bioconductor: limma | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2018.00397

Analysis of Mouse Brain Transcriptome After Experimental Duvenhage Virus Infection Shows Activation of Innate Immune Response and Pyroptotic Cell Death Pathway
Cited by: 9
Author(s): Penelope Koraka, Benedict Martina, Henk-Jan van den Ham, Fatiha Zaaraoui-Boutahar, Wilfred F. J. van IJcken, Jouke M. Roose, Geert van Amerongen, Arno C. Andeweg, A.D.M.E. Osterhaus
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.24357

APIM-peptide targeting PCNA improves the efficacy of docetaxel treatment in the TRAMP mouse model of prostate cancer
Cited by: 31
Author(s): Caroline Krogh Søgaard, Siver Andreas Moestue, Morten Rye, Jana Kim, Anala Nepal, Nina‐Beate Liabakk, Siri Bachke, Tone Frost Bathen, Marit Otterlei, Deborah K. Hill
Software Mentions: 1
Published: almost 7 years ago

10.18632/oncotarget.24370

<i>In silico</i>analysis of expression data during the early priming stage of liver regeneration after partial hepatectomy in rat
Cited by: 4
Author(s): Yin Li, Xueqiang Guo, Chunyan Zhang, Zhihui Cai, Chi Xu
Software Mentions: 1
Published: almost 7 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

10.1038/s41598-018-32173-z

Integration of Molecular Interactome and Targeted Interaction Analysis to Identify a COPD Disease Network Module
Cited by: 33
Author(s): Amitabh Sharma, Maksim Kitsak, Michael H. Cho, Asher Ameli, Xiaobo Zhou, Zhiqiang Jiang, James D. Crapo, Terri H. Beaty, Jörg Menche, Per Bakke, Marc Santolini, Edwin K. Silverman
Software Mentions: 1
Published: about 6 years ago

10.1007/s00204-020-02697-3

Calretinin is a novel candidate marker for adverse ovarian effects of early life exposure to mixtures of endocrine disruptors in the rat
Cited by: 6
Author(s): Hanna Katarina Lilith Johansson, Terje Svingen, Julie Boberg, Paul A. Fowler, David Stead, Anne Marie Vinggaard, Panagiotis Filis
Software Mentions: 1
Published: over 4 years ago

10.1186/s40478-018-0544-y

Network-based analysis of oligodendrogliomas predicts novel cancer gene candidates within the region of the 1p/19q co-deletion
Cited by: 26
Author(s): Josef Gladitz, Barbara Klink, Michael Seifert
Software Mentions: 1
Published: over 6 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

10.1007/s00204-018-2239-3

Prenatal arsenic exposure is associated with increased plasma IGFBP3 concentrations in 9-year-old children partly via changes in DNA methylation
Cited by: 29
Author(s): Anda R. Gliga, Karin Engström, Maria Kippler, Helena Skröder, Sultan Ahmed, Marie Vahter, Rubhana Raqib, Karin Broberg
Software Mentions: 1
Published: over 6 years ago

10.1007/s00401-016-1550-4

Glycolytic-to-oxidative fiber-type switch and mTOR signaling activation are early-onset features of SBMA muscle modified by high-fat diet
Cited by: 67
Author(s): Anna Rocchi, Carmelo Milioto, Sara Parodi, Andrea Armirotti, Doriana Borgia, Matteo Pellegrini, Anna Urciuolo, Sibilla Molon, Valeria Morbidoni, Manuela Marabita, Vanina Romanello, Pamela Gatto, Bert Blaauw, Paolo Bonaldo, Fabio Sambataro, Diane M. Robins, Andrew P. Lieberman, Gian Domenico Sorarù, Lodovica Vergani, Marco Sandri, Maria Pennuto
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms160816816

Differential DNA Methylation in Relation to Age and Health Risks of Obesity
Cited by: 36
Author(s): María L. Mansego, Fermı́n I. Milagro, M. Ángeles Zulet, María J. Moreno-Aliaga, J. Alfredo Martínéz
Software Mentions: 1
Published: over 9 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

10.3389/fmicb.2012.00284

Comparison of Sepsis-Induced Transcriptomic Changes in a Murine Model to Clinical Blood Samples Identifies Common Response Patterns
Cited by: 15
Author(s): Sandro Lambeck, Martina Weber, Falk A. Gonnert, Ralf Mrowka, Michael Bauer
Software Mentions: 1
Published: almost 13 years ago

