Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: genefilter
https://packages.ecosyste.ms/registries/bioconductor.org/packages/genefilter
genefilter: methods for filtering genes from high-throughput experiments
2 versions
Latest release: 12 months ago
65 dependent packages
3,148,119 downloads total
Papers Mentioning genefilter 142
10.18632/oncotarget.25420
Comparative molecular characterization of typical and exceptional responders in glioblastomaCited by: 14
Author(s): Kristin Wipfler, Adam Cornish, Chittibabu Guda
Software Mentions: 2
Published: over 6 years ago
10.1002/ece3.1098
Mating system variation drives rapid evolution of the female transcriptome in<i>Drosophila pseudoobscura</i>Cited by: 18
Author(s): Elina Immonen, Rhonda R. Snook, Michael G. Ritchie
Software Mentions: 2
Published: over 10 years ago
10.1016/j.celrep.2018.02.027
S. aureus Evades Macrophage Killing through NLRP3-Dependent Effects on Mitochondrial TraffickingCited by: 62
Author(s): Taylor S. Cohen, Michelle L. Boland, Brandon B. Boland, Virginia Takahashi, Andrey Tovchigrechko, Young Lee, Aimee D. Wilde, Mark J. Mazaitis, Omari Jones-Nelson, Christine Tkaczyk, Rajiv Raja, C. Kendall Stover, Bret R. Sellman
Software Mentions: 2
Published: over 6 years ago
10.1155/2016/4369431
Integrated Analysis of DNA Methylation and mRNA Expression Profiles Data to Identify Key Genes in Lung AdenocarcinomaCited by: 15
Author(s): Xiang Jin, Xingang Liu, Xiaodan Li, Yinghui Guan
Software Mentions: 2
Published: almost 9 years ago
10.1186/1752-0509-3-55
A graphical model approach for inferring large-scale networks integrating gene expression and genetic polymorphismCited by: 30
Author(s): Jen-Hwa Chu, Scott T. Weiss, Vincent J. Carey, Benjamin A. Raby
Software Mentions: 2
Published: over 15 years ago
10.1186/s12864-015-1896-3
Weight-reduction through a low-fat diet causes differential expression of circulating microRNAs in obese C57BL/6 miceCited by: 42
Author(s): Ching‐Hua Hsieh, Cheng-Shyuan Rau, Shao-Chun Wu, Johnson Chia‐Shen Yang, Yi-Chan Wu, Tsu-Hsiang Lu, Siou-Ling Tzeng, Chi‐Chuan Wu, Ching-Yi Lin
Software Mentions: 2
Published: about 9 years ago
10.1186/s12864-016-3119-y
Australian black field crickets show changes in neural gene expression associated with socially-induced morphological, life-history, and behavioral plasticityCited by: 12
Author(s): Michael M. Kasumovic, Zhiliang Chen, Marc R. Wilkins
Software Mentions: 2
Published: almost 8 years ago
10.12688/f1000research.4524.1
KEGGscape: a Cytoscape app for pathway data integrationCited by: 63
Author(s): Kozo Nishida, Keiichiro Ono, Shigehiko Kanaya, Koichi Takahashi
Software Mentions: 2
Published: over 10 years ago
10.1186/1471-2407-6-200
Selection of suitable reference genes for accurate normalization of gene expression profile studies in non-small cell lung cancerCited by: 89
Author(s): Silvia Saviozzi, Francesca Cordero, Marco Lo Iacono, Silvia Novello, Scagliotti V. Giorgio, Raffaele Calogero
Software Mentions: 2
Published: about 18 years ago
10.1111/acel.12505
Advanced aging phenotype is revealed by epigenetic modifications in rat liver after <i>in utero</i> malnutritionCited by: 18
Author(s): Hye Heo, Jessica N. Tozour, Fabien Delahaye, Yongmei Zhao, Lingguang Cui, Nir Barzilai, Francine Einstein
Software Mentions: 2
Published: about 8 years ago
10.18632/oncotarget.15681
The histone demethylase<i>KDM3A</i>regulates the transcriptional program of the androgen receptor in prostate cancer cellsCited by: 74
