bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1186/s12864-018-5066-2

A comparative analysis of library prep approaches for sequencing low input translatome samples
Cited by: 52
Author(s): Yang Song, Béatrice Milon, Sandra Ott, Xüna Zhao, Lisa Sadzewicz, Amol C. Shetty, Erich T. Boger, Luke J. Tallon, Robert J. Morell, Anup Mahurkar, Ronna Hertzano
Software Mentions: 6
Published: almost 8 years ago

10.1186/s12859-019-3121-x

A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons
Cited by: 2
Author(s): Stanislav Listopad, Trina M. Norden-Krichmar
Software Mentions: 6
Published: almost 7 years ago

10.18632/aging.102817

Identification of prognostic immune-related genes in the tumor microenvironment of endometrial cancer
Cited by: 61
Author(s): Peigen Chen, Yongtao Yang, Yu Zhang, Senwei Jiang, Xiaomao Li, Jing Wan
Software Mentions: 6
Published: over 6 years ago

10.1186/s12864-015-1840-6

Male and female mice show significant differences in hepatic transcriptomic response to 2,3,7,8-tetrachlorodibenzo-p-dioxin
Cited by: 38
Author(s): Jamie Lee, Stephenie D. Prokopec, John D. Watson, Ren Sun, Raimo Pohjanvirta, Paul C. Boutros
Software Mentions: 6
Published: about 11 years ago

10.1371/journal.pone.0102610

Potential Therapeutic Targets for Oral Cancer: ADM, TP53, EGFR, LYN, CTLA4, SKIL, CTGF, CD70
Cited by: 28
Author(s): Saurabh Bundela, Anjana Sharma, Prakash S. Bisen
Software Mentions: 6
Published: about 12 years ago

10.1186/1471-2164-10-439

Relative power and sample size analysis on gene expression profiling data
Cited by: 64
Author(s): Maarten van Iterson, Peter A C ‘t Hoen, Paola Pedotti, Guido Hooiveld, Johan T. den Dunnen, Gjb van Ommen, JM Boer, R.M. Menezes
Software Mentions: 6
Published: almost 17 years ago

10.1038/s41421-020-00200-x

Single-cell transcriptome atlas of lung adenocarcinoma featured with ground glass nodules
Cited by: 45
Author(s): Tao Lu, Xiaodong Yang, Yu Shi, Mengnan Zhao, Guoshu Bi, Jiaqi Liang, Zhencong Chen, Yiwei Huang, Wei Jiang, Lin Zhang, Junjie Xi, Shuai Wang, Yong Yang, Cheng Zhan, Qun Wang, Liang Tan
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12859-015-0610-4

Factors affecting the accuracy of a class prediction model in gene expression data
Cited by: 17
Author(s): Putri W. Novianti, Victor L. Jong, Kit C. B. Roes, Marinus J.C. Eijkemans
Software Mentions: 6
Published: about 11 years ago

10.1186/s40168-018-0526-0

Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems
Cited by: 299
Author(s): Shuo Jiao, Weimin Chen, Jieli Wang, Nini Du, Qiaoping Li, Gehong Wei
Software Mentions: 6
Published: about 8 years ago

10.18632/aging.202603

Functional analysis of brain derived neurotrophic factor (BDNF) in Huntington’s disease
Cited by: 6
Author(s): Zhike Zhou, Shanshan Zhong, Rongwei Zhang, Kexin Kang, Xiaoqian Zhang, Ying Xu, Chuansheng Zhao, Mei Zhao
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0106397

RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data
Cited by: 138
Author(s): Mehmet K. Samur
Software Mentions: 6
Published: almost 12 years ago

10.1186/s12859-020-03715-y

MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments
Cited by: 8
Author(s): Brian Vestal, Camille M. Moore, Elizabeth Wynn, Laura Saba, Tasha E. Fingerlin, Katerina Kechris
Software Mentions: 6
Published: about 6 years ago