10.18632/aging.102765

Testicular biopsies microarray analysis reveals circRNAs are involved in the pathogenesis of non-obstructive azoospermia
Cited by: 8
Author(s): Hao Bo, Zhizhong Liu, Ruiling Tang, Guanghui Gong, Xingming Wang, Han Zhang, Fang Zhu, Dai Zhou, Wenbing Zhu, Yue‐Qiu Tan, Liqing Fan
Software Mentions: 1
Published: almost 5 years ago

10.3389/fmicb.2017.00276

Apoptosis, Toll-like, RIG-I-like and NOD-like Receptors Are Pathways Jointly Induced by Diverse Respiratory Bacterial and Viral Pathogens
Cited by: 21
Author(s): Isidoro Martı́nez, Juan Carlos Oliveros, Isabel Cuesta, Jorge de la Barrera, Vicente Ausina, Cristina Casals, Alba de Lorenzo, Ernesto Garcı́a, Belén García-Fojeda, Junkal Garmendía, Mar González-Nicolau, Alícia Lacoma, Margarita Menéndez, David Moranta, Amelia Nieto, Juan Ortı́n, Alicia Pérez-González, Cristina Prat, Elisa Ramos‐Sevillano, Verónica Regueiro, Ariel Rodríguez-Frandsen, Dolores Solı́s, José Yuste, José A. Bengoechea, José A. Melero
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2016.00229

Different Transcriptional Responses from Slow and Fast Growth Rate Strains of Listeria monocytogenes Adapted to Low Temperature
Cited by: 24
Author(s): Ninoska Cordero, Felipe Rodríguez Maza, Helen Navea-Perez, Andrés Aravena, Bárbara Marquez-Fontt, Paola Navarrete, Guillermo Figueroa, Maurício González, Mauricio Latorre, Angélica Reyes-Jara
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2021.638640

Silver Nanoparticles Induce a Triclosan-Like Antibacterial Action Mechanism in Multi-Drug Resistant Klebsiella pneumoniae
Cited by: 19
Author(s): Vikram Pareek, Stéphanie Devineau, Sathesh K Sivasankaran, Arpit Bhargava, Jitendra Panwar, Shabarinath Srikumar, Séamus Fanning
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmicb.2020.01301

NF-κB/TWIST1 Mediates Migration and Phagocytosis of Macrophages in the Mice Model of Implant-Associated Staphylococcus aureus Osteomyelitis
Cited by: 13
Author(s): Yutian Wang, Yihuang Lin, Ching‐Li Cheng, Pengyu Chen, Ping Zhang, Hangtian Wu, Kaiqun Li, Ye Deng, Jikun Qian, Xianrong Zhang, Bin Yu
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2164-13-243

The genes and enzymes of the carotenoid metabolic pathway in Vitis vinifera L.
Cited by: 109
Author(s): Philip R. Young, Justin Graham Lashbrooke, Erik Alexandersson, Dan Jacobson, C. Moser, Riccardo Velasco, Melané A. Vivier
Software Mentions: 1
Published: over 12 years ago

10.1038/tp.2016.78

Differential expression of transcriptional regulatory units in the prefrontal cortex of patients with bipolar disorder: potential role of early growth response gene 3
Cited by: 27
Author(s): Bianca Pfaffenseller, Pedro Vieira da Silva Magalhães, Marco Antônio De Bastiani, Mauro A. A. Castro, Amelia L. Gallitano, Flávio Kapczinski, Fábio Klamt
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2017.00539

Outlining Core Pathways of Amyloid Toxicity in Bacteria with the RepA-WH1 Prionoid
Cited by: 15
Author(s): Laura Molina García, María Moreno-del Álamo, Pedro Botías, Zaira Martín‐Moldes, María Rosario Salinas Fernández, Alicia Sánchez-Gorostiaga, Aída Alonso-del Valle, Juan Nogales, Jesús García-Cantalejo, Rafael Giraldo
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2018.02084

Clostridium difficile Biofilm: Remodeling Metabolism and Cell Surface to Build a Sparse and Heterogeneously Aggregated Architecture
Cited by: 46
Author(s): Isabelle Poquet, Laure Saujet, Alexis Canette, Marc Monot, Jovana Mihajlovic, Jean‐Marc Ghigo, Olga Soutourina, Romain Briandet, Isabelle Martin‐Verstraete, Bruno Dupuy
Software Mentions: 1
Published: about 6 years ago

10.7717/peerj.6375

Identification of special key genes for alcohol-related hepatocellular carcinoma through bioinformatic analysis
Cited by: 16
Author(s): Xiuzhi Zhang, Chunyan Kang, Ningning Li, Xiaoli Liu, Jinzhong Zhang, Fenglan Gao, Liping Dai
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms17040568

