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: limma

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

Linear Models for Microarray Data
3 versions
Latest release: about 1 year ago
314 dependent packages
4,663,292 downloads total

Papers Mentioning limma 7,776

10.1038/s41419-020-2477-1
Deficiency in the autophagy modulator Dram1 exacerbates pyroptotic cell death of Mycobacteria-infected macrophages
Cited by: 22
Author(s): Rui Zhang, Mónica Varela, Gabriel Forn-Cuní, Vincenzo Torraca, Michiel van der Vaart, Annemarie H. Meijer
Software Mentions: 7
Published: over 4 years ago
10.7554/eLife.29312
Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis
Cited by: 35
Author(s): Isabelle Bergiers, Tallulah Andrews, Özge Vargel Bölükbaşı, Andreas Buneß, Ewa Janosz, Natalia López-Anguita, Kerstin Ganter, Kinga Kosim, Cemre Celen, Gülce Itır Perçin, Paul Collier, Bianka Baying, Vladimı́r Beneš, Martin Hemberg, Christophe Lancrin
Software Mentions: 7
Published: over 6 years ago
10.7554/eLife.41627
Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming
Cited by: 38
Author(s): Mirko Francesconi, Bruno Di Stefano, Clara Berenguer, Luísa de Andrés-Aguayo, Marcos Plana-Carmona, María Méndez-Lago, Amy Guillaumet-Adkins, Gustavo Rodríguez-Esteban, Marta Gut, Holger Heyn, Ben Liu, Thomas Graf
Software Mentions: 7
Published: over 5 years ago
10.1186/s13045-017-0406-2
Analyses of caspase-1-regulated transcriptomes in various tissues lead to identification of novel IL-1β-, IL-18- and sirtuin-1-independent pathways
Cited by: 43
Author(s): Yafeng Li, Gayani Nanayakkara, Yu Sun, Xinyuan Li, Luqiao Wang, Ramón Cueto, Ying Shao, Hangfei Fu, Candice Johnson, Jiali Cheng, Xiongwen Chen, Wenhui Hu, Jun Yu, Eric T. Choi, Hong Wang, Xiaofeng Yang
Software Mentions: 7
Published: almost 8 years ago
10.1038/s41420-021-00451-x
A novel defined pyroptosis-related gene signature for predicting the prognosis of ovarian cancer
Cited by: 256
Author(s): Ying Yang, Qinjin Dai, Hongbo Qi
Software Mentions: 7
Published: over 3 years ago
10.1093/gigascience/giy167
SMAGEXP: a galaxy tool suite for transcriptomics data meta-analysis
Cited by: 2
Author(s): Samuel Blanck, Guillemette Marot
Software Mentions: 7
Published: almost 6 years ago
10.1136/jitc-2020-001519
Transcriptional analysis of multiple ovarian cancer cohorts reveals prognostic and immunomodulatory consequences of ERV expression
Cited by: 10
Author(s): Marina Natoli, John Gallon, Haonan Lu, Ala Amgheib, David J. Pinato, Francesco Mauri, Teresa Marafioti, Ayse U. Akarca, Ines Ullmo, Jacey Ip, Eric O. Aboagye, Robert E. Brown, Anastasios Karadimitris, Sadaf Ghaem‐Maghami
Software Mentions: 7
Published: almost 4 years ago
10.1186/1471-2164-15-452
Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding
Cited by: 52
Author(s): Arun Kommadath, Hua Bao, Adriano S. Arantes, Graham Plastow, Christopher K. Tuggle, Shawn M. D. Bearson, Le Luo Guan, Paul Stothard
Software Mentions: 7
Published: over 10 years ago
10.1136/jitc-2020-001335
Druggable epigenetic suppression of interferon-induced chemokine expression linked to <i>MYCN</i> amplification in neuroblastoma
Cited by: 15
Author(s): Johanna A Seier, Julia Reinhardt, Kritika Saraf, Susanna S. Ng, Julian Philipp Layer, Dillon Corvino, Kristina Althoff, Frank A. Giordano, Alexander Schramm, Matthias Fischer, Michael Hölzel
Software Mentions: 7
Published: over 3 years ago
10.3389/fimmu.2019.02616
Microarray Gene Expression Dataset Re-analysis Reveals Variability in Influenza Infection and Vaccination
Cited by: 12
Author(s): Lavida R. K. Rogers, Gustavo de los Campos, George I. Mias
Software Mentions: 7
Published: about 5 years ago
10.7554/eLife.51413
Endothelial heterogeneity across distinct vascular beds during homeostasis and inflammation
Cited by: 190
Author(s): Ankit Jambusaria, Zhigang Hong, Lianghui Zhang, Shubhi Srivastava, Arundhati Jana, Péter T. Tóth, Yang Dai, Asrar B. Malik, Jalees Rehman
Software Mentions: 7
Published: almost 5 years ago
10.1371/journal.pone.0116508
