaohui Huang
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.101751

miRNA-mRNA crosstalk in myocardial ischemia induced by calcified aortic valve stenosis
Cited by: 12
Author(s): Chenyang Duan, Zhijun Cao, Fuqin Tang, Jian Zhao, Chunshui Liang, Hong Liu, Xiao Ye, Liangming Liu, Rong Ma
Software Mentions: 4
Published: over 7 years ago

10.3389/fonc.2020.590861

Clinical and Biological Significances of a Ferroptosis-Related Gene Signature in Glioma
Cited by: 89
Author(s): Shenghua Zhuo, Zhimin Chen, Yibei Yang, Jinben Zhang, Jianming Tang, Kun Yang
Software Mentions: 4
Published: over 5 years ago

10.1186/s12885-021-07930-5

The construction and validation of an RNA binding protein-related prognostic model for bladder cancer
Cited by: 17
Author(s): Fengxia Chen, Qingqing Wang, Youwen Zhou
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.56221

Ageing compromises mouse thymus function and remodels epithelial cell differentiation
Cited by: 83
Author(s): Jeanette Baran-Gale, Michael D. Morgan, Stefano Maio, Fatima Dhalla, Irene Calvo‐Asensio, Mary E. Deadman, Adam E. Handel, Ashley Maynard, Steven Chen, Foad Green, Rene Sit, Norma Neff, Spyros Darmanis, Weilun Tan, Andy P May, John C. Marioni, Chris P. Ponting, Georg A. Holländer
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41420-021-00462-8

NR5A2 transcriptional activation by BRD4 promotes pancreatic cancer progression by upregulating GDF15
Cited by: 10
Author(s): Feng Guo, Yingke Zhou, Hui Guo, Dianyun Ren, Xin Jin, Heshui Wu
Software Mentions: 4
Published: over 5 years ago

10.1038/s41421-020-0157-z

Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human
Cited by: 119
Author(s): Juanjuan Zhao, Shuye Zhang, Yang Liu, Xiaomeng He, Mengmeng Qu, Gang Xu, Hongbo Wang, Man Huang, Jing Pan, Zhenwen Liu, Zhiwei Li, Lei Liu, Zheng Zhang
Software Mentions: 4
Published: over 6 years ago

10.3389/fimmu.2020.590618

A TP53-Associated Immune Prognostic Signature for the Prediction of Overall Survival and Therapeutic Responses in Muscle-Invasive Bladder Cancer
Cited by: 32
Author(s): Xiangkun Wu, Daojun Lv, Chao Cai, Zhijian Zhao, Ming Wang, Wenzhe Chen, Yongda Liu
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.684052

Low Energy Electron Irradiation Is a Potent Alternative to Gamma Irradiation for the Inactivation of (CAR-)NK-92 Cells in ATMP Manufacturing
Cited by: 11
Author(s): Lia Walcher, Ann-Kathrin Kistenmacher, Charline Sommer, Sebastian Böhlen, Christina Ziemann, Susann Dehmel, Armin Braun, U. Sandy Tretbar, Stephan Klöß, Axel Schambach, Michael Morgan, Dennis Löffler, Christoph Kämpf, Conny Blumert, Kristin Reiche, Jana Beckmann, Ulla König, Bastian Standfest, Martin Thoma, Gustavo R. Makert, Sebastian Ulbert, Uta Kossatz-Böhlert, Ulrike Köhl, Anna Dünkel, Frank Stephan
Software Mentions: 4
Published: about 5 years ago

10.1038/s41421-020-00218-1

3D landscape of Hepatitis B virus interactions with human chromatins
Cited by: 20
Author(s): Bo Yang, Boyuan Li, Lingfei Jia, Yongpeng Jiang, Xin Wang, Shaodong Jiang, Shunda Du, Ji Xiong, Pengyuan Yang
Software Mentions: 4
Published: over 5 years ago

10.3389/fbioe.2020.00266

Characterization of lncRNA-Associated ceRNA Network to Reveal Potential Prognostic Biomarkers in Lung Adenocarcinoma
Cited by: 8
Author(s): Yang Wang, Ruyi He, Lixin Ma
Software Mentions: 4
Published: over 6 years ago

10.3389/fbioe.2020.00206

Predicting the Risk of Melanoma Metastasis Using an Immune Risk Score in the Melanoma Cohort
Cited by: 4
Author(s): Yang Sheng, Cheng Yan-ping, Tong Liu, Ning Liu, Yufeng Liu, Geyu Liang
Software Mentions: 4
Published: over 6 years ago