10.1155/2020/5816763

Screening of T Cell-Related Long Noncoding RNA-MicroRNA-mRNA Regulatory Networks in Non-Small-Cell Lung Cancer
Cited by: 6
Author(s): Jinping Duan, Yuefen Pan, Yang Xi, Liping Zhong, Jia Yin, Jingying Xu, Zhuang Jing, Shuwen Han
Software Mentions: 6
Published: almost 6 years ago

10.1093/gigascience/giaa117

Correcting for experiment-specific variability in expression compendia can remove underlying signals
Cited by: 16
Author(s): Alexandra Lee, YoSon Park, Georgia Doing, Deborah A. Hogan, Casey S. Greene
Software Mentions: 6
Published: almost 6 years ago

10.3389/fonc.2021.697198

A Pyroptosis-Related Gene Signature for Predicting Survival in Glioblastoma
Cited by: 40
Author(s): Xinyu Li, Luyu Zhang, Xueyuan Li, Xitao Yang, Lixin Su
Software Mentions: 6
Published: about 5 years ago

10.3389/fonc.2021.597536

Systems Biomedicine of Primary and Metastatic Colorectal Cancer Reveals Potential Therapeutic Targets
Cited by: 7
Author(s): Mehran Piran, Neda Sepahi, Afagh Moattari, A. M. Rahimi, Ali Ghanbariasad
Software Mentions: 6
Published: about 5 years ago

10.3390/life11020115

A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression
Cited by: 6
Author(s): Theodora-Dafni Michalettou, Ioannis Michalopoulos, Sylvain V. Costes, Christine E. Hellweg, Megumi Hada, Alexandros G. Georgakilas
Software Mentions: 6
Published: over 5 years ago

10.1186/s12920-019-0571-y

Stoichioproteomics reveal oxygen usage bias, key proteins and pathways in glioma
Cited by: 4
Author(s): Yuan Yin, Bo Li, Ke‐Jie Mou, Muhammad Tahir Khan, Aman Chandra Kaushik, Dong‐Qing Wei, Yujuan Zhang
Software Mentions: 6
Published: about 7 years ago

10.1186/1471-2105-13-102

Workflows for microarray data processing in the Kepler environment
Cited by: 14
Author(s): Thomas Stropp, Timothy M. McPhillips, Bertram Ludäscher, Mark Bieda
Software Mentions: 6
Published: over 14 years ago

10.1080/21655979.2020.1847398

Development of cancer prognostic signature based on pan-cancer proteomics
Cited by: 6
Author(s): Weiguo Huang, Jianhui Chen, Wanqing Weng, Yukai Xiang, Hongqi Shi, Yunfeng Shan
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0175657

Age, gender and UV-exposition related effects on gene expression in in vivo aged short term cultivated human dermal fibroblasts
Cited by: 28
Author(s): Wolfgang Kaisers, Petra Boukamp, Hans Jürgen Stark, Holger Schwender, Julia Tigges, Jean Krutmann, Heiner Schaal
Software Mentions: 6
Published: over 9 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

10.1186/s12859-015-0751-5

Comparative study on gene set and pathway topology-based enrichment methods
Cited by: 61
Author(s): Michaela Bayerlová, Klaus Jung, Frank Krämer, Florian Klemm, Annalen Bleckmann, Tim Beißbarth
Software Mentions: 6
Published: almost 11 years ago

10.3389/fonc.2020.01001

Network-Based Approach to Identify the Antiproliferative Mechanisms of Bruceine D in Breast Cancer From the Cancer Genome Atlas
Cited by: 3
Author(s): Sai Tian, Rui Jiang, Weidong Zhang
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0252096

Application of multi-omics data integration and machine learning approaches to identify epigenetic and transcriptomic differences between in vitro and in vivo produced bovine embryos
Cited by: 9
Author(s): María Belén Rabaglino, Alan M. O’Doherty, Jan Bojsen-Møller Secher, Patrick Lonergan, Poul Hyttel, Trudee Fair, Haja N. Kadarmideen
Software Mentions: 6
Published: over 5 years ago

