10.1186/s12859-017-1498-y

Evaluation of logistic regression models and effect of covariates for case–control study in RNA-Seq analysis
Cited by: 15
Author(s): Seung Hoan Choi, Adam Labadorf, Richard H. Myers, Kathryn L. Lunetta, Josée Dupuis, Anita L. DeStefano
Software Mentions: 10
Published: over 9 years ago

10.1186/s12864-016-2737-8

Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery
Cited by: 55
Author(s): Zhilong Jia, Ying Liu, Naiyang Guan, Xiaochen Bo, Zhi-Gang Luo, Michael R. Barnes
Software Mentions: 10
Published: about 10 years ago

10.3389/pore.2021.594649

Bcl-2 Associated Athanogene 2 (BAG2) is Associated With Progression and Prognosis of Hepatocellular Carcinoma: A Bioinformatics-Based Analysis
Cited by: 7
Author(s): Xi Zhang, Junjun Zhang, Yang Liu, Jie Li, Juan Tan, Zewen Song
Software Mentions: 10
Published: over 5 years ago

10.1155/2020/1468980

Construction and Analysis of lncRNA-Mediated ceRNA Network in Nasopharyngeal Carcinoma Based on Weighted Correlation Network Analysis
Cited by: 7
Author(s): Zhenning Zou, Shuguang Liu, Yanping Ha, Bowan Huang
Software Mentions: 10
Published: almost 6 years ago

10.1007/s00401-020-02224-9

Altered DNA methylation profiles in blood from patients with sporadic Creutzfeldt–Jakob disease
Cited by: 14
Author(s): Luke C. Dabin, Fernando Guntoro, Tracy Campbell, Tony Bélicard, Adam R. Smith, Rebecca G. Smith, Rachel Raybould, Jonathan M. Schott, Katie Lunnon, Peter Sarkies, John Collinge, Simon Mead, Emmanuelle Viré
Software Mentions: 10
Published: almost 6 years ago

10.1186/s12859-021-04055-1

Juxtapose: a gene-embedding approach for comparing co-expression networks
Cited by: 8
Author(s): Katie Ovens, Farhad Maleki, B. Frank Eames, Ian McQuillan
Software Mentions: 10
Published: over 5 years ago

10.1038/s41598-020-57760-x

Resident and phytometer plants host comparable rhizosphere fungal communities in managed grassland ecosystems
Cited by: 8
Author(s): Ricardo Schöps, Kezia Goldmann, Lotte Korell, Helge Bruelheide, Tesfaye Wubet, François Buscot
Software Mentions: 10
Published: over 6 years ago

10.1186/s12920-020-00754-5

Identification of potential crucial genes in atrial fibrillation: a bioinformatic analysis
Cited by: 15
Author(s): Junguo Zhang, Xin Huang, Xiaojie Wang, Yanhui Gao, Li Liu, Ziyi Li, Xuejiao Chen, Jie Zeng, Zebing Ye, Guowei Li
Software Mentions: 10
Published: about 6 years ago

10.3389/fonc.2021.704038

Fatty Acid Metabolism-Related lncRNAs Are Potential Biomarkers for Predicting the Overall Survival of Patients With Colorectal Cancer
Cited by: 13
Author(s): Yue Peng, Chang Xu, Jun Wen, Yuanchuan Zhang, Meng Wang, Xiaoxiao Liu, Kang Zhao, Zheng Wang, Yanjun Liu, Tongtong Zhang
Software Mentions: 10
Published: about 5 years ago

10.3389/fgene.2021.692953

Identification of the Real Hub Gene and Construction of a Novel Prognostic Signature for Pancreatic Adenocarcinoma Based on the Weighted Gene Co-expression Network Analysis and Least Absolute Shrinkage and Selection Operator Algorithms
Cited by: 15
Author(s): Qihang Yuan, Jie Ren, Zhizhou Wang, Ji Li, Dawei Deng, Dong Shang
Software Mentions: 10
Published: almost 5 years ago

10.1111/jcmm.14918

An outcome model for human bladder cancer: A comprehensive study based on weighted gene co‐expression network analysis
Cited by: 24
Author(s): Yaoyi Xiong, Lushun Yuan, Jing Xiong, Huimin Xu, Yongwen Luo, Gang Wang, Lingao Ju, Yu Xiao, Xinghuan Wang
Software Mentions: 10
Published: over 6 years ago

10.3389/fgene.2021.584164

Four Novel Prognostic Genes Related to Prostate Cancer Identified Using Co-expression Structure Network Analysis
Cited by: 14
Author(s): Tao Feng, Dechao Wei, Qiankun Li, Xiaobing Yang, Yili Han, Yunping Luo, Yongguang Jiang
Software Mentions: 10
Published: over 5 years ago

10.7554/eLife.62250

Age-related changes in polycomb gene regulation disrupt lineage fidelity in intestinal stem cells
Cited by: 11
Author(s): Helen M Tauc, Imilce A. Rodriguez‐Fernandez, Jason A. Hackney, Michał Pawlak, Tal Oron, Jerome Korzelius, Hagar F. Moussa, Subhra Chaudhuri, Zora Modrušan, Bruce A Edgar, Heinrich Jasper
Software Mentions: 10
Published: over 5 years ago

