bioconductor: limma | Projects | Ecosyste.ms: Papers

10.3389/fgene.2021.632359

Construction of a circRNA-miRNA-mRNA Regulatory Network Reveals Potential Mechanism and Treatment Options for Osteosarcoma
Cited by: 6
Author(s): Yi He, Haiting Zhou, Wei Wang, Haoran Xu, Hao Cheng
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2021.750827

Bioinformatics Analysis Identified miR-584-5p and Key miRNA-mRNA Networks Involved in the Osteogenic Differentiation of Human Periodontal Ligament Stem Cells
Cited by: 2
Author(s): Chengze Wang, Lingling Dong, Ying Wang, Zhiwei Jiang, Jing Zhang, Guoli Yang
Software Mentions: 2
Published: almost 5 years ago

10.3389/fgene.2015.00014

Toxicogenomics profiling of bone marrow from rats treated with topotecan in combination with oxaliplatin: a mechanistic strategy to inform combination toxicity
Cited by: 9
Author(s): Myrtle A. Davis, Jianying Li, Enid M. Knight, Sandy Eldridge, Kellye K. Daniels, Pierre R. Bushel
Software Mentions: 2
Published: over 11 years ago

10.3389/fgene.2021.666106

ESPL1 Is a Novel Prognostic Biomarker Associated With the Malignant Features of Glioma
Cited by: 5
Author(s): Zhendong Liu, Xiaoyu Lian, Xiuru Zhang, Yongjie Zhu, Wang Zhang, Jialin Wang, Hongbo Wang, Binfeng Liu, Zhishuai Ren, Mengjun Zhang, Mingyang Li, Yanzheng Gao
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2020.627459

Construction of Circular RNA–MicroRNA–Messenger RNA Regulatory Network of Recurrent Implantation Failure to Explore Its Potential Pathogenesis
Cited by: 6
Author(s): Jiahuan Luo, Li Zhu, Ning Zhou, Yuanyuan Zhang, Lirong Zhang, Ruopeng Zhang
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2020.595477

Bioinformatics Analysis Reveals an Association Between Cancer Cell Stemness, Gene Mutations, and the Immune Microenvironment in Stomach Adenocarcinoma
Cited by: 16
Author(s): Zaisheng Ye, Miao Zheng, Yi Zeng, Shenghong Wei, Yi Wang, Zhitao Lin, Chen Shu, Ying Xie, Qinqin Zheng, Luchuan Chen
Software Mentions: 2
Published: almost 6 years ago

10.3389/fgene.2020.578143

Key Molecules and Pathways Underlying Sporadic Amyotrophic Lateral Sclerosis: Integrated Analysis on Gene Expression Profiles of Motor Neurons
Cited by: 10
Author(s): Jianing Lin, Pian Huang, Wei-Neng Chen, Cheng-Hui Ye, Huanxing Su, Xiaoli Yao
Software Mentions: 2
Published: almost 6 years ago

10.3389/fgene.2020.605767

The Construction and Analysis of Tumor-Infiltrating Immune Cells and ceRNA Networks in Bladder Cancer
Cited by: 9
Author(s): Aimin Jiang, Na Liu, Shengjie Bai, Jingjing Wang, Huan Gao, Xiaoqiang Zheng, Xiao Fu, Mengdi Ren, Xiaoni Zhang, Tao Tian, Zhiping Ruan, Yu Yao, Xuan Liang
Software Mentions: 2
Published: almost 6 years ago

10.3389/fgene.2020.572194

Identification of Common Differentially Expressed Genes and Potential Therapeutic Targets in Ulcerative Colitis and Rheumatoid Arthritis
Cited by: 9
Author(s): Yueying Chen, Hanyang Li, Lijie Lai, Qi Feng, Jun Shen
Software Mentions: 2
Published: almost 6 years ago

10.3389/fgene.2021.680125

Revisiting an Expression Dataset of Discordant Inflammatory Bowel Disease Twin Pairs Using a Mutation Burden Test Reveals CYP2C18 as a Novel Marker
Cited by: 4
Author(s): Juan Du, Jie Yin, Haojie Du, Jiawei Zhang
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2018.00746

A Comprehensive Analysis of Fibroblast Growth Factor Receptor 2b Signaling on Epithelial Tip Progenitor Cells During Early Mouse Lung Branching Morphogenesis
Cited by: 36
Author(s): Matthew R. Jones, Salma Dilai, Arun Lingampally, Cho-Ming Chao, Soula Danopoulos, Gianni Carraro, Regina T. Mukhametshina, Jochen Wilhelm, Eveline Baumgart-Vogt, Denise Al Alam, Chengshui Chen, Parviz Minoo, Jin San Zhang, Savério Bellusci
Software Mentions: 2
Published: over 7 years ago

10.3389/fgene.2020.578002

CD52 Is a Prognostic Biomarker and Associated With Tumor Microenvironment in Breast Cancer
Cited by: 21
Author(s): Jianxin Wang, Guangchen Zhang, Yang Sui, Yang Zhong, Yinzhu Chu, Hailing Tang, Binbin Guo, Cong Zhang, Changjun Wu
Software Mentions: 2
Published: almost 6 years ago