10.1186/s40170-020-00217-6

Therapy-induced lipid uptake and remodeling underpin ferroptosis hypersensitivity in prostate cancer
Cited by: 56
Author(s): Kaylyn D. Tousignant, Anja Rockstroh, Berwyck L. J. Poad, Ali Talebi, Reuben S. E. Young, Atefeh Taherian Fard, Rajesh Gupta, Tuo Zang, Chenwei Wang, Melanie Lehman, Johan Swinnen, Stephen J. Blanksby, Colleen C. Nelson, Martin C. Sadowski
Software Mentions: 6
Published: about 6 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/s12864-020-6684-z

Transcriptomic analysis of marine endophytic fungi extract identifies highly enriched anti-fungal fractions targeting cancer pathways in HepG2 cell lines
Cited by: 7
Author(s): Ethel J. S. Blessie, Wasco Wruck, Benaiah Annertey Abbey, Audrey Ncube, Nina Graffmann, Vincent Amarh, Patrick Kobina Arthur, James Adjaye
Software Mentions: 6
Published: over 6 years ago

10.18632/aging.103807

Identification of long-term survival-associated gene in breast cancer
Cited by: 12
Author(s): Shipeng Ning, Hui Li, Kun Qiao, Qin Wang, Meiying Shen, Yujuan Kang, Yanling Yin, Jiena Liu, Lei Liu, Siyu Hou, Yunlong Wang, Shouping Xu, Da Pang
Software Mentions: 6
Published: almost 6 years ago

10.1038/leu.2015.172

Genome-scale definition of the transcriptional programme associated with compromised PU.1 activity in acute myeloid leukaemia
Cited by: 15
Author(s): Jonathan Sive, Silvia Basilico, Rebecca Hannah, Sarah Kinston, Fernando J. Calero-Nieto, Berthold Göttgens
Software Mentions: 6
Published: about 11 years ago

10.1002/cam4.3133

Charactering tumor microenvironment reveals stromal‐related transcription factors promote tumor carcinogenesis in gastric cancer
Cited by: 14
Author(s): Haining Liu, Shujuan Ni, Hanbo Wang, Qiongyan Zhang, Wei-Hung Weng
Software Mentions: 6
Published: over 6 years ago

10.3389/fonc.2021.675545

Identification of a Ferroptosis-Related LncRNA Signature as a Novel Prognosis Model for Lung Adenocarcinoma
Cited by: 52
Author(s): Lu Lu, Leping Liu, Qiangqiang Zhao, Rong Gui, Qiancheng Zhao
Software Mentions: 6
Published: about 5 years ago

10.3389/fnins.2019.00392

Data-Driven Analysis of Age, Sex, and Tissue Effects on Gene Expression Variability in Alzheimer's Disease
Cited by: 19
Author(s): Lavida R. K. Brooks, George I. Mias
Software Mentions: 6
Published: over 7 years ago

10.1002/cam4.4161

Integrated pan‐cancer of AURKA expression and drug sensitivity analysis reveals increased expression of AURKA is responsible for drug resistance
Cited by: 12
Author(s): Noushin Miralaei, Ahmad Majd, Kamran Ghaedi, Maryam Peymani, Masoomeh Safaei
Software Mentions: 6
Published: about 5 years ago

10.1186/1471-2164-10-270

Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events
Cited by: 110
Author(s): Sônia Sousa Melo Cavalcanti de Albuquerque, Céline Carret, Ana Rita Grosso, Alice S. Tarun, Xinxia Peng, Stefan H. I. Kappe, Miguel Prudêncio, Maria M. Mota
Software Mentions: 6
Published: about 17 years ago

10.1002/cam4.3984

Signature based on metabolic‐related gene pairs can predict overall survival of osteosarcoma patients
Cited by: 8
Author(s): Long‐Qing Li, Liang‐Hao Zhang, Yongjie Yuan, Xin Lu, Yi Zhang, Yong‐Kui Liu, Wen Jiang, Manhas Abdul Khader, Tao Liu, Jiazhen Li, Yan Zhang
Software Mentions: 6
Published: over 5 years ago

