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: bioconductor: DOSE

https://packages.ecosyste.ms/registries/bioconductor.org/packages/DOSE

Disease Ontology Semantic and Enrichment analysis
2 versions
Latest release: about 1 year ago
25 dependent packages
1,049,684 downloads total

Papers Mentioning DOSE 138

10.3389/fmolb.2020.570702
Prognostic Prediction Using a Stemness Index-Related Signature in a Cohort of Gastric Cancer
Cited by: 27
Author(s): Xiaowei Chen, Dawei Zhang, Fei Jiang, Yan Shen, Xin Li, Xin Hu, Pingmin Wei, Xiaobing Shen
Software Mentions: 24
Published: about 4 years ago
10.3390/ijms22031075
A Novel Epigenetic Machine Learning Model to Define Risk of Progression for Hepatocellular Carcinoma Patients
Cited by: 7
Author(s): Luca Bedon, Michele Dal Bo, Monica Mossenta, Davide Busato, Giuseppe Toffoli, Maurizio Polano
Software Mentions: 13
Published: almost 4 years ago
10.1155/2021/5575286
Screening and Bioinformatics Analysis of Competitive Endogenous RNA Regulatory Network ––Related to Circular RNA in Breast Cancer
Cited by: 3
Author(s): Tao Wang, Yi Zhang, Yan He, Yang Liu, Qi Peng
Software Mentions: 12
Published: about 3 years ago
10.3390/cancers13081788
Analysis of Intra-Tumoral Macrophages and T Cells in Non-Small Cell Lung Cancer (NSCLC) Indicates a Role for Immune Checkpoint and CD200-CD200R Interactions
Cited by: 7
Author(s): Anders Tøndell, Yashwanth Subbannayya, Sissel Gyrid Freim Wahl, Arnar Flatberg, Sveinung Sørhaug, Magne Børset, Markus Haug
Software Mentions: 12
Published: over 3 years ago
10.1186/s12957-021-02175-9
A prognostic model for hepatocellular carcinoma based on apoptosis-related genes
Cited by: 15
Author(s): Renjie Liu, Guifu Wang, Chi Zhang, Dou‐Sheng Bai
Software Mentions: 12
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
10.3389/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
10.1080/21655979.2020.1822715
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
10.3389/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
10.1186/s12974-018-1113-9
Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness
Cited by: 45
Author(s): David G. Ashbrook, Benjamin Hing, Lindsay T. Michalovicz, Kimberly A. Kelly, Julie V. Miller, Wilfred C. de Vega, Diane B. Miller, Gordon Broderick, James P. O’Callaghan, Patrick O. McGowan
Software Mentions: 9
Published: over 6 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/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
10.7150/ijms.50704
Integral Analysis of the RNA Binding Protein-associated Prognostic Model for Renal Cell Carcinoma
Cited by: 11
Author(s): Qin Xin, Zhengfang Liu, Yan Kou, Zhiqing Fang, Yi‐Ming Fan
Software Mentions: 9
Published: almost 4 years ago
10.3389/fphar.2021.621359
Compound Dihuang Granule Inhibits Nigrostriatal Pathway Apoptosis in Parkinson’s Disease by Suppressing the JNK/AP-1 Pathway
Cited by: 8
Author(s): Li Wang, Yufang Yang, Long Chen, Zhu-qing He, Dian-yong Bi, Lei Zhang, Yuanfu Xu, Jiancheng He
Software Mentions: 9
Published: over 3 years ago
10.3390/cancers13102498
Comparative Transcriptomics of Immune Checkpoint Inhibitor Myocarditis Identifies Guanylate Binding Protein 5 and 6 Dysregulation
Cited by: 16
Author(s): Daniel Finke, Markus Heckmann, Janek Salatzki, Johannes Riffel, Esther Herpel, Lucie Heinzerling, Benjamin Meder, Mirko Völkers, Oliver Müller, Norbert Frey, Hugo A. Katus, Florian Leuschner, Ziya Kaya, Lorenz Lehmann
Software Mentions: 9
Published: over 3 years ago
10.3389/fcvm.2020.586871
Predicting Diagnostic Gene Biomarkers Associated With Immune Infiltration in Patients With Acute Myocardial Infarction
Cited by: 64
Author(s): Enfa Zhao, Hang Xie, Yushun Zhang
Software Mentions: 8
Published: about 4 years ago
10.1155/2020/2507074
A Network Pharmacology-Based Identification Study on the Mechanism of Xiao-Xu-Ming Decoction for Cerebral Ischemic Stroke