10.1002/1878-0261.12850

High‐throughput proteomics of breast cancer interstitial fluid: identification of tumor subtype‐specific serologically relevant biomarkers
Cited by: 13
Author(s): Thilde Terkelsen, Maria Pernemalm, Pavel Gromov, Anna‐Lise Børresen‐Dale, Anders Krogh, Vilde Drageset Haakensen, Janne Lethiö, Elena Papaleo, Irina Gromova
Software Mentions: 10
Published: over 5 years ago

10.1172/jci.insight.145854

Cell-autonomous retinoic acid receptor signaling has stage-specific effects on mouse enteric nervous system
Cited by: 6
Author(s): Tao Gao, Elizabeth C. Wright-Jin, Rajarshi Sengupta, Jessica B. Anderson, Robert O. Heuckeroth
Software Mentions: 10
Published: about 5 years ago

10.3389/fgene.2021.616686

Identifying Differentially Expressed Genes of Zero Inflated Single Cell RNA Sequencing Data Using Mixed Model Score Tests
Cited by: 2
Author(s): Zhiqiang He, Yueyun Pan, Fang Shao, Hui Wang
Software Mentions: 10
Published: over 5 years ago

10.1186/s12575-018-0067-8

Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results
Cited by: 23
Author(s): Shitao Zhao, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 10
Published: over 8 years ago

10.1155/2021/2191709

Establishment of an Immune-Related Gene Signature for Risk Stratification for Patients with Glioma
Cited by: 2
Author(s): Jiaxue He, Chun Zeng, Yong Long
Software Mentions: 10
Published: almost 5 years ago

10.1155/2020/5858092

Profiles of Immune Infiltration and Prognostic Immunoscore in Lung Adenocarcinoma
Cited by: 9
Author(s): Yanyan Li, Liping Tao, Weiyang Cai
Software Mentions: 10
Published: about 6 years ago

10.1111/jcmm.15848

m6A RNA methylation regulators could contribute to the occurrence of chronic obstructive pulmonary disease
Cited by: 43
Author(s): Xinwei Huang, Dongjin Lv, Yao Xiao, Min Li, Hong Zhang
Software Mentions: 10
Published: almost 6 years ago

10.1002/1878-0261.12747

Identification and validation of a combined hypoxia and immune index for triple‐negative breast cancer
Cited by: 57
Author(s): Shaoquan Zheng, Yutian Zou, Jie Liang, Weikai Xiao, Anli Yang, Tiebao Meng, Shilin Lu, Zhong-Bing Luo, Xiaoming Xie
Software Mentions: 10
Published: about 6 years ago

10.1155/2021/5567392

Construction and Validation of a Novel Prognostic Signature for Intestinal Type of Gastric Cancer
Cited by: 3
Author(s): Fan Zhang, Ewetse Paul Maswikiti, Yucai Wei, Wenzhang Wu, Yumin Li
Software Mentions: 10
Published: about 5 years ago

10.1038/s41598-020-76881-x

Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis
Cited by: 81
Author(s): Luis A. Corchete, Elizabeta A. Rojas, Diego Alonso-López, Javier De Las Rivas, Norma C. Gutiérrez, F.J. Burguillo
Software Mentions: 10
Published: almost 6 years ago

10.3390/cancers13133371

Meta-Analysis of Microdissected Breast Tumors Reveals Genes Regulated in the Stroma but Hidden in Bulk Analysis
Cited by: 7
Author(s): Aurora Savino, Niccolò De Marzo, Paolo Provero, Valeria Poli
Software Mentions: 10
Published: about 5 years ago

10.1016/j.devcel.2018.01.022

Innate Immune Response and Off-Target Mis-splicing Are Common Morpholino-Induced Side Effects in Xenopus
Cited by: 40
Author(s): George E. Gentsch, Thomas Spruce, Rita S. Monteiro, Nick Owens, Stephen R. Martin, James C. Smith
Software Mentions: 10
Published: over 8 years ago

10.1371/journal.pgen.1007102

Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content
Cited by: 16
Author(s): Daniele Colombo, Lukas Burger, Tuncay Baubec, Dirk Schübeler
Software Mentions: 10
Published: over 8 years ago

10.1242/dev.169474

An integrated transcriptional analysis of the developing human retina
Cited by: 67
Author(s): Carla Mellough, R. Bauer, Joseph Collin, Birthe Dorgau, Darin Zerti, David Dolan, Carl M. Jones, Osagie Izuogu, Min Yu, Dean Hallam, Jannetta S. Steyn, Kathryn White, David Steel, Mauro Santibanez‐Koref, David Elliott, Michael S. Jackson, Susan Lindsay, Sushma Nagaraja Grellscheid, Majlinda Lako
Software Mentions: 10
Published: over 7 years ago

10.1371/journal.pone.0041762

Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines.
Cited by: 7
Author(s): Matthew P Davis, Cei Abreu‐Goodger, Stijn van Dongen, Dong Lu, P. Täte, Nenad Bartoniček, Claudia Kutter, Pentao Liu, William C. Skarnes, Anton J. Enright, Ian Dunham
Software Mentions: 10
Published: over 14 years ago