10.1186/s13040-021-00261-y

A prognostic model based on seven immune-related genes predicts the overall survival of patients with hepatocellular carcinoma
Cited by: 6
Author(s): Qian Yan, Wenjiang Zheng, Boqing Wang, Baoqian Ye, Huiyan Luo, Xinqian Yang, Ping Zhang, Xiongwen Wang
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0037714

Dynamic Gene Expression in the Human Cerebral Cortex Distinguishes Children from Adults
Cited by: 32
Author(s): Kirstin N. Sterner, Amy Weckle, Harry T. Chugani, Adi L. Tarca, Chet C. Sherwood, Patrick R. Hof, Christopher W. Kuzawa, Amy M. Boddy, Asad Abbas, Ryan L. Raaum, Lucie Grégoire, Leonard Lipovich, Lawrence I. Grossman, Monica Uddin, Morris Goodman, Derek E. Wildman
Software Mentions: 6
Published: over 14 years ago

10.1371/journal.pone.0066826

A Comparative Analysis of Transcription Factor Expression during Metazoan Embryonic Development
Cited by: 31
Author(s): Alicia N. Schep, Boris Adryan
Software Mentions: 6
Published: about 13 years ago

10.1186/1471-2105-9-86

The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
Cited by: 75
Author(s): Frédéric Chalmel, Michael Primig
Software Mentions: 6
Published: over 18 years ago

10.18632/aging.102683

DNAH10 mutation correlates with cisplatin sensitivity and tumor mutation burden in small-cell lung cancer
Cited by: 19
Author(s): Man Li, Anqi Lin, Peng Luo, Weitao Shen, Dan Xiao, Lan-ying Gou, Jian Zhang, Linlang Guo
Software Mentions: 6
Published: over 6 years ago

10.3389/fonc.2021.685065

Comprehensive Landscape of Ovarian Cancer Immune Microenvironment Based on Integrated Multi-Omics Analysis
Cited by: 4
Author(s): Jiacheng Shen, Tingwei Liu, Qiaoli Bei, Shaohua Xu
Software Mentions: 6
Published: about 5 years ago

10.3389/fnmol.2021.637143

Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data
Cited by: 7
Author(s): Jordan Sicherman, Dwight F. Newton, Paul Pavlidis, Etienne Sibille, Shreejoy J. Tripathy
Software Mentions: 6
Published: over 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

10.1186/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

10.1002/cam4.3576

Establishment and validation of a prognostic nomogram based on a novel five‐DNA methylation signature for survival in endometrial cancer patients
Cited by: 6
Author(s): Xingchen Li, Fufen Yin, Fan Yuan, Yuan Cheng, Yangyang Dong, Jingyi Zhou, Zhiqi Wang, Jianliu Wang
Software Mentions: 6
Published: over 5 years ago

10.1002/cam4.4115

Development and validation of a PBRM1‐associated immune prognostic model for clear cell renal cell carcinoma
Cited by: 5
Author(s): Jiayi Chen, Chunlin Yao, Nan Qiao, Yangyang Ge, Jianhua Li, Yun Lin, Shanglong Yao
Software Mentions: 6
Published: almost 5 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

10.1371/journal.pone.0134011

A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis.
Cited by: 7
Author(s): Gabriela D. A. Guardia, Luís Ferreira Pires, Ricardo Zorzetto Nicoliello Vêncio, Kelen Cristina Ribeiro Malmegrim, Cléver Ricardo Guareis de Farias
Software Mentions: 6
Published: over 11 years ago

10.18632/aging.203190

Immune infiltration and a ferroptosis-associated gene signature for predicting the prognosis of patients with endometrial cancer
Cited by: 32
Author(s): Wenwu Yin, Liao Fuchun, Mengjie Chen, Xiaoqing Qin, Hao Lai, Yuan Lin, Desheng Yao
Software Mentions: 6
Published: about 5 years ago

