cran: pheatmap | Projects | Ecosyste.ms: Papers

10.18632/aging.202589

The aging-related risk signature in colorectal cancer
Cited by: 40
Author(s): Taohua Yue, Shanwen Chen, Jing Zhu, Shuqin Guo, Zhihao Huang, Pengyuan Wang, Shuai Zuo, Yucun Liu
Software Mentions: 6
Published: over 5 years ago

10.7150/jca.42531

Identification of the key genes and characterizations of Tumor Immune Microenvironment in Lung Adenocarcinoma (LUAD) and Lung Squamous Cell Carcinoma (LUSC)
Cited by: 24
Author(s): Lemeng Zhang, Jianhua Chen, Tianli Cheng, Hua Yang, Haitao Li, Changqie Pan
Software Mentions: 6
Published: over 6 years ago

10.1016/j.immuni.2020.03.011

Stromal Cells Covering Omental Fat-Associated Lymphoid Clusters Trigger Formation of Neutrophil Aggregates to Capture Peritoneal Contaminants
Cited by: 47
Author(s): Lucy H. Jackson-Jones, Peter Smith, Jordan Raymond Portman, Marlene S Magalhaes, Katie J. Mylonas, Matthieu Vermeren, Mark Nixon, Beth E. P. Henderson, Ross Dobie, Sonja Vermeren, Laura Denby, Neil C. Henderson, Damian J. Mole, C Benezech
Software Mentions: 6
Published: over 6 years ago

10.1016/j.immuni.2021.08.011

Adenosine-to-inosine editing of endogenous Z-form RNA by the deaminase ADAR1 prevents spontaneous MAVS-dependent type I interferon responses
Cited by: 58
Author(s): Qingli Tang, Rachel E. Rigby, George R. Young, Astrid Korning Hvidt, Tanja Davis, Tiong Kit Tan, Anne Bridgeman, Alain Townsend, George Kassiotis, Jan Rehwinkel
Software Mentions: 6
Published: almost 5 years ago

10.3389/fgene.2021.668311

Construction of a circRNA-Related Prognostic Risk Score Model for Predicting the Immune Landscape of Lung Adenocarcinoma
Cited by: 0
Author(s): Huawei Li, Jun Wang, Linyou Zhang
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pntd.0009633

Identification of potential biomarkers in dengue via integrated bioinformatic analysis
Cited by: 5
Author(s): Lisha Xie, Xin Yin, Jie Bi, Hongyu Luo, Xun‐Jie Cao, Yu-Wen Ma, Ye-Ling Liu, Jianwen Su, Geng-Ling Lin, Xu‐Guang Guo
Software Mentions: 6
Published: about 5 years ago

10.1093/gigascience/giaa116

The Dynamic Proteome of Oligodendrocyte Lineage Differentiation Features Planar Cell Polarity and Macroautophagy Pathways
Cited by: 8
Author(s): Paria Pooyan, Razieh Karamzadeh, Mehdi Mirzaei, Anna Meyfour, Ardeshir Amirkhan, Yunqi Wu, Vivek Gupta, Hossein Baharvand, Mohammad Javan, Ghasem Hosseini Salekdeh
Software Mentions: 6
Published: almost 6 years ago

10.1155/2021/8842105

Comparison of the Fatty Acid Metabolism Pathway in Pan-Renal Cell Carcinoma: Evidence from Bioinformatics
Cited by: 1
Author(s): Ping Wu, Yingkun Xu, Jiayi Li, Xiaowei Li, Peizhi Zhang, Ningke Ruan, Cong Zhang, Panpan Sun, Qifei Wang, Guangzhen Wu
Software Mentions: 6
Published: over 5 years ago

10.3390/biom9010012

Integrated Transcriptome Analysis Reveals Plant Hormones Jasmonic Acid and Salicylic Acid Coordinate Growth and Defense Responses upon Fungal Infection in Poplar
Cited by: 63
Author(s): Jie Luo, Wenxiu Xia, Pei Cao, Zheng’ang Xiao, Yan Zhang, Meifeng Liu, Chengjun Zhan, Nian Wang
Software Mentions: 6
Published: over 7 years ago

10.1080/19490976.2021.1900995

Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment
Cited by: 21
Author(s): Kang Kang, Lejla Imamovic, Maria-Anna Misiakou, Maria Bornakke Sørensen, Yoshitaro Heshiki, Yueqiong Ni, Tingting Zheng, Jun Li, Mostafa Mostafa Hashim Ellabaan, Marta Colomer-Lluch, Anne A Rode, Peter Bytzer, Gianni Panagiotou, Morten Otto Alexander Sommer
Software Mentions: 6
Published: over 5 years ago

10.1186/s40168-018-0449-9

The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool
Cited by: 113
Author(s): Jo De Vrieze, Ameet J. Pinto, William T. Sloan, Umer Zeeshan Ijaz
Software Mentions: 6
Published: over 8 years ago

10.1186/s12866-020-01987-1

Long-term effects of mixed planting on arbuscular mycorrhizal fungal communities in the roots and soils of Juglans mandshurica plantations
Cited by: 7
Author(s): Ji Li, Zhang Yan, Yuchun Yang, Lü Yang, Na Yang, Depeng Zhang
Software Mentions: 6
Published: almost 6 years ago

