bioconductor: limma | Projects | Ecosyste.ms: Papers

10.3390/cells9102329

Complexity of Brassica oleracea–Alternaria brassicicola Susceptible Interaction Reveals Downregulation of Photosynthesis at Ultrastructural, Transcriptional, and Physiological Levels
Cited by: 16
Author(s): Violetta Katarzyna Macioszek, Magdalena Gapińska, Agnieszka Żmieńko, Mirosław Sobczak, Andrzej Skoczowski, Jakub Oliwa, Andrzej K. Kononowicz
Software Mentions: 1
Published: about 6 years ago

10.1186/s12859-015-0808-5

Practical impacts of genomic data “cleaning” on biological discovery using surrogate variable analysis
Cited by: 50
Author(s): Andrew E. Jaffe, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinbergern, Joshua G. Chenoweth, Ronald D.G. McKay, Jeffrey T. Leek, Carlo Colantuoni
Software Mentions: 1
Published: about 11 years ago

10.3390/cells10020325

Genetic Perturbation of Pyruvate Dehydrogenase Kinase 1 Modulates Growth, Angiogenesis and Metabolic Pathways in Ovarian Cancer Xenografts
Cited by: 8
Author(s): Carolina Venturoli, Ilaria Piga, Matteo Curtarello, Martina Verza, Giovanni Esposito, Santina Venuto, Filippo Navaglia, Angela Grassi, Stefano Indraccolo
Software Mentions: 1
Published: almost 6 years ago

10.3390/cells9061333

Heterogeneity of Metabolic Vulnerability in Imatinib-Resistant Gastrointestinal Stromal Tumor
Cited by: 11
Author(s): Wen‐Shih Huang, Jianlu Gao, Ziqing Chen, Hao Shi, Jing Yuan, Huanhuan Cui, Chun‐Nan Yeh, Robert Bränström, Catharina Larsson, Shuijie Li, Weng‐Onn Lui
Software Mentions: 1
Published: over 6 years ago

10.3389/fnmol.2018.00497

Circular RNA Expression Alteration and Bioinformatics Analysis in Rats After Traumatic Spinal Cord Injury
Cited by: 45
Author(s): Chuan Qin, Changbin Liu, Degang Yang, Feng Gao, Xin Zhang, Chao Zhang, Liyong Du, Mingliang Yang, Jianjun Li
Software Mentions: 1
Published: almost 8 years ago

10.3390/cells9061327

Role of microRNA 690 in Mediating Angiotensin II Effects on Inflammation and Endoplasmic Reticulum Stress
Cited by: 14
Author(s): Kalhara R. Menikdiwela, Latha Ramalingam, Mostafa M. Abbas, Halima Bensmail, Shane Scoggin, Nishan S. Kalupahana, Asha Palat, Preethi H. Gunaratne, Naima Moustaid‐Moussa
Software Mentions: 1
Published: over 6 years ago

10.3390/cells9040859

Failure to Down-Regulate miR-154 Expression in Early Postnatal Mouse Lung Epithelium Suppresses Alveologenesis, with Changes in Tgf-β Signaling Similar to those Induced by Exposure to Hyperoxia
Cited by: 6
Author(s): Cho-Ming Chao, Gianni Carraro, Zvonimir A. Rako, Johannes Kolck, Jamschid Sedighi, Volker Zimmermann, Alena Moiseenko, Jochen Wilhelm, Brittany M. Young, Chong Lei, Jin Wu, Adriana Contreras, Parviz Minoo, Guillermo Barreto, David Warburton, Savério Bellusci
Software Mentions: 1
Published: over 6 years ago

10.3389/fneur.2021.672570

A Rare Variant of ANK3 Is Associated With Intracranial Aneurysm
Cited by: 3
Author(s): Junyu Liu, Xin Liao, Jilin Zhou, Bingyang Li, Lu Xu, Songlin Liu, Yifeng Li, Dejian Yuan, Chongyu Hu, Weixi Jiang, Junxia Yan
Software Mentions: 1
Published: over 5 years ago