10.3389/fgene.2020.583629

Identification of Molecular Markers Associated With the Pathophysiology and Treatment of Lupus Nephritis Based on Integrated Transcriptome Analysis
Cited by: 8
Author(s): Meng Yao, Congcong Gao, Chunyi Zhang, Xing Di, Wenfang Liang, Wenbo Sun, Qianqian Wang, Zhaohui Zheng
Software Mentions: 2
Published: almost 6 years ago

10.3389/fgene.2021.685371

Identification of Distinct Molecular Patterns and a Four-Gene Signature in Colon Cancer Based on Invasion-Related Genes
Cited by: 3
Author(s): Yanfang Dong, Tao Shang, HaiXin Ji, Xiukou Zhou, Zhi Chen
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2020.00401

Immune-Related Prognostic Model in Colon Cancer: A Gene Expression-Based Study
Cited by: 4
Author(s): Haojie Yang, Wei Jin, Lun Hua, Dan Gan, Can Cui, Changpeng Han, Zhenyi Wang
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2014.00131

Identification of potential therapeutic targets in a model of neuropathic pain
Cited by: 13
Author(s): Hemalatha B. Raju, Zoë A. Englander, Enrico Capobianco, Nicholas F. Tsinoremas, Jessica K. Lerch
Software Mentions: 2
Published: over 12 years ago

10.3389/fgene.2021.579900

Enhanced Expression of CNTD2/CCNP Predicts Poor Prognosis in Bladder Cancer Based on the GSE13507
Cited by: 0
Author(s): Mancheng Gong, Erlin Song, Guiying Huang, Wenjun Ni, Wenjing Dong, Runqiang Yuan
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2019.00023

Identification of Important Effector Proteins in the FOXJ1 Transcriptional Network Associated With Ciliogenesis and Ciliary Function
Cited by: 23
Author(s): Ishita Mukherjee, Sudipto Roy, Saikat Chakrabarti
Software Mentions: 2
Published: over 7 years ago

10.3389/fimmu.2020.597741

RNA Sequencing Keloid Transcriptome Associates Keloids With Th2, Th1, Th17/Th22, and JAK3-Skewing
Cited by: 43
Author(s): Jianni Wu, Ester Del Duca, Michael M. Espino, Alyssa Gontzes, Inna Cueto, Ning Zhang, Yeriel Estrada, Ana B. Pavel, James G. Krueger, Emma Guttman‐Yassky
Software Mentions: 2
Published: almost 6 years ago

10.3389/fimmu.2020.01933

Construction of a Prognostic Immune Signature for Squamous-Cell Lung Cancer to Predict Survival
Cited by: 6
Author(s): Rui Lian Chen, Jing Zhou, Yang Cao, Liankang Sun, Shan Su, Xiao Jie Deng, Jie Lin, Zhi Wei Xiao, Zhuang Zhong Chen, Si Yu Wang, Li Zhu Lin
Software Mentions: 2
Published: about 6 years ago

10.3389/fimmu.2020.00194

Rheumatoid Arthritis Patients, Both Newly Diagnosed and Methotrexate Treated, Show More DNA Methylation Differences in CD4+ Memory Than in CD4+ Naïve T Cells
Cited by: 14
Author(s): Kari Guderud, Line Hagen Sunde, Siri Tennebø Flåm, Marthe Thoresen Mæhlen, Maria D Mjaavatten, Siri Lillegraven, Anna‐Birgitte Aga, Ida Marie Evenrød, Ellen Sauar Norli, Bettina Kulle Andreassen, Sören Franzenburg, André Franke, Espen A. Haavardsholm, Simon Rayner, Kristina Gervin, Benedicte A. Lie
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2021.705308

RGC-32 Acts as a Hub to Regulate the Transcriptomic Changes Associated With Astrocyte Development and Reactive Astrocytosis
Cited by: 1
Author(s): Alexandru Tatomir, Austin Beltrand, Vinh Nguyen, Jean-Paul Courneya, Dallas Boodhoo, Cornelia Cudrici, Dafin F. Mureşanu, Violeta Rus, Tudor C. Badea, Horea Rus
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2021.665407

A Novel Immune-Related Seventeen-Gene Signature for Predicting Early Stage Lung Squamous Cell Carcinoma Prognosis
Cited by: 16
Author(s): Tao Fan, Zhiliang Lu, Yu Liu, Li-Yu Wang, He Tian, Zheng Yang, Bo Zheng, Liyan Xue, Fengwei Tan, Qi Xue, Shugeng Gao, Chunxiang Li, Jie He
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2019.01535

IL-6 Mediated Transcriptional Programming of Naïve CD4+ T Cells in Early Rheumatoid Arthritis Drives Dysregulated Effector Function
Cited by: 14
Author(s): Laura A. Ridgley, Amy E. Anderson, Nicola J Maney, Najib Naamane, Andrew Skelton, Catherine A. Lawson, Paul Emery, John D. Isaacs, Ruaidhrı́ J. Carmody, Arthur G. Pratt
Software Mentions: 2
Published: about 7 years ago

10.3389/fimmu.2020.584048

Foxp3+ Regulatory T Cells Inhibit CCl4-Induced Liver Inflammation and Fibrosis by Regulating Tissue Cellular Immunity
Cited by: 20
Author(s): Yoshinobu Ikeno, Daiya Ohara, Yusuke Takeuchi, Hidenobu Watanabe, Gen Kondoh, Kojiro Taura, Shinji Üemoto, Keiji Hirota
Software Mentions: 2
Published: almost 6 years ago