10.3389/fmolb.2021.607090

Identification of an IRGP Signature to Predict Prognosis and Immunotherapeutic Efficiency in Bladder Cancer
Cited by: 12
Author(s): Lianghao Zhang, Long‐Qing Li, Yonghao Zhan, Zhaowei Zhu, Xuepei Zhang
Software Mentions: 6
Published: over 5 years ago

10.3389/fmolb.2020.608368

Identification and Development of a Novel 4-Gene Immune-Related Signature to Predict Osteosarcoma Prognosis
Cited by: 12
Author(s): Mingde Cao, Junhui Zhang, Haiyan Xu, Zhujian Lin, Hong Chang, Yuchen Wang, Xusheng Huang, Xiang Chen, Hua Wang, Yancheng Song
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0180322

Affected pathways and transcriptional regulators in gene expression response to an ultra-marathon trail: Global and independent activity approaches
Cited by: 6
Author(s): María Maqueda, Emma Roca, Daniel Brotons, José Manuel Nieto Soria, Alexandre Perera
Software Mentions: 6
Published: almost 9 years ago

10.3389/fmolb.2020.582911

Comprehensive Analysis of the Relationships Between Tumor Mutation Burden With Immune Infiltrates in Cervical Cell Carcinoma
Cited by: 9
Author(s): Cankun Zhou, Chaomei Li, Shunqing Peng, Liangcheng Zhou, Huan Li
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0183517

Integrated analysis of long non-coding RNAs in human gastric cancer: An in silico study
Cited by: 7
Author(s): Han Wang, Zhenyu Zhang, Bangshun He, Yu Xu, Jun Zhang, Weijun Cao
Software Mentions: 6
Published: about 9 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

10.3389/fmolb.2021.675651

Construction and External Validation of a Ferroptosis-Related Gene Signature of Predictive Value for the Overall Survival in Bladder Cancer
Cited by: 28
Author(s): Jingchao Liu, Hong Ma, Lingfeng Meng, Xiaodong Liu, Zhengtong Lv, Yaoguang Zhang, Qianqian Wang
Software Mentions: 6
Published: over 5 years ago

10.3389/fmolb.2021.636991

Identifying Dendritic Cell–Related Genes Through a Co-Expression Network to Construct a 12-Gene Risk-Scoring Model for Predicting Hepatocellular Carcinoma Prognosis
Cited by: 7
Author(s): Chao-Yuan Huang, Xiaotao Jiang, Yuancheng Huang, Lina Zhao, Peiwu Li, Fengbin Liu
Software Mentions: 6
Published: over 5 years ago

10.3389/fmolb.2021.628546

Identification of Molecular Subtypes and Key Genes of Atherosclerosis Through Gene Expression Profiles
Cited by: 3
Author(s): Yujia Yang, Yuchen Cai, Yuan Zhang, Yuanfu Xu, Zhiqiang Xu
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0254829

Tumor infiltrating lymphocytes associated competitive endogenous RNA networks as predictors of outcome in hepatic carcinoma based on WGCNA analysis
Cited by: 1
Author(s): Ying He, Xu Rui, Li Peng, Xiaoyu Hu
Software Mentions: 6
Published: about 5 years ago

10.1186/1752-0509-8-S4-S5

Network-based biomarkers enhance classical approaches to prognostic gene expression signatures
Cited by: 18
Author(s): Rebecca Barter, Sarah-Jane Schramm, Graham J. Mann, Jean Yee Hwa Yang
Software Mentions: 6
Published: over 11 years ago

10.3389/fmolb.2021.644620

Pan-Cancer Prognostic, Immunity, Stemness, and Anticancer Drug Sensitivity Characterization of N6-Methyladenosine RNA Modification Regulators in Human Cancers
Cited by: 24
Author(s): Rui Li, Yunhong Yin, Xiu-Li Ji, Xiao Liu, Jianping Li, Yi-Qing Qu
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0068414

NanoMiner — Integrative Human Transcriptomics Data Resource for Nanoparticle Research
Cited by: 20
Author(s): Lingjia Kong, Soile Tuomela, Lauri Hahne, Helena Ahlfors, Olli Yli‐Harja, Bengt Fadeel, Riitta Lahesmaa, Reija Autio
Software Mentions: 6
Published: about 13 years ago

