Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: limma

https://packages.ecosyste.ms/registries/bioconductor.org/packages/limma

Linear Models for Microarray Data
3 versions
Latest release: about 1 year ago
314 dependent packages
4,663,292 downloads total

Papers Mentioning limma 7,776

10.3389/fnins.2020.00081
Identification of Blood Circular RNAs as Potential Biomarkers for Acute Ischemic Stroke
Cited by: 31
Author(s): Dan Lu, Eric S. Ho, Hongcheng Mai, Jiankun Zang, Yanfang Liu, Yufeng Li, Bing Yang, Yan Ding, Chi Kwan Tsang, Anding Xu
Software Mentions: 2
Published: almost 5 years ago
10.3389/fnins.2021.678548
Gene Expression Analysis in Three Posttraumatic Stress Disorder Cohorts Implicates Inflammation and Innate Immunity Pathways and Uncovers Shared Genetic Risk With Major Depressive Disorder
Cited by: 10
Author(s): Melanie E. Garrett, Xue Qin, Divya Mehta, Michelle F. Dennis, Christine E. Marx, Gerald A. Grant, VA Mid-Atlantic Mirecc Workgroup, Ptsd Initiative, Injury, Murray B. Stein, Nathan A. Kimbrel, Jean C. Beckham, Michael A. Hauser, Allison Ashley‐Koch
Software Mentions: 2
Published: over 3 years ago
10.3389/fnins.2014.00346
The Drosophila surface glia transcriptome: evolutionary conserved blood-brain barrier processes
Cited by: 108
Author(s): Michael K. DeSalvo, Samantha J. Hindle, Zeid M. Rusan, Souvinh Orng, Mark Eddison, Kyle Halliwill, Roland J. Bainton
Software Mentions: 2
Published: about 10 years ago
10.3389/fonc.2021.746763
A Novel Seven Gene Signature-Based Prognostic Model to Predict Distant Metastasis of Lymph Node-Negative Triple-Negative Breast Cancer
Cited by: 4
Author(s): Weiping Peng, Caijin Lin, Shanshan Jing, Guan-Hua Su, Xi Jin, Gen-Hong Di, Zhi‐Ming Shao
Software Mentions: 2
Published: about 3 years ago
10.3389/fonc.2021.636093
Identification of Methylation-Regulated Differentially Expressed Genes and Related Pathways in Hepatocellular Carcinoma: A Study Based on TCGA Database and Bioinformatics Analysis
Cited by: 12
Author(s): Liang Yu, Bin Ma, Peng Jiang, Hongmei Yang
Software Mentions: 2
Published: over 3 years ago
10.3389/fonc.2020.00097
Targeting Metabolic Deregulation Landscapes in Breast Cancer Subtypes
Cited by: 15
Author(s): Erandi A. Serrano-Carbajal, Jesús Espinal-Enríquez, Enrique Hernández‐Lemus
Software Mentions: 2
Published: almost 5 years ago
10.3389/fphar.2020.575765
Regulatory Master Genes Identification and Drug Repositioning by Integrative mRNA-miRNA Network Analysis for Acute Type A Aortic Dissection
Cited by: 7
Author(s): Junjun Fang, Zongfu Pan, Hao Yu, Shuanying Yang, Xiaoping Hu, Xiaoyang Lu, Li Lü
Software Mentions: 2
Published: almost 4 years ago
10.3389/fphar.2021.693982
Resveratrol Alleviates Dextran Sulfate Sodium-Induced Acute Ulcerative Colitis in Mice by Mediating PI3K/Akt/VEGFA Pathway
Cited by: 12
Author(s): Fang Zhu, Jujia Zheng, Fang Xu, Yiyuan Xi, Jun Chen, Xiaorong Xu
Software Mentions: 2
Published: over 3 years ago
10.3389/fphar.2019.00385
DNMT Inhibitors Increase Methylation in the Cancer Genome
Cited by: 61
Author(s): Anil Giri, Tero Aittokallio
Software Mentions: 2
Published: over 5 years ago
10.3389/fphar.2019.00625
Losmapimod Protected Epileptic Rats From Hippocampal Neuron Damage Through Inhibition of the MAPK Pathway
Cited by: 6
Author(s): Min Li, Lexiang Cui, Xuebing Feng, Chao Wang, Yinmeng Zhang, Lijie Wang, Ying Ding, Teng Zhao
Software Mentions: 2
Published: over 5 years ago
10.3389/fphar.2021.627126
Blood microRNA Signatures Serve as Potential Diagnostic Biomarkers for Hepatic Sinusoidal Obstruction Syndrome Caused by Gynura japonica Containing Pyrrolizidine Alkaloids
Cited by: 3
Author(s): Xunjiang Wang, Wei Zhang, Yongfeng Yang, Yiran Chen, Yuzheng Zhuge, Aizhen Xiong, Li Yang, Zhengtao Wang
Software Mentions: 2
Published: almost 4 years ago
10.3389/fphar.2020.00284
An Integrated Pharmacology-Based Analysis for Antidepressant Mechanism of Chinese Herbal Formula Xiao-Yao-San
Cited by: 35
Author(s): Naijun Yuan, Lian Gong, Kairui Tang, Liangliang He, Wenzhi Hao, Xiaojuan Li, Qingyu Ma, Jiaxu Chen
Software Mentions: 2
Published: over 4 years ago
10.3389/fphar.2020.00630
Early Response to the Plant Toxin Stenodactylin in Acute Myeloid Leukemia Cells Involves Inflammatory and Apoptotic Signaling
Cited by: 8
Author(s): Daniele Mercatelli, Massimo Bortolotti, Vibeke Andresen, André Sulen, Letizia Polito, Bjørn Tore Gjertsen, Andrea Bolognesi
Software Mentions: 2
Published: over 4 years ago
10.3389/fphys.2018.00236
Arachidonic Acid Metabolism Pathway Is Not Only Dominant in Metabolic Modulation but Associated With Phenotypic Variation After Acute Hypoxia Exposure
