bioconductor: limma | Projects | Ecosyste.ms: Papers

10.7717/peerj.11733

Identification of a circadian gene signature that predicts overall survival in lung adenocarcinoma
Cited by: 2
Author(s): Xinliang Gao, Mingbo Tang, Suyan Tian, Jialin Li, Wei Liu
Software Mentions: 7
Published: about 5 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: over 7 years ago

10.3390/microorganisms8101592

Gut Microbiome in Children from Indigenous and Urban Communities in México: Different Subsistence Models, Different Microbiomes
Cited by: 12
Author(s): Andrés Sánchez-Quinto, Daniel Cerqueda‐García, Luisa I. Falcón, Osiris Gaona, Santiago Martínez-Correa, Javier Nieto, Isaac González‐Santoyo
Software Mentions: 7
Published: almost 6 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: about 8 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 6 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: over 9 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 7 years ago

10.3389/fonc.2020.542140

Identification of Immune-Related lncRNA Signature to Predict Prognosis and Immunotherapeutic Efficiency in Bladder Cancer
Cited by: 19
Author(s): Lianghao Zhang, Long‐Qing Li, Yonghao Zhan, Jian‐Ge Wang, Zhaowei Zhu, Xuepei Zhang
Software Mentions: 7
Published: over 5 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 6 years ago

10.18632/aging.202417

Overexpression of TICRR and PPIF confer poor prognosis in endometrial cancer identified by gene co-expression network analysis
Cited by: 13
Author(s): Linlin Yang, Yunxia Cui, Xiao Sun, Yudong Wang
Software Mentions: 7
Published: over 5 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 8 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 5 years ago

10.18632/aging.102518

A twenty gene-based gene set variation score reflects the pathological progression from cirrhosis to hepatocellular carcinoma
Cited by: 21
Author(s): Yan Lin, Rong Liang, Jiazhou Ye, Qian Li, Ziyu Liu, Xing Gao, Xuemin Piao, Rongyun Mai, Donghua Zou, Lianying Ge
Software Mentions: 7
Published: almost 7 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: over 11 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 5 years ago

10.18632/aging.103671

Target RNA modification for epigenetic drug repositioning in neuroblastoma: computational omics proximity between repurposing drug and disease
Cited by: 6
Author(s): Pei Ma, Lifeng Yue, Sen Zhang, Da‐Cheng Hao, Zhihong Wu, Lijia Xu, Guanhua Du, Pei‐Gen Xiao
Software Mentions: 7
Published: almost 6 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 13 years ago

10.7554/eLife.30952

Transcriptomic and proteomic landscape of mitochondrial dysfunction reveals secondary coenzyme Q deficiency in mammals
Cited by: 158
Author(s): Inge Kühl, María Miranda, Ilian Atanassov, Irina Kuznetsova, Yvonne Hinze, Arnaud Mourier, Aleksandra Filipovska, Nils‐Göran Larsson
Software Mentions: 7
Published: almost 9 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 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 13 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 7 years ago

10.1155/2021/1801873

Identification of Key Functional Modules and Immunomodulatory Regulators of Hepatocellular Carcinoma
Cited by: 2
Author(s): Dan Luo, Xiang Zhang, Xiaokai Li, Gang Chen
Software Mentions: 7
Published: about 5 years ago

10.7554/eLife.60223

Analysis of the immune response to sciatic nerve injury identifies efferocytosis as a key mechanism of nerve debridement
Cited by: 64
Author(s): Ashley L. Kalinski, Choya Yoon, Lucas D. Huffman, Patrick C. Duncker, Rafi Kohen, Ryan Passino, Hannah Hafner, Craig Johnson, Riki Kawaguchi, Kevin S. Carbajal, Juan Sebastián Jara, Edmund R. Hollis, Daniel H. Geschwind, Benjamin M. Segal, Roman J. Giger
Software Mentions: 7
Published: almost 6 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 8 years ago

10.1371/journal.pcbi.1008354

Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines
Cited by: 5
Author(s): Chen Xie, Cemalettin Bekpen, Sven Künzel, Maryam Keshavarz, Rebecca Krebs-Wheaton, Neva Škrabar, Kristian K. Ullrich, Wenyu Zhang, Diethard Tautz
Software Mentions: 7
Published: almost 6 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: almost 6 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 12 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: over 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 6 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 5 years ago