Cited by: 8
Author(s): Dehui Li, Yifan Su, Cheng-Yi Sun, Huanfang Fan, Weijuan Gao
Software Mentions: 8
Published: about 4 years ago
10.1007/s00018-018-2898-5
Celiac disease biomarkers identified by transcriptome analysis of small intestinal biopsies
Cited by: 32
Author(s): Hanna Bragde, Ulf Jansson, Mats Fredrikson, Ewa Grodzinsky, Jan Söderman
Software Mentions: 8
Published: over 6 years ago
10.1371/journal.pone.0249691
Profiling DNA break sites and transcriptional changes in response to contextual fear learning
Cited by: 25
Author(s): Ryan Stott, Oleg Kritsky, Li‐Huei Tsai
Software Mentions: 8
Published: over 3 years ago
10.1371/journal.pone.0107957
Simulation Studies as Designed Experiments: The Comparison of Penalized Regression Models in the “Large p, Small n” Setting
Cited by: 13
Author(s): Elias Chaibub Neto, J. Christopher Bare, Adam A. Margolin
Software Mentions: 8
Published: about 10 years ago
10.3389/fmolb.2021.711239
Identification of Hub Genes and Pathways Associated With Idiopathic Pulmonary Fibrosis via Bioinformatics Analysis
Cited by: 15
Author(s): Hanxi Wan, Xinwei Huang, Peilin Cong, Mengfan He, Aiwen Chen, Tingmei Wu, Danqing Dai, Wanrong Li, Xiao-Fei Gao, Tian Li, Huazheng Liang, Lize Xiong
Software Mentions: 8
Published: over 3 years ago
10.1186/s41065-021-00201-0
Identification and validation of hub genes of synovial tissue for patients with osteoarthritis and rheumatoid arthritis
Cited by: 10
Author(s): Yanzhi Ge, Zuxiang Chen, Yanbin Fu, Xue Xiao, Haipeng Xu, Peijian Tong, Li Zhou
Software Mentions: 8
Published: about 3 years ago
10.1038/s41419-021-03552-8
Transcriptional profiling reveals the transcription factor networks regulating the survival of striatal neurons
Cited by: 12
Author(s): Lin Yang, 智慧 蘇, Zi-Wu Wang, Zhenmeiyu Li, Zicong Shang, Heng Du, Shuai Liu, Dashi Qi, Zhengang Yang, Zhejun Xu, Zhuangzhi Zhang
Software Mentions: 8
Published: over 3 years ago
10.1186/s12920-019-0562-z
Clustering analysis of microRNA and mRNA expression data from TCGA using maximum edge-weighted matching algorithms
Cited by: 9
Author(s): Lizhong Ding, Zheyun Feng, Yongsheng Bai
Software Mentions: 8
Published: over 5 years ago
10.1371/journal.pone.0207359
Chronic lifestyle diseases display seasonal sensitive comorbid trend in human population evidence from Google Trends
Cited by: 14
Author(s): Jai Chand Patel, Pankaj Khurana, Y. K. Sharma, Bhuvnesh Kumar, R. Sugadev
Software Mentions: 8
Published: almost 6 years ago
10.3389/fphar.2020.00076
Efficacy of Chinese Herbal Formula Sini Zuojin Decoction in Treating Gastroesophageal Reflux Disease: Clinical Evidence and Potential Mechanisms
Cited by: 10
Author(s): Shaowei Li, Mengfen Huang, Guojing Wu, Wei-Han Huang, Zhanhui Huang, Xiaoqian Yang, Jinming Ou, Qipeng Wei, Chengli Liu, YU Shaoyuan
Software Mentions: 7
Published: over 4 years ago
10.3389/fnmol.2018.00225
NFIX Circular RNA Promotes Glioma Progression by Regulating miR-34a-5p via Notch Signaling Pathway
Cited by: 86
Author(s): Haidong Xu, Yu Zhang, Qi Ling, Lijuan Ding, Hong Jiang, Haojun Yu
Software Mentions: 7
Published: over 6 years ago
10.1186/s12967-019-1909-0
ALS blood expression profiling identifies new biomarkers, patient subgroups, and evidence for neutrophilia and hypoxia
Cited by: 38
Author(s): William R. Swindell, Colin Kruse, Edward O. List, Darlene E. Berryman, John J. Kopchick
Software Mentions: 7
Published: over 5 years ago
10.18632/aging.202982
Prognostic value of members of NFAT family for pan-cancer and a prediction model based on NFAT2 in bladder cancer
Cited by: 4
Author(s): Zhou-Tong Dai, Xiang Yuan, Yundan Wang, Lidao Bao, Jun Wang, Jiapeng Li, Huimin Zhang, Zhongxin Lu, Sreenivasan Ponnambalam, Xing–Hua Liao
Software Mentions: 7
Published: over 3 years ago
