bioconductor: limma | Projects | Ecosyste.ms: Papers

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 5 years ago

10.3390/ijms21239218

Transcriptome Remodeling in Gradual Development of Inverse Resistance between Paclitaxel and Cisplatin in Ovarian Cancer Cells
Cited by: 9
Author(s): Jolanta Szenajch, Alicja Szabelska‐Berȩsewicz, Aleksandra Świercz, Joanna Zyprych-Walczak, Idzi Siatkowski, Michał Góralski, Agnieszka Synowiec, Luiza Handschuh
Software Mentions: 7
Published: over 5 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: over 6 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

10.3389/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 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

10.1042/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: almost 6 years ago

10.3389/fmicb.2020.00995

Microbiota in the Rhizosphere and Seed of Rice From China, With Reference to Their Transmission and Biogeography
Cited by: 31
Author(s): Xin Zhou, Jinting Wang, Z.F. Zhang, Wei Li, Wen Chen, Lei Cai
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pone.0215565

A robust data-driven genomic signature for idiopathic pulmonary fibrosis with applications for translational model selection
Cited by: 6
Author(s): Ron Ammar, Pitchumani Sivakumar, Gábor Járai, John Ryan Thompson
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: over 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

10.1038/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: almost 7 years ago

10.1371/journal.pone.0183933

Tensor decomposition-based unsupervised feature extraction applied to matrix products for multi-view data processing
Cited by: 24
Author(s): Y-h. Taguchi
Software Mentions: 7
Published: almost 9 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.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

10.1002/1873-3468.14180

Genome‐scale metabolic modelling of SARS‐CoV‐2 in cancer cells reveals an increased shift to glycolytic energy production
Cited by: 13
Author(s): Elisabeth Yaneske, Guido Zampieri, Loris Bertoldi, Giuseppe Benvenuto, Claudio Angione
Software Mentions: 7
Published: almost 5 years ago

10.1111/acel.13344

Senescence‐associated β‐galactosidase reveals the abundance of senescent CD8+ T cells in aging humans
Cited by: 62
Author(s): Ricardo Iván Martínez-Zamudio, Hannah K Dewald, Themistoklis Vasilopoulos, Lisa Gittens-Williams, Patricia Fitzgerald-Bocarsly, Utz Herbig
Software Mentions: 7
Published: over 5 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: about 8 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

10.12688/f1000research.9005.3

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
Cited by: 297
Author(s): Charity W. Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Tian Li, Gordon K. Smyth, Matthew E. Ritchie
Software Mentions: 7
Published: over 7 years ago

10.1186/s12859-020-03722-z

PAWER: protein array web exploreR
Cited by: 4
Author(s): Dmytro Fishman, Ivan Kuzmin, Priit Adler, Jaak Vilo, Hedi Peterson
Software Mentions: 7
Published: almost 6 years ago

10.12688/f1000research.11290.1

Gene length and detection bias in single cell RNA sequencing protocols
Cited by: 71
Author(s): Belinda Phipson, Luke Zappia, Alicia Oshlack
Software Mentions: 7
Published: over 9 years ago

10.12688/f1000research.6030.2

AGA: Interactive pipeline for reproducible gene expression and DNA methylation data analyses
Cited by: 3
Author(s): Michael Considine, Hilary S. Parker, Yingying Wei, Xaio Xia, Leslie Cope, Michael F. Ochs, Elana J. Fertig
Software Mentions: 7
Published: almost 11 years ago

10.18632/aging.202269

Immune profile of the tumor microenvironment and the identification of a four-gene signature for lung adenocarcinoma
Cited by: 15
Author(s): Tao Fan, Mark Zhu, Li-Yu Wang, Yu Liu, He Tian, Zheng Yang, Fengwei Tan, Nan Sun, Chunxiang Li, Jie He
Software Mentions: 7
Published: over 5 years ago

10.1155/2021/6629842

DOCK4 Is a Platinum-Chemosensitive and Prognostic-Related Biomarker in Ovarian Cancer
Cited by: 6
Author(s): Qianqian Zhao, Jie Zhong, Ping Lü, Xiao Feng, Ying Han, Chenqi Ling, Wenxiu Guo, Weijin Zhou, Fudong Yu
Software Mentions: 7
Published: over 5 years ago

10.3390/medicina55060269

A Robust Approach for Identification of Cancer Biomarkers and Candidate Drugs
Cited by: 10
Author(s): Shahjaman, Rezanur Rahman, S. M. Shahinul Islam, Md. Nurul Haque Mollah
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: 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