Prognostic Value of MicroRNAs in Preoperative Treated Rectal Cancer
Cited by: 16
Author(s): Azadeh Azizian, Ingo Epping, Frank Krämer, Peter Jo, Markus Bernhardt, Julia Kitz, Gabriela Salinas, Hendrik A. Wolff, Marian Grade, Tim Beißbarth, B. Michael Ghadimi, Jochen Gaedcke
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2020.01553

Increased Antibody Response to Fucosylated Oligosaccharides and Fucose-Carrying Bacteroides Species in Crohn’s Disease
Cited by: 7
Author(s): Katharina Kappler, Yi Lasanajak, David F. Smith, Lennart Opitz, Thierry Hennet
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0101970

A Functional Genomic Screen for Evolutionarily Conserved Genes Required for Lifespan and Immunity in Germline-Deficient C. elegans
Cited by: 23
Author(s): Amit Sinha, Robbie Rae
Software Mentions: 1
Published: over 10 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

10.3390/ijms17050665

Characterization of Micro-RNA Changes during the Progression of Type 2 Diabetes in Zucker Diabetic Fatty Rats
Cited by: 47
Author(s): Denis Delić, Claudia Eisele, RM Schmid, Gerd Luippold, Eric Mayoux, Rolf Grempler
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2019.02007

Regulation of Early Host Immune Responses Shapes the Pathogenicity of Avian Influenza A Virus
Cited by: 9
Author(s): Jiya Sun, Jingfeng Wang, Xuye Yuan, Xiangwei Wu, Tianqi Sui, Aiping Wu, Genhong Cheng, Taijiao Jiang
Software Mentions: 1
Published: about 5 years ago

10.18632/oncotarget.25087

Transcriptome based individualized therapy of refractory pediatric sarcomas: feasibility, tolerability and efficacy
Cited by: 14
Author(s): Bushra Weidenbusch, Günther Richter, Marie Sophie Kesper, Monika Guggemoos, Katja Gall, Carolin Prexler, И. В. Казанцев, Alexandra Sipol, Ларс Линднер, Michaela Nathrath, Olaf Witt, Katja Specht, Frigga Beitinger, Carolin Knebel, Stuart Hosie, Rüdiger von Eisenhardt-Rothe, Wilko Weichert, Irene Teichert-von Luettichau, Stefan Burdach
Software Mentions: 1
Published: over 6 years ago

10.1007/s00204-014-1279-6

From transient transcriptome responses to disturbed neurodevelopment: role of histone acetylation and methylation as epigenetic switch between reversible and irreversible drug effects
Cited by: 70
Author(s): Nina V. Balmer, Stefanie Klima, Eugen Rempel, Violeta N. Ivanova, Raivo Kolde, Matthias K. Weng, Kesavan Meganathan, Margit Henry, Agapios Sachinidis, Michael R. Berthold, Jan G. Hengstler, Jörg Rahnenführer, Tanja Waldmann, Marcel Leist
Software Mentions: 1
Published: over 10 years ago

10.3389/fmicb.2016.00320

Genome-Wide Expression Profiling Reveals S100B as Biomarker for Invasive Aspergillosis
Cited by: 6
Author(s): Andreas Dix, Kristin Czakai, Jan Springer, Mirjam Fließer, Michael Bonin, Reinhard Guthke, Anna Lena Schmitt, Hermann Einsele, Jörg Linde, Jürgen Löffler
Software Mentions: 1
Published: over 8 years ago

10.3390/microarrays3040263

Expression Comparison of Oil Biosynthesis Genes in Oil Palm Mesocarp Tissue Using Custom Array
Cited by: 12
Author(s): Yick Ching Wong, Qi Bin Kwong, Heng Leng Lee, Chuang Kee Ong, Sean Mayes, Fook Tim Chew, David R. Appleton, Harikrishna Kulaveerasingam
Software Mentions: 1
Published: about 10 years ago

10.3389/fmicb.2020.596440

CircRNA-1806 Decreases T Cell Apoptosis and Prolongs Survival of Mice After Cryptococcal Infection by Sponging miRNA-126
Cited by: 4
Author(s): Lei Zhang, Keming Zhang, Wenzhang Fang, Hang Li, Yingfang Li, Weiwei Jiang, Dongying Hu, Carolina Coelho, Xiaogang Liu, Liangqi Cai, Wanqing Liao, Weihua Pan
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2015.00051

Heat shock proteins IbpA and IbpB are required for NlpI-participated cell division in Escherichia coli
Cited by: 9
Author(s): Jing Tao, Yu Sang, Qihui Teng, Jinjing Ni, Kevin Yi Yang, Stephen Kwok‐Wing Tsui, Yufeng Yao
Software Mentions: 1
Published: almost 10 years ago