10.7717/peerj.11018

Integrated analysis of immune-related long noncoding RNAs as diagnostic biomarkers in psoriasis
Cited by: 13
Author(s): Feixiang Fan, Zhen Huang, Yongfeng Chen
Software Mentions: 7
Published: over 5 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: over 5 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 5 years ago

10.3390/genes12081179

Dysregulation of Synaptic Signaling Genes Is Involved in Biology of Uterine Leiomyoma
Cited by: 2
Author(s): Jovan Krsteski, Mario Gorenjak, Igor But, Maja Pakiž, Uroš Potočnik
Software Mentions: 7
Published: about 5 years ago

10.1186/s13058-020-01379-3

Acquired mutations and transcriptional remodeling in long-term estrogen-deprived locoregional breast cancer recurrences
Cited by: 19
Author(s): Nolan Priedigkeit, Kai Ding, William Horne, Jay K. Kolls, Tian Du, Peter C. Lucas, Jens-Uwe Blohmer, Carsten Denkert, A Machleidt, Barbara Ingold-Heppner, Steffi Oesterreich, Adrian V. Lee
Software Mentions: 7
Published: almost 6 years ago

10.1186/s12864-016-2816-x

EventPointer: an effective identification of alternative splicing events using junction arrays
Cited by: 28
Author(s): Juan Pablo Romero, Ander Muniategui, Fernando J. de Miguel, Ander Aramburu, Luis M. Montuenga, Rubén Pı́o, Ángel Rubio
Software Mentions: 7
Published: over 10 years ago

10.3389/fimmu.2020.01900

Biomarkers of the Response to Immune Checkpoint Inhibitors in Metastatic Urothelial Carcinoma
Cited by: 5
Author(s): Siteng Chen, Ning Zhang, Tao Wang, Encheng Zhang, Xiang Wang, Junhua Zheng
Software Mentions: 7
Published: about 6 years ago

10.1186/s40478-020-00908-7

Epigenetic modulation of AREL1 and increased HLA expression in brains of multiple system atrophy patients
Cited by: 18
Author(s): Rasmus Rydbirk, Jonas Folke, Florence Busato, Elodie Roché, Alisha Shahzad Chauhan, Annemette Løkkegaard, Anne Mette Hejl, Matthias Bode, Morten Blaabjerg, Mette Møller, Erik Hvid Danielsen, Tomasz Brudek, Bente Pakkenberg, Jörg Tost, Susana Aznar
Software Mentions: 7
Published: over 6 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: about 8 years ago

10.1016/j.celrep.2020.107930

Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras
Cited by: 17
Author(s): Nele Merret Hollmann, Pravin Kumar Ankush Jagtap, Paweł Masiewicz, Tanit Guitart, Bernd Simon, Jan Provazník, Frank Stein, Per Haberkant, Lara Sweetapple, Laura Villacorta, Dylan Mooijman, Vladimı́r Beneš, Mikhail M. Savitski, Fátima Gebauer, Janosch Hennig
Software Mentions: 7
Published: over 6 years ago

10.18632/aging.102844

Development of a four-gene prognostic model for pancreatic cancer based on transcriptome dysregulation
Cited by: 19
Author(s): Jie Yan, Liangcai Wu, Congwei Jia, Shuangni Yu, Zhaohui Lü, Yueping Sun, Jie Chen
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: almost 6 years ago

10.1186/s12935-021-02086-5

PODN is a prognostic biomarker and correlated with immune infiltrates in osteosarcoma
Cited by: 9
Author(s): Feng Yao, Zhenxin Zhu, Jun Wen, Fu Yong Zhang, Zheng Zhang, Lei Zhu, Guang Hao Su, Quan Yuan, Yun Fang Zhen, Xiao Dong Wang
Software Mentions: 7
Published: about 5 years ago

10.3389/fnins.2021.621121

Analysis of the Neuroproteome Associated With Cell Therapy After Intranigral Grafting in a Mouse Model of Parkinson Disease
Cited by: 1
Author(s): Hassan Dakik, Sarah Mantash, Ali Nehme, Firas Kobeissy, Masoud Zabet-Moghaddam, Parvin Mirzaei, Yehia Mechref, Afsaneh Gaillard, Laetitia Prestoz, Kazem Zibara
Software Mentions: 7
Published: over 5 years ago

10.1186/s12935-021-02212-3

Midkine promotes glioblastoma progression via PI3K-Akt signaling
Cited by: 14
Author(s): Beiquan Hu, Chao Qin, Li Li, Lei Wei, Xianlun Mo, Huasheng Fan, Yuanhua Lei, Feng Wang, Donghua Zou
Software Mentions: 7
Published: about 5 years ago

