bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1038/s41598-020-70596-9

Identification of potential diagnostic gene biomarkers in patients with osteoarthritis
Cited by: 13
Author(s): Xinling Wang, Yu Yang, Yong Huang, Zhu Ming-shuang, Rigao Chen, Zhanghui Liao, Shipeng Yang
Software Mentions: 8
Published: about 6 years ago

10.1186/s12957-018-1519-y

Identification of hub genes with diagnostic values in pancreatic cancer by bioinformatics analyses and supervised learning methods
Cited by: 23
Author(s): Chunyang Li, Xiaoxi Zeng, Haopeng Yu, Yuanxia Gu, Wei Zhang
Software Mentions: 8
Published: almost 8 years ago

10.1038/s41598-020-75541-4

Stromal microenvironment promoted infiltration in esophageal adenocarcinoma and squamous cell carcinoma: a multi-cohort gene-based analysis
Cited by: 6
Author(s): Jiali Li, Zhao-Yi Zeng, Xueping Jiang, Nannan Zhang, Yanping Gao, Yuan Luo, Wenjie Sun, Shuying Li, Jiangbo Ren, Yan Gong, Conghua Xie
Software Mentions: 8
Published: almost 6 years ago

10.3389/fcell.2021.653357

Combination of Immune-Related Genomic Alterations Reveals Immune Characterization and Prediction of Different Prognostic Risks in Ovarian Cancer
Cited by: 2
Author(s): Xibo Zhao, Shanshan Cong, Qiuyan Guo, Yan Cheng, Tian Liang, Jing Wang, Guangmei Zhang
Software Mentions: 8
Published: over 5 years ago

10.1186/s12935-020-01588-y

A four prognosis-associated lncRNAs (PALnc) based risk score system reflects immune cell infiltration and predicts patient survival in pancreatic cancer
Cited by: 14
Author(s): Hongkai Zhuang, Shanzhou Huang, Zixuan Zhou, Zuyi Ma, Zedan Zhang, Chuanzhao Zhang, Baohua Hou
Software Mentions: 8
Published: almost 6 years ago

10.1371/journal.pone.0183264

The transcriptional profiling of human in vivo-generated plasma cells identifies selective imbalances in monoclonal gammopathies
Cited by: 12
Author(s): Luis M. Valor, Beatriz Rodrı́guez-Bayona, Ana Ramos-Amaya, José A. Brieva, Antonio Campos‐Caro
Software Mentions: 8
Published: about 9 years ago

10.3389/fmed.2021.644053

Comprehensive Analysis Identifies Potential Ferroptosis-Associated mRNA Therapeutic Targets in Ovarian Cancer
Cited by: 16
Author(s): Jiyan Zhang, Jie Xi, Ping Huang, Saitian Zeng
Software Mentions: 8
Published: over 5 years ago

10.3389/fonc.2021.561763

Predict Colon Cancer by Pairing Plasma miRNAs: Establishment of a Normalizer-Free, Cross-Platform Model
Cited by: 3
Author(s): Dashan Qin, Qingdong Guo, Rui Wei, Si Liu, Shoumin Zhu, Shutian Zhang, Li Min
Software Mentions: 8
Published: over 5 years ago

10.1097/MD.0000000000027374

Identification and validation of a hypoxia-related prognostic signature in clear cell renal cell carcinoma patients
Cited by: 7
Author(s): Zhengtian Li, Gang Du, Rong Zhao, Weibo Yang, Chan Li, Jun Huang, Zhenpei Wen, Hening Li, Bo Zhang
Software Mentions: 8
Published: about 5 years ago

10.3389/fgene.2019.01331

Reproducibility of Methods to Detect Differentially Expressed Genes from Single-Cell RNA Sequencing
Cited by: 50
Author(s): Tian Mou, Wenjiang Deng, Fengyun Gu, Yudi Pawitan, Trung Nghia Vu
Software Mentions: 8
Published: over 6 years ago

10.3389/fgene.2021.647353

Identification of Hub Genes and Their Correlation With Immune Infiltration Cells in Hepatocellular Carcinoma Based on GEO and TCGA Databases
Cited by: 22
Author(s): Rui Huang, Jinying Liu, Hui Li, Lierui Zheng, Haojun Jin, Yaqing Zhang, Wei Ma, Junhong Su, Min Wang, Kun Yang
Software Mentions: 8
Published: over 5 years ago