10.3389/fmicb.2018.01142

Analysis of Beijing Douzhir Microbiota by High-Throughput Sequencing and Isolation of Acidogenic, Starch-Flocculating Strains
Cited by: 2
Author(s): Yan Xu, Yu Yang, Yuan Tian, Yuhong Su, Xiaona Li, Zhen Zhang, Hongyan Zhu, Jiahong Han, Huajiang Zhang, Liying Liu, Lili Zhang
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.25264

Highly expressed placental miRNAs control key biological processes in human cancer cell lines
Cited by: 10
Author(s): Daniel Onofre Vidal, Anelisa Ramão, Daniel Guariz Pinheiro, Bruna Rodrigues Muys, Julio C. C. Lorenzi, Cleidson de Pádua Alves, Dalila Lucíola Zanette, Greice Andreotti de Molfetta, Geraldo Duarte, Wilson A. Silva
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-11-235

Plasmodium falciparum spermidine synthase inhibition results in unique perturbation-specific effects observed on transcript, protein and metabolite levels
Cited by: 29
Author(s): John Vw Becker, Linda Mtwisha, Bridget Genevieve Crampton, Stoyan Stoychev, Anna C. van Brummelen, Shaun Reeksting, Abraham I. Louw, Lyn‐Marié Birkholtz, D Mancama
Software Mentions: 1
Published: over 14 years ago

10.1007/s00204-020-02779-2

Hepatotoxic pyrrolizidine alkaloids induce DNA damage response in rat liver in a 28-day feeding study
Cited by: 24
Author(s): Johanna Ebmeyer, Josef Daniel Rasinger, Jan G. Hengstler, Dirk Schaudien, Otto Creutzenberg, Alfonso Lampen, Albert Braeuning, Stefanie Hessel‐Pras
Software Mentions: 1
Published: over 4 years ago

10.3390/ijms17081260

Bioinformatics and Microarray Analysis of miRNAs in Aged Female Mice Model Implied New Molecular Mechanisms for Impaired Fracture Healing
Cited by: 29
Author(s): Bing He, Zongkang Zhang, Jin Liu, Yao He, Tao Tang, Jie Li, Baosheng Guo, Aiping Lü, Bao-Ting Zhang, Ge Zhang
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-9-474

Differential gene expression profiles are dependent upon method of peripheral blood collection and RNA isolation
Cited by: 88
Author(s): Adam Asare, Svetlana A Kolchinsky, Gongxun Zhong, Thomas J. Wang, Khadir Raddassi, Katarzyna Bourcier, Vicki Seyfert-Margolis
Software Mentions: 1
Published: about 16 years ago

10.3389/fmicb.2020.01939

Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile
Cited by: 38
Author(s): Olga Soutourina, Thomas Dubois, Marc Monot, Pavel V. Shelyakin, Laure Saujet, Pierre Boudry, Mikhail S. Gelfand, Bruno Dupuy, Isabelle Martin‐Verstraete
Software Mentions: 1
Published: over 4 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

10.3390/toxics8010012

Potential of Inactivated Bifidobacterium Strain in Attenuating Benzo(A)Pyrene Exposure-Induced Damage in Colon Epithelial Cells In Vitro
Cited by: 7
Author(s): Mengfan Xu, Lili Fu, Junwen Zhang, Tao Wang, Junfeng Fan, Baoqing Zhu, Piotr Dziugan, Bolin Zhang
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0192746

Species-specific regulation of angiogenesis by glucocorticoids reveals contrasting effects on inflammatory and angiogenic pathways
Cited by: 10
Author(s): Ruth Morgan, John Keen, Daniel L. Halligan, Alan O’Callaghan, Ruth Andrew, Dawn E W Livingstone, Amber J Abernethie, Giorgia Maltese, Brian R. Walker, Patrick W. F. Hadoke
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13690-021-00588-2

Identification of a prognostic long noncoding RNA signature in lung squamous cell carcinoma: a population-based study with a mean follow-up of 3.5 years
Cited by: 7
Author(s): Rongjiong Zheng, Mengdi Zheng, Mingming Wang, Feijie Lu, Meiling Hu
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms18061298

Using Coexpression Protein Interaction Network Analysis to Identify Mechanisms of Danshensu Affecting Patients with Coronary Heart Disease
Cited by: 24
Author(s): Mengqi Huo, Zhixin Wang, Dongxue Wu, Yanling Zhang, Yu Qiao
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-018-4518-z

