bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1186/1471-2105-13-86

DNA methylation arrays as surrogate measures of cell mixture distribution
Cited by: 2,436
Author(s): E. Andrés Houseman, William P. Accomando, Devin C. Koestler, Brock C. Christensen, Carmen J. Marsit, Heather H. Nelson, John K. Wiencke, Karl T. Kelsey
Software Mentions: 1
Published: over 12 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 12 years ago

10.1371/journal.pone.0054248

Lack of RsmA-Mediated Control Results in Constant Hypervirulence, Cell Elongation, and Hyperflagellation in Pectobacterium wasabiae
Cited by: 25
Author(s): Viia Kõiv, Liis Andresen, Martin Broberg, Jekaterina Frolova, Panu Somervuo, Petri Auvinen, Minna Pirhonen, Tanel Tenson, Andres Mäe
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2105-7-261

Empirical array quality weights in the analysis of microarray data
Cited by: 270
Author(s): Matthew E. Ritchie, Dileepa S. Diyagama, Jody Neilson, Ryan K. van Laar, Alexander Dobrovic, Andrew Holloway, Gordon K. Smyth
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0140467

Genome-Wide DNA Methylation Patterns of Bovine Blastocysts Developed In Vivo from Embryos Completed Different Stages of Development In Vitro
Cited by: 67
Author(s): Dessie Salilew‐Wondim, Éric Fournier, M. Hoelker, Mohammed Saeed‐Zidane, Ernst Tholen, Christian Looft, Christiane Neuhoff, U. Besenfelder, V. Havlíček, F. Rings, Dominic Gagné, Marc‐André Sirard, Claude Robert, Habib A. Shojaei Saadi, Ahmed Gad, K. Schellander, Dawit Tesfaye
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0063825

Global Gene Expression Profiling in PAI-1 Knockout Murine Heart and Kidney: Molecular Basis of Cardiac-Selective Fibrosis
Cited by: 33
Author(s): Asish K. Ghosh, Sheila B. Murphy, Raj Kishore, Douglas E. Vaughan
Software Mentions: 1
Published: over 11 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 4 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 4 years ago

10.1371/journal.pone.0082473

Molecular Strategies of the Caenorhabditis elegans Dauer Larva to Survive Extreme Desiccation
Cited by: 97
Author(s): Cihan Erkut, Andrej Vasilj, Sebastian Boland, Bianca Habermann, Andrej Shevchenko, Teymuras V. Kurzchalia
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2105-10-45

Comparison of small n statistical tests of differential expression applied to microarrays
Cited by: 75
Author(s): Carl Murie, Owen Z. Woody, Anna Y. Lee, Robert Nadon
Software Mentions: 1
Published: almost 16 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 4 years ago

10.1371/journal.pone.0044609

In Vivo Functional Requirement of the Mouse Ifitm1 Gene for Germ Cell Development, Interferon Mediated Immune Response and Somitogenesis
Cited by: 10
Author(s): Ingeborg Klymiuk, Lukas Kenner, Thure Adler, Dirk H. Busch, Auke Boersma, Martin Irmler, Valérie Gailus‐Durner, Helmut Fuchs, Nicole R. Leitner, Mathias Müller, Ralf Kühn, Michaela Schlederer, Irina Treise, Martin Hrabé de Angelis, Johannes Beckers
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0086490

Genome and Transcriptome Analysis of the Basidiomycetous Yeast Pseudozyma antarctica Producing Extracellular Glycolipids, Mannosylerythritol Lipids
Cited by: 34
Author(s): Tomotake Morita, Hideaki Koike, Hiroko Hagiwara, Emi Ito, Masayuki Machida, Shun Sato, Hiroshi Habe, Daï Kitamoto
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0003279

Single-Species Microarrays and Comparative Transcriptomics
Cited by: 17
Author(s): Frédéric J. J. Chain, Dora Ilieva, Ben Evans
Software Mentions: 1
Published: about 16 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 5 years ago

10.1186/1471-2105-9-409

Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios
Cited by: 121
Author(s): Johan Staaf, Johan Vallon‐Christersson, David Lindgren, Gunnar Juliusson, Richard Rosenquist, Mattias Höglund, Åke Borg, Markus Ringnér
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0068415