Author(s): Stephen Wilson, Lingling Fan, Natasha Sahgal, Jianfei Qi, Fabian V. Filipp
Software Mentions: 2
Published: over 7 years ago
10.3389/fimmu.2018.02870
Theiler's Virus-Mediated Immunopathology in the CNS and Heart: Roles of Organ-Specific Cytokine and Lymphatic ResponsesCited by: 15
Author(s): Seiichi Omura, Eiichiro Kawai, Fumitaka Sato, Nicholas E. Martinez, Alireza Minagar, Mahmoud Al‐Kofahi, J. Winny Yun, Urška Cvek, Marjan Trutschl, J. Steven Alexander, Ikuo Tsunoda
Software Mentions: 2
Published: almost 6 years ago
10.3389/fimmu.2019.00516
Bioinformatics Analyses Determined the Distinct CNS and Peripheral Surrogate Biomarker Candidates Between Two Mouse Models for Progressive Multiple SclerosisCited by: 11
Author(s): Seiichi Omura, Fumitaka Sato, Nicholas E. Martinez, Ah-Mee Park, Mitsugu Fujita, Nikki J. Kennett, Urška Cvek, Alireza Minagar, J. Steven Alexander, Ikuo Tsunoda
Software Mentions: 2
Published: over 5 years ago
10.14252/foodsafetyfscj.D-20-00032
Effect of Transgenic Rootstock Grafting on the Omics Profiles in TomatoCited by: 9
Author(s): Hiroaki Kodama, Taira Miyahara, Taichi Oguchi, Takashi Tsujimoto, Yoshihiro Ozeki, Toshiki Ogawa, Yube Yamaguchi, Daisaku Ohta
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0123316
Gene Profiling Characteristics of Radioadaptive Response in AG01522 Normal Human FibroblastsCited by: 18
Author(s): Jue Hou, Fan Wang, Peizhong Kong, K.N. Yu, Hongzhi Wang, Wei Han
Software Mentions: 2
Published: over 9 years ago
10.3390/jcdd8040045
Transcriptome Analysis Reveals Differential Gene Expression between the Closing Ductus Arteriosus and the Patent Ductus Arteriosus in HumansCited by: 5
Author(s): Junichi Saito, Tomoyuki Kojima, Shota Tanifuji, Yuko Kato, Shuntaro Oka, Yukio Ichikawa, Etsuko Miyagi, Tsuyoshi Tachibana, Toshihide Asou, Utako Yokoyama
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0044998
Myelin-Derived Lipids Modulate Macrophage Activity by Liver X Receptor ActivationCited by: 54
Author(s): Jeroen F. J. Bogie, Silke Timmermans, Vân Anh Huynh-Thu, Alexandre Irrthum, Hubert J.M. Smeets, Jan Åke Gustafsson, Knut R. Steffensen, Monique Mulder, Piet Stinissen, Niels Hellings, Jerome J. A. Hendriks
Software Mentions: 2
Published: about 12 years ago
10.1186/1748-717X-9-111
Integrating microRNA and mRNA expression profiles in response to radiation-induced injury in rat lungCited by: 27
Author(s): Ling Xie, Jundong Zhou, Shuyu Zhang, Qing Chen, Renchun Lai, Wei‐Qun Ding, Chuanjun Song, Xingjun Meng, Jinchang Wu
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0077936
Profiling Circulating MicroRNA Expression in Experimental Sepsis Using Cecal Ligation and PunctureCited by: 56
Author(s): Shao-Chun Wu, Johnson Chia‐Shen Yang, Cheng-Shyuan Rau, Yi‐Chun Chen, Tsu-Hsiang Lu, Ming‐Wei Lin, Siou-Ling Tzeng, Yi-Chan Wu, Chi‐Chuan Wu, Ching‐Hua Hsieh
Software Mentions: 2
Published: almost 11 years ago
10.7717/peerj.2775
Network-based analysis of differentially expressed genes in cerebrospinal fluid (CSF) and blood reveals new candidate genes for multiple sclerosisCited by: 46
Author(s): Nahid Safari-Alighiarloo, Mostafa Rezaei‐Tavirani, Mohammad Taghi Taghizadeh, Seyyed Mohammad Tabatabaei, Saeed Namaki
Software Mentions: 2
Published: almost 8 years ago
10.18632/oncotarget.20076
mRNA expression profiles obtained from microdissected pancreatic cancer cells can predict patient survivalCited by: 4