Large Scale Aggregate Microarray Analysis Reveals Three Distinct Molecular Subclasses of Human Preeclampsia
Cited by: 90
Author(s): Katherine Leavey, Shannon Bainbridge, Brian Cox
Software Mentions: 7
Published: almost 10 years ago
10.26508/lsa.201800085
Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cells
Cited by: 29
Author(s): Constantine Mylonas, Peter Tessarz
Software Mentions: 7
Published: over 6 years ago
10.1155/2020/2415374
Identifying 4 Novel lncRNAs as Potential Biomarkers for Acute Rejection and Graft Loss of Renal Allograft
Cited by: 7
Author(s): Zedan Zhang, Yanlin Tang, Hongkai Zhuang, Enyu Lin, Lu Xie, Xiaoqiang Feng, Jiayi Zeng, Yanjun Liu, Jiumin Liu, Yuming Yu
Software Mentions: 7
Published: about 4 years ago
10.1371/journal.pone.0201751
Pancreatic cancer survival analysis defines a signature that predicts outcome
Cited by: 52
Author(s): Pichai Raman, Ravikanth Maddipati, Kian Huat Lim, Aydın Tözeren
Software Mentions: 7
Published: over 6 years ago
10.3389/fgene.2021.684002
Regulation of Long Non-coding RNA KCNQ1OT1 Network in Colorectal Cancer Immunity
Cited by: 5
Author(s): Junjie Liu, Wei Lv, Shuling Li, Jingwen Deng
Software Mentions: 7
Published: about 3 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
10.1186/s13073-016-0334-8
Panx3 links body mass index and tumorigenesis in a genetically heterogeneous mouse model of carcinogen-induced cancer
Cited by: 12
Author(s): Kyle Halliwill, David A. Quigley, Hio Chung Kang, Reyno Del Rosario, David G. Ginzinger, Allan Balmain
Software Mentions: 7
Published: over 8 years ago
10.1038/s41421-021-00312-y
A single-cell atlas of liver metastases of colorectal cancer reveals reprogramming of the tumor microenvironment in response to preoperative chemotherapy
Cited by: 42
Author(s): Li-Heng Che, Jingwen Li, Jian-Ping Huo, Rong Luo, Rui-Ming Xu, He Cai, Yuqing Li, Anni Zhou, Pinbo Huang, Yongyu Chen, Weijian Ni, Yunxia Zhou, Yuan-Yuan Liu, Huiyan Li, Rong Zhou, Ming Hui, Jianming Li
Software Mentions: 7
Published: about 3 years ago
10.1371/journal.pone.0196836
Multiclass classification for skin cancer profiling based on the integration of heterogeneous gene expression series
Cited by: 17
Author(s): Juan Manuel Gálvez, Daniel Castillo, José Benavente Herrera, Belén San Román, Olga Valenzuela, Francisco M. Ortuño Guzman, Ignacio Rojas
Software Mentions: 7
Published: over 6 years ago
10.1038/s41598-020-77727-2
Gene expression in diapausing rotifer eggs in response to divergent environmental predictability regimes
Cited by: 21
Author(s): Eva Tarazona, José Ignacio Lucas-Lledó, Marı́a José Carmona, Eduardo M. García‐Roger
Software Mentions: 7
Published: almost 4 years ago
10.1186/s12967-020-02697-y
A novel immune classification reveals distinct immune escape mechanism and genomic alterations: implications for immunotherapy in hepatocellular carcinoma
Cited by: 58
Author(s): Zaoqu Liu, Yuyuan Zhang, Chengcheng Shi, Xueliang Zhou, Kaihao Xu, Dechao Jiao, Zhenqiang Sun, Xinwei Han
Software Mentions: 7
Published: almost 4 years ago
10.1371/journal.pone.0216793
Patterns of gene expression characterize T1 and T3 clear cell renal cell carcinoma subtypes
Cited by: 4
Author(s): A. Borys, Michał Seweryn, Tomasz Gołąbek, Łukasz Bełch, Agnieszka Klimkowska, Justyna Totoń‐Żurańska, Julita Machlowska, Piotr Chłosta, Krzysztof Okoń, Paweł Wołkow
Software Mentions: 7
Published: over 5 years ago
10.1002/ctm2.500
Single‐cell transcriptomes reveal heterogeneity of high‐grade serous ovarian carcinoma
Cited by: 29
Author(s): Qian Hao, Jiajia Li, Qinghua Zhang, Fei Xu, Bangxiang Xie, Hua Lu, Xiaohua Wu, Xiang Zhou
Software Mentions: 7
Published: over 3 years ago
10.1371/journal.ppat.1006767
Comparative transcriptome profiling of virulent and non-virulent Trypanosoma cruzi underlines the role of surface proteins during infection
Cited by: 50
Author(s): Ashton T. Belew, Caroline Junqueira, Gabriela F. Rodrigues-Luiz, Bruna M. Valente, Antônio Edson Rocha Oliveira, Rafael B. Polidoro, Luciana W. Zuccherato, Daniella Castanheira Bartholomeu, Sérgio Schenkman, Ricardo T. Gazzinelli, Barbara A. Burleigh, Najib M. El-Sayed, Santuza Maria Ribeiro Teixeira