Identification of placental nutrient transporters associated with intrauterine growth restriction and pre-eclampsia
Cited by: 57
Author(s): Xiao Huang, Pascale Anderle, Lu Hostettler, Marc Baumann, Daniel Surbek, Edgar Ontsouka, Christiane Albrecht
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-13-76

Sexual and asexual oogenesis require the expression of unique and shared sets of genes in the insect Acyrthosiphon pisum
Cited by: 33
Author(s): Aurore Gallot, Shuji Shigenobu, Tomomi Hashiyama, Stéphanie Jaubert-Possamai, Denis Tagu
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-016-2580-y

Prediction of hybrid performance in maize with a ridge regression model employed to DNA markers and mRNA transcription profiles
Cited by: 26
Author(s): Carola Zenke-Philippi, Alexander Thiemann, Felix Seifert, Tobias A. Schrag, Albrecht E. Melchinger, Stefan Scholten, Matthias Frisch
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0020966

Expression Profiling of FSHD-1 and FSHD-2 Cells during Myogenic Differentiation Evidences Common and Distinctive Gene Dysregulation Patterns
Cited by: 39
Author(s): Stefania Cheli, Stéphanie François, Beatrice Bodega, Francesco Ferrari, Elena Tenedini, Enrica Roncaglia, Sérgio Ferrari, Enrico Ginelli, Raffaella Meneveri
Software Mentions: 1
Published: over 13 years ago

10.1186/s12864-021-07994-4

Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection
Cited by: 3
Author(s): Christopher P. Kozakiewicz, Alexandra K. Fraik, Austin H. Patton, Manuel Ruiz‐Aravena, David G. Hamilton, Rodrigo Hamede, Hamish McCallum, Paul A. Hohenlohe, Mark J. Margres, Matthew T. Jones, Andrew Storfer
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.pone.0135102

Comprehensive Assessment of Host Responses to 5-Fluorouracil-Induced Oral Mucositis through Transcriptomic Analysis
Cited by: 8
Author(s): Chung‐Ta Chang, Chien Yun Hsiang, Tin Yun Ho, Chung Ze Wu, Hsiang Hsi Hong, Yi Huang
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-37909-5

Pancreatic adenocarcinomas with mature blood vessels have better overall survival
Cited by: 74
Author(s): Eriko Katsuta, Qianya Qi, Xuan Peng, Steven N. Hochwald, Li Yan, Kazuaki Takabe
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-016-3458-8

CNVs into the wild: screening the genomes of conifer trees (Picea spp.) reveals fewer gene copy number variations in hybrids and links to adaptation
Cited by: 27
Author(s): Julien Prunier, S. Caron, John Mackay
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-11-6

An evolutionary consequence of dosage compensation on Drosophila melanogaster female X-chromatin structure?
Cited by: 35
Author(s): Yu Zhang, Brian Oliver
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12864-018-5220-x

RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database
Cited by: 19
Author(s): Pierre R. Bushel, Florian Caiment, Han Wu, Raegan O’Lone, Frank Day, John N. Calley, Aaron T. Smith, Jianying Li
Software Mentions: 1
Published: about 6 years ago

10.1007/s00403-014-1476-4

The effect of two endogenous retinoids on the mRNA expression profile in human primary keratinocytes, focusing on genes causing autosomal recessive congenital ichthyosis
Cited by: 13
Author(s): Hans Törmä, Anders Bergström, G. Ghiasifarahani, Berit Berne
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-13-173

Genome-wide expression profiling shows transcriptional reprogramming in Fusarium graminearum by Fusarium graminearum virus 1-DK21 infection
Cited by: 33
Author(s): Won Kyong Cho, Jisuk Yu, Kyung-Mi Lee, Moonil Son, Kyung-Hee Min, Yin-Won Lee, Kook‐Hyung Kim
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-14-869

TE-array—a high throughput tool to study transposon transcription
Cited by: 12
Author(s): Veena P. Gnanakkan, Andrew E. Jaffe, Lixin Dai, Jie Fu, Sarah J. Wheelan, Hyam I. Levitsky, Jef D. Boeke, Kathleen H. Burns
Software Mentions: 1
Published: almost 11 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: over 10 years ago

10.18632/aging.102092

Exosomes derived from microRNA-199a-overexpressing mesenchymal stem cells inhibit glioma progression by down-regulating AGAP2
Cited by: 67
Author(s): Lei Yu, Si Gui, Yawei Liu, Xiaoyu Qiu, Guozhong Zhang, Xian Zhang, Jun Pan, Jun Fan, Songtao Qi, Binghui Qiu
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-12-81