10.1038/s42003-020-0842-3

Loss of the branched-chain amino acid transporter CD98hc alters the development of colonic macrophages in mice
Cited by: 17
Author(s): Philipp Wuggenig, Berna Kaya, Hassan Melhem, C. Korcan Ayata, Swiss Ibd Cohort Investigators, Petr Hrúz, Emre Sayan, Hideki Tsumura, Morihiro Ito, Julien Roux, Jan Hendrik Niess
Software Mentions: 10
Published: over 6 years ago

10.3389/fgene.2021.695130

A Novel Signature Constructed by Immune-Related LncRNA Predicts the Immune Landscape of Colorectal Cancer
Cited by: 7
Author(s): Mengyu Sun, Tongyue Zhang, Yijun Wang, Wenjie Huang, Limin Xia
Software Mentions: 10
Published: about 5 years ago

10.1371/journal.ppat.1005996

A Mouse Model of Chronic West Nile Virus Disease
Cited by: 44
Author(s): Jessica B. Graham, Jessica L. Swarts, Courtney Wilkins, Sunil Thomas, Richard Green, Aimee Sekine, Kathleen Voss, Reneé C. Ireton, Michael A. Mooney, Gabrielle Choonoo, Darla R. Miller, Piper M. Treuting, Fernando Pardo Manuel de Villena, Martin T. Ferris, Shannon K. McWeeney, Michael Gale, Jennifer M. Lund
Software Mentions: 10
Published: almost 10 years ago

10.1186/s12711-021-00614-5

Influence of genetics and the pre-vaccination blood transcriptome on the variability of antibody levels after vaccination against Mycoplasma hyopneumoniae in pigs
Cited by: 8
Author(s): Fany Blanc, Tatiana Maroilley, Manuel Revilla, Gaëtan Lemonnier, Jean Jacques Leplat, Yvon Billon, Laure Ravon, Olivier Bouchez, Jean Pierre Bidanel, Bertrand Bed’Hom, Marie-Hélène Pinard-van Der Laan, Jordi Estellé, Claire Rogel‐Gaillard
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.pcbi.1007803

Methodological challenges in translational drug response modeling in cancer: A systematic analysis with FORESEE
Cited by: 9
Author(s): Lisa-Katrin Turnhoff, Ali Hadizadeh Esfahani, Andreas Schuppert
Software Mentions: 10
Published: over 6 years ago

10.1016/j.celrep.2019.10.024

Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis
Cited by: 227
Author(s): Ross Dobie, John Wilson-Kanamori, Beth E. P. Henderson, J. F. Smith, Kylie P. Matchett, Jordan Raymond Portman, Karolina Wallenborg, Simone Picelli, Анна Загорска, Swetha Pendem, Thomas E. Hudson, Max C. Wu, Grant R. Budas, David G. Breckenridge, Ewen M Harrison, Damian J. Mole, Stephen J. Wigmore, Prakash Ramachandran, Chris P. Ponting, Sarah A. Teichmann, John C. Marioni, Neil C. Henderson
Software Mentions: 10
Published: almost 7 years ago

10.3389/fgene.2020.586602

Multi-Approach Bioinformatics Analysis of Curated Omics Data Provides a Gene Expression Panorama for Multiple Cancer Types
Cited by: 13
Author(s): Bruno César Feltes, Joice de Faria Poloni, Itamar José Guimarães Nunes, Sara Socorro Faria, Márcio Dorn
Software Mentions: 10
Published: over 5 years ago

10.1186/s40168-021-01104-y

Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome
Cited by: 22
Author(s): Alexandra J. Roth‐Schulze, Megan A. S. Penno, Katrina Ngui, Helena Oakey, Esther Bandala‐Sanchez, Andrew C. Smith, Theo R. Allnutt, Rebecca L. Thomson, Peter Vuillermin, Maria E. Craig, William D. Rawlinson, Elizabeth A. Davis, Mark Harris, Georgia Soldatos, Peter Colman, John M. Wentworth, Aveni Haynes, Simon C. Barry, Richard Sinnott, Grant Morahan, Naiara G. Bediaga, Gordon K. Smyth, Anthony T. Papenfuss, Jennifer Couper, Leonard C. Harrison
Software Mentions: 10
Published: about 5 years ago

10.1002/embj.201386825

Key regulators control distinct transcriptional programmes in blood progenitor and mast cells
Cited by: 48
Author(s): Fernando J. Calero-Nieto, Felicia Ng, Nicola K. Wilson, Rebecca Hannah, Victoria Moignard, Ana Leal-Cervantes, Isabel Jimenez-Madrid, Evangelia Diamanti, Lorenz Wernisch, Berthold Göttgens
Software Mentions: 10
Published: over 12 years ago

10.3390/ijms22179601

In Silico Methods for the Identification of Diagnostic and Favorable Prognostic Markers in Acute Myeloid Leukemia
Cited by: 7
Author(s): Hande Öngün Yılmaz, Halil Ibrahim Toy, Stephan Marquardt, Gökhan Karakülah, Can Küçük, Panagiota I. Kontou, Stella Logotheti, Athanasia Pavlopoulou
Software Mentions: 10
Published: almost 5 years ago