Software Mentions: 7
Published: almost 7 years ago
10.3389/fimmu.2021.672158
Analysis of Tumor Microenvironment Characteristics in Bladder Cancer: Implications for Immune Checkpoint Inhibitor Therapy
Cited by: 21
Author(s): Xingyu Chen, Haotian Chen, Dong He, Ying Cheng, Yuxing Zhu, Mengqing Xiao, Hua Lan, Zhanwang Wang, Ke Cao
Software Mentions: 7
Published: over 3 years ago
10.1111/jcmm.16275
Identification of key candidate biomarkers for severe influenza infection by integrated bioinformatical analysis and initial clinical validation
Cited by: 7
Author(s): Shuai Liu, Zhisheng Huang, Xiaoyan Deng, Xiaohui Zou, Hui Li, Shengrui Mu, Bin Cao
Software Mentions: 7
Published: almost 4 years ago
10.1186/s13059-021-02466-0
Acute depletion of CTCF rewires genome-wide chromatin accessibility
Cited by: 26
Author(s): Beisi Xu, Hong Wang, Shaela Wright, Judith Hyle, Yang Zhang, Ying Shao, Mingming Niu, Yiping Fan, Wojciech Rosikiewicz, Mohamed Nadhir Djekidel, Junmin Peng, Rui Lu, Chunliang Li
Software Mentions: 7
Published: over 3 years ago
10.1186/s12864-016-3317-7
A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data
Cited by: 32
Author(s): Yongli Hu, Takeshi Hase, Hui Peng Li, Shyam Prabhakar, Hiroaki Kitano, See Ket Ng, Samik Ghosh, Lionel Wee
Software Mentions: 7
Published: almost 8 years ago
10.1186/s12894-021-00795-7
Comprehensive analysis of tumour mutational burden and its clinical significance in prostate cancer
Cited by: 14
Author(s): Limin Wang, Shucheng Pan, Binbin Zhu, Zhenliang Yu, Wei Wang
Software Mentions: 7
Published: almost 4 years ago
10.1186/s12864-020-06888-1
A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples
Cited by: 6
Author(s): Huamei Li, Ingo G. H. Schmidt‐Wolf, Wenglong Ming, Xiao Sun, Hongde Liu
Software Mentions: 7
Published: about 4 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
10.1186/1471-2164-14-445
The Saccharomyces cerevisiae transcriptome as a mirror of phytochemical variation in complex extracts of Equisetum arvense from America, China, Europe and India
Cited by: 20
Author(s): R. Kimberley Cook, James R. Hennell, Samiuela Lee, Cheang Khoo, Maria Carles, Vincent J. Higgins, Suresh Govindaraghavan, Nikolaus J. Sucher
Software Mentions: 7
Published: over 11 years ago
10.1186/s13148-018-0510-3
Multifactorial analysis of the stochastic epigenetic variability in cord blood confirmed an impact of common behavioral and environmental factors but not of in vitro conception
Cited by: 25
Author(s): Davide Gentilini, Edgardo Somigliana, Luca Pagliardini, Elisa Rabellotti, Paolo Garagnani, Luisa Bernardinelli, Enrico Papaleo, Massimo Candiani, Anna Maria Di Blasio, Paola Viganò
Software Mentions: 7
Published: over 6 years ago
10.3389/fgene.2021.702695
Identification and Elucidation of the Protective isomiRs in Lung Cancer Patient Prognosis
Cited by: 1
Author(s): Fu-Mei Hsieh, Su-Ting Lai, Ming-Fong Wu, Chen-Ching Lin
Software Mentions: 7
Published: about 3 years ago
10.1371/journal.pone.0076051
Alterations in miRNA Levels in the Dentate Gyrus in Epileptic Rats
Cited by: 79
Author(s): Anna Bot, Konrad J. Dębski, Katarzyna Łukasiuk
Software Mentions: 7
Published: about 11 years ago
10.3389/fgene.2021.678780
Identification of a Four-Gene Signature With Prognostic Significance in Endometrial Cancer Using Weighted-Gene Correlation Network Analysis
Cited by: 7
Author(s): Shijin Huang, Lihong Pang, Changqiang Wei
Software Mentions: 7
Published: about 3 years ago
10.1042/BSR20203336
Comprehensive analysis of tumor mutation burden and immune microenvironment in gastric cancer
Cited by: 17
Author(s): Jie Yu, QianYun Zhang, Mengchuan Wang, Shi-Dong Liang, Hongyun Huang, Lang Xie, Chunhui Cui
Software Mentions: 7
Published: almost 4 years ago
10.7150/jca.53831
Development and Validation of an Immune-Related Long Non-coding RNA Prognostic Model in Glioma
Cited by: 5
Author(s): Xiaowei Qiu, Yuan Tian, Jingnan Xu, Xin Jiang, Zeyu Liu, Xuewei Qi, Xin Chang, Jianxin Zhao, Jinchang Huang