10.3389/fimmu.2021.679458

Comparative Proteomic Analysis Reveals Varying Impact on Immune Responses in Phorbol 12-Myristate-13-Acetate-Mediated THP-1 Monocyte-to-Macrophage Differentiation
Cited by: 21
Author(s): Sneha M. Pinto, Hera Kim, Yashwanth Subbannayya, Miriam S. Giambelluca, Korbinian Bösl, Liv Ryan, Animesh Sharma, Richard K. Kandasamy
Software Mentions: 4
Published: about 5 years ago

10.3389/fimmu.2020.594540

The Monocytes That Repopulate in Mice After Cyclophosphamide Treatment Acquire a Neutrophil Precursor Gene Signature and Immunosuppressive Activity
Cited by: 5
Author(s): Zhi Chun Ding, Nada S. Aboelella, Locke J. Bryan, Huidong Shi, Gang Zhou
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.630988

Transcriptomic Profiling of Fibropapillomatosis in Green Sea Turtles (Chelonia mydas) From South Texas
Cited by: 9
Author(s): Nicholas B. Blackburn, Ana C Leandro, Nina Nahvi, Mariana A. Devlin, Marcelo Leandro, Ignacio Martinez Escobedo, Juan M. Peralta, Jeff George, Brian A. Stacy, Thomas W. deMaar, John Blangero, Megan Keniry, Joanne E. Curran
Software Mentions: 4
Published: over 5 years ago

10.3389/fmolb.2021.692130

RNA m1A Methyltransferase TRMT6 Predicts Poorer Prognosis and Promotes Malignant Behavior in Glioma
Cited by: 22
Author(s): Beibei Wang, Lihua Niu, Zhengyang Wang, Zhihua Zhao
Software Mentions: 4
Published: almost 5 years ago

10.1111/cpr.13096

Base editing‐mediated perturbation of endogenous PKM1/2 splicing facilitates isoform‐specific functional analysis in vitro and in vivo
Cited by: 6
Author(s): Jianxiang Lin, Susu Wu, Qingmei Shen, Jie Liu, Shisheng Huang, Guangdun Peng, Yong Qiao
Software Mentions: 4
Published: about 5 years ago

10.1111/cpr.12885

NUP98‐HOXA10hd fusion protein sustains multi‐lineage haematopoiesis of lineage‐committed progenitors in transplant setting
Cited by: 2
Author(s): Yong Dong, Kaitao Wang, Qitong Weng, Tongjie Wang, Pingwei Zhou, Xiaofei Liu, Geng Yang, Lijuan Liu, Hongling Wu, Jinyong Wang, Juan Du
Software Mentions: 4
Published: about 6 years ago

10.3389/fimmu.2021.638066

Cross-Tissue Transcriptomic Analysis Leveraging Machine Learning Approaches Identifies New Biomarkers for Rheumatoid Arthritis
Cited by: 13
Author(s): Dmitry Rychkov, Jessica Neely, Tomiko Oskotsky, Steven Yu, Noah Perlmutter, Joanne Nititham, Alexander Carvidi, Melissa A. Krueger, Andrew J. Gross, Lindsey A. Criswell, Judith F. Ashouri, Marina Sirota
Software Mentions: 4
Published: about 5 years ago

10.18632/aging.202943

Identification of key pathways and genes in carotid atherosclerosis through bioinformatics analysis of RNA-seq data
Cited by: 2
Author(s): Zhongchen Li, Jiheng Hao, Kun Chen, Qunlong Jiang, Peijian Wang, Xiaohui Xing, Jiyue Wang, Yinjiang Zhang, Yi Xiao, Liyong Zhang
Software Mentions: 4
Published: about 5 years ago

10.3389/fmolb.2021.696072

Decreased Expression of PACSIN1 in Brain Glioma Samples Predicts Poor Prognosis
Cited by: 6
Author(s): Zimu Zhou, Zhiyuan Jia, Xi-an Fu, Rui Ma, Ren Yuting, Yuan Wang, Tao Wen, Ming Ma, Yinlong Liu, Enfang Shan
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2021.641756

Chemotranscriptomic Profiling Defines Drug-Specific Signatures of the Glycopeptide Antibiotics Dalbavancin, Vancomycin and Chlorobiphenyl-Vancomycin in a VanB-Type-Resistant Streptomycete
Cited by: 0
Author(s): Andrew Hesketh, Giselda Bucca, Colin P. Smith, Hee‐Jeon Hong
Software Mentions: 4
Published: over 5 years ago

