cran: ggalluvial | Projects | Ecosyste.ms: Papers

10.1155/2021/6613151

Genomic and Transcriptome Analysis to Identify the Role of the mTOR Pathway in Kidney Renal Clear Cell Carcinoma and Its Potential Therapeutic Significance
Cited by: 6
Author(s): Xiangyu Che, Xiaochen Qi, Yingkun Xu, Qifei Wang, Guangzhen Wu
Software Mentions: 19
Published: over 3 years ago

10.12688/f1000research.22139.2

scRepertoire: An R-based toolkit for single-cell immune receptor analysis
Cited by: 121
Author(s): Nicholas Borcherding, Nicholas L. Bormann, Gloria Kraus
Software Mentions: 16
Published: over 4 years ago

10.1038/s42003-021-01796-w

Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults
Cited by: 73
Author(s): Rong Xu, Renfei Lu, Tao Zhang, Qian Wu, Wei Cai, Xudong Han, Zhenzhou Wan, Xia Jin, Zhigang Zhang, Chiyu Zhang
Software Mentions: 15
Published: almost 4 years ago

10.3389/fimmu.2021.557994

Investigation of Genetic Determinants of Glioma Immune Phenotype by Integrative Immunogenomic Scale Analysis
Cited by: 10
Author(s): Binghao Zhao, Yuekun Wang, Yaning Wang, Congxin Dai
Software Mentions: 14
Published: over 3 years ago

10.1128/AEM.01225-21

Dynamics of the Human Nasal Microbiota and Staphylococcus aureus CC398 Carriage in Pig Truck Drivers across One Workweek
Cited by: 7
Author(s): Anna Cäcilia Ingham, Tinna Ravnholt Urth, Raphael N. Sieber, Marc Stegger, Sofie Marie Edslev, Øystein Angen, Anders Rhod Larsen
Software Mentions: 13
Published: about 3 years ago

10.1038/s41421-021-00321-x

Dynamics of TCR repertoire and T cell function in COVID-19 convalescent individuals
Cited by: 23
Author(s): Lingjie Luo, Wenhua Liang, Jianfeng Pang, Gang Xu, Yingying Chen, Xinrong Guo, Xin Wang, Yi Zhao, Yang-dian Lai, Yang Liu, Bin Li, Bing Su, Shuye Zhang, Michal Baniyash, Lei Shen, Lei Chen, Yun Ling, Ying Wang, Qiming Liang, Hongzhou Lu, Zheng Zhang, Feng Wang
Software Mentions: 12
Published: about 3 years ago

10.1099/mgen.0.000503

Rapid molecular evolution of Spiroplasma symbionts of Drosophila
Cited by: 13
Author(s): Michael Gerth, Humberto Martínez-Montoya, Paulino Ramirez, Florent Masson, Joanne S. Griffin, Rodolfo Aramayo, Stefanos Siozios, Bruno Lemaître, Mariana Mateos, Gregory D. D. Hurst
Software Mentions: 11
Published: almost 4 years ago

10.1155/2021/2291899

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

10.3390/microorganisms9071487

Changes in Skin and Nasal Microbiome and Staphylococcal Species Following Treatment of Atopic Dermatitis with Dupilumab
Cited by: 20
Author(s): Caroline Meyer Olesen, Anna Cäcilia Ingham, Simon Francis Thomsen, Maja‐Lisa Clausen, Paal Skytt Andersen, Sofie Marie Edslev, Yasemin Topal Yüksel, Emma Guttman‐Yassky, Tove Agner
Software Mentions: 10
Published: over 3 years ago

10.3389/fmolb.2021.657087

N6-Methyladenosine RNA Methylation Regulator-Related Alternative Splicing (AS) Gene Signature Predicts Non–Small Cell Lung Cancer Prognosis
Cited by: 16
Author(s): Zhenyu Zhao, Qidong Cai, Peng-Fei Zhang, Boxue He, Ping Xiong, Guangxu Tu, Weilin Peng, Li Wang, Fenglei Yu, Xiang Wang
Software Mentions: 8
Published: over 3 years ago

10.3389/fonc.2020.535985

Biomarker Discovery for the Carcinogenic Heterogeneity Between Colon and Rectal Cancers Based on lncRNA-Associated ceRNA Network Analysis
Cited by: 24
Author(s): Xin Qi, Yuxin Lin, Xingyun Liu, Jiajia Chen, Bairong Shen
Software Mentions: 8
Published: about 4 years ago