10.1186/s12872-021-02092-5
The GEnetic Syntax Score: a genetic risk assessment implementation tool grading the complexity of coronary artery disease—rationale and design of the GESS study
Cited by: 11
Author(s): Ioannis S. Vizirianakis, Fani Chatzopoulou, Αndreas S. Papazoglou, Efstratios Karagiannidis, Georgios Sofdis, Nikolaos Stalikas, Christos Stefopoulos, Konstantinos Kyritsis, Nikolaos Mittas, Nikoleta F. Theodoroula, Aggeliki Lampri, Eleni Mezarli, Αναστάσιος Κάρτας, Dimitrios Chatzidimitriou, Anna Papa-Konidari, Eleftherios Angelis, Ηaralambos Karvounis, Georgios Sianos
Software Mentions: 7
Published: over 3 years ago
10.1186/1756-0500-5-360
LXtoo: an integrated live Linux distribution for the bioinformatics community
Cited by: 5
Author(s): Guangchuang Yu, Li-Gen Wang, Xiaohong Meng, Qing-Yu He
Software Mentions: 7
Published: over 12 years ago
10.1002/cam4.3434
The clinical value and potential molecular mechanism of the downregulation of MAOA in hepatocellular carcinoma tissues
Cited by: 20
Author(s): Yu‐Yan Pang, Jian‐Di Li, Gao Li, Xia Yang, Yi‐Wu Dang, Zhiyong Lai, Li‐Min Liu, Jie Yang, Huayu Wu, Rong‐Quan He, Zhi‐Guang Huang, Dandan Xiong, Lihua Yang, Lin Shi, Wei‐Jia Mo, Deng Tang, Huiping Lu, Gang Chen
Software Mentions: 7
Published: about 4 years ago
10.1038/s41598-021-88694-7
Tumor mutation burden (TMB)-associated signature constructed to predict survival of lung squamous cell carcinoma patients
Cited by: 13
Author(s): Yan Duan, Yi Chen
Software Mentions: 7
Published: over 3 years ago
10.1002/1878-0261.12923
Epigenetic and transcriptional analysis reveals a core transcriptional program conserved in clonal prostate cancer metastases
Cited by: 8
Author(s): Tesa Severson, Yanyun Zhu, Angelo M. De Marzo, Tracy Jones, Jonathan W. Simons, William G. Nelson, Srinivasan Yegnasubramanian, Matthew L. Freedman, Lodewyk F.A. Wessels, Andries M. Bergman, Michael C. Haffner, Wilbert Zwart
Software Mentions: 7
Published: over 3 years ago
10.1093/database/baz151
LeukmiR: a database for miRNAs and their targets in acute lymphoblastic leukemia
Cited by: 13
Author(s): Abdul Rawoof, Guruprasadh Swaminathan, Shrish Tiwari, Rekha A. Nair, Lekha Dinesh Kumar
Software Mentions: 7
Published: almost 5 years ago
10.1155/2021/8897313
Systematic Investigation of the Effect of Powerful Tianma Eucommia Capsule on Ischemic Stroke Using Network Pharmacology
Cited by: 4
Author(s): Pengcheng Feng, Guixia Li, Yuandong Huang, Jinhong Pei
Software Mentions: 7
Published: over 3 years ago
10.7150/thno.56141
Distinct placental molecular processes associated with early-onset and late-onset preeclampsia
Cited by: 31
Author(s): Zhonglu Ren, Yunfei Gao, Yue Gao, Guanmei Liang, Qian Chen, Sijia Jiang, Xiaoxue Yang, Cui-Xia Fan, Haizhen Wang, Jing Wang, Yi‐Wu Shi, Chaoqun Xiao, Ming Zhong, Xinping Yang
Software Mentions: 6
Published: almost 4 years ago
10.3389/fgene.2020.00099
A FITM1-Related Methylation Signature Predicts the Prognosis of Patients With Non-Viral Hepatocellular Carcinoma
Cited by: 4
Author(s): J Chen, X Wang, Wei Li, Chao Shang, T Chen, Y Chen
Software Mentions: 6
Published: over 4 years ago
10.3389/fgene.2021.654517
Identification of Key Genes Associated With the Process of Hepatitis B Inflammation and Cancer Transformation by Integrated Bioinformatics Analysis
Cited by: 7
Author(s): Jingyuan Zhang, Xinkui Liu, Wei Zhou, Shan Lu, Chao Wu, Zhishan Wu, Runping Liu, Xiaojiaoyang Li, Jiarui Wu, Yingying Liu, Siyu Guo, Shanshan Jia, Xiaomeng Zhang, Miaomiao Wang
Software Mentions: 6
Published: about 3 years ago
10.1098/rsos.191480
Mid and hindgut transcriptome profiling analysis of Atlantic salmon ( Salmon salar ) under unpredictable chronic stress
Cited by: 2
Author(s): Signe Dille Løvmo, Angelico Madaro, Paul Whatmore, Tora Bardal, Mari‐Ann Östensen, Simen Rød Sandve, Rolf Erik Olsen