10.3390/cells9071726

miR-22-3p Negatively Affects Tumor Progression in T-Cell Acute Lymphoblastic Leukemia
Cited by: 13
Author(s): Valentina Saccomani, Angela Grassi, Erich Piovan, Deborah Bongiovanni, Ludovica Di Martino, Sonia Minuzzo, Valeria Tosello, Paola Zanovello
Software Mentions: 1
Published: over 6 years ago

10.3390/cells7110184

Cytogenetic and Transcriptomic Analysis of Human Endometrial MSC Retaining Proliferative Activity after Sublethal Heat Shock
Cited by: 9
Author(s): М. А. Шилина, Т. М. Гринчук, Olga V. Anatskaya, Alexander E. Vinogradov, Л. Л. Алексеенко, Artem Elmuratov, Nikolay Nikolsky
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2105-9-S4-S9

Reconstructing networks of pathways via significance analysis of their intersections
Cited by: 29
Author(s): Mirko Francesconi, Daniel Remondini, Nicola Neretti, John M. Sedivy, Leon N. Cooper, E. Verondini, Luciano Milanesi, Gastone Castellani
Software Mentions: 1
Published: over 18 years ago

10.3390/cells8010015

A Role for Circular Non-Coding RNAs in the Pathogenesis of Sporadic Parathyroid Adenomas and the Impact of Gender-Specific Epigenetic Regulation
Cited by: 12
Author(s): Maria P. Yavropoulou, Christos Poulios, Nikolaos Michalopoulos, Ariadni Gatzou, Sofia Chrisafi, Stylianos Mantalovas, Theodossis S Papavramidis, Emily Daskalaki, Electra Sofou, Kalliopi Kotsa, Ισαάκ Κεσίσογλου, Pantelis Zebekakis, John G. Yovos
Software Mentions: 1
Published: almost 8 years ago

10.1155/2018/6451298

LCK as a Potential Therapeutic Target for Acute Rejection after Kidney Transplantation: A Bioinformatics Clue
Cited by: 6
Author(s): Linpei Jia, Rufu Jia, Yinping Li, Xiaoxia Li, Qiang Jia, Hong‐Liang Zhang
Software Mentions: 1
Published: over 8 years ago

10.3389/fneur.2021.624696

The Delayed Neuropathological Consequences of Traumatic Brain Injury in a Community-Based Sample
Cited by: 20
Author(s): Nadia Postupna, Shannon Rose, Laura E. Gibbons, Natalie M Coleman, Leanne L Hellstern, Kayla Ritchie, Angela Wilson, Eiron Cudaback, Xianwu Li, Erica J. Melief, Allison Beller, Jeremy A. Miller, Amber Nolan, Desiree A. Marshall, Rod Walker, Thomas J. Montine, Eric B. Larson, Paul K. Crane, Richard G. Ellenbogen, Edward S. Lein, Kristen Dams-O’Connor, C. Dirk Keene
Software Mentions: 1
Published: over 5 years ago

10.3389/fneur.2020.00978

Single-Arm, Non-randomized, Time Series, Single-Subject Study of Fecal Microbiota Transplantation in Multiple Sclerosis
Cited by: 43
Author(s): Phillip A. Engen, Antonia M. Zaferiou, Heather Rasmussen, Ankur Naqib, Stefan J. Green, Louis Fogg, Christopher B. Forsyth, Shohreh Raeisi, Bruce R. Hamaker, Ali Keshavarzian
Software Mentions: 1
Published: about 6 years ago

10.3389/fneur.2021.666750

Identification of Circular RNAs Related to Vascular Endothelial Proliferation, Migration, and Angiogenesis After Spinal Cord Injury Using Microarray Analysis in Female Mice
Cited by: 4
Author(s): Xin Ye, Yilei Chen, Jiasheng Wang, Jian Chen, Ying Yao, Linlin Wang, Fengdong Zhao
Software Mentions: 1
Published: about 5 years ago