Author(s): Ana-Bárbara García-García, M. Carmen Gómez-Mateo, Rebeca Hilario, Pilar Rentero-Garrido, Álvaro Martínez‐Doménech, Verónica González-Albert, Andrés Cervantes, Pablo Marín-García, Felipe Javier Chaves, Antonio Ferrández‐Izquierdo, Luís Sabater
Software Mentions: 2
Published: about 7 years ago
10.1038/srep42460
Variation-preserving normalization unveils blind spots in gene expression profilingCited by: 18
Author(s): Carlos P. Roca, Susana I. L. Gomes, Mónica J.B. Amorim, Janeck J. Scott-Fordsmand
Software Mentions: 2
Published: over 7 years ago
10.3892/mmr.2015.3794
Identification of genes associated with laryngeal squamous cell carcinoma samples based on bioinformatic analysisCited by: 6
Author(s): Bo Yang, Xiaoyong Bao
Software Mentions: 2
Published: over 9 years ago
10.1186/1471-2148-11-47
Evolutionary origins of Brassicaceae specific genes in Arabidopsis thalianaCited by: 140
Author(s): Mark T.A. Donoghue, Channa Keshavaiah, Sandesh H Swamidatta, Charles Spillane
Software Mentions: 2
Published: over 13 years ago
10.1007/s10549-017-4652-3
Functional transcriptomic annotation and protein–protein interaction network analysis identify NEK2, BIRC5, and TOP2A as potential targets in obese patients with luminal A breast cancerCited by: 31
Author(s): Miriam Nuncia-Cantarero, Sandra Martínez-Canales, Fernando Andrés-Pretel, Gabriel Santpere, Alberto Ocaña, Eva M Moya
Software Mentions: 2
Published: over 6 years ago
10.1186/s13058-016-0676-6
Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancerCited by: 24
Author(s): Marsela Braunstein, Linda M. Liao, Nicola Lyttle, Nazleen Lobo, Karen Taylor, Paul M. Krzyzanowski, Irina Kalatskaya, Cindy Q. Yao, Lincoln Stein, Paul C. Boutros, Christopher Twelves, Richard Marcellus, John M.S. Bartlett, Melanie Spears
Software Mentions: 2
Published: over 8 years ago
10.1038/s41598-020-72078-4
Esterified carotenoids are synthesized in petals of carnation (Dianthus caryophyllus) and accumulate in differentiated chromoplastsCited by: 10
Author(s): Luna Iijima, Sanae Kishimoto, Akemi Ohmiya, Masafumi Yagi, Emi Okamoto, Taira Miyahara, Takashi Tsujimoto, Yoshihiro Ozeki, Nahoko Uchiyama, Takashi Hakamatsuka, Takanobu Kouno, Emilio Cano, Mitsuru Shimizu, Masahiro Nishihara
Software Mentions: 2
Published: about 4 years ago
10.1186/s13287-018-0950-x
New insights into the genic and metabolic characteristics of induced pluripotent stem cells from polycystic ovary syndrome womenCited by: 15
Author(s): Zheying Min, Qian Gao, Xiumei Zhang, Yong Fan, Tao Tan, Rong Li, Yue Zhao, Yang Yu
Software Mentions: 2
Published: about 6 years ago
10.7150/thno.48247
MED13L integrates Mediator-regulated epigenetic control into lung cancer radiosensitivityCited by: 17
Author(s): Nasha Zhang, Ying Song, Yeyang Xu, Jiandong Liu, Yue Shen, Lixin Zhou, Jinming Yu, Ming Yang
Software Mentions: 2
Published: almost 5 years ago
10.1155/2013/458278
Transcriptional Response of Bovine Monocyte-Derived Macrophages after the Infection with Different Argentinean<i>Mycobacterium bovis</i>IsolatesCited by: 7
Author(s): Karina Caimi, Federico Carlos Blanco, Marcelo Soria, Fabiana Bigi
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.pone.0189087
New roles for nuclear EGFR in regulating the stability and translation of mRNAs associated with VEGF signalingCited by: 17
Author(s): Klaus Dittmann, Claus Mayer, Stefan Czemmel, Stephan M. Huber, H. Peter Rodemann
Software Mentions: 1