10.3389/fgene.2019.00025

LncRNAs GIHCG and SPINT1-AS1 Are Crucial Factors for Pan-Cancer Cells Sensitivity to Lapatinib
Cited by: 20
Author(s): Zhen Xiang, Shuzheng Song, Zhenggang Zhu, Wenhong Sun, Jaron E. Gifts, Sam Q. Sun, Qiushi Shauna Li, Yingyan Yu, Keqin Kathy Li
Software Mentions: 6
Published: over 7 years ago

10.1186/s40168-020-00917-7

Spatial heterogeneity of bacterial colonization across different gut segments following inter-species microbiota transplantation
Cited by: 56
Author(s): Na Li, Bo Zuo, Shimeng Huang, Benhua Zeng, Dandan Han, Tiantian Li, Ting Liu, Zhenhua Wu, Hong Wei, Jiangchao Zhao, Junjun Wang
Software Mentions: 6
Published: over 5 years ago

10.1002/1878-0261.12709

HPV‐related methylation‐based reclassification and risk stratification of cervical cancer
Cited by: 25
Author(s): Shuanying Yang, Ying Wu, Shuqian Wang, Peng Xu, Yao Deng, Meng Wang, Kang Liu, Tian Tian, Yuyao Zhu, Na Li, Linghui Zhou, Zhijun Dai, Huafeng Kang
Software Mentions: 6
Published: about 6 years ago

10.1002/1878-0261.12965

The ZEB2‐dependent EMT transcriptional programme drives therapy resistance by activating nucleotide excision repair genes ERCC1 and ERCC4 in colorectal cancer
Cited by: 14
Author(s): Rahul Sreekumar, Hajir AlSaihati, Muhammad Emaduddin, Karwan A. Moutasim, Massimiliano Mellone, Ashish Patel, Seval Kılıç, Metin Çetįn, Sule Erdemir, Marta Salgado Navio, Maria A. Lopez, Nathan Curtis, Tamer Yağcı, John Primrose, Brendan D. Price, Geert Berx, Gareth J. Thomas, Eugene Tulchinsky, Alex H. Mirnezami, Emre Sayan
Software Mentions: 6
Published: over 5 years ago

10.18632/aging.102746

Identification of an immune-related risk signature for predicting prognosis in clear cell renal cell carcinoma
Cited by: 34
Author(s): Xiaoliang Hua, Juan Chen, Yang Su, Chaozhao Liang
Software Mentions: 6
Published: over 6 years ago

10.3389/fcell.2021.664843

Characterization of DNA Methylation and Screening of Epigenetic Markers in Polycystic Ovary Syndrome
Cited by: 9
Author(s): Pengbo Cao, Weihao Yang, Peijun Wang, Xihe Li, Buhe Nashun
Software Mentions: 6
Published: about 5 years ago

10.1186/s40168-021-01144-4

Trophic level drives the host microbiome of soil invertebrates at a continental scale
Cited by: 14
Author(s): Dong Zhu, Manuel Delgado‐Baquerizo, Jing Ding, Michael R. Gillings, Yong‐Guan Zhu
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12876-021-01734-4

Identification of the angiogenesis related genes for predicting prognosis of patients with gastric cancer
Cited by: 9
Author(s): Shu Zheng, Zizhen Zhang, Ning Ding, Jiawei Sun, Yaowang Lin, Jingyu Chen, Jing Zhong, Liming Shao, Zhenghua Lin, Min Xue
Software Mentions: 6
Published: over 5 years ago

10.3389/fonc.2020.579868

Hypoxia-Associated Prognostic Markers and Competing Endogenous RNA Co-Expression Networks in Breast Cancer
Cited by: 20
Author(s): Peng Gong, You-Cheng Shao, Shu‐Chun Huang, Yifan Zeng, Xianglin Yuan, Jingjing Xu, Weinan Yin, Lei Wei, Jingwei Zhang
Software Mentions: 6
Published: over 5 years ago

10.3389/fcell.2021.724860

Integrative Analysis of Biomarkers Through Machine Learning Identifies Stemness Features in Colorectal Cancer
Cited by: 7
Author(s): Ran Wei, Jichuan Quan, Shuofeng Li, Hengchang Liu, Xu Guan, Zheng Jiang, Xishan Wang
Software Mentions: 6
Published: almost 5 years ago

10.3389/fonc.2020.00424

BTK Has Potential to Be a Prognostic Factor for Lung Adenocarcinoma and an Indicator for Tumor Microenvironment Remodeling: A Study Based on TCGA Data Mining
Cited by: 82
Author(s): Kewei Bi, Xin Wei, Xiaoxue Qin, Bo Li
Software Mentions: 6
Published: over 6 years ago

10.1186/s12872-021-02166-4

Identification of biomarkers associated with metabolic cardiovascular disease using mRNA-SNP-miRNA regulatory network analysis
Cited by: 4
Author(s): Zhiyuan Fan, Wei Peng, Zhiwen Wang, Ling Zhang, Kuo Li
Software Mentions: 6
Published: about 5 years ago