Software Mentions: 7
Published: almost 4 years ago
10.3389/fimmu.2021.691811
Immune Infiltrating Cells-Derived Risk Signature Based on Large-scale Analysis Defines Immune Landscape and Predicts Immunotherapy Responses in Glioma Tumor Microenvironment
Cited by: 36
Author(s): Nan Zhang, Hao Zhang, Zeyu Wang, Ziyu Dai, Xun Zhang, Quan Cheng, Zhixiong Liu
Software Mentions: 7
Published: over 3 years ago
10.3389/fcell.2021.659294
Ubiquitin Modification Patterns of Clear Cell Renal Cell Carcinoma and the Ubiquitin Score to Aid Immunotherapy and Targeted Therapy
Cited by: 5
Author(s): Peng Zhou, Yuchao Lu, Xiufen Yang, Jin‐Zhou Xu, Chen‐Qian Liu, Qi‐Dong Xia, Junlin Lu, Shaogang Wang, Jia Hu
Software Mentions: 7
Published: over 3 years ago
10.7150/jca.50716
Detection of Pancreatic Ductal Adenocarcinoma by A qPCR-based Normalizer-free Circulating Extracellular Vesicles RNA Signature
Cited by: 6
Author(s): Dashan Qin, Yu Zhao, Qingdong Guo, Shoumin Zhu, Shutian Zhang, Li Min
Software Mentions: 7
Published: almost 4 years ago
10.1002/ece3.7901
Linking ecology, morphology, and metabolism: Niche differentiation in sympatric populations of closely related species of the genus <i>Littorina</i> (<i>Neritrema</i>)
Cited by: 7
Author(s): Arina L. Maltseva, Marina A. Varfolomeeva, Roman V. Ayanka, Elizaveta R. Gafarova, Egor A. Repkin, Polina Pavlova, Alexei L. Shavarda, Natalia A. Mikhailova, Andrei I. Granovitch
Software Mentions: 7
Published: over 3 years ago
10.1186/s12864-019-6308-7
Human gene expression variability and its dependence on methylation and aging
Cited by: 23
Author(s): Nasser Bashkeel, Theodore J. Perkins, Mads Kærn, Jonathan M. Lee
Software Mentions: 7
Published: almost 5 years ago
10.7150/jca.47557
Identification of a prognostic 4-mRNA signature in laryngeal squamous cell carcinoma
Cited by: 1
Author(s): Cheng Zhang, Bin Shen, Xinwei Chen, Shang Gao, Xiaohua Ying, Pin Dong
Software Mentions: 7
Published: almost 4 years ago
10.3389/fonc.2021.618187
CCR4, CCR8, and P2RY14 as Prognostic Factors in Head and Neck Squamous Cell Carcinoma Are Involved in the Remodeling of the Tumor Microenvironment
Cited by: 9
Author(s): Liangliang Meng, Xiaoxi He, Hong Qin, Bo Qiao, Xiao Zhang, Bin Wu, Xiaobo Zhang, Yingtian Wei, Jing Li, Zhaoxiang Ye, Yueyong Xiao
Software Mentions: 7
Published: almost 4 years ago
10.3389/fimmu.2018.01444
Elucidating T Cell Activation-Dependent Mechanisms for Bifurcation of Regulatory and Effector T Cell Differentiation by Multidimensional and Single-Cell Analysis
Cited by: 10
Author(s): Alla Bradley, Takeji Hashimoto, M. Ono
Software Mentions: 7
Published: over 6 years ago
10.1042/BSR20200935
WGCNA reveals key gene modules regulated by the combined treatment of colon cancer with PHY906 and CPT11
Cited by: 21
Author(s): Shuqin Xing, Yafei Wang, Kaiwen Hu, Fen Wang, Tao Sun, Quanwang Li
Software Mentions: 7
Published: about 4 years ago
10.3389/fgene.2021.744113
Identification and Validation of Hypoxia-Related lncRNA Signature as a Prognostic Model for Hepatocellular Carcinoma
Cited by: 8
Author(s): Chengke Zhou, Huajun Zhang, Liqing Lu
Software Mentions: 7
Published: about 3 years ago
10.3389/fimmu.2021.639634
Development and Validation of a Novel Prognostic Model for Acute Myeloid Leukemia Based on Immune-Related Genes
Cited by: 10
Author(s): Ran Li, Zuoyou Ding, Peng Jin, Shishuang Wu, Ge Jiang, Rufang Xiang, Wenfang Wang, Zhen Jin, Xiaoyang Li, Kai Xue, Xiaolu Wu, Junmin Li
Software Mentions: 7
Published: over 3 years ago
10.15252/msb.20188497
netDx: interpretable patient classification using integrated patient similarity networks
Cited by: 59
Author(s): Shraddha Pai, Shirley Hui, Ruth Isserlin, Manjool Shah, Hussam Kaka, Gary D. Bader
Software Mentions: 7
Published: almost 6 years ago
10.1002/jcsm.12556
An epigenetic clock for human skeletal muscle
Cited by: 58
Author(s): Sarah Voisin, Nicholas R. Harvey, Larisa M. Haupt, Lyn R. Griffiths, Kevin J. Ashton, Vernon G. Coffey, Thomas Doering, Jamie-Lee M Thompson, Christian Benedict, Jonathan Cedernaes, Maléne E. Lindholm, Jeffrey M. Craig, David S. Rowlands, Adam P. Sharples, Steve Horvath, Nir Eynon