Cited by: 8
Author(s): Chang Liu, Bao Liu, Lu Liu, Erlong Zhang, Bind-da Sun, Gang Xu, Jian Chen, Yuqi Gao
Software Mentions: 2
Published: over 6 years ago
10.3389/fphys.2012.00339
A Systems Biology Approach to Deciphering the Etiology of Steatosis Employing Patient-Derived Dermal Fibroblasts and iPS Cells
Cited by: 18
Author(s): Justyna Józefczuk, Karl Kashofer, Ramesh Ummanni, Frauke Henjes, Samrina Rehman, Suzanne Geenen, Wasco Wruck, Christian Regenbrecht, Andriani Daskalaki, Christoph Wierling, Paola Turano, Ivano Bertini, Ulrike Korf, Kurt Zatloukal, Hans V. Westerhoff, Hans Lehrach, James Adjaye
Software Mentions: 2
Published: almost 13 years ago
10.3389/fphys.2017.00723
N-acetylcysteine Counteracts Adipose Tissue Macrophage Infiltration and Insulin Resistance Elicited by Advanced Glycated Albumin in Healthy Rats
Cited by: 10
Author(s): Karolline S. da Silva, Paula Ramos Pinto, N. Fabre, Diogo Bugano Diniz Gomes, Karina Thieme, Lígia Shimabukuro Okuda, Rodrigo Tallada Iborra, Vanessa G. Freitas, Maria Heloísa Massola Shimizu, Walcy Rosolia Teodoro, Suely Kazue Nagahashi Marie, Tom M. Woods, Margaret A. Brimble, Russell Pickford, Kerry‐Anne Rye, Maristela Mitiko Okamoto, Sérgio Catanozi, Maria L. Correa-Giannela, Ubiratan Fabres Machado, Marisa Passarelli
Software Mentions: 2
Published: about 7 years ago
10.3389/fphys.2020.629542
Calcium-Sensing Receptor Participates in High Glucose-Induced EndMT in Primary Human Aortic Endothelial Cells
Cited by: 2
Author(s): Cheng Yuan, Lihua Ni, Xianqin Yang, Changjiang Zhang, Xiaoyan Wu
Software Mentions: 2
Published: almost 4 years ago
10.3389/fpls.2017.01006
Key Components of Different Plant Defense Pathways Are Dispensable for Powdery Mildew Resistance of the Arabidopsis mlo2 mlo6 mlo12 Triple Mutant
Cited by: 35
Author(s): Harald Kühn, Justine Lorek, Mark Kwaaitaal, Chiara Consonni, Katia Becker, Cristina Micali, Emiel Ver Loren van Themaat, Paweł Bednarek, Tom M. Raaymakers, Michela Appiano, Yuling Bai, Dorothea Meldau, Stephani Baum, Uwe Conrath, Ivo Feußner, Ralph Panstruga
Software Mentions: 2
Published: over 7 years ago
10.3389/fpls.2017.01905
Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases
Cited by: 24
Author(s): J. Alberto Romero Navarro, Wilbert Phillips‐Mora, Adriana Arciniegas-Leal, Allan Mata-Quirós, Niina Haiminen, Guiliana Mustiga, Donald Livingstone, Harm van Bakel, David N. Kuhn, Laxmi Parida, Andrew Kasarskis, Juan Carlos Motamayor
Software Mentions: 2
Published: about 7 years ago
10.3389/fpls.2018.00023
GSHR, a Web-Based Platform Provides Gene Set-Level Analyses of Hormone Responses in Arabidopsis
Cited by: 1
Author(s): Xiaojuan Ran, Jian Liu, Meifang Qi, Yuejun Wang, Jingfei Cheng, Yijing Zhang
Software Mentions: 2
Published: almost 7 years ago
10.3389/fpls.2015.01157
Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice
Cited by: 57
Author(s): Shuchi Smita, Amit Katiyar, Viswanathan Chinnusamy, Dev Mani Pandey, Kailash C. Bansal
Software Mentions: 2
Published: almost 9 years ago
10.3389/fpls.2019.01704
Dual Transcriptome and Metabolic Analysis of Vitis vinifera cv. Pinot Noir Berry and Botrytis cinerea During Quiescence and Egressed Infection
Cited by: 20
Author(s): Zeraye Mehari Haile, G. Malacarne, S. Pilati, Paolo Sonego, Marco Moretto, Domenico Masuero, Urška Vrhovšek, Kristof Engelen, Elena Baraldi, C. Moser
Software Mentions: 2
Published: almost 5 years ago
10.3389/fpls.2019.01323
Transcriptome Analysis of the Hierarchical Response of Histone Deacetylase Proteins That Respond in an Antagonistic Manner to Salinity Stress
Cited by: 13
Author(s): Minoru Ueda, Atsushi Matsui, S. Watanabe, Makoto Kobayashi, Kazuki Saito, Maho Tanaka, Junko Ishida, Miyako Kusano, Mitsunori Seo, Motoaki Seki
Software Mentions: 2
Published: about 5 years ago
10.3389/fpls.2016.00326
Influence of Light and Temperature on Gene Expression Leading to Accumulation of Specific Flavonol Glycosides and Hydroxycinnamic Acid Derivatives in Kale (Brassica oleracea var. sabellica)
Cited by: 46
Author(s): Susanne Neugart, Angelika Krumbein, Rita Zrenner
Software Mentions: 2
Published: over 8 years ago
10.3389/fpls.2016.01055
Phytochrome and Ethylene Signaling Integration in Arabidopsis Occurs via the Transcriptional Regulation of Genes Co-targeted by PIFs and EIN3
Cited by: 22
Author(s): Jinkil Jeong, Keunhwa Kim, Mi Eon Kim, Hye Gi Kim, Gwi Suk Heo, Ohkmae Kim Park, Youn‐Il Park, Giltsu Choi, Eunkyoo Oh
Software Mentions: 2
Published: over 8 years ago
10.3389/fpls.2019.00192