10.1111/jcmm.16619

Systematic profiling of invasion‐related gene signature predicts prognostic features of lung adenocarcinoma
Cited by: 17
Author(s): Ping Yu, L. Tong, Yujia Song, Hui Qü, Ying Chen
Software Mentions: 10
Published: about 5 years ago

10.3389/fonc.2021.729103

Identification of Iron Metabolism-Related Genes as Prognostic Indicators for Lower-Grade Glioma
Cited by: 17
Author(s): Shenbin Xu, Zefeng Wang, Juan Ye, Shuhao Mei, Jianmin Zhang
Software Mentions: 10
Published: almost 5 years ago

10.3389/fgene.2021.739520

Construction of a Prognostic Model in Lung Adenocarcinoma Based on Ferroptosis-Related Genes
Cited by: 6
Author(s): Min Liang, Mafeng Chen, Yao Zhong, Satwant Singh, Sandeep Singh
Software Mentions: 10
Published: almost 5 years ago

10.3390/ijms22031190

Genome-Wide DNA Methylation Analysis of a Cohort of 41 Patients Affected by Oculo-Auriculo-Vertebral Spectrum (OAVS)
Cited by: 12
Author(s): Valentina Guida, Luciano Calzari, Maria Teresa Fadda, Francesca Piceci‐Sparascio, María Cristina Digilio, Laura Bernardini, Francesco Brancati, Teresa Mattina, Daniela Melis, Francesca Forzano, Silvana Briuglia, Tommaso Mazza, Sebastiano Bianca, Enza Maria Valente, Leila Bagherjad Salehi, Paolo Prontera, Mario Pagnoni, Romano Tenconi, Bruno Dallapiccola, Giorgio Iannetti, Luigi Corsaro, Alessandro De Luca, Davide Gentilini
Software Mentions: 10
Published: over 5 years ago

10.3389/fgene.2020.569572

Aberrantly Methylated-Differentially Expressed Genes Identify Novel Atherosclerosis Risk Subtypes
Cited by: 6
Author(s): Yuzhou Xue, Yongzheng Guo, Suxin Luo, Wei Zhou, Jun Xiang, Yuansong Zhu, Zhenxian Xiang, Ju Shen
Software Mentions: 10
Published: over 5 years ago

10.3389/fonc.2018.00659

The Role of COL5A2 in Patients With Muscle-Invasive Bladder Cancer: A Bioinformatics Analysis of Public Datasets Involving 787 Subjects and 29 Cell Lines
Cited by: 28
Author(s): Xiangyu Meng, Mingjun Shi, Zhao-Yi Zeng, Chen Chen, Tong-Zu Liu, Qiuji Wu, Shuo Li
Software Mentions: 10
Published: over 7 years ago

10.1186/gb-2004-5-10-r80

Cited by: 10,848
Author(s): Robert Gentleman, Vincent J. Carey, Douglas M. Bates, Benjamin M. Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Maria Iacus, Rafael A. Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony Rossini, Günther Sawitzki, Colin A. Smith, Gordon K. Smyth, Luke Tierney, Jean Yee Hwa Yang, Jianhua Zhang
Software Mentions: 10
Published: over 22 years ago

10.3389/fonc.2021.644956

A New Oxaliplatin Resistance-Related Gene Signature With Strong Predicting Ability in Colon Cancer Identified by Comprehensive Profiling
Cited by: 6
Author(s): Qiu Sheng Lin, Liang Luo, Hua Wang
Software Mentions: 10
Published: over 5 years ago

10.3389/fgene.2019.00279

Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis
Cited by: 46
Author(s): Verónica Jiménez-Jacinto, Alejandro Sánchez-Flores, Leticia Vega‐Alvarado
Software Mentions: 10
Published: over 7 years ago

10.3389/fonc.2021.643465

Identification of the Roles of a Stemness Index Based on mRNA Expression in the Prognosis and Metabolic Reprograming of Pancreatic Ductal Adenocarcinoma
Cited by: 6
Author(s): Rong Tang, Xiaomeng Liu, Wei Wang, Jie Hua, Jin Xu, Chen Liang, Qingcai Meng, Jiang Liu, Bo Zhang, Xianjun Yu, Si Shi
Software Mentions: 10
Published: over 5 years ago

10.1186/gb-2014-15-2-r29

voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Cited by: 4,221
Author(s): Charity W. Law, Yunshun Chen, Wei Shi, Gordon K. Smyth
Software Mentions: 10
Published: over 12 years ago

10.1371/journal.pcbi.1008947

Chromosomal neighbourhoods allow identification of organ specific changes in gene expression
Cited by: 1
Author(s): Rishi Das Roy, Outi Hallikas, Mona M. Christensen, Élodie Renvoisé, Jukka Jernvall
Software Mentions: 10
Published: almost 5 years ago

10.3390/ijms21051754

MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data
Cited by: 10
Author(s): Enrico Gaffo, Michele Bortolomeazzi, Andrea Bisognin, Piero Di Battista, Federica Lovisa, Lara Mussolin, Stefania Bortoluzzi
Software Mentions: 10
Published: over 6 years ago