10.3389/fimmu.2021.697157

Integrated Bioinformatics and Validation Reveal Potential Biomarkers Associated With Progression of Primary Sjögren’s Syndrome
Cited by: 16
Author(s): Ning Li, Lei Li, Mengyao Wu, Yusi Li, Jie Yang, Yi‐Cheng Wu, Hui Xu, Danyang Luo, Youhe Gao, Xiaochun Fei, Liting Jiang
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2019.00468

CD117 (c-Kit) Is Expressed During CD8+ T Cell Priming and Stratifies Sensitivity to Apoptosis According to Strength of TCR Engagement
Cited by: 19
Author(s): Guido Frumento, Jianmin Zuo, Kriti Verma, Wayne Croft, Pradeep Ramagiri, Frederick Chen, Paul Moss
Software Mentions: 2
Published: over 7 years ago

10.3389/fimmu.2020.00075

NK Cell Priming From Endogenous Homeostatic Signals Is Modulated by CIS
Cited by: 24
Author(s): Rebecca B. Delconte, Geoffrey Guittard, Wilford Goh, Soroor Hediyeh-Zadeh, Robert J. Hennessy, Jai Rautela, Melissa J. Davis, Fernando Souza-Fonseca-Guimarães, Jacques A. Nunès, Nicholas D. Huntington
Software Mentions: 2
Published: over 6 years ago

10.3389/fmed.2021.674523

Expression and Pathogenic Analysis of Integrin Family Genes in Systemic Sclerosis
Cited by: 4
Author(s): Di Xu, Ting Li, Ke Wang, Rong Mu
Software Mentions: 2
Published: about 5 years ago

10.3389/fmed.2020.619453

Association of Cigarette Smoking, COPD, and Lung Cancer With Expression of SARS-CoV-2 Entry Genes in Human Airway Epithelial Cells
Cited by: 11
Author(s): Youlun Ju, Brigitte Kasper, Frank Petersen, Xinhua Yu
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2021.727104

The Role of graRS in Regulating Virulence and Antimicrobial Resistance in Methicillin-Resistant Staphylococcus aureus
Cited by: 4
Author(s): Le Chen, Zihui Wang, Tao Xu, Hongfei Ge, Fang Zhou, Xiaoyi Zhu, Xianhui Li, Di Qu, Cheng Zheng, Yang Wu, Keqing Zhao
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2021.706934

The Small Protein YmoA Controls the Csr System and Adjusts Expression of Virulence-Relevant Traits of Yersinia pseudotuberculosis
Cited by: 5
Author(s): Katja Böhme, Ann Kathrin Heroven, Stephanie Lobedann, Yuzhu Guo, Anne-Sophie Stolle, Petra Dersch
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2021.724676

A Global Analysis of Photoreceptor-Mediated Transcriptional Changes Reveals the Intricate Relationship Between Central Metabolism and DNA Repair in the Filamentous Fungus Trichoderma atroviride
Cited by: 7
Author(s): Enrique Pola-Sánchez, José Manuel Villalobos-Escobedo, Nohemí Carreras-Villaseñor, Pedro Martı́nez-Hernández, Emma Beatriz Beltrán-Hernández, Edgardo Ulises Esquivel-Naranjo, Alfredo Herrera‐Estrella
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2020.01635

DNA-Binding and Transcription Activation by Unphosphorylated Response Regulator AgrR From Cupriavidus metallidurans Involved in Silver Resistance
Cited by: 11
Author(s): Muntasir Ali, Ann Provoost, Kristel Mijnendonckx, Rob Van Houdt, Daniël Charlier
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2019.00092

Exposure to Sub-inhibitory Concentrations of the Chemosensitizer 1-(1-Naphthylmethyl)-Piperazine Creates Membrane Destabilization in Multi-Drug Resistant Klebsiella pneumoniae
Cited by: 19
Author(s): João Anes, Sathesh K Sivasankaran, Dechamma Mundanda Muthappa, Séamus Fanning, Shabarinath Srikumar
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2014.00402

Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification
Cited by: 36
Author(s): David H. Keating, Yaoping Zhang, Irene M. Ong, Sean J. McIlwain, Eduardo Morales, Jeffrey A. Grass, Mary Tremaine, William Bothfeld, Alan Higbee, Arne Ulbrich, Allison J. Balloon, Michael S. Westphall, Josh Aldrich, Mary Lipton, Joonhoon Kim, Oleg V. Moskvin, Yury V. Bukhman, Joshua J. Coon, Patricia J. Kiley, Donna M. Bates, Robert Landick
Software Mentions: 2
Published: about 12 years ago

10.3389/fmicb.2019.02303

Caecal Microbiota of Experimentally Campylobacter jejuni-Infected Chickens at Different Ages
Cited by: 18
Author(s): Julia Hankel, Klaus Jung, Henrike Kuder, Birgit Keller, Christoph A. Keller, Eric Galvez, Till Strowig, Christian Visscher
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2021.680101

Dysbiosis of Gut Microbiota in Patients With Acute Myocardial Infarction
Cited by: 38
Author(s): Ying Han, Zhaowei Gong, Guizhi Sun, Jing Xu, Changlu Qi, Weiju Sun, Huijie Jiang, Peigang Cao, Hong Ju
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2021.663019