Transcriptome Profiling and Genome-Wide Association Studies Reveal GSTs and Other Defense Genes Involved in Multiple Signaling Pathways Induced by Herbicide Safener in Grain Sorghum
Cited by: 23
Author(s): You Soon Baek, Loren V. Goodrich, Patrick J. Brown, Brandon T. James, Stephen P. Moose, Kris N. Lambert, Dean E. Riechers
Software Mentions: 2
Published: over 5 years ago
10.3389/fpls.2014.00046
Role of callose synthases in transfer cell wall development in tocopherol deficient Arabidopsis mutants
Cited by: 31
Author(s): Hiroshi Maéda, Wan Song, Tammy L. Sage, Dean DellaPenna
Software Mentions: 2
Published: almost 11 years ago
10.3389/fpls.2021.679047
Trajectories of Homoeolog-Specific Expression in Allotetraploid Tragopogon castellanus Populations of Independent Origins
Cited by: 1
Author(s): J. Lucas Boatwright, Cheng‐Ting Yeh, Heng-Cheng Hu, Alfonso Susanna, Douglas E. Soltis, Pamela S. Soltis, Patrick S. Schnable, W. Brad Barbazuk
Software Mentions: 2
Published: over 3 years ago
10.3389/fpls.2017.01093
Abscisic Acid Is a Major Regulator of Grape Berry Ripening Onset: New Insights into ABA Signaling Network
Cited by: 106
Author(s): S. Pilati, Giorgia Bagagli, Paolo Sonego, Marco Moretto, D. Brazzale, Giulia Castorina, Laura Simoni, Chiara Tonelli, Graziano Guella, Kristof Engelen, Massimo Galbiati, C. Moser
Software Mentions: 2
Published: over 7 years ago
10.3389/fpls.2016.00925
A De Novo-Assembly Based Data Analysis Pipeline for Plant Obligate Parasite Metatranscriptomic Studies
Cited by: 7
Author(s): Li Guo, Kelly S. Allen, Greg Deiulio, Yong Zhang, Angela M. Madeiras, Robert L. Wick, Lijun Ma
Software Mentions: 2
Published: over 8 years ago
10.3389/fpls.2017.00632
Differences in Flower Transcriptome between Grapevine Clones Are Related to Their Cluster Compactness, Fruitfulness, and Berry Size
Cited by: 28
Author(s): Jérôme Grimplet, Javier Tello, Natalia Laguna, Javier Ibáñez
Software Mentions: 2
Published: over 7 years ago
10.3389/fpls.2015.00308
Minimal evidence for consistent changes in maize DNA methylation patterns following environmental stress
Cited by: 75
Author(s): Steven R. Eichten, Nathan M. Springer
Software Mentions: 2
Published: over 9 years ago
10.3389/fpls.2015.01260
Microarray Meta-Analysis Focused on the Response of Genes Involved in Redox Homeostasis to Diverse Abiotic Stresses in Rice
Cited by: 20
Author(s): Joao Braga de Abreu Neto, Michael Frei
Software Mentions: 2
Published: almost 9 years ago
10.3389/fnsys.2017.00075
Gene Network Construction from Microarray Data Identifies a Key Network Module and Several Candidate Hub Genes in Age-Associated Spatial Learning Impairment
Cited by: 7
Author(s): Raihan K. Uddin, Shiva M. Singh
Software Mentions: 2
Published: about 7 years ago
10.1534/g3.111.001115
Correlation of Global MicroRNA Expression With Basal Cell Carcinoma Subtype
Cited by: 35
Author(s): Christopher Heffelfinger, Zhengqing Ouyang, Anna Engberg, David J. Leffell, Allison Hanlon, Patricia B. Gordon, Wei Zheng, Hongyu Zhao, M Snyder, Allen E. Bale
Software Mentions: 2
Published: almost 13 years ago
10.1534/g3.113.008029
Genome-Wide Gene Expression Effects of Sex Chromosome Imprinting in<i>Drosophila</i>
Cited by: 26
Author(s): Bernardo Lemos, Alan T. Branco, Pan Jiang, Daniel L. Hartl, Colin D. Meiklejohn
Software Mentions: 2
Published: almost 11 years ago
10.1534/g3.117.040089
Comparative Transcriptomics of Malaria Mosquito Testes: Function, Evolution, and Linkage
Cited by: 8
Author(s): Bryan J. Cassone, Raissa G. G. Kay, Matthew P. Daugherty, Bradley J. White
Software Mentions: 2
Published: over 7 years ago
10.1534/g3.117.043828
Unique Allelic eQTL Clusters in Human MHC Haplotypes
Cited by: 19
Author(s): Tze Hau Lam, Meixin Shen, Matthew Zirui Tay, Ee Chee Ren
Software Mentions: 2
Published: over 7 years ago
10.1534/g3.119.400430
Combining Transcriptomics and Proteomics Reveals Potential Post-transcriptional Control of Gene Expression After Light Exposure in <i>Metarhizium acridum</i>
Cited by: 14
Author(s): Guilherme Thomaz Pereira Brancini, Márcia E. S. Ferreira, Drauzio E.N. Rangel, Gilberto Úbida Leite Braga
Software Mentions: 2
Published: over 5 years ago
10.1534/g3.119.400469
Investigating the Influence of Glycerol on the Utilization of Glucose in <i>Yarrowia lipolytica</i> Using RNA-Seq-Based Transcriptomics
Cited by: 11
Author(s): Patrice Lubuta, Mhairi Workman, Eduard J. Kerkhoven, Christopher Workman
Software Mentions: 2
Published: about 5 years ago
10.1534/g3.120.401718
The Utility of Resolving Asthma Molecular Signatures Using Tissue-Specific Transcriptome Data
Cited by: 11