Software Mentions: 6
Published: almost 5 years ago
10.1038/s41598-020-57716-1
Ontology-driven integrative analysis of omics data through Onassis
Cited by: 9
Author(s): Eugenia Galeota, Kamal Kishore, Mattia Pelizzola
Software Mentions: 6
Published: almost 5 years ago
10.1186/s13059-015-0815-x
The estrous cycle surpasses sex differences in regulating the transcriptome in the rat medial prefrontal cortex and reveals an underlying role of early growth response 1
Cited by: 48
Author(s): Florian Duclot, Mohamed Kabbaj
Software Mentions: 6
Published: almost 9 years ago
10.3389/fvets.2019.00214
Transcriptomic Profiling of Duodenal Epithelium Reveals Temporally Dynamic Impacts of Direct Duodenal Starch-Infusion During Dry Period of Dairy Cattle
Cited by: 2
Author(s): Congjun Li, Shudai Lin, María Jose Ranilla-García, VI Ransom L. Baldwin
Software Mentions: 6
Published: over 5 years ago
10.1128/mSystems.00163-21
Oral Epithelial Cells Distinguish between <i>Candida</i> Species with High or Low Pathogenic Potential through MicroRNA Regulation
Cited by: 5
Author(s): Márton Horváth, Gábor Nagy, Nóra Zsindely, László Bodai, Péter Horváth, Csaba Vágvölgyi, Joshua D. Nosanchuk, Renáta Tóth, Attila Gácser
Software Mentions: 6
Published: over 3 years ago
10.3389/fimmu.2021.676173
Interleukin-17A Causes Osteoarthritis-Like Transcriptional Changes in Human Osteoarthritis-Derived Chondrocytes and Synovial Fibroblasts In Vitro
Cited by: 20
Author(s): Jolet Y Mimpen, Mathew Baldwin, Adam P. Cribbs, Martin Philpott, Andrew Carr, Stephanie G. Dakin, Sarah Snelling
Software Mentions: 6
Published: over 3 years ago
10.1186/s13046-021-02015-4
LncRNA CARMN overexpression promotes prognosis and chemosensitivity of triple negative breast cancer via acting as miR143-3p host gene and inhibiting DNA replication
Cited by: 15
Author(s): Xiaonan Sheng, Huijuan Dai, Yueyao Du, Jing Peng, Rui Sha, Fan Yang, Liheng Zhou, Yingsong Lin, Shuguang Xu, Yifan Wu, Weiqiang Yin, Jinsong Lu
Software Mentions: 6
Published: over 3 years ago
10.1038/s41420-021-00547-4
Impairment of neuronal mitochondrial function by l-DOPA in the absence of oxygen-dependent auto-oxidation and oxidative cell damage
Cited by: 5
Author(s): Philipp Hörmann, Sylvie Delcambre, Jasmin E. Hanke, Robert Geffers, Marcel Leist, Karsten Hiller
Software Mentions: 6
Published: over 3 years ago
10.3389/fonc.2021.684242
Integrated Analysis of a Competing Endogenous RNA Network Reveals a Prognostic lncRNA Signature in Bladder Cancer
Cited by: 2
Author(s): Mou Peng, Cheng Xu, Xiong Wang, Yi Lee, Yinhuai Wang
Software Mentions: 6
Published: over 3 years ago
10.1038/s41598-020-72671-7
Molecular signatures of anthroponotic cutaneous leishmaniasis in the lesions of patients infected with Leishmania tropica
Cited by: 10
Author(s): Nasrin Masoudzadeh, Malin Östensson, Josefine Persson, Vahid Mashayekhi Goyonlo, Christopher Agbajogu, Yasaman Taslimi, Reza Erfanian Salim, Farnaz Zahedifard, Amir Mizbani, Housein Malekafzali Ardekani, Bronwyn M. Gunn, Sima Rafati, Ali M. Harandi
Software Mentions: 6
Published: about 4 years ago
10.1155/2020/5786053
Integrating Network Pharmacology with Molecular Docking to Unravel the Active Compounds and Potential Mechanism of Simiao Pill Treating Rheumatoid Arthritis
Cited by: 16
Author(s): Mengshi Tang, Xiaoqing Xie, Pan Yi, Jin Seok Kang, Jiafen Liao, Wenqun Li, Fen Li
Software Mentions: 6
Published: about 4 years ago
10.1186/s13195-021-00862-z
Prediction of differentially expressed microRNAs in blood as potential biomarkers for Alzheimer’s disease by meta-analysis and adaptive boosting ensemble learning
Cited by: 26
Author(s): Sze Chung Yuen, Xueya Liang, Hongmei Zhu, Yongliang Jia, Siu-wai Leung
Software Mentions: 5
Published: over 3 years ago
10.18632/aging.102871