Pathological Features of Enterovirus 71-Associated Brain and Lung Damage in Mice Based on Quantitative Proteomic Analysis
Cited by: 9
Author(s): Yuefei Jin, Dong Liu, Tiantian Sun, Yue Du, Yanlei Gao, Ronghua Ding, Wangquan Ji, Weiguo Zhang, Haiyan Yang, Shuaiyin Chen, Guangcai Duan
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2015.00171

Biomarker-based classification of bacterial and fungal whole-blood infections in a genome-wide expression study
Cited by: 24
Author(s): Andreas Dix, Kerstin Hünniger, Michael Weber, Reinhard Guthke, Oliver Kurzai, Jörg Linde
Software Mentions: 2
Published: over 11 years ago

10.3389/fmicb.2021.687888

Thermonucleases Contribute to Staphylococcus aureus Biofilm Formation in Implant-Associated Infections–A Redundant and Complementary Story
Cited by: 15
Author(s): Jia Yu, Feng Jiang, Feiyang Zhang, Musha Hamushan, Jiafei Du, Yanjie Mao, Qiaojie Wang, Pei Han, Jin Tang, Hao Shen
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2019.00429

Comparative Description of the Expression Profile of Interferon-Stimulated Genes in Multiple Cell Lineages Targeted by HIV-1 Infection
Cited by: 17
Author(s): Hirofumi Aso, Jumpei Ito, Yoshio Koyanagi, Kei Sato
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2020.01973

Monocyte and Macrophage-Mediated Pathology and Protective Immunity During Schistosomiasis
Cited by: 15
Author(s): Camila Oliveira Silva Souza, Luiz Gustavo Gardinassi, Vanderlei Rodrigues, Lúcia Helena Faccioli
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2017.01556

Transcriptomic Analyses Reveal Differential Gene Expression of Immune and Cell Death Pathways in the Brains of Mice Infected with West Nile Virus and Chikungunya Virus
Cited by: 21
Author(s): Stephanie M. Lim, Henk-Jan van den Ham, Minoushka Oduber, Eurydice Martina, Fatiha Zaaraoui-Boutahar, Jeroen M. Roose, Wilfred F. J. van IJcken, Albert D. M. E. Osterhaus, Arno C. Andeweg, Penelope Koraka, Byron Martina
Software Mentions: 2
Published: about 9 years ago

10.3389/fmicb.2019.01247

Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum
Cited by: 15
Author(s): Wonyong Kim, Brad Cavinder, Robert H. Proctor, Kerry O’Donnell, Jeffrey P. Townsend, Frances Trail
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2018.00361

ArgR of Streptomyces coelicolor Is a Pleiotropic Transcriptional Regulator: Effect on the Transcriptome, Antibiotic Production, and Differentiation in Liquid Cultures
Cited by: 17
Author(s): Alma Botas, Rosario Pérez‐Redondo, Antonio Rodríguez‐García, Rubén Álvarez-Álvarez, Paula Yagüe, Ángel Manteca, Paloma Liras
Software Mentions: 2
Published: over 8 years ago

10.3389/fmolb.2021.567730

A Novel Nine Apoptosis-Related Genes Signature Predicting Overall Survival for Kidney Renal Clear Cell Carcinoma and its Associations with Immune Infiltration
Cited by: 13
Author(s): Yi Wang, Yinhao Chen, Bingye Zhu
Software Mentions: 2
Published: over 5 years ago

10.3389/fonc.2020.615472

Multi-Omics Analysis of Brain Metastasis Outcomes Following Craniotomy
Cited by: 28
Author(s): Jing Su, Qianqian Song, Shadi Qasem, Stacey S. O’Neill, Jingyun Lee, Cristina M. Furdui, Boris Pasche, Linda J. Metheny-Barlow, Adrianna Henson Masters, Hui-Wen Lo, Fei Xing, Kounosuke Watabe, Lance D. Miller, Stephen B. Tatter, Adrian W. Laxton, Christopher T. Whitlow, Michael D. Chan, M. Soike, Jimmy Ruiz
Software Mentions: 2
Published: over 5 years ago

10.3389/fonc.2020.618902

Comprehensively Analyzed Macrophage-Regulated Genes Indicate That PSMA2 Promotes Colorectal Cancer Progression
Cited by: 6
Author(s): J. Qi, Zhiqiu Hu, Shaoqun Liu, Fan Li, Sheng Wang, Wuqing Wang, Xia Sheng, Feng Li
Software Mentions: 2
Published: over 5 years ago

10.3389/fonc.2020.599816

Identification of Iron Metabolism-Related Gene Signatures for Predicting the Prognosis of Patients With Sarcomas
Cited by: 6
Author(s): Jianyi Li, Chuan Hu, Yukun Du, Xiaojie Tang, Chen Shao, Tongshuai Xu, Zheng Zhao, Huiqiang Hu, Yingyi Sheng, Jianwei Guo, Yongming Xi
Software Mentions: 2
Published: over 5 years ago

10.3389/fonc.2020.01421

Analysis of Differentially Expressed Long Non-coding RNAs and the Associated TF-mRNA Network in Tongue Squamous Cell Carcinoma
Cited by: 6
Author(s): Mi Zhang, Zexi Chen, Sihui Zhang, Ling Wu, Yinghui Jie, Ying Liao, Yue Huang, Chen Chen Jiang, Bin Shi
Software Mentions: 2
Published: about 6 years ago