Author(s): Debajyoti Ghosh, Lili Ding, Jonathan A. Bernstein, Tesfaye B. Mersha
Software Mentions: 2
Published: about 4 years ago
10.1093/g3journal/jkab077
Highly effective proximate labeling in <i>Drosophila</i>
Cited by: 21
Author(s): Bo Zhang, Yuanbing Zhang, Ji‐Long Liu
Software Mentions: 2
Published: over 3 years ago
10.1007/s10120-018-0859-1
E-cadherin-deficient cells have synthetic lethal vulnerabilities in plasma membrane organisation, dynamics and function
Cited by: 25
Author(s): Tanis Godwin, S. Thomas Kelly, Tom P. Brew, Nicola Bougen-Zhukov, Andrew Single, Augustine Chen, Cassie E. Stylianou, Lawrence D. Harris, Sophie K. Currie, Bryony J. Telford, Henry Beetham, Gary B. Evans, Michael A. Black, Parry Guilford
Software Mentions: 2
Published: over 6 years ago
10.1111/jcmm.16084
Herbal formula LLKL ameliorates hyperglycaemia, modulates the gut microbiota and regulates the gut‐liver axis in Zucker diabetic fatty rats
Cited by: 12
Author(s): Mei Li, Lei Ding, Yuli Hu, Lingling Qin, You Wu, Wei Liu, Lili Wu, Tonghua Liu
Software Mentions: 2
Published: about 4 years ago
10.1111/jcmm.15573
Human bone marrow mesenchymal stem cell‐derived extracellular vesicles impede the progression of cervical cancer via the miR‐144‐3p/CEP55 pathway
Cited by: 13
Author(s): Meng Qin, Baofang Zhang, Ying‐Ming Zhang, Shuyan Wang, Xiaohui Zhu
Software Mentions: 2
Published: almost 4 years ago
10.1111/jcmm.16400
Cytoglobin promotes sensitivity to ferroptosis by regulating p53‐YAP1 axis in colon cancer cells
Cited by: 38
Author(s): Shazhou Ye, Mingjun Xu, Tingwei Zhu, Jiayi Chen, Shanping Shi, Haizhong Jiang, Qingfang Zheng, Qi Liao, Xiaoyun Ding, Yang Xi
Software Mentions: 2
Published: almost 4 years ago
10.1111/jcmm.16419
Circular RNA circANAPC2 mediates the impairment of endochondral ossification by miR‐874‐3p/SMAD3 signalling pathway in idiopathic short stature
Cited by: 12
Author(s): Xijuan Liu, Du Zhi, Xuan Yao, Tianle Sheng, Jinghong Yuan, Jingyu Jia
Software Mentions: 2
Published: over 3 years ago
10.1111/jcmm.16402
Integrated study of miR‐215 promoting breast cancer cell apoptosis by targeting RAD54B
Cited by: 8
Author(s): Mingyuan Wang, Jingnan Liao, Chang Tan, Hong Zhou, Jinjin Wang, Kangkai Wang, Yiming Li, Wei Wu
Software Mentions: 2
Published: almost 4 years ago
10.1111/jcmm.16494
Construction of an immune‐related LncRNA signature with prognostic significance for bladder cancer
Cited by: 15
Author(s): Wenjie Luo, Xi Tian, Wenhao Xu, Yuanyuan Qu, Wenkai Zhu, Jie Wu, Chao Ma, Hai-Liang Zhang, Dingwei Ye, Yiping Zhu
Software Mentions: 2
Published: over 3 years ago
10.1111/jcmm.16439
Fructose‐1,6‐bisphosphatase aggravates oxidative stress‐induced apoptosis in asthma by suppressing the Nrf2 pathway
Cited by: 9
Author(s): Jiapeng Hu, Jia Wang, Chunlu Li, Yunxiao Shang
Software Mentions: 2
Published: over 3 years ago
10.1111/jcmm.16612
MiR‐193b deregulation is associated with Parkinson's disease
Cited by: 13
Author(s): Masoud Baghi, Elaheh Yadegari, Mohsen Rostamian Delavar, Maryam Peymani, Mazdak Ganjalikhani‐Hakemi, Mehri Salari, Mohammad Hossein Nasr-Esfahani, Timothy L. Megraw, Kamran Ghaedi
Software Mentions: 2
Published: over 3 years ago
10.1002/jcp.27049
<b>Intratumor lactate levels reflect HER2 addiction status in HER2‐positive breast cancer</b>
Cited by: 29
Author(s): Lorenzo Castagnoli, Egidio Iorio, Matteo Dugo, Ada Koschorke, Simona Faraci, Rossella Canese, Patrizia Casalini, Patrizia Nanni, Claudio Vernieri, Massimo Di Nicola, Daniele Morelli, Elda Tagliabue, Serenella M. Pupa
Software Mentions: 2
Published: over 6 years ago
10.1002/jcp.29067
Identification of hub genes and construction of transcriptional regulatory network for the progression of colon adenocarcinoma hub genes and TF regulatory network of colon adenocarcinoma
Cited by: 23
Author(s): Shuxun Wei, Jinshui Chen, Yu Fang Huang, Qiang Sun, Haolu Wang, Xiaowen Liang, Zhiqian Hu, Xinxing Li
Software Mentions: 2
Published: about 5 years ago
10.1186/1758-2946-5-30
Drug repositioning: a machine-learning approach through data integration
Cited by: 255
Author(s): Francesco Napolitano, Yan Zhao, Vânia M. Moreira, Roberto Tagliaferri, Juha Kere, Mauro D’Amato, Dario Greco
Software Mentions: 2
Published: over 11 years ago
10.1111/jcpp.12740
Longitudinal epigenetic predictors of amygdala:hippocampus volume ratio
Cited by: 26
Author(s): Esther Walton, Charlotte A.M. Cecil, Matthew Suderman, Jingyu Liu, Jessica A. Turner, Vince D. Calhoun, Stefan Ehrlich, Caroline L Relton, Edward D. Barker
Software Mentions: 2
Published: over 7 years ago
10.1210/clinem/dgab072