Population transcriptomics of Drosophila melanogaster females
Cited by: 45
Author(s): Lena Müller, Stephan Hütter, Rayna Stamboliyska, Sarah S. Saminadin-Peter, Wolfgang Stephan, John Parsch
Software Mentions: 1
Published: almost 14 years ago

10.1038/s41598-019-38985-x

Transcriptome-wide analysis of filarial extract-primed human monocytes reveal changes in LPS-induced PTX3 expression levels
Cited by: 2
Author(s): Benedikt C. Buerfent, Lina Gölz, Andrea Hofmann, Heiko Rühl, Wiebke Stamminger, Nadine Fricker, Timo Hess, Johannes Oldenburg, Markus M. Nöthen, Johannes Schumacher, Marc P. Hübner, Achim Hoerauf
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-15-829

Profiling of the embryonic Atlantic halibut (Hippoglossus hippoglossus L.) transcriptome reveals maternal transcripts as potential markers of embryo quality
Cited by: 29
Author(s): Maren Mommens, Jorge M.O. Fernandes, Knut Erik Tollefsen, Ian A. Johnston, Igor Babiak
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-019-39010-x

Transcriptomic and genomic structural variation analyses on grape cultivars reveal new insights into the genotype-dependent responses to water stress
Cited by: 15
Author(s): Claudia Rita Catacchio, Fiammetta Alagna, Rocco Perniola, Carlo Bergamini, Silvia Rotunno, Francesco Maria Calabrese, Pasquale Crupi, Donato Antonacci, Mario Ventura, Maria Francesca Cardone
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-015-1393-8

Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level
Cited by: 70
Author(s): Roland Prielhofer, Stephanie P. Cartwright, Alexandra B. Graf, Minoska Valli, Roslyn M. Bill, Diethard Mattanovich, Brigitte Gasser
Software Mentions: 1
Published: over 9 years ago

10.7717/peerj.9086

Identification of key genes associated with progression and prognosis for lung squamous cell carcinoma
Cited by: 10
Author(s): Xu Ma, Hongyi Ren, Ruoyu Peng, Yi Li, Liang Ming
Software Mentions: 1
Published: over 4 years ago

10.3390/ijms18122728

Identification of Differentially Expressed miRNAs in Colorado Potato Beetles (Leptinotarsa decemlineata (Say)) Exposed to Imidacloprid
Cited by: 18
Author(s): Mathieu D. Morin, Pierre J. Lyons, Nicolas Crapoulet, Sébastien Boquel, Pier Jr Morin
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2164-10-236

Transcriptomics reveals extensive inducible biotransformation in the soil-dwelling invertebrate Folsomia candida exposed to phenanthrene
Cited by: 65
Author(s): Benjamin Nota, Mirte Bosse, Bauke Ylstra, Nico M. van Straalen, Dick Roelofs
Software Mentions: 1
Published: almost 16 years ago

10.1128/AEM.00638-16

Pichia pastoris Exhibits High Viability and a Low Maintenance Energy Requirement at Near-Zero Specific Growth Rates
Cited by: 42
Author(s): Corinna Rebnegger, Tim Vos, Alexandra B. Graf, Minoska Valli, Jack T. Pronk, Pascale Daran‐Lapujade, Diethard Mattanovich
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-12-123

Comparative tissue transcriptomics reveal prompt inter-organ communication in response to local bacterial kidney infection
Cited by: 15
Author(s): Jorrit Boekel, Örjan Källskog, Monica Rydén-Aulin, Mikael Rhen, Agneta Richter‐Dahlfors
Software Mentions: 1
Published: over 13 years ago

10.3390/antiox10010025

Crosstalk between Long-Term Sublethal Oxidative Stress and Detrimental Inflammation as Potential Drivers for Age-Related Retinal Degeneration
Cited by: 11
Author(s): Lara Macchioni, Davide Chiasserini, Letizia Mezzasoma, Magdalena Davidescu, Pier Luigi Orvietani, Katia Fettucciari, Leonardo Salviati, Barbara Cellini, Ilaria Bellezza
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0184095

The transcriptional landscape of Rhizoctonia solani AG1-IA during infection of soybean as defined by RNA-seq
Cited by: 15
Author(s): Tanya Copley, Raj Duggavathi, Suha Jabaji
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0192689

Gene set analysis of post-lactational mammary gland involution gene signatures in inflammatory and triple-negative breast cancer
Cited by: 21
Author(s): Arvind Bambhroliya, Renae D. Van Wyhe, Swaminathan Kumar, Bisrat G. Debeb, Jay P. Reddy, S. Van Laere, Randa El‐Zein, Arvind Rao, Wendy A. Woodward
Software Mentions: 1
Published: over 6 years ago