10.1186/s12864-018-4689-7

Gene copy number variation in natural populations of Plasmodium falciparum in Eastern Africa
Cited by: 12
Author(s): Joan Simam, Martin K. Rono, Joyce M. Ngoi, Mary Nyonda, Sachel Mok, Kevin Marsh, Zbynek Bozdech, Margaret J. Mackinnon
Software Mentions: 7
Published: over 8 years ago

10.1155/2021/5555634

Downregulation of ATP6V1A Involved in Alzheimer’s Disease via Synaptic Vesicle Cycle, Phagosome, and Oxidative Phosphorylation
Cited by: 15
Author(s): Zhike Zhou, Jun Bai, Shanshan Zhong, Rongwei Zhang, Kexin Kang, Xiaoqian Zhang, Ying Xu, Chuansheng Zhao, Mei Zhao
Software Mentions: 7
Published: over 5 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: over 8 years ago

10.18632/aging.203017

Identification of key transcriptome biomarkers based on a vital gene module associated with pathological changes in Alzheimer’s disease
Cited by: 11
Author(s): Tong Zhang, Yang Shen, Yiqing Guo, Junyan Yao
Software Mentions: 7
Published: about 5 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

10.18632/aging.103999

CCL5-dependent mast cell infiltration into the tumor microenvironment in clear cell renal cell carcinoma patients
Cited by: 12
Author(s): Tianjie Liu, Qing Xia, Haibao Zhang, Zixi Wang, Wenjie Yang, Xiao Gu, Tao Hou, Yule Chen, Xinqi Pei, Guodong Zhu, Dalin He, Lei Li, Shan Xu
Software Mentions: 7
Published: almost 6 years ago

10.1002/evl3.245

Widespread cryptic variation in genetic architecture between the sexes
Cited by: 11
Author(s): Wouter van der Bijl, Judith E. Mank
Software Mentions: 7
Published: about 5 years ago

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

10.15252/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

10.15252/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: over 8 years ago

10.1186/s13000-021-01118-y

Identification of immune-infiltrating cell-related biomarkers in hepatocellular carcinoma based on gene co-expression network analysis
Cited by: 6
Author(s): Yinghui Hou, Guizhi Zhang
Software Mentions: 7
Published: about 5 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

10.1242/dev.199561

Global proteomic analyses of human cytotrophoblast differentiation/invasion
Cited by: 4
Author(s): Hao Chen, Katherine E. Williams, Elaine Kwan, Mirhan Kapidzic, Kenisha A. Puckett, Rayyan Aburajab, Joshua F. Robinson, Susan J. Fisher
Software Mentions: 7
Published: about 5 years ago

10.1111/jcmm.16321

Characterization of an endoplasmic reticulum stress‐related signature to evaluate immune features and predict prognosis in glioma
Cited by: 29
Author(s): Qing Zhang, Gefei Guan, Cheng Peng, Wen Cheng, Lianhe Yang, Anhua Wu
Software Mentions: 7
Published: over 5 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

10.3390/genes11040400

Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant
Cited by: 7
Author(s): Alexandre Rêgo, Samridhi Chaturvedi, Amy L. Springer, Alexandra M. Lish, Caroline L. Barton, Karen M. Kapheim, Frank J. Messina, Zachariah Gompert
Software Mentions: 7
Published: over 6 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

10.1186/1471-2105-9-46

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

10.18632/aging.202982

Prognostic value of members of NFAT family for pan-cancer and a prediction model based on NFAT2 in bladder cancer
Cited by: 4
Author(s): Zhou-Tong Dai, Xiang Yuan, Yundan Wang, Lidao Bao, Jun Wang, Jiapeng Li, Huimin Zhang, Zhongxin Lu, Sreenivasan Ponnambalam, Xing–Hua Liao
Software Mentions: 7
Published: over 5 years ago

10.18632/aging.102571

Identification of molecular correlations of RBM8A with autophagy in Alzheimer's disease
Cited by: 40
Author(s): Donghua Zou, Rongjie Li, Xiaohua Huang, Guoying Chen, Ying Liu, Youshi Meng, Yimei Wang, Yuan Wu, Ying Mao
Software Mentions: 7
Published: over 6 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

10.1186/s13059-014-0465-4

DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging
Cited by: 84
Author(s): Belinda Phipson, Alicia Oshlack
Software Mentions: 7
Published: almost 12 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