Gene Expression Profiling of Immune-Competent Human Cells Exposed to Engineered Zinc Oxide or Titanium Dioxide Nanoparticles
Cited by: 87
Author(s): Soile Tuomela, Reija Autio, Tina Buerki-Thurnherr, Osman Arslan, Andrea Kunzmann, Britta Andersson-Willman, Peter Wick, Sanjay Mathur, Annika Scheynius, Harald F. Krug, Bengt Fadeel, Riitta Lahesmaa
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0041041

Role of Heat-Stable Enterotoxins in the Induction of Early Immune Responses in Piglets after Infection with Enterotoxigenic Escherichia coli
Cited by: 59
Author(s): Michaela Loos, Marisa Geens, Stijn Schauvliege, Frank Gasthuys, Jan van der Meulen, J. Daniel Dubreuil, Bruno Goddeeris, Theodoor Niewold, Eric Cox
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0159010

Gremlin-1 Overexpression in Mouse Lung Reduces Silica-Induced Lymphocyte Recruitment – A Link to Idiopathic Pulmonary Fibrosis through Negative Correlation with CXCL10 Chemokine
Cited by: 11
Author(s): Katri Koli, Eva Sutinen, Mikko Rönty, Pia Rantakari, Vittorio Fortino, Ville Pulkkinen, Dario Greco, Petra Sipilä, Marjukka Myllärniemi
Software Mentions: 1
Published: over 8 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 9 years ago

10.1371/journal.pone.0194229

Pure flavonoid epicatechin and whole genome gene expression profiles in circulating immune cells in adults with elevated blood pressure: A randomised double-blind, placebo-controlled, crossover trial
Cited by: 25
Author(s): Diederik Esser, Johanna M. Geleijnse, Juri C. Matualatupauw, James I Dower, Daan Kromhout, P.C.H. Hollman, Lydia A. Afman
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0207470

CRB3 and the FERM protein EPB41L4B regulate proliferation of mammary epithelial cells through the release of amphiregulin
Cited by: 2
Author(s): Stephanie Walker, Laura M. Selfors, Ben Margolis, Joan S. Brugge
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0058104

Identification and Characterization of MicroRNAs Controlled by the Osteoblast-Specific Transcription Factor Osterix
Cited by: 46
Author(s): Chen Qin, Wenbin Liu, Krishna M. Sinha, Hideyo Yasuda, Benoít de Crombrugghe
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0189153

Altered intragenic DNA methylation of HOOK2 gene in adipose tissue from individuals with obesity and type 2 diabetes
Cited by: 21
Author(s): Sandra Rodríguez-Rodero, Edelmiro Menéndez Torre, Gustavo Fernández-Bayón, Paula Morales Sánchez, Lourdes Sanz, Estrella Olga Turienzo Santos, Juan José González, Ceferino Martínez-Faedo, Lorena Suárez-Gutiérrez, Jessica Ares Blanco, Lucía Díaz-Naya, Alicia Martín-Nieto, Juan Luís Fernández-Morera, Mario F. Fraga, Elías Delgado
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0069694

A Strong Anti-Inflammatory Signature Revealed by Liver Transcription Profiling of Tmprss6−/− Mice
Cited by: 8
Author(s): Michela Riba, Marco Rausa, Melissa Sorosina, Davide Cittaro, Josè Manuel Garcia Manteiga, Antonella Nai, Alessia Pagani, Filippo Martinelli Boneschi, Elia Stupka, Clara Camaschella, Laura Silvestri
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0185611

A proteomics approach to identify targets of the ubiquitin-like molecule Urm1 in Drosophila melanogaster
Cited by: 10
Author(s): Behzad Khoshnood, Ingrid Dacklin, Caroline Grabbe
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0165913

Novel Gene Expression Profile of Women with Intrinsic Skin Youthfulness by Whole Transcriptome Sequencing
Cited by: 11
Author(s): Jin Xu, Robert C. Spitale, Linna Guan, Ryan A. Flynn, Enrique Torre, Rui Li, Inbar Raber, Kun Qu, Dale Kern, Helen Knaggs, Howard Y. Chang, Anne Lynn S. Chang
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0187581

Circular RNA profile of infantile hemangioma by microarray analysis
Cited by: 17
Author(s): Cong Fu, Ruihua Lv, Guangqi Xu, Linfeng Zhang, Jianhai Bi, Li Lin, Xiaowen Liu, Ran Huo
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0008066