Software Mentions: 7
Published: almost 5 years ago
10.15252/emmm.202013180
Intraductal xenografts show lobular carcinoma cells rely on their own extracellular matrix and LOXL1
Cited by: 21
Author(s): George Sflomos, Laura Battista, Patrick Aouad, Fabio De Martino, Valentina Scabia, Athina Stravodimou, Ayyakkannu Ayyanan, Assia Ifticene‐Treboux, Philipp Bücher, Maryse Fiche, Giovanna Ambrosini, Cathrin Brisken, Rls
Software Mentions: 7
Published: almost 4 years ago
10.1016/j.virol.2021.03.019
Zika virus infection during pregnancy protects against secondary infection in the absence of CD8+ cells
Cited by: 3
Author(s): Blake Schouest, Brandon J Beddingfield, Margaret H. Gilbert, Rudolf P. Bohm, Faith Schiro, Pyone P. Aye, Antonito T. Panganiban, Diogo M. Magnani, Nicholas J. Maness
Software Mentions: 7
Published: over 3 years ago
10.1038/srep29042
Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana
Cited by: 35
Author(s): Frédéric Bouché, Maria D’Aloia, Pierre Tocquin, Guillaume Lobet, Nathalie Detry, Claire Périlleux
Software Mentions: 7
Published: over 8 years ago
10.3390/bios3030238
A Comparison of Methods for RNA-Seq Differential Expression Analysis and a New Empirical Bayes Approach
Cited by: 20
Author(s): Sergiusz Wesołowski, Marc R. Birtwistle, Grzegorz A. Rempała
Software Mentions: 7
Published: over 11 years ago
10.1038/s41598-017-13397-x
The effect of insecticide synergist treatment on genome-wide gene expression in a polyphagous pest
Cited by: 28
Author(s): Simon Snoeck, Robert Greenhalgh, Luc Tirry, Richard M. Clark, Thomas Van Leeuwen, Wannes Dermauw
Software Mentions: 7
Published: about 7 years ago
10.3389/fgene.2021.714639
Development and Validation of a Gene Mutation-Associated Nomogram for Hepatocellular Carcinoma Patients From Four Countries
Cited by: 5
Author(s): Tingping Huang, Tao Yan, Gonghai Chen, Chunqing Zhang
Software Mentions: 7
Published: about 3 years ago
10.3389/fcell.2021.659080
ANXA1 as a Prognostic and Immune Microenvironmental Marker for Gliomas Based on Transcriptomic Analysis and Experimental Validation
Cited by: 8
Author(s): Zhongxiao Lin, Ming‐Shien Wen, Enxing Yu, Xiao Yan Lin, Hua Wang, Jiayu Chen, Chaojie Yao, Hengli Zhang, Junnan Ru, Kankai Wang, Ying Zhang, Lijie Huang, Qichuan Zhuge, Shuxu Yang
Software Mentions: 7
Published: over 3 years ago
10.1038/s41416-019-0571-x
Prognosis and modulation mechanisms of COMMD6 in human tumours based on expression profiling and comprehensive bioinformatics analysis
Cited by: 24
Author(s): Mi Yang, Weiqiang Huang, Yaling Sun, Huazhen Liang, Min Chen, Xixi Wu, Xiaoqing Wang, Longshan Zhang, Xiaobin Cheng, Yu Fan, Hua Pan, Longhua Chen, Jian Guan
Software Mentions: 7
Published: about 5 years ago
10.3389/fcell.2021.618313
Long Non-coding RNA Expression Patterns in Stomach Adenocarcinoma Serve as an Indicator of Tumor Mutation Burden and Are Associated With Tumor-Infiltrating Lymphocytes and Microsatellite Instability
Cited by: 6
Author(s): Dongdong Yang, Jianan Yu, Bing Han, Yue Sun, Steven Mo, Jing Hu
Software Mentions: 7
Published: almost 4 years ago
10.1186/s12864-018-4896-2
Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands
Cited by: 8
Author(s): Panagiotis Moulos, Αλέξανδρος Αλεξανδράτος, Ioannis Nellas, Skarlatos G. Dedos
Software Mentions: 7
Published: over 6 years ago
10.3389/fncel.2020.612560
Proteomic Characterization of Human Neural Stem Cells and Their Secretome During in vitro Differentiation
Cited by: 19
Author(s): Jakub Červenka, Jiřina Tylečková, Helena Kupcová Skalníková, Kateřina Vodičková Kepková, Ievgeniia Poliakh, Ivona Valeková, Lucie Pfeiferová, Michal Kolář, Michaela Vaškovičová, Tereza Pánková, Petr Vodička
Software Mentions: 7
Published: almost 4 years ago
10.3390/cancers13163929
Maturation State-Specific Alternative Splicing in FLT3-ITD and NPM1 Mutated AML
Cited by: 4
Author(s): Anna Wojtuszkiewicz, Inge van der Werf, Stephan Hütter, Wencke Walter, Constance Baer, Wolfgang Kern, Jeroen Janssen, Gert J. Ossenkoppele, Claudia Haferlach, Jacqueline Cloos, Torsten Haferlach