Differential Mitochondrial Gene Expression in Adipose Tissue Following Weight Loss Induced by Diet or Bariatric Surgery
Cited by: 12
Author(s): Birgitta W. van der Kolk, Maheswary Muniandy, Dorota Kaminska, Marcus Alvarez, Arthur Ko, Min‐Hua Zong, Armand Valsesia, Dominique Langin, Maija Vaittinen, Mirva Pääkkönen, Riikka Jokinen, Sanna Kaye, Sini Heinonen, Kirsi A. Virtanen, Daniel P. Andersson, Ville Männistö, Wim H. M. Saris, Arne Astrup, Mikael Rydén, Ellen E. Blaak, Päivi Pajukanta, Jussi Pihlajamäki, Kirsi H. Pietiläinen
Software Mentions: 2
Published: almost 4 years ago
10.1172/JCI124725
microRNA-142–mediated repression of phosphodiesterase 3B critically regulates peripheral immune tolerance
Cited by: 38
Author(s): Nelomi Anandagoda, Joanna Willis, Arnulf Hertweck, Luke B. Roberts, Ian Jackson, M. Refik Gökmen, Richard G. Jenner, Jane K. Howard, Graham M. Lord
Software Mentions: 2
Published: almost 6 years ago
10.1172/JCI86924
Extracellular matrix proteomics identifies molecular signature of symptomatic carotid plaques
Cited by: 108
Author(s): Sarah R. Langley, Karin Willeit, Athanasios Didangelos, Ljubica Matic, Philipp Skroblin, Javier Barallobre-Barreiro, Mariette Lengquist, Gregor Rungger, Alexander Kapustin, Ludmilla Kedenko, Chris Molenaar, Ruifang Lu, Temo Barwari, Gonca Suna, Xiaoke Yin, Bernhard Iglseder, Bernhard Paulweber, Peter Willeit, Joseph Shalhoub, Gérard Pasterkamp, Alun H. Davies, Claudia Monaco, Ulf Hedin, Catherine M. Shanahan, Johann Willeit, Stefan Kiechl, Manuel Mayr
Software Mentions: 2
Published: over 7 years ago
10.1172/JCI134132
Orally bioavailable CDK9/2 inhibitor shows mechanism-based therapeutic potential in MYCN-driven neuroblastoma
Cited by: 38
Author(s): Evon Poon, Tong Liang, Yann Jamin, Susanne Walz, Colin Kwok, Anne Hakkert, Karen Barker, Zuzanna Urban, Khin Thway, Rhamy Zeid, Albert Hallsworth, Gary Box, Marli E. Ebus, Marco P. Licciardello, Yordan Sbirkov, Glori Lazaro, Elizabeth Calton, Barbara Martins Da Costa, Melanie Valenti, Alexis de Haven Brandon, Hannah Webber, Nicolas Tardif, Gilberto S. Almeida, Rossitza Christova, Gunther Boysen, Mark W. Richards, Giuseppe Barone, Anthony M. Ford, Richard Bayliss, Paul A. Clarke, Johann S. de Bono, Nathanael S. Gray, Julian Blagg, Simon P. Robinson, Suzanne A. Eccles, Daniella Zheleva, James E. Bradner, Jan J. Molenaar, Igor Vivanco, Martin Eilers, Paul Workman, Charles Y. Lin, Louis Chesler
Software Mentions: 2
Published: about 4 years ago
10.1002/jcla.23428
Hsa_circ_0023642 promotes proliferation, invasion, and migration of gastric cancer by sponging microRNA‐223
Cited by: 6
Author(s): Yi Zhang, Lei Xia, Jing Wu, Xinyu Xu, Gang Li
Software Mentions: 2
Published: over 4 years ago
10.3390/jcm7110419
Unique MicroRNA and mRNA Interactions in EGFR-Mutated Lung Adenocarcinoma
Cited by: 13
Author(s): Sophia Subat, Kentaro Inamura, Hironori Ninomiya, Hiroko Nagano, Sakae Okumura
Software Mentions: 2
Published: about 6 years ago
10.3390/jcm8111772
A CTC-Cluster-Specific Signature Derived from OMICS Analysis of Patient-Derived Xenograft Tumors Predicts Outcomes in Basal-Like Breast Cancer
Cited by: 35
Author(s): Hariprasad Thangavel, Carmine De Angelis, Suhas Vasaikar, Raksha Bhat, Mohit Kumar Jolly, Chandandeep Nagi, Chad J. Creighton, Ken Chen, Lacey E. Dobrolecki, Jason T. George, Tanya Kumar, Noor Mazin Abdulkareem, Sufeng Mao, Agostina Nardone, Mothaffar F. Rimawi, C. Kent Osborne, Michael T. Lewis, Herbert Levine, Bing Zhang, Rachel Schiff, Mario Giuliano, Meghana V. Trivedi
Software Mentions: 2
Published: about 5 years ago
10.3390/jcm9051338
Genome-Wide Analysis of the DNA Methylation Profile Identifies the Fragile Histidine Triad (FHIT) Gene as a New Promising Biomarker of Crohn’s Disease
Cited by: 8
Author(s): Tae-Oh Kim, Dong Il Park, Yu Han, Keunsoo Kang, Sae-Gwang Park, Hae Ryoun Park, Joo Mi Yi
Software Mentions: 2
Published: over 4 years ago
10.3390/jcm10122680
Methylation Status of Corticotropin-Releasing Factor (CRF) Receptor Genes in Colorectal Cancer
Cited by: 8
Author(s): Μαρία Παναγοπούλου, Antonia Cheretaki, Makrina Karaglani, Ioanna Balgkouranidou, Eirini Biziota, Kyriakos Amarantidis, Nikolaos Xenidis, Stylianos Kakolyris, Stavroula Baritaki, Εkaterini Chatzaki
Software Mentions: 2
Published: over 3 years ago
10.1155/2020/4178639
Identification of Susceptibility Modules and Genes for Cardiovascular Disease in Diabetic Patients Using WGCNA Analysis
Cited by: 41
Author(s): Weiwei Liang, Fangfang Sun, Yingxin Zhao, Peng-Fei Shan, Han-Yu Lou
Software Mentions: 2
Published: over 4 years ago
10.1093/jxb/erv285
