bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1155/2020/5717498

An Integrated Autophagy-Related Long Noncoding RNA Signature as a Prognostic Biomarker for Human Endometrial Cancer: A Bioinformatics-Based Approach
Cited by: 14
Author(s): Ziwei Wang, Jun Zhang, Yan Liu, Rong Zhao, Xing Zhou, Hongbo Wang
Software Mentions: 8
Published: almost 4 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: almost 4 years ago

10.1186/s13059-019-1855-4

Common DNA sequence variation influences 3-dimensional conformation of the human genome
Cited by: 66
Author(s): David U. Gorkin, Yunjiang Qiu, Ming Hu, Kipper Fletez-Brant, Tristin Liu, Anthony Schmitt, Amina Noor, Joshua Chiou, Kyle J. Gaulton, Jonathan Sebat, Yun Li, Kasper D. Hansen, Bing Ren
Software Mentions: 8
Published: almost 5 years ago

10.1038/s41598-017-13731-3

The Role of Chromatin Density in Cell Population Heterogeneity during Stem Cell Differentiation
Cited by: 16
Author(s): Mahdi Golkaram, Jaeshin Jang, Stefan Hellander, Kenneth S. Kosik, Linda R. Petzold
Software Mentions: 8
Published: about 7 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 3 years ago

10.3389/fnins.2021.613329

Integrated Transcriptional Profiling Analysis and Immune-Related Risk Model Construction for Intracranial Aneurysm Rupture
Cited by: 4
Author(s): Dezhi Shan, Xing Guo, Guozheng Yang, Zheng He, Rongrong Zhao, Hao Xue, Gang Li
Software Mentions: 8
Published: over 3 years ago

10.1038/tp.2016.275

A methylome-wide mQTL analysis reveals associations of methylation sites with GAD1 and HDAC3 SNPs and a general psychiatric risk score
Cited by: 28
Author(s): Diana‐Maria Ciuculete, Adrian Boström, Sarah Voisin, H. Philipps, Olga E. Titova, Marcus Bandstein, Lamia Nikontovic, Michael J. Williams, Jessica Mwinyi, Helgi B. Schiöth
Software Mentions: 8
Published: almost 8 years ago

10.1371/journal.pone.0248889

Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms
Cited by: 10
Author(s): Jozsef Karman, Jing Wang, Corneliu Bodea, Sherry Cao, Marc C. Levesque
Software Mentions: 8
Published: over 3 years ago

10.1155/2015/789516

Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local Normalization
Cited by: 6
Author(s): Yongchao Dou, Xiaoli Guo, Lingling Yuan, David R. Holding, Chi Zhang
Software Mentions: 8
Published: almost 10 years ago

10.1016/j.immuni.2019.02.006

Anti-commensal IgG Drives Intestinal Inflammation and Type 17 Immunity in Ulcerative Colitis
Cited by: 121
Author(s): Tomas Castro‐Dopico, Thomas W. Dennison, John R. Ferdinand, Rebeccah J. Mathews, Aaron Fleming, Dean Clift, Benjamin J Stewart, Chenzhi Jing, Konstantina Strongili, Larisa I. Labzin, Edward J M Monk, Kourosh Saeb‐Parsy, Clare E. Bryant, Simon Clare, Miles Parkes, Menna R. Clatworthy
Software Mentions: 8
Published: over 5 years ago

10.18632/aging.103475

Constructing a global transcriptional regulatory landscape for early non-small cell lung cancer to identify hub genes and key pathways
Cited by: 6
Author(s): Jianlong Bu, Pinyi Zhang, Kaibin Zhu, Yubo Yan, Bowen Shi, Junfeng Wang, Shidong Xu
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pmed.1002223

Master Regulators of Oncogenic KRAS Response in Pancreatic Cancer: An Integrative Network Biology Analysis
Cited by: 38
Author(s): Shivan Sivakumar, Inês de Santiago, L Chlon, Florian Markowetz
Software Mentions: 8
Published: almost 8 years ago