10.3389/fgene.2020.595757

Periostin Contributes to Immunoglobulin a Nephropathy by Promoting the Proliferation of Mesangial Cells: A Weighted Gene Correlation Network Analysis
Cited by: 4
Author(s): Jinlong Wu, Qisheng Lin, Shu Li, Xinghua Shao, Xuying Zhu, Minfang Zhang, Wenyan Zhou, Zhaohui Ni
Software Mentions: 7
Published: over 5 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 9 years ago

10.3389/fcell.2021.726716

Identification of an Immune-Related Long Noncoding RNA Pairs Model to Predict Survival and Immune Features in Gastric Cancer
Cited by: 8
Author(s): Shenglei Song, Shuhao Liu, Zhewei Wei, Xinghan Jin, Deli Mao, Yulong He, Bo Li, Changhua Zhang
Software Mentions: 7
Published: about 5 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: about 5 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 5 years ago

10.1186/s12935-021-02050-3

Constructe a novel 5 hypoxia genes signature for cervical cancer
Cited by: 13
Author(s): Yang Yang, Yaling Li, Ruiqun Qi, Lan Zhang
Software Mentions: 7
Published: over 5 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 5 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 5 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: almost 9 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 7 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 10 years ago

10.1186/s12859-019-3016-x

NPA: an R package for computing network perturbation amplitudes using gene expression data and two-layer networks
Cited by: 6
Author(s): Florian Martin, Sylvain Gubian, Marja Talikka, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 7
Published: about 7 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 5 years ago

10.3389/fgene.2019.01372

4See: A Flexible Browser to Explore 4C Data
Cited by: 12
Author(s): Yousra Ben Zouari, Angeliki Platania, Anne Molitor, Tom Sexton
Software Mentions: 7
Published: over 6 years ago

10.1186/s12935-019-1028-2

Expression profile analysis identifies IER3 to predict overall survival and promote lymph node metastasis in tongue cancer
Cited by: 10
Author(s): Fang Xiao, Yinhua Dai, Yujiao Hu, Mengmeng Lu, Qun Dai
Software Mentions: 7
Published: almost 7 years ago

10.3389/fgene.2021.678436

Development of an Immune-Related LncRNA Prognostic Signature for Glioma
Cited by: 8
Author(s): Yudong Cao, Hecheng Zhu, Jun Tan, Yin Wu, Quanwei Zhou, Zhaoqi Xin, Zhaoping Wu, Zhipeng Jiang, Youwei Guo, Yirui Kuang, Can Li, Ming Zhao, Xingjun Jiang, Jian Peng, Chao Ren
Software Mentions: 7
Published: over 5 years ago

10.1016/j.ccell.2020.08.016

Metabolic Imaging Detects Resistance to PI3Kα Inhibition Mediated by Persistent FOXM1 Expression in ER+ Breast Cancer
Cited by: 35
Author(s): Susana Ros, Alan J. Wright, Paula D’Santos, De‐En Hu, Robin Hesketh, Yaniv Lubling, Dimitra Georgopoulou, Giulia Lerda, Dominique‐Laurent Couturier, Pedram Razavi, Rapahel Pelossof, Ankita Batra, Elizabeth Mannion, David Y. Lewis, Alistair Martin, Richard D. Baird, Mafalda Oliveira, Leonora W. de Boo, Sabine C. Linn, Maurizio Scaltriti, Oscar M. Rueda, Alejandra Bruna, Carlos Caldas, Kevin M. Brindle
Software Mentions: 7
Published: about 6 years ago

10.1016/j.ccell.2019.08.008

An Evolutionarily Conserved Function of Polycomb Silences the MHC Class I Antigen Presentation Pathway and Enables Immune Evasion in Cancer
Cited by: 314
Author(s): Marian L. Burr, Christina E Sparbier, Kah Lok Chan, Yih-Chih Chan, Ariena Kersbergen, Enid Y.N. Lam, Elizabeth Azidis-Yates, Dane Vassiliadis, Charles C. Bell, Omer Gilan, Susan Jackson, Lavinia Tan, Stephen Q. Wong, Sebastian Hollizeck, Ewa M. Michalak, Hannah V. Siddle, Michael T. McCabe, Rab K. Prinjha, Glen R Guerra, Benjamin Solomon, Shahneen Sandhu, Sarah‐Jane Dawson, Paul A. Beavis, Richard W. Tothill, Carleen Cullinane, Paul J. Lehner, Kate D. Sutherland, Mark A. Dawson
Software Mentions: 7
Published: about 7 years ago