The<i>IDA/IDA-LIKE</i>and<i>PIP/PIP-LIKE</i>gene families in<i>Arabidopsis</i>: phylogenetic relationship, expression patterns, and transcriptional effect of the PIPL3 peptide
Cited by: 64
Author(s): Ane Kjersti Vie, Javad Najafi, Bin Liu, Per Winge, Melinka A. Butenko, Karina S. Hornslien, Robert P. Kumpf, Reidunn B. Aalen, Atle M. Bones, Tore Brembu
Software Mentions: 2
Published: over 9 years ago
10.1093/jxb/erv516
Kresoxim-methyl primes<i>Medicago truncatula</i>plants against abiotic stress factors via altered reactive oxygen and nitrogen species signalling leading to downstream transcriptional and metabolic readjustment
Cited by: 28
Author(s): Panagiota Filippou, Chrystalla Antoniou, Toshihiro Obata, Katrien Van Der Kelen, Vaggelis Harokopos, Loukas Kanetis, Vassilis Aidinis, Frank Van Breusegem, Alisdair R. Fernie, Vasileios Fotopoulos
Software Mentions: 2
Published: almost 9 years ago
10.1093/jxb/erw350
The build-up of osmotic stress responses within the growing root apex using kinematics and RNA-sequencing
Cited by: 12
Author(s): Mathilde Royer, David Cohen, Nathalie Aubry, Vera Vendramin, Simone Scalabrin, Federica Cattonaro, Marie‐Béatrice Bogeat‐Triboulot, Irène Hummel
Software Mentions: 2
Published: about 8 years ago
10.1093/jxb/erx168
The IDA-LIKE peptides IDL6 and IDL7 are negative modulators of stress responses in Arabidopsis thaliana
Cited by: 28
Author(s): Ane Kjersti Vie, Javad Najafi, Per Winge, Ester Cattan, Michael Wrzaczek, Jaakko Kangasjärvi, Gad Miller, Tore Brembu, Atle M. Bones
Software Mentions: 2
Published: over 7 years ago
10.1093/jxb/erx254
Diversity of cis-regulatory elements associated with auxin response in Arabidopsis thaliana
Cited by: 43
Author(s): Pavel Cherenkov, Daria D. Novikova, N. A. Omelyanchuk, Victor G. Levitsky, Ivo Große, Dolf Weijers, В. В. Миронова
Software Mentions: 2
Published: over 7 years ago
10.1093/jxb/erw474
Nod factors potentiate auxin signaling for transcriptional regulation and lateral root formation inMedicago truncatula
Cited by: 15
Author(s): Violaine Herrbach, Ximena Chirinos, David Rodrı́guez-Lázaro, Kokoévi Agbévénou, Rémy Vincent, Stéphanie Pateyron, Stéphanie Huguet, Sandrine Balzergue, Asher Pasha, Nicholas J. Provart, Clare Gough, Sandra Bensmihen
Software Mentions: 2
Published: almost 8 years ago
10.1093/jxb/eraa099
Transcriptional analysis of arogenate dehydratase genes identifies a link between phenylalanine biosynthesis and lignin biosynthesis
Cited by: 9
Author(s): Jorge El-Azaz, Fernando De la Torre, María Belén Pascual, Sandrine Debille, Francis Canlet, Luc Harvengt, Jean-François Trontin, Concepción Ávila
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.ppat.1000604
Lethal Influenza Virus Infection in Macaques Is Associated with Early Dysregulation of Inflammatory Related Genes
Cited by: 197
Author(s): Cristian Cillóniz, Kyoko Shinya, Xinxia Peng, Marcus J. Korth, Sean Proll, Lauri Aicher, Victoria S. Carter, Jean Chang, Darwyn Kobasa, Friedericke Feldmann, James E. Strong, Heinz Feldmann, Yoshihiro Kawaoka, Michael G. Katze
Software Mentions: 2
Published: about 15 years ago
10.1371/journal.ppat.1002315
Severe Acute Respiratory Syndrome Coronavirus Envelope Protein Regulates Cell Stress Response and Apoptosis
Cited by: 175
Author(s): Marta L. DeDiego, José L. Nieto-Torres, Jose M. Jiménez-Guardeño, José Ángel Regla-Nava, Enrique Álvarez, Juan Carlos Oliveros, Jincun Zhao, Craig Fett, Stanley Perlman, Luis Enjuanes
Software Mentions: 2
Published: about 13 years ago
10.1371/journal.ppat.1004079
Exposure-Dependent Control of Malaria-Induced Inflammation in Children
Cited by: 135
Author(s): Sílvia Portugal, Jacqueline Moebius, Jeff Skinner, Safiatou Doumbo, Didier Doumtabé, Younoussou Koné, Seydou Dia, Kishore Kanakabandi, Daniel E. Sturdevant, Kimmo Virtaneva, Stephen F. Porcella, Shanping Li, Ogobara K. Doumbo, Kassoum Kayentao, Aissata Ongoïba, Boubacar Traoré, Peter D. Crompton
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.ppat.1004662
Prion Infections and Anti-PrP Antibodies Trigger Converging Neurotoxic Pathways
Cited by: 74
Author(s): U. Herrmann, Tiziana Sonati, Jeppe Falsig, Regina Reimann, Paolo Dametto, Tracy O’Connor, Bei Li, Agnes Lau, Simone Hornemann, Silvia Sorce, Uli Wagner, Despina Sanoudou, Adriano Aguzzi
Software Mentions: 2
Published: almost 10 years ago
10.1371/journal.ppat.1005263
Interferon-γ Inhibits Ebola Virus Infection
Cited by: 69
Author(s): Bethany A. Rhein, Linda S. Powers, Kai J. Rogers, Manu Anantpadma, Brajesh K. Singh, Yoshio Sakurai, Thomas B. Bair, Catherine L. Miller-Hunt, Patrick L. Sinn, Robert A. Davey, Martha M. Monick, Wendy Maury
