bioconductor: oligo | Projects | Ecosyste.ms: Papers

10.1186/1471-2156-15-81

Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations
Cited by: 16
Author(s): Robert B. Scharpf, Lynn Mireles, Qiong Yang, Anna Köttgen, Ingo Ruczinski, Katalin Suszták, Eitan Halper-Stromberg, Adrienne Tin, Stephen Cristiano, Aravinda Chakravarti, Eric Boerwinkle, Caroline S. Fox, Josef Coresh, W. H. Linda Kao
Software Mentions: 56
Published: almost 11 years ago

10.1371/journal.pcbi.1000227

Analyzing ChIP-chip Data Using Bioconductor
Cited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Software Mentions: 39
Published: almost 16 years ago

10.1371/journal.pcbi.1007792

eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research
Cited by: 38
Author(s): Augusto Anguita‐Ruiz, Alberto Segura‐Delgado, Rafael Alcalá, Concepción M. Aguilera, Jesús Alcalá‐Fdez
Software Mentions: 23
Published: over 4 years ago

10.3389/fimmu.2019.02887

Meta-Analysis of in vitro-Differentiated Macrophages Identifies Transcriptomic Signatures That Classify Disease Macrophages in vivo
Cited by: 29
Author(s): Hung Jen Chen, Andrew Y. Li Yim, Guillermo R. Griffith, Wouter J. de Jonge, Marcel M.A.M. Mannens, Enrico Ferrero, Peter Henneman, Menno P.J. de Winther
Software Mentions: 13
Published: almost 5 years ago

10.12688/f1000research.8967.2

An end to end workflow for differential gene expression using Affymetrix microarrays
Cited by: 16
Author(s): Bernd Klaus, Stefanie Reisenauer
Software Mentions: 13
Published: over 6 years ago

10.1186/1471-2105-11-194

Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data
Cited by: 32
Author(s): Benedikt Zacher, Pei Fen Kuan, Achim Tresch
Software Mentions: 12
Published: over 14 years ago

10.3390/cancers13122903

Integrative Transcriptomic Analysis Reveals Distinctive Molecular Traits and Novel Subtypes of Collecting Duct Carcinoma
Cited by: 6
Author(s): Chiara Gargiuli, Pierangela Sepe, Anna Tessari, Tyler Sheetz, Maurizio Colecchia, F.G.M. De Braud, Giuseppe Procopio, Marialuisa Sensi, Elena Verzoni, Matteo Dugo
Software Mentions: 11
Published: over 3 years ago

10.1371/journal.pone.0224750

Gene expression microarray public dataset reanalysis in chronic obstructive pulmonary disease
Cited by: 3
Author(s): Lavida R. K. Rogers, Madison Verlinde, George I. Mias
Software Mentions: 10
Published: almost 5 years ago

10.1371/journal.pone.0256016

Integration of chronological omics data reveals mitochondrial regulatory mechanisms during the development of hepatocellular carcinoma
Cited by: 2
Author(s): J. Noé García-Chávez, Verónica Rocío Vásquez-Garzón, Mercedes G. López, Saúl Villa‐Treviño, Rafaél Montiel
Software Mentions: 10
Published: about 3 years ago

10.1186/s40478-018-0548-7

Proteomic analysis of Medulloblastoma reveals functional biology with translational potential
Cited by: 35
Author(s): Samuel Rivero-Hinojosa, Ling San Lau, Mojca Stampar, Jerome A. Staal, Huizhen Zhang, Heather Gordish‐Dressman, Paul A. Northcott, Stefan M. Pfister, Michael D. Taylor, Kristy J. Brown, Brian R. Rood
Software Mentions: 10
Published: over 6 years ago

10.1038/s41598-019-46168-x

Cytotoxic unsaturated electrophilic compounds commonly target the ubiquitin proteasome system
Cited by: 16
Author(s): Karthik Selvaraju, Arjan Mofers, Paola Pellegrini, Johannes Salomonsson, Alexandra Ahlner, Vivian Morad, Ellin-Kristina Hillert, Belén Espinosa, Elias S.J. Arnér, Lasse Jensen, Jonas Malmström, Maria V. Turkina, Pádraig D’Arcy, Michael A. Walters, Maria Sunnerhagen, Stig Linder
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.ppat.1005996

A Mouse Model of Chronic West Nile Virus Disease
Cited by: 44
Author(s): Jessica B. Graham, Jessica L. Swarts, Courtney Wilkins, Sunil Thomas, Richard Green, Aimee Sekine, Kathleen Voss, Reneé C. Ireton, Michael A. Mooney, Gabrielle Choonoo, Darla R. Miller, Piper M. Treuting, Fernando Pardo Manuel de Villena, Martin T. Ferris, Shannon K. McWeeney, Michael Gale, Jennifer M. Lund
Software Mentions: 10
Published: about 8 years ago

10.1155/2021/6657397

Identifying Stage II Colorectal Cancer Recurrence Associated Genes by Microarray Meta-Analysis and Building Predictive Models with Machine Learning Algorithms
Cited by: 2
Author(s): Wei Lu, Xiang Pan, Siqi Dai, Dongliang Fu, Maxwell Hwang, Yaowu Zhu, Lina Zhang, Jingsun Wei, Xianglong Kong, Jun Li, Qian Xiao, Kefeng Ding
Software Mentions: 9
Published: over 3 years ago