10.1371/journal.pgen.1009531

Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetes
Cited by: 12
Author(s): Anthony Aylward, Mei-Lin Okino, Paola Benaglio, Joshua Chiou, Elisha Beebe, José Padilla, Sharlene Diep, Kyle J. Gaulton
Software Mentions: 10
Published: over 5 years ago

10.1186/s40246-019-0226-2

Size matters: how sample size affects the reproducibility and specificity of gene set analysis
Cited by: 28
Author(s): Farhad Maleki, Katie Ovens, Ian McQuillan, Anthony Kusalik
Software Mentions: 10
Published: almost 7 years ago

10.1016/j.ebiom.2015.09.027

Distinct Transcriptional and Anti-Mycobacterial Profiles of Peripheral Blood Monocytes Dependent on the Ratio of Monocytes: Lymphocytes
Cited by: 58
Author(s): Vivek Naranbhai, Helen A. Fletcher, Rachel Tanner, Matthew K. O’Shea, Helen McShane, Benjamin P. Fairfax, Julian C. Knight, Adrian V. S. Hill
Software Mentions: 9
Published: almost 11 years ago

10.3389/fgene.2021.691465

ARG2, MAP4K5 and TSTA3 as Diagnostic Markers of Steroid-Induced Osteonecrosis of the Femoral Head and Their Correlation With Immune Infiltration
Cited by: 10
Author(s): Rongguo Yu, Jiayu Zhang, Youguang Zhuo, Hong Xu, Jie Ye, Susu Tang, Nannan Liu, Yiyuan Zhang
Software Mentions: 9
Published: about 5 years ago

10.3389/fgene.2021.661988

Identification of Aging-Related Genes Associated With Clinical and Prognostic Features of Hepatocellular Carcinoma
Cited by: 12
Author(s): Xingte Chen, Lei Wang, Liang Hong, Zhiying Su, Xiaohong Zhong, Han Zhou, Xueqing Zhang, Junxin Wang, Lingdong Shao
Software Mentions: 9
Published: about 5 years ago

10.1016/j.celrep.2019.01.041

RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types
Cited by: 510
Author(s): Gianni Monaco, Bernett Lee, Weili Xu, Seri Mustafah, You Yi Hwang, Christophe Carré, Nicolas Burdin, Lucian Visan, Michele Ceccarelli, Michael Poidinger, Alfred Zippelius, João Pedro de Magalhães, Anis Larbi
Software Mentions: 9
Published: over 7 years ago

10.3389/fgene.2020.00785

Systematic Evaluation of the Diagnostic and Prognostic Significance of Competitive Endogenous RNA Networks in Prostate Cancer
Cited by: 3
Author(s): Zihu Guo, Han Liang, Yingxue Fu, Ziyin Wu, Yaohua Ma, Yueping Liu, Haiqing Wang, Li Jiang, Shengnan Liang, Zhenzhong Wang, Furong Li, Wei Xiao, Jingbo Wang, Yonghua Wang
Software Mentions: 9
Published: about 6 years ago

10.3389/fonc.2021.698856

A Novel Ferroptosis-Related Gene Model for Overall Survival Predictions of Bladder Urothelial Carcinoma Patients
Cited by: 9
Author(s): Min Zhang, Xin Zhang, Minghang Yu, Wei Zhang, Di Zhang, Song Zeng, Xi Wang, Xiaosong Hu
Software Mentions: 9
Published: about 5 years ago

10.3390/ijms21134763

The Differential Effect of Carbon Dots on Gene Expression and DNA Methylation of Human Embryonic Lung Fibroblasts as a Function of Surface Charge and Dose
Cited by: 15
Author(s): Michal Šíma, Kristýna Vrbová, Táňa Závodná, K. Hoňková, Irena Chvojková, Antonín Ambrož, Jǐŕı Kléma, Andrea Rössnerová, Kateřina Poláková, Tomáš Malina, Jan Belza, Jan Topinka, Pavel Rőssner
Software Mentions: 9
Published: about 6 years ago

10.1186/s13229-019-0262-8

Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer
Cited by: 25
Author(s): Jaume Forés-Martos, Ferrán Catalá-López, Jon Sánchez-Valle, Kristina Ibáñez, Héctor Tejero, Helena Palma-Gudiel, Joan Climent, Véra Pancaldi, Lourdes Fañanás, Celso Arango, Mara Parellada, Anaı̈s Baudot, Daniel Vogt, John L.R. Rubenstein, Alfonso Valencia, Rafael Tabarés‐Seisdedos
Software Mentions: 9
Published: over 7 years ago

10.1186/s12918-016-0349-1

DGCA: A comprehensive R package for Differential Gene Correlation Analysis
Cited by: 156
Author(s): Andrew McKenzie, Igor Katsyv, Won Min Song, Minghui Wang, Bin Zhang
Software Mentions: 9
Published: almost 10 years ago

10.1038/s41598-018-31780-0

DNA hypermethylation and differential gene expression associated with Klinefelter syndrome
Cited by: 67
Author(s): Anne Skakkebæk, Morten Muhlig Nielsen, Christian Trolle, Søren Vang, Henrik Hornshøj, Jakob Hedegaard, Mikkel Wallentin, Anders Bojesen, Jens Michael Hertz, Jens Fedder, John R. Østergaard, Jakob Skou Pedersen, Claus Højbjerg Gravholt
Software Mentions: 9
Published: almost 8 years ago