10.1155/2021/6661625

Identification of Immune-Related Prognostic Biomarkers Associated with HPV-Positive Head and Neck Squamous Cell Carcinoma
Cited by: 6
Author(s): Yifei Chen, Jin Nie, Xiangsheng Li, Tao Fan, Xiaowen Deng, Dan Liang, Gui‐Lin Song
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12859-021-04197-2

Hypergraph models of biological networks to identify genes critical to pathogenic viral response
Cited by: 29
Author(s): Song Feng, Emily Heath, Brett Jefferson, Cliff Joslyn, Henry Kvinge, Hugh D. Mitchell, Brenda Praggastis, Amie J. Eisfeld, Amy C. Sims, Larissa B. Thackray, Shufang Fan, Kevin B. Walters, Peter Halfmann, Danielle Westhoff-Smith, Qing Tan, Vineet D. Menachery, Timothy P. Sheahan, Adam S. Cockrell, Jacob Kocher, Kelly G. Stratton, Natalie C. Heller, Lisa Bramer, Michael S. Diamond, Ralph S. Baric, Katrina M. Waters, Yoshihiro Kawaoka, Jason McDermott, Emilie Purvine
Software Mentions: 1
Published: over 5 years ago

10.3389/fnins.2019.00633

Meta-Analysis of Gene Expression and Identification of Biological Regulatory Mechanisms in Alzheimer's Disease
Cited by: 35
Author(s): Lining Su, Sufen Chen, Chenqing Zheng, Wei H, Xiu–Peng Song
Software Mentions: 1
Published: over 7 years ago

10.3389/fnins.2020.00488

Identification of the Hub Genes Related to Nerve Injury-Induced Neuropathic Pain
Cited by: 6
Author(s): Kai Wang, Yi Duan, Zhuang Yu, Binhai Zhu, Shuiqing Li, Xiaoguang Liu
Software Mentions: 1
Published: over 6 years ago

10.1155/2015/952184

Electroporated Antigen-Encoding mRNA Is Not a Danger Signal to Human Mature Monocyte-Derived Dendritic Cells
Cited by: 6
Author(s): Stefanie Hoyer, Kerstin F. Gerer, Isabell A. Pfeiffer, Sabrina Prommersberger, Sandra Höfflin, Tanushree Jaitly, Luca Beltrame, Duccio Cavalieri, Gerold Schuler, Julio Vera, Niels Schaft, Jan Dörrie
Software Mentions: 1
Published: almost 12 years ago

10.1016/j.stem.2012.02.023

The Germ Cell Determinant Blimp1 Is Not Required for Derivation of Pluripotent Stem Cells
Cited by: 22
Author(s): Siqin Bao, Harry G. Leitch, Astrid Gillich, Jennifer Nichols, Fuchou Tang, Shinseog Kim, Caroline Lee, Thomas P. Zwaka, Xihe Li, M. Azim Surani
Software Mentions: 1
Published: over 14 years ago

10.1038/s41422-019-0181-4

AIF-regulated oxidative phosphorylation supports lung cancer development
Cited by: 56
Author(s): Rao S, Laura Mondragón, Blanka Pranjic, Toshikatsu Hanada, Gautier Stoll, Thomas Köcher, Peng Zhang, Alexander Jais, Alexander Lercher, Andréas Bergthaler, Daniel Schramek, Katharina Haigh, Valentina Sica, Marion Leduc, Nazanine Modjtahedi, Tsung-Pin Pai, Masahiro Onji, Iris Uribesalgo, Reiko Hanada, I. Kozieradzki, Rubina Koglgruber, Shane J. F. Cronin, Zhi‐Gang She, Franz Quehenberger, Helmut Popper, Lukas Kenner, Jody J. Haigh, Oliver Kepp, Malgorzata Rak, Kaican Cai, Guido Kroemer, Josef Penninger
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0019640

A Nonparametric Mean-Variance Smoothing Method to Assess Arabidopsis Cold Stress Transcriptional Regulator CBF2 Overexpression Microarray Data
Cited by: 3
Author(s): Patrick J. Hu, Tapabrata Maiti
Software Mentions: 1
Published: over 15 years ago