10.1186/1471-2105-14-254

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments
Cited by: 49
Author(s): Mikel Esnaola, Pedro Puig, David Herrera González, Robert Castelo, Juan R. González
Software Mentions: 9
Published: about 11 years ago

10.1016/j.mad.2021.111437

Transcriptomic profiling of long- and short-lived mutant mice implicates mitochondrial metabolism in ageing and shows signatures of normal ageing in progeroid mice
Cited by: 6
Author(s): Matías Fuentealba, Daniel K. Fabian, Handan Melike Dönertaş, Janet Thornton, Linda Partridge
Software Mentions: 9
Published: over 3 years ago

10.1038/s41598-019-55434-x

QuantSeq. 3′ Sequencing combined with Salmon provides a fast, reliable approach for high throughput RNA expression analysis
Cited by: 28
Author(s): Susan M. Corley, Niamh M. Troy, Anthony Bosco, Marc R. Wilkins
Software Mentions: 9
Published: almost 5 years ago

10.3389/fnins.2020.00209

A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer’s Disease
Cited by: 6
Author(s): Sze Chung Yuen, Hongmei Zhu, Siu-wai Leung
Software Mentions: 9
Published: over 4 years ago

10.3389/fimmu.2021.649551

TSPAN1, TMPRSS4, SDR16C5, and CTSE as Novel Panel for Pancreatic Cancer: A Bioinformatics Analysis and Experiments Validation
Cited by: 11
Author(s): Yi-Jun Hua, Tiandong Li, Hua Wang, Jinyu Wu, Chuncheng Yi, Jianxiang Shi, Peng Wang, Chunhua Song, Liping Dai, Guozhong Jiang, Yuguang Huang, Yu Ye, Jitian Li
Software Mentions: 8
Published: over 3 years ago

10.1186/s40478-017-0421-0

Integrated analysis of genetic, behavioral, and biochemical data implicates neural stem cell-induced changes in immunity, neurotransmission and mitochondrial function in Dementia with Lewy Body mice
Cited by: 5
Author(s): Anita Lakatos, Natalie R.S. Goldberg, Mathew Blurton‐Jones
Software Mentions: 8
Published: over 7 years ago

10.3390/ijms21072337

Differential Targeting of Gr-MDSCs, T Cells and Prostate Cancer Cells by Dactolisib and Dasatinib
Cited by: 10
Author(s): Guoqiang Lü, Zhijian Jin, Xin Lü
Software Mentions: 8
Published: over 4 years ago

10.3390/ijms22179426

Gravitational Force—Induced 3D Chromosomal Conformational Changes Are Associated with Rapid Transcriptional Response in Human T Cells
Cited by: 14
Author(s): Christian Vahlensieck, Cora S. Thiel, Ye Zhang, Andreas Huge, Oliver Ullrich
Software Mentions: 8
Published: about 3 years ago

10.1371/journal.pone.0183264

The transcriptional profiling of human in vivo-generated plasma cells identifies selective imbalances in monoclonal gammopathies
Cited by: 12
Author(s): Luis M. Valor, Beatriz Rodrı́guez-Bayona, Ana Ramos-Amaya, José A. Brieva, Antonio Campos‐Caro
Software Mentions: 8
Published: about 7 years ago

10.1016/j.csbj.2020.06.023

Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities
Cited by: 10
Author(s): Susan Idicula‐Thomas, Ulka Gawde, Sameeksha Bhaye, Khushal Pokar, Gary D. Bader
Software Mentions: 8
Published: almost 5 years ago

10.3390/ijms20215412

Analysis of Transcriptome, Selected Intracellular Signaling Pathways, Proliferation and Apoptosis of LNCaP Cells Exposed to High Leptin Concentrations
Cited by: 12
Author(s): Marta Szyszka, Lukasz Paschke, Marianna Tyczewska, Karol Jopek, Piotr Celichowski, Paulina Milecka, G. F. Sultanova, Ewelina Stelcer, Agnieszka Malińska, Ludwik K. Malendowicz, Marcin Ruciński
Software Mentions: 7
Published: about 5 years ago

10.1186/s13045-017-0406-2

Analyses of caspase-1-regulated transcriptomes in various tissues lead to identification of novel IL-1β-, IL-18- and sirtuin-1-independent pathways
Cited by: 43
Author(s): Yafeng Li, Gayani Nanayakkara, Yu Sun, Xinyuan Li, Luqiao Wang, Ramón Cueto, Ying Shao, Hangfei Fu, Candice Johnson, Jiali Cheng, Xiongwen Chen, Wenhui Hu, Jun Yu, Eric T. Choi, Hong Wang, Xiaofeng Yang
Software Mentions: 7
Published: almost 8 years ago

10.1016/j.jim.2016.02.023

Comparative genomics analysis of mononuclear phagocyte subsets confirms homology between lymphoid tissue-resident and dermal XCR1+ DCs in mouse and human and distinguishes them from Langerhans cells
Cited by: 44
Author(s): Sabrina Carpentier, Thien‐Phong Vu Manh, Rabie Chelbi, Sandrine Henri, Bernard Malissen, Muzlifah Haniffa, Florent Ginhoux, Marc Dalod
Software Mentions: 7
Published: over 8 years ago

10.3389/pore.2021.604730

Identification of Key Genes Involved in Pancreatic Ductal Adenocarcinoma with Diabetes Mellitus Based on Gene Expression Profiling Analysis
Cited by: 4
Author(s): Wenbai Zhou, Yujing Wang, Hongmei Gao, Ying Jia, Yuanxin Xu, Xiaojing Wan, Zhiying Zhang, Haiqiao Yu, Shuang Yan
Software Mentions: 7
Published: over 3 years ago

