bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1042/BSR20194365

Identification of crucial aberrantly methylated and differentially expressed genes related to cervical cancer using an integrated bioinformatics analysis
Cited by: 10
Author(s): Xiaoling Ma, Jinhui Liu, Hui Wang, Yi Jiang, Yicong Wan, Yankai Xia, Wenjun Cheng
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.ppat.1004419

Leishmania donovani Infection Causes Distinct Epigenetic DNA Methylation Changes in Host Macrophages
Cited by: 109
Author(s): Alexandra K. Marr, Julia L. MacIsaac, Ruiwei Jiang, Adriana M. Airo, Michæl S. Kobor, W. Robert McMaster
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.ppat.1004542

Targeted Changes of the Cell Wall Proteome Influence Candida albicans Ability to Form Single- and Multi-strain Biofilms
Cited by: 52
Author(s): Vitor Cabral, Sadri Znaidi, Larry P. Walker, Hélène Martin-Yken, Étienne Dague, Mélanie Legrand, Keunsook Lee, Murielle Chauvel, Arnaud Firon, Tristan Rossignol, Mathias L. Richard, Carol A. Munro, Sophie Bachellier‐Bassi, Christophe d’Enfert
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.ppat.1004630

Cell Cycle-Independent Phospho-Regulation of Fkh2 during Hyphal Growth Regulates Candida albicans Pathogenesis
Cited by: 25
Author(s): Jamie A. Greig, Ian Sudbery, Jonathan P. Richardson, Julian R. Naglik, Yan Ming Wang, Peter E. Sudbery
Software Mentions: 1
Published: almost 10 years ago

10.1042/BSR20201401

Computational analysis and verification of molecular genetic targets for glioblastoma
Cited by: 7
Author(s): Xue Li, Haibing Liu, Yehuang Chen, Liangfeng Wei, Jingfang Hong
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0014026

Dynamic, Large-Scale Profiling of Transcription Factor Activity from Live Cells in 3D Culture
Cited by: 29
Author(s): Michael Weiss, Beatriz Peñalver Bernabé, Abigail D. Bellis, Linda J. Broadbelt, Jacqueline S. Jeruss, Lonnie D. Shea
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0095929

Combinatorial Communication in Bacteria: Implications for the Origins of Linguistic Generativity
Cited by: 19
Author(s): Thomas C. Scott‐Phillips, James Gurney, Alasdair Ivens, Stephen P. Diggle, Roman Popat
Software Mentions: 1
Published: over 10 years ago

10.1042/BSR20181783

Integrated analyses of lncRNAs microarray profiles and mRNA–lncRNA coexpression in smooth muscle cells under hypoxic and normoxic conditions
Cited by: 6
Author(s): Qinshuo Zhao, Dating Sun, Yuanyuan Li, Jin Qin, Jiangtao Yan
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.ppat.1005772

Spliceosome SNRNP200 Promotes Viral RNA Sensing and IRF3 Activation of Antiviral Response
Cited by: 22
Author(s): Nicolas Tremblay, Martin Baril, Laurent Chatel‐Chaix, Salwa Es-Saad, Alex Young Park, Robert K. Koenekoop, Daniel Lamarre
Software Mentions: 1
Published: over 8 years ago

10.1042/BSR20200980

Identification of prognosis-related genes in the tumor microenvironment of stomach adenocarcinoma by TCGA and GEO datasets
Cited by: 22
Author(s): Na Ren, Bin Liang, Yunhui Li
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0176204

microRNA-125a-3p is regulated by MyD88 in Legionella pneumophila infection and targets NTAN1
Cited by: 8
Author(s): Elisa Jentho, M. Kirby Bodden, Christine Schulz, Anna Lena Jung, Kerstin Seidel, Bernd Schmeck, Wilhelm Bertrams
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0017691

Unifying Gene Expression Measures from Multiple Platforms Using Factor Analysis
Cited by: 16
Author(s): Xin Victoria Wang, Roel G.W. Verhaak, Elizabeth Purdom, Paul T. Spellman, Terence P. Speed
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.ppat.1006103

Autophagy Is an Innate Mechanism Associated with Leprosy Polarization
Cited by: 42
Author(s): Bruno Jorge de Andrade Silva, Mayara Garcia de Mattos Barbosa, Priscila Ribeiro Andrade, Helen Ferreira, José Augusto da Costa Nery, Suzana Côrte-Real, Gilberto Marcelo Sperandio da Silva, Patrícia Sammarco Rosa, Mario Fabri, Euzenir Nunes Sarno, Roberta Olmo Pinheiro
Software Mentions: 1
Published: almost 8 years ago

10.1042/BSR20192724

Profiles of immune cell infiltration in head and neck squamous carcinoma
Cited by: 18
Author(s): Bin Liang, Tao Ye, Tianjiao Wang
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0027413