10.7150/jca.41983

Predictive value of hypoxia, metabolism and immune factors for prognosis in hepatocellular carcinoma: a retrospective analysis and multicenter validation study
Cited by: 4
Author(s): Peng Lin, Dong‐Yue Wen, Gang Chen, Yi‐Wu Dang, Yun He, Hong Yang
Software Mentions: 4
Published: over 6 years ago

10.1038/s41422-020-00458-6

Mutual dependency between lncRNA LETN and protein NPM1 in controlling the nucleolar structure and functions sustaining cell proliferation
Cited by: 25
Author(s): Xianteng Wang, Xiaolin Hu, Wanlu Song, Hui Xu, Zhao Xiao, Rongxia Huang, Qing-Ran Bai, Fan Zhang, Yongzhen Chen, Yu Liu, Jau–Shiung Fang, Xin Li, Qin Shen, Haitao Zhao, Xuerui Yang
Software Mentions: 4
Published: over 5 years ago

10.7150/jca.44436

DNA methylation profiling to predict overall survival risk in gastric cancer: development and validation of a nomogram to optimize clinical management
Cited by: 7
Author(s): Xianxiong Ma, Hengyu Chen, Guobin Wang, Lei Li, Kaixiong Tao
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.101847

Integrated DNA methylation and gene expression analysis in the pathogenesis of coronary artery disease
Cited by: 30
Author(s): Miao Liu, Rong Yin, Qinghui Zhang, Xi‐Jiang Hu, Feng Huang, Wu-Xian Chen, Xiaoli Cao, Jin‐Zhen Wu
Software Mentions: 4
Published: over 7 years ago

10.1042/BSR20211280

Identification of hub genes in colorectal cancer based on weighted gene co-expression network analysis and clinical data from The Cancer Genome Atlas
Cited by: 23
Author(s): Yu Zhang, Jia Luo, Zhe Liu, Xudong Li, Ying Ma, Bohang Zhang, Yuxuan Chen, Xiaofeng Li, Zhi-Guo Feng, Ningning Yang, Dayun Feng, Lei Wang, Xiu–Peng Song
Software Mentions: 4
Published: about 5 years ago

10.1042/BSR20194337

Mining TCGA database for tumor mutation burden and their clinical significance in bladder cancer
Cited by: 71
Author(s): Jia Lv, Yongze Zhu, Alin Ji, Qi Zhang, Guodong Liao
Software Mentions: 4
Published: over 6 years ago

10.1172/jci.insight.145029

Nrf2 overexpression rescues the RPE in mouse models of retinitis pigmentosa
Cited by: 30
Author(s): David M. Wu, Xuke Ji, Maryna V. Ivanchenko, M. S. Chung, Mary E. Piper, Parimal Rana, Sean K. Wang, Y. Y. Xue, Emma R. West, Sophia R. Zhao, Hongbin Xu, Marcelo Cicconet, Wenjun Xiong, Constance L. Cepko
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.203178

Identification of differentially expressed genes-related prognostic risk model for survival prediction in breast carcinoma patients
Cited by: 1
Author(s): Jinyu Li, Gena Huang, Caixia Ren, Ning Wang, Silei Sui, Zuowei Zhao, Man Li
Software Mentions: 4
Published: about 5 years ago

10.1042/BSR20203459

CXCL10 is a potential biomarker and associated with immune infiltration in human papillary thyroid cancer
Cited by: 10
Author(s): Xiaojing Qin, Lin Xu, Guoqiang Xue, Huiying Fan, Haoyu Wang, Jing Wu, Da Pei
Software Mentions: 4
Published: over 5 years ago

10.1002/2211-5463.12983

Identification of modules and novel prognostic biomarkers in liver cancer through integrated bioinformatics analysis
Cited by: 5
Author(s): Bo Shen, Kun Li, Yuting Zhang
Software Mentions: 4
Published: almost 6 years ago

10.18632/aging.102782

A nomogram combining long non-coding RNA expression profiles and clinical factors predicts survival in patients with bladder cancer
Cited by: 30
Author(s): Yifan Wang, Du Li, Xuemei Yang, Juan Li, Peilong Li, Yinghui Zhao, Weili Duan, Yingjie Chen, Yunshan Wang, Hongzhi Mao, Chuanxin Wang
Software Mentions: 4
Published: over 6 years ago

10.7150/jca.49262

Pathologic evolution-related Gene Analysis based on both single-cell and bulk transcriptomics in Colorectal Cancer
Cited by: 3
Author(s): Jiali Li, Zhao-Yi Zeng, Jiarui Chen, Xingyu Liu, Xueping Jiang, Wenjie Sun, Yuan Luo, Jiangbo Ren, Yan Gong, Conghua Xie
Software Mentions: 4
Published: over 6 years ago