10.1128/mBio.01369-21

HIV-1 Vpr Induces Widespread Transcriptomic Changes in CD4 <sup>+</sup> T Cells Early Postinfection
Cited by: 6
Author(s): Hélène Bauby, Christopher Ward, Rupert Hugh-White, Chad M. Swanson, Reiner Schulz, Caroline Goujon, Michael H. Malim
Software Mentions: 8
Published: over 5 years ago

10.3389/fcell.2021.686664

Systematic Characterization of Novel Immune Gene Signatures Predicts Prognostic Factors in Hepatocellular Carcinoma
Cited by: 4
Author(s): Dafeng Xu, Yu Wang, Junzhen Wu, Yuliang Zhang, Zhehao Liu, Yonghai Chen, Jinfang Zheng
Software Mentions: 8
Published: about 5 years ago

10.1016/j.isci.2021.102762

NANOS2 is a sequence-specific mRNA-binding protein that promotes transcript degradation in spermatogonial stem cells
Cited by: 9
Author(s): Azzurra Codino, Tomasz W. Turowski, Louie N. van de Lagemaat, Ivayla Ivanova, Andrea Tavosanis, Christian Much, Tania Auchynnikava, Lina Vasiliauskaitė, Marcos Morgan, Juri Rappsilber, Robin Allshire, Kamil R. Kranc, David Tollervey, Dónal O’Carroll
Software Mentions: 8
Published: over 5 years ago

10.3389/fcell.2021.665869

Enhancing Fatty Acid Catabolism of Macrophages Within Aberrant Breast Cancer Tumor Microenvironment Can Re-establish Antitumor Function
Cited by: 4
Author(s): Yucui Gu, Xingjian Niu, Lei Yin, Yiran Wang, Yue Yang, Xudong Yang, Qingyuan Zhang, Hongfei Ji
Software Mentions: 8
Published: over 5 years ago

10.1038/s41597-020-00696-8

Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients
Cited by: 10
Author(s): Antonio Federico, Veera Hautanen, Nils Christian, Andreas Kremer, Angela Serra, Dario Greco
Software Mentions: 8
Published: almost 6 years ago

10.1128/mSystems.01356-20

Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities
Cited by: 26
Author(s): Jingjie Du, Ahmed A. Zayed, Kristina A. Kigerl, Kylie Zane, Matthew B. Sullivan, Phillip G. Popovich
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pcbi.1008748

A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways
Cited by: 6
Author(s): Martín Garrido‐Rodriguez, Daniel López-López, Francisco Ortuño, María Peña‐Chilet, Eduardo Muñóz, Marco A. Calzado, Joaquı́n Dopazo
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pcbi.1006378

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets
Cited by: 45
Author(s): Davide Risso, Liam Purvis, Russell B. Fletcher, Diya Das, John Ngai, Sandrine Dudoit, Elizabeth Purdom
Software Mentions: 8
Published: about 8 years ago

10.1371/journal.pone.0187722

Plasma microRNA profiling: Exploring better biomarkers for lymphoma surveillance
Cited by: 47
Author(s): Drirh Khare, Neta Goldschmidt, Aya Bardugo, Devorah Gur‐Wahnon, Iddo Z. Ben‐Dov, Batia Avni
Software Mentions: 8
Published: almost 9 years ago

10.1007/s13365-020-00931-3

Transcriptional signatures of Zika virus infection in astrocytes
Cited by: 3
Author(s): Blake Schouest, Tiffany A. Peterson, Dawn Szeltner, Elizabeth A. Scheef, Melody Baddoo, Nathan Ungerleider, Erik K. Flemington, Andrew G. MacLean, Nicholas J. Maness
Software Mentions: 8
Published: over 5 years ago

10.3389/fonc.2020.558596

Development and Validation of Autophagy-Related Gene Signature and Nomogram for Predicting Survival in Oral Squamous Cell Carcinoma
Cited by: 25
Author(s): Chen Hou, Hao Cai, Yue Zhu, Shuojin Huang, Song Fan, Jinsong Hou
Software Mentions: 8
Published: almost 6 years ago

10.1038/s41598-020-68665-0

MAF1 is a chronic repressor of RNA polymerase III transcription in the mouse
Cited by: 15
Author(s): Nicolas Bonhoure, Viviane Praz, Robyn D. Moir, Gilles Willemin, François Mange, Catherine Moret, Ian M. Willis, Nouria Hernandez
Software Mentions: 8
Published: about 6 years ago