Spatial and Temporal Analysis of Gene Expression during Growth and Fusion of the Mouse Facial Prominences
Cited by: 55
Author(s): Weiguo Feng, Sonia M. Leach, Hannah Tipney, Tzulip Phang, Mark W. Geraci, Richard A. Spritz, Lawrence Hunter, Trevor Williams
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0010215

Immunoregulatory Actions of Epithelial Cell PPAR γ at the Colonic Mucosa of Mice with Experimental Inflammatory Bowel Disease
Cited by: 42
Author(s): Saroj Kant Mohapatra, Amir J. Guri, Montserrat Climent, Cristina Goena Vives, Adria Carbo, William Horne, Raquel Hontecillas, Josep Bassaganya‐Riera
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0020041

Glioblastoma Models Reveal the Connection between Adult Glial Progenitors and the Proneural Phenotype
Cited by: 136
Author(s): Liang Liu, Adam M. Sonabend, Paolo Guarnieri, Craig Soderquist, Thomas Ludwig, Steven Rosenfeld, Jeffrey N. Bruce, Peter Canoll
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0190066

Whole genome microarray analysis of neural progenitor C17.2 cells during differentiation and validation of 30 neural mRNA biomarkers for estimation of developmental neurotoxicity
Cited by: 13
Author(s): Kristina Attoff, Anda R. Gliga, Jessica Lundqvist, Ulf Norinder, Anna Forsby
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0125611

Genomic Instability of Osteosarcoma Cell Lines in Culture: Impact on the Prediction of Metastasis Relevant Genes
Cited by: 35
Author(s): Roman Muff, Pramod C. Rath, Ram Mohan Ram Kumar, Knut Husmann, Walter Born, Michael Baudis, Bruno Fuchs
Software Mentions: 1
Published: over 9 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 3 years ago

10.1371/journal.pone.0052079

Deletion of Chromosomes 13q and 14q Is a Common Feature of Tumors with BRCA2 Mutations
Cited by: 14
Author(s): Audrey Rouault, Guillaume Banneau, Gaëtan MacGrogan, Natalie Jones, Nabila Elarouci, Emmanuelle Barouk-Simonet, Laurence Venat, Isabelle Coupier, Éric Letouzé, Aurélien de Reyniès, Françoise Bonnet, Richard Iggo, Nicolas Sévenet, Michel Longy
Software Mentions: 1
Published: almost 12 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 3 years ago

10.3389/fphar.2020.00512

Quercetin Attenuates Atherosclerosis via Modulating Oxidized LDL-Induced Endothelial Cellular Senescence
Cited by: 51
Author(s): Yuehua Jiang, Ling-Yu Jiang, Yongcheng Wang, Daifu Ma, Xiao Li
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0166923

Identifying Causal Genes at the Multiple Sclerosis Associated Region 6q23 Using Capture Hi-C
Cited by: 31
Author(s): Paul Martin, Amanda McGovern, Jonathan Massey, Stefan Schoenfelder, Kate Duffus, Annie Yarwood, Anne Barton, Jane Worthington, Peter Fraser, Stephen Eyre, Gisela Orozco
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pgen.1004452

zic-1 Expression in Planarian Neoblasts after Injury Controls Anterior Pole Regeneration
Cited by: 64
Author(s): Constanza Vásquez-Doorman, Christian P. Petersen
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1006716

Epistatic interaction between the lipase-encoding genes Pnpla2 and Lipe causes liposarcoma in mice
Cited by: 31
Author(s): Jianli Wu, Christoph Preuß, Shu Pei Wang, Hao Yang, Bo Ji, Gregory W. Carter, Rebecca A. Gladdy, Grégor Andelfinger, Grant A. Mitchell
Software Mentions: 1
Published: over 7 years ago

10.3389/fphar.2020.01138

Discovery of Selenocysteine as a Potential Nanomedicine Promotes Cartilage Regeneration With Enhanced Immune Response by Text Mining and Biomedical Databases
Cited by: 5
Author(s): Jing Ye, Bingbing Xu, Bao-Shi Fan, Jiying Zhang, Fu‐Zhen Yuan, Yourong Chen, Zewen Sun, Xin Yan, Yifan Song, Shi-Tang Song, Meng Yang, Jia‐Kuo Yu
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pgen.1004597

Oligoasthenoteratozoospermia and Infertility in Mice Deficient for miR-34b/c and miR-449 Loci
Cited by: 104
Author(s): Stefano Comazzetto, Monica Di Giacomo, Karsten Rasmussen, Christian Much, Chiara Azzi, Emerald Perlas, Marcos Morgan, Dónal O’Carroll
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pgen.1002645