10.3389/fonc.2020.01532

Complement C7 (C7), a Potential Tumor Suppressor, Is an Immune-Related Prognostic Biomarker in Prostate Cancer (PC)
Cited by: 12
Author(s): Zhao Chun-hua, Xin Yan, Guo-Wei Du, Kurerban Tuoheti, Xiaojie Bai, Hua-Hui Wu, Ren‐Jie Zhang, Guan-Fa Xiao, Tong-Zu Liu
Software Mentions: 2
Published: about 6 years ago

10.3389/fonc.2021.583083

COL5A2 Promotes Proliferation and Invasion in Prostate Cancer and Is One of Seven Gleason-Related Genes That Predict Recurrence-Free Survival
Cited by: 26
Author(s): Xiaohan Ren, Xinglin Chen, Kai Fang, Xu Zhang, Xiao‐Hong Wei, Tong-Tong Zhang, Guangyao Li, Zhongwen Lü, Ninghong Song, Shangqian Wang, Chao Qin
Software Mentions: 2
Published: over 5 years ago

10.3389/fonc.2019.01474

Comprehensive Analysis of Competitive Endogenous RNAs Network, Being Associated With Esophageal Squamous Cell Carcinoma and Its Emerging Role in Head and Neck Squamous Cell Carcinoma
Cited by: 11
Author(s): Donghu Yu, Xiaolan Ruan, Jingyu Huang, Weidong Hu, Chen Chen, Yu Xu, Jian Hou, Sheng Li
Software Mentions: 2
Published: over 6 years ago

10.3389/fonc.2021.626663

Construction of Novel lncRNA–miRNA–mRNA Network Associated With Recurrence and Identification of Immune-Related Potential Regulatory Axis in Hepatocellular Carcinoma
Cited by: 22
Author(s): Tian Zhan, Xiang Gao, Guoguang Wang, Ли Фан, Jian Shen, Lu Chen, Lei Xu, Yuan Li, Jianping Zhang
Software Mentions: 2
Published: about 5 years ago

10.3389/fonc.2021.676124

Malignant Tumor Purity Reveals the Driven and Prognostic Role of CD3E in Low-Grade Glioma Microenvironment
Cited by: 10
Author(s): Xiuqin Lu, Chuanyu Li, Wenhao Xu, Yuanyuan Wu, Jian Wang, Shuxian Chen, Ye Zhang, Hao Huang, Haiyang Huang, Wangrui Liu
Software Mentions: 2
Published: about 5 years ago

10.3389/fonc.2020.01147

Development and Validation of a Gene Signature for Prediction of Relapse in Stage I Testicular Germ Cell Tumors
Cited by: 2
Author(s): Jianguo Zhou, Jie Yang, Sanli Jin, Siyu Xiao, Lei Shi, Zhang Ting-you, Hu Ma, Udo S. Gaipl
Software Mentions: 2
Published: about 6 years ago

10.3389/fonc.2021.627504

A New RBPs-Related Signature Predicts the Prognosis of Colon Adenocarcinoma Patients
Cited by: 16
Author(s): Kai‐Kai Chang, Chong Yuan, Xueguang Liu
Software Mentions: 2
Published: over 5 years ago

10.3389/fonc.2021.615967

Identification of Proteins Deregulated by Platinum-Based Chemotherapy as Novel Biomarkers and Therapeutic Targets in Non-Small Cell Lung Cancer
Cited by: 4
Author(s): Sarah-Louise Ryan, Keyur A. Dave, Sam Beard, Martina Gyimesi, M. McTaggart, Katherine B. Sahin, Christopher J. Molloy, Neha S. Gandhi, Eric D. Boittier, Connor O’Leary, Esha Shah, Emma Bolderson, Anne‐Marie Baird, Derek J. Richard, Kenneth J. O’Byrne, Mark N. Adams
Software Mentions: 2
Published: over 5 years ago

10.3389/fonc.2021.634075

Development and Validation of Novel Biomarkers Related to M2 Macrophages Infiltration by Weighted Gene Co-Expression Network Analysis in Prostate Cancer
Cited by: 7
Author(s): Ning Xu, Ru‐Nan Dong, Tingting Lin, Lin Tian, Yunzhi Lin, Shao‐Hao Chen, Jiang Zhu, Zhi‐Bin Ke, Fei Huang, Ye‐Hui Chen, Xue-Yi Xue
Software Mentions: 2
Published: about 5 years ago

10.3389/fonc.2021.714866

Identification of Hub Genes Related to Liver Metastasis of Colorectal Cancer by Integrative Analysis
Cited by: 9
Author(s): Sicheng Liu, Yaguang Zhang, Su Zhang, Lei Qiu, Bo Zhang, Junhong Han
Software Mentions: 2
Published: about 5 years ago

10.3389/fonc.2021.698835

SNAP25 Inhibits Glioma Progression by Regulating Synapse Plasticity via GLS-Mediated Glutaminolysis
Cited by: 13
Author(s): Qiongzhen Huang, Changlin Lian, Yaoyuan Dong, Huijun Zeng, Boyang Liu, Ningbo Xu, Zhenyan He
Software Mentions: 2
Published: about 5 years ago