10.1371/journal.pone.0053544

Visualising the Cross-Level Relationships between Pathological and Physiological Processes and Gene Expression: Analyses of Haematological Diseases
Cited by: 13
Author(s): M. Ono, Reiko Tanaka, Manabu Kano, Toshio Sugiman
Software Mentions: 6
Published: over 13 years ago

10.1186/s12885-021-08341-2

Identification of the prognostic value of ferroptosis-related gene signature in breast cancer patients
Cited by: 55
Author(s): Ding Wang, Guodong Wei, Jiangwei Ma, Shuai Cheng, Longyuan Jia, Xinyue Song, Ming Zhang, Mingyi Ju, Lin Wang, Lin Zhao, Shijie Xin
Software Mentions: 6
Published: over 5 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

10.3389/fmolb.2021.615084

Development of a Machine Learning-Based Autophagy-Related lncRNA Signature to Improve Prognosis Prediction in Osteosarcoma Patients
Cited by: 12
Author(s): Guangzhi Zhang, Zhi-Xi Wu, Chunying Li, Enhui Ren, Wenhua Yuan, Yajun Deng, Qiqi Xie
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0012657

A Comprehensive and Universal Method for Assessing the Performance of Differential Gene Expression Analyses
Cited by: 13
Author(s): Mikhail G. Dozmorov, Joel M. Guthridge, Robert E. Hurst, Igor Dozmorov
Software Mentions: 6
Published: almost 16 years ago

10.1186/s12935-021-01804-3

Prognostic and predictive value of FCER1G in glioma outcomes and response to immunotherapy
Cited by: 11
Author(s): Houshi Xu, Qiangqiang Zhu, Lan Tang, Junkun Jiang, Huiwen Yuan, Anke Zhang, Meiqing Lou
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pgen.1008749

Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago
Cited by: 29
Author(s): Heini M. Natri, Katalina Bobowik, Pradiptajati Kusuma, Chelzie Crenna Darusallam, Guy S. Jacobs, Georgi Hudjashov, J. Stephen Lansing, Herawati Sudoyo, Nicholas E. Banovich, Murray P. Cox, Irene Gallego Romero
Software Mentions: 6
Published: over 6 years ago

10.3389/fimmu.2020.606338

Specific Induction of Double Negative B Cells During Protective and Pathogenic Immune Responses
Cited by: 33
Author(s): Christoph Ruschil, Gisela Gabernet, Gildas Lepennetier, Simon Heumos, Miriam Kaminski, Zsuzsanna Hracskó, Martin Irmler, Johannes Beckers, Ulf Ziemann, Sven Nahnsen, Gregory P. Owens, Jeffrey L. Bennett, Bernhard Hemmer, Markus C. Kowarik
Software Mentions: 6
Published: over 5 years ago

10.3389/fmolb.2021.619110

Screening and Identification of Key Common and Specific Genes and Their Prognostic Roles in Different Molecular Subtypes of Breast Cancer
Cited by: 7
Author(s): Na Sun, Peng Gao, Yanling Li, Zexuan Yan, Zaihui Peng, Yi Zhang, Fei Han, Xiaowei Qi
Software Mentions: 6
Published: over 5 years ago

10.3390/nu13041340

Ileal Lactase Expression Associates with Lactase Persistence Genotypes
Cited by: 1
Author(s): Jan Krzysztof Nowak, Emilia Dybska, Marzena Dworacka, Natallia Tsikhan, Victoria Kononets, Saule Bermagambetova, Jarosław Walkowiak
Software Mentions: 6
Published: over 5 years ago

10.1186/s12885-019-6101-7

A large cohort study identifying a novel prognosis prediction model for lung adenocarcinoma through machine learning strategies
Cited by: 43
Author(s): Yin Li, Di Ge, Jie Gu, Fan Xu, Qinqing Zhu
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pone.0096376