10.1186/s12943-020-01170-0

m6A regulator-mediated methylation modification patterns and tumor microenvironment infiltration characterization in gastric cancer
Cited by: 600
Author(s): Bo Zhang, Qiong Wu, Ben Li, Defeng Wang, Lei Wang, You Zhou
Software Mentions: 9
Published: over 6 years ago

10.1016/j.celrep.2019.11.077

Integrated Epigenome, Exome, and Transcriptome Analyses Reveal Molecular Subtypes and Homeotic Transformation in Uterine Fibroids
Cited by: 42
Author(s): Jitu W. George, Huihui Fan, Benjamin K. Johnson, Tyler J. Carpenter, Kelly K. Foy, Anindita Chatterjee, Amanda L. Patterson, Julie Koeman, Marie Adams, Zachary Madaj, David Chesla, Erica E. Marsh, Timothy J. Triche, Hui Shen, Jose Teixeira
Software Mentions: 9
Published: over 6 years ago

10.3389/fonc.2020.626912

Molecular Subtypes and CD4+ Memory T Cell-Based Signature Associated With Clinical Outcomes in Gastric Cancer
Cited by: 15
Author(s): Zhikun Ning, Cegui Hu, Chao Huang, Jiang Liu, Taicheng Zhou, Zhen Zong
Software Mentions: 9
Published: over 5 years ago

10.1186/s13041-020-00681-7

Brain transcriptome analysis reveals subtle effects on mitochondrial function and iron homeostasis of mutations in the SORL1 gene implicated in early onset familial Alzheimer’s disease
Cited by: 22
Author(s): Karissa Barthelson, Stephen Pederson, Morgan Newman, Michael Lardelli
Software Mentions: 9
Published: almost 6 years ago

10.3389/fonc.2021.695006

Tumor-Infiltrating PD-1hiCD8+-T-Cell Signature as an Effective Biomarker for Immune Checkpoint Inhibitor Therapy Response Across Multiple Cancers
Cited by: 7
Author(s): Zhenyu Yang, Yulan Deng, Jinghui Cheng, Shiyou Wei, Hao Luo, Lunxu Liu
Software Mentions: 9
Published: almost 5 years ago

10.3390/ijms21145044

Epigenome Wide Association and Stochastic Epigenetic Mutation Analysis on Cord Blood of Preterm Birth
Cited by: 10
Author(s): Elena Spada, Luciano Calzari, Luigi Corsaro, Teresa Fazia, Monica Mencarelli, Anna Maria Di Blasio, Luisa Bernardinelli, G. Zangheri, Michele Vignali, Davide Gentilini
Software Mentions: 9
Published: about 6 years ago

10.1186/s13059-016-1000-6

Blood lipids influence DNA methylation in circulating cells
Cited by: 149
Author(s): Koen F. Dekkers, Maarten van Iterson, Roderick C. Slieker, Matthijs Moed, Marc Jan Bonder, M.A. van Galen, Hailiang Mei, Daria V. Zhernakova, Leonard H van den Berg, Joris Deelen, Jenny van Dongen, Diana van Heemst, Albert Hofman, Jouke Jan Hottenga, Carla Kallen, Casper G. Schalkwijk, Coen D. A. Stehouwer, Ettje F. Tigchelaar, André G. Uitterlinden, Gonneke Willemsen, Alexandra Zhernakova, Lude Franke, Peter A.C. ’t Hoen, Ritsert C. Jansen, Joyce B. J. van Meurs, Dorret I. Boomsma, Cornelia M. van Duijn, Marleen M.J. van Greevenbroek, Jan H. Veldink, Cisca Wijmenga, Erik W. van Zwet, P. Eline Slagboom, J. Wouter Jukema, Bastiaan T. Heijmans
Software Mentions: 9
Published: about 10 years ago

10.1155/2021/6290261

Identification of a Tumor Microenvironment-Related Gene Signature Indicative of Disease Prognosis and Treatment Response in Colon Cancer
Cited by: 24
Author(s): Wenzheng Chen, Jianfeng Huang, Jianbo Xiong, Pengcheng Fu, Changyu Chen, Yi Liu, Zhengrong Li, Zhigang Jie, Yi Cao
Software Mentions: 9
Published: about 5 years ago

10.3389/fgene.2020.570325

Construction of a Nomogram Based on a Hypoxia-Related lncRNA Signature to Improve the Prediction of Gastric Cancer Prognosis
Cited by: 29
Author(s): Qian Chen, Lang Hu, Kaihua Chen
Software Mentions: 9
Published: almost 6 years ago

10.3389/fonc.2021.619242

The Identification and Validation of Two Heterogenous Subtypes and a Risk Signature Based on Ferroptosis in Hepatocellular Carcinoma
Cited by: 40
Author(s): Xinwei Han, Libo Wang, Long Liu, Taoyuan Lu, Dechao Jiao, Yuling Sun, Xinwei Han
Software Mentions: 9
Published: over 5 years ago