Prognostic value of immune-related genes in the tumor microenvironment of lung adenocarcinoma and lung squamous cell carcinoma
Cited by: 52
Author(s): Yan Qu, Bo Cheng, Ningsheng Shao, Yibin Jia, Qingxu Song, Bingxu Tan, Jianbo Wang
Software Mentions: 5
Published: over 4 years ago
10.1038/s41598-020-66721-3
Cardiac transcriptional and metabolic changes following thoracotomy
Cited by: 0
Author(s): Markus Heckmann, Ashraf Yusuf Rangrez, Daniel Finke, Andreas Jungmann, Julia S. Kreußer, Alexandra Rosskopf, Nesrin Schmiedel, Hugo A. Katus, Norbert Frey, Oliver Müller
Software Mentions: 5
Published: over 4 years ago
10.3389/fmicb.2020.01943
Commonalities and Differences in the Transcriptional Response of the Model Fungus Saccharomyces cerevisiae to Different Commercial Graphene Oxide Materials
Cited by: 4
Author(s): Felix Laguna-Teno, María Suárez-Diez, Juan Antonio Tamayo-Ramos
Software Mentions: 5
Published: over 4 years ago
10.3389/fonc.2020.605097
An Integrative Pan-Cancer Analysis Revealing LCN2 as an Oncogenic Immune Protein in Tumor Microenvironment
Cited by: 33
Author(s): Wen‐Xiu Xu, Jian Zhang, Yu-Ting Hua, Su-Jin Yang, Dandan Wang, Jinhai Tang
Software Mentions: 5
Published: almost 4 years ago
10.1155/2020/5217405
Based on Network Pharmacology to Explore the Molecular Targets and Mechanisms of Gegen Qinlian Decoction for the Treatment of Ulcerative Colitis
Cited by: 43
Author(s): Meiqi Wei, He Li, Qifang Li, Yi Qiao, Qun Ma, Ruining Xie, Rong Wang, Yuan Liu, Chao Wei, Bingbing Li, Canlei Zheng, Bing Sun, Bin Yu
Software Mentions: 5
Published: almost 4 years ago
10.3389/fgene.2021.722803
Identification of Potential Biomarkers for Psoriasis by DNA Methylation and Gene Expression Datasets
Cited by: 9
Author(s): Yong Liu, Shengnan Cui, Jiayi Sun, Xin Yan, Dongran Han
Software Mentions: 5
Published: about 3 years ago
10.1038/s41392-020-00457-4
Longitudinal transcriptome analyses show robust T cell immunity during recovery from COVID-19
Cited by: 55
Author(s): Hong Zheng, Min Xu, Cui Xian Yang, Ren Rong Tian, Mi Zhang, Jian Jian Li, Xi Cheng Wang, Zhao Ding, Gui Mei Li, Xiaolu Li, Yu He, Xing-qi Dong, Yong Yao, Yong Zheng
Software Mentions: 5
Published: almost 4 years ago
10.3389/fgene.2021.670240
IGFBP2 Is a Potential Master Regulator Driving the Dysregulated Gene Network Responsible for Short Survival in Glioblastoma Multiforme
Cited by: 6
Author(s): Manasa Kalya, Alexander Kel, Darius Wlochowitz, Edgar Wingender, Tim Beißbarth
Software Mentions: 5
Published: over 3 years ago
10.18632/aging.102278
Association between promoter DNA methylation and gene expression in the pathogenesis of ischemic stroke
Cited by: 20
Author(s): Guo-Xiong Deng, Ning Xu, Qi Huang, Jin-Yue Tan, Zhao Zhang, Xianfeng Li, Jinru Wei
Software Mentions: 5
Published: about 5 years ago
10.3390/v13061129
Evidence of Transcriptional Shutoff by Pathogenic Viral Haemorrhagic Septicaemia Virus in Rainbow Trout
Cited by: 4
Author(s): Irene Cano, Eduarda M. Santos, Karen Moore, Audrey Farbos, Ronny van Aerle
Software Mentions: 5
Published: over 3 years ago
10.1186/2043-9113-4-8
comoR: a software for disease comorbidity risk assessment
Cited by: 82
Author(s): Mohammad Ali Moni, Píetro Lió
Software Mentions: 5
Published: almost 11 years ago
10.3389/fonc.2021.685980
Role of NRP1 in Bladder Cancer Pathogenesis and Progression
Cited by: 15
Author(s): Yun Dong, Weiming Ma, Zengliang Shi, Zhiguo Zhang, Jing Zhou, Yang Li, Shaoqi Zhang, Kun Pang, Bibo Li, Wen-da Zhang, Tao Fan, Guanghao Zhu, Xue Li, Rui Li, Ying Liu, Lin Hao, Conghui Han
Software Mentions: 5
Published: over 3 years ago
10.3389/fonc.2021.705939
Identification of the Effects of Chondroitin Sulfate on Inhibiting CDKs in Colorectal Cancer Based on Bioinformatic Analysis and Experimental Validation
Cited by: 1
