bioconductor: limma | Projects | Ecosyste.ms: Papers

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

10.1186/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/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: over 7 years ago

10.1111/jcmm.15939

Prognostic value and immune cell infiltration of hypoxic phenotype‐related gene signatures in glioblastoma microenvironment
Cited by: 10
Author(s): Kai Xiao, Jun Tan, Jian Yuan, Gang Peng, Wenyong Long, Jun Su, Yao Xiao, Qian Xiao, Changwu Wu, Chaoying Qin, Lili Hu, Kaili Liu, Shunlian Liu, Hao Zhou, Yichong Ning, Xiaojuan Ding, Qing Liu
Software Mentions: 11
Published: almost 6 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

10.1016/j.xpro.2021.100397

Protocol for comprehensive RNA sequencing analysis of murine long non-coding RNAs during aging
Cited by: 0
Author(s): Xinyue Lu, Qi Zhou, Jin Liu, Li Sun
Software Mentions: 11
Published: over 5 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

10.3389/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

10.1371/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: almost 15 years ago

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

10.1186/1756-0500-3-81

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

10.1111/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

10.1186/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

10.1371/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: almost 9 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

10.3389/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: over 5 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

10.1155/2021/6616908

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

10.1186/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: almost 10 years ago

10.3389/fonc.2021.626654

Identification of a Novel Four-Gene Signature Correlated With the Prognosis of Patients With Hepatocellular Carcinoma: A Comprehensive Analysis
Cited by: 7
Author(s): Weihua Zhu, Lixin Ru, Zhenchao Ma
Software Mentions: 11
Published: over 5 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/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

10.3389/pore.2021.1609852

Identification of a Gene Prognostic Model of Gastric Cancer Based on Analysis of Tumor Mutation Burden
Cited by: 9
Author(s): Weijun Ma, Weidong Li, Xu Liu, Lu Liu, Xinbing Yu, Liping Yang, Mingxu Da
Software Mentions: 11
Published: almost 5 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/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

10.1186/1471-2164-9-419

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/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

10.3389/fonc.2021.709077

Pyroptosis-Related Gene Signatures Can Robustly Diagnose Skin Cutaneous Melanoma and Predict the Prognosis
Cited by: 57
Author(s): Anji Ju, Jintian Tang, Shuohua Chen, Yan Fu, Yongzhang Luo
Software Mentions: 11
Published: about 5 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

10.1038/s41598-019-48495-5

Latent-period stool proteomic assay of multiple sclerosis model indicates protective capacity of host-expressed protease inhibitors
Cited by: 9
Author(s): Carlos Gutiérrez González, Stephanie Tankou, Laura M. Cox, Ellen P. Casavant, Howard L. Weiner, Joshua E. Elias
Software Mentions: 11
Published: about 7 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

10.1016/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

10.1155/2009/201325

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

10.3389/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

10.3390/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

10.3390/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

10.1038/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: over 7 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

10.1074/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: almost 6 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/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

10.7554/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: about 6 years ago

10.7554/eLife.64846

NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1
Cited by: 36
Author(s): Carolina Marques, Thomas Unterkircher, Paula Kroon, Barbara Oldrini, Annalisa Izzo, Yuliia Dramaretska, Roberto Ferrarese, Eva Kling, Oliver Schnell, Sven Nelander, Erwin F. Wagner, Latifa Bakiri, Gaetano Gargiulo, Maria Stella Carro, Massimo Squatrito
Software Mentions: 11
Published: about 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

10.1186/s12864-017-3819-y

RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples
Cited by: 67
Author(s): Petr V. Nazarov, Arnaud Muller, Tony Kaoma, Nathalie Nicot, Cristina Máximo, Philippe Birembaut, Nhan L. Tran, Gunnar Dittmar, Laurent Vallar
Software Mentions: 11
Published: over 9 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

10.3389/fimmu.2021.664845

CD2 Is a Novel Immune-Related Prognostic Biomarker of Invasive Breast Carcinoma That Modulates the Tumor Microenvironment
Cited by: 24
Author(s): Yanzhu Chen, Zhishang Meng, Lin Zhang, Feng Liu
Software Mentions: 11
Published: over 5 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

10.3389/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

10.1186/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

10.3389/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

10.3389/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

10.1534/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

10.1128/mSystems.00200-20

High-Throughput Stool Metaproteomics: Method and Application to Human Specimens
Cited by: 14
Author(s): Carlos Gutiérrez González, Hannah C. Wastyk, Madeline Topf, Christopher D. Gardner, Justin L. Sonnenburg, Joshua E. Elias
Software Mentions: 11
Published: about 6 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

10.1093/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

10.15252/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

10.1002/1878-0261.12117

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

10.1155/2021/6664386

Hypoxia Molecular Characterization in Hepatocellular Carcinoma Identifies One Risk Signature and Two Nomograms for Clinical Management
Cited by: 23
Author(s): Xinwei Han, Long Liu, Taoyuan Lu, Libo Wang, Zhaonan Li, Dechao Jiao, Xinwei Han
Software Mentions: 11
Published: over 5 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/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

10.1155/2021/7404927

A Comprehensive Multiomics Analysis Identified Ubiquilin 4 as a Promising Prognostic Biomarker of Immune-Related Therapy in Pan-Cancer
Cited by: 4
Author(s): Jie Li, Ye Tong, Zhi Wang, Yi Liu, Xiaofeng Dai, Yubing Zhu
Software Mentions: 10
Published: almost 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