DNA Replication Timing Is Maintained Genome-Wide in Primary Human Myoblasts Independent of D4Z4 Contraction in FSH Muscular Dystrophy
Cited by: 21
Author(s): Benjamin D. Pope, Koji Tsumagari, Dana Battaglia, Tyrone Ryba, Ichiro Hiratani, Melanie Ehrlich, David M. Gilbert
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0123047

Dose-Dependent Effects of Morphine Exposure on mRNA and microRNA (miR) Expression in Hippocampus of Stressed Neonatal Mice
Cited by: 17
Author(s): Ryan M. McAdams, Ronald J. McPherson, Richard P. Beyer, Theo K. Bammler, Frederico M. Farin, Sandra E. Juul
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.ppat.1006676

Mycobacterium tuberculosis infection modulates adipose tissue biology
Cited by: 34
Author(s): Macarena Beigier-Bompadre, Georgina N. Montagna, Anja A. Kühl, Laura Lozza, January Weiner, Andreas Kupz, Alexis Vogelzang, Hans-Joachim Mollenkopf, Delia Löwe, Silke Bandermann, Anca Dorhoi, Volker Brinkmann, Kai Matuschewski, Stefan H. E. Kaufmann
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0233445

Identification of feature risk pathways of smoking-induced lung cancer based on SVM
Cited by: 6
Author(s): Rongjun Chen, Jiaqi Lin
Software Mentions: 1
Published: over 4 years ago

10.1042/BSR20180775

Analysis of anti-osteoporosis function of chlorogenic acid by gene microarray profiling in ovariectomy rat model
Cited by: 21
Author(s): Min Jun, Zhen Yuan, Qiao Zhang, Sijian Lin, Kai Wang, Jun Luo
Software Mentions: 1
Published: about 6 years ago

10.1042/BSR20201713

Identification of biomarkers associated with synovitis in rheumatoid arthritis by bioinformatics analyses
Cited by: 5
Author(s): Zhaoyan Li, Meng Xu, Ronghang Li, Zhe Zhu, Yuzhe Liu, Zhenwu Du, Guizhen Zhang, Yang Song
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.ppat.1007145

Non-linear hierarchy of the quorum sensing signalling pathway in bloodstream form African trypanosomes
Cited by: 34
Author(s): Lindsay McDonald, Mathieu Cayla, Alasdair Ivens, Binny M. Mony, Paula MacGregor, Eleanor Silvester, Kirsty Ross McWilliam, Keith R. Matthews
Software Mentions: 1
Published: over 6 years ago

10.1042/BSR20193823

Identification of novel biomarkers and candidate small molecule drugs in rheumatoid arthritis and osteoarthritis based on bioinformatics analysis of high-throughput data
Cited by: 9
Author(s): Bin Zuo, Junfeng Zhu, Fei Xiao, Chenglong Wang, Yun Shen, Xiao Chen
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0004563

Integrative Analysis of Epigenetic Modulation in Melanoma Cell Response to Decitabine: Clinical Implications
Cited by: 57
Author(s): Ruth Halaban, Michael Krauthammer, Mattia Pelizzola, Elaine Cheng, Daniela Kovacs, Mario Sznol, Stephan Ariyan, Deepak Narayan, Antonella Bacchiocchi, Annette M. Molinaro, Yuval Kluger, Min Deng, Nam Tran, Wengeng Zhang, Mauro Picardo, Jan J. Enghild
Software Mentions: 1
Published: almost 16 years ago

10.1042/BSR20201946

Circular RNA expression profiles in umbilical cord blood exosomes from normal and gestational diabetes mellitus patients
Cited by: 24
Author(s): Mingtao Cao, Le Zhang, Yongcheng Lin, Zhengying Li, Jianjuan Xu, Zhonghua Shi, Zhong Chen, Jinqi Ma, Juan Wen
Software Mentions: 1
Published: about 4 years ago

10.1042/BSR20182274

EPHA3 enhances macrophage autophagy and apoptosis by disrupting the mTOR signaling pathway in mice with endometriosis
Cited by: 8
Author(s): Hongmei Xu, Yu-Hang Gao, Yang Shu, Yi Wang, Qingyang Shi
Software Mentions: 1
Published: over 5 years ago

10.1042/BSR20200390

MIR600HG suppresses metastasis and enhances oxaliplatin chemosensitivity by targeting ALDH1A3 in colorectal cancer
Cited by: 19
Author(s): Yi Yao, Nan Li
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-016-3068-5

Dysregulation of mitotic machinery genes precedes genome instability during spontaneous pre-malignant transformation of mouse ovarian surface epithelial cells
Cited by: 10
Author(s): Ulises Urzúa, Sandra Ampuero, Katherine F. Roby, Garrison A. Owens, David J. Munroe
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0125228