Large Sex Differences in Chicken Behavior and Brain Gene Expression Coincide with Few Differences in Promoter DNA-Methylation
Cited by: 38
Author(s): Daniel Nätt, Beatrix Agnvall, Per Jensen
Software Mentions: 6
Published: over 12 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

10.1186/s12885-021-08431-1

Five metastasis-related mRNAs signature predicting the survival of patients with liver hepatocellular carcinoma
Cited by: 7
Author(s): Chao Chen, Yan Qun Liu, Shi Qiu, Ya Li, Ning Jun Yu, Kang Liu, Li Ming Zhong
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0257072

Cytochrome P450-2D6: A novel biomarker in liver cancer health disparity
Cited by: 7
Author(s): Zahraa I. Khamis, Xiaodong Pang, Zihan Cui, Qing-Xiang Amy Sang, Jinfeng Zhang
Software Mentions: 6
Published: almost 5 years ago

10.20892/j.issn.2095-3941.2020.0073

Single-cell RNA-seq reveals the immune escape and drug resistance mechanisms of mantle cell lymphoma
Cited by: 23
Author(s): Liang Wang, Steven Mo, Xin Li, Yuanyuan He, Jing Yang
Software Mentions: 6
Published: over 6 years ago

10.3389/fimmu.2021.671201

Identification and Validation of the Signatures of Infiltrating Immune Cells in the Eutopic Endometrium Endometria of Women With Endometriosis
Cited by: 22
Author(s): Xinglong Wu, Jin-Jiao Chen, Huiling Zhou, Yu Wu, Fei Lin, Jing Shi, Hong-Zhen Wu, Hai-Qun Xiao, Wei Wang
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12967-020-02597-1

Transcriptome analysis identifies putative multi-gene signature distinguishing benign and malignant pancreatic head mass
Cited by: 8
Author(s): Bishnupriya Chhatriya, Moumita Mukherjee, Sukanta Ray, Barsha Saha, Somdatta Lahiri, Sandip Halder, Indranil Ghosh, Sujan Khamrui, Kshaunish Das, Samsiddhi Bhattacharjee, Saroj Kant Mohapatra, Srikanta Goswami
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12885-021-08083-1

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

10.1186/s12967-020-02545-z

Development and validation of a robust immune-related prognostic signature in early-stage lung adenocarcinoma
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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

10.1371/journal.pone.0219747

2,3,7,8-Tetrachlorodibenzo-p-dioxin modifies alternative splicing in mouse liver
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Author(s): Ana B. Villaseñor-Altamirano, John D. Watson, Stephenie D. Prokopec, Cindy Q. Yao, Paul C. Boutros, Raimo Pohjanvirta, Jesús Valdés‐Flores, Guillermo Elizondo
Software Mentions: 6
Published: about 7 years ago

10.18632/aging.102714

ISG20 serves as a potential biomarker and drives tumor progression in clear cell renal cell carcinoma
Cited by: 22
Author(s): Tianbo Xu, Hailong Ruan, Su Gao, Jingchong Liu, Yuenan Liu, Zhengshuai Song, Qi Cao, Keshan Wang, Lin Bao, Di Liu, Junwei Tong, Jian Shi, Huageng Liang, Hongmei Yang, Ke Chen, Xiaoping Zhang
Software Mentions: 6
Published: over 6 years ago

10.1155/2021/6347592

Macrophages M1-Related Prognostic Signature in Hepatocellular Carcinoma
Cited by: 2
Author(s): Hao Zhang, Lin Sun, Xiao Hu
Software Mentions: 6
Published: almost 5 years ago

10.18632/aging.103695

Glioblastoma cell differentiation trajectory predicts the immunotherapy response and overall survival of patients
Cited by: 26
Author(s): Zihao Wang, Xiaopeng Guo, Lu Gao, Yu Wang, Wenbin Ma, Bing Xing
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

10.1155/2020/2319194

Immune-Related lncRNA Correlated with Transcription Factors Provide Strong Prognostic Prediction in Gliomas
Cited by: 4
Author(s): Yantao Tian, Yiquan Ke, Yanxia Ma
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12935-020-01179-x