10.3389/fimmu.2019.02616

Microarray Gene Expression Dataset Re-analysis Reveals Variability in Influenza Infection and Vaccination
Cited by: 12
Author(s): Lavida R. K. Rogers, Gustavo de los Campos, George I. Mias
Software Mentions: 7
Published: about 5 years ago

10.1186/s12967-017-1174-z

24h-gene variation effect of combined bevacizumab/erlotinib in advanced non-squamous non-small cell lung cancer using exon array blood profiling
Cited by: 9
Author(s): Florent Baty, Markus Joerger, Martin Früh, Dirk Klingbiel, Francesco Zappa, Martin Brutsche
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pone.0196836

Multiclass classification for skin cancer profiling based on the integration of heterogeneous gene expression series
Cited by: 17
Author(s): Juan Manuel Gálvez, Daniel Castillo, José Benavente Herrera, Belén San Román, Olga Valenzuela, Francisco M. Ortuño Guzman, Ignacio Rojas
Software Mentions: 7
Published: over 6 years ago

10.3390/ijms21134629

Differences in Gene Expression Profile of Primary Tumors in Metastatic and Non-Metastatic Papillary Thyroid Carcinoma—Do They Exist?
Cited by: 5
Author(s): Sylwia Szpak‐Ulczok, Aleksandra Pfeifer, Dagmara Rusinek, Małgorzata Oczko-Wojciechowska, M. Kowalska, Tomasz Tyszkiewicz, Marta Cieślicka, Daria Handkiewicz-Junak, Krzysztof Fujarewicz, Dariusz Lange, Ewa Chmielik, Ewa Zembala‐Nożyńska, Sebastian Student, Agnieszka Kotecka-Blicharz, Aneta Kluczewska-Gałka, Barbara Jarząb, Agnieszka Czarniecka, Michał Jarząb, Jolanta Krajewska
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-021-92036-y

Capitalizing on transcriptome profiling to optimize and identify targets for promoting early murine folliculogenesis in vitro
Cited by: 6
Author(s): Andrea Jones, Beatriz Peñalver Bernabé, Vasantha Padmanabhan, Jun Li, Ariella Shikanov
Software Mentions: 7
Published: over 3 years ago

10.1186/s12967-016-0906-9

Centrosome associated genes pattern for risk sub-stratification in multiple myeloma
Cited by: 13
Author(s): Fedor Kryukov, Pavel Němec, Lenka Radová, Elena V. Kryukova, Samuel Adeyinka Okubote, Jiří Minařík, Zdena Štefániková, Luděk Pour, Roman Hájek
Software Mentions: 7
Published: over 8 years ago

10.3390/genes11070802

Convergence of Prognostic Gene Signatures Suggests Underlying Mechanisms of Human Prostate Cancer Progression
Cited by: 6
Author(s): Bogdan A. Luca, Vincent Moulton, Christopher Ellis, Shea P. Connell, Daniel Brewer, Christopher S. Cooper
Software Mentions: 6
Published: over 4 years ago

10.3390/cancers12061597

TERT Promoter Mutations and Their Impact on Gene Expression Profile in Papillary Thyroid Carcinoma
Cited by: 11
Author(s): Dagmara Rusinek, Aleksandra Pfeifer, Marta Cieślicka, M. Kowalska, Agnieszka Pawlaczek, Jolanta Krajewska, Sylwia Szpak‐Ulczok, Tomasz Tyszkiewicz, Monika Halczok, Agnieszka Czarniecka, Ewa Zembala‐Nożyńska, Mykola Chekan, Roman Lamch, Daria Handkiewicz-Junak, Aleksandra Ledwoń, Ewa Paliczka-Cieślik, Aleksandra Kropińska, Barbara Jarząb, Małgorzata Oczko-Wojciechowska
Software Mentions: 6
Published: over 4 years ago

10.3390/cancers12092416

Systems Biology Approaches Reveal Potential Phenotype-Modifier Genes in Neurofibromatosis Type 1
Cited by: 7
Author(s): Thayne Woycinck Kowalski, Larissa Brussa Reis, Tiago Finger Andreis, Patrícia Ashton‐Prolla, Clévia Rosset
Software Mentions: 6
Published: about 4 years ago

10.1186/s12864-016-2849-1

Deciphering transcriptome profiles of peripheral blood mononuclear cells in response to PRRSV vaccination in pigs
Cited by: 26
Author(s): M. S. Islam, Christine Große‐Brinkhaus, Maren Pröll, Muhammad Jasim Uddin, Sharmin Aqter Rony, Dawit Tesfaye, Ernst Tholen, Michael Hölker, K. Schellander, Christiane Neuhoff
Software Mentions: 6
Published: about 8 years ago

10.7554/eLife.23361

A chloroplast retrograde signal, 3’-phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination
Cited by: 116
Author(s): Wannarat Pornsiriwong, Gonzalo M. Estavillo, Kai Xun Chan, Estee E-Ling Tee, Diep R Ganguly, Peter A. Crisp, Su Yin Phua, Chenchen Zhao, Jiaen Qiu, Jiyoung Park, Miing Tiem Yong, Nazia Nisar, Arun Kumar Yadav, Benjamin Schwessinger, John P. Rathjen, Christopher I. Cazzonelli, Philippa B. Wilson, Matthew Gilliham, Zhong‐Hua Chen, Barry J. Pogson
Software Mentions: 6
Published: over 7 years ago