Software Mentions: 7
Published: over 3 years ago
10.1371/journal.pcbi.1006792
IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis
Cited by: 25
Author(s): Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison J. Miller, Anne Fennell, Qin Ma
Software Mentions: 7
Published: almost 6 years ago
10.1038/s41598-017-10853-6
The Schistosoma mansoni genome encodes thousands of long non-coding RNAs predicted to be functional at different parasite life-cycle stages
Cited by: 39
Author(s): Elton J. R. Vasconcelos, Luis DaSilva, David S. Pires, Guilherme M. Lavezzo, Adriana S. A. Pereira, Murilo Sena Amaral, Sérgio Verjovski-Almeida
Software Mentions: 7
Published: about 7 years ago
10.3389/fonc.2021.657094
LINC01977 Promotes Breast Cancer Progression and Chemoresistance to Doxorubicin by Targeting miR-212-3p/GOLM1 Axis
Cited by: 12
Author(s): Zheng Li, Yaming Li, Xiaolong Wang, Yiran Liang, Dan Luo, Dianwen Han, Chen Li, Tong Chen, Hanwen Zhang, Ying Liu, Zekun Wang, Bing Chen, Limin Wang, Wenjing Zhao, Qifeng Yang
Software Mentions: 7
Published: over 3 years ago
10.15252/msb.20178041
Molecular transitions in early progenitors during human cord blood hematopoiesis
Cited by: 120
Author(s): Shiwei Zheng, Efthymia Papalexi, Andrew Butler, William Stephenson, Rahul Satija
Software Mentions: 7
Published: almost 7 years ago
10.1371/journal.pgen.1009294
Molecular asymmetry in the cephalochordate embryo revealed by single-blastomere transcriptome profiling
Cited by: 4
Author(s): Che-Yi Lin, Mei-Yeh Jade Lu, Jia-Xing Yue, Kun-Lung Li, Yann Le Pétillon, Luok Wen Yong, Yihua Chen, Fu‐Yu Tsai, Yu-Feng Lyu, Cheng-Yi Chen, Sheng-Ping L. Hwang, Yi-Hsien Su, Jr-Kai Yu
Software Mentions: 7
Published: almost 4 years ago
10.1007/s10549-019-05135-w
A high-risk luminal A dominant breast cancer subtype with increased mobility
Cited by: 21
Author(s): Liping Guo, Guoji Chen, Wen Zhang, Lülin Zhou, Ting Xiao, Di Xia, Yipeng Wang, Feng Li, Kaitai Zhang
Software Mentions: 7
Published: almost 6 years ago
10.3389/fonc.2020.01409
Development and Validation of a Tumor Mutation Burden–Related Immune Prognostic Model for Lower-Grade Glioma
Cited by: 43
Author(s): Yin Wu, Xingjun Jiang, Jun Tan, Zhaoqi Xin, Quanwei Zhou, Chaohong Zhan, Xianyong Fu, Zhaoping Wu, Youwei Guo, Zhipeng Jiang, Chao Ren, Guihua Tang
Software Mentions: 7
Published: over 4 years ago
10.3390/cancers12082310
Systematic Analysis of Aberrant Biochemical Networks and Potential Drug Vulnerabilities Induced by Tumor Suppressor Loss in Malignant Pleural Mesothelioma
Cited by: 15
Author(s): Haitang Yang, Duo Xu, Yang Zhang, Feng Yao, Heng Zhao, Ralph A. Schmid, Ren‐Wang Peng
Software Mentions: 7
Published: over 4 years ago
10.3389/fcell.2021.637400
Integrated Bioinformatical Analysis Identifies GIMAP4 as an Immune-Related Prognostic Biomarker Associated With Remodeling in Cervical Cancer Tumor Microenvironment
Cited by: 16
Author(s): Fangfang Xu, Jiacheng Shen, Shaohua Xu
Software Mentions: 7
Published: almost 4 years ago
10.1186/s12864-021-07593-3
Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response
Cited by: 23
Author(s): Florencia Schlamp, Sofie Y. N. Delbare, Angela M. Early, Martin T. Wells, Sumanta Basu, Andrew G. Clark
Software Mentions: 7
Published: over 3 years ago
10.3390/cancers13071730
Identification and Validation of an Immune-Associated RNA-Binding Proteins Signature to Predict Clinical Outcomes and Therapeutic Responses in Glioma Patients
Cited by: 11
Author(s): Ruotong Tian, Yimin Li, Qian Liu, Minfeng Shu
Software Mentions: 7
Published: over 3 years ago
10.15252/emmm.201910606
Novel Alzheimer risk genes determine the microglia response to amyloid‐β but not to TAU pathology
Cited by: 149
Author(s): Annerieke Sierksma, Ashley Lu, Renzo Mancuso, Nicola Fattorelli, Nicola Thrupp, Evgenia Salta, Jesus Zoco, David Blum, Luc Buée, Bart De Strooper, Mark Fiers
Software Mentions: 7
Published: almost 5 years ago
10.1042/BSR20200492