10.3389/fonc.2020.00183

Genomics and Prognosis Analysis of Epithelial-Mesenchymal Transition in Glioma
Cited by: 54
Author(s): Chuming Tao, Kai Huang, Jin Shi, Qing Hu, Kuangxun Li, Xingen Zhu
Software Mentions: 2
Published: over 6 years ago

10.3389/fonc.2020.591739

Prognostic Signatures Based on Thirteen Immune-Related Genes in Colorectal Cancer
Cited by: 15
Author(s): Xiaobo Ma, Yuanyuan Xu, Min Zhu, Lu Wang
Software Mentions: 2
Published: over 5 years ago

10.3389/fonc.2020.547942

CircRNA_000864 Upregulates B-cell Translocation Gene 2 Expression and Represses Migration and Invasion in Pancreatic Cancer Cells by Binding to miR-361-3p
Cited by: 20
Author(s): Lei Huang, Junxiang Han, Huifan Yu, Jialing Liu, Lili Gui, Zhengkun Wu, Xinxu Zhao, Shiqi Su, Gaohang Fu, Fēi Li
Software Mentions: 2
Published: over 5 years ago

10.3389/fonc.2020.00605

LUM Expression and Its Prognostic Significance in Gastric Cancer
Cited by: 32
Author(s): Xiaowei Chen, Xin Li, Xin Hu, Fei Jiang, Yan Shen, Rui Xu, Leilei Wu, Pingmin Wei, Xiaobing Shen
Software Mentions: 2
Published: over 6 years ago

10.3389/fonc.2021.692774

An Adaptive Transfer-Learning-Based Deep Cox Neural Network for Hepatocellular Carcinoma Prognosis Prediction
Cited by: 7
Author(s): Hua Chai, Xia Long, Lei Zhang, Jiarui Yang, Zhongyue Zhang, Xiangjun Qian, Yuedong Yang, Weidong Pan
Software Mentions: 2
Published: almost 5 years ago

10.3389/fonc.2020.575737

Combination of T-Cell Bispecific Antibodies With PD-L1 Checkpoint Inhibition Elicits Superior Anti-Tumor Activity
Cited by: 25
Author(s): Johannes Sam, Sara Colombetti, Tanja Fauti, Andreas Roller, Marlene Biehl, Linda Fahrni, Valeria Nicolini, Mario Perro, Tapan K. Nayak, Esther Bommer, Anne Schoenle, Μaria Karagianni, Marine Le Clech, Nathalie Steinhoff, Christian Klein, Pablo Umaña, Marina Bacac
Software Mentions: 2
Published: almost 6 years ago

10.3389/fonc.2021.711736

A Novel Prognostic Model Based on Autophagy-Related Long Non-Coding RNAs for Clear Cell Renal Cell Carcinoma
Cited by: 11
Author(s): Xinyuan Li, Haitao Yu, Zongjie Wei, Xin Gou, Simin Liang, Fu Liu
Software Mentions: 2
Published: about 5 years ago

10.3389/fped.2021.576585

Identification of Potential Diagnostic Gene Targets for Pediatric Sepsis Based on Bioinformatics and Machine Learning
Cited by: 2
Author(s): Ying Qiao, Bo Zhang, Ying Liu
Software Mentions: 2
Published: over 5 years ago

10.3389/fped.2021.617298

Differential Expression Profiles and Functional Analysis of Long Non-coding RNAs in Children With Dilated Cardiomyopathy
Cited by: 0
Author(s): Dongxiao Cai, Bo Han, Wei Sun, Li Zhang, Jing Wang, Diandong Jiang, Honglei Jia
Software Mentions: 2
Published: over 5 years ago

10.3389/fphar.2020.622212

Ursolic Acid Regulates Cell Cycle and Proliferation in Colon Adenocarcinoma by Suppressing Cyclin B1
Cited by: 9
Author(s): Minhui Yang, Changxiao Hu, Yibo Cao, Wei Liang, Xiangdong Yang, Tianbao Xiao
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-018-1451-z

Post-translational buffering leads to convergent protein expression levels between primates
Cited by: 32
Author(s): Sidney H. Wang, Chiaowen Joyce Hsiao, Zia Khan, Jonathan K. Pritchard
Software Mentions: 2
Published: about 8 years ago

10.1186/s13059-020-02258-y

Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals
Cited by: 84
Author(s): Guiomar Martín, Yamile Márquez, Federica Mantica, Paula Duque, Manuel Irimia
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-021-02436-6

Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers
Cited by: 3
Author(s): Marie Zufferey, Yuanlong Liu, Daniele Tavernari, Marco Mina, Giovanni Ciriello
Software Mentions: 2
Published: about 5 years ago

10.1186/gm519

miR-638 regulates gene expression networks associated with emphysematous lung destruction
Cited by: 63
Author(s): Stephanie A. Christenson, Corry‐Anke Brandsma, Joshua D. Campbell, Darryl A. Knight, Dmitri V. Pechkovsky, James C. Hogg, Wim Timens, Dirkje S. Postma, Marc E. Lenburg, Avrum Spira
Software Mentions: 2
Published: over 13 years ago