10.1186/s13229-019-0287-z

A meta-analysis of two high-risk prospective cohort studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood
Cited by: 12
Author(s): Charles E. Mordaunt, Bo Y. Park, Kelly M. Bakulski, Jason I. Feinberg, Lisa Croen, Christine Ladd‐Acosta, Craig J. Newschaffer, Heather E. Volk, Sally J Ozonoff, Irva Hertz‐Picciotto, Janine M. LaSalle, Rebecca Jean Schmidt, M. Daniele Fallin
Software Mentions: 6
Published: about 5 years ago

10.1038/srep21518

Activation of the TGFβ pathway impairs endothelial to haematopoietic transition
Cited by: 32
Author(s): Özge Vargel, Yang Zhang, Kinga Kosim, Kerstin Ganter, Sophia Föehr, Yannicka Mardenborough, Maya Shvartsman, Anton J. Enright, Jeroen Krijgsveld, Christophe Lancrin
Software Mentions: 6
Published: over 8 years ago

10.1186/1471-2164-14-14

Quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity
Cited by: 26
Author(s): Katie S Viljoen, Jonathan M. Blackburn
Software Mentions: 6
Published: almost 12 years ago

10.3389/fimmu.2020.606338

Specific Induction of Double Negative B Cells During Protective and Pathogenic Immune Responses
Cited by: 33
Author(s): Christoph Ruschil, Gisela Gabernet, Gildas Lepennetier, Simon Heumos, Miriam Kaminski, Zsuzsanna Hracskó, Martin Irmler, Johannes Beckers, Ulf Ziemann, Sven Nahnsen, Gregory P. Owens, Jeffrey L. Bennett, Bernhard Hemmer, Markus C. Kowarik
Software Mentions: 6
Published: almost 4 years ago

10.3390/life11020115

A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression
Cited by: 6
Author(s): Theodora-Dafni Michalettou, Ioannis Michalopoulos, Sylvain V. Costes, Christine E. Hellweg, Megumi Hada, Alexandros G. Georgakilas
Software Mentions: 6
Published: almost 4 years ago

10.3389/fphar.2016.00142

Comparative Transcriptome Analysis Identifies CCDC80 as a Novel Gene Associated with Pulmonary Arterial Hypertension
Cited by: 22
Author(s): Shota Sasagawa, Yuhei Nishimura, Hirofumi Sawada, Eric Erquan Zhang, Shiko Okabe, Soichiro Murakami, Yoshifumi Ashikawa, Mizuki Yuge, Koki Kawaguchi, Reiko Kawase, Yoshihide Mitani, Kazuo Maruyama, Toshio Tanaka
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0101581

Analysis of the Transcriptome in Hyperoxic Lung Injury and Sex-Specific Alterations in Gene Expression
Cited by: 25
Author(s): Krithika Lingappan, Chandramouleeswaran Srinivasan, Weiwu Jiang, Lihua Wang, Xanthi I. Couroucli, Bhagavatula Moorthy
Software Mentions: 6
Published: over 10 years ago

10.3389/fimmu.2020.00851

Gene Expression Profiling of PDGFRA Mutant GIST Reveals Immune Signatures as a Specific Fingerprint of D842V Exon 18 Mutation
Cited by: 10
Author(s): Valentina Indio, Gloria Ravegnini, Annalisa Astolfi, Milena Urbini, Maristella Saponara, Antonio De Leo, Elisa Gruppioni, Giuseppe Tarantino, Sabrina Angelini, Andrea Pession, Maria Abbondanza Pantaleo, Margherita Nannini
Software Mentions: 6
Published: over 4 years ago

10.1186/s12864-020-6684-z

Transcriptomic analysis of marine endophytic fungi extract identifies highly enriched anti-fungal fractions targeting cancer pathways in HepG2 cell lines
Cited by: 7
Author(s): Ethel J. S. Blessie, Wasco Wruck, Benaiah Annertey Abbey, Audrey Ncube, Nina Graffmann, Vincent Amarh, Patrick Kobina Arthur, James Adjaye
Software Mentions: 6
Published: over 4 years ago

10.3389/fgene.2016.00031

A Consensus Network of Gene Regulatory Factors in the Human Frontal Lobe
Cited by: 17
Author(s): Stefano Berto, Alvaro Perdomo‐Sabogal, Daniel Gerighausen, Jing Qin, Katja Nowick
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0219747

2,3,7,8-Tetrachlorodibenzo-p-dioxin modifies alternative splicing in mouse liver
Cited by: 5
Author(s): Ana B. Villaseñor-Altamirano, John D. Watson, Stephenie D. Prokopec, Cindy Q. Yao, Paul C. Boutros, Raimo Pohjanvirta, Jesús Valdés‐Flores, Guillermo Elizondo
Software Mentions: 6
Published: over 5 years ago

10.1534/g3.117.041624

Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross
Cited by: 35
Author(s): Richard Green, Courtney Wilkins, Sunil Thomas, Aimee Sekine, Duncan M. Hendrick, Kathleen Voss, Reneé C. Ireton, Michael A. Mooney, Jennifer T. Go, Gabrielle Choonoo, Sophia Jeng, Fernando P Pardo Manuel De Villena, Martin T. Ferris, Shannon K. McWeeney, Michael Gale
Software Mentions: 6
Published: over 7 years ago