10.1371/journal.ppat.1009933

Trypanosoma brucei triggers a broad immune response in the adipose tissue
Cited by: 11
Author(s): Henrique Machado, Tiago Bizarra-Rebelo, Mariana Sequeira, Sandra Trindade, Tãnia Carvalho, Filipa Rijo‐Ferreira, Barbara Rentroia‐Pacheco, Karine Serre, Luísa M. Figueiredo
Software Mentions: 8
Published: about 5 years ago

10.1186/s13148-020-00931-4

TWIST1 DNA methylation is a cell marker of airway and parenchymal lung fibroblasts that are differentially methylated in asthma
Cited by: 7
Author(s): Rachel L. Clifford, Chen Xi Yang, Nick Fishbane, J. Patel, Julia L. MacIsaac, Lisa M. McEwen, Sean May, Marcos Castellanos-Uribe, Parameswaran Nair, Ma’en Obeidat, Michæl S. Kobor, Alan J. Knox, Tillie-Louise Hackett
Software Mentions: 8
Published: about 6 years ago

10.1371/journal.pone.0069624

Transcriptomic Analysis of Insulin-Sensitive Tissues from Anti-Diabetic Drug Treated ZDF Rats, a T2DM Animal Model
Cited by: 4
Author(s): Yo Na Kim, Sangok Kim, Il Yong Kim, Jae Hoon Shin, Sooyoung Cho, Sun Shin Yi, Wankyu Kim, Kyung Sub Kim, Sanghyuk Lee, Je Kyung Seong
Software Mentions: 8
Published: about 13 years ago

10.3389/fonc.2021.654388

MYD88 Is a Potential Prognostic Gene and Immune Signature of Tumor Microenvironment for Gliomas
Cited by: 13
Author(s): Qinglong Guo, Xing Xiao, Jinsen Zhang
Software Mentions: 8
Published: over 5 years ago

10.7717/peerj.12070

Prognostic impact of a lymphocyte activation-associated gene signature in GBM based on transcriptome analysis
Cited by: 1
Author(s): Yujia Lan, Erjie Zhao, Xinxin Zhang, Xiaojing Zhu, Linyun Wan, Aditya Suru, Yanyan Ping, Yihan Wang
Software Mentions: 8
Published: about 5 years ago

10.3389/fonc.2020.01198

Immune Landscape of the Tumor Microenvironment Identifies Prognostic Gene Signature CD4/CD68/CSF1R in Osteosarcoma
Cited by: 25
Author(s): Yi-Jiang Song, Yanyang Xu, Xuejun Zhu, Jianchang Fu, Cong Deng, Hongmin Chen, Huaiyuan Xu, Guohui Song, Jinchang Lu, Qinglian Tang, Jin Wang
Software Mentions: 8
Published: about 6 years ago

10.3389/fgene.2021.650554

Exploration of the Role of m6 A RNA Methylation Regulators in Malignant Progression and Clinical Prognosis of Ovarian Cancer
Cited by: 4
Author(s): Qinglv Wei, Dan Yang, Xiaoyi Liu, Hongyan Zhao, Yang Yu, Jing Xu, Tao Liu, Ping Yi
Software Mentions: 8
Published: over 5 years ago

10.1038/s41598-020-62354-8

Differential stromal reprogramming in benign and malignant naturally occurring canine mammary tumours identifies disease-modulating stromal components
Cited by: 18
Author(s): Parisa Amini, Sina Nassiri, Alexandra Malbon, Enni Markkanen
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pone.0255708

Identification of key genes and immune infiltration modulated by CPAP in obstructive sleep apnea by integrated bioinformatics analysis
Cited by: 3
Author(s): Cheng Fan, Sisi Huang, Chunhua Xiang, Tianhui An, Yi Song
Software Mentions: 8
Published: about 5 years ago

10.1002/cam4.4156

Comprehensive analysis of a new prognosis signature based on histone deacetylases in clear cell renal cell carcinoma
Cited by: 6
Author(s): Fajuan Cheng, Bin Zheng, Jianwei Wang, Guiting Zhao, Zhongshun Yao, Zhihong Niu
Software Mentions: 8
Published: about 5 years ago

10.3389/fcvm.2020.575275

Reactivation of Atrium Genes Is a Primer for Heart Infarction or Regeneration
Cited by: 1
Author(s): Yang Zhen
Software Mentions: 8
Published: almost 6 years ago