Innate Responses Induced by Whole Inactivated Virus or Subunit Influenza Vaccines in Cultured Dendritic Cells Correlate with Immune Responses In Vivo
Cited by: 19
Author(s): Maaike Stoel, Jan Pool, Jacqueline de Vries-Idema, Fatiha Zaaraoui-Boutahar, M Bijl, Arno C. Andeweg, Jan Wilschut, Anke Huckriede
Software Mentions: 1
Published: over 9 years ago

10.1155/2020/4728947

An Autophagy-Related Long Noncoding RNA Signature Contributes to Poor Prognosis in Colorectal Cancer
Cited by: 35
Author(s): Jingsun Wei, Xin Ge, Yang Tang, Yuntao Qian, Wei Lu, Kai Jiang, Yunxia Fang, Maxwell Hwang, Dongliang Fu, Qian Xiao, Kefeng Ding
Software Mentions: 1
Published: about 4 years ago

10.1042/BSR20191503

Systematic large-scale meta-analysis identifies miRNA-429/200a/b and miRNA-141/200c clusters as biomarkers for necrotizing enterocolitis in newborn
Cited by: 16
Author(s): Hong Liu, Yibiao Wang
Software Mentions: 1
Published: about 5 years ago

10.1042/BSR20191985

Time series expression pattern of key genes reveals the molecular process of esophageal cancer
Cited by: 2
Author(s): Jiafu Wang, Xiang Xie, Yifeng Sun
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0137696

Computational Identification of Post Translational Modification Regulated RNA Binding Protein Motifs
Cited by: 7
Author(s): Andrew S. Brown, Bidyut K. Mohanty, Philip H. Howe
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0077281

Mammosphere Formation in Breast Carcinoma Cell Lines Depends upon Expression of E-cadherin
Cited by: 166
Author(s): Juan Manuel Iglesias, Izaskun Beloqui, Francisco García‐García, Olatz Leis, Alejandro Vázquez-Martín, Arrate Eguiara, Sílvia Cufí, Pavon Andres, Javier A. Menendez, Joaquı́n Dopazo, Ángel G. Martín
Software Mentions: 1
Published: about 11 years ago

10.1038/s41598-017-14814-x

Disease-relevant signalling-pathways in head and neck cancer: Taspase1’s proteolytic activity fine-tunes TFIIA function
Cited by: 8
Author(s): Alena Gribko, Angelina Hahlbrock, Sebastian Strieth, Sven Becker, Jan Hagemann, Max Deichelbohrer, Andreas Hildebrandt, Negusse Habtemichael, Désirée Wünsch
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-017-15023-2

Altered B-lymphopoiesis in mice with deregulated thrombopoietin signaling
Cited by: 3
Author(s): Amanda E. Au, Marion Lebois, Starling A. Sim, Ping Cannon, Jason Corbin, Pradnya Gangatirkar, Craig D. Hyland, Diane Moujalled, Angelika Rutgersson, Fatme Yassinson, Benjamin T. Kile, Kylie D. Mason, Ashley P. Ng, Warren S. Alexander, Emma C. Josefsson
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0068464

An Improved Method for TAL Effectors DNA-Binding Sites Prediction Reveals Functional Convergence in TAL Repertoires of Xanthomonas oryzae Strains
Cited by: 80
Author(s): Álvaro L. Pérez‐Quintero, Luis M. Rodriguez-R, Alexis Dereeper, Carolina Martínez López, Ralf Koebnik, Boris Szurek, Sébastien Cunnac
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0074184

Expression Signature as a Biomarker for Prenatal Diagnosis of Trisomy 21
Cited by: 13
Author(s): Marija Volk, Aleš Maver, Luca Lovrečić, Peter Juvan, Borut Peterlin
Software Mentions: 1
Published: about 11 years ago

10.1038/s41598-017-15348-y

Serotonin drives the acquisition of a profibrotic and anti-inflammatory gene profile through the 5-HT7R-PKA signaling axis
Cited by: 38
Author(s): Ángeles Domínguez-Soto, Alicia Usategui, Mateo de las Casas-Engel, Miriam Simón-Fuentes, Concha Nieto, Víctor D. Cuevas, Miguel A. Vega, José L. Pablos, Ángel L. Corbí
Software Mentions: 1
Published: about 7 years ago

10.1186/1755-8794-7-35

A systems biology approach to understand the pathophysiological mechanisms of cardiac pathological hypertrophy associated with rosiglitazone
Cited by: 18
Author(s): Lars Verschuren, Peter Y. Wielinga, Thomas Kelder, Marijana Radonjić, Kanita Salic, Robert Kleemann, Ben van Ommen, Teake Kooistra
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-017-16005-0

Comprehensive functional enrichment analysis of male infertility
Cited by: 23
Author(s): Seyyed Mohammad Razavi, Marjan Sabbaghian, Mahdi Jalili, Adeleh Divsalar, Olaf Wolkenhauer, Ali Salehzadeh‐Yazdi
Software Mentions: 1
Published: about 7 years ago