10.1038/s41598-018-19451-6

Cross-species transcriptional analysis reveals conserved and host-specific neoplastic processes in mammalian glioma
Cited by: 20
Author(s): Nina P. Connolly, Amol C. Shetty, Jesse A. Stokum, Ina Hoeschele, Marni B. Siegel, C. Ryan Miller, Anthony J. Kim, Cheng‐Ying Ho, Eduardo Dávila, J. Marc Simard, Scott E. Devine, John H. Rossmeisl, Eric C. Holland, Jeffrey A. Winkles, Graeme F. Woodworth
Software Mentions: 6
Published: almost 7 years ago

10.3389/fgene.2021.618277

Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder
Cited by: 7
Author(s): Mateusz Garbulowski, Karolina Smolińska, Klev Diamanti, Gang Pan, Khurram Maqbool, Lars Feuk, Jan Komorowski
Software Mentions: 6
Published: over 3 years ago

10.7554/eLife.04530

The long non-coding RNA Dali is an epigenetic regulator of neural differentiation
Cited by: 142
Author(s): Vladislava Chalei, Stephen N. Sansom, Lesheng Kong, Sheena Lee, Juan Montiel, Keith W. Vance, Chris P. Ponting
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pbio.3001166

Neural stem cells traffic functional mitochondria via extracellular vesicles
Cited by: 79
Author(s): Luca Peruzzotti-Jametti, Joshua D. Bernstock, Cory M. Willis, Giulia Manferrari, Rebecca Rogall, Erika Fernández-Vizarra, James C Williamson, Alice Braga, Aletta van den Bosch, Tommaso Leonardi, Grzegorz Krzak, Ágnes Kittel, Cristiane Benincá, Nunzio Vicario, Sisareuth Tan, Carlos Bastos, Iacopo Bicci, Nunzio Iraci, JA Smith, Ben Peacock, Karin H. Müller, Paul J. Lehner, Edit I. Buzás, Nuno Faria, Massimo Zeviani, Christian Frezza, Alain Brisson, Nicholas J Matheson, Carlo Viscomi, Stefano Pluchino
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pbio.3000091

Non-proteolytic ubiquitin modification of PPARγ by Smurf1 protects the liver from steatosis
Cited by: 16
Author(s): Kun Yan Zhu, Yi Tang, Xuan Xu, Hien Dang, Liu-Ya Tang, Xiang Wang, Xin Wei Wang, Ying E. Zhang
Software Mentions: 5
Published: almost 6 years ago

10.3390/ijms21030751

Effect of Bortezomib on Global Gene Expression in PC12-Derived Nerve Cells
Cited by: 10
Author(s): Karolina Łuczkowska, Dorota Rogińska, Zofia Ulańczyk, Bogusław Machaliński
Software Mentions: 5
Published: almost 5 years ago

10.15252/emmm.202012461

Combination therapies induce cancer cell death through the integrated stress response and disturbed pyrimidine metabolism
Cited by: 12
Author(s): Goetz Hartleben, Kenji Schorpp, Yongseok Kwon, Barbara Betz, Foivos-Filippos Tsokanos, Zahra Dantes, A Schäfer, Ina Rothenaigner, José Manuel Monroy Kuhn, Pauline Morigny, Lisa Mehr, Sean Lin, Susanne Seitz, Janina Tokarz, Anna Artati, Jerzy Adamsky, Oliver Plettenburg, Dominik Lutter, Martin Irmler, Johannes Beckers, Maximilian Reichert, Kamyar Hadian, Anja Zeigerer, Stephan Herzig, Mauricio Berriel Díaz
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-021-82067-w

Calcium calmodulin kinase II activity is required for cartilage homeostasis in osteoarthritis
Cited by: 11
Author(s): Giovanna Nalesso, Anne‐Sophie Thorup, S. Eldridge, Armando M. De Palma, Amanpreet Kaur, Kiran Peddireddi, Kevin Blighe, Sharmila Rana, B. Stott, Tonia L. Vincent, B.L. Thomas, Jessica Bertrand, J. Sherwood, Antonella Fioravanti, Costantino Pitzalis, Francesco Dell’Accio
Software Mentions: 5
Published: over 3 years ago

10.1155/2019/9651380

Integrated Bioinformatics Analysis of Hub Genes and Pathways in Anaplastic Thyroid Carcinomas
Cited by: 14
Author(s): Xueren Gao, Jianguo Wang, Shulong Zhang
Software Mentions: 5
Published: almost 6 years ago

10.1016/j.molp.2020.07.010

The IBI1 Receptor of β-Aminobutyric Acid Interacts with VOZ Transcription Factors to Regulate Abscisic Acid Signaling and Callose-Associated Defense
Cited by: 25
Author(s): Roland E. Schwarzenbacher, Grace Wardell, Joost H. M. Stassen, Emily Guest, Peijun Zhang, Estrella Luna, Jurriaan Ton
Software Mentions: 5
Published: about 4 years ago

10.1186/s12864-015-1546-9

Activation of defence pathways in Scots pine bark after feeding by pine weevil (Hylobius abietis)
Cited by: 31
Author(s): Andriy Kovalchuk, Tommaso Raffaello, Emad Jaber, Susanna Keriö, Rajendra P. Ghimire, W. Walter Lorenz, Jeffrey F. D. Dean, Jarmo K. Holopainen, Fred O. Asiegbu
Software Mentions: 5
Published: over 9 years ago