Author(s): Yingyu Zhou, Xuyang Li, Yuki Morita, Satoshi Hachimura, Takuya Miyakawa, Sachiko Takahashi, Masaru Tanokura
Software Mentions: 5
Published: about 3 years ago
10.1038/s41598-019-39318-8
Identifying Windows of Susceptibility by Temporal Gene Analysis
Cited by: 9
Author(s): Kristin P. Bennett, Elisabeth M. Brown, Hannah De los Santos, Matthew Poegel, Thomas R. Kiehl, Evan W. Patton, Spencer Norris, Sally Temple, John S. Erickson, Deborah L. McGuinness, Nathan C. Boles
Software Mentions: 5
Published: over 5 years ago
10.1371/journal.pone.0115692
HPOSim: An R Package for Phenotypic Similarity Measure and Enrichment Analysis Based on the Human Phenotype Ontology
Cited by: 49
Author(s): Yue Deng, Lin Gao, Bingbo Wang, Guo Xia-zhen
Software Mentions: 5
Published: almost 10 years ago
10.1186/s12885-021-07887-5
Metabolic alterations in meningioma reflect the clinical course
Cited by: 2
Author(s): Waseem Masalha, Karam Daka, Jakob Woerner, Nils Pompe, Stefan Weber, Daniel Delev, Marie T. Krüger, Oliver Schnell, Jürgen Beck, Dieter Henrik Heiland, Juergen Grauvogel
Software Mentions: 4
Published: over 3 years ago
10.18632/aging.202452
Evaluation of the prognostic values of solute carrier (SLC) family 39 genes for patients with lung adenocarcinoma
Cited by: 8
Author(s): Haoming Zhou, Yingbo Zhu, Huizhong Qi, Liang Liang, Hao Wu, Jingping Yuan, Qingyong Hu
Software Mentions: 4
Published: almost 4 years ago
10.3390/plants10050919
Transcriptomic Analysis of Radish (Raphanus sativus L.) Spontaneous Tumor
Cited by: 2
Author(s): А.А. Ткаченко, И. Е. Додуева, Varvara E. Tvorogova, Alexander V. Predeus, Olga Pravdina, Ksenia Kuznetsova, Л. А. Лутова
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pbio.3000849
In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age
Cited by: 203
Author(s): Nicole A P Lieberman, Vikas Peddu, Hong Xie, Lasata Shrestha, Meei Li Huang, Megan Mears, Maria N.B. Cajimat, Dennis A. Bente, Pei Yong Shi, Francesca T. Bovier, Pavitra Roychoudhury, Keith R. Jerome, Anne Moscona, Matteo Porotto, Alexander L. Greninger
Software Mentions: 4
Published: about 4 years ago
10.1371/journal.pntd.0008424
Differential gene expression elicited by ZIKV infection in trophoblasts from congenital Zika syndrome discordant twins
Cited by: 17
Author(s): Murilo Sena Amaral, Ernesto Goulart, Luiz C. Caires-Júnior, David A. Morales-Vicente, Alessandra Soares‐Schanoski, Roselane P. Gomes, Giovanna Gonçalves de Oliveira Olberg, Renato Mancini Astray, Jorge Kalil, Mayana Zatz, Sérgio Verjovski-Almeida
Software Mentions: 4
Published: over 4 years ago
10.7150/thno.46142
A panel of eight microRNAs is a good predictive parameter for triple-negative breast cancer relapse
Cited by: 42
Author(s): Hsiao-Chin Hong, Ching-Te Chuang, Wei‐Chih Huang, Shun-Long Weng, Chia-Hung Chen, Kuang-Hsin Chang, Kuang‐Wen Liao, Hsien-Da Huang
Software Mentions: 4
Published: almost 5 years ago
10.18632/aging.103083
Nudix hydrolase 1 is a prognostic biomarker in hepatocellular carcinoma
Cited by: 6
Author(s): Qifeng Ou, Ning Ma, Zhenzhen Yu, Rongchang Wang, Yucheng Hou, Ziming Wang, Fan Chen, Wen Li, Jiong Bi, Jiachi Ma, Longjuan Zhang, Shan Qiao, Xiaohui Huang
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pone.0234986
Molecular analyses of glioblastoma stem-like cells and glioblastoma tissue
Cited by: 7
Author(s): Marco Wallenborn, Leiming Xu, Holger Kirsten, Leili Rohani, Daniela Rudolf, Peter Ahnert, Christian Schmidt, R. Schulz, Mandy Richter, Wolfgang Krupp, Wolf Mueller, Adiv A. Johnson, Jürgen Meixensberger, Heidrun Holland
Software Mentions: 4
Published: over 4 years ago
10.1186/s40364-021-00302-y
Lower BCL11B expression is associated with adverse clinical outcome for patients with myelodysplastic syndrome
Cited by: 7