10.1186/s12920-019-0566-8

Discovery of stroke-related blood biomarkers from gene expression network models
Cited by: 13
Author(s): Konstantinos Theofilatos, Aigli Korfiati, Seferina Mavroudi, Matthew C. Cowperthwaite, Max Shpak
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0060051

FOXQ1, a Novel Target of the Wnt Pathway and a New Marker for Activation of Wnt Signaling in Solid Tumors
Cited by: 52
Author(s): Jon Christensen, Susanne Bentz, Thierry Sengstag, V. Prasad Shastri, Pascale Anderle
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0169286

Molecular Characteristics of High-Dose Melphalan Associated Oral Mucositis in Patients with Multiple Myeloma: A Gene Expression Study on Human Mucosa
Cited by: 10
Author(s): Mette Marcussen, Julie Støve Bødker, Henrik Bærbak Christensen, Preben Johansen, Søren Laurentius Nielsen, Ilse Christiansen, Olav J. Bergmann, Martin Bøgsted, Karen Dybkær, Mogens Vyberg, Hans Erik Johnsen
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-017-17776-2

Purification of replicating pancreatic β-cells for gene expression studies
Cited by: 3
Author(s): Reyes Carballar, Maria de Lluc Canyelles, Claudia Fernández, Yasmina Martí, Sarah Bonnin, Esther Castaño, Eduard Montanya, Noèlia Téllez
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-017-17840-x

Plant-derived compounds strigolactone GR24 and pinosylvin activate SIRT1 and enhance glucose uptake in rat skeletal muscle cells
Cited by: 18
Author(s): Shalem Modi, Nagendra Yaluri, Tarja Kokkola, Markku Laakso
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-017-18034-1

Effects of maternal obesity on Wharton’s Jelly mesenchymal stromal cells
Cited by: 8
Author(s): Heba Badraiq, Aleksandra Čvoro, Antonio Galleu, Marisa Simon, Cristian Miere, Carl Hobbs, Reiner Schulz, RC Siow, Francesco Dazzi, Duško Ilić
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-017-18041-2

Detection of Cystic Fibrosis Serological Biomarkers Using a T7 Phage Display Library
Cited by: 6
Author(s): H. S. Talwar, Samer Najeeb Hanoudi, Andreea Geamanu, Dana G. Kissner, Sorin Drăghici, Lobelia Samavati
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-017-17545-1

Comprehensive Expression Analysis of microRNAs and mRNAs in Synovial Tissue from a Mouse Model of Early Post-Traumatic Osteoarthritis
Cited by: 23
Author(s): Louise H. W. Kung, Varshini Ravi, Lynn Rowley, Katrina M. Bell, Christopher B. Little, John F. Bateman
Software Mentions: 1
Published: almost 7 years ago

10.1155/2021/5193913

Identification of Differentially Expressed Circular RNAs as miRNA Sponges in Lung Adenocarcinoma
Cited by: 4
Author(s): Yuechao Liu, Xin Wang, Lulu Bi, Hongbo Huo, Yan Shi, Yimeng Cui, Yaowen Cui, Ruixue Gu, Dexin Jia, Shuai Zhang, Li Cai, Xiaomei Li, Ying Xing
Software Mentions: 1
Published: about 3 years ago

10.1155/2021/6610511

Osthole Inhibits Breast Cancer Progression through Upregulating Tumor Suppressor GNG7
Cited by: 11
Author(s): Jie Mei, Zhihui Wang, Shaojie Zhao, Yan Zhang
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-017-18519-z

Comparative Analysis of Gene Expression Profiles of Human Dental Fluorosis and Kashin-Beck Disease
Cited by: 6
Author(s): Zhang Qiang, Jing Ma, Haiqing Liu, Duolong He, Lilin Chen, Honglu Wu, Hong Jiang, Qing Lü, Shenglu Bai
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0180660

A three-microRNA signature as a diagnostic and prognostic marker in clear cell renal cancer: An In Silico analysis
Cited by: 30
Author(s): Bin Liang, Jianying Zhao, Xuan Wang
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.15662

PIF* promotes brain re-myelination locally while regulating systemic inflammation- clinically relevant multiple sclerosis <i>M.smegmatis</i> model
Cited by: 17
Author(s): Giuseppe Migliara, Martin Mueller, Alessia Piermattei, Chaya Brodie, Michael J. Paidas, Eytan R. Barnea, Francesco Ria
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0086296

Transcriptomic Analysis of Liquid Non-Sporulating Streptomyces coelicolor Cultures Demonstrates the Existence of a Complex Differentiation Comparable to That Occurring in Solid Sporulating Cultures
Cited by: 39
Author(s): Paula Yagüe, Antonio Rodríguez‐García, María Teresa López-García, Beatriz Rioseras, Juan F. Martı́n, Jesús Sánchez, Ángel Manteca
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0135605