10.1186/s13148-021-01064-y

DNA methylation and gene expression integration in cardiovascular disease
Cited by: 21
Author(s): Guillermo Palou-Márquez, Isaac Subirana, Lara Nonell, Alba Fernández‐Sanlés, Roberto Elosúa
Software Mentions: 5
Published: over 3 years ago

10.1186/1744-8069-10-7

A Comparison of RNA-Seq and Exon Arrays for Whole Genome Transcription Profiling of the L5 Spinal Nerve Transection Model of Neuropathic Pain in the Rat
Cited by: 72
Author(s): James R. Perkins, Ana Antunes-Martins, Margarita Calvo, John Grist, Werner Rust, RM Schmid, Tobias Hildebrandt, Matthias Kohl, Christine A. Orengo, Stephen B. McMahon, David L.H. Bennett
Software Mentions: 5
Published: almost 11 years ago

10.1038/s41598-019-48589-0

Inhibition of GATA2 restrains cell proliferation and enhances apoptosis and chemotherapy mediated apoptosis in human GATA2 overexpressing AML cells
Cited by: 7
Author(s): Juan Bautista Menendez-Gonzalez, Samantha Sinnadurai, Alex Gibbs, Leigh-anne Thomas, Maria Konstantinou, Alfonso Garcia-Valverde, Magali Boyer, Zhengke Wang, Ashleigh S. Boyd, Allison Blair, Rhys G. Morgan, Neil P. Rodrigues
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-017-08010-0

Small secreted proteins from the necrotrophic conifer pathogen Heterobasidion annosum s.l. (HaSSPs) induce cell death in Nicotiana benthamiana
Cited by: 25
Author(s): Tommaso Raffaello, Fred O. Asiegbu
Software Mentions: 5
Published: about 7 years ago

10.1038/srep13135

Unique Toll-Like Receptor 4 Activation by NAMPT/PBEF Induces NFκB Signaling and Inflammatory Lung Injury
Cited by: 119
Author(s): Sara M. Camp, Ermelinda Ceco, Carrie Evenoski, Sergei M. Danilov, Tong Zhou, Eddie T. Chiang, Liliana Moreno‐Vinasco, Brandon Mapes, Jieling Zhao, Gamze Gürsoy, Mary Elizabeth Brown, Djanybek Adyshev, Shahid Siddiqui, Hector Quijada, Saad Sammani, Eleftheria Letsiou, Laleh Saadat, Mohammed Yousef, Ting Wang, Jie Liang, Joe G.N. Garcia
Software Mentions: 5
Published: about 9 years ago

10.1093/database/baaa012

CancerLivER: a database of liver cancer gene expression resources and biomarkers
Cited by: 19
Author(s): Harpreet Kaur, Sherry Bhalla, Dilraj Kaur, Gajendra P. S. Raghava
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-016-3460-1

Enumerateblood – an R package to estimate the cellular composition of whole blood from Affymetrix Gene ST gene expression profiles
Cited by: 8
Author(s): Casey P. Shannon, Robert Balshaw, Virginia Chen, Zsuzsanna Hollander, Mustafa Toma, Bruce M. McManus, J. Mark FitzGerald, Don D. Sin, Raymond T. Ng, Scott J. Tebbutt
Software Mentions: 5
Published: almost 8 years ago

10.3390/ijms22115744

BRAF Inhibitors Induce Feedback Activation of RAS Pathway in Thyroid Cancer Cells
Cited by: 8
Author(s): Elisa Bonaldi, Chiara Gargiuli, Loris De Cecco, Arianna Micali, Maria Grazia Rizzetti, Angela Greco, Maria Grazia Borrello, Emanuela Minna
Software Mentions: 5
Published: over 3 years ago

10.12688/wellcomeopenres.11253.2

A genomic atlas of human adrenal and gonad development
Cited by: 46
Author(s): Ignacio del Valle, Federica Buonocore, Andrew Duncan, Lin Lin, Martino Barenco, Rahul Parnaik, Sonia Shah, Michael Hubank, Dianne Gerrelli, John C. Achermann
Software Mentions: 5
Published: about 7 years ago

10.1186/1471-2164-15-472

Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment
Cited by: 43
Author(s): Rebecca Worsley Hunt, Anthony Mathelier, Luis del Peso, Wyeth W. Wasserman
Software Mentions: 5
Published: over 10 years ago

10.3390/ijms21186499

MiR-581/SMAD7 Axis Contributes to Colorectal Cancer Metastasis: A Bioinformatic and Experimental Validation-Based Study
Cited by: 12
Author(s): Xiaojuan Zhao, Shuzhen Liu, Bianbian Yan, Jin Yang, Erfei Chen
Software Mentions: 5
Published: about 4 years ago

10.1155/2013/192548

Expression of Bmi-1 in Pediatric Brain Tumors as a New Independent Prognostic Marker of Patient Survival
Cited by: 10
Author(s): Shirin Farivar, Reza Keikha, Reza Shiari, Farzaneh Jadali
Software Mentions: 4
Published: almost 12 years ago

10.7554/eLife.63838

Inducible mechanisms of disease tolerance provide an alternative strategy of acquired immunity to malaria
Cited by: 39
Author(s): Wiebke Nahrendorf, Alasdair Ivens, Philip J. Spence
Software Mentions: 4
Published: over 3 years ago