Coordinate Regulation of Lipid Metabolism by Novel Nuclear Receptor Partnerships
Cited by: 81
Author(s): Pranali Pathare, Alex Lin, Karin E. Bornfeldt, Stefan Taubert, Marc R. Van Gilst
Software Mentions: 1
Published: over 12 years ago

10.3389/fphar.2021.654985

Development and Validation of an Interleukin-6 Nomogram to Predict Primary Non-response to Infliximab in Crohn’s Disease Patients
Cited by: 4
Author(s): Yueying Chen, Hanyang Li, Qi Feng, Jun Shen
Software Mentions: 1
Published: over 3 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 16 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 3 years ago

10.1371/journal.pgen.1004348

Fine Tuning of the UPR by the Ubiquitin Ligases Siah1/2
Cited by: 32
Author(s): Marzia Scortegagna, Hyungsoo Kim, Jianliang Li, Heng‐Chen Yao, Laurence M. Brill, Jaeseok Han, Eric Lau, David D.L. Bowtell, Gabriel Haddad, Randal J. Kaufman, Ze’ev A. Ronai
Software Mentions: 1
Published: over 10 years ago

10.3389/fphar.2020.551786

Regulation of Pain Genes—Capsaicin vs Resiniferatoxin: Reassessment of Transcriptomic Data
Cited by: 10
Author(s): Rajeev K. Singla, Adiba Sultana, Shahin Alam, Bairong Shen
Software Mentions: 1
Published: about 4 years ago

10.3389/fphar.2017.00923

PSORS1C1 Hypomethylation Is Associated with Allopurinol-Induced Severe Cutaneous Adverse Reactions during Disease Onset Period: A Multicenter Retrospective Case-Control Clinical Study in Han Chinese
Cited by: 10
Author(s): Bao Sun, Lin Cheng, Yan Xiong, Lei Hu, Zhicheng Luo, Maojun Zhou, Ji Li, Hongfu Xie, Fazhong He, Xiaoqing Yuan, Xiaoping Chen, Hong‐Hao Zhou, Zhao‐Qian Liu, Xiang Chen, Wei Zhang
Software Mentions: 1
Published: almost 7 years ago

10.7554/eLife.38430

Thalidomide promotes degradation of SALL4, a transcription factor implicated in Duane Radial Ray syndrome
Cited by: 282
Author(s): Katherine A. Donovan, Jian An, Radosław P. Nowak, Jingting Yuan, Emma C. Fink, Bethany C. Berry, Benjamin L. Ebert, Eric S. Fischer
Software Mentions: 1
Published: over 6 years ago

10.3389/fphar.2021.682713

Ginsenoside Rb1 Lessens Gastric Precancerous Lesions by Interfering With β-Catenin/TCF4 Interaction
Cited by: 9
Author(s): Jinhao Zeng, Xiao Ma, Ziyi Zhao, Yu Chen, Jundong Wang, Yanwei Hao, Jun-Rong Yu, Zhongzhen Zeng, Nianzhi Chen, Maoyuan Zhao, Jian-Yuan Tang, Daoyin Gong
Software Mentions: 1
Published: about 3 years ago

10.3389/fphar.2013.00009

Monitoring Response and Resistance to the Novel Arsenical Darinaparsin in an AML Patient
Cited by: 4
Author(s): Torsten Holm Nielsen, Nathalie A. Johnson, Nicolas Garnier, Stanley Kwan, Yao Lu, Eftihia Cocolakis, Josée Hébert, Robert Morgan, Éric R. Paquet, Kevin P. Callahan, Craig T. Jordan, Sarit Assouline, Wilson H. Miller, Koren K. Mann
Software Mentions: 1
Published: almost 12 years ago

10.3389/fphar.2021.723488

Sulfasalazine Sensitizes Polyhematoporphyrin-Mediated Photodynamic Therapy in Cholangiocarcinoma by Targeting xCT
Cited by: 5
Author(s): Yuanna Zheng, Xiangshui Miao, Xiong Li, Bo Chen, Fanyun Kong, Jiangjiao Zhou, Zhong-Tao Liu, Yu Wen, Zijian Zhang, Heng Zou
Software Mentions: 1
Published: over 3 years ago