10.1038/s41421-021-00274-1

Integrating longitudinal clinical laboratory tests with targeted proteomic and transcriptomic analyses reveal the landscape of host responses in COVID-19
Cited by: 21
Author(s): Yun Tan, Wei Zhang, Zhaoqin Zhu, Na Qiao, Yun Ling, Mingquan Guo, Tong Yin, Hai Fang, Xiaoguang Xu, Gang Lu, Peipei Zhang, Shuangshuang Yang, Ziyu Fu, Dongguo Liang, Yinyin Xie, Ruihong Zhang, Lu Jiang, Shuting Yu, Jing Lu, Fang-Ying Jiang, Jian Chen, Chenlu Xiao, Shengyue Wang, Shuo Chen, Xiu‐Wu Bian, Hongzhou Lu, Feng Liu, Sai‐Juan Chen
Software Mentions: 9
Published: about 5 years ago

10.1371/journal.pgen.1009259

Loss of endocytosis-associated RabGEF1 causes aberrant morphogenesis and altered autophagy in photoreceptors leading to retinal degeneration
Cited by: 9
Author(s): Passley Hargrove-Grimes, Anupam Mondal, Jessica Gumerson, Jacob Nellissery, Angel Aponte, Linn Gieser, Haohua Qian, Robert N Fariss, Juan S. Bonifacino, Tiansen Li, Anand Swaroop
Software Mentions: 9
Published: over 5 years ago

10.1186/s13148-020-0824-9

Maternal diabetes and obesity influence the fetal epigenome in a largely Hispanic population
Cited by: 18
Author(s): Heather E. Rizzo, Elia N. Escaname, Nicholas B. Alana, Elizabeth Lavender, Jonathan Gelfond, Roman Fernandez, Matthew A. Hibbs, Julie King, Nicholas Carr, Cynthia L. Blanco
Software Mentions: 9
Published: over 6 years ago

10.3390/metabo11040211

gcProfileMakeR: An R Package for Automatic Classification of Constitutive and Non-Constitutive Metabolites
Cited by: 3
Author(s): Fernando Pérez-Sánz, Victoria Ruiz-Hernández, Marta I. Terry, Sara Arce-Gallego, Julia Weiß, Pedro J. Navarro, Marcos Egea‐Cortines
Software Mentions: 9
Published: over 5 years ago

10.3389/fonc.2021.711020

Integration of scRNA-Seq and Bulk RNA-Seq to Analyse the Heterogeneity of Ovarian Cancer Immune Cells and Establish a Molecular Risk Model
Cited by: 37
Author(s): Leilei Liang, Jing Yu, Jian Li, Ning Li, Jing Liu, Lin Xiu, Jia Zeng, Tiantian Wang, Lingying Wu
Software Mentions: 9
Published: almost 5 years ago

10.3389/fnins.2020.00209

A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer’s Disease
Cited by: 6
Author(s): Sze Chung Yuen, Hongmei Zhu, Siu-wai Leung
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pone.0209656

A distinct epigenetic profile distinguishes stenotic from non-inflamed fibroblasts in the ileal mucosa of Crohn’s disease patients
Cited by: 14
Author(s): Andrew Y. Li Yim, Jessica R. de Bruyn, Nicolette W. Duijvis, Catriona Sharp, Enrico Ferrero, Wouter J. de Jonge, Manon E. Wildenberg, Marcel M.A.M. Mannens, Christianne J. Buskens, Geert R. D’Haens, Peter Henneman, Anje A. te Velde
Software Mentions: 9
Published: over 7 years ago

10.1016/j.mad.2021.111437

Transcriptomic profiling of long- and short-lived mutant mice implicates mitochondrial metabolism in ageing and shows signatures of normal ageing in progeroid mice
Cited by: 6
Author(s): Matías Fuentealba, Daniel K. Fabian, Handan Melike Dönertaş, Janet Thornton, Linda Partridge
Software Mentions: 9
Published: over 5 years ago

10.1038/s41598-020-66998-4

Comparison of differential accessibility analysis strategies for ATAC-seq data
Cited by: 26
Author(s): Paul Gontarz, Shuhua Fu, Xiaoyun Xing, Shaopeng Liu, Benpeng Miao, Viktoriia Bazylianska, Akhil Sharma, Pamela A. F. Madden, K. Lynn Cates, Andrew S. Yoo, Anna Moszczyńska, Ting Wang, Bo Zhang
Software Mentions: 9
Published: about 6 years ago

10.1038/s41598-021-98998-3

VCAM1 expression in the myocardium is associated with the risk of heart failure and immune cell infiltration in myocardium
Cited by: 19
Author(s): Tongyu Wang, Jiahu Tian, Yinji Jin
Software Mentions: 9
Published: almost 5 years ago

10.7150/thno.53092

Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapy
Cited by: 7
Author(s): Xin Lai, Florian S. Dreyer, Martina Cantone, Martin Eberhardt, Kerstin F. Gerer, Tanushree Jaitly, Steffen Uebe, Christopher Lischer, Arif B. Ekici, Jürgen Wittmann, Hans‐Martin Jäck, Niels Schaft, Jan Dörrie, Julio Vera
Software Mentions: 9
Published: over 5 years ago