10.3389/fphar.2019.00303

Transcriptome-Wide Effects of Sphingosine Kinases Knockdown in Metastatic Prostate and Breast Cancer Cells: Implications for Therapeutic Targeting
Cited by: 17
Author(s): Heba Alshaker, Qi Wang, Daniel Brewer, Dmitri Pchejetski
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-14-882

VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine)
Cited by: 55
Author(s): D. Wong, Crystal Sweetman, Damian Paul Drew, Christopher M. Ford
Software Mentions: 4
Published: almost 11 years ago

10.3389/fphar.2016.00126

EP300 Protects from Light-Induced Retinopathy in Zebrafish
Cited by: 13
Author(s): Reiko Kawase, Yuhei Nishimura, Yoshifumi Ashikawa, Shota Sasagawa, Soichiro Murakami, Mizuki Yuge, Shiko Okabe, Koki Kawaguchi, Hiroshi Yamamoto, Kazumi Moriyuki, Shinsaku Yamane, Kazuhiro Tsuruma, Masamitsu Shimazawa, Hideaki Hara, Toshio Tanaka
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.64680

Urocortin-3 neurons in the mouse perifornical area promote infant-directed neglect and aggression
Cited by: 23
Author(s): Anita E. Autry, Wu Zheng, Vikrant Kapoor, Johannes Kohl, Dhananjay Bambah-Mukku, Nimrod D. Rubinstein, Brenda Marin-Rodriguez, Ilaria Carta, Victoria Sedwick, Ming Tang, Catherine Dulac
Software Mentions: 4
Published: about 3 years ago

10.1186/s12859-015-0669-y

Equalizer reduces SNP bias in Affymetrix microarrays
Cited by: 6
Author(s): David A. Quigley
Software Mentions: 4
Published: over 9 years ago

10.7717/peerj.7135

Comprehensive analysis of an lncRNA-miRNA-mRNA competing endogenous RNA network in pulpitis
Cited by: 31
Author(s): Fangcao Lei, Han Zhang, Xiaoli Xie
Software Mentions: 4
Published: over 5 years ago

10.1155/2018/1243858

Characterization of Transcription Termination-Associated RNAs: New Insights into their Biogenesis, Tailing, and Expression in Primary Tumors
Cited by: 4
Author(s): Ilaria Laudadio, Sara Formichetti, Silvia Gioiosa, Filippos Klironomos, Nikolaus Rajewsky, Giuseppe Macino, Claudia Carissimi, Valerio Fulci
Software Mentions: 4
Published: almost 7 years ago

10.1002/JLB.3A0617-261R

Effects of anti-inflammatory drugs on the expression of tryptophan-metabolism genes by human macrophages
Cited by: 22
Author(s): Tim Regan, Andrew C. Gill, Sara Clohisey, Mark W. Barnett, Carmine M. Pariante, Neil A. Harrison, David Hume, Edward T. Bullmore, Tom C. Freeman
Software Mentions: 4
Published: almost 7 years ago

10.1016/j.pain.2013.05.021

HDAC inhibitors attenuate the development of hypersensitivity in models of neuropathic pain
Cited by: 127
Author(s): Franziska Denk, Wenlong Huang, Ben S. Sidders, Angela Bithell, Megan Crow, John Grist, Simone Sharma, Daniel Ziemek, Andrew S.C. Rice, Noel J. Buckley, Stephen B. McMahon
Software Mentions: 4
Published: about 11 years ago

10.1002/embj.201386225

The long non-coding RNA Paupar regulates the expression of both local and distal genes
Cited by: 183
Author(s): Keith W. Vance, Stephen N. Sansom, Sheena Lee, Vladislava Chalei, Lesheng Kong, Sarah Cooper, Peter L. Oliver, Chris P. Ponting
Software Mentions: 4
Published: almost 11 years ago

10.3390/ijms21062249

AHR Signaling Dampens Inflammatory Signature in Neonatal Skin γδ T Cells
Cited by: 11
Author(s): Katja Merches, Alfonso Schiavi, Heike Weighardt, Swantje Steinwachs, Nadine Teichweyde, Irmgard Förster, K Hochrath, Beatrix Schumak, Natascia Ventura, Patrick Petzsch, Karl Köhrer, Charlotte Esser
Software Mentions: 4
Published: over 4 years ago

10.1016/j.dib.2016.06.001

Microarray dataset of Jurkat cells following miR-93 over-expression
Cited by: 0
Author(s): Silvia Gioiosa, Lorena Verduci, Gianluca Azzalin, Claudia Carissimi, Valerio Fulci, Giuseppe Macino
Software Mentions: 4
Published: about 8 years ago

10.1186/s12864-017-4186-4

The gene SMART study: method, study design, and preliminary findings
Cited by: 45
Author(s): Xu Yan, Nir Eynon, Ioannis Papadimitriou, Jujiao Kuang, Fiona Munson, Oren Tirosh, Lannie O’Keefe, Lyn R. Griffiths, Kevin J. Ashton, Nuala M. Byrne, Yannis Pitsiladis, David Bishop
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-018-29847-z

The reciprocal interplay between TNFα and the circadian clock impacts on cell proliferation and migration in Hodgkin lymphoma cells
Cited by: 26
Author(s): Marconi Abreu, Alireza Basti, Nikolaï Genov, Gianluigi Mazzoccoli, Angela Relógio
Software Mentions: 4
Published: over 6 years ago