Next Generation Sequencing Analysis Reveals Segmental Patterns of microRNA Expression in Mouse Epididymal Epithelial Cells
Cited by: 42
Author(s): Brett Nixon, Simone J. Stanger, Bettina P. Mihalas, Jackson N. Reilly, Andy Anderson, Matthew D. Dun, Sonika Tyagi, Janet E. Holt, Eileen A. McLaughlin
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0179797

The RNA uridyltransferase Zcchc6 is expressed in macrophages and impacts innate immune responses
Cited by: 10
Author(s): Elyse Kozlowski, Gregory A. Wasserman, Marcos Morgan, Dónal O’Carroll, Nora-Guadalupe P. Ramirez, Suryaram Gummuluru, Jasmine Rah, Adam C. Gower, Michael H. Ieong, Lee J. Quinton, Joseph P. Mizgerd, Matthew R. Jones
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0031777

Endoplasmic Reticulum Stress-Sensing Mechanism Is Activated in Entamoeba histolytica upon Treatment with Nitric Oxide
Cited by: 55
Author(s): Julien Santi-Rocca, Spenser S. Smith, Christian Weber, Erika Pineda, Chung-Chau Hon, Emma Saavedra, Alfonso Olivos-García, Sandrine Rousseau, Marie‐Agnès Dillies, Jean‐Yves Coppée, Nancy Guillén
Software Mentions: 1
Published: over 12 years ago

10.1038/s41598-018-20457-3

Conserved DNA Methylation Signatures in Early Maternal Separation and in Twins Discordant for CO2 Sensitivity
Cited by: 13
Author(s): Francesca Giannese, Alessandra Luchetti, Giulia Barbiera, Valentina Lampis, Claudio Zanettini, Gun Peggy Knudsen, Simona Scaini, Dejan Lazarevic, Davide Cittaro, Francesca R. D’Amato, Marco Battaglia
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-20161-2

ITGB1-dependent upregulation of Caveolin-1 switches TGFβ signalling from tumour-suppressive to oncogenic in prostate cancer
Cited by: 24
Author(s): Teijo Pellinen, Sami Blom, Sara Rubio Sánchez, Katja Välimäki, John-Patrick Mpindi, Hind Azegrouz, Raffaele Strippoli, Raquel Nieto, Mariano Vitón, Irene Palacios, Riku Turkki, Yinhai Wang, Miguel Sánchez-Álvarez, Stig Nordling, Anna Bützow, Tuomas Mirtti, Antti Rannikko, Marı́a C. Montoya, Olli Kallioniemi, Miguel Á. del Pozo
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-20885-1

Laminar Flow Attenuates Macrophage Migration Inhibitory Factor Expression in Endothelial Cells
Cited by: 9
Author(s): Congzhen Qiao, Shengdi Li, Haocheng Lu, Fan Meng, Yanbo Fan, Yanhong Guo, Y. Eugene Chen, Jifeng Zhang
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0019556

Technical Variability Is Greater than Biological Variability in a Microarray Experiment but Both Are Outweighed by Changes Induced by Stimulation
Cited by: 26
Author(s): Penelope A Bryant, Gordon K. Smyth, Roy M. Robins-Browne, Nigel Curtis
Software Mentions: 1
Published: over 13 years ago

10.1038/s41598-018-21201-7

Development of a primary human Small Intestine-on-a-Chip using biopsy-derived organoids
Cited by: 479
Author(s): Magdalena Kasendra, Alessio Tovaglieri, Alexandra Sontheimer-Phelps, Hossein Baharvand, Amir Bein, Angeliki Chalkiadaki, William Scholl, Cheng Zhang, Hannah Rickner, Camilla A. Richmond, Hu Li, David T. Breault, Donald E. Ingber
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-21684-4

Molecular basis of differential nitrogen use efficiencies and nitrogen source preferences in contrasting Arabidopsis accessions
Cited by: 19
Author(s): Jochen Menz, Tim Range, Johannes Trini, Uwe Ludewig, Benjamin Neuhäuser
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-21337-6

CD38 promotes pristane-induced chronic inflammation and increases susceptibility to experimental lupus by an apoptosis-driven and TRPM2-dependent mechanism
Cited by: 24
Author(s): Sonia García‐Rodríguez, Antonio Rosal-Vela, Davide Botta, Luz Milbeth Cumba Garcia, Esther Zumaquero, Verónica Prados-Maniviesa, Daniela Cerezo-Wallis, Nicola Lo Buono, José-Ángel Robles-Guirado, Salvador Guerrero, Elena González-Paredes, Eduardo Andrés-León, Ángel L. Corbí, Matthias Mack, Friedrich Koch-Nolte, Ramón Merino, Mercedes Zubiaur, Frances E. Lund, Jaime Sancho
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-23129-4

Baseline mRNA expression differs widely between common laboratory strains of zebrafish
Cited by: 16
Author(s): Lindsay A. Holden, Kim H. Brown
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-23492-2