10.7554/eLife.52535

Tuberculosis-associated IFN-I induces Siglec-1 on tunneling nanotubes and favors HIV-1 spread in macrophages
Cited by: 25
Author(s): Maeva Dupont, Shanti Souriant, Luciana Balboa, Thien‐Phong Vu Manh, Karine Pingris, Stella Rousset, Céline Cougoule, Yoann Rombouts, Renaud Poincloux, Myriam Ben Neji, Carolina Allers, Deepak Kaushal, Marcelo J. Kuroda, Susana Benet, Javier Martínez-Picado, Nuria Izquierdo‐Useros, Marı́a del Carmen Sasiain, Isabelle Maridonneau‐Parini, Olivier Neyrolles, Christel Vérollet, Geanncarlo Lugo-Villarino
Software Mentions: 1
Published: over 4 years ago

10.3389/fphar.2019.01171

The Modulatory Properties of Astragalus membranaceus Treatment on Triple-Negative Breast Cancer: An Integrated Pharmacological Method
Cited by: 24
Author(s): Cun Liu, Kejia Wang, Jing Zhuang, Chundi Gao, Huayao Li, Lijuan Liu, Fubin Feng, Chao Zhou, Yubin Kang, Laijun Deng, Lu Wang, Jia Li, Changgang Sun
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pgen.1000671

Compensatory Evolution of Gene Regulation in Response to Stress by Escherichia coli Lacking RpoS
Cited by: 91
Author(s): Daniel M. Stoebel, Karsten Hokamp, Charles J. Dorman
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pgen.1000021

The Mediator Subunit MDT-15 Confers Metabolic Adaptation to Ingested Material
Cited by: 101
Author(s): Stefan Taubert, Malene Hansen, Marc R. Van Gilst, Samantha Cooper, Keith R. Yamamoto
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pgen.1002824

Genome-Wide Association Analysis in Asthma Subjects Identifies SPATS2L as a Novel Bronchodilator Response Gene
Cited by: 108
Author(s): Blanca E. Himes, Xiaofeng Jiang, Ruoxi Hu, Ann Chen Wu, Jessica Lasky‐Su, Barbara J. Klanderman, John Ziniti, Jody Senter-Sylvia, John J. Lima, Charles G. Irvin, Stephen P. Peters, Deborah A. Meyers, Eugene R. Bleecker, Michiaki Kubo, Mayumi Tamari, Yusuke Nakamura, Stanley J. Szefler, Robert F. Lemanske, Robert S. Zeiger, Robert C. Strunk, Fernando D. Martínez, John P. Hanrahan, Gerard H. Koppelman, Dirkje S. Postma, Maartje A.E. Nieuwenhuis, Judith M. Vonk, Reynold A. Panettieri, Amy Markezich, Elliot Israel, Vincent J. Carey, Kelan G. Tantisira, Augusto A. Litonjua, Quan Lu, Scott T. Weiss
Software Mentions: 1
Published: over 12 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 13 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 15 years ago

10.1186/s13018-021-02464-9

Bioinformatics analysis and identification of genes and molecular pathways in steroid-induced osteonecrosis of the femoral head
Cited by: 8
Author(s): Tianye Lin, Weijian Chen, Peng Yang, Ziqi Li, Qiushi Wei, Liqing Du, Haibin Wang, Wei He, Qingwen Zhang
Software Mentions: 1
Published: over 3 years ago

10.3389/fphys.2020.572605

Long Non-coding RNA MIAT Knockdown Prevents the Formation of Intracranial Aneurysm by Downregulating ENC1 via MYC
Cited by: 6
Author(s): Xinguo Li, Hang Zhao, Jihui Liu, Jing Tong
Software Mentions: 1
Published: almost 4 years ago

10.7554/eLife.07839

Functional evidence implicating chromosome 7q22 haploinsufficiency in myelodysplastic syndrome pathogenesis
Cited by: 14
Author(s): Jasmine C. Wong, Kelley Weinfurtner, Maria del pilar Alzamora, Scott C. Kogan, Michael R. Burgess, Yan Zhang, Joy Nakitandwe, Jing Ma, Jinjun Cheng, Shann-Ching Chen, Theodore Ho, Johanna Flach, Damien Reynaud, Emmanuelle Passegué, James R. Downing, Kevin Shannon
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1008439