10.20892/j.issn.2095-3941.2020.0402

The m6A methylation landscape stratifies hepatocellular carcinoma into 3 subtypes with distinct metabolic characteristics
Cited by: 17
Author(s): Xiaotian Shen, Beiyuan Hu, Jing Xu, Wei Qin, Yan Fu, Shun Wang, Qiongzhu Dong, Lun–Xiu Qin
Software Mentions: 7
Published: almost 7 years ago

10.3389/fpls.2021.639631

Local Duplication of TIR-NBS-LRR Gene Marks Clubroot Resistance in Brassica napus cv. Tosca
Cited by: 11
Author(s): Piotr M. Kopec, Katarzyna Mikołajczyk, E. Jajor, A. Perek, Joanna Nowakowska, Christian Obermeier, Harmeet Singh Chawla, M. Korbas, I. Bartkowiak-Broda, Wojciech M. Karłowski
Software Mentions: 7
Published: over 5 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 6 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 5 years ago

10.1093/bib/bbt086

Comparison of software packages for detecting differential expression in RNA-seq studies
Cited by: 317
Author(s): Fatemeh Seyednasrollah, Asta Laiho, Laura L. Elo
Software Mentions: 7
Published: almost 13 years ago

10.1186/1471-2105-16-S11-S4

Epiviz: a view inside the design of an integrated visual analysis software for genomics
Cited by: 3
Author(s): Florin Chelaru, Héctor Corrada Bravo
Software Mentions: 7
Published: about 11 years ago

10.1093/bib/bbz126

Systematic evaluation of differential splicing tools for RNA-seq studies
Cited by: 99
Author(s): Arfa Mehmood, Asta Laiho, Mikko S Venäläinen, Aidan McGlinchey, Ning Wang, Laura L. Elo
Software Mentions: 7
Published: almost 7 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: about 6 years ago

10.1186/1471-2105-9-46

EzArray: A web-based highly automated Affymetrix expression array data management and analysis system
Cited by: 16
Author(s): Yuerong Zhu, Yuelin J. Zhu, Wei Xu
Software Mentions: 7
Published: over 18 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 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: over 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: over 5 years ago

10.1155/2020/2837906

Integrative Analysis of Three Novel Competing Endogenous RNA Biomarkers with a Prognostic Value in Lung Adenocarcinoma
Cited by: 7
Author(s): Juan Tan, Weimin Wang, Bin Song, Yawei Song, Zili Meng
Software Mentions: 7
Published: about 6 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: about 5 years ago

10.1371/journal.pgen.1002704

Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue
Cited by: 45
Author(s): Leopold Parts, Åsa K. Hedman, Sarah Keildson, Andrew Knights, Cei Abreu‐Goodger, Martijn van de Bunt, José Afonso Guerra-Assunção, Nenad Bartoniček, Stijn van Dongen, Reedik Mägi, James Nisbet, Amy Barrett, Mattias Rantalainen, Alexandra C. Nica, Michael A. Quail, Kerrin S. Small, Daniel Glass, Anton J. Enright, John Winn, Panos Deloukas, Emmanouil T. Dermitzakis, Mark I. McCarthy, Timothy D. Spector, Richard Durbin, Cecilia M. Lindgren
Software Mentions: 7
Published: over 14 years ago

10.1186/s12859-018-2445-2

Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance
Cited by: 44
Author(s): Alyssa Baccarella, Claire Williams, Jay Z. Parrish, Charles C. Kim
Software Mentions: 7
Published: almost 8 years ago

10.3389/fgene.2021.604714

Coupling of Co-expression Network Analysis and Machine Learning Validation Unearthed Potential Key Genes Involved in Rheumatoid Arthritis
Cited by: 8
Author(s): Jianwei Xiao, Rongsheng Wang, Xu Cai, Zhizhong Ye
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: about 5 years ago

10.3389/fcell.2021.648279

Prognostic Value of a Novel Signature With Nine Hepatitis C Virus-Induced Genes in Hepatic Cancer by Mining GEO and TCGA Databases
Cited by: 5
Author(s): Jianming Wei, Bo Wang, Xibo Gao, Daqing Sun
Software Mentions: 7
Published: about 5 years ago