Author(s): Xin Huang, Cunte Chen, Mengjun Zhong, Suxia Geng, Yujie Zhao, Minming Li, Chenxin Deng, Lizhi Zeng, Ping Wu, Zhihui Lu, Jianyu Weng, Xin Du, Yangqiu Li
Software Mentions: 4
Published: over 3 years ago
10.1186/s12864-018-5170-3
Long non-coding RNAs have age-dependent diurnal expression that coincides with age-related changes in genome-wide facultative heterochromatin
Cited by: 19
Author(s): Jinhee Park, William J. Belden
Software Mentions: 4
Published: about 6 years ago
10.3390/ijms20051182
Temporal Splicing Switches in Elements of the TNF-Pathway Identified by Computational Analysis of Transcriptome Data for Human Cell Lines
Cited by: 6
Author(s): Nikolaï Genov, Alireza Basti, Marconi Abreu, Angela Relógio
Software Mentions: 4
Published: over 5 years ago
10.1186/s12986-019-0366-3
A novel lncRNA-miRNA-mRNA triple network identifies lncRNA TWF1 as an important regulator of miRNA and gene expression in coronary artery disease
Cited by: 15
Author(s): Miao Liu, Rui-Xing Yin, Qinghui Zhang, Xi‐Jiang Hu, Feng Huang, Wu-Xian Chen, Xiaoli Cao, Jin‐Zhen Wu
Software Mentions: 4
Published: over 5 years ago
10.1002/2211-5463.12982
Metabolomic analysis of fibrotic mice combined with public RNA‐Seq human lung data reveal potential diagnostic biomarker candidates for lung fibrosis
Cited by: 8
Author(s): Yosui Nojima, Yoshito Takeda, Yohei Maeda, Takeshi Bamba, Eiichiro Fukusaki, Mari Itoh, Kenji Mizuguchi, Atsushi Kumanogoh
Software Mentions: 4
Published: about 4 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: almost 5 years ago
10.3389/fcell.2015.00028
How to build personalized multi-omics comorbidity profiles
Cited by: 46
Author(s): Mohammad Ali Moni, Píetro Lió
Software Mentions: 4
Published: over 9 years ago
10.3389/fgene.2020.613744
Integrated Weighted Gene Co-expression Network Analysis Identified That TLR2 and CD40 Are Related to Coronary Artery Disease
Cited by: 6
Author(s): Bin Qi, Jianhong Chen, Tao Lin, Chuan-Meng Zhu, Yong Wang, Guo-Xiong Deng, Miao Liu
Software Mentions: 4
Published: almost 4 years ago
10.3389/fimmu.2021.716606
Augmented Expansion of Treg Cells From Healthy and Autoimmune Subjects via Adult Progenitor Cell Co-Culture
Cited by: 5
Author(s): James L. Reading, Valerie D. Roobrouck, Caroline Hull, Pablo D. Becker, Jelle Beyens, Alice Valentin-Torres, Dominic A. Boardman, Estefania Nova Lamperti, Samantha R. Stubblefield, Giovanna Lombardi, Robert Deans, Anthony E. Ting, Timothy Tree
Software Mentions: 4
Published: about 3 years ago
10.3389/fimmu.2021.666163
Transcriptomic Signature Differences Between SARS-CoV-2 and Influenza Virus Infected Patients
Cited by: 22
Author(s): Stéphanie Bibert, Nicolas Guex, João Lourenço, Thomas Brahier, Matthaios Papadimitriou-Olivgeris, Lauro Damonti, Oriol Manuel, Robin Liechti, Lou Götz, Jonathan Tschopp, Mathieu Quinodoz, Péter Vollenweider, Jean‐Luc Pagani, Mauro Oddo, Olivier Hügli, Frédéric Lamoth, Véronique Erard, Cathy Voide, Mauro Delorenzi, Nathalie Rufer, Fabio Candotti, Carlo Rivolta, Noémie Boillat‐Blanco, Pierre‐Yves Bochud
Software Mentions: 4
Published: over 3 years ago
10.1186/s12944-019-1142-0
LncRNA SNHG8 is identified as a key regulator of acute myocardial infarction by RNA-seq analysis
Cited by: 26
Author(s): Liuan Zhuo, Yi-Tao Wen, Yong Wang, Zhi-Fang Liang, Gang Wu, Nong Mei-dan, Miao Liu
Software Mentions: 4
Published: about 5 years ago
10.1038/s41598-021-93616-8
MicroRNA-378a-3p is overexpressed in psoriasis and modulates cell cycle arrest in keratinocytes via targeting BMP2 gene
Cited by: 7
Author(s): Wipasiri Soonthornchai, Pattarin Tangtanatakul, Kornvalee Meesilpavikkai, Virgil A. S. H. Dalm, Patipark Kueanjinda, Jongkonnee Wongpiyabovorn
Software Mentions: 4
Published: over 3 years ago
10.18632/aging.104004
Integrated analysis of transcriptomic and metabolomic data demonstrates the significant role of pyruvate carboxylase in the progression of ovarian cancer