Software Mentions: 2
Published: about 9 years ago
10.1371/journal.ppat.1005936
Combined Activity of DCL2 and DCL3 Is Crucial in the Defense against Potato Spindle Tuber Viroid
Cited by: 49
Author(s): Κωνσταντίνα Κατσαρού, Eleni Mavrothalassiti, Wannes Dermauw, Thomas Van Leeuwen, Kriton Kalantidis
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.ppat.1006576
Malaria-induced interferon-γ drives the expansion of Tbethi atypical memory B cells
Cited by: 122
Author(s): Nyamekye Obeng-Adjei, Sílvia Portugal, Prasida Holla, Shanping Li, Hyung Sun Sohn, Abhijit A. Ambegaonkar, Jeff Skinner, Georgina Bowyer, Ogobara K. Doumbo, Boubacar Traoré, Susan K. Pierce, Peter D. Crompton
Software Mentions: 2
Published: about 7 years ago
10.1371/journal.ppat.1006788
Lower temperatures reduce type I interferon activity and promote alphaviral arthritis
Cited by: 34
Author(s): Natalie A. Prow, Bing Tang, Joy Gardner, Thuy T. Le, Adam Taylor, Yee Suan Poo, Eri Nakayama, Thiago Dominguez Crespo Hirata, Helder I. Nakaya, Andrii Slonchak, Pamela Mukhopadhyay, Suresh Mahalingam, Wayne A. Schroder, William B. Klimstra, Andreas Suhrbier
Software Mentions: 2
Published: almost 7 years ago
10.1371/journal.ppat.1006871
Liver macrophage-associated inflammation correlates with SIV burden and is substantially reduced following cART
Cited by: 18
Author(s): Bridget S. Fisher, Richard Green, Rachel Brown, Matthew P. Wood, Tiffany Hensley-McBain, Cole Fisher, Jean Chang, Andrew D. Miller, William J. Bosche, Jeffrey D. Lifson, Maud Mavigner, Charlene Miller, Michael Gale, Guido Silvestri, Ann Chahroudi, Nichole R. Klatt, Donald L. Sodora
Software Mentions: 2
Published: almost 7 years ago
10.1371/journal.ppat.1007276
Cellular sheddases are induced by Merkel cell polyomavirus small tumour antigen to mediate cell dissociation and invasiveness
Cited by: 24
Author(s): Nnenna Nwogu, James R. Boyne, Samuel J. Dobson, Krzysztof Poterlowicz, G. Eric Blair, Andrew Macdonald, Jamel Mankouri, Adrian Whitehouse
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.ppat.1007298
Microvesicles from malaria-infected red blood cells activate natural killer cells via MDA5 pathway
Cited by: 48
Author(s): Weijian Ye, Marvin Chew, Jue Hou, Fritz Lai, Stije J. Leopold, Hooi Linn Loo, Aniruddha Ghose, A. K. Dutta, Yi‐Ping Phoebe Chen, Eng Eong Ooi, Nicholas J. White, Arjen M. Dondorp, Peter R. Preiser, Jianzhu Chen
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.ppat.1007528
Antagonistic paralogs control a switch between growth and pathogen resistance in C. elegans
Cited by: 62
Author(s): Kirthi C. Reddy, Tal Dror, Ryan Underwood, Guled A. Osman, Corrina R. Elder, Christopher A. Desjardins, Christina A. Cuomo, Michalis Barkoulas, Emily R. Troemel
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.ppat.1007684
The TLR4 adaptor TRAM controls the phagocytosis of Gram-negative bacteria by interacting with the Rab11-family interacting protein 2
Cited by: 26
Author(s): Astrid Skjesol, Mariya Yurchenko, Korbinian Bösl, Caroline S. Gravastrand, Kaja Elisabeth Nilsen, Lene Melsæther Grøvdal, Federica Agliano, Francesco Patanè, Germana Lentini, Hera Kim, Giuseppe Teti, A. Sharma, Richard K. Kandasamy, Bjørnar Sporsheim, Kristian K. Starheim, Douglas T. Golenbock, Harald Stenmark, Mary W. McCaffrey, Terje Espevik, Harald Husebye
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.ppat.1007748
CD8+ T cells retain protective functions despite sustained inhibitory receptor expression during Epstein-Barr virus infection in vivo
Cited by: 42
Author(s): Bithi Chatterjee, Yun Deng, Angelika Holler, Nicolás Gonzalo Núñez, Tarik Azzi, Liliana Danusia Vanoaica, Anne Müller, Hana Zdimerova, Olga Antsiferova, Andrea Zbinden, Riccarda Capaul, Johannes H. Dreyer, David Nadal, Burkhard Becher, Mark D. Robinson, Hans J. Stauss, Christian Münz
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.ppat.1007841
DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes
Cited by: 37
Author(s): Taylor M. Nye, Kristin M. Jacob, Elena K. Holley, Juan M Nevarez, Suzanne Dawid, Lyle A. Simmons, Michael Watson
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.ppat.1007880
Systems analysis of subjects acutely infected with the Chikungunya virus
Cited by: 26