10.1042/BSR20201491

Exploration of immune-related genes in high and low tumor mutation burden groups of chromophobe renal cell carcinoma
Cited by: 9
Author(s): Lei Li, Xi Chen, Lu Hao, Qiuyan Chen, Haosheng Liu, Qing Zhou
Software Mentions: 4
Published: about 6 years ago

10.1155/2021/8834578

Identification of Potential Gene and MicroRNA Biomarkers of Acute Kidney Injury
Cited by: 3
Author(s): Siyang Wang, Jie Gao, Yiwei Song, Guangyan Cai, Xiangmei Chen
Software Mentions: 4
Published: over 5 years ago

10.1155/2020/8962090

Identification of Differentially Expressed lncRNAs and mRNAs in Children with Acquired Aplastic Anemia by RNA Sequencing
Cited by: 1
Author(s): Shaoying Lu, Xiaoxiao Song, Jing Chen, Xuguang Qiao
Software Mentions: 4
Published: about 6 years ago

10.1155/2021/9933136

Identification of Biomarkers for Predicting Allograft Rejection following Kidney Transplantation Based on the Weighted Gene Coexpression Network Analysis
Cited by: 2
Author(s): Lijun Wang, Xiao-Bo Ma, Hongying Xia, Xun Sun, Yu Lu, Qian Yang, Zongqiang Hu, Yi‐Fang Zhao, Wei Hu, Jianghua Ran
Software Mentions: 4
Published: about 5 years ago

10.18632/aging.102228

Prognostic value of a hypoxia-related microRNA signature in patients with colorectal cancer
Cited by: 31
Author(s): Yongmei Yang, Ailin Qu, Qi Wu, Xin Zhang, Lili Wang, Chen Li, Zhaogang Dong, Du Li, Chuanxin Wang
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.202901

High expression of COMMD7 is an adverse prognostic factor in acute myeloid leukemia
Cited by: 12
Author(s): Kongfei Li, Lieguang Chen, Hua Zhang, Lu Wang, Keya Sha, Xiaohong Du, Daiyang Li, Zhong-Zheng Zheng, Renzhi Pei, Ying Lu, Hongyan Tong
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2018.03137

The Schistosomiasis SpleenOME: Unveiling the Proteomic Landscape of Splenomegaly Using Label-Free Mass Spectrometry
Cited by: 6
Author(s): Miguel Cosenza-Contreras, Renata Alves de Oliveira e Castro, Bruno Mattei, Jonatan Marques Campos, Gustavo Gonçalves Silva, Nívia Carolina Nogueira de Paiva, Rodrigo Dian de Oliveira Aguiar-Soares, Cláudia Martins Carneiro, Luís Afonso, William Castro-Borges
Software Mentions: 4
Published: over 7 years ago

10.7150/jca.48664

MMP9 and IGFBP1 Regulate Tumor Immune and Drive Tumor Progression in Clear Cell Renal Cell Carcinoma
Cited by: 13
Author(s): Tianbo Xu, Su Gao, Jingchong Liu, Yu Huang, Ke Chen, Xiaoping Zhang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41416-020-0799-5

A novel stratification framework for predicting outcome in patients with prostate cancer
Cited by: 8
Author(s): Bogdan A. Luca, Vincent Moulton, Christopher Ellis, Dylan R. Edwards, Colin Campbell, Rosalin Cooper, Jeremy Clark, Daniel Brewer, Christopher S. Cooper
Software Mentions: 4
Published: over 6 years ago

10.1016/j.bbih.2021.100265

Transcriptional profiling of macaque microglia reveals an evolutionary preserved gene expression program
Cited by: 4
Author(s): Marissa Dubbelaar, Chairi Misrielal, Jeffrey J. Bajramović, Saskia M. Burm, Ella A. Zuiderwijk‐Sick, Nieske Brouwer, Corien Grit, Susanne M. Kooistra, Sueli Mieko Oba-Shinjo, Suely Kazue Nagahashi Marie, Hendrikus Boddeke, Bart J. L. Eggen
Software Mentions: 4
Published: about 5 years ago

10.1186/s41065-019-0100-1

A co-expression network for differentially expressed genes in bladder cancer and a risk score model for predicting survival
Cited by: 16
Author(s): Zihao Chen, Guojun Liu, Aslam Hossain, И. Г. Данилова, Mikhail A. Bolkov, Guoqing Liu, Irina A. Tuzankina, Wanlong Tan
Software Mentions: 4
Published: about 7 years ago

Projects: bioconductor: clusterProfiler

Science Score: 75/100

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Papers Mentioning clusterProfiler 2,223