10.18632/aging.203300

LncRNA CCAT1 promotes prostate cancer cells proliferation, migration, and invasion through regulation of miR-490-3p/FRAT1 axis
Cited by: 9
Author(s): Xiaowei Cai, Yiheng Dai, Peng Gao, Guanyu Ren, Dingcai Cheng, Bo Wang, Yi Wang, Jian Yu, Yueyao Du, Xizhi Wang, Boxin Xue
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0106076

Long Non-Coding RNAs Differentially Expressed between Normal versus Primary Breast Tumor Tissues Disclose Converse Changes to Breast Cancer-Related Protein-Coding Genes
Cited by: 33
Author(s): Kristin Reiche, Katharina Kasack, S Schreiber, Torben Lüders, Eldri Undlien Due, Bjørn Naume, Margit Riis, Vessela N. Kristensen, Friedemann Horn, Anne Lise Børresen-Dale, Jörg Hackermüller, Lars Oliver Baumbusch
Software Mentions: 1
Published: about 12 years ago

10.18632/oncotarget.12103

Profiles of miRNAs matched to biology in aromatase inhibitor resistant breast cancer
Cited by: 12
Author(s): Reiner Hoppe, Ping Fan, Florian Büttner, Stefan Winter, Amit Tyagi, Heather E. Cunliffe, V. Craig Jordan, Hiltrud Brauch
Software Mentions: 1
Published: about 10 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: almost 16 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 12 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 9 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 15 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 15 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 11 years ago

10.3389/fnins.2013.00033

Peripheral blood RNA gene expression profiling in patients with bacterial meningitis
Cited by: 38
Author(s): Margit Lill, Sulev Kõks, Ursel Soomets, Leonard C. Schalkwyk, Cathy Fernandes, Irja Lutsar, Pille Taba
Software Mentions: 1
Published: almost 14 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 6 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: over 17 years ago

10.1186/1471-2105-12-197

Linear and non-linear dependencies between copy number aberrations and mRNA expression reveal distinct molecular pathways in breast cancer
Cited by: 37
Author(s): Hiroko Kato Solvang, Ole Christian Lingjærde, Arnoldo Frigessi, Anne‐Lise Børresen‐Dale, Vessela N. Kristensen
Software Mentions: 1
Published: over 15 years ago

10.3389/fnins.2013.00021

The Effect of Nicotinamide on Gene Expression in a Traumatic Brain Injury Model
Cited by: 16
Author(s): Gail D. Anderson, Todd C. Peterson, Fred M. Farin, Theo K. Bammler, Richard P. Beyer, Eric D. Kantor, Michael R. Hoane
Software Mentions: 1
Published: almost 14 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 11 years ago

10.1186/1471-2105-11-27

Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach
Cited by: 101
Author(s): Dirk Repsilber, Sabine Kern, Anna Telaar, Gerhard Walzl, Gillian F. Black, Joachim Selbig, Shreemanta K. Parida, Stefan H. E. Kaufmann, Marc Jacobsen
Software Mentions: 1
Published: almost 17 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 11 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 13 years ago

10.3389/fonc.2020.01008

Identification of Immune-Related Prognostic Biomarkers Based on the Tumor Microenvironment in 20 Malignant Tumor Types With Poor Prognosis
Cited by: 8
Author(s): Yu Liu, Hao Zhou, Jing Zheng, Xiaojun Zeng, Wei Yu, Wei Liu, Gan Huang, Yang Zhang, Weiling Fu
Software Mentions: 1
Published: over 6 years ago

10.3389/fonc.2020.00333

Alterations in Immune-Related Genes as Potential Marker of Prognosis in Breast Cancer
Cited by: 21
Author(s): Bei Li, Rongxin Geng, Qi Wu, Qian Yang, Si Sun, Shan Zhu, Zhiliang Xu
Software Mentions: 1
Published: over 6 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 13 years ago