10.1186/s12920-020-00808-8

Biomarker discovery in attention deficit hyperactivity disorder: RNA sequencing of whole blood in discordant twin and case-controlled cohorts
Cited by: 11
Author(s): Timothy A. McCaffrey, Georges St. Laurent, Dmitry Shtokalo, Денис Антонец, Yuri Vyatkin, Dan Jones, Eleanor Battison, Joel T. Nigg
Software Mentions: 7
Published: almost 6 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: almost 7 years ago

10.1038/s41597-019-0095-5

Multi omics analysis of fibrotic kidneys in two mouse models
Cited by: 25
Author(s): Mira Pavkovic, Lorena Pantano, Cory V. Gerlach, Sergine Brutus, Sarah A. Boswell, Robert A. Everley, Jagesh V. Shah, Shannan Ho Sui, Vishal S. Vaidya
Software Mentions: 7
Published: about 7 years ago

10.1186/s12920-021-01081-z

Identification and validation of a novel immune-related signature associated with macrophages and CD8 T cell infiltration predicting overall survival for hepatocellular carcinoma
Cited by: 2
Author(s): Junyu Huo, Liqun Wu, Yunjin Zang
Software Mentions: 7
Published: almost 5 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: almost 6 years ago

10.3389/fonc.2021.698278

A Focal Adhesion-Related Gene Signature Predicts Prognosis in Glioma and Correlates With Radiation Response and Immune Microenvironment
Cited by: 7
Author(s): Haonan Li, Guohui Wang, Wenyan Wang, Jie Pan, Huandi Zhou, Xuetao Han, Linlin Su, Zhenghui Ma, Liubing Hou, Xiaoying Xue
Software Mentions: 7
Published: almost 5 years ago

10.1053/j.gastro.2017.10.007

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome
Cited by: 199
Author(s): Kate J. Howell, Judith Kraiczy, Komal Nayak, Marco Gasparetto, Alex Ross, Claire Lee, Tim N. Mak, Bon–Kyoung Koo, Nitin Kumar, Trevor D. Lawley, Anupam Sinha, Philip Rosenstiel, Robert Heuschkel, Oliver Stegle, Matthias Zilbauer
Software Mentions: 7
Published: over 8 years ago

10.3390/genes10100778

DNA Methylation Markers for Pan-Cancer Prediction by Deep Learning
Cited by: 48
Author(s): Biao Liu, Yulu Liu, Xingxin Pan, Mengyao Li, Shuang Yang, Shuai Cheng Li
Software Mentions: 7
Published: almost 7 years ago

10.1002/cti2.1127

High‐dimensional analyses reveal a distinct role of T‐cell subsets in the immune microenvironment of gastric cancer
Cited by: 18
Author(s): Minyu Wang, Yen-Yu Huang, Joseph C Kong, Yu Sun, Daniela Tantalo, Han Xian Aw Yeang, Le Ying, Feng Yan, Dakang Xu, Heloise M. Halse, Natasha Di Costanzo, Ian Gordon, Catherine Mitchell, Laura K. Mackay, Rita A. Busuttil, Paul J. Neeson, Alex Boussioutas
Software Mentions: 7
Published: over 6 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

10.1016/j.csbj.2021.04.056

A computational analysis of transcriptional profiles from CD8(+) T lymphocytes reveals potential mechanisms of HIV/AIDS control and progression
Cited by: 3
Author(s): Sergey Ivanov, Dmitry Filimonov, O. Tarasova
Software Mentions: 7
Published: over 5 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: about 8 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: over 6 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: about 7 years ago

10.3389/fonc.2021.632459

Construction and Validation of a Novel Eight-Gene Risk Signature to Predict the Progression and Prognosis of Bladder Cancer
Cited by: 3
Author(s): Ruiliang Wang, Zongtai Zheng, Shun Mao, Wentao Zhang, Ji Liu, Cheng Li, Shenghua Liu, Xudong Yao
Software Mentions: 7
Published: about 5 years ago

10.1186/1471-2105-12-267

SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data
Cited by: 39
Author(s): Xutao Deng
Software Mentions: 7
Published: about 15 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

10.3389/fonc.2020.01444

Development and Validation of an m6A RNA Methylation Regulator-Based Signature for Prognostic Prediction in Cervical Squamous Cell Carcinoma
Cited by: 32
Author(s): Jianji Pan, Lichao Xu, Hongda Pan
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

10.3389/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

10.3389/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: about 5 years ago

10.18632/aging.102200

Identification and validation of four hub genes involved in the plaque deterioration of atherosclerosis
Cited by: 12
Author(s): Peipei Chen, Yuexin Chen, Wei Wu, Lianfeng Chen, Xufei Yang, Shuyang Zhang
Software Mentions: 7
Published: almost 7 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