10.1186/s41065-021-00201-0

Identification and validation of hub genes of synovial tissue for patients with osteoarthritis and rheumatoid arthritis
Cited by: 10
Author(s): Yanzhi Ge, Zuxiang Chen, Yanbin Fu, Xue Xiao, Haipeng Xu, Peijian Tong, Li Zhou
Software Mentions: 8
Published: about 3 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 3 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 6 years ago

10.3389/fcimb.2020.00194

Delineation and Modulation of the Natural Killer Cell Transcriptome in Rhesus Macaques During ZIKV and SIV Infections
Cited by: 2
Author(s): Malika Aïd, Daniel R. Ram, Steven E. Bosinger, Dan H. Barouch, R. Keith Reeves
Software Mentions: 8
Published: over 4 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: almost 5 years ago

10.3390/jcm9092955

Optimized Identification of Advanced Chronic Kidney Disease and Absence of Kidney Disease by Combining Different Electronic Health Data Resources and by Applying Machine Learning Strategies
Cited by: 8
Author(s): Christoph Weber, Lena Röschke, Luise Modersohn, Christina Lohr, Tobias Kolditz, Udo Hahn, Danny Ammon, Boris Betz, Michael Kiehntopf
Software Mentions: 8
Published: about 4 years ago

10.3389/fcimb.2018.00326

In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of Leishmania-Infected Macrophages
Cited by: 16
Author(s): Patrícia Sampaio Tavares Veras, Pablo Ivan Pereira Ramos, Juliana Perrone Bezerra de Menezes
Software Mentions: 8
Published: about 6 years ago

10.1186/s13059-019-1747-7

Cell type-specific epigenetic links to schizophrenia risk in the brain
Cited by: 65
Author(s): Isabel Mendizabal, Stefano Berto, Noriyoshi Usui, Kazuya Toriumi, Paramita Chatterjee, Connor Douglas, Iksoo Huh, Hyeonsoo Jeong, Thomas S. Layman, Carol A. Tamminga, Todd M. Preuss, Genevieve Konopka, Soojin V. Yi
Software Mentions: 8
Published: over 5 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 12 years ago

10.1186/s12859-020-3506-x

Negative binomial additive model for RNA-Seq data analysis
Cited by: 16
Author(s): Ruwei Xu, Pei Fen Kuan
Software Mentions: 8
Published: over 4 years ago

10.3389/fcell.2021.704242

Two Similar Signatures for Predicting the Prognosis and Immunotherapy Efficacy of Stomach Adenocarcinoma Patients
Cited by: 4
Author(s): Taohua Yue, Shuai Zuo, Jing Zhu, Shuqin Guo, Zhihao Huang, Jichang Li, Xin Wang, Yucun Liu, Shanwen Chen, Pengyuan Wang
Software Mentions: 8
Published: over 3 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: over 3 years ago

10.1186/1471-2164-12-507

Chipster: user-friendly analysis software for microarray and other high-throughput data
Cited by: 294
Author(s): M Aleksi Kallio, Jarno Tuimala, Taavi Hupponen, Petri Klemelä, Massimiliano Gentile, Ilari Scheinin, M.K. Koski, Janne Käki, Eija Korpelainen
Software Mentions: 8
Published: about 13 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 3 years ago

10.3389/fcell.2021.642650

A Novel CpG Methylation Risk Indicator for Predicting Prognosis in Bladder Cancer
Cited by: 9
Author(s): Yufeng Guo, Jun Yin, Yuanheng Dai, Yu-Dong Guan, Pinjin Chen, Yongqiang Chen, Chen‐Zheng Huang, Yong‐Jie Lu, Lirong Zhang, Dae‐Kyu Song
Software Mentions: 8
Published: about 3 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: about 9 years ago

10.3389/fimmu.2021.749459

A Machine Learning Model to Predict the Triple Negative Breast Cancer Immune Subtype
Cited by: 24
Author(s): Zihao Chen, Maoli Wang, Rudy Leon De Wilde, Ruifa Feng, Mingqiang Su, Wenjie Shi
Software Mentions: 8
Published: about 3 years ago