10.1186/gm550

Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity
Cited by: 10
Author(s): Nadia M. Penrod, Casey S. Greene, Jason H. Moore
Software Mentions: 2
Published: over 12 years ago

10.1186/s13073-014-0075-5

Alteration in basal and depolarization induced transcriptional network in iPSC derived neurons from Timothy syndrome
Cited by: 72
Author(s): Yuan Tian, Irina Voineagu, Sergiu P. Pașca, Hyejung Won, Vijayendran Chandran, Steve Horvath, Ricardo E. Dolmetsch, Daniel H. Geschwind
Software Mentions: 2
Published: almost 12 years ago

10.1186/s13073-014-0097-z

Linking hypothetical knowledge patterns to disease molecular signatures for biomarker discovery in Alzheimer’s disease
Cited by: 7
Author(s): Ashutosh Malhotra, Erfan Younesi, Shweta Bagewadi, Martin Hofmann‐Apitius
Software Mentions: 2
Published: almost 12 years ago

10.1186/s13073-016-0345-5

Characterisation of the global transcriptional response to heat shock and the impact of individual genetic variation
Cited by: 3
Author(s): Peter Humburg, Narelle J. Maugeri, Wanseon Lee, Bert Mohr, Julian C. Knight
Software Mentions: 2
Published: about 10 years ago

10.1186/s13073-016-0347-3

Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model
Cited by: 34
Author(s): Nils Grabole, Jitao David Zhang, Stefan Aigner, Nadine Ruderisch, Veronica Costa, Felix Weber, Michel Theron, Nikolaos Berntenis, Olivia Spleiss, Martin Ebeling, G Yeo, Ravi Jagasia, Anna Kiialainen
Software Mentions: 2
Published: almost 10 years ago

10.1186/s13073-016-0381-1

Allele-specific expression in the human heart and its application to postoperative atrial fibrillation and myocardial ischemia
Cited by: 6
Author(s): Martin I. Sigurdsson, Louis A. Saddic, Mahyar Heydarpour, Tzuu-Wang Chang, Prem Shekar, Sary F. Aranki, Gregory S. Couper, Stanton K. Shernan, J. G. Seidman, Simon C. Body, Jochen D. Muehlschlegel
Software Mentions: 2
Published: almost 10 years ago

10.1186/s13073-017-0443-z

DNA methylation-based chromatin compartments and ChIP-seq profiles reveal transcriptional drivers of prostate carcinogenesis
Cited by: 15
Author(s): Poppy Simmonds, Erick Loomis, Ed Curry
Software Mentions: 2
Published: over 9 years ago

10.1186/s13073-020-00759-w

Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma
Cited by: 14
Author(s): Emma E. Thompson, Quynh Dang, Blair Mitchell-Handley, Kavitha Rajendran, Sumati Ram-Mohan, Julian Solway, Carole Ober, Ramaswamy Krishnan
Software Mentions: 2
Published: about 6 years ago

10.1186/s13073-020-00808-4

Identification of epigenome-wide DNA methylation differences between carriers of APOE ε4 and APOE ε2 alleles
Cited by: 18
Author(s): Richard M Martin, Kadi Vaher, Mairead Lesley Bermingham, Stewart W. Morris, Andrew D. Bretherick, Yanni Zeng, Konrad Rawlik, Carmen Amador, Archie Campbell, Chris Haley, Caroline Hayward, David J. Porteous, Andrew M. McIntosh, Riccardo E. Marioni, Kathryn Evans
Software Mentions: 2
Published: over 5 years ago

10.1016/j.gpb.2020.02.002

CRISPR Screens Identify Essential Cell Growth Mediators in BRAF Inhibitor-resistant Melanoma
Cited by: 14
Author(s): Ziyi Li, Binbin Wang, Shengqing Gu, Peng Jiang, Avinash Sahu, Chen-Hao Chen, Tong Han, Sailing Shi, Xiaoqing Wang, Nicole Traugh, Hailing Liu, Yin Liu, Qiu Liang Wu, Myles Brown, Tengfei Xiao, Genevieve M. Boland, X. Shirley Liu
Software Mentions: 2
Published: over 6 years ago

10.1080/19490976.2019.1651596

Mucosal IgG in inflammatory bowel disease – a question of (sub)class?
Cited by: 10
Author(s): Tomas Castro‐Dopico, Menna R. Clatworthy
Software Mentions: 2
Published: about 7 years ago

10.1002/hsr2.202

A prognostic risk model based on immune‐related genes predicts overall survival of patients with hepatocellular carcinoma
Cited by: 2
Author(s): Banglun Pan, Lin Liu, Wei Li
Software Mentions: 2
Published: almost 6 years ago

10.1002/hep.29877

Impact of Interferon Lambda 4 Genotype on Interferon‐Stimulated Gene Expression During Direct‐Acting Antiviral Therapy for Hepatitis C
Cited by: 17
Author(s): Narayan Ramamurthy, Emanuele Marchi, Azim Ansari, Vincent Pedergnana, Angela R. McLean, Emma Hudson, Rory Bowden, Chris C. A. Spencer, Eleanor Barnes, Paul Klenerman
Software Mentions: 2
Published: about 8 years ago