10.3389/fnins.2021.682247

Decreased MEF2A Expression Regulated by Its Enhancer Methylation Inhibits Autophagy and May Play an Important Role in the Progression of Alzheimer’s Disease
Cited by: 8
Author(s): Hui Li, Rui Wang, Xuqi Guo, Yugang Jiang
Software Mentions: 7
Published: about 5 years ago

10.3390/ijms19061808

Co-Expression Network Analysis of AMPK and Autophagy Gene Products during Adipocyte Differentiation
Cited by: 8
Author(s): Mahmoud Ahmed, Jin Seok Hwang, Trang Huyen Lai, Sahib Zada, Huynh Quoc Nguyen, Trang Min Pham, Miyong Yun, Deok Ryong Kim
Software Mentions: 7
Published: about 8 years ago

10.3389/fmolb.2021.651525

Potential Role of NEU1 in Hepatocellular Carcinoma: A Study Based on Comprehensive Bioinformatical Analysis
Cited by: 5
Author(s): Zhulin Wu, Li He, Lina Yang, Xuehong Fang, Lisheng Peng
Software Mentions: 7
Published: almost 5 years ago

10.7554/eLife.62800

Mapping immune variation and var gene switching in naive hosts infected with Plasmodium falciparum
Cited by: 18
Author(s): Kathryn H. Milne, Alasdair Ivens, Adam J. Reid, Magda E. Lotkowska, Áine O’Toole, Geetha Sankaranarayanan, Diana Muñoz Sandoval, Wiebke Nahrendorf, Clément Regnault, Nick J. Edwards, Sarah E. Silk, Ruth Payne, Angela M. Minassian, Navin Venkatraman, Mandy Sanders, Adrian V. S. Hill, Michael P. Barrett, Matthew Berriman, Simon J. Draper, J. Alexandra Rowe, Philip J. Spence
Software Mentions: 7
Published: over 5 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
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Author(s): Zaoqu Liu, Yuyuan Zhang, Chengcheng Shi, Xueliang Zhou, Kaihao Xu, Dechao Jiao, Zhenqiang Sun, Xinwei Han
Software Mentions: 7
Published: over 5 years ago

10.3389/fmolb.2021.624951

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

10.3390/ijms19102903

Identification of a Prognostic Hypoxia-Associated Gene Set in IDH-Mutant Glioma
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Author(s): Philip Dao Trong, Saskia Rösch, Heimo Mairbäurl, Stefan Pusch, Andreas Unterberg, Christel Herold‐Mende, Rolf Warta
Software Mentions: 7
Published: almost 8 years ago

10.1155/2017/5310198

Robust Significance Analysis of Microarrays by Minimum <i>β</i>-Divergence Method
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Author(s): Shahjaman, Nishith Kumar, Md. Manir Hossain Mollah, Shakil Ahmed, Anjuman Ara Begum, S. M. Shahinul Islam, Md. Nurul Haque Mollah
Software Mentions: 7
Published: over 9 years ago

10.1186/s12864-016-3260-7

DeSigN: connecting gene expression with therapeutics for drug repurposing and development
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Author(s): Bernard Kok Bang Lee, Kai Hung Tiong, Jit Kang Chang, Chee Sun Liew, Zainal Ariff Abdul Rahman, Aik Choon Tan, Tsung Fei Khang, Sok Ching Cheong
Software Mentions: 7
Published: over 9 years ago

10.3389/fmolb.2021.645845

A Novel Defined Risk Signature of the Ferroptosis-Related Genes for Predicting the Prognosis of Ovarian Cancer
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Author(s): Ying Yang, Qinjin Dai, Shuhong Li, Jie He, Hongbo Qi
Software Mentions: 7
Published: over 5 years ago

10.1186/s12885-020-06777-6

The DNA hypermethylation phenotype of colorectal cancer liver metastases resembles that of the primary colorectal cancers
Cited by: 11
Author(s): Stephany Orjuela, Mirco Menigatti, Peter Schraml, Patryk Kambakamba, Mark D. Robinson, Giancarlo Marra
Software Mentions: 7
Published: over 6 years ago

10.1186/s12885-020-07345-8

Identification of a metabolism-related gene expression prognostic model in endometrial carcinoma patients
Cited by: 19
Author(s): Pinping Jiang, Wei Sun, Ningmei Shen, Xin Huang, Shilong Fu
Software Mentions: 7
Published: almost 6 years ago