10.18632/aging.102979

Development of a prognostic index and screening of potential biomarkers based on immunogenomic landscape analysis of colorectal cancer
Cited by: 33
Author(s): Lin Kang, Jun Huang, Haiwei Luo, Chen Luo, Xiaojian Zhu, Fanqin Bu, Han Xiao, Xiao Li, Zhengming Zhu
Software Mentions: 6
Published: over 6 years ago

10.3389/fcell.2021.690167

Sex-Specific Development in Haplodiploid Honeybee Is Controlled by the Female-Embryo-Specific Activation of Thousands of Intronic LncRNAs
Cited by: 0
Author(s): Miao Wang, Dong Chen, Huoqing Zheng, Luping Zhao, Xiao‐Feng Xue, Fengyun Yu, Yu Zhang, Chao Cheng, Qingsheng Niu, Shuai Wang, Yi Zhang, Liming Wu
Software Mentions: 6
Published: about 5 years ago

10.1080/21655979.2020.1840731

Bioinformatics analysis to screen key prognostic genes in the breast cancer tumor microenvironment
Cited by: 9
Author(s): Qian Ye, Xiaofei Han, Zhengsheng Wu
Software Mentions: 6
Published: over 6 years ago

10.1186/s12894-021-00880-x

Cross-talk and clinical value of m[superscript 6]A regulatory gene in bladder cancer
Cited by: 0
Author(s): Benzheng Zhou, Qin Luo, Ye Zhang
Software Mentions: 6
Published: almost 5 years ago

10.3390/plants10061039

Comparative Analysis of Re-Annotated Genes Provides Insight into Evolutionary Divergence and Expressions of Aquaporin Family in Pepper
Cited by: 2
Author(s): Yeon Mi Lee, Geun Young Chae, Min Kyung Kim, Seungill Kim
Software Mentions: 6
Published: about 5 years ago

10.1186/s12885-021-08520-1

Computational analysis for identification of early diagnostic biomarkers and prognostic biomarkers of liver cancer based on GEO and TCGA databases and studies on pathways and biological functions affecting the survival time of liver cancer
Cited by: 21
Author(s): Shuangquan Gao, Jian Gang, Man Yu, Guiliang Xin, Huixin Tan
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pbio.3000948

Absence of nuclear receptors LXRs impairs immune response to androgen deprivation and leads to prostate neoplasia
Cited by: 3
Author(s): Laura Bousset, Amandine Septier, Julio Buñay, Allison Voisin, Rachel Guiton, Christelle Damon-Soubeyrant, Yoan Renaud, Angélique De Haze, Vincent Sapin, Anne Fogli, Amandine Rambur, Cyrille de Joussineau, Ayhan Kocer, Amalia Trousson, Joëlle Henry-Berger, Marcus Höring, Gerhard Liebisch, Silke Matysik, Jean-Marc A. Lobaccaro, Laurence Morel, Silvère Baron
Software Mentions: 6
Published: over 5 years ago

10.18632/aging.203166

Identification and validation of inferior prognostic genes associated with immune signatures and chemotherapy outcome in acute myeloid leukemia
Cited by: 7
Author(s): Jie Wang, Hao Jian-ping, Nazim Uddin, Yun Wu, Rong Chen, Dongfeng Li, Dai-qin Xiong, Nan Ding, Jianhua Yang, Xiaowen Ding
Software Mentions: 6
Published: about 5 years ago

10.7717/peerj.4402

Comparative genomic analysis of a new tellurite-resistantPsychrobacterstrain isolated from the Antarctic Peninsula
Cited by: 19
Author(s): Claudia Muñoz-Villagrán, Katterinne N. Mendez, Fabián A. Cornejo, Maximiliano Figueroa, Agustina Undabarrena, Eduardo Morales, Mauricio Arenas-Salinas, Felipe Arenas, Eduardo Castro-Nallar, Claudio C. Vásquez
Software Mentions: 6
Published: over 8 years ago

10.3389/fcell.2021.622021

Identification of Potential ceRNA Network and Patterns of Immune Cell Infiltration in Systemic Sclerosis-Associated Interstitial Lung Disease
Cited by: 6
Author(s): Qiuhong Wu, Yang Liu, Yan Xie, Shixiong Wei, Yi Liu
Software Mentions: 6
Published: about 5 years ago

10.1186/s12885-021-08083-1

Gene expression and immune infiltration in melanoma patients with different mutation burden
Cited by: 8
Author(s): Liwei Wang, Chuanxi Fu, Rui Li, Lei Shi, Guosheng Zhao, Yan Zhang
Software Mentions: 6
Published: over 5 years ago

10.3389/fcell.2021.682002

Identification of CDK2-Related Immune Forecast Model and ceRNA in Lung Adenocarcinoma, a Pan-Cancer Analysis
Cited by: 34
Author(s): Tingting Liu, Rui Li, Huo Chen, Jianping Li, Jie Yao, Xiu-Li Ji, Yi-Qing Qu
Software Mentions: 6
Published: about 5 years ago