10.7717/peerj.7942

A genomic-clinical nomogram predicting recurrence-free survival for patients diagnosed with hepatocellular carcinoma
Cited by: 6
Author(s): Junjie Kong, Tao Wang, Shu Shen, Zifei Zhang, Xianwei Yang, Wentao Wang
Software Mentions: 8
Published: almost 7 years ago

10.1038/s41598-019-48746-5

Gene Expression Predicts Histological Severity and Reveals Distinct Molecular Profiles of Nonalcoholic Fatty Liver Disease
Cited by: 93
Author(s): Stephen A. Hoang, Abdul M. Oseini, Ryan E. Feaver, Banumathi K. Cole, Amon Asgharpour, Robert Vincent, Mohammad Shadab Siddiqui, Mark Lawson, Nathan Day, Justin M. Taylor, Brian R. Wamhoff, Faridoddin Mirshahi, Melissa J. Contos, Michael O. Idowu, Arun J. Sanyal
Software Mentions: 8
Published: about 7 years ago

10.1371/journal.pone.0159921

BEclear: Batch Effect Detection and Adjustment in DNA Methylation Data
Cited by: 19
Author(s): Ruslan Akulenko, Markus Merl, Volkhard Helms
Software Mentions: 8
Published: about 10 years ago

10.7717/peerj.1360

Getting the most out of RNA-seq data analysis
Cited by: 22
Author(s): Tsung Fei Khang, Ching Yee Lau
Software Mentions: 8
Published: almost 11 years ago

10.1002/cam4.3655

Immune landscape and a promising immune prognostic model associated with TP53 in early‐stage lung adenocarcinoma
Cited by: 17
Author(s): Chia-Chien Wu, Rong Xiang, Lin Wei
Software Mentions: 8
Published: almost 6 years ago

10.1186/s13148-016-0230-5

Peripheral blood methylation profiling of female Crohn’s disease patients
Cited by: 40
Author(s): Andrew Y. Li Yim, Nicolette W. Duijvis, Jing Hua Zhao, Wouter J. de Jonge, Geert R. D’Haens, Marcel M.A.M. Mannens, Adri N. Mul, Anje A. te Velde, Peter Henneman
Software Mentions: 8
Published: over 10 years ago

10.7717/peerj.11233

Identification of a ferroptosis-related gene signature (FRGS) for predicting clinical outcome in lung adenocarcinoma
Cited by: 11
Author(s): Sheng Wang, Chunlei Wu, Dehua Mao, Quanteng Hu
Software Mentions: 8
Published: over 5 years ago

10.1084/jem.20201833

ADAR and hnRNPC deficiency synergize in activating endogenous dsRNA-induced type I IFN responses
Cited by: 7
Author(s): Anna‐Maria Herzner, Zia Khan, Eric L. Van Nostrand, Sara M. Chan, Trinna Cuellar, Ronald Chen, Ximo Pechuan-Jorge, László G. Kömüves, Margaret Solon, Zora Modrušan, Benjamin Haley, G Yeo, Timothy W. Behrens, Matthew L. Albert
Software Mentions: 8
Published: about 5 years ago

10.3389/fonc.2021.642144

Complement C1q (C1qA, C1qB, and C1qC) May Be a Potential Prognostic Factor and an Index of Tumor Microenvironment Remodeling in Osteosarcoma
Cited by: 33
Author(s): Longhao Chen, Jinfu Liu, Yan Lu, Xinyu He, Chi Zhang, Huanyi Zhou
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0143970

A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren’s Syndrome
Cited by: 37
Author(s): Katherine James, Shereen Al-Ali, Jessica Tarn, Simon Cockell, Colin S. Gillespie, Victoria Hindmarsh, James Locke, Sheryl Mitchell, Dennis Lendrem, Simon Bowman, Elizabeth Price, Colin Pease, Paul Emery, Peter Lanyon, John Hunter, Monica Gupta, Michèle Bombardieri, Nurhan Sutcliffe, Costantino Pitzalis, John McLaren, Annie Cooper, Marian Regan, Ian Giles, David Isenberg, Vadivelu Saravanan, David Coady, Bhaskar Dasgupta, Neil McHugh, Steven Young-Min, Robert J. Moots, Nagui Gendi, Mohammed Akil, Bridget Griffiths, Anil Wipat, Julia L. Newton, David Jones, John D. Isaacs, Jennifer Hallinan, Wan‐Fai Ng
Software Mentions: 8
Published: almost 11 years ago

10.3389/fcvm.2020.586871

Predicting Diagnostic Gene Biomarkers Associated With Immune Infiltration in Patients With Acute Myocardial Infarction
Cited by: 64
Author(s): Enfa Zhao, Hang Xie, Yushun Zhang
Software Mentions: 8
Published: almost 6 years ago