Author(s): Alessandra Soares‐Schanoski, Natália Baptista Cruz, Luíza Antunes de Castro-Jorge, Roberto Gameiro de Carvalho, Cliomar Alves dos Santos, Nancy da Rós, Ursula de Oliveira, Danuza Duarte Costa, Cecília Luiza Simões Santos, Marielton dos Passos Cunha, Maria Leonor S. Oliveira, Juliana Cardoso Alves, Regina Adalva de Lucena Couto Océa, Danielle Rodrigues Ribeiro, André Nicolau Aquime Gonçalves, Patrícia Gonzalez-Dias, Andreas Suhrbier, Paolo Marinho de Andrade Zanotto, Inácio L.M. Junqueira-de-Azevedo, Dario S. Zamboni, Roque Pacheco de Almeida, Paulo Lee Ho, Jorge Kalil, Milton Yutaka Nishiyama-Jr, Helder I. Nakaya
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.ppat.1007960
Dafachronic acid promotes larval development in Haemonchus contortus by modulating dauer signalling and lipid metabolism
Cited by: 31
Author(s): Guangxu Ma, Tao Wang, Pasi K. Korhonen, Neil D. Young, Shuai Nie, Ching‐Seng Ang, Nicholas A. Williamson, Gavin E. Reid, Robin B. Gasser
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-017-16070-5
Hypomethylation of HOXA4 promoter is common in Silver-Russell syndrome and growth restriction and associates with stature in healthy children
Cited by: 11
Author(s): Mari Muurinen, Katariina Hannula-Jouppi, Lovisa E. Reinius, Cilla Söderhäll, Simon Kebede Merid, Anna Bergström, Erik Melén, Göran Pershagen, Marita Lipsanen‐Nyman, Dario Greco, Juha Kere
Software Mentions: 2
Published: about 7 years ago
10.1038/s41598-017-16201-y
Cartilage intermediate layer protein 1 (CILP1): A novel mediator of cardiac extracellular matrix remodelling
Cited by: 34
Author(s): Frans A. van Nieuwenhoven, Chantal Munts, Roel C Op't Veld, Arantxa González, Javier Dı́ez, Stéphane Heymans, Blanche Schroen, Marc van Bilsen
Software Mentions: 2
Published: about 7 years ago
10.1038/s41598-017-16627-4
A flexible ontology for inference of emergent whole cell function from relationships between subcellular processes
Cited by: 24
Author(s): Jens Hansen, David Meretzky, Simeneh Woldesenbet, Gustavo Stolovitzky, Ravi Iyengar
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41598-017-18308-8
A central role for PI3K-AKT signaling pathway in linking SAMHD1-deficiency to the type I interferon signature
Cited by: 26
Author(s): Changhoon Oh, Jeongmin Ryoo, Kiwon Park, Baek Kim, Michele B. Daly, DongYeon Cho, Kwangseog Ahn
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41598-017-18370-2
ModuleDiscoverer: Identification of regulatory modules in protein-protein interaction networks
Cited by: 53
Author(s): Sebastian Vlaic, Theresia Conrad, Christian Tokarski-Schnelle, Mika Gustafsson, Uta Dahmen, Reinhard Guthke, Stefan Schuster
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41598-018-23772-x
Association between DNA methylation in cord blood and maternal smoking: The Hokkaido Study on Environment and Children’s Health
Cited by: 34
Author(s): Kunio Miyake, Akio Kawaguchi, Ryuichi Miura, Sachiko Kobayashi, Nguyen Quoc Vuong Tran, Sumitaka Kobayashi, Chihiro Miyashita, Atsuko Araki, Takeo Kubota, Zentaro Yamagata, Reiko Kishi
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-24256-8
Proteomic profiling of human cancer pseudopodia for the identification of anti-metastatic drug candidates
Cited by: 7
Author(s): Sunkyu Choi, Aditya Bhagwat, Rasha Al Mismar, Neha Goswami, Hisham Ben Hamidane, Lu Sun, Johannes Graumann
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-24232-2
Translational study identifies XPF and MUS81 as predictive biomarkers for oxaliplatin-based peri-operative chemotherapy in patients with esophageal adenocarcinoma
Cited by: 8
Author(s): Thomas P. MacGregor, R Carter, Richard Gillies, John M. Findlay, Christiana Kartsonaki, Francesc Castro-Giner, Natasha Sahgal, L M Wang, Runjan Chetty, Nicholas Maynard, Jean‐Baptiste Cazier, Francesca M. Buffa, Peter J. McHugh, Ian Tomlinson, Mark R. Middleton, Ricky A. Sharma
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-23505-0
Proteomic analysis of plasma extracellular vesicles reveals mitochondrial stress upon HTLV-1 infection
Cited by: 22
Author(s): Patricia Jeannin, Thibault Chaze, Quentin Giai Gianetto, Mariette Matondo, Olivier Gout, Antoine Gessain, Philippe V. Afonso
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-27306-3
Transcriptomic and neurochemical analysis of the stellate ganglia in mice highlights sex differences
Cited by: 13
Author(s): Richard Bayles, Antoinette Olivas, Quin E. Denfeld, William R. Woodward, Suzanne S. Fei, Lina Gao, Beth A. Habecker
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-27646-0
Independent regulation of Plasmodium falciparum rif gene promoters
Cited by: 5
Author(s): Rosana Beatriz Duque Araujo, Tatiane Macedo Silva, Charlotte Kaiser, Gabriela Fernandes Leite, Diego Peres Alonso, Paulo Eduardo Martins Ribolla, Gerd Wunderlich
Software Mentions: 2
Published: over 6 years ago