10.1002/cam4.2983

Comprehensive insights on pivotal prognostic signature involved in clear cell renal cell carcinoma microenvironment using the ESTIMATE algorithm
Cited by: 30
Author(s): Jun Luo, Yi Xie, Yuxiao Zheng, Chenji Wang, Feng Qi, Jiateng Hu, Yixiang Xu
Software Mentions: 11
Published: over 6 years ago

10.3389/fmolb.2021.559800

KIF18B is a Prognostic Biomarker and Correlates with Immune Infiltrates in Pan-Cancer
Cited by: 9
Author(s): Mengjun Qiu, Qiushuang Wang, Qiuting Li, Lisheng Zhu, Yanan Li, Shengli Yang, Zhifan Xiong
Software Mentions: 11
Published: over 5 years ago

10.1111/jcmm.15615

Gene regulation network analysis reveals core genes associated with survival in glioblastoma multiforme
Cited by: 15
Author(s): Lan Jiang, Min Zhong, Tianbing Chen, Xiaolong Zhu, Hui Yang, Kun Lv
Software Mentions: 11
Published: about 6 years ago

10.3389/fmolb.2021.684050

Characterization of Hypoxia-Related Molecular Subtypes in Clear Cell Renal Cell Carcinoma to Aid Immunotherapy and Targeted Therapy via Multi-Omics Analysis
Cited by: 10
Author(s): Weimin Zhong, Hongbin Zhong, Fengling Zhang, Chaoqun Huang, Yao Lin, Jian Huang
Software Mentions: 11
Published: about 5 years ago

10.1016/j.ebiom.2018.04.010

Genomic Response to Vitamin D Supplementation in the Setting of a Randomized, Placebo-Controlled Trial
Cited by: 28
Author(s): Antonio J. Berlanga‐Taylor, Katharine Plant, Andrew Dahl, Evelyn Lau, Michael Hill, David Sims, Andreas Heger, Jonathan Emberson, Jane Armitage, Robert Clarke, Julian C. Knight
Software Mentions: 11
Published: over 8 years ago

10.15252/emmm.201911900

Epigenetic gene expression links heart failure to memory impairment
Cited by: 13
Author(s): Rezaul Islam, Dawid Lbik, M. Sadman Sakib, Raoul Maximilian Hofmann, Tea Berulava, Martí Jiménez Mausbach, Julia Cha, Maria Amélia Azevêdo Goldberg, Elerdashvili Vakhtang, Christian Schiffmann, Anke Zieseniß, Dörthe M. Katschinski, Farahnaz Sananbenesi, Karl Toischer, André Fischer
Software Mentions: 11
Published: over 5 years ago

10.3389/fcell.2021.621618

Functional Assessment of Four Novel Immune-Related Biomarkers in the Pathogenesis of Clear Cell Renal Cell Carcinoma
Cited by: 7
Author(s): Daojun Lv, Xiangkun Wu, Ming Wang, Wenzhe Chen, Shuxin Yang, Yongda Liu, Guohua Zeng, Danan Gu
Software Mentions: 11
Published: over 5 years ago

10.3389/fonc.2021.646060

Immune-Related Gene SERPINE1 Is a Novel Biomarker for Diffuse Lower-Grade Gliomas via Large-Scale Analysis
Cited by: 20
Author(s): Xiaoming Huang, Fenglin Zhang, Dong He, Xiaoshuai Ji, Jiajia Gao, Wenqing Liu, Yunda Wang, Qian Liu, Tao Xin
Software Mentions: 11
Published: over 5 years ago

10.1155/2021/2291899

Crosstalk between Heart Failure and Cognitive Impairment via hsa-miR-933/RELB/CCL21 Pathway
Cited by: 8
Author(s): Wenxiao Feng, Jie Yang, Wen‐Chao Song, Yi-Tao Xue
Software Mentions: 11
Published: almost 5 years ago