Profiles of overall survival-related gene expression-based risk signature and their prognostic implications in clear cell renal cell carcinoma
Cited by: 3
Author(s): Zihao He, Tuo Deng, Xiaolu Duan, Guohua Zeng
Software Mentions: 7
Published: about 4 years ago
10.3389/fonc.2021.729340
Tumor Mutation Burden-Associated LINC00638/miR-4732-3p/ULBP1 Axis Promotes Immune Escape via PD-L1 in Hepatocellular Carcinoma
Cited by: 15
Author(s): Qi Feng, Xiaojing Du, Zhiying Zhao, Ding Zhang, Mengli Huang, Yuezong Bai, Biwei Yang, Wenxing Qin, Jinglin Xia
Software Mentions: 7
Published: about 3 years ago
10.1038/s41598-019-53843-6
Monocytes affect bone mineral density in pre- and postmenopausal women through ribonucleoprotein complex biogenesis by integrative bioinformatics analysis
Cited by: 8
Author(s): Kang-Wen Xiao, Jiali Li, Zhao-Yi Zeng, Zhibo Liu, Zhiqiang Hou, Xin Yan, Lin Cai
Software Mentions: 7
Published: about 5 years ago
10.3389/fonc.2021.734873
DNA Methylation Regulator-Meditated Modification Patterns Define the Distinct Tumor Microenvironment in Lung Adenocarcinoma
Cited by: 3
Author(s): Dejian Yuan, Zehong Wei, Yicheng Wang, Cheng Fang, Yujie Zeng, Yang Li, Shangyu Zhang, Jianbo Li, Renkuan Tang
Software Mentions: 7
Published: about 3 years ago
10.3389/fonc.2021.674394
Comprehensive Analysis of Cyclin Family Gene Expression in Colon Cancer
Cited by: 12
Author(s): Jieling Li, Liyuan Zhou, Ying Liu, Lingzhi Yang, Dayi Jiang, Kuan Li, Shouqi Xie, Wang Xiao, Shaoxiang Wang
Software Mentions: 7
Published: over 3 years ago
10.3389/fonc.2020.00033
PLXNC1 Enhances Carcinogenesis Through Transcriptional Activation of IL6ST in Gastric Cancer
Cited by: 9
Author(s): Jie Chen, Haining Liu, Jinggui Chen, Bo Sun, Jianghong Wu, Chunyan Du
Software Mentions: 7
Published: almost 5 years ago
10.3389/fimmu.2021.634127
Immunophenotyping of Peripheral Blood Mononuclear Cells in Septic Shock Patients With High-Dimensional Flow Cytometry Analysis Reveals Two Subgroups With Differential Responses to Immunostimulant Drugs
Cited by: 4
Author(s): Ya Wang, Brian Gloss, Benjamin Tang, Suat Dervish, Brigitte Santner-Nanan, Christina Whitehead, Kristy Masters, Kristen K. Skarratt, Sally Teoh, Stephen D. Schibeci, Nicole Fewings, Chrystelle Brignone, Frédéric Triebel, David R. Booth, Anthony S. McLean, Marek Nalos
Software Mentions: 7
Published: over 3 years ago
10.3390/e21030242
A Method Based on Differential Entropy-Like Function for Detecting Differentially Expressed Genes Across Multiple Conditions in RNA-Seq Studies
Cited by: 1
Author(s): Zhuo Wang, Shuilin Jin, Chiping Zhang
Software Mentions: 7
Published: over 5 years ago
10.3389/fcell.2021.651593
An Immune-Related Long Non-Coding RNA Signature to Predict the Prognosis of Ewing’s Sarcoma Based on a Machine Learning Iterative Lasso Regression
Cited by: 4
Author(s): Enhui Ren, Yajun Deng, Wenhua Yuan, Guangzhi Zhang, Zhi-Xi Wu, Chunying Li, Qiqi Xie
Software Mentions: 7
Published: over 3 years ago
10.3389/fonc.2020.00061
The Prognostic Significance of Metabolic Syndrome and a Related Six-lncRNA Signature in Esophageal Squamous Cell Carcinoma
Cited by: 18
Author(s): Yu Liu, Li-Yu Wang, Hengchang Liu, Chunxiang Li, Jie He
Software Mentions: 7
Published: almost 5 years ago
10.1128/mSystems.00280-19
Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single <i>Ctena orbiculata</i> (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition
Cited by: 7
Author(s): Shen Jean Lim, Louie C. Alexander, Annette Summers Engel, Audrey Paterson, Laurie C. Anderson, Barbara J. Campbell
Software Mentions: 7
Published: over 5 years ago
10.3389/fonc.2021.660242
Identification and Validation of a Five-Gene Signature Associated With Overall Survival in Breast Cancer Patients
Cited by: 6
Author(s): Xiaolong Wang, Chen Li, Tong Chen, Wenhao Li, Hanwen Zhang, Dong Zhang, Ying Liu, Dianwen Han, Yaming Li, Zheng Li, Dan Luo, Ning Zhang, Qifeng Yang
Software Mentions: 7
Published: over 3 years ago
10.1042/BSR20204340
TIGIT-related transcriptome profile and its association with tumor immune microenvironment in breast cancer