10.3389/fonc.2020.01411

Comparison of Stage 4 and Stage 4s Neuroblastoma Identifies Autophagy-Related Gene and LncRNA Signatures Associated With Prognosis
Cited by: 12
Author(s): Xinyao Meng, Honglin Li, Erhu Fang, Jiexiong Feng, Xiaoli Zhao
Software Mentions: 8
Published: over 4 years ago

10.1186/s12866-021-02222-1

Patterns of yeast diversity distribution and its drivers in rhizosphere soil of Hami melon orchards in different regions of Xinjiang
Cited by: 7
Author(s): Shanshan Zhu, Yonghui Lei, Chong Wang, Yu‐Mei Wei, Chuncheng Wang, Yanfei Sun
Software Mentions: 8
Published: over 3 years ago

10.7150/ijms.47224

Construction and Validation of a Protein Prognostic Model for Lung Squamous Cell Carcinoma
Cited by: 5
Author(s): Xisheng Fang, Xia Liu, Chengyin Weng, Yong Wu, Baoxiu Li, Haibo Mao, Mingyu Guan, Lin Lü, Guolong Liu
Software Mentions: 7
Published: almost 5 years ago

10.1155/2021/2628824

A Potential ceRNA Network for Neurological Damage in Preterm Infants
Cited by: 7
Author(s): Hui‐Zi Jin, Xinlan Liang, Zhenyu Cai
Software Mentions: 7
Published: over 3 years ago

10.1155/2020/7147824

Construction of Protein-related Risk Score Model in Bladder Urothelial Carcinoma
Cited by: 5
Author(s): Qizhan Luo, Xiaobo Zhang
Software Mentions: 7
Published: over 4 years ago

10.7717/peerj.11219

Construction and validation of an RNA-binding protein-associated prognostic model for colorectal cancer
Cited by: 8
Author(s): Yifei Miao, Hongling Zhang, Bai-Horng Su, Jiangtao Wang, Wuxia Quan, Qiutian Li, Denghai Mi
Software Mentions: 7
Published: over 3 years ago

10.1186/s12885-021-08462-8

Construction and comprehensive analysis of a ceRNA network to reveal potential prognostic biomarkers for lung adenocarcinoma
Cited by: 12
Author(s): Lei Gao, Ling Zhang
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0257510

Environmental DNA gives comparable results to morphology-based indices of macroinvertebrates in a large-scale ecological assessment
Cited by: 17
Author(s): Jeanine Brantschen, Rosetta C. Blackman, Jean‐Claude Walser, Florian Altermatt
Software Mentions: 7
Published: about 3 years ago

10.7554/eLife.68812

Impact of asymptomatic Plasmodium falciparum infection on the risk of subsequent symptomatic malaria in a longitudinal cohort in Kenya
Cited by: 14
Author(s): Kelsey M. Sumner, Judith Mangeni, Andrew Obala, Elizabeth Freedman, Lucy Abel, Steven R. Meshnick, Jessie K. Edwards, Brian W. Pence, Wendy Prudhomme-O’Meara, Steve M. Taylor
Software Mentions: 7
Published: over 3 years ago

10.1007/s12020-020-02434-x

Using The Cancer Genome Atlas data to refine the 8th edition of the American Joint Committee on Cancer staging for papillary thyroid carcinoma
Cited by: 3
Author(s): Anello Marcello Poma, Elisabetta Macerola, Liborio Torregrossa, Rossella Elisei, Ferruccio Santini, Fulvio Basolo
Software Mentions: 7
Published: about 4 years ago

10.3389/fgene.2020.577585

Development of an miRNA-Array-Based Diagnostic Signature for Periodontitis
Cited by: 11
Author(s): Sanli Jin, Jianguo Zhou, Xiaoyan Guan, Guohui Bai, Jianguo Liu, Liangwen Chen
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41598-021-90538-3

Identification of prognostic biomarkers related to the tumor microenvironment in thyroid carcinoma
Cited by: 6
Author(s): Junwei Du, Guoquan Li, Yang-sen Li, Xinguang Qiu
Software Mentions: 6
Published: over 3 years ago