10.18632/aging.102847

Risk score based on expression of five novel genes predicts survival in soft tissue sarcoma
Cited by: 21
Author(s): Hao Gu, Zhang Chao, Jia Guo, Min Yang, Hongshan Zhong, Wei Jin, Yang Liu, Liping Gao, Renxiong Wei
Software Mentions: 9
Published: over 6 years ago

10.1186/s12859-016-1321-1

GEN3VA: aggregation and analysis of gene expression signatures from related studies
Cited by: 17
Author(s): Gregory W. Gundersen, Kathleen M. Jagodnik, Holly Woodland, Nicholas F. Fernandez, Kevin Sani, Anders B. Dohlman, Peter M.U. Ung, Caroline D. Monteiro, Avner Schlessinger, Avi Ma’ayan
Software Mentions: 9
Published: almost 10 years ago

10.1186/s12935-020-1113-6

Construction of a novel gene-based model for prognosis prediction of clear cell renal cell carcinoma
Cited by: 81
Author(s): Zedan Zhang, Enyu Lin, Hongkai Zhuang, Lu Xie, Xiaoqiang Feng, Jiumin Liu, Yuming Yu
Software Mentions: 9
Published: over 6 years ago

10.1186/1471-2164-16-S7-S14

Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads
Cited by: 12
Author(s): Hung I Harry Chen, Yuanhang Liu, Yi Zou, Zhao Lai, Devanand Sarkar, Yufei Huang, Yidong Chen
Software Mentions: 9
Published: about 11 years ago

10.3389/fmolb.2020.604252

Prognostic Model of Colorectal Cancer Constructed by Eight Immune-Related Genes
Cited by: 14
Author(s): Shuting Wen, Lina He, Zhuotai Zhong, Hong Mi, Fengbin Liu
Software Mentions: 9
Published: over 5 years ago

10.1186/s12885-020-6638-5

Multiple m6A RNA methylation modulators promote the malignant progression of hepatocellular carcinoma and affect its clinical prognosis
Cited by: 33
Author(s): Nanfang Qu, Sanyu Qin, Xuemei Zhang, Xiaotong Bo, Zhengchun Liu, Chao Tan, Guiqiong Wen, Haixing Jiang
Software Mentions: 9
Published: over 6 years ago

10.1155/2021/7408893

Identification of a Four-lncRNA Prognostic Signature for Colon Cancer Based on Genome Instability
Cited by: 2
Author(s): Duo Yun, Zhimin Yang
Software Mentions: 9
Published: almost 5 years ago

10.1186/s12859-016-0994-9

Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments
Cited by: 79
Author(s): Ran Bi, Peng Liu
Software Mentions: 9
Published: over 10 years ago

10.1186/s12885-019-6235-7

lionessR: single sample network inference in R
Cited by: 22
Author(s): Marieke L. Kuijjer, Ping-Han Hsieh, John Quackenbush, Kimberly Glass
Software Mentions: 9
Published: almost 7 years ago

10.1002/cam4.4203

Comprehensive analysis of pan‐cancer reveals potential of ASF1B as a prognostic and immunological biomarker
Cited by: 25
Author(s): Xinyao Hu, Hua Zhu, Xiaoyu Zhang, Xueling He, Ximing Xu
Software Mentions: 9
Published: almost 5 years ago

10.18632/aging.104064

Clinical and prognostic pan-cancer analysis of m6A RNA methylation regulators in four types of endocrine system tumors
Cited by: 29
Author(s): Kai Li, Hui Luo, Hui Luo, Xiao Zhu
Software Mentions: 9
Published: over 5 years ago

10.1186/s40425-018-0422-y

33rd Annual Meeting & Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2018)
Cited by: 36
Author(s):
Software Mentions: 9
Published: almost 8 years ago

10.1371/journal.pone.0199274

Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats
Cited by: 25
Author(s): Boris Zybailov, Galina Glazko, Yasir Rahmatallah, Dmitri S. Andreyev, Taylor McElroy, Oleg Karaduta, Stephanie D. Byrum, Lisa Orr, Alan J. Tackett, Samuel G. Mackintosh, Ricky D. Edmondson, Dorothy A. Kieffer, Roy J. Martin, Sean H. Adams, Nosratola D. Vaziri, John M. Arthur
Software Mentions: 9
Published: over 7 years ago

10.1002/cam4.2774

Identification of prognostic genes in adrenocortical carcinoma microenvironment based on bioinformatic methods
Cited by: 39
Author(s): Xiao Li, Yang Gao, Zicheng Xu, Zheng Zhang, Yuxiao Zheng, Feng Qi
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pone.0220518

Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne)
Cited by: 4
Author(s): Albert Fradera-Sola, Ann Thomas, Dagmara Gasior, John A. Harper, Matthew J. Hegarty, Ian Armstead, Narcís Fernández-Fuentes
Software Mentions: 9
Published: about 7 years ago

10.1038/s41388-018-0450-6

The miR-96 and RARγ signaling axis governs androgen signaling and prostate cancer progression
Cited by: 40
Author(s): Mark D. Long, Prashant Singh, James R. Russell, Gerard Llimos, Spencer R. Rosario, Abbas Rizvi, Patrick R. van den Berg, Jason Kirk, Lara E. Sucheston‐Campbell, Dominic J. Smiraglia, Moray J. Campbell
Software Mentions: 9
Published: about 8 years ago