10.1089/ars.2018.7551

Putative Role of Nuclear Factor-Kappa B But Not Hypoxia-Inducible Factor-1α in Hypoxia-Dependent Regulation of Oxidative Stress in Hematopoietic Stem and Progenitor Cells
Cited by: 7
Author(s): Camilla Halvarsson, Emma Rörby, Pernilla Eliasson, Stefan Lang, Shamit Soneji, Jan Ingvar Jönsson
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-13-447

Genetic module and miRNome trait analyses reflect the distinct biological features of endothelial progenitor cells from different anatomic locations
Cited by: 22
Author(s): Cheng-Chung Cheng, Hung-Hao Lo, Tse‐Shun Huang, Yi-Chieh Cheng, Shi-Ting Chang, Shing‐Jyh Chang, Hsei–Wei Wang
Software Mentions: 1
Published: about 12 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

10.1186/1471-2164-15-1114

Genes associated with thermosensitive genic male sterility in rice identified by comparative expression profiling
Cited by: 21
Author(s): Yufang Pan, Qiaofeng Li, Zhizheng Wang, Yang Wang, Rui Ma, Lili Zhu, Guangcun He, Rongzhi Chen
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41598-019-40811-3

Comprehensive analysis of the GATA transcription factor gene family in breast carcinoma using gene microarrays, online databases and integrated bioinformatics
Cited by: 14
Author(s): Shan Yu, Xuepeng Jiang, Juan Li, Chao Li, Mian Guo, Fei Ye, Maomao Zhang, Yu‐Fei Jiao, Bin Guo
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-41059-7

The Nuclear Receptor and Clock Repressor Rev-erbα Suppresses Myogenesis
Cited by: 32
Author(s): Somik Chatterjee, Hongshan Yin, Weini Li, Jeongkyung Lee, Vijay Yechoor, Ke Ma
Software Mentions: 1
Published: over 5 years ago

10.1136/annrheumdis-2018-214539

Synovial cellular and molecular signatures stratify clinical response to csDMARD therapy and predict radiographic progression in early rheumatoid arthritis patients
Cited by: 177
Author(s): Frances Humby, Myles Lewis, Nandhini Ramamoorthi, Jason A. Hackney, Michael R. Barnes, Michèle Bombardieri, Audi Setiadi, Stephen Kelly, F Bene, Maria DiCicco, Sudeh Riahi, Vidalba Rocher, Nora Ng, Ilias Lazarou, Rebecca Hands, Désirée van der Heijde, Robert Landewé, Annette H M van der Helm-van Mil, Alberto Cauli, Iain B. McInnes, Christopher D. Buckley, Ernest Choy, Peter Taylor, Michael J. Townsend, Costantino Pitzalis
Software Mentions: 1
Published: over 5 years ago

10.3389/fonc.2020.571524

Identification of Key Gene Signatures Associated With Bone Metastasis in Castration-Resistant Prostate Cancer Using Co-Expression Analysis
Cited by: 5
Author(s): Zhongxiang Yu, Hanlin Zou, Huihao Wang, Qi Li, Dong Yu
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0017245

Mutant Analysis in Arabidopsis Provides Insight into the Molecular Mode of Action of the Auxinic Herbicide Dicamba
Cited by: 61
Author(s): Cynthia Gleason, Rhonda C. Foley, Karam B. Singh
Software Mentions: 1
Published: over 13 years ago

10.1080/07853890.2021.1966087

Screening differentially expressed genes between endometriosis and ovarian cancer to find new biomarkers for endometriosis
Cited by: 8
Author(s): Zhenzhen Lu, Ying Gao
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0127286

CEMP1 Induces Transformation in Human Gingival Fibroblasts
Cited by: 16
Author(s): Mercedes Bermúdez, Iván Imaz-Rosshandler, Claudia Rangel‐Escareño, Margarita Zeichner‐David, Higinio Arzate, Gabriela Mercado
Software Mentions: 1
Published: over 9 years ago

10.3389/fonc.2020.01031

Identification of Aberrantly Methylated Differentially CpG Sites in Hepatocellular Carcinoma and Their Association With Patient Survival
Cited by: 2
Author(s): Renguo Guan, Weimin Guo, Wang Hong, Ye Lin, Xiongfeng Zou, Ning Shi, Dongyang Yang, Yu Zhou, Zhixiang Jian, Haosheng Jin, Weidong Lin, Min Yu
Software Mentions: 1
Published: over 4 years ago