10.3389/fcell.2021.681745

Comprehensive Analysis of the Immune Infiltrates and PD-L1 of m6A RNA Methylation Regulators in Hepatocellular Carcinoma
Cited by: 9
Author(s): Yali Xu, Xueling He, Junjian Deng, Lin Xiong, Yue Li, Xiaoyu Zhang, Wenliang Chen, Xin Liu, Ximing Xu
Software Mentions: 8
Published: over 3 years ago

10.1186/s12906-020-02939-y

A bioinformatics investigation into the pharmacological mechanisms of javanica oil emulsion injection in non-small cell lung cancer based on network pharmacology methodologies
Cited by: 3
Author(s): Mengwei Ni, Xinkui Liu, Ziqi Meng, Shuyu Liu, Shanshan Jia, Yingying Liu, Wei Zhou, Jiarui Wu, Jingyuan Zhang, Siyu Guo, Jialin Li, Haojia Wang, Xiaomeng Zhang
Software Mentions: 8
Published: over 4 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: about 5 years ago

10.3389/fcell.2021.712230

A Novel Ferroptosis-Related Prognostic Signature Reveals Macrophage Infiltration and EMT Status in Bladder Cancer
Cited by: 19
Author(s): Yi‐Lin Yan, Jinming Cai, Zhengnan Huang, Xiangqian Cao, Pengyu Tang, Zeyi Wang, Fang Zhang, Shujie Xia, Bing Shen
Software Mentions: 8
Published: over 3 years ago

10.3389/fonc.2020.574939

Identification of an Immune-Related Gene Signature Based on Immunogenomic Landscape Analysis to Predict the Prognosis of Adult Acute Myeloid Leukemia Patients
Cited by: 19
Author(s): Ruiqi Zhu, Huishan Tao, Wenyi Lin, Liang Tang, Yu Hu
Software Mentions: 8
Published: about 4 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 5 years ago

10.1371/journal.pone.0240824

A novel computational approach for predicting complex phenotypes in Drosophila (starvation-sensitive and sterile) by deriving their gene expression signatures from public data
Cited by: 0
Author(s): Dobril Ivanov, Gerrit Bostelmann, Benoît Lan-Leung, Julie Williams, Linda Partridge, Valentina Escott‐Price, Janet M. Thornton
Software Mentions: 8
Published: about 4 years ago

10.1007/s00018-018-2898-5

Celiac disease biomarkers identified by transcriptome analysis of small intestinal biopsies
Cited by: 32
Author(s): Hanna Bragde, Ulf Jansson, Mats Fredrikson, Ewa Grodzinsky, Jan Söderman
Software Mentions: 8
Published: over 6 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 3 years ago

10.1186/1471-2105-11-450

Filtering, FDR and power
Cited by: 43
Author(s): Maarten van Iterson, Judith M. Boer, Renée X. de Menezes
Software Mentions: 8
Published: about 14 years ago

10.3389/fonc.2018.00100

Genomic DNA Methylation-Derived Algorithm Enables Accurate Detection of Malignant Prostate Tissues
Cited by: 35
Author(s): Erfan Aref‐Eshghi, Laila C. Schenkel, Peter Ainsworth, Hanxin Lin, David I. Rodenhiser, Jean‐Claude Cutz, Bekim Sadiković
Software Mentions: 8
Published: over 6 years ago

10.1016/j.celrep.2019.10.018

Aryl Hydrocarbon Receptor Contributes to the Transcriptional Program of IL-10-Producing Regulatory B Cells
Cited by: 91
Author(s): Christopher Piper, Elizabeth C. Rosser, Kristīne Oļeiņika, Kiran Nistala, Thomas Krausgruber, André F. Rendeiro, Aggelos Banos, Ignat Drozdov, Matteo Villa, Scott Thomson, Georgina Xanthou, Christoph Bock, Brigitta Stockinger, Claudia Mauri
Software Mentions: 8
Published: about 5 years ago

10.1093/bib/bbv069

Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline
Cited by: 45
Author(s): Yasir Rahmatallah, Frank Emmert‐Streib, Galina Glazko
Software Mentions: 8
Published: about 9 years ago

10.1186/s12859-021-04114-7

Streamlining differential exon and 3′ UTR usage with diffUTR
Cited by: 3
Author(s): Stefan Gerber, Gerhard Schratt, Pierre-Luc Germain
Software Mentions: 8
Published: over 3 years ago