10.3390/nu12041042

Green Tea Polyphenol EGCG Attenuates MDSCs-mediated Immunosuppression through Canonical and Non-Canonical Pathways in a 4T1 Murine Breast Cancer Model
Cited by: 33
Author(s): Ping Xu, Feng Yan, Yuhai Zhao, Xiangbo Chen, Shili Sun, Yuefei Wang, Le Ying
Software Mentions: 6
Published: over 6 years ago

10.3389/fcell.2021.633747

Transcriptome Analysis Reveals Differentially Expressed Genes and Long Non-coding RNAs Associated With Fecundity in Sheep Hypothalamus With Different FecB Genotypes
Cited by: 10
Author(s): Si Chen, Xiaofei Guo, Xiaoyun He, Ran Di, Xiaosheng Zhang, Jinlong Zhang, Xiangyu Wang
Software Mentions: 6
Published: about 5 years ago

10.3389/fonc.2019.00221

Non-coding and Coding Transcriptional Profiles Are Significantly Altered in Pediatric Retinoblastoma Tumors
Cited by: 25
Author(s): Swetha Rajasekaran, Lakshmi Dhevi N. Selvan, Kathleen Dotts, Ranjith Kumar, Pukhraj Rishi, Vikas Khetan, Madhoolika Bisht, Karthikeyan Sivaraman, Subrmanian Krishnakumar, Debashis Sahoo, Moray J. Campbell, Sailaja Elchuri, Wayne Miles
Software Mentions: 6
Published: over 7 years ago

10.3390/microorganisms9030492

The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort Study
Cited by: 11
Author(s): Barry Linnane, Aaron M. Walsh, Calum J. Walsh, Fiona Crispie, Órla O’Sullivan, Paul D. Cotter, Michael McDermott, J. A. A. Renwick, Paul McNally
Software Mentions: 6
Published: over 5 years ago

10.3389/fonc.2021.587479

Identification of Mitochondrial-Related Prognostic Biomarkers Associated With Primary Bile Acid Biosynthesis and Tumor Microenvironment of Hepatocellular Carcinoma
Cited by: 21
Author(s): Tao Zhang, Yingli Nie, Jian Gu, Kailin Cai, Xiangdong Chen, Huili Li, Jiliang Wang
Software Mentions: 6
Published: over 5 years ago

10.3389/fcell.2021.672248

Immune Infiltrates of m6A RNA Methylation-Related lncRNAs and Identification of PD-L1 in Patients With Primary Head and Neck Squamous Cell Carcinoma
Cited by: 25
Author(s): Ziyi Feng, Haoyu Gao, Tianda Feng
Software Mentions: 6
Published: about 5 years ago

10.3390/microorganisms9020208

Aquatic Bacterial Diversity, Community Composition and Assembly in the Semi-Arid Inner Mongolia Plateau: Combined Effects of Salinity and Nutrient Levels
Cited by: 29
Author(s): Xiangming Tang, Guobo Xie, Kwang‐Tsao Shao, Wei Tian, Guang Gao, Boqiang Qin
Software Mentions: 6
Published: over 5 years ago

10.3389/fcell.2021.686909

Multi-Omics Data Integration Analysis of an Immune-Related Gene Signature in LGG Patients With Epilepsy
Cited by: 13
Author(s): Quan Cheng, Weiwei Duan, Shiqing He, Chen Li, Hui Cao, Kun Liu, Weijie Ye, Bo Yuan, Zhiwei Xia
Software Mentions: 6
Published: about 5 years ago

10.1186/s12885-020-06741-4

A novel risk score model based on eight genes and a nomogram for predicting overall survival of patients with osteosarcoma
Cited by: 30
Author(s): Guangzhi Wu, Minglei Zhang
Software Mentions: 6
Published: about 6 years ago

10.1186/s12967-020-02545-z

Development and validation of a robust immune-related prognostic signature in early-stage lung adenocarcinoma
Cited by: 13
Author(s): Pancheng Wu, Yi Zheng, Yanyu Wang, Yadong Wang, Ning Liang
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12967-020-02689-y

Three hematologic/immune system-specific expressed genes are considered as the potential biomarkers for the diagnosis of early rheumatoid arthritis through bioinformatics analysis
Cited by: 60
Author(s): Qi Cheng, Xin Chen, Huaxiang Wu, Yan Du
Software Mentions: 6
Published: over 5 years ago

10.3389/fonc.2019.00692

Transcriptomic Analysis Identifies RNA Binding Proteins as Putative Regulators of Myelopoiesis and Leukemia
Cited by: 16
Author(s): Subha Saha, Krushna Chandra Murmu, Mayukh Biswas, Sohini Chakraborty, Jhinuk Basu, Swati Madhulika, Srinivasa Prasad Kolapalli, Santosh Chauhan, Amitava Sengupta, Punit Prasad
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pbio.3000675

SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution
Cited by: 35
Author(s): Alexandros Sountoulidis, Andreas Liontos, Hong Phuong Nguyen, Alexandra B. Firsova, Athanasios Fysikopoulos, Xiaoyan Qian, Werner Seeger, Erik Sundström, Mats Nilsson, Christos Samakovlis
Software Mentions: 6
Published: over 5 years ago