Cited by: 8
Author(s): Qin Zhang, Chaowei Gao, Jianqiang Shao, Zunyi Wang
Software Mentions: 7
Published: almost 4 years ago
10.3389/fimmu.2020.585168
Distinct Age-Related Epigenetic Signatures in CD4 and CD8 T Cells
Cited by: 40
Author(s): Bin Hu, Rohit R. Jadhav, Claire E. Gustafson, Sabine Le Saux, Zhongde Ye, Xuanying Li, Lu Tian, Cornelia M. Weyand, Jörg J. Goronzy
Software Mentions: 7
Published: about 4 years ago
10.15252/emmm.202012525
<scp>LSD</scp> 1 inhibition induces differentiation and cell death in Merkel cell carcinoma
Cited by: 36
Author(s): Lukas Leiendecker, Pauline S. Jung, Izabela Krecioch, Tobias Neumann, Alexander Schleiffer, Karl Mechtler, Thomas Wiesner, Anna C. Obenauf
Software Mentions: 7
Published: about 4 years ago
10.3389/fcell.2021.682261
Immunity-Related Gene Signature Identifies Subtypes Benefitting From Adjuvant Chemotherapy or Potentially Responding to PD1/PD-L1 Blockage in Pancreatic Cancer
Cited by: 3
Author(s): Qian Hao, Hongzhe Li, Junjie Xie, Xiang Lü, Fanlu Li, Weishen Wang, Xiaomei Tang, Minmin Shi, Longyang Jiang, Hongwei Li, Hao Chen, Chenghong Peng, Zhiwei Xu, Xiaxing Deng, Baiyong Shen
Software Mentions: 7
Published: over 3 years ago
10.3389/fonc.2021.654185
Overexpression of GINS4 Is Associated With Tumor Progression and Poor Survival in Hepatocellular Carcinoma
Cited by: 6
Author(s): Ziying Zhang, Peng Chen, Hui Xie, Peiguo Cao
Software Mentions: 7
Published: over 3 years ago
10.1371/journal.pone.0147249
Cell and Microvesicle Urine microRNA Deep Sequencing Profiles from Healthy Individuals: Observations with Potential Impact on Biomarker Studies
Cited by: 43
Author(s): Iddo Z. Ben‐Dov, Veronica M. Whalen, Béatrice Goilav, Klaas E.A. Max, Thomas Tuschl
Software Mentions: 7
Published: almost 9 years ago
10.1186/s10194-021-01285-9
Identification of disease- and headache-specific mediators and pathways in migraine using blood transcriptomic and metabolomic analysis
Cited by: 13
Author(s): Tímea Aczél, Tamás Körtési, József Kun, Péter Urbán, Witold Bauer, Róbert Herczeg, Robert Farkaš, K Kovács, Barna Vásárhelyi, Gellért Balázs Karvaly, Attila Gyenesei, Bernadett Tuka, János Tajti, László Vécsei, Kata Bölcskei, Zsuzsanna Helyes
Software Mentions: 7
Published: about 3 years ago
10.1002/jev2.12127
Inflammasome‐induced extracellular vesicles harbour distinct RNA signatures and alter bystander macrophage responses
Cited by: 26
Author(s): Christina F. Budden, Linden J. Gearing, Romina Kaiser, Lena Standke, Paul J. Hertzog, Eicke Latz
Software Mentions: 7
Published: over 3 years ago
10.1038/s41598-020-64794-8
Integrative genomics approach identifies molecular features associated with early-stage ovarian carcinoma histotypes
Cited by: 12
Author(s): Hanna Engqvist, Toshima Z. Parris, Jana Biermann, Elisabeth Werner Rönnerman, Peter Larsson, Karin Sundfeldt, Anikó Kovács, Per Karlsson, Khalil Helou
Software Mentions: 7
Published: over 4 years ago
10.1371/journal.pone.0159138
Technical Advances of the Recombinant Antibody Microarray Technology Platform for Clinical Immunoproteomics
Cited by: 26
Author(s): Payam Delfani, Linda Dexlin Mellby, Malin Nordström, Andreas Holmér, Mattias Ohlsson, Carl Borrebaeck, Christer Wingren
Software Mentions: 7
Published: over 8 years ago
10.15252/embr.201642378
Linear ubiquitination by <scp>LUBEL</scp> has a role in <i>Drosophila</i> heat stress response
Cited by: 31
Author(s): Tomoko Asaoka, Jorge Almagro, Christine Ehrhardt, Yi-Chun Isabella Tsai, Alexander Schleiffer, Luiza Deszcz, Sini Junttila, Leonie Ringrose, Karl Mechtler, Anoop Kavirayani, Attila Gyenesei, Kay Hofmann, Peter Duchek, Katrin Rittinger, Fumiyo Ikeda
Software Mentions: 7
Published: about 8 years ago
10.3389/fcell.2021.665364
Hypoxia Constructing the Prognostic Model of Colorectal Adenocarcinoma and Related to the Immune Microenvironment
Cited by: 11
Author(s): Yuanyuan Zhang, Feng Yang, Xiaohong Peng, Xiaoyü Li, Na Luo, Wenjun Zhu, Min Fu, Qianxia Li, Guangyuan Hu
Software Mentions: 7
Published: over 3 years ago