10.1038/s41438-019-0119-5

What makes turnips: anatomy, physiology and transcriptome during early stages of its hypocotyl-tuber development
Cited by: 23
Author(s): Mengyang Li, Niccolò Bassetti, Stefan Petrasch, Ningwen Zhang, Johan Bucher, Shuxing Shen, Zhao Jian-jun, Guusje Bonnema
Software Mentions: 2
Published: over 7 years ago

10.1038/s41438-019-0212-9

Genome-wide transcriptome analysis reveals molecular pathways involved in leafy head formation of Chinese cabbage (Brassica rapa)
Cited by: 10
Author(s): Xiaoxue Sun, Ram Kumar Basnet, Zhichun Yan, Johan Bucher, Chengcheng Cai, Jianjun Zhao, Guusje Bonnema
Software Mentions: 2
Published: almost 7 years ago

10.1002/iid3.375

Data mining combined with experiments to validate CEP55 as a prognostic biomarker in colorectal cancer
Cited by: 8
Author(s): Lin Kang, Xiaojian Zhu, Chen Luo, Fanqin Bu, Jinfeng Zhu, Zhengming Zhu
Software Mentions: 2
Published: almost 6 years ago

10.1111/imcb.12399

GPR43 regulates marginal zone B‐cell responses to foreign and endogenous antigens
Cited by: 9
Author(s): Leona Rohrbeck, Mónika Ádori, Shan Wang, Chenfei He, Christopher Andrew Tibbitt, Mark Chernyshev, Madle Sirel, Ulf Ribacke, Ben Murrell, Mohammad Bohlooly‐Y, Mikael C. I. Karlsson, Gunilla B. Karlsson Hedestam, Jonathan M. Coquet
Software Mentions: 2
Published: almost 6 years ago

10.1172/jci.insight.93739

Neonatal and adult recent thymic emigrants produce IL-8 and express complement receptors CR1 and CR2
Cited by: 43
Author(s): Marcin Ł. Pękalski, Arcadio Rubio Garćıa, Ricardo C. Ferreira, Daniel B. Rainbow, Deborah J. Smyth, Meghavi Mashar, Jane Brady, Natalia Savinykh, Xaquín Castro Dopico, Sumiyya Mahmood, Simon Duley, Helen Stevens, Neil Walker, Antony J. Cutler, Frank Waldron‐Lynch, David B. Dunger, Claire Shannon-Lowe, Alasdair Coles, Joanne L. Jones, Chris Wallace, John A. Todd, Linda S. Wicker
Software Mentions: 2
Published: about 9 years ago

10.1038/srep23002

Effects of Systemically Administered Hydrocortisone on the Human Immunome
Cited by: 113
Author(s): Matthew J. Olnes, Yuri Kotliarov, Angélique Biancotto, Foo Cheung, Jinguo Chen, Rongye Shi, Huizhi Zhou, Ena Wang, John S. Tsang, Robert B. Nussenblatt
Software Mentions: 2
Published: over 10 years ago

10.1038/srep24141

Implication of Long noncoding RNAs in the endothelial cell response to hypoxia revealed by RNA-sequencing
Cited by: 113
Author(s): Christine Voellenkle, José Manuel García-Manteiga, Simona Pedrotti, Alessandra Perfetti, Ilario De Toma, D. Da Silva, Biagina Maimone, Simona Greco, Pasquale Fasanaro, Pasquale Creo, Germana Zaccagnini, Carlo Gaetano, Fabio Martelli
Software Mentions: 2
Published: over 10 years ago

10.1038/srep26822

Analysis of the dynamic co-expression network of heart regeneration in the zebrafish
Cited by: 27
Author(s): Sophie Rodius, Ganna Androsova, Lou Götz, Robin Liechti, Isaac Crespo, Susanne Merz, Petr V. Nazarov, Nigel Klein, Céline Jeanty, Juan Manuel González‐Rosa, Arnaud Muller, François Bernardin, Simone P. Niclou, Laurent Vallar, Nadia Mercader, Mark Ibberson, Ioannis Xénarios, Francisco Azuaje
Software Mentions: 2
Published: over 10 years ago

10.1038/srep28261

Fibroblasts profiling in scarring trachoma identifies IL-6 as a functional component of a fibroblast-macrophage pro-fibrotic and pro-inflammatory feedback loop
Cited by: 28
Author(s): Jenny Z. Kechagia, Daniel G. Ezra, Matthew J. Burton, Maryse Bailly
Software Mentions: 2
Published: about 10 years ago

10.1038/srep28415

The space of enzyme regulation in HeLa cells can be inferred from its intracellular metabolome
Cited by: 13
Author(s): Christian Diener, Felipe Muñoz-Gonzalez, Sergio Encarnación, Osbaldo Resendis‐Antonio
Software Mentions: 2
Published: about 10 years ago

10.1038/srep29604

Decreased expression of Calpain-9 predicts unfavorable prognosis in patients with gastric cancer
Cited by: 24
Author(s): Peike Peng, Weicheng Wu, Junjie Zhao, Shushu Song, Xuefei Wang, Dongwei Jia, Miaomiao Shao, Mingming Zhang, Lili Li, Lan Wang, Fangfang Duan, Ran Zhao, Caiting Yang, Hao Wu, Jie Zhang, Zhongliang Shen, Yuanyuan Ruan, Jianxin Gu
Software Mentions: 2
Published: about 10 years ago

Projects: bioconductor: limma

Science Score: 78/100

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Papers Mentioning limma 7,776