Expression profile analysis identifies key genes as prognostic markers for metastasis of osteosarcoma
Cited by: 12
Author(s): Xiaoqing Guan, Zhiyuan Guan, Chunli Song
Software Mentions: 6
Published: over 6 years ago

10.1155/2021/5583400

Identification and Validation of Autophagy-Related Gene Nomograms to Predict the Prognostic Value of Patients with Cervical Cancer
Cited by: 3
Author(s): Jinqun Jiang, Hongxing Xu, Yihao Wang, Hai Lü
Software Mentions: 6
Published: about 5 years ago

10.1186/s12885-021-08052-8

Comprehensive analysis of immune-related prognostic genes in the tumour microenvironment of hepatocellular carcinoma
Cited by: 2
Author(s): Weike Gao, Luan Li, Xinyin Han, Siyao Liu, Chengzhen Li, Guanying Yu, Lei Zhang, Dongsheng Zhang, Caiyun Liu, Erhong Meng, Shuai Hong, Dongliang Wang, Peiming Guo, Guangjun Shi
Software Mentions: 6
Published: over 5 years ago

10.1186/s12967-021-03012-z

Cancer-associated fibroblast infiltration in gastric cancer: the discrepancy in subtypes pathways and immunosuppression
Cited by: 18
Author(s): Xu Liu, Li Yao, Jingkun Qu, Lin Liu, Ning Lü, Jiansheng Wang, Zhang Jia
Software Mentions: 6
Published: about 5 years ago

10.1155/2021/5552623

Integrative Functional Genomic Analysis of Molecular Signatures and Mechanistic Pathways in the Cell Cycle Underlying Alzheimer’s Disease
Cited by: 5
Author(s): Zhike Zhou, Jun Bai, Shanshan Zhong, Rongwei Zhang, Kexin Kang, Xiaoqian Zhang, Ying Xu, Chuansheng Zhao, Mei Zhao
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0015581

Therapeutic Implications of GIPC1 Silencing in Cancer
Cited by: 21
Author(s): Thomas Chittenden, Jane Pak, Renee Rubio, Hai‐Ling Margaret Cheng, Kristina M. Holton, Niall Prendergast, Vladimir Glinskii, Yi Cai, Aedín C. Culhane, Stefan Bentink, Mathew Schwede, Jessica C. Mar, Eleanor Howe, Martin J. Aryee, Răzvan Sultana, Anthony A. Lanahan, Jennifer Taylor, Chris Holmes, William C. Hahn, Jean J. Zhao, J. Dirk Iglehart, John Quackenbush
Software Mentions: 6
Published: over 15 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

10.1186/s13058-019-1098-z

A subgroup of microRNAs defines PTEN-deficient, triple-negative breast cancer patients with poorest prognosis and alterations in RB1, MYC, and Wnt signaling
Cited by: 33
Author(s): Dong‐Yu Wang, Deena M.A. Gendoo, Yaacov Ben‐David, James R. Woodgett, Eldad Zacksenhaus
Software Mentions: 6
Published: over 7 years ago

10.1523/JNEUROSCI.1675-19.2019

Midkine-a Is Required for Cell Cycle Progression of Müller Glia during Neuronal Regeneration in the Vertebrate Retina
Cited by: 28
Author(s): Mikiko Nagashima, Travis S. D’Cruz, Antoinette Eyram Danku, Doneen Hesse, Christopher J. Sifuentes, Pamela A. Raymond, Peter F. Hitchcock
Software Mentions: 6
Published: over 6 years ago

10.3390/ijms20020263

Molecular Network-Based Drug Prediction in Thyroid Cancer
Cited by: 14
Author(s): Xingyu Xu, Hang Long, Baohang Xi, Binbin Ji, Zejun Li, Yunyue Dang, Cheng Jiang, Yao Yao, Jialiang Yang
Software Mentions: 6
Published: over 7 years ago

Projects: bioconductor: limma

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Papers Mentioning limma 7,776