10.1371/journal.ppat.1009602

Single cell analysis of host response to helminth infection reveals the clonal breadth, heterogeneity, and tissue-specific programming of the responding CD4+ T cell repertoire
Cited by: 5
Author(s): Ivy K. Brown, Nathan Dyjack, Mindy M. Miller, S. Harsha Krovi, Cydney Rios, Rachel A. Woolaver, Laura Harmacek, Ting-Hui Tu, Brian P. O’Connor, Thomas Danhorn, Brian Vestal, Laurent Gapin, Clemencia Pinilla, Max A. Seibold, James Scott‐Browne, Radleigh Santos, R. Lee Reinhardt
Software Mentions: 8
Published: over 5 years ago

10.12688/f1000research.13196.2

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR
Cited by: 42
Author(s): Yunshun Chen, Bhupinder Pal, Jane E. Visvader, Gordon K. Smyth
Software Mentions: 8
Published: almost 8 years ago

10.1186/gb-2013-14-9-r95

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
Cited by: 594
Author(s): Franck Rapaport, Raya Khanin, Yupu Liang, Mono Pirun, Azra Krek, Paul Zumbo, Christopher E. Mason, Nicholas D. Socci, Doron Betel
Software Mentions: 8
Published: almost 14 years ago

10.1155/2021/8859996

Potential Prognostic Biomarkers of Lung Adenocarcinoma Based on Bioinformatic Analysis
Cited by: 17
Author(s): Jili Hou, Yong Cheng
Software Mentions: 8
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
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: 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

10.3390/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

10.1155/2021/5555634

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

10.1186/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 7 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: about 12 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.2021.639642

Immune-Related Genes Are Prognostic Markers for Prostate Cancer Recurrence
Cited by: 10
Author(s): Min Fu, Qiang Wang, Hanbo Wang, Ying Dai, Jin Wang, Weiting Kang, Zilian Cui, Xunbo Jin
Software Mentions: 7
Published: about 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
Cited by: 37
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

10.3390/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: about 7 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: almost 7 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 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

10.1186/s13148-021-01145-y

Childhood-onset dystonia-causing KMT2B variants result in a distinctive genomic hypermethylation profile
Cited by: 17
Author(s): Andrea Ciolfi, Aidin Foroutan, Alessandro Capuano, Lucia Pedace, Lorena Travaglini, Simone Pizzi, Marco Andreani, Evelina Miele, Federica Invernizzi, Chiara Reale, Celeste Panteghini, Maria Iascone, Marcello Niceta, Ralitza H. Gavrilova, Laura Schultz‐Rogers, Emanuele Agolini, Maria Francesca Bedeschi, Paolo Prontera, Matteo Garibaldi, Serena Galosi, Vincenzo Leuzzi, Paola Soliveri, Rory J. Olson, Giovanna Zorzi, Barbara Garavaglia, Marco Tartaglia, Bekim Sadiković
Software Mentions: 7
Published: about 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

10.12688/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: almost 8 years ago

10.1186/s13148-018-0453-8

Peripheral blood epi-signature of Claes-Jensen syndrome enables sensitive and specific identification of patients and healthy carriers with pathogenic mutations in KDM5C
Cited by: 55
Author(s): Laila C. Schenkel, Erfan Aref‐Eshghi, Cindy Skinner, Peter Ainsworth, Hanxin Lin, Guillaume Paré, David I. Rodenhiser, Charles E. Schwartz, Bekim Sadiković
Software Mentions: 7
Published: over 8 years ago

10.1371/journal.pone.0014524

DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
Cited by: 493
Author(s): Fabienne Brenet, Michelle Moh, Patricia Funk, Erika Feierstein, Agnès Viale, Nicholas D. Socci, Joseph M. Scandura
Software Mentions: 7
Published: over 15 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: about 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

10.1128/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: about 7 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

10.1186/s13148-019-0658-5

Gene domain-specific DNA methylation episignatures highlight distinct molecular entities of ADNP syndrome
Cited by: 65
Author(s): Eric G. Bend, Erfan Aref‐Eshghi, David B. Everman, R. Curtis Rogers, Sara Cathey, Eloise J. Prijoles, Michael J. Lyons, Heather L. Davis, Katie Clarkson, Karen W. Gripp, Dong Liu, Elizabeth Bhoj, Elaine H. Zackai, Paul R. Mark, Hákon Hákonarson, Laurie A. Demmer, Michael A. Levy, Jennifer Kerkhof, Alan Stuart, David I. Rodenhiser, Michael J. Friez, Roger E. Stevenson, Charles E. Schwartz, Bekim Sadiković
Software Mentions: 7
Published: over 7 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: about 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: about 6 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 6 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 5 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