10.3390/cancers12010045

N-Terminal Truncated Myb with New Transcriptional Activity Produced Through Use of an Alternative MYB Promoter in Salivary Gland Adenoid Cystic Carcinoma
Cited by: 11
Author(s): Candace A. Frerich, Hailey N. Sedam, Huining Kang, Yoshitsugu Mitani, Adel K. El‐Naggar, Scott A. Ness
Software Mentions: 8
Published: almost 5 years ago

10.3390/cancers13143621

HPV Infection Leaves a DNA Methylation Signature in Oropharyngeal Cancer Affecting Both Coding Genes and Transposable Elements
Cited by: 10
Author(s): Diego Camuzi, Luisa Aguirre Buexm, Simone De Queiroz Chaves Lourenço, Davide Degli Esposti, Cyrille Cuenin, Monique de Souza Almeida Lopes, Francesca Manara, Fazlur Rahman Talukdar, Zdenko Herceg, Luís Felipe Ribeiro Pinto, Sheila Coelho Soares-Lima
Software Mentions: 8
Published: over 3 years ago

10.1186/s13073-021-00866-2

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium
Cited by: 21
Author(s): Silva Kasela, Victor E. Ortega, Molly Martorella, Suresh Garudadri, Jennifer Nguyen, Elizabeth J. Ampleford, Anu Pasanen, Srilaxmi Nerella, Kristina L. Buschur, Igor Barjaktarević, R. Graham Barr, Eugene R. Bleecker, Russell P. Bowler, Alejandro P. Comellas, Christopher B. Cooper, David Couper, Gerard J. Criner, Jeffrey L. Curtis, MeiLan K. Han, Nadia N. Hansel, Eric A. Hoffman, Robert J. Kaner, Jerry A. Krishnan, Fernando J. Martínez, Merry-Lynn McDonald, Deborah A. Meyers, Robert Paine, Stephen P. Peters, Mario Castro, Loren C. Denlinger, Serpil C. Erzurum, John V. Fahy, Elliot Israel, Nizar N. Jarjour, Bruce D. Levy, Xingnan Li, Wendy C. Moore, Sally E. Wenzel, Joe Zein, Charles Langelier, Prescott G. Woodruff, Tuuli Lappalainen, Stephanie A. Christenson
Software Mentions: 8
Published: over 3 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 3 years ago

10.1016/j.molcel.2019.01.009

Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing
Cited by: 195
Author(s): Alba Rodríguez-Meira, Gemma Buck, Sally-Ann Clark, Benjamin Povinelli, Verónica Alcolea, Eleni Louka, Simon J. McGowan, Angela Hamblin, Nikolaos Sousos, Nikolaos Barkas, Alice Giustacchini, Bethan Psaila, Sten Eirik W. Jacobsen, Supat Thongjuea, Adam J. Mead
Software Mentions: 8
Published: over 5 years ago

10.3389/fonc.2020.01411

Comparison of Stage 4 and Stage 4s Neuroblastoma Identifies Autophagy-Related Gene and LncRNA Signatures Associated With Prognosis
Cited by: 12
Author(s): Xinyao Meng, Honglin Li, Erhu Fang, Jiexiong Feng, Xiaoli Zhao
Software Mentions: 8
Published: over 4 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 3 years ago

10.1186/s13229-017-0119-y

Exaggerated CpH methylation in the autism-affected brain
Cited by: 30
Author(s): Shannon Ellis, Saloni Gupta, Anna Moes, Andrew B. West, Dan E. Arking
Software Mentions: 7
Published: almost 8 years ago

10.1186/1471-2105-16-S5-S10

Using epigenomics data to predict gene expression in lung cancer
Cited by: 40
Author(s): Jeffery Li, Travers Ching, Sijia Huang, Lana X. Garmire
Software Mentions: 7
Published: over 9 years ago