10.3389/fonc.2020.570654

Prognostic Role of Tumor Mutation Burden Combined With Immune Infiltrates in Skin Cutaneous Melanoma Based on Multi-Omics Analysis
Cited by: 16
Author(s): Junya Yan, Xiaowen Wu, Jiayi Yu, Yanyan Zhu, Shundong Cang
Software Mentions: 11
Published: almost 6 years ago

10.3389/fonc.2020.00691

Immunoscore Predicts Survival in Early-Stage Lung Adenocarcinoma Patients
Cited by: 12
Author(s): Zihuan Zhao, Dan Zhao, Jianguo Xia, Yichuan Wang, Buhai Wang
Software Mentions: 11
Published: over 6 years ago

10.7554/eLife.58705

Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants
Cited by: 23
Author(s): Liis Kolberg, Nurlan Kerimov, Hedi Peterson, Kaur Alasoo
Software Mentions: 11
Published: almost 6 years ago

10.3389/fgene.2021.733715

Development and Validation of a Novel Gene Signature for Predicting the Prognosis by Identifying m5C Modification Subtypes of Cervical Cancer
Cited by: 2
Author(s): Jing Yu, Leilei Liang, Jing Liu, Tingting Liu, Jian Li, Lin Xiu, Jia Zeng, Tiantian Wang, Di Wang, Lijun Liang, Dawei Xie, Ding-Xiong Chen, Jusheng An, Lingying Wu
Software Mentions: 11
Published: almost 5 years ago

10.3389/fgene.2021.620705

Identification of Tumor Microenvironment-Related Prognostic Genes in Sarcoma
Cited by: 6
Author(s): Dongjun Dai, Lanyu Xie, Yongjie Shui, Jinfan Li, Qichun Wei
Software Mentions: 11
Published: over 5 years ago

10.3390/cancers13122903

Integrative Transcriptomic Analysis Reveals Distinctive Molecular Traits and Novel Subtypes of Collecting Duct Carcinoma
Cited by: 6
Author(s): Chiara Gargiuli, Pierangela Sepe, Anna Tessari, Tyler Sheetz, Maurizio Colecchia, F.G.M. De Braud, Giuseppe Procopio, Marialuisa Sensi, Elena Verzoni, Matteo Dugo
Software Mentions: 11
Published: about 5 years ago

10.3389/fgene.2015.00040

Integrating multi-omic features exploiting Chromosome Conformation Capture data
Cited by: 9
Author(s): Ivan Merelli, Fabio Tordini, Maurizio Drocco, Marco Aldinucci, Píetro Lió, Luciano Milanesi
Software Mentions: 11
Published: over 11 years ago

10.1038/s41598-021-88698-3

In-depth transcriptomic analysis of human retina reveals molecular mechanisms underlying diabetic retinopathy
Cited by: 23
Author(s): Kolja Becker, H. Klein, Eric J. Simon, Coralie Viollet, Christian Haslinger, Germán Leparc, Christian Schultheis, Victor Chong, Markus H. Kuehn, Francesc Fernández-Albert, Remko A. Bakker
Software Mentions: 11
Published: over 5 years ago

10.1186/s12859-019-2968-1

Visualization methods for differential expression analysis
Cited by: 6
Author(s): Lindsay Rutter, Adrienne N. Moran Lauter, Michelle A. Graham, Dianne Cook
Software Mentions: 11
Published: almost 7 years ago

10.1074/mcp.TIR120.002155

ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis
Cited by: 129
Author(s): Johannes Griss, Guilherme Viteri, Konstantinos Sidiropoulos, Vy Kim Nguyen, Antonio Fabregat, Henning Hermjakob
Software Mentions: 11
Published: over 5 years ago

10.1186/s12575-021-00152-w

N6-Methyladenosine Related Long Non-Coding RNAs and Immune Cell Infiltration in the Tumor Microenvironment of Gastric Cancer
Cited by: 9
Author(s): Zhong Lin Yu, Zheng Zhu
Software Mentions: 11
Published: about 5 years ago