10.1093/gigascience/giaa137

Long-read assembly of the Brassica napus reference genome Darmor-bzh
Cited by: 50
Author(s): Mathieu Rousseau‐Gueutin, Caroline Belser, Corinne Da Silva, Gautier Richard, Benjamin Istace, Corinne Cruaud, Cyril Falentin, Franz Boideau, Julien Boutte, Régine Delourme, Gwenaëlle Deniot, Stéfan Engelen, Julie Ferreira de Carvalho, Arnaud Lemainque, Loeiz Maillet, Jérôme Morice, Patrick Wincker, Anne‐Marie Chèvre, Jean‐Marc Aury
Software Mentions: 6
Published: almost 4 years ago

10.3389/fpsyt.2020.00384

Effectiveness of Open-Ended Psychotherapy Under Clinically Representative Conditions
Cited by: 6
Author(s): Magnus Nordmo, Nils Martin Sønderland, Odd E. Havik, Dag Erik Eilertsen, Jon T. Monsen, Ole André Solbakken
Software Mentions: 6
Published: over 4 years ago

10.1186/s12935-020-01423-4

Identification of a three-long noncoding RNA prognostic model involved competitive endogenous RNA in kidney renal clear cell carcinoma
Cited by: 21
Author(s): Di Zhang, Song Zeng, Xiaopeng Hu
Software Mentions: 6
Published: over 4 years ago

10.3389/fonc.2021.670138

Integrated Analysis of ceRNA Network Reveals Prognostic and Metastasis Associated Biomarkers in Breast Cancer
Cited by: 8
Author(s): Qian Da, Qinghui Zheng, Danping Wu, Buyun Ye, Yang‐Yang Qian, Tao Zhou, Jie Qiu, Xuli Meng
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-021-90489-9

Auxiliary rapid identification of pathogenic and antagonistic microorganisms associated with Coptis chinensis root rot by high-throughput sequencing
Cited by: 7
Author(s): Hailang Liao, Ling Huang, Na Li, Wenjia Ke, Yiqing Xiang, Yuntong Ma
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2019.00684

Increase in DNA Damage by MYCN Knockdown Through Regulating Nucleosome Organization and Chromatin State in Neuroblastoma
Cited by: 3
Author(s): Xinjie Hu, Weisheng Zheng, Qianshu Zhu, Liang Gu, Yanhua Du, Zhe Han, Xiaobai Zhang, Daniel Carter, Belamy B. Cheung, Andong Qiu, Cizhong Jiang
Software Mentions: 5
Published: over 5 years ago

10.3390/nu13072193

The Effect of a Lifestyle Intervention on Type 2 Diabetes Pathophysiology and Remission: The Stevenshof Pilot Study
Cited by: 5
Author(s): Iris M de Hoogh, Johanneke E. Oosterman, W. Otten, Anne-Margreeth Krijger, Susanne Berbée-Zadelaar, Wilrike J. Pasman, Ben van Ommen, Hanno Pijl, Suzan Wopereis
Software Mentions: 5
Published: over 3 years ago

10.1002/cam4.3481

Integrated genomic analysis identifies a genetic mutation model predicting response to immune checkpoint inhibitors in melanoma
Cited by: 22
Author(s): Junjie Jiang, Yongfeng Ding, Mengjie Wu, Yanyan Chen, Xiadong Lyu, Jun Lü, Haiyong Wang, Lisong Teng
Software Mentions: 5
Published: about 4 years ago

10.1155/2021/9954370

Identification of the Ferroptosis-Associated Gene Signature to Predict the Prognostic Status of Endometrial Carcinoma Patients
Cited by: 5
Author(s): Jinlong Qin, Xiaowen Shao, Lei Wu, Hongling Du
Software Mentions: 5
Published: about 3 years ago

10.3389/fgene.2021.619821

Comprehensive Profiling Reveals Distinct Microenvironment and Metabolism Characterization of Lung Adenocarcinoma
Cited by: 3
Author(s): Li Chang, Chen Tian, Yangyang Liu, Jinyan Liang, Yue Zeng, Qifan Yang, Yuting Liu, Di Wu, Jingjing Wu, Juanjuan Wang, Kai Zhang, Fei Gu, Yue Hu, Li Liu
Software Mentions: 5
Published: over 3 years ago

10.1155/2021/8848227

A Novel Autophagy-Related lncRNA Gene Signature to Improve the Prognosis of Patients with Melanoma
Cited by: 10
Author(s): Yi Ding, Li Tian, Min Li, Tuersong Tayier, Meilin Zhang, Long Chen, Shumei Feng
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2021.690509

