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

10.3389/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: 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

10.3389/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: about 5 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

10.3389/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

10.3389/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

10.1111/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/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

10.3390/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

10.1038/s41598-021-96712-x

Pan-transcriptome identifying master genes and regulation network in response to drought and salt stresses in Alfalfa (Medicago sativa L.)
Cited by: 12
Author(s): César A. Medina, Deborah A. Samac, Long‐Xi Yu
Software Mentions: 11
Published: almost 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

10.1186/1471-2164-9-419

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

10.3389/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

10.1155/2021/6616908

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: about 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: over 19 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

10.1128/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

10.18632/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/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

10.1371/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

10.1155/2021/6664386

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

10.1371/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

10.18632/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

10.1038/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: almost 7 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: about 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

10.3389/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

10.1186/1471-2105-10-74

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

10.1186/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

10.15252/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

10.1074/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/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

10.1016/j.celrep.2020.107908

Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models
Cited by: 174
Author(s): Ying-Wooi Wan, Rami Al‐Ouran, Carl Grant Mangleburg, Thanneer M. Perumal, Tom V. Lee, Katherine S. Allison, Vivek Swarup, Cory C. Funk, Chris Gaiteri, Mariet Allen, Minghui Wang, Sarah M. Neuner, Catherine C. Kaczorowski, Vivek Philip, Gareth R. Howell, Heidi Martini‐Stoica, Hui Zheng, Hongkang Mei, Xiaoyan Zhong, Jungwoo Wren Kim, Valina L. Dawson, Ted M. Dawson, Ping‐Chieh Pao, Li‐Huei Tsai, Jean‐Vianney Haure‐Mirande, Michelle E. Ehrlich, Paramita Chakrabarty, Yona Levites, Xue Wang, Eric B. Dammer, Gyan Srivastava, Sumit Mukherjee, Solveig K. Sieberts, Larsson Omberg, Kristen K. Dang, James A. Eddy, Phil Snyder, Yooree Chae, Sandeep Amberkar, Wenbin Wei, Winston Hide, Christoph Preuß, Ayla Ergün, Philip J. Ebert, David Airey, Sara Mostafavi, Lei Yu, Hans‐Ulrich Klein, Gregory W. Carter, David A. Collier, Todd E. Golde, Aĺlan I. Levey, David A. Bennett, Karol Estrada, T. Matthew Townsend, Bin Zhang, Eric E. Schadt, Philip L. De Jager, Nathan D. Price, Nilüfer Ertekin-Taner, Zhandong Liu, Zhandong Liu, Lara M. Mangravite, Benjamin A. Logsdon
Software Mentions: 11
Published: about 6 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/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: about 9 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

10.1186/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: almost 7 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

10.1016/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/s12935-021-02041-4

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

10.7554/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

10.7554/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

10.3390/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

10.3389/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

10.1038/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/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

10.3389/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

10.3389/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

10.1002/1878-0261.12117

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

10.1002/1878-0261.12134

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

10.1371/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

10.1093/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

10.3390/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

10.1534/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

10.1155/2021/2291899

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

10.1002/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

10.3390/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

10.1155/2020/6539398

Distinguishing Kawasaki Disease from Febrile Infectious Disease Using Gene Pair Signatures
Cited by: 1
Author(s): Jiayong Zhong, Qingsheng Huang, Yanfei Wang, Huan Gao, Hongling Jia, Jun Fan, Huiying Liang
Software Mentions: 10
Published: over 6 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

10.1155/2020/1468980

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

10.3390/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

10.3390/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

10.1038/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

10.1371/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

10.1371/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

10.1111/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

10.1002/1878-0261.12850

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.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.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

10.1002/1878-0261.12747

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

10.1097/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: about 5 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/fonc.2020.01710

Prognostic Implications of Metabolism Related Gene Signature in Cutaneous Melanoma
Cited by: 14
Author(s): Furong Zeng, Juan Su, Cong Peng, Mengting Liao, Shuang Zhao, Ying Guo, Xiang Chen, Guangtong Deng
Software Mentions: 10
Published: almost 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

10.3390/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/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

10.1155/2008/147563

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

10.3390/ijms21051754

MiR&amp;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

10.1016/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

10.3389/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

10.1242/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

10.1038/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: almost 5 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

10.1155/2021/2191709

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

10.3389/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/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

10.1038/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

10.3389/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/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/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

10.3389/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

10.3389/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

10.1186/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.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

10.1111/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/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