10.3390/microorganisms9010002

Genomic Analysis of Antimicrobial Resistance Genotype-to-Phenotype Agreement in Helicobacter pylori
Cited by: 15
Author(s): Tal Domanovich-Asor, Yair Motro, Boris Khalfin, Hillary A. Craddock, Avi Peretz, Jacob Moran-Gilad
Software Mentions: 6
Published: over 5 years ago

10.3389/fonc.2021.617289

Derivation and Validation of a Prognostic Model for Cancer Dependency Genes Based on CRISPR-Cas9 in Gastric Adenocarcinoma
Cited by: 16
Author(s): Wenjie Zhou, Junqing Li, Xiufen Lu, Fangjie Liu, Tailai An, Xing Xiao, Zi Chong Kuo, Wenhui Wu, Yulong He
Software Mentions: 6
Published: over 5 years ago

10.3389/fonc.2020.544610

Identification of Four Immune Subtypes in Bladder Cancer Based on Immune Gene Sets
Cited by: 25
Author(s): Chaozhi Tang, Jiakang Ma, Xiuli Liu, Zhengchun Liu
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12967-020-02260-9

Identification of key genes controlling breast cancer stem cell characteristics via stemness indices analysis
Cited by: 42
Author(s): Jianying Pei, Yanxia Wang, Yan Li
Software Mentions: 6
Published: over 6 years ago

10.1186/s40168-020-00854-5

Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria
Cited by: 52
Author(s): Xingxing Jian, Yinghong Zhu, Jian Ouyang, Yihui Wang, Qian Lei, Jiliang Xia, Yongjun Guan, Jingyu Zhang, Jiaojiao Guo, Yanjuan He, Jinuo Wang, Jian Li, Jingchao Lin, Mingming Su, Guancheng Li, Minghua Wu, Lugui Qiu, Juanjuan Xiang, Lu Xie, Jia Wang, Wen Zhou
Software Mentions: 6
Published: about 6 years ago

10.1186/s12885-020-07438-4

A 38-gene model comprised of key TET2-associated genes shows additive utility to high-risk prostate cancer cases in the prognostication of biochemical recurrence
Cited by: 1
Author(s): Shivani Kamdar, Neil Fleshner, Bharati Bapat
Software Mentions: 6
Published: almost 6 years ago

10.7717/peerj.7141

Comparison of soil bacterial community and functional characteristics following afforestation in the semi-arid areas
Cited by: 27
Author(s): Jiaojiao Deng, Yan Zhang, You Yin, Xu Zhu, Wenxu Zhu, Yongbin Zhou
Software Mentions: 6
Published: about 7 years ago

10.1186/s40168-019-0689-3

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease
Cited by: 184
Author(s): Almut Heinken, Dmitry A. Ravcheev, Federico Baldini, Laurent Heirendt, Ronan M. T. Fleming, Ines Thiele
Software Mentions: 6
Published: over 7 years ago

10.1186/s40168-020-0783-6

Dietary effects on gut microbiota of the mesquite lizard Sceloporus grammicus (Wiegmann, 1828) across different altitudes
Cited by: 36
Author(s): Nina Montoya‐Ciriaco, Selene Gómez-Acata, Ligia Catalina Muñoz-Arenas, Luc Dendooven, Arturo Estrada–Torres, Aníbal H. Díaz de la Vega‐Pérez, Yendi E. Navarro‐Noya
Software Mentions: 6
Published: over 6 years ago

10.1186/s40168-020-00806-z

RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs
Cited by: 178
Author(s): Leyuan Li, Zhibin Ning, Xu Zhang, Janice Mayne, Kai Cheng, Alain Stintzi, Daniel Figeys
Software Mentions: 6
Published: over 6 years ago

10.3389/fmolb.2020.620765

Development and External Validation of a Novel Immune Checkpoint–Related Gene Signature for Prediction of Overall Survival in Hepatocellular Carcinoma
Cited by: 11
Author(s): Enfa Zhao, Shimin Chen, Yujie Dang
Software Mentions: 6
Published: over 5 years ago

10.1002/2211-5463.13211

Prognostic biomarker identification and tumor classification in breast cancer patients by methylation and transcriptome analysis
Cited by: 4
Author(s): Xiongdong Zhong, Guoying Zhong
Software Mentions: 6
Published: about 5 years ago

10.1002/2211-5463.12692

Multidimensional profiling of drug‐treated cells by Imaging Mass Cytometry
Cited by: 33
Author(s): Alexandre Bouzekri, Amanda Esch, Olga Ornatsky
Software Mentions: 6
Published: about 7 years ago

10.3389/fmolb.2020.00148

Friend or Foe: Prognostic and Immunotherapy Roles of BTLA in Colorectal Cancer
Cited by: 23
Author(s): Jingjing Song, Lihui Wu
Software Mentions: 6
Published: about 6 years ago