Published: almost 7 years ago
10.1186/s13059-020-1936-4
A post-transcriptional program of chemoresistance by AU-rich elements and TTP in quiescent leukemic cellsCited by: 21
Author(s): Sooncheol Lee, Douglas S. Micalizzi, Samuel S. Truesdell, Syed I. A. Bukhari, Myriam Boukhali, Jennifer Lombardi‐Story, Yasutaka Kato, Min‐Kyung Choo, Ipsita Dey‐Guha, Fei Ji, Benjamin Nicholson, David T. Myers, Dongjun Lee, Maria Antonietta Mazzola, Radhika Raheja, Adam Langenbucher, Nicholas J. Haradhvala, Michael S. Lawrence, Roopali Gandhi, Christopher Tiedje, Manuel D. Díaz-Muñoz, David A. Sweetser, Ruslan I. Sadreyev, David B. Sykes, Wilhelm Haas, Daniel A. Haber, Shyamala Maheswaran, Shobha Vasudevan
Software Mentions: 1
Published: over 4 years ago
10.1186/s12864-016-2671-9
Immediate and long-term transcriptional response of hind muscle tissue to transient variation of incubation temperature in broilersCited by: 6
Author(s): Watcharapong Naraballobh, Nares Trakooljul, Eduard Muráni, Ronald M. Brunner, Carsten Krischek, Sabine Janisch, Michael Wicke, Siriluck Ponsuksili, Klaus Wimmers
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pone.0179230
Identification and prediction of alternative transcription start sites that generate rod photoreceptor-specific transcripts from ubiquitously expressed genesCited by: 6
Author(s): Evgenya Y. Popova, Anna C. Salzberg, Chen Yang, Samuel Shao Min Zhang, Colin J. Barnstable
Software Mentions: 1
Published: over 7 years ago
10.1002/2211-5463.12659
Low expression of <i>WWC1</i> , a tumor suppressor gene, is associated with aggressive breast cancer and poor survival outcomeCited by: 12
Author(s): Zhanwei Wang, Dionyssios Katsaros, Nicoletta Biglia, Siyan Yi, Yuanyuan Fu, Maarit Tiirikainen, Herbert Yu
Software Mentions: 1
Published: over 5 years ago
10.3389/fgene.2019.01007
Mining Public Toxicogenomic Data Reveals Insights and Challenges in Delineating Liver Steatosis Adverse Outcome PathwaysCited by: 14
Author(s): Mohamed Diwan M. AbdulHameed, Venkat R. Pannala, Anders Wallqvist
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.pone.0054365
Frequency and Prognostic Impact of CEBPA Proximal, Distal and Core Promoter Methylation in Normal Karyotype AML: A Study on 623 CasesCited by: 24
Author(s): Annette Fasan, Tamara Alpermann, Claudia Haferlach, Vera Grossmann, Andreas Roller, Alexander Kohlmann, Christiane Eder, Wolfgang Kern, Torsten Haferlach, Susanne Schnittger
Software Mentions: 1
Published: over 11 years ago
10.3390/md15050136
Transcriptomic Profiling of the Allorecognition Response to Grafting in the Demosponge Amphimedon queenslandicaCited by: 3
Author(s): Laura F. Grice, Bernard M. Degnan
Software Mentions: 1
Published: over 7 years ago
10.3390/biom7010015
The Genomic Impact of DNA CpG Methylation on Gene Expression; Relationships in Prostate CancerCited by: 72
Author(s): Mark D. Long, Dominic J. Smiraglia, Moray J. Campbell
Software Mentions: 1
Published: over 7 years ago
10.1038/s41598-019-54336-2
Subendothelial stiffness alters endothelial cell traction force generation while exerting a minimal effect on the transcriptomeCited by: 41
Author(s): Effie Bastounis, Yi‐Ting Yeh, Julie A. Theriot
Software Mentions: 1
Published: almost 5 years ago
10.3390/ijms21010332
Network Medicine Approach for Analysis of Alzheimer’s Disease Gene Expression DataCited by: 10
Author(s): David S. Cohen, Alexander Pilozzi, Xudong Huang
Software Mentions: 1
Published: almost 5 years ago