Identification of potential key protein interaction networks of BK virus nephropathy in patients receiving kidney transplantation
Cited by: 12
Author(s): Linpei Jia, Wenbin Fu, Rufu Jia, Leiyun Wu, Xiaoxia Li, Qiang Jia, Hong‐Liang Zhang
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0118226

Selection of Reference Genes for qPCR- and ddPCR-Based Analyses of Gene Expression in Senescing Barley Leaves
Cited by: 39
Author(s): Agnieszka Żmieńko, Anna Samelak-Czajka, Michał Góralski, Ewa Sobieszczuk‐Nowicka, Piotr Kozlowski, Marek Figlerowicz
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0039126

Transcriptional Responses of Resistant and Susceptible Fish Clones to the Bacterial Pathogen Flavobacterium psychrophilum
Cited by: 51
Author(s): Christelle Langevin, M. Mar Blanco, Samuel Martín, Luc Jouneau, Jean‐François Bernardet, Armel Houel, Aurélie Lunazzi, Éric Duchaud, Christian Michel, Edwige Quillet, Pierre Boudinot
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0045899

Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray
Cited by: 28
Author(s): Paula Fernández, Marcelo Soria, David Blesa, Julio Dirienzo, Sebastián Moschen, Máximo Rivarola, Bernardo Clavijo, Sergio González, Lucila Peluffo, Dario Príncipi, Guillermo A. A. Dosio, Luis Aguirrezábal, Francisco García‐García, Ana Conesa, H. Esteban Hopp, Joaquı́n Dopazo, Ruth Amelia Heinz, Norma Paniego
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0033284

Genome-Wide DNA Methylation Indicates Silencing of Tumor Suppressor Genes in Uterine Leiomyoma
Cited by: 102
Author(s): Antònia Navarro, Ping Yin, Diana Monsivais, Simon Lin, Pan Du, Jian Jun Wei, Serdar E. Bulun
Software Mentions: 1
Published: over 12 years ago

10.1186/s12920-020-00799-6

Comprehensive analysis of angiogenesis-related genes and pathways in early diabetic retinopathy
Cited by: 18
Author(s): Chufeng Gu, Thashi Lhamo, Chen Zou, Chuandi Zhou, Tong Su, Deji Draga, Da Luo, Zhi Zheng, Li Yin, Qinghua Qiu
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0035119

Seasonal Changes in Patterns of Gene Expression in Avian Song Control Brain Regions
Cited by: 42
Author(s): Christopher K. Thompson, John Meitzen, Kirstin Replogle, Jenny Drnevich, Karin Lent, Anne Marie Wissman, Federico M. Farin, Theo K. Bammler, Richard P. Beyer, David F. Clayton, David J. Perkel, Eliot A. Brenowitz
Software Mentions: 1
Published: over 12 years ago

10.1186/s12920-020-0657-6

DNA hypermethylation associated with upregulated gene expression in prostate cancer demonstrates the diversity of epigenetic regulation
Cited by: 64
Author(s): Ieva Rauluševičiūtė, Finn Drabløs, Morten Rye
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-018-24282-6

Dynamic transcriptomic analysis of Ischemic Injury in a Porcine Pre-Clinical Model mimicking Donors Deceased after Circulatory Death
Cited by: 14
Author(s): Sébastien Giraud, Clara Steichen, Géraldine Allain, Pierre Couturier, Delphine Labourdette, Sophie Lamarre, Virginie Ameteau, Solenne Tillet, Patrick Hannaert, Raphaël Thuillier, Thierry Hauet
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-24546-1

The observed alteration in BCL2 expression following lithium treatment is influenced by the choice of normalization method
Cited by: 7
Author(s): Odeya Damri, Galila Agam, Lilah Toker
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0006718

Identification of Keratinocyte Growth Factor as a Target of microRNA-155 in Lung Fibroblasts: Implication in Epithelial-Mesenchymal Interactions
Cited by: 190
Author(s): Nicolas Pottier, Thomas Maurin, B. Chevalier, Marie-Pierre Puisségur, Kévin Lebrigand, Karine Robbe-Sermesant, Thomas Bertero, Christian L. Lino Cardenas, Elisabeth Courcot, Géraldine Rios, Sandra Fourré, Jean-Marc Lo-Guidice, Brice Marcet, Bruno Cardinaud, Pascal Barbry, Bernard Mari
Software Mentions: 1
Published: over 15 years ago

10.1186/s12920-021-01087-7

Integrated bioinformatics analysis of core regulatory elements involved in keloid formation
Cited by: 4
Author(s): Chuying Li, Mei-Tong Jin, Yinli Luo, Zhehu Jin, Long-Quan Pi
Software Mentions: 1
Published: about 3 years ago