Cited by: 9
Author(s): Hongjing Shang, Jianfeng Zheng, Jinyi Tong
Software Mentions: 3
Published: about 4 years ago
10.1186/s12859-020-3408-y
AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species
Cited by: 16
Author(s): Zhenmin Du, Qi Hu, Xinxing Liu, Kai Zou, Emmanuel Konadu Sarkodie, Xueduan Liu, Fei Gao
Software Mentions: 3
Published: over 4 years ago
10.1186/s12906-021-03215-3
A network pharmacology perspective for deciphering potential mechanisms of action of Solanum nigrum L. in bladder cancer
Cited by: 17
Author(s): Yun Dong, Lin Hao, Kun Fang, Xing Han, Hui Yu, Jianjun Zhang, Longjun Cai, Tao Fan, Wen-da Zhang, Kun Pang, Weiming Ma, Xitao Wang, Conghui Han
Software Mentions: 3
Published: almost 4 years ago
10.3390/v12080804
Respiratory Syncytial Virus Infection Induces Chromatin Remodeling to Activate Growth Factor and Extracellular Matrix Secretion Pathways
Cited by: 20
Author(s): Xiaofang Xu, Dianhua Qiao, Morgan Mann, Roberto P. Garofalo, Allan R. Brasier
Software Mentions: 3
Published: over 4 years ago
10.7717/peerj.3175
Profiling transcriptomes of human SH-SY5Y neuroblastoma cells exposed to maleic acid
Cited by: 7
Author(s): Chia-Chi Wang, Yin Chi Lin, Yin-Hua Cheng, Chun Wei Tung
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pone.0235670
UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization
Cited by: 8
Author(s): Duc-Hau Le
Software Mentions: 3
Published: over 4 years ago
10.1242/dev.196022
scRNA sequencing uncovers a TCF4-dependent transcription factor network regulating commissure development in mouse
Cited by: 6
Author(s): Marie-Theres Wittmann, Sayako Katada, Elisabeth Sock, Philipp Kirchner, Arif B. Ekici, Michael Wegner, Kinichi Nakashima, Dieter Chichung Lie, André Reis
Software Mentions: 3
Published: over 3 years ago
10.3389/fonc.2021.691771
Inflammatory Environment Promotes the Adhesion of Tumor Cells to Brain Microvascular Endothelial Cells
Cited by: 4
Author(s): Ke Wang, Shuang Dong, Doaa Higazy, Li-Jing Jin, Qing-Cui Zou, Haowei Chen, Aakif Inayat, Sheng Hu, Min Cui
Software Mentions: 3
Published: over 3 years ago
10.3389/fphar.2021.690118
Identification of Tumor Necrosis Factor-Alpha (TNF-α) Inhibitor in Rheumatoid Arthritis Using Network Pharmacology and Molecular Docking
Cited by: 23
Author(s): Liang Bai, Hao Chen, Peng Zhou, Jun Yu
Software Mentions: 3
Published: over 3 years ago
10.1186/s13321-015-0077-3
ChemDIS: a chemical–disease inference system based on chemical–protein interactions
Cited by: 13
Author(s): Chun Wei Tung
Software Mentions: 3
Published: over 9 years ago
10.1038/s41598-019-54603-2
A novel circRNA-miRNA-mRNA network identifies circ-YOD1 as a biomarker for coronary artery disease
Cited by: 49
Author(s): Miao Liu, Rui-Xing Yin, Qinghui Zhang, Pei-Juan Liao, Yong Wang, Rong-Jun Nie, Hui Li
Software Mentions: 3
Published: almost 5 years ago
10.1038/s41598-020-77606-w
The absence of (TCAGGG)n repeats in some telomeres, combined with variable responses to NR2F2 depletion, suggest that this nuclear receptor plays an indirect role in the alternative lengthening of telomeres
Cited by: 5
Author(s): Ahmed S. N. Alhendi, Nicola J. Royle
Software Mentions: 3
Published: almost 4 years ago
10.1186/s12967-020-02321-z
Development and validation of a survival model for lung adenocarcinoma based on autophagy-associated genes
Cited by: 20
Author(s): Xiaofei Wang, Shuang Yao, Zengtuan Xiao, Jialin Gong, Li Zuo, Baoai Han, Zhen Fa Zhang
Software Mentions: 3
Published: over 4 years ago
10.1186/s12967-019-1776-8
Circulating miR-3659 may be a potential biomarker of dyslipidemia in patients with obesity
Cited by: 12
Author(s): Miao Liu, Rui-Xing Yin, Shang Ling Pan, Shuo Yang, De Zhai Yang, Wei Lin
Software Mentions: 3
Published: almost 6 years ago