Loss of thymidine kinase 1 inhibits lung cancer growth and metastatic attributes by reducing GDF15 expression
Cited by: 32
Author(s): Parmanand Malvi, Radoslav Janoštiak, Arvindhan Nagarajan, Guoping Cai, Narendra Wajapeyee
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pgen.1000773

Alternative Splicing Events Are a Late Feature of Pathology in a Mouse Model of Spinal Muscular Atrophy
Cited by: 209
Author(s): Dirk Bäumer, Sheena Lee, George Nicholson, Joanna L. Davies, Nicholas J. Parkinson, Lyndsay M. Murray, Thomas H. Gillingwater, Olaf Ansorge, Kay E. Davies, Kevin Talbot
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pgen.1006801

C. elegans DAF-16/FOXO interacts with TGF-ß/BMP signaling to induce germline tumor formation via mTORC1 activation
Cited by: 21
Author(s): Wenjing Qi, Yizhen Yan, Dietmar Pfeifer, Erika Donner von Gromoff, Yimin Wang, Wolfgang Maier, Ralf Baumeister
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1000223

Variations in Stress Sensitivity and Genomic Expression in Diverse S. cerevisiae Isolates
Cited by: 181
Author(s): Daniel J. Kvitek, Jessica L. Will, Audrey P. Gasch
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pgen.1005216

Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature
Cited by: 29
Author(s): Samantha M. Thomas, Courtney L Kagan, Bryan J. Pavlovic, Jonathan E. Burnett, Kristen Patterson, Jonathan K. Pritchard, Yoav Gilad
Software Mentions: 1
Published: over 9 years ago

10.3389/fphys.2018.00132

Key Inflammatory Processes in Human NASH Are Reflected in Ldlr−/−.Leiden Mice: A Translational Gene Profiling Study
Cited by: 34
Author(s): Martine C. Morrison, Robert Kleemann, Arianne van Koppen, Roeland Hanemaaijer, Lars Verschuren
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pgen.1005486

A Large-Scale Functional Analysis of Putative Target Genes of Mating-Type Loci Provides Insight into the Regulation of Sexual Development of the Cereal Pathogen Fusarium graminearum
Cited by: 65
Author(s): Hee-Kyoung Kim, Seong-Mi Jo, Gi-Yong Kim, Da-Woon Kim, Yeon-Ki Kim, Sung-Hwan Yun
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pgen.1004203

Cleavage Factor I Links Transcription Termination to DNA Damage Response and Genome Integrity Maintenance in Saccharomyces cerevisiae
Cited by: 18
Author(s): Hélène Gaillard, Andrés Aguilera
Software Mentions: 1
Published: over 10 years ago

10.3389/fphys.2018.01635

Inflammation and Mechanical Stress Stimulate Osteogenic Differentiation of Human Aortic Valve Interstitial Cells
Cited by: 30
Author(s): Maria Bogdanova, Aleksandra Kostina, Katarina Zihlavnikova Enayati, Arsenii Zabirnyk, Anna Malashicheva, Kåre‐Olav Stensløkken, Gareth J. Sullivan, Mari-Liis Kaljusto, John‐Peder Escobar Kvitting, Anna Kostareva, Jarle Vaage, Arkady Rutkovskiy
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pgen.1005415

BMP Inhibition in Seminomas Initiates Acquisition of Pluripotency via NODAL Signaling Resulting in Reprogramming to an Embryonal Carcinoma
Cited by: 54
Author(s): Daniel Nettersheim, Sina Jostes, Rakesh Kumar Sharma, Simon Schneider, Andrea Hofmann, Humberto J. Ferreira, Per Hoffmann, Glen Kristiansen, Manel Esteller, Hubert Schorle
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1002515

Neurophysiological Defects and Neuronal Gene Deregulation in Drosophila mir-124 Mutants
Cited by: 45
Author(s): Kailiang Sun, Jakub Orzechowski Westholm, Kazuya Tsurudome, Joshua W. Hagen, Yubing Lu, Minoree Kohwi, Doron Betel, Fen‐Biao Gao, A. Pejmun Haghighi, Chris Q. Doe, Eric C. Lai
Software Mentions: 1
Published: almost 13 years ago

10.3389/fphys.2019.01112

Circular RNA Expression Profiling and Selection of Key Circular RNAs in the Hypothalamus of Heat-Acclimated Rats
Cited by: 8
Author(s): Lijun Fan, Gaihong An, Shang Wang, Xuewei Chen, Ying Liu, Zhifeng Liu, Qiang Ma, Jing Wang
Software Mentions: 1
Published: over 5 years ago