Identification and Validation of a Ferroptosis-Related Long Non-coding RNA Signature for Predicting the Outcome of Lung Adenocarcinoma
Cited by: 27
Author(s): Zhiyuan Zheng, Qian Zhang, Wei Wu, Yu Xue, Shuhan Liu, Qiaoqian Chen, Lin Dong
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2021.547333

The Immune Heterogeneity Between Pulmonary Adenocarcinoma and Squamous Cell Carcinoma: A Comprehensive Analysis Based on lncRNA Model
Cited by: 11
Author(s): Tao Yan, Guoyuan Ma, Kai Wang, Weidong Liu, W. L. Zhong, Jiajun Du
Software Mentions: 4
Published: over 3 years ago

10.1007/s00384-020-03744-2

Response to neoadjuvant treatment among rectal cancer patients in a population-based cohort
Cited by: 1
Author(s): Elizabeth Alwers, Lina Jansen, Jakob Nikolas Kather, Efrat L. Amitay, Hendrik Bläker, Matthias Kloor, Katrin E. Tagscherer, Wilfried Roth, Esther Herpel, Jenny Chang‐Claude, Hermann Brenner, Michael Hoffmeister
Software Mentions: 4
Published: about 4 years ago

10.18632/aging.203184

The circadian clock is associated with prognosis and immune infiltration in stomach adenocarcinoma
Cited by: 13
Author(s): Zhihao Huang, Aoxiao He, Jiakun Wang, Hongmei Lü, Rongguiyi Zhang, Linquan Wu, Qian Feng
Software Mentions: 4
Published: over 3 years ago

10.3389/fonc.2019.00649

Construction and Investigation of a lncRNA-Associated ceRNA Regulatory Network in Cholangiocarcinoma
Cited by: 32
Author(s): Junyu Long, Jianping Xiong, Yi Bai, Jianshan Mao, Jianzhen Lin, Weiyu Xu, Hui Zhang, Shuguang Chen, Hong Zhao
Software Mentions: 3
Published: over 5 years ago

10.18632/aging.202150

A TP53-based immune prognostic model for muscle-invasive bladder cancer
Cited by: 6
Author(s): Hongyan Li, Lu Han, Wanli Cui, Yufan Huang, Xin Jin
Software Mentions: 3
Published: almost 4 years ago

10.1128/AEM.02541-20

Colonization of Naive Roots from Populus tremula × alba Involves Successive Waves of Fungi and Bacteria with Different Trophic Abilities
Cited by: 9
Author(s): F. Fracchia, Lauralie Mangeot-Peter, Lea Jacquot, Francis Martin, Claire Veneault‐Fourrey, Aurélie Deveau
Software Mentions: 3
Published: over 3 years ago

10.1155/2020/1872962

Development of Autophagy Signature-Based Prognostic Nomogram for Refined Glioma Survival Prognostication
Cited by: 5
Author(s): Yuxiang Fan, Xinyu Peng, Baoqin Li, Gang Zhao
Software Mentions: 3
Published: about 4 years ago

10.3390/biomedicines9050546

Weighted Gene Co-Expression Network Analysis Reveals Key Genes and Potential Drugs in Abdominal Aortic Aneurysm
Cited by: 5
Author(s): Kejia Kan, Feng Guo, Lei Zhu, Prama Pallavi, Martin Sigl, Michael Keese
Software Mentions: 3
Published: over 3 years ago

10.7717/peerj.6091

Screening of prognostic biomarkers for endometrial carcinoma based on a ceRNA network
Cited by: 6
Author(s): Mingjun Zheng, Rui Gou, Wenchao Zhang, Xin Nie, Jing Wang, Lingling Gao, Juanjuan Liu, Xiao Li, Bei Lin
Software Mentions: 3
Published: almost 6 years ago

10.1155/2021/8849977

A Risk Signature with Autophagy-Related Long Noncoding RNAs for Predicting the Prognosis of Clear Cell Renal Cell Carcinoma: Based on the TCGA Database and Bioinformatics
Cited by: 14
Author(s): Yundong Xuan, Wei-Hao Chen, Kan Liu, Yu Tang Gao, Shidong Zuo, Baojun Wang, Xin Ma, Xu Zhang
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2021.683714

Gut Microbial SNPs Induced by High-Fiber Diet Dominate Nutrition Metabolism and Environmental Adaption of Faecalibacterium prausnitzii in Obese Children
Cited by: 7
Author(s): Hui Li, Liping Zhao, Menghui Zhang
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2020.597569