10.3389/fonc.2020.585452

Mechanism and Molecular Network of RBM8A-Mediated Regulation of Oxaliplatin Resistance in Hepatocellular Carcinoma
Cited by: 9
Author(s): Rong Liang, Jinyan Zhang, Zhihui Liu, Ziyu Liu, Qian Li, Xi Luo, Yongqiang Li, Jiazhou Ye, Yan Lin
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2164-7-252

Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma
Cited by: 451
Author(s): Ilhem Diboun, Lorenz Wernisch, Christine A. Orengo, M Koltzenburg
Software Mentions: 1
Published: about 18 years ago

10.1186/1471-2164-13-274

Defining new criteria for selection of cell-based intestinal models using publicly available databases
Cited by: 46
Author(s): Jon Christensen, Sara El-Gebali, Manuela Natoli, Thierry Sengstag, Mauro Delorenzi, Susanne Bentz, Hanifa Bouzourène, Martı́n Rumbo, Armando Felsani, Sanna Siissalo, Jouni Hirvonen, Maya R Vila, Piercarlo Saletti, Michel Aguet, Pascale Anderle
Software Mentions: 1
Published: over 12 years ago

10.7717/peerj.10830

The methylation level of TFAP2A is a potential diagnostic biomarker for retinoblastoma: an analytical validation study
Cited by: 4
Author(s): Qi Zeng, Sha Wang, Jia Tan, Lu Chen, Jinwei Wang
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.2839

Transcriptomic response of maize primary roots to low temperatures at seedling emergence
Cited by: 15
Author(s): Mauro Di Fenza, Bridget Hogg, Jim Grant, Susanne Barth
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-018-5413-3

Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species
Cited by: 20
Author(s): Rahul Rane, Stephen L. Pearce, Fang Li, Chris Coppin, Michele Schiffer, Jennifer Shirriffs, Carla M. Sgrò, Philippa C. Griffin, Guojie Zhang, Siu Fai Lee, Ary A. Hoffmann, John G. Oakeshott
Software Mentions: 1
Published: almost 6 years ago

10.18632/oncotarget.25728

Epigenetic activation of HORMAD1 in basal-like breast cancer: role in Rucaparib sensitivity
Cited by: 24
Author(s): Xian Wang, Ying Tan, Xianlong Cao, Jin Ah Kim, Tianmeng Chen, Yiheng Hu, Matthew Wexler, Xiaosong Wang
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0158774

RIPK3 Is Largely Dispensable for RIG-I-Like Receptor- and Type I Interferon-Driven Transcriptional Responses to Influenza A Virus in Murine Fibroblasts
Cited by: 6
Author(s): Shoko Nogusa, Michael Slifker, Justin P. Ingram, Roshan J. Thapa, Siddharth Balachandran
Software Mentions: 1
Published: over 8 years ago

10.1186/s13018-021-02390-w

Identification of key genes and pathways of BMP-9-induced osteogenic differentiation of mesenchymal stem cells by integrated bioinformatics analysis
Cited by: 12
Author(s): Jiaqi Wu, Lin-Bo Mao, Lingfeng Liu, Yongmei Li, Jian Wu, Jiao Yao, Fenghuan Zhang, Tingyu Liu, Ling Yuan
Software Mentions: 1
Published: over 3 years ago

10.18632/aging.202845

NET1 promotes HCC growth and metastasis in vitro and in vivo via activating the Akt signaling pathway
Cited by: 4
Author(s): Zhenhua Chen, Qian‐Zhi Ni, Xiuping Zhang, Ning Ma, Jing-Kai Feng, Kang Wang, Jingjing Li, Dong Xie, Xiaochun Ma, Shuqun Cheng
Software Mentions: 1
Published: over 3 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

10.1186/s12864-020-6768-9

PretiMeth: precise prediction models for DNA methylation based on single methylation mark
Cited by: 4
Author(s): Jie Tang, Jianxiao Zou, Xiaoran Zhang, Mei Fan, Qi Tian, Shuyao Fu, Shihong Gao, Shicai Fan
Software Mentions: 1
Published: over 4 years ago

10.3390/ani10091680

Identification of the Key microRNAs and miRNA-mRNA Interaction Networks during the Ovarian Development of Hens
Cited by: 8
Author(s): Jing Li, Chong Li, Qi Li, Wenting Li, Hong Li, Guoxi Li, Xiangtao Kang, Xiaojun Liu, Yadong Tian
Software Mentions: 1
Published: about 4 years ago

Projects: bioconductor: limma

Papers Mentioning limma 7,776