10.1186/s40168-019-0781-8

Metagenomic analysis reveals the microbiome and resistome in migratory birds
Cited by: 96
Author(s): Jintao Cao, Yongfei Hu, Fei Liu, Yanan Wang, Yuhai Bi, Na Lv, Jing Li, Baoli Zhu, George F. Gao
Software Mentions: 6
Published: over 6 years ago

10.7717/peerj.8505

Identification and validation of key modules and hub genes associated with the pathological stage of oral squamous cell carcinoma by weighted gene co-expression network analysis
Cited by: 10
Author(s): Xuegang Hu, Genban Sun, Zhiqiang Shi, Hui Ni, Shan Jiang
Software Mentions: 6
Published: over 6 years ago

10.3390/ijms22168482

Multicellular Human Cardiac Organoids Transcriptomically Model Distinct Tissue-Level Features of Adult Myocardium
Cited by: 17
Author(s): Charles M. Kerr, Dylan Richards, Donald R. Menick, Kristine Y. DeLeon‐Pennell, Ying Mei
Software Mentions: 6
Published: about 5 years ago

10.1093/femsec/fiz108

Diversity of tryptophan halogenases in sponges of the genus Aplysina
Cited by: 9
Author(s): Johanna Gutleben, Jasper J. Koehorst, Kyle McPherson, Shirley A. Pomponi, René H. Wijffels, Hauke Smidt, Detmer Sipkema
Software Mentions: 6
Published: about 7 years ago

10.1099/mgen.0.000064

In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages
Cited by: 95
Author(s): Danielle J. Ingle, Mary Valcanis, Alex Kuzevski, Marija Tauschek, Michael Inouye, Timothy P. Stinear, Myron M. Levine, Roy M. Robins-Browne, Kathryn E. Holt
Software Mentions: 6
Published: about 10 years ago

10.12688/f1000research.17149.2

Hub genes in a pan-cancer co-expression network show potential for predicting drug responses
Cited by: 0
Author(s): Francisco Azuaje, Tony Kaoma, Céline Jeanty, Petr V. Nazarov, Arnaud Muller, Sang Yoon Kim, Gunnar Dittmar, Anna Golebiewska, Simone P. Niclou
Software Mentions: 6
Published: over 7 years ago

10.18632/oncotarget.15749

Gene regulatory pattern analysis reveals essential role of core transcriptional factors’ activation in triple-negative breast cancer
Cited by: 15
Author(s): Li Min, Cheng Zhang, Like Qu, Jialiang Huang, Lan Jiang, Jiafei Liu, Luca Pinello, Guo‐Cheng Yuan, Chengchao Shou
Software Mentions: 6
Published: over 9 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: about 6 years ago

10.7717/peerj.3051

Taxonomic and functional trait diversity of wild bees in different urban settings
Cited by: 97
Author(s): Étienne Normandin, Nicolas J. Vereecken, Christopher M. Buddle, Valérie Fournier
Software Mentions: 6
Published: over 9 years ago

10.15252/emmm.202012118

The mutational landscape of the <scp>SCAN</scp> ‐B real‐world primary breast cancer transcriptome
Cited by: 30
Author(s): Christian Brueffer, Sergii Gladchuk, Christof Winter, Johan Vallon‐Christersson, Cecilia Hegardt, Jari Häkkinen, Anthony George, Yilun Chen, Anna Ehinger, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Åke Borg, Lao H. Saal
Software Mentions: 6
Published: almost 6 years ago

10.1002/ece3.7861

Effects of ecological environment and host genotype on the phyllosphere bacterial communities of cigar tobacco (Nicotiana tabacum L.)
Cited by: 9
Author(s): Lei Xing, Jianlei Yang, Yuping Jia, Xiaobing Hu, Yi Liu, Heng Xu, Huaqun Yin, Juan Li, Zhenxie Yi
Software Mentions: 6
Published: about 5 years ago

10.1128/mSphere.00843-20

Pseudomonas aeruginosa Volatilome Characteristics and Adaptations in Chronic Cystic Fibrosis Lung Infections
Cited by: 10
Author(s): Thomas J. Davis, Ava V. Karanjia, Charity N. Bhebhe, Sarah B. West, Matthew Richardson, Heather D. Bean
Software Mentions: 6
Published: almost 6 years ago

10.1128/mBio.02399-20

Hemozoin Promotes Lung Inflammation via Host Epithelial Activation
Cited by: 1
Author(s): Shivang S. Shah, David A. Fidock, Alice Prince
Software Mentions: 6
Published: over 5 years ago

10.3390/microorganisms8081225

Lactobacillus Mucosae Strain Promoted by a High-Fiber Diet in Genetic Obese Child Alleviates Lipid Metabolism and Modifies Gut Microbiota in ApoE-/- Mice on a Western Diet
Cited by: 19
Author(s): Tianyi Jiang, Huan Wu, Xin Yang, Yue Li, Ziyi Zhang, Feng Chen, Liping Zhao, Chenhong Zhang
Software Mentions: 6
Published: about 6 years ago