Identification and Validation of an Autophagy-Related lncRNA Signature for Patients With Breast Cancer
Cited by: 13
Author(s): Ruyue Zhang, Qingwen Zhu, Dengke Yin, Zichang Yang, Jiahao Guo, Jingmin Zhang, Yubing Zhou, Jane Yu
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.58722

Typical and atypical language brain organization based on intrinsic connectivity and multitask functional asymmetries
Cited by: 21
Author(s): Loïc Labache, Bernard Mazoyer, Marc Joliot, Fabrice Crivello, Isabelle Hesling, Nathalie Tzourio‐Mazoyer
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-021-92115-0

Development and validation of an individualized immune prognostic model in stage I–III lung squamous cell carcinoma
Cited by: 10
Author(s): Qifan Yang, Di Wu, Jian Wang, Li Ba, Chen Tian, Yuting Liu, Yue Hu, Li Liu
Software Mentions: 2
Published: over 3 years ago

10.1186/s13002-020-00406-z

The uses of fig (Ficus) by five ethnic minority communities in Southern Shan State, Myanmar
Cited by: 4
Author(s): Aye Mya Mon, Yinxian Shi, Xuefei Yang, Pyae Phyo Hein, Thaung Naing Oo, Cory Whitney, Yongping Yang
Software Mentions: 2
Published: about 4 years ago

10.7150/jca.40621

The Prediction of Survival in Hepatocellular Carcinoma Based on A Four Long Non-coding RNAs Expression Signature
Cited by: 5
Author(s): Zongxing Yang, Yuhan Yang, Gang Zhou, Yan Luo, Wenjun Yang, Yuan Zhou, Jin Yang
Software Mentions: 2
Published: almost 5 years ago

10.18632/aging.102334

CircUBAP2-mediated competing endogenous RNA network modulates tumorigenesis in pancreatic adenocarcinoma
Cited by: 46
Author(s): Rongjie Zhao, Junjie Ni, Lu Si, Sujing Jiang, Lixin You, Hao Líu, Jiawei Shou, Chongya Zhai, Wei Zhang, Shengpeng Shao, Xinmei Yang, Hongming Pan, Weidong Han
Software Mentions: 2
Published: about 5 years ago

10.1111/jcmm.16251

Analysis of changes in circular RNA expression and construction of ceRNA networks in human dilated cardiomyopathy
Cited by: 14
Author(s): Lin Zhou, Yongchao Zhao, Fangjie Dai, Enyong Su, Fuhai Li, Yan Yan
Software Mentions: 2
Published: almost 4 years ago

10.3390/cancers13133123

Molecular Alterations in Relation to Histopathological Characteristics in a Large Series of Pediatric Papillary Thyroid Carcinoma from a Single Institution
Cited by: 10
Author(s): Elisabetta Macerola, Agnese Proietti, Anello Marcello Poma, Clara Ugolini, Liborio Torregrossa, Paola Vignali, Alessio Basolo, Gabriele Materazzi, Rossella Elisei, Ferruccio Santini, Fulvio Basolo
Software Mentions: 2
Published: over 3 years ago

10.1186/s12884-020-03533-3

Apgar score and neonatal mortality in China: an observational study from a national surveillance system
Cited by: 13
Author(s): Yi Mu, Mingrong Li, Junwu Zhu, Yanping Wang, Aiyun Xing, Zheng Liu, Yanxia Xie, Xiaodong Wang, Juan Liang
Software Mentions: 1
Published: almost 4 years ago

10.3389/fimmu.2021.671503

Rituximab Associated Hypogammaglobulinemia in Autoimmune Disease
Cited by: 38
Author(s): Joanna Tieu, Rona Smith, Seerapani Gopaluni, Dinakantha Kumararatne, Mark McClure, Ania Manson, S. B. Houghton, David Jayne
Software Mentions: 1
Published: over 3 years ago

10.1097/MD.0000000000017679

The national maternal near miss surveillance in China
Cited by: 14
Author(s): Yi Mu, Xiaodong Wang, Xiaohong Li, Zheng Liu, Mingrong Li, Yanping Wang, Qi Li, Kui Deng, Jun Zhu, Juan Liang
Software Mentions: 1
Published: about 5 years ago

Projects: cran: ggalluvial

Papers Mentioning ggalluvial 57