10.1038/s41598-018-25512-7

Expressional analysis of disease-relevant signalling-pathways in primary tumours and metastasis of head and neck cancers
Cited by: 16
Author(s): Dorothée Goesswein, Negusse Habtemichael, Aslihan Gerhold‐Ay, Johanna Mazur, Désirée Wünsch, Shirley K. Knauer, Julian Künzel, Christoph Matthias, Sebastian Strieth, Roland H. Stauber
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0190334

Stage-specific IFN-induced and IFN gene expression reveal convergence of type I and type II IFN and highlight their role in both acute and chronic stage of pathogenic SIV infection
Cited by: 10
Author(s): Nadia Echebli, Nicolas Tchitchek, Stéphanie Dupuy, Timothée Bruel, Caroline Passaes, Nathalie Bosquet, Roger Le Grand, Christine Bourgeois, Benoît Favier, Rémi Cheynier, Olivier Lambotte, Bruno Vaslin
Software Mentions: 1
Published: almost 7 years ago

10.18632/oncotarget.6379

Different prognostic impact of<i>STK11</i>mutations in non-squamous non-small-cell lung cancer
Cited by: 59
Author(s): Nicolas Pécuchet, Pierre Laurent‐Puig, Audrey Lupo, Antoine Legras, Marco Alifano, Karine Pallier, Audrey Didelot, Laure Gibault, Claire Danel, Pierre‐Alexandre Just, Marc Riquet, Françoise Le Pimpec-Barthes, Diane Damotte, Elizabeth Fabre, Hélène Blons
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-018-26944-x

Mitochondrial function is impaired in the skeletal muscle of pre-frail elderly
Cited by: 66
Author(s): Pénélope Andreux, Marcus P.J. van Diemen, Maxime R. Heezen, Johan Auwerx, Chris Rinsch, Geert Jan Groeneveld, Anurag Singh
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-26865-9

Identifying conserved UV exposure genes and mechanisms
Cited by: 6
Author(s): Susana I. L. Gomes, Carlos P. Roca, Janeck J. Scott-Fordsmand, Mónica J.B. Amorim
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0213078

Differential expression of miRNAs in acute myeloid leukemia quantified by Nextgen sequencing of whole blood samples
Cited by: 13
Author(s): Aakriti Pandita, Poornima Ramadas, Aarati Poudel, Nibal Saad, Ankit Anand, Alina Basnet, Dongliang Wang, Frank A. Middleton, Diana M. Gilligan
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0127003

Level of Fatty Acid Binding Protein 5 (FABP5) Is Increased in Sputum of Allergic Asthmatics and Links to Airway Remodeling and Inflammation
Cited by: 30
Author(s): Hille Suojalehto, Pia Anneli Sofia Kinaret, Maritta Kilpeläinen, Elina Toskala, Niina Ahonen, Henrik Wolff, Harri Alenius, Anne Puustinen
Software Mentions: 1
Published: over 9 years ago

10.1186/s12920-015-0103-3

Integrated genomics has identified a new AT/RT-like yet INI1-positive brain tumor subtype among primary pediatric embryonal tumors
Cited by: 14
Author(s): Donald Ming Tak Ho, Chuan Chi Shih, Muh Lii Liang, Chan Yen Tsai, Tsung Han Hsieh, Chin Han Tsai, Shih Chieh Lin, Ting Chang, Meng En Chao, Hsei Wei Wang, Tai-Tong Wong
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0106973

The Cultural Divide: Exponential Growth in Classical 2D and Metabolic Equilibrium in 3D Environments
Cited by: 52
Author(s): Krzysztof Wrzesinski, Adelina Rogowska-Wrzesińska, Rattiyaporn Kanlaya, Kamil Borkowski, Veit Schwämmle, Jie Dai, Kira Joensen, Katarzyna Wojdyła, Vasco Botelho Carvalho, Stephen J. Fey
Software Mentions: 1
Published: about 10 years ago

10.1016/j.isci.2021.102676

A human multi-cellular model shows how platelets drive production of diseased extracellular matrix and tissue invasion
Cited by: 26
Author(s): Beatrice Malacrida, Sam Nichols, Eleni Maniati, Roanne R. Jones, Robin Delanie-Smith, Reza Roozitalab, Eleanor J. Tyler, Morgan Thomas, Gina Boot, Jonas Mackerodt, Michelle Lockley, Martin M. Knight, Frances R. Balkwill, Oliver M.T. Pearce
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-018-27900-5

Comparative Analysis of Mutant Huntingtin Binding Partners in Yeast Species
Cited by: 5
Author(s): Yanding Zhao, Ashley A. Zurawel, Nicole P. Jenkins, Martin L. Duennwald, Chao Cheng, Arminja N. Kettenbach, Surachai Supattapone
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0008583

Transglutaminase 2, a Novel Regulator of Eicosanoid Production in Asthma Revealed by Genome-Wide Expression Profiling of Distinct Asthma Phenotypes
Cited by: 62
Author(s): Teal S. Hallstrand, Mark M. Wurfel, Ying Lü, Zhanglin Ni, Michael H. Gelb, William A. Altemeier, Richard P. Beyer, Moira L. Aitken, William R. Henderson
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0089406