10.1186/s13072-021-00411-w

Sensitivity of cohesin–chromatin association to high-salt treatment corroborates non-topological mode of loop extrusion
Cited by: 4
Author(s): Arkadiy K. Golov, Anastasia V. Golova, А. В. Гаврилов, Sergey V. Razin
Software Mentions: 6
Published: about 5 years ago

10.3390/ijms21228769

Physiological Changes in Barley mlo-11 Powdery Mildew Resistance Conditioned by Tandem Repeat Copy Number
Cited by: 3
Author(s): Cynthia Ge, Paula Moolhuijzen, Lee T. Hickey, Elzette Wentzel, Wei‐Wei Deng, Eric Dinglasan, Simon R. Ellwood
Software Mentions: 6
Published: over 5 years ago

10.1155/2020/8841859

Establishment and Validation of a Prognostic Risk Model for Autophagy-Related Genes in Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Wenkai Han, Xiaoyan Xu, Kai Che, Guofeng Ma, Danxia Li, Mingxin Zhang, Wei Jiao, Haitao Niu
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12920-021-01003-z

Repeat to gene expression ratios in leukemic blast cells can stratify risk prediction in acute myeloid leukemia
Cited by: 5
Author(s): Megumi Onishi-Seebacher, Galina Erikson, Zoe Sawitzki, Devon P. Ryan, Gabriele Greve, Michael Lübbert, Thomas Jenuwein
Software Mentions: 6
Published: about 5 years ago

10.1186/s41065-020-00169-3

Identification of differentially expressed genes, signaling pathways and immune infiltration in rheumatoid arthritis by integrated bioinformatics analysis
Cited by: 8
Author(s): Yanzhi Ge, Li Zhou, Zuxiang Chen, Yingying Mao, Ting Li, Peijian Tong
Software Mentions: 6
Published: over 5 years ago

10.26508/lsa.202000731

Exploiting somatic piRNAs in Bemisia tabaci enables novel gene silencing through RNA feeding
Cited by: 18
Author(s): Mosharrof Mondal, Judith K. Brown, Alex S. Flynt
Software Mentions: 6
Published: about 6 years ago

10.3389/fmolb.2021.619027

Gene Expression Subtyping Reveals Immune alterations:TCGA Database for Prognosis in Ovarian Serous Cystadenocarcinoma
Cited by: 4
Author(s): Chao Feng, Yan Xu, Yuanyuan Liu, Lixia Zhu, Le Wang, Xueying Cui, Jingjing Lü, Yan Zhang, Lina Zhou, Min-Bin Chen, Zhiqin Zhang, Ping Li
Software Mentions: 6
Published: almost 5 years ago

10.1101/2020.07.19.210955

Interferons and viruses induce a novel primate-specific isoform dACE2 and not the SARS-CoV-2 receptor ACE2
Cited by: 19
Author(s): Olusegun O. Onabajo, Abdul Rouf Banday, Wusheng Yan, Adeola Obajemu, Megan L. Stanifer, Deanna M. Santer, Óscar Flórez-Vargas, Helen Piontkivska, Joselin M. Vargas, Carmon Kee, D. Lorne Tyrrell, Juan L. Mendoza, Steeve Boulant, Ludmila Prokunina‐Olsson
Software Mentions: 6
Published: about 6 years ago

10.1186/s12967-017-1201-0

Whole blood gene expression in adolescent chronic fatigue syndrome: an exploratory cross-sectional study suggesting altered B cell differentiation and survival
Cited by: 46
Author(s): Chinh Bkrong Nguyen, Lene Alsøe, Jessica M. Lindvall, Dag Sulheim, Even Fagermoen, Anette Winger, Mari Kaarbø, Hilde Nilsen, Vegard Bruun Wyller
Software Mentions: 6
Published: over 9 years ago

10.1038/s41598-021-82306-0

Terroir and vintage discrimination of Malbec wines based on phenolic composition across multiple sites in Mendoza, Argentina
Cited by: 17
Author(s): Roy Urvieta, Gregory V. Jones, Fernando Buscema, Rubén Bottini, A. Fontana
Software Mentions: 6
Published: over 5 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: almost 6 years ago

10.1186/s40246-021-00313-8

Identification of differentially expressed genes and signaling pathways in human conjunctiva and reproductive tract infected with Chlamydia trachomatis
Cited by: 3
Author(s): Guodong Zhu, Xun‐Jie Cao, Yaping Li, Jiaxin Li, Zi-Jian Leng, Lisha Xie, Xu‐Guang Guo
Software Mentions: 6
Published: over 5 years ago

10.1186/s40246-021-00323-6

An ensemble of the iCluster method to analyze longitudinal lncRNA expression data for psoriasis patients
Cited by: 2
Author(s): Suyan Tian, Chi Wang
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-018-23989-w

A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition
Cited by: 90
Author(s): Jennifer L. Pechal, Carl J. Schmidt, Heather R. Jordan, M. Eric Benbow
Software Mentions: 6
Published: over 8 years ago