10.1038/s41421-021-00312-y

A single-cell atlas of liver metastases of colorectal cancer reveals reprogramming of the tumor microenvironment in response to preoperative chemotherapy
Cited by: 42
Author(s): Li-Heng Che, Jingwen Li, Jian-Ping Huo, Rong Luo, Rui-Ming Xu, He Cai, Yuqing Li, Anni Zhou, Pinbo Huang, Yongyu Chen, Weijian Ni, Yunxia Zhou, Yuan-Yuan Liu, Huiyan Li, Rong Zhou, Ming Hui, Jianming Li
Software Mentions: 7
Published: about 3 years ago

10.1186/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: about 4 years ago

10.3389/fonc.2020.00061

The Prognostic Significance of Metabolic Syndrome and a Related Six-lncRNA Signature in Esophageal Squamous Cell Carcinoma
Cited by: 18
Author(s): Yu Liu, Li-Yu Wang, Hengchang Liu, Chunxiang Li, Jie He
Software Mentions: 7
Published: almost 5 years ago

10.3389/fonc.2021.618187

CCR4, CCR8, and P2RY14 as Prognostic Factors in Head and Neck Squamous Cell Carcinoma Are Involved in the Remodeling of the Tumor Microenvironment
Cited by: 9
Author(s): Liangliang Meng, Xiaoxi He, Hong Qin, Bo Qiao, Xiao Zhang, Bin Wu, Xiaobo Zhang, Yingtian Wei, Jing Li, Zhaoxiang Ye, Yueyong Xiao
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41420-021-00451-x

A novel defined pyroptosis-related gene signature for predicting the prognosis of ovarian cancer
Cited by: 256
Author(s): Ying Yang, Qinjin Dai, Hongbo Qi
Software Mentions: 7
Published: over 3 years ago

10.7554/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 3 years ago

10.3390/microorganisms9061116

Environmental Conditions Modulate the Transcriptomic Response of Both Caulobacter crescentus Morphotypes to Cu Stress
Cited by: 2
Author(s): Laurens Maertens, Pauline Cherry, Françoise Tilquin, Rob Van Houdt, Jean-Yves Matroule
Software Mentions: 7
Published: over 3 years ago

10.3390/microorganisms8101505

Reanalysis of Gene Expression Profiles of CD4+ T Cells Treated with HIV-1 Latency Reversal Agents
Cited by: 3
Author(s): Antônio Victor Campos Coelho, Romero Marinho de Moura, Sérgio Crovella
Software Mentions: 7
Published: about 4 years ago

10.1038/s41419-020-2477-1

Deficiency in the autophagy modulator Dram1 exacerbates pyroptotic cell death of Mycobacteria-infected macrophages
Cited by: 22
Author(s): Rui Zhang, Mónica Varela, Gabriel Forn-Cuní, Vincenzo Torraca, Michiel van der Vaart, Annemarie H. Meijer
Software Mentions: 7
Published: over 4 years ago

10.3390/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: about 4 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: almost 4 years ago

10.1186/1471-2105-14-91

A comparison of methods for differential expression analysis of RNA-seq data
Cited by: 725
Author(s): Charlotte Soneson, Mauro Delorenzi
Software Mentions: 7
Published: over 11 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: about 4 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: about 4 years ago

10.1186/s40168-021-01013-0

animalcules: interactive microbiome analytics and visualization in R
Cited by: 16
Author(s): Yue Zhao, Anthony Federico, Tyler Faits, Solaiappan Manimaran, Daniel Segrè, Stefano Monti, W. Evan Johnson
Software Mentions: 7
Published: over 3 years ago

10.1186/s10194-021-01285-9

Identification of disease- and headache-specific mediators and pathways in migraine using blood transcriptomic and metabolomic analysis
Cited by: 13
Author(s): Tímea Aczél, Tamás Körtési, József Kun, Péter Urbán, Witold Bauer, Róbert Herczeg, Robert Farkaš, K Kovács, Barna Vásárhelyi, Gellért Balázs Karvaly, Attila Gyenesei, Bernadett Tuka, János Tajti, László Vécsei, Kata Bölcskei, Zsuzsanna Helyes
Software Mentions: 7
Published: about 3 years ago

10.18632/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: over 3 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: about 6 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 3 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: about 4 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 4 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 3 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: over 6 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: over 3 years ago