10.3389/fphys.2020.00804

microRNA-9 Inhibits Vulnerable Plaque Formation and Vascular Remodeling via Suppression of the SDC2-Dependent FAK/ERK Signaling Pathway in Mice With Atherosclerosis
Cited by: 13
Author(s): Ruihong Zhang, Bai Song, Xiaojian Hong, Zhiyuan Shen, Li Sui, Siyu Wang
Software Mentions: 1
Published: over 4 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: almost 17 years ago

10.18632/aging.102995

PHTF2 regulates lipids metabolism in gastric cancer
Cited by: 12
Author(s): Yuling Chi, Haiyan Wang, Fengsong Wang, Mingcui Ding
Software Mentions: 1
Published: over 4 years ago

10.3389/fphys.2020.00621

Regulatory T Cells as a Novel Candidate for Cell-Based Therapy in Kidney Disease
Cited by: 2
Author(s): Junyu Lu, Jianfeng Zhang, Menghua Chen, Chun Chen, Zhengzhao Li, Liao Pinhu
Software Mentions: 1
Published: over 4 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 13 years ago

10.1371/journal.pgen.1003081

dJun and Vri/dNFIL3 Are Major Regulators of Cardiac Aging in Drosophila
Cited by: 50
Author(s): Véronique Monnier, Magali Iché-Torres, Michaël Rera, Vincent Contremoulins, Céline Guichard, Nathalie Lalevée, Hervé Tricoire, Laurent Perrin
Software Mentions: 1
Published: almost 12 years ago

10.3389/fphys.2019.00619

Comparative Expression Profiling of Wild Type Drosophila Malpighian Tubules and von Hippel-Lindau Haploinsufficient Mutant
Cited by: 2
Author(s): Marilena Ignesti, Davide Andrenacci, Bettina Fischer, Valeria Cavaliere, Giuseppe Gargiulo
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1003630

Fine Time Course Expression Analysis Identifies Cascades of Activation and Repression and Maps a Putative Regulator of Mammalian Sex Determination
Cited by: 82
Author(s): Steven C. Munger, Anirudh Raju Natarajan, Loren L. Looger, Uwe Ohler, Blanche Capel
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1003967

A Novel Intergenic ETnII-β Insertion Mutation Causes Multiple Malformations in Polypodia Mice
Cited by: 6
Author(s): Jessica A. Lehoczky, Peedikayil E. Thomas, Kevin M. Patrie, Kailey M. Owens, Lisa M. Villarreal, Kenneth Galbraith, Joe Washburn, Craig Johnson, Bryant J. Gavino, Alexander D. Borowsky, Kathleen J. Millen, Paul Wakenight, William D. Law, Margaret L. Van Keuren, Galina B. Gavrilina, Elizabeth D. Hughes, Thomas L. Saunders, Lesil E Brihn, Joseph H. Nadeau, Jeffrey W. Innis
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12859-018-2117-2

Robust volcano plot: identification of differential metabolites in the presence of outliers
Cited by: 25
Author(s): Nishith Kumar, Md. Rakibul Hoque, Masahiro Sugimoto
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.0020159

Evidence for Diversity in Transcriptional Profiles of Single Hematopoietic Stem Cells
Cited by: 47
Author(s): Carlos A. Ramos, Teresa A Bowman, Nathan C. Boles, Akil Merchant, Yayun Zheng, Irma Parra, Suzanne A.W. Fuqua, Chad A. Shaw, Margaret A. Goodell
Software Mentions: 1
Published: about 18 years ago

10.1186/1471-2105-14-59

Active subnetwork recovery with a mechanism-dependent scoring function; with application to angiogenesis and organogenesis studies
Cited by: 3
Author(s): Ilana Lichtenstein, Michael A. Charleston, Tibério Caetano, Jennifer R. Gamble, Mathew A. Vadas
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pgen.1003945

Mouse BAZ1A (ACF1) Is Dispensable for Double-Strand Break Repair but Is Essential for Averting Improper Gene Expression during Spermatogenesis
Cited by: 30
Author(s): James A. Dowdle, Monika Mehta, Elizabeth M. Kass, Bao Q. Vuong, Akiko Inagaki, Dieter Egli, Maria Jasin, Scott Keeney
Software Mentions: 1
Published: about 11 years ago