10.1161/CIRCULATIONAHA.120.046464

Hyperglycemia Induces Trained Immunity in Macrophages and Their Precursors and Promotes Atherosclerosis
Cited by: 75
Author(s): Laurienne Edgar, Naveed Akbar, Adam Braithwaite, Thomas Krausgruber, Héctor Gallart-Ayala, Jade Bailey, Alastair Corbin, Tariq E. Khoyratty, Joshua T Chai, Mohammad Alkhalil, André F. Rendeiro, Klemen Žiberna, Ritu Arya, Thomas J. Cahill, Christoph Bock, Jurga Laurencikiene, Mark J. Crabtree, Madeleine E. Lemieux, Niels P. Riksen, Mihai G. Netea, Craig E. Wheelock, Keith M. Channon, Mikael Rydén, Irina A. Udalova, Ricardo Carnicer, Robin P. Choudhury
Software Mentions: 6
Published: almost 5 years ago

10.1161/CIRCULATIONAHA.119.039596

Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins
Cited by: 74
Author(s): Sonia Chothani, Sebastian Schäfer, Eleonora Adami, V. Sivakumar, Anissa A. Widjaja, Sarah R. Langley, Jessie Tan, Mao Wang, Nicholas M Quaife, Chee Jian Pua, G. D’Agostino, Shamini Guna Shekeran, Benjamin L. George, Si Ching Lim, Elaine Yiqun Cao, Sebastiaan van Heesch, Franziska Witte, Leanne E. Felkin, Eleni G. Christodoulou, Jinqiao Dong, Susanne Blachut, Giannino Patone, Paul J.R. Barton, Norbert Hübner, Stuart A. Cook, Owen J. L. Rackham
Software Mentions: 6
Published: almost 7 years ago

10.1128/mSystems.00017-19

Probiotic Bifidobacterium lactis V9 Regulates the Secretion of Sex Hormones in Polycystic Ovary Syndrome Patients through the Gut-Brain Axis
Cited by: 128
Author(s): Jiachao Zhang, Zhihong Sun, Shuaiming Jiang, Xiaoye Bai, Chenchen Ma, Qingyun Peng, Kaining Chen, Haibo Chang, Tuanyu Fang, Heping Zhang
Software Mentions: 6
Published: over 7 years ago

10.1038/s41598-019-44902-z

Evaluation of ultra-low input RNA sequencing for the study of human T cell transcriptome
Cited by: 12
Author(s): Jingya Wang, Sadiye Amcaoglu Rieder, Jincheng Wu, Susana Hayes, Rebecca Halpin, Melissa de los Reyes, Yashaswi Shrestha, Roland Kolbeck, Rajiv Raja
Software Mentions: 6
Published: about 7 years ago

10.1038/s41598-019-46932-z

DMSO cryopreservation is the method of choice to preserve cells for droplet-based single-cell RNA sequencing
Cited by: 73
Author(s): Christian T. Wohnhaas, Germán Leparc, Francesc Fernández-Albert, David Kind, Florian Gantner, Coralie Viollet, Tobias Hildebrandt, Patrick Baum
Software Mentions: 6
Published: about 7 years ago

10.1186/s13148-018-0582-0

Differential open chromatin profile and transcriptomic signature define depot-specific human subcutaneous preadipocytes: primary outcomes
Cited by: 20
Author(s): Adeline Divoux, Katalin Sandor, Dóra Bojcsuk, Amlan Talukder, Xiaoman Li, Bálint László Bálint, Timothy F. Osborne, Steven R. Smith
Software Mentions: 6
Published: over 7 years ago

10.1038/s41598-019-50864-z

Circular RNA differential expression in blood cell populations and exploration of circRNA deregulation in pediatric acute lymphoblastic leukemia
Cited by: 62
Author(s): Enrico Gaffo, Elena Boldrin, Anna Dal Molin, Silvia Bresolin, Annagiulia Bonizzato, Luca Trentin, Chiara Frasson, Klaus‐Michael Debatin, Lueder Hinrich Meyer, Geertruy te Kronnie, Stefania Bortoluzzi
Software Mentions: 6
Published: almost 7 years ago

10.1002/ctm2.156

A three‐lncRNA signature of pretreatment biopsies predicts pathological response and outcome in esophageal squamous cell carcinoma with neoadjuvant chemoradiotherapy
Cited by: 17
Author(s): Chaoqi Zhang, Zhihui Zhang, Guochao Zhang, Liyan Xue, Haijun Yang, Yuejun Luo, Xiaoli Zheng, Yonglei Zhang, Yufen Yuan, Ruixue Lei, Zhaoyang Yang, Bo Zheng, Zhen Zhang, Le Wang, Yun Cao, Sihui Wang, Feng Wang, Lingling Fang, Qingpeng Zeng, Jiagen Li, Shugeng Gao, Qi Xue, Nan Sun, Jie He
Software Mentions: 6
Published: about 6 years ago

10.1038/s42003-021-02012-5

High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans
Cited by: 22
Author(s): Alexandra Schoenle, Manon Hohlfeld, Karoline Hermanns, Frédéric Mahé, Colomban de Vargas, Frank Nitsche, Hartmut Arndt
Software Mentions: 6
Published: over 5 years ago

Projects: cran: pheatmap

Science Score: 75/100

Penalties:

Papers Mentioning pheatmap 2,572