10.1186/s12885-015-1539-8

Identifying novel hypoxia-associated markers of chemoresistance in ovarian cancer
Cited by: 34
Author(s): Lynda McEvoy, Sharon O’Toole, Cathy Spillane, C Martín, Michael Gallagher, Britta K. Stordal, Gordon Blackshields, Orla Sheils, John O’Leary
Software Mentions: 4
Published: over 9 years ago

10.1186/s13041-020-00685-3

Neuronal activity regulates alternative exon usage
Cited by: 5
Author(s): Johanna Denkena, Andrea Zaisser, Barbara Merz, Bertram Klinger, Dietmar Kuhl, Nils Blüthgen, Guido Hermey
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-018-38310-y

Msx1 loss suppresses formation of the ectopic crypts developed in the Apc-deficient small intestinal epithelium
Cited by: 5
Author(s): Monika Horázná, Lucie Janečková, Jiří Švec, Oľga Babošová, Dušan Hrčkulák, Martina Vojtěchová, Kateřina Galušková, Eva Šloncová, Michal Kolář, Hynek Strnad, Vladimír Kořínek
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-017-02761-6

Transcription Factor Networks derived from Breast Cancer Stem Cells control the immune response in the Basal subtype
Cited by: 27
Author(s): Willian A. da Silveira, Patrícia Vianna Bonini Palma, Renata Danielle Sicchieri, Rolando A R Villacis, Larissa Raquel Mouro Mandarano, Tatiane Oliveira, Heriton Mr Antonio, Jurandyr Moreira de Andrade, Valdair Francisco Muglia, Sílvia Regina Rogatto, Charles Theillet, Stanislas du Manoir, Daniel Guimarães Tiezzi
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0179265

Cancer cell redirection biomarker discovery using a mutual information approach
Cited by: 7
Author(s): Kimberly Roche, F. Alex Feltus, Jang Pyo Park, Marie–May Coissieux, Chenyan Chang, Vera B. S. Chan, Mohamed Bentires‐Alj, Brian W. Booth
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-018-28185-4

Early alteration of epigenetic-related transcription in Huntington’s disease mouse models
Cited by: 35
Author(s): Irati Hervás-Corpión, Deisy Guiretti, Manuel Alcaráz-Iborra, Román Olivares, Antonio Campos‐Caro, Ángel Barco, Luis M. Valor
Software Mentions: 4
Published: over 6 years ago

10.3390/genes12020299

Analysis of the Differential Gene and Protein Expression Profiles of Corneal Epithelial Cells Stimulated with Alternating Current Electric Fields
Cited by: 5
Author(s): Bhavani S. Kowtharapu, Jyoti Damaraju, Nitesh Kumar Singh, Josefin Ziebart, Rainer Bader, Dirk Koczan, Oliver Stachs
Software Mentions: 4
Published: over 3 years ago

10.3390/genes11070815

Cortical Granule Distribution and Expression Pattern of Genes Regulating Cellular Component Size, Morphogenesis, and Potential to Differentiation are Related to Oocyte Developmental Competence and Maturational Capacity In Vivo and In Vitro
Cited by: 10
Author(s): Magdalena Kulus, Wiesława Kranc, Michal Ješeta, Patrycja Sujka‐Kordowska, Aneta Konwerska, Sylwia Ciesiółka, Piotr Celichowski, Lisa Moncrieff, Ievgeniia Kocherova, Małgorzata Józkowiak, Jakub Kulus, Maria Wieczorkiewicz, Hanna Piotrowska‐Kempisty, Mariusz T. Skowroński, Dorota Bukowska, Marie Machatková, Šárka Hanuláková, Paul Mozdziak, J. M. Jaśkowski, Bartosz Kempisty, Paweł Antosik
Software Mentions: 4
Published: over 4 years ago

10.3390/genes12091363

Meta-Analysis of Brain Gene Expression Data from Mouse Model Studies of Maternal Immune Activation Using Poly(I:C)
Cited by: 4
Author(s): Aodán Laighneach, Lieve Desbonnet, John Kelly, Gary Donohoe, Derek W. Morris
Software Mentions: 4
Published: about 3 years ago

10.1186/bcr3684

Transforming growth factor beta receptor type III is a tumor promoter in mesenchymal-stem like triple negative breast cancer
Cited by: 45
Author(s): Bojana Jovanović, J. Scott Beeler, Michael W. Pickup, Anna Chytil, Agnieszka E. Gorska, William J. Ashby, Brian D. Lehmann, Andries Zijlstra, Jennifer A. Pietenpol, Harold L. Moses
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0102091

Pesticide Methoxychlor Promotes the Epigenetic Transgenerational Inheritance of Adult-Onset Disease through the Female Germline
Cited by: 191
Author(s): Mohan Manikkam, M. Muksitul Haque, Carlos Guerrero-Bosagna, Eric Nilsson, Michael K. Skinner
Software Mentions: 4
Published: over 10 years ago

10.1186/s12864-015-1984-4

Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network
Cited by: 34
Author(s): Maria Pires Pacheco, Elisabeth John, Tony Kaoma, Merja Heinäniemi, Nathalie Nicot, Laurent Vallar, Jean-Luc Bueb, Lasse Sinkkonen, Thomas Sauter
Software Mentions: 4
Published: about 9 years ago

Projects: bioconductor: oligo

Papers Mentioning oligo 204