10.3389/fpls.2015.00682

Analysis of global gene expression profile of rice in response to methylglyoxal indicates its possible role as a stress signal molecule
Cited by: 50
Author(s): Charanpreet Kaur, Hemant R. Kushwaha, Ananda Mustafiz, Ashwani Pareek, Sudhir K. Sopory, Sneh L. Singla‐Pareek
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2105-8-218

Novel and simple transformation algorithm for combining microarray data sets
Cited by: 12
Author(s): Ki Yeol Kim, Dong Hyuk Ki, Hana Jeong, Hei Cheul Jeung, Hyun Cheol Chung, Sun Young Rha
Software Mentions: 1
Published: over 17 years ago

10.7554/eLife.14926

Polycomb enables primitive endoderm lineage priming in embryonic stem cells
Cited by: 27
Author(s): Robert S. Illingworth, Jurriaan Hölzenspies, Fabian V Roske, Wendy A. Bickmore, Joshua M. Brickman
Software Mentions: 1
Published: about 8 years ago

10.3389/fpls.2015.01198

From Accumulation to Degradation: Reprogramming Polyamine Metabolism Facilitates Dark-Induced Senescence in Barley Leaf Cells
Cited by: 27
Author(s): Ewa Sobieszczuk‐Nowicka, Szymon Kubala, Agnieszka Żmieńko, Arleta Małecka, Jolanta Legocka
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pgen.1002749

Cohesin Proteins Promote Ribosomal RNA Production and Protein Translation in Yeast and Human Cells
Cited by: 81
Author(s): Tania Bose, Kenneth K. Lee, Shuai Lü, Baoshan Xu, Bethany Harris, Brian D. Slaughter, Jay R. Unruh, Alexander S. Garrett, William McDowell, Andrew Box, Hua Li, Allison Peak, Sreekumar Ramachandran, Chris Seidel, Jennifer L. Gerton
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1003427

Evolution after Introduction of a Novel Metabolic Pathway Consistently Leads to Restoration of Wild-Type Physiology
Cited by: 45
Author(s): Sean M. Carroll, Christopher J. Marx
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1000982

Arabidopsis thaliana Chromosome 4 Replicates in Two Phases That Correlate with Chromatin State
Cited by: 68
Author(s): Tae Jin Lee, Pete E. Pascuzzi, Sharon B. Settlage, Randall W. Shultz, Miloš Tanurdžić, Pablo D. Rabinowicz, Margit Menges, Ping Zheng, Dorrie Main, James A. H. Murray, Bryon Sosinski, George C. Allen, Robert A. Martienssen, Linda Hanley‐Bowdoin, Matthew Vaughn, William F. Thompson
Software Mentions: 1
Published: over 14 years ago

10.1186/s13018-020-01641-6

Knockdown of long non-coding RNA PVT1 induces apoptosis of fibroblast-like synoviocytes through modulating miR-543-dependent SCUBE2 in rheumatoid arthritis
Cited by: 19
Author(s): Junxia Wang, Xianghui Kong, Haijian Hu, Shunfang Shi
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pgen.1001120

Genetic Deletion of the Desmosomal Component Desmoplakin Promotes Tumor Microinvasion in a Mouse Model of Pancreatic Neuroendocrine Carcinogenesis
Cited by: 50
Author(s): Matthew G. H. Chun, Douglas Hanahan
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pgen.1005232

Cell Cycle Control by the Master Regulator CtrA in Sinorhizobium meliloti
Cited by: 88
Author(s): Francesco Pini, Nicole J. De Nisco, Lorenzo Ferri, Jon Penterman, Antonella Fioravanti, Matteo Brilli, Alessio Mengoni, Marco Bazzicalupo, Patrick H. Viollier, Graham C. Walker, Emanuele G. Biondi
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1008600

The coordinate actions of calcineurin and Hog1 mediate the stress response through multiple nodes of the cell cycle network
Cited by: 10
Author(s): Cassandra M. Leech, Mackenzie J. Flynn, Heather E. Arsenault, Jianhong Ou, Haibo Li, Lihua Julie Zhu, Jennifer A. Benanti
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pgen.1005334

Epigenetic Aging Signatures Are Coherently Modified in Cancer
Cited by: 94
Author(s): Qiong Lin, Wolfgang Wagner
Software Mentions: 1
Published: over 9 years ago

Projects: bioconductor: limma

Papers Mentioning limma 7,776