10.3389/fmolb.2020.562441

Novel Molecular Subtypes Associated With 5mC Methylation and Their Role in Hepatocellular Carcinoma Immunotherapy
Cited by: 12
Author(s): Zhuomao Mo, Zhirui Cao, Shaoju Luo, Yan Chen, Shijun Zhang
Software Mentions: 7
Published: almost 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

10.1186/1471-2164-11-349

Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3
Cited by: 70
Author(s): RM Schmid, Patrick Baum, Carina Ittrich, Katrin Fundel‐Clemens, Wolfgang Huber, Benedikt Brors, Roland Eils, Andreas Weith, Detlev Mennerich, Karsten Quast
Software Mentions: 7
Published: about 16 years ago

10.1371/journal.pone.0079729

DCGL v2.0: An R Package for Unveiling Differential Regulation from Differential Co-expression
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Author(s): Jing Yang, Hui Yu, Baohong Liu, Zhongming Zhao, Lei Liu, Liangxiao Ma, Yixue Li, Yuanyuan Li
Software Mentions: 7
Published: over 12 years ago

10.3389/fmolb.2021.656145

Identification and Exploration of Novel Macrophage M2-Related Biomarkers and Potential Therapeutic Agents in Endometriosis
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Author(s): Zhongqi Cui, Ramesh Singh Bhandari, Lei Qin, Mingzhi Lu, Lei Zhang, Mengmei Zhang, Fenyong Sun, Lijin Feng, Shasha Zhao
Software Mentions: 7
Published: about 5 years ago

10.1186/s13287-020-01823-3

Multiomics global landscape of stemness-related gene clusters in adipose-derived mesenchymal stem cells
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Author(s): Guan-Ming Lu, Yong-Xian Rong, Zheng Liang, Dong-Lin Hunag, Yuju Ma, Zhizhai Luo, Fengyao Wu, Xinheng Liu, Yu Liu, Steven Mo, Zhongquan Qi, Hong-Mian Li
Software Mentions: 7
Published: about 6 years ago

10.3389/fmolb.2021.705008

CUX1 Facilitates the Development of Oncogenic Properties Via Activating Wnt/β-Catenin Signaling Pathway in Glioma
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Author(s): Fang Fěng, Zongqing Zhao, Yunfei Zhou, Yalin Cheng, Xiujie Wu, Xueyuan Heng
Software Mentions: 7
Published: about 5 years ago

10.1155/2021/2628824

A Potential ceRNA Network for Neurological Damage in Preterm Infants
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Author(s): Hui‐Zi Jin, Xinlan Liang, Zhenyu Cai
Software Mentions: 7
Published: almost 5 years ago

10.3389/fmolb.2021.656204

Understanding the Holobiont: Crosstalk Between Gut Microbiota and Mitochondria During Long Exercise in Horse
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Author(s): Núria Mach, Marco Moroldo, Andrea Rau, Jérôme Lecardonnel, Laurence Le Moyec, Céline Robert, Éric Barrey
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0196117

Identification of a neutrophil-related gene expression signature that is enriched in adult systemic lupus erythematosus patients with active nephritis: Clinical/pathologic associations and etiologic mechanisms
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Author(s): Joan E. Wither, Stephenie D. Prokopec, Babak Noamani, Nan-Hua Chang, Dennisse Bonilla, Zahi Touma, Carmen Ávila-Casado, Heather N. Reich, James W. Scholey, Paul R. Fortin, Paul C. Boutros, Carolina Landolt-Marticorena
Software Mentions: 7
Published: over 8 years ago

10.18632/aging.202417

Overexpression of TICRR and PPIF confer poor prognosis in endometrial cancer identified by gene co-expression network analysis
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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
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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

10.1038/s41598-021-94343-w

Gene expression analysis method integration and co-expression module detection applied to rare glucide metabolism disorders using ExpHunterSuite
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Author(s): Fernando M. Jabato, José Córdoba-Caballero, Elena Rojano, Carlos Romá‐Mateo, Pascual Sanz, Belén Pérez, Diana Gallego, Pedro Seoane, Juan A. G. Ranea, James R. Perkins
Software Mentions: 7
Published: about 5 years ago

10.1038/s41598-021-93509-w

Mapping the landscape of chromatin dynamics during naïve CD4+ T-cell activation
Cited by: 9
Author(s): Muhammad Munir Iqbal, Michael Serralha, Parwinder Kaur, David Martino
Software Mentions: 7
Published: about 5 years ago

Projects: bioconductor: limma

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Papers Mentioning limma 7,776