10.18632/oncotarget.12257

Integration of zebrafish fin regeneration genes with expression data of human tumors <i>in silico</i> uncovers potential novel melanoma markers
Cited by: 26
Author(s): Martin Hagedorn, Géraldine Siegfried, Katarzyna B. Hooks, Abdel‐Majid Khatib
Software Mentions: 1
Published: about 10 years ago

10.3389/fonc.2020.567021

JAG1, Regulated by microRNA-424-3p, Involved in Tumorigenesis and Epithelial–Mesenchymal Transition of High Proliferative Potential-Pituitary Adenomas
Cited by: 9
Author(s): Yiyuan Chen, Bin Li, Jiaxuan Feng, Qiuyue Fang, Jinhua Cheng, Weiyan Xie, Chuzhong Li, Sen Cheng, Yazhou Zhang, Hua Gao
Software Mentions: 1
Published: almost 6 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 13 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 13 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 10 years ago

10.3389/fonc.2019.00685

4T1 Mammary Carcinoma Colonization of Metastatic Niches Is Accelerated by Obesity
Cited by: 21
Author(s): Gabriela Coeli Menezes Evangelista, Pollyanna Amaral Salvador, Sara Malaguti Andrade Soares, Luciana Rodrigues Carvalho Barros, Felipe Henrique da Cunha Xavier, Luiza Macedo Abdo, Ana Cristina Moura Gualberto, Gilson Costa Macedo, Maria Alejandra Clavijo-Salomon, Jacy Gameiro
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2105-9-117

A mixture model approach to sample size estimation in two-sample comparative microarray experiments
Cited by: 14
Author(s): Tommy S Jørstad, Herman Midelfart, Atle M. Bones
Software Mentions: 1
Published: over 18 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 9 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 13 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 11 years ago

10.1186/1471-2105-12-134

SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects
Cited by: 69
Author(s): Alexis Dereeper, Stéphane Nicolas, Loïc Le Cunff, Roberto Baciliéri, Agnès Doligez, Jean‐Pierre Péros, Manuel Ruiz, Patrice This
Software Mentions: 1
Published: over 15 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 9 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 14 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 15 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 11 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 14 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 14 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 14 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 14 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: about 17 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 9 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 7 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 11 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 12 years ago

10.3389/fonc.2021.592393

Clinical and Genetic Predictive Models for the Prediction of Pathological Complete Response to Optimize the Effectiveness for Trastuzumab Based Chemotherapy
Cited by: 1
Author(s): Lun Li, Min Chen, Shuyue Zheng, Hanlu Li, Weiru Chi, Bingqiu Xiu, Qi Zhang, Jian Hou, Wang Jia, Jiong Wu
Software Mentions: 1
Published: over 5 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 17 years ago

10.3389/fonc.2021.700084

A New Prognostic Risk Signature of Eight Ferroptosis-Related Genes in the Clear Cell Renal Cell Carcinoma
Cited by: 8
Author(s): Ji Chen, Yating Zhan, Rongrong Zhang, Bin Chen, Junting Huang, Chunxue Li, Wenjie Zhang, Yajing Wang, Yuxiang Gao, Jianjian Zheng, Yeping Li
Software Mentions: 1
Published: over 5 years ago

10.1093/infdis/jiy420

Impact of Zostavax Vaccination on T-Cell Accumulation and Cutaneous Gene Expression in the Skin of Older Humans After Varicella Zoster Virus Antigen–Specific Challenge
Cited by: 10
Author(s): Nayna Patel, Milica Vukmanovic‐Stejic, Mayte Suárez‐Fariñas, Emma S. Chambers, Daisy Sandhu, Judilyn Fuentes‐Duculan, Neil A. Mabbott, M.H.A. Rustin, James G. Krueger, Arne N. Akbar
Software Mentions: 1
Published: about 8 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 12 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: about 19 years ago

Projects: bioconductor: limma

Science Score: 78/100

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Papers Mentioning limma 7,776