10.1002/1878-0261.12117

Recurrence-associated gene signature optimizes recurrence-free survival prediction of colorectal cancer
Cited by: 37
Author(s): Xianglong Tian, Xiaoqiang Zhu, Tingting Yan, Chuangqi Yu, Chaoqin Shen, Ye Hu, Jie Hong, Haoyan Chen, Jing‐Yuan Fang
Software Mentions: 11
Published: almost 9 years ago

10.18632/aging.203242

Glycolysis- and immune-related novel prognostic biomarkers of Ewing's sarcoma: glucuronic acid epimerase and triosephosphate isomerase 1
Cited by: 9
Author(s): Jie Jiang, Xinli Zhan, Guoyong Xu, Tuo Liang, Chaojie Yu, Shijie Liao, Liyi Chen, Shengsheng Huang, Xuhua Sun, Ming Yi, Zide Zhang, Yuanlin Yao, Chong Liu
Software Mentions: 11
Published: about 5 years ago

10.3389/fbioe.2020.00101

The Integrated Transcriptome Bioinformatics Analysis Identifies Key Genes and Cellular Components for Spinal Cord Injury-Related Neuropathic Pain
Cited by: 8
Author(s): Runzhi Huang, Tong Meng, Rui Zhu, Lijuan Zhao, Dianwen Song, Huabin Yin, Zongqiang Huang, Liming Cheng, Jie Zhang
Software Mentions: 11
Published: over 6 years ago

10.1371/journal.pone.0188873

A comprehensive analysis of breast cancer microbiota and host gene expression
Cited by: 105
Author(s): Kevin J. Thompson, James N. Ingle, Xiaojia Tang, Nicholas Chia, Patricio Jeraldo, Marina Walther-Antonio, Karunya K. Kandimalla, Stephen Johnson, Jingwen Yao, Sean C. Harrington, Vera J. Suman, Liewei Wang, Richard Weinshilboum, Judy C. Boughey, Jean Pierre A. Kocher, Heidi Nelson, Matthew P. Goetz, Krishna R. Kalari
Software Mentions: 11
Published: over 8 years ago

10.3389/fonc.2014.00147

An Integrative Analysis of Meningioma Tumors Reveals the Determinant Genes and Pathways of Malignant Transformation
Cited by: 7
Author(s): José Carlos Iglesias Gómez, Adrián Mosquera Orgueira
Software Mentions: 11
Published: about 12 years ago

10.3389/fcvm.2021.624714

Identification of Potential Biomarkers and Immune Infiltration Characteristics in Idiopathic Pulmonary Arterial Hypertension Using Bioinformatics Analysis
Cited by: 21
Author(s): Haowei Zeng, Xiaoqin Liu, Yushun Zhang
Software Mentions: 11
Published: over 5 years ago

10.1534/g3.120.401270

Application of Transcriptional Gene Modules to Analysis of <i>Caenorhabditis elegans</i>’ Gene Expression Data
Cited by: 7
Author(s): Michael Cary, Katie Podshivalova, Cynthia Kenyon
Software Mentions: 11
Published: almost 6 years ago

10.1093/g3journal/jkab104

Strongyloides RNA-seq Browser: a web-based software platform for on-demand bioinformatics analyses of Strongyloides species
Cited by: 2
Author(s): Astra S. Bryant, Stephanie F. DeMarco, Elissa A. Hallem
Software Mentions: 11
Published: over 5 years ago

10.1002/1878-0261.12134

Tissue glycomics distinguish tumour sites in women with advanced serous adenocarcinoma
Cited by: 21
Author(s): Merrina Anugraham, Francis Jacob, Arun Everest‐Dass, Andreas Schoetzau, Sheri Nixdorf, Neville F. Hacker, Daniel Fink, Viola Heinzelmann‐Schwarz, Nicolle H. Packer
Software Mentions: 11
Published: almost 9 years ago