10.3389/fcell.2021.688798

QSOX2 Is an E2F1 Target Gene and a Novel Serum Biomarker for Monitoring Tumor Growth and Predicting Survival in Advanced NSCLC
Cited by: 3
Author(s): Yaqi Li, Mei Liu, Zhuoxian Zhang, Libin Deng, Zhenyu Zhai, Hua Liu, Yiting Wang, Cheng Zhang, Jianping Xiong, Chao Shi
Software Mentions: 7
Published: about 5 years ago

10.3389/fphys.2021.609770

Construction of Prognostic Risk Prediction Model of Oral Squamous Cell Carcinoma Based on Nine Survival-Associated Metabolic Genes
Cited by: 10
Author(s): Zhun Huang, Yangyang Yao, Ting‐Yu Chen, Yifan Zhao, Chao Zhang, Yu‐Ming Niu
Software Mentions: 7
Published: over 5 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: over 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 6 years ago

10.3389/fonc.2020.553399

CD8+ T Cell Co-Expressed Genes Correlate With Clinical Phenotype and Microenvironments of Urothelial Cancer
Cited by: 20
Author(s): Yutao Wang, Kexin Yan, Jiaxing Lin, Yang Liu, Jianfeng Wang, Xuejie Li, Xinxin Li, Zhixiong Hua, Zhenhua Zheng, Jianxiu Shi, Siqing Sun, Jianbin Bi
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0079729

DCGL v2.0: An R Package for Unveiling Differential Regulation from Differential Co-expression
Cited by: 76
Author(s): Jing Yang, Hui Yu, Baohong Liu, Zhongming Zhao, Lei Liu, Liangxiao Ma, Yixue Li, Yuanyuan Li
Software Mentions: 7
Published: almost 13 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: over 6 years ago

10.1186/s12859-017-1619-7

Meta-analysis approach as a gene selection method in class prediction: does it improve model performance? A case study in acute myeloid leukemia
Cited by: 4
Author(s): Putri W. Novianti, Victor L. Jong, Kit C. B. Roes, Marinus J.C. Eijkemans
Software Mentions: 7
Published: over 9 years ago

10.1186/s13293-020-00312-9

Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data
Cited by: 27
Author(s): Kimberly C. Olney, Sarah M. Brotman, Jocelyn P. Andrews, Valeria A. Valverde-Vesling, Melissa A. Wilson
Software Mentions: 7
Published: about 6 years ago

10.3389/fmolb.2020.587822

A Novel Prognostic Model of Endometrial Carcinoma Based on Clinical Variables and Oncogenomic Gene Signature
Cited by: 5
Author(s): Fang Deng, Jing Mu, Changzheng Qu, Fang Yang, Xing Liu, Xiaomin Zhang, Xiaoning Peng
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 5 years ago

10.7554/eLife.57843

Increased longevity due to sexual activity in mole-rats is associated with transcriptional changes in the HPA stress axis
Cited by: 17
Author(s): Arne Sahm, Matthias Platzer, Philipp Koch, Yoshiyuki Henning, Martin Bens, Marco Groth, Hynek Burda, Sabine Begall, Saskia Ting, Moritz Goetz, Paul Van Daele, Magdalena Staniszewska, Jasmin Klose, Pedro Fragoso Costa, Steve Hoffmann, Karol Szafranski, Philip Dammann
Software Mentions: 7
Published: over 5 years ago

10.1186/s13062-016-0169-7

Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls
Cited by: 26
Author(s): Paweł P. Łabaj, David P. Kreil
Software Mentions: 7
Published: almost 10 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: over 5 years ago

10.3389/fonc.2021.671892

A Liquid-Liquid Phase Separation-Related Gene Signature as Prognostic Biomarker for Epithelial Ovarian Cancer
Cited by: 9
Author(s): Yan Qiu, Min Pan, Xuemei Chen
Software Mentions: 7
Published: over 5 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: over 7 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 6 years ago

10.3389/fmolb.2021.624951

Metabolism-Relevant Molecular Classification Identifies Tumor Immune Microenvironment Characterization and Immunotherapeutic Effect in Cervical Cancer
Cited by: 4
Author(s): Luyi Li, Hui Gao, Danhan Wang, Hao Jiang, Hongzhu Wang, Jiajian Yu, Xin Jiang, Changjiang Huang
Software Mentions: 7
Published: over 5 years ago

Projects: bioconductor: limma

Science Score: 78/100

Bonuses:

Penalties:

Papers Mentioning limma 7,776