10.3389/fnbeh.2019.00157

Early Life Stress Restricts Translational Reactivity in CA3 Neurons Associated With Altered Stress Responses in Adulthood
Cited by: 37
Author(s): Jordan Marrocco, Jason D. Gray, Joshua F. Kogan, Nathan R. Einhorn, Emma M. O’Cinneide, Todd G. Rubin, Thomas Carroll, Eric F. Schmidt, Bruce S. McEwen
Software Mentions: 7
Published: about 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: about 9 years ago

10.3389/fgene.2020.566579

Bioinformatics Analysis Discovers Microtubular Tubulin Beta 6 Class V (TUBB6) as a Potential Therapeutic Target in Glioblastoma
Cited by: 12
Author(s): Lan Jiang, Xiaolong Zhu, Hui Yang, Tianbing Chen, Kun Lv
Software Mentions: 7
Published: about 6 years ago

10.1038/s41597-021-00809-x

A multi-center cross-platform single-cell RNA sequencing reference dataset
Cited by: 14
Author(s): Xin Chen, Zujun Yang, Wanqiu Chen, Yongmei Zhao, Andrew Farmer, Bao Tran, Vyacheslav Furtak, Malcolm Moos, Wenming Xiao, Charles Wang
Software Mentions: 7
Published: over 5 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: about 5 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: over 7 years ago

10.1038/s41597-019-0207-2

Compendiums of cancer transcriptomes for machine learning applications
Cited by: 13
Author(s): Su Bin Lim, Swee Jin Tan, Wan-Teck Lim, Chwee Teck Lim
Software Mentions: 7
Published: almost 7 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/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

10.12688/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

10.1038/s41598-019-55453-8

MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment
Cited by: 2
Author(s): Andigoni Malousi, Sofia Kouidou, Maria Tsagiopoulou, Nikos Papakonstantinou, Emmanouil Bouras, Elisavet Georgiou, Georgios Tzimagiorgis, Kostas Stamatopoulos
Software Mentions: 7
Published: almost 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

10.3389/fonc.2021.626961

Identification of Stemness Characteristics Associated With the Immune Microenvironment and Prognosis in Gastric Cancer
Cited by: 15
Author(s): Deli Mao, Zhijun Zhou, Shenglei Song, Dongsheng Li, Yulong He, Zhewei Wei, Changhua Zhang
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2020.00895

Identification of Hub Genes Associated With Hepatocellular Carcinoma Using Robust Rank Aggregation Combined With Weighted Gene Co-expression Network Analysis
Cited by: 10
Author(s): Hongjiang Song, Na Ding, Shang Li, Jianlong Liao, Aimin Xie, Youtao Yu, Chunlong Zhang, Caifang Ni
Software Mentions: 7
Published: about 6 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

10.1371/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

10.3389/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

10.7717/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

10.1371/journal.pone.0201830

Exposure to a firefighting overhaul environment without respiratory protection increases immune dysregulation and lung disease risk
Cited by: 14
Author(s): Stephen J. Gainey, Gavin P. Horn, Albert E. Towers, Maci L. Oelschlager, Vincent L. Tir, Jenny Drnevich, Kenneth W. Fent, Stephen Kerber, Denise L. Smith, Gregory G. Freund
Software Mentions: 7
Published: about 8 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: 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: over 7 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

10.3390/cells10092215

Autophagy-Associated IL-15 Production Is Involved in the Pathogenesis of Leprosy Type 1 Reaction
Cited by: 0
Author(s): Bruno Jorge de Andrade Silva, Tamiris Lameira Bittencourt, Thyago Leal-Calvo, Mayara Abud Mendes, Rhana Berto da Silva Prata, Mayara Garcia de Mattos Barbosa, Priscila Ribeiro Andrade, Suzana Côrte-Real, Gilberto Marcelo Sperandio da Silva, Milton Ozório Moraes, Euzenir Nunes Sarno, Roberta Olmo Pinheiro
Software Mentions: 7
Published: about 5 years ago

Projects: bioconductor: limma

Science Score: 78/100

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Papers Mentioning limma 7,776