10.18632/aging.202957

Integrative analysis identifies key mRNA biomarkers for diagnosis, prognosis, and therapeutic targets of HCV-associated hepatocellular carcinoma
Cited by: 8
Author(s): Yongqiang Zhang, Yuqin Tang, Chengbin Guo, Gen Li
Software Mentions: 11
Published: over 5 years ago

10.1186/s12894-019-0479-z

Where is the limit of prostate cancer biomarker research? Systematic investigation of potential prognostic and diagnostic biomarkers
Cited by: 2
Author(s): Anika Kremer, Tobias Kremer, Glen Kristiansen, Yuri Tolkach
Software Mentions: 11
Published: about 7 years ago

10.1186/s12935-021-02041-4

Ten-gene signature reveals the significance of clinical prognosis and immuno-correlation of osteosarcoma and study on novel skeleton inhibitors regarding MMP9
Cited by: 17
Author(s): Weihang Li, Ziyi Ding, Dong Wang, Chengfei Li, Yikai Pan, Yingjing Zhao, Hongzhe Zhao, Tianxing Lu, Rui Xu, Shilei Zhang, Bin Yuan, Yunlong Zhao, Yanjiang Yin, Yuan Gao, Jing Li, Ming Yan
Software Mentions: 11
Published: about 5 years ago

10.3389/fimmu.2021.599207

Molecular and Clinical Characterization of LAG3 in Breast Cancer Through 2994 Samples
Cited by: 15
Author(s): Qiang Liu, Yihang Qi, Jie Zhai, Xiangyi Kong, Xiangyu Wang, Zhongzhao Wang, Yi Fang, Jing Wang
Software Mentions: 11
Published: about 5 years ago

10.1186/s12935-021-01795-1

Identification and development of a novel invasion-related gene signature for prognosis prediction in colon adenocarcinoma
Cited by: 15
Author(s): Jiahua Liu, Chunhui Jiang, Chunjie Xu, Dongyang Wang, Ya Shen, Ye Liu, Lei Gu
Software Mentions: 11
Published: over 5 years ago

10.1186/1756-0500-3-81

Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays
Cited by: 17
Author(s): Colin S. Gillespie, Guiyuan Lei, Richard J. Boys, Amanda Greenall, Darren J. Wilkinson
Software Mentions: 11
Published: over 16 years ago

10.1371/journal.pcbi.1007665

CAncer bioMarker Prediction Pipeline (CAMPP)—A standardized framework for the analysis of quantitative biological data
Cited by: 8
Author(s): Thilde Terkelsen, Anders Krogh, Elena Papaleo
Software Mentions: 11
Published: over 6 years ago

10.1186/1471-2105-10-74

RGG: A general GUI Framework for R scripts
Cited by: 7
Author(s): Ilhami Visne, Erkan Dilaveroǧlu, Klemens Vierlinger, Martin Lauss, Ahmet Yıldız, Andreas Weinhäusel, Christa Noehammer, Friedrich Leisch, Albert Kriegner
Software Mentions: 11
Published: over 17 years ago

10.1016/j.ccell.2017.08.017

Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma
Cited by: 662
Author(s): Alan Mackay, Anna Burford, Diana Carvalho, Elisa Izquierdo, Janat Fazal-Salom, Kathryn R. Taylor, Lynn Bjerke, Matthew Clarke, Maria Vinci, Meera Nandhabalan, Sara Temelso, Sergey Popov, Valeria Molinari, Pichai Raman, Angela J. Waanders, Harry Han, Saumya Gupta, Lynley V. Marshall, Stergios Zacharoulis, Sucheta Vaidya, Henry Mandeville, Leslie Bridges, Andrew Martin, Safa Al‐Sarraj, Christopher Chandler, Ho Keung Ng, Xingang Li, Kun Mu, Saoussen Trabelsi, Dorra H’mida-Ben Brahim, Alexei N. Kisljakov, Д. М. Коновалов, Andrew S. Moore, Ángel M. Carcaboso, Mariona Suñol, Carmen de Torres, Ofelia Cruz, Jaume Mora, Л. И. Шац, João N. Stávale, Lucas Tadeu Bidinotto, Rui Manuel Reis, Natacha Entz‐Werlé, Michael Farrell, Jane Cryan, Darach Crimmins, John Caird, Jane Pears, Michelle Monje, Marie‐Anne Debily, David Castel, Jacques Grill, Cynthia Hawkins, Hamid Nikbakht, Nada Jabado, Suzanne J. Baker, Stefan M. Pfister, David Jones, Maryam Fouladi, André O. von Bueren, Michael Baudis, Adam Resnick, Chris Jones
Software Mentions: 11
Published: almost 9 years ago

10.1186/s12935-020-01393-7

Small nucleolar RNAs signature (SNORS) identified clinical outcome and prognosis of bladder cancer (BLCA)
Cited by: 5
Author(s): Rui Cao, Bo Ma, Lushun Yuan, Gang Wang, Ye Tian
Software Mentions: 11
Published: about 6 years ago

10.1186/s13058-021-01451-6

Transcriptome and genome evolution during HER2-amplified breast neoplasia
Cited by: 3
Author(s): Peipei Lu, Joseph W. Foley, Chunfang Zhu, Katherine McNamara, Korsuk Sirinukunwattana, Sujay Vennam, Sushama Varma, Hamid Fehri, Arunima Srivastava, Shirley Zhu, Jens Rittscher, Parag Mallick, Christina Curtis, Robert B. West
Software Mentions: 11
Published: about 5 years ago

10.3390/diagnostics10030171

GRB10 and E2F3 as Diagnostic Markers of Osteoarthritis and Their Correlation with Immune Infiltration
Cited by: 56
Author(s): Yajun Deng, Enhui Ren, Wenhua Yuan, Guang-Zhi Zhang, Zhi-Xi Wu, Qiqi Xie
Software Mentions: 11
Published: over 6 years ago

10.1016/j.csbj.2021.05.040

Robustness of differential gene expression analysis of RNA-seq
Cited by: 31
Author(s): Alexey Stupnikov, Caitríona E. McInerney, Kienan I. Savage, Stuart McIntosh, Frank Emmert‐Streib, Richard D. Kennedy, Manuel Salto-Tellez, Kevin M. Prise, Darragh G. McArt
Software Mentions: 11
Published: over 5 years ago

10.1155/2009/201325

Analysis of Array-CGH Data Using the R and Bioconductor Software Suite
Cited by: 8
Author(s): Winfried Hofmann, Anja Weigmann, Marcel Tauscher, Britta Skawran, Tim Focken, R Buurman, Luzie U. Wingen, Brigitte Schlegelberger, Doris Steinemann
Software Mentions: 11
Published: over 17 years ago

10.1186/1471-2105-7-509

CoXpress: differential co-expression in gene expression data
Cited by: 149
Author(s): Michael Watson
Software Mentions: 11
Published: almost 20 years ago

10.1186/s12859-016-1386-x

Robust differential expression analysis by learning discriminant boundary in multi-dimensional space of statistical attributes
Cited by: 0
Author(s): Yuanzhe Bei, Pengyu Hong
Software Mentions: 11
Published: over 9 years ago

10.3390/ijms221910302

The Impact of m1A Methylation Modification Patterns on Tumor Immune Microenvironment and Prognosis in Oral Squamous Cell Carcinoma
Cited by: 17
Author(s): Li Gao, Ru Chen, Masahiro Sugimoto, Masanobu Mizuta, Yo Kishimoto, Koichi Omori
Software Mentions: 11
Published: almost 5 years ago

10.1186/s12885-019-5965-x

Distinct signatures of lung cancer types: aberrant mucin O-glycosylation and compromised immune response
Cited by: 32
Author(s): Marta Lucchetta, Isabelle da Piedade, Mohamed Mounir, Marina Vabistsevits, Thilde Terkelsen, Elena Papaleo
Software Mentions: 11
Published: about 7 years ago

10.3389/fimmu.2020.612784

Integrated Analysis of the ETS Family in Melanoma Reveals a Regulatory Role of ETV7 in the Immune Microenvironment
Cited by: 14
Author(s): Hui Qü, Hui Zhao, Xi Zhang, Yang Liu, Feng Li, Li-Yan Sun, Zewen Song
Software Mentions: 11
Published: over 5 years ago

10.7717/peerj.10680

Homologous recombination repair rathway and RAD54L in early-stage lung adenocarcinoma
Cited by: 5
Author(s): Shaoyong Zheng, Lan Yao, Fasheng Li, Luyu Huang, Yunfang Yu, Zenan Lin, Hao Li, Xiance Jin, Michael Lanuti, Haiyu Zhou
Software Mentions: 11
Published: over 5 years ago

10.1155/2021/6616908

Interpreting the Molecular Mechanisms of Yinchenhao Decoction on Hepatocellular Carcinoma through Absorbed Components Based on Network Pharmacology
Cited by: 5
Author(s): Jijia Sun, Tao Han, Tao Yang, Yunhui Chen, Jihan Huang
Software Mentions: 11
Published: over 5 years ago

10.3390/cancers12030692

Hypoxia-Induced Adaptations of miRNomes and Proteomes in Melanoma Cells and Their Secreted Extracellular Vesicles
Cited by: 29
Author(s): Geoffroy Walbrecq, Odile Lecha, Anthoula Gaigneaux, Miriam Rebecca Fougeras, Demetra Philippidou, Christiane Margue, Miléne Tetsi Nomigni, François Bernardin, Gunnar Dittmar, Iris Behrmann, Stephanie Kreis
Software Mentions: 11
Published: over 6 years ago

10.3390/ijms20225621

APOBEC3-Mediated RNA Editing in Breast Cancer is Associated with Heightened Immune Activity and Improved Survival
Cited by: 45
Author(s): Mariko Asaoka, Takashi Ishikawa, Kazuaki Takabe, Santosh K. Patnaik
Software Mentions: 11
Published: almost 7 years ago

10.3389/fgene.2021.692426

A Ferroptosis-Related Gene Signature Identified as a Novel Prognostic Biomarker for Colon Cancer
Cited by: 15
Author(s): Xin Qi, Rui Wang, Yuxin Lin, Donghui Yan, Jiachen Zuo, Jiajia Chen, Bairong Shen
Software Mentions: 11
Published: about 5 years ago

10.1038/s41598-019-44765-4

Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression
Cited by: 35
Author(s): Ingrid Tarr, Emma McCann, Beben Benyamin, Timothy J. Peters, Natalie A. Twine, Katharine Y. Zhang, Qiongyi Zhao, Zong Hong Zhang, Dominic B. Rowe, Garth A. Nicholson, Denis C. Bauer, Susan J. Clark, Ian P. Blair, Kelly L. Williams
Software Mentions: 11
Published: about 7 years ago

10.3390/jcm9041055

Whole-Genome DNA Methylation Profiling of CD14+ Monocytes Reveals Disease Status and Activity Differences in Crohn’s Disease Patients
Cited by: 12
Author(s): Andrew Y. Li Yim, Nicolette W. Duijvis, Mohammed Ghiboub, Catriona Sharp, Enrico Ferrero, Marcel M.A.M. Mannens, Geert D’Haens, Wouter J. de Jonge, Anje A. te Velde, Peter Henneman
Software Mentions: 11
Published: over 6 years ago

10.1186/1471-2164-9-419

Transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in liver: Comparison of rat and mouse
Cited by: 74
Author(s): Paul C. Boutros, Rui Yan, Ivy D. Moffat, Raimo Pohjanvirta, Allan B. Okey
Software Mentions: 11
Published: over 18 years ago

10.1186/1756-0500-5-282

Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results
Cited by: 9
Author(s): Yilin Dai, Ling Guo, Meng Li, Yibu Chen
Software Mentions: 11
Published: about 14 years ago

10.3390/cancers11081104

Differential Expression of DNA Repair Genes in Prognostically-Favorable versus Unfavorable Uveal Melanoma
Cited by: 10
Author(s): Mehmet Doğrusöz, Andrea Ruschel Träsel, Jinfeng Cao, Selҫuk Ҫolak, Sake I. van Pelt, Wilma G. M. Kroes, Amina F.A.S. Teunisse, Samar Alsafadi, Sjoerd G. van Duinen, Gregorius P M Luyten, Pieter A. van der Velden, Adriana Amaro, Ulrich Pfeffer, Aart G. Jochemsen, Martine J. Jager
Software Mentions: 11
Published: about 7 years ago

10.3389/fgene.2021.609174

METTL14 Acts as a Potential Regulator of Tumor Immune and Progression in Clear Cell Renal Cell Carcinoma
Cited by: 11
Author(s): Tianbo Xu, Su Gao, Hailong Ruan, Jingchong Liu, Yuenan Liu, Di Liu, Junwei Tong, Jian Shi, Hongmei Yang, Ke Chen, Xiaoping Zhang
Software Mentions: 11
Published: about 5 years ago

10.1371/journal.pcbi.1002276

BeadArray Expression Analysis Using Bioconductor
Cited by: 50
Author(s): Matthew E. Ritchie, Mark J. Dunning, Mike L. Smith, Wei Shi, Andy G. Lynch
Software Mentions: 11
Published: over 14 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

10.1186/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

10.1038/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

10.1186/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

10.18632/aging.202279

Exploration of the immune cell infiltration-related gene signature in the prognosis of melanoma
Cited by: 19
Author(s): Yongquan Zeng, Yue Zeng, Hang Yin, Fengxia Chen, Qingqing Wang, Xiaoyan Yu, Youwen Zhou
Software Mentions: 10
Published: over 5 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

10.1111/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

10.1371/journal.pone.0251804

Influence of genetic background and dietary oleic acid on gut microbiota composition in Duroc and Iberian pigs
Cited by: 4
Author(s): Adrián López-García, Rita Benítez, Yolanda Núñez, E. Gómez-Izquierdo, E. de Mercado, Juan García‐Casco, Óscar González-Recio, C. J. López‐Bote, Jordi Estellé, Cristina Óvilo
Software Mentions: 10
Published: over 5 years ago

10.1155/2008/147563

Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data: Tools for the First Steps
Cited by: 6
Author(s): Grier P. Page, Issa Coulibaly
Software Mentions: 10
Published: about 18 years ago

10.1186/s12859-017-1847-x

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
Cited by: 42
Author(s): Joseph N. Paulson, Cho-Yi Chen, Camila M. Lopes‐Ramos, Marieke L. Kuijjer, John Platig, Abhijeet R. Sonawane, Maud Fagny, Kimberly Glass, John Quackenbush
Software Mentions: 10
Published: almost 9 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

10.1371/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/s13059-021-02368-1

treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses
Cited by: 4
Author(s): Ronald Huang, Charlotte Soneson, Pierre‐Luc Germain, Thomas Schmidt, Christian von Mering, Mark D. Robinson
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.pone.0256016

Integration of chronological omics data reveals mitochondrial regulatory mechanisms during the development of hepatocellular carcinoma
Cited by: 2
Author(s): J. Noé García-Chávez, Verónica Rocío Vásquez-Garzón, Mercedes G. López, Saúl Villa‐Treviño, Rafaél Montiel
Software Mentions: 10
Published: about 5 years ago

10.1186/s13059-021-02337-8

Best practices on the differential expression analysis of multi-species RNA-seq
Cited by: 36
Author(s): Matthew Chung, Vincent M. Bruno, David A. Rasko, Christina A. Cuomo, José F. Muñoz, Jonathan Livny, Amol Shetty, Anup Mahurkar, Julie C. Dunning Hotopp
Software Mentions: 10
Published: over 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: about 5 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

10.1186/s13059-018-1466-5

Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data
Cited by: 40
Author(s): Alemu Takele Assefa, Katrijn De Paepe, Celine Everaert, Pieter Mestdagh, Olivier Thas, Jo Vandesompele
Software Mentions: 10
Published: about 8 years ago

10.1002/cam4.4117

A comprehensive analysis of immune infiltration in the tumor microenvironment of osteosarcoma
Cited by: 17
Author(s): Hao Yang, Liang Zhao, Yang Zhang, Fangfang Li
Software Mentions: 10
Published: about 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

10.1186/s12935-021-01965-1

Elevated expression of LPCAT1 predicts a poor prognosis and is correlated with the tumour microenvironment in endometrial cancer
Cited by: 9
Author(s): Tianyi Zhao, Min Han, Xiaohong Ma, Lina Wei, Yixin Hou, Rui Sun, Jie Jiang
Software Mentions: 10
Published: over 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

10.18632/aging.103517

Identifying CpG methylation signature as a promising biomarker for recurrence and immunotherapy in non–small-cell lung carcinoma
Cited by: 13
Author(s): Ruihan Luo, Song Jing, Xiao Xiao, Zhengbo Xie, Zhuochen Zhao, Wanfeng Zhang, Shiqi Miao, Yongyao Tang, Longke Ran
Software Mentions: 10
Published: about 6 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

10.1186/s12859-019-3146-1

A comparative study of topology-based pathway enrichment analysis methods
Cited by: 51
Author(s): Jing Ma, Ali Shojaie, George Michailidis
Software Mentions: 10
Published: almost 7 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.2021.643465

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

10.3389/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

10.1371/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

10.1371/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

10.18632/aging.102087

Identification of hub genes in prostate cancer using robust rank aggregation and weighted gene co-expression network analysis
Cited by: 71
Author(s): Zhenyu Song, Chongxi Fan, Zhiyuan Zhuo, Zhe Ma, Wenzhi Li, Gang Chen
Software Mentions: 10
Published: about 7 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

10.1007/s10456-020-09743-9

Epigenetic regulation of the lineage specificity of primary human dermal lymphatic and blood vascular endothelial cells
Cited by: 16
Author(s): Carlotta Tacconi, Yuliang He, Luca Ducoli, Michael Detmar
Software Mentions: 10
Published: almost 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

10.3389/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

10.1242/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

10.7717/peerj.1845

A molecular classification of human mesenchymal stromal cells
Cited by: 42
Author(s): Florian Rohart, Elizabeth A. Mason, Nicholas Matigian, Rowland Mosbergen, Othmar Korn, Tyrone Chen, Suzanne Butcher, Jatin Patel, Kerry Atkinson, Kiarash Khosrotehrani, Nicholas M. Fisk, Kim‐Anh Lê Cao, Christine A. Wells
Software Mentions: 10
Published: over 10 years ago

10.1186/s12859-017-1539-6

Model based heritability scores for high-throughput sequencing data
Cited by: 9
Author(s): Pratyaydipta Rudra, Wenmei Shi, Brian Vestal, Pamela Russell, Aaron Odell, Robin D. Dowell, Richard A. Radcliffe, Laura Saba, Katerina Kechris
Software Mentions: 10
Published: over 9 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