JAK2-Centered Interactome Hotspot Identified by an Integrative Network Algorithm in Acute Stanford Type A Aortic Dissection
Cited by: 16
Author(s): Ping Sun, Duojiao Wu, Andrew E. Teschendorff, Tao Hong, Linyan Wang, Mengjia Qian, Chunsheng Wang, Xiangdong Wang
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-018-28168-5

Identification of novel ΔNp63α-regulated miRNAs using an optimized small RNA-Seq analysis pipeline
Cited by: 5
Author(s): Suraj Sakaram, Michael P. Craig, Natasha T. Hill, Amjad A. Aljagthmi, Christian M. Garrido, Oleg Paliy, Michael Bottomley, Michael L. Raymer, Madhavi Kadakia
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0000781

Sterility and Gene Expression in Hybrid Males of Xenopus laevis and X. muelleri
Cited by: 58
Author(s): John H. Malone, Thomas H. Chrzanowski, Pawel Michalak
Software Mentions: 1
Published: over 17 years ago

10.1038/s41598-018-28563-y

Fatty liver is associated with blood pathways of inflammatory response, immune system activation and prothrombotic state in Young Finns Study
Cited by: 10
Author(s): Tuukka Taipale, Ilkka Seppälä, Emma Raitoharju, Nina Mononen, Leo-Pekka Lyytikäinen, Thomas Illig, Mélanie Waldenberger, Markus Juonala, Nina Hutri‐Kähönen, Niku Oksala, Mika Kähönen, Olli T. Raitakari, Terho Lehtimäki
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-29107-0

Differentially Methylated Genes in Saliva are linked to Childhood Stress
Cited by: 52
Author(s): Ligia A. Papale, Leslie J. Seltzer, Andy Madrid, Seth D. Pollak, Reid S. Alisch
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-29593-2

Mediation analysis reveals common mechanisms of RUNX1 point mutations and RUNX1/RUNX1T1 fusions influencing survival of patients with acute myeloid leukemia
Cited by: 9
Author(s): Roman Hornung, Vindi Jurinović, Aarif M.N. Batcha, Stefanos A. Bamopoulos, Maja Rothenberg‐Thurley, Susanne Amler, Maria Cristina Sauerland, Wolfgang E. Berdel, Bernhard Wörmann, Stefan K. Bohlander, Jan Braess, Wolfgang Hiddemann, Sören Lehmann, Sylvain Mareschal, Karsten Spiekermann, Klaus H. Metzeler, Tobias Herold, Anne‐Laure Boulesteix
Software Mentions: 1
Published: over 6 years ago

10.1186/1755-8794-6-41

Transcriptome signatures in Helicobacter pylori-infected mucosa identifies acidic mammalian chitinase loss as a corpus atrophy marker
Cited by: 49
Author(s): Intawat Nookaew, Kaisa Thorell, Kuntal Worah, Shugui Wang, Martin L. Hibberd, Henrik Sjövall, Sven Pettersson, Jens Nielsen, Samuel Lundin
Software Mentions: 1
Published: about 11 years ago

10.1186/1755-8794-7-13

Childhood abuse is associated with methylation of multiple loci in adult DNA
Cited by: 147
Author(s): Matthew Suderman, Nada Borghol, Jane J. Pappas, Snehal M Pinto Pereira, Marcus Pembrey, Clyde Hertzman, Chris Power, Moshe Szyf
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0063283

A Cocoa Peptide Protects Caenorhabditis elegans from Oxidative Stress and β-Amyloid Peptide Toxicity
Cited by: 67
Author(s): Patricia Martorell, Esther Bataller, Silvia Llopis, Núria González, Beatriz Tarazona Álvarez, Fernando Montón, Pepa Ortiz, Daniel Ramón, Salvador Genovés
Software Mentions: 1
Published: over 11 years ago

10.18632/oncotarget.10949

Prognostic value of molecular events from negative surgical margin of non-small-cell lung cancer
Cited by: 7
Author(s): Bangrong Cao, Feng Li, Dongfang Lu, Yan Liu, Yu Liu, Shu Guo, Ning Han, Xiangyang Liu, Yousheng Mao, Jie He, Shujun Cheng, Yanning Gao, Kaitai Zhang
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-30313-z

The Overlap of Lung Tissue Transcriptome of Smoke Exposed Mice with Human Smoking and COPD
Cited by: 17
Author(s): Ma’en Obeidat, Anna Dvorkin‐Gheva, Xuan Li, Yohan Bossé, Corry‐Anke Brandsma, David C. Nickle, Philip M. Hansbro, Rosa Faner, Àlvar Agustí, Peter D. Paré, Martin R. Stämpfli, Don D. Sin
Software Mentions: 1
Published: over 6 years ago

Projects: bioconductor: limma

Papers Mentioning limma 7,776