10.1186/s12864-016-3317-7

A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data
Cited by: 32
Author(s): Yongli Hu, Takeshi Hase, Hui Peng Li, Shyam Prabhakar, Hiroaki Kitano, See Ket Ng, Samik Ghosh, Lionel Wee
Software Mentions: 7
Published: almost 8 years ago

10.3389/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 3 years ago

10.1128/mSystems.00280-19

Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single <i>Ctena orbiculata</i> (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition
Cited by: 7
Author(s): Shen Jean Lim, Louie C. Alexander, Annette Summers Engel, Audrey Paterson, Laurie C. Anderson, Barbara J. Campbell
Software Mentions: 7
Published: over 5 years ago

10.1186/1471-2105-16-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: over 9 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: over 3 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 3 years ago

10.3390/cancers13071730

Identification and Validation of an Immune-Associated RNA-Binding Proteins Signature to Predict Clinical Outcomes and Therapeutic Responses in Glioma Patients
Cited by: 11
Author(s): Ruotong Tian, Yimin Li, Qian Liu, Minfeng Shu
Software Mentions: 7
Published: over 3 years ago

10.1186/1471-2105-9-46

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: almost 17 years ago

10.1186/s12935-020-01429-y

Establishment of the prognostic index of lung squamous cell carcinoma based on immunogenomic landscape analysis
Cited by: 11
Author(s): Jianguo Zhang, Jianzhong Zhang, Cheng Yuan, Yuan Luo, Yangyi Li, Panpan Dai, Wenjie Sun, Nannan Zhang, Jiangbo Ren, Mengjie Zhang, Yan Gong, Conghua Xie
Software Mentions: 7
Published: over 4 years ago

10.1186/s13287-020-01823-3

Multiomics global landscape of stemness-related gene clusters in adipose-derived mesenchymal stem cells
Cited by: 8
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: over 4 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 3 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: almost 5 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: about 4 years ago

10.3390/cancers13163929

Maturation State-Specific Alternative Splicing in FLT3-ITD and NPM1 Mutated AML
Cited by: 4
Author(s): Anna Wojtuszkiewicz, Inge van der Werf, Stephan Hütter, Wencke Walter, Constance Baer, Wolfgang Kern, Jeroen Janssen, Gert J. Ossenkoppele, Claudia Haferlach, Jacqueline Cloos, Torsten Haferlach
Software Mentions: 7
Published: over 3 years ago

10.1186/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 4 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 5 years ago

10.3389/fmolb.2021.665222

Identification of the m6A RNA Methylation Regulators WTAP as a Novel Prognostic Biomarker and Genomic Alterations in Cutaneous Melanoma
Cited by: 12
Author(s): Ziyi Feng, Ting Wang, Xin Su, Shu Guo
Software Mentions: 7
Published: over 3 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 3 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: almost 4 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
Cited by: 7
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: over 3 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 3 years ago

10.3389/fmolb.2021.645845

A Novel Defined Risk Signature of the Ferroptosis-Related Genes for Predicting the Prognosis of Ovarian Cancer
Cited by: 23
Author(s): Ying Yang, Qinjin Dai, Shuhong Li, Jie He, Hongbo Qi
Software Mentions: 7
Published: over 3 years ago

10.3390/ijms19102903

Identification of a Prognostic Hypoxia-Associated Gene Set in IDH-Mutant Glioma
Cited by: 27
Author(s): Philip Dao Trong, Saskia Rösch, Heimo Mairbäurl, Stefan Pusch, Andreas Unterberg, Christel Herold‐Mende, Rolf Warta
Software Mentions: 7
Published: about 6 years ago

10.3390/cancers12082310

Systematic Analysis of Aberrant Biochemical Networks and Potential Drug Vulnerabilities Induced by Tumor Suppressor Loss in Malignant Pleural Mesothelioma
Cited by: 15
Author(s): Haitang Yang, Duo Xu, Yang Zhang, Feng Yao, Heng Zhao, Ralph A. Schmid, Ren‐Wang Peng
Software Mentions: 7
Published: over 4 years ago

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