10.1371/journal.pone.0224750

Gene expression microarray public dataset reanalysis in chronic obstructive pulmonary disease
Cited by: 3
Author(s): Lavida R. K. Rogers, Madison Verlinde, George I. Mias
Software Mentions: 10
Published: almost 7 years ago

10.1155/2021/6365459

Identification of a Pyroptosis-Related Gene Signature for Prediction of Overall Survival in Lung Adenocarcinoma
Cited by: 14
Author(s): Donghai Zheng, Lv Bian, Minglang Wang, Luoqing Wang, Yilian Wang
Software Mentions: 10
Published: almost 5 years ago

10.1038/s41416-020-0887-6

UGT2B17 modifies drug response in chronic lymphocytic leukaemia
Cited by: 12
Author(s): Éric P. Allain, Michèle Rouleau, Katrina Vanura, Sophie Tremblay, Joanie Vaillancourt, Vincent Bat, Patrick Caron, Lyne Villeneuve, Adrien Labriet, Véronique Turcotte, Trang Le, Medhat Shehata, Susanne Schnabl, Dita Demirtas, Rainer Hubmann, Charles Joly-Beauparlant, Arnaud Droit, Ulrich Jäger, Philipp B. Staber, Éric Lévesque, Chantal Guillemette
Software Mentions: 10
Published: over 6 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

10.1042/BSR20201734

Identification prognosis-associated immune genes in colon adenocarcinoma
Cited by: 16
Author(s): Yifei Miao, Jiangtao Wang, Xueping Ma, Yuan Yang, Denghai Mi
Software Mentions: 10
Published: almost 6 years ago

10.1371/journal.pone.0034594

Heterogeneity of Inflammatory and Cytokine Networks in Chronic Plaque Psoriasis
Cited by: 71
Author(s): William R. Swindell, Xianying Xing, Philip E. Stuart, Cynthia S. Chen, Abhishek Aphale, Rajan P. Nair, John J. Voorhees, James T. Elder, Andrew Johnston, Jóhann E. Guðjónsson
Software Mentions: 10
Published: over 14 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

10.1371/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

10.1371/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

10.7717/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/s12859-021-04055-1

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

10.1155/2020/5858092

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

10.3390/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: about 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

10.18632/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

10.3390/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

10.1186/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/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

10.1038/s41598-021-96236-4

A novel prognostic signature of immune-related lncRNA pairs in lung adenocarcinoma
Cited by: 5
Author(s): Yang Liu, Qiuhong Wu, Xuejiao Fan, Wen Li, Yong Li, Hui Zhu, Qinghua Zhou, Jinming Yu
Software Mentions: 10
Published: about 5 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

10.1155/2008/147563

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: over 18 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

10.3389/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: almost 6 years ago

10.3389/fmolb.2021.649363

Weighted Gene Co-expression Network Analysis Identifies CALD1 as a Biomarker Related to M2 Macrophages Infiltration in Stage III and IV Mismatch Repair-Proficient Colorectal Carcinoma
Cited by: 7
Author(s): Hongliang Zheng, Yuge Bai, Jingui Wang, Shanwen Chen, Junling Zhang, Jing Zhu, Yucun Liu, Xin 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

10.3390/cells10050977

Identification of 15 lncRNAs Signature for Predicting Survival Benefit of Advanced Melanoma Patients Treated with Anti-PD-1 Monotherapy
Cited by: 22
Author(s): Jianguo Zhou, Bo Liang, Jianguo Liu, Sanli Jin, Sisi He, Benjamin Frey, Ning Gu, Rainer Fietkau, Markus Hecht, Hu Ma, Udo S. Gaipl
Software Mentions: 10
Published: over 5 years ago

10.3389/fonc.2021.747300

High Throughput Transcriptome Data Analysis and Computational Verification Reveal Immunotherapy Biomarkers of Compound Kushen Injection for Treating Triple-Negative Breast Cancer
Cited by: 2
Author(s): Xinkui Liu, Yang Wu, Yingying Zhang, Dechao Bu, Chao Wu, Shan Lu, Zhihong Huang, Yurong Song, Yi Zhao, Fengying Guo, Peizhi Ye, Changgeng Fu, Liangliang Shen, Jingyuan Zhang, Haojia Wang, Xianchun Duan, Jiarui Wu
Software Mentions: 10
Published: almost 5 years ago

10.3389/fmolb.2021.692530

Ferroptosis-Related Gene Signature and Patterns of Immune Infiltration Predict the Overall Survival in Patients With Lung Adenocarcinoma
Cited by: 5
Author(s): Yuxuan Wang, Weikang Chen, Minqi Zhu, Lei Xian
Software Mentions: 10
Published: about 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

10.1097/MD.0000000000026068

MiRNA-based model for predicting the TMB level in colon adenocarcinoma based on a LASSO logistic regression method
Cited by: 1
Author(s): Zhengtian Li, Lingling Jiang, Rong Zhao, Jun Huang, Weibo Yang, Zhenpei Wen, Bo Zhang, Gang Du
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

10.1126/sciadv.abc3781

Extensive tissue-specific expression variation and novel regulators underlying circadian behavior
Cited by: 21
Author(s): Maria Litovchenko, Antonio C. A. Meireles-Filho, Michael Frochaux, R. Bevers, Alessio Prunotto, Ane Martín Anduaga, Brian Hollis, Vincent Gardeux, Virginie Braman, Julie Russeil, Sebastián Kadener, Matteo Dal Peraro, Bart Deplancke
Software Mentions: 10
Published: over 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

10.1186/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

10.1371/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

10.1111/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

Projects: bioconductor: limma

Science Score: 78/100

Bonuses:

